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{"doc_key": "PMID26970688_abstract", "dataset": "pickle", "sentences": [["Acer", "pseudoplatanus", "seeds", "are", "characterized", "by", "a", "deep", "physiological", "embryo", "dormancy", "that", "requires", "a", "few", "weeks", "of", "cold", "stratification", "in", "order", "to", "promote", "germination", "."], ["Understanding", "the", "function", "of", "proteins", "and", "their", "related", "metabolic", "pathways", ",", "in", "conjunction", "with", "the", "plant", "hormones", "implicated", "in", "the", "breaking", "of", "seed", "dormancy", ",", "would", "expand", "our", "knowledge", "pertaining", "to", "this", "process", "."], ["In", "this", "study", ",", "a", "proteomic", "approach", "was", "used", "to", "analyze", "the", "changes", "occurring", "in", "seeds", "in", "response", "to", "cold", "stratification", ",", "which", "leads", "to", "dormancy", "release", "."], ["In", "addition", ",", "the", "involvement", "of", "abscisic", "(", "ABA", ")", "and", "gibberellic", "acids", "(", "GA", ")", "was", "also", "examined", "."], ["Fifty-three", "proteins", "showing", "significant", "changes", "were", "identified", "by", "mass", "spectrometry", "."], ["An", "effect", "of", "ABA", "on", "protein", "variation", "was", "observed", "at", "the", "beginning", "of", "stratification", ",", "while", "the", "influence", "of", "GA", "on", "protein", "abundance", "was", "observed", "during", "the", "middle", "phase", "of", "stratification", "."], ["The", "majority", "of", "proteins", "associated", "with", "dormancy", "breaking", "in", "the", "presence", "of", "only", "water", ",", "and", "also", "ABA", "or", "GA", ",", "were", "classified", "as", "being", "involved", "in", "metabolism", "and", "genetic", "information", "processing", "."], ["For", "metabolic-related", "proteins", ",", "the", "effect", "of", "ABA", "on", "protein", "abundance", "was", "stimulatory", "for", "half", "of", "the", "proteins", "and", "inhibitory", "for", "half", "of", "the", "proteins", "."], ["On", "the", "other", "hand", ",", "the", "effect", "on", "genetic", "information", "processing", "related", "proteins", "was", "stimulatory", "."], ["GA", "was", "found", "to", "upregulate", "both", "metabolic-related", "and", "genetic", "information", "processing-related", "proteins", "."], ["While", "seed", "dormancy", "breaking", "depends", "on", "proteins", "involved", "in", "a", "variety", "of", "processes", ",", "proteins", "associated", "with", "methionine", "metabolism", "(", "adenosine", "kinase", ",", "methionine", "synthase", ")", "and", "glycine-rich", "RNA", "binding", "proteins", "appear", "to", "be", "of", "particular", "importance", "."]], "ner": [[[0, 2, "Plant_region"]], [[40, 41, "Plant_hormone"]], [], [[93, 102, "Plant_hormone"]], [], [[121, 121, "Plant_hormone"], [137, 137, "Plant_hormone"]], [[167, 167, "Plant_hormone"], [169, 169, "Plant_hormone"]], [[190, 190, "Plant_hormone"]], [], [[225, 225, "Plant_hormone"]], [[255, 256, "Biochemical_pathway"], [258, 259, "Protein"], [261, 262, "Protein"], [265, 268, "Protein"]]], "relations": [[], [], [], [], [], [], [], [], [], [], [[258, 259, 255, 256, "interacts"], [261, 262, 255, 256, "interacts"]]]}
