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Induction of NF-KB during monocyte differentiation by HIV type 1 infection.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91079577:0", "type": "list", "id": "abstracts:91079577:0:negation"}
Induction of NF-KB during monocyte differentiation by HIV type 1 infection.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91079577:0", "type": "list", "id": "abstracts:91079577:0:speculation"}
The production of human immunodeficiency virus type 1 (HIV-1) progeny was followed in the U937 promonocytic cell line after stimulation either with retinoic acid or PMA, and in purified human monocytes and macrophages.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91079577:1", "type": "list", "id": "abstracts:91079577:1:negation"}
The production of human immunodeficiency virus type 1 (HIV-1) progeny was followed in the U937 promonocytic cell line after stimulation either with retinoic acid or PMA, and in purified human monocytes and macrophages.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91079577:1", "type": "list", "id": "abstracts:91079577:1:speculation"}
Electrophoretic mobility shift assays and Southwestern blotting experiments were used to detect the binding of cellular transactivation factor NF-KB to the double repeat-KB enhancer sequence located in the long terminal repeat.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91079577:2", "type": "list", "id": "abstracts:91079577:2:negation"}
Electrophoretic mobility shift assays and Southwestern blotting experiments were used to detect the binding of cellular transactivation factor NF-KB to the double repeat-KB enhancer sequence located in the long terminal repeat.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91079577:2", "type": "list", "id": "abstracts:91079577:2:speculation"}
PMA treatment, and not retinoic acid treatment of the U937 cells acts in inducing NF-KB expression in the nuclei.
Every negation cue in the text, as written.
{ "text": [ "not" ], "answer_start": [ 19 ] }
{"field": "negation_cues", "group": "abstracts:91079577:3", "type": "list", "id": "abstracts:91079577:3:negation"}
PMA treatment, and not retinoic acid treatment of the U937 cells acts in inducing NF-KB expression in the nuclei.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91079577:3", "type": "list", "id": "abstracts:91079577:3:speculation"}
PMA treatment, and not retinoic acid treatment of the U937 cells acts in inducing NF-KB expression in the nuclei.
The full scope of the negation cue 'not' at [19, 22) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "not retinoic acid treatment of the U937 cells" ], "answer_start": [ 19 ] }
{"field": "negation_scope_0", "group": "abstracts:91079577:3", "type": "list", "id": "abstracts:91079577:3:X1.4.1", "cue_spans": [[19, 22]]}
In nuclear extracts from monocytes or macrophages, induction of NF-KB occurred only if the cells were previously infected with HIV-1.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91079577:4", "type": "list", "id": "abstracts:91079577:4:negation"}
In nuclear extracts from monocytes or macrophages, induction of NF-KB occurred only if the cells were previously infected with HIV-1.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91079577:4", "type": "list", "id": "abstracts:91079577:4:speculation"}
When U937 cells were infected with HIV-1, no induction of NF-KB factor was detected, whereas high level of progeny virions was produced, suggesting that this factor was not required for viral replication.
Every negation cue in the text, as written.
{ "text": [ "no", "not" ], "answer_start": [ 42, 169 ] }
{"field": "negation_cues", "group": "abstracts:91079577:5", "type": "list", "id": "abstracts:91079577:5:negation"}
When U937 cells were infected with HIV-1, no induction of NF-KB factor was detected, whereas high level of progeny virions was produced, suggesting that this factor was not required for viral replication.
Every speculation cue in the text, as written.
{ "text": [ "suggesting" ], "answer_start": [ 137 ] }
{"field": "speculation_cues", "group": "abstracts:91079577:5", "type": "list", "id": "abstracts:91079577:5:speculation"}
When U937 cells were infected with HIV-1, no induction of NF-KB factor was detected, whereas high level of progeny virions was produced, suggesting that this factor was not required for viral replication.
The full scope of the negation cue 'not' at [169, 172) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "not required for viral replication" ], "answer_start": [ 169 ] }
{"field": "negation_scope_0", "group": "abstracts:91079577:5", "type": "list", "id": "abstracts:91079577:5:X1.6.1", "cue_spans": [[169, 172]]}
When U937 cells were infected with HIV-1, no induction of NF-KB factor was detected, whereas high level of progeny virions was produced, suggesting that this factor was not required for viral replication.
