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{"doc_key": "PMID21533105_abstract", "dataset": "pickle", "sentences": [["Fusarium", "species", "cause", "serious", "diseases", "in", "cereal", "staple", "food", "crops", "such", "as", "wheat", "and", "maize", "."], ["Currently", ",", "the", "mechanisms", "underlying", "resistance", "to", "Fusarium-caused", "diseases", "are", "still", "largely", "unknown", "."], ["In", "the", "present", "study", ",", "we", "employed", "a", "combined", "proteomic", "and", "transcriptomic", "approach", "to", "investigate", "wheat", "genes", "responding", "to", "F.", "graminearum", "infection", "that", "causes", "Fusarium", "head", "blight", "(", "FHB", ")", "."], ["We", "found", "a", "total", "of", "163", "genes", "and", "37", "proteins", "that", "were", "induced", "by", "infection", "."], ["These", "genes", "and", "proteins", "were", "associated", "with", "signaling", "pathways", "mediated", "by", "salicylic", "acid", "(", "SA", ")", ",", "jasmonic", "acid", "(", "JA", ")", ",", "ethylene", "(", "ET", ")", ",", "calcium", "ions", ",", "phosphatidic", "acid", "(", "PA", ")", ",", "as", "well", "as", "with", "reactive", "oxygen", "species", "(", "ROS", ")", "production", "and", "scavenging", ",", "antimicrobial", "compound", "synthesis", ",", "detoxification", ",", "and", "cell", "wall", "fortification", "."], ["We", "compared", "the", "time-course", "expression", "profiles", "between", "FHB-resistant", "Wangshuibai", "plants", "and", "susceptible", "Meh0106", "mutant", "plants", "of", "a", "selected", "set", "of", "genes", "that", "are", "critical", "to", "the", "plants", "'", "resistance", "and", "defense", "reactions", "."], ["A", "biphasic", "phenomenon", "was", "observed", "during", "the", "first", "24", "h", "after", "inoculation", "(", "hai", ")", "in", "the", "resistant", "plants", "."], ["The", "SA", "and", "Ca(2", "+", ")", "signaling", "pathways", "were", "activated", "within", "6", "hai", "followed", "by", "the", "JA", "mediated", "defense", "signaling", "activated", "around", "12", "hai", "."], ["ET", "signaling", "was", "activated", "between", "these", "two", "phases", "."], ["Genes", "for", "PA", "and", "ROS", "synthesis", "were", "induced", "during", "the", "SA", "and", "JA", "phases", ",", "respectively", "."], ["The", "delayed", "activation", "of", "the", "SA", "defense", "pathway", "in", "the", "mutant", "was", "associated", "with", "its", "susceptibility", "."], ["After", "F.", "graminearum", "infection", ",", "the", "endogenous", "contents", "of", "SA", "and", "JA", "in", "Wangshuibai", "and", "the", "mutant", "changed", "in", "a", "manner", "similar", "to", "the", "investigated", "genes", "corresponding", "to", "the", "individual", "pathways", "."], ["A", "few", "genes", "for", "resistance-related", "cell", "modification", "and", "phytoalexin", "production", "were", "also", "identified", "."], ["This", "study", "provided", "important", "clues", "for", "designing", "strategies", "to", "curb", "diseases", "caused", "by", "Fusarium", "."]], "ner": [[[0, 1, "Multicellular_organism"], [6, 9, "Multicellular_organism"], [12, 12, "Multicellular_organism"], [14, 14, "Multicellular_organism"]], [[23, 24, "Biochemical_process"]], [[45, 46, "DNA"], [49, 51, "Biochemical_process"], [54, 56, "Biochemical_process"], [58, 58, "Biochemical_process"]], [], [[88, 89, "Plant_hormone"], [91, 91, "Plant_hormone"], [94, 95, "Plant_hormone"], [97, 97, "Plant_hormone"], [100, 100, "Plant_hormone"], [102, 102, "Plant_hormone"], [105, 106, "Element"], [108, 109, "Organic_compound_other"], [111, 111, "Organic_compound_other"], [118, 126, "Biochemical_process"], [135, 137, "Biochemical_process"], [128, 130, "Biochemical_process"]], [[147, 148, "Multicellular_organism"], [151, 153, "Multicellular_organism"]], [], [[193, 199, "Biochemical_pathway"], [208, 211, "Biochemical_process"]], [[217, 218, "Biochemical_process"]], [[228, 231, "Biochemical_pathway"], [236, 236, "Plant_hormone"], [238, 238, "Plant_hormone"]], [[248, 250, "Biochemical_pathway"]], [[261, 263, "Multicellular_organism"], [269, 269, "Plant_hormone"], [271, 271, "Plant_hormone"], [273, 273, "Multicellular_organism"]], [[300, 301, "Biochemical_process"]], [[319, 319, "Multicellular_organism"]]], "relations": [[[0, 1, 12, 12, "inhibits"], [0, 1, 14, 14, "inhibits"]], [], [[49, 51, 54, 56, "produces"], [49, 51, 58, 58, "produces"]], [], [], [], [], [], [], [[236, 236, 228, 231, "interacts"], [238, 238, 228, 231, "interacts"]], [], [[269, 269, 273, 273, "is-in"], [271, 271, 273, 273, "is-in"]], [], []]}
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{"doc_key": "PMID21287176_abstract", "dataset": "pickle", "sentences": [["Proteomics", "has", "contributed", "to", "defining", "the", "specific", "functions", "of", "genes", "and", "proteins", "involved", "in", "plant-pathogen", "interactions", "."], ["Proteomic", "studies", "have", "led", "to", "the", "identification", "of", "many", "pathogenicity", "and", "defense-related", "genes", "and", "proteins", "expressed", "during", "phytopathogen", "infections", ",", "resulting", "in", "the", "collection", "of", "an", "enormous", "amount", "of", "data", "."], ["However", ",", "the", "molecular", "basis", "of", "plant-pathogen", "interactions", "remains", "an", "intensely", "active", "area", "of", "investigation", "."], ["In", "this", "review", ",", "the", "role", "of", "differential", "analysis", "of", "proteins", "expressed", "during", "fungal", ",", "bacterial", ",", "and", "viral", "infection", "is", "discussed", ",", "as", "well", "as", "the", "role", "of", "JA", "and", "SA", "in", "the", "production", "of", "stress", "related", "proteins", "."], ["Resistance", "acquired", "upon", "induction", "of", "stress", "related", "proteins", "in", "intact", "plant", "leaves", "is", "mediated", "by", "potentiation", "of", "pathogens", "via", "signal", "elicitors", "."], ["Stress", "related", "genes", "extensively", "used", "in", "biotechnology", "had", "been", "cited", "."], ["Stress", "related", "proteins", "identified", "must", "be", "followed", "through", "for", "studying", "the", "molecular", "mechanism", "for", "plant", "defense", "against", "pathogens", "."]], "ner": [[], [], [], [[93, 93, "Plant_hormone"], [95, 95, "Plant_hormone"]], [], [], []], "relations": [[], [], [], [], [], [], []]}
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{"doc_key": "PMID24264441_abstract", "dataset": "pickle", "sentences": [["The", "effect", "of", "calcium", "on", "the", "secretion", "of", "\u03b1-amylase", "(", "EC", "3.2.1.1", ")", "and", "other", "hydrolases", "from", "aleurone", "layers", "of", "barley", "(", "Hordeum", "vulgare", "L.", "cv", ".", "Himalaya", ")", "was", "studied", "."], ["Withdrawal", "of", "Ca(2", "+", ")", "from", "the", "incubation", "medium", "of", "aleurone", "layers", "preincubated", "in", "5", "\u03bcM", "gibberellic", "acid", "(", "GA3", ")", "and", "5", "mM", "CaCl2", "results", "in", "a", "70", "-", "80", "%", "reduction", "in", "the", "secretion", "of", "\u03b1-amylase", "activity", "to", "the", "incubation", "medium", "."], ["Agar-gel", "electrophoresis", "shows", "that", "the", "reduction", "in", "\u03b1-amylase", "activity", "following", "Ca(2", "+", ")", "withdrawal", "is", "correlated", "with", "the", "disappearance", "of", "group", "B", "isoenzymes", "from", "the", "incubation", "medium", "."], ["The", "secretion", "of", "isoenzymes", "of", "group", "A", "is", "unaffected", "by", "Ca(2", "+", ")", "."], ["The", "addition", "of", "Ca(2", "+", ")", "stimulates", "the", "secretion", "of", "group-B", "isoenzymes", "but", "has", "no", "measurable", "effect", "on", "either", "the", "\u03b1-amylase", "activity", "or", "the", "isoenzyme", "pattern", "of", "aleurone-layer", "extracts", "."], ["Pulse-labelling", "experiments", "with", "[(35)S]methionine", "show", "that", "Ca(2", "+", ")", "withdrawal", "results", "in", "a", "reduction", "in", "the", "secretion", "of", "labelled", "polypeptides", "into", "the", "incubation", "medium", "."], ["Immunochemical", "studies", "also", "show", "that", ",", "in", "the", "absence", "of", "Ca(2", "+", ")", ",", "\u03b1-amylase", "isoenzymes", "of", "group", "B", "are", "not", "secreted", "into", "the", "incubation", "medium", "."], ["In", "addition", "to", "its", "effect", "on", "\u03b1-amylase", ",", "Ca(2", "+", ")", "influences", "the", "secretion", "of", "other", "proteins", "including", "several", "acid", "hydrolases", "."], ["The", "secretion", "of", "these", "other", "proteins", "shows", "the", "same", "dependence", "on", "Ca(2", "+", ")", "concentration", "as", "does", "that", "of", "\u03b1-amylase", "."], ["Other", "cations", "can", "promote", "the", "secretion", "of", "\u03b1-amylase", "to", "less", "and", "varying", "extents", "."], ["Strontium", "is", "85", "%", "as", "effective", "as", "Ca(2", "+", ")", "while", "Ba(2", "+", ")", "is", "only", "10", "%", "as", "effective", "."], ["We", "conclude", "that", "Ca(2", "+", ")", "regulates", "the", "secretion", "of", "enzymes", "and", "other", "proteins", "from", "the", "aleurone", "layer", "of", "barley", "."]], "ner": [[[3, 3, "Element"], [8, 8, "Protein"], [10, 11, "Protein"], [15, 15, "Protein"], [20, 20, "Multicellular_organism"], [22, 27, "Multicellular_organism"]], [[34, 36, "Element"], [48, 49, "Plant_hormone"], [69, 70, "Biochemical_process"], [51, 51, "Plant_hormone"], [56, 56, "Inorganic_compound_other"]], [[83, 84, "Biochemical_process"], [86, 88, "Element"], [96, 98, "Protein"]], [[114, 116, "Element"]], [[121, 123, "Element"], [128, 129, "Protein"], [138, 139, "Biochemical_process"], [142, 143, "Biochemical_process"]], [[151, 151, "Organic_compound_other"], [154, 156, "Element"]], [[183, 185, "Element"], [187, 188, "Protein"]], [[206, 206, "Protein"], [208, 210, "Element"], [219, 220, "Protein"]], [[233, 235, "Element"], [241, 241, "Protein"]], [[250, 250, "Protein"]], [[257, 257, "Element"], [264, 266, "Element"], [268, 270, "Element"]], [[281, 283, "Element"], [297, 297, "Multicellular_organism"]]], "relations": [[[8, 8, 20, 20, "is-in"], [8, 8, 22, 27, "is-in"], [10, 11, 20, 20, "is-in"], [10, 11, 22, 27, "is-in"], [15, 15, 20, 20, "is-in"], [15, 15, 22, 27, "is-in"]], [], [], [], [[121, 123, 128, 129, "activates"]], [], [], [[208, 210, 206, 206, "interacts"], [208, 210, 219, 220, "interacts"]], [], [], [], []]}
{"doc_key": "PMID17644730_abstract", "dataset": "pickle", "sentences": [["GIBBERELLIN", "INSENSITIVE", "DWARF1", "(", "GID1", ")", "encodes", "a", "soluble", "gibberellin", "(", "GA", ")", "receptor", "that", "shares", "sequence", "similarity", "with", "a", "hormone-sensitive", "lipase", "(", "HSL", ")", "."], ["Previously", ",", "a", "yeast", "two-hybrid", "(", "Y2H", ")", "assay", "revealed", "that", "the", "GID1-GA", "complex", "directly", "interacts", "with", "SLENDER", "RICE1", "(", "SLR1", ")", ",", "a", "DELLA", "repressor", "protein", "in", "GA", "signaling", "."], ["Here", ",", "we", "demonstrated", ",", "by", "pull-down", "and", "bimolecular", "fluorescence", "complementation", "(", "BiFC", ")", "experiments", ",", "that", "the", "GA-dependent", "GID1-SLR1", "interaction", "also", "occurs", "in", "planta", "."], ["GA(4", ")", "was", "found", "to", "have", "the", "highest", "affinity", "to", "GID1", "in", "Y2H", "assays", "and", "is", "the", "most", "effective", "form", "of", "GA", "in", "planta", "."], ["Domain", "analyses", "of", "SLR1", "using", "Y2H", ",", "gel", "filtration", ",", "and", "BiFC", "methods", "revealed", "that", "the", "DELLA", "and", "TVHYNP", "domains", "of", "SLR1", "are", "required", "for", "the", "GID1-SLR1", "interaction", "."], ["To", "identify", "the", "important", "regions", "of", "GID1", "for", "GA", "and", "SLR1", "interactions", ",", "we", "used", "many", "different", "mutant", "versions", "of", "GID1", ",", "such", "as", "the", "spontaneous", "mutant", "GID1s", ",", "N-", "and", "C-terminal", "truncated", "GID1s", ",", "and", "mutagenized", "GID1", "proteins", "with", "conserved", "amino", "acids", "replaced", "with", "Ala.", "The", "amino", "acid", "residues", "important", "for", "SLR1", "interaction", "completely", "overlapped", "the", "residues", "required", "for", "GA", "binding", "that", "were", "scattered", "throughout", "the", "GID1", "molecule", "."], ["When", "we", "plotted", "these", "residues", "on", "the", "GID1", "structure", "predicted", "by", "analogy", "with", "HSL", "tertiary", "structure", ",", "many", "residues", "were", "located", "at", "regions", "corresponding", "to", "the", "substrate", "binding", "pocket", "and", "lid", "."], ["Furthermore", ",", "the", "GA-GID1", "interaction", "was", "stabilized", "by", "SLR1", "."], ["Based", "on", "these", "observations", ",", "we", "proposed", "a", "molecular", "model", "for", "interaction", "between", "GA", ",", "GID1", ",", "and", "SLR1", "."]], "ner": [[[0, 2, "DNA"], [4, 4, "DNA"], [20, 21, "Protein"], [23, 23, "Protein"], [8, 13, "Protein"]], [[43, 44, "Protein"], [46, 46, "Protein"], [50, 52, "Protein"], [38, 39, "Protein"], [54, 55, "Biochemical_process"]], [[75, 77, "Biochemical_process"]], [[104, 104, "Plant_hormone"], [93, 93, "Protein"], [83, 84, "Plant_hormone"]], [[111, 111, "Protein"], [129, 129, "Protein"], [124, 127, "Protein"], [134, 135, "Biochemical_process"]], [[197, 198, "Biochemical_process"], [143, 143, "Protein"], [157, 157, "Protein"], [166, 170, "Protein"], [189, 190, "Biochemical_process"], [204, 205, "Protein"], [173, 175, "Protein"], [145, 148, "Biochemical_process"], [162, 164, "Protein"]], [[214, 214, "Protein"], [220, 220, "Protein"]], [[247, 247, "Protein"], [242, 243, "Biochemical_process"]], [[262, 262, "Plant_hormone"], [264, 264, "Protein"], [267, 267, "Protein"]]], "relations": [[[0, 2, 8, 13, "produces"], [4, 4, 8, 13, "produces"]], [[38, 39, 43, 44, "interacts"], [38, 39, 46, 46, "interacts"], [43, 44, 54, 55, "is-in"], [46, 46, 54, 55, "is-in"]], [], [[83, 84, 93, 93, "interacts"]], [[124, 127, 129, 129, "is-in"], [124, 127, 134, 135, "interacts"], [129, 129, 134, 135, "interacts"]], [], [], [[247, 247, 242, 243, "interacts"]], [[262, 262, 264, 264, "interacts"], [262, 262, 267, 267, "interacts"], [264, 264, 267, 267, "interacts"]]]}
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{"doc_key": "PMID32238850_abstract", "dataset": "pickle", "sentences": [["In", "response", "to", "infestation", "by", "herbivores", ",", "rice", "plants", "rapidly", "biosynthesize", "defense", "compounds", "by", "activating", "a", "series", "of", "defense-related", "pathways", "."], ["However", ",", "which", "defensive", "compounds", "in", "rice", "are", "effective", "against", "herbivores", "remains", "largely", "unknown", "."], ["We", "found", "that", "the", "infestation", "of", "white-backed", "planthopper", "(", "WBPH", ")", "Sogatella", "furcifera", "gravid", "females", "significantly", "increased", "levels", "of", "jasmonic", "acid", "(", "JA", ")", ",", "jasmonoyl-isoleucine", "(", "JA-Ile", ")", "and", "H(2)O(2", ")", ",", "and", "reduced", "the", "level", "of", "ethylene", "in", "rice", ";", "levels", "of", "11", "of", "the", "tested", "12", "phenolamides", "(", "PAs", ")", "were", "subsequently", "enhanced", "."], ["In", "contrast", ",", "WBPH", "nymph", "infestation", "had", "no", "effect", "on", "levels", "of", "JA", ",", "JA-Ile", ",", "ethylene", "and", "H(2)O(2", ")", "in", "rice", ",", "and", "enhanced", "levels", "of", "only", "2", "of", "12", "PAs", "."], ["Moreover", ",", "infestation", "by", "brown", "planthopper", "Nilaparvata", "lugens", "gravid", "females", "also", "affected", "the", "production", "of", "these", "PAs", "differently", "."], ["Bioassays", "revealed", "that", "4", "PAs", "-", "N-feruloylputrescine", ",", "N-feruloyltyramine", ",", "feruloylagmatine", "and", "N1,N10-diferuloylspermidine", "-", "were", "toxic", "to", "newly", "emerged", "WBPH", "female", "adults", "."], ["Our", "results", "suggest", "that", "WBPH-", "or", "BPH-induced", "biosynthesis", "of", "PAs", "in", "rice", "seems", "to", "be", "shaped", "primarily", "by", "the", "specific", "profile", "of", "defense-related", "signals", "elicited", "by", "the", "herbivore", "and", "that", "PAs", "play", "a", "role", "in", "conferring", "the", "resistance", "to", "WBPH", "on", "rice", "."]], "ner": [[[7, 8, "Multicellular_organism"]], [[27, 27, "Multicellular_organism"]], [[55, 56, "Plant_hormone"], [58, 58, "Plant_hormone"], [61, 61, "Plant_hormone"], [63, 63, "Plant_hormone"], [66, 67, "Inorganic_compound_other"], [74, 74, "Plant_hormone"], [76, 76, "Multicellular_organism"], [85, 85, "Organic_compound_other"], [87, 87, "Organic_compound_other"], [42, 50, "Multicellular_organism"]], [[105, 105, "Plant_hormone"], [109, 109, "Plant_hormone"], [111, 112, "Inorganic_compound_other"], [114, 114, "Multicellular_organism"], [124, 124, "Organic_compound_other"], [96, 97, "Multicellular_organism"], [107, 107, "Plant_hormone"]], [[130, 135, "Multicellular_organism"], [142, 142, "Organic_compound_other"]], [[149, 149, "Organic_compound_other"], [151, 151, "Organic_compound_other"], [153, 153, "Organic_compound_other"], [155, 155, "Organic_compound_other"], [157, 157, "Organic_compound_other"], [164, 166, "Multicellular_organism"]], [[177, 177, "Organic_compound_other"], [179, 179, "Multicellular_organism"], [198, 198, "Organic_compound_other"], [207, 207, "Multicellular_organism"], [209, 209, "Multicellular_organism"], [172, 175, "Biochemical_process"]]], "relations": [[], [], [[42, 50, 55, 56, "activates"], [42, 50, 58, 58, "activates"], [42, 50, 61, 61, "activates"], [42, 50, 63, 63, "activates"], [42, 50, 66, 67, "activates"], [42, 50, 74, 74, "inhibits"], [42, 50, 85, 85, "activates"], [42, 50, 87, 87, "activates"], [55, 56, 76, 76, "is-in"], [58, 58, 76, 76, "is-in"], [61, 61, 76, 76, "is-in"], [63, 63, 76, 76, "is-in"], [66, 67, 76, 76, "is-in"]], [[96, 97, 124, 124, "activates"], [105, 105, 114, 114, "is-in"], [107, 107, 114, 114, "is-in"], [109, 109, 114, 114, "is-in"], [111, 112, 114, 114, "is-in"]], [[130, 135, 142, 142, "interacts"]], [[157, 157, 164, 166, "inhibits"], [155, 155, 164, 166, "inhibits"], [153, 153, 164, 166, "inhibits"], [151, 151, 164, 166, "inhibits"]], [[172, 175, 177, 177, "produces"], [198, 198, 207, 207, "inhibits"], [172, 175, 179, 179, "is-in"], [207, 207, 209, 209, "interacts"]]]}
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{"doc_key": "PMID33084931_abstract", "dataset": "pickle", "sentences": [["Genome", "wide", "association", "studies", "enabled", "prediction", "of", "many", "candidate", "genes", "for", "flowering", ",", "maturity", "and", "plant", "height", "under", "differing", "day-length", "conditions", "."], ["Some", "genes", "were", "envisaged", "only", "from", "derived", "B.", "rapa", "."], ["Flowering", "and", "plant", "height", "are", "the", "key", "life", "history", "traits", "."], ["These", "are", "crucial", "for", "adaptation", "and", "productivity", "."], ["Current", "investigations", "aimed", "to", "examine", "genotypic", "differences", "governing", "days", "to", "flowering", ",", "maturity", "and", "plant", "height", "under", "contrasting", "day-length", "conditions", ";", "and", "identify", "genomic", "regions", "governing", "the", "observed", "phenotypic", "variations", "."], ["An", "association", "panel", "comprising", "195", "inbred", "lines", ",", "representing", "natural", "(", "NR", ")", "and", "derived", "(", "DR", ")", "forms", "of", "Brassica", "rapa", "(", "AA", ";", "2n", "\u2009", "=", "\u2009", "20", ")", ",", "was", "evaluated", "at", "two", "sowing", "dates", "and", "two", "locations", ",", "representing", "different", "day-length", "regimes", "."], ["Derived", "B.", "rapa", "is", "a", "unique", "pre-breeding", "material", "extracted", "from", "B.", "juncea", "(", "AABB", ";", "2n", "\u2009", "=", "\u2009", "36", ")", "."], ["Population", "structure", "analysis", ",", "using", "DArT", "genotypes", "established", "derived", "B.", "rapa", "as", "a", "genetic", "resource", "distinct", "from", "natural", "B.", "rapa", "."], ["Genome", "wide", "association", "studies", "facilitated", "detection", "of", "many", "trait", "associated", "SNPs", "."], ["Chromosomes", "A03", ",", "A05", "and", "A09", "harboured", "majority", "of", "these", "."], ["Functional", "annotation", "of", "the", "associated", "SNPs", "and", "surrounding", "genome", "space(s", ")", "helped", "to", "predict", "43", "candidate", "genes", "."], ["Many", "of", "these", "were", "predicted", "under", "specific", "day-length", "conditions", "."], ["Important", "among", "these", "were", "the", "genes", "encoding", "floral", "meristem", "identity", "(", "SPL3", ",", "SPL15", ",", "AP3", ",", "BAM2", ")", ",", "photoperiodic", "responses", "(", "COL2", ",", "AGL18", ",", "SPT", ",", "NF-YC4", ")", ",", "gibberellic", "acid", "biosynthesis", "(", "GA1", ")", "and", "regulation", "of", "flowering", "(", "EBS", ")", "."], ["Some", "of", "the", "predicted", "genes", "were", "detected", "for", "DR", "subpanel", "alone", "."], ["Genes", "controlling", "hormones", ",", "auxins", "and", "gibberellins", "appeared", "important", "for", "the", "regulation", "of", "plant", "height", "."], ["Many", "of", "the", "significant", "SNPs", "were", "located", "on", "chromosomes", "harbouring", "previously", "reported", "QTLs", "and", "candidate", "genes", "."], ["The", "identified", "loci", "may", "be", "used", "for", "marker-assisted", "selection", "after", "due", "validation", "."]], "ner": [[], [[29, 30, "Multicellular_organism"]], [], [], [], [[102, 103, "Multicellular_organism"]], [[139, 140, "Multicellular_organism"], [129, 131, "Multicellular_organism"]], [[156, 157, "Multicellular_organism"], [159, 161, "Multicellular_organism"], [168, 170, "Multicellular_organism"]], [], [[185, 185, "DNA"], [187, 187, "DNA"], [189, 189, "DNA"]], [], [], [[234, 234, "DNA"], [236, 236, "DNA"], [238, 238, "DNA"], [240, 240, "DNA"], [246, 246, "DNA"], [248, 248, "DNA"], [250, 250, "DNA"], [252, 252, "DNA"], [259, 259, "DNA"], [266, 266, "DNA"], [255, 257, "Biochemical_pathway"]], [], [[285, 285, "Plant_hormone"], [287, 287, "Plant_hormone"]], [], []], "relations": [[], [], [], [], [], [], [[139, 140, 129, 131, "produces"]], [], [], [], [], [], [[259, 259, 255, 257, "is-in"]], [], [], [], []]}
{"doc_key": "PMID32615387_abstract", "dataset": "pickle", "sentences": [["Hot", "peppers", "are", "sensitive", "to", "low", "temperature", ",", "and", "seed", "browning", "significantly", "reduces", "the", "fruit", "quality", "."], ["This", "study", "aims", "to", "clarify", "the", "mechanisms", "of", "seed", "browning", "in", "terms", "of", "metabolite", "changes", "."], ["Metabolites", "were", "analysed", "during", "a", "30-day-storage", "period", "at", "2", "\u00a0", "\u00b0", "C", "and", "10", "\u00a0", "\u00b0", "C", "."], ["Gamma-aminobutyric", "acid", ",", "tyrosine", ",", "phenylalanine", ",", "and", "isoleucine", "concentrations", "were", "significantly", "higher", "at", "2", "\u00a0", "\u00b0", "C", "storage", "than", "at", "10", "\u00a0", "\u00b0", "C", "."], ["Reactive", "oxygen", "species", "(", "ROS", ")", "generation", "was", "associated", "with", "seed", "browning", "."], ["Transcription", "of", "jasmonic", "acid", "synthesis", "and", "ROS", "scavenging", "genes", "were", "higher", "in", "hot", "peppers", "stored", "at", "2", "\u00a0", "\u00b0", "C", "than", "those", "stored", "at", "10", "\u00a0", "\u00b0", "C", "."], ["This", "study", "elucidated", "the", "mechanisms", "underlying", "seed", "browning", "and", "chill", "damage", "in", "hot", "peppers", "during", "storage", "at", "low", "temperatures", "and", "our", "findings", "may", "help", "improve", "hot", "peppers", "'", "quality", "following", "harvesting", "."]], "ner": [[[0, 1, "Multicellular_organism"]], [], [], [[51, 52, "Organic_compound_other"], [54, 54, "Amino_acid_monomer"], [56, 56, "Amino_acid_monomer"], [59, 59, "Amino_acid_monomer"]], [[77, 83, "Biochemical_process"]], [[102, 103, "Multicellular_organism"], [92, 98, "DNA"]], [[131, 132, "Multicellular_organism"]]], "relations": [[], [], [], [], [], [[92, 98, 102, 103, "is-in"]], []]}
