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CL-cell

Id Subject Object Predicate Lexical cue cl_id
T1 1197-1231 Cell denotes peripheral blood mononuclear cells http://purl.obolibrary.org/obo/CL:0000842|http://purl.obolibrary.org/obo/CL:2000001

sentences

Id Subject Object Predicate Lexical cue
T1 0-170 Sentence denotes Potent and stable attenuation of live-HIV-1 by gain of a proteolysis-resistant inhibitor of NF-kappaB (IkappaB-alphaS32/36A) and the implications for vaccine development.
T2 171-294 Sentence denotes Live-attenuated human immunodeficiency viruses (HIVs) are candidates for Acquired Immunodeficiency Syndrome (AIDS) vaccine.
T3 295-526 Sentence denotes Based on the simian immunodeficiency virus (SIV) model for AIDS, loss-of-function (e.g. deletion of accessory genes such as nef) has been forwarded as a primary approach for creating enfeebled, but replication-competent, HIV-1/SIV.
T4 527-663 Sentence denotes Regrettably, recent evidence suggests that loss-of-function alone is not always sufficient to prevent the emergence of virulent mutants.
T5 664-802 Sentence denotes New strategies that attenuate via mechanisms distinct from loss-of-function are needed for enhancing the safety phenotype of viral genome.
T6 803-927 Sentence denotes Here, we propose gain-of-function to be used simultaneously with loss-of-function as a novel approach for attenuating HIV-1.
T7 928-1082 Sentence denotes We have constructed an HIV-1 genome carrying the cDNA of a proteolysis-resistant nuclear factor-kappaB inhibitor (IkappaB-alphaS32/36A) in the nef region.
T8 1083-1232 Sentence denotes HIV-1 expressing IkappaB-alphaS32/36A down-regulates viral expression and is highly attenuated in both Jurkat and peripheral blood mononuclear cells.
T9 1233-1455 Sentence denotes We provide formal proof that the phenotypic and attenuating characteristics of IkappaB-alphaS32/36A permit its stable maintenance in a live, replicating HIV-1 despite 180 days of forced ex vivo passaging in tissue culture.
T10 1456-1571 Sentence denotes As compared with other open-reading frames embedded into HIV/SIV genome, this degree of stability is unprecedented.
T11 1572-1730 Sentence denotes Thus, IkappaB-alphaS32/36A offers proof-of-principle that artifactually gained functions, when used to attenuate the replication of live HIV-1, can be stable.
T12 1731-1883 Sentence denotes These findings illustrate gain-of-function as a feasible strategy for developing safer live-attenuated HIVs to be tested as candidates for AIDS vaccine.

Glycosmos6-MAT

Id Subject Object Predicate Lexical cue
T1 1208-1213 http://purl.obolibrary.org/obo/MAT_0000083 denotes blood
T2 1208-1213 http://purl.obolibrary.org/obo/MAT_0000315 denotes blood

jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 57-88 protein denotes proteolysis-resistant inhibitor
T2 92-101 protein denotes NF-kappaB
T3 103-123 protein denotes IkappaB-alphaS32/36A
T4 419-422 DNA denotes nef
T5 789-801 DNA denotes viral genome
T6 951-963 DNA denotes HIV-1 genome
T7 977-981 DNA denotes cDNA
T8 987-1040 protein denotes proteolysis-resistant nuclear factor-kappaB inhibitor
T9 1042-1062 protein denotes IkappaB-alphaS32/36A
T10 1071-1081 DNA denotes nef region
T11 1100-1120 protein denotes IkappaB-alphaS32/36A
T12 1186-1192 cell_line denotes Jurkat
T13 1197-1231 cell_type denotes peripheral blood mononuclear cells
T14 1312-1332 protein denotes IkappaB-alphaS32/36A
T15 1479-1498 DNA denotes open-reading frames
T16 1513-1527 DNA denotes HIV/SIV genome
T17 1578-1598 protein denotes IkappaB-alphaS32/36A

