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{"doc_key": "PMID16716453_abstract", "dataset": "pickle", "sentences": [["Calcium-dependent", "protein", "kinases", "(", "CPKs", ")", "play", "important", "roles", "in", "multiple", "signal", "transduction", "pathways", "but", "the", "precise", "role", "of", "individual", "CPK", "is", "largely", "unknown", "."], ["We", "isolated", "two", "cDNAs", "encoding", "two", "CPK", "isoforms", "(", "Cicer", "arietinum", "CPKs-CaCPK1", "and", "CaCPK2", ")", "of", "chickpea", "."], ["Their", "expression", "in", "various", "organs", "and", "in", "response", "to", "various", "phytohormones", ",", "and", "dehydration", ",", "high", "salt", "stress", "and", "fungal", "spore", "in", "excised", "leaves", "as", "well", "as", "localization", "in", "leaf", "and", "stem", "tissues", "were", "analyzed", "in", "this", "study", "."], ["CaCPK1", "protein", "and", "its", "activity", "were", "ubiquitous", "in", "all", "tissues", "examined", "."], ["In", "contrast", ",", "CaCPK2", "transcript", ",", "CaCPK2", "protein", "and", "its", "activity", "were", "almost", "undetectable", "in", "flowers", "and", "fruits", "."], ["Both", "CaCPK1", "and", "CaCPK2", "transcripts", "and", "proteins", "were", "abundant", "in", "roots", "but", "in", "minor", "quantities", "in", "leaves", "and", "stems", "."], ["Of", "the", "three", "phytohormones", "tested", ",", "viz", ".", "indole-3-acetic", "acid", "(", "IAA", ")", ",", "gibberellin", "(", "GA(3", ")", ")", "and", "benzyladenine", "(", "BA", ")", ",", "only", "BA", "increased", "both", "CaCPK1", "and", "CaCPK2", "transcripts", ",", "proteins", "and", "their", "activities", "."], ["GA(3", ")", "induced", "accumulation", "of", "CaCPK2", "transcript", "and", "protein", "but", "CaCPK1", "remained", "unaffected", "."], ["The", "expression", "of", "CaCPK1", "and", "CaCPK2", "in", "leaves", "was", "enhanced", "in", "response", "to", "high", "salt", "stress", "."], ["Treatments", "with", "Aspergillus", "sp.", "spores", "increased", "expression", "of", "CaCPK1", "in", "chickpea", "leaf", "tissue", "but", "had", "no", "effect", "on", "CaCPK2", "."], ["Excised", "leaves", "subjected", "to", "dehydration", "showed", "increase", "in", "CaCPK2", "expression", "but", "not", "in", "CaCPK1", "."], ["Both", "isoforms", "were", "located", "in", "the", "plasma", "membrane", "(", "PM", ")", "and", "chloroplast", "membrane", "of", "leaf", "mesophyll", "cells", "as", "well", "as", "in", "the", "PM", "of", "stem", "xylem", "parenchyma", "cells", "."], ["These", "results", "suggest", "specific", "roles", "for", "CaCPK", "isoforms", "in", "phytohormone/defense/stress", "signaling", "pathways", "."]], "ner": [[[0, 2, "Protein"], [4, 4, "Protein"], [20, 20, "Protein"]], [[31, 32, "Protein"], [34, 38, "Multicellular_organism"], [41, 41, "Multicellular_organism"]], [[53, 53, "Plant_hormone"], [59, 59, "Inorganic_compound_other"]], [[82, 83, "Protein"]], [[97, 98, "RNA"], [100, 101, "Protein"]], [[114, 119, "Organic_compound_other"]], [[136, 136, "Plant_hormone"], [141, 142, "Plant_hormone"], [144, 144, "Plant_hormone"], [147, 147, "Plant_hormone"], [149, 150, "Plant_hormone"], [153, 153, "Plant_hormone"], [155, 155, "Plant_hormone"], [159, 159, "Plant_hormone"], [162, 165, "RNA"]], [[172, 173, "Plant_hormone"], [177, 180, "Organic_compound_other"], [182, 182, "Protein"]], [[189, 189, "DNA"], [191, 191, "DNA"], [200, 200, "Inorganic_compound_other"]], [[205, 207, "Cell"], [211, 211, "DNA"], [213, 215, "Tissue"], [221, 221, "DNA"]], [[231, 232, "Biochemical_process"], [236, 236, "DNA"]], [], [[274, 275, "Protein"], [277, 279, "Biochemical_pathway"]]], "relations": [[], [[34, 38, 41, 41, "is-in"]], [], [], [], [], [[159, 159, 162, 165, "activates"]], [[172, 173, 177, 180, "activates"]], [[200, 200, 191, 191, "activates"], [200, 200, 189, 189, "activates"]], [[205, 207, 211, 211, "activates"], [211, 211, 213, 215, "is-in"]], [], [], [[274, 275, 277, 279, "is-in"]]]}
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{"doc_key": "PMID33793923_abstract", "dataset": "pickle", "sentences": [["The", "potassium", "ion", "(", "K+", ")", "is", "vital", "for", "plant", "growth", "and", "development", ",", "and", "K+-deprivation", "leads", "to", "reduced", "crop", "yields", "."], ["Here", "we", "describe", "phenotypic", ",", "transcriptomic", ",", "and", "mutant", "analyses", "to", "investigate", "the", "signaling", "mechanisms", "mediating", "root", "architectural", "changes", "in", "Arabidopsis", "(", "Arabidopsis", "thaliana", ")", "Columbia", "."], ["We", "showed", "effects", "on", "root", "architecture", "are", "mediated", "through", "a", "reduction", "in", "cell", "division", "in", "the", "lateral", "root", "(", "LR", ")", "meristems", ",", "the", "rate", "of", "LR", "initiation", "is", "reduced", "but", "LR", "density", "is", "unaffected", ",", "and", "primary", "root", "growth", "is", "reduced", "only", "slightly", "."], ["This", "was", "primarily", "regulated", "through", "gibberellic", "acid", "(", "GA", ")", "signaling", ",", "which", "leads", "to", "the", "accumulation", "of", "growth-inhibitory", "DELLA", "proteins", "."], ["The", "short", "LR", "phenotype", "was", "rescued", "by", "exogenous", "application", "of", "GA", "but", "not", "of", "auxin", "or", "by", "the", "inhibition", "of", "ethylene", "signaling", "."], ["RNA-seq", "analysis", "showed", "upregulation", "by", "K+-deprivation", "of", "the", "transcription", "factors", "JUNGBRUNNEN1", "(", "JUB1", ")", "and", "the", "C-repeat-binding", "factor", "(CBF)/dehydration-responsive", "element-binding", "factor", "1", "regulon", ",", "which", "are", "known", "to", "regulate", "GA", "signaling", "and", "levels", "that", "regulate", "DELLAs", "."], ["Transgenic", "overexpression", "of", "JUB1", "and", "CBF1", "enhanced", "responses", "to", "K+", "stress", "."], ["Attenuation", "of", "the", "reduced", "LR", "growth", "response", "occurred", "in", "mutants", "of", "the", "CBF1", "target", "gene", "SFR6", ",", "implicating", "a", "role", "for", "JUB1", ",", "CBF1", ",", "and", "SFR6", "in", "the", "regulation", "of", "LR", "growth", "in", "response", "to", "K+-deprivation", "via", "DELLAs", "."], ["We", "propose", "this", "represents", "a", "mechanism", "to", "limit", "horizontal", "root", "growth", "in", "conditions", "where", "K+", "is", "available", "deeper", "in", "the", "soil", "."]], "ner": [[[1, 2, "Element"], [4, 4, "Element"], [15, 15, "Biochemical_process"]], [[42, 47, "Multicellular_organism"]], [], [[99, 104, "Biochemical_process"], [112, 114, "Protein"]], [[126, 126, "Plant_hormone"], [130, 