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{"doc_key": "PMID16169960_abstract", "dataset": "pickle", "sentences": [["Fungal", "elicitor", "prepared", "from", "the", "cell", "walls", "of", "Aspergillum", "niger", "induces", "multiple", "responses", "of", "Hypericum", "perforatum", "cells", ",", "including", "nitric", "oxide", "(", "NO", ")", "generation", ",", "jasmonic", "acid", "(", "JA", ")", "biosynthesis", ",", "and", "hypericin", "production", "."], ["To", "determine", "the", "role", "of", "NO", "and", "JA", "in", "elicitor-induced", "hypericin", "production", ",", "we", "study", "the", "effects", "of", "NO", "scavenger", "2-", "to", "4-carboxyphenyl-4,4", ",", "5,5-tetramethylimidazoline-1-oxyl-3-oxide", "(", "cPITO", ")", ",", "nitric", "oxide", "synthase", "inhibitor", "S", ",", "S'-1,3-phenylene-bis(1,2-ethanediyl)-bis-isothiourea", ",", "and", "inhibitors", "of", "the", "octadecanoid", "pathway", "on", "elicitor-induced", "NO", "generation", ",", "JA", "biosynthesis", ",", "and", "hypericin", "production", "."], 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{"doc_key": "PMID25914698_abstract", "dataset": "pickle", "sentences": [["Jasmonic", "acid", "(", "JA", ")", "and", "nitric", "oxide", "(", "NO", ")", "are", "well-characterized", "signaling", "molecules", "in", "plant", "defense", "responses", "."], ["However", ",", "their", "roles", "in", "plant", "defense", "against", "root-knot", "nematode", "(", "RKN", ",", "Meloidogyne", "incognita", ")", "infection", "are", "largely", "unknown", "."], ["In", "this", "study", ",", "we", "found", "that", "the", "transcript", "levels", "of", "the", "JA-", "and", "NO-related", "biosynthetic", "and", "signaling", "component", "genes", "were", "induced", "after", "RKN", "infection", "."], ["Application", "of", "exogenous", "JA", "and", "sodium", "nitroprusside", "(", "SNP", ";", "a", "NO", "donor", ")", "significantly", "decreased", "the", "number", "of", "egg", "masses", "in", "tomato", "roots", "after", "RKN", "infection", "and", "partially", "alleviated", "RKN-induced", "decreases", "in", "plant", "fresh", "weight", "and", "net", "photosynthetic", "rate", "."], ["These", "molecules", "also", "alleviated", "RKN-induced", "increases", "in", "root", "electrolyte", "leakage", "and", "membrane", "peroxidation", "."], ["Importantly", ",", "NO", "scavenger", "partially", "inhibited", "JA-induced", "RKN", "defense", "."], ["The", "pharmacological", "inhibition", "of", "JA", "biosynthesis", "significantly", "increased", "the", "plants", "'", "susceptibility", "to", "RKNs", ",", "which", "was", "effectively", "alleviated", "by", "SNP", "application", ",", "showing", "that", "NO", "may", "be", "involved", "in", "the", "JA-dependent", "RKN", "defense", "pathway", "."], ["Furthermore", ",", "both", "JA", "and", "SNP", "induced", "increases", "in", "protease", "inhibitor", "2", "(", "PI2", ")", "gene", "expression", "after", "RKN", "infestation", "."], ["Silencing", "of", "PI2", "compromised", "both", "JA-", "and", "SNP-induced", "RKN", "defense", "responses", ",", "suggesting", "that", "the", "PI2", "gene", "mediates", "JA-", "and", "NO-induced", "defense", "against", "RKNs", "."], ["This", "work", "will", "be", "important", "for", "deepening", "the", "understanding", "of", "the", "mechanisms", "involved", "in", "basal", "defense", "against", "RKN", "attack", "in", "plants", "."]], "ner": [[[6, 7, "Inorganic_compound_other"], [3, 3, "Plant_hormone"], [0, 1, "Plant_hormone"], [9, 9, "Inorganic_compound_other"]], [[31, 31, "Multicellular_organism"], [28, 29, "Multicellular_organism"], [33, 34, "Multicellular_organism"]], [[53, 60, "DNA"], [64, 65, "Biochemical_process"]], [[78, 78, "Inorganic_compound_other"], [92, 93, "Biochemical_process"], [70, 70, "Plant_hormone"], [89, 90, "Plant_region"], [75, 75, "Inorganic_compound_other"], [72, 73, "Inorganic_compound_other"]], [[119, 120, "Biochemical_process"]], [[128, 130, "Biochemical_process"], [124, 125, "Inorganic_compound_other"]], [[152, 152, "Inorganic_compound_other"], [157, 