The full scope of the negation cue 'no' at [42, 44) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "no induction of NF-KB factor was detected" ], "answer_start": [ 42 ] }
{"field": "negation_scope_1", "group": "abstracts:91079577:5", "type": "list", "id": "abstracts:91079577:5:X1.6.3", "cue_spans": [[42, 44]]}
When U937 cells were infected with HIV-1, no induction of NF-KB factor was detected, whereas high level of progeny virions was produced, suggesting that this factor was not required for viral replication.
The full scope of the speculation cue 'suggesting' at [137, 147) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "suggesting that this factor was not required for viral replication" ], "answer_start": [ 137 ] }
{"field": "speculation_scope_2", "group": "abstracts:91079577:5", "type": "list", "id": "abstracts:91079577:5:X1.6.2", "cue_spans": [[137, 147]]}
These results indicate that in monocytic cell lineage, HIV-1 could mimic some differentiation/activation stimuli allowing nuclear NF-KB expression.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91079577:6", "type": "list", "id": "abstracts:91079577:6:negation"}
These results indicate that in monocytic cell lineage, HIV-1 could mimic some differentiation/activation stimuli allowing nuclear NF-KB expression.
Every speculation cue in the text, as written.
{ "text": [ "indicate that", "could" ], "answer_start": [ 14, 61 ] }
{"field": "speculation_cues", "group": "abstracts:91079577:6", "type": "list", "id": "abstracts:91079577:6:speculation"}
These results indicate that in monocytic cell lineage, HIV-1 could mimic some differentiation/activation stimuli allowing nuclear NF-KB expression.
The full scope of the speculation cue 'could' at [61, 66) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "could mimic some differentiation/activation stimuli allowing nuclear NF-KB expression" ], "answer_start": [ 61 ] }
{"field": "speculation_scope_0", "group": "abstracts:91079577:6", "type": "list", "id": "abstracts:91079577:6:X1.7.1", "cue_spans": [[61, 66]]}
These results indicate that in monocytic cell lineage, HIV-1 could mimic some differentiation/activation stimuli allowing nuclear NF-KB expression.
The full scope of the speculation cue 'indicate that' at [14, 27) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "indicate that in monocytic cell lineage, HIV-1 could mimic some differentiation/activation stimuli allowing nuclear NF-KB expression" ], "answer_start": [ 14 ] }
{"field": "speculation_scope_1", "group": "abstracts:91079577:6", "type": "list", "id": "abstracts:91079577:6:X1.7.2", "cue_spans": [[14, 27]]}
Positive and negative regulation of immunoglobulin gene expression by a novel B-cell-specific enhancer element.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91094881:0", "type": "list", "id": "abstracts:91094881:0:negation"}
Positive and negative regulation of immunoglobulin gene expression by a novel B-cell-specific enhancer element.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91094881:0", "type": "list", "id": "abstracts:91094881:0:speculation"}
A new B-cell-specific enhancer element has been identified 3' of E4 and the octamerlike motifs in the human immunoglobulin heavy-chain gene enhancer.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91094881:1", "type": "list", "id": "abstracts:91094881:1:negation"}
A new B-cell-specific enhancer element has been identified 3' of E4 and the octamerlike motifs in the human immunoglobulin heavy-chain gene enhancer.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91094881:1", "type": "list", "id": "abstracts:91094881:1:speculation"}
Tandem copies of this 67-bp MnlI-AluI fragment, when fused to the chloramphenicol acetyltransferase gene driven by the conalbumin promoter, stimulated transcription in B cells but not in Jurkat T cells or HeLa cells.
Every negation cue in the text, as written.
{ "text": [ "not" ], "answer_start": [ 180 ] }
{"field": "negation_cues", "group": "abstracts:91094881:2", "type": "list", "id": "abstracts:91094881:2:negation"}
Tandem copies of this 67-bp MnlI-AluI fragment, when fused to the chloramphenicol acetyltransferase gene driven by the conalbumin promoter, stimulated transcription in B cells but not in Jurkat T cells or HeLa cells.
Every speculation cue in the text, as written.
