5100009@unknown@formal@none@1@S@Assuming that the 23rd amino acid is also encoded by a stop codon, we systematically predicted proteins that contain stop-codon-encoded amino acids from 191 prokaryotic genomes.@(((:tag . "VBG") (:stem . "assume") (:form . "Assuming") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . "RB") (:stem . "systematically") (:form . "systematically")\n  (:end . 84) (:start . 70) (:id . 57))\n ((:tag . "VBD") (:stem . "predict") (:form . "predicted") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 103)\n  (:start . 95) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 116)\n  (:start . 109) (:id . 61))\n ((:tag . "JJ") (:stem . "stop-codon-encoded") (:form . "stop-codon-encoded")\n  (:end . 135) (:start . 117) (:id . 62))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 141)\n  (:start . 136) (:id . 63))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 147)\n  (:start . 142) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . "CD") (:stem . "191") (:form . "191") (:end . 156) (:start . 153)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "prokaryotic") (:form . "prokaryotic") (:end . 168)\n  (:start . 157) (:id . 67))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 176)\n  (:start . 169) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x1.10.1) (:span 0 8)))\n (:hscopes ((:id . :x1.10.1) (:span 0 65)))\n (:identifiers (:sid . :s1.10) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100019@unknown@formal@none@1@S@Two such amino acids have been discovered to date: selenocysteine 34 and pyrrolysine 56.@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "discover") (:form . "discovered") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n  (:end . 65) (:start . 51) (:id . 52))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 84)\n  (:start . 73) (:id . 55))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.20) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100029@unknown@formal@none@1@S@Because genome sequences of various prokaryotes are available today, there will be a chance to discover the novel amino acid via analysis of these genomes.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "prokaryote") (:form . "prokaryotes") (:end . 47)\n  (:start . 36) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 61)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "today") (:form . "today") (:end . 67) (:start . 62)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 51))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 91)\n  (:start . 85) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "VB") (:stem . "discover") (:form . "discover") (:end . 103)\n  (:start . 95) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 113)\n  (:start . 108) (:id . 60))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 119)\n  (:start . 114) (:id . 61))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 128) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 137)\n  (:start . 129) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 146)\n  (:start . 141) (:id . 66))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 154)\n  (:start . 147) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.30) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100039@unknown@formal@none@1@S@By enumerating ORFs that have an inframe stop codon from genomes and examining their evolutionary conservation, candidate proteins can be predicted.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "enumerate") (:form . "enumerating") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "examine") (:form . "examining") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 84)\n  (:start . 79) (:id . 55))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 97)\n  (:start . 85) (:id . 56))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 110)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 58))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 121)\n  (:start . 112) (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 130)\n  (:start . 122) (:id . 60))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 134) (:start . 131)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 137) (:start . 135)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 147)\n  (:start . 138) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.40) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100049@unknown@formal@none@1@S@If we enumerate all iORFs from microbial genomes, most of the readthrough genes will be included in them.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "enumerate") (:form . "enumerate") (:end . 15)\n  (:start . 6) (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "microbial") (:form . "microbial") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 73)\n  (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 96)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.50) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100059@unknown@formal@none@1@S@(a) Schematic illustration of an interrupted ORF (iORF).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "illustration") (:form . "illustration") (:end . 26)\n  (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "interrupted") (:form . "interrupted") (:end . 44)\n  (:start . 33) (:id . 49))\n ((:tag . "NNP") (:stem . "ORF") (:form . "ORF") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "iORF") (:form . "iORF") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.60) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100069@unknown@formal@none@1@S@In this way, they can be eliminated as candidates.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 17) (:start . 13)\n  (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "eliminate") (:form . "eliminated") (:end . 35)\n  (:start . 25) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 49)\n  (:start . 39) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 50) (:start . 49)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s1.70) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100079@unknown@formal@none@1@S@The prediction schema is shown in Figure 2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "schema") (:form . "schema") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.80) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100089@unknown@formal@none@1@S@A flowchart of the prediction procedure@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "flowchart") (:form . "flowchart") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 39)\n  (:start . 30) (:id . 47)))@@@1@6@((:identifiers (:sid . :s1.90) (:did . :1471-2105-8-225) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5100099@unknown@formal@none@1@S@There were 94,690 iORFs that have interspecific hits.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "CD") (:stem . "94,690") (:form . "94,690") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "interspecific") (:form . "interspecific")\n  (:end . 47) (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.100) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100109@unknown@formal@none@1@S@Hence, three-step filtering procedures were applied to remove the false positives.@(((:tag . "RB") (:stem . "hence") (:form . "Hence") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "three-step") (:form . "three-step") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.110) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100119@unknown@formal@none@1@S@Of the 14 families, 11 were found in our prediction result.@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 33) (:start . 28)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 40) (:start . 37)\n  (:id . 51))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 51)\n  (:start . 41) (:id . 52))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 58)\n  (:start . 52) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.120) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100129@unknown@formal@none@1@S@For example, "GSU2293 + downstream" means that the iORF consists of the gene GSU2293 and its downstream sequence.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "GSU2293") (:form . "GSU2293") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "downstream") (:form . "downstream") (:end . 34)\n  (:start . 24) (:id . 48))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 41) (:start . 36)\n  (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 64)\n  (:start . 56) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 56))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gsu2293") (:form . "GSU2293") (:end . 84)\n  (:start . 77) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 103)\n  (:start . 93) (:id . 61))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 112)\n  (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.130) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100139@unknown@formal@none@1@S@The rest is a cluster of TetR-like transcriptional regulators from Methanosarcina acetivorans and M. barkeri.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "rest") (:form . "rest") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "tetr-like") (:form . "TetR-like") (:end . 34)\n  (:start . 25) (:id . 48))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 50) (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 61)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Methanosarcina") (:form . "Methanosarcina")\n  (:end . 81) (:start . 67) (:id . 52))\n ((:tag . "NNP") (:stem . "acetivorans") (:form . "acetivorans") (:end . 93)\n  (:start . 82) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "M.") (:form . "M.") (:end . 100) (:start . 98)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "barkeri") (:form . "barkeri") (:end . 108)\n  (:start . 101) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.140) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100149@unknown@formal@none@1@S@There were two such clusters (Table 1).@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s1.150) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100159@unknown@formal@none@1@S@A protein Dpro_2 contains yet another inframe stop codon (TAG) at the column 189.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "dpro_2") (:form . "Dpro_2") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "TAG") (:form . "TAG") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 76)\n  (:start . 70) (:id . 56))\n ((:tag . "CD") (:stem . "189") (:form . "189") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.160) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100169@unknown@formal@none@1@S@However, computational analysis of sequences immediately downstream of the inframe stop codons failed to identify SECIS elements, which is a hallmark of selenocysteine-containing genes.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n  (:end . 22) (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . "RB") (:stem . "immediately") (:form . "immediately") (:end . 56)\n  (:start . 45) (:id . 48))\n ((:tag . "RB") (:stem . "downstream") (:form . "downstream") (:end . 67)\n  (:start . 57) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 82)\n  (:start . 75) (:id . 52))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 87) (:start . 83)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 94)\n  (:start . 88) (:id . 54))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 101)\n  (:start . 95) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 56))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 113)\n  (:start . 105) (:id . 57))\n ((:tag . "NN") (:stem . "secis") (:form . "SECIS") (:end . 119)\n  (:start . 114) (:id . 58))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 128)\n  (:start . 120) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 135)\n  (:start . 130) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 138) (:start . 136)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 140) (:start . 139)\n  (:id . 63))\n ((:tag . "NN") (:stem . "hallmark") (:form . "hallmark") (:end . 149)\n  (:start . 141) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "selenocysteine-containing")\n  (:form . "selenocysteine-containing") (:end . 178) (:start . 153)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 184)\n  (:start . 179) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 68)))@@@1@27@((:ncues ((:id . :x1.170.1) (:span 95 101)))\n (:nscopes ((:id . :x1.170.1) (:span 95 128)))\n (:identifiers (:sid . :s1.170) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100179@unknown@formal@none@1@S@Stop codon usage in the pre-filtering clusters@(((:tag . "NNP") (:stem . "Stop") (:form . "Stop") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "pre-filtering") (:form . "pre-filtering")\n  (:end . 37) (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 46)\n  (:start . 38) (:id . 48)))@@@1@7@((:identifiers (:sid . :s1.180) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|SectionTitle|)))@oe@9-2-2011
5100189@unknown@formal@none@1@S@Discrepancies of stop codon usages between the inframe and C-terminal stop codons@(((:tag . "NNS") (:stem . "discrepancy") (:form . "Discrepancies") (:end . 13)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "usage") (:form . "usages") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 42)\n  (:start . 35) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 69)\n  (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 81)\n  (:start . 75) (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.190) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|FigureLegend|)))@oe@9-2-2011
5100199@unknown@formal@none@1@S@Sensitivity of this test is not high because many organisms that utilize selenocysteine were below the defined threshold.@(((:tag . "NN") (:stem . "sensitivity") (:form . "Sensitivity") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 59)\n  (:start . 50) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "utilize") (:form . "utilize") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "selenocysteine") (:form . "selenocysteine")\n  (:end . 87) (:start . 73) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 110)\n  (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 120)\n  (:start . 111) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.200) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100209@unknown@formal@none@1@S@Perrodou et al. 19 constructed a database of predicted recoding events in microbes.@(((:tag . "NNP") (:stem . "Perrodou") (:form . "Perrodou") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "construct") (:form . "constructed") (:end . 30)\n  (:start . 19) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . "VBG") (:stem . "recode") (:form . "recoding") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 70)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "microbe") (:form . "microbes") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.210) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100219@unknown@formal@none@1@S@Dimethylamine methyltransferases also lack non-readthrough homologs.@(((:tag . "NNP") (:stem . "Dimethylamine") (:form . "Dimethylamine")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "methyltransferas") (:form . "methyltransferases")\n  (:end . 32) (:start . 14) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 37) (:start . 33)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 42) (:start . 38)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "non-readthrough") (:form . "non-readthrough")\n  (:end . 58) (:start . 43) (:id . 46))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 67)\n  (:start . 59) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 48)))@@@1@7@((:ncues ((:id . :x1.220.1) (:span 38 42)))\n (:nscopes ((:id . :x1.220.1) (:span 38 67)))\n (:identifiers (:sid . :s1.220) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100229@unknown@formal@none@1@S@However, almost no novel candidates for readthrough genes were predicted.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 35)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "readthrough") (:form . "readthrough") (:end . 51)\n  (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.230) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100239@unknown@formal@none@1@S@Yet another possibility is that the 23rd amino acid exists but is not encoded by stop codons.@(((:tag . "RB") (:stem . "yet") (:form . "Yet") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 92)\n  (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x1.240.2) (:span 12 23)))\n (:ncues ((:id . :x1.240.1) (:span 66 69)))\n (:hscopes ((:id . :x1.240.2) (:span 12 92)))\n (:nscopes ((:id . :x1.240.1) (:span 66 92)))\n (:identifiers (:sid . :s1.240) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100249@unknown@formal@none@1@S@Such selenoproteins identified through our screening of nearly 200 microbial genomes were selenoprotein A and only one uncertain candidate.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n  (:end . 19) (:start . 5) (:id . 43))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 30)\n  (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 38)\n  (:start . 31) (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 42) (:start . 39)\n  (:id . 46))\n ((:tag . "NN") (:stem . "screening") (:form . "screening") (:end . 52)\n  (:start . 43) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 48))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 62)\n  (:start . 56) (:id . 49))\n ((:tag . "CD") (:stem . "200") (:form . "200") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "microbial") (:form . "microbial") (:end . 76)\n  (:start . 67) (:id . 51))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 84)\n  (:start . 77) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 89) (:start . 85)\n  (:id . 53))\n ((:tag . "NN") (:stem . "selenoprotein") (:form . "selenoprotein")\n  (:end . 103) (:start . 90) (:id . 54))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 105) (:start . 104)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 114) (:start . 110)\n  (:id . 57))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "uncertain") (:form . "uncertain") (:end . 128)\n  (:start . 119) (:id . 59))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 138)\n  (:start . 129) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.250) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100259@unknown@formal@none@1@S@Although many of the currently known selenoproteins and pyrrolysine proteins were successfully detected, no candidate for the 23rd amino acid was discovered.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "selenoprotein") (:form . "selenoproteins")\n  (:end . 51) (:start . 37) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "pyrrolysine") (:form . "pyrrolysine") (:end . 67)\n  (:start . 56) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 76)\n  (:start . 68) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 81) (:start . 77)\n  (:id . 52))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 94)\n  (:start . 82) (:id . 53))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 103)\n  (:start . 95) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 55))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 107) (:start . 105)\n  (:id . 56))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 117)\n  (:start . 108) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 121) (:start . 118)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "23rd") (:form . "23rd") (:end . 130) (:start . 126)\n  (:id . 60))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 136)\n  (:start . 131) (:id . 61))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 141) (:start . 137)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 145) (:start . 142)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "discover") (:form . "discovered") (:end . 156)\n  (:start . 146) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 65)))@@@1@24@((:ncues ((:id . :x1.260.1) (:span 105 107)))\n (:nscopes ((:id . :x1.260.1) (:span 105 156)))\n (:identifiers (:sid . :s1.260) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100269@unknown@formal@none@1@S@A total of 328 complete genome sequences of prokaryotes were downloaded from the KEGG FTP site 25 in April 2006.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "328") (:form . "328") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "prokaryote") (:form . "prokaryotes") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "KEGG") (:form . "KEGG") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "FTP") (:form . "FTP") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "April") (:form . "April") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.270) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100279@unknown@formal@none@1@S@Similarly, iORFs were compared with RNA genes using BLASTN, and those matched with the RNAs were removed.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "iorf") (:form . "iORFs") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "BLASTN") (:form . "BLASTN") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "match") (:form . "matched") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "rna") (:form . "RNAs") (:end . 91) (:start . 87)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 104)\n  (:start . 97) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.280) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100289@unknown@formal@none@1@S@Subsequently, conservation of the inframe stop codons in each cluster was examined.@(((:tag . "RB") (:stem . "subsequently") (:form . "Subsequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 26)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "inframe") (:form . "inframe") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.290) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100299@unknown@formal@none@1@S@Then, 2Δl = 2(lfree – lfix) approximately follows the χ2 distribution with one degree of freedom.@(((:tag . "RB") (:stem . "then") (:form . "Then") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "2δl") (:form . "2Δl") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "FW") (:stem . "2(lfree") (:form . "2(lfree") (:end . 19)\n  (:start . 12) (:id . 46))\n ((:tag . "NN") (:stem . "–") (:form . "–") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "lfix") (:form . "lfix") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 41) (:start . 28) (:id . 50))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 49)\n  (:start . 42) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "χ2") (:form . "χ2") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 69)\n  (:start . 57) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 85)\n  (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "freedom") (:form . "freedom") (:end . 96)\n  (:start . 89) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.300) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100309@unknown@formal@none@1@S@If the N- and C-terminal parts of an iORF have distinct but closely arranged BLAST hits in other genomes, it strongly suggests the iORF is actually two adjacent genes.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "N-") (:form . "N-") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 24)\n  (:start . 14) (:id . 46))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 55)\n  (:start . 47) (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 67)\n  (:start . 60) (:id . 54))\n ((:tag . "VBN") (:stem . "arrange") (:form . "arranged") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 96) (:start . 91)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 104)\n  (:start . 97) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 117)\n  (:start . 109) (:id . 63))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 126)\n  (:start . 118) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "NN") (:stem . "iorf") (:form . "iORF") (:end . 135) (:start . 131)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 138) (:start . 136)\n  (:id . 67))\n ((:tag . "RB") (:stem . "actually") (:form . "actually") (:end . 147)\n  (:start . 139) (:id . 68))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 151) (:start . 148)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 160)\n  (:start . 152) (:id . 70))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 166)\n  (:start . 161) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x1.310.1) (:span 118 126)))\n (:hscopes ((:id . :x1.310.1) (:span 118 166)))\n (:identifiers (:sid . :s1.310) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100319@unknown@formal@none@1@S@The matrix elements were subsequently normalized to the number of alignments N.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 37)\n  (:start . 25) (:id . 46))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 48)\n  (:start . 38) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 62)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 76)\n  (:start . 66) (:id . 52))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 78) (:start . 77)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s1.320) (:did . :1471-2105-8-225)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100329@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s2.3) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5100339@unknown@formal@none@1@S@Comparison of the prediction dataset to other available human interaction datasets estimates the false positive rate of the new method to be below 80% which is competitive with other methods.@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 55)\n  (:start . 46) (:id . 49))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 61) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 73)\n  (:start . 62) (:id . 51))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 82)\n  (:start . 74) (:id . 52))\n ((:tag . "VBZ") (:stem . "estimate") (:form . "estimates") (:end . 92)\n  (:start . 83) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 102) (:start . 97)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 111)\n  (:start . 103) (:id . 56))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 116) (:start . 112)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 127) (:start . 124)\n  (:id . 60))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 134)\n  (:start . 128) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 140) (:start . 138)\n  (:id . 63))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 146)\n  (:start . 141) (:id . 64))\n ((:tag . "CD") (:stem . "80") (:form . "80") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 156)\n  (:start . 151) (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 159) (:start . 157)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "competitive") (:form . "competitive") (:end . 171)\n  (:start . 160) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 176) (:start . 172)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 182)\n  (:start . 177) (:id . 71))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 190)\n  (:start . 183) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x2.13.1) (:span 83 92)))\n (:hscopes ((:id . :x2.13.1) (:span 83 190)))\n (:identifiers (:sid . :s2.13) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100349@unknown@formal@none@1@S@Interactions determined by high-throughput methods are generally considered to be less reliable than those obtained by low-throughput studies 1314 and as a consequence efforts are also underway to extract evidence for interactions from the literature 151617.@(((:tag . "NNS") (:stem . "interaction") (:form . "Interactions") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 23)\n  (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 26) (:start . 24)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "high-throughput") (:form . "high-throughput")\n  (:end . 42) (:start . 27) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 50)\n  (:start . 43) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n  (:id . 47))\n ((:tag . "RB") (:stem . "generally") (:form . "generally") (:end . 64)\n  (:start . 55) (:id . 48))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 75)\n  (:start . 65) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 81) (:start . 79)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 86) (:start . 82)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "reliable") (:form . "reliable") (:end . 95)\n  (:start . 87) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 100) (:start . 96)\n  (:id . 54))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 106)\n  (:start . 101) (:id . 55))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 115)\n  (:start . 107) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 118) (:start . 116)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "low-throughput") (:form . "low-throughput")\n  (:end . 133) (:start . 119) (:id . 58))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 141)\n  (:start . 134) (:id . 59))\n ((:tag . "CD") (:stem . "1314") (:form . "1314") (:end . 146) (:start . 142)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 153) (:start . 151)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 155) (:start . 154)\n  (:id . 63))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 167)\n  (:start . 156) (:id . 64))\n ((:tag . "NNS") (:stem . "effort") (:form . "efforts") (:end . 175)\n  (:start . 168) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 179) (:start . 176)\n  (:id . 66))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 184) (:start . 180)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "underway") (:form . "underway") (:end . 193)\n  (:start . 185) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 196) (:start . 194)\n  (:id . 69))\n ((:tag . "VB") (:stem . "extract") (:form . "extract") (:end . 204)\n  (:start . 197) (:id . 70))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 213)\n  (:start . 205) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 217) (:start . 214)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 230)\n  (:start . 218) (:id . 73))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 235) (:start . 231)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 239) (:start . 236)\n  (:id . 75))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 250)\n  (:start . 240) (:id . 76))\n ((:tag . "CD") (:stem . "151617") (:form . "151617") (:end . 257)\n  (:start . 251) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 258) (:start . 257)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x2.23.1) (:span 65 75)))\n (:hscopes ((:id . :x2.23.1) (:span 0 141)))\n (:identifiers (:sid . :s2.23) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100359@unknown@formal@none@1@S@For example, the major complexes in yeast have been predicted by this strategy 25.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 61)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.33) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100369@unknown@formal@none@1@S@4) Predictors based on functional features exploit non-sequence information to infer interactions.@(((:tag . "LS") (:stem . "4") (:form . "4") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "NNS") (:stem . "predictor") (:form . "Predictors") (:end . 13)\n  (:start . 3) (:id . 44))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "VBP") (:stem . "exploit") (:form . "exploit") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "JJ") (:stem . "non-sequence") (:form . "non-sequence") (:end . 63)\n  (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 75)\n  (:start . 64) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "VB") (:stem . "infer") (:form . "infer") (:end . 84) (:start . 79)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 97)\n  (:start . 85) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.43) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100379@unknown@formal@none@1@S@Although, many computational methods have investigated the prediction of protein-protein interactions, few have so far been applied to the human proteome.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n  (:end . 28) (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 54)\n  (:start . 42) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 49))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 69)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n  (:end . 88) (:start . 73) (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 101)\n  (:start . 89) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 106) (:start . 103)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 111) (:start . 107)\n  (:id . 56))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 114) (:start . 112)\n  (:id . 57))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 131)\n  (:start . 124) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 134) (:start . 132)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 144)\n  (:start . 139) (:id . 63))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 153)\n  (:start . 145) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.53) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100389@unknown@formal@none@1@S@Results and discussion@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 22)\n  (:start . 12) (:id . 44)))@@@1@3@((:identifiers (:sid . :s2.63) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5100399@unknown@formal@none@1@S@In the absence of the Transitive module, the Preliminary Score is used as the final likelihood ratio output by the predictor.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 32)\n  (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "Preliminary") (:end . 56)\n  (:start . 45) (:id . 51))\n ((:tag . "NN") (:stem . "score") (:form . "Score") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 94)\n  (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 100) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 107)\n  (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 110) (:start . 108)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 62))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 124)\n  (:start . 115) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 64)))@@@1@23@((:ncues ((:id . :x2.73.1) (:span 7 14)))\n (:nscopes ((:id . :x2.73.1) (:span 7 39)))\n (:identifiers (:sid . :s2.73) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100409@unknown@formal@none@1@S@The final likelihood ratio is then the product of the preliminary score calculated in panel A and the likelihood ratio output by the transitive module in panel B.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "preliminary") (:end . 65)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 82)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 118)\n  (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 125)\n  (:start . 119) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 143)\n  (:start . 133) (:id . 65))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 150)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 153) (:start . 151)\n  (:id . 67))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 159)\n  (:start . 154) (:id . 68))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 161) (:start . 160)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.83) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100419@unknown@formal@none@1@S@The evaluation of this ratio is difficult because not all true interactions are known.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 75)\n  (:start . 63) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.93) (:did . :1471-2105-8-239) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100429@unknown@formal@none@1@S@However, since the highest likelihood ratio for the expression datasets that we consider is 33, they are not sufficient on their own to predict interacting protein pairs with a posterior odds ratio above 1.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 62)\n  (:start . 52) (:id . 51))\n ((:tag . "VBZ") (:stem . "dataset") (:form . "datasets") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 119)\n  (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 128)\n  (:start . 123) (:id . 64))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "VB") (:stem . "predict") (:form . "predict") (:end . 143)\n  (:start . 136) (:id . 67))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 155)\n  (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 163)\n  (:start . 156) (:id . 69))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 169)\n  (:start . 164) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 174) (:start . 170)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 176) (:start . 175)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 186)\n  (:start . 177) (:id . 73))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 191) (:start . 187)\n  (:id . 74))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 197)\n  (:start . 192) (:id . 75))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 203)\n  (:start . 198) (:id . 76))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 205) (:start . 204)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 78)))@@@1@37@((:ncues ((:id . :x2.103.1) (:span 105 108)))\n (:nscopes ((:id . :x2.103.1) (:span 105 205)))\n (:identifiers (:sid . :s2.103) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100439@unknown@formal@none@1@S@Additionally, this combination circumvents possible problems of dependence between these features.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 30)\n  (:start . 19) (:id . 45))\n ((:tag . "VBZ") (:stem . "circumvent") (:form . "circumvents") (:end . 42)\n  (:start . 31) (:id . 46))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 51)\n  (:start . 43) (:id . 47))\n ((:tag . "NNS") (:stem . "problem") (:form . "problems") (:end . 60)\n  (:start . 52) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dependence") (:form . "dependence") (:end . 74)\n  (:start . 64) (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 82)\n  (:start . 75) (:id . 51))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 88) (:start . 83)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 97)\n  (:start . 89) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x2.113.1) (:span 43 51)))\n (:hscopes ((:id . :x2.113.1) (:span 43 97)))\n (:identifiers (:sid . :s2.113) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100449@unknown@formal@none@1@S@When investigated as a separate feature, the chi-square score of co-occurrence of domain pairs correlates well with the likelihood of interaction of protein pairs that contain these domains, with the highest chi-square score bin obtaining a likelihood ratio of 14, as shown in Figure 3A.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 17)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "chi-square") (:form . "chi-square") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "co-occurrence") (:form . "co-occurrence")\n  (:end . 78) (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 88)\n  (:start . 82) (:id . 55))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "correlate") (:form . "correlates") (:end . 105)\n  (:start . 95) (:id . 57))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 110) (:start . 106)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 130)\n  (:start . 120) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 62))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 145)\n  (:start . 134) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 64))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 156)\n  (:start . 149) (:id . 65))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 162)\n  (:start . 157) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 167) (:start . 163)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 175)\n  (:start . 168) (:id . 68))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 181)\n  (:start . 176) (:id . 69))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 189)\n  (:start . 182) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 195) (:start . 191)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 73))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 207)\n  (:start . 200) (:id . 74))\n ((:tag . "JJ") (:stem . "chi-square") (:form . "chi-square") (:end . 218)\n  (:start . 208) (:id . 75))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 224)\n  (:start . 219) (:id . 76))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 228) (:start . 225)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "obtain") (:form . "obtaining") (:end . 238)\n  (:start . 229) (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 240) (:start . 239)\n  (:id . 79))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 251)\n  (:start . 241) (:id . 80))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 257)\n  (:start . 252) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 260) (:start . 258)\n  (:id . 82))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 263) (:start . 261)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 264) (:start . 263)\n  (:id . 84))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 267) (:start . 265)\n  (:id . 85))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 273)\n  (:start . 268) (:id . 86))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 276) (:start . 274)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 283)\n  (:start . 277) (:id . 88))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 286) (:start . 284)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 287) (:start . 286)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s2.123) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100459@unknown@formal@none@1@S@The transitive module enhances the preliminary likelihood score (PS) (calculated using the group A modules) by considering the local topology of the resulting network which is assessed using the neighborhood topology score as detailed in the Methods section.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "preliminary") (:end . 46)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 57)\n  (:start . 47) (:id . 48))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 63) (:start . 58)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PS") (:form . "PS") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 80)\n  (:start . 70) (:id . 54))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 106)\n  (:start . 99) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 110) (:start . 108)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "consider") (:form . "considering") (:end . 122)\n  (:start . 111) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 132)\n  (:start . 127) (:id . 64))\n ((:tag . "NN") (:stem . "topology") (:form . "topology") (:end . 141)\n  (:start . 133) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 158)\n  (:start . 149) (:id . 68))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 166)\n  (:start . 159) (:id . 69))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 172)\n  (:start . 167) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 184)\n  (:start . 176) (:id . 72))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 190) (:start . 185)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n  (:id . 74))\n ((:tag . "NN") (:stem . "neighborhood") (:form . "neighborhood") (:end . 207)\n  (:start . 195) (:id . 75))\n ((:tag . "NN") (:stem . "topology") (:form . "topology") (:end . 216)\n  (:start . 208) (:id . 76))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 222)\n  (:start . 217) (:id . 77))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 225) (:start . 223)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "detail") (:form . "detailed") (:end . 234)\n  (:start . 226) (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 237) (:start . 