157, "Inorganic_compound_other"], [163, 166, "Biochemical_pathway"], [136, 137, "Biochemical_pathway"], [145, 145, "Multicellular_organism"]], [[177, 184, "Biochemical_process"], [171, 171, "Plant_hormone"], [173, 173, "Inorganic_compound_other"], [186, 186, "Multicellular_organism"]], [[212, 212, "Multicellular_organism"], [207, 210, "Biochemical_process"], [191, 191, "DNA"], [194, 199, "Biochemical_process"], [204, 205, "DNA"]], [[231, 231, "Multicellular_organism"]]], "relations": [[], [], [[64, 65, 53, 60, "activates"]], [[92, 93, 89, 90, "interacts"], [70, 70, 92, 93, "inhibits"], [72, 73, 92, 93, "inhibits"], [75, 75, 92, 93, "inhibits"]], [], [[124, 125, 128, 130, "inhibits"]], [[157, 157, 163, 166, "interacts"]], [[173, 173, 177, 184, "activates"], [171, 171, 177, 184, "activates"]], [[204, 205, 207, 210, "interacts"], [207, 210, 212, 212, "inhibits"]], []]}
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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", "°", "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"]], []]}
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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"]]]}
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{"doc_key": "PMID9800210_abstract", "dataset": "pickle", "sentences": [["The", "wound", "response", "of", "tomato", "plants", "has", "been", "extensively", "studied", ",", "and", "provides", "a", "useful", "model", "to", "understand", "signal", "transduction", "events", "leading", "from", "injury", "to", "marker", "gene", "expression", "."], ["The", "principal", "markers", "that", "have", "been", "used", "in", "these", "studies", "are", "genes", "encoding", "proteinase", "inhibitor", "(", "pin", ")", "proteins", "."], ["Activation", "of", "pin", "genes", "occurs", "in", "the", "wounded", "leaf", "and", "in", "distant", "unwounded", "leaves", "of", "the", "plant", "."], ["This", "paper", "reviews", "current", "understanding", "of", "signalling", "pathways", "in", "the", "wounded", "leaf", ",", "and", "in", "the", "systemically", "responding", "unwounded", "leaves", "."], ["First", ",", "the", "nature", "of", "known", "elicitors", "and", "their", "potential", "roles", "in", "planta", "are", "discussed", ",", "in", "particular", ",", "oligogalacturonides", ",", "jasmonates", "and", "the", "peptide", "signal", ",", "systemin", "."], ["Inhibitors", "of", "wound-induced", "proteinase", "inhibitor", "(", "pin", ")", "expression", "are", "also", "reviewed", ",", "with", "particular", "reference", "to", "phenolics", ",", "sulphydryl", "reagents", "and", "fusicoccin", "."], ["In", "each", "section", ",", "results", "obtained", "from", "the", "bioassay", "are", "considered", "within", "the", "wider", "context", "of", "data", "from", "mutants", "and", "from", "transgenic", "plants", "with", "altered", "levels", "of", "putative", "signalling", "components", "."], ["Following", "this", "introduction", ",", "current", "models", "for", "pin", "gene", "regulation", "are", "described", "and", "discussed", ",", "together", "with", "a", "summary", "for", "the", "involvement", "of", "phosphorylation-dephosphorylation", "in", "wound", "signalling", "."], ["Finally", ",", "a", "new", "model", "for", "wound-induced", "pin", "gene", "expression", "is", "presented", ",", "arising", "from", "recent", "data", "from", "the", "author", "'s", "laboratory", "."]], "ner": [[[4, 5, "Multicellular_organism"]], [[42, 47, "Protein"]], [[51, 52, "DNA"]], [], [[107, 107, "Organic_compound_other"], [109, 109, "Plant_hormone"], [115, 115, "Peptide"]], [[119, 125, "Biochemical_process"], [134, 134, "Organic_compound_other"], [136, 137, "Organic_compound_other"], [139, 139, "Organic_compound_other"]], [], [[179, 181, "Biochemical_process"], [195, 195, "Biochemical_process"]], [[206, 209, "Biochemical_process"]]], "relations": [[], [], [], [], [], [[134, 134, 119, 125, "inhibits"], [136, 137, 119, 125, "inhibits"], [139, 139, 119, 125, "inhibits"]], [], [], []]}