130, "Plant_hormone"], [136, 137, "Biochemical_process"]], [[144, 144, "Biochemical_process"], [149, 149, "DNA"], [151, 151, "DNA"], [155, 161, "DNA"], [168, 169, "Biochemical_process"], [174, 174, "Protein"]], [[179, 179, "DNA"], [181, 181, "DNA"], [185, 185, "Element"]], [[200, 203, "DNA"], [209, 209, "DNA"], [211, 211, "DNA"], [214, 214, "DNA"], [224, 224, "Biochemical_process"], [226, 226, "Protein"]], [[242, 242, "Element"]]], "relations": [[], [], [], [[99, 104, 112, 114, "activates"]], [], [[144, 144, 149, 149, "activates"], [144, 144, 151, 151, "activates"], [144, 144, 155, 161, "activates"], [149, 149, 168, 169, "interacts"], [151, 151, 168, 169, "interacts"], [155, 161, 168, 169, "interacts"]], [[179, 179, 185, 185, "interacts"], [181, 181, 185, 185, "interacts"]], [[209, 209, 224, 224, "interacts"], [211, 211, 224, 224, "interacts"], [214, 214, 224, 224, "interacts"], [209, 209, 226, 226, "interacts"], [211, 211, 226, 226, "interacts"], [214, 214, 226, 226, "interacts"]], []]}
{"doc_key": "PMID26881925_abstract", "dataset": "pickle", "sentences": [["Effects", "of", "α-ketol", "linolenic", "acid", "(", "KODA", ")", "application", "on", "endogenous", "abscisic", "acid", "(", "ABA", ")", ",", "jasmonic", "acid", "(", "JA", ")", ",", "and", "aromatic", "volatiles", "were", "investigated", "in", "'", "Kyoho", "'", "grapes", "(", "Vitis", "labrusca", "×", "Vitis", "vinifera", ")", "infected", "by", "a", "pathogen", "(", "Glomerella", "cingulata", ")", "."], ["The", "expressions", "of", "9-cis-epoxycarotenoid", "dioxygenase", "(", "VvNCED1", ")", ",", "ABA", "8'-hydroxylase", "(", "VvCYP707A1", ")", ",", "lipoxygenase", "(", "VvLOX", ")", ",", "and", "allene", "oxide", "synthase", "(", "VvAOS", ")", "were", "also", "examined", "."], ["The", "grape", "berries", "were", "dipped", "in", "0.1mM", "KODA", "solution", "before", "inoculation", "with", "the", "pathogen", "and", "stored", "at", "25", "°", "C", "for", "12", "days", "."], ["The", "development", "of", "infection", "was", "significantly", "suppressed", "upon", "KODA", "treatment", "."], ["Endogenous", "ABA", ",", "JA", "and", "phaseic", "acid", "(", "PA", ")", "were", "induced", "in", "inoculated", "berries", "."], ["KODA", "application", "before", "inoculation", "increased", "endogenous", "ABA", ",", "PA", "and", "JA", "through", "the", "activation", "of", "VvNCED1", ",", "VvCYP707A1", "and", "VvAOS", "genes", ",", "respectively", "."], ["In", "addition", ",", "terpenes", ",", "methyl", "salicylate", "(", "Me-SA", ")", "and", "C6-aldehydes", "such", "as", "(E)-2-hexenal", "and", "cis-3-hexenal", "associated", "with", "fungal", "resistance", "also", "increased", "in", "KODA-treated", "berries", "during", "storage", "."], ["These", "results", "suggest", "that", "the", "synergistic", "effect", "of", "JA", ",", "ABA", ",", "and", "some", "aromatic", "volatiles", "induced", "by", "KODA", "application", "may", "provide", "resistance", "to", "pathogen", "infection", "in", "grape", "berries", "."]], "ner": [[[2, 4, "Organic_compound_other"], [6, 6, "Organic_compound_other"], [11, 12, "Plant_hormone"], [14, 14, "Plant_hormone"], [20, 20, "Plant_hormone"], [17, 18, "Plant_hormone"], [29, 32, "Multicellular_organism"], [34, 38, "Multicellular_organism"], [45, 46, "Multicellular_organism"]], [[52, 53, "DNA"], [55, 55, "DNA"], [58, 59, "DNA"], [61, 61, "DNA"], [64, 64, "DNA"], [66, 66, "DNA"], [70, 72, "DNA"], [74, 74, "DNA"]], [[87, 87, "Organic_compound_other"], [81, 82, "Plant_region"]], [[112, 112, "Organic_compound_other"]], [[120, 121, "Organic_compound_other"], [123, 123, "Organic_compound_other"], [116, 116, "Plant_hormone"], [118, 118, "Plant_hormone"]], [[131, 131, "Organic_compound_other"], [139, 139, "Organic_compound_other"], [137, 137, "Plant_hormone"], [141, 141, "Plant_hormone"], [146, 151, "DNA"]], [[169, 169, "Organic_compound_other"], [166, 166, "Organic_compound_other"], [171, 171, "Organic_compound_other"], [160, 161, "Plant_hormone"], [163, 163, "Plant_hormone"], [158, 158, "Organic_compound_other"]], [[202, 202, "Organic_compound_other"], [192, 192, "Plant_hormone"], [194, 194, "Plant_hormone"], [211, 212, "Plant_region"]]], "relations": [[], [], [], [], [], [[131, 131, 137, 137, "activates"], [131, 131, 139, 139, "activates"], [131, 131, 141, 141, "activates"], [131, 131, 146, 151, "activates"]], [], [[202, 202, 192, 192, "activates"], [202, 202, 194, 194, "activates"]]]}
{"doc_key": "PMID26348016_abstract", "dataset": "pickle", "sentences": [["Apoplast", ",", "the", "diffusional", "space", "between", "plant", "cell", "plasma", "membranes", ",", "is", "an", "important", "medium", "for", "signaling", "within", "and", "between", "the", "cells", "."], ["Apoplastic", "reactive", "oxygen", "species", "(", "ROS", ")", "are", "crucial", "signaling", "molecules", "in", "various", "biological", "processes", "."], ["ROS", "signaling", "is", "interconnected", "with", "the", "response", "to", "several", "hormones", ",", "including", "jasmonic", "acid", "(", "JA", ")", ",", "salicylic", "acid", "(", "SA", ")", "and", "ethylene", "."], ["Using", "ozone", "(", "O3", ")", "to", "activate", "apoplastic", "ROS", "signaling", ",", "we", "performed", "global", "and", "targeted", "analysis", "of", "transcriptional", "changes", "and", "cell", "death", "assays", "to", "dissect", "the", "contribution", "of", "hormone", "signaling", "and", "various", "transcription", "factors", "(", "TFs", ")", "in", "the", "regulation", "of", "gene", "expression", "and", "cell", "death", "."], ["The", "contributions", "of", "SA", ",", "JA", ",", "and", "ethylene", "were", "assessed", "through", "analysis", "of", "single", ",", "double", ",", "and", "triple", "mutants", "deficient", "in", "biosynthesis", "or", "signaling", "for", "all", "three", "hormones", "."], ["Even", "in", "the", "triple", "mutant", ",", "the", "global", "gene", "expression", "responses", "to", "O3", "were", "mostly", "similar", "to", "the", "wild-type", "."], ["Cell", "death", "in", "the", "JA", "receptor", "mutant", "coi1", "-", "16", "was", "suppressed", "by", "impairment", "of", "the", "NADPH", "oxidase", "RBOHF", ",", "suggesting", "a", "role", "for", "a", "ROS", "signal", "in", "limiting", "the", "spread", "of", "cell", "death", "."], ["In", "response", "to", "apoplastic", "ROS", ",", "there", "is", "not", "a", "single", "signaling", "pathway", "that", "regulates", "gene", "expression", "or", "cell", "death", "."], ["Instead", ",", "several", "pathways", "regulate", "the", "apoplastic", "ROS", "response", "via", "combinatorial", "or", "overlapping", "mechanisms", "."]], "ner": [[], [[28, 28, "Inorganic_compound_other"], [23, 26, "Inorganic_compound_other"]], [[39, 40, "Biochemical_process"], [51, 52, "Plant_hormone"], [54, 54, "Plant_hormone"], [57, 58, "Plant_hormone"], [60, 60, "Plant_hormone"], [63, 63, "Plant_hormone"]], [[66, 66, "Inorganic_compound_other"], [68, 68, "Inorganic_compound_other"], [72, 74, "Biochemical_process"]], [[116, 116, "Plant_hormone"], [121, 121, "Plant_hormone"], [118, 118, "Plant_hormone"]], [[156, 156, "Inorganic_compound_other"]], [[189, 189, "Inorganic_compound_other"], [168, 173, "Multicellular_organism"], [180, 182, "Protein"]], [[202, 203, "Inorganic_compound_other"]], [[226, 228, "Biochemical_process"]]], "relations": [[], [], [[51, 52, 39, 40, "interacts"], [54, 54, 39, 40, "interacts"], [57, 58, 39, 40, "interacts"], [60, 60, 39, 40, "interacts"], [63, 63, 39, 40, "interacts"]], [[66, 66, 72, 74, "activates"], [68, 68, 72, 74, "activates"]], [], [], [], [], []]}
