Datasets:
jnlpba

Tasks: named-entity-recognition

Task Categories: token-classification

Languages: English

Multilinguality: monolingual

Size Categories: 10K<n<100K

Language Creators: expert-generated

Annotations Creators: expert-generated

Source Datasets: extended|other-genia-v3.02

Licenses: unknown

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id (string)	tokens (sequence)	ner_tags (sequence)
"1"	[ "IL-2", "gene", "expression", "and", "NF-kappa", "B", "activation", "through", "CD28", "requires", "reactive", "oxygen", "production", "by", "5-lipoxygenase", "." ]	[ 1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0 ]
"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", "." ]	[ 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 9, 0, 0, 0, 0, 0 ]
"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", "." ]	[ 0, 7, 8, 8, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 9, 10, 0, 9, 10, 0, 9, 0, 0 ]
"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", "." ]	[ 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 9, 0 ]
"5"	[ "Our", "data", "suggest", "that", "lipoxygenase", "metabolites", "activate", "ROI", "formation", "which", "then", "induce", "IL-2", "expression", "via", "NF-kappa", "B", "activation", "." ]	[ 0, 0, 0, 0, 9, 10, 0, 0, 0, 0, 0, 0, 9, 0, 0, 9, 10, 0, 0 ]
"6"	[ "These", "findings", "should", "be", "useful", "for", "therapeutic", "strategies", "and", "the", "development", "of", "immunosuppressants", "targeting", "the", "CD28", "costimulatory", "pathway", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0 ]
"7"	[ "The", "peri-kappa", "B", "site", "mediates", "human", "immunodeficiency", "virus", "type", "2", "enhancer", "activation", "in", "monocytes", "but", "not", "in", "T", "cells", "." ]	[ 0, 1, 2, 2, 0, 1, 2, 2, 2, 2, 2, 0, 0, 7, 0, 0, 0, 7, 8, 0 ]
"8"	[ "Human", "immunodeficiency", "virus", "type", "2", "(", "HIV-2", ")", ",", "like", "HIV-1", ",", "causes", "AIDS", "and", "is", "associated", "with", "AIDS", "cases", "primarily", "in", "West", "Africa", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"9"	[ "HIV-1", "and", "HIV-2", "display", "significant", "differences", "in", "nucleic", "acid", "sequence", "and", "in", "the", "natural", "history", "of", "clinical", "disease", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"10"	[ "Consistent", "with", "these", "differences", ",", "we", "have", "previously", "demonstrated", "that", "the", "enhancer/promoter", "region", "of", "HIV-2", "functions", "quite", "differently", "from", "that", "of", "HIV-1", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"11"	[ "Whereas", "activation", "of", "the", "HIV-1", "enhancer", "following", "T-cell", "stimulation", "is", "mediated", "largely", "through", "binding", "of", "the", "transcription", "factor", "NF-kappa", "B", "to", "two", "adjacent", "kappa", "B", "sites", "in", "the", "HIV-1", "long", "terminal", "repeat", ",", "activation", "of", "the", "HIV-2", "enhancer", "in", "monocytes", "and", "T", "cells", "is", "dependent", "on", "four", "cis-acting", "elements", ":", "a", "single", "kappa", "B", "site", ",", "two", "purine-rich", "binding", "sites", ",", "PuB1", "and", "PuB2", ",", "and", "a", "pets", "site", "." ]	[ 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 9, 10, 0, 0, 0, 1, 2, 2, 0, 0, 1, 2, 2, 2, 0, 0, 0, 0, 1, 2, 0, 7, 0, 7, 8, 0, 0, 0, 0, 1, 2, 0, 0, 0, 1, 2, 2, 0, 0, 1, 2, 2, 0, 1, 0, 1, 0, 0, 0, 1, 2, 0 ]
"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", "." ]	[ 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 1, 2, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 1, 2, 0 ]