{ "text": [ "or" ], "answer_start": [ 202 ] }
{"field": "speculation_cues", "group": "abstracts:91094881:2", "type": "list", "id": "abstracts:91094881:2:speculation"}
Tandem copies of this 67-bp MnlI-AluI fragment, when fused to the chloramphenicol acetyltransferase gene driven by the conalbumin promoter, stimulated transcription in B cells but not in Jurkat T cells or HeLa cells.
The full scope of the negation cue 'not' at [180, 183) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "not in Jurkat T cells or HeLa cells" ], "answer_start": [ 180 ] }
{"field": "negation_scope_0", "group": "abstracts:91094881:2", "type": "list", "id": "abstracts:91094881:2:X2.3.2", "cue_spans": [[180, 183]]}
Tandem copies of this 67-bp MnlI-AluI fragment, when fused to the chloramphenicol acetyltransferase gene driven by the conalbumin promoter, stimulated transcription in B cells but not in Jurkat T cells or HeLa cells.
The full scope of the speculation cue 'or' at [202, 204) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "Jurkat T cells or HeLa cells" ], "answer_start": [ 187 ] }
{"field": "speculation_scope_1", "group": "abstracts:91094881:2", "type": "list", "id": "abstracts:91094881:2:X2.3.1", "cue_spans": [[202, 204]]}
Footprinting analysis revealed that the identical sequence CCGAAACTGAAAAGG, designated E6, was protected by nuclear extracts from B cells, T cells, or HeLa cells.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91094881:3", "type": "list", "id": "abstracts:91094881:3:negation"}
Footprinting analysis revealed that the identical sequence CCGAAACTGAAAAGG, designated E6, was protected by nuclear extracts from B cells, T cells, or HeLa cells.
Every speculation cue in the text, as written.
{ "text": [ "or" ], "answer_start": [ 148 ] }
{"field": "speculation_cues", "group": "abstracts:91094881:3", "type": "list", "id": "abstracts:91094881:3:speculation"}
Footprinting analysis revealed that the identical sequence CCGAAACTGAAAAGG, designated E6, was protected by nuclear extracts from B cells, T cells, or HeLa cells.
The full scope of the speculation cue 'or' at [148, 150) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "B cells, T cells, or HeLa cells" ], "answer_start": [ 130 ] }
{"field": "speculation_scope_0", "group": "abstracts:91094881:3", "type": "list", "id": "abstracts:91094881:3:X2.4.1", "cue_spans": [[148, 150]]}
Gel mobility shift assays using a synthetic E6 motif detected a B-cell-specific complex in addition to a ubiquitous band found also in T cells and HeLa cells.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91094881:4", "type": "list", "id": "abstracts:91094881:4:negation"}
Gel mobility shift assays using a synthetic E6 motif detected a B-cell-specific complex in addition to a ubiquitous band found also in T cells and HeLa cells.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91094881:4", "type": "list", "id": "abstracts:91094881:4:speculation"}
In agreement with the results of gel retardation assays, tandem copies of the E6 motif stimulated transcription in ARH77 and Raji cells but not in Jurkat or HeLa cells.
Every negation cue in the text, as written.
{ "text": [ "not" ], "answer_start": [ 140 ] }
{"field": "negation_cues", "group": "abstracts:91094881:5", "type": "list", "id": "abstracts:91094881:5:negation"}
In agreement with the results of gel retardation assays, tandem copies of the E6 motif stimulated transcription in ARH77 and Raji cells but not in Jurkat or HeLa cells.
Every speculation cue in the text, as written.
{ "text": [ "or" ], "answer_start": [ 154 ] }
{"field": "speculation_cues", "group": "abstracts:91094881:5", "type": "list", "id": "abstracts:91094881:5:speculation"}
In agreement with the results of gel retardation assays, tandem copies of the E6 motif stimulated transcription in ARH77 and Raji cells but not in Jurkat or HeLa cells.
The full scope of the negation cue 'not' at [140, 143) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "not in Jurkat or HeLa cells" ], "answer_start": [ 140 ] }
{"field": "negation_scope_0", "group": "abstracts:91094881:5", "type": "list", "id": "abstracts:91094881:5:X2.6.2", "cue_spans": [[140, 143]]}
In agreement with the results of gel retardation assays, tandem copies of the E6 motif stimulated transcription in ARH77 and Raji cells but not in Jurkat or HeLa cells.