235)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 241) (:start . 238)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Methods") (:form . "Methods") (:end . 249)\n  (:start . 242) (:id . 82))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 257)\n  (:start . 250) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 258) (:start . 257)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s2.133) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100469@unknown@formal@none@1@S@Independence of all modules used in our predictor was verified by calculating Pearson correlation coefficients for all pairs of modules.@(((:tag . "NN") (:stem . "independence") (:form . "Independence") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 77)\n  (:start . 66) (:id . 53))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 97)\n  (:start . 86) (:id . 55))\n ((:tag . "NNS") (:stem . "coefficient") (:form . "coefficients") (:end . 110)\n  (:start . 98) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 114) (:start . 111)\n  (:id . 57))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 124)\n  (:start . 119) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 135)\n  (:start . 128) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.143) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100479@unknown@formal@none@1@S@Table 3 summarizes the characteristics of 19 different predictors and shows accuracy measures.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "summarize") (:form . "summarizes") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "characteristic") (:form . "characteristics")\n  (:end . 38) (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 54)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "predictor") (:form . "predictors") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 75) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 84)\n  (:start . 76) (:id . 53))\n ((:tag . "NNS") (:stem . "measure") (:form . "measures") (:end . 93)\n  (:start . 85) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.153) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100489@unknown@formal@none@1@S@As the scores of the predictors increase, so do the number of interactions predicted above different posterior odds ratio thresholds (see lower portion of Table 3).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "predictor") (:form . "predictors") (:end . 31)\n  (:start . 21) (:id . 47))\n ((:tag . "VBP") (:stem . "increase") (:form . "increase") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "VB") (:stem . "do") (:form . "do") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 58)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 74)\n  (:start . 62) (:id . 55))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 84)\n  (:start . 75) (:id . 56))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 100)\n  (:start . 91) (:id . 58))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 110)\n  (:start . 101) (:id . 59))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 115) (:start . 111)\n  (:id . 60))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 121)\n  (:start . 116) (:id . 61))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 132)\n  (:start . 122) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 143) (:start . 138)\n  (:id . 65))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 151)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 160)\n  (:start . 155) (:id . 68))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 162) (:start . 161)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.163) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100499@unknown@formal@none@1@S@It is this predictor that is further analyzed in the next sections.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 45)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 66)\n  (:start . 58) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.173) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100509@unknown@formal@none@1@S@As shown in Table 4, the predictors trained on datasets containing 100 times more negatives than positives perform significantly better than those trained on datasets containing equal numbers of positives and negatives.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "predictor") (:form . "predictors") (:end . 35)\n  (:start . 25) (:id . 49))\n ((:tag . "VBN") (:stem . "train") (:form . "trained") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 55)\n  (:start . 47) (:id . 52))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 66)\n  (:start . 56) (:id . 53))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 96) (:start . 92)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 106)\n  (:start . 97) (:id . 59))\n ((:tag . "VBP") (:stem . "perform") (:form . "perform") (:end . 114)\n  (:start . 107) (:id . 60))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 128) (:start . 115) (:id . 61))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 135)\n  (:start . 129) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 140) (:start . 136)\n  (:id . 63))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 146)\n  (:start . 141) (:id . 64))\n ((:tag . "VBN") (:stem . "train") (:form . "trained") (:end . 154)\n  (:start . 147) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 157) (:start . 155)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 166)\n  (:start . 158) (:id . 67))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 177)\n  (:start . 167) (:id . 68))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 183)\n  (:start . 178) (:id . 69))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 191)\n  (:start . 184) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 204)\n  (:start . 195) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 218)\n  (:start . 209) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.183) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100519@unknown@formal@none@1@S@A criticism of randomly chosen negatives is that they will contain some true interactors.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "criticism") (:form . "criticism") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "interactor") (:form . "interactors") (:end . 88)\n  (:start . 77) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.193) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100529@unknown@formal@none@1@S@The localization-derived negative trained predictor tested on sets containing localization-derived negatives achieves a lower accuracy than that of the random negative trained predictor tested on a test set containing randomly-generated negatives (0.0686 +/- 0.0010 vs 0.0747 +/- 0.0022).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "localization-derived")\n  (:form . "localization-derived") (:end . 24) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 33)\n  (:start . 25) (:id . 44))\n ((:tag . "JJ") (:stem . "trained") (:form . "trained") (:end . 41)\n  (:start . 34) (:id . 45))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 51)\n  (:start . 42) (:id . 46))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 58) (:start . 52)\n  (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 61) (:start . 59)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 66) (:start . 62)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 77)\n  (:start . 67) (:id . 50))\n ((:tag . "JJ") (:stem . "localization-derived")\n  (:form . "localization-derived") (:end . 98) (:start . 78) (:id . 51))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 108)\n  (:start . 99) (:id . 52))\n ((:tag . "VBZ") (:stem . "achieve") (:form . "achieves") (:end . 117)\n  (:start . 109) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 54))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 125) (:start . 120)\n  (:id . 55))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 134)\n  (:start . 126) (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 139) (:start . 135)\n  (:id . 57))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 144) (:start . 140)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 158)\n  (:start . 152) (:id . 61))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 167)\n  (:start . 159) (:id . 62))\n ((:tag . "JJ") (:stem . "trained") (:form . "trained") (:end . 175)\n  (:start . 168) (:id . 63))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 185)\n  (:start . 176) (:id . 64))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 192)\n  (:start . 186) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 195) (:start . 193)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 197) (:start . 196)\n  (:id . 67))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 202) (:start . 198)\n  (:id . 68))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 206) (:start . 203)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 217)\n  (:start . 207) (:id . 70))\n ((:tag . "JJ") (:stem . "randomly-generated") (:form . "randomly-generated")\n  (:end . 236) (:start . 218) (:id . 71))\n ((:tag . "NNS") (:stem . "negative") (:form . "negatives") (:end . 246)\n  (:start . 237) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 248) (:start . 247)\n  (:id . 73))\n ((:tag . "CD") (:stem . "0.0686") (:form . "0.0686") (:end . 254)\n  (:start . 248) (:id . 74))\n ((:tag . "SYM") (:stem . "+/-") (:form . "+/-") (:end . 258) (:start . 255)\n  (:id . 75))\n ((:tag . "CD") (:stem . "0.0010") (:form . "0.0010") (:end . 265)\n  (:start . 259) (:id . 76))\n ((:tag . "IN") (:stem . "vs") (:form . "vs") (:end . 268) (:start . 266)\n  (:id . 77))\n ((:tag . "CD") (:stem . "0.0747") (:form . "0.0747") (:end . 275)\n  (:start . 269) (:id . 78))\n ((:tag . "SYM") (:stem . "+/-") (:form . "+/-") (:end . 279) (:start . 276)\n  (:id . 79))\n ((:tag . "CD") (:stem . "0.0022") (:form . "0.0022") (:end . 286)\n  (:start . 280) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 287) (:start . 286)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.203) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100539@unknown@formal@none@1@S@As shown in Figure 4A, all modules contribute positively (i.e. contribute a likelihood ratio greater than 1.0) to the prediction of a certain proportion of the interactions in the LR400 dataset.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "4a") (:form . "4A") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 34)\n  (:start . 27) (:id . 49))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 45)\n  (:start . 35) (:id . 50))\n ((:tag . "RB") (:stem . "positively") (:form . "positively") (:end . 56)\n  (:start . 46) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 73)\n  (:start . 63) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 86)\n  (:start . 76) (:id . 56))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 63))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 128)\n  (:start . 118) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 141)\n  (:start . 134) (:id . 67))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 152)\n  (:start . 142) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 172)\n  (:start . 160) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 73))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 185)\n  (:start . 180) (:id . 74))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 193)\n  (:start . 186) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.213) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100549@unknown@formal@none@1@S@Few interactions in the LR400 dataset are predicted on the basis of having interacting orthologs in worm or fly alone.@(((:tag . "JJ") (:stem . "few") (:form . "Few") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 74) (:start . 68)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 86)\n  (:start . 75) (:id . 55))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 96)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "worm") (:form . "worm") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 111) (:start . 108)\n  (:id . 60))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 117)\n  (:start . 112) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.223) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100559@unknown@formal@none@1@S@The Combined and Transitive modules contribute the most to the prediction of interactions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "combined") (:form . "Combined") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "transitive") (:form . "Transitive") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 89)\n  (:start . 77) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.233) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100569@unknown@formal@none@1@S@The right side of the curve illustrates the number of interactions that are predicted above likelihood ratios of 400 and more.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "curve") (:form . "curve") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "illustrate") (:form . "illustrates") (:end . 39)\n  (:start . 28) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 66)\n  (:start . 54) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 85)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "CD") (:stem . "400") (:form . "400") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.243) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100579@unknown@formal@none@1@S@As the posterior odds ratio increases, the false positive rate decreases and the ratio of the true positive rate divided by the false positive ratio increases.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "decrease") (:form . "decreases") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 107)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 112) (:start . 108)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 133)\n  (:start . 128) (:id . 65))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 142)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 148)\n  (:start . 143) (:id . 67))\n ((:tag . "NNS") (:stem . "increase") (:form . "increases") (:end . 158)\n  (:start . 149) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.253) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100589@unknown@formal@none@1@S@We estimated false positive rates for each of the datasets by comparing them two by two to one of the reference datasets, thus generating 4 to 6 different estimates of false positive rates for each computational dataset, as shown in Figure 6A (the two Lehner datasets were not compared to each other, which is why they have fewer FPR estimates).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "estimate") (:form . "estimated") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "compare") (:form . "comparing") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 111)\n  (:start . 102) (:id . 62))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 120)\n  (:start . 112) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 126) (:start . 122)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "generate") (:form . "generating") (:end . 137)\n  (:start . 127) (:id . 66))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 139) (:start . 138)\n  (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 68))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 154)\n  (:start . 145) (:id . 70))\n ((:tag . "NNS") (:stem . "estimate") (:form . "estimates") (:end . 164)\n  (:start . 155) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 173)\n  (:start . 168) (:id . 73))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 182)\n  (:start . 174) (:id . 74))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 188)\n  (:start . 183) (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 192) (:start . 189)\n  (:id . 76))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 197) (:start . 193)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n  (:end . 211) (:start . 198) (:id . 78))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 219)\n  (:start . 212) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 220) (:start . 219)\n  (:id . 80))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 223) (:start . 221)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 229)\n  (:start . 224) (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 232) (:start . 230)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 239)\n  (:start . 233) (:id . 84))\n ((:tag . "NN") (:stem . "6a") (:form . "6A") (:end . 242) (:start . 240)\n  (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 244) (:start . 243)\n  (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 247) (:start . 244)\n  (:id . 87))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 251) (:start . 248)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "Lehner") (:form . "Lehner") (:end . 258)\n  (:start . 252) (:id . 89))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 267)\n  (:start . 259) (:id . 90))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 272) (:start . 268)\n  (:id . 91))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 276) (:start . 273)\n  (:id . 92))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 285)\n  (:start . 277) (:id . 93))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 288) (:start . 286)\n  (:id . 94))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 293) (:start . 289)\n  (:id . 95))\n ((:tag . "NN") (:stem . "other") (:form . "other") (:end . 299)\n  (:start . 294) (:id . 96))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 300) (:start . 299)\n  (:id . 97))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 306)\n  (:start . 301) (:id . 98))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 309) (:start . 307)\n  (:id . 99))\n ((:tag . "WRB") (:stem . "why") (:form . "why") (:end . 313) (:start . 310)\n  (:id . 100))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 318) (:start . 314)\n  (:id . 101))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 323) (:start . 319)\n  (:id . 102))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 329) (:start . 324)\n  (:id . 103))\n ((:tag . "NN") (:stem . "fpr") (:form . "FPR") (:end . 333) (:start . 330)\n  (:id . 104))\n ((:tag . "NNS") (:stem . "estimate") (:form . "estimates") (:end . 343)\n  (:start . 334) (:id . 105))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 344) (:start . 343)\n  (:id . 106))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 345) (:start . 344)\n  (:id . 107)))@@@1@66@((:ncues ((:id . :x2.263.1) (:span 273 276)))\n (:nscopes ((:id . :x2.263.1) (:span 243 299)))\n (:identifiers (:sid . :s2.263) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100599@unknown@formal@none@1@S@The number and overlap of distinct proteins (shown in B) and distinct interactions (shown in C) are shown for the LR400 dataset, the Rhodes prediction dataset and the June 2006 version of the HPRD.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 69)\n  (:start . 61) (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 82)\n  (:start . 70) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 89) (:start . 84)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 99) (:start . 96)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 105)\n  (:start . 100) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 109) (:start . 106)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 65))\n ((:tag . "NN") (:stem . "lr400") (:form . "LR400") (:end . 119)\n  (:start . 114) (:id . 66))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 127)\n  (:start . 120) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Rhodes") (:form . "Rhodes") (:end . 139)\n  (:start . 133) (:id . 70))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 150)\n  (:start . 140) (:id . 71))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 158)\n  (:start . 151) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "June") (:form . "June") (:end . 171) (:start . 167)\n  (:id . 75))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 176) (:start . 172)\n  (:id . 76))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 184)\n  (:start . 177) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 196) (:start . 192)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s2.273) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100609@unknown@formal@none@1@S@Using such a threshold, the authors claim to predict 180 010 human interactions.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "VBP") (:stem . "claim") (:form . "claim") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "VB") (:stem . "predict") (:form . "predict") (:end . 52)\n  (:start . 45) (:id . 51))\n ((:tag . "CD") (:stem . "180") (:form . "180") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "CD") (:stem . "010") (:form . "010") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 66) (:start . 61)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 79)\n  (:start . 67) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.283) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100619@unknown@formal@none@1@S@Such examples include interactions that allow the formation of well-known protein complexes such as the proteasome, the MCM protein complex involved in the initiation of genome replication, replication factor C, the TBP/TAF complex (TBP-associated factors) and the EIF complex (eukaryotic translation initiation factors).@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 34)\n  (:start . 22) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "allow") (:form . "allow") (:end . 45) (:start . 40)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "well-known") (:form . "well-known") (:end . 73)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 91)\n  (:start . 82) (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 96) (:start . 92)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 99) (:start . 97)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 56))\n ((:tag . "NN") (:stem . "proteasome") (:form . "proteasome") (:end . 114)\n  (:start . 104) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "MCM") (:form . "MCM") (:end . 123) (:start . 120)\n  (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 131)\n  (:start . 124) (:id . 61))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 139)\n  (:start . 132) (:id . 62))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 148)\n  (:start . 140) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 151) (:start . 149)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 65))\n ((:tag . "NN") (:stem . "initiation") (:form . "initiation") (:end . 166)\n  (:start . 156) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n  (:id . 67))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 176)\n  (:start . 170) (:id . 68))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 188)\n  (:start . 177) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 70))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 201)\n  (:start . 190) (:id . 71))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 208)\n  (:start . 202) (:id . 72))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 210) (:start . 209)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 215) (:start . 212)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "TBP/TAF") (:form . "TBP/TAF") (:end . 223)\n  (:start . 216) (:id . 76))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 231)\n  (:start . 224) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 233) (:start . 232)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "tbp-associated") (:form . "TBP-associated")\n  (:end . 247) (:start . 233) (:id . 79))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 255)\n  (:start . 248) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 256) (:start . 255)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 260) (:start . 257)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 264) (:start . 261)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "EIF") (:form . "EIF") (:end . 268) (:start . 265)\n  (:id . 84))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 276)\n  (:start . 269) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 278) (:start . 277)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 288)\n  (:start . 278) (:id . 87))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 300)\n  (:start . 289) (:id . 88))\n ((:tag . "NN") (:stem . "initiation") (:form . "initiation") (:end . 311)\n  (:start . 301) (:id . 89))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 319)\n  (:start . 312) (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 320) (:start . 319)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 321) (:start . 320)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s2.293) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100629@unknown@formal@none@1@S@-TCPTP was predicted to interact with STAT6 at a posterior odds ratio of 4300.@(((:tag . "NNP") (:stem . "-TCPTP") (:form . "-TCPTP") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "stat6") (:form . "STAT6") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "CD") (:stem . "4300") (:form . "4300") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.303) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100639@unknown@formal@none@1@S@-Sam68 and Smad2 achieve a predicted posterior odds ratio of 32.@(((:tag . "NNP") (:stem . "-Sam68") (:form . "-Sam68") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Smad2") (:form . "Smad2") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "achieve") (:form . "achieve") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "odd") (:form . "odds") (:end . 51) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.313) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100649@unknown@formal@none@1@S@A subset of our novel predictions have been independently validated by identifying recent reports that experimentally investigated and confirmed that these protein pairs do interact.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 33)\n  (:start . 22) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 57) (:start . 44) (:id . 50))\n ((:tag . "VBN") (:stem . "validate") (:form . "validated") (:end . 67)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 82)\n  (:start . 71) (:id . 53))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 89)\n  (:start . 83) (:id . 54))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n  (:id . 56))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 117) (:start . 103) (:id . 57))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 130)\n  (:start . 118) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 144)\n  (:start . 135) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n  (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 155)\n  (:start . 150) (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 163)\n  (:start . 156) (:id . 63))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 169)\n  (:start . 164) (:id . 64))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 172) (:start . 170)\n  (:id . 65))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 181)\n  (:start . 173) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.323) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100659@unknown@formal@none@1@S@Additionally, some proteins were not recovered in the conversion between different identifiers.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "recover") (:form . "recovered") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "conversion") (:form . "conversion") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 72)\n  (:start . 65) (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "NNS") (:stem . "identifier") (:form . "identifiers") (:end . 94)\n  (:start . 83) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 55)))@@@1@14@((:ncues ((:id . :x2.333.1) (:span 33 36)))\n (:nscopes ((:id . :x2.333.1) (:span 14 94)))\n (:identifiers (:sid . :s2.333) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100669@unknown@formal@none@1@S@In addition, positive to negative ratios of 1:1 and 1:100 were considered.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "CD") (:stem . "1:1") (:form . "1:1") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1:100") (:form . "1:100") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 73)\n  (:start . 63) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.343) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100679@unknown@formal@none@1@S@The transparency of the method allows the straightforward determination of which features are most predictive of interaction at the level of the whole proteome as well as for individual protein pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "transparency") (:form . "transparency") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "straightforward") (:form . "straightforward")\n  (:end . 57) (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "determination") (:form . "determination")\n  (:end . 71) (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 80) (:start . 75)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 89)\n  (:start . 81) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 93) (:start . 90)\n  (:id . 54))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 98) (:start . 94)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 109)\n  (:start . 99) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 57))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 124)\n  (:start . 113) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 127) (:start . 125)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 60))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 137)\n  (:start . 132) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 150)\n  (:start . 145) (:id . 64))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 159)\n  (:start . 151) (:id . 65))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 162) (:start . 160)\n  (:id . 66))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 167) (:start . 163)\n  (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 170) (:start . 168)\n  (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 174) (:start . 171)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 185)\n  (:start . 175) (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 193)\n  (:start . 186) (:id . 71))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 199)\n  (:start . 194) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.353) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100689@unknown@formal@none@1@S@When a particular state of a feature occurs only in positive examples (known interacting proteins), the likelihoods are set to the highest non-infinite value of any state for that feature (to avoid infinite values).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 60)\n  (:start . 52) (:id . 52))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 88)\n  (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "likelihood") (:form . "likelihoods") (:end . 115)\n  (:start . 104) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 138)\n  (:start . 131) (:id . 66))\n ((:tag . "JJ") (:stem . "non-infinite") (:form . "non-infinite") (:end . 151)\n  (:start . 139) (:id . 67))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n  (:id . 69))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 164) (:start . 161)\n  (:id . 70))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 170)\n  (:start . 165) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 174) (:start . 171)\n  (:id . 72))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 179) (:start . 175)\n  (:id . 73))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 187)\n  (:start . 180) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 191) (:start . 189)\n  (:id . 76))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 197)\n  (:start . 192) (:id . 77))\n ((:tag . "JJ") (:stem . "infinite") (:form . "infinite") (:end . 206)\n  (:start . 198) (:id . 78))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 213)\n  (:start . 207) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s2.363) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100699@unknown@formal@none@1@S@Thus, between the two releases of the HPRD, there was a large increase in the number of interactions for this subset of proteins and this is likely to continue for at least the next few releases.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "release") (:form . "releases") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "HPRD") (:form . "HPRD") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 49) (:start . 44)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 53) (:start . 50)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 55) (:start . 54)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 61) (:start . 56)\n  (:id . 55))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 70)\n  (:start . 62) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 58))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 84)\n  (:start . 78) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 100)\n  (:start . 88) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n  (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 109) (:start . 105)\n  (:id . 63))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 116)\n  (:start . 110) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 128)\n  (:start . 120) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 67))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 137) (:start . 133)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 140) (:start . 138)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 147)\n  (:start . 141) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 150) (:start . 148)\n  (:id . 71))\n ((:tag . "VB") (:stem . "continue") (:form . "continue") (:end . 159)\n  (:start . 151) (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 163) (:start . 160)\n  (:id . 73))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 166) (:start . 164)\n  (:id . 74))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 172)\n  (:start . 167) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 181) (:start . 177)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 185) (:start . 182)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "release") (:form . "releases") (:end . 194)\n  (:start . 186) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x2.373.1) (:span 141 147)))\n (:hscopes ((:id . :x2.373.1) (:span 133 194)))\n (:identifiers (:sid . :s2.373) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100709@unknown@formal@none@1@S@Pearson correlations were calculated for all 56620761 transcript pairs and correlation values were grouped into 20 bins of increasing co-expression.@(((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "correlation") (:form . "correlations") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "CD") (:stem . "56620761") (:form . "56620761") (:end . 53)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "transcript") (:form . "transcript") (:end . 64)\n  (:start . 54) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 70) (:start . 65)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 86)\n  (:start . 75) (:id . 52))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 93)\n  (:start . 87) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 98) (:start . 94)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "group") (:form . "grouped") (:end . 106)\n  (:start . 99) (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 111) (:start . 107)\n  (:id . 56))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 114) (:start . 112)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 119) (:start . 115)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . "NN") (:stem . "co-expression") (:form . "co-expression")\n  (:end . 147) (:start . 134) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.383) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100719@unknown@formal@none@1@S@The orthology module has four additional bins: two bin for human pairs that have interacting paralogs in human (a medium and a low confidence bin which use the same definition as above for the model organisms), one bin for human pairs that have interacting homologs in more than one organism (these can be orthologs in yeast, worm or fly, or paralogs in human) and one bin for human pairs that have only non-interacting orthologs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "orthology") (:form . "orthology") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 70) (:start . 65)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 92)\n  (:start . 81) (:id . 57))\n ((:tag . "NNS") (:stem . "paralog") (:form . "paralogs") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 120)\n  (:start . 114) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 130) (:start . 127)\n  (:id . 66))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 141)\n  (:start . 131) (:id . 67))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 145) (:start . 142)\n  (:id . 68))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 151)\n  (:start . 146) (:id . 69))\n ((:tag . "VBP") (:stem . "use") (:form . "use") (:end . 155) (:start . 152)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 164) (:start . 160)\n  (:id . 72))\n ((:tag . "NN") (:stem . "definition") (:form . "definition") (:end . 175)\n  (:start . 165) (:id . 73))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 178) (:start . 176)\n  (:id . 74))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 184)\n  (:start . 179) (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 188) (:start . 185)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 77))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 198)\n  (:start . 193) (:id . 78))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 208)\n  (:start . 199) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 209) (:start . 208)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 210) (:start . 209)\n  (:id . 81))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 214) (:start . 211)\n  (:id . 82))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 218) (:start . 215)\n  (:id . 83))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 222) (:start . 219)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 228)\n  (:start . 223) (:id . 85))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 234)\n  (:start . 229) (:id . 86))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 239) (:start . 235)\n  (:id . 87))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 244) (:start . 240)\n  (:id . 88))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 256)\n  (:start . 245) (:id . 89))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 265)\n  (:start . 257) (:id . 90))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 268) (:start . 266)\n  (:id . 91))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 273) (:start . 269)\n  (:id . 92))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 278) (:start . 274)\n  (:id . 93))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 282) (:start . 279)\n  (:id . 94))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 291)\n  (:start . 283) (:id . 95))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 293) (:start . 292)\n  (:id . 96))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 298)\n  (:start . 293) (:id . 97))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 302) (:start . 299)\n  (:id . 98))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 305) (:start . 303)\n  (:id . 99))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 315)\n  (:start . 306) (:id . 100))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 318) (:start . 316)\n  (:id . 101))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 324)\n  (:start . 319) (:id . 102))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 325) (:start . 324)\n  (:id . 103))\n ((:tag . "NN") (:stem . "worm") (:form . "worm") (:end . 330) (:start . 326)\n  (:id . 104))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 333) (:start . 331)\n  (:id . 105))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 337) (:start . 334)\n  (:id . 106))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 338) (:start . 337)\n  (:id . 107))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 341) (:start . 339)\n  (:id . 108))\n ((:tag . "NNS") (:stem . "paralog") (:form . "paralogs") (:end . 350)\n  (:start . 342) (:id . 109))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 353) (:start . 351)\n  (:id . 110))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 359)\n  (:start . 354) (:id . 111))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 360) (:start . 359)\n  (:id . 112))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 364) (:start . 361)\n  (:id . 113))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 368) (:start . 365)\n  (:id . 114))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 372) (:start . 369)\n  (:id . 115))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 376) (:start . 373)\n  (:id . 116))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 382)\n  (:start . 377) (:id . 117))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 388)\n  (:start . 383) (:id . 118))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 393) (:start . 389)\n  (:id . 119))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 398) (:start . 394)\n  (:id . 120))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 403) (:start . 399)\n  (:id . 121))\n ((:tag . "JJ") (:stem . "non-interacting") (:form . "non-interacting")\n  (:end . 419) (:start . 404) (:id . 122))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 429)\n  (:start . 420) (:id . 123))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 430) (:start . 429)\n  (:id . 124)))@@@1@83@((:identifiers (:sid . :s2.393) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100729@unknown@formal@none@1@S@Additionally, Pfam 74 domain pairs known to interact from three-dimensional structures 75 were included in the highest Chi-square score bin.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "CD") (:stem . "74") (:form . "74") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "three-dimensional") (:form . "three-dimensional")\n  (:end . 75) (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 86)\n  (:start . 76) (:id . 53))\n ((:tag . "CD") (:stem . "75") (:form . "75") (:end . 89) (:start . 87)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 103)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 118)\n  (:start . 111) (:id . 59))\n ((:tag . "JJ") (:stem . "chi-square") (:form . "Chi-square") (:end . 129)\n  (:start . 119) (:id . 60))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 135)\n  (:start . 130) (:id . 61))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.403) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100739@unknown@formal@none@1@S@Disorder module@(((:tag . "NN") (:stem . "disorder") (:form . "Disorder") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 15) (:start . 9)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.413) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100749@unknown@formal@none@1@S@It does this by considering the local topology of the network predicted by the integration of the Group A modules as depicted in Figure 2.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "consider") (:form . "considering") (:end . 27)\n  (:start . 16) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "topology") (:form . "topology") (:end . 46)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 90)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Group") (:form . "Group") (:end . 103)\n  (:start . 98) (:id . 59))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 113)\n  (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "depict") (:form . "depicted") (:end . 125)\n  (:start . 117) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 135)\n  (:start . 129) (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 137) (:start . 136)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.423) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100759@unknown@formal@none@1@S@For a given set of neighbors, T increases as the interactions with these neighbors become more likely (as the sum of se increases).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "neighbor") (:form . "neighbors") (:end . 28)\n  (:start . 19) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 31) (:start . 30)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 41)\n  (:start . 32) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 61)\n  (:start . 49) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 72) (:start . 67)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "neighbor") (:form . "neighbors") (:end . 82)\n  (:start . 73) (:id . 56))\n ((:tag . "VBP") (:stem . "become") (:form . "become") (:end . 89)\n  (:start . 83) (:id . 57))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 101)\n  (:start . 95) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "NN") (:stem . "sum") (:form . "sum") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 64))\n ((:tag . "NN") (:stem . "se") (:form . "se") (:end . 119) (:start . 117)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "increase") (:form . "increases") (:end . 129)\n  (:start . 120) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s2.433) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100769@unknown@formal@none@1@S@Accuracy measurements@(((:tag . "NN") (:stem . "accuracy") (:form . "Accuracy") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 21)\n  (:start . 9) (:id . 43)))@@@1@2@((:identifiers (:sid . :s2.443) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|SectionTitle|)))@oe@9-2-2011