"13"	[ "This", "site", "is", "conserved", "among", "isolates", "of", "HIV-2", "and", "the", "closely", "related", "simian", "immunodeficiency", "virus", ",", "and", "transfection", "assays", "show", "this", "site", "to", "mediate", "HIV-2", "enhancer", "activation", "following", "stimulation", "of", "monocytic", "but", "not", "T-cell", "lines", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 5, 0, 0, 5, 6, 0 ]
"14"	[ "This", "is", "the", "first", "description", "of", "an", "HIV-2", "enhancer", "element", "which", "displays", "such", "monocyte", "specificity", ",", "and", "no", "comparable", "enhancer", "element", "has", "been", "clearly", "defined", "for", "HIV-1", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0 ]
"15"	[ "While", "a", "nuclear", "factor", "(", "s", ")", "from", "both", "peripheral", "blood", "monocytes", "and", "T", "cells", "binds", "the", "peri-kappa", "B", "site", ",", "electrophoretic", "mobility", "shift", "assays", "suggest", "that", "either", "a", "different", "protein", "binds", "to", "this", "site", "in", "monocytes", "versus", "T", "cells", "or", "that", "the", "protein", "recognizing", "this", "enhancer", "element", "undergoes", "differential", "modification", "in", "monocytes", "and", "T", "cells", ",", "thus", "supporting", "the", "transfection", "data", "." ]	[ 0, 0, 9, 10, 0, 0, 0, 0, 0, 7, 8, 8, 0, 7, 8, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 7, 8, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 7, 0, 7, 8, 0, 0, 0, 0, 0, 0, 0 ]
"16"	[ "Further", ",", "while", "specific", "constitutive", "binding", "to", "the", "peri-kappa", "B", "site", "is", "seen", "in", "monocytes", ",", "stimulation", "with", "phorbol", "esters", "induces", "additional", ",", "specific", "binding", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"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", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 7, 8, 0, 0, 0, 0, 0 ]
"18"	[ "E1A", "gene", "expression", "induces", "susceptibility", "to", "killing", "by", "NK", "cells", "following", "immortalization", "but", "not", "adenovirus", "infection", "of", "human", "cells", "." ]	[ 1, 2, 0, 0, 0, 0, 0, 0, 7, 8, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0 ]
"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", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 7, 8, 0 ]
"20"	[ "Only", "stably", "transfected", "target", "cells", "exhibited", "cytolytic", "susceptibility", ",", "despite", "expression", "of", "equivalent", "levels", "of", "E1A", "proteins", "in", "Ad-infected", "targets", "." ]	[ 0, 0, 5, 6, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 5, 6, 0 ]
"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", "." ]	[ 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0, 0, 1, 2, 0, 0, 9, 10, 10, 10, 0, 0, 7, 8, 0 ]
"22"	[ "This", "differential", "effect", "of", "E1A", "expression", "on", "the", "cytolytic", "phenotypes", "of", "infected", "and", "stably", "transfected", "human", "cells", "suggests", "that", "human", "NK", "cells", "provide", "an", "effective", "immunologic", "barrier", "against", "the", "in", "vivo", "survival", "and", "neoplastic", "progression", "of", "E1A-immortalized", "cells", "that", "may", "emerge", "from", "the", "reservoir", "of", "persistently", "infected", "cells", "in", "the", "human", "host", "." ]	[ 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0, 0, 7, 8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 6, 0, 0, 0, 0, 0, 0, 0, 7, 8, 8, 0, 0, 0, 0, 0 ]
"23"	[ "Distinct", "signaling", "properties", "identify", "functionally", "different", "CD4", "epitopes", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 10, 0 ]