The full scope of the speculation cue 'or' at [154, 156) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "Jurkat or HeLa" ], "answer_start": [ 147 ] }
{"field": "speculation_scope_1", "group": "abstracts:91094881:5", "type": "list", "id": "abstracts:91094881:5:X2.6.1", "cue_spans": [[154, 156]]}
Furthermore, a mutant E6 motif lost both in vitro binding activity and in vivo enhancer activity.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91094881:6", "type": "list", "id": "abstracts:91094881:6:negation"}
Furthermore, a mutant E6 motif lost both in vitro binding activity and in vivo enhancer activity.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91094881:6", "type": "list", "id": "abstracts:91094881:6:speculation"}
In striking contrast to the mouse Ig heavy-chain enhancer, in which the octamer motif acts as a B-cell-specific enhancer element, the human enhancer contains an octamerlike sequence with one base substitution which bound octamer-binding proteins with only very low affinity and showed no enhancer activity of its own.
Every negation cue in the text, as written.
{ "text": [ "no" ], "answer_start": [ 285 ] }
{"field": "negation_cues", "group": "abstracts:91094881:7", "type": "list", "id": "abstracts:91094881:7:negation"}
In striking contrast to the mouse Ig heavy-chain enhancer, in which the octamer motif acts as a B-cell-specific enhancer element, the human enhancer contains an octamerlike sequence with one base substitution which bound octamer-binding proteins with only very low affinity and showed no enhancer activity of its own.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91094881:7", "type": "list", "id": "abstracts:91094881:7:speculation"}
In striking contrast to the mouse Ig heavy-chain enhancer, in which the octamer motif acts as a B-cell-specific enhancer element, the human enhancer contains an octamerlike sequence with one base substitution which bound octamer-binding proteins with only very low affinity and showed no enhancer activity of its own.
The full scope of the negation cue 'no' at [285, 287) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "no enhancer activity of its own" ], "answer_start": [ 285 ] }
{"field": "negation_scope_0", "group": "abstracts:91094881:7", "type": "list", "id": "abstracts:91094881:7:X2.8.1", "cue_spans": [[285, 287]]}
Interestingly, the MnlI-AluI fragment could suppress the basal-level activity of the conalbumin promoter in both Jurkat and HeLa cells.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91094881:8", "type": "list", "id": "abstracts:91094881:8:negation"}
Interestingly, the MnlI-AluI fragment could suppress the basal-level activity of the conalbumin promoter in both Jurkat and HeLa cells.
Every speculation cue in the text, as written.
{ "text": [ "could" ], "answer_start": [ 38 ] }
{"field": "speculation_cues", "group": "abstracts:91094881:8", "type": "list", "id": "abstracts:91094881:8:speculation"}
Interestingly, the MnlI-AluI fragment could suppress the basal-level activity of the conalbumin promoter in both Jurkat and HeLa cells.
The full scope of the speculation cue 'could' at [38, 43) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "could suppress the basal-level activity of the conalbumin promoter in both Jurkat and HeLa cells" ], "answer_start": [ 38 ] }
{"field": "speculation_scope_0", "group": "abstracts:91094881:8", "type": "list", "id": "abstracts:91094881:8:X2.9.1", "cue_spans": [[38, 43]]}
Moreover, simian virus 40 enhancer activity was blocked by the MnlI-AluI fragment in HeLa cells but not in B cells.
Every negation cue in the text, as written.
{ "text": [ "not" ], "answer_start": [ 100 ] }
{"field": "negation_cues", "group": "abstracts:91094881:9", "type": "list", "id": "abstracts:91094881:9:negation"}
Moreover, simian virus 40 enhancer activity was blocked by the MnlI-AluI fragment in HeLa cells but not in B cells.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91094881:9", "type": "list", "id": "abstracts:91094881:9:speculation"}
Moreover, simian virus 40 enhancer activity was blocked by the MnlI-AluI fragment in HeLa cells but not in B cells.
The full scope of the negation cue 'not' at [100, 103) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "not in B cells" ], "answer_start": [ 100 ] }
{"field": "negation_scope_0", "group": "abstracts:91094881:9", "type": "list", "id": "abstracts:91094881:9:X2.10.1", "cue_spans": [[100, 103]]}
Thus, the novel enhancer element identified in this study is probably a target site for both positive and negative factors.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91094881:10", "type": "list", "id": "abstracts:91094881:10:negation"}
Thus, the novel enhancer element identified in this study is probably a target site for both positive and negative factors.