5100779@unknown@formal@none@1@S@The area under ROC curves is often used as a summary measure of accuracy.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "curve") (:form . "curves") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "summary") (:form . "summary") (:end . 52)\n  (:start . 45) (:id . 52))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 60)\n  (:start . 53) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 72)\n  (:start . 64) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.453) (:did . :1471-2105-8-239)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100789@unknown@formal@none@1@S@SCOPE outperformed a broad range of existing motif discovery algorithms on the same dataset by a statistically significant margin.@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "outperforme") (:form . "outperformed") (:end . 18)\n  (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "broad") (:form . "broad") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 91)\n  (:start . 84) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 110) (:start . 97) (:id . 58))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 122)\n  (:start . 111) (:id . 59))\n ((:tag . "NN") (:stem . "margin") (:form . "margin") (:end . 129)\n  (:start . 123) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.9) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100799@unknown@formal@none@1@S@Motif finding programs rely on a search algorithm to optimize a motif model (an abstract representation of a set of transcription factor binding sites).@(((:tag . "NN") (:stem . "motif") (:form . "Motif") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "rely") (:form . "rely") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "VB") (:stem . "optimize") (:form . "optimize") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "abstract") (:form . "abstract") (:end . 88)\n  (:start . 80) (:id . 57))\n ((:tag . "NN") (:stem . "representation") (:form . "representation")\n  (:end . 103) (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 129) (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 136)\n  (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 144)\n  (:start . 137) (:id . 65))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.19) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100809@unknown@formal@none@1@S@Even assuming that optimal parameter settings exist for a motif finding program for each specific situation, for the typical biologist looking to identify motifs in a set of uncharacterized sequences, acquiring such expertise is an onerous task.@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "assume") (:form . "assuming") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "optimal") (:form . "optimal") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "VBP") (:stem . "exist") (:form . "exist") (:end . 51) (:start . 46)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 97)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "situation") (:form . "situation") (:end . 107)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "typical") (:form . "typical") (:end . 124)\n  (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "biologist") (:form . "biologist") (:end . 134)\n  (:start . 125) (:id . 62))\n ((:tag . "VBG") (:stem . "look") (:form . "looking") (:end . 142)\n  (:start . 135) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 145) (:start . 143)\n  (:id . 64))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 154)\n  (:start . 146) (:id . 65))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 161)\n  (:start . 155) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 166) (:start . 165)\n  (:id . 68))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 170) (:start . 167)\n  (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "uncharacterized") (:form . "uncharacterized")\n  (:end . 189) (:start . 174) (:id . 71))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 199)\n  (:start . 190) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "acquire") (:form . "acquiring") (:end . 210)\n  (:start . 201) (:id . 74))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 215) (:start . 211)\n  (:id . 75))\n ((:tag . "NN") (:stem . "expertise") (:form . "expertise") (:end . 225)\n  (:start . 216) (:id . 76))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 228) (:start . 226)\n  (:id . 77))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 231) (:start . 229)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "onerous") (:form . "onerous") (:end . 239)\n  (:start . 232) (:id . 79))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 244) (:start . 240)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x3.29.1) (:span 5 13)))\n (:hscopes ((:id . :x3.29.1) (:span 5 107)))\n (:identifiers (:sid . :s3.29) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100819@unknown@formal@none@1@S@Ensemble methods, well known in the machine learning community 9, are typically composed of multiple methods comprising different search strategies (or the same search strategies with different initiation settings or random restarts) with a unified objective function.@(((:tag . "JJ") (:stem . "ensemble") (:form . "Ensemble") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "machine") (:form . "machine") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "VBG") (:stem . "learn") (:form . "learning") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "community") (:form . "community") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 79)\n  (:start . 70) (:id . 55))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 88)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 100)\n  (:start . 92) (:id . 58))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 108)\n  (:start . 101) (:id . 59))\n ((:tag . "VBG") (:stem . "comprise") (:form . "comprising") (:end . 119)\n  (:start . 109) (:id . 60))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 129)\n  (:start . 120) (:id . 61))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 136)\n  (:start . 130) (:id . 62))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 147)\n  (:start . 137) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 151) (:start . 149)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 160) (:start . 156)\n  (:id . 67))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 167)\n  (:start . 161) (:id . 68))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 178)\n  (:start . 168) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 183) (:start . 179)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 193)\n  (:start . 184) (:id . 71))\n ((:tag . "NN") (:stem . "initiation") (:form . "initiation") (:end . 204)\n  (:start . 194) (:id . 72))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 213)\n  (:start . 205) (:id . 73))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 216) (:start . 214)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 223)\n  (:start . 217) (:id . 75))\n ((:tag . "NNS") (:stem . "restart") (:form . "restarts") (:end . 232)\n  (:start . 224) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 233) (:start . 232)\n  (:id . 77))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 238) (:start . 234)\n  (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 240) (:start . 239)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "unified") (:form . "unified") (:end . 248)\n  (:start . 241) (:id . 80))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 258)\n  (:start . 249) (:id . 81))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 267)\n  (:start . 259) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 268) (:start . 267)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s3.39) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100829@unknown@formal@none@1@S@Rather than randomly restarting the same search algorithm or comparing multiple search strategies that all search for the same global optimum (and are potentially vulnerable to the same local optima), our algorithm assumes that the ""biological significance surface"" primarily consists of three local optima, and that one of these peaks represents the global optimum.@(((:tag . "RB") (:stem . "rather") (:form . "Rather") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "VBG") (:stem . "restart") (:form . "restarting") (:end . 31)\n  (:start . 21) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "compare") (:form . "comparing") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 79)\n  (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 86)\n  (:start . 80) (:id . 53))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 97)\n  (:start . 87) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n  (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 106) (:start . 103)\n  (:id . 56))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 113)\n  (:start . 107) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . 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"of") (:end . 289) (:start . 287)\n  (:id . 88))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 295)\n  (:start . 290) (:id . 89))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 301)\n  (:start . 296) (:id . 90))\n ((:tag . "NNS") (:stem . "optimum") (:form . "optima") (:end . 308)\n  (:start . 302) (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 309) (:start . 308)\n  (:id . 92))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 313) (:start . 310)\n  (:id . 93))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 318) (:start . 314)\n  (:id . 94))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 322) (:start . 319)\n  (:id . 95))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 325) (:start . 323)\n  (:id . 96))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 331)\n  (:start . 326) (:id . 97))\n ((:tag . "NNS") (:stem . "peak") (:form . "peaks") (:end . 337)\n  (:start . 332) (:id . 98))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 348)\n  (:start . 338) (:id . 99))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 352) (:start . 349)\n  (:id . 100))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 359)\n  (:start . 353) (:id . 101))\n ((:tag . "NN") (:stem . "optimum") (:form . "optimum") (:end . 367)\n  (:start . 360) (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 368) (:start . 367)\n  (:id . 103)))@@@1@62@((:hcues ((:id . :x3.49.1) (:span 215 222)) ((:id . :x3.49.2) (:span 151 162))\n  ((:id . :x3.49.3) (:span 58 60)))\n (:ncues ((:id . :x3.49.4) (:span 0 11)))\n (:hscopes ((:id . :x3.49.1) (:span 215 367))\n  ((:id . :x3.49.2) (:span 151 173)) ((:id . :x3.49.3) (:span 12 199)))\n (:nscopes ((:id . :x3.49.4) (:span 0 199)))\n (:identifiers (:sid . :s3.49) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100839@unknown@formal@none@1@S@The ultimate goal of a motif finder is to identify the specific subsequences Û in U that act as binding sites for the transcription factor(s) that regulate G.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "ultimate") (:form . "ultimate") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "goal") (:form . "goal") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "finder") (:form . "finder") (:end . 35)\n  (:start . 29) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 63)\n  (:start . 55) (:id . 53))\n ((:tag . "NNS") (:stem . "subsequence") (:form . "subsequences") (:end . 76)\n  (:start . 64) (:id . 54))\n ((:tag . "VBP") (:stem . "û") (:form . "Û") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "act") (:form . "act") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 95) (:start . 93)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 103)\n  (:start . 96) (:id . 61))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 109)\n  (:start . 104) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 64))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 131) (:start . 118) (:id . 65))\n ((:tag . "NN") (:stem . "factor(s)") (:form . "factor(s)") (:end . 141)\n  (:start . 132) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 146) (:start . 142)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "regulate") (:form . "regulate") (:end . 155)\n  (:start . 147) (:id . 68))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 157) (:start . 156)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.59) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100849@unknown@formal@none@1@S@BEAM and SPACER are run independently; PRISM runs on the top 100 motifs output by BEAM.@(((:tag . "NN") (:stem . "beam") (:form . "BEAM") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "SPACER") (:form . "SPACER") (:end . 15)\n  (:start . 9) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "run") (:form . "run") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 37) (:start . 24) (:id . 47))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "prism") (:form . "PRISM") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "run") (:form . "runs") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "BEAM") (:form . "BEAM") (:end . 86) (:start . 82)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.69) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100859@unknown@formal@none@1@S@In general, we seek to maximize -log(p(M = m)).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "seek") (:form . "seek") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "VB") (:stem . "maximize") (:form . "maximize") (:end . 31)\n  (:start . 23) (:id . 48))\n ((:tag . "JJ") (:stem . "-log(p(M") (:form . "-log(p(M") (:end . 40)\n  (:start . 32) (:id . 49))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.79) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100869@unknown@formal@none@1@S@In contrast, we have proposed that all characters should not be treated equally, but should be penalized in proportion to the information provided by them 1112.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "character") (:form . "characters") (:end . 49)\n  (:start . 39) (:id . 50))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . "RB") (:stem . "equally") (:form . "equally") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 91)\n  (:start . 85) (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "penalize") (:form . "penalized") (:end . 104)\n  (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 118)\n  (:start . 108) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 121) (:start . 119)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 64))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 137)\n  (:start . 126) (:id . 65))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 146)\n  (:start . 138) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 149) (:start . 147)\n  (:id . 67))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 154) (:start . 150)\n  (:id . 68))\n ((:tag . "CD") (:stem . "1112") (:form . "1112") (:end . 159) (:start . 155)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x3.89.1) (:span 85 91)) ((:id . :x3.89.2) (:span 50 56))\n  ((:id . :x3.89.4) (:span 21 29)))\n (:ncues ((:id . :x3.89.3) (:span 57 60)))\n (:hscopes ((:id . :x3.89.1) (:span 85 154)) ((:id . :x3.89.2) (:span 35 79))\n  ((:id . :x3.89.4) (:span 21 154)))\n (:nscopes ((:id . :x3.89.3) (:span 35 79)))\n (:identifiers (:sid . :s3.89) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100879@unknown@formal@none@1@S@These objective functions were as follows: position bias (based on the Kolmogorov-Smirnov, or KS, statistic), overrepresentation (a Poisson-based measure based on how often a motif occurs in U) and coverage (a Poisson-based measure based on how many upstream sequences contain the motif).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Kolmogorov-Smirnov") (:form . "Kolmogorov-Smirnov")\n  (:end . 89) (:start . 71) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "KS") (:form . "KS") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "statistic") (:form . "statistic") (:end . 107)\n  (:start . 98) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n  (:end . 128) (:start . 110) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "poisson-based") (:form . "Poisson-based")\n  (:end . 145) (:start . 132) (:id . 66))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 153)\n  (:start . 146) (:id . 67))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 159)\n  (:start . 154) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 162) (:start . 160)\n  (:id . 69))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 166) (:start . 163)\n  (:id . 70))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 172)\n  (:start . 167) (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 174) (:start . 173)\n  (:id . 72))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 180)\n  (:start . 175) (:id . 73))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 187)\n  (:start . 181) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 190) (:start . 188)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 197) (:start . 194)\n  (:id . 78))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 206)\n  (:start . 198) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 208) (:start . 207)\n  (:id . 80))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 209) (:start . 208)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "poisson-based") (:form . "Poisson-based")\n  (:end . 223) (:start . 210) (:id . 82))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 231)\n  (:start . 224) (:id . 83))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 237)\n  (:start . 232) (:id . 84))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 240) (:start . 238)\n  (:id . 85))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 244) (:start . 241)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 249) (:start . 245)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 258)\n  (:start . 250) (:id . 88))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 268)\n  (:start . 259) (:id . 89))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 276)\n  (:start . 269) (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 280) (:start . 277)\n  (:id . 91))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 286)\n  (:start . 281) (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 287) (:start . 286)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s3.99) (:did . :1471-2105-8-249) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5100889@unknown@formal@none@1@S@Non-degenerate 6-mers from S. cerevisiae were scored according to Sig scores based on (a) Overrepresentation, (b) Overrepresentation-KS, (c) Coverage and (d) KS metrics of statistical significance.@(((:tag . "JJ") (:stem . "non-degenerate") (:form . "Non-degenerate")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "6-mer") (:form . "6-mers") (:end . 21)\n  (:start . 15) (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "score") (:form . "scored") (:end . 52)\n  (:start . 46) (:id . 48))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 62)\n  (:start . 53) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sig") (:form . "Sig") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 76)\n  (:start . 70) (:id . 52))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 82) (:start . 77)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Overrepresentation") (:form . "Overrepresentation")\n  (:end . 108) (:start . 90) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "NN") (:stem . "overrepresentation-ks")\n  (:form . "Overrepresentation-KS") (:end . 135) (:start . 114) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Coverage") (:form . "Coverage") (:end . 149)\n  (:start . 141) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 70))\n ((:tag . "LS") (:stem . "d") (:form . "d") (:end . 156) (:start . 155)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 72))\n ((:tag . "NN") (:stem . "ks") (:form . "KS") (:end . 160) (:start . 158)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "metric") (:form . "metrics") (:end . 168)\n  (:start . 161) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 183)\n  (:start . 172) (:id . 76))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 196)\n  (:start . 184) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.109) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100899@unknown@formal@none@1@S@We used the overrepresentation objective function for the other species, as our upstream definitions for those species were of variable length due to the available annotations.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n  (:end . 30) (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "objective") (:form . "objective") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 49)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 63) (:start . 58)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . "NNS") (:stem . "definition") (:form . "definitions") (:end . 100)\n  (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n  (:id . 57))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 110)\n  (:start . 105) (:id . 58))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 118)\n  (:start . 111) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 123) (:start . 119)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 135)\n  (:start . 127) (:id . 62))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 142)\n  (:start . 136) (:id . 63))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 146) (:start . 143)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 163)\n  (:start . 154) (:id . 67))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 175)\n  (:start . 164) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.119) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100909@unknown@formal@none@1@S@Performance at different overrepresentation Sig values on synthetic data.@(((:tag . "NNP") (:stem . "Performance") (:form . "Performance") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n  (:end . 43) (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "sig") (:form . "Sig") (:end . 47) (:start . 44)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 54)\n  (:start . 48) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 57) (:start . 55)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 67)\n  (:start . 58) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 72) (:start . 68)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.129) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100919@unknown@formal@none@1@S@SCOPE's reported accuracy was significantly higher than any of its component algorithms (Table 1).@(((:tag . "NN") (:stem . "scope") (:form . "SCOPE") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 43) (:start . 30) (:id . 47))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 50) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 87)\n  (:start . 77) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.139) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100929@unknown@formal@none@1@S@Average and standard error of sensitivity and PPV for the component algorithms of SCOPE on all 78 regulons@(((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 41)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PPV") (:form . "PPV") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 78)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 106)\n  (:start . 98) (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.149) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|FigureLegend|)))@oe@9-2-2011
5100939@unknown@formal@none@1@S@One rule that may prove effective is to weight the output of each algorithm according to (for example) the frequency of occurrence of each class of motif (non-degenerate, short degenerate or long degenerate) in the species or by learning the appropriate weights on a representative training set, creating, in effect, a Naïve Bayesian Network.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "VB") (:stem . "prove") (:form . "prove") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . 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"on") (:end . 264) (:start . 262)\n  (:id . 89))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 266) (:start . 265)\n  (:id . 90))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 281) (:start . 267) (:id . 91))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 290)\n  (:start . 282) (:id . 92))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 294) (:start . 291)\n  (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 295) (:start . 294)\n  (:id . 94))\n ((:tag . "VBG") (:stem . "create") (:form . "creating") (:end . 304)\n  (:start . 296) (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 305) (:start . 304)\n  (:id . 96))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 308) (:start . 306)\n  (:id . 97))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 315)\n  (:start . 309) (:id . 98))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 316) (:start . 315)\n  (:id . 99))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 318) (:start . 317)\n  (:id . 100))\n ((:tag . "NNP") (:stem . "Naïve") (:form . "Naïve") (:end . 324)\n  (:start . 319) (:id . 101))\n ((:tag . "NNP") (:stem . "Bayesian") (:form . "Bayesian") (:end . 333)\n  (:start . 325) (:id . 102))\n ((:tag . "NNP") (:stem . "Network") (:form . "Network") (:end . 341)\n  (:start . 334) (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 342) (:start . 341)\n  (:id . 104)))@@@1@63@((:hcues ((:id . :x3.159.1) (:span 14 17)))\n (:hscopes ((:id . :x3.159.1) (:span 14 33)))\n (:identifiers (:sid . :s3.159) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100949@unknown@formal@none@1@S@Motif model abbreviations: cons = consensus; PWM = position weight matrix; mis = consensus with predefined number of allowed non-position-specific mismatches.@(((:tag . "NN") (:stem . "motif") (:form . "Motif") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n  (:end . 25) (:start . 12) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "con") (:form . "cons") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PWM") (:form . "PWM") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "=") (:form . "=") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 59)\n  (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "mis") (:form . "mis") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "=") (:form . "=") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 90)\n  (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "predefine") (:form . "predefined") (:end . 106)\n  (:start . 96) (:id . 60))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 113)\n  (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "allow") (:form . "allowed") (:end . 124)\n  (:start . 117) (:id . 63))\n ((:tag . "JJ") (:stem . "non-position-specific")\n  (:form . "non-position-specific") (:end . 146) (:start . 125) (:id . 64))\n ((:tag . "NNS") (:stem . "mismatch") (:form . "mismatches") (:end . 157)\n  (:start . 147) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.169) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100959@unknown@formal@none@1@S@Performance comparisons@(((:tag . "NNP") (:stem . "Performance") (:form . "Performance") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 23)\n  (:start . 12) (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.179) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|FigureLegend|)))@oe@9-2-2011
5100969@unknown@formal@none@1@S@By these measures, SCOPE was the only program that scored highly in both sensitivity and PPV (ranking first and second respectively).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "measure") (:form . "measures") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 45)\n  (:start . 38) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "score") (:form . "scored") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 84)\n  (:start . 73) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "PPV") (:form . "PPV") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "rank") (:form . "ranking") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 107)\n  (:start . 102) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 118)\n  (:start . 112) (:id . 63))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 131)\n  (:start . 119) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.189) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100979@unknown@formal@none@1@S@Therefore, sets of genes identified from co-expression data may often contain multiple extraneous upstream sequences.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 35)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "co-expression") (:form . "co-expression")\n  (:end . 54) (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "JJ") (:stem . "extraneous") (:form . "extraneous") (:end . 97)\n  (:start . 87) (:id . 55))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 106)\n  (:start . 98) (:id . 56))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 116)\n  (:start . 107) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x3.199.1) (:span 60 63)))\n (:hscopes ((:id . :x3.199.1) (:span 60 116)))\n (:identifiers (:sid . :s3.199) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100989@unknown@formal@none@1@S@Increasing quantities of randomly selected upstream regions were added to each regulon.@(((:tag . "VBG") (:stem . "increase") (:form . "Increasing") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "quantity") (:form . "quantities") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 42)\n  (:start . 34) (:id . 46))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 51)\n  (:start . 43) (:id . 47))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 59)\n  (:start . 52) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 64) (:start . 60)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 70) (:start . 65)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 78) (:start . 74)\n  (:id . 52))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 86)\n  (:start . 79) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.209) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5100999@unknown@formal@none@1@S@Conversely, the PWM-based methods have an apparently more powerful motif model 17, but their search strategies cannot guarantee optimality and often terminate at local optima.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "pwm-based") (:form . "PWM-based") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "RB") (:stem . "apparently") (:form . "apparently") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "powerful") (:form . "powerful") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 78) (:start . 73)\n  (:id . 53))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 92)\n  (:start . 87) (:id . 57))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 99)\n  (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 110)\n  (:start . 100) (:id . 59))\n ((:tag . "JJ") (:stem . "cannot") (:form . "cannot") (:end . 117)\n  (:start . 111) (:id . 60))\n ((:tag . "VB") (:stem . "guarantee") (:form . "guarantee") (:end . 127)\n  (:start . 118) (:id . 61))\n ((:tag . "NN") (:stem . "optimality") (:form . "optimality") (:end . 138)\n  (:start . 128) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 63))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 148)\n  (:start . 143) (:id . 64))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 158)\n  (:start . 149) (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 161) (:start . 159)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 167)\n  (:start . 162) (:id . 67))\n ((:tag . "NNS") (:stem . "optimum") (:form . "optima") (:end . 174)\n  (:start . 168) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 69)))@@@1@28@((:ncues ((:id . :x3.219.1) (:span 111 117)))\n (:nscopes ((:id . :x3.219.1) (:span 111 138)))\n (:identifiers (:sid . :s3.219) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101009@unknown@formal@none@1@S@In this light, SCOPE can be seen as leveraging the second key observation by embracing the No Free Lunch Theorem:: rather than boost average performance by taking the average results of three general purpose algorithms, SCOPE uses highly specialized algorithms and assumes each will perform strongly on some regulons and weakly on others (and that the unified scoring metric can tell the difference).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "light") (:form . "light") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 32) (:start . 28)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 35) (:start . 33)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "leverage") (:form . "leveraging") (:end . 46)\n  (:start . 36) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 73)\n  (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "embrace") (:form . "embracing") (:end . 86)\n  (:start . 77) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "No") (:form . "No") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Free") (:form . "Free") (:end . 98) (:start . 94)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Lunch") (:form . "Lunch") (:end . 104)\n  (:start . 99) (:id . 61))\n ((:tag . "NNP") (:stem . "Theorem") (:form . "Theorem") (:end . 112)\n  (:start . 105) (:id . 62))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 114) (:start . 113)\n  (:id . 64))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 121)\n  (:start . 115) (:id . 65))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 126) (:start . 122)\n  (:id . 66))\n ((:tag . "VB") (:stem . "boost") (:form . "boost") (:end . 132)\n  (:start . 127) (:id . 67))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 140)\n  (:start . 133) (:id . 68))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 152)\n  (:start . 141) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "take") (:form . "taking") (:end . 162)\n  (:start . 156) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 174)\n  (:start . 167) (:id . 73))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 182)\n  (:start . 175) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 75))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 191)\n  (:start . 186) (:id . 76))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 199)\n  (:start . 192) (:id . 77))\n ((:tag . "NN") (:stem . "purpose") (:form . "purpose") (:end . 207)\n  (:start . 200) (:id . 78))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 218)\n  (:start . 208) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 219) (:start . 218)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 225)\n  (:start . 220) (:id . 81))\n ((:tag . "NNS") (:stem . "use") (:form . "uses") (:end . 230) (:start . 226)\n  (:id . 82))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 237)\n  (:start . 231) (:id . 83))\n ((:tag . "VBN") (:stem . "specialize") (:form . "specialized") (:end . 249)\n  (:start . 238) (:id . 84))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 260)\n  (:start . 250) (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 264) (:start . 261)\n  (:id . 86))\n ((:tag . "VBZ") (:stem . "assume") (:form . "assumes") (:end . 272)\n  (:start . 265) (:id . 87))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 277) (:start . 273)\n  (:id . 88))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 282) (:start . 278)\n  (:id . 89))\n ((:tag . "VB") (:stem . "perform") (:form . "perform") (:end . 290)\n  (:start . 283) (:id . 90))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 299)\n  (:start . 291) (:id . 91))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 302) (:start . 300)\n  (:id . 92))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 307) (:start . 303)\n  (:id . 93))\n ((:tag . "NNS") (:stem . "regulon") (:form . "regulons") (:end . 316)\n  (:start . 308) (:id . 94))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 320) (:start . 317)\n  (:id . 95))\n ((:tag . "RB") (:stem . "weakly") (:form . "weakly") (:end . 327)\n  (:start . 321) (:id . 96))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 330) (:start . 328)\n  (:id . 97))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 337)\n  (:start . 331) (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . 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"difference") (:end . 398)\n  (:start . 388) (:id . 109))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 399) (:start . 398)\n  (:id . 110))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 400) (:start . 399)\n  (:id . 111)))@@@1@70@((:hcues ((:id . :x3.229.1) (:span 265 272))\n  ((:id . :x3.229.3) (:span 21 24)))\n (:ncues ((:id . :x3.229.2) (:span 115 126)))\n (:hscopes ((:id . :x3.229.1) (:span 265 399))\n  ((:id . :x3.229.3) (:span 15 112)))\n (:nscopes ((:id . :x3.229.2) (:span 115 218)))\n (:identifiers (:sid . :s3.229) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101019@unknown@formal@none@1@S@This observation could be leveraged by a search algorithm that explicitly searches for motifs matching this unique structure.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 22) (:start . 17)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "leverage") (:form . "leveraged") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "RB") (:stem . "explicitly") (:form . "explicitly") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "VBZ") (:stem . "search") (:form . "searches") (:end . 82)\n  (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 93)\n  (:start . 87) (:id . 55))\n ((:tag . "VBG") (:stem . "match") (:form . "matching") (:end . 102)\n  (:start . 94) (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 107) (:start . 103)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 114)\n  (:start . 108) (:id . 58))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 124)\n  (:start . 115) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x3.239.1) (:span 17 22)))\n (:hscopes ((:id . :x3.239.1) (:span 17 124)))\n (:identifiers (:sid . :s3.239) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101029@unknown@formal@none@1@S@An important factor to consider when taking the best of multiple runs is the relative size of the search space.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "VB") (:stem . "consider") (:form . "consider") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "take") (:form . "taking") (:end . 43) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "run") (:form . "runs") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 104)\n  (:start . 98) (:id . 60))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 110)\n  (:start . 105) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.249) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101039@unknown@formal@none@1@S@Whereas previous performance comparisons attempt to optimize the parameters of the programs in question 467 or allow expert users to tune their own programs and manually filter both the input and output 5 we intentionally made our comparisons between programs without manually optimizing any parameters for any species so as to emulate typical use conditions.@(((:tag . "IN") (:stem . "whereas") (:form . "Whereas") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 28)\n  (:start . 17) (:id . 44))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 40)\n  (:start . 29) (:id . 45))\n ((:tag . "VBP") (:stem . "attempt") (:form . "attempt") (:end . 48)\n  (:start . 41) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 47))\n ((:tag . 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"any") (:end . 310) (:start . 307)\n  (:id . 88))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 318)\n  (:start . 311) (:id . 89))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 321) (:start . 319)\n  (:id . 90))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 324) (:start . 322)\n  (:id . 91))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 327) (:start . 325)\n  (:id . 92))\n ((:tag . "VB") (:stem . "emulate") (:form . "emulate") (:end . 335)\n  (:start . 328) (:id . 93))\n ((:tag . "JJ") (:stem . "typical") (:form . "typical") (:end . 343)\n  (:start . 336) (:id . 94))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 347) (:start . 344)\n  (:id . 95))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 358)\n  (:start . 348) (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 359) (:start . 358)\n  (:id . 97)))@@@1@56@((:ncues ((:id . :x3.259.1) (:span 260 267)))\n (:nscopes ((:id . :x3.259.1) (:span 260 358)))\n (:identifiers (:sid . :s3.259) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101049@unknown@formal@none@1@S@Whereas a background set of promoter regions is easy to identify, it is not clear how to define a reasonable genomic sample of enhancers.@(((:tag . "IN") (:stem . "whereas") (:form . "Whereas") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "easy") (:form . "easy") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 81) (:start . 76)\n  (:id . 57))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 59))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 95)\n  (:start . 89) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "reasonable") (:form . "reasonable") (:end . 108)\n  (:start . 98) (:id . 62))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 116)\n  (:start . 109) (:id . 63))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 123)\n  (:start . 117) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "enhancer") (:form . "enhancers") (:end . 136)\n  (:start . 127) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x3.269.1) (:span 72 81)))\n (:hscopes ((:id . :x3.269.1) (:span 72 136)))\n (:identifiers (:sid . :s3.269) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101059@unknown@formal@none@1@S@By dividing the search space into tractable domains, SCOPE mitigates the potential liabilities associated with ensemble methods, resulting in a program that is capable of finding cis-regulatory elements of arbitrary length, degree of degeneracy, motif orientation and frequency of occurrence.