{"doc_key": "PMID28584068_abstract", "dataset": "pickle", "sentences": [["In", "tobacco", "(", "Nicotiana", "tabacum", ")", ",", "nicotine", "is", "the", "predominant", "alkaloid", "."], ["It", "is", "produced", "in", "the", "roots", "and", "accumulated", "mainly", "in", "the", "leaves", "."], ["Jasmonates", "play", "a", "central", "signaling", "role", "in", "damage-induced", "nicotine", "formation", "."], ["The", "genome", "sequence", "of", "tobacco", "provides", "us", "an", "almost", "complete", "inventory", "of", "structural", "and", "regulatory", "genes", "involved", "in", "nicotine", "pathway", "."], ["Phylogenetic", "and", "expression", "analyses", "revealed", "a", "series", "of", "structural", "genes", "of", "the", "nicotine", "pathway", ",", "forming", "a", "regulon", ",", "under", "the", "control", "of", "jasmonate-responsive", "ETHYLENE", "RESPONSE", "FACTOR", "(", "ERF", ")", "transcription", "factors", "."], ["The", "duplication", "of", "NAD", "and", "polyamine", "metabolic", "pathways", "and", "the", "subsequent", "recruitment", "of", "duplicated", "primary", "metabolic", "genes", "into", "the", "nicotine", "biosynthesis", "regulon", "were", "suggested", "to", "be", "the", "drivers", "for", "pyridine", "and", "pyrrolidine", "ring", "formation", "steps", "early", "in", "the", "pathway", "."], ["Transcriptional", "regulation", "by", "ERF", "and", "cooperatively", "acting", "MYC2", "transcription", "factors", "are", "corroborated", "by", "the", "frequent", "occurrence", "of", "cognate", "cis-regulatory", "elements", "of", "the", "factors", "in", "the", "promoter", "regions", "of", "the", "downstream", "structural", "genes", "."], ["The", "allotetraploid", "tobacco", "has", "homologous", "clusters", "of", "ERF", "genes", "on", "different", "chromosomes", ",", "which", "are", "possibly", "derived", "from", "two", "ancestral", "diploids", "and", "include", "either", "nicotine-controlling", "ERF189", "or", "ERF199", "A", "large", "chromosomal", "deletion", "was", "found", "within", "one", "allele", "of", "the", "nicotine-controlling", "NICOTINE2", "locus", ",", "which", "is", "part", "of", "one", "of", "the", "ERF", "gene", "clusters", ",", "and", "which", "has", "been", "used", "to", "breed", "tobacco", "cultivars", "with", "a", "low-nicotine", "content", "."]], "ner": [[[3, 4, "Multicellular_organism"], [7, 7, "Organic_compound_other"], [11, 11, "Organic_compound_other"], [1, 1, "Multicellular_organism"]], [], [[26, 26, "Plant_hormone"], [33, 35, "Biochemical_process"]], [[55, 56, "Biochemical_pathway"], [41, 41, "Multicellular_organism"]], [[70, 71, "Biochemical_pathway"], [81, 89, "Protein"]], [[94, 98, "Biochemical_pathway"], [110, 112, "DNA"], [120, 124, "Biochemical_process"]], [[138, 140, "Protein"], [134, 134, "Protein"]], [[171, 172, "DNA"], [203, 205, "DNA"], [188, 189, "DNA"], [191, 191, "DNA"], [166, 166, "Multicellular_organism"], [214, 216, "DNA"], [225, 226, "Multicellular_organism"]]], "relations": [[[7, 7, 1, 1, "is-in"], [7, 7, 3, 4, "is-in"]], [], [[26, 26, 33, 35, "interacts"]], [], [[81, 89, 70, 71, "interacts"]], [], [[134, 134, 138, 140, "interacts"]], [[171, 172, 166, 166, "is-in"], [203, 205, 214, 216, "is-in"]]]}
{"doc_key": "PMID4638107_abstract", "dataset": "pickle", "sentences": [["Both", "gibberellic", "acid", "and", "abscisic", "acid", "inhibit", "the", "light", "induced", "synthesis", "of", "amaranthin", "in", "Amaranthus", "tricolor", "seedlings", "."], ["The", "auxin", ",", "indolyl-3-acetic", "acid", "has", "no", "effect", "."], ["The", "protein/RNA", "inhibitors", ",", "cycloheximide", "and", "8-azaguanine", ",", "also", "reduced", "the", "levels", "of", "amaranthin", "produced", "."]], "ner": [[[1, 2, "Plant_hormone"], [4, 5, "Plant_hormone"], [14, 16, "Multicellular_organism"], [12, 12, "Organic_compound_other"]], [[19, 19, "Plant_hormone"], [21, 22, "Plant_hormone"]], [[31, 31, "Organic_compound_other"], [33, 33, "Organic_compound_other"], [40, 40, "Organic_compound_other"]]], "relations": [[[4, 5, 12, 12, "inhibits"], [1, 2, 12, 12, "inhibits"], [12, 12, 14, 16, "is-in"]], [], [[33, 33, 40, 40, "inhibits"], [31, 31, 40, 40, "inhibits"]]]}
{"doc_key": "PMID16660470_abstract", "dataset": "pickle", "sentences": [["Gibberellic", "acid", "(", "GA(3", ")", ")", "promotes", "and", "continuous", "gold", "light", "inhibits", "germination", "of", "seeds", "of", "a", "dwarf", "strain", "(", "WB-2", ")", "of", "watermelon", "[", "Citrullus", "lanatus", "(", "Thunb", ".", ")", "Matsu", ".", "and", "Nakai", "]", "."], ["Osmotic", "inhibition", "of", "germination", "with", "mannitol", "in", "light-grown", "seeds", "of", "WB-2", "was", "only", "slightly", "reversed", "by", "GA(3", ")", "at", "the", "concentrations", "used", ",", "whereas", ",", "GA(3", ")", "substantially", "relieved", "osmotic", "inhibition", "in", "dark-grown", "seeds", "."], ["The", "effects", "of", "GA(3", ")", "and", "gold", "light", "on", "development", "of", "catalase", "and", "invertase", "activities", "and", "on", "levels", "of", "free", "amino", "acids", "in", "germinating", "seeds", "of", "WB-2", "were", "examined", "."], ["Light", "depressed", "development", "of", "catalase", "and", "invertase", "activity", "."], ["Levels", "of", "free", "amino", "acids", "increased", "more", "slowly", "in", "embryonic", "axes", "of", "light-", "than", "dark-incubated", "seeds", ",", "but", "in", "cotyledons", "higher", "levels", "of", "amino", "acids", "were", "maintained", "in", "light-grown", "seeds", "."], ["GA(3", ")", "accelerated", "the", "development", "of", "catalase", "activity", "in", "whole", "embryos", "and", "invertase", "activity", "in", "embryonic", "axes", ",", "but", "did", "not", "significantly", "affect", "invertase", "activity", "in", "cotyledons", "during", "germination", "."], ["GA(3", ")", "had", "little", "effect", "on", "amino", "acid", "pools", "in", "cotyledons", "and", "embryonic", "axes", "."]], "ner": [[[0, 