Every speculation cue in the text, as written.
{ "text": [ "probably" ], "answer_start": [ 61 ] }
{"field": "speculation_cues", "group": "abstracts:91094881:10", "type": "list", "id": "abstracts:91094881:10:speculation"}
Thus, the novel enhancer element identified in this study is probably a target site for both positive and negative factors.
The full scope of the speculation cue 'probably' at [61, 69) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "probably a target site for both positive and negative factors" ], "answer_start": [ 61 ] }
{"field": "speculation_scope_0", "group": "abstracts:91094881:10", "type": "list", "id": "abstracts:91094881:10:X2.11.1", "cue_spans": [[61, 69]]}
The NF kappa B independent cis-acting sequences in HIV-1 LTR responsive to T-cell activation.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91101115:0", "type": "list", "id": "abstracts:91101115:0:negation"}
The NF kappa B independent cis-acting sequences in HIV-1 LTR responsive to T-cell activation.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91101115:0", "type": "list", "id": "abstracts:91101115:0:speculation"}
The rate of transcription initiation directed by the long terminal repeat (LTR) of HIV-1 increases in response to mitogenic stimuli of T cells.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91101115:1", "type": "list", "id": "abstracts:91101115:1:negation"}
The rate of transcription initiation directed by the long terminal repeat (LTR) of HIV-1 increases in response to mitogenic stimuli of T cells.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91101115:1", "type": "list", "id": "abstracts:91101115:1:speculation"}
Here we show that the response of the HIV-1 LTR may be governed by two independent sequences located 5' to the site of transcription initiation sequences that bind either NFAT-1 or NF kappa B.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91101115:2", "type": "list", "id": "abstracts:91101115:2:negation"}
Here we show that the response of the HIV-1 LTR may be governed by two independent sequences located 5' to the site of transcription initiation sequences that bind either NFAT-1 or NF kappa B.
Every speculation cue in the text, as written.
{ "text": [ "may" ], "answer_start": [ 48 ] }
{"field": "speculation_cues", "group": "abstracts:91101115:2", "type": "list", "id": "abstracts:91101115:2:speculation"}
Here we show that the response of the HIV-1 LTR may be governed by two independent sequences located 5' to the site of transcription initiation sequences that bind either NFAT-1 or NF kappa B.
The full scope of the speculation cue 'may' at [48, 51) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "the response of the HIV-1 LTR may be governed by two independent sequences located 5' to the site of transcription initiation sequences that bind either NFAT-1 or NF kappa B" ], "answer_start": [ 18 ] }
{"field": "speculation_scope_0", "group": "abstracts:91101115:2", "type": "list", "id": "abstracts:91101115:2:X3.3.1", "cue_spans": [[48, 51]]}
The rate of LTR-directed gene expression increased in response to treatment with either a phorbol ester or tumor necrosis factor alpha if either the NFAT-1 or NF kappa B binding sites were deleted, but failed to respond to these mitogenic stimuli if both sequences were absent.
Every negation cue in the text, as written.
{ "text": [ "failed" ], "answer_start": [ 202 ] }
{"field": "negation_cues", "group": "abstracts:91101115:3", "type": "list", "id": "abstracts:91101115:3:negation"}
The rate of LTR-directed gene expression increased in response to treatment with either a phorbol ester or tumor necrosis factor alpha if either the NFAT-1 or NF kappa B binding sites were deleted, but failed to respond to these mitogenic stimuli if both sequences were absent.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91101115:3", "type": "list", "id": "abstracts:91101115:3:speculation"}
The rate of LTR-directed gene expression increased in response to treatment with either a phorbol ester or tumor necrosis factor alpha if either the NFAT-1 or NF kappa B binding sites were deleted, but failed to respond to these mitogenic stimuli if both sequences were absent.