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "divide") (:form . "dividing") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "tractable") (:form . "tractable") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "SCOPE") (:form . "SCOPE") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "mitigate") (:form . "mitigates") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "liability") (:form . "liabilities") (:end . 94)\n  (:start . 83) (:id . 55))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 105)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "ensemble") (:form . "ensemble") (:end . 119)\n  (:start . 111) (:id . 58))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 127)\n  (:start . 120) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 138)\n  (:start . 129) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 143) (:start . 142)\n  (:id . 63))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 151)\n  (:start . 144) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 156) (:start . 152)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 159) (:start . 157)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "capable") (:form . "capable") (:end . 167)\n  (:start . 160) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "find") (:form . "finding") (:end . 178)\n  (:start . 171) (:id . 69))\n ((:tag . "JJ") (:stem . "cis-regulatory") (:form . "cis-regulatory")\n  (:end . 193) (:start . 179) (:id . 70))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 202)\n  (:start . 194) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "arbitrary") (:form . "arbitrary") (:end . 215)\n  (:start . 206) (:id . 73))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 222)\n  (:start . 216) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n  (:id . 75))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 230)\n  (:start . 224) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 233) (:start . 231)\n  (:id . 77))\n ((:tag . "NN") (:stem . "degeneracy") (:form . "degeneracy") (:end . 244)\n  (:start . 234) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 245) (:start . 244)\n  (:id . 79))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 251)\n  (:start . 246) (:id . 80))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 263)\n  (:start . 252) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 267) (:start . 264)\n  (:id . 82))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 277)\n  (:start . 268) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 280) (:start . 278)\n  (:id . 84))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 291)\n  (:start . 281) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 292) (:start . 291)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s3.279) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101069@unknown@formal@none@1@S@As in Hu et al. 4, we define accuracy to be the Phi score between the known and predicted binding sites.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Hu") (:form . "Hu") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 15) (:start . 12)\n  (:id . 46))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 21) (:start . 19)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "define") (:form . "define") (:end . 28)\n  (:start . 22) (:id . 50))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 37)\n  (:start . 29) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 43) (:start . 41)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Phi") (:form . "Phi") (:end . 51) (:start . 48)\n  (:id . 55))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 57) (:start . 52)\n  (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 65)\n  (:start . 58) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 75) (:start . 70)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 89)\n  (:start . 80) (:id . 61))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 97)\n  (:start . 90) (:id . 62))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 103) (:start . 98)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.289) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101079@unknown@formal@none@1@S@The most common statistical test in motif finding is based on overrepresentation, which can be roughly defined as the probability that a motif m that is observed C(m) times in the regulon would occur at least C(m) times in a random collection of the same number of genes.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "overrepresentation") (:form . "overrepresentation")\n  (:end . 80) (:start . 62) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "RB") (:stem . "roughly") (:form . "roughly") (:end . 102)\n  (:start . 95) (:id . 58))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 129)\n  (:start . 118) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 142)\n  (:start . 137) (:id . 65))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 152) (:start . 150)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 161)\n  (:start . 153) (:id . 69))\n ((:tag . "JJ") (:stem . "C(m)") (:form . "C(m)") (:end . 166) (:start . 162)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 172)\n  (:start . 167) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 73))\n ((:tag . "NN") (:stem . "regulon") (:form . "regulon") (:end . 187)\n  (:start . 180) (:id . 74))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 193)\n  (:start . 188) (:id . 75))\n ((:tag . "VB") (:stem . "occur") (:form . "occur") (:end . 199)\n  (:start . 194) (:id . 76))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 202) (:start . 200)\n  (:id . 77))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 208)\n  (:start . 203) (:id . 78))\n ((:tag . "CD") (:stem . "C(m)") (:form . "C(m)") (:end . 213) (:start . 209)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 219)\n  (:start . 214) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 224) (:start . 223)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 231)\n  (:start . 225) (:id . 83))\n ((:tag . "NN") (:stem . "collection") (:form . "collection") (:end . 242)\n  (:start . 232) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 245) (:start . 243)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 249) (:start . 246)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 254) (:start . 250)\n  (:id . 87))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 261)\n  (:start . 255) (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 264) (:start . 262)\n  (:id . 89))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 270)\n  (:start . 265) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s3.299) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101089@unknown@formal@none@1@S@Transcription factors often require their binding sites to be located in a restricted range relative to the start of transcription.@(((:tag . "NNP") (:stem . "Transcription") (:form . "Transcription")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 21)\n  (:start . 14) (:id . 43))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 27) (:start . 22)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 35)\n  (:start . 28) (:id . 45))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 41)\n  (:start . 36) (:id . 46))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 49)\n  (:start . 42) (:id . 47))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 55) (:start . 50)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 69)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 85)\n  (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 91) (:start . 86)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "start") (:form . "start") (:end . 113)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 130) (:start . 117) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.309) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101099@unknown@formal@none@1@S@The reference sample Y is defined as the set of starting positions of m in all upstream regions in the genome.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "y") (:form . "Y") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "start") (:form . "starting") (:end . 56)\n  (:start . 48) (:id . 52))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 87)\n  (:start . 79) (:id . 58))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 95)\n  (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 61))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 109)\n  (:start . 103) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.319) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101109@unknown@formal@none@1@S@Such an assumption may be overly generous – as the TBP example above makes clear, the transcriptional machinery of a cell is clearly able to differentiate between the two strands.@(((:tag . "PDT") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "RB") (:stem . "overly") (:form . "overly") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "JJ") (:stem . "generous") (:form . "generous") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "–") (:form . "–") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "TBP") (:form . "TBP") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 62)\n  (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "make") (:form . "makes") (:end . 74) (:start . 69)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 101) (:start . 86) (:id . 59))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 111)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 116) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 121) (:start . 117)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 124) (:start . 122)\n  (:id . 64))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 132)\n  (:start . 125) (:id . 65))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 137) (:start . 133)\n  (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n  (:id . 67))\n ((:tag . "VB") (:stem . "differentiate") (:form . "differentiate")\n  (:end . 154) (:start . 141) (:id . 68))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 162)\n  (:start . 155) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 70))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 170) (:start . 167)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 178)\n  (:start . 171) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x3.329.1) (:span 19 22)))\n (:hscopes ((:id . :x3.329.1) (:span 19 41)))\n (:identifiers (:sid . :s3.329) (:did . :1471-2105-8-249)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101119@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.7) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5101129@unknown@formal@none@1@S@One way to understand a protein's function is to look at its composition of conserved domains.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 21)\n  (:start . 11) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "VB") (:stem . "look") (:form . "look") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "composition") (:form . "composition") (:end . 72)\n  (:start . 61) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 85)\n  (:start . 76) (:id . 57))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 93)\n  (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.17) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101139@unknown@formal@none@1@S@The structural evidence lends strong support to the inferred domain pair, resulting in a high confidence set of domain pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "lend") (:form . "lends") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "inferred") (:form . "inferred") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 67)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 93) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 104)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 118)\n  (:start . 112) (:id . 61))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 124)\n  (:start . 119) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x4.27.1) (:span 52 60)) ((:id . :x4.27.2) (:span 24 44)))\n (:hscopes ((:id . :x4.27.1) (:span 52 72)) ((:id . :x4.27.2) (:span 24 72)))\n (:identifiers (:sid . :s4.27) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101149@unknown@formal@none@1@S@How conserved are domain–domain pairs between species, and how many interacting domain pairs are still unknown?@(((:tag . "WRB") (:stem . "how") (:form . "How") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "domain–domain") (:form . "domain–domain")\n  (:end . 31) (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 53)\n  (:start . 46) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 79)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 86)\n  (:start . 80) (:id . 54))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 92) (:start . 87)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 102) (:start . 97)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 110)\n  (:start . 103) (:id . 58))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 111) (:start . 110)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x4.37.1) (:span 103 110)))\n (:hscopes ((:id . :x4.37.1) (:span 59 110)))\n (:identifiers (:sid . :s4.37) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101159@unknown@formal@none@1@S@Given that 74% of all UniProt proteins contain at least one Pfam match, this is not by itself surprising.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "CD") (:stem . "74") (:form . "74") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "UniProt") (:form . "UniProt") (:end . 29)\n  (:start . 22) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 38)\n  (:start . 30) (:id . 49))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 70) (:start . 65)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 79) (:start . 77)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 83) (:start . 80)\n  (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 93)\n  (:start . 87) (:id . 61))\n ((:tag . "JJ") (:stem . "surprising") (:form . "surprising") (:end . 104)\n  (:start . 94) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 63)))@@@1@22@((:ncues ((:id . :x4.47.1) (:span 80 83)))\n (:nscopes ((:id . :x4.47.1) (:span 80 104)))\n (:identifiers (:sid . :s4.47) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101169@unknown@formal@none@1@S@The relatively low iPfam coverage is by itself a disappointing finding.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "disappointing") (:form . "disappointing")\n  (:end . 62) (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.57) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101179@unknown@formal@none@1@S@In the following paragraph, we will call the experimental interactions that contain an iPfam domain pair the covered experimental interactions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "paragraph") (:form . "paragraph") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "call") (:form . "call") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 57)\n  (:start . 45) (:id . 51))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 70)\n  (:start . 58) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 83)\n  (:start . 76) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 99)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 116)\n  (:start . 109) (:id . 60))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 129)\n  (:start . 117) (:id . 61))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 142)\n  (:start . 130) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.67) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101189@unknown@formal@none@1@S@In both H. sapiens (blue) and S. cerevisiae (green) a small number of iPfam domain pairs covers a large fraction of the interactome, whereas in E. coli, no iPfam domain occurs in more than 4 experimental interactions at a time.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 24) (:start . 20)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n  (:id . 49))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 32) (:start . 30)\n  (:id . 50))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 43)\n  (:start . 33) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 50) (:start . 45)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 59) (:start . 54)\n  (:id . 56))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 66)\n  (:start . 60) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 75) (:start . 70)\n  (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 82)\n  (:start . 76) (:id . 60))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 88) (:start . 83)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "cover") (:form . "covers") (:end . 95)\n  (:start . 89) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 103) (:start . 98)\n  (:id . 64))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 112)\n  (:start . 104) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 67))\n ((:tag . "NN") (:stem . "interactome") (:form . "interactome") (:end . 131)\n  (:start . 120) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 69))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 140)\n  (:start . 133) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "E.") (:form . "E.") (:end . 146) (:start . 144)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "coli") (:form . "coli") (:end . 151) (:start . 147)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 74))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 155) (:start . 153)\n  (:id . 75))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 161)\n  (:start . 156) (:id . 76))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 168)\n  (:start . 162) (:id . 77))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 175)\n  (:start . 169) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 178) (:start . 176)\n  (:id . 79))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 183) (:start . 179)\n  (:id . 80))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 188) (:start . 184)\n  (:id . 81))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 190) (:start . 189)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 203)\n  (:start . 191) (:id . 83))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 216)\n  (:start . 204) (:id . 84))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 219) (:start . 217)\n  (:id . 85))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 221) (:start . 220)\n  (:id . 86))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 226) (:start . 222)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 88)))@@@1@47@((:ncues ((:id . :x4.77.1) (:span 153 155)))\n (:nscopes ((:id . :x4.77.1) (:span 153 226)))\n (:identifiers (:sid . :s4.77) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101199@unknown@formal@none@1@S@We reasoned that if there are iPfam domain pairs that act as reusable modules in protein interactions, then highly connected proteins should also be more likely to contain promiscuous iPfam domain pairs and vice-versa.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "reason") (:form . "reasoned") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "act") (:form . "act") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "reusable") (:form . "reusable") (:end . 69)\n  (:start . 61) (:id . 54))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 88)\n  (:start . 81) (:id . 57))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 101)\n  (:start . 89) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 107) (:start . 103)\n  (:id . 60))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 114)\n  (:start . 108) (:id . 61))\n ((:tag . "JJ") (:stem . "connected") (:form . "connected") (:end . 124)\n  (:start . 115) (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 140)\n  (:start . 134) (:id . 64))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 145) (:start . 141)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 148) (:start . 146)\n  (:id . 66))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 153) (:start . 149)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 160)\n  (:start . 154) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n  (:id . 69))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 171)\n  (:start . 164) (:id . 70))\n ((:tag . "JJ") (:stem . "promiscuous") (:form . "promiscuous") (:end . 183)\n  (:start . 172) (:id . 71))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 189)\n  (:start . 184) (:id . 72))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 196)\n  (:start . 190) (:id . 73))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 202)\n  (:start . 197) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 206) (:start . 203)\n  (:id . 75))\n ((:tag . "NN") (:stem . "vice-versa") (:form . "vice-versa") (:end . 217)\n  (:start . 207) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x4.87.1) (:span 134 140 154 160))\n  ((:id . :x4.87.3) (:span 3 11)))\n (:hscopes ((:id . :x4.87.1) (:span 108 217))\n  ((:id . :x4.87.3) (:span 3 217)))\n (:identifiers (:sid . :s4.87) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101209@unknown@formal@none@1@S@The correlation is outlined by dotted lines.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "outline") (:form . "outlined") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "dot") (:form . "dotted") (:end . 37) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.97) (:did . :1471-2105-8-259) (:did-type . :bmc_id)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101219@unknown@formal@none@1@S@Looking for example at the covered experimental interactions in H. sapiens(Additional file 1), only 8 out of the 100 most frequent iPfam domain pairs are seen in intrachain interactions exclusively, while 61 are exclusive to interchain interactions and 31 are seen in both.@(((:tag . "VBG") (:stem . "look") (:form . "Looking") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 47)\n  (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 60)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sapiens(Additional") (:form . "sapiens(Additional")\n  (:end . 85) (:start . 67) (:id . 52))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 90) (:start . 86)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 92) (:start . 91)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 105) (:start . 102)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 121) (:start . 117)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 130)\n  (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 136)\n  (:start . 131) (:id . 65))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 143)\n  (:start . 137) (:id . 66))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 149)\n  (:start . 144) (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 153) (:start . 150)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 158) (:start . 154)\n  (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "intrachain") (:form . "intrachain") (:end . 172)\n  (:start . 162) (:id . 71))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 185)\n  (:start . 173) (:id . 72))\n ((:tag . "RB") (:stem . "exclusively") (:form . "exclusively") (:end . 197)\n  (:start . 186) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 198) (:start . 197)\n  (:id . 74))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 204)\n  (:start . 199) (:id . 75))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 207) (:start . 205)\n  (:id . 76))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 211) (:start . 208)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "exclusive") (:form . "exclusive") (:end . 221)\n  (:start . 212) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 224) (:start . 222)\n  (:id . 79))\n ((:tag . "VB") (:stem . "interchain") (:form . "interchain") (:end . 235)\n  (:start . 225) (:id . 80))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 248)\n  (:start . 236) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 252) (:start . 249)\n  (:id . 82))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 255) (:start . 253)\n  (:id . 83))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 259) (:start . 256)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 264) (:start . 260)\n  (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 267) (:start . 265)\n  (:id . 86))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 272) (:start . 268)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 273) (:start . 272)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s4.107) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101229@unknown@formal@none@1@S@3671 out of a total of 5380 interacting protein pairs from the PDB contain an iPfam domain pair that does not interact in one complex structure but does so in another.@(((:tag . "CD") (:stem . "3671") (:form . "3671") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 19) (:start . 14)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "CD") (:stem . "5380") (:form . "5380") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 39)\n  (:start . 28) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 74)\n  (:start . 67) (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 90)\n  (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 95) (:start . 91)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 105) (:start . 101)\n  (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 118)\n  (:start . 110) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 64))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 125) (:start . 122)\n  (:id . 65))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 133)\n  (:start . 126) (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 143)\n  (:start . 134) (:id . 67))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 147) (:start . 144)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 152) (:start . 148)\n  (:id . 69))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n  (:id . 71))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 166)\n  (:start . 159) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 73)))@@@1@32@((:ncues ((:id . :x4.117.1) (:span 106 109)))\n (:nscopes ((:id . :x4.117.1) (:span 106 143)))\n (:identifiers (:sid . :s4.117) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101239@unknown@formal@none@1@S@We also analysed the full dataset of protein complexes.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.127) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101249@unknown@formal@none@1@S@Within the 3 to 19% of experimental interactions covered by iPfam, we analysed the conservation of iPfam domain pairs between species.@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 19) (:start . 18)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 35)\n  (:start . 23) (:id . 49))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 48)\n  (:start . 36) (:id . 50))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 78)\n  (:start . 70) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 95)\n  (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 104) (:start . 99)\n  (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 111)\n  (:start . 105) (:id . 61))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 117)\n  (:start . 112) (:id . 62))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 125)\n  (:start . 118) (:id . 63))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 133)\n  (:start . 126) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.137) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101259@unknown@formal@none@1@S@The iPfam domains in these pairs are related to housekeeping activities such as translation, replication or ATP synthesis.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "housekeeping") (:form . "housekeeping") (:end . 60)\n  (:start . 48) (:id . 51))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 91)\n  (:start . 80) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 104)\n  (:start . 93) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "ATP") (:form . "ATP") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.147) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101269@unknown@formal@none@1@S@From these random results, we derive a P value of 3.6 · 10-30 that the observed correlation is random.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "derive") (:form . "derive") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 52))\n ((:tag . "CD") (:stem . "3.6") (:form . "3.6") (:end . 53) (:start . 50)\n  (:id . 53))\n ((:tag . "NN") (:stem . "·") (:form . "·") (:end . 55) (:start . 54)\n  (:id . 54))\n ((:tag . "CD") (:stem . "10-30") (:form . "10-30") (:end . 61) (:start . 56)\n  (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 66) (:start . 62)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 79)\n  (:start . 71) (:id . 58))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 91)\n  (:start . 80) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 101)\n  (:start . 95) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.157) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101279@unknown@formal@none@1@S@ΨS The proteome size for species S@(((:tag . "VBZ") (:stem . "ψs") (:form . "ΨS") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "proteome") (:form . "proteome") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 34) (:start . 33)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.167) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101289@unknown@formal@none@1@S@The estimates for the total number of iPfam domain pairs ranges from 33813 to 120511, with an average of 76918.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "estimate") (:form . "estimates") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "range") (:form . "ranges") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "CD") (:stem . "33813") (:form . "33813") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "CD") (:stem . "120511") (:form . "120511") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . "CD") (:stem . "76918") (:form . "76918") (:end . 110)\n  (:start . 105) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.177) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101299@unknown@formal@none@1@S@The estimated total number of iPfam domains in all species@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 58)\n  (:start . 51) (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.187) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101309@unknown@formal@none@1@S@This in turn creates new targets for future structural genomics projects 30.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "turn") (:form . "turn") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "create") (:form . "creates") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "genomic") (:form . "genomics") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "project") (:form . "projects") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.197) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101319@unknown@formal@none@1@S@In fact, we find the most frequent iPfam domain pairs to be recognition domains in signal transduction.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 16) (:start . 12)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 25) (:start . 21)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 34)\n  (:start . 26) (:id . 49))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 40) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 71)\n  (:start . 60) (:id . 55))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 79)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 102)\n  (:start . 90) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.207) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101329@unknown@formal@none@1@S@While all such estimates should be taken with caution, our results show that at best 10% of all structural domain pairs are represented in iPfam.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "estimate") (:form . "estimates") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "caution") (:form . "caution") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 60))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 95) (:start . 92)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 106)\n  (:start . 96) (:id . 62))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 113)\n  (:start . 107) (:id . 63))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 119)\n  (:start . 114) (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 123) (:start . 120)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 135)\n  (:start . 124) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n  (:id . 67))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 144)\n  (:start . 139) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.217) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101339@unknown@formal@none@1@S@They found only 16 orthologous interacting protein pairs that were conserved in S. cerevisiae, C. elegans, D. melanogaster and H. sapiens.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 30)\n  (:start . 19) (:id . 46))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 42)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 93)\n  (:start . 83) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 105)\n  (:start . 98) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 122) (:start . 110) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "H.") (:form . "H.") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 137)\n  (:start . 130) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.227) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101349@unknown@formal@none@1@S@In this study, we addressed the utility of current knowledge about structural domain interactions in order to interpret experimental protein interactions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "address") (:form . "addressed") (:end . 27)\n  (:start . 18) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "utility") (:form . "utility") (:end . 39)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 50)\n  (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 60)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 77)\n  (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 84)\n  (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 97)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 106)\n  (:start . 101) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 109) (:start . 107)\n  (:id . 59))\n ((:tag . "VB") (:stem . "interpret") (:form . "interpret") (:end . 119)\n  (:start . 110) (:id . 60))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 132)\n  (:start . 120) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 140)\n  (:start . 133) (:id . 62))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 153)\n  (:start . 141) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s4.237) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101359@unknown@formal@none@1@S@A wide range of databases were used to cover as many distinct experimental data sets as possible.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 25)\n  (:start . 16) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "VB") (:stem . "cover") (:form . "cover") (:end . 44) (:start . 39)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 61)\n  (:start . 53) (:id . 53))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 74)\n  (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 96)\n  (:start . 88) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.247) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101369@unknown@formal@none@1@S@Species@(((:tag . "NNP") (:stem . "Specie") (:form . "Species") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.257) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|SectionTitle|)))@oe@9-2-2011
5101379@unknown@formal@none@1@S@All such interacting domain pairs are stored in a database together with detailed information on the residues involved 13.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "store") (:form . "stored") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 93)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 109)\n  (:start . 101) (:id . 58))\n ((:tag . "VBD") (:stem . "involve") (:form . "involved") (:end . 118)\n  (:start . 110) (:id . 59))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.267) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101389@unknown@formal@none@1@S@Species distribution of iPfam domain pairs@(((:tag . "NNP") (:stem . "Species") (:form . "Species") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ipfam") (:form . "iPfam") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 42) (:start . 37)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s4.277) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|FigureLegend|)))@oe@9-2-2011
5101399@unknown@formal@none@1@S@Random networks@(((:tag . "NNP") (:stem . "Random") (:form . "Random") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 15)\n  (:start . 7) (:id . 43)))@@@1@2@((:identifiers (:sid . :s4.287) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|SectionTitle|)))@oe@9-2-2011
5101409@unknown@formal@none@1@S@Where appropriate, the inverse probability P(X > x) = 1 - f(x; μ, σ) was applied.@(((:tag . "WRB") (:stem . "where") (:form . "Where") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "inverse") (:form . "inverse") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 42)\n  (:start . 31) (:id . 47))\n ((:tag . "NNP") (:stem . "P(X") (:form . "P(X") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "SYM") (:stem . "x") (:form . "x") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "NN") (:stem . "f(x") (:form . "f(x") (:end . 61) (:start . 58)\n  (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . "SYM") (:stem . "μ") (:form . "μ") (:end . 64) (:start . 63)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "σ") (:form . "σ") (:end . 67) (:start . 66)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 72) (:start . 69)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 80)\n  (:start . 73) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.297) (:did . :1471-2105-8-259)\n  (:did-type . :bmc_id) (:dtype . :|Biological_full_article|)\n  (:dpart . :|Text|)))@oe@9-2-2011