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{"doc_key": "PMID31450090_abstract", "dataset": "pickle", "sentences": [["Changes", "in", "specialized", "metabolites", "were", "analyzed", "in", "wheat", "leaves", "inoculated", "with", "Bipolaris", "sorokiniana", ",", "the", "causal", "agent", "of", "spot", "blotch", "of", "Poaceae", "species", "."], ["HPLC", "analysis", "detected", "the", "accumulation", "of", "six", "compounds", "in", "B.", "sorokiniana-infected", "leaves", "."], ["Of", "these", ",", "we", "purified", "two", "compounds", "by", "silica", "gel", "and", "ODS", "column", "chromatography", "and", "preparative", "HPLC", ",", "and", "identified", "them", "as", "cinnamic", "acid", "amides", ",", "N-cinnamoyl-9-hydroxy-8-oxotryptamine", "and", "N-cinnamoyl-8-oxotryptamine", ",", "by", "spectroscopic", "analyses", "."], ["The", "remaining", "four", "compounds", "were", "predicted", "to", "be", "p-coumaric", "acid", "amides", "of", "hydroxyputrescine", ",", "hydroxyagmatine", ",", "hydroxydehydroagmatine", ",", "and", "agmatine", "by", "mass", "spectrometry", "."], ["The", "accumulation", "of", "two", "cinnamic", "acid", "amides", "was", "also", "induced", "by", "Fusarium", "graminearum", "infection", ",", "and", "by", "treatment", "with", "CuCl(2", ")", ",", "jasmonic", "acid", ",", "and", "isopentenyladenine", "."], ["Antifungal", "activity", "of", "these", "amides", "was", "shown", "by", "inhibition", "of", "conidial", "germination", "and", "germ", "tube", "elongation", "of", "F.", "graminearum", "and", "Alternaria", "brassicicola", ",", "indicating", "that", "they", "act", "as", "phytoalexins", "."], ["The", "accumulation", "of", "these", "amides", "also", "detected", "in", "barley", "leaves", "treated", "with", "CuCl(2", ")", "."], ["We", "examined", "the", "accumulation", "of", "25", "phenylamides", "in", "B.", "sorokiniana-infected", "wheat", "leaves", "using", "LC-MS/MS", "."], ["Hydroxycinnamic", "acid", "amides", "of", "tryptamine", ",", "serotonin", ",", "putrescine", ",", "and", "agmatine", ",", "were", "induced", "after", "infection", "with", "B.", "sorokiniana", "."], ["Thus", ",", "the", "induced", "accumulation", "of", "two", "groups", "of", "phenylamides", ",", "cinnamic", "acid", "amides", "with", "indole", "amines", ",", "and", "p-coumaric", "acid", "amides", "with", "putrescine", "and", "agmatine", "related", "amines", ",", "represents", "a", "major", "metabolic", "response", "of", "wheat", "to", "pathogen", "infection", "."]], "ner": [[[7, 8, "Plant_region"], [11, 12, "Multicellular_organism"], [21, 22, "Multicellular_organism"], [18, 19, "Biochemical_process"]], [[33, 35, "Plant_region"]], [[63, 63, "Organic_compound_other"], [59, 61, "Organic_compound_other"], [65, 65, "Organic_compound_other"]], [[85, 85, "Organic_compound_other"], [87, 87, "Organic_compound_other"], [79, 81, "Organic_compound_other"], [83, 83, "Organic_compound_other"], [90, 90, "Organic_compound_other"]], [[106, 108, "Biochemical_process"], [99, 101, "Organic_compound_other"], [114, 115, "Inorganic_compound_other"], [117, 118, "Plant_hormone"], [121, 121, "Plant_hormone"]], [[140, 141, "Multicellular_organism"], [127, 127, "Organic_compound_other"], [143, 144, "Multicellular_organism"], [151, 151, "Organic_compound_other"]], [[161, 162, "Plant_region"], [165, 166, "Inorganic_compound_other"], [157, 157, "Organic_compound_other"]], [[174, 174, "Organic_compound_other"], [176, 179, "Plant_region"]], [[194, 194, "Organic_compound_other"], [201, 202, "Multicellular_organism"], [183, 185, "Organic_compound_other"], [187, 187, "Organic_compound_other"], [191, 191, "Organic_compound_other"], [189, 189, "Organic_compound_other"]], [[215, 217, "Organic_compound_other"], [219, 220, "Organic_compound_other"], [223, 225, "Organic_compound_other"], [227, 231, "Organic_compound_other"], [213, 213, "Organic_compound_other"], [239, 239, "Multicellular_organism"]]], "relations": [[[11, 12, 21, 22, "interacts"]], [], [], [], [[106, 108, 99, 101, "activates"], [114, 115, 99, 101, "activates"], [117, 118, 99, 101, "activates"], [121, 121, 99, 101, "activates"]], [[127, 127, 140, 141, "inhibits"], [127, 127, 143, 144, "inhibits"]], [[157, 157, 161, 162, "is-in"], [165, 166, 157, 157, "activates"]], [[174, 174, 176, 179, "is-in"]], [[201, 202, 183, 185, "activates"], [187, 187, 183, 185, "produces"], [189, 189, 183, 185, "produces"], [191, 191, 183, 185, "produces"], [194, 194, 183, 185, "produces"]], [[239, 239, 213, 213, "produces"], [239, 239, 215, 217, "produces"], [239, 239, 219, 220, "produces"], [239, 239, 223, 225, "produces"], [239, 239, 227, 231, "produces"]]]}
{"doc_key": "PMID16041570_abstract", "dataset": "pickle", "sentences": [["Chemically", "synthesized", "2-hydroxyethyl", "jasmonate", "(", "HEJA", ")", "was", "for", "the", "first", "time", "employed", "to", "induce", "the", "ginsenoside", "biosynthesis", "and", "to", "manipulate", "the", "product", "heterogeneity", "in", "plant", "cell", "cultures", "."], ["The", "dose", "response", "and", "timing", "of", "HEJA", "elicitation", "were", "investigated", "in", "cell", "suspension", "cultures", "of", "Panax", "notoginseng", "."], ["The", "optimal", "concentration", "and", "timing", "of", "HEJA", "addition", "for", "both", "cell", "growth", "and", "ginsenoside", "accumulation", "was", "identified", "to", "be", "200", "microM", "added", "on", "day", "4", "."], ["It", "was", "interestingly", "found", "that", "HEJA", "could", "stimulate", "ginsenosides", "biosynthesis", "and", "change", "their", "heterogeneity", "more", "efficiently", "than", "methyl", "jasmonate", "(", "MJA", ")", ",", "i.e.", ",", "the", "total", "ginsenoside", "content", "and", "the", "Rb/Rg", "ratio", "increased", "about", "60", "and", "30", "%", "with", "HEJA", "elicitation", "than", "that", "by", "MJA", ",", "respectively", "."], ["The", "activity", "of", "Rb1", "biosynthetic", "enzyme", ",", "i.e.", ",", "UDPG-ginsenoside", "Rd", "glucosyltransferase", "(", "UGRdGT", ")", ",", "was", "also", "higher", "in", "the", "former", "case", "."], ["A", "maximal", "production", "titer", "of", "ginsenoside", "Rg1", ",", "Re", ",", "Rb1", ",", "and", "Rd", "was", "47.4+/-4.8", ",", "52.3+/-4.4", ",", "190+/-18", ",", "and", "12.1+/-2.5", "mg/l", "with", "HEJA", "elicitation", ",", "which", "was", "about", "1.3-", ",", "1.3-", ",", "1.7-", ",", "and", "2.1-fold", "than", "that", "using", "MJA", ",", "respectively", "."], ["Early", "signal", "events", "in", "plant", "defense", "response", ",", "including", "oxidative", "burst", "and", "jasmonic", "acid", "(", "JA", ")", "biosynthesis", ",", "were", "also", "examined", "."], ["Levels", "of", "H2O2", "and", "NO", "in", "medium", "and", "L-phenylalanine", "ammonia", "lyase", "activity", "in", "cells", "were", "not", "affected", "by", "addition", "of", "MJA", "and", "HEJA", "."], ["On", "the", "other", "hand", ",", "the", "JA", "content", "in", "cells", "was", "increased", "with", "external", "jasmonates", "elicitation", ",", "and", "it", "was", "inhibited", "with", "the", "addition", "of", "JA", "biosynthesis", "inhibitors", "."], ["The", "results", "suggest", "that", "oxidative", "burst", "might", "not", "be", "involved", "in", "the", "jasmonates-elicited", "signal", "transduction", "pathway", ",", "and", "MJA", "and", "HEJA", "may", "induce", "the", "ginsenoside", "biosynthesis", "via", "induction", "of", "endogenous", "JA", "biosynthesis", "and", "key", "enzymes", "(", "such", "as", "UGRdGT", ")", "in", "the", "ginsenoside", "biosynthetic", "pathway", "of", "P.", "notoginseng", "cells", "."], ["The", "information", "is", "useful", "for", "hyperproduction", "of", "plant-specific", "heterogeneous", "products", "."]], "ner": [[[2, 3, "Plant_hormone"], [5, 5, "Plant_hormone"], [16, 17, "Biochemical_pathway"]], [[35, 35, "Plant_hormone"], [44, 45, "Multicellular_organism"]], [[53, 53, "Plant_hormone"], [60, 61, "Biochemical_process"]], [[78, 78, "Plant_hormone"], [90, 91, "Plant_hormone"], [93, 93, "Plant_hormone"], [100, 100, "Organic_compound_other"], [113, 113, "Plant_hormone"], [118, 118, "Plant_hormone"], [81, 82, "Biochemical_pathway"]], [[125, 127, "Protein"], [131, 133, "Protein"], [135, 135, "Protein"]], [[151, 159, "Organic_compound_other"], [171, 171, "Plant_hormone"], [188, 188, "Plant_hormone"]], [[204, 209, "Biochemical_pathway"]], [[217, 217, "Inorganic_compound_other"], [219, 219, "Inorganic_compound_other"], [235, 235, "Plant_hormone"], [237, 237, "Plant_hormone"], [223, 226, "Biochemical_process"]], [[245, 245, "Plant_hormone"], [253, 253, "Plant_hormone"], [264, 266, "Organic_compound_other"]], [[280, 283, "Biochemical_pathway"], [286, 286, "Plant_hormone"], [288, 288, "Plant_hormone"], [306, 306, "Protein"], [310, 312, "Biochemical_pathway"], [292, 293, "Biochemical_pathway"], [298, 299, "Biochemical_pathway"], [314, 316, "Cell"]], []], "relations": [[[5, 5, 16, 17, "activates"], [2, 3, 16, 17, "activates"]], [], [], [[78, 78, 81, 82, "activates"], [90, 91, 81, 82, "activates"], [93, 93, 81, 82, "activates"], [113, 113, 100, 100, "activates"], [118, 118, 100, 100, "activates"]], [], [[171, 171, 151, 159, "activates"], [188, 188, 151, 159, "activates"]], [], [], [[264, 266, 245, 245, "inhibits"], [253, 253, 245, 245, "activates"]], [[288, 288, 292, 293, "activates"], [286, 286, 292, 293, "activates"], [286, 286, 298, 299, "interacts"], [288, 288, 298, 299, "interacts"], [286, 286, 306, 306, "interacts"], [288, 288, 306, 306, "interacts"], [310, 312, 314, 316, "is-in"], [306, 306, 310, 312, "is-in"]], []]}
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{"doc_key": "PMID28106116_abstract", "dataset": "pickle", "sentences": [["Potential", "of", "MoSM1", ",", "encoding", "for", "a", "cerato-platanin", "protein", "from", "Magnaporthe", "oryzae", ",", "in", "improvement", "of", "rice", "disease", "resistance", "was", "examined", "."], ["Transient", "expression", "of", "MoSM1", "in", "rice", "leaves", "initiated", "hypersensitive", "response", "and", "upregulated", "expression", "of", "defense", "genes", "."], ["When", "transiently", "expressed", "in", "tobacco", "leaves", ",", "MoSM1", "targeted", "to", "plasma", "membrane", "."], ["The", "MoSM1-overexpressing", "(", "MoSM1-OE", ")", "transgenic", "rice", "lines", "showed", "an", "improved", "resistance", ",", "as", "revealed", "by", "the", "reduced", "disease", "severity", "and", "decreased", "in", "planta", "pathogen", "growth", ",", "against", "2", "strains", "belonging", "to", "two", "different", "races", "of", "M.", "oryzae", ",", "causing", "blast", "disease", ",", "and", "against", "2", "strains", "of", "Xanthomonas", "oryzae", "pv", ".", "oryzae", ",", "causing", "bacterial", "leaf", "blight", "disease", "."], ["However", ",", "no", "alteration", "in", "resistance", "to", "sheath", "blight", "disease", "was", "observed", "in", "MoSM1-OE", "lines", "."], ["The", "MoSM1-OE", "plants", "contained", "elevated", "levels", "of", "salicylic", "acid", "(", "SA", ")", "and", "jasmonic", "acid", "(", "JA", ")", "and", "constitutively", "activated", "the", "expression", "of", "SA", "and", "JA", "signaling-related", "regulatory", "and", "defense", "genes", "."], ["Furthermore", ",", "the", "MoSM1-OE", "plants", "had", "no", "effect", "on", "drought", "and", "salt", "stress", "tolerance", "and", "on", "grain", "yield", "."], ["We", "conclude", "that", "MoSM1", "confers", "a", "broad-spectrum", "resistance", "against", "different", "pathogens", "through", "modulating", "SA-", "and", "JA-mediated", "signaling", "pathways", "without", "any", "penalty", "on", "abiotic", "stress", "tolerance", "and", "grain", "yield", ",", "providing", "a", "promising", "potential", "for", "application", "of", "MoSM1", "in", "improvement", "of", "disease", "resistance", "in", "crops", "."]], "ner": [[[2, 2, "DNA"], [7, 8, "Protein"], [10, 11, "Multicellular_organism"], [16, 18, "Biochemical_process"]], [[25, 25, "DNA"], [27, 28, "Plant_region"], [30, 31, "Biochemical_process"]], [[43, 44, "Plant_region"], [46, 46, "DNA"]], [[53, 59, "Multicellular_organism"], [88, 89, "Multicellular_organism"], [92, 93, "Biochemical_process"], [100, 104, "Unicellular_organism"], [107, 110, "Biochemical_process"]], [[119, 121, "Biochemical_process"], [125, 126, "Multicellular_organism"]], [[129, 130, "Multicellular_organism"], [135, 136, "Plant_hormone"], [138, 138, "Plant_hormone"], [141, 142, "Plant_hormone"], [144, 144, "Plant_hormone"], [152, 159, "DNA"]], [[164, 165, "Multicellular_organism"], [170, 174, "Biochemical_process"]], [[183, 183, "DNA"], [193, 197, "Biochemical_pathway"], [216, 216, "DNA"]]], "relations": [[[2, 2, 7, 8, "produces"], [7, 8, 10, 11, "is-in"]], [[25, 25, 30, 31, "activates"]], [], [[53, 59, 88, 89, "inhibits"], [88, 89, 92, 93, "produces"], [53, 59, 100, 104, "inhibits"], [100, 104, 107, 110, "produces"]], [], [[135, 136, 129, 130, "is-in"], [138, 138, 129, 130, "is-in"], [141, 142, 129, 130, "is-in"], [144, 144, 129, 130, "is-in"], [129, 130, 152, 159, "activates"]], [], [[183, 183, 193, 197, "interacts"]]]}
{"doc_key": "PMID19034497_abstract", "dataset": "pickle", "sentences": [["Auxin", "is", "one", "of", "the", "most", "important", "phytohormones", "and", "exerts", "pleiotropic", "effects", "on", "plant", "growth", "and", "development", "."], ["Aux/IAA", "and", "auxin", "response", "factor", "(", "ARF", ")", "are", "two", "important", "protein", "families", "that", "are", "well", "recognized", "for", "their", "roles", "in", "auxin-mediated", "responses", "."], ["Aux/IAA", "proteins", "are", "short-lived", "transcriptional", "regulators", "that", "mediate", "auxin", "responses", "through", "interaction", "with", "ARF", "transcription", "factors", "."], ["Here", ",", "we", "systematically", "compared", "the", "genomic", "organization", "of", "the", "two", "families", "in", "rice", "."], ["The", "expression", "profiles", "of", "both", "families", "were", "compared", "to", "show", "possible", "association", "of", "the", "two", "gene", "families", "at", "expression", "level", ",", "which", "would", "help", "reveal", "their", "synergistic", "relationships", "and", "functions", "."], ["The", "expression", "profile", "analysis", "of", "Aux/IAA", "and", "ARF", "genes", "in", "30", "organs/tissues", "(", "collected", "from", "an", "entire", "life", "cycle", "of", "rice", ")", "suggested", "that", "Aux/IAA", "and", "ARF", "genes", "are", "expressed", "in", "very", "diverse", "patterns", "."], ["In", "general", ",", "the", "genes", "showing", "similar", "expression", "patterns", "tended", "to", "be", "in", "the", "same", "phylogenetic", "subgroup", "even", "though", "their", "expression", "patterns", "were", "not", "always", "the", "same", "."], ["Hierarchical", "cluster", "analysis", "revealed", "that", "there", "are", "eight", "pairs", "of", "IAA", "and", "ARF", "genes", ",", "with", "each", "pair", "showing", "highly", "correlated", "expression", "."], ["The", "expression", "levels", "of", "the", "IAA", "gene", "family", "were", "also", "checked", "under", "various", "hormone", "treatments", "including", "abscisic", "acid", ",", "kinetin", ",", "gibberellin", ",", "jasmonic", "acid", ",", "auxin", "and", "brassinolide", "."], ["The", "results", "indicated", "that", "most", "of", "the", "IAA", "genes", "respond", "to", "at", "least", "one", "of", "the", "treatments", "."], ["Furthermore", ",", "DNA", "chip", "and", "real-time", "PCR", "results", "show", "that", "many", "genes", "in", "these", "families", "were", "responsive", "to", "various", "abiotic", "stresses", ",", "indicating", "an", "interaction", "between", "plant", "growth", "and", "abiotic", "stress", "."], ["The", "effect", "of", "abiotic", "stress", "on", "plant", "growth", "and", "auxin", "distribution", "was", "further", "confirmed", "with", "the", "root", "growth", "of", "DR5-GUS", "transgenic", "rice", "under", "mannitol", "treatment", ",", "in", "which", "a", "close", "association", "between", "mannitol-induced", "changes", "of", "auxin", "distribution", "and", "root", "growth", "was", "observed", "."]], "ner": [[[0, 0, "Plant_hormone"], [7, 7, "Plant_hormone"]], [[18, 18, "Protein"], [20, 22, "Protein"], [24, 24, "Protein"], [39, 40, "Biochemical_process"]], [[42, 43, "Protein"], [50, 51, "Biochemical_process"], [55, 57, "Protein"]], [[72, 72, "Multicellular_organism"]], [], [[110, 113, "DNA"], [129, 132, "DNA"], [125, 125, "Multicellular_organism"]], [], [[178, 181, "DNA"]], [[207, 208, "Plant_hormone"], [212, 212, "Plant_hormone"], [214, 215, "Plant_hormone"], [217, 217, "Plant_hormone"], [196, 198, "DNA"], [210, 210, "Organic_compound_other"], [219, 219, "Organic_compound_other"]], [[228, 229, "DNA"]], [], [[280, 281, "Biochemical_process"], [306, 307, "Biochemical_process"], [290, 292, "Multicellular_organism"], [294, 294, "Organic_compound_other"]]], "relations": [[], [[24, 24, 39, 40, "interacts"], [20, 22, 39, 40, "interacts"], [18, 18, 39, 40, "interacts"]], [[42, 43, 55, 57, "interacts"], [42, 43, 50, 51, "interacts"]], [], [], [[110, 113, 125, 125, "is-in"]], [], [], [], [], [], [[306, 307, 290, 292, "is-in"]]]}
{"doc_key": "PMID10972869_abstract", "dataset": "pickle", "sentences": [["Recent", "evidence", "suggests", "that", "oxidized", "lipid-derived", "molecules", "play", "significant", "roles", "in", "inducible", "plant", "defence", "responses", "against", "microbial", "pathogens", ",", "either", "by", "directly", "deterring", "parasite", "multiplication", ",", "or", "as", "signals", "involved", "in", "the", "induction", "of", "sets", "of", "defence", "genes", "."], ["The", "synthesis", "of", "these", "oxylipins", "was", "hypothesized", "to", "be", "initiated", "by", "the", "phospholipase", "A2-mediated", "release", "of", "unsaturated", "fatty", "acids", "from", "membrane", "lipids", "."], ["Here", ",", "we", "demonstrate", "that", ",", "in", "tobacco", "leaves", "reacting", "hypersensitively", "to", "tobacco", "mosaic", "virus", ",", "a", "strong", "increase", "in", "soluble", "phospholipase", "A2", "(", "PLA2", ")", "activity", "occurs", "at", "the", "onset", "of", "necrotic", "lesion", "appearance", "."], ["This", "rapid", "PLA2", "activation", "occurred", "before", "the", "accumulation", "of", "12-oxophytodienoic", "and", "jasmonic", "acids", ",", "two", "fatty", "acid-derived", "defence", "signals", "."], ["Three", "PLA2", "isoforms", "were", "separated", "and", "the", "most", "active", "enzyme", "was", "partially", "purified", ",", "its", "N-terminal", "sequence", "displaying", "similarity", "with", "patatin", ",", "the", "major", "storage", "protein", "in", "potato", "tubers", "."], ["Three", "related", "tobacco", "patatin-like", "cDNAs", ",", "called", "NtPat1", ",", "NtPat2", "and", "NtPat3", ",", "were", "cloned", ",", "with", "NtPat2", "encoding", "the", "PLA2", "isolated", "from", "infected", "leaves", "."], ["RT-PCR", "experiments", "showed", "a", "rapid", "transcriptional", "activation", "of", "the", "three", "NtPat", "genes", "in", "virus-infected", "leaves", ",", "preceding", "the", "increase", "in", "PLA2", "activity", "."], ["Recombinant", "NtPat1", "and", "NtPat3", "enzymes", "were", "active", "in", "an", "assay", "using", "labelled", "bacterial", "membranes", ",", "and", "also", "displayed", "high", "bona", "fide", "PLA2", "activity", "on", "phosphatidylcholine", "substrate", "."], ["These", "results", "point", "to", "a", "possible", "new", "role", "of", "patatin-like", "phospholipases", "in", "inducible", "plant", "defence", "responses", "."], ["The", "induction", "kinetics", "together", "with", "the", "enzymatic", "activity", "data", "indicate", "that", "the", "NtPat", "proteins", "may", "provide", "precursors", "for", "oxylipin", "synthesis", "during", "the", "hypersensitive", "response", "to", "pathogens", "."]], "ner": [[], [[43, 43, "Organic_compound_other"], [55, 57, "Organic_compound_other"], [59, 60, "Organic_compound_other"]], [[69, 70, "Plant_region"], [74, 76, "Virus"], [83, 84, "Protein"], [86, 86, "Protein"]], [[100, 101, "Biochemical_process"], [107, 110, "Plant_hormone"], [113, 116, "Biochemical_process"]], [[119, 120, "Protein"], [138, 138, "Protein"], [145, 146, "Plant_region"]], [[150, 152, "DNA"], [155, 155, "DNA"], [157, 157, "DNA"], [159, 159, "DNA"], [165, 165, "DNA"], [168, 168, "Protein"]], [[184, 185, "DNA"], [194, 195, "Biochemical_process"]], [[197, 201, "Protein"], [218, 219, "Biochemical_process"], [221, 221, "Organic_compound_other"]], [[233, 234, "Protein"]], [[253, 254, "Protein"], [259, 260, "Biochemical_process"], [263, 264, "Biochemical_process"]]], "relations": [[], [[55, 57, 59, 60, "is-in"]], [[74, 76, 69, 70, "inhibits"], [74, 76, 83, 84, "activates"], [74, 76, 86, 86, "activates"]], [], [[138, 138, 145, 146, "is-in"]], [[165, 165, 168, 168, "produces"]], [], [], [], [[253, 254, 259, 260, "interacts"]]]}
{"doc_key": "PMID11299384_abstract", "dataset": "pickle", "sentences": [["Azospirillum", "species", "are", "plant", "growth-promotive", "bacteria", "whose", "beneficial", "effects", "have", "been", "postulated", "to", "be", "partially", "due", "to", "production", "of", "phytohormones", ",", "including", "gibberellins", "(", "GAs", ")", "."], ["In", "this", "work", ",", "Azospirillum", "brasilense", "strain", "Cd", "and", "Azospirillum", "lipoferum", "strain", "USA", "5b", "promoted", "sheath", "elongation", "growth", "of", "two", "single", "gene", "GA-deficient", "dwarf", "rice", "(", "Oryza", "sativa", ")", "mutants", ",", "dy", "and", "dx", ",", "when", "the", "inoculated", "seedlings", "were", "supplied", "with", "[17,17", "-", "2H2]GA20-glucosyl", "ester", "or", "[", "17,17-", "2H2]GA20-glucosyl", "ether", "."], ["Results", "of", "capillary", "gas", "chromatography-mass", "spectrometry", "analysis", "show", "that", "this", "growth", "was", "due", "primarily", "to", "release", "of", "the", "aglycone", "[17,17", "-", "2H2]GA20", "and", "its", "subsequent", "3beta-hydroxylation", "to", "[17,17", "-", "2H2]GA1", "by", "the", "microorganism", "for", "the", "dy", "mutant", ",", "and", "by", "both", "the", "rice", "plant", "and", "microorganism", "for", "the", "dx", "mutant", "."]], "ner": [[[19, 19, "Plant_hormone"], [22, 22, "Plant_hormone"], [24, 24, "Plant_hormone"], [0, 1, "Unicellular_organism"]], [[69, 72, "Organic_compound_other"], [74, 77, "Organic_compound_other"], [31, 34, "Unicellular_organism"], [36, 40, "Unicellular_organism"], [58, 58, "Multicellular_organism"], [60, 60, "Multicellular_organism"], [47, 56, "Multicellular_organism"]], [[97, 100, "Organic_compound_other"], [121, 122, "Multicellular_organism"], [106, 108, "Organic_compound_other"], [114, 115, "Multicellular_organism"], [127, 128, "Multicellular_organism"], [104, 104, "Biochemical_process"]]], "relations": [[], [[36, 40, 47, 56, "interacts"], [31, 34, 47, 56, "interacts"], [31, 34, 58, 58, "interacts"], [36, 40, 60, 60, "interacts"], [31, 34, 60, 60, "interacts"], [36, 40, 58, 58, "interacts"], [69, 72, 31, 34, "interacts"], [74, 77, 31, 34, "interacts"], [69, 72, 36, 40, "interacts"], [74, 77, 36, 40, "interacts"]], [[97, 100, 106, 108, "produces"], [104, 104, 106, 108, "produces"], [104, 104, 97, 100, "interacts"]]]}