"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", "." ]	[ 0, 9, 10, 0, 0, 9, 10, 0, 9, 10, 10, 10, 10, 10, 0, 7, 8, 0, 0, 0, 0, 0, 0, 0 ]
"25"	[ "We", "have", "investigated", "the", "effect", "of", "CD4", "triggering", "on", "T", "cell", "activating", "signals", "in", "a", "lymphoma", "model", "using", "monoclonal", "antibodies", "(", "mAb", ")", "which", "recognize", "different", "CD4", "epitopes", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 9, 0, 0, 0, 0, 9, 10, 0 ]
"26"	[ "We", "demonstrate", "that", "CD4", "triggering", "delivers", "signals", "capable", "of", "activating", "the", "NF-AT", "transcription", "factor", "which", "is", "required", "for", "interleukin-2", "gene", "expression", "." ]	[ 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 9, 0, 0, 0 ]
"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", "." ]	[ 0, 0, 9, 10, 0, 9, 10, 0, 0, 0, 0, 0, 0, 9, 10, 10, 9, 0, 9, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0 ]
"28"	[ "Lack", "of", "full", "activation", "of", "NF-AT", "could", "be", "correlated", "to", "a", "dramatically", "reduced", "capacity", "to", "induce", "calcium", "flux", "and", "could", "be", "complemented", "with", "a", "calcium", "ionophore", "." ]	[ 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"29"	[ "The", "results", "identify", "functionally", "distinct", "epitopes", "on", "the", "CD4", "coreceptor", "involved", "in", "activation", "of", "the", "Ras/protein", "kinase", "C", "and", "calcium", "pathways", "." ]	[ 0, 0, 0, 0, 0, 9, 0, 0, 9, 10, 0, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0 ]
"30"	[ "Ligand-dependent", "repression", "of", "the", "erythroid", "transcription", "factor", "GATA-1", "by", "the", "estrogen", "receptor", "." ]	[ 0, 0, 0, 0, 9, 10, 10, 9, 0, 0, 9, 10, 0 ]
"31"	[ "High-dose", "estrogen", "administration", "induces", "anemia", "in", "mammals", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0 ]
"32"	[ "In", "chickens", ",", "estrogens", "stimulate", "outgrowth", "of", "bone", "marrow-derived", "erythroid", "progenitor", "cells", "and", "delay", "their", "maturation", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 7, 8, 8, 8, 8, 0, 0, 0, 0, 0 ]
"33"	[ "This", "delay", "is", "associated", "with", "down-regulation", "of", "many", "erythroid", "cell-specific", "genes", ",", "including", "alpha-", "and", "beta-globin", ",", "band", "3", ",", "band", "4.1", ",", "and", "the", "erythroid", "cell-specific", "histone", "H5", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 10, 9, 0 ]
"34"	[ "We", "show", "here", "that", "estrogens", "also", "reduce", "the", "number", "of", "erythroid", "progenitor", "cells", "in", "primary", "human", "bone", "marrow", "cultures", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 8, 0, 5, 6, 6, 6, 6, 0 ]
"35"	[ "To", "address", "potential", "mechanisms", "by", "which", "estrogens", "suppress", "erythropoiesis", ",", "we", "have", "examined", "their", "effects", "on", "GATA-1", ",", "an", "erythroid", "transcription", "factor", "that", "participates", "in", "the", "regulation", "of", "the", "majority", "of", "erythroid", "cell-specific", "genes", "and", "is", "necessary", "for", "full", "maturation", "of", "erythrocytes", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 7, 0 ]