5101419@unknown@formal@none@1@S@Finally, ectopic expression of neur in D-mib mutant larvae rescues the wing D-mib phenotype, indicating that Neur can compensate for the lack of D-mib activity.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "neur") (:form . "neur") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "VBZ") (:stem . "rescue") (:form . "rescues") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "wing") (:form . "wing") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 81) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 103)\n  (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "VB") (:stem . "compensate") (:form . "compensate") (:end . 128)\n  (:start . 118) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 132) (:start . 129)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 64))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 150)\n  (:start . 145) (:id . 67))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 159)\n  (:start . 151) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x5.10.2) (:span 93 108)))\n (:ncues ((:id . :x5.10.1) (:span 137 141)))\n (:hscopes ((:id . :x5.10.2) (:span 93 159)))\n (:nscopes ((:id . :x5.10.1) (:span 137 159)))\n (:identifiers (:sid . :s5.10) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101429@unknown@formal@none@1@S@Conversely, Ser (but not Dl) is specifically required for segmental patterning [5].@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n  (:id . 50))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 44)\n  (:start . 32) (:id . 51))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 53)\n  (:start . 45) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "segmental") (:form . "segmental") (:end . 67)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "patterning") (:form . "patterning") (:end . 78)\n  (:start . 68) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 59)))@@@1@18@((:ncues ((:id . :x5.20.1) (:span 21 24)))\n (:nscopes ((:id . :x5.20.1) (:span 21 28)))\n (:identifiers (:sid . :s5.20) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101439@unknown@formal@none@1@S@Third, two distinct E3 ubiquitin ligases, Neuralized (Neur) and Mind bomb (Mib), have recently been shown to regulate Dl endocytosis and N activation in Drosophila and Danio rerio, respectively [18,19,20,21,22,23,24,25].@(((:tag . "RB") (:stem . "third") (:form . "Third") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "e3") (:form . "E3") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ubiquitin") (:form . "ubiquitin") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "ligas") (:form . "ligases") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Neuralized") (:form . "Neuralized") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "mind") (:form . "Mind") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "bomb") (:form . "bomb") (:end . 73) (:start . 69)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 78) (:start . 75)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 85) (:start . 81)\n  (:id . 61))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 94)\n  (:start . 86) (:id . 62))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 99) (:start . 95)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 105)\n  (:start . 100) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 65))\n ((:tag . "VB") (:stem . "regulate") (:form . "regulate") (:end . 117)\n  (:start . 109) (:id . 66))\n ((:tag . "NN") (:stem . "dl") (:form . "Dl") (:end . 120) (:start . 118)\n  (:id . 67))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 132)\n  (:start . 121) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 138) (:start . 137)\n  (:id . 70))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 149)\n  (:start . 139) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 152) (:start . 150)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 163)\n  (:start . 153) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Danio") (:form . "Danio") (:end . 173)\n  (:start . 168) (:id . 75))\n ((:tag . "NN") (:stem . "rerio") (:form . "rerio") (:end . 179)\n  (:start . 174) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 77))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 193)\n  (:start . 181) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 195) (:start . 194)\n  (:id . 79))\n ((:tag . "CD") (:stem . "18,19,20,21,22,23,24,25")\n  (:form . "18,19,20,21,22,23,24,25") (:end . 218) (:start . 195) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 219) (:start . 218)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s5.30) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101449@unknown@formal@none@1@S@How endocytosis of Dl leads to the activation of N remains to be elucidated.@(((:tag . "WRB") (:stem . "how") (:form . "How") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 45)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 58)\n  (:start . 51) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "elucidate") (:form . "elucidated") (:end . 75)\n  (:start . 65) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x5.40.1) (:span 51 75)))\n (:hscopes ((:id . :x5.40.1) (:span 0 75)))\n (:identifiers (:sid . :s5.40) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101459@unknown@formal@none@1@S@We report here that D-mib, like D. rerio Mib, appears to regulate Dl signaling during leg segmentation, wing vein formation, and lateral inhibition in the adult notum.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "report") (:form . "report") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "rerio") (:form . "rerio") (:end . 40) (:start . 35)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Mib") (:form . "Mib") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 53)\n  (:start . 46) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "VB") (:stem . "regulate") (:form . "regulate") (:end . 65)\n  (:start . 57) (:id . 55))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 68) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 78)\n  (:start . 69) (:id . 57))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 85)\n  (:start . 79) (:id . 58))\n ((:tag . "NN") (:stem . "leg") (:form . "leg") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "segmentation") (:form . "segmentation") (:end . 102)\n  (:start . 90) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "wing") (:form . "wing") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "vein") (:form . "vein") (:end . 113) (:start . 109)\n  (:id . 63))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 123)\n  (:start . 114) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 136)\n  (:start . 129) (:id . 67))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 147)\n  (:start . 137) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 160)\n  (:start . 155) (:id . 71))\n ((:tag . "NN") (:stem . "notum") (:form . "notum") (:end . 166)\n  (:start . 161) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x5.50.1) (:span 46 53)))\n (:hscopes ((:id . :x5.50.1) (:span 20 166)))\n (:identifiers (:sid . :s5.50) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101469@unknown@formal@none@1@S@Insertion of this P-element confers late pupal lethality.@(((:tag . "NNP") (:stem . "Insertion") (:form . "Insertion") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "P-element") (:form . "P-element") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "VBZ") (:stem . "confer") (:form . "confers") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "RB") (:stem . "late") (:form . "late") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "pupal") (:form . "pupal") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s5.60) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101479@unknown@formal@none@1@S@First, lethality of homozygous D-mib1 pupae is associated with the insertion of a P-element into the 5? UTR of the D-mib gene.@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 30)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "d-mib1") (:form . "D-mib1") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "pupae") (:form . "pupae") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 57)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "p-element") (:form . "P-element") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "utr") (:form . "UTR") (:end . 107) (:start . 104)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 120)\n  (:start . 115) (:id . 64))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 125) (:start . 121)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s5.70) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101489@unknown@formal@none@1@S@Open reading frames are shown in black.@(((:tag . "JJ") (:stem . "open") (:form . "Open") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "black") (:form . "black") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s5.80) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101499@unknown@formal@none@1@S@D-mib (E) and Ser (F) mutant flies showed similar wing loss phenotypes.@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 17) (:start . 14)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 48))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 20) (:start . 19)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 21) (:start . 20)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 28)\n  (:start . 22) (:id . 51))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 34) (:start . 29)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 41) (:start . 35)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 49)\n  (:start . 42) (:id . 54))\n ((:tag . "NN") (:stem . "wing") (:form . "wing") (:end . 54) (:start . 50)\n  (:id . 55))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 59) (:start . 55)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 70)\n  (:start . 60) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.90) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101509@unknown@formal@none@1@S@D-mib Regulates Dl Signaling@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "Regulates") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Signaling") (:form . "Signaling") (:end . 28)\n  (:start . 19) (:id . 45)))@@@1@4@((:identifiers (:sid . :s5.100) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5101519@unknown@formal@none@1@S@Finally, the vein phenotype seen in D-mib hypomorphic flies is similar to the one seen in Dlts mutant flies [39].@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "vein") (:form . "vein") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "hypomorphic") (:form . "hypomorphic") (:end . 53)\n  (:start . 42) (:id . 50))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 81) (:start . 78)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Dlt") (:form . "Dlts") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 101)\n  (:start . 95) (:id . 60))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 107) (:start . 102)\n  (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "CD") (:stem . "39") (:form . "39") (:end . 111) (:start . 109)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s5.110) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101529@unknown@formal@none@1@S@We then studied in more detail the function of D-mib during wing development.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "study") (:form . "studied") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "VBG") (:stem . "wing") (:form . "wing") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 76)\n  (:start . 65) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.120) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101539@unknown@formal@none@1@S@Thus, the D-mib wing phenotype may result from defective N inductive signaling at the D-V boundary.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 15) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "wing") (:form . "wing") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "result") (:form . "result") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "defective") (:form . "defective") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "inductive") (:form . "inductive") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "D-V") (:form . "D-V") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "boundary") (:form . "boundary") (:end . 98)\n  (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x5.130.1) (:span 31 34)))\n (:hscopes ((:id . :x5.130.1) (:span 31 98)))\n (:identifiers (:sid . :s5.130) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101549@unknown@formal@none@1@S@D-mib co-localized with Ser, Dl, and N at the apical cortex (Figure 3B–3D???).@(((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "co-localized") (:form . "co-localized") (:end . 18)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 41) (:start . 39)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "apical") (:form . "apical") (:end . 52)\n  (:start . 46) (:id . 53))\n ((:tag . "NN") (:stem . "cortex") (:form . "cortex") (:end . 59)\n  (:start . 53) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 67)\n  (:start . 61) (:id . 56))\n ((:tag . "NNP") (:stem . "3B–3D") (:form . "3B–3D") (:end . 73) (:start . 68)\n  (:id . 57))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 74) (:start . 73)\n  (:id . 58))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 75) (:start . 74)\n  (:id . 59))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 76) (:start . 75)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s5.140) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101559@unknown@formal@none@1@S@(E–E??) D-mib (green in [E and E?]) co-localized with Dl (red in [E and E??]) at the apical cortex of wing pouch cells.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E–E") (:form . "E–E") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 6) (:start . 5) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 7) (:start . 6) (:id . 46))\n ((:tag . "JJ") (:stem . "d-mib") (:form . "D-mib") (:end . 13) (:start . 8)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 20) (:start . 15)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n  (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 25) (:start . 24)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 26) (:start . 25)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 32) (:start . 31)\n  (:id . 54))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 33) (:start . 32)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 34) (:start . 33)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "co-localize") (:form . "co-localized") (:end . 48)\n  (:start . 36) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 56) (:start . 54)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 61) (:start . 58)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 66) (:start . 65)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 67) (:start . 66)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 73) (:start . 72)\n  (:id . 67))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 74) (:start . 73)\n  (:id . 68))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 75) (:start . 74)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 76) (:start . 75)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 71))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 80) (:start . 78)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "apical") (:form . "apical") (:end . 91)\n  (:start . 85) (:id . 74))\n ((:tag . "NN") (:stem . "cortex") (:form . "cortex") (:end . 98)\n  (:start . 92) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "wing") (:form . "wing") (:end . 106) (:start . 102)\n  (:id . 77))\n ((:tag . "NN") (:stem . "pouch") (:form . "pouch") (:end . 112)\n  (:start . 107) (:id . 78))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 118)\n  (:start . 113) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s5.150) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101569@unknown@formal@none@1@S@(B) and (D) show high-magnification views of the areas boxed in (A) and (C), respectively.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 10) (:start . 9)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 11) (:start . 10)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 16) (:start . 12)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "high-magnification") (:form . "high-magnification")\n  (:end . 35) (:start . 17) (:id . 50))\n ((:tag . "NNS") (:stem . "view") (:form . "views") (:end . 41) (:start . 36)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 54) (:start . 49)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "box") (:form . "boxed") (:end . 60) (:start . 55)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 66) (:start . 65)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 74) (:start . 73)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 64))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 89)\n  (:start . 77) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s5.160) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101579@unknown@formal@none@1@S@We therefore conclude that the D-mib gene is required to regulate the level of Ser at the apical cortex of wing disc cells.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "VB") (:stem . "regulate") (:form . "regulate") (:end . 65)\n  (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "apical") (:form . "apical") (:end . 96)\n  (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "cortex") (:form . "cortex") (:end . 103)\n  (:start . 97) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "wing") (:form . "wing") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "disc") (:form . "disc") (:end . 116) (:start . 112)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 122)\n  (:start . 117) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s5.170) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101589@unknown@formal@none@1@S@Clone boundaries are outlined in (H and H?) and (J and J?).@(((:tag . "NNP") (:stem . "Clone") (:form . "Clone") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "outline") (:form . "outlined") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 35) (:start . 34)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 50) (:start . 49)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 56) (:start . 55)\n  (:id . 57))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 57) (:start . 56)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.180) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101599@unknown@formal@none@1@S@The uptake of anti-Ser and anti-Dl antibodies was then assessed using secondary antibodies.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "anti-ser") (:form . "anti-Ser") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "anti-dl") (:form . "anti-Dl") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 79)\n  (:start . 70) (:id . 53))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 90)\n  (:start . 80) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.190) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101609@unknown@formal@none@1@S@(C–C??) and (F–F??) show confocal z-sections.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C–C") (:form . "C–C") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 6) (:start . 5) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 7) (:start . 6) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "F–F") (:form . "F–F") (:end . 16) (:start . 13)\n  (:id . 49))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 17) (:start . 16)\n  (:id . 50))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 18) (:start . 17)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 24) (:start . 20)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 33)\n  (:start . 25) (:id . 54))\n ((:tag . "NNS") (:stem . "z-section") (:form . "z-sections") (:end . 44)\n  (:start . 34) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.200) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101619@unknown@formal@none@1@S@Loss of D-mib activity in large dorsal clones of D-mib2 mutant cells resulted in a loss of Cut expression at the D-V interface (Figure 6A and 6B).@(((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "d-mib2") (:form . "D-mib2") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 77)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Cut") (:form . "Cut") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 105)\n  (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "D-V") (:form . "D-V") (:end . 116) (:start . 113)\n  (:id . 63))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 126)\n  (:start . 117) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 134)\n  (:start . 128) (:id . 66))\n ((:tag . "NN") (:stem . "6a") (:form . "6A") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 68))\n ((:tag . "NN") (:stem . "6b") (:form . "6B") (:end . 144) (:start . 142)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s5.210) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101629@unknown@formal@none@1@S@A similar rescue was observed with a YFP::D-mib protein (Figure 7B–7B?)”, indicating that YFP::D-mib is functional.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "YFP::D-mib") (:form . "YFP::D-mib") (:end . 47)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "NNP") (:stem . "7B–7B?)”") (:form . "7B–7B?)”") (:end . 74)\n  (:start . 64) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 86)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "YFP::D-mib") (:form . "YFP::D-mib") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 116)\n  (:start . 106) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x5.220.1) (:span 76 91)))\n (:hscopes ((:id . :x5.220.1) (:span 76 116)))\n (:identifiers (:sid . :s5.220) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101639@unknown@formal@none@1@S@D-mib Acts Downstream of Ser and Upstream of Activated N@(((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNPS") (:stem . "Acts") (:form . "Acts") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Downstream") (:form . "Downstream") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Upstream") (:form . "Upstream") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Activated") (:form . "Activated") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 56) (:start . 55)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s5.230) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5101649@unknown@formal@none@1@S@Expression of Neur in dorsal cells was sufficient to compensate for the loss of D-mib activity (D).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 49)\n  (:start . 39) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "VB") (:stem . "compensate") (:form . "compensate") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 94)\n  (:start . 86) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.240) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101659@unknown@formal@none@1@S@We conclude that ectopic expression of Neur compensates for the loss of D-mib activity.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "compensate") (:form . "compensates") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 77) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 86)\n  (:start . 78) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.250) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101669@unknown@formal@none@1@S@Second, expression of D-mib in the dorsal Ser-signaling cells was sufficient to rescue the D-mib mutant wing phenotype.@(((:tag . "RB") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "JJ") (:stem . "ser-signaling") (:form . "Ser-signaling")\n  (:end . 55) (:start . 42) (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 76)\n  (:start . 66) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "VB") (:stem . "rescue") (:form . "rescue") (:end . 86)\n  (:start . 80) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "wing") (:form . "wing") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.260) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101679@unknown@formal@none@1@S@Interestingly, the strong requirement for Dl and Ser endocytosis seen in Drosophila is not conserved in Caenorhabditis elegans, in which secreted ligands have been shown to be functional [58,59].@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 37)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 64)\n  (:start . 53) (:id . 51))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 100)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Caenorhabditis") (:form . "Caenorhabditis")\n  (:end . 118) (:start . 104) (:id . 59))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 126)\n  (:start . 119) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 136)\n  (:start . 131) (:id . 63))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 145)\n  (:start . 137) (:id . 64))\n ((:tag . "NNS") (:stem . "ligand") (:form . "ligands") (:end . 153)\n  (:start . 146) (:id . 65))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 158) (:start . 154)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 163) (:start . 159)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 169)\n  (:start . 164) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 172) (:start . 170)\n  (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 175) (:start . 173)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 186)\n  (:start . 176) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 188) (:start . 187)\n  (:id . 72))\n ((:tag . "CD") (:stem . "58,59") (:form . "58,59") (:end . 193)\n  (:start . 188) (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 194) (:start . 193)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 75)))@@@1@34@((:ncues ((:id . :x5.270.1) (:span 87 90)))\n (:nscopes ((:id . :x5.270.1) (:span 15 186)))\n (:identifiers (:sid . :s5.270) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101689@unknown@formal@none@1@S@The functional differences observed between D-mib and neur cannot be simply explained by obvious differences in molecular activity and/or substrate specificity.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 26)\n  (:start . 15) (:id . 44))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 35)\n  (:start . 27) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 43)\n  (:start . 36) (:id . 46))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 49) (:start . 44)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "NN") (:stem . "neur") (:form . "neur") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 65)\n  (:start . 59) (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "RB") (:stem . "simply") (:form . "simply") (:end . 75)\n  (:start . 69) (:id . 52))\n ((:tag . "VBN") (:stem . "explain") (:form . "explained") (:end . 85)\n  (:start . 76) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 96)\n  (:start . 89) (:id . 55))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 108)\n  (:start . 97) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 121)\n  (:start . 112) (:id . 58))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 130)\n  (:start . 122) (:id . 59))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 137)\n  (:start . 131) (:id . 60))\n ((:tag . "NN") (:stem . "substrate") (:form . "substrate") (:end . 147)\n  (:start . 138) (:id . 61))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 159)\n  (:start . 148) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 63)))@@@1@22@((:ncues ((:id . :x5.280.1) (:span 59 65)))\n (:nscopes ((:id . :x5.280.1) (:span 0 159)))\n (:identifiers (:sid . :s5.280) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101699@unknown@formal@none@1@S@Whether endogenous Neur binds and activates Ser remains to be tested.@(((:tag . "IN") (:stem . "whether") (:form . "Whether") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 68) (:start . 62)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 53)))@@@1@12@((:hcues ((:id . :x5.290.1) (:span 0 7)))\n (:hscopes ((:id . :x5.290.1) (:span 0 47)))\n (:identifiers (:sid . :s5.290) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101709@unknown@formal@none@1@S@In conclusion, Neur and D-mib appear to have similar molecular activities in the regulation of Dl and Ser endocytosis but distinct developmental functions in Drosophila.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "conclusion") (:form . "conclusion") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Neur") (:form . "Neur") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "D-mib") (:form . "D-mib") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 52)\n  (:start . 45) (:id . 51))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 73)\n  (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 91)\n  (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Dl") (:form . "Dl") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "endocytosis") (:form . "endocytosis") (:end . 117)\n  (:start . 106) (:id . 61))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 130)\n  (:start . 122) (:id . 63))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 144) (:start . 131) (:id . 64))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 154)\n  (:start . 145) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 168)\n  (:start . 158) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x5.300.1) (:span 30 36)))\n (:hscopes ((:id . :x5.300.1) (:span 15 168)))\n (:identifiers (:sid . :s5.300) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101719@unknown@formal@none@1@S@Sequence analysis of the D-mib3 and D-mib4 alleles was carried on PCR products prepared from genomic DNA prepared from D-mib3/D-mib2 and D-mib4/D-mib2 mutant pupae.@(((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "d-mib3") (:form . "D-mib3") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "d-mib4") (:form . "D-mib4") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 113)\n  (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "NN") (:stem . "d-mib3/d-mib2") (:form . "D-mib3/D-mib2")\n  (:end . 132) (:start . 119) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 62))\n ((:tag . "NN") (:stem . "d-mib4/d-mib2") (:form . "D-mib4/D-mib2")\n  (:end . 150) (:start . 137) (:id . 63))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 157)\n  (:start . 151) (:id . 64))\n ((:tag . "NNS") (:stem . "pupa") (:form . "pupae") (:end . 163)\n  (:start . 158) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s5.310) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101729@unknown@formal@none@1@S@Rabbit polyclonal anti-D-mib antibodies were raised against the CYNERKTDDSELPGN peptide (CovalAb, Lyon, France).@(((:tag . "NN") (:stem . "rabbit") (:form . "Rabbit") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "polyclonal") (:form . "polyclonal") (:end . 17)\n  (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "anti-d-mib") (:form . "anti-D-mib") (:end . 28)\n  (:start . 18) (:id . 44))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 39)\n  (:start . 29) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "raise") (:form . "raised") (:end . 51)\n  (:start . 45) (:id . 47))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 59)\n  (:start . 52) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cynerktddselpgn") (:form . "CYNERKTDDSELPGN")\n  (:end . 79) (:start . 64) (:id . 50))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 87)\n  (:start . 80) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "CovalAb") (:form . "CovalAb") (:end . 96)\n  (:start . 89) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Lyon") (:form . "Lyon") (:end . 102) (:start . 98)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "France") (:form . "France") (:end . 110)\n  (:start . 104) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s5.320) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101739@unknown@formal@none@1@S@Following three medium changes and a 45-min chase period, wing discs were fixed and incubated with secondary antibodies.@(((:tag . "VBG") (:stem . "follow") (:form . "Following") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "45-min") (:form . "45-min") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "chase") (:form . "chase") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "wing") (:form . "wing") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "disc") (:form . "discs") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 108)\n  (:start . 99) (:id . 59))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 119)\n  (:start . 109) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.330) (:did . :pmc1064853) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101749@unknown@formal@none@1@S@We also studied several divergent proteins encoded by the sea urchin and lancelet genomes that are 25%-30% identical to the RAG1 N-terminal domain and the RAG1 core.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "study") (:form . "studied") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "JJ") (:stem . "divergent") (:form . "divergent") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 89)\n  (:start . 82) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "CD") (:stem . "25%-30") (:form . "25%-30") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 116)\n  (:start . 107) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 62))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 128) (:start . 124)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 139)\n  (:start . 129) (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 146)\n  (:start . 140) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 159) (:start . 155)\n  (:id . 68))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 164) (:start . 160)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.10) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101759@unknown@formal@none@1@S@In addition to this combinatorial diversity, further diversity is generated by small insertions and deletions at junctions between the joined segments.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "combinatorial") (:form . "combinatorial")\n  (:end . 33) (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 84) (:start . 79)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "insertion") (:form . "insertions") (:end . 95)\n  (:start . 85) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "deletion") (:form . "deletions") (:end . 109)\n  (:start . 100) (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "junction") (:form . "junctions") (:end . 122)\n  (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 130)\n  (:start . 123) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "joined") (:form . "joined") (:end . 141)\n  (:start . 135) (:id . 62))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 150)\n  (:start . 142) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.20) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101769@unknown@formal@none@1@S@In vertebrates, in vivo RAG-mediated transpositions are strongly suppressed, probably to minimize potential harm to genome function.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "rag-mediated") (:form . "RAG-mediated") (:end . 36)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n  (:end . 51) (:start . 37) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "VBN") (:stem . "suppress") (:form . "suppressed") (:end . 75)\n  (:start . 65) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 52))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "VB") (:stem . "minimize") (:form . "minimize") (:end . 97)\n  (:start . 89) (:id . 55))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 107)\n  (:start . 98) (:id . 56))\n ((:tag . "NN") (:stem . "harm") (:form . "harm") (:end . 112) (:start . 108)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 122)\n  (:start . 116) (:id . 59))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 131)\n  (:start . 123) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x6.30.1) (:span 77 85)))\n (:hscopes ((:id . :x6.30.1) (:span 77 131)))\n (:identifiers (:sid . :s6.30) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101779@unknown@formal@none@1@S@Genomes of plants and vertebrates seem to be free of any recognizable Transib transposons (Figure 1).@(((:tag . "NNS") (:stem . "genome") (:form . "Genomes") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "free") (:form . "free") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "recognizable") (:form . "recognizable") (:end . 69)\n  (:start . 57) (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 89)\n  (:start . 78) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 97)\n  (:start . 91) (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 99) (:start . 98)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x6.40.1) (:span 34 38)))\n (:hscopes ((:id . :x6.40.1) (:span 0 89)))\n (:identifiers (:sid . :s6.40) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101789@unknown@formal@none@1@S@In fungi, the Transib TPase was detected in soybean rust only.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fungus") (:form . "fungi") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 40)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "soybean") (:form . "soybean") (:end . 51)\n  (:start . 44) (:id . 51))\n ((:tag . "NN") (:stem . "rust") (:form . "rust") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.50) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101799@unknown@formal@none@1@S@To achieve that, we combined protein sequences of the seven known Transib TPases with the set of all GenBank proteins.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "achieve") (:form . "achieve") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "combine") (:form . "combined") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 73)\n  (:start . 66) (:id . 54))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 80) (:start . 74)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 108)\n  (:start . 101) (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 117)\n  (:start . 109) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.60) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101809@unknown@formal@none@1@S@The more diverse the TPases used in determining the PSSM, the more accurate is the approximation; some of the insect Transib TPases are less than 30% identical to each other, as shown in Figure 2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 27) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 47)\n  (:start . 36) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 75)\n  (:start . 67) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "approximation") (:form . "approximation")\n  (:end . 96) (:start . 83) (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 116)\n  (:start . 110) (:id . 63))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 124)\n  (:start . 117) (:id . 64))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 131)\n  (:start . 125) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 135) (:start . 132)\n  (:id . 66))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 140) (:start . 136)\n  (:id . 67))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 145) (:start . 141)\n  (:id . 68))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 148) (:start . 146)\n  (:id . 69))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 149) (:start . 148)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 159)\n  (:start . 150) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n  (:id . 72))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 167) (:start . 163)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 173)\n  (:start . 168) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 75))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 177) (:start . 175)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 183)\n  (:start . 178) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 193)\n  (:start . 187) (:id . 79))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 195) (:start . 194)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s6.70) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101819@unknown@formal@none@1@S@At the same time, recently sequenced genomes of honeybee, roundworms, fish, frog, mammals, sea squirts, plants, and fungi (except soybean rust) do not contain any detectable Transib transposons (see Figure 1).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 26)\n  (:start . 18) (:id . 47))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 36)\n  (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "honeybee") (:form . "honeybee") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "roundworm") (:form . "roundworms") (:end . 68)\n  (:start . 58) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "fish") (:form . "fish") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "frog") (:form . "frog") (:end . 80) (:start . 76)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 89)\n  (:start . 82) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 94) (:start . 91)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "squirt") (:form . "squirts") (:end . 102)\n  (:start . 95) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 110)\n  (:start . 104) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "fungus") (:form . "fungi") (:end . 121)\n  (:start . 116) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 68))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 129)\n  (:start . 123) (:id . 69))\n ((:tag . "NN") (:stem . "soybean") (:form . "soybean") (:end . 137)\n  (:start . 130) (:id . 70))\n ((:tag . "NN") (:stem . "rust") (:form . "rust") (:end . 142) (:start . 138)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 72))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 146) (:start . 144)\n  (:id . 73))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 150) (:start . 147)\n  (:id . 74))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 158)\n  (:start . 151) (:id . 75))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 162) (:start . 159)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 173)\n  (:start . 163) (:id . 77))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 181)\n  (:start . 174) (:id . 78))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 193)\n  (:start . 182) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 80))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 198) (:start . 195)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 205)\n  (:start . 199) (:id . 82))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 207) (:start . 206)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 208) (:start . 207)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 85)))@@@1@44@((:ncues ((:id . :x6.80.1) (:span 147 150)))\n (:nscopes ((:id . :x6.80.1) (:span 147 193)))\n (:identifiers (:sid . :s6.80) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101829@unknown@formal@none@1@S@Each empty cell indicates that the corresponding TPase query was not used at the particular stage of PSI-BLAST analysis.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "empty") (:form . "empty") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 48)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 60) (:start . 55)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 91)\n  (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 97) (:start . 92)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 110)\n  (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 119)\n  (:start . 111) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 61)))@@@1@20@((:ncues ((:id . :x6.90.1) (:span 65 68)))\n (:nscopes ((:id . :x6.90.1) (:span 31 119)))\n (:identifiers (:sid . :s6.90) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101839@unknown@formal@none@1@S@This includes the distances between the second D and E residues, which are much longer in Transib transposons (206–214 aa) and RAG1 (253 aa) than in DDE TPases from other studied superfamilies (e.g., approximately 35-aa in Mariner/Tc1 [23], 2-aa in P [23], approximately 35-aa in Harbinger [24], with hAT as an exception (325-aa, [25]).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 70) (:start . 65)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 79) (:start . 75)\n  (:id . 56))\n ((:tag . "RBR") (:stem . "longer") (:form . "longer") (:end . 86)\n  (:start . 80) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 97)\n  (:start . 90) (:id . 59))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 109)\n  (:start . 98) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 61))\n ((:tag . "CD") (:stem . "206–214") (:form . "206–214") (:end . 118)\n  (:start . 111) (:id . 62))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 121) (:start . 119)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 131) (:start . 127)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 67))\n ((:tag . "CD") (:stem . "253") (:form . "253") (:end . 136) (:start . 133)\n  (:id . 68))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 139) (:start . 137)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 70))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 145) (:start . 141)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "DDE") (:form . "DDE") (:end . 152) (:start . 149)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 159)\n  (:start . 153) (:id . 74))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 164) (:start . 160)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 170)\n  (:start . 165) (:id . 76))\n ((:tag . "VBN") (:stem . "study") (:form . "studied") (:end . 178)\n  (:start . 171) (:id . 77))\n ((:tag . "NNS") (:stem . "superfamily") (:form . "superfamilies")\n  (:end . 192) (:start . 179) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 79))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 198) (:start . 194)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 199) (:start . 198)\n  (:id . 81))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 213) (:start . 200) (:id . 82))\n ((:tag . "JJ") (:stem . "35-aa") (:form . "35-aa") (:end . 219)\n  (:start . 214) (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 84))\n ((:tag . "NN") (:stem . "mariner/tc1") (:form . "Mariner/Tc1") (:end . 234)\n  (:start . 223) (:id . 85))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 236) (:start . 235)\n  (:id . 86))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 238) (:start . 236)\n  (:id . 87))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 239) (:start . 238)\n  (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 240) (:start . 239)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "2-aa") (:form . "2-aa") (:end . 245) (:start . 241)\n  (:id . 90))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 248) (:start . 246)\n  (:id . 91))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 250) (:start . 249)\n  (:id . 92))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 252) (:start . 251)\n  (:id . 93))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 254) (:start . 252)\n  (:id . 94))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 255) (:start . 254)\n  (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 256) (:start . 255)\n  (:id . 96))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 270) (:start . 257) (:id . 97))\n ((:tag . "JJ") (:stem . "35-aa") (:form . "35-aa") (:end . 276)\n  (:start . 271) (:id . 98))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 279) (:start . 277)\n  (:id . 99))\n ((:tag . "NNP") (:stem . "Harbinger") (:form . "Harbinger") (:end . 289)\n  (:start . 280) (:id . 100))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 291) (:start . 290)\n  (:id . 101))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 293) (:start . 291)\n  (:id . 102))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 294) (:start . 293)\n  (:id . 103))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 295) (:start . 294)\n  (:id . 104))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 300) (:start . 296)\n  (:id . 105))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 304) (:start . 301)\n  (:id . 106))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 307) (:start . 305)\n  (:id . 107))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 310) (:start . 308)\n  (:id . 108))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 320)\n  (:start . 311) (:id . 109))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 322) (:start . 321)\n  (:id . 110))\n ((:tag . "JJ") (:stem . "325-aa") (:form . "325-aa") (:end . 328)\n  (:start . 322) (:id . 111))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 329) (:start . 328)\n  (:id . 112))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 331) (:start . 330)\n  (:id . 113))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 333) (:start . 331)\n  (:id . 114))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 334) (:start . 333)\n  (:id . 115))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 335) (:start . 334)\n  (:id . 116))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 336) (:start . 335)\n  (:id . 117)))@@@1@76@((:identifiers (:sid . :s6.100) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101849@unknown@formal@none@1@S@Based on this information, the function of these motifs in Transib TPases is expected to be similar to that in RAG1.