1, "Plant_hormone"], [3, 4, "Plant_hormone"], [23, 23, "Multicellular_organism"], [25, 34, "Multicellular_organism"], [20, 20, "Multicellular_organism"], [9, 10, "Inorganic_compound_other"]], [[42, 42, "Organic_compound_other"], [53, 54, "Plant_hormone"], [62, 63, "Plant_hormone"], [47, 47, "Multicellular_organism"]], [[75, 76, "Plant_hormone"], [98, 98, "Multicellular_organism"], [83, 86, "Biochemical_process"], [91, 93, "Amino_acid_monomer"], [78, 79, "Inorganic_compound_other"]], [[106, 109, "Biochemical_process"]], [[113, 115, "Amino_acid_monomer"]], [[142, 143, "Plant_hormone"], [148, 149, "Biochemical_process"], [165, 166, "Biochemical_process"], [154, 155, "Biochemical_process"]], [[172, 173, "Plant_hormone"]]], "relations": [[], [], [[91, 93, 98, 98, "is-in"], [83, 86, 98, 98, "is-in"]], [], [], [[142, 143, 148, 149, "activates"], [142, 143, 154, 155, "activates"]], []]}
{"doc_key": "PMID16664167_abstract", "dataset": "pickle", "sentences": [["Effects", "of", "ethylene", ",", "gibberellins", ",", "and", "kinetin", "on", "the", "germination", "of", "two", "lots", "of", "Chenopodium", "album", "L.", "seeds", ",", "collected", "from", "the", "field", "in", "1982", "and", "1983", ",", "were", "studied", "in", "relation", "to", "the", "availability", "of", "nitrate", "."], ["The", "experiments", "were", "conducted", "in", "darkness", "and", "at", "temperatures", "ranging", "from", "12", "to", "32", "degrees", "C.", "Ethylene", "induced", "over", "75", "%", "germination", "in", "the", "1983", "seed", "but", "had", "little", "effect", "on", "the", "1982", "seed", "."], ["Nitrate", "was", "only", "slightly", "promotive", "in", "either", "of", "the", "two", "seed", "lots", "."], ["A", "combination", "of", "ethylene", "and", "nitrate", ",", "however", ",", "acted", "synergistically", "on", "1982", "seed", ",", "resulting", "in", "as", "much", "germination", "as", "that", "induced", "in", "1983", "seed", "by", "ethylene", "alone", "."], ["In", "1983", "seed", ",", "a", "combination", "of", "ethylene", "and", "nitrate", "was", "only", "marginally", "more", "effective", "than", "ethylene", "."], ["A", "similar", "relationship", "was", "observed", "in", "the", "effects", "of", "gibberellic", "acid(4", "+", "7", ")", "(", "GA(4", "+", "7", ")", ")", "and", "nitrate", "on", "seeds", "from", "the", "two", "lots", "."], ["The", "1982", "seed", ",", "which", "responded", "synergistically", "to", "combinations", "of", "nitrate", "with", "ethylene", "or", "GA(4", "+", "7", ")", "was", "found", "to", "contain", "an", "extremely", "low", "endogenous", "level", "of", "nitrate", "as", "compared", "to", "1983", "seed", "."], ["Thus", ",", "high", "levels", "of", "either", "endogenous", "or", "applied", "nitrate", "appeared", "to", "enhance", "the", "germination", "response", "to", "ethylene", "or", "GA(4", "+", "7).Kinetin", "had", "no", "effect", "on", "1982", "seed", "and", "only", "a", "small", "promotive", "effect", "on", "1983", "seed", "."], ["There", "was", "no", "synergism", "between", "kinetin", "and", "nitrate", "in", "either", "of", "the", "seed", "lots", "."]], "ner": [[[2, 2, "Plant_hormone"], [4, 4, "Plant_hormone"], [7, 7, "Plant_hormone"], [15, 18, "Plant_region"], [37, 37, "Inorganic_compound_other"]], [[55, 55, "Plant_hormone"]], [[74, 74, "Inorganic_compound_other"]], [[90, 90, "Plant_hormone"], [92, 92, "Inorganic_compound_other"], [114, 114, "Plant_hormone"]], [[124, 124, "Plant_hormone"], [126, 126, "Inorganic_compound_other"], [133, 133, "Plant_hormone"]], [[144, 148, "Plant_hormone"], [150, 153, "Plant_hormone"], [156, 156, "Inorganic_compound_other"]], [[174, 174, "Inorganic_compound_other"], [176, 176, "Plant_hormone"], [178, 181, "Plant_hormone"], [192, 192, "Inorganic_compound_other"]], [[208, 208, "Inorganic_compound_other"], [216, 216, "Plant_hormone"]], [[242, 242, "Plant_hormone"], [244, 244, "Inorganic_compound_other"]]], "relations": [[], [], [], [], [], [], [], [], []]}
{"doc_key": "PMID26767749_abstract", "dataset": "pickle", "sentences": [["The", "plant-specific", "WUSCHEL-related", "homeobox", "(", "WOX", ")", "nuclear", "proteins", "have", "important", "roles", "in", "the", "transcriptional", "regulation", "of", "many", "developmental", "processes", "."], ["Among", "the", "rice", "(", "Oryza", "sativa", ")", "WOX", "proteins", ",", "a", "loss", "of", "OsWOX3A", "function", "in", "narrow", "leaf2", "(", "nal2", ")", "nal3", "double", "mutants", "(", "termed", "nal2/3", ")", "causes", "pleiotropic", "effects", ",", "such", "as", "narrow", "and", "curly", "leaves", ",", "opened", "spikelets", ",", "narrow", "grains", ",", "more", "tillers", ",", "and", "fewer", "lateral", "roots", ",", "but", "almost", "normal", "plant", "height", "."], ["To", "examine", "OsWOX3A", "function", "in", "more", "detail", ",", "transgenic", "rice", "overexpressing", "OsWOX3A", "(", "OsWOX3A-OX", ")", "were", "generated", ";", "unexpectedly", ",", "all", "of", "them", "consistently", "exhibited", "severe", "dwarfism", "with", "very", "short", "and", "wide", "leaves", ",", "a", "phenotype", "that", "resembles", "that", "of", "gibberellic", "acid", "(GA)-deficient", "or", "GA-insensitive", "mutants", "."], ["Exogenous", "GA3", "treatment", "fully", "rescued", "the", "developmental", "defects", "of", "OsWOX3A-OX", "plants", ",", "suggesting", "that", "constitutive", "overexpression", "of", "OsWOX3A", "downregulates", "GA", "biosynthesis", "."], ["Quantitative", "analysis", "of", "GA", "intermediates", "revealed", "significantly", "reduced", "levels", "of", "GA20", "and", "bioactive", "GA1", "in", "OsWOX3A-OX", ",", "possibly", "due", "to", "downregulation", "of", "the", "expression", "of", "KAO", ",", "which", "encodes", "ent-kaurenoic", "acid", "oxidase", ",", "a", "GA", "biosynthetic", "enzyme", "."], ["Yeast", "one-hybrid", "and", "electrophoretic", "mobility", "shift", "assays", "revealed", "that", "OsWOX3A", "directly", "interacts", "with", "the", "KAO", "promoter", "."], ["OsWOX3A", "expression", "is", "drastically", "and", "temporarily", "upregulated", "by", "GA3", "and", "downregulated", "by", "paclobutrazol", ",", "a", "blocker", "of", "GA", "biosynthesis", "."], ["These", "data", "indicate", "that", "OsWOX3A", "is", "a", "GA-responsive", "gene", "and", "functions", "in", "the", "negative", "feedback", "regulation", "of", "the", "GA", "biosynthetic", "pathway", "for", "GA", "homeostasis", "to", "maintain", "the", "threshold", "levels", "of", "endogenous", "GA", "intermediates", "throughout", "development", "."]], "ner": [[[1, 