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{"doc_key": "PMID32158118_abstract", "dataset": "pickle", "sentences": [["Menthol", "mint", "(", "Mentha", "arvensis", "L.", ")", "cultivation", "is", "significantly", "affected", "by", "the", "heavy", "metals", "like", "cadmium", "(", "Cd", ")", "which", "also", "imposes", "severe", "health", "hazards", "."], ["Two", "menthol", "mint", "cultivars", "namely", "Kosi", "and", "Kushal", "were", "evaluated", "under", "Cd", "stress", "conditions", "."], ["Impact", "of", "plant", "growth", "regulators", "(", "PGRs", ")", "like", "salicylic", "acid", "(", "SA", ")", ",", "gibberellic", "acid", "(", "GA(3", ")", ")", "and", "triacontanol", "(", "Tria", ")", "on", "Cd", "stress", "tolerance", "was", "assessed", "."], ["Reduced", "growth", ",", "photosynthetic", "parameters", ",", "mineral", "nutrient", "concentration", ",", "and", "increased", "oxidative", "stress", "biomarkers", "like", "electrolyte", "leakage", ",", "malondialdehyde", ",", "and", "hydrogen", "peroxide", "contents", "were", "observed", "under", "Cd", "stress", "."], ["Differential", "upregulation", "of", "proline", "content", "and", "antioxidant", "activities", "under", "Cd", "stress", "was", "observed", "in", "both", "the", "cultivars", "."], ["Interestingly", ",", "low", "electrolyte", "leakage", ",", "lipid", "peroxidation", ",", "hydrogen", "peroxide", "and", "Cd", "concentration", "in", "leaves", "were", "observed", "in", "Kushal", "compared", "to", "Kosi", "."], ["Among", "all", "the", "PGRs", "tested", ",", "SA", "proved", "to", "be", "the", "\u00a0", "best", "in", "improving", "Cd-stress", "tolerance", "in", "both", "the", "cultivars", "but", "Kushal", "responded", "better", "than", "Kosi", "."]], "ner": [[[0, 1, "Multicellular_organism"], [3, 5, "Multicellular_organism"], [16, 16, "Element"], [18, 18, "Element"]], [[28, 30, "Multicellular_organism"], [32, 32, "Multicellular_organism"], [34, 34, "Multicellular_organism"], [38, 38, "Element"]], [[69, 71, "Biochemical_process"], [44, 46, "Plant_hormone"], [48, 48, "Plant_hormone"], [51, 52, "Plant_hormone"], [54, 54, "Plant_hormone"], [57, 58, "Plant_hormone"], [60, 61, "Plant_hormone"], [64, 64, "Plant_hormone"], [66, 66, "Plant_hormone"]], [[103, 103, "Element"], [94, 94, "Organic_compound_other"], [97, 98, "Inorganic_compound_other"], [91, 92, "Biochemical_process"]], [[115, 115, "Element"], [109, 109, "Amino_acid_monomer"]], [[143, 143, "Multicellular_organism"], [146, 146, "Multicellular_organism"], [136, 136, "Element"], [130, 131, "Biochemical_process"], [133, 134, "Inorganic_compound_other"], [127, 128, "Biochemical_process"]], [[170, 170, "Multicellular_organism"], [174, 174, "Multicellular_organism"], [163, 164, "Biochemical_process"], [151, 151, "Plant_hormone"], [154, 154, "Plant_hormone"]]], "relations": [[], [], [], [[103, 103, 91, 92, "activates"], [103, 103, 94, 94, "activates"], [103, 103, 97, 98, "activates"]], [[115, 115, 109, 109, "interacts"]], [[136, 136, 143, 143, "is-in"], [133, 134, 143, 143, "is-in"], [130, 131, 143, 143, "is-in"], [127, 128, 143, 143, "is-in"], [127, 128, 146, 146, "is-in"], [130, 131, 146, 146, "is-in"], [133, 134, 146, 146, "is-in"], [136, 136, 146, 146, "is-in"]], [[154, 154, 163, 164, "activates"], [163, 164, 170, 170, "is-in"], [163, 164, 174, 174, "is-in"]]]}
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{"doc_key": "PMID16169957_abstract", "dataset": "pickle", "sentences": [["We", "analyzed", "expression", "of", "marker", "genes", "for", "three", "defense", "pathways", "during", "infection", "by", "Cauliflower", "mosaic", "virus", "(", "CaMV", ")", ",", "a", "compatible", "pathogen", "of", "Arabidopsis", "(", "Arabidopsis", "thaliana", ")", ",", "using", "luciferase", "reporter", "transgenes", "and", "directly", "by", "measuring", "transcript", "abundance", "."], ["Expression", "of", "PR-1", ",", "a", "marker", "for", "salicylic", "acid", "signaling", ",", "was", "very", "low", "until", "8", "d", "postinoculation", "and", "then", "rose", "sharply", ",", "coinciding", "with", "the", "rise", "in", "virus", "levels", "."], ["In", "contrast", ",", "as", "early", "as", "2", "h", "postinoculation", ",", "transcriptional", "up-regulation", "of", "GST1-a", "marker", "for", "reactive", "oxygen", "species-and", "PDF1.2-a", "marker", "for", "jasmonic", "acid/ethylene", "defense", "signaling-was", "detectable", "in", "the", "virus-inoculated", "leaf", "and", "systemically", ".", "In", "parallel", "with", "the", "activation", "of", "GST1", ",", "H(2)O(2", ")", "accumulated", "locally", "and", "systemically", "in", "virus-", "but", "not", "mock-inoculated", "plants", "."], ["However", ",", "in", "plants", "inoculated", "with", "infectious", "CaMV", "DNA", "rather", "than", "virus", "particles", ",", "the", "onset", "of", "systemic", "luciferase", "activity", "was", "delayed", "by", "24", "to", "48", "h", ",", "suggesting", "that", "virion", "structural", "proteins", "act", "as", "the", "elicitor", "."], ["This", "phenomenon", ",", "which", "we", "term", "the", "rapid", "systemic", "response", ",", "preceded", "virus", "movement", "from", "the", "inoculated", "leaf", ";", "therefore", ",", "the", "systemic", "signal", "is", "not", "viral", "."], ["Systemic", ",", "but", "not", "local", ",", "H(2)O(2", ")", "accumulation", "was", "abolished", "in", "rbohDF", "double", "mutants", "and", "in", "etr1", "-", "1", "and", "ein2", "-", "1", "mutants", ",", "implicating", "NADPH", "oxidase", "and", "ethylene", "signaling", "in", "the", "generation", "and", "transduction", "of", "the", "response", "."], ["Ethylene", ",", "but", "not", "rbohDF", "mutants", ",", "also", "showed", "reduced", "susceptibility", "to", "CaMV", ",", "whereas", "in", "NahG", "transgenics", ",", "virus", "levels", "were", "similar", "to", "wild", "type", "."], ["These", "findings", "implicate", "reactive", "oxygen", "species", "and", "ethylene", "in", "signaling", "in", "response", "to", "CaMV", "infection", ",", "but", "suggest", "that", "salicylic", "acid", "does", "not", "play", "an", "effective", "role", "."]], "ner": [[[13, 15, "Virus"], [17, 17, "Virus"], [24, 24, "Multicellular_organism"], [26, 27, "Multicellular_organism"], [31, 33, "DNA"]], [[48, 50, "Biochemical_process"], [43, 43, "DNA"]], [[114, 115, "Inorganic_compound_other"], [112, 112, "DNA"], [91, 92, "DNA"], [85, 86, "DNA"]], [[133, 135, "DNA"], [145, 146, "Biochemical_process"]], [], [[199, 201, "Biochemical_process"], [205, 207, "Multicellular_organism"], [220, 221, "Protein"], [223, 224, "Biochemical_process"], [210, 217, "Multicellular_organism"]], [[234, 234, "Plant_hormone"], [246, 246, "Virus"], [238, 239, "Multicellular_organism"], [250, 251, "Multicellular_organism"]], [[264, 266, "Inorganic_compound_other"], [268, 268, "Plant_hormone"], [280, 281, "Plant_hormone"], [274, 275, "Biochemical_process"]]], "relations": [[[13, 15, 24, 24, "interacts"], [13, 15, 26, 27, "interacts"], [17, 17, 24, 24, "interacts"], [17, 17, 26, 27, "interacts"]], [[43, 43, 48, 50, "is-in"]], [], [[133, 135, 145, 146, "inhibits"]], [], [[220, 221, 199, 201, "interacts"], [223, 224, 199, 201, "interacts"]], [[234, 234, 246, 246, "inhibits"]], [[268, 268, 274, 275, "interacts"], [264, 266, 274, 275, "interacts"]]]}
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{"doc_key": "PMID14555690_abstract", "dataset": "pickle", "sentences": [["Plants", "under", "stress", "from", "both", "biotic", "and", "abiotic", "sources", "produce", "increased", "levels", "of", "ethylene", ",", "which", "is", "perceived", "by", "ethylene", "receptors", "and", "triggers", "cellular", "responses", "further", "downstream", "."], ["Protein", "phosphorylation", "and", "dephosphorylation", "were", "implicated", "in", "the", "regulation", "of", "ethylene", "induction", "by", "stresses", "based", "on", "studies", "using", "protein", "kinase", "and", "phosphatase", "inhibitors", "."], ["However", ",", "the", "kinase(s", ")", "involved", "remains", "to", "be", "determined", "."], ["Using", "a", "conditional", "gain-of-function", "transgenic", "system", ",", "we", "demonstrate", "that", "the", "activation", "of", "SIPK", ",", "a", "tobacco", "mitogen-activated", "protein", "kinase", "(", "MAPK", ")", ",", "by", "NtMEK2DD", ",", "an", "active", "mutant", "of", "the", "upstream", "kinase", "of", "SIPK", ",", "resulted", "in", "a", "dramatic", "increase", "in", "ethylene", "production", "."], ["The", "increase", "in", "ethylene", "after", "the", "activation", "of", "SIPK", "coincided", "with", "a", "dramatic", "increase", "in", "1-aminocyclopropane-1-carboxylic", "acid", "(", "ACC", ")", "synthase", "(", "ACS", ")", "activity", ",", "which", "was", "followed", "by", "the", "activation", "of", "a", "subgroup", "of", "ACS", "and", "ACC", "oxidase", "(", "ACO", ")", "genes", ",", "suggesting", "that", "either", "the", "activation", "of", "unidentified", "ACS(s", ")", "or", "post-transcriptional", "regulation", "is", "involved", "."], ["Infection", "with", "Tobacco", "mosaic", "virus", "(", "TMV", ")", ",", "which", "is", "known", "to", "activate", "the", "SIPK", "cascade", "and", "induce", "ethylene", "biosynthesis", ",", "also", "induced", "the", "same", "ACSs", "and", "ACOs", "."], ["After", "ethylene", "production", "in", "NtMEK2DD", "plants", ",", "strong", "activation", "of", "ETHYLENE-RESPONSE", "FACTOR", "(", "ERF", ")", "genes", "was", "observed", ",", "similar", "to", "the", "effect", "in", "NN", "tobacco", "plants", "infected", "with", "TMV", "."], ["In", "contrast", "to", "previous", "reports", ",", "no", "major", "increase", "in", "jasmonic", "acid", "(", "JA", ")", "and", "methyl", "jasmonate", "(", "MJ", ")", "was", "detected", "after", "the", "activation", "of", "SIPK/WIPK", "in", "NtMEK2DD", "transgenic", "plants", "."], ["These", "results", "suggest", "that", "the", "induction", "of", "ethylene", "but", "not", "JA/MJ", "is", "involved", "in", "plant", "defense", "responses", "mediated", "by", "the", "NtMEK2-SIPK/WIPK", "pathway", "."]], "ner": [[[13, 13, "Plant_hormone"], [19, 20, "Protein"]], [[38, 39, "Biochemical_process"], [46, 50, "Organic_compound_other"], [28, 31, "Biochemical_process"]], [[55, 56, "Protein"]], [[106, 107, "Biochemical_process"], [76, 76, "Protein"], [84, 84, "Protein"], [96, 96, "Protein"], [98, 98, "Protein"], [88, 88, "Protein"], [79, 82, "Protein"]], [[112, 112, "Plant_hormone"], [117, 117, "Protein"], [124, 133, "Biochemical_process"], [161, 162, "Protein"], [145, 152, "DNA"]], [[195, 195, "Protein"], [197, 197, "Protein"], [171, 173, "Virus"], [175, 175, "Virus"], [184, 185, "Biochemical_pathway"], [188, 189, "Biochemical_pathway"]], [[200, 201, "Biochemical_process"], [203, 204, "Multicellular_organism"], [223, 225, "Multicellular_organism"], [228, 228, "Virus"], [209, 214, "DNA"]], [[243, 243, "Plant_hormone"], [240, 241, "Plant_hormone"], [246, 247, "Plant_hormone"], [249, 249, "Plant_hormone"], [259, 261, "Multicellular_organism"]], [[270, 270, "Plant_hormone"], [283, 284, "Biochemical_pathway"]]], "relations": [[[19, 20, 13, 13, "interacts"]], [[28, 31, 38, 39, "interacts"]], [], [[88, 88, 76, 76, "activates"], [76, 76, 106, 107, "activates"]], [[117, 117, 112, 112, "activates"], [117, 117, 124, 133, "activates"], [117, 117, 145, 152, "activates"]], [[171, 173, 184, 185, "activates"], [175, 175, 184, 185, "activates"], [171, 173, 188, 189, "activates"], [171, 173, 195, 195, "activates"], [171, 173, 197, 197, "activates"], [175, 175, 188, 189, "activates"], [175, 175, 195, 195, "activates"], [175, 175, 197, 197, "activates"]], [[200, 201, 209, 214, "activates"], [200, 201, 203, 204, "is-in"]], [], [[270, 270, 283, 284, "interacts"]]]}
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{"doc_key": "PMID11094982_abstract", "dataset": "pickle", "sentences": [["The", "induction", "of", "alpha-amylase", "triggered", "by", "gibberellic", "acid", "in", "barley", "embryos", "is", "repressed", "by", "sugars", "."], ["We", "investigated", "the", "effects", "of", "glucose", "on", "the", "gibberellin", "signal", "transduction", "pathway", "to", "localize", "the", "site", "of", "interaction", "of", "the", "sugar/hormone", "signalling", "pathways", "."], ["Our", "results", "indicate", "that", "glucose", "represses", "gibberellin", "signalling", "late", "along", "this", "hormone", "transduction", "pathway", ",", "downstream", "of", "transcription", "of", "the", "gibberellin-modulated", "transcriptional", "activator", "(", "GAMYB", ")", "needed", "for", "alpha-amylase", "induction", "."], ["This", "result", "suggests", "either", "that", "glucose", "repression", "is", "transduced", "by", "a", "pathway", "independent", "of", "gibberellin", "signalling", "or", "that", "repression", "occurs", "at", "the", "level", "of", "GAMYB", "translation", "."]], "ner": [[[3, 3, "Organic_compound_other"], [6, 7, "Plant_hormone"], [9, 10, "Multicellular_organism"]], [[21, 21, "Organic_compound_other"], [24, 27, "Biochemical_pathway"], [36, 38, "Biochemical_process"]], [[44, 44, "Organic_compound_other"], [46, 47, "Biochemical_pathway"], [60, 62, "Protein"], [64, 64, "Protein"], [68, 69, "Biochemical_pathway"]], [[85, 86, "Biochemical_pathway"], [95, 96, "Biochemical_process"], [76, 77, "Biochemical_process"]]], "relations": [[[6, 7, 3, 3, "activates"], [3, 3, 9, 10, "is-in"]], [], [[44, 44, 46, 47, "inhibits"], [68, 69, 64, 64, "interacts"], [68, 69, 60, 62, "interacts"]], []]}
{"doc_key": "PMID18941053_abstract", "dataset": "pickle", "sentences": [["Seed", "germination", "is", "antagonistically", "controlled", "by", "the", "phytohormones", "gibberellic", "acid", "(", "GA", ")", "and", "abscisic", "acid", "(", "ABA", ")", "."], ["GA", "promotes", "seed", "germination", "by", "enhancing", "the", "proteasome-mediated", "destruction", "of", "RGL2", "(", "for", "RGA-LIKE2", ")", ",", "a", "key", "DELLA", "factor", "repressing", "germination", "."], ["By", "contrast", ",", "ABA", "blocks", "germination", "by", "inducing", "ABI5", "(", "for", "ABA-INSENSITIVE5", ")", ",", "a", "basic", "domain/leucine", "zipper", "transcription", "factor", "repressing", "germination", "."], ["Decreased", "GA", "synthesis", "leads", "to", "an", "increase", "in", "endogenous", "ABA", "levels", "through", "a", "stabilized", "RGL2", ",", "a", "process", "that", "may", "involve", "XERICO", ",", "a", "RING-H2", "zinc", "finger", "factor", "promoting", "ABA", "synthesis", "."], ["In", "turn", ",", "increased", "endogenous", "ABA", "synthesis", "is", "necessary", "to", "elevate", "not", "only", "ABI5", "RNA", "and", "protein", "levels", "but", "also", ",", "critically", ",", "those", "of", "RGL2", "."], ["Increased", "ABI5", "protein", "is", "ultimately", "responsible", "for", "preventing", "seed", "germination", "when", "GA", "levels", "are", "reduced", "."], ["However", ",", "overexpression", "of", "ABI5", "was", "not", "sufficient", "to", "repress", "germination", ",", "as", "ABI5", "activity", "requires", "phosphorylation", "."], ["The", "endogenous", "ABI5", "phosphorylation", "and", "inhibition", "of", "germination", "could", "be", "recapitulated", "by", "the", "addition", "of", "a", "SnRK2", "protein", "kinase", "to", "the", "ABI5", "overexpression", "line", "."], ["In", "sleepy1", "mutant", "seeds", ",", "RGL2", "overaccumulates", ";", "germination", "of", "these", "seeds", "can", "occur", "under", "conditions", "that", "produce", "low", "ABI5", "expression", "."], ["These", "data", "support", "the", "notion", "that", "ABI5", "acts", "as", "the", "final", "common", "repressor", "of", "germination", "in", "response", "to", "changes", "in", "ABA", "and", "GA", "levels", "."]], "ner": [[[7, 18, "Plant_hormone"], [0, 1, "Biochemical_process"]], [[20, 20, "Plant_hormone"], [33, 33, "Protein"], [22, 23, "Biochemical_process"], [27, 28, "Biochemical_process"], [38, 39, "Protein"], [30, 30, "Protein"]], [[46, 46, "Plant_hormone"], [51, 51, "Protein"], [54, 54, "Protein"], [58, 62, "Protein"]], [[75, 75, "Plant_hormone"], [67, 68, "Biochemical_pathway"], [87, 87, "Protein"], [95, 96, "Biochemical_pathway"], [90, 93, "Protein"], [79, 80, "Protein"]], [[103, 104, "Biochemical_pathway"], [123, 123, "Protein"], [111, 114, "Organic_compound_other"]], [[136, 136, "Plant_hormone"], [126, 127, "Protein"], [133, 134, "Biochemical_process"]], [[145, 145, "Protein"], [154, 154, "Protein"]], [[161, 162, "Biochemical_process"], [175, 177, "Protein"], [180, 182, "Multicellular_organism"]], [[185, 187, "Plant_region"], [189, 189, "Protein"], [203, 204, "Biochemical_process"]], [[226, 226, "Plant_hormone"], [228, 228, "Plant_hormone"], [212, 212, "Protein"]]], "relations": [[[7, 18, 0, 1, "interacts"]], [[20, 20, 22, 23, "activates"], [20, 20, 27, 28, "activates"], [33, 33, 22, 23, "inhibits"], [27, 28, 30, 30, "inhibits"], [27, 28, 33, 33, "inhibits"], [30, 30, 22, 23, "inhibits"]], [[46, 46, 54, 54, "activates"], [46, 46, 51, 51, "activates"]], [[67, 68, 79, 80, "interacts"], [87, 87, 95, 96, "activates"], [79, 80, 75, 75, "activates"]], [[103, 104, 111, 114, "activates"], [103, 104, 123, 123, "activates"]], [[126, 127, 133, 134, "inhibits"]], [], [[175, 177, 161, 162, "activates"]], [[189, 189, 185, 187, "is-in"]], [[212, 212, 226, 226, "interacts"], [212, 212, 228, 228, "interacts"]]]}
{"doc_key": "PMID17464219_abstract", "dataset": "pickle", "sentences": [["The", "mitogen-activated", "protein", "kinase", "(", "MAPK", ")", "signaling", "cascade", "is", "critical", "for", "regulating", "plant", "defense", "systems", "against", "various", "kinds", "of", "pathogen", "and", "environmental", "stresses", "."], ["One", "component", "of", "this", "cascade", ",", "the", "MAP", "kinase", "kinases", "(", "MAPKK", ")", ",", "has", "not", "yet", "been", "shown", "to", "be", "induced", "in", "plants", "following", "biotic", "attacks", ",", "such", "as", "those", "by", "insects", "and", "fungi", "."], ["We", "describe", "here", "a", "gene", "coding", "for", "a", "blast", "(", "Magnaporthe", "grisea)-", "and", "insect", "(", "Nilaparvata", "lugens)-responsive", "putative", "MAPK", "kinase", ",", "OmMKK1", "(", "Oryza", "minuta", "MAPKK", "1", ")", ",", "which", "was", "identified", "in", "a", "library", "of", "O.", "minuta", "expressed", "sequence", "tags", "(", "ESTs", ")", "."], ["Two", "copies", "of", "OmMKK1", "are", "present", "in", "the", "O.", "minuta", "genome", "."], ["They", "encode", "a", "predicted", "protein", "with", "molecular", "mass", "39", "kDa", "and", "pI", "of", "6.2", "."], ["Transcript", "patterns", "following", "imbibition", "of", "plant", "hormones", "such", "as", "methyl", "jasmonic", "acid", "(", "MeJA", ")", ",", "ethephone", ",", "salicylic", "acid", "(", "SA", ")", "and", "abscisic", "acid", "(", "ABA", ")", ",", "as", "well", "as", "exposure", "to", "methyl", "viologen", "(", "MV", ")", ",", "revealed", "that", "the", "expression", "of", "OmMKK1", "is", "related", "to", "defense", "response", "signaling", "pathways", "."], ["A", "comparative", "analysis", "of", "OmMKK1", "and", "its", "O.", "sativa", "ortholog", "OsMKK1", "showed", "that", "both", "were", "induced", "by", "stress-related", "hormones", "and", "biotic", "stresses", ",", "but", "that", "the", "kinetics", "of", "their", "responses", "differed", "despite", "their", "high", "amino", "acid", "sequence", "identity", "(", "96", "%", ")", "."]], "ner": [[[1, 8, "Biochemical_process"]], [[32, 34, "Protein"], [36, 36, "Protein"]], [[69, 80, "Protein"], [82, 82, "Protein"], [84, 87, "Protein"], [97, 98, "Multicellular_organism"]], [[109, 109, "DNA"], [114, 116, "DNA"]], [], [[138, 139, "Plant_hormone"], [142, 144, "Plant_hormone"], [146, 146, "Plant_hormone"], [149, 149, "Plant_hormone"], [151, 152, "Plant_hormone"], [154, 154, "Plant_hormone"], [157, 158, "Plant_hormone"], [160, 160, "Plant_hormone"], [168, 169, "Organic_compound_other"], [171, 171, "Organic_compound_other"], [179, 179, "DNA"]], [[192, 192, "DNA"], [195, 196, "Multicellular_organism"], [198, 198, "DNA"]]], "relations": [[], [], [[82, 82, 97, 98, "is-in"], [84, 87, 97, 98, "is-in"], [69, 80, 97, 98, "is-in"]], [[109, 109, 114, 116, "is-in"]], [], [], [[198, 198, 195, 196, "is-in"]]]}
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{"doc_key": "PMID26374894_abstract", "dataset": "pickle", "sentences": [["Plant", "growth", "and", "development", "are", "controlled", "by", "nine", "structurally", "distinct", "small", "molecules", "termed", "phytohormones", "."], ["Over", "the", "last", "20", "years", ",", "the", "molecular", "basis", "of", "their", "signal", "transduction", ",", "from", "receptors", "to", "transcription", "factors", ",", "has", "been", "dissected", "using", "mainly", "Arabidopsis", "thaliana", "and", "rice", "as", "model", "systems", "."], ["Phytohormones", "can", "be", "broadly", "classified", "into", "two", "distinct", "groups", "on", "the", "basis", "of", "whether", "the", "subcellular", "localization", "of", "their", "receptors", "is", "in", "the", "cytoplasm", "or", "nucleus", ",", "and", "hence", "soluble", ",", "or", "membrane-bound", ",", "and", "hence", "insoluble", "."], ["Soluble", "receptors", ",", "which", "control", "the", "responses", "to", "auxin", ",", "jasmonates", ",", "gibberellins", ",", "strigolactones", "and", "salicylic", "acid", ",", "signal", "either", "directly", "or", "indirectly", "via", "the", "destruction", "of", "regulatory", "proteins", "."], ["Responses", "to", "abscisic", "acid", "are", "primarily", "mediated", "by", "soluble", "receptors", "that", "indirectly", "regulate", "the", "phosphorylation", "of", "targeted", "proteins", "."], ["Insoluble", "receptors", ",", "which", "control", "the", "responses", "to", "cytokinins", ",", "brassinosteroids", "and", "ethylene", ",", "transduce", "their", "signal", "through", "protein", "phosphorylation", "."], ["This", "chapter", "provides", "a", "comparison", "of", "the", "different", "components", "of", "these", "signalling", "systems", ",", "and", "discusses", "the", "similarities", "and", "differences", "between", "them", "."]], "ner": [[[13, 13, "Plant_hormone"]], [[40, 41, "Multicellular_organism"], [43, 43, "Multicellular_organism"]], [[48, 48, "Plant_hormone"]], [[86, 87, "Protein"], [94, 94, "Plant_hormone"], [96, 96, "Plant_hormone"], [98, 98, "Plant_hormone"], [100, 100, "Plant_hormone"], [102, 103, "Plant_hormone"]], [[119, 120, "Plant_hormone"], [125, 126, "Protein"]], [[136, 137, "Protein"], [144, 144, "Plant_hormone"], [146, 146, "Plant_hormone"], [148, 148, "Plant_hormone"], [154, 155, "Biochemical_process"]], []], "relations": [[], [], [], [[86, 87, 94, 94, "interacts"], [86, 87, 96, 96, "interacts"], [86, 87, 98, 98, "interacts"], [86, 87, 100, 100, "interacts"], [86, 87, 102, 103, "interacts"]], [[119, 120, 125, 126, "interacts"]], [[136, 137, 144, 144, "interacts"], [136, 137, 146, 146, "interacts"], [136, 137, 148, 148, "interacts"], [136, 137, 154, 155, "activates"]], []]}