@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 25)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "NNP") (:stem . "TPases") (:form . "TPases") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 99)\n  (:start . 92) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 115) (:start . 111)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x6.110.1) (:span 77 85)))\n (:hscopes ((:id . :x6.110.1) (:span 27 115)))\n (:identifiers (:sid . :s6.110) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101859@unknown@formal@none@1@S@Starting positions of the motifs immediately follow the corresponding protein names.@(((:tag . "VBG") (:stem . "start") (:form . "Starting") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "RB") (:stem . "immediately") (:form . "immediately") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "VBP") (:stem . "follow") (:form . "follow") (:end . 51)\n  (:start . 45) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 69)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 77)\n  (:start . 70) (:id . 51))\n ((:tag . "NNS") (:stem . "name") (:form . "names") (:end . 83) (:start . 78)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.120) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101869@unknown@formal@none@1@S@(A) Frequencies of the most frequent nucleotides at each position of the consensus sequence of the 5? TIRs of transposons that belong to 20 families of Transib transposons identified in fruit flies and mosquitoes.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "frequency") (:form . "Frequencies") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 36)\n  (:start . 28) (:id . 49))\n ((:tag . "NNS") (:stem . "nucleotide") (:form . "nucleotides") (:end . 48)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 65)\n  (:start . 57) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 82)\n  (:start . 73) (:id . 56))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 91)\n  (:start . 83) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "tir") (:form . "TIRs") (:end . 106) (:start . 102)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 121)\n  (:start . 110) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "belong") (:form . "belong") (:end . 133)\n  (:start . 127) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 139) (:start . 137)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 148)\n  (:start . 140) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 159)\n  (:start . 152) (:id . 71))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 171)\n  (:start . 160) (:id . 72))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 182)\n  (:start . 172) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 185) (:start . 183)\n  (:id . 74))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 191)\n  (:start . 186) (:id . 75))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 197) (:start . 192)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 201) (:start . 198)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 212)\n  (:start . 202) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.130) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101879@unknown@formal@none@1@S@In one study [12], 35 of 38 (92%) TSDs generated during RAG-mediated intermolecular transposition were 5 bp long, and the remaining 8% were either 4 or 3 bp long.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 48))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 21) (:start . 19)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 50))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 27) (:start . 25)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 29) (:start . 28)\n  (:id . 52))\n ((:tag . "CD") (:stem . "92") (:form . "92") (:end . 31) (:start . 29)\n  (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 32) (:start . 31)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 38) (:start . 34)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 48)\n  (:start . 39) (:id . 57))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 55)\n  (:start . 49) (:id . 58))\n ((:tag . "JJ") (:stem . "rag-mediated") (:form . "RAG-mediated") (:end . 68)\n  (:start . 56) (:id . 59))\n ((:tag . "JJ") (:stem . "intermolecular") (:form . "intermolecular")\n  (:end . 83) (:start . 69) (:id . 60))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n  (:end . 97) (:start . 84) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 102) (:start . 98)\n  (:id . 62))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 104) (:start . 103)\n  (:id . 63))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 107) (:start . 105)\n  (:id . 64))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 112) (:start . 108)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 131)\n  (:start . 122) (:id . 69))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 133) (:start . 132)\n  (:id . 70))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 134) (:start . 133)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 139) (:start . 135)\n  (:id . 72))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 146)\n  (:start . 140) (:id . 73))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 148) (:start . 147)\n  (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 151) (:start . 149)\n  (:id . 75))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 153) (:start . 152)\n  (:id . 76))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 156) (:start . 154)\n  (:id . 77))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 161) (:start . 157)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.140) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101889@unknown@formal@none@1@S@Both RAG1/2-mediated and Transib transpositions show strong preference for GC-rich target sites [12–14,32], even though genomes hosting Transib transposons are AT-rich (Figure S4; Table 2).@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "rag1/2-mediated") (:form . "RAG1/2-mediated")\n  (:end . 20) (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n  (:end . 47) (:start . 33) (:id . 46))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 52) (:start . 48)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 59)\n  (:start . 53) (:id . 48))\n ((:tag . "NN") (:stem . "preference") (:form . "preference") (:end . 70)\n  (:start . 60) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 74) (:start . 71)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "gc-rich") (:form . "GC-rich") (:end . 82)\n  (:start . 75) (:id . 51))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 89)\n  (:start . 83) (:id . 52))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 95) (:start . 90)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 97) (:start . 96)\n  (:id . 54))\n ((:tag . "CD") (:stem . "12–14,32") (:form . "12–14,32") (:end . 105)\n  (:start . 97) (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 106) (:start . 105)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 112) (:start . 108)\n  (:id . 58))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 119)\n  (:start . 113) (:id . 59))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 127)\n  (:start . 120) (:id . 60))\n ((:tag . "VBG") (:stem . "host") (:form . "hosting") (:end . 135)\n  (:start . 128) (:id . 61))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 143)\n  (:start . 136) (:id . 62))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 155)\n  (:start . 144) (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 159) (:start . 156)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "at-rich") (:form . "AT-rich") (:end . 167)\n  (:start . 160) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 175)\n  (:start . 169) (:id . 67))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 178) (:start . 176)\n  (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 179) (:start . 178)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 185)\n  (:start . 180) (:id . 70))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 187) (:start . 186)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s6.150) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101899@unknown@formal@none@1@S@RAG1 Core–Like Sequences in the Sea Urchin, Lancelet, Starlet Sea Anemone, and Hydra Genomes@(((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Core–Like") (:form . "Core–Like") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "Sequence") (:form . "Sequences") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Urchin") (:form . "Urchin") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Lancelet") (:form . "Lancelet") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Starlet") (:form . "Starlet") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "NNP") (:stem . "Sea") (:form . "Sea") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Anemone") (:form . "Anemone") (:end . 73)\n  (:start . 66) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Hydra") (:form . "Hydra") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "NNPS") (:stem . "Genome") (:form . "Genomes") (:end . 92)\n  (:start . 85) (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.160) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5101909@unknown@formal@none@1@S@Although the two proteins are only 38% identical to each other, they share common features: (1) their N-terminal portions are missing and the RAG1-like sequences start at positions 17 or 18; (2) in both proteins the first aa residue overlaps with the acceptor splice site; and (3) their similarity to RAG1 starts at positions corresponding to position 470 of the human RAG1.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 48)\n  (:start . 39) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 81)\n  (:start . 75) (:id . 57))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 90)\n  (:start . 82) (:id . 58))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 94) (:start . 93)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 101)\n  (:start . 96) (:id . 63))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 112)\n  (:start . 102) (:id . 64))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 121)\n  (:start . 113) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 125) (:start . 122)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "miss") (:form . "missing") (:end . 133)\n  (:start . 126) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 151)\n  (:start . 142) (:id . 70))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 161)\n  (:start . 152) (:id . 71))\n ((:tag . "VBP") (:stem . "start") (:form . "start") (:end . 167)\n  (:start . 162) (:id . 72))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 170) (:start . 168)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 180)\n  (:start . 171) (:id . 74))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 183) (:start . 181)\n  (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 186) (:start . 184)\n  (:id . 76))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 189) (:start . 187)\n  (:id . 77))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 190) (:start . 189)\n  (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 192) (:start . 191)\n  (:id . 79))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 193) (:start . 192)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 197) (:start . 195)\n  (:id . 82))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 202) (:start . 198)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 211)\n  (:start . 203) (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 215) (:start . 212)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 221)\n  (:start . 216) (:id . 86))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 224) (:start . 222)\n  (:id . 87))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 232)\n  (:start . 225) (:id . 88))\n ((:tag . "VBZ") (:stem . "overlap") (:form . "overlaps") (:end . 241)\n  (:start . 233) (:id . 89))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 246) (:start . 242)\n  (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 250) (:start . 247)\n  (:id . 91))\n ((:tag . "NN") (:stem . "acceptor") (:form . "acceptor") (:end . 259)\n  (:start . 251) (:id . 92))\n ((:tag . "NN") (:stem . "splice") (:form . "splice") (:end . 266)\n  (:start . 260) (:id . 93))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 271) (:start . 267)\n  (:id . 94))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 272) (:start . 271)\n  (:id . 95))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 276) (:start . 273)\n  (:id . 96))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 278) (:start . 277)\n  (:id . 97))\n ((:tag . "LS") (:stem . "3") (:form . "3") (:end . 279) (:start . 278)\n  (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 280) (:start . 279)\n  (:id . 99))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 286)\n  (:start . 281) (:id . 100))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 297)\n  (:start . 287) (:id . 101))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 300) (:start . 298)\n  (:id . 102))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 305) (:start . 301)\n  (:id . 103))\n ((:tag . "VBZ") (:stem . "start") (:form . "starts") (:end . 312)\n  (:start . 306) (:id . 104))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 315) (:start . 313)\n  (:id . 105))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 325)\n  (:start . 316) (:id . 106))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 339)\n  (:start . 326) (:id . 107))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 342) (:start . 340)\n  (:id . 108))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 351)\n  (:start . 343) (:id . 109))\n ((:tag . "CD") (:stem . "470") (:form . "470") (:end . 355) (:start . 352)\n  (:id . 110))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 358) (:start . 356)\n  (:id . 111))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 362) (:start . 359)\n  (:id . 112))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 368)\n  (:start . 363) (:id . 113))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 373) (:start . 369)\n  (:id . 114))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 374) (:start . 373)\n  (:id . 115)))@@@1@74@((:ncues ((:id . :x6.170.1) (:span 126 133)))\n (:nscopes ((:id . :x6.170.1) (:span 96 133)))\n (:identifiers (:sid . :s6.170) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101919@unknown@formal@none@1@S@Using these trace sequences, we partially assembled a hydra gene, called RAG1L_NM, which encodes the RAG1 core–like protein.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "VBD") (:stem . "assemble") (:form . "assembled") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 72) (:start . 66)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RAG1L_NM") (:form . "RAG1L_NM") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 96)\n  (:start . 89) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 115)\n  (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 123)\n  (:start . 116) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.180) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101929@unknown@formal@none@1@S@Names of these elements are shown above the rectangles.@(((:tag . "NNS") (:stem . "name") (:form . "Names") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "rectangle") (:form . "rectangles") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.190) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101939@unknown@formal@none@1@S@Furthermore, we found that unassembled WGS trace sequences encode two other proteins, P4_SP and P5_SP, similar to the N-terminal RAG1 domain (Figure 6).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "unassembled") (:form . "unassembled") (:end . 38)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "wgs") (:form . "WGS") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 58)\n  (:start . 49) (:id . 50))\n ((:tag . "VBP") (:stem . "encode") (:form . "encode") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "P4_SP") (:form . "P4_SP") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "P5_SP") (:form . "P5_SP") (:end . 101)\n  (:start . 96) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 110)\n  (:start . 103) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 140)\n  (:start . 134) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 148)\n  (:start . 142) (:id . 67))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.200) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101949@unknown@formal@none@1@S@To test whether the reported sea urchin sequences represent a true RAG1-like match, we cut off the ring finger motif and repeated the BLASTP search against all GenBank proteins.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "cut") (:form . "cut") (:end . 90) (:start . 87)\n  (:id . 57))\n ((:tag . "RP") (:stem . "off") (:form . "off") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 110)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 116)\n  (:start . 111) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "repeat") (:form . "repeated") (:end . 129)\n  (:start . 121) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "BLASTP") (:form . "BLASTP") (:end . 140)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 147)\n  (:start . 141) (:id . 67))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 155)\n  (:start . 148) (:id . 68))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 159) (:start . 156)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 167)\n  (:start . 160) (:id . 70))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 176)\n  (:start . 168) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x6.210.1) (:span 8 15)))\n (:hscopes ((:id . :x6.210.1) (:span 8 82)))\n (:identifiers (:sid . :s6.210) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101959@unknown@formal@none@1@S@The sea urchin and lancelet proteins are marked by “_SP” and “_BF” following the identification numbers of the corresponding contigs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 47) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "_SP") (:form . "_SP") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "_BF") (:form . "_BF") (:end . 65) (:start . 62)\n  (:id . 56))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 66) (:start . 65)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 76)\n  (:start . 67) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 59))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 95) (:start . 81) (:id . 60))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 103)\n  (:start . 96) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 124)\n  (:start . 111) (:id . 64))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 132)\n  (:start . 125) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.220) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101969@unknown@formal@none@1@S@As shown in this paper, the RAG1 core was derived from a Transib TPase, but given the low identity between the Transib TPase and the RAG1 core (14%–17%) it is not clear whether the ancestral transposon was a member of the group of canonical Transib transposons preserved in modern genomes of insects, hydra, and sea urchin (see Figure 1), or a member of an unknown group of Transib transposons that encoded a TPase that was more similar to RAG1 core than to the canonical TPase from the currently known Transib transposons.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "paper") (:form . "paper") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 32) (:start . 28)\n  (:id . 49))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 37) (:start . 33)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 49)\n  (:start . 42) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 54) (:start . 50)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 64)\n  (:start . 57) (:id . 55))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 70) (:start . 65)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 75) (:start . 72)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 81) (:start . 76)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 89) (:start . 86)\n  (:id . 61))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 98)\n  (:start . 90) (:id . 62))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 106)\n  (:start . 99) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 118)\n  (:start . 111) (:id . 65))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 124)\n  (:start . 119) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 68))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 137) (:start . 133)\n  (:id . 69))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 142) (:start . 138)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 71))\n ((:tag . "CD") (:stem . "14%–17") (:form . "14%–17") (:end . 150)\n  (:start . 144) (:id . 72))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 151) (:start . 150)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 74))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 155) (:start . 153)\n  (:id . 75))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 158) (:start . 156)\n  (:id . 76))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 162) (:start . 159)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 168)\n  (:start . 163) (:id . 78))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 176)\n  (:start . 169) (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "ancestral") (:form . "ancestral") (:end . 190)\n  (:start . 181) (:id . 81))\n ((:tag . "NN") (:stem . "transposon") (:form . "transposon") (:end . 201)\n  (:start . 191) (:id . 82))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 205) (:start . 202)\n  (:id . 83))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 207) (:start . 206)\n  (:id . 84))\n ((:tag . "NN") (:stem . "member") (:form . "member") (:end . 214)\n  (:start . 208) (:id . 85))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 217) (:start . 215)\n  (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 221) (:start . 218)\n  (:id . 87))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 227)\n  (:start . 222) (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 230) (:start . 228)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "canonical") (:form . "canonical") (:end . 240)\n  (:start . 231) (:id . 90))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 248)\n  (:start . 241) (:id . 91))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 260)\n  (:start . 249) (:id . 92))\n ((:tag . "VBN") (:stem . "preserve") (:form . "preserved") (:end . 270)\n  (:start . 261) (:id . 93))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 273) (:start . 271)\n  (:id . 94))\n ((:tag . "JJ") (:stem . "modern") (:form . "modern") (:end . 280)\n  (:start . 274) (:id . 95))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 288)\n  (:start . 281) (:id . 96))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 291) (:start . 289)\n  (:id . 97))\n ((:tag . "NNS") (:stem . "insect") (:form . "insects") (:end . 299)\n  (:start . 292) (:id . 98))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 300) (:start . 299)\n  (:id . 99))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 306)\n  (:start . 301) (:id . 100))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 307) (:start . 306)\n  (:id . 101))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 311) (:start . 308)\n  (:id . 102))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 315) (:start . 312)\n  (:id . 103))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 322)\n  (:start . 316) (:id . 104))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 324) (:start . 323)\n  (:id . 105))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 327) (:start . 324)\n  (:id . 106))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 334)\n  (:start . 328) (:id . 107))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 336) (:start . 335)\n  (:id . 108))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 337) (:start . 336)\n  (:id . 109))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 338) (:start . 337)\n  (:id . 110))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 341) (:start . 339)\n  (:id . 111))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 343) (:start . 342)\n  (:id . 112))\n ((:tag . "NN") (:stem . "member") (:form . "member") (:end . 350)\n  (:start . 344) (:id . 113))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 353) (:start . 351)\n  (:id . 114))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 356) (:start . 354)\n  (:id . 115))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 364)\n  (:start . 357) (:id . 116))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 370)\n  (:start . 365) (:id . 117))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 373) (:start . 371)\n  (:id . 118))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 381)\n  (:start . 374) (:id . 119))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 393)\n  (:start . 382) (:id . 120))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 398) (:start . 394)\n  (:id . 121))\n ((:tag . "VBD") (:stem . "encode") (:form . "encoded") (:end . 406)\n  (:start . 399) (:id . 122))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 408) (:start . 407)\n  (:id . 123))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 414)\n  (:start . 409) (:id . 124))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 419) (:start . 415)\n  (:id . 125))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 423) (:start . 420)\n  (:id . 126))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 428) (:start . 424)\n  (:id . 127))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 436)\n  (:start . 429) (:id . 128))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 439) (:start . 437)\n  (:id . 129))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 444) (:start . 440)\n  (:id . 130))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 449) (:start . 445)\n  (:id . 131))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 454) (:start . 450)\n  (:id . 132))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 457) (:start . 455)\n  (:id . 133))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 461) (:start . 458)\n  (:id . 134))\n ((:tag . "JJ") (:stem . "canonical") (:form . "canonical") (:end . 471)\n  (:start . 462) (:id . 135))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 477)\n  (:start . 472) (:id . 136))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 482) (:start . 478)\n  (:id . 137))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 486) (:start . 483)\n  (:id . 138))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 496)\n  (:start . 487) (:id . 139))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 502)\n  (:start . 497) (:id . 140))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 510)\n  (:start . 503) (:id . 141))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 522)\n  (:start . 511) (:id . 142))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 523) (:start . 522)\n  (:id . 143)))@@@1@102@((:hcues ((:id . :x6.230.1) (:span 339 341))\n  ((:id . :x6.230.2) (:span 169 176)) ((:id . :x6.230.3) (:span 159 168)))\n (:hscopes ((:id . :x6.230.1) (:span 206 522))\n  ((:id . :x6.230.2) (:span 169 522)) ((:id . :x6.230.3) (:span 159 522)))\n (:identifiers (:sid . :s6.230) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101979@unknown@formal@none@1@S@Nevertheless, based on the orientations and relative positions of these transposons, none of them appears to be associated with the RAG1-like sequences (see Figure 5).@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "orientation") (:form . "orientations") (:end . 39)\n  (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 105)\n  (:start . 98) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 122)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "rag1-like") (:form . "RAG1-like") (:end . 141)\n  (:start . 132) (:id . 64))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 151)\n  (:start . 142) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 156) (:start . 153)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 163)\n  (:start . 157) (:id . 68))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 165) (:start . 164)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x6.240.2) (:span 98 105)))\n (:ncues ((:id . :x6.240.1) (:span 85 89)))\n (:hscopes ((:id . :x6.240.2) (:span 85 151)))\n (:nscopes ((:id . :x6.240.1) (:span 85 151)))\n (:identifiers (:sid . :s6.240) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101989@unknown@formal@none@1@S@In the sea urchin, lancelet, hydra, and starlet sea anemone genomes, the RAG1 core–like sequences and the N-terminal domain–like sequences do not appear to be linked to each other or to any other proteins.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "lancelet") (:form . "lancelet") (:end . 27)\n  (:start . 19) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hydra") (:form . "hydra") (:end . 34) (:start . 29)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "NN") (:stem . "starlet") (:form . "starlet") (:end . 47)\n  (:start . 40) (:id . 52))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 51) (:start . 48)\n  (:id . 53))\n ((:tag . "NN") (:stem . "anemone") (:form . "anemone") (:end . 59)\n  (:start . 52) (:id . 54))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 67)\n  (:start . 60) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 57))\n ((:tag . "NN") (:stem . "rag1") (:form . "RAG1") (:end . 77) (:start . 73)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "core–like") (:form . "core–like") (:end . 87)\n  (:start . 78) (:id . 59))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 97)\n  (:start . 88) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 116)\n  (:start . 106) (:id . 63))\n ((:tag . "JJ") (:stem . "domain–like") (:form . "domain–like") (:end . 128)\n  (:start . 117) (:id . 64))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 138)\n  (:start . 129) (:id . 65))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 141) (:start . 139)\n  (:id . 66))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 152)\n  (:start . 146) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 155) (:start . 153)\n  (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 165)\n  (:start . 159) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 168) (:start . 166)\n  (:id . 72))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 173) (:start . 169)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 179)\n  (:start . 174) (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 182) (:start . 180)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 185) (:start . 183)\n  (:id . 76))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 189) (:start . 186)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 195)\n  (:start . 190) (:id . 78))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 204)\n  (:start . 196) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x6.250.2) (:span 146 152)))\n (:ncues ((:id . :x6.250.1) (:span 142 145)))\n (:hscopes ((:id . :x6.250.2) (:span 69 204)))\n (:nscopes ((:id . :x6.250.1) (:span 69 204)))\n (:identifiers (:sid . :s6.250) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5101999@unknown@formal@none@1@S@Again, it is unclear if this part is not present in sea urchins or simply undetectable due to its small size and the high sequence divergence.@(((:tag . "RB") (:stem . "again") (:form . "Again") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 33) (:start . 29)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 40) (:start . 37)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 48)\n  (:start . 41) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 55) (:start . 52)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "urchin") (:form . "urchins") (:end . 63)\n  (:start . 56) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 66) (:start . 64)\n  (:id . 56))\n ((:tag . "RB") (:stem . "simply") (:form . "simply") (:end . 73)\n  (:start . 67) (:id . 57))\n ((:tag . "JJ") (:stem . "undetectable") (:form . "undetectable") (:end . 86)\n  (:start . 74) (:id . 58))\n ((:tag . "IN") (:stem . "due") (:form . "due") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 97) (:start . 94)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 103) (:start . 98)\n  (:id . 62))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 108) (:start . 104)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 121) (:start . 117)\n  (:id . 66))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 130)\n  (:start . 122) (:id . 67))\n ((:tag . "NN") (:stem . "divergence") (:form . "divergence") (:end . 141)\n  (:start . 131) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x6.260.2) (:span 64 66)) ((:id . :x6.260.3) (:span 21 23))\n  ((:id . :x6.260.4) (:span 13 20)))\n (:ncues ((:id . :x6.260.1) (:span 37 40)))\n (:hscopes ((:id . :x6.260.2) (:span 37 63))\n  ((:id . :x6.260.3) (:span 21 141)) ((:id . :x6.260.4) (:span 13 141)))\n (:nscopes ((:id . :x6.260.1) (:span 37 86)))\n (:identifiers (:sid . :s6.260) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102009@unknown@formal@none@1@S@The observed sequence similarity between the RAG1 and Transib TPase protein can help to identify aa residues in the TPase that are crucial for transposition of Transib transposons.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 40)\n  (:start . 33) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 75)\n  (:start . 68) (:id . 52))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "JJ") (:stem . "aa") (:form . "aa") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 108)\n  (:start . 100) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 121)\n  (:start . 116) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 138)\n  (:start . 131) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n  (:id . 65))\n ((:tag . "NN") (:stem . "transposition") (:form . "transposition")\n  (:end . 156) (:start . 143) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 159) (:start . 157)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 167)\n  (:start . 160) (:id . 68))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 179)\n  (:start . 168) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x6.270.1) (:span 76 79)))\n (:hscopes ((:id . :x6.270.1) (:span 76 179)))\n (:identifiers (:sid . :s6.270) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102019@unknown@formal@none@1@S@Second, although RAG1/2-mediated transpositions are characterized by 5-bp (sometimes 4-bp) TSDs, all known hAT transposons are characterized by 8-bp TSDs.@(((:tag . "RB") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "rag1/2-mediated") (:form . "RAG1/2-mediated")\n  (:end . 32) (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "transposition") (:form . "transpositions")\n  (:end . 47) (:start . 33) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 51) (:start . 48)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 65) (:start . 52) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 68) (:start . 66)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 73) (:start . 69)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 51))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 84)\n  (:start . 75) (:id . 52))\n ((:tag . "JJ") (:stem . "4-bp") (:form . "4-bp") (:end . 89) (:start . 85)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "TSD") (:form . "TSDs") (:end . 95) (:start . 91)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 106)\n  (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 110) (:start . 107)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 122)\n  (:start . 111) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 140) (:start . 127) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 143) (:start . 141)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "8-bp") (:form . "8-bp") (:end . 148) (:start . 144)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 153) (:start . 149)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.280) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102029@unknown@formal@none@1@S@Partially assembled S. purpuratus contig sequences were downloaded on 12 August 2004 from the Baylor College of Medicine through the Web site at ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Spurpuratus/blast/Spur20030922-genome.@(((:tag . "RB") (:stem . "partially") (:form . "Partially") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "assemble") (:form . "assembled") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "purpuratus") (:form . "purpuratus") (:end . 33)\n  (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 40)\n  (:start . 34) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 50)\n  (:start . 41) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 66)\n  (:start . 56) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 69) (:start . 67)\n  (:id . 50))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "August") (:form . "August") (:end . 79)\n  (:start . 73) (:id . 52))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 84) (:start . 80)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Baylor") (:form . "Baylor") (:end . 100)\n  (:start . 94) (:id . 56))\n ((:tag . "NNP") (:stem . "College") (:form . "College") (:end . 108)\n  (:start . 101) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Medicine") (:form . "Medicine") (:end . 120)\n  (:start . 112) (:id . 59))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 128)\n  (:start . 121) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 136) (:start . 133)\n  (:id . 62))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 141) (:start . 137)\n  (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "NN")\n  (:stem\n   . "ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Spurpuratus/blast/Spur20030922-genome")\n  (:form\n   . "ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Spurpuratus/blast/Spur20030922-genome")\n  (:end . 218) (:start . 145) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.290) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102039@unknown@formal@none@1@S@To avoid background noise introduced by mutations, Transib relics, whose TPase-coding regions contained numerous stop codons and indels, were ignored unless several copies were available.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "relic") (:form . "relics") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 72) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "tpase-coding") (:form . "TPase-coding") (:end . 85)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 103)\n  (:start . 94) (:id . 56))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 112)\n  (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 117) (:start . 113)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "codon") (:form . "codons") (:end . 124)\n  (:start . 118) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "indel") (:form . "indels") (:end . 135)\n  (:start . 129) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 141) (:start . 137)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "ignore") (:form . "ignored") (:end . 149)\n  (:start . 142) (:id . 64))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 156)\n  (:start . 150) (:id . 65))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 164)\n  (:start . 157) (:id . 66))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 171)\n  (:start . 165) (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 176) (:start . 172)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 186)\n  (:start . 177) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.300) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102049@unknown@formal@none@1@S@A standalone 2001 version of PSI (Position-Specific Iterating)-BLAST [18,45] was used for detection of proteins that were significantly similar to TPases encoded by Transib and other superfamilies of DNA transposons.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "standalone") (:form . "standalone") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PSI") (:form . "PSI") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "position-specific") (:form . "Position-Specific")\n  (:end . 51) (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "Iterating)-BLAST") (:form . "Iterating)-BLAST")\n  (:end . 68) (:start . 52) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "CD") (:stem . "18,45") (:form . "18,45") (:end . 75) (:start . 70)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 99)\n  (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 111)\n  (:start . 103) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 121) (:start . 117)\n  (:id . 61))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 135) (:start . 122) (:id . 62))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 143)\n  (:start . 136) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 153)\n  (:start . 147) (:id . 65))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 161)\n  (:start . 154) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 164) (:start . 162)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 172)\n  (:start . 165) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 182)\n  (:start . 177) (:id . 70))\n ((:tag . "NNS") (:stem . "superfamily") (:form . "superfamilies")\n  (:end . 196) (:start . 183) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 199) (:start . 197)\n  (:id . 72))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 203) (:start . 200)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "transposon") (:form . "transposons") (:end . 215)\n  (:start . 204) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s6.310) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102059@unknown@formal@none@1@S@The following protocol describes the procedure: (1) Use a GenBank set combined with N number of Transib TPases (in our studies, N was equal to 7, 13, and 18), (2) run PSI-BLAST against GenBank combined with TPases using each TPase as a query or seed, (3) select only Transib TPase sequences with E-values less than 10-5 to define the PSSM, (4) take the best E-value (Ei) obtained by PSI-BLAST for RAG1s when PSSM is constructed without RAG1, then (5) repeat these operations for different numbers (N) of TPases.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "describe") (:form . "describes") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "VB") (:stem . "use") (:form . "Use") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 65)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 78)\n  (:start . 70) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 92)\n  (:start . 86) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 103)\n  (:start . 96) (:id . 61))\n ((:tag . "NNP") (:stem . "TPas") (:form . "TPases") (:end . 110)\n  (:start . 104) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 64))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 118) (:start . 115)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 126)\n  (:start . 119) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 129) (:start . 128)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 133) (:start . 130)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 139)\n  (:start . 134) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 71))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 144) (:start . 143)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 73))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 148) (:start . 146)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n  (:id . 76))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 156) (:start . 154)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 80))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 161) (:start . 