The full scope of the negation cue 'failed' at [202, 208) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "failed to respond to these mitogenic stimuli if both sequences were absent" ], "answer_start": [ 202 ] }
{"field": "negation_scope_0", "group": "abstracts:91101115:3", "type": "list", "id": "abstracts:91101115:3:X3.4.1", "cue_spans": [[202, 208]]}
The HIV-1 mutant virus containing both NF kappa B and NFAT-1 deletion was able to replicate although at a much decreased growth rate, while the deletion of NFAT-1 alone increased the viral growth rate in Jurkat cells.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91101115:4", "type": "list", "id": "abstracts:91101115:4:negation"}
The HIV-1 mutant virus containing both NF kappa B and NFAT-1 deletion was able to replicate although at a much decreased growth rate, while the deletion of NFAT-1 alone increased the viral growth rate in Jurkat cells.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91101115:4", "type": "list", "id": "abstracts:91101115:4:speculation"}
Neither deletion of NF kappa B nor deletion of NFAT-1 decreased activation of viral replication by phorbol ester.
Every negation cue in the text, as written.
{ "text": [ "Neither", "nor" ], "answer_start": [ 0, 31 ] }
{"field": "negation_cues", "group": "abstracts:91101115:5", "type": "list", "id": "abstracts:91101115:5:negation"}
Neither deletion of NF kappa B nor deletion of NFAT-1 decreased activation of viral replication by phorbol ester.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91101115:5", "type": "list", "id": "abstracts:91101115:5:speculation"}
Neither deletion of NF kappa B nor deletion of NFAT-1 decreased activation of viral replication by phorbol ester.
The full scope of the negation cue 'Neither' at [0, 7), 'nor' at [31, 34) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "Neither deletion of NF kappa B nor deletion of NFAT-1 decreased activation of viral replication by phorbol ester" ], "answer_start": [ 0 ] }
{"field": "negation_scope_0", "group": "abstracts:91101115:5", "type": "list", "id": "abstracts:91101115:5:X3.6.1", "cue_spans": [[0, 7], [31, 34]]}
Specific depletion of the B-cell population induced by aberrant expression of human interferon regulatory factor 1 gene in transgenic mice.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:0", "type": "list", "id": "abstracts:91110562:0:negation"}
Specific depletion of the B-cell population induced by aberrant expression of human interferon regulatory factor 1 gene in transgenic mice.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91110562:0", "type": "list", "id": "abstracts:91110562:0:speculation"}
Interferons (IFNs) are well known both as antiviral proteins and as potent regulators of cell growth and differentiation.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:1", "type": "list", "id": "abstracts:91110562:1:negation"}
Interferons (IFNs) are well known both as antiviral proteins and as potent regulators of cell growth and differentiation.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91110562:1", "type": "list", "id": "abstracts:91110562:1:speculation"}
In fact, IFNs inhibit growth of various normal and transformed cell types.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:2", "type": "list", "id": "abstracts:91110562:2:negation"}
In fact, IFNs inhibit growth of various normal and transformed cell types.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91110562:2", "type": "list", "id": "abstracts:91110562:2:speculation"}
Previously, a nuclear factor, IRF-1 (interferon regulatory factor 1), which binds to type I IFN and some IFN-inducible gene promoters, was identified and cloned.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:3", "type": "list", "id": "abstracts:91110562:3:negation"}
Previously, a nuclear factor, IRF-1 (interferon regulatory factor 1), which binds to type I IFN and some IFN-inducible gene promoters, was identified and cloned.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91110562:3", "type": "list", "id": "abstracts:91110562:3:speculation"}
Since the IRF-1 gene is both virus and IFN inducible, an intriguing issue is raised as to whether the IRF-1 gene is functioning in IFN-mediated regulation of cell growth and differentiation.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:4", "type": "list", "id": "abstracts:91110562:4:negation"}
Since the IRF-1 gene is both virus and IFN inducible, an intriguing issue is raised as to whether the IRF-1 gene is functioning in IFN-mediated regulation of cell growth and differentiation.
Every speculation cue in the text, as written.
{ "text": [ "issue is raised", "whether" ], "answer_start": [ 68, 90 ] }
{"field": "speculation_cues", "group": "abstracts:91110562:4", "type": "list", "id": "abstracts:91110562:4:speculation"}
Since the IRF-1 gene is both virus and IFN inducible, an intriguing issue is raised as to whether the IRF-1 gene is functioning in IFN-mediated regulation of cell growth and differentiation.