"36"	[ "We", "demonstrate", "that", "the", "transcriptional", "activity", "of", "GATA-1", "is", "strongly", "repressed", "by", "the", "estrogen", "receptor", "(", "ER", ")", "in", "a", "ligand-dependent", "manner", "and", "that", "this", "repression", "is", "reversible", "in", "the", "presence", "of", "4-hydroxytamoxifen", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 9, 10, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"37"	[ "ER", "-mediated", "repression", "of", "GATA-1", "activity", "occurs", "on", "an", "artificial", "promoter", "containing", "a", "single", "GATA-binding", "site", ",", "as", "well", "as", "in", "the", "context", "of", "an", "intact", "promoter", "which", "is", "normally", "regulated", "by", "GATA-1", "." ]	[ 9, 0, 0, 0, 9, 0, 0, 0, 0, 1, 2, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 9, 0 ]
"38"	[ "GATA-1", "and", "ER", "bind", "to", "each", "other", "in", "vitro", "in", "the", "absence", "of", "DNA", "." ]	[ 9, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"39"	[ "In", "coimmunoprecipitation", "experiments", "using", "transfected", "COS", "cells", ",", "GATA-1", "and", "ER", "associate", "in", "a", "ligand-dependent", "manner", "." ]	[ 0, 0, 0, 0, 0, 5, 6, 0, 9, 0, 9, 0, 0, 0, 0, 0, 0 ]
"40"	[ "Mapping", "experiments", "indicate", "that", "GATA-1", "and", "the", "ER", "form", "at", "least", "two", "contacts", ",", "which", "involve", "the", "finger", "region", "and", "the", "N-terminal", "activation", "domain", "of", "GATA-1", "." ]	[ 0, 0, 0, 0, 9, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 10, 0, 9, 0 ]
"41"	[ "We", "speculate", "that", "estrogens", "exert", "effects", "on", "erythropoiesis", "by", "modulating", "GATA-1", "activity", "through", "protein-protein", "interaction", "with", "the", "ER", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 9, 0 ]
"42"	[ "(", "ABSTRACT", "TRUNCATED", "AT", "250", "WORDS", ")" ]	[ 0, 0, 0, 0, 0, 0, 0 ]
"43"	[ "Mouse", "interleukin-2", "receptor", "alpha", "gene", "expression", "." ]	[ 1, 2, 2, 2, 2, 0, 0 ]
"44"	[ "Interleukin-1", "and", "interleukin-2", "control", "transcription", "via", "distinct", "cis-acting", "elements", "." ]	[ 9, 0, 9, 0, 0, 0, 0, 1, 2, 0 ]
"45"	[ "We", "have", "shown", "that", "interleukin-1", "(", "IL-1", ")", "and", "IL-2", "control", "IL-2", "receptor", "alpha", "(", "IL-2R", "alpha", ")", "gene", "transcription", "in", "CD4-CD8-", "murine", "T", "lymphocyte", "precursors", "." ]	[ 0, 0, 0, 0, 9, 0, 9, 0, 0, 9, 0, 1, 2, 2, 2, 2, 2, 2, 2, 0, 0, 5, 6, 6, 6, 6, 0 ]
"46"	[ "Here", "we", "map", "the", "cis-acting", "elements", "that", "mediate", "interleukin", "responsiveness", "of", "the", "mouse", "IL-2R", "alpha", "gene", "using", "a", "thymic", "lymphoma-derived", "hybridoma", "(", "PC60", ")", "." ]	[ 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 0, 0, 5, 6, 6, 0, 5, 0, 0 ]
"47"	[ "The", "transcriptional", "response", "of", "the", "IL-2R", "alpha", "gene", "to", "stimulation", "by", "IL-1", "+", "IL-2", "is", "biphasic", "." ]	[ 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 9, 0, 9, 0, 0, 0 ]
"48"	[ "IL-1", "induces", "a", "rapid", ",", "protein", "synthesis-independent", "appearance", "of", "IL-2R", "alpha", "mRNA", "that", "is", "blocked", "by", "inhibitors", "of", "NF-kappa", "B", "activation", "." ]	[ 9, 0, 0, 0, 0, 0, 0, 0, 0, 3, 4, 4, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0 ]
"49"	[ "It", "also", "primes", "cells", "to", "become", "IL-2", "responsive", "and", "thereby", "prepares", "the", "second", "phase", ",", "in", "which", "IL-2", "induces", "a", "100-fold", "further", "increase", "in", "IL-2R", "alpha", "transcripts", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 3, 4, 4, 0 ]