{"doc_key": "PMID30727640_abstract", "dataset": "pickle", "sentences": [["High-frequency", "bud", "break", "and", "multiple", "shoots", "were", "induced", "in", "apical", "shoot", "buds", "and", "nodal", "explants", "ofMorus", "cathayana", ",", "M.", "lhou", "andM.", "serrata", "on", "Murashige", "and", "Skoog", "(", "MS", ")", "medium", "containing", "0.5", "-", "1.0", "mg/l", "6-benzylaminopurine", "(", "BAP", ")", "."], ["Addition", "of", "gibberellic", "acid", "(", "0.4", "mg/l", ")", "along", "with", "BAP", "induced", "faster", "bud", "break", "both", "in", "apical", "shoot", "buds", "and", "nodal", "explants", "and", "also", "enhanced", "the", "frequency", "of", "bud", "break", "in", "all", "three", "species", "."], ["Shoot", "culture", "initiation", "was", "greatly", "influenced", "by", "explant", "type", ",", "explant", "age", "and", "explanting", "season", "."], ["The", "shoots", "were", "successfully", "rooted", "on", "half-strength", "MS", "medium", "containing", "a", "combination", "of", "indole-3-acetic", "acid", ",", "indole-3-butyric", "acid", "and", "indole-3-propionic", "acid", ",", "each", "at", "1.0", "mg/l", "."], ["The", "plantlets", "were", "successfully", "acclimated", "and", "eventually", "established", "in", "soil", "."]], "ner": [[[18, 19, "Multicellular_organism"], [35, 35, "Organic_compound_other"], [37, 37, "Organic_compound_other"]], [[50, 50, "Organic_compound_other"], [42, 43, "Plant_hormone"]], [], [[105, 106, "Organic_compound_other"], [108, 109, "Organic_compound_other"], [111, 112, "Organic_compound_other"]], []], "relations": [[], [], [], [], []]}
{"doc_key": "PMID12223598_abstract", "dataset": "pickle", "sentences": [["Lettuce", "(", "Lactuca", "sativa", "L.", ")", "endosperm", "cell", "walls", "isolated", "prior", "to", "radicle", "emergence", "underwent", "autohydrolysis", ",", "the", "rate", "of", "which", "was", "correlated", "with", "whether", "radicle", "emergence", "would", "subsequently", "occur", "."], ["Extraction", "of", "endosperm", "cell", "walls", "with", "6", "M", "LiCl", "suppressed", "autohydrolysis", ",", "and", "the", "desalted", "extract", "possessed", "activity", "that", "was", "capable", "of", "hydrolyzing", "purified", "locust", "bean", "galactomannan", "but", "not", "arabinogalactan", ",", "carboxymethylcellulose", ",", "glucomannan", ",", "polygalacturonic", "acid", ",", "tomato", "galactomannan", ",", "or", "native", "lettuce", "endosperm", "cell", "walls", "."], ["Some", "hydrolytic", "activity", "was", "detected", "on", "endosperm", "cell", "walls", "if", "they", "were", "modified", "by", "partial", "trifluoroacetic", "acid", "hydrolysis", "or", "pretreatment", "with", "guanidinium", "thiocyanate", "."], ["In", "extended", "incubations", "the", "cell", "wall", "enzyme", "extract", "released", "only", "large", "molecular", "mass", "fragments", "from", "locust", "bean", "galactomannan", ",", "indicating", "primarily", "endo-activity", "."], ["Galactomannan-hydrolyzing", "activity", "in", "the", "cell", "wall", "extract", "increased", "as", "a", "function", "of", "imbibition", "time", "and", "was", "greatest", "just", "prior", "to", "radicle", "emergence", "."], ["Thermoinhibition", "(", "imbibition", "at", "32[deg]C", ")", "or", "treatment", "with", "abscisic", "acid", "at", "a", "temperature", "optimal", "