8, "Protein"]], [[23, 29, "Protein"], [34, 35, "Biochemical_process"], [37, 44, "Multicellular_organism"], [47, 47, "Multicellular_organism"]], [[82, 82, "Protein"], [88, 89, "Multicellular_organism"], [93, 93, "Multicellular_organism"], [120, 125, "Multicellular_organism"], [91, 91, "DNA"]], [[128, 128, "Plant_hormone"], [146, 147, "Biochemical_pathway"], [136, 137, "Multicellular_organism"], [144, 144, "DNA"]], [[159, 159, "Plant_hormone"], [162, 162, "Plant_hormone"], [178, 180, "Protein"], [164, 164, "Multicellular_organism"], [152, 153, "Organic_compound_other"], [174, 174, "DNA"], [183, 185, "Protein"]], [[196, 196, "Protein"], [201, 202, "DNA"]], [[212, 212, "Plant_hormone"], [216, 216, "Organic_compound_other"], [221, 222, "Biochemical_pathway"], [204, 205, "Biochemical_process"]], [[242, 244, "Biochemical_pathway"], [231, 232, "DNA"], [228, 228, "DNA"], [255, 256, "Organic_compound_other"], [246, 247, "Biochemical_process"]]], "relations": [[], [], [[82, 82, 93, 93, "is-in"]], [[144, 144, 146, 147, "inhibits"]], [[174, 174, 178, 180, "produces"]], [[196, 196, 201, 202, "interacts"]], [[212, 212, 204, 205, "activates"], [216, 216, 204, 205, "inhibits"], [216, 216, 221, 222, "inhibits"]], [[228, 228, 242, 244, "interacts"], [228, 228, 246, 247, "interacts"]]]}
{"doc_key": "PMID30887305_abstract", "dataset": "pickle", "sentences": [["BACKGROUND", ":", "Salt", "stress", "is", "a", "devastating", "environmental", "stress", "that", "causes", "plant", "growth", "inhibition", "and", "yield", "reduction", "."], ["OBJECTIVE", ":", "The", "identification", "of", "salt-tolerant", "genes", "brings", "hope", "for", "the", "generation", "of", "salinity-tolerant", "crop", "plants", "through", "molecular", "breeding", "."], ["METHODS", ":", "In", "this", "study", ",", "one", "salt-sensitive", "and", "one", "salt-tolerant", "maize", "inbred", "line", "were", "screened", "from", "242", "maize", "inbred", "lines", "."], ["Reactive", "oxygen", "species", "(ROS)-related", "enzyme", "activities", "were", "detected", "and", "salt-responsive", "comparative", "transcriptome", "analysis", "was", "performed", "for", "control", "and", "220", "mM", "NaCl", "treated", "maize", "leaves", "."], ["RESULTS", ":", "Salt-tolerant", "maize", "inbred", "line", "(", "L87", ")", "showed", "higher", "ROS-related", "enzyme", "(", "SOD", ",", "POD", ",", "APX", "and", "CAT", ")", "activities", "and", "accumulated", "relatively", "lower", "levels", "of", "ROS", "under", "salt", "stress", "."], ["Of", "the", "total", "DEGs", ",", "1856", "upregulated", "DEGs", "were", "specific", "to", "L87", ",", "including", "stress", "tolerance-related", "members", "of", "the", "70kDa", "family", "of", "heat", "shock", "proteins", "(", "Hsp70s", ")", "and", "aquaporins", "."], ["The", "DEGs", "involved", "in", "the", "abscisic", "acid", "(", "ABA", ")", ",", "ethylene", ",", "jasmonic", "acid", "(", "JA", ")", "and", "salicylic", "acid", "(", "SA", ")", "signal", "transduction", "pathways", "may", "determine", "the", "difference", "in", "salt", "tolerance", "between", "the", "two", "varieties", ",", "especially", "one", "central", "component", "SnRK2", ",", "that", "positively", "regulates", "ABA", "signaling", "and", "was", "only", "upregulated", "in", "L87", "."], ["Analysis", "of", "DEGs", "related", "to", "ROS", "scavenging", "showed", "that", "some", "peroxidase", "(", "POD", ")", ",", "glutathione", "S-transferase", "(", "GST", ")", ",", "catalase", "(", "CAT", ")", "and", "superoxide", "dismutase", "(", "SOD", ")", "genes", "specific", "to", "L87", "probably", "enhanced", "its", "salt", "tolerance", "."], ["The", "analysis", "of", "differentially", "expressed", "transcription", "factors", "(", "TFs", ")", "suggested", "that", "WRKY", "TFs", "could", "contribute", "to", "the", "difference", "in", "salt", "tolerance", "between", "the", "two", "maize", "lines", "."], ["CONCLUSION", ":", "Compared", "with", "Salt-sensitive", "maize", "inbred", "line", "(", "L29", ")", ",", "L87", "exhibits", "specific", "regulatory", "mechanisms", "related", "to", "salt", "tolerance", ",", "including", "plant", "hormone", "interactions", ",", "ROS", "scavenging", "and", "the", "regulation", "of", "TFs", "."], ["Our", "study", "identifies", "new", "candidate", "genes", "that", "may", "regulate", "maize", "tolerance", "to", "salt", "stress", "and", "provides", "useful", "information", "for", "breeding", "maize", "with", "high", "salt", "resistance", "."]], "ner": [[[2, 2, "Inorganic_compound_other"]], [[23, 24, "DNA"]], [[45, 51, "Multicellular_organism"], [56, 58, "Multicellular_organism"]], [[60, 65, "Biochemical_process"], [82, 83, "Plant_region"], [80, 80, "Inorganic_compound_other"]], [[87, 90, "Multicellular_organism"], [92, 92, "Multicellular_organism"], [96, 107, "Biochemical_process"], [114, 114, "Inorganic_compound_other"], [116, 116, "Inorganic_compound_other"]], [[130, 130, "Multicellular_organism"], [138, 143, "Protein"], [145, 145, "Protein"], [148, 148, "Protein"]], [[155, 176, "Biochemical_pathway"], [182, 183, "Biochemical_process"], [193, 193, "Protein"], [198, 199, "Biochemical_process"], [205, 205, "Multicellular_organism"]], [[212, 213, "Biochemical_process"], [217, 238, "DNA"], [241, 241, "Multicellular_organism"], [245, 246, "Biochemical_process"]], [[260, 261, "Protein"], [268, 269, "Biochemical_process"], [273, 274, "Multicellular_organism"]], [[280, 283, "Multicellular_organism"], [285, 285, "Multicellular_organism"], [288, 288, "Multicellular_organism"], [295, 296, "Biochemical_process"], [303, 304, "Biochemical_process"]], [[320, 321, "Biochemical_process"], [334, 335, "Biochemical_process"], [323, 323, "Inorganic_compound_other"], [331, 331, "Multicellular_organism"]]], "relations": [[], [], [], [], [[96, 107, 87, 90, "is-in"], [96, 107, 92, 92, "is-in"]], [[138, 143, 130, 130, "is-in"], [145, 145, 130, 130, "is-in"], [148, 148, 130, 130, "is-in"]], [[193, 193, 198, 199, "activates"], [193, 193, 205, 205, "is-in"]], [[217, 238, 241, 241, "is-in"]], [], [[303, 304, 288, 288, "is-in"], [295, 296, 303, 304, "interacts"]], [[320, 321, 323, 323, "inhibits"]]]}