"50"	[ "Transient", "transfection", "experiments", "show", "that", "several", "elements", "in", "the", "promoter-proximal", "region", "of", "the", "IL-2R", "alpha", "gene", "contribute", "to", "IL-1", "responsiveness", ",", "most", "importantly", "an", "NF-kappa", "B", "site", "conserved", "in", "the", "human", "and", "mouse", "gene", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 1, 2, 2, 0, 0, 9, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 1, 2, 2, 2, 0 ]
"51"	[ "IL-2", "responsiveness", ",", "on", "the", "other", "hand", ",", "depends", "on", "a", "78-nucleotide", "segment", "1.3", "kilobases", "upstream", "of", "the", "major", "transcription", "start", "site", "." ]	[ 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 1, 2, 2, 2, 0 ]
"52"	[ "This", "segment", "functions", "as", "an", "IL-2-inducible", "enhancer", "and", "lies", "within", "a", "region", "that", "becomes", "DNase", "I", "hypersensitive", "in", "normal", "T", "cells", "in", "which", "IL-2R", "alpha", "expression", "has", "been", "induced", "." ]	[ 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0, 0, 7, 8, 0, 0, 9, 10, 0, 0, 0, 0, 0 ]
"53"	[ "IL-2", "responsiveness", "requires", "three", "distinct", "elements", "within", "the", "enhancer", "." ]	[ 9, 0, 0, 0, 0, 1, 0, 0, 1, 0 ]
"54"	[ "Two", "of", "these", "are", "potential", "binding", "sites", "for", "STAT", "proteins", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0 ]
"55"	[ "Hematopoietic", "lineage", "commitment", ":", "role", "of", "transcription", "factors", "." ]	[ 7, 8, 0, 0, 0, 0, 9, 10, 0 ]
"56"	[ "This", "review", "focuses", "on", "the", "roles", "of", "transcription", "factors", "in", "hematopoietic", "lineage", "commitment", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0, 0, 0, 0 ]
"57"	[ "A", "brief", "introduction", "to", "lineage", "commitment", "and", "asymmetric", "cell", "division", "is", "followed", "by", "a", "discussion", "of", "several", "methods", "used", "to", "identify", "transcription", "factors", "important", "in", "specifying", "hematopoietic", "cell", "types", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0, 0, 7, 8, 8, 0 ]
"58"	[ "Next", "is", "presented", "a", "discussion", "of", "the", "use", "of", "embryonic", "stem", "cells", "in", "the", "analysis", "of", "hematopoietic", "gene", "expression", "and", "the", "use", "of", "targeted", "gene", "disruption", "to", "analyze", "the", "role", "of", "transcription", "factors", "in", "hematopoiesis", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 8, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0, 0 ]
"59"	[ "Finally", ",", "the", "status", "of", "our", "current", "knowledge", "concerning", "the", "roles", "of", "transcription", "factors", "in", "the", "commitment", "to", "erythroid", ",", "myeloid", "and", "lymphoid", "cell", "types", "is", "summarized", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0, 0, 0, 7, 8, 8, 8, 8, 8, 8, 0, 0, 0 ]
"60"	[ "Epstein-Barr", "virus", "replicative", "gene", "transcription", "during", "de", "novo", "infection", "of", "human", "thymocytes", ":", "simultaneous", "early", "expression", "of", "BZLF-1", "and", "its", "repressor", "RAZ", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0, 0, 0, 0, 0, 9, 0, 0, 0, 9, 0 ]
"61"	[ "Epstein-Barr", "virus", "(", "EBV", ")", "is", "known", "to", "infect", "B", "cells", "and", "epithelial", "cells", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0, 7, 8, 0 ]
"62"	[ "We", "and", "others", "have", "shown", "that", "EBV", "can", "also", "infect", "a", "subset", "of", "thymocytes", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0 ]
"63"	[ "Infection", "of", "thymocytes", "was", "accompanied", "by", "the", "appearance", "of", "linear", "EBV", "genome", "within", "8", "hr", "of", "infection", "." ]	[ 0, 0, 7, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0 ]