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-170 Sentence denotes Potent and stable attenuation of live-HIV-1 by gain of a proteolysis-resistant inhibitor of NF-kappaB (IkappaB-alphaS32/36A) and the implications for vaccine development.
S2 171-294 Sentence denotes Live-attenuated human immunodeficiency viruses (HIVs) are candidates for Acquired Immunodeficiency Syndrome (AIDS) vaccine.
S3 295-526 Sentence denotes Based on the simian immunodeficiency virus (SIV) model for AIDS, loss-of-function (e.g. deletion of accessory genes such as nef) has been forwarded as a primary approach for creating enfeebled, but replication-competent, HIV-1/SIV.
S4 527-663 Sentence denotes Regrettably, recent evidence suggests that loss-of-function alone is not always sufficient to prevent the emergence of virulent mutants.
S5 664-802 Sentence denotes New strategies that attenuate via mechanisms distinct from loss-of-function are needed for enhancing the safety phenotype of viral genome.
S6 803-927 Sentence denotes Here, we propose gain-of-function to be used simultaneously with loss-of-function as a novel approach for attenuating HIV-1.
S7 928-1082 Sentence denotes We have constructed an HIV-1 genome carrying the cDNA of a proteolysis-resistant nuclear factor-kappaB inhibitor (IkappaB-alphaS32/36A) in the nef region.
S8 1083-1232 Sentence denotes HIV-1 expressing IkappaB-alphaS32/36A down-regulates viral expression and is highly attenuated in both Jurkat and peripheral blood mononuclear cells.
S9 1233-1455 Sentence denotes We provide formal proof that the phenotypic and attenuating characteristics of IkappaB-alphaS32/36A permit its stable maintenance in a live, replicating HIV-1 despite 180 days of forced ex vivo passaging in tissue culture.
S10 1456-1571 Sentence denotes As compared with other open-reading frames embedded into HIV/SIV genome, this degree of stability is unprecedented.
S11 1572-1730 Sentence denotes Thus, IkappaB-alphaS32/36A offers proof-of-principle that artifactually gained functions, when used to attenuate the replication of live HIV-1, can be stable.
S12 1731-1883 Sentence denotes These findings illustrate gain-of-function as a feasible strategy for developing safer live-attenuated HIVs to be tested as candidates for AIDS vaccine.

genia-medco-coref

Id Subject Object Predicate Lexical cue
C1 33-43 NP denotes live-HIV-1
C2 55-124 NP denotes a proteolysis-resistant inhibitor of NF-kappaB (IkappaB-alphaS32/36A)
C3 244-293 NP denotes Acquired Immunodeficiency Syndrome (AIDS) vaccine
C4 360-423 NP denotes loss-of-function (e.g. deletion of accessory genes such as nef)
C5 570-592 NP denotes loss-of-function alone
C6 664-678 NP denotes New strategies
C7 679-683 NP denotes that
C8 723-739 NP denotes loss-of-function
C9 820-836 NP denotes gain-of-function
C10 868-884 NP denotes loss-of-function
C11 985-1063 NP denotes a proteolysis-resistant nuclear factor-kappaB inhibitor (IkappaB-alphaS32/36A)
C12 1244-1256 NP denotes formal proof
C13 1257-1261 NP denotes that
C14 1312-1332 NP denotes IkappaB-alphaS32/36A
C15 1340-1343 NP denotes its
C16 1578-1598 NP denotes IkappaB-alphaS32/36A
C17 1606-1624 NP denotes proof-of-principle
C18 1625-1629 NP denotes that
C19 1704-1714 NP denotes live HIV-1
C20 1757-1773 NP denotes gain-of-function
C21 1870-1882 NP denotes AIDS vaccine
R1 C5 C4 coref-ident loss-of-function alone,loss-of-function (e.g. deletion of accessory genes such as nef)
R2 C7 C6 coref-relat that,New strategies
R3 C8 C5 coref-ident loss-of-function,loss-of-function alone
R4 C10 C8 coref-ident loss-of-function,loss-of-function
R5 C11 C2 coref-ident a proteolysis-resistant nuclear factor-kappaB inhibitor (IkappaB-alphaS32/36A),a proteolysis-resistant inhibitor of NF-kappaB (IkappaB-alphaS32/36A)
R6 C13 C12 coref-relat that,formal proof
R7 C14 C11 coref-ident IkappaB-alphaS32/36A,a proteolysis-resistant nuclear factor-kappaB inhibitor (IkappaB-alphaS32/36A)
R8 C15 C14 coref-pron its,IkappaB-alphaS32/36A
R9 C16 C14 coref-ident IkappaB-alphaS32/36A,IkappaB-alphaS32/36A
R10 C18 C17 coref-relat that,proof-of-principle
R11 C19 C1 coref-ident live HIV-1,live-HIV-1
R12 C20 C9 coref-ident gain-of-function,gain-of-function
R13 C21 C3 coref-ident AIDS vaccine,Acquired Immunodeficiency Syndrome (AIDS) vaccine