{"doc_key": "PMID25873659_abstract", "dataset": "pickle", "sentences": [["High", "temperature", "(", "HT", ")", ",", "high", "humidity", "(", "HH", ")", ",", "and", "pathogen", "infection", "often", "co-occur", "and", "negatively", "affect", "plant", "growth", "."], ["However", ",", "these", "stress", "factors", "and", "plant", "responses", "are", "generally", "studied", "in", "isolation", "."], ["The", "mechanisms", "of", "synergistic", "responses", "to", "combined", "stresses", "are", "poorly", "understood", "."], ["We", "isolated", "the", "subgroup", "IIb", "WRKY", "family", "member", "CaWRKY6", "from", "Capsicum", "annuum", "and", "performed", "quantitative", "real-time", "PCR", "analysis", "."], ["CaWRKY6", "expression", "was", "upregulated", "by", "individual", "or", "simultaneous", "treatment", "with", "HT", ",", "HH", ",", "combined", "HT", "and", "HH", "(", "HTHH", ")", ",", "and", "Ralstonia", "solanacearum", "inoculation", ",", "and", "responded", "to", "exogenous", "application", "of", "jasmonic", "acid", "(", "JA", ")", ",", "ethephon", ",", "and", "abscisic", "acid", "(", "ABA", ")", "."], ["Virus-induced", "gene", "silencing", "of", "CaWRKY6", "enhanced", "pepper", "plant", "susceptibility", "to", "R.", "solanacearum", "and", "HTHH", ",", "and", "downregulated", "the", "hypersensitive", "response", "(", "HR", ")", ",", "JA-", ",", "ethylene", "(ET)-", ",", "and", "ABA-induced", "marker", "gene", "expression", ",", "and", "thermotolerance-associated", "expression", "of", "CaHSP24", ",", "ER-small", "CaSHP", ",", "and", "Chl-small", "CaHSP", "."], ["CaWRKY6", "overexpression", "in", "pepper", "attenuated", "the", "HTHH-induced", "suppression", "of", "resistance", "to", "R.", "solanacearum", "infection", "."], ["CaWRKY6", "bound", "to", "and", "activated", "the", "CaWRKY40", "promoter", "in", "planta", ",", "which", "is", "a", "pepper", "WRKY", "that", "regulates", "heat-stress", "tolerance", "and", "R.", "solanacearum", "resistance", "."], ["CaWRKY40", "silencing", "significantly", "blocked", "HR-induced", "cell", "death", "and", "reduced", "transcriptional", "expression", "of", "CaWRKY40", "."], ["These", "data", "suggest", "that", "CaWRKY6", "is", "a", "positive", "regulator", "of", "R.", "solanacearum", "resistance", "and", "heat-stress", "tolerance", ",", "which", "occurs", "in", "part", "by", "activating", "CaWRKY40", "."]], "ner": [[], [], [], [[52, 57, "DNA"], [59, 60, "Multicellular_organism"]], [[68, 69, "Biochemical_process"], [91, 92, "Unicellular_organism"], [101, 102, "Plant_hormone"], [104, 104, "Plant_hormone"], [107, 107, "Plant_hormone"], [110, 111, "Plant_hormone"], [113, 113, "Plant_hormone"]], [[120, 120, "DNA"], [122, 123, "Multicellular_organism"], [126, 127, "Unicellular_organism"], [134, 135, "Biochemical_process"], [137, 137, "Biochemical_process"], [140, 149, "Biochemical_process"], [155, 155, "DNA"], [157, 158, "DNA"], [161, 162, "DNA"]], [[164, 165, "Biochemical_process"], [167, 167, "Multicellular_organism"], [175, 177, "Biochemical_process"]], [[179, 179, "DNA"], [185, 186, "DNA"], [193, 194, "DNA"], [200, 202, "Biochemical_process"]], [[204, 205, "Biochemical_process"], [208, 210, "Biochemical_process"], [216, 216, "DNA"]], [[222, 222, "DNA"], [228, 230, "Biochemical_process"], [241, 241, "DNA"]]], "relations": [[], [], [], [[52, 57, 59, 60, "is-in"]], [[91, 92, 68, 69, "activates"], [101, 102, 68, 69, "interacts"], [104, 104, 68, 69, "interacts"], [107, 107, 68, 69, "interacts"], [110, 111, 68, 69, "interacts"], [113, 113, 68, 69, "interacts"]], [[126, 127, 122, 123, "inhibits"]], [[164, 165, 175, 177, "inhibits"], [164, 165, 167, 167, "is-in"]], [[179, 179, 185, 186, "activates"], [185, 186, 200, 202, "interacts"]], [[204, 205, 208, 210, "inhibits"], [204, 205, 216, 216, "inhibits"]], [[222, 222, 228, 230, "activates"], [222, 222, 241, 241, "activates"]]]}
{"doc_key": "PMID31734917_abstract", "dataset": "pickle", "sentences": [["Jasmonates", "are", "essential", "engineers", "of", "plant", "defense", "responses", "against", "many", "pests", ",", "including", "herbivorous", "insects", "."], ["Herbivory", "induces", "the", "production", "of", "jasmonic", "acid", "(", "JA", ")", "and", "its", "bioactive", "conjugate", "jasmonoyl-L-isoleucine", "(", "JA-Ile", ")", ",", "which", "then", "triggers", "a", "large", "transcriptional", "reprogramming", "to", "promote", "plant", "acclimation", "."], ["The", "contribution", "of", "the", "JA", "pathway", ",", "including", "its", "components", "and", "regulators", ",", "to", "defense", "responses", "against", "insect", "herbivory", "can", "be", "evaluated", "by", "conducting", "bioassays", "with", "a", "wide", "range", "of", "host", "plants", "and", "insect", "pests", "."], ["Here", ",", "we", "describe", "a", "detailed", "and", "reproducible", "protocol", "for", "testing", "feeding", "behavior", "of", "the", "generalist", "herbivore", "Spodoptera", "littoralis", "on", "the", "model", "plant", "Arabidopsis", "thaliana", "and", "hence", "infer", "the", "contribution", "of", "JA-mediated", "plant", "defense", "responses", "to", "a", "chewing", "insect", "."]], "ner": [[[0, 0, "Plant_hormone"]], [[30, 30, "Plant_hormone"], [32, 32, "Plant_hormone"], [21, 22, "Plant_hormone"], [24, 24, "Plant_hormone"]], [[51, 52, "Biochemical_pathway"]], [[100, 101, "Multicellular_organism"], [106, 107, "Multicellular_organism"], [114, 117, "Biochemical_process"]]], "relations": [[], [], [], []]}
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{"doc_key": "PMID25919406_abstract", "dataset": "pickle", "sentences": [["During", "a", "compatible", "interaction", ",", "the", "sebacinoid", "root-associated", "fungi", "Piriformospora", "indica", "and", "Sebacina", "vermifera", "induce", "modification", "of", "root", "morphology", "and", "enhance", "shoot", "growth", "in", "Arabidopsis", "thaliana", "."], ["The", "genomic", "traits", "common", "in", "these", "two", "fungi", "were", "investigated", "and", "compared", "with", "those", "of", "other", "root-associated", "fungi", "and", "saprotrophs", "."], ["The", "transcriptional", "responses", "of", "the", "two", "sebacinoid", "fungi", "and", "of", "Arabidopsis", "roots", "to", "colonization", "at", "three", "different", "symbiotic", "stages", "were", "analyzed", "by", "custom-designed", "microarrays", "."], ["We", "identified", "key", "genomic", "features", "characteristic", "of", "sebacinoid", "fungi", ",", "such", "as", "expansions", "for", "gene", "families", "involved", "in", "hydrolytic", "activities", ",", "carbohydrate-binding", "and", "protein-protein", "interaction", "."], ["Additionally", ",", "we", "show", "that", "colonization", "of", "Arabidopsis", "correlates", "with", "the", "induction", "of", "salicylic", "acid", "catabolism", "and", "accumulation", "of", "jasmonate", "and", "glucosinolates", "(", "GSLs", ")", "."], ["Genes", "involved", "in", "root", "developmental", "processes", "were", "specifically", "induced", "by", "S.", "vermifera", "at", "later", "stages", "during", "interaction", "."], ["Using", "different", "Arabidopsis", "indole-GSLs", "mutants", "and", "measurement", "of", "secondary", "metabolites", ",", "we", "demonstrate", "the", "importance", "of", "the", "indolic", "glucosinolate", "pathway", "in", "the", "growth", "restriction", "of", "P.", "indica", "and", "S.", "vermifera", "and", "we", "identify", "indole-phytoalexins", "and", "specifically", "indole-carboxylic", "acids", "derivatives", "as", "potential", "key", "players", "in", "the", "maintenance", "of", "a", "mutualistic", "interaction", "with", "root", "endophytes", "."]], "ner": [[[9, 10, "Multicellular_organism"], [24, 25, "Multicellular_organism"], [12, 13, "Multicellular_organism"]], [], [[54, 55, "Multicellular_organism"], [58, 59, "Plant_region"]], [[80, 81, "Multicellular_organism"]], [[106, 106, "Multicellular_organism"], [112, 114, "Biochemical_process"], [118, 118, "Plant_hormone"], [120, 120, "Organic_compound_other"], [122, 122, "Organic_compound_other"]], [[135, 136, "Multicellular_organism"]], [[145, 147, "Multicellular_organism"], [168, 169, "Multicellular_organism"], [171, 172, "Multicellular_organism"], [160, 162, "Biochemical_pathway"], [176, 176, "Organic_compound_other"], [179, 181, "Organic_compound_other"]]], "relations": [[[9, 10, 24, 25, "interacts"], [12, 13, 24, 25, "interacts"]], [], [], [], [], [], [[160, 162, 168, 169, "inhibits"], [160, 162, 171, 172, "inhibits"]]]}
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{"doc_key": "PMID31125282_abstract", "dataset": "pickle", "sentences": [["Tritrophic", "interactions", "involving", "a", "biocontrol", "agent", ",", "a", "pathogen", ",", "and", "a", "plant", "have", "been", "analyzed", "predominantly", "from", "the", "perspective", "of", "the", "biocontrol", "agent", "."], ["To", "explore", "the", "adaptive", "strategies", "of", "wheat", "in", "response", "to", "beneficial", ",", "pathogenic", ",", "and", "combined", "microorganisms", ",", "we", "performed", "the", "first", "comprehensive", "transcriptomic", ",", "proteomic", ",", "and", "biochemical", "analysis", "in", "wheat", "roots", "after", "exposure", "to", "Bacillus", "velezensis", "CC09", ",", "Gaeumannomyces", "graminis", "var", ".", "tritici", ",", "and", "their", "combined", "colonization", ",", "respectively", "."], ["The", "transcriptional", "or", "translational", "programming", "of", "wheat", "roots", "inoculated", "with", "beneficial", "B.", "velezensis", "showed", "mild", "alterations", "compared", "with", "that", "of", "pathogenic", "G.", "graminis", "var", ".", "tritici", "."], ["However", ",", "the", "combination", "of", "B.", "velezensis", "and", "G.", "graminis", "var", ".", "tritici", "activated", "a", "larger", "transcriptional", "or", "translational", "program", "than", "for", "each", "single", "microorganism", ",", "although", "the", "gene", "expression", "pattern", "was", "similar", "to", "that", "of", "individual", "infection", "by", "G.", "graminis", "var", ".", "tritici", ",", "suggesting", "a", "prioritization", "of", "defense", "against", "G.", "graminis", "var", ".", "tritici", "infection", "."], ["Surprisingly", ",", "pathogen-associated", "molecular", "pattern-triggered", "immunity", "and", "effector-triggered", "immunity", "made", "wheat", "pretreated", "with", "B.", "velezensis", "more", "sensitive", "to", "subsequent", "G.", "graminis", "var", ".", "tritici", "infection", "."], ["Additionally", ",", "B.", "velezensis", "triggered", "a", "salicylic", "acid", "(SA)-dependent", "mode", "of", "induced", "systemic", "resistance", "that", "resembles", "pathogen-induced", "systemic", "acquired", "resistance", "."], ["Wheat", "plants", "mainly", "depend", "on", "SA-mediated", "resistance", ",", "and", "not", "that", "mediated", "by", "jasmonic", "acid", "(", "JA", ")", ",", "against", "the", "necrotrophic", "pathogen", "G.", "graminis", "var", ".", "tritici", "."], ["Moreover", ",", "SA-JA", "interactions", "resulted", "in", "antagonistic", "effects", "regardless", "of", "the", "type", "of", "microorganisms", "in", "wheat", "."], ["Further", "enhancement", "of", "SA-dependent", "defense", "responses", "such", "as", "lignification", "to", "the", "combined", "infection", "was", "shown", "to", "reduce", "the", "level", "of", "induced", "JA-dependent", "defense", "against", "subsequent", "infection", "with", "G.", "graminis", "var", ".", "tritici", "."], ["Altogether", ",", "our", "results", "demonstrate", "how", "the", "hexaploid", "monocot", "wheat", "responds", "to", "beneficial", "or", "pathogenic", "microorganisms", "and", "prolongs", "the", "onset", "of", "take-all", "disease", "through", "modulation", "of", "cell", "reprogramming", "and", "signaling", "events", "."]], "ner": [[[0, 1, "Biochemical_process"]], [[31, 31, "Multicellular_organism"], [56, 57, "Plant_region"], [61, 63, "Unicellular_organism"], [65, 69, "Multicellular_organism"]], [[84, 85, "Plant_region"], [89, 90, "Unicellular_organism"], [99, 103, "Multicellular_organism"]], [[110, 111, "Unicellular_organism"], [113, 117, "Multicellular_organism"], [144, 148, "Multicellular_organism"], [156, 161, "Biochemical_process"]], [[165, 168, "Biochemical_process"], [170, 171, "Biochemical_process"], [173, 173, "Multicellular_organism"], [176, 177, "Unicellular_organism"], [182, 187, "Multicellular_organism"]], [[191, 192, "Unicellular_organism"], [195, 196, "Plant_hormone"], [200, 202, "Biochemical_process"], [205, 208, "Biochemical_process"]], [[210, 211, "Multicellular_organism"], [215, 216, "Biochemical_process"], [223, 224, "Plant_hormone"], [226, 226, "Plant_hormone"], [233, 237, "Multicellular_organism"]], [[241, 242, "Biochemical_process"], [254, 254, "Multicellular_organism"]], [[259, 261, "Biochemical_process"], [277, 278, "Biochemical_process"], [283, 287, "Multicellular_organism"]], [[296, 298, "Multicellular_organism"]]], "relations": [[], [], [[84, 85, 89, 90, "interacts"], [99, 103, 84, 85, "inhibits"]], [], [[165, 168, 182, 187, "activates"], [170, 171, 182, 187, "activates"], [176, 177, 173, 173, "interacts"], [176, 177, 170, 171, "interacts"], [176, 177, 165, 168, "interacts"], [182, 187, 173, 173, "is-in"]], [[191, 192, 200, 202, "activates"], [195, 196, 200, 202, "interacts"]], [[215, 216, 233, 237, "inhibits"]], [[241, 242, 254, 254, "is-in"]], [[259, 261, 277, 278, "inhibits"], [277, 278, 283, 287, "interacts"]], []]}
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{"doc_key": "PMID28390170_abstract", "dataset": "pickle", "sentences": [["Phytohormones", ",", "such", "as", "salicylic", "acid", "(", "SA", ")", ",", "ethylene", "(", "ET", ")", "and", "jasmonic", "acid", "(", "JA", ")", ",", "play", "key", "roles", "in", "plant", "defence", "following", "pathogen", "attack", "."], ["The", "involvement", "of", "these", "hormones", "in", "susceptibility", "following", "Fusarium", "oxysporum", "(", "Fo", ")", "infection", "has", "mostly", "been", "studied", "in", "Arabidopsis", "thaliana", "."], ["However", ",", "Fo", "causes", "vascular", "wilt", "disease", "in", "a", "broad", "range", "of", "crops", ",", "including", "tomato", "(", "Solanum", "lycopersicum", ")", "."], ["Surprisingly", "little", "is", "known", "about", "the", "involvement", "of", "these", "phytohormones", "in", "the", "susceptibility", "of", "tomato", "towards", "Fo", "f.", "sp.", "lycopersici", "(", "Fol", ")", "."], ["Here", ",", "we", "investigate", "their", "involvement", "by", "the", "analysis", "of", "the", "expression", "of", "ET", ",", "JA", "and", "SA", "marker", "genes", "following", "Fol", "infection", ",", "and", "by", "bioassays", "of", "tomato", "mutants", "affected", "in", "either", "hormone", "production", "or", "perception", "."], ["Fol", "inoculation", "triggered", "the", "expression", "of", "SA", "and", "ET", "marker", "genes", ",", "showing", "the", "activation", "of", "these", "pathways", "."], ["NahG", "tomato", ",", "in", "which", "SA", "is", "degraded", ",", "became", "hypersusceptible", "to", "Fol", "infection", "and", "showed", "stronger", "disease", "symptoms", "than", "wild-type", "."], ["In", "contrast", ",", "ACD", "and", "Never", "ripe", "(", "Nr", ")", "mutants", ",", "in", "which", "ET", "biosynthesis", "and", "perception", ",", "respectively", ",", "are", "impaired", ",", "showed", "decreased", "disease", "symptoms", "and", "reduced", "fungal", "colonization", "on", "infection", "."], ["The", "susceptibility", "of", "the", "def1", "tomato", "mutant", ",", "and", "a", "prosystemin", "over-expressing", "line", ",", "in", "which", "JA", "signalling", "is", "compromised", "or", "constitutively", "activated", ",", "respectively", ",", "was", "unaltered", "."], ["Our", "results", "show", "that", "SA", "is", "a", "negative", "and", "ET", "a", "positive", "regulator", "of", "Fol", "susceptibility", "."], ["The", "SA", "and", "ET", "signalling", "pathways", "appear", "to", "act", "synergistically", ",", "as", "an", "intact", "ET", "pathway", "is", "required", "for", "the", "induction", "of", "an", "SA", "marker", "gene", ",", "and", "vice", "versa", "."]], "ner": [[[0, 0, "Plant_hormone"], [4, 5, "Plant_hormone"], [7, 7, "Plant_hormone"], [10, 10, "Plant_hormone"], [12, 12, "Plant_hormone"], [15, 16, "Plant_hormone"]], [[39, 44, "Biochemical_process"], [50, 51, "Multicellular_organism"]], [[55, 55, "Multicellular_organism"], [57, 59, "Biochemical_process"], [68, 68, "Multicellular_organism"], [70, 71, "Multicellular_organism"]], [[83, 83, "Plant_hormone"], [88, 88, "Multicellular_organism"], [90, 93, "Multicellular_organism"], [95, 95, "Multicellular_organism"]], [[111, 117, "DNA"], [119, 120, "Biochemical_process"], [126, 127, "Multicellular_organism"]], [[136, 136, "Multicellular_organism"], [142, 146, "DNA"]], [[155, 156, "Multicellular_organism"], [160, 160, "Plant_hormone"], [167, 168, "Biochemical_process"]], [[180, 187, "Multicellular_organism"], [191, 194, "Biochemical_process"]], [[216, 218, "Multicellular_organism"], [222, 224, "Multicellular_organism"], [228, 229, "Biochemical_process"]], [[245, 245, "Plant_hormone"], [250, 250, "Plant_hormone"], [255, 256, "Biochemical_process"]], [[259, 263, "Biochemical_pathway"], [272, 273, "Biochemical_pathway"], [281, 283, "DNA"]]], "relations": [[], [], [[55, 55, 57, 59, "produces"], [55, 55, 68, 68, "interacts"], [55, 55, 70, 71, "interacts"]], [[90, 93, 88, 88, "inhibits"], [95, 95, 88, 88, "inhibits"]], [], [[136, 136, 142, 146, "activates"]], [[167, 168, 155, 156, "inhibits"]], [], [], [[245, 245, 255, 256, "activates"], [250, 250, 255, 256, "inhibits"]], [[272, 273, 281, 283, "activates"], [281, 283, 272, 273, "activates"]]]}
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{"doc_key": "PMID30092129_abstract", "dataset": "pickle", "sentences": [["Mitogen-activated", "protein", "kinases", "(", "MAPKs", ")", "play", "an", "important", "role", "in", "defense", "responses", "to", "biotic", "and", "abiotic", "stresses", "."], ["In", "order", "to", "investigate", "the", "role", "of", "SlMAPK3", "in", "tomato", "plant", "resistance", "to", "Botrytis", "cinerea", ",", "two", "lines", "of", "slmapk3", "mutants", "and", "wild-type", "(", "WT", ")", "tomato", "plants", "were", "used", "."], ["The", "results", "showed", "that", "slmapk3", "mutants", "were", "more", "susceptible", "to", "B.", "cinerea", "and", "that", "knockout", "of", "SlMAPK3", "reduced", "the", "activities", "of", "defense", "enzymes", "and", "enhanced", "the", "accumulation", "of", "reactive", "oxygen", "species", "(", "ROS", ")", "."], ["Furthermore", ",", "we", "detected", "the", "expressions", "of", "salicylic", "acid", "(", "SA", ")", "and", "jasmonic", "acid", "(", "JA", ")", "signaling-related", "genes", "and", "found", "that", "knockout", "of", "SlMAPK3", "enhanced", "the", "expressions", "of", "SlPR1", ",", "SlPAD4", "and", "SlEDS1", ",", "whereas", "\u00a0", "reduced", "the", "expressions", "of", "SlLoxC", ",", "SlPI", "I", "\u00a0", "and", "SlPI", "II", "and", "enhanced", "the", "expressions", "of", "SlJAZ1", "and", "SlMYC2", "."], ["We", "postulate", "that", "SlMAPK3", "plays", "a", "positive", "role", "in", "tomato", "plant", "resistance", "to", "B.", "cinerea", "through", "regulating", "ROS", "accumulation", "and", "SA", "and", "JA", "defense", "signaling", "pathways", "."]], "ner": [[[0, 2, "Protein"], [4, 4, "Protein"]], [[26, 26, "Protein"], [32, 33, "Multicellular_organism"], [38, 39, "Multicellular_organism"], [45, 46, "Multicellular_organism"], [28, 30, "Biochemical_process"]], [[60, 61, "Multicellular_organism"], [66, 66, "DNA"], [78, 80, "Inorganic_compound_other"], [82, 82, "Inorganic_compound_other"], [54, 55, "Multicellular_organism"]], [[92, 104, "DNA"], [110, 110, "DNA"], [115, 115, "DNA"], [117, 117, "DNA"], [119, 119, "DNA"], [127, 127, "DNA"], [133, 134, "DNA"], [129, 130, "DNA"], [140, 140, "DNA"], [142, 142, "DNA"]], [[147, 147, "DNA"], [157, 158, "Multicellular_organism"], [161, 162, "Biochemical_process"], [164, 169, "Biochemical_pathway"], [153, 155, "Biochemical_process"]]], "relations": [[], [[28, 30, 32, 33, "inhibits"]], [[60, 61, 54, 55, "inhibits"], [66, 66, 78, 80, "activates"], [66, 66, 82, 82, "activates"]], [[110, 110, 115, 115, "activates"], [110, 110, 117, 117, "activates"], [110, 110, 119, 119, "activates"], [110, 110, 142, 142, "activates"], [110, 110, 140, 140, "activates"], [110, 110, 133, 134, "inhibits"], [110, 110, 129, 130, "inhibits"], [110, 110, 127, 127, "inhibits"]], [[153, 155, 157, 158, "inhibits"], [147, 147, 153, 155, "activates"], [161, 162, 147, 147, "interacts"], [164, 169, 147, 147, "interacts"]]]}
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{"doc_key": "PMID32196677_abstract", "dataset": "pickle", "sentences": [["Multiple", "isoforms", "of", "chitinases", "participate", "in", "plant", "defense", "against", "outside", "invaders", "."], ["However", ",", "the", "functions", "of", "hydrolase", "family", "19", "(", "GH19", ")", "chitinases", "on", "pest", "control", "remain", "largely", "unknown", "."], ["Here", "we", "reported", "the", "isolation", "and", "functional", "analysis", "of", "a", "gene", "CsChi19", ",", "which", "encodes", "a", "GH19", "endochitinase", "protein", "of", "332", "amino", "acid", "residues", "from", "tea", "plant", "(", "Camellia", "sinensis", ")", "."], ["CsChi19", "expression", "levels", "were", "upregulated", "in", "response", "to", "mechanical", "wounding", ",", "infestation", "by", "two", "important", "pests", ":", "the", "tea", "geometrid", "Ectropis", "grisescens", "and", "the", "tea", "green", "leafhopper", "Empoasca", "(", "Matsumurasca", ")", "onukii", ",", "a", "fungal", "pathogen", "Colletotrichum", "fructicola", ",", "and", "treatment", "with", "two", "phytohormones", ":", "jasmonic", "acid", "(", "JA", ")", "and", "salicylic", "acid", "."], ["CsChi19", "was", "heterologously", "expressed", "in", "Escherichia", "coli", ",", "and", "its", "catalytic", "function", "was", "further", "elucidated", "."], ["The", "protein", "could", "hydrolyze", "colloidal", "chitin", ",", "and", "the", "optimum", "temperature", "and", "pH", "for", "its", "activity", "was", "40", "\u00b0", "C", "and", "pH", "5.0", "."], ["CsChi19", "were", "found", "to", "be", "toxic", "to", "tea", "pests", "when", "they", "were", "fed", "on", "artificial", "diets", "containing", "this", "protein", "."], ["Interestingly", ",", "the", "regurgitant", "derived", "from", "E.", "grisescens", "fed", "with", "artificial", "diets", "containing", "CsChi19", "protein", "induced", "stronger", "expression", "of", "CsMPK3", ",", "more", "JA", "burst", ",", "more", "accumulation", "of", "defense-related", "secondary", "metabolites", ",", "and", "more", "emission", "of", "volatiles", "than", "the", "regurgitant", "derived", "from", "E.", "grisescens", "fed", "only", "with", "artificial", "diets", "."], ["Our", "results", "provide", "first", "evidence", "that", "CsChi19", "is", "involved", "in", "mediating", "a", "novel", "defense", "mechanism", "of", "tea", "plant", "through", "altering", "the", "composition", "of", "the", "regurgitant", "."]], "ner": [[[3, 3, "Protein"]], [[17, 23, "Protein"]], [[42, 42, "DNA"], [47, 49, "Protein"], [56, 57, "Multicellular_organism"], [59, 60, "Multicellular_organism"]], [[63, 64, "Biochemical_process"], [83, 84, "Multicellular_organism"], [81, 82, "Multicellular_organism"], [87, 89, "Multicellular_organism"], [90, 94, "Multicellular_organism"], [99, 100, "Multicellular_organism"], [106, 106, "Plant_hormone"], [108, 109, "Plant_hormone"], [111, 111, "Plant_hormone"], [114, 115, "Plant_hormone"]], [[117, 117, "DNA"], [122, 123, "Unicellular_organism"]], [[137, 138, "Organic_compound_other"]], [[157, 157, "DNA"], [164, 165, "Multicellular_organism"]], [[183, 184, "Multicellular_organism"], [190, 191, "Protein"], [196, 196, "DNA"], [199, 200, "Biochemical_process"], [219, 220, "Multicellular_organism"]], [[233, 233, "DNA"], [243, 244, "Multicellular_organism"]]], "relations": [[], [], [[42, 42, 47, 49, "produces"], [47, 49, 56, 57, "is-in"], [47, 49, 59, 60, "is-in"]], [[81, 82, 63, 64, "activates"], [83, 84, 63, 64, "activates"], [87, 89, 63, 64, "activates"], [90, 94, 63, 64, "activates"], [99, 100, 63, 64, "activates"], [108, 109, 63, 64, "activates"], [111, 111, 63, 64, "activates"], [114, 115, 63, 64, "activates"]], [], [], [[157, 157, 164, 165, "inhibits"]], [[190, 191, 196, 196, "activates"], [190, 191, 199, 200, "activates"], [183, 184, 196, 196, "activates"], [183, 184, 199, 200, "activates"], [183, 184, 190, 191, "interacts"]], []]}