The full scope of the speculation cue 'whether' at [90, 97) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "whether the IRF-1 gene is functioning in IFN-mediated regulation of cell growth and differentiation" ], "answer_start": [ 90 ] }
{"field": "speculation_scope_0", "group": "abstracts:91110562:4", "type": "list", "id": "abstracts:91110562:4:X4.5.1", "cue_spans": [[90, 97]]}
Since the IRF-1 gene is both virus and IFN inducible, an intriguing issue is raised as to whether the IRF-1 gene is functioning in IFN-mediated regulation of cell growth and differentiation.
The full scope of the speculation cue 'issue is raised' at [68, 83) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "issue is raised as to whether the IRF-1 gene is functioning in IFN-mediated regulation of cell growth and differentiation" ], "answer_start": [ 68 ] }
{"field": "speculation_scope_1", "group": "abstracts:91110562:4", "type": "list", "id": "abstracts:91110562:4:X4.5.2", "cue_spans": [[68, 83]]}
In this study, we generated transgenic mice carrying the human IRF-1 gene linked to the human immunoglobulin heavy-chain enhancer.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:5", "type": "list", "id": "abstracts:91110562:5:negation"}
In this study, we generated transgenic mice carrying the human IRF-1 gene linked to the human immunoglobulin heavy-chain enhancer.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91110562:5", "type": "list", "id": "abstracts:91110562:5:speculation"}
In the transgenic mice, all the lymphoid tissues examined showed a dramatic reduction in the number of B lymphocytes (B cells).
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:6", "type": "list", "id": "abstracts:91110562:6:negation"}
In the transgenic mice, all the lymphoid tissues examined showed a dramatic reduction in the number of B lymphocytes (B cells).
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91110562:6", "type": "list", "id": "abstracts:91110562:6:speculation"}
Preparation and analysis of bone marrow cells from the chimeric mice indicated that the bone marrow is the effective site for specific depletion of the B-cell population.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:7", "type": "list", "id": "abstracts:91110562:7:negation"}
Preparation and analysis of bone marrow cells from the chimeric mice indicated that the bone marrow is the effective site for specific depletion of the B-cell population.
Every speculation cue in the text, as written.
{ "text": [ "indicated that" ], "answer_start": [ 69 ] }
{"field": "speculation_cues", "group": "abstracts:91110562:7", "type": "list", "id": "abstracts:91110562:7:speculation"}
Preparation and analysis of bone marrow cells from the chimeric mice indicated that the bone marrow is the effective site for specific depletion of the B-cell population.
The full scope of the speculation cue 'indicated that' at [69, 83) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "indicated that the bone marrow is the effective site for specific depletion of the B-cell population" ], "answer_start": [ 69 ] }
{"field": "speculation_scope_0", "group": "abstracts:91110562:7", "type": "list", "id": "abstracts:91110562:7:X4.8.1", "cue_spans": [[69, 83]]}
In fact, transgenic bone marrow cells cocultured with a bone marrow-derived stromal cell line revealed an altered B-cell maturation pattern.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91110562:8", "type": "list", "id": "abstracts:91110562:8:negation"}
In fact, transgenic bone marrow cells cocultured with a bone marrow-derived stromal cell line revealed an altered B-cell maturation pattern.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91110562:8", "type": "list", "id": "abstracts:91110562:8:speculation"}
Identification and cloning of TCF-1, a T lymphocyte-specific transcription factor containing a sequence-specific HMG box.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91114695:0", "type": "list", "id": "abstracts:91114695:0:negation"}
Identification and cloning of TCF-1, a T lymphocyte-specific transcription factor containing a sequence-specific HMG box.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91114695:0", "type": "list", "id": "abstracts:91114695:0:speculation"}
CD3-epsilon expression is controlled by a downstream T lymphocyte-specific enhancer element.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91114695:1", "type": "list", "id": "abstracts:91114695:1:negation"}
CD3-epsilon expression is controlled by a downstream T lymphocyte-specific enhancer element.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91114695:1", "type": "list", "id": "abstracts:91114695:1:speculation"}
We report the identification of a T cell-specific transcription factor, TCF-1, binding to this element.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91114695:2", "type": "list", "id": "abstracts:91114695:2:negation"}
We report the identification of a T cell-specific transcription factor, TCF-1, binding to this element.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91114695:2", "type": "list", "id": "abstracts:91114695:2:speculation"}
The multimerized recognition motif of TCF-1 constituted a T cell-specific enhancer.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91114695:3", "type": "list", "id": "abstracts:91114695:3:negation"}
The multimerized recognition motif of TCF-1 constituted a T cell-specific enhancer.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91114695:3", "type": "list", "id": "abstracts:91114695:3:speculation"}
Subsequent cloning of TCF-1 identified three splice alternatives.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91114695:4", "type": "list", "id": "abstracts:91114695:4:negation"}
Subsequent cloning of TCF-1 identified three splice alternatives.