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 33-43 virus denotes live-HIV-1
T2 57-88 protein_family_or_group denotes proteolysis-resistant inhibitor
T3 92-101 protein_complex denotes NF-kappaB
T4 103-123 protein_molecule denotes IkappaB-alphaS32/36A
T5 150-169 other_name denotes vaccine development
T6 171-217 virus denotes Live-attenuated human immunodeficiency viruses
T7 219-223 virus denotes HIVs
T8 244-293 other_name denotes Acquired Immunodeficiency Syndrome (AIDS) vaccine
T9 308-349 virus denotes simian immunodeficiency virus (SIV) model
T10 354-358 other_name denotes AIDS
T11 360-376 other_name denotes loss-of-function
T12 419-422 DNA_domain_or_region denotes nef
T13 516-525 virus denotes HIV-1/SIV
T14 570-586 other_name denotes loss-of-function
T15 646-662 virus denotes virulent mutants
T16 723-739 other_name denotes loss-of-function
T17 789-801 DNA_family_or_group denotes viral genome
T18 820-836 other_name denotes gain-of-function
T19 868-884 other_name denotes loss-of-function
T20 921-926 virus denotes HIV-1
T21 951-956 virus denotes HIV-1
T22 977-981 DNA_family_or_group denotes cDNA
T23 987-1040 protein_family_or_group denotes proteolysis-resistant nuclear factor-kappaB inhibitor
T24 1042-1062 protein_molecule denotes IkappaB-alphaS32/36A
T25 1071-1074 DNA_domain_or_region denotes nef
T26 1083-1088 virus denotes HIV-1
T27 1100-1120 protein_molecule denotes IkappaB-alphaS32/36A
T28 1136-1152 other_name denotes viral expression
T29 1186-1192 cell_line denotes Jurkat
T30 1197-1231 cell_type denotes peripheral blood mononuclear cells
T31 1312-1332 protein_molecule denotes IkappaB-alphaS32/36A
T32 1386-1391 virus denotes HIV-1
T33 1440-1454 other_artificial_source denotes tissue culture
T34 1479-1498 DNA_family_or_group denotes open-reading frames
T35 1513-1527 DNA_family_or_group denotes HIV/SIV genome
T36 1578-1598 protein_molecule denotes IkappaB-alphaS32/36A
T37 1704-1708 virus denotes live
T38 1709-1714 virus denotes HIV-1
T39 1757-1773 other_name denotes gain-of-function
T40 1818-1833 virus denotes live-attenuated
T41 1834-1838 virus denotes HIVs
T42 1870-1882 other_name denotes AIDS vaccine

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 193-209 HP_0002721 denotes immunodeficiency
T2 253-269 HP_0002721 denotes Immunodeficiency
T3 315-331 HP_0002721 denotes immunodeficiency

HP-phenotype

Id Subject Object Predicate Lexical cue hp_id
T1 193-209 Phenotype denotes immunodeficiency HP:0002721
T2 253-269 Phenotype denotes Immunodeficiency HP:0002721
T3 315-331 Phenotype denotes immunodeficiency HP:0002721

mondo_disease

Id Subject Object Predicate Lexical cue mondo_id
T1 193-209 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T2 244-278 Disease denotes Acquired Immunodeficiency Syndrome http://purl.obolibrary.org/obo/MONDO_0012268
T3 280-284 Disease denotes AIDS http://purl.obolibrary.org/obo/MONDO_0012268
T4 315-331 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T5 339-342 Disease denotes SIV http://purl.obolibrary.org/obo/MONDO_0010029
T6 354-358 Disease denotes AIDS http://purl.obolibrary.org/obo/MONDO_0012268
T7 522-525 Disease denotes SIV http://purl.obolibrary.org/obo/MONDO_0010029
T8 1517-1520 Disease denotes SIV http://purl.obolibrary.org/obo/MONDO_0010029
T9 1870-1874 Disease denotes AIDS http://purl.obolibrary.org/obo/MONDO_0012268

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 187-192 OrganismTaxon denotes human 9606
T2 308-337 OrganismTaxon denotes simian immunodeficiency virus 11723
T3 339-342 OrganismTaxon denotes SIV 11723
T4 522-525 OrganismTaxon denotes SIV 11723
T5 1517-1520 OrganismTaxon denotes SIV 11723

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1197-1231 Body_part denotes peripheral blood mononuclear cells http://purl.obolibrary.org/obo/CL_0000842|http://purl.obolibrary.org/obo/CL_2000001
T3 1440-1446 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

Anatomy-MAT

Id Subject Object Predicate Lexical cue mat_id
T1 1208-1213 Body_part denotes blood http://purl.obolibrary.org/obo/MAT_0000083|http://purl.obolibrary.org/obo/MAT_0000315