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PubMed:21135151 JSONTXT

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LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
8431 10-14 GeneOrGeneProduct denotes CCR5 NCBIGene:1234
8432 14-21 SequenceVariant denotes delta32 c|DEL||32
8433 73-78 OrganismTaxon denotes HIV-1 NCBITaxon:11676
8434 206-235 GeneOrGeneProduct denotes C-C chemokine receptor type 5 NCBIGene:1234
8435 237-241 GeneOrGeneProduct denotes CCR5 NCBIGene:1234
8436 303-308 OrganismTaxon denotes HIV-1 NCBITaxon:11676
8437 933-937 GeneOrGeneProduct denotes CCR5 NCBIGene:1234
8438 1028-1033 GeneOrGeneProduct denotes gp120 NCBIGene:3700
8439 1065-1070 OrganismTaxon denotes HIV-1 NCBITaxon:11676
8440 1130-1139 DiseaseOrPhenotypicFeature denotes infection MESH:D007239
8441 1160-1174 DiseaseOrPhenotypicFeature denotes HIV-1-infected MESH:D015658
8442 1205-1209 GeneOrGeneProduct denotes CCR5 NCBIGene:1234
8443 1216-1221 OrganismTaxon denotes HIV-1 NCBITaxon:11676
8444 1276-1280 GeneOrGeneProduct denotes CCR5 NCBIGene:1234
8445 1284-1287 SequenceVariant denotes Δ32 c|DEL||32
8446 1351-1360 DiseaseOrPhenotypicFeature denotes infection MESH:D007239
8447 1488-1495 OrganismTaxon denotes patient NCBITaxon:9606
8448 1838-1845 OrganismTaxon denotes patient NCBITaxon:9606
8449 1974-1978 GeneOrGeneProduct denotes CCR5 NCBIGene:1234
8450 2062-2069 OrganismTaxon denotes patient NCBITaxon:9606
8451 2095-2099 DiseaseOrPhenotypicFeature denotes AIDS MESH:D000163

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T6 1251-1415 Sentence denotes Presence or absence of a CCR5 wt/Δ32 genotype and progressive or long-term nonprogressive course of infection stratify the clinical populations in a two-way design.
T1 0-183 Sentence denotes Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models.
T2 184-499 Sentence denotes The interplay between C-C chemokine receptor type 5 (CCR5) host genetic background, disease progression, and intrahost HIV-1 evolutionary dynamics remains unclear because differences in viral evolution between hosts limit the ability to draw conclusions across hosts stratified into clinically relevant populations.
T3 500-646 Sentence denotes Similar inference problems are proliferating across many measurably evolving pathogens for which intrahost sequence samples are readily available.
T4 647-909 Sentence denotes To this end, we propose novel hierarchical phylogenetic models (HPMs) that incorporate fixed effects to test for differences in dynamics across host populations in a formal statistical framework employing stochastic search variable selection and model averaging.
T5 910-1250 Sentence denotes To clarify the role of CCR5 host genetic background and disease progression on viral evolutionary patterns, we obtain gp120 envelope sequences from clonal HIV-1 variants isolated at multiple time points in the course of infection from populations of HIV-1-infected individuals who only harbored CCR5-using HIV-1 variants at all time points.
T7 1416-1706 Sentence denotes As compared with the standard approach of analyzing sequences from each patient independently, the HPM provides more efficient estimation of evolutionary parameters such as nucleotide substitution rates and d(N)/d(S) rate ratios, as shown by significant shrinkage of the estimator variance.
T8 1707-1856 Sentence denotes The fixed effects also correct for nonindependence of data between populations and results in even further shrinkage of individual patient estimates.
T9 1857-2004 Sentence denotes Model selection suggests an association between nucleotide substitution rate and disease progression, but a role for CCR5 genotype remains elusive.
T10 2005-2241 Sentence denotes Given the absence of clear d(N)/d(S) differences between patient groups, delayed onset of AIDS symptoms appears to be solely associated with lower viral replication rates rather than with differences in selection on amino acid fixation.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 73-78 OrganismTaxon denotes HIV-1 NCBItxid:11676
T2 303-308 OrganismTaxon denotes HIV-1 NCBItxid:11676
T3 1065-1070 OrganismTaxon denotes HIV-1 NCBItxid:11676
T4 1160-1165 OrganismTaxon denotes HIV-1 NCBItxid:11676
T5 1216-1221 OrganismTaxon denotes HIV-1 NCBItxid:11676

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 2095-2099 DiseaseOrPhenotypicFeature denotes AIDS 0012268

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 14-21 SequenceVariant denotes delta32
T2 1284-1287 SequenceVariant denotes Δ32