Every speculation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "speculation_cues", "group": "abstracts:91114695:4", "type": "list", "id": "abstracts:91114695:4:speculation"}
TCF-1 contained a single DNA-binding HMG box most closely related to similar boxes in the putative mammalian sex-determining gene SRY and in the Schizosaccharomyces pombe Mc mating type gene.
Every negation cue in the text, as written.
{ "text": [], "answer_start": [] }
{"field": "negation_cues", "group": "abstracts:91114695:5", "type": "list", "id": "abstracts:91114695:5:negation"}
TCF-1 contained a single DNA-binding HMG box most closely related to similar boxes in the putative mammalian sex-determining gene SRY and in the Schizosaccharomyces pombe Mc mating type gene.
Every speculation cue in the text, as written.
{ "text": [ "putative" ], "answer_start": [ 90 ] }
{"field": "speculation_cues", "group": "abstracts:91114695:5", "type": "list", "id": "abstracts:91114695:5:speculation"}
TCF-1 contained a single DNA-binding HMG box most closely related to similar boxes in the putative mammalian sex-determining gene SRY and in the Schizosaccharomyces pombe Mc mating type gene.
The full scope of the speculation cue 'putative' at [90, 98) (zero-based characters, end-exclusive). Return every scope segment.
{ "text": [ "putative mammalian sex-determining gene SRY" ], "answer_start": [ 90 ] }
{"field": "speculation_scope_0", "group": "abstracts:91114695:5", "type": "list", "id": "abstracts:91114695:5:X5.6.1", "cue_spans": [[90, 98]]}
End of preview. Expand in Data Studio

BioScope negation and speculation spans

Expert annotations of negation and speculation cues and their scopes in biomedical abstracts and full papers (the clinical part, whose text is masked, is left out). Every sentence asks for the negation and speculation cues and the scope of each cue. BioScope has no native split: abstracts gets a deterministic document-disjoint 80/10/10 split (crc32(DocID) % 100); papers has only 9 documents and stays train-only.

Data-only mirror of the original distribution (SHA256 b20b525506f7), documented by bioscope.py. Reproduce with scripts/repackage_dataset/span_structure.py; provenance.json records hashes, settings and counts. License: cc-by-2.0 (evidence). Public biological abstracts and papers only; article texts retain their original terms. Clinical masked text excluded.

Schema: context, question, answers (text, answer_start: every span, not alternatives) and JSON-string metadata (field, sentence group). Used by the extraction config of tasksource-jev-typed-decisions.

Citation

Please cite the original dataset:

@article{vincze2008bioscope,
    title = {The {BioScope} corpus: biomedical texts annotated for uncertainty, negation and their scopes},
    author = {Vincze, Veronika and Szarvas, Gy{\"o}rgy and Farkas, Rich{\'a}rd and M{\'o}ra, Gy{\"o}rgy and Csirik, J{\'a}nos},
    journal = {BMC Bioinformatics},
    volume = {9},
    number = {Suppl 11},
    pages = {S9},
    year = {2008},
    url = {https://doi.org/10.1186/1471-2105-9-S11-S9},
}

Citing tasksource

If you use tasksource, its standardized task annotations, or datasets derived from them in published research, please cite the tasksource paper (Sileo, LREC-COLING 2024).

@inproceedings{sileo-2024-tasksource,
    title = "tasksource: A Large Collection of {NLP} tasks with a Structured Dataset Preprocessing Framework",
    author = "Sileo, Damien",
    booktitle = "Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)",
    month = may,
    year = "2024",
    address = "Torino, Italia",
    publisher = "ELRA and ICCL",
    url = "https://aclanthology.org/2024.lrec-main.1361",
    doi = "10.63317/2h4pkr685mkq",
    pages = "15655--15684",
}
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