{"doc_key": "PMID16661216_abstract", "dataset": "pickle", "sentences": [["Suspension", "cultures", "were", "incubated", "in", "the", "presence", "and", "absence", "of", "gibberellic", "acid", "(", "GA(3", ")", ")", "in", "an", "attempt", "to", "define", "a", "new", "experimental", "system", "for", "study", "of", "the", "molecular", "action", "of", "gibberellins", "upon", "growth", "."], ["Unlike", "many", "suspension", "cultures", ",", "an", "auxin-independent", "green", "clone", "from", "spinach", "(", "Spinacia", "oleracea", "L.", ")", "and", "an", "auxin-dependent", "line", "of", "\"", "Paul", "'s", "Scarlet", "\"", "rose", "(", "Rosa", "sp.", ")", "were", "promoted", "in", "expansion", "growth", "by", "GA(3", ")", "at", "10(-11", ")", "to", "10(-6", ")", "molar", "."], ["In", "Rosa", "the", "cells", "also", "elongated", "upon", "GA(3", ")", "treatment", "whereas", "in", "Spinacia", "they", "remained", "isodiametric", "."], ["Attempts", "were", "made", "to", "intensify", "the", "response", "."], ["The", "effect", "of", "GA(3", ")", "in", "Spinacia", "was", "stronger", "when", "gas", "exchange", "between", "the", "culture", "and", "the", "laboratory", "air", "was", "facilitated", "."], ["The", "response", "of", "Rosa", "was", "dependent", "on", "the", "presence", "of", "a", "cytokinin", ",", "although", "this", "culture", "did", "not", "require", "exogenous", "cytokinin", "for", "serial", "subculture", "."], ["GA(3", ")", "antagonized", "the", "growth", "retardant", "AMO-1618", "in", "Rosa", "but", "not", "in", "Spinacia", "."], ["In", "general", ",", "conditions", "that", "enhanced", "growth", "also", "rendered", "GA(3", ")", "a", "more", "effective", "promoter", ";", "conversely", ",", "GA(3", ")", "tended", "to", "become", "inhibitory", "under", "conditions", "that", "permitted", "only", "slow", "growth", "."]], "ner": [[[10, 11, "Plant_hormone"], [13, 14, "Plant_hormone"], [32, 32, "Plant_hormone"]], [[73, 74, "Plant_hormone"], [48, 50, "Multicellular_organism"], [57, 62, "Multicellular_organism"], [64, 65, "Multicellular_organism"], [46, 46, "Multicellular_organism"], [42, 44, "Multicellular_organism"]], [[90, 91, "Plant_hormone"], [95, 95, "Multicellular_organism"], [84, 84, "Multicellular_organism"]], [], [[111, 112, "Plant_hormone"], [114, 114, "Multicellular_organism"]], [[133, 133, "Multicellular_organism"], [141, 141, "Plant_hormone"], [150, 150, "Plant_hormone"]], [[155, 156, "Plant_hormone"], [161, 161, "Organic_compound_other"], [163, 163, "Multicellular_organism"], [167, 167, "Multicellular_organism"]], [[178, 179, "Plant_hormone"], [187, 188, "Plant_hormone"]]], "relations": [[], [], [], [], [], [], [[155, 156, 161, 161, "inhibits"], [155, 156, 163, 163, "is-in"]], []]}
{"doc_key": "PMID16663540_abstract", "dataset": "pickle", "sentences": [["Abscisic", "acid", "(", "ABA", ")", ",", "auxins", ",", "cytokinins", ",", "gibberellic", "acid", ",", "alone", "or", "in", "combination", "were", "tested", "for", "their", "effects", "on", "short-term", "sucrose", "uptake", "in", "sugar", "beet", "(", "Beta", "vulgaris", "cv", "USH-20", ")", "roots", "."], ["The", "effect", "of", "ABA", "on", "active", "sucrose", "uptake", "varied", "from", "no", "effect", "to", "the", "more", "generally", "observed", "1.4-to", "3.0-fold", "stimulation", "."], ["A", "racemic", "mixture", "of", "ABA", "and", "its", "trans", "isomer", "were", "more", "stimulatory", "than", "ABA", "alone", "."], ["Pretreating", "and/or", "simultaneously", "treating", "the", "tissue", "with", "K(+", ")", "or", "IAA", "prevented", "the", "ABA", "response", "while", "cytokinins", "and", "gibberellic", "acid", "did", "not", "."], ["While", "the", "variable", "sensitivities", "of", "beet", "root", "to", "ABA", "may", "somehow", "be", "related", "to", "the", "auxin", "and", "alkali", "cation", "status", "of", "the", "tissue", ",", "tissue", "sensitivity", "to", "ABA", "was", "not", "correlated", "with", "ABA", "uptake", ",", "accumulation", ",", "or", "metabolic", "patterns", "."], ["In", "contrast", "to", "ABA", ",", "indoleacetic", "acid", "(", "IAA", ")", "and", "other", "auxins", "strongly", "inhibited", "active", "sucrose", "uptake", "in", "beet", "roots", "."], ["Cytokinins", "enhanced", "the", "auxin-induced", "inhibition", "of", "sucrose", "uptake", "but", "ABA", "and", "gibberellic", "acid", "did", "not", "modify", "or", "counteract", "the", "auxin", "effect", "."], ["Trans-zeatin", ",", "benzyladenine", ",", "kinetin", ",", "and", "gibberellins", "had", "no", "effect", "on", "active", "sucrose", "uptake", "."], ["None", "of", "the", "hormones", "or", "hormone", "mixtures", "tested", "had", "any", "significant", "effect", "on", "passive", "sucrose", "uptake", "."], ["The", "effects", "of", "IAA", "and", "ABA", "on", "sucrose", "uptake", "were", "detectable", "within", "1", "h", "suggesting", "a", "rather", "close", "relationship", "between", "the", "physiological", "activities", "of", "IAA", "and", "ABA", "and", "the", "operation", "of", "the", "active", "transport", "system", "."]], "ner": [[[0, 1, "Plant_hormone"], [3, 3, "Plant_hormone"], [6, 6, "Plant_hormone"], [10, 11, "Plant_hormone"], [8, 8, "Plant_hormone"], [27, 35, "Plant_region"], [24, 25, "Biochemical_process"]], [[40, 40, "Plant_hormone"], [42, 44, "Biochemical_process"]], [[62, 62, "Plant_hormone"], [71, 71, "Plant_hormone"]], [[92, 93, "Plant_hormone"], [84, 84, "Plant_hormone"], [81, 82, "Element"], [87, 88, "Biochemical_pathway"], [90, 90, "Plant_hormone"]], [[124, 124, "Plant_hormone"], [105, 105, "Plant_hormone"], [102, 103, "Plant_region"], [112, 112, "Plant_hormone"], [114, 115, "Element"], [129, 130, "Biochemical_process"]], [[143, 144, "Plant_hormone"], [146, 146, "Plant_hormone"], [141, 141, "Plant_hormone"], [157, 158, "Plant_region"], [150, 150, "Plant_hormone"], [153, 155, "Biochemical_process"]], [[169, 169, "Plant_hormone"], [171, 172, "Plant_hormone"], [163, 164, "Biochemical_process"], [179, 179, "Plant_hormone"], [160, 160, "Plant_hormone"], [166, 167, "Biochemical_process"]], [[182, 182, "Plant_hormone"], [186, 186, "Plant_hormone"], [184, 184, "Organic_compound_other"], [189, 189, "Plant_hormone"], [194, 196, "Biochemical_process"]], [[211, 213, "Biochemical_process"]], [[241, 241, "Plant_hormone"], [239, 239, "Plant_hormone"], [218, 218, "Plant_hormone"], [220, 220, "Plant_hormone"], [222, 223, "Biochemical_process"]]], "relations": [[[24, 25, 27, 35, "is-in"]], [[40, 40, 42, 44, "interacts"]], [], [[84, 84, 87, 88, "inhibits"], [81, 82, 87, 88, "inhibits"]], [], [[143, 144, 153, 155, "inhibits"], [146, 146, 153, 155, "inhibits"], [150, 150, 153, 155, "inhibits"], [153, 155, 157, 158, "is-in"]], [[160, 160, 163, 164, "activates"], [163, 164, 166, 167, "inhibits"]], [], [], [[218, 218, 222, 223, "interacts"], [220, 220, 222, 223, "interacts"]]]}
{"doc_key": "PMID28001315_abstract", "dataset": "pickle", "sentences": [["Artemisinin", "is", "a", "type", "of", "sesquiterpene", "lactone", "well", "known", "as", "an", "antimalarial", "drug", ",", "and", "is", "specifically", "produced", "in", "glandular", "trichomes", "of", "Artemisia", "annua", "."], ["However", ",", "the", "regulatory", "network", "for", "the", "artemisinin", "biosynthetic", "pathway", "remains", "poorly", "understood", "."], ["Exploration", "of", "trichome-specific", "transcription", "factors", "would", "facilitate", "the", "elucidation", "of", "regulatory", "mechanism", "of", "artemisinin", "biosynthesis", "."], ["The", "WRKY", "transcription", "factor", "GLANDULAR", "TRICHOME-SPECIFIC", "WRKY", "1", "(", "AaGSW1", ")", "was", "cloned", "and", "analysed", "in", "A.", "\u00a0", "annua", "."], ["AaGSW1", "exhibited", "similar", "expression", "patterns", "to", "the", "trichome-specific", "genes", "of", "the", "artemisinin", "biosynthetic", "pathway", "and", "AP2/ERF", "transcription", "factor", "AaORA", "."], ["A", "\u03b2-glucuronidase", "(", "GUS", ")", "staining", "assay", "further", "demonstrated", "that", "AaGSW1", "is", "a", "glandular", "trichome-specific", "transcription", "factor", "."], ["AaGSW1", "positively", "regulates", "CYP71AV1", "and", "AaORA", "expression", "by", "directly", "binding", "to", "the", "W-box", "motifs", "in", "their", "promoters", "."], ["Overexpression", "of", "AaGSW1", "in", "A.", "\u00a0", "annua", "significantly", "improves", "artemisinin", "and", "dihydroartemisinic", "acid", "contents", ";", "moreover", ",", "AaGSW1", "can", "be", "directly", "regulated", "by", "AaMYC2", "and", "AabZIP1", ",", "which", "are", "positive", "regulators", "of", "jasmonate", "(JA)-", "and", "abscisic", "acid", "(ABA)-mediated", "artemisinin", "biosynthetic", "pathways", ",", "respectively", "."], ["These", "results", "demonstrate", "that", "AaGSW1", "is", "a", "glandular", "trichome-specific", "WRKY", "transcription", "factor", "and", "a", "positive", "regulator", "in", "the", "artemisinin", "biosynthetic", "pathway", "."], ["Moreover", ",", "we", "propose", "that", "two", "trifurcate", "feed-forward", "pathways", "involving", "AaGSW1", ",", "CYP71AV1", "and", "AaMYC2/AabZIP1", "function", "in", "the", "JA/ABA", "response", "in", "A.", "\u00a0", "annua", "."]], "ner": [[[0, 0, "Organic_compound_other"], [5, 6, "Organic_compound_other"], [22, 23, "Multicellular_organism"]], [[32, 34, "Biochemical_pathway"]], [[52, 53, "Biochemical_pathway"], [41, 43, "Protein"]], [[56, 62, "Protein"], [64, 64, "Protein"]], [[86, 88, "Biochemical_pathway"], [75, 75, "Protein"], [82, 83, "DNA"], [90, 93, "Protein"]], [[105, 105, "Protein"], [108, 111, "Protein"]], [[113, 113, "Protein"], [116, 119, "Biochemical_process"], [125, 126, "DNA"]], [[140, 140, "Organic_compound_other"], [142, 143, "Organic_compound_other"], [163, 171, "Biochemical_pathway"], [133, 133, "Protein"], [148, 148, "Protein"], [154, 154, "Protein"], [156, 156, "Protein"]], [[193, 195, "Biochemical_pathway"], [179, 179, "Protein"], [182, 186, "Protein"]], [[207, 207, "Protein"], [209, 209, "Protein"], [211, 211, "Protein"], [215, 216, "Biochemical_process"]]], "relations": [[[22, 23, 0, 0, "produces"]], [], [], [], [], [], [[113, 113, 116, 119, "activates"], [125, 126, 113, 113, "interacts"]], [[133, 133, 140, 140, "activates"], [133, 133, 142, 143, "activates"], [148, 148, 154, 154, "interacts"], [148, 148, 156, 156, "interacts"], [156, 156, 163, 171, "activates"], [154, 154, 163, 171, "activates"]], [[179, 179, 193, 195, "activates"]], [[207, 207, 215, 216, "interacts"], [209, 209, 215, 216, "interacts"], [211, 211, 215, 216, "interacts"]]]}
{"doc_key": "PMID29464725_abstract", "dataset": "pickle", "sentences": [["Gibberellin", "(", "GA", ")", "regulates", "various", "plant", "growth", "and", "developmental", "processes", ",", "but", "its", "role", "in", "pathogen", "attack", ",", "and", "especially", "nematode-plant", "interactions", ",", "still", "remains", "to", "be", "elucidated", "."], ["An", "in-depth", "characterization", "of", "the", "role", "of", "GA", "in", "nematode", "infection", "was", "conducted", "using", "mutant", "lines", "of", "rice", ",", "chemical", "inhibitors", ",", "and", "phytohormone", "measurements", "."], ["Our", "results", "showed", "that", "GA", "influences", "rice-Meloidogyne", "graminicola", "interactions", "in", "a", "concentration-dependent", "manner", "."], ["Foliar", "spray", "of", "plants", "with", "a", "low", "concentration", "of", "gibberellic", "acid", "enhanced", "nematode", "infection", "."], ["Biosynthetic", "and", "signaling", "mutants", "confirmed", "the", "importance", "of", "gibberellin", "for", "rice", "susceptibility", "to", "M.", "\u00a0", "graminicola", "infection", "."], ["Our", "study", "also", "demonstrates", "that", "GA", "signaling", "suppresses", "jasmonate", "(JA)-mediated", "defense", "against", "M.", "\u00a0", "graminicola", ",", "and", "likewise", "the", "JA-induced", "defense", "against", "M.", "\u00a0", "graminicola", "requires", "SLENDER", "RICE1", "(SLR1)-mediated", "repression", "of", "the", "GA", "pathway", "."], ["In", "contrast", "to", "observations", "from", "other", "plant-pathogen", "interactions", ",", "GA", "plays", "a", "dominant", "role", "over", "JA", "in", "determining", "susceptibility", "to", "M.", "\u00a0", "graminicola", "in", "rice", "."], ["This", "GA-induced", "nematode", "susceptibility", "was", "largely", "independent", "of", "auxin", "biosynthesis", ",", "but", "relied", "on", "auxin", "transport", "."], ["In", "conclusion", ",", "we", "showed", "that", "GA-JA", "antagonistic", "crosstalk", "is", "at", "the", "forefront", "of", "the", "interaction", "between", "rice", "and", "M.", "\u00a0", "graminicola", ",", "and", "SLR1", "plays", "a", "central", "role", "in", "the", "JA-mediated", "defense", "response", "in", "rice", "against", "this", "nematode", "."]], "ner": [[[0, 0, "Plant_hormone"], [2, 2, "Plant_hormone"], [21, 22, "Biochemical_process"]], [[37, 37, "Plant_hormone"], [47, 47, "Multicellular_organism"], [53, 53, "Plant_hormone"], [39, 40, "Biochemical_process"]], [[60, 60, "Plant_hormone"], [62, 64, "Biochemical_process"]], [[79, 80, "Plant_hormone"], [82, 83, "Biochemical_process"]], [[93, 93, "Plant_hormone"], [95, 96, "Biochemical_process"]], [[108, 109, "Biochemical_process"], [111, 113, "Biochemical_process"], [122, 123, "Biochemical_process"], [129, 132, "Biochemical_process"], [135, 136, "Biochemical_pathway"]], [[147, 147, "Plant_hormone"], [153, 153, "Plant_hormone"], [162, 162, "Multicellular_organism"]], [[165, 167, "Biochemical_process"], [172, 173, "Biochemical_pathway"], [178, 179, "Biochemical_process"]], [[187, 189, "Biochemical_process"], [198, 198, "Multicellular_organism"], [212, 214, "Biochemical_process"], [216, 216, "Multicellular_organism"], [219, 219, "Multicellular_organism"], [205, 205, "Protein"]]], "relations": [[], [], [[60, 60, 62, 64, "interacts"]], [[79, 80, 82, 83, "activates"]], [[93, 93, 95, 96, "interacts"]], [[108, 109, 111, 113, "inhibits"], [129, 132, 135, 136, "inhibits"], [129, 132, 122, 123, "interacts"]], [[147, 147, 153, 153, "interacts"], [147, 147, 162, 162, "is-in"]], [[165, 167, 178, 179, "interacts"]], [[187, 189, 198, 198, "interacts"], [212, 214, 216, 216, "is-in"], [212, 214, 219, 219, "interacts"], [205, 205, 212, 214, "is-in"]]]}
{"doc_key": "PMID19516980_abstract", "dataset": "pickle", "sentences": [["Many", "induced", "responses", "in", "plants", "are", "systemic", "."], ["Therefore", ",", "root-induced", "responses", "may", "alter", "leaf", "quality", "for", "shoot", "herbivores", "."], ["Previously", ",", "we", "found", "that", "root", "and", "shoot", "application", "of", "jasmonic", "acid", "(", "JA", ")", "to", "feral", "Brassica", "oleracea", "both", "induced", "glucosinolates", "in", "the", "leaves", "."], ["However", ",", "the", "types", "of", "glucosinolates", "that", "increased", "in", "root-", "and", "shoot", "induced", "plants", "were", "different", "."], ["Here", "we", "analyse", "whether", "primary", "metabolites", ",", "such", "as", "sugars", "and", "amino", "acids", ",", "are", "also", "differentially", "affected", "."], ["Moreover", ",", "we", "test", "whether", "chemical", "differences", "in", "root-", "and", "shoot-induced", "plants", "differentially", "affect", "growth", "of", "the", "generalist", "Mamestra", "brassicae", "and", "the", "specialist", "Pieris", "rapae", "."], ["Comprehensive", "analysis", "of", "glucosinolates", ",", "amino", "acid", "and", "sugars", "with", "principal", "component", "analysis", "revealed", "that", "leaf", "chemical", "profiles", "were", "affected", "both", "by", "JA", "application", "and", "by", "the", "organ", "that", "was", "induced", "."], ["Shoot-induction", "increased", "indole", "glucosinolates", ",", "whereas", "root-induction", "induced", "aliphatic", "glucosinolates", "in", "the", "leaves", "."], ["Leaves", "of", "shoot-induced", "plants", "had", "lower", "total", "sugar", "and", "total", "amino", "acid", "levels", ",", "whereas", "in", "root-induced", "plants", "only", "total", "sugar", "levels", "were", "significantly", "decreased", "."], ["(Iso)leucine", "responded", "significantly", "different", "from", "the", "general", "trend", ",", "which", "allowed", "us", "to", "discuss", "the", "potential", "role", "of", "Myb", "transcription", "factors", "which", "are", "coordinating", "JA-induced", "glucosinolate", "and", "amino", "acid", "responses", "in", "Arabidopsis", "thaliana", "."], ["Both", "M.", "brassicae", "and", "P.", "rapae", "grew", "the", "slowest", "on", "leaves", "of", "shoot-induced", "plants", "."], ["M.", "brassicae", "growth", "and", "survival", "was", "also", "reduced", "on", "root-induced", "plants", ",", "whereas", "P.", "rapae", "growth", "on", "these", "plants", "was", "similar", "to", "that", "on", "controls", "."], ["Specialist", "and", "generalist", "herbivores", "thus", "are", "differentially", "affected", "by", "the", "chemical", "changes", "after", "root", "and", "shoot-JA", "application", "."]], "ner": [[], [], [[30, 31, "Plant_hormone"], [33, 33, "Plant_hormone"], [36, 38, "Multicellular_organism"], [41, 41, "Organic_compound_other"]], [[51, 51, "Organic_compound_other"]], [], [[100, 101, "Multicellular_organism"], [105, 106, "Multicellular_organism"]], [[111, 111, "Organic_compound_other"], [130, 130, "Plant_hormone"]], [[142, 143, "Organic_compound_other"], [148, 149, "Organic_compound_other"]], [], [[180, 180, "Amino_acid_monomer"], [198, 200, "Protein"], [204, 209, "Biochemical_process"], [211, 212, "Multicellular_organism"]], [[215, 216, "Multicellular_organism"], [218, 219, "Multicellular_organism"]], [[229, 230, "Multicellular_organism"], [242, 243, "Multicellular_organism"]], []], "relations": [[], [], [[30, 31, 41, 41, "activates"], [33, 33, 41, 41, "activates"]], [], [], [], [], [], [], [[198, 200, 204, 209, "interacts"], [198, 200, 211, 212, "is-in"]], [], [], []]}
{"doc_key": "PMID22442409_abstract", "dataset": "pickle", "sentences": [["The", "phloem", "plays", "a", "crucial", "role", "in", "assimilate", "and", "nutrient", "transport", ",", "pathogen", "response", ",", "and", "plant", "growth", "and", "development", "."], ["Yet", ",", "few", "species", "have", "yielded", "pure", "phloem", "exudate", "and", ",", "if", "proteins", "need", "to", "be", "analysed", ",", "those", "species", "may", "not", "have", "sequenced", "genomes", ",", "making", "identification", "difficult", "."], ["The", "enrichment", "of", "Arabidopsis", "thaliana", "phloem", "exudate", "in", "amounts", "large", "enough", "to", "allow", "for", "metabolite", "and", "protein", "analysis", "is", "described", "."], ["Using", "this", "method", ",", "it", "was", "possible", "to", "identify", "65", "proteins", "present", "in", "the", "Arabidopsis", "phloem", "exudate", "."], ["The", "majority", "of", "these", "proteins", "could", "be", "grouped", "by", "response", "to", "pathogens", ",", "stress", ",", "or", "hormones", ",", "carbon", "metabolism", ",", "protein", "interaction", ",", "modification", ",", "and", "turnover", ",", "and", "transcription", "factors", "."], ["It", "was", "also", "possible", "to", "detect", "11", "proteins", "that", "play", "a", "role", "in", "lipid/fatty", "acid", "metabolism", "(", "aspartic", "protease", ",", "putative", "3-\u03b2-hydroxysteroid", "dehydrogenase", ",", "UDP-sulphoquinovose", "synthase/SQD1", ",", "lipase", ",", "PIG-P-like", "protein", ":", "phosphatidylinositol-N-acetylglucosaminyltransferase", ")", ",", "storage", "(", "glycine-rich", "protein", ")", ",", "binding", "(", "annexin", ",", "lipid-associated", "family", "protein", ",", "GRP17/oleosin", ")", ",", "and/or", "signalling", "(", "annexin", ",", "putative", "lipase", ",", "PIG-P-like", "protein", ")", "."], ["Along", "with", "putative", "lipid-binding", "proteins", ",", "several", "lipids", "and", "fatty", "acids", "could", "be", "identified", "."], ["Only", "a", "few", "examples", "exist", "of", "lipids", "(", "jasmonic", "acid", ",", "oxylipins", ")", "or", "lipid-binding", "proteins", "(", "DIR1", ",", "acyl-CoA-binding", "protein", ")", "in", "the", "phloem", "."], ["Finding", "hydrophobic", "compounds", "in", "an", "aqueous", "environment", "is", "not", "without", "precedence", "in", "biological", "systems", ":", "human", "blood", "contains", "a", "variety", "of", "lipids", ",", "many", "of", "which", "play", "a", "significant", "role", "in", "human", "health", "."], ["In", "blood", ",", "lipids", "are", "transported", "while", "bound", "to", "proteins", "."], ["The", "present", "findings", "of", "lipids", "and", "lipid-binding", "proteins", "in", "phloem", "exudates", "suggest", "that", "a", "similar", "long-distance", "lipid", "signalling", "exists", "in", "plants", "and", "may", "play", "an", "important", "role", "in", "plant", "growth", "and", "development", "."]], "ner": [[], [], [[54, 57, "Organic_compound_other"]], [[86, 88, "Organic_compound_other"]], [[108, 109, "Biochemical_process"]], [[140, 141, "Protein"], [143, 145, "Protein"], [150, 150, "Protein"], [160, 161, "Protein"], [166, 166, "Protein"], [168, 170, "Protein"], [178, 178, "Protein"], [180, 181, "Protein"], [183, 184, "Protein"], [136, 138, "Biochemical_process"], [152, 153, "Protein"], [155, 155, "Protein"]], [[189, 191, "Protein"], [196, 197, "Organic_compound_other"]], [[210, 211, "Plant_hormone"], [213, 213, "Organic_compound_other"], [219, 219, "Protein"], [221, 222, "Protein"], [216, 217, "Protein"]], [[243, 244, "Tissue"], [259, 260, "Biochemical_process"]], [], [[279, 280, "Protein"], [288, 290, "Biochemical_process"]]], "relations": [[], [], [], [], [], [[140, 141, 136, 138, "is-in"], [143, 145, 136, 138, "is-in"], [150, 150, 136, 138, "is-in"], [152, 153, 136, 138, "is-in"], [155, 155, 136, 138, "is-in"]], [], [], [], [], []]}
{"doc_key": "PMID33232332_abstract", "dataset": "pickle", "sentences": [["Plant", "grafting", "is", "a", "sequential", "wound", "healing", "process", "."], ["However", ",", "whether", "wounding", "induces", "a", "different", "jasmonic", "acid", "(", "JA", ")", "response", "within", "half", "a", "day", "(", "12", "h", ")", "after", "grafting", "or", "non-grafting", "remains", "unclear", "."], ["Using", "the", "tomato", "hypocotyl", "grafting", "method", ",", "we", "show", "that", "grafting", "alleviates", "the", "asymmetrical", "accumulation", "of", "JA", "and", "jasmonic", "acid", "isoleucine", "conjugate", "(", "JA-Ile", ")", "in", "scion", "and", "rootstock", "caused", "by", "wounding", ",", "and", "from", "2", "h", "after", "tomato", "micrografting", ",", "grafting", "obviously", "restored", "the", "level", "of", "JA-Ile", "in", "the", "scion", "and", "rootstock", "."], ["Meanwhile", ",", "five", "JA-related", "genes", ",", "SlLOX11", ",", "SlAOS", ",", "SlCOI1", ",", "SlLAPA", "and", "SlJA2L", ",", "are", "detected", "and", "show", "significant", "changes", "in", "transcriptional", "expression", "patterns", "within", "12", "h", "of", "grafting", ",", "from", "asymmetrical", "to", "symmetrical", ",", "when", "the", "expression", "of", "30", "JA-", "and", "defense-related", "genes", "were", "analyzed", "."], ["The", "results", "indicated", "that", "grafting", "alleviates", "the", "asymmetrical", "JA", "and", "defense", "response", "between", "scion", "and", "rootstock", "of", "the", "tomato", "hypocotyl", "within", "12", "h", "as", "induced", "by", "wounding", "."], ["Moreover", ",", "we", "demonstrate", "that", "in", "the", "very", "early", "hours", "after", "grafting", ",", "JA-related", "genes", "may", "be", "involved", "in", "a", "molecular", "mechanism", "that", "changes", "asymmetrical", "expression", "as", "induced", "by", "wounding", "between", "scion", "and", "rootstock", ",", "thereby", "promoting", "wound", "healing", "and", "grafting", "success", "."]], "ner": [[], [[16, 21, "Biochemical_process"]], [[53, 53, "Plant_hormone"], [55, 58, "Plant_hormone"], [60, 60, "Plant_hormone"], [84, 84, "Plant_hormone"], [39, 40, "Plant_region"], [75, 75, "Multicellular_organism"]], [[97, 97, "DNA"], [101, 101, "DNA"], [94, 95, "DNA"], [99, 99, "DNA"], [103, 103, "DNA"], [105, 105, "DNA"], [133, 136, "DNA"]], [[148, 151, "Biochemical_process"], [158, 159, "Plant_region"]], [[181, 182, "DNA"]]], "relations": [[], [], [], [], [], []]}