"64"	[ "Circularization", "of", "the", "EBV", "genome", "was", "not", "detected", "." ]	[ 0, 0, 0, 1, 2, 0, 0, 0, 0 ]
"65"	[ "This", "is", "in", "contrast", "to", "the", "infection", "in", "B", "cells", "where", "the", "genome", "can", "circularize", "within", "24", "hr", "of", "infection", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
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"67"	[ "The", "appearance", "of", "a", "novel", "fusion", "transcript", "(", "RAZ", ")", ",", "which", "comprised", "regions", "of", "the", "BZLF-1", "locus", "and", "the", "adjacent", "BRLF-1", "locus", ",", "was", "detected", "by", "RT-PCR", "." ]	[ 0, 0, 0, 0, 0, 9, 10, 0, 9, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0 ]
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"73"	[ "Rather", ",", "EBV", "remains", "in", "a", "linear", "configuration", "from", "which", "replicative", "genes", "are", "transcribed", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0 ]
"74"	[ "Identification", "and", "purification", "of", "human", "Stat", "proteins", "activated", "in", "response", "to", "interleukin-2", "." ]	[ 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 9, 0 ]
"75"	[ "A", "key", "cytokine", "induced", "during", "the", "immune", "response", "is", "IL-2", "." ]	[ 0, 0, 9, 0, 0, 0, 0, 0, 0, 9, 0 ]
"76"	[ "Following", "T", "cell", "activation", ",", "the", "genes", "encoding", "IL-2", "and", "the", "various", "chains", "of", "its", "receptor", "are", "transcriptionally", "induced", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"77"	[ "In", "turn", ",", "secreted", "IL-2", "serves", "to", "stimulate", "the", "proliferation", "and", "differentiation", "of", "T", "lymphocytes", "." ]	[ 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0 ]
"78"	[ "Several", "recent", "studies", "have", "implicated", "Jak", "kinases", "in", "the", "signaling", "pathway", "induced", "by", "IL-2", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0 ]
"79"	[ "Following", "this", "lead", ",", "we", "set", "out", "to", "identify", "transcription", "factors", "induced", "in", "response", "to", "IL-2", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0, 0, 0, 9, 0 ]
"80"	[ "Human", "peripheral", "blood", "lymphocytes", "were", "observed", "to", "contain", "several", "IL-2", "-inducible", "DNA", "binding", "activities", "." ]	[ 7, 8, 8, 8, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0 ]
"81"	[ "Similar", "activities", "were", "also", "observed", "in", "a", "transformed", "human", "lymphocyte", "line", ",", "termed", "YT", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 5, 6, 6, 6, 0, 0, 5, 0 ]
"82"	[ "We", "have", "purified", "these", "activities", "and", "found", "that", "the", "principal", "IL-2-inducible", "component", "bears", "significant", "relatedness", "to", "a", "prolactin-induced", "transcription", "factor", "first", "identified", "in", "sheep", "mammary", "gland", "tissue", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 7, 8, 8, 8, 0 ]
"83"	[ "We", "hypothesize", "that", "activation", "of", "this", "protein", ",", "designated", "hStat5", ",", "helps", "govern", "the", "biological", "effects", "of", "IL-2", "during", "the", "immune", "response", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0 ]
