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id (string)tokens (json)ner_tags (json)
1
[ "IL-2", "gene", "expression", "and", "NF-kappa", "B", "activation", "through", "CD28", "requires", "reactive", "oxygen", "production", "by", "5-lipoxygenase", "." ]
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2
[ "Activation", "of", "the", "CD28", "surface", "receptor", "provides", "a", "major", "costimulatory", "signal", "for", "T", "cell", "activation", "resulting", "in", "enhanced", "production", "of", "interleukin-2", "(", "IL-2", ")", "and", "cell", "proliferation", "." ]
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3
[ "In", "primary", "T", "lymphocytes", "we", "show", "that", "CD28", "ligation", "leads", "to", "the", "rapid", "intracellular", "formation", "of", "reactive", "oxygen", "intermediates", "(", "ROIs", ")", "which", "are", "required", "for", "CD28", "-mediated", "activation", "of", "the", "NF-kappa", "B", "/", "CD28-responsive", "complex", "and", "IL-2", "expression", "." ]
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4
[ "Delineation", "of", "the", "CD28", "signaling", "cascade", "was", "found", "to", "involve", "protein", "tyrosine", "kinase", "activity", ",", "followed", "by", "the", "activation", "of", "phospholipase", "A2", "and", "5-lipoxygenase", "." ]
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5
[ "Our", "data", "suggest", "that", "lipoxygenase", "metabolites", "activate", "ROI", "formation", "which", "then", "induce", "IL-2", "expression", "via", "NF-kappa", "B", "activation", "." ]
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6
[ "These", "findings", "should", "be", "useful", "for", "therapeutic", "strategies", "and", "the", "development", "of", "immunosuppressants", "targeting", "the", "CD28", "costimulatory", "pathway", "." ]
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7
[ "The", "peri-kappa", "B", "site", "mediates", "human", "immunodeficiency", "virus", "type", "2", "enhancer", "activation", "in", "monocytes", "but", "not", "in", "T", "cells", "." ]
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8
[ "Human", "immunodeficiency", "virus", "type", "2", "(", "HIV-2", ")", ",", "like", "HIV-1", ",", "causes", "AIDS", "and", "is", "associated", "with", "AIDS", "cases", "primarily", "in", "West", "Africa", "." ]
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9
[ "HIV-1", "and", "HIV-2", "display", "significant", "differences", "in", "nucleic", "acid", "sequence", "and", "in", "the", "natural", "history", "of", "clinical", "disease", "." ]
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10
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11
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12
[ "We", "have", "now", "identified", "a", "novel", "cis-acting", "element", "within", "the", "HIV-2", "enhancer", ",", "immediately", "upstream", "of", "the", "kappa", "B", "site", ",", "designated", "peri-kappa", "B", "." ]
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13
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14
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15
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16
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17
[ "Understanding", "the", "monocyte-specific", "function", "of", "the", "peri-kappa", "B", "factor", "may", "ultimately", "provide", "insight", "into", "the", "different", "role", "monocytes", "and", "T", "cells", "play", "in", "HIV", "pathogenesis", "." ]
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18
[ "E1A", "gene", "expression", "induces", "susceptibility", "to", "killing", "by", "NK", "cells", "following", "immortalization", "but", "not", "adenovirus", "infection", "of", "human", "cells", "." ]
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19
[ "Adenovirus", "(", "Ad", ")", "infection", "and", "E1A", "transfection", "were", "used", "to", "model", "changes", "in", "susceptibility", "to", "NK", "cell", "killing", "caused", "by", "transient", "vs", "stable", "E1A", "expression", "in", "human", "cells", "." ]
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20
[ "Only", "stably", "transfected", "target", "cells", "exhibited", "cytolytic", "susceptibility", ",", "despite", "expression", "of", "equivalent", "levels", "of", "E1A", "proteins", "in", "Ad-infected", "targets", "." ]
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21
[ "The", "inability", "of", "E1A", "gene", "products", "to", "induce", "cytolytic", "susceptibility", "during", "infection", "was", "not", "explained", "by", "an", "inhibitory", "effect", "of", "viral", "infection", "on", "otherwise", "susceptible", "target", "cells", "or", "by", "viral", "gene", "effects", "on", "class", "I", "MHC", "antigen", "expression", "on", "target", "cells", "." ]
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22
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23
[ "Distinct", "signaling", "properties", "identify", "functionally", "different", "CD4", "epitopes", "." ]
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24
[ "The", "CD4", "coreceptor", "interacts", "with", "non-polymorphic", "regions", "of", "major", "histocompatibility", "complex", "class", "II", "molecules", "on", "antigen-presenting", "cells", "and", "contributes", "to", "T", "cell", "activation", "." ]
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25
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26
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27
[ "Whereas", "different", "anti-CD4", "mAb", "or", "HIV-1", "gp120", "could", "all", "trigger", "activation", "of", "the", "protein", "tyrosine", "kinases", "p56lck", "and", "p59fyn", "and", "phosphorylation", "of", "the", "Shc", "adaptor", "protein", ",", "which", "mediates", "signals", "to", "Ras", ",", "they", "differed", "significantly", "in", "their", "ability", "to", "activate", "NF-AT", "." ]
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28
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29
[ "The", "results", "identify", "functionally", "distinct", "epitopes", "on", "the", "CD4", "coreceptor", "involved", "in", "activation", "of", "the", "Ras/protein", "kinase", "C", "and", "calcium", "pathways", "." ]
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30
[ "Ligand-dependent", "repression", "of", "the", "erythroid", "transcription", "factor", "GATA-1", "by", "the", "estrogen", "receptor", "." ]
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31
[ "High-dose", "estrogen", "administration", "induces", "anemia", "in", "mammals", "." ]
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32
[ "In", "chickens", ",", "estrogens", "stimulate", "outgrowth", "of", "bone", "marrow-derived", "erythroid", "progenitor", "cells", "and", "delay", "their", "maturation", "." ]
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33
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34
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35
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36
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37