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{"doc_key": "PMID29062306_abstract", "dataset": "pickle", "sentences": [["Certain", "plant", "growth", "promoting", "bacteria", "have", "ability", "to", "ameliorate", "abiotic", "and/or", "biotic", "stressors", ",", "which", "can", "be", "exploited", "to", "enhance", "plant", "growth", "and", "productivity", "of", "the", "plants", "under", "stress", "conditions", "."], ["Therefore", ",", "the", "present", "study", "aimed", "to", "examine", "the", "role", "of", "a", "rhizospheric", "bacterial", "isolate", "SBP-9", "isolated", "from", "Sorghum", "bicolor", "(", "i", ")", "in", "promoting", "the", "wheat", "plant", "growth", "under", "salinity", "stress", ",", "and", "(", "ii", ")", "in", "enhancing", "the", "defense", "response", "in", "wheat", "against", "fungal", "pathogen", "\"", "Fusarium", "graminearum", ".", "\"", "The", "test", "isolate", "possessed", "plant", "growth", "promoting", "(", "PGP", ")", "traits", "including", "ACC", "deaminase", "(", "ACCD", ")", ",", "gibberellic", "acid", ",", "indole", "acetic", "acid", "(", "IAA", ")", ",", "siderophore", ",", "and", "inorganic", "phosphate", "solubilization", "."], ["Under", "salt", "(", "NaCl", ")", "stress", ",", "inoculation", "of", "this", "isolate", "to", "wheat", "plant", "significantly", "increased", "plant", "growth", "in", "terms", "of", "various", "growth", "parameters", "such", "as", "shoot", "length/root", "length", "(", "20", "-", "39", "%", ")", ",", "fresh", "weight/dry", "weight", "(", "28", "-", "42", "%", ")", ",", "and", "chlorophyll", "content", "(", "24", "-", "56", "%", ")", "following", "inoculation", "of", "test", "isolate", "SBP-9", "."], ["Bacterial", "inoculation", "decreased", "the", "level", "of", "proline", ",", "and", "malondialdehyde", ",", "whereas", "elevated", "the", "antioxidative", "enzymatic", "activities", "of", "superoxide-dismutase", "(", "SOD", ";", "28", "-", "41", "%", ")", ",", "catalase", "(", "CAT", ";", "24", "-", "56", "%", ")", ",", "and", "peroxidase", "(", "POX", ";", "26", "-", "44", "%", ")", "."], ["Furthermore", ",", "it", "also", "significantly", "decreased", "the", "Na(+", ")", "accumulation", "in", "both", "shoot", "and", "roots", "in", "the", "range", "of", "25", "-", "32", "%", ",", "and", "increased", "the", "K(+", ")", "uptake", "by", "20", "-", "28", "%", ",", "thereby", "favoring", "the", "K(+)/Na(+", ")", "ratio", "."], ["On", "the", "other", "hand", ",", "the", "test", "isolate", "also", "enhanced", "the", "level", "of", "defense", "enzymes", "like", "\u03b2-1", ",", "3", "glucanase", ",", "phenylalanine", "ammonia", "lyase", "(", "PAL", ")", ",", "peroxidae", "(", "PO", ")", ",", "and", "polyphenol", "oxidase", "(", "PPO", ")", ",", "which", "can", "protect", "plants", "from", "the", "infection", "of", "pathogens", "."], ["The", "result", "of", "colonization", "test", "showed", "an", "ability", "of", "the", "test", "isolate", "to", "successfully", "colonize", "the", "wheat", "plants", "."], ["These", "results", "indicate", "that", "Stenotrophomonas", "maltophilia", "SBP-9", "has", "potential", "to", "promote", "the", "wheat", "growth", "under", "biotic", "and", "abiotic", "(", "salt", ")", "stressors", "directly", "or", "indirectly", "and", "can", "be", "further", "tested", "at", "field", "level", "for", "exploitation", "as", "bioinoculant", "."]], "ner": [[], [[49, 50, "Multicellular_organism"], [57, 59, "Biochemical_process"], [95, 96, "Protein"], [98, 98, "Protein"], [101, 102, "Plant_hormone"], [104, 106, "Plant_hormone"], [74, 74, "Multicellular_organism"], [79, 80, "Multicellular_organism"], [108, 108, "Plant_hormone"], [111, 111, "Organic_compound_other"], [114, 116, "Biochemical_process"], [43, 46, "Unicellular_organism"]], [[130, 131, "Multicellular_organism"], [119, 119, "Inorganic_compound_other"], [121, 121, "Inorganic_compound_other"], [165, 165, "Organic_compound_other"], [176, 178, "Unicellular_organism"]], [[186, 186, "Amino_acid_monomer"], [189, 189, "Organic_compound_other"], [198, 198, "Protein"], [200, 200, "Protein"], [208, 208, "Protein"], [219, 219, "Protein"], [210, 210, "Protein"], [221, 221, "Protein"]], [[236, 238, "Biochemical_process"], [256, 258, "Biochemical_process"]], [[288, 291, "Protein"], [293, 295, "Protein"], [297, 297, "Protein"], [300, 300, "Protein"], [302, 302, "Protein"], [306, 307, "Protein"], [309, 309, "Protein"]], [[338, 339, "Multicellular_organism"]], [[353, 354, "Biochemical_process"], [345, 347, "Unicellular_organism"], [360, 360, "Inorganic_compound_other"]]], "relations": [[], [[43, 46, 49, 50, "interacts"], [79, 80, 74, 74, "interacts"]], [[176, 178, 165, 165, "activates"]], [], [], [], [], [[345, 347, 353, 354, "activates"], [345, 347, 360, 360, "interacts"]]]}
{"doc_key": "PMID15740005_abstract", "dataset": "pickle", "sentences": [["A", "rapid", ",", "selective", ",", "sensitive", ",", "accurate", ",", "and", "inexpensive", "immunosensor", "for", "gibberellin", "acid", "detection", "was", "designed", "by", "coupling", "immunoassay", "with", "the", "square", "wave", "anodic", "stripping", "voltammetry", "(", "SWASV", ")", "technique", "involving", "copper", "ion", "labeled", "antigen", "in", "the", "competitive", "immunoreaction", "."], ["The", "response", "signal", "expressed", "as", "the", "percentage", "of", "current", "reduction", "CR", "%", "(", "y", ")", "is", "linearly", "related", "to", "the", "concentration", "of", "GA", "(", "x", ")", "in", "the", "1", "microg/mL", "to", "approximately", "150", "microg/mL", "range", "with", "a", "regression", "equation", "of", "the", "form", "y", "=", "0.44x", "+", "15.59", "and", "a", "correlation", "coefficient", "of", "0.99", "."], ["The", "results", "of", "the", "immunosensor", "assay", "were", "compared", "with", "those", "obtained", "by", "HPLC", "and", "ELISA", ",", "which", "show", "a", "satisfactory", "agreement", "."], ["The", "immunosensor", "was", "used", "to", "determine", "the", "GA", "content", "in", "the", "hybrid", "rice", "grain", "samples", "taken", "in", "the", "growing", "period", "."]], "ner": [[[13, 14, "Plant_hormone"], [33, 34, "Element"]], [[64, 64, "Plant_hormone"]], [], [[125, 125, "Plant_hormone"], [129, 131, "Plant_region"]]], "relations": [[], [], [], []]}
{"doc_key": "PMID10580327_abstract", "dataset": "pickle", "sentences": [["Jasmonic", "acid", "is", "a", "carbocyclic", "fatty", "acid", "that", "is", "biosynthesized", "from", "alpha-linolenic", "acid", "in", "several", "steps", "."], ["The", "formation", "of", "the", "ring", "structure", "of", "jasmonic", "acid", "is", "catalyzed", "by", "the", "enzyme", "allene", "oxide", "cyclase", "(", "EC", "5.3.99.6", ")", "and", "involves", "the", "cyclization", "of", "an", "unstable", "allene", "oxide", "into", "the", "cyclopentenone", "12-oxo-10,15(Z)-phytodienoic", "acid", "."], ["In", "this", "study", ",", "a", "number", "of", "allene", "oxides", "were", "generated", ",", "and", "their", "enzymatic", "and", "nonenzymatic", "cyclization", "into", "cyclopentenones", "was", "investigated", "."], ["Nonenzymatic", "cyclization", "was", "observed", "with", "allene", "oxides", "having", "one", "pair", "of", "conjugated", "double", "bonds", "and", "an", "additional", "isolated", "double", "bond", "in", "the", "beta", ",", "gamma", "position", "relative", "to", "the", "epoxide", "group", ",", "i.e.", ",", "the", "partial", "structure", "4,5-epoxy-1,3,7-octatriene", "."], ["Enzymatic", "cyclization", "took", "place", "provided", "that", "this", "structural", "element", "was", "inserted", "in", "the", "fatty", "acid", "chain", "with", "its", "epoxide", "group", "in", "the", "n-6,7", "position", "and", "the", "isolated", "double", "bond", "in", "the", "n-3", "position", "."], ["A", "number", "of", "oxygenated", "fatty", "acids", "having", "structural", "features", "in", "common", "with", "the", "natural", "allene", "oxides", "were", "tested", "as", "inhibitors", "of", "allene", "oxide", "cyclase", "."], ["Fatty", "acids", "having", "an", "allene", "oxide", "structure", "in", "the", "n-6,7", "position", "but", "lacking", "the", "double", "bond", "in", "the", "n-3", "position", ",", "as", "well", "as", "fatty", "acids", "having", "a", "saturated", "epoxide", "group", "in", "the", "n-6,7", "position", ",", "served", "as", "competitive", "inhibitors", "of", "the", "enzyme", "."], ["Data", "on", "the", "substrate", "specificity", "of", "allene", "oxide", "synthase", "(", "EC", "4.2.1.92", ")", "from", "corn", "seeds", "indicated", "that", "fatty", "acid", "hydroperoxides", "with", "a", "double", "bond", "at", "n-3", "and", "with", "the", "hydroperoxide", "function", "at", "n-6", "exhibit", "the", "highest", "affinity", "but", "the", "slowest", "reaction", "velocity", "."]], "ner": [[[0, 1, "Plant_hormone"], [11, 12, "Organic_compound_other"], [4, 6, "Organic_compound_other"]], [[24, 25, "Plant_hormone"], [31, 33, "Protein"], [35, 36, "Protein"], [49, 51, "Organic_compound_other"], [44, 46, "Organic_compound_other"]], [[60, 61, "Organic_compound_other"], [72, 72, "Organic_compound_other"]], [[113, 113, "Organic_compound_other"], [81, 82, "Organic_compound_other"], [105, 106, "Organic_compound_other"]], [[133, 134, "Organic_compound_other"], [128, 130, "Organic_compound_other"]], [[152, 154, "Organic_compound_other"], [162, 164, "Organic_compound_other"], [170, 172, "Protein"]], [[178, 179, "Organic_compound_other"], [174, 175, "Organic_compound_other"], [198, 199, "Organic_compound_other"], [202, 204, "Organic_compound_other"]], [[224, 226, "Protein"], [228, 229, "Protein"], [232, 233, "Plant_region"], [236, 238, "Organic_compound_other"], [248, 249, "Biochemical_process"]]], "relations": [[[11, 12, 0, 1, "produces"]], [[44, 46, 49, 51, "produces"], [31, 33, 24, 25, "produces"], [35, 36, 24, 25, "produces"], [35, 36, 44, 46, "interacts"], [31, 33, 44, 46, "interacts"]], [], [[105, 106, 81, 82, "is-in"]], [[133, 134, 128, 130, "is-in"]], [], [[178, 179, 174, 175, "is-in"], [202, 204, 198, 199, "is-in"]], [[224, 226, 232, 233, "is-in"], [228, 229, 232, 233, "is-in"]]]}
{"doc_key": "PMID12777041_abstract", "dataset": "pickle", "sentences": [["Calmodulin", "(", "CaM", ")", "plays", "an", "important", "role", "in", "sensing", "and", "transducing", "changes", "in", "cellular", "Ca2", "+", "concentration", "in", "response", "to", "several", "biotic", "and", "abiotic", "stresses", "."], ["Although", "CaM", "is", "implicated", "in", "plant-pathogen", "interactions", ",", "its", "molecular", "targets", "and", "their", "role", "in", "defense", "signaling", "pathway(s", ")", "are", "poorly", "understood", "."], ["To", "elucidate", "the", "signaling", "pathways", "that", "link", "CaM", "to", "defense", "responses", ",", "we", "screened", "a", "cDNA", "library", "constructed", "from", "bean", "leaves", "undergoing", "a", "hypersensitive", "response", "(", "HR", ")", "with", "radiolabeled", "CaM", "isoforms", "."], ["A", "total", "of", "26", "putative", "CBPs", "were", "identified", "."], ["Sequencing", "of", "the", "cDNAs", "revealed", "that", "they", "represent", "8", "different", "genes", "."], ["They", "are", "homologues", "of", "previously", "identified", "CaM-binding", "proteins", "(", "CBPs", ")", "in", "other", "systems", "."], ["However", ",", "some", "CBPs", "are", "novel", "members", "of", "known", "CBP", "families", "."], ["The", "proteins", "encoded", "by", "these", "clones", "bound", "CaM", "in", "a", "Ca2", "+", "-dependent", "manner", "."], ["To", "determine", "if", "these", "CBPs", "are", "involved", "in", "plant", "defense", "responses", ",", "we", "analyzed", "their", "expression", "in", "bean", "leaves", "inoculated", "with", "compatible", ",", "incompatible", "and", "nonpathogenic", "bacterial", "strains", "."], ["Expression", "of", "three", "CBPs", "including", "an", "isoform", "of", "cyclic", "nucleotide-gated", "channels", "(", "PvCNGC-A", ")", "and", "two", "hypothetical", "proteins", "(", "PvCBP60-C", "and", "PvCBP60-D", ")", "was", "induced", "whereas", "the", "expression", "of", "two", "other", "isoforms", "of", "CNGCs", "(", "PvCNGC-B", "and", "PvCNGC-C", ")", "was", "repressed", "in", "response", "to", "incompatible", "pathogens", "."], ["The", "expression", "of", "the", "rest", ",", "a", "small", "auxin", "up", "RNA", "(", "PvSAUR1", ")", "and", "two", "hypothetical", "proteins", "(", "PvCBP60-A", "and", "PvCBP60-B", ")", ",", "was", "not", "changed", "."], ["The", "expression", "of", "most", "of", "the", "pathogen-regulated", "genes", "was", "also", "affected", "by", "salicylic", "acid", ",", "jasmonic", "acid", ",", "hydrogen", "peroxide", "and", "a", "fungal", "elicitor", ",", "which", "are", "known", "to", "induce", "defense", "responses", "."], ["Our", "results", "strongly", "suggest", "that", "at", "least", "five", "bean", "CBPs", "are", "involved", "in", "plant", "defense", "responses", "."]], "ner": [[[14, 16, "Element"], [0, 0, "Protein"], [2, 2, "Protein"]], [[28, 28, "Protein"]], [[57, 57, "Protein"], [79, 81, "Protein"], [69, 70, "Plant_region"], [73, 74, "Biochemical_pathway"], [76, 76, "Biochemical_pathway"]], [[88, 88, "Protein"]], [], [[110, 111, "Protein"], [113, 113, "Protein"]], [[122, 122, "Protein"], [128, 129, "Protein"]], [[138, 138, "Protein"]], [[150, 150, "Protein"], [163, 164, "Plant_region"]], [[178, 178, "Protein"], [187, 187, "Protein"], [194, 194, "Protein"], [196, 196, "Protein"], [210, 210, "Protein"], [181, 185, "Protein"], [206, 208, "Protein"], [212, 212, "Protein"]], [[241, 241, "Protein"], [243, 243, "Protein"], [229, 232, "RNA"], [234, 234, "RNA"]], [[262, 263, "Plant_hormone"], [265, 266, "Plant_hormone"], [268, 269, "Inorganic_compound_other"]], [[291, 292, "Protein"]]], "relations": [[[0, 0, 14, 16, "interacts"], [2, 2, 14, 16, "interacts"]], [], [], [], [], [], [], [], [[150, 150, 163, 164, "is-in"]], [], [], [], []]}
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{"doc_key": "PMID18945932_abstract", "dataset": "pickle", "sentences": [["Selected", "strains", "of", "nonpathogenic", "rhizobacteria", "can", "reduce", "disease", "in", "foliar", "tissues", "through", "the", "induction", "of", "a", "defense", "state", "known", "as", "induced", "systemic", "resistance", "(", "ISR", ")", "."], ["Compared", "with", "the", "large", "body", "of", "information", "on", "ISR", "in", "dicotyledonous", "plants", ",", "little", "is", "known", "about", "the", "mechanisms", "underlying", "rhizobacteria-induced", "resistance", "in", "cereal", "crops", "."], ["Here", ",", "we", "demonstrate", "the", "ability", "of", "Pseudomonas", "fluorescens", "WCS374r", "to", "trigger", "ISR", "in", "rice", "(", "Oryza", "sativa", ")", "against", "the", "leaf", "blast", "pathogen", "Magnaporthe", "oryzae", "."], ["Using", "salicylic", "acid", "(SA)-nonaccumulating", "NahG", "rice", ",", "an", "ethylene-insensitive", "OsEIN2", "antisense", "line", ",", "and", "the", "jasmonate-deficient", "mutant", "hebiba", ",", "we", "show", "that", "this", "WCS374r-induced", "resistance", "is", "regulated", "by", "an", "SA-independent", "but", "jasmonic", "acid/ethylene-modulated", "signal", "transduction", "pathway", "."], ["Bacterial", "mutant", "analysis", "uncovered", "a", "pseudobactin-type", "siderophore", "as", "the", "crucial", "determinant", "responsible", "for", "ISR", "elicitation", "."], ["Root", "application", "of", "WCS374r-derived", "pseudobactin", "(", "Psb374", ")", "primed", "naive", "leaves", "for", "accelerated", "expression", "of", "a", "pronounced", "multifaceted", "defense", "response", ",", "consisting", "of", "rapid", "recruitment", "of", "phenolic", "compounds", "at", "sites", "of", "pathogen", "entry", ",", "concerted", "expression", "of", "a", "diverse", "set", "of", "structural", "defenses", ",", "and", "a", "timely", "hyperinduction", "of", "hydrogen", "peroxide", "formation", "putatively", "driving", "cell", "wall", "fortification", "."], ["Exogenous", "SA", "application", "alleviated", "this", "Psb374-modulated", "defense", "priming", ",", "while", "Psb374", "pretreatment", "antagonized", "infection-induced", "transcription", "of", "SA-responsive", "PR", "genes", ",", "suggesting", "that", "the", "Psb374-", "and", "SA-modulated", "signaling", "pathways", "are", "mutually", "antagonistic", "."], ["Interestingly", ",", "in", "sharp", "contrast", "to", "WCS374r-mediated", "ISR", ",", "chemical", "induction", "of", "blast", "resistance", "by", "the", "SA", "analog", "benzothiadiazole", "was", "independent", "of", "jasmonic", "acid/ethylene", "signaling", "and", "involved", "the", "potentiation", "of", "SA-responsive", "gene", "expression", "."], ["Together", ",", "these", "results", "offer", "novel", "insights", "into", "the", "signaling", "circuitry", "governing", "induced", "resistance", "against", "M.", "oryzae", "and", "suggest", "that", "rice", "is", "endowed", "with", "multiple", "blast-effective", "resistance", "pathways", "."]], "ner": [[[20, 22, "Biochemical_process"], [24, 24, "Biochemical_process"]], [[35, 35, "Biochemical_process"], [47, 48, "Biochemical_process"], [50, 51, "Multicellular_organism"]], [[60, 62, "Unicellular_organism"], [65, 65, "Biochemical_process"], [69, 70, "Multicellular_organism"], [77, 78, "Multicellular_organism"], [67, 67, "Multicellular_organism"], [74, 76, "Multicellular_organism"]], [[81, 85, "Multicellular_organism"], [88, 91, "Multicellular_organism"], [95, 97, "Multicellular_organism"], [103, 104, "Biochemical_process"], [109, 115, "Biochemical_pathway"]], [[122, 123, "Organic_compound_other"], [130, 131, "Biochemical_process"]], [[159, 160, "Organic_compound_other"], [139, 139, "Organic_compound_other"], [136, 137, "Organic_compound_other"], [182, 184, "Biochemical_process"], [187, 189, "Biochemical_process"]], [[192, 192, "Plant_hormone"], [201, 201, "Organic_compound_other"], [207, 209, "DNA"], [196, 198, "Biochemical_process"], [214, 218, "Biochemical_pathway"]], [[229, 230, "Biochemical_process"], [239, 241, "Plant_hormone"], [245, 247, "Biochemical_process"], [253, 255, "Biochemical_process"], [235, 236, "Biochemical_process"]], [[272, 273, "Multicellular_organism"], [277, 277, "Multicellular_organism"], [282, 284, "Biochemical_pathway"]]], "relations": [[], [[47, 48, 50, 51, "is-in"]], [[60, 62, 65, 65, "activates"], [65, 65, 67, 67, "is-in"], [65, 65, 69, 70, "is-in"], [65, 65, 74, 76, "inhibits"], [65, 65, 77, 78, "inhibits"]], [[109, 115, 103, 104, "interacts"]], [[122, 123, 130, 131, "activates"]], [[136, 137, 159, 160, "activates"], [136, 137, 182, 184, "activates"], [139, 139, 159, 160, "activates"], [139, 139, 182, 184, "activates"]], [[192, 192, 196, 198, "inhibits"], [201, 201, 207, 209, "inhibits"]], [[239, 241, 235, 236, "activates"], [239, 241, 253, 255, "interacts"]], [[282, 284, 277, 277, "is-in"]]]}
{"doc_key": "PMID19073963_abstract", "dataset": "pickle", "sentences": [["When", "plants", "are", "attacked", "by", "pathogens", ",", "they", "defend", "themselves", "with", "an", "arsenal", "of", "defence", "mechanisms", ",", "both", "passive", "and", "active", "."], ["The", "active", "defence", "responses", ",", "which", "require", "de", "novo", "protein", "synthesis", ",", "are", "regulated", "through", "a", "complex", "and", "interconnected", "network", "of", "signalling", "pathways", "that", "mainly", "involve", "three", "molecules", ",", "salicylic", "acid", "(", "SA", ")", ",", "jasmonic", "acid", "(", "JA", ")", ",", "and", "ethylene", "(", "ET", ")", ",", "and", "which", "results", "in", "the", "synthesis", "of", "pathogenesis-related", "(", "PR", ")", "proteins", "."], ["Microbe", "or", "elicitor-induced", "signal", "transduction", "pathways", "lead", "to", "(", "i", ")", "the", "reinforcement", "of", "cell", "walls", "and", "lignification", ",", "(", "ii", ")", "the", "production", "of", "antimicrobial", "metabolites", "(", "phytoalexins", ")", ",", "and", "(", "iii", ")", "the", "production", "of", "reactive", "oxygen", "species", "(", "ROS", ")", "and", "reactive", "nitrogen", "species", "(", "RNS", ")", "."], ["Among", "the", "proteins", "induced", "during", "the", "host", "plant", "defence", ",", "class", "III", "plant", "peroxidases", "(", "EC", "1.11.1.7", ";", "hydrogen", "donor", ":", "H(2)O(2", ")", "oxidoreductase", ",", "Prxs", ")", "are", "well", "known", "."], ["They", "belong", "to", "a", "large", "multigene", "family", ",", "and", "participate", "in", "a", "broad", "range", "of", "physiological", "processes", ",", "such", "as", "lignin", "and", "suberin", "formation", ",", "cross-linking", "of", "cell", "wall", "components", ",", "and", "synthesis", "of", "phytoalexins", ",", "or", "participate", "in", "the", "metabolism", "of", "ROS", "and", "RNS", ",", "both", "switching", "on", "the", "hypersensitive", "response", "(", "HR", ")", ",", "a", "form", "of", "programmed", "host", "cell", "death", "at", "the", "infection", "site", "associated", "with", "limited", "pathogen", "development", "."], ["The", "present", "review", "focuses", "on", "these", "plant", "defence", "reactions", "in", "which", "Prxs", "are", "directly", "or", "indirectly", "involved", ",", "and", "ends", "with", "the", "signalling", "pathways", ",", "which", "regulate", "Prx", "gene", "expression", "during", "plant", "defence", "."], ["How", "they", "are", "integrated", "within", "the", "complex", "network", "of", "defence", "responses", "of", "any", "host", "plant", "cell", "will", "be", "the", "cornerstone", "of", "future", "research", "."]], "ner": [[], [[51, 52, "Plant_hormone"], [54, 54, "Plant_hormone"], [60, 60, "Plant_hormone"], [66, 66, "Plant_hormone"], [64, 64, "Plant_hormone"], [57, 58, "Plant_hormone"], [76, 80, "Protein"]], [[99, 99, "Biochemical_process"], [110, 110, "Organic_compound_other"], [120, 122, "Inorganic_compound_other"], [124, 124, "Inorganic_compound_other"], [127, 129, "Inorganic_compound_other"], [131, 131, "Inorganic_compound_other"]], [[144, 147, "Protein"], [155, 157, "Protein"], [159, 159, "Protein"], [149, 150, "Protein"], [152, 152, "Element"]], [[215, 216, "Biochemical_process"], [218, 218, "Biochemical_process"], [185, 188, "Biochemical_process"], [199, 199, "Organic_compound_other"], [207, 207, "Inorganic_compound_other"], [209, 209, "Inorganic_compound_other"], [224, 227, "Biochemical_process"]], [[249, 249, "Protein"], [265, 267, "Biochemical_process"]], []], "relations": [[], [[51, 52, 76, 80, "activates"], [54, 54, 76, 80, "activates"], [57, 58, 76, 80, "activates"], [64, 64, 76, 80, "activates"], [66, 66, 76, 80, "activates"], [60, 60, 76, 80, "activates"]], [], [], [], [], []]}
