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PubMed:9356353 JSONTXT

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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 0-8 protein denotes TNFalpha
T2 29-45 protein denotes protein kinase A
T3 82-91 DNA denotes HIV-1 LTR
T4 121-152 DNA denotes TRE-like cAMP response elements
T5 154-174 protein denotes Activating protein-1
T6 176-180 protein denotes AP-1
T7 190-213 DNA denotes TPA responsive elements
T8 215-218 DNA denotes TRE
T9 250-279 DNA denotes transcription initiation site
T10 287-296 DNA denotes U5 region
T11 304-330 DNA denotes HIV-1 long terminal repeat
T12 332-335 DNA denotes LTR
T13 344-372 DNA denotes downstream sequence elements
T14 381-384 DNA denotes DSE
T15 400-404 protein denotes AP-1
T16 409-417 protein denotes CREB/ATF
T17 418-439 protein denotes transcription factors
T18 476-479 DNA denotes DSE
T19 489-513 DNA denotes cAMP-responsive elements
T20 515-518 DNA denotes CRE
T21 572-585 protein denotes cholera toxin
T22 587-590 protein denotes Ctx
T23 634-650 protein denotes protein kinase A
T24 652-655 protein denotes PKA
T25 732-741 DNA denotes HIV-1 DSE
T26 813-816 protein denotes Ctx
T27 821-829 protein denotes TNFalpha
T28 831-834 protein denotes Ctx
T29 849-857 protein denotes TNFalpha
T30 861-869 protein denotes IL-1beta
T31 907-918 protein denotes p24 antigen
T32 933-954 cell_line denotes U1 promonocytic cells
T33 980-1003 DNA denotes LTR reporter constructs
T34 1035-1044 DNA denotes DSE sites
T35 1059-1062 DNA denotes LTR
T36 1091-1094 protein denotes Ctx
T37 1099-1107 protein denotes TNFalpha
T38 1140-1143 protein denotes Ctx
T39 1148-1156 protein denotes IL-1beta
T40 1184-1192 protein denotes TNFalpha
T41 1197-1205 protein denotes IL-1beta
T42 1241-1245 protein denotes /PKA
T43 1295-1303 cell_line denotes U1 cells
T44 1317-1320 DNA denotes DSE
T45 1330-1333 DNA denotes TRE
T46 1395-1399 protein denotes AP-1
T47 1425-1433 protein denotes TNFalpha
T48 1445-1453 protein denotes IL-1beta
T49 1470-1473 protein denotes Ctx
T50 1513-1517 protein denotes AP-1
T51 1571-1605 DNA denotes TRE-like cAMP-responsive DSE sites
T52 1617-1639 DNA denotes 5'-untranslated leader
T53 1694-1702 protein denotes TNFalpha
T54 1715-1719 protein denotes /PKA
T55 1739-1742 DNA denotes DSE
T56 1747-1750 DNA denotes TRE
T57 1769-1788 protein denotes CREB/ATF homodimers
T58 1832-1835 DNA denotes DSE
T59 1841-1853 protein denotes heterodimers
T60 1871-1897 protein denotes AP-1 and CREB/ATF proteins

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-153 Sentence denotes TNFalpha cooperates with the protein kinase A pathway to synergistically increase HIV-1 LTR transcription via downstream TRE-like cAMP response elements.
S2 154-337 Sentence denotes Activating protein-1 (AP-1) binding TPA responsive elements (TRE) are located downstream of the transcription initiation site in the U5 region of the HIV-1 long terminal repeat (LTR).
S3 338-440 Sentence denotes These downstream sequence elements, termed DSE, can bind both AP-1 and CREB/ATF transcription factors.
S4 441-685 Sentence denotes Recently, we demonstrated that the DSE are also cAMP-responsive elements (CRE), since they mediated activation signals elicited by cholera toxin (Ctx), a potent activator of the cAMP-dependent protein kinase A (PKA) signal transduction pathway.
S5 686-830 Sentence denotes In the present study, we demonstrate that the HIV-1 DSE can mediate the transcriptional synergy elicited by the combination of Ctx and TNFalpha.
S6 831-955 Sentence denotes Ctx combined with TNFalpha or IL-1beta to produce a synergistic increase in p24 antigen production in U1 promonocytic cells.
S7 956-1304 Sentence denotes Transfection studies of LTR reporter constructs indicated that mutation of the DSE sites abrogated the LTR-mediated synergy induced by Ctx and TNFalpha, whereas the synergy induced by Ctx and IL-1beta was unaffected, suggesting TNFalpha and IL-1beta cooperate differently with the cAMP/PKA activation pathway to induce HIV-1 expression in U1 cells.
S8 1305-1424 Sentence denotes Because the DSE are also TRE sites, we assessed the effect of the agonist combinations on AP-1-dependent transcription.
S9 1425-1541 Sentence denotes TNFalpha as well as IL-1beta cooperated with Ctx to produce a synergistic activation of AP-1-mediated transcription.
S10 1542-1728 Sentence denotes These data indicate that the TRE-like cAMP-responsive DSE sites within the 5'-untranslated leader can mediate the transcriptional cooperativity between TNFalpha and the cAMP/PKA pathway.
S11 1729-1898 Sentence denotes Since the DSE and TRE sites cannot bind CREB/ATF homodimers, we propose a mechanism in which the HIV-1 DSE bind heterodimers composed of both AP-1 and CREB/ATF proteins.