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38
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39
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40
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41
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42
[ "(", "ABSTRACT", "TRUNCATED", "AT", "250", "WORDS", ")" ]
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43
[ "Mouse", "interleukin-2", "receptor", "alpha", "gene", "expression", "." ]
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44
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45
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46
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47
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48
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49
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50
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51
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52
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53
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54
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55
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56
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57
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59
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60
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61
[ "Epstein-Barr", "virus", "(", "EBV", ")", "is", "known", "to", "infect", "B", "cells", "and", "epithelial", "cells", "." ]
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62
[ "We", "and", "others", "have", "shown", "that", "EBV", "can", "also", "infect", "a", "subset", "of", "thymocytes", "." ]
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63
[ "Infection", "of", "thymocytes", "was", "accompanied", "by", "the", "appearance", "of", "linear", "EBV", "genome", "within", "8", "hr", "of", "infection", "." ]
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64
[ "Circularization", "of", "the", "EBV", "genome", "was", "not", "detected", "." ]
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65
[ "This", "is", "in", "contrast", "to", "the", "infection", "in", "B", "cells", "where", "the", "genome", "can", "circularize", "within", "24", "hr", "of", "infection", "." ]
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70
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71
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72
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73
[ "Rather", ",", "EBV", "remains", "in", "a", "linear", "configuration", "from", "which", "replicative", "genes", "are", "transcribed", "." ]
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74
[ "Identification", "and", "purification", "of", "human", "Stat", "proteins", "activated", "in", "response", "to", "interleukin-2", "." ]
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75
[ "A", "key", "cytokine", "induced", "during", "the", "immune", "response", "is", "IL-2", "." ]
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76
[ "Following", "T", "cell", "activation", ",", "the", "genes", "encoding", "IL-2", "and", "the", "various", "chains", "of", "its", "receptor", "are", "transcriptionally", "induced", "." ]
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77
[ "In", "turn", ",", "secreted", "IL-2", "serves", "to", "stimulate", "the", "proliferation", "and", "differentiation", "of", "T", "lymphocytes", "." ]
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78
[ "Several", "recent", "studies", "have", "implicated", "Jak", "kinases", "in", "the", "signaling", "pathway", "induced", "by", "IL-2", "." ]
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79
[ "Following", "this", "lead", ",", "we", "set", "out", "to", "identify", "transcription", "factors", "induced", "in", "response", "to", "IL-2", "." ]
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80
[ "Human", "peripheral", "blood", "lymphocytes", "were", "observed", "to", "contain", "several", "IL-2", "-inducible", "DNA", "binding", "activities", "." ]
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81
[ "Similar", "activities", "were", "also", "observed", "in", "a", "transformed", "human", "lymphocyte", "line", ",", "termed", "YT", "." ]
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82
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83
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84
[ "E2F-1", "and", "a", "cyclin-like", "DNA", "repair", "enzyme", ",", "uracil-DNA", "glycosylase", ",", "provide", "evidence", "for", "an", "autoregulatory", "mechanism", "for", "transcription", "." ]
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85
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86
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87
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88
[ "We", "also", "provide", "evidence", "for", "the", "functional", "relationship", "between", "the", "cyclin-like", "UDG", "gene", "product", "and", "E2F", "." ]
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89
[ "High", "levels", "of", "UDG", "expression", "in", "a", "transient", "transfection", "assay", "result", "in", "the", "down-regulation", "of", "transcriptional", "activity", "through", "elements", "specific", "for", "E2F", "-mediated", "transcription", "." ]
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90
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91
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92
[ "This", "implicates", "E2F", "as", "a", "multifunctional", "target", "for", "proteins", "and", "enzymes", ",", "possibly", ",", "responsive", "to", "DNA", "damage", "through", "the", "negative", "effect", "of", "UDG", "on", "E2F", "-mediated", "transcriptional", "activity", "." ]
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93
[ "Cellular", "and", "molecular", "mechanisms", "of", "IFN-gamma", "production", "induced", "by", "IL-2", "and", "IL-12", "in", "a", "human", "NK", "cell", "line", "." ]
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94
[ "Interferon-gamma", "(", "IFN-gamma", ")", "is", "an", "important", "immunoregulatory", "protein", "produced", "predominantly", "by", "T", "cells", "and", "large", "granular", "lymphocytes", "(", "LGL", ")", "in", "response", "to", "different", "extracellular", "signals", "." ]
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95
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96
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97
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98
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99
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100
[ "The", "results", "suggest", "that", "activation", "of", "protein", "kinase", "C", ",", "but", "not", "new", "protein", "synthesis", ",", "is", "required", "for", "IL-2", "induction", "of", "IFN-gamma", "and", "GM-CSF", "cytoplasmic", "mRNA", "." ]
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End of preview (truncated to 100 rows)