{"doc_key": "PMID16086245_abstract", "dataset": "pickle", "sentences": [["Increasing", "sucrose", "from", "20", "to", "50", "g", "l(-1", ")", "in", "Uncaria", "tomentosa", "cell", "suspension", "cultures", "enhanced", "ursolic", "acid", "and", "oleanolic", "acid", "production", "from", "129", "+", "/-", "61", "to", "553", "+", "/-", "193", "microg", "g(-1", ")", "cell", "dry", "wt", "."], ["The", "maximal", "concentration", "of", "both", "triterpenes", "(", "1680", "+", "/-", "39", "microg", "g(-1", ")", "cell", "dry", "wt", ")", "was", "8", "days", "after", "elicitation", "by", "jasmonic", "acid", ",", "while", "yeast", "extract", "or", "citrus", "pectin", "treatments", "produced", "1189", "+", "/-", "20", "or", "1120", "+", "/-", "26", "microg", "g(-1", ")", "cell", "dry", "wt", ",", "respectively", "."], ["The", "ratio", "of", "ursolic", "acid", ":", "oleanolic", "acid", "was", "constant", "at", "70:30", "."]], "ner": [[[1, 1, "Organic_compound_other"], [16, 21, "Biochemical_process"], [10, 12, "Cell"]], [[44, 44, "Organic_compound_other"], [63, 64, "Plant_hormone"], [67, 68, "Organic_compound_other"], [70, 71, "Organic_compound_other"]], [[95, 96, "Organic_compound_other"], [98, 99, "Organic_compound_other"]]], "relations": [[[1, 1, 16, 21, "activates"]], [[63, 64, 44, 44, "interacts"], [67, 68, 44, 44, "interacts"], [70, 71, 44, 44, "interacts"]], []]}
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{"doc_key": "PMID29017819_abstract", "dataset": "pickle", "sentences": [["Jasmonates", "(", "JAs", ")", "are", "signals", "in", "plant", "stress", "responses", "and", "development", "."], ["One", "of", "the", "first", "observed", "and", "prominent", "responses", "to", "JAs", "is", "the", "induction", "of", "biosynthesis", "of", "different", "groups", "of", "secondary", "compounds", "."], ["Among", "them", "are", "nicotine", ",", "isoquinolines", ",", "glucosinolates", ",", "anthocyanins", ",", "benzophenanthridine", "alkaloids", ",", "artemisinin", ",", "and", "terpenoid", "indole", "alkaloids", "(", "TIAs", ")", ",", "such", "as", "vinblastine", "."], ["This", "brief", "review", "describes", "modes", "of", "action", "of", "JAs", "in", "the", "biosynthesis", "of", "anthocyanins", ",", "nicotine", ",", "TIAs", ",", "glucosinolates", "and", "artemisinin", "."], ["After", "introducing", "JA", "biosynthesis", ",", "the", "central", "role", "of", "the", "SCF(COI1)-JAZ", "co-receptor", "complex", "in", "JA", "perception", "and", "MYB-type", "and", "MYC-type", "transcription", "factors", "is", "described", "."], ["Brief", "comments", "are", "provided", "on", "primary", "metabolites", "as", "precursors", "of", "secondary", "compounds", "."], ["Pathways", "for", "the", "biosynthesis", "of", "anthocyanin", ",", "nicotine", ",", "TIAs", ",", "glucosinolates", "and", "artemisinin", "are", "described", "with", "an", "emphasis", "on", "JA-dependent", "transcription", "factors", ",", "which", "activate", "or", "repress", "the", "expression", "of", "essential", "genes", "encoding", "enzymes", "in", "the", "biosynthesis", "of", "these", "secondary", "compounds", "."], ["Applied", "aspects", "are", "discussed", "using", "the", "biotechnological", "formation", "of", "artemisinin", "as", "an", "example", "of", "JA-induced", "biosynthesis", "of", "secondary", "compounds", "in", "plant", "cell", "factories", "."]], "ner": [[[0, 0, "Plant_hormone"], [2, 2, "Plant_hormone"]], [[22, 22, "Plant_hormone"]], [[38, 38, "Organic_compound_other"], [40, 40, "Organic_compound_other"], [42, 42, "Organic_compound_other"], [44, 44, "Organic_compound_other"], [46, 47, "Organic_compound_other"], [49, 49, "Organic_compound_other"], [52, 54, "Organic_compound_other"], [56, 56, "Organic_compound_other"], [61, 61, "Organic_compound_other"]], [[71, 71, "Plant_hormone"], [76, 76, "Organic_compound_other"], [78, 78, "Organic_compound_other"], [80, 80, "Organic_compound_other"], [82, 82, "Organic_compound_other"], [84, 84, "Organic_compound_other"]], [[88, 89, "Biochemical_pathway"], [96, 98, "Protein"], [100, 101, "Biochemical_process"], [103, 107, "Protein"]], [], [[129, 129, "Organic_compound_other"], [131, 131, "Organic_compound_other"], [133, 133, "Organic_compound_other"], [135, 135, "Organic_compound_other"], [137, 137, "Organic_compound_other"], [144, 146, "Protein"]], [[176, 176, "Organic_compound_other"], [181, 182, "Biochemical_process"]]], "relations": [[], [], [], [], [[96, 98, 100, 101, "is-in"], [96, 98, 103, 107, "interacts"]], [], [[144, 146, 129, 129, "interacts"], [144, 146, 131, 131, "interacts"], [144, 146, 133, 133, "interacts"], [144, 146, 135, 135, "interacts"], [144, 146, 137, 137, "interacts"]], []]}
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{"doc_key": "PMID27660055_abstract", "dataset": "pickle", "sentences": [["BACKGROUND", "AND", "AIMS", ":", "Current", "strategies", "for", "increased", "crop", "protection", "of", "susceptible", "tomato", "plants", "against", "pathogen", "infections", "include", "treatment", "with", "synthetic", "chemicals", ",", "application", "of", "natural", "pathogen-derived", "compounds", "or", "transfer", "of", "resistance", "genes", "from", "wild", "tomato", "species", "within", "breeding", "programmes", "."], ["In", "this", "study", ",", "a", "series", "of", "45", "genes", "potentially", "involved", "in", "defence", "mechanisms", "was", "retrieved", "from", "the", "genome", "sequence", "of", "inbred", "reference", "tomato", "cultivar", "Solanum", "lycopersicum", "'", "Heinz", "1706", "'", "."], ["The", "aim", "of", "the", "study", "was", "to", "analyse", "expression", "of", "these", "selected", "genes", "in", "wild", "and", "cultivated", "tomato", "plants", "contrasting", "in", "resistance", "to", "the", "biotrophic", "pathogen", "Oidium", "neolycopersici", ",", "the", "causative", "agent", "of", "powdery", "mildew", "."], ["Plants", "were", "treated", "either", "solely", "with", "potential", "resistance", "inducers", "or", "by", "inducers", "together", "with", "the", "pathogen", "."], ["METHODS", ":", "The", "resistance", "against", "O.", "neolycopersici", "infection", "as", "well", "as", "RT-PCR-based", "analysis", "of", "gene", "expression", "in", "response", "to", "the", "oomycete", "elicitor", "oligandrin", "and", "chemical", "agent", "β-aminobutyric", "acid", "(", "BABA", ")", "were", "investigated", "in", "the", "highly", "susceptible", "domesticated", "inbred", "genotype", "Solanum", "lycopersicum", "'", "Amateur", "'", "and", "resistant", "wild", "genotype", "Solanum", "habrochaites", "."], ["KEY", "RESULTS", ":", "Differences", "in", "basal", "expression", "levels", "of", "defensins", ",", "germins", ",", "β-1,3-glucanases", ",", "heveins", ",", "chitinases", ",", "osmotins", "and", "PR1", "proteins", "in", "non-infected", "and", "non-elicited", "plants", "were", "observed", "between", "the", "highly", "resistant", "and", "susceptible", "genotypes", "."], ["Moreover", ",", "these", "defence", "genes", "showed", "an", "extensive", "up-regulation", "following", "O.", "neolycopersici", "infection", "in", "both", "genotypes", "."], ["Application", "of", "BABA", "and", "elicitin", "induced", "expression", "of", "multiple", "defence-related", "transcripts", "and", ",", "through", "different", "mechanisms", ",", "enhanced", "resistance", "against", "powdery", "mildew", "in", "the", "susceptible", "tomato", "genotype", "."], ["CONCLUSIONS", ":", "The", "results", "indicate", "that", "non-specific", "resistance", "in", "the", "resistant", "genotype", "S.", "habrochaites", "resulted", "from", "high", "basal", "levels", "of", "transcripts", "with", "proven", "roles", "in", "defence", "processes", "."], ["In", "the", "susceptible", "genotype", "S.", "lycopersicum", "'", "Amateur", "'", ",", "oligandrin-", "and", "BABA-induced", "resistance", "involved", "different", "signalling", "pathways", ",", "with", "BABA-treated", "leaves", "displaying", "direct", "activation", "of", "the", "ethylene-dependent", "signalling", "pathway", ",", "in", "contrast", "to", "previously", "reported", "jasmonic", "acid-mediated", "signalling", "for", "elicitins", "."]], "ner": [[[34, 36, "Multicellular_organism"], [12, 13, "Multicellular_organism"]], [[66, 71, "Multicellular_organism"], [64, 64, "Multicellular_organism"]], [[87, 91, "Multicellular_organism"], [106, 107, "Biochemical_process"], [99, 100, "Multicellular_organism"]], [], [[148, 148, "Protein"], [166, 170, "Multicellular_organism"], [131, 133, "Biochemical_process"], [152, 153, "Organic_compound_other"], [155, 155, "Organic_compound_other"], [175, 176, "Multicellular_organism"]], [[189, 189, "Protein"], [191, 191, "Protein"], [193, 193, "Protein"], [195, 195, "Protein"], [197, 197, "Protein"], [199, 200, "Protein"], [187, 187, "Protein"]], [[226, 228, "Biochemical_process"]], [[237, 237, "Protein"], [253, 254, "Biochemical_process"], [258, 259, "Multicellular_organism"], [235, 235, "Organic_compound_other"]], [[273, 274, "Multicellular_organism"]], [[299, 302, "Biochemical_process"], [316, 318, "Biochemical_pathway"], [329, 329, "Protein"], [293, 297, "Multicellular_organism"], [325, 327, "Biochemical_process"]]], "relations": [[], [], [[99, 100, 106, 107, "produces"]], [], [], [], [], [[237, 237, 253, 254, "inhibits"], [235, 235, 253, 254, "inhibits"]], [], [[299, 302, 293, 297, "is-in"], [316, 318, 293, 297, "is-in"], [325, 327, 329, 329, "interacts"]]]}
{"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"]], []]}
{"doc_key": "PMID33330509_abstract", "dataset": "pickle", "sentences": [["Germination", "is", "a", "process", "of", "seed", "sprouting", "that", "facilitates", "embryo", "growth", "."], ["The", "breakdown", "of", "reserved", "starch", "in", "the", "endosperm", "into", "simple", "sugars", "is", "essential", "for", "seed", "germination", "and", "subsequent", "seedling", "growth", "."], ["At", "the", "early", "stage", "of", "germination", ",", "gibberellic", "acid", "(", "GA", ")", "activates", "transcription", "factor", "GAMYB", "to", "promote", "de", "novo", "synthesis", "of", "isoforms", "of", "α-amylase", "in", "the", "aleurone", "layer", "and", "scutellar", "epithelium", "of", "the", "embryo", "."], ["Here", ",", "we", "demonstrate", "that", "wheat", "germination", "is", "regulated", "by", "plant", "target", "of", "rapamycin", "(", "TOR", ")", "signaling", "."], ["TOR", "is", "a", "central", "component", "of", "the", "essential-nutrient-dependent", "pathway", "controlling", "cell", 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{"doc_key": "PMID26194557_abstract", "dataset": "pickle", "sentences": [["Ginseng", "is", "one", "of", "the", "most", "important", "plants", "in", "oriental", "medicine", "."], ["The", "pharmacological", "effects", "of", "this", "medicinal", "herb", "are", "mostly", "correlated", "to", "the", "major", "bioactive", "triterpene", "saponin", ",", "called", "ginsenoside", "."], ["Due", "to", "the", "long", "cultivation", "period", "of", "ginseng", "and", "increased", "ginsenoside", "level", "in", "aged", "root", ",", "we", "need", "to", "develop", "strategies", "to", "increase", "ginseng", "productivity", "in", "cell", "and", "tissue", "culture", "in", "a", "faster", "way", "."], ["Elicitation", "is", "already", "considered", "to", "improve", "the", "yield", "of", "this", "valuable", "secondary", "metabolite", ";", "especially", ",", "different", "types", ",", "timings", ",", "and", "durations", "of", "elicitation", "could", "affect", "the", "ginsenoside", "production", "and", "heterogeneity", "."], ["Activation", "of", "ginsenoside", "biosynthetic", "genes", "and", "ginsenoside", "accumulation", "mediated", "by", "elicitor-induced", "signaling", "molecules", "would", "be", "helpful", "for", "commercial", "production", "of", "individual", "ginsenosides", "."], ["Jasmonic", "acid", "is", "the", "well-known", "signaling", "molecule", "which", "mainly", "involved", "in", "ginsenoside", "accumulation", "."], ["Ca(2", "+", ")", "spiking", "and", "reactive", "oxygen", "species", ",", "nitric", "oxide", ",", "and", "ethylene", "production", "are", "other", "messengers", "which", "mediate", "production", "of", "ginsenoside", "."], ["This", "review", "highlights", "the", "elicitation", "strategies", "for", "production", "of", "the", "ginsenoside", "based", "on", "the", "principle", "of", "putative", "signal", "transduction", "pathways", "."]], "ner": [[[0, 0, "Multicellular_organism"]], [[30, 30, "Organic_compound_other"], [25, 27, "Organic_compound_other"]], [[39, 39, "Multicellular_organism"], [42, 42, "Organic_compound_other"], [55, 55, "Multicellular_organism"]], [[95, 96, "Biochemical_pathway"]], [[102, 104, "DNA"], [121, 121, "Organic_compound_other"], [106, 107, "Biochemical_process"]], [[123, 124, "Plant_hormone"], [134, 135, "Biochemical_process"]], [[142, 151, "Biochemical_process"], [159, 159, "Organic_compound_other"], [137, 140, "Biochemical_process"]], [[171, 171, "Organic_compound_other"]]], "relations": [[], [], [], [], [], [[123, 124, 134, 135, "interacts"]], [[137, 140, 159, 159, "interacts"], [142, 151, 159, 159, "interacts"]], []]}
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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"]], []]}