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 0-6 GeneOrGeneProduct denotes Impact
T2 102-111 GeneOrGeneProduct denotes processes
T3 134-141 GeneOrGeneProduct denotes testing
T4 206-235 GeneOrGeneProduct denotes C-C chemokine receptor type 5
T5 237-241 GeneOrGeneProduct denotes CCR5
T6 339-346 GeneOrGeneProduct denotes unclear
T7 400-405 GeneOrGeneProduct denotes limit
T8 500-507 GeneOrGeneProduct denotes Similar
T9 552-556 GeneOrGeneProduct denotes many
T10 636-645 GeneOrGeneProduct denotes available
T11 655-658 GeneOrGeneProduct denotes end
T12 671-676 GeneOrGeneProduct denotes novel
T13 751-755 GeneOrGeneProduct denotes test
T14 808-812 GeneOrGeneProduct denotes in a
T15 933-937 GeneOrGeneProduct denotes CCR5
T16 1028-1033 GeneOrGeneProduct denotes gp120
T24 1243-1249 GeneOrGeneProduct denotes points
T17 1034-1042 GeneOrGeneProduct denotes envelope
T18 1092-1100 GeneOrGeneProduct denotes multiple
T19 1101-1105 GeneOrGeneProduct denotes time
T20 1106-1112 GeneOrGeneProduct denotes points
T21 1205-1209 GeneOrGeneProduct denotes CCR5
T22 1234-1237 GeneOrGeneProduct denotes all
T23 1238-1242 GeneOrGeneProduct denotes time
T25 1276-1280 GeneOrGeneProduct denotes CCR5
T26 1316-1320 GeneOrGeneProduct denotes long
T27 1321-1325 GeneOrGeneProduct denotes term
T28 1395-1399 GeneOrGeneProduct denotes in a
T29 1801-1805 GeneOrGeneProduct denotes even
T30 1974-1978 GeneOrGeneProduct denotes CCR5
T31 2221-2231 GeneOrGeneProduct denotes amino acid

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 0-6 GeneOrGeneProduct denotes Impact
T2 206-235 GeneOrGeneProduct denotes C-C chemokine receptor type 5
T3 237-241 GeneOrGeneProduct denotes CCR5
T4 339-346 GeneOrGeneProduct denotes unclear
T5 500-507 GeneOrGeneProduct denotes Similar
T6 671-676 GeneOrGeneProduct denotes novel
T7 933-937 GeneOrGeneProduct denotes CCR5
T8 1028-1033 GeneOrGeneProduct denotes gp120
T9 1034-1042 GeneOrGeneProduct denotes envelope
T10 1092-1100 GeneOrGeneProduct denotes multiple
T11 1205-1209 GeneOrGeneProduct denotes CCR5
T12 1276-1280 GeneOrGeneProduct denotes CCR5
T13 1321-1325 GeneOrGeneProduct denotes term
T14 1801-1805 GeneOrGeneProduct denotes even
T15 1974-1978 GeneOrGeneProduct denotes CCR5
T16 2221-2231 GeneOrGeneProduct denotes amino acid

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 50-69 DiseaseOrPhenotypicFeature denotes disease progression D018450
T2 268-287 DiseaseOrPhenotypicFeature denotes disease progression D018450
T3 966-985 DiseaseOrPhenotypicFeature denotes disease progression D018450
T4 1130-1139 DiseaseOrPhenotypicFeature denotes infection D007239
T5 1351-1360 DiseaseOrPhenotypicFeature denotes infection D007239
T6 1938-1957 DiseaseOrPhenotypicFeature denotes disease progression D018450
T7 2095-2099 DiseaseOrPhenotypicFeature denotes AIDS D000163

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 206-235 GeneOrGeneProduct denotes C-C chemokine receptor type 5
T2 237-241 GeneOrGeneProduct denotes CCR5
T3 933-937 GeneOrGeneProduct denotes CCR5
T4 1028-1033 GeneOrGeneProduct denotes gp120
T5 1034-1042 GeneOrGeneProduct denotes envelope
T6 1205-1209 GeneOrGeneProduct denotes CCR5
T7 1276-1280 GeneOrGeneProduct denotes CCR5
T8 1974-1978 GeneOrGeneProduct denotes CCR5

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 1130-1139 DiseaseOrPhenotypicFeature denotes infection 0005550
T2 1351-1360 DiseaseOrPhenotypicFeature denotes infection 0005550
T3 2095-2099 DiseaseOrPhenotypicFeature denotes AIDS 0012268