for", "germination", "(", "25[deg]C", ")", "suppressed", "both", "germination", "and", "endosperm", "cell", "wall", "mannanase", "activity", ",", "whereas", "alleviation", "of", "thermoinhibition", "with", "gibberellic", "acid", "was", "accompanied", "by", "significant", "enhancement", "of", "mannanase", "activity", "."], ["We", "conclude", "that", "a", "cell", "wall-bound", "endo-[beta]-mannanase", "is", "expressed", "in", "lettuce", "endosperm", "prior", "to", "radicle", "emergence", "and", "is", "regulated", "by", "the", "same", "conditions", "that", "govern", "germination", "."]], "ner": [[[0, 8, "Cell_component"]], [[39, 39, "Inorganic_compound_other"], [55, 57, "Organic_compound_other"], [60, 60, "Organic_compound_other"], [62, 62, "Organic_compound_other"], [64, 64, "Organic_compound_other"], [66, 67, "Organic_compound_other"], [69, 70, "Organic_compound_other"], [73, 77, "Cell_component"]], [[94, 96, "Biochemical_process"], [100, 101, "Organic_compound_other"]], [[118, 120, "Organic_compound_other"]], [[126, 127, "Biochemical_process"]], [[158, 159, "Plant_hormone"], [173, 177, "Biochemical_process"], [184, 185, "Plant_hormone"], [192, 193, "Biochemical_process"]], [[199, 201, "Protein"], [205, 206, "Tissue"]]], "relations": [[], [], [], [], [], [[158, 159, 173, 177, "inhibits"], [184, 185, 192, 193, "activates"]], [[199, 201, 205, 206, "is-in"]]]}
{"doc_key": "PMID33357541_abstract", "dataset": "pickle", "sentences": [["GP-1", ",", "a", "novel", "glycoprotein", "from", "Streptomyces", "sp.", "ZX01", "has", "a", "plant", "immunity-inducing", "effect", "."], ["GP-1-treated", "plants", "exhibited", "enhanced", "systemic", "resistance", "with", "a", "significant", "reduction", "in", "TMV", "lesions", "on", "tobacco", "leaves", ",", "but", "its", "antiviral", "mechanism", "remains", "unclear", "."], ["In", "this", "study", ",", "early", "plant", "defense-related", "responses", ",", "such", "as", "Ca(2", "+", ")", "influx", ",", "callose", "apposition", ",", "oxidative", "burst", ",", "hypersensitive", "response", ",", "programmed", "cell", "death", ",", "increase", "in", "nitric", "oxide", "(", "NO", ")", ",", "and", "stomatal", "closure", ",", "were", "investigated", "under", "GP-1", "treatment", ",", "and", "the", "mechanism", "of", "how", "GP-1", "induces", "viral", "resistance", "in", "Nicotiana", "benthamiana", "was", "studied", "."], ["Results", "showed", "that", "GP-1", "induced", "[Ca(2+)](cyt", ")", "rapidly", "in", "tobacco", "leaves", "and", "suspended", "cells", ",", "followed", "by", "reactive", "oxygen", "species", "(", "ROS", ")", "and", "NO", "elevation", "."], ["Transcriptome", "analysis", "showed", "significant", "differences", "in", "expression", "levels", "between", "the", "GP-1-treated", "N.", "benthamiana", "and", "the", "control", "and", "showed", "significantly", "upregulated", "and", "enriched", "pathways", "including", "defense", "and", "immune", "reaction", "."], ["Similar", "to", "typical", "pathogen-associated", "molecular", "patterns", ",", "GP-1", "induced", "callose", "deposition", "and", "stomatal", "closure", "to", "form", "defense", "barriers", "against", "pathogen", "invasion", "."], ["The", "expression", "of", "defense-related", "genes", "further", "confirmed", "the", "above", "conclusions", "."], ["By", "analyzing", "transcriptome", "in", "N.", "benthamiana", "and", "the", "contents", "of", "salicylic", "acid", "(", "SA", ")", "and", "jasmonic", "acid", "(", "JA", ")", ",", "GP-1", "enhanced", "viral", "resistance", "of", "tobacco", "by", "improving", "the", "SA", "and", "JA", "contents", ",", "strengthening", "plant", "secondary", "metabolites