genia-medco-coref

Id Subject Object Predicate Lexical cue
C1 0-8 NP denotes TNFalpha
C2 154-219 NP denotes Activating protein-1 (AP-1) binding TPA responsive elements (TRE)
C3 338-372 NP denotes These downstream sequence elements
C4 381-384 NP denotes DSE
C5 472-479 NP denotes the DSE
C6 527-531 NP denotes they
C7 572-591 NP denotes cholera toxin (Ctx)
C8 593-684 NP denotes a potent activator of the cAMP-dependent protein kinase A (PKA) signal transduction pathway
C9 728-741 NP denotes the HIV-1 DSE
C11 813-816 NP denotes Ctx
C12 821-829 NP denotes TNFalpha
C10 813-829 NP denotes Ctx and TNFalpha
C13 831-834 NP denotes Ctx
C14 849-857 NP denotes TNFalpha
C15 861-869 NP denotes IL-1beta
C16 933-954 NP denotes U1 promonocytic cells
C18 1091-1094 NP denotes Ctx
C19 1099-1107 NP denotes TNFalpha
C17 1091-1107 NP denotes Ctx and TNFalpha
C20 1140-1143 NP denotes Ctx
C21 1148-1156 NP denotes IL-1beta
C23 1184-1192 NP denotes TNFalpha
C24 1197-1205 NP denotes IL-1beta
C22 1184-1205 NP denotes TNFalpha and IL-1beta
C25 1295-1303 NP denotes U1 cells
C26 1313-1320 NP denotes the DSE
C27 1330-1339 NP denotes TRE sites
C29 1425-1433 NP denotes TNFalpha
C30 1445-1453 NP denotes IL-1beta
C28 1425-1453 NP denotes TNFalpha as well as IL-1beta
C31 1470-1473 NP denotes Ctx
C32 1694-1702 NP denotes TNFalpha
C33 1735-1742 NP denotes the DSE
C34 1747-1756 NP denotes TRE sites
C35 1801-1812 NP denotes a mechanism
C36 1816-1821 NP denotes which
C37 1822-1835 NP denotes the HIV-1 DSE
R1 C3 C2 coref-ident These downstream sequence elements,Activating protein-1 (AP-1) binding TPA responsive elements (TRE)
R2 C4 C3 coref-ident DSE,These downstream sequence elements
R3 C6 C5 coref-pron they,the DSE
R4 C8 C7 coref-appos a potent activator of the cAMP-dependent protein kinase A (PKA) signal transduction pathway,cholera toxin (Ctx)
R5 C11 C7 coref-ident Ctx,cholera toxin (Ctx)
R6 C12 C1 coref-ident TNFalpha,TNFalpha
R7 C14 C12 coref-ident TNFalpha,TNFalpha
R8 C18 C13 coref-ident Ctx,Ctx
R9 C19 C14 coref-ident TNFalpha,TNFalpha
R10 C17 C10 coref-ident Ctx and TNFalpha,Ctx and TNFalpha
R11 C20 C18 coref-ident Ctx,Ctx
R12 C21 C15 coref-ident IL-1beta,IL-1beta
R13 C23 C19 coref-ident TNFalpha,TNFalpha
R14 C24 C21 coref-ident IL-1beta,IL-1beta
R15 C25 C16 coref-ident U1 cells,U1 promonocytic cells
R16 C26 C5 coref-ident the DSE,the DSE
R17 C29 C23 coref-ident TNFalpha,TNFalpha
R18 C30 C24 coref-ident IL-1beta,IL-1beta
R19 C28 C22 coref-ident TNFalpha as well as IL-1beta,TNFalpha and IL-1beta
R20 C31 C20 coref-ident Ctx,Ctx
R21 C32 C29 coref-ident TNFalpha,TNFalpha
R22 C33 C26 coref-ident the DSE,the DSE
R23 C34 C27 coref-ident TRE sites,TRE sites
R24 C36 C35 coref-relat which,a mechanism
R25 C37 C9 coref-ident the HIV-1 DSE,the HIV-1 DSE