{"doc_key": "PMID15842626_abstract", "dataset": "pickle", "sentences": [["Staphylococcus", "aureus", "is", "a", "ubiquitous", "gram-positive", "bacterium", "that", "can", "cause", "superficial", "to", "serious", "systemic", "infections", "in", "animals", "and", "humans", "."], ["Here", "we", "report", "the", "development", "of", "a", "plant", "infection", "model", "to", "study", "the", "pathogenesis", "of", "this", "bacterium", "."], ["Three", "global", "regulatory", "mutants", ",", "RN6911", "(", "agr-", ")", ",", "ALC", "488", "(", "sarA-", ")", "ALC", "842", "(", "sarA-/agr-", ")", "and", "an", "alpha-toxin", "mutant", "defective", "in", "biofilm", "formation", "(", "DU1090", ")", "which", "are", "attenuated", "in", "animal", "pathogenesis", ",", "were", "also", "attenuated", "in", "their", "ability", "to", "infect", "plants", ",", "suggesting", "that", "these", "regulators", "that", "mediate", "synthesis", "of", "virulence", "factors", "essential", "for", "animal", "pathogenesis", "are", "also", "required", "for", "plant", "pathogenesis", "."], ["Further", ",", "using", "Arabidopsis", "plants", "altered", "in", "defense", "responses", "such", "as", "the", "transgenic", "lines", "NahG", "[", "defective", "in", "salicylic", "acid", "(", "SA", ")", "accumulation", "]", ",", "and", "35S-LOX2-", "(", "defective", "in", "jasmonic", "acid", "production", "and", "hyper-accumulator", "of", "SA", ")", ",", "and", "mutants", "ics1", "(", "depleted", "in", "SA", "accumulation", ")", ",", "and", "npr1", "-", "1", "(", "non-expressor", "of", "pathogenesis-related", "protein", ")", "we", "show", "that", "resistance", "of", "Arabidopsis", "to", "typical", "plant", "pathogens", "and", "the", "animal", "pathogen", "S.", "aureus", "is", "conserved", "and", "is", "mediated", "by", "SA", "."], ["The", "data", "presented", "here", "suggest", "that", "Arabidopsis", "thaliana", "resistance", "to", "S.", "aureus", "is", "mediated", "either", "by", "a", "direct", "effect", "of", "SA", "on", "the", "pathogen", ",", "specifically", "one", "that", "affects", "the", "attachment/aggregate", "formation", "on", "the", "root", "surface", "and", "reduces", "the", "pathogen", "'s", "virulence", ",", "or", "by", "SA-dependent", ",", "NPR1-independent", "host", "responses", "."]], "ner": [[[0, 1, "Unicellular_organism"], [18, 18, "Multicellular_organism"]], [], [[60, 61, "Unicellular_organism"], [67, 67, "Unicellular_organism"], [43, 43, "Unicellular_organism"], [45, 45, "Unicellular_organism"], [48, 49, "Unicellular_organism"], [51, 51, "Unicellular_organism"], [53, 54, "Unicellular_organism"], [56, 56, "Unicellular_organism"]], [[110, 111, "Multicellular_organism"], [144, 144, "Plant_hormone"], [172, 172, "Multicellular_organism"], [189, 189, "Plant_hormone"], [134, 134, "Multicellular_organism"], [158, 160, "Multicellular_organism"], [181, 182, "Unicellular_organism"], [121, 121, "Multicellular_organism"], [138, 140, "Biochemical_process"], [149, 149, "Multicellular_organism"], [153, 154, "Biochemical_process"], [162, 165, "Multicellular_organism"], [125, 130, "Biochemical_process"]], [[201, 202, "Unicellular_organism"], [211, 211, "Plant_hormone"], [236, 240, "Biochemical_process"], [197, 199, "Biochemical_process"]]], "relations": [[[0, 1, 18, 18, "inhibits"]], [], [], [[144, 144, 134, 134, "is-in"], [189, 189, 181, 182, "interacts"], [181, 182, 172, 172, "interacts"]], [[211, 211, 201, 202, "interacts"], [211, 211, 197, 199, "interacts"], [197, 199, 201, 202, "inhibits"], [236, 240, 197, 199, "interacts"]]]}
{"doc_key": "PMID22080599_abstract", "dataset": "pickle", "sentences": [["Plants", "coordinate", "and", "tightly", "regulate", "pathogen", "defense", "by", "the", "mostly", "antagonistic", "salicylate", "(SA)-", "and", "jasmonate", "(JA)-mediated", "signaling", "pathways", "."], ["Here", ",", "we", "show", "that", "the", "previously", "uncharacterized", "glucosyltransferase", "UGT76B1", "is", "a", "novel", "player", "in", "this", "SA-JA", "signaling", "crosstalk", "."], ["UGT76B1", "was", "selected", "as", "the", "top", "stress-induced", "isoform", "among", "all", "122", "members", "of", "the", "Arabidopsis", "thaliana", "UGT", "family", "."], ["Loss", "of", "UGT76B1", "function", "leads", "to", "enhanced", "resistance", "to", "the", "biotrophic", "pathogen", "Pseudomonas", "syringae", "and", "accelerated", "senescence", "but", "increased", "susceptibility", "toward", "necrotrophic", "Alternaria", "brassicicola", "."], ["This", "is", "accompanied", "by", "constitutively", "elevated", "SA", "levels", "and", "SA-related", "marker", "gene", "expression", ",", "whereas", "JA-dependent", "markers", "are", "repressed", "."], ["Conversely", ",", "UGT76B1", "overexpression", "has", "the", "opposite", "effect", "."], ["Thus", ",", "UGT76B1", "attenuates", "SA-dependent", "plant", "defense", "in", "the", "absence", "of", "infection", ",", "promotes", "the", "JA", "response", ",", "and", "delays", "senescence", "."], ["The", "ugt76b1", "phenotypes", "were", "SA", "dependent", ",", "whereas", "UGT76B1", "overexpression", "indicated", "that", "this", "gene", "possibly", "also", "has", "a", "direct", "effect", "on", "the", "JA", "pathway", "."], ["Nontargeted", "metabolomic", "analysis", "of", "UGT76B1", "knockout", "and", "overexpression", "lines", "using", "ultra-high-resolution", "mass", "spectrometry", "and", "activity", "assays", "with", "the", "recombinant", "enzyme", "led", "to", "the", "ab", "initio", "identification", "of", "isoleucic", "acid", "(", "2-hydroxy-3-methyl-pentanoic", "acid", ")", "as", "a", "substrate", "of", "UGT76B1", "."], ["Exogenously", "applied", "isoleucic", "acid", "increased", "resistance", "against", "P.", "syringae", "infection", "."], ["These", "findings", "indicate", "a", "novel", "link", "between", "amino", "acid-related", "molecules", "and", "plant", "defense", "that", "is", "mediated", "by", "small-molecule", "glucosylation", "."]], "ner": [[[11, 17, "Biochemical_pathway"]], [[27, 28, "Protein"], [35, 37, "Biochemical_process"]], [[39, 39, "Protein"], [53, 56, "Protein"]], [[60, 61, "Biochemical_process"], [70, 71, "Unicellular_organism"], [80, 81, "Multicellular_organism"]], [[89, 89, "Plant_hormone"], [92, 95, "Biochemical_process"], [98, 99, "DNA"]], [[105, 106, "Biochemical_process"]], [[114, 114, "Protein"], [116, 118, "Biochemical_process"], [127, 128, "Biochemical_process"]], [[138, 138, "Plant_hormone"], [142, 143, "Biochemical_process"], [156, 157, "Biochemical_process"]], [[163, 167, "Multicellular_organism"], [186, 187, "Organic_compound_other"], [189, 190, "Organic_compound_other"], [196, 196, "Protein"]], [[200, 201, "Organic_compound_other"], [205, 207, "Biochemical_process"]], [[226, 227, "Biochemical_process"]]], "relations": [[], [[27, 28, 35, 37, "is-in"]], [], [], [], [], [[114, 114, 116, 118, "interacts"], [114, 114, 127, 128, "activates"]], [], [[196, 196, 189, 190, "interacts"], [196, 196, 186, 187, "interacts"]], [[200, 201, 205, 207, "inhibits"]], []]}
{"doc_key": "PMID14676968_abstract", "dataset": "pickle", "sentences": [["Brassinosteroids", "(", "BRs", ")", "are", "a", "group", "of", "naturally", "occurring", "plant", "steroidal", "compounds", "with", "wide-ranging", "biological", "activity", "that", "offer", "the", "unique", "possibility", "of", "increasing", "crop", "yields", "through", "both", "changing", "plant", "metabolism", "and", "protecting", "plants", "from", "environmental", "stresses", "."], ["In", "recent", "years", ",", "genetic", "and", "biochemical", "studies", "have", "established", "an", "essential", "role", "for", "BRs", "in", "plant", "development", ",", "and", "on", "this", "basis", "BRs", "have", "been", "given", "the", "stature", "of", "a", "phytohormone", "."], ["A", "remarkable", "feature", "of", "BRs", "is", "their", "potential", "to", "increase", "resistance", "in", "plants", "to", "a", "wide", "spectrum", "of", "stresses", ",", "such", "as", "low", "and", "high", "temperatures", ",", "drought", ",", "high", "salt", ",", "and", "pathogen", "attack", "."], ["Despite", "this", ",", "only", "a", "few", "studies", "aimed", "at", "understanding", "the", "mechanism", "by", "which", "BRs", "promote", "stress", "resistance", "have", "been", "undertaken", "."], ["Studies", "of", "the", "BR", "signaling", "pathway", "and", "BR", "gene-regulating", "properties", "indicate", "that", "there", "is", "cross-talk", "between", "BRs", "and", "other", "hormones", ",", "including", "those", "with", "established", "roles", "in", "plant", "defense", "responses", "such", "as", "abscisic", "acid", ",", "jasmonic", "acid", ",", "and", "ethylene", "."], ["Recent", "studies", "aimed", "at", "understanding", "how", "BRs", "modulate", "stress", "responses", "suggest", "that", "complex", "molecular", "changes", "underlie", "BR-induced", "stress", "tolerance", "in", "plants", "."], ["Analyses", "of", "these", "changes", "should", "generate", "exciting", "results", "in", "the", "future", "and", "clarify", "whether", "the", "ability", "of", "BRs", "to", "increase", "plant", "resistance", "to", "a", "range", "of", "stresses", "lies", "in", "the", "complex", "interactions", "of", "BRs", "with", "other", "hormones", "."], ["Future", "studies", "should", "also", "elucidate", "if", "BRI1", ",", "an", "essential", "component", "of", "the", "BR", "receptor", ",", "directly", "participates", "in", "stress", "response", "signaling", "through", "interactions", "with", "ligands", "and", "proteins", "involved", "in", "plant", "defense", "responses", "."]], "ner": [[[0, 0, "Plant_hormone"], [2, 2, "Plant_hormone"]], [[52, 52, "Plant_hormone"], [61, 61, "Plant_hormone"], [69, 69, "Plant_hormone"]], [[75, 75, "Plant_hormone"], [101, 101, "Organic_compound_other"]], [[121, 121, "Plant_hormone"]], [[132, 134, "Biochemical_pathway"], [136, 136, "Plant_hormone"], [145, 145, "Plant_hormone"], [161, 162, "Plant_hormone"], [164, 165, "Plant_hormone"], [168, 168, "Plant_hormone"]], [[176, 176, "Plant_hormone"], [186, 188, "Biochemical_process"]], [[209, 209, "Plant_hormone"], [225, 225, "Plant_hormone"]], [[236, 236, "Protein"], [243, 244, "Protein"]]], "relations": [[], [], [], [], [[145, 145, 161, 162, "interacts"], [145, 145, 164, 165, "interacts"], [145, 145, 168, 168, "interacts"]], [], [], [[236, 236, 243, 244, "is-in"]]]}
{"doc_key": "PMID10198087_abstract", "dataset": "pickle", "sentences": [["Two", "key", "genes", "in", "terpenoid", "indole", "alkaloid", "biosynthesis", ",", "Tdc", "and", "Str", ",", "encoding", "tryptophan", "decarboxylase", "and", "strictosidine", "synthase", ",", "respectively", ",", "are", "coordinately", "induced", "by", "fungal", "elicitors", "in", "suspension-cultured", "Catharanthus", "roseus", "cells", "."], ["We", "have", "studied", "the", "roles", "of", "the", "jasmonate", "biosynthetic", "pathway", "and", "of", "protein", "phosphorylation", "in", "signal", "transduction", "initiated", "by", "a", "partially", "purified", "elicitor", "from", "yeast", "extract", "."], ["In", "addition", "to", "activating", "Tdc", "and", "Str", "gene", "expression", ",", "the", "elicitor", "also", "induced", "the", "biosynthesis", "of", "jasmonic", "acid", "."], ["The", "jasmonate", "precursor", "alpha-linolenic", "acid", "or", "methyl", "jasmonate", "(", "MeJA", ")", "itself", "induced", "Tdc", "and", "Str", "gene", "expression", "when", "added", "exogenously", "."], ["Diethyldithiocarbamic", "acid", ",", "an", "inhibitor", "of", "jasmonate", "biosynthesis", ",", "blocked", "both", "the", "elicitor-induced", "formation", "of", "jasmonic", "acid", "and", "the", "activation", "of", "terpenoid", "indole", "alkaloid", "biosynthetic", "genes", "."], ["The", "protein", "kinase", "inhibitor", "K-252a", "abolished", "both", "elicitor-induced", "jasmonate", "biosynthesis", "and", "MeJA-induced", "Tdc", "and", "Str", "gene", "expression", "."], ["Analysis", "of", "the", "expression", "of", "Str", "promoter/gusA", "fusions", "in", "transgenic", "C.", "roseus", "cells", "showed", "that", "the", "elicitor", "and", "MeJA", "act", "at", "the", "transcriptional", "level", "."], ["These", "results", "demonstrate", "that", "the", "jasmonate", "biosynthetic", "pathway", "is", "an", "integral", "part", "of", "the", "elicitor-triggered", "signal", "transduction", "pathway", "that", "results", "in", "the", "coordinate", "expression", "of", "the", "Tdc", "and", "Str", "genes", "and", "that", "protein", "kinases", "act", "both", "upstream", "and", "downstream", "of", "jasmonates", "."]], "ner": [[[4, 7, "Biochemical_pathway"], [9, 9, "DNA"], [11, 11, "DNA"], [14, 15, "Protein"], [17, 18, "Protein"], [29, 32, "Cell"]], [[41, 43, "Biochemical_pathway"], [46, 47, "Biochemical_process"], [58, 59, "Organic_compound_other"]], [[65, 69, "Biochemical_process"], [78, 79, "Plant_hormone"]], [[82, 85, "Plant_hormone"], [87, 88, "Plant_hormone"], [90, 90, "Plant_hormone"], [94, 98, "Biochemical_process"]], [[103, 104, "Organic_compound_other"], [109, 110, "Biochemical_pathway"], [118, 119, "Plant_hormone"], [124, 128, "DNA"]], [[131, 134, "Organic_compound_other"], [137, 139, "Biochemical_process"], [141, 146, "Biochemical_process"]], [[153, 155, "DNA"], [157, 160, "Cell"], [166, 166, "Plant_hormone"]], [[178, 180, "Biochemical_pathway"], [187, 190, "Biochemical_pathway"], [199, 202, "DNA"], [205, 206, "Protein"], [213, 213, "Plant_hormone"]]], "relations": [[[9, 9, 14, 15, "produces"], [11, 11, 17, 18, "produces"]], [], [], [[87, 88, 94, 98, "activates"], [90, 90, 94, 98, "activates"], [82, 85, 94, 98, "activates"]], [[103, 104, 109, 110, "inhibits"], [103, 104, 124, 128, "inhibits"], [103, 104, 118, 119, "inhibits"]], [[131, 134, 137, 139, "inhibits"], [131, 134, 141, 146, "inhibits"]], [], [[178, 180, 187, 190, "is-in"], [187, 190, 199, 202, "interacts"]]]}
{"doc_key": "PMID27072931_abstract", "dataset": "pickle", "sentences": [["BACKGROUND", ":", "The", "plant-specific", "TCP", "transcription", "factor", "family", ",", "which", "is", "involved", "in", "the", "regulation", "of", "cell", "growth", "and", "proliferation", ",", "performs", "diverse", "functions", "in", "multiple", "aspects", "of", "plant", "growth", "and", "development", "."], ["However", ",", "no", "comprehensive", "analysis", "of", "the", "TCP", "family", "in", "watermelon", "(", "Citrullus", "lanatus", ")", "has", "been", "undertaken", "previously", "."], ["RESULTS", ":", "A", "total", "of", "27", "watermelon", "TCP", "encoding", "genes", "distributed", "on", "nine", "chromosomes", "were", "identified", "."], ["Phylogenetic", "analysis", "clustered", "the", "genes", "into", "11", "distinct", "subgroups", "."], ["Furthermore", ",", "phylogenetic", "and", "structural", "analyses", "distinguished", "two", "homology", "classes", "within", "the", "ClTCP", "family", ",", "designated", "Class", "I", "and", "Class", "II", "."], ["The", "Class", "II", "genes", "were", "differentiated", "into", "two", "subclasses", ",", "the", "CIN", "subclass", "and", "the", "CYC/TB1", "subclass", "."], ["The", "expression", "patterns", "of", "all", "members", "were", "determined", "by", "semi-quantitative", "PCR", "."], ["The", "functions", "of", "two", "ClTCP", "genes", ",", "ClTCP14a", "and", "ClTCP15", ",", "in", "regulating", "plant", "height", "were", "confirmed", "by", "ectopic", "expression", "in", "Arabidopsis", "wild-type", "and", "ortholog", "mutants", "."], ["CONCLUSIONS", ":", "This", "study", "represents", "the", "first", "genome-wide", "analysis", "of", "the", "watermelon", "TCP", "gene", "family", ",", "which", "provides", "valuable", "information", "for", "understanding", "the", "classification", "and", "functions", "of", "the", "TCP", "genes", "in", "watermelon", "."]], "ner": [[[3, 7, "DNA"]], [[40, 41, "DNA"], [43, 43, "Multicellular_organism"], [45, 46, "Multicellular_organism"]], [[59, 62, "DNA"]], [], [[92, 93, "DNA"]], [[113, 114, "DNA"], [117, 118, "DNA"]], [], [[136, 137, "DNA"], [139, 139, "DNA"], [141, 141, "DNA"], [153, 157, "Multicellular_organism"]], [[170, 173, "DNA"], [187, 188, "DNA"], [190, 190, "Multicellular_organism"]]], "relations": [[], [[40, 41, 43, 43, "is-in"], [40, 41, 45, 46, "is-in"]], [], [], [], [], [], [], [[187, 188, 190, 190, "is-in"]]]}
{"doc_key": "PMID24519835_abstract", "dataset": "pickle", "sentences": [["1", "."], ["The", "development", "of", "flower", "buds", "inSoldanella", "minima", "grown", "at", "15", "\u00b0", "or", "above", "is", "stopped", "at", "the", "stage", "of", "sporogenous", "cells", "in", "the", "anthers", "."], ["2", ".", "Low", "temperature", "overcomes", "this", "inhibition", ",", "resulting", "in", "microsporogenesis", "and", "subsequent", "flowering", "."], ["Microsporogenesis", "must", "thus", "be", "considered", "as", "a", "phase", "initiated", "only", "at", "low", "temperature", "."], ["Photoperiod", "does", "not", "seem", "to", "playa", "decisive", "role", "in", "this", "process", "."], ["3", ".", "Applied", "gibberellic", "acid", "substitutes", "for", "the", "cold", "requirement", "of", "the", "flower", "buds", "."]], "ner": [[], [], [], [], [], [[71, 72, "Plant_hormone"]]], "relations": [[], [], [], [], [], []]}
{"doc_key": "PMID24724816_abstract", "dataset": "pickle", "sentences": [["The", "behavior", "of", "naturally", "virulent", "Meloidogyne", "isolates", "toward", "the", "tomato", "resistance", "gene", "Mi", "in", "major", "tomato-growing", "areas", "in", "Israel", "was", "studied", "for", "the", "first", "time", "."], ["Virulence", "of", "seven", "selected", "isolates", "was", "confirmed", "over", "three", "successive", "generations", "on", "resistant", "(", "Mi-carrying", ")", "and", "susceptible", "(", "non-Mi-carrying", ")", "tomato", "cultivars", "."], ["Diagnostic", "markers", "verified", "the", "predominance", "of", "Meloidogyne", "javanica", "among", "virulent", "isolates", "selected", "on", "resistant", "tomato", "cultivars", "or", "rootstocks", "."], ["To", "better", "understand", "the", "determinants", "of", "nematode", "selection", "on", "Mi-carrying", "plants", ",", "reproduction", "of", "Mi-avirulent", "and", "virulent", "isolates", "Mjav1", "and", "Mjv2", ",", "respectively", ",", "measured", "as", "eggs", "per", "gram", "of", "root", ",", "on", "non-Mi-carrying", ",", "heterozygous", "(", "Mi/mi", ")", "and", "homozygous", "(", "Mi/Mi", ")", "genotypes", "was", "evaluated", "."], ["Although", "no", "reproduction", "of", "Mjav1", "was", "observed", "on", "Mi/Mi", "genotypes", ",", "some", "reproduction", "was", "consistently", "observed", "on", "Mi/mi", "plants", ";", "reproduction", "of", "Mjv2", "on", "the", "homozygous", "and", "heterozygous", "genotypes", "was", "similar", "to", "that", "on", "susceptible", "cultivars", ",", "suggesting", "a", "limited", "quantitative", "effect", "of", "the", "Mi", "gene", "."], ["Histological", "examination", "of", "giant", "cells", "induced", "by", "Mi-virulent", "versus", "avirulent", "isolates", "confirmed", "the", "high", "virulence", "of", "Mjv2", "on", "Mi/mi", "and", "Mi/Mi", "genotypes", ",", "allowing", "the", "formation", "of", "well-developed", "giant-cell", "systems", "despite", "the", "Mi", "gene", "."], ["Analysis", "of", "the", "plant", "defense", "response", "in", "tomato", "Mi/Mi", ",", "Mi/mi", ",", "and", "mi/mi", "genotypes", "to", "both", "avirulent", "and", "virulent", "isolates", "was", "investigated", "by", "quantitative", "real-time", "polymerase", "chain", "reaction", "."], ["Although", "the", "jasmonate", "(JA)-signaling", "pathway", "was", "clearly", "upregulated", "by", "avirulent", "and", "virulent", "isolates", "on", "the", "susceptible", "(", "not", "carrying", "Mi", ")", "and", "heterozygous", "(", "Mi/mi", ")", "plants", ",", "no", "change", "in", "signaling", "was", "observed", "in", "the", "homozygous", "(", "Mi/Mi", ")", "resistant", "line", "following", "incompatible", "interaction", "with", "the", "avirulent", "isolate", "."], ["Thus", ",", "similar", "to", "infection", "promoted", "by", "the", "avirulent", "isolate", "on", "the", "susceptible", "genotype", ",", "the", "Mi-virulent", "isolate", "induced", "the", "JA-dependent", "pathway", ",", "which", "might", "promote", "tomato", "susceptibility", "during", "the", "compatible", "interaction", "with", "the", "homozygous", "(", "Mi/Mi", ")", "resistant", "line", "."], ["These", "results", "have", "important", "consequences", "for", "the", "management", "of", "Mi", "resistance", "genes", "for", "ensuring", "sustainable", "tomato", "farming", "."]], "ner": [[[9, 12, "DNA"], [5, 6, "Multicellular_organism"]], [[38, 48, "Multicellular_organism"]], [[56, 57, "Multicellular_organism"], [64, 67, "Multicellular_organism"]], [[75, 75, "Multicellular_organism"], [78, 79, "Multicellular_organism"], [83, 89, "Multicellular_organism"], [102, 113, "Multicellular_organism"]], [[121, 121, "Multicellular_organism"], [139, 139, "Multicellular_organism"], [125, 126, "Multicellular_organism"], [134, 135, "Multicellular_organism"], [161, 162, "DNA"]], [[180, 180, "Multicellular_organism"], [171, 174, "Organic_compound_other"], [182, 185, "Multicellular_organism"], [196, 197, "DNA"]], [[206, 213, "Multicellular_organism"]], [[231, 233, "Biochemical_pathway"], [248, 248, "DNA"], [253, 253, "DNA"], [267, 267, "DNA"]], [[305, 305, "Multicellular_organism"], [299, 300, "Biochemical_pathway"], [295, 296, "Multicellular_organism"], [315, 315, "DNA"]], [[335, 335, "Multicellular_organism"], [329, 331, "DNA"]]], "relations": [[], [], [], [], [[121, 121, 134, 135, "interacts"], [139, 139, 134, 135, "interacts"], [139, 139, 125, 126, "interacts"]], [[180, 180, 182, 185, "inhibits"]], [], [], [[295, 296, 299, 300, "activates"]], []]}
{"doc_key": "PMID15749761_abstract", "dataset": "pickle", "sentences": [["Histone", "acetylation", "is", "modulated", "through", "the", "action", "of", "histone", "acetyltransferases", "and", "deacetylases", ",", "which", "play", "key", "roles", "in", "the", "regulation", "of", "eukaryotic", "gene", "expression", "."], ["Previously", ",", "we", "have", "identified", "a", "yeast", "histone", "deacetylase", "REDUCED", "POTASSIUM", "DEPENDENCY3", "(", "RPD3", ")", "homolog", ",", "HISTONE", "DEACETYLASE19", "(", "HDA19", ")", "(", "AtRPD3A", ")", ",", "in", "Arabidopsis", "thaliana", "."], ["Here", ",", "we", "report", "further", "study", "of", "the", "expression", "and", "function", "of", "HDA19", "."], ["Analysis", "of", "Arabidopsis", "plants", "containing", "the", "HDA19:beta-glucuronidase", "fusion", "gene", "revealed", "that", "HDA19", "was", "expressed", "throughout", "the", "life", "of", "the", "plant", "and", "in", "most", "plant", "organs", "examined", "."], ["In", "addition", ",", "the", "expression", "of", "HDA19", "was", "induced", "by", "wounding", ",", "the", "pathogen", "Alternaria", "brassicicola", ",", "and", "the", "plant", "hormones", "jasmonic", "acid", "and", "ethylene", "."], ["Using", "green", "fluorescent", "protein", "fusion", ",", "we", "demonstrated", "that", "HDA19", "accumulated", "in", "the", "nuclei", "of", "Arabidopsis", "cells", "."], ["Overexpression", "of", "HDA19", "in", "35S", ":", "HDA19", "plants", "decreased", "histone", "acetylation", "levels", ",", "whereas", "downregulation", "of", "HDA19", "in", "HDA19-RNA", "interference", "(", "RNAi", ")", "plants", "increased", "histone", "acetylation", "levels", "."], ["In", "comparison", "with", "wild-type", "plants", ",", "35S", ":", "HDA19", "transgenic", "plants", "had", "increased", "expression", "of", "ETHYLENE", "RESPONSE", "FACTOR1", "and", "were", "more", "resistant", "to", "the", "pathogen", "A.", "brassicicola", "."], ["The", "expression", "of", "jasmonic", "acid", "and", "ethylene", "regulated", "PATHOGENESIS-RELATED", "genes", ",", "Basic", "Chitinase", "and", "beta-1,3-Glucanase", ",", "was", "upregulated", "in", "35S", ":", "HDA19", "plants", "but", "downregulated", "in", "HDA19-RNAi", "plants", "."], ["Our", "studies", "provide", "evidence", "that", "HDA19", "may", "regulate", "gene", "expression", "involved", "in", "jasmonic", "acid", "and", "ethylene", "signaling", "of", "pathogen", "response", "in", "Arabidopsis", "."]], "ner": [[[0, 1, "Biochemical_process"], [8, 11, "Protein"]], [[42, 43, "DNA"], [45, 45, "DNA"], [52, 53, "Multicellular_organism"], [48, 48, "DNA"], [31, 40, "DNA"]], [[67, 67, "DNA"]], [[75, 77, "DNA"], [80, 80, "DNA"], [71, 71, "Multicellular_organism"]], [[102, 102, "DNA"], [110, 111, "Multicellular_organism"], [115, 120, "Plant_hormone"]], [[131, 131, "Protein"], [137, 138, "Cell"]], [[156, 156, "DNA"], [142, 142, "DNA"], [149, 150, "Biochemical_process"], [165, 166, "Biochemical_process"], [144, 147, "Multicellular_organism"], [158, 163, "Multicellular_organism"]], [[184, 186, "DNA"], [194, 195, "Multicellular_organism"], [175, 179, "Multicellular_organism"]], [[208, 209, "DNA"], [211, 211, "DNA"], [216, 219, "Multicellular_organism"], [223, 224, "Multicellular_organism"], [200, 206, "DNA"]], [[231, 231, "DNA"], [247, 247, "Multicellular_organism"], [238, 242, "Biochemical_process"]]], "relations": [[[8, 11, 0, 1, "interacts"]], [[31, 40, 52, 53, "is-in"], [42, 43, 52, 53, "is-in"], [45, 45, 52, 53, "is-in"], [48, 48, 52, 53, "is-in"]], [], [], [[110, 111, 102, 102, "activates"], [115, 120, 102, 102, "activates"]], [[131, 131, 137, 138, "is-in"]], [[142, 142, 144, 147, "is-in"], [142, 142, 149, 150, "inhibits"], [156, 156, 158, 163, "is-in"], [156, 156, 165, 166, "activates"]], [[184, 186, 175, 179, "is-in"], [175, 179, 194, 195, "inhibits"]], [], [[231, 231, 238, 242, "interacts"], [238, 242, 247, 247, "is-in"]]]}