160)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 82))\n ((:tag . "VB") (:stem . "run") (:form . "run") (:end . 166) (:start . 163)\n  (:id . 83))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 176)\n  (:start . 167) (:id . 84))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 184)\n  (:start . 177) (:id . 85))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 192)\n  (:start . 185) (:id . 86))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 201)\n  (:start . 193) (:id . 87))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 206) (:start . 202)\n  (:id . 88))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 213)\n  (:start . 207) (:id . 89))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 219) (:start . 214)\n  (:id . 90))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 224) (:start . 220)\n  (:id . 91))\n ((:tag . "NN") (:stem . "tpase") (:form . "TPase") (:end . 230)\n  (:start . 225) (:id . 92))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 233) (:start . 231)\n  (:id . 93))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 235) (:start . 234)\n  (:id . 94))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 241)\n  (:start . 236) (:id . 95))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 244) (:start . 242)\n  (:id . 96))\n ((:tag . "NN") (:stem . "seed") (:form . "seed") (:end . 249) (:start . 245)\n  (:id . 97))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 250) (:start . 249)\n  (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 252) (:start . 251)\n  (:id . 99))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 253) (:start . 252)\n  (:id . 100))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 254) (:start . 253)\n  (:id . 101))\n ((:tag . "VBP") (:stem . "select") (:form . "select") (:end . 261)\n  (:start . 255) (:id . 102))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 266) (:start . 262)\n  (:id . 103))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 274)\n  (:start . 267) (:id . 104))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 280)\n  (:start . 275) (:id . 105))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 290)\n  (:start . 281) (:id . 106))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 295) (:start . 291)\n  (:id . 107))\n ((:tag . "NNS") (:stem . "e-value") (:form . "E-values") (:end . 304)\n  (:start . 296) (:id . 108))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 309) (:start . 305)\n  (:id . 109))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 314) (:start . 310)\n  (:id . 110))\n ((:tag . "CD") (:stem . "10-5") (:form . "10-5") (:end . 319) (:start . 315)\n  (:id . 111))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 322) (:start . 320)\n  (:id . 112))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 329)\n  (:start . 323) (:id . 113))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 333) (:start . 330)\n  (:id . 114))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 338) (:start . 334)\n  (:id . 115))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 339) (:start . 338)\n  (:id . 116))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 341) (:start . 340)\n  (:id . 117))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 342) (:start . 341)\n  (:id . 118))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 343) (:start . 342)\n  (:id . 119))\n ((:tag . "VBP") (:stem . "take") (:form . "take") (:end . 348) (:start . 344)\n  (:id . 120))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 352) (:start . 349)\n  (:id . 121))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 357) (:start . 353)\n  (:id . 122))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 365)\n  (:start . 358) (:id . 123))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 367) (:start . 366)\n  (:id . 124))\n ((:tag . "NNP") (:stem . "Ei") (:form . "Ei") (:end . 369) (:start . 367)\n  (:id . 125))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 370) (:start . 369)\n  (:id . 126))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 379)\n  (:start . 371) (:id . 127))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 382) (:start . 380)\n  (:id . 128))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 392)\n  (:start . 383) (:id . 129))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 396) (:start . 393)\n  (:id . 130))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1s") (:end . 402)\n  (:start . 397) (:id . 131))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 407) (:start . 403)\n  (:id . 132))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 412) (:start . 408)\n  (:id . 133))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 415) (:start . 413)\n  (:id . 134))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 427)\n  (:start . 416) (:id . 135))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 435)\n  (:start . 428) (:id . 136))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 440) (:start . 436)\n  (:id . 137))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 441) (:start . 440)\n  (:id . 138))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 446) (:start . 442)\n  (:id . 139))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 448) (:start . 447)\n  (:id . 140))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 449) (:start . 448)\n  (:id . 141))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 450) (:start . 449)\n  (:id . 142))\n ((:tag . "VBP") (:stem . "repeat") (:form . "repeat") (:end . 457)\n  (:start . 451) (:id . 143))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 463)\n  (:start . 458) (:id . 144))\n ((:tag . "NNS") (:stem . "operation") (:form . "operations") (:end . 474)\n  (:start . 464) (:id . 145))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 478) (:start . 475)\n  (:id . 146))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 488)\n  (:start . 479) (:id . 147))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 496)\n  (:start . 489) (:id . 148))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 498) (:start . 497)\n  (:id . 149))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 499) (:start . 498)\n  (:id . 150))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 500) (:start . 499)\n  (:id . 151))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 503) (:start . 501)\n  (:id . 152))\n ((:tag . "NNS") (:stem . "tpas") (:form . "TPases") (:end . 510)\n  (:start . 504) (:id . 153))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 511) (:start . 510)\n  (:id . 154)))@@@1@113@((:ncues ((:id . :x6.320.1) (:span 428 435)))\n (:nscopes ((:id . :x6.320.1) (:span 428 440)))\n (:identifiers (:sid . :s6.320) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102069@unknown@formal@none@1@S@One of the 5-bp TSDs flanking the 3? terminus of a Transib was excluded in each case.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "5-bp") (:form . "5-bp") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "tsd") (:form . "TSDs") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 45)\n  (:start . 37) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 58)\n  (:start . 51) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 62) (:start . 59)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 71)\n  (:start . 63) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 79) (:start . 75)\n  (:id . 58))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 84) (:start . 80)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.330) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102079@unknown@formal@none@1@S@Multiple Alignment of the RAG1 Core and Transib TPase Proteins@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "Alignment") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RAG1") (:form . "RAG1") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Core") (:form . "Core") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 62)\n  (:start . 54) (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.340) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5102089@unknown@formal@none@1@S@Dots indicate nucleotide identity with the consensus sequence; hyphens represent alignment gaps.@(((:tag . "NNS") (:stem . "dot") (:form . "Dots") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "hyphen") (:form . "hyphens") (:end . 70)\n  (:start . 63) (:id . 51))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 80)\n  (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 90)\n  (:start . 81) (:id . 53))\n ((:tag . "NNS") (:stem . "gap") (:form . "gaps") (:end . 95) (:start . 91)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.350) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102099@unknown@formal@none@1@S@(G) TransibN1_SP family from sea urchin.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "TransibN1_SP") (:form . "TransibN1_SP") (:end . 16)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sea") (:form . "sea") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "urchin") (:form . "urchin") (:end . 39)\n  (:start . 33) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.360) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102109@unknown@formal@none@1@S@Structure of hAT 5? Termini@(((:tag . "NN") (:stem . "structure") (:form . "Structure") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "hat") (:form . "hAT") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Termini") (:form . "Termini") (:end . 27)\n  (:start . 20) (:id . 47)))@@@1@6@((:identifiers (:sid . :s6.370) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5102119@unknown@formal@none@1@S@Columns 1 and 2 list common and Latin names of species whose genomes contain Transib TPase sequences.@(((:tag . "NNS") (:stem . "column") (:form . "Columns") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 9) (:start . 8)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 27)\n  (:start . 21) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "latin") (:form . "Latin") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "name") (:form . "names") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 54)\n  (:start . 47) (:id . 52))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 68)\n  (:start . 61) (:id . 54))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 76)\n  (:start . 69) (:id . 55))\n ((:tag . "NNP") (:stem . "Transib") (:form . "Transib") (:end . 84)\n  (:start . 77) (:id . 56))\n ((:tag . "NNP") (:stem . "TPase") (:form . "TPase") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 100)\n  (:start . 91) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.380) (:did . :pmc1131882) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102129@unknown@formal@none@1@S@A Role for Adenosine Deaminase in Drosophila Larval Development@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Role") (:form . "Role") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Adenosine") (:form . "Adenosine") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "NNP") (:stem . "Deaminase") (:form . "Deaminase") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 44)\n  (:start . 34) (:id . 48))\n ((:tag . "NNP") (:stem . "Larval") (:form . "Larval") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "NNP") (:stem . "Development") (:form . "Development") (:end . 63)\n  (:start . 52) (:id . 50)))@@@1@9@((:identifiers (:sid . :s7.1) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5102139@unknown@formal@none@1@S@Adenosine deaminase (ADA) is an enzyme present in all organisms that catalyzes the irreversible deamination of adenosine and deoxyadenosine to inosine and deoxyinosine.@(((:tag . "NNP") (:stem . "Adenosine") (:form . "Adenosine") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "deaminase") (:form . "deaminase") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "ADA") (:form . "ADA") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 63)\n  (:start . 54) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "catalyze") (:form . "catalyzes") (:end . 78)\n  (:start . 69) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "irreversible") (:form . "irreversible") (:end . 95)\n  (:start . 83) (:id . 57))\n ((:tag . "NN") (:stem . "deamination") (:form . "deamination") (:end . 107)\n  (:start . 96) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 120)\n  (:start . 111) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 61))\n ((:tag . "NN") (:stem . "deoxyadenosine") (:form . "deoxyadenosine")\n  (:end . 139) (:start . 125) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "NN") (:stem . "inosine") (:form . "inosine") (:end . 150)\n  (:start . 143) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 65))\n ((:tag . "NN") (:stem . "deoxyinosine") (:form . "deoxyinosine") (:end . 167)\n  (:start . 155) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.11) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102149@unknown@formal@none@1@S@The predominant source of extracellular adenosine during systemic activation of the stress system is the sympathetic nervous system [7].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "predominant") (:form . "predominant") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 39) (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 49)\n  (:start . 40) (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 56)\n  (:start . 50) (:id . 48))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 65)\n  (:start . 57) (:id . 49))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 76)\n  (:start . 66) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 52))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 90)\n  (:start . 84) (:id . 53))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 97)\n  (:start . 91) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 100) (:start . 98)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "sympathetic") (:form . "sympathetic") (:end . 116)\n  (:start . 105) (:id . 57))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 124)\n  (:start . 117) (:id . 58))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 131)\n  (:start . 125) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 133) (:start . 132)\n  (:id . 60))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 134) (:start . 133)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.21) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102159@unknown@formal@none@1@S@We also demonstrated that adenosine functions as a negative signal for cell proliferation and concluded that ADGFs stimulate cell growth in vitro by depletion of extracellular adenosine [16].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 20)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "VBZ") (:stem . "function") (:form . "functions") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 89) (:start . 76) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "conclude") (:form . "concluded") (:end . 103)\n  (:start . 94) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "ADGF") (:form . "ADGFs") (:end . 114)\n  (:start . 109) (:id . 58))\n ((:tag . "VBP") (:stem . "stimulate") (:form . "stimulate") (:end . 124)\n  (:start . 115) (:id . 59))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 129) (:start . 125)\n  (:id . 60))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 136)\n  (:start . 130) (:id . 61))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 62))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 145)\n  (:start . 140) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 148) (:start . 146)\n  (:id . 64))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 158)\n  (:start . 149) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 175) (:start . 162) (:id . 67))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 185)\n  (:start . 176) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 187) (:start . 186)\n  (:id . 69))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 189) (:start . 187)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 190) (:start . 189)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.31) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102169@unknown@formal@none@1@S@Some homozygous third-instar larvae can be found alive in the vial even after 10 d of development.@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "third-instar") (:form . "third-instar") (:end . 28)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 35)\n  (:start . 29) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 39) (:start . 36)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "alive") (:form . "alive") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "vial") (:form . "vial") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 77) (:start . 72)\n  (:id . 54))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "d") (:form . "d") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 97)\n  (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.41) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102179@unknown@formal@none@1@S@This result confirms that the mutant phenotype is caused by the mutation in the ADGF-A gene.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "confirm") (:form . "confirms") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 86)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.51) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102189@unknown@formal@none@1@S@Each experiment was repeated at least four times (with 20–30 animals in each vial) and the standard error is shown.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "repeat") (:form . "repeated") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "CD") (:stem . "20–30") (:form . "20–30") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "vial") (:form . "vial") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 99)\n  (:start . 91) (:id . 60))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 105)\n  (:start . 100) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 114)\n  (:start . 109) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.61) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102199@unknown@formal@none@1@S@However, neither of the two lines carrying the mutated version of the UAS-ADGF-A (producing full-length protein detected by anti-myc antibody; see Materials and Methods) showed any rescue of the mutant phenotype.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "neither") (:form . "neither") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "UAS-ADGF-A") (:form . "UAS-ADGF-A") (:end . 80)\n  (:start . 70) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 103)\n  (:start . 92) (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 111)\n  (:start . 104) (:id . 59))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 120)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "anti-myc") (:form . "anti-myc") (:end . 132)\n  (:start . 124) (:id . 62))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 141)\n  (:start . 133) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 142) (:start . 141)\n  (:id . 64))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 156)\n  (:start . 147) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 168)\n  (:start . 161) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 69))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 176)\n  (:start . 170) (:id . 70))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 180) (:start . 177)\n  (:id . 71))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 187)\n  (:start . 181) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 190) (:start . 188)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 201)\n  (:start . 195) (:id . 75))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 211)\n  (:start . 202) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 77)))@@@1@36@((:ncues ((:id . :x7.71.1) (:span 9 16)))\n (:nscopes ((:id . :x7.71.1) (:span 9 211)))\n (:identifiers (:sid . :s7.71) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102209@unknown@formal@none@1@S@This process is similar to normal metamorphic changes, in which the hemocytes are first released from the front lobes, and the posterior lobes disperse later.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "metamorphic") (:form . "metamorphic") (:end . 45)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 77)\n  (:start . 68) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 87) (:start . 82)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "release") (:form . "released") (:end . 96)\n  (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "front") (:form . "front") (:end . 111)\n  (:start . 106) (:id . 60))\n ((:tag . "NNS") (:stem . "lobe") (:form . "lobes") (:end . 117)\n  (:start . 112) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 136)\n  (:start . 127) (:id . 65))\n ((:tag . "NNS") (:stem . "lobe") (:form . "lobes") (:end . 142)\n  (:start . 137) (:id . 66))\n ((:tag . "VBP") (:stem . "disperse") (:form . "disperse") (:end . 151)\n  (:start . 143) (:id . 67))\n ((:tag . "RB") (:stem . "later") (:form . "later") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.81) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102219@unknown@formal@none@1@S@Hemocyte Abnormalities in adgf-a Mutant Larvae@(((:tag . "NNP") (:stem . "Hemocyte") (:form . "Hemocyte") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "abnormality") (:form . "Abnormalities") (:end . 22)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "adgf-a") (:form . "adgf-a") (:end . 32)\n  (:start . 26) (:id . 45))\n ((:tag . "NNP") (:stem . "Mutant") (:form . "Mutant") (:end . 39)\n  (:start . 33) (:id . 46))\n ((:tag . "NNP") (:stem . "Larvae") (:form . "Larvae") (:end . 46)\n  (:start . 40) (:id . 47)))@@@1@6@((:identifiers (:sid . :s7.91) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5102229@unknown@formal@none@1@S@Crystal Cells in Late Third Instar Larvae@(((:tag . "JJ") (:stem . "crystal") (:form . "Crystal") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Cell") (:form . "Cells") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Late") (:form . "Late") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Third") (:form . "Third") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Instar") (:form . "Instar") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NNP") (:stem . "Larvae") (:form . "Larvae") (:end . 41)\n  (:start . 35) (:id . 48)))@@@1@7@((:identifiers (:sid . :s7.101) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5102239@unknown@formal@none@1@S@The number of hemocytes is also reduced, but to a lesser extent in larvae rescued by Cg-Gal4/UAS-ADGF-A.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "JJR") (:stem . "less") (:form . "lesser") (:end . 56) (:start . 50)\n  (:id . 53))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 63)\n  (:start . 57) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 73)\n  (:start . 67) (:id . 56))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 81)\n  (:start . 74) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Cg-Gal4/UAS-ADGF-A") (:form . "Cg-Gal4/UAS-ADGF-A")\n  (:end . 103) (:start . 85) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.111) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102249@unknown@formal@none@1@S@No rescue of the phenotype, including body shape of escaping pupae, was observed.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "shape") (:form . "shape") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "escape") (:form . "escaping") (:end . 60)\n  (:start . 52) (:id . 52))\n ((:tag . "NN") (:stem . "pupae") (:form . "pupae") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 80)\n  (:start . 72) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 57)))@@@1@16@((:ncues ((:id . :x7.121.1) (:span 0 2)))\n (:nscopes ((:id . :x7.121.1) (:span 0 80)))\n (:identifiers (:sid . :s7.121) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102259@unknown@formal@none@1@S@However, the delay in development and block of pupariation (Figure 6B), as well as the pupal body shape, were not influenced by this mutation.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "delay") (:form . "delay") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 33)\n  (:start . 22) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "block") (:form . "block") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "pupariation") (:form . "pupariation") (:end . 58)\n  (:start . 47) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "6b") (:form . "6B") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 74) (:start . 72)\n  (:id . 57))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 79) (:start . 75)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "pupal") (:form . "pupal") (:end . 92) (:start . 87)\n  (:id . 61))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 97) (:start . 93)\n  (:id . 62))\n ((:tag . "NN") (:stem . "shape") (:form . "shape") (:end . 103) (:start . 98)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 109) (:start . 105)\n  (:id . 65))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 113) (:start . 110)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "influence") (:form . "influenced") (:end . 124)\n  (:start . 114) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 127) (:start . 125)\n  (:id . 68))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 132) (:start . 128)\n  (:id . 69))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 141)\n  (:start . 133) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 71)))@@@1@30@((:ncues ((:id . :x7.131.1) (:span 110 113)))\n (:nscopes ((:id . :x7.131.1) (:span 9 141)))\n (:identifiers (:sid . :s7.131) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102269@unknown@formal@none@1@S@Previous results suggest that fat body disintegration might be caused by the action of hemocytes.@(((:tag . "JJ") (:stem . "previous") (:form . "Previous") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "fat") (:form . "fat") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "disintegration") (:form . "disintegration")\n  (:end . 53) (:start . 39) (:id . 48))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 59) (:start . 54)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 69)\n  (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 96)\n  (:start . 87) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x7.141.1) (:span 54 59)) ((:id . :x7.141.2) (:span 17 24)))\n (:hscopes ((:id . :x7.141.1) (:span 30 96))\n  ((:id . :x7.141.2) (:span 17 96)))\n (:identifiers (:sid . :s7.141) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102279@unknown@formal@none@1@S@Mutation in a Putative Adenosine Receptor Suppresses the Block of Pupariation in adgf-a@(((:tag . "NN") (:stem . "mutation") (:form . "Mutation") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "putative") (:form . "Putative") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "NNP") (:stem . "Adenosine") (:form . "Adenosine") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NNP") (:stem . "Receptor") (:form . "Receptor") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "VBZ") (:stem . "suppress") (:form . "Suppresses") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Block") (:form . "Block") (:end . 62) (:start . 57)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Pupariation") (:form . "Pupariation") (:end . 77)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "NN") (:stem . "adgf-a") (:form . "adgf-a") (:end . 87)\n  (:start . 81) (:id . 54)))@@@1@13@((:hcues ((:id . :x7.151.1) (:span 14 22)))\n (:hscopes ((:id . :x7.151.1) (:span 14 41)))\n (:identifiers (:sid . :s7.151) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5102289@unknown@formal@none@1@S@Ecdysone Regulation of Development in adgf-a@(((:tag . "NNP") (:stem . "Ecdysone") (:form . "Ecdysone") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 19)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Development") (:form . "Development") (:end . 34)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "NN") (:stem . "adgf-a") (:form . "adgf-a") (:end . 44)\n  (:start . 38) (:id . 47)))@@@1@6@((:identifiers (:sid . :s7.161) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5102299@unknown@formal@none@1@S@The delayed development and low pupariation rate in the adgf-a mutant larvae (see Figures 2A and 7A) could be caused by an effect on hormonal regulation of development.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "delay") (:form . "delayed") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pupariation") (:form . "pupariation") (:end . 43)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "adgf-a") (:form . "adgf-a") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 76)\n  (:start . 70) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "7a") (:form . "7A") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 106)\n  (:start . 101) (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 116)\n  (:start . 110) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 119) (:start . 117)\n  (:id . 64))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 122) (:start . 120)\n  (:id . 65))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 129)\n  (:start . 123) (:id . 66))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 132) (:start . 130)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "hormonal") (:form . "hormonal") (:end . 141)\n  (:start . 133) (:id . 68))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 152)\n  (:start . 142) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 167)\n  (:start . 156) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x7.171.1) (:span 101 106)))\n (:hscopes ((:id . :x7.171.1) (:span 0 167)))\n (:identifiers (:sid . :s7.171) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102309@unknown@formal@none@1@S@All analyzed adgf-a mutant larvae carrying the Sgs?3-GFP construct showed normal expression of Sgs-GFP in salivary glands (Figure 7D).@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "adgf-a") (:form . "adgf-a") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sgs?3-GFP") (:form . "Sgs?3-GFP") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 66)\n  (:start . 57) (:id . 50))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 73) (:start . 67)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 91)\n  (:start . 81) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sgs-GFP") (:form . "Sgs-GFP") (:end . 102)\n  (:start . 95) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "salivary") (:form . "salivary") (:end . 114)\n  (:start . 106) (:id . 57))\n ((:tag . "NNS") (:stem . "gland") (:form . "glands") (:end . 121)\n  (:start . 115) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 129)\n  (:start . 123) (:id . 60))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 132) (:start . 130)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.181) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102319@unknown@formal@none@1@S@Overexpression of ADGF-A in animals with a hypomorphic cact combination (cactE8/cactIIIG) increased the adult survival rate almost 4-fold (Figure 8A).@(((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 24)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "hypomorphic") (:form . "hypomorphic") (:end . 54)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "cact") (:form . "cact") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 71)\n  (:start . 60) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "cactE8/cactIIIG") (:form . "cactE8/cactIIIG")\n  (:end . 88) (:start . 73) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 99)\n  (:start . 90) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 109)\n  (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 118)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 130)\n  (:start . 124) (:id . 60))\n ((:tag . "RB") (:stem . "4-fold") (:form . "4-fold") (:end . 137)\n  (:start . 131) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 145)\n  (:start . 139) (:id . 63))\n ((:tag . "NN") (:stem . "8a") (:form . "8A") (:end . 148) (:start . 146)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.191) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102329@unknown@formal@none@1@S@(B) Percentage of late third instar larvae presenting melanotic tumor formation.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "percentage") (:form . "Percentage") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 28) (:start . 23)\n  (:id . 48))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 35)\n  (:start . 29) (:id . 49))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 42)\n  (:start . 36) (:id . 50))\n ((:tag . "VBG") (:stem . "present") (:form . "presenting") (:end . 53)\n  (:start . 43) (:id . 51))\n ((:tag . "JJ") (:stem . "melanotic") (:form . "melanotic") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 79)\n  (:start . 70) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.201) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102339@unknown@formal@none@1@S@This suggests a function for ADGF-A within the lymph gland.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "ADGF-A") (:form . "ADGF-A") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "lymph") (:form . "lymph") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gland") (:form . "gland") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 52)))@@@1@11@((:hcues ((:id . :x7.211.1) (:span 5 13)))\n (:hscopes ((:id . :x7.211.1) (:span 5 58)))\n (:identifiers (:sid . :s7.211) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102349@unknown@formal@none@1@S@Constitutive activation of Toll signaling leads to developmental arrest and hematopoietic defects associated with melanotic tumor formation [35], similar to the phenotype of the adgf-a mutant.@(((:tag . "JJ") (:stem . "constitutive") (:form . "Constitutive") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 23)\n  (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Toll") (:form . "Toll") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 41)\n  (:start . 32) (:id . 46))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 47) (:start . 42)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 64) (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "arrest") (:form . "arrest") (:end . 71)\n  (:start . 65) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "hematopoietic") (:form . "hematopoietic")\n  (:end . 89) (:start . 76) (:id . 52))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 97)\n  (:start . 90) (:id . 53))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 108)\n  (:start . 98) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 113) (:start . 109)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "melanotic") (:form . "melanotic") (:end . 123)\n  (:start . 114) (:id . 56))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 129)\n  (:start . 124) (:id . 57))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 139)\n  (:start . 130) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 141) (:start . 140)\n  (:id . 59))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 143) (:start . 141)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 144) (:start . 143)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 153)\n  (:start . 146) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 156) (:start . 154)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 65))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 170)\n  (:start . 161) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 68))\n ((:tag . "NN") (:stem . "adgf-a") (:form . "adgf-a") (:end . 184)\n  (:start . 178) (:id . 69))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 191)\n  (:start . 185) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.221) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102359@unknown@formal@none@1@S@One of the most remarkable features of the adgf-a mutant phenotype is the disintegration of the fat body in third-instar larvae, another indication of precocious metamorphic changes since the disintegration normally occurs much later, during pupal life.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "remarkable") (:form . "remarkable") (:end . 26)\n  (:start . 16) (:id . 46))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "adgf-a") (:form . "adgf-a") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 66)\n  (:start . 57) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "disintegration") (:form . "disintegration")\n  (:end . 88) (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "fat") (:form . "fat") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 104) (:start . 100)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "third-instar") (:form . "third-instar") (:end . 120)\n  (:start . 108) (:id . 61))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 127)\n  (:start . 121) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 63))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 136)\n  (:start . 129) (:id . 64))\n ((:tag . "NN") (:stem . "indication") (:form . "indication") (:end . 147)\n  (:start . 137) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "precocious") (:form . "precocious") (:end . 161)\n  (:start . 151) (:id . 67))\n ((:tag . "JJ") (:stem . "metamorphic") (:form . "metamorphic") (:end . 173)\n  (:start . 162) (:id . 68))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 181)\n  (:start . 174) (:id . 69))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 187)\n  (:start . 182) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 71))\n ((:tag . "NN") (:stem . "disintegration") (:form . "disintegration")\n  (:end . 206) (:start . 192) (:id . 72))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 215)\n  (:start . 207) (:id . 73))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 222)\n  (:start . 216) (:id . 74))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 227) (:start . 223)\n  (:id . 75))\n ((:tag . "RB") (:stem . "later") (:form . "later") (:end . 233)\n  (:start . 228) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 234) (:start . 233)\n  (:id . 77))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 241)\n  (:start . 235) (:id . 78))\n ((:tag . "JJ") (:stem . "pupal") (:form . "pupal") (:end . 247)\n  (:start . 242) (:id . 79))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 252) (:start . 248)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x7.231.1) (:span 137 147)))\n (:hscopes ((:id . :x7.231.1) (:span 137 181)))\n (:identifiers (:sid . :s7.231) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102369@unknown@formal@none@1@S@Possible Signaling Role for Adenosine@(((:tag . "JJ") (:stem . "possible") (:form . "Possible") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Signaling") (:form . "Signaling") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "NNP") (:stem . "Role") (:form . "Role") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Adenosine") (:form . "Adenosine") (:end . 37)\n  (:start . 28) (:id . 46)))@@@1@5@((:hcues ((:id . :x7.241.1) (:span 0 8)))\n (:hscopes ((:id . :x7.241.1) (:span 0 37)))\n (:identifiers (:sid . :s7.241) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5102379@unknown@formal@none@1@S@One possible explanation for the developmental delay and failure to pupariate is that the adgf-a mutation affects the production or release of ecdysteroid hormones from the major endocrine organ of the Drosophila larva—the ring gland.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "explanation") (:form . "explanation") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 46) (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "delay") (:form . "delay") (:end . 52) (:start . 47)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "failure") (:form . "failure") (:end . 64)\n  (:start . 57) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "VB") (:stem . "pupariate") (:form . "pupariate") (:end . 77)\n  (:start . 68) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "adgf-a") (:form . "adgf-a") (:end . 96)\n  (:start . 90) (:id . 56))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 113)\n  (:start . 106) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 59))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 128)\n  (:start . 118) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 131) (:start . 129)\n  (:id . 61))\n ((:tag . "NN") (:stem . "release") (:form . "release") (:end . 139)\n  (:start . 132) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "NN") (:stem . "ecdysteroid") (:form . "ecdysteroid") (:end . 154)\n  (:start . 143) (:id . 64))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 163)\n  (:start . 155) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 168) (:start . 164)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 178)\n  (:start . 173) (:id . 68))\n ((:tag . "JJ") (:stem . "endocrine") (:form . "endocrine") (:end . 188)\n  (:start . 179) (:id . 69))\n ((:tag . "NN") (:stem . "organ") (:form . "organ") (:end . 194)\n  (:start . 189) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 197) (:start . 195)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 201) (:start . 198)\n  (:id . 72))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 212)\n  (:start . 202) (:id . 73))\n ((:tag . "NN") (:stem . "larva") (:form . "larva") (:end . 218)\n  (:start . 213) (:id . 74))\n ((:tag . "NN") (:stem . "—") (:form . "—") (:end . 219) (:start . 218)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 222) (:start . 219)\n  (:id . 76))\n ((:tag . "NN") (:stem . "ring") (:form . "ring") (:end . 227) (:start . 223)\n  (:id . 77))\n ((:tag . "NN") (:stem . "gland") (:form . "gland") (:end . 233)\n  (:start . 228) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x7.251.2) (:span 4 12)))\n (:ncues ((:id . :x7.251.1) (:span 57 64)))\n (:hscopes ((:id . :x7.251.2) (:span 4 77)))\n (:nscopes ((:id . :x7.251.1) (:span 57 77)))\n (:identifiers (:sid . :s7.251) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102389@unknown@formal@none@1@S@Work using adenosine-receptor deficient mammalian cells also suggested the existence of a novel, undefined adenosine signaling mechanism [44].@(((:tag . "NNP") (:stem . "Work") (:form . "Work") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "adenosine-receptor") (:form . "adenosine-receptor")\n  (:end . 29) (:start . 11) (:id . 44))\n ((:tag . "JJ") (:stem . "deficient") (:form . "deficient") (:end . 39)\n  (:start . 30) (:id . 45))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 49)\n  (:start . 40) (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 55) (:start . 50)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 60) (:start . 56)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "suggest") (:form . "suggested") (:end . 70)\n  (:start . 61) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 50))\n ((:tag . "NN") (:stem . "existence") (:form . "existence") (:end . 84)\n  (:start . 75) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 95) (:start . 90)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "undefined") (:form . "undefined") (:end . 106)\n  (:start . 97) (:id . 56))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 116)\n  (:start . 107) (:id . 57))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 126)\n  (:start . 117) (:id . 58))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 136)\n  (:start . 127) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 138) (:start . 137)\n  (:id . 60))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 140) (:start . 138)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 141) (:start . 140)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x7.261.1) (:span 61 70)))\n (:hscopes ((:id . :x7.261.1) (:span 61 136)))\n (:identifiers (:sid . :s7.261) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102399@unknown@formal@none@1@S@This would be consistent with the role of adenosine as a “stress hormone” in mammals [6].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 64)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 72)\n  (:start . 