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 0-8 protein_molecule denotes TNFalpha
T2 29-45 protein_molecule denotes protein kinase A
T3 82-87 virus denotes HIV-1
T4 121-152 DNA_family_or_group denotes TRE-like cAMP response elements
T5 154-174 protein_molecule denotes Activating protein-1
T6 176-180 protein_molecule denotes AP-1
T7 190-213 DNA_family_or_group denotes TPA responsive elements
T8 215-218 DNA_family_or_group denotes TRE
T9 250-279 DNA_domain_or_region denotes transcription initiation site
T10 287-296 DNA_domain_or_region denotes U5 region
T11 304-309 virus denotes HIV-1
T12 332-335 DNA_domain_or_region denotes LTR
T13 344-372 DNA_family_or_group denotes downstream sequence elements
T14 381-384 DNA_domain_or_region denotes DSE
T15 400-404 protein_molecule denotes AP-1
T16 409-417 protein_molecule denotes CREB/ATF
T17 418-439 protein_family_or_group denotes transcription factors
T18 476-479 DNA_domain_or_region denotes DSE
T19 489-513 DNA_family_or_group denotes cAMP-responsive elements
T20 515-518 DNA_family_or_group denotes CRE
T21 572-585 protein_molecule denotes cholera toxin
T22 587-590 protein_molecule denotes Ctx
T23 619-633 other_name denotes cAMP-dependent
T24 634-650 protein_molecule denotes protein kinase A
T25 652-655 protein_molecule denotes PKA
T26 732-737 virus denotes HIV-1
T27 738-741 DNA_domain_or_region denotes DSE
T28 813-816 protein_molecule denotes Ctx
T29 821-829 protein_molecule denotes TNFalpha
T30 831-834 protein_molecule denotes Ctx
T31 849-857 protein_molecule denotes TNFalpha
T32 861-869 protein_molecule denotes IL-1beta
T33 907-918 protein_molecule denotes p24 antigen
T34 933-954 cell_line denotes U1 promonocytic cells
T35 980-1003 DNA_family_or_group denotes LTR reporter constructs
T36 1035-1038 DNA_domain_or_region denotes DSE
T37 1059-1062 DNA_domain_or_region denotes LTR
T38 1091-1094 protein_molecule denotes Ctx
T39 1099-1107 protein_molecule denotes TNFalpha
T40 1140-1143 protein_molecule denotes Ctx
T41 1148-1156 protein_molecule denotes IL-1beta
T42 1184-1192 protein_molecule denotes TNFalpha
T43 1197-1205 protein_molecule denotes IL-1beta
T44 1237-1241 nucleotide denotes cAMP
T45 1241-1245 protein_molecule denotes /PKA
T46 1275-1280 virus denotes HIV-1
T47 1295-1303 cell_line denotes U1 cells
T48 1317-1320 DNA_domain_or_region denotes DSE
T49 1330-1333 DNA_family_or_group denotes TRE
T50 1395-1399 protein_molecule denotes AP-1
T51 1425-1433 protein_molecule denotes TNFalpha
T52 1445-1453 protein_molecule denotes IL-1beta
T53 1470-1473 protein_molecule denotes Ctx
T54 1513-1517 protein_molecule denotes AP-1
T55 1571-1574 DNA_family_or_group denotes TRE
T56 1596-1599 DNA_domain_or_region denotes DSE
T57 1617-1639 DNA_domain_or_region denotes 5'-untranslated leader
T58 1694-1702 protein_molecule denotes TNFalpha
T59 1711-1715 nucleotide denotes cAMP
T60 1715-1719 protein_molecule denotes /PKA
T61 1739-1742 DNA_domain_or_region denotes DSE
T62 1747-1750 DNA_family_or_group denotes TRE
T63 1769-1777 protein_molecule denotes CREB/ATF
T64 1832-1835 DNA_domain_or_region denotes DSE
T65 1841-1853 protein_complex denotes heterodimers