Dataset Card for JNLPBA

Dataset Summary

The data came from the GENIA version 3.02 corpus (Kim et al., 2003). This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus.

Supported Tasks and Leaderboards

NER

Languages

English

Dataset Structure

Data Instances

{ 'id': '1', 'tokens': ['IL-2', 'gene', 'expression', 'and', 'NF-kappa', 'B', 'activation', 'through', 'CD28', 'requires', 'reactive', 'oxygen', 'production', 'by', '5-lipoxygenase', '.'], 'ner_tags': [1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0], }

Data Fields

  • id: Sentence identifier.
  • tokens: Array of tokens composing a sentence.
  • ner_tags: Array of tags, where 0 indicates no bio-entity mentioned, 1 signals the first token of a bio-entity and 2 the subsequent bio-entity tokens.

Data Splits

Train samples: 37094 Validation samples: 7714

Dataset Creation

Curation Rationale

[Needs More Information]

Source Data

Initial Data Collection and Normalization

[Needs More Information]

Who are the source language producers?

[Needs More Information]

Annotations

Annotation process

[Needs More Information]

Who are the annotators?

[Needs More Information]

Personal and Sensitive Information

[Needs More Information]

Considerations for Using the Data

Social Impact of Dataset

[Needs More Information]

Discussion of Biases

[Needs More Information]

Other Known Limitations

[Needs More Information]

Additional Information

Dataset Curators

[Needs More Information]

Licensing Information

[Needs More Information]

Citation Information

@inproceedings{collier-kim-2004-introduction, title = "Introduction to the Bio-entity Recognition Task at {JNLPBA}", author = "Collier, Nigel and Kim, Jin-Dong", booktitle = "Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications ({NLPBA}/{B}io{NLP})", month = aug # " 28th and 29th", year = "2004", address = "Geneva, Switzerland", publisher = "COLING", url = "https://aclanthology.org/W04-1213", pages = "73--78", }

Contributions

Thanks to @edugp for adding this dataset.

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Models trained or fine-tuned on jnlpba