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{"doc_key": "PMID30076223_abstract", "dataset": "pickle", "sentences": [["Nitrogen", "dioxide", "(", "NO(2", ")", ")", "forms", "in", "plants", "under", "stress", "conditions", ",", "but", "little", "is", "known", "about", "its", "physiological", "functions", "."], ["Here", ",", "we", "explored", "the", "physiological", "functions", "of", "NO(2", ")", "in", "plant", "cells", "using", "short-term", "fumigation", "of", "Arabidopsis", "(", "Arabidopsis", "thaliana", ")", "for", "1", "h", "with", "10", "\u00b5L", "L(-1", ")", "NO(2", ".", ")", "Although", "leaf", "symptoms", "were", "absent", ",", "the", "expression", "of", "genes", "related", "to", "pathogen", "resistance", "was", "induced", "."], ["Fumigated", "plants", "developed", "basal", "disease", "resistance", ",", "or", "pattern-triggered", "immunity", ",", "against", "the", "necrotrophic", "fungus", "Botrytis", "cinerea", "and", "the", "hemibiotrophic", "bacterium", "Pseudomonas", "syringae", "Functional", "salicylic", "acid", "and", "jasmonic", "acid", "(", "JA", ")", "signaling", "pathways", "were", "both", "required", "for", "the", "full", "expression", "of", "NO(2)-induced", "resistance", "against", "B.", "cinerea", "An", "early", "peak", "of", "salicylic", "acid", "accumulation", "immediately", "after", "NO(2", ")", "exposure", "was", "followed", "by", "a", "transient", "accumulation", "of", "oxophytodienoic", "acid", "."], ["The", "simultaneous", "NO(2)-induced", "expression", "of", "genes", "involved", "in", "jasmonate", "biosynthesis", "and", "jasmonate", "catabolism", "resulted", "in", "the", "complete", "suppression", "of", "JA", "and", "JA-isoleucine", "(", "JA-Ile", ")", "accumulation", ",", "which", "was", "accompanied", "by", "a", "rise", "in", "the", "levels", "of", "their", "catabolic", "intermediates", "12-OH-JA", ",", "12-OH-JA-Ile", ",", "and", "12-COOH-JA-Ile", "."], ["NO(2)-treated", "plants", "emitted", "the", "volatile", "monoterpene", "\u03b1-pinene", "and", "the", "sesquiterpene", "longifolene", "(", "syn", ".", "junipene", ")", ",", "which", "could", "function", "in", "signaling", "or", "direct", "defense", "against", "pathogens", "."], ["NO(2)-triggered", "B.", "cinerea", "resistance", "was", "dependent", "on", "enhanced", "early", "callose", "deposition", "and", "CYTOCHROME", "P450", "79B2", "(", "CYP79B2", ")", ",", "CYP79B3", ",", "and", "PHYTOALEXIN", "DEFICIENT3", "gene", "functions", "but", "independent", "of", "camalexin", ",", "CYP81F2", ",", "and", "4-OH-indol-3-ylmethylglucosinolate", "derivatives", "."], ["In", "sum", ",", "exogenous", "NO(2", ")", "triggers", "basal", "pathogen", "resistance", ",", "pointing", "to", "a", "possible", "role", "for", "endogenous", "NO(2", ")", "in", "defense", "signaling", "."], ["Additionally", ",", "this", "study", "revealed", "the", "involvement", "of", "jasmonate", "catabolism", "and", "volatiles", "in", "pathogen", "immunity", "."]], "ner": [[[0, 1, "Inorganic_compound_other"], [3, 4, "Inorganic_compound_other"]], [[30, 31, "Inorganic_compound_other"], [52, 54, "Inorganic_compound_other"], [41, 42, "Multicellular_organism"], [39, 39, "Multicellular_organism"]], [[128, 129, "Inorganic_compound_other"], [87, 88, "Multicellular_organism"], [93, 94, "Unicellular_organism"], [117, 118, "Multicellular_organism"], [123, 125, "Biochemical_process"], [138, 139, "Organic_compound_other"], [80, 81, "Biochemical_pathway"], [114, 115, "Biochemical_process"], [96, 105, "Biochemical_pathway"]], [[149, 150, "Biochemical_pathway"], [152, 153, "Biochemical_pathway"], [160, 166, "Biochemical_process"], [181, 181, "Organic_compound_other"], [183, 183, "Organic_compound_other"], [186, 186, "Organic_compound_other"], [143, 144, "Biochemical_process"]], [[192, 194, "Organic_compound_other"], [197, 198, "Organic_compound_other"], [202, 202, "Organic_compound_other"]], [[216, 219, "Biochemical_process"], [228, 230, "DNA"], [232, 232, "DNA"], [235, 235, "DNA"], [238, 239, "DNA"], [225, 226, "Biochemical_process"], [245, 245, "Organic_compound_other"], [250, 251, "Organic_compound_other"], [247, 247, "DNA"]], [[271, 272, "Inorganic_compound_other"], [257, 258, "Inorganic_compound_other"]], [[285, 286, "Biochemical_pathway"]]], "relations": [[], [], [[80, 81, 87, 88, "inhibits"], [80, 81, 93, 94, "inhibits"], [128, 129, 123, 125, "activates"], [128, 129, 138, 139, "activates"], [96, 105, 114, 115, "interacts"], [114, 115, 117, 118, "inhibits"]], [[143, 144, 160, 166, "inhibits"], [143, 144, 181, 181, "activates"], [143, 144, 183, 183, "activates"], [143, 144, 186, 186, "activates"], [143, 144, 149, 150, "interacts"], [143, 144, 152, 153, "interacts"]], [], [[216, 219, 225, 226, "interacts"], [216, 219, 228, 230, "interacts"], [216, 219, 232, 232, "interacts"], [216, 219, 235, 235, "interacts"], [216, 219, 238, 239, "interacts"]], [], []]}
{"doc_key": "PMID21831212_abstract", "dataset": "pickle", "sentences": [["Ethylene", "responsive", "factors", "(", "ERFs", ")", "are", "a", "large", "family", "of", "plant-specific", "transcription", "factors", "that", "are", "involved", "in", "the", "regulation", "of", "plant", "development", "and", "stress", "responses", "."], ["However", ",", "little", "to", "nothing", "is", "known", "about", "their", "role", "in", "herbivore-induced", "defense", "."], ["We", "discovered", "a", "nucleus-localized", "ERF", "gene", "in", "rice", "(", "Oryza", "sativa", ")", ",", "OsERF3", ",", "that", "was", "rapidly", "up-regulated", "in", "response", "to", "feeding", "by", "the", "rice", "striped", "stem", "borer", "(", "SSB", ")", "Chilo", "suppressalis", "."], ["Antisense", "and", "over-expression", "of", "OsERF3", "revealed", "that", "it", "positively", "affects", "transcript", "levels", "of", "two", "mitogen-activated", "protein", "kinases", "(", "MAPKs", ")", "and", "two", "WRKY", "genes", "as", "well", "as", "concentrations", "of", "jasmonate", "(", "JA", ")", ",", "salicylate", "(", "SA", ")", "and", "the", "activity", "of", "trypsin", "protease", "inhibitors", "(", "TrypPIs", ")", "."], ["OsERF3", "was", "also", "found", "to", "mediate", "the", "resistance", "of", "rice", "to", "SSB", "."], ["On", "the", "other", "hand", ",", "OsERF3", "was", "slightly", "suppressed", "by", "the", "rice", "brown", "planthopper", "(", "BPH", ")", "Nilaparvata", "lugens", "(", "St\u00e5l", ")", "and", "increased", "susceptibility", "to", "this", "piercing", "sucking", "insect", ",", "possibly", "by", "suppressing", "H(2)O(2", ")", "biosynthesis", "."], ["We", "propose", "that", "OsERF3", "affects", "early", "components", "of", "herbivore-induced", "defense", "responses", "by", "suppressing", "MAPK", "repressors", "and", "modulating", "JA", ",", "SA", ",", "ethylene", "and", "H(2)O(2", ")", "pathways", "as", "well", "as", "plant", "resistance", "."], ["Our", "results", "also", "illustrate", "that", "OsERF3", "acts", "as", "a", "central", "switch", "that", "gears", "the", "plant", "'s", "metabolism", "towards", "an", "appropriate", "response", "to", "chewing", "or", "piercing/sucking", "insects", "."]], "ner": [[[0, 2, "Protein"], [4, 4, "Protein"]], [], [[44, 46, "DNA"], [48, 48, "Multicellular_organism"], [50, 51, "Multicellular_organism"], [54, 54, "DNA"], [66, 69, "Multicellular_organism"], [71, 71, "Multicellular_organism"], [73, 74, "Multicellular_organism"]], [[80, 80, "DNA"], [90, 92, "Protein"], [94, 94, "Protein"], [98, 99, "DNA"], [105, 105, "Plant_hormone"], [107, 107, "Plant_hormone"], [110, 110, "Plant_hormone"], [112, 112, "Plant_hormone"], [118, 120, "Protein"], [122, 122, "Protein"]], [[125, 125, "DNA"], [134, 134, "Multicellular_organism"], [136, 136, "Multicellular_organism"]], [[143, 143, "DNA"], [149, 151, "Multicellular_organism"], [153, 153, "Multicellular_organism"], [155, 159, "Multicellular_organism"], [172, 174, "Biochemical_process"]], [[179, 179, "DNA"], [189, 190, "Protein"], [193, 201, "Biochemical_pathway"]], [[213, 213, "DNA"]]], "relations": [[], [], [[44, 46, 48, 48, "is-in"], [44, 46, 50, 51, "is-in"], [54, 54, 48, 48, "is-in"], [54, 54, 50, 51, "is-in"], [66, 69, 54, 54, "activates"], [71, 71, 54, 54, "activates"], [73, 74, 54, 54, "activates"]], [[80, 80, 90, 92, "activates"], [80, 80, 94, 94, "activates"], [80, 80, 98, 99, "activates"], [80, 80, 105, 105, "activates"], [80, 80, 107, 107, "activates"], [80, 80, 110, 110, "activates"], [80, 80, 112, 112, "activates"], [80, 80, 118, 120, "activates"], [80, 80, 122, 122, "activates"]], [[125, 125, 136, 136, "inhibits"], [134, 134, 136, 136, "interacts"]], [[149, 151, 143, 143, "inhibits"], [153, 153, 143, 143, "inhibits"], [155, 159, 143, 143, "inhibits"]], [[179, 179, 189, 190, "inhibits"], [179, 179, 193, 201, "interacts"]], []]}
{"doc_key": "PMID24318175_abstract", "dataset": "pickle", "sentences": [["Abscisic-acid", "(", "ABA", ")", "levels", "were", "determined", "in", "triticale", "6A190", "kernels", "at", "various", "stages", "of", "development", "from", "anthesis", "to", "maturity", "."], ["ABA", "reached", "a", "maximum", "at", "ca", "."], ["22", "d", "post-anthesis", "and", "declined", "rapidly", "12", "d", "later", "."], ["Associated", "with", "drying", "of", "the", "kernel", "at", "maturity", "there", "was", "a", "rapid", "increase", "in", "the", "endogenous", "level", "of", "\u03b1-amylase", ",", "apparently", "based", "upon", "de-novo", "synthesis", "."], ["Simultaneously", "there", "were", "visible", "signs", "of", "degradation", "of", "the", "large", "starch", "grains", "in", "the", "starchy", "endosperm", "."], ["Regulation", "of", "\u03b1-amylase", "production", "in", "the", "kernel", "by", "exogenous", "gibberellic", "acid", "(", "GA3", ")", "was", "only", "evident", "in", "the", "almost", "mature", "kernel", "(", "30", "-", "40", "d", "after", "anthesis", ")", "and", "then", "only", "if", "these", "kernels", "were", "first", "dried", "artificially", "."], ["Furthermore", ",", "little", "\u03b1-amylase", "mRNA", "could", "be", "detected", "prior", "to", "kernel", "maturity", "and", "water", "loss", "."], ["Thus", ",", "the", "high", "levels", "of", "gibberellin", "(", "GA", ")", "that", "have", "been", "found", "early", "in", "kernel", "development", "in", "cereals", "do", "not", "appear", "to", "control", "the", "later", "production", "of", "\u03b1-amylase", "and", "onset", "of", "kernel", "germination", "in", "the", "ear", "of", "triticale", "."], ["However", ",", "the", "presence", "of", "high", "levels", "of", "ABA", "until", "maturity", "could", "prevent", "early", "germination", "and", "premature", "production", "of", "\u03b1-amylase", "."], ["Kernels", "of", "triticale", "6A190", "are", "characteristically", "shrivelled", "and", "non-dormant", "at", "maturity", "."], ["The", "relevance", "of", "changes", "in", "the", "capacity", "of", "kernels", "to", "respond", "to", "and", "produce", "GA", "and", "ABA", "is", "discussed", "in", "relation", "to", "problems", "of", "harvest", "dormancy", "in", "cereals", "."]], "ner": [[[0, 0, "Plant_hormone"], [2, 2, "Plant_hormone"], [8, 10, "Plant_region"]], [[21, 21, "Plant_hormone"]], [], [[56, 56, "Protein"]], [], [[83, 84, "Biochemical_process"], [90, 91, "Plant_hormone"], [93, 93, "Plant_hormone"]], [[125, 126, "RNA"]], [[144, 144, "Plant_hormone"], [146, 146, "Plant_hormone"], [157, 157, "Multicellular_organism"], [167, 167, "Protein"], [177, 177, "Multicellular_organism"]], [[187, 187, "Plant_hormone"], [198, 198, "Protein"]], [[202, 203, "Multicellular_organism"]], [[226, 226, "Plant_hormone"], [228, 228, "Plant_hormone"], [239, 239, "Multicellular_organism"]]], "relations": [[], [], [], [], [], [[90, 91, 83, 84, "interacts"], [93, 93, 83, 84, "interacts"]], [], [[146, 146, 157, 157, "is-in"], [144, 144, 157, 157, "is-in"], [167, 167, 177, 177, "is-in"]], [[187, 187, 198, 198, "inhibits"]], [], []]}
{"doc_key": "PMID24493088_abstract", "dataset": "pickle", "sentences": [["The", "activities", "of", "(\u00b1)-abscisic", "acid", "and", "a", "number", "of", "compounds", "derived", "from", "p-coumaric", "acid", "and", "coumarin", "and", "their", "interaction", "with", "gibberellic", "acid", "in", "the", "control", "of", "the", "elongation", "of", "the", "first", "wheat", "leaf", "are", "examined", "."], ["(\u00b1)-Abscisic", "acid", "strongly", "inhibits", "leaf", "growth", "in", "the", "presence", "as", "well", "as", "in", "the", "absence", "of", "gibberellic", "acid", ",", "but", "the", "inhibition", "is", "greater", "in", "the", "presence", "of", "gibberellic", "acid", "(", "3", "\u03bcg/l", "already", "have", "an", "observable", "effect", ")", "."], ["Among", "other", "compounds", ",", "only", "ferulic", "acid", "and", "coumarin", "significantly", "reduce", "leaf", "elongation", ",", "and", "they", "are", "effective", "only", "at", "high", "concentrations", "(", "1.44", "\u00b7", "10(-4", ")", "M/l", ")", "."]], "ner": [[[12, 13, "Organic_compound_other"], [15, 15, "Organic_compound_other"], [20, 21, "Plant_hormone"], [31, 32, "Plant_region"], [3, 4, "Plant_hormone"]], [[52, 53, "Plant_hormone"], [64, 65, "Plant_hormone"], [36, 37, "Plant_hormone"]], [[81, 82, "Organic_compound_other"], [84, 84, "Organic_compound_other"]]], "relations": [[], [[36, 37, 52, 53, "interacts"], [36, 37, 64, 65, "interacts"]], []]}
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{"doc_key": "PMID12746525_abstract", "dataset": "pickle", "sentences": [["The", "role", "of", "ethylene", "(", "ET", ")", "signaling", "in", "the", "responses", "of", "two", "hybrid", "aspen", "(", "Populus", "tremula", "L.", "x", "P.", "tremuloides", "Michx", ".", ")", "clones", "to", "chronic", "ozone", "(", "O(3", ")", ";", "75", "nL", "L(-1", ")", ")", "was", "investigated", "."], ["The", "hormonal", "responses", "differed", "between", "the", "clones", ";", "the", "O(3)-sensitive", "clone", "51", "had", "higher", "ET", "evolution", "than", "the", "tolerant", "clone", "200", "during", "the", "exposure", ",", "whereas", "the", "free", "salicylic", "acid", "concentration", "in", "clone", "200", "was", "higher", "than", "in", "clone", "51", "."], ["The", "cellular", "redox", "status", ",", "measured", "as", "glutathione", "redox", "balance", ",", "did", "not", "differ", "between", "the", "clones", "suggesting", "that", "the", "O(3", ")", "lesions", "were", "not", "a", "result", "of", "deficient", "antioxidative", "capacity", "."], ["The", "buildup", "of", "salicylic", "acid", "during", "chronic", "O(3", ")", "exposure", "might", "have", "prevented", "the", "up-regulation", "of", "ET", "biosynthesis", "in", "clone", "200", "."], ["Blocking", "of", "ET", "perception", "with", "1-methylcyclopropene", "protected", "both", "clones", "from", "the", "decrease", "in", "net", "photosynthesis", "during", "chronic", "exposure", "to", "O(3", ")", "."], ["After", "a", "pretreatment", "with", "low", "O(3", ")", "for", "9", "d", ",", "an", "acute", "1.5-fold", "O(3", ")", "elevation", "caused", "necrosis", "in", "the", "O(3)-sensitive", "clone", "51", ",", "which", "increased", "substantially", "when", "ET", "perception", "was", "blocked", "."], ["The", "results", "suggest", "that", "in", "hybrid", "aspen", ",", "ET", "signaling", "had", "a", "dual", "role", "depending", "on", "the", "severity", "of", "the", "stress", "."], ["ET", "accelerated", "leaf", "senescence", "under", "low", "O(3", ")", ",", "but", "under", "acute", "O(3", ")", "elevation", ",", "ET", "signaling", "seemed", "to", "be", "required", "for", "protection", "from", "necrotic", "cell", "death", "."]], "ner": [[[3, 7, "Biochemical_process"], [28, 28, "Inorganic_compound_other"], [30, 31, "Inorganic_compound_other"], [13, 25, "Multicellular_organism"]], [[50, 52, "Multicellular_organism"], [55, 56, "Biochemical_process"], [60, 61, "Multicellular_organism"], [68, 70, "Plant_hormone"], [73, 74, "Multicellular_organism"], [79, 80, "Multicellular_organism"]], [[89, 89, "Organic_compound_other"], [102, 103, "Inorganic_compound_other"]], [[117, 118, "Plant_hormone"], [121, 122, "Inorganic_compound_other"], [130, 131, "Biochemical_pathway"], [133, 134, "Multicellular_organism"]], [[138, 139, "Biochemical_pathway"], [141, 141, "Organic_compound_other"], [155, 156, "Inorganic_compound_other"]], [[163, 164, "Inorganic_compound_other"], [172, 173, "Inorganic_compound_other"], [179, 181, "Multicellular_organism"], [187, 188, "Biochemical_pathway"]], [[197, 198, "Multicellular_organism"], [200, 201, "Biochemical_process"]], [[220, 221, "Inorganic_compound_other"], [226, 227, "Inorganic_compound_other"], [214, 214, "Plant_hormone"], [230, 231, "Biochemical_process"], [216, 217, "Biochemical_process"]]], "relations": [[], [[68, 70, 73, 74, "is-in"], [68, 70, 79, 80, "is-in"]], [], [[130, 131, 133, 134, "is-in"], [121, 122, 117, 118, "activates"]], [[141, 141, 138, 139, "inhibits"]], [[172, 173, 179, 181, "inhibits"]], [[200, 201, 197, 198, "is-in"]], [[214, 214, 216, 217, "activates"]]]}
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{"doc_key": "PMID25596183_abstract", "dataset": "pickle", "sentences": [["The", "hemibiotrophic", "fungus", "Zymoseptoria", "tritici", "causes", "Septoria", "tritici", "blotch", "disease", "of", "wheat", "(", "Triticum", "aestivum", ")", "."], ["Pathogen", "reproduction", "on", "wheat", "occurs", "without", "cell", "penetration", ",", "suggesting", "that", "dynamic", "and", "intimate", "intercellular", "communication", "occurs", "between", "fungus", "and", "plant", "throughout", "the", "disease", "cycle", "."], ["We", "used", "deep", "RNA", "sequencing", "and", "metabolomics", "to", "investigate", "the", "physiology", "of", "plant", "and", "pathogen", "throughout", "an", "asexual", "reproductive", "cycle", "of", "Z.", "tritici", "on", "wheat", "leaves", "."], ["Over", "3,000", "pathogen", "genes", ",", "more", "than", "7,000", "wheat", "genes", ",", "and", "more", "than", "300", "metabolites", "were", "differentially", "regulated", "."], ["Intriguingly", ",", "individual", "fungal", "chromosomes", "contributed", "unequally", "to", "the", "overall", "gene", "expression", "changes", "."], ["Early", "transcriptional", "down-regulation", "of", "putative", "host", "defense", "genes", "was", "detected", "in", "inoculated", "leaves", "."], ["There", "was", "little", "evidence", "for", "fungal", "nutrient", "acquisition", "from", "the", "plant", "throughout", "symptomless", "colonization", "by", "Z.", "tritici", ",", "which", "may", "instead", "be", "utilizing", "lipid", "and", "fatty", "acid", "stores", "for", "growth", "."], ["However", ",", "the", "fungus", "then", "subsequently", "manipulated", "specific", "plant", "carbohydrates", ",", "including", "fructan", "metabolites", ",", "during", "the", "switch", "to", "necrotrophic", "growth", "and", "reproduction", "."], ["This", "switch", "coincided", "with", "increased", "expression", "of", "jasmonic", "acid", "biosynthesis", "genes", "and", "large-scale", "activation", "of", "other", "plant", "defense", "responses", "."], ["Fungal", "genes", "encoding", "putative", "secondary", "metabolite", "clusters", "and", "secreted", "effector", "proteins", "were", "identified", "with", "distinct", "infection", "phase-specific", "expression", "patterns", ",", "although", "functional", "analysis", "suggested", "that", "many", "have", "overlapping/redundant", "functions", "in", "virulence", "."], ["The", "pathogenic", "lifestyle", "of", "Z.", "tritici", "on", "wheat", "revealed", "through", "this", "study", ",", "involving", "initial", "defense", "suppression", "by", "a", "slow-growing", "extracellular", "and", "nutritionally", "limited", "pathogen", "followed", "by", "defense", "(", "hyper", ")", "activation", "during", "reproduction", ",", "reveals", "a", "subtle", "modification", "of", "the", "conceptual", "definition", "of", "hemibiotrophic", "plant", "infection", "."]], "ner": [[[13, 14, "Multicellular_organism"], [11, 11, "Multicellular_organism"], [3, 4, "Multicellular_organism"], [6, 9, "Biochemical_process"]], [[20, 20, "Multicellular_organism"]], [[64, 65, "Multicellular_organism"], [67, 68, "Plant_region"]], [[78, 78, "Multicellular_organism"]], [], [], [[133, 134, "Multicellular_organism"], [143, 144, "Organic_compound_other"]], [[161, 162, "Organic_compound_other"]], [[180, 182, "Biochemical_pathway"]], [], [[229, 230, "Multicellular_organism"]]], "relations": [[[3, 4, 11, 11, "interacts"], [3, 4, 13, 14, "interacts"], [3, 4, 6, 9, "produces"]], [], [], [], [], [], [], [], [], [], []]}
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{"doc_key": "PMID24095919_abstract", "dataset": "pickle", "sentences": [["The", "plant", "hormone", "ethylene", "is", "involved", "in", "many", "physiological", "processes", ",", "including", "plant", "growth", ",", "development", "and", "senescence", "."], ["Ethylene", "also", "plays", "a", "pivotal", "role", "in", "plant", "response", "or", "adaptation", "under", "biotic", "and", "abiotic", "stress", "conditions", "."], ["In", "plants", ",", "ethylene", "production", "often", "enhances", "the", "tolerance", "to", "sub-optimal", "environmental", "conditions", "."], ["This", "role", "is", "particularly", "important", "from", "both", "ecological", "and", "agricultural", "point", "of", "views", "."], ["Among", "the", "abiotic", "stresses", ",", "the", "role", "of", "ethylene", "in", "plants", "under", "nutrient", "stress", "conditions", "has", "not", "been", "completely", "investigated", "."], ["In", "literature", "few", "reports", "are", "available", "on", "the", "interaction", "among", "ethylene", "and", "macro-", "or", "micro-nutrients", "."], ["However", ",", "the", "published", "works", "clearly", "demonstrated", "that", "several", "mineral", "nutrients", "largely", "affect", "ethylene", "biosynthesis", "and", "perception", "with", "a", "strong", "influence", "on", "plant", "physiology", "."], ["The", "aim", "of", "this", "review", "is", "to", "revisit", "the", "old", "findings", "and", "recent", "advances", "of", "knowledge", "regarding", "the", "sub-optimal", "nutrient", "conditions", "on", "the", "effect", "of", "ethylene", "biosynthesis", "and", "perception", "in", "plants", "."], ["The", "effect", "of", "deficiency", "or", "excess", "of", "the", "single", "macronutrient", "or", "micronutrient", "on", "the", "ethylene", "pathway", "and", "plant", "responses", "are", "reviewed", "and", "discussed", "."], ["The", "synergistic", "and", "antagonist", "effect", "of", "the", "different", "mineral", "nutrients", "on", "ethylene", "plant", "responses", "is", "critically", "analyzed", "."], ["Moreover", ",", "this", "review", "highlights", "the", "status", "of", "information", "between", "nutritional", "stresses", "and", "plant", "response", ",", "emphasizing", "the", "topics", "that", "should", "be", "further", "investigated", "."]], "ner": [[[1, 3, "Plant_hormone"]], [[19, 19, "Plant_hormone"]], [[40, 41, "Biochemical_process"]], [], [[73, 73, "Plant_hormone"]], [[96, 96, "Plant_hormone"]], [[115, 116, "Biochemical_pathway"]], [[152, 155, "Biochemical_process"]], [[173, 174, "Biochemical_pathway"]], [[194, 196, "Biochemical_process"]], []], "relations": [[], [], [], [], [], [], [], [], [], [], []]}
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