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{"doc_key": "PMID30681911_abstract", "dataset": "pickle", "sentences": [["Ramularia", "leaf", "spot", "disease", "(", "RLS", ")", ",", "caused", "by", "the", "ascomycete", "fungus", "Ramularia", "collo-cygni", ",", "has", "emerged", "as", "a", "major", "economic", "disease", "of", "barley", "."], ["No", "substantial", "resistance", "has", "been", "identified", ",", "so", "far", ",", "among", "barley", "genotypes", "and", ",", "based", "on", "the", "epidemiology", "of", "the", "disease", ",", "a", "quantitative", "genetic", "determinacy", "of", "RLS", "has", "been", "suggested", "."], ["The", "relative", "contributions", "of", "barley", "and", "R.", "collo-cygni", "genetics", "to", "disease", "infection", "and", "epidemiology", "are", "practically", "unknown", "."], ["Here", ",", "we", "present", "an", "integrated", "genome-wide", "analysis", "of", "host", "and", "pathogen", "transcriptome", "landscapes", "identified", "in", "a", "sensitive", "barley", "cultivar", "following", "infection", "by", "an", "aggressive", "R.", "collo-cygni", "isolate", "."], ["We", "compared", "transcriptional", "responses", "in", "the", "infected", "and", "noninfected", "leaf", "samples", "in", "order", "to", "identify", "which", "molecular", "events", "are", "associated", "with", "RLS", "symptom", "development", "."], ["We", "found", "a", "large", "proportion", "of", "R.", "collo-cygni", "genes", "to", "be", "expressed", "in", "planta", "and", "that", "many", "were", "also", "closely", "associated", "with", "the", "infection", "stage", "."], ["The", "transition", "from", "surface", "to", "apoplastic", "colonization", "was", "associated", "with", "downregulation", "of", "cell", "wall-degrading", "genes", "and", "upregulation", "of", "nutrient", "uptake", "and", "resistance", "to", "oxidative", "stresses", "."], ["Interestingly", ",", "the", "production", "of", "secondary", "metabolites", "was", "dynamically", "regulated", "within", "the", "fungus", ",", "indicating", "that", "R.", "collo-cygni", "produces", "a", "diverse", "panel", "of", "toxic", "compounds", "according", "to", "the", "infection", "stage", "."], ["A", "defense", "response", "against", "R.", "collo-cygni", "was", "identified", "in", "barley", "at", "the", "early", ",", "asymptomatic", "infection", "and", "colonization", "stages", "."], ["We", "found", "activation", "of", "ethylene", "signaling", ",", "jasmonic", "acid", "signaling", ",", "and", "phenylpropanoid", "and", "flavonoid", "pathways", "to", "be", "highly", "induced", ",", "indicative", "of", "a", "classical", "response", "to", "necrotrophic", "pathogens", "."], ["Disease", "development", "was", "found", "to", "be", "associated", "with", "gene", "expression", "patterns", "similar", "to", "those", "found", "at", "the", "onset", "of", "leaf", "senescence", ",", "when", "nutrients", ",", "possibly", ",", "are", "used", "by", "the", "infecting", "fungus", "."], ["These", "analyses", ",", "combining", "both", "barley", "and", "R.", "collo-cygni", "transcript", "profiles", ",", "demonstrate", "the", "activation", "of", "complex", "transcriptional", "programs", "in", "both", "organisms", "."]], "ner": [[[0, 3, "Biochemical_process"], [5, 5, "Biochemical_process"], [13, 14, "Multicellular_organism"], [24, 24, "Multicellular_organism"]], [[54, 54, "Biochemical_process"], [37, 38, "Multicellular_organism"]], [[63, 63, "Multicellular_organism"], [65, 66, "Multicellular_organism"]], [[102, 104, "Multicellular_organism"], [95, 96, "Multicellular_organism"]], [[127, 127, "Biochemical_process"]], [[137, 139, "DNA"]], [[169, 171, "DNA"]], [[199, 200, "Multicellular_organism"]], [[218, 219, "Multicellular_organism"], [223, 223, "Multicellular_organism"]], [[238, 239, "Biochemical_process"], [241, 243, "Biochemical_process"], [246, 249, "Biochemical_pathway"]], [], [[303, 308, "RNA"]]], "relations": [[[13, 14, 5, 5, "produces"], [13, 14, 0, 3, "produces"], [13, 14, 24, 24, "inhibits"]], [], [], [], [], [], [], [], [], [], [], []]}
{"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": "PMID26582034_abstract", "dataset": "pickle", "sentences": [["BACKGROUND", ":", "Postharvest", "fruit", "conservation", "relies", "on", "low", "temperatures", "and", "manipulations", "of", "hormone", "metabolism", "to", "maintain", "sensory", "properties", "."], ["Peaches", "are", "susceptible", "to", "chilling", "injuries", ",", "such", "as", "'", "woolliness", "'", "that", "is", "caused", "by", "juice", "loss", "leading", "to", "a", "'", "wooly", "'", "fruit", "texture", "."], ["Application", "of", "gibberellic", "acid", "at", "the", "initial", "stages", "of", "pit", "hardening", "impairs", "woolliness", "incidence", ",", "however", "the", "mechanisms", "controlling", "the", "response", "remain", "unknown", "."], ["We", "have", "employed", "genome", "wide", "transcriptional", "profiling", "to", "investigate", "the", "effects", "of", "gibberellic", "acid", "application", "and", "cold", "storage", "on", "harvested", "peaches", "."], ["RESULTS", ":", "Approximately", "half", "of", "the", "investigated", "genes", "exhibited", "significant", "differential", "expression", "in", "response", "to", "the", "treatments", "."], ["Cellular", "and", "developmental", "process", "gene", "ontologies", "were", "overrepresented", "among", "the", "differentially", "regulated", "genes", ",", "whereas", "sequences", "in", "cell", "death", "and", "immune", "response", "categories", "were", "underrepresented", "."], ["Gene", "set", "enrichment", "demonstrated", "a", "predominant", "role", "of", "cold", "storage", "in", "repressing", "the", "transcription", "of", "genes", "associated", "to", "cell", "wall", "metabolism", "."], ["In", "contrast", ",", "genes", "involved", "in", "hormone", "responses", "exhibited", "a", "more", "complex", "transcriptional", "response", ",", "indicating", "an", "extensive", "network", "of", "crosstalk", "between", "hormone", "signaling", "and", "low", "temperatures", "."], ["Time", "course", "transcriptional", "analyses", "demonstrate", "the", "large", "contribution", "of", "gene", "expression", "regulation", "on", "the", "biochemical", "changes", "leading", "to", "woolliness", "in", "peach", "."], ["CONCLUSION", ":", "Overall", ",", "our", "results", "provide", "insights", "on", "the", "mechanisms", "controlling", "the", "complex", "phenotypes", "associated", "to", "postharvest", "textural", "changes", "in", "peach", "and", "suggest", "that", "hormone", "mediated", "reprogramming", "previous", "to", "pit", "hardening", "affects", "the", "onset", "of", "chilling", "injuries", "."]], "ner": [[], [[19, 19, "Plant_region"]], [[48, 49, "Plant_hormone"]], [[82, 83, "Plant_hormone"], [90, 90, "Plant_region"]], [], [], [[154, 156, "Biochemical_process"]], [], [[206, 206, "Plant_region"]], [[229, 229, "Plant_region"]]], "relations": [[], [], [], [], [], [], [], [], [], []]}