"84"	[ "E2F-1", "and", "a", "cyclin-like", "DNA", "repair", "enzyme", ",", "uracil-DNA", "glycosylase", ",", "provide", "evidence", "for", "an", "autoregulatory", "mechanism", "for", "transcription", "." ]	[ 9, 0, 0, 9, 10, 10, 10, 0, 9, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"85"	[ "The", "cell", "cycle-dependent", "transcription", "factor", ",", "E2F-1", ",", "regulates", "the", "cyclin", "-like", "species", "of", "the", "DNA", "repair", "enzyme", "uracil-DNA", "glycosylase", "(", "UDG", ")", "gene", "in", "human", "osteosarcoma", "(", "Saos-2", ")", "cells", "." ]	[ 0, 9, 10, 10, 10, 0, 9, 0, 0, 0, 9, 0, 0, 0, 0, 9, 10, 10, 1, 2, 2, 2, 2, 2, 0, 5, 6, 6, 6, 6, 6, 0 ]
"86"	[ "We", "demonstrate", ",", "through", "the", "deletion", "of", "the", "human", "UDG", "promoter", "sequences", ",", "that", "expression", "of", "E2F-1", "activates", "the", "UDG", "promoter", "through", "several", "E2F", "sites", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 0, 0, 0, 0, 9, 0, 0, 1, 2, 0, 0, 1, 2, 0 ]
"87"	[ "The", "major", "putative", "downstream", "site", "for", "E2F", ",", "located", "in", "the", "first", "exon", ",", "serves", "as", "a", "target", "for", "E2F-1/DP1", "complex", "binding", "in", "vitro", "." ]	[ 0, 1, 2, 2, 2, 0, 9, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0, 0, 0 ]
"88"	[ "We", "also", "provide", "evidence", "for", "the", "functional", "relationship", "between", "the", "cyclin-like", "UDG", "gene", "product", "and", "E2F", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 10, 10, 0, 9, 0 ]
"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", "." ]	[ 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 9, 0, 0, 0 ]
"90"	[ "Overexpression", "of", "UDG", "in", "Saos", "2", "cells", "was", "observed", "to", "delay", "growth", "late", "in", "G1", "phase", "and", "transiently", "arrest", "these", "cells", "from", "progressing", "into", "the", "S", "phase", "." ]	[ 0, 0, 9, 0, 5, 6, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
"91"	[ "This", "hypothetical", "model", "integrates", "one", "mechanism", "of", "DNA", "repair", "with", "the", "cell", "cycle", "control", "of", "gene", "transcription", ",", "likely", "through", "E2F", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0 ]
"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", "." ]	[ 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 9, 0, 0, 0, 0 ]
"93"	[ "Cellular", "and", "molecular", "mechanisms", "of", "IFN-gamma", "production", "induced", "by", "IL-2", "and", "IL-12", "in", "a", "human", "NK", "cell", "line", "." ]	[ 0, 0, 0, 0, 0, 9, 0, 0, 0, 9, 0, 9, 0, 0, 5, 6, 6, 6, 0 ]
"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", "." ]	[ 9, 0, 9, 0, 0, 0, 0, 9, 10, 0, 0, 0, 7, 8, 0, 7, 8, 8, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0 ]
"95"	[ "In", "particular", ",", "two", "interleukins", "(", "ILs", ")", ",", "IL-2", "and", "IL-12", ",", "have", "been", "shown", "to", "be", "potent", "inducers", "of", "IFN-gamma", "gene", "expression", "in", "both", "T", "cells", "and", "LGL", "." ]	[ 0, 0, 0, 0, 9, 0, 9, 0, 0, 9, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 7, 8, 0, 7, 0 ]
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"99"	[ "To", "investigate", "the", "signaling", "pathways", "involved", "in", "the", "gene", "induction", ",", "five", "inhibitors", ",", "cyclosporin", "A", "(", "CsA", ")", ",", "transforming", "growth", "factor-beta", ",", "cycloheximide", ",", "genistein", ",", "and", "staurosporine", "A", ",", "were", "used", "in", "analyzing", "the", "effects", "of", "IL-2", "and", "IL-12", "on", "NK3.3", "cells", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 9, 0, 5, 6, 0 ]
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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

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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