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 50-69 DiseaseOrPhenotypicFeature denotes disease progression D018450
T2 73-76 DiseaseOrPhenotypicFeature denotes HIV DISEASE
T3 268-287 DiseaseOrPhenotypicFeature denotes disease progression D018450
T4 303-306 DiseaseOrPhenotypicFeature denotes HIV DISEASE
T5 966-985 DiseaseOrPhenotypicFeature denotes disease progression D018450
T6 1065-1068 DiseaseOrPhenotypicFeature denotes HIV DISEASE
T7 1130-1139 DiseaseOrPhenotypicFeature denotes infection D007239
T8 1160-1174 DiseaseOrPhenotypicFeature denotes HIV-1-infected DISEASE
T9 1216-1219 DiseaseOrPhenotypicFeature denotes HIV DISEASE
T10 1351-1360 DiseaseOrPhenotypicFeature denotes infection D007239
T11 1938-1957 DiseaseOrPhenotypicFeature denotes disease progression D018450
T12 2095-2099 DiseaseOrPhenotypicFeature denotes AIDS D000163

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 1160-1174 DiseaseOrPhenotypicFeature denotes HIV-1-infected DISEASE
T2 2095-2099 DiseaseOrPhenotypicFeature denotes AIDS D000163

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 813-819 ChemicalEntity denotes formal http://purl.obolibrary.org/obo/CHEBI_48341

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 73-78 OrganismTaxon denotes HIV-1
T2 303-308 OrganismTaxon denotes HIV-1
T3 1065-1070 OrganismTaxon denotes HIV-1
T4 1160-1165 OrganismTaxon denotes HIV-1
T5 1216-1221 OrganismTaxon denotes HIV-1
T6 1488-1495 OrganismTaxon denotes patient
T7 1838-1845 OrganismTaxon denotes patient
T8 2062-2069 OrganismTaxon denotes patient

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T1 813-819 ChemicalEntity denotes formal http://purl.obolibrary.org/obo/CHEBI_48341
T8 1974-1978 GeneOrGeneProduct denotes CCR5
T7 1276-1280 GeneOrGeneProduct denotes CCR5
T6 1205-1209 GeneOrGeneProduct denotes CCR5
T5 1034-1042 GeneOrGeneProduct denotes envelope
T4 1028-1033 GeneOrGeneProduct denotes gp120
T3 933-937 GeneOrGeneProduct denotes CCR5
T2 237-241 GeneOrGeneProduct denotes CCR5
T75148 206-235 GeneOrGeneProduct denotes C-C chemokine receptor type 5
T20950 2095-2099 DiseaseOrPhenotypicFeature denotes AIDS D000163
T56817 1160-1174 DiseaseOrPhenotypicFeature denotes HIV-1-infected DISEASE
T90594 2062-2069 OrganismTaxon denotes patient
T15102 1838-1845 OrganismTaxon denotes patient
T98533 1488-1495 OrganismTaxon denotes patient
T14126 1216-1221 OrganismTaxon denotes HIV-1
T24839 1160-1165 OrganismTaxon denotes HIV-1
T59051 1065-1070 OrganismTaxon denotes HIV-1
T296 303-308 OrganismTaxon denotes HIV-1
T72741 73-78 OrganismTaxon denotes HIV-1
T89493 1284-1287 SequenceVariant denotes Δ32
T28822 14-21 SequenceVariant denotes delta32

DisGeNET

Id Subject Object Predicate Lexical cue
T0 1028-1033 gene:3700 denotes gp120
T1 1065-1068 disease:C0019693 denotes HIV
T2 1028-1033 gene:3700 denotes gp120
T3 1160-1163 disease:C0019693 denotes HIV
T4 1028-1033 gene:3700 denotes gp120
T5 1216-1219 disease:C0019693 denotes HIV
R1 T0 T1 associated_with gp120,HIV
R2 T2 T3 associated_with gp120,HIV
R3 T4 T5 associated_with gp120,HIV

Allie

Id Subject Object Predicate Lexical cue
SS1_21135151_1_0 206-235 expanded denotes C-C chemokine receptor type 5
SS2_21135151_1_0 237-241 abbr denotes CCR5
SS1_21135151_3_0 677-709 expanded denotes hierarchical phylogenetic models
SS2_21135151_3_0 711-715 abbr denotes HPMs
AE1_21135151_1_0 SS1_21135151_1_0 SS2_21135151_1_0 abbreviatedTo C-C chemokine receptor type 5,CCR5
AE1_21135151_3_0 SS1_21135151_3_0 SS2_21135151_3_0 abbreviatedTo hierarchical phylogenetic models,HPMs

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 14-21 DNAMutation:|DEL||32 denotes delta32