65) (:id . 55))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 84)\n  (:start . 77) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 87) (:start . 86)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 88) (:start . 87)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x7.271.1) (:span 5 10)))\n (:hscopes ((:id . :x7.271.1) (:span 5 84)))\n (:identifiers (:sid . :s7.271) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102409@unknown@formal@none@1@S@A mutation in the adenosine receptor gene on Chromosome III was produced by the ends-out targeting method (ED, unpublished data) and is referred to here as adoR.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "adenosine") (:form . "adenosine") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Chromosome") (:form . "Chromosome") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . "CD") (:stem . "iii") (:form . "III") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "ends-out") (:form . "ends-out") (:end . 88)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ED") (:form . "ED") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 122)\n  (:start . 111) (:id . 62))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 127)\n  (:start . 123) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 144)\n  (:start . 136) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 147) (:start . 145)\n  (:id . 68))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 152) (:start . 148)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "adoR") (:form . "adoR") (:end . 160) (:start . 156)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.281) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102419@unknown@formal@none@1@S@To recognize homozygous larvae, balancer chromosomes with the GFP marker were used: CyO Pw+mW.hs=Ubi-GFP.S65TPAD1 (BL-4559) and TM3 Pw+mC=ActGFPJMR2 Ser (BL-4888).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "recognize") (:form . "recognize") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 30)\n  (:start . 24) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "balancer") (:form . "balancer") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 52)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 72)\n  (:start . 66) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 82) (:start . 78)\n  (:id . 54))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "CyO") (:form . "CyO") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Pw+mW.hs=Ubi-GFP.S65TPAD1")\n  (:form . "Pw+mW.hs=Ubi-GFP.S65TPAD1") (:end . 113) (:start . 88) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "BL-4559") (:form . "BL-4559") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "TM3") (:form . "TM3") (:end . 131) (:start . 128)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Pw+mC=ActGFPJMR2") (:form . "Pw+mC=ActGFPJMR2")\n  (:end . 148) (:start . 132) (:id . 63))\n ((:tag . "NNP") (:stem . "Ser") (:form . "Ser") (:end . 152) (:start . 149)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 65))\n ((:tag . "NN") (:stem . "bl-4888") (:form . "BL-4888") (:end . 161)\n  (:start . 154) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.291) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102429@unknown@formal@none@1@S@Fat body observation@(((:tag . "NNP") (:stem . "Fat") (:form . "Fat") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 20)\n  (:start . 9) (:id . 44)))@@@1@3@((:identifiers (:sid . :s7.301) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5102439@unknown@formal@none@1@S@To observe hemocyte morphology, samples were analyzed at least 10 min after the deposition of solution with hemocytes, in order to allow the cells to adhere to the surface of the slide.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "observe") (:form . "observe") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "hemocyte") (:form . "hemocyte") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "deposition") (:form . "deposition") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "solution") (:form . "solution") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "hemocyte") (:form . "hemocytes") (:end . 117)\n  (:start . 108) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 127)\n  (:start . 122) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 64))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 136)\n  (:start . 131) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 146)\n  (:start . 141) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n  (:id . 68))\n ((:tag . "VB") (:stem . "adhere") (:form . "adhere") (:end . 156)\n  (:start . 150) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 159) (:start . 157)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 71))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 171)\n  (:start . 164) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 74))\n ((:tag . "NN") (:stem . "slide") (:form . "slide") (:end . 184)\n  (:start . 179) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.311) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102449@unknown@formal@none@1@S@The sequence encoding the myc-tag 5?- GAGCAAAAGCTCATTTCTGAAGAGGACTTG-3? plus a stop codon was inserted into XbaI site of pUAST (using the XbaI site on the 5? end and the NheI site on the 3? end) cut by XhoI/XbaI.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "myc-tag") (:form . "myc-tag") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "CD") (:stem . "5?-") (:form . "5?-") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "gagcaaaagctcatttctgaagaggacttg-3")\n  (:form . "GAGCAAAAGCTCATTTCTGAAGAGGACTTG-3") (:end . 70) (:start . 38)\n  (:id . 48))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 71) (:start . 70)\n  (:id . 49))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 76) (:start . 72)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n  (:id . 51))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 89) (:start . 84)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 93) (:start . 90)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 102)\n  (:start . 94) (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 107) (:start . 103)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 112) (:start . 108)\n  (:id . 57))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 117) (:start . 113)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 59))\n ((:tag . "NN") (:stem . "puast") (:form . "pUAST") (:end . 126)\n  (:start . 121) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 133) (:start . 128)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 142) (:start . 138)\n  (:id . 64))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 147) (:start . 143)\n  (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 157) (:start . 156)\n  (:id . 69))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 161) (:start . 158)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "NheI") (:form . "NheI") (:end . 174) (:start . 170)\n  (:id . 73))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 179) (:start . 175)\n  (:id . 74))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 182) (:start . 180)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 186) (:start . 183)\n  (:id . 76))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 188) (:start . 187)\n  (:id . 77))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 189) (:start . 188)\n  (:id . 78))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 193) (:start . 190)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "cut") (:form . "cut") (:end . 198) (:start . 195)\n  (:id . 81))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 201) (:start . 199)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "XhoI/XbaI") (:form . "XhoI/XbaI") (:end . 211)\n  (:start . 202) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s7.321) (:did . :pmc1135298) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102459@unknown@formal@none@1@S@A comparison of programmed cell death between species@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "program") (:form . "programmed") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 53)\n  (:start . 46) (:id . 49)))@@@1@8@((:identifiers (:sid . :s8.1) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5102469@unknown@formal@none@1@S@Programmed cell death has long been known to be a part of normal development, but it was not until the discovery of the first genes essential for the phenomenon that our understanding of the events leading up to the deliberate elimination of a cell began to take shape.@(((:tag . "VBN") (:stem . "program") (:form . "Programmed") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 64)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 76)\n  (:start . 65) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 88) (:start . 85)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 98) (:start . 93)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 62))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 112)\n  (:start . 103) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 125)\n  (:start . 120) (:id . 66))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 131)\n  (:start . 126) (:id . 67))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 141)\n  (:start . 132) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 145) (:start . 142)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 149) (:start . 146)\n  (:id . 70))\n ((:tag . "NN") (:stem . "phenomenon") (:form . "phenomenon") (:end . 160)\n  (:start . 150) (:id . 71))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 165) (:start . 161)\n  (:id . 72))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 169) (:start . 166)\n  (:id . 73))\n ((:tag . "NN") (:stem . "understanding") (:form . "understanding")\n  (:end . 183) (:start . 170) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 186) (:start . 184)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 190) (:start . 187)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 197)\n  (:start . 191) (:id . 77))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 205)\n  (:start . 198) (:id . 78))\n ((:tag . "RB") (:stem . "up") (:form . "up") (:end . 208) (:start . 206)\n  (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 211) (:start . 209)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 215) (:start . 212)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "deliberate") (:form . "deliberate") (:end . 226)\n  (:start . 216) (:id . 82))\n ((:tag . "NN") (:stem . "elimination") (:form . "elimination") (:end . 238)\n  (:start . 227) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 241) (:start . 239)\n  (:id . 84))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 243) (:start . 242)\n  (:id . 85))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 248) (:start . 244)\n  (:id . 86))\n ((:tag . "VBD") (:stem . "begin") (:form . "began") (:end . 254)\n  (:start . 249) (:id . 87))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 257) (:start . 255)\n  (:id . 88))\n ((:tag . "VB") (:stem . "take") (:form . "take") (:end . 262) (:start . 258)\n  (:id . 89))\n ((:tag . "NN") (:stem . "shape") (:form . "shape") (:end . 268)\n  (:start . 263) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s8.11) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102479@unknown@formal@none@1@S@Drosophila has at least eight caspases, five of which have been at least partially characterized (Dcp-1, Dcp-2/Dredd, drICE, Dronc, and Decay) and three uncharacterized ones found encoded in the genome sequence [7].@(((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "CD") (:stem . "eight") (:form . "eight") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "caspas") (:form . "caspases") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 63) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 72) (:start . 67)\n  (:id . 55))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 82)\n  (:start . 73) (:id . 56))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 96) (:start . 83) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Dcp-1") (:form . "Dcp-1") (:end . 103)\n  (:start . 98) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Dcp-2/Dredd") (:form . "Dcp-2/Dredd") (:end . 116)\n  (:start . 105) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "drICE") (:form . "drICE") (:end . 123)\n  (:start . 118) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Dronc") (:form . "Dronc") (:end . 130)\n  (:start . 125) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Decay") (:form . "Decay") (:end . 141)\n  (:start . 136) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 70))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 152)\n  (:start . 147) (:id . 71))\n ((:tag . "JJ") (:stem . "uncharacterized") (:form . "uncharacterized")\n  (:end . 168) (:start . 153) (:id . 72))\n ((:tag . "NNS") (:stem . "one") (:form . "ones") (:end . 173) (:start . 169)\n  (:id . 73))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 179)\n  (:start . 174) (:id . 74))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 187)\n  (:start . 180) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 190) (:start . 188)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n  (:id . 77))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 201)\n  (:start . 195) (:id . 78))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 210)\n  (:start . 202) (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 212) (:start . 211)\n  (:id . 80))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 213) (:start . 212)\n  (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 214) (:start . 213)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.21) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102489@unknown@formal@none@1@S@Like CED-4, Apaf-1 requires dATP for caspase activation, but Apaf-1 requires cytochrome c in addition [14].@(((:tag . "IN") (:stem . "like") (:form . "Like") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ced-4") (:form . "CED-4") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Apaf-1") (:form . "Apaf-1") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "datp") (:form . "dATP") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "caspase") (:form . "caspase") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Apaf-1") (:form . "Apaf-1") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 76)\n  (:start . 68) (:id . 54))\n ((:tag . "NN") (:stem . "cytochrome") (:form . "cytochrome") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 89) (:start . 88)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 106) (:start . 105)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.31) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102499@unknown@formal@none@1@S@The rate of mitochondrial release of cytochrome c in mammalian cells undergoing apoptosis was recently measured and found to be rapid [18].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "mitochondrial") (:form . "mitochondrial")\n  (:end . 25) (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "release") (:form . "release") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cytochrome") (:form . "cytochrome") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "undergo") (:form . "undergoing") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 89)\n  (:start . 80) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 102)\n  (:start . 94) (:id . 56))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 111)\n  (:start . 103) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 121)\n  (:start . 116) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 127) (:start . 125)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s8.41) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102509@unknown@formal@none@1@S@A third group shows that peptide caspase inhibitors can block Drosophila Bok-mediated apoptosis in cell culture, lending support to a model in which expression of Bok protein leads to caspase activation [24].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "caspase") (:form . "caspase") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "VB") (:stem . "block") (:form . "block") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 72)\n  (:start . 62) (:id . 52))\n ((:tag . "JJ") (:stem . "bok-mediated") (:form . "Bok-mediated") (:end . 85)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 95)\n  (:start . 86) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 103) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 111)\n  (:start . 104) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "lend") (:form . "lending") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 128)\n  (:start . 121) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 139)\n  (:start . 134) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 148)\n  (:start . 143) (:id . 65))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 159)\n  (:start . 149) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Bok") (:form . "Bok") (:end . 166) (:start . 163)\n  (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 174)\n  (:start . 167) (:id . 69))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 180)\n  (:start . 175) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 183) (:start . 181)\n  (:id . 71))\n ((:tag . "NN") (:stem . "caspase") (:form . "caspase") (:end . 191)\n  (:start . 184) (:id . 72))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 202)\n  (:start . 192) (:id . 73))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 204) (:start . 203)\n  (:id . 74))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 206) (:start . 204)\n  (:id . 75))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 207) (:start . 206)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s8.51) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102519@unknown@formal@none@1@S@One notable exception is that the C.elegans homologs of IAPs do not appear to function in programmed cell death.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "notable") (:form . "notable") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNPS") (:stem . "C.elegans") (:form . "C.elegans") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "iap") (:form . "IAPs") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "program") (:form . "programmed") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 111)\n  (:start . 106) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x8.61.2) (:span 68 74)))\n (:ncues ((:id . :x8.61.1) (:span 64 67)))\n (:hscopes ((:id . :x8.61.2) (:span 30 111)))\n (:nscopes ((:id . :x8.61.1) (:span 30 111)))\n (:identifiers (:sid . :s8.61) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102529@unknown@formal@none@1@S@Also, Hid has been shown to be negatively regulated by survival signals mediated by receptor tyrosine kinases through the Ras and mitogen-activated protein (MAP) kinase pathway, which is also well conserved in mammals [28,29].@(((:tag . "RB") (:stem . "also") (:form . "Also") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Hid") (:form . "Hid") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 18) (:start . 14)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "RB") (:stem . "negatively") (:form . "negatively") (:end . 41)\n  (:start . 31) (:id . 50))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 51)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 63)\n  (:start . 55) (:id . 53))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 92)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "tyrosine") (:form . "tyrosine") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "kinase") (:form . "kinases") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 117)\n  (:start . 110) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 61))\n ((:tag . "NNPS") (:stem . "Ras") (:form . "Ras") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "mitogen-activated") (:form . "mitogen-activated")\n  (:end . 147) (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 155)\n  (:start . 148) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "MAP") (:form . "MAP") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 168)\n  (:start . 162) (:id . 69))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 176)\n  (:start . 169) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 183)\n  (:start . 178) (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 186) (:start . 184)\n  (:id . 73))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 191) (:start . 187)\n  (:id . 74))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 196) (:start . 192)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 206)\n  (:start . 197) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 209) (:start . 207)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 217)\n  (:start . 210) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 219) (:start . 218)\n  (:id . 79))\n ((:tag . "CD") (:stem . "28,29") (:form . "28,29") (:end . 224)\n  (:start . 219) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 225) (:start . 224)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.71) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102539@unknown@formal@none@1@S@The observation that transcription of both reaper and dark/hac-1/dapaf-1 can be induced by ionizing radiation suggests that these death-inducing signals can feed into the cell death pathway at multiple points.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 34) (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "reaper") (:form . "reaper") (:end . 49)\n  (:start . 43) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dark/hac-1/dapaf-1") (:form . "dark/hac-1/dapaf-1")\n  (:end . 72) (:start . 54) (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 76) (:start . 73)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 79) (:start . 77)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 87)\n  (:start . 80) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "ionize") (:form . "ionizing") (:end . 99)\n  (:start . 91) (:id . 55))\n ((:tag . "NN") (:stem . "radiation") (:form . "radiation") (:end . 109)\n  (:start . 100) (:id . 56))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 118)\n  (:start . 110) (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 123) (:start . 119)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 129)\n  (:start . 124) (:id . 59))\n ((:tag . "JJ") (:stem . "death-inducing") (:form . "death-inducing")\n  (:end . 144) (:start . 130) (:id . 60))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 152)\n  (:start . 145) (:id . 61))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 156) (:start . 153)\n  (:id . 62))\n ((:tag . "VB") (:stem . "feed") (:form . "feed") (:end . 161) (:start . 157)\n  (:id . 63))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 166) (:start . 162)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 65))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 175) (:start . 171)\n  (:id . 66))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 181)\n  (:start . 176) (:id . 67))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 189)\n  (:start . 182) (:id . 68))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 192) (:start . 190)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 201)\n  (:start . 193) (:id . 70))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 208)\n  (:start . 202) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x8.81.1) (:span 153 156))\n  ((:id . :x8.81.2) (:span 110 118)))\n (:hscopes ((:id . :x8.81.1) (:span 153 208))\n  ((:id . :x8.81.2) (:span 110 208)))\n (:identifiers (:sid . :s8.81) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102549@unknown@formal@none@1@S@Loss-of-function mutants in diap1 have a very striking early embryonic phenotype: virtually all cells display an apoptotic morphology, as well as displaying DNA fragmentation seen by TUNEL labeling, four to five hours into development [47,49,50].@(((:tag . "JJ") (:stem . "loss-of-function") (:form . "Loss-of-function")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 24)\n  (:start . 17) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 44))\n ((:tag . "NN") (:stem . "diap1") (:form . "diap1") (:end . 33) (:start . 28)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "striking") (:form . "striking") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 60) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 80)\n  (:start . 71) (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "RB") (:stem . "virtually") (:form . "virtually") (:end . 91)\n  (:start . 82) (:id . 54))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 101) (:start . 96)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 109)\n  (:start . 102) (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "apoptotic") (:form . "apoptotic") (:end . 122)\n  (:start . 113) (:id . 59))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 61))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 137) (:start . 135)\n  (:id . 62))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 142) (:start . 138)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 145) (:start . 143)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "display") (:form . "displaying") (:end . 156)\n  (:start . 146) (:id . 65))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 160) (:start . 157)\n  (:id . 66))\n ((:tag . "NN") (:stem . "fragmentation") (:form . "fragmentation")\n  (:end . 174) (:start . 161) (:id . 67))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 179) (:start . 175)\n  (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 182) (:start . 180)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "TUNEL") (:form . "TUNEL") (:end . 188)\n  (:start . 183) (:id . 70))\n ((:tag . "NN") (:stem . "labeling") (:form . "labeling") (:end . 197)\n  (:start . 189) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 198) (:start . 197)\n  (:id . 72))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 203) (:start . 199)\n  (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 206) (:start . 204)\n  (:id . 74))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 211) (:start . 207)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 217)\n  (:start . 212) (:id . 76))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 222) (:start . 218)\n  (:id . 77))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 234)\n  (:start . 223) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 236) (:start . 235)\n  (:id . 79))\n ((:tag . "CD") (:stem . "47,49,50") (:form . "47,49,50") (:end . 244)\n  (:start . 236) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 245) (:start . 244)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.91) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102559@unknown@formal@none@1@S@Conservation of key regulators of programmed cell death between species@(((:tag . "NNP") (:stem . "Conservation") (:form . "Conservation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "program") (:form . "programmed") (:end . 44)\n  (:start . 34) (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 63)\n  (:start . 56) (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 71)\n  (:start . 64) (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.101) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5102569@unknown@formal@none@1@S@While it is clear that the search for homologs of known cell death genes has been greatly facilitated by the availability of the entire genome sequence for C. elegans, Drosophila, and humans, there are limitations to this strategy.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 66) (:start . 61)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 72) (:start . 67)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 81) (:start . 77)\n  (:id . 57))\n ((:tag . "RB") (:stem . "greatly") (:form . "greatly") (:end . 89)\n  (:start . 82) (:id . 58))\n ((:tag . "VBN") (:stem . "facilitate") (:form . "facilitated") (:end . 101)\n  (:start . 90) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "availability") (:form . "availability") (:end . 121)\n  (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 135)\n  (:start . 129) (:id . 65))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 142)\n  (:start . 136) (:id . 66))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 151)\n  (:start . 143) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 155) (:start . 152)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 158) (:start . 156)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 166)\n  (:start . 159) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 178)\n  (:start . 168) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 179) (:start . 178)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 183) (:start . 180)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "human") (:form . "humans") (:end . 190)\n  (:start . 184) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 76))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 197)\n  (:start . 192) (:id . 77))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 201) (:start . 198)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "limitation") (:form . "limitations") (:end . 213)\n  (:start . 202) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 216) (:start . 214)\n  (:id . 80))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 221) (:start . 217)\n  (:id . 81))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 230)\n  (:start . 222) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.111) (:did . :pmc138857) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102579@unknown@formal@none@1@S@Because sex chromosomes appeared relatively late in evolution, dosage compensation evolved independently in different organisms and is accomplished by distinct mechanisms.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "sex") (:form . "sex") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 43)\n  (:start . 33) (:id . 46))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 48) (:start . 44)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 61)\n  (:start . 52) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 69)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "compensation") (:form . "compensation") (:end . 82)\n  (:start . 70) (:id . 52))\n ((:tag . "VBD") (:stem . "evolve") (:form . "evolved") (:end . 90)\n  (:start . 83) (:id . 53))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 104) (:start . 91) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 117)\n  (:start . 108) (:id . 56))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 127)\n  (:start . 118) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 134) (:start . 132)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "accomplish") (:form . "accomplished") (:end . 147)\n  (:start . 135) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 150) (:start . 148)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 159)\n  (:start . 151) (:id . 62))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 170)\n  (:start . 160) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.7) (:did . :pmc138894) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102589@unknown@formal@none@1@S@It is assumed that Xist RNA provides a mark for specific histones (for example, histone macroH2A1.2), as well as proteins deacetylating histones and methylating many of the X-linked genes at GpC dinucleotides [9,10,11]; all these events are important for maintaining the silenced state of the inactivated X.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "assume") (:form . "assumed") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Xist") (:form . "Xist") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . 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5102599@unknown@formal@none@1@S@The three recent papers [1,2,3] have now started to address the role of the roX genes in this process and investigated which MSL proteins interact with the roX RNAs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "paper") (:form . "papers") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "CD") (:stem . "1,2,3") (:form . "1,2,3") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "start") (:form . "started") (:end . 48)\n  (:start . 41) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "VB") (:stem . "address") (:form . "address") (:end . 59)\n  (:start . 52) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "roX") (:form . "roX") (:end . 79) (:start . 76)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 85) (:start . 80)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 93) (:start . 89)\n  (:id . 61))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 101)\n  (:start . 94) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 118)\n  (:start . 106) (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 124)\n  (:start . 119) (:id . 65))\n ((:tag . "NN") (:stem . "msl") (:form . "MSL") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 137)\n  (:start . 129) (:id . 67))\n ((:tag . "VBP") (:stem . "interact") (:form . "interact") (:end . 146)\n  (:start . 138) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 151) (:start . 147)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "roX") (:form . "roX") (:end . 159) (:start . 156)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNAs") (:end . 164) (:start . 160)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.27) (:did . :pmc138894) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102609@unknown@formal@none@1@S@They found that roX1 and roX2 RNAs are associated with the X chromosome at different stages and sites during the assembly of the DCC.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "rox1") (:form . "roX1") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "rox2") (:form . "roX2") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "rna") (:form . "RNAs") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 49)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "X") (:form . "X") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 71)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 84)\n  (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 91)\n  (:start . 85) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 108)\n  (:start . 102) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "DCC") (:form . "DCC") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s9.37) (:did . :pmc138894) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102619@unknown@formal@none@1@S@The HAT domain of MOF is responsible for histone H4 acetylation, both in vivo and in vitro, as shown by Smith et al. [3].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "HAT") (:form . "HAT") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "MOF") (:form . "MOF") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 36)\n  (:start . 25) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "histone") (:form . "histone") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "h4") (:form . "H4") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "acetylation") (:form . "acetylation") (:end . 63)\n  (:start . 52) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 90) (:start . 85)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 94) (:start . 92)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 100) (:start . 95)\n  (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 103) (:start . 101)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Smith") (:form . "Smith") (:end . 109)\n  (:start . 104) (:id . 64))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 112) (:start . 110)\n  (:id . 65))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 116) (:start . 113)\n  (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n  (:id . 67))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 119) (:start . 118)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 120) (:start . 119)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.47) (:did . :pmc138894) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102629@unknown@formal@none@1@S@It is intriguing to speculate that the chromodomain of other remodeling proteins also exert their activity through RNA interactions and that RNAs might be more common than generally appreciated in transcriptional regulation.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "intrigue") (:form . "intriguing") (:end . 16)\n  (:start . 6) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VB") (:stem . "speculate") (:form . "speculate") (:end . 29)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "chromodomain") (:form . "chromodomain") (:end . 51)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "remodel") (:form . "remodeling") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "exert") (:form . "exert") (:end . 91) (:start . 86)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 97)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 106)\n  (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 118) (:start . 115)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 131)\n  (:start . 119) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 140) (:start . 136)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "rna") (:form . "RNAs") (:end . 145) (:start . 141)\n  (:id . 63))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 151)\n  (:start . 146) (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 154) (:start . 152)\n  (:id . 65))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 159) (:start . 155)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 166)\n  (:start . 160) (:id . 67))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 171) (:start . 167)\n  (:id . 68))\n ((:tag . "RB") (:stem . "generally") (:form . "generally") (:end . 181)\n  (:start . 172) (:id . 69))\n ((:tag . "VBN") (:stem . "appreciate") (:form . "appreciated") (:end . 193)\n  (:start . 182) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 196) (:start . 194)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 212) (:start . 197) (:id . 72))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 223)\n  (:start . 213) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x9.57.1) (:span 146 151)) ((:id . :x9.57.2) (:span 20 29)))\n (:hscopes ((:id . :x9.57.1) (:span 146 223))\n  ((:id . :x9.57.2) (:span 20 223)))\n (:identifiers (:sid . :s9.57) (:did . :pmc138894) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102639@unknown@formal@none@1@S@Multiple RNA-protein interactions within the DCC@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "rna-protein") (:form . "RNA-protein") (:end . 20)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 33)\n  (:start . 21) (:id . 44))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 40)\n  (:start . 34) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "DCC") (:form . "DCC") (:end . 48) (:start . 45)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s9.67) (:did . :pmc138894) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5102649@unknown@formal@none@1@S@Evidence from co-immunoprecipitation experiments indicates that MSL1 and MSL2 interact directly with each other, a notion supported by the MSL1-MSL2 association at the 35 chromosomal entry sites in the absence of any other MSLs (the preDCC; Figure 1).@(((:tag . "NN") (:stem . "evidence") (:form . "Evidence") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "co-immunoprecipitation")\n  (:form . "co-immunoprecipitation") (:end . 36) (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 48)\n  (:start . 37) (:id . 45))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 58)\n  (:start . 49) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 63) (:start . 59)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "MSL1") (:form . "MSL1") (:end . 68) (:start . 64)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "MSL2") (:form . "MSL2") (:end . 77) (:start . 73)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "interact") (:form . "interact") (:end . 86)\n  (:start . 78) (:id . 51))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 95)\n  (:start . 87) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 100) (:start . 96)\n  (:id . 53))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 105) (:start . 101)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 111)\n  (:start . 106) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 114) (:start . 113)\n  (:id . 57))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 121)\n  (:start . 115) (:id . 58))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 131)\n  (:start . 122) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 61))\n ((:tag . "NN") (:stem . "msl1-msl2") (:form . "MSL1-MSL2") (:end . 148)\n  (:start . 139) (:id . 62))\n ((:tag . "NN") (:stem . "association") (:form . "association") (:end . 160)\n  (:start . 149) (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 163) (:start . 161)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 65))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 170) (:start . 168)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "chromosomal") (:form . "chromosomal") (:end . 182)\n  (:start . 171) (:id . 67))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 188)\n  (:start . 183) (:id . 68))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 194)\n  (:start . 189) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 197) (:start . 195)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 201) (:start . 198)\n  (:id . 71))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 209)\n  (:start . 202) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 212) (:start . 210)\n  (:id . 73))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 216) (:start . 213)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 222)\n  (:start . 217) (:id . 75))\n ((:tag . "NNS") (:stem . "msl") (:form . "MSLs") (:end . 227) (:start . 223)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 229) (:start . 228)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 232) (:start . 229)\n  (:id . 78))\n ((:tag . "NN") (:stem . "predcc") (:form . "preDCC") (:end . 239)\n  (:start . 233) (:id . 79))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 240) (:start . 239)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 247)\n  (:start . 241) (:id . 81))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 249) (:start . 248)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 250) (:start . 249)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x9.77.1) (:span 49 63)))\n (:hscopes ((:id . :x9.77.1) (:span 49 111)))\n (:identifiers (:sid . :s9.77) (:did . :pmc138894) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5102659@unknown@formal@none@1@S@Although roX1 mutant males are fully viable [7], it was suggested that roX1 mutant males lacking a large number of additional genes, including roX2, have a lethal dosage-compensation phenotype because the DCC fails to assemble on the X chromosome [19].@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "rox1") (:form . "roX1") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "male") (:form . "males") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "(") (:stem . "[") (:form . 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5102669@unknown@formal@none@1@S@Not unlike in Drosophila, the DCC complex of C. elegans is also assembled in an ordered sequence, but no RNAs have been identified that might be involved in this assembly process [20]; either there will be yet another surprising turn in this multifaceted process or the CroX (C. elegans roX) RNAs wait to be discovered.@(((:tag . "RB") (:stem . "not") (:form . "Not") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "unlike") (:form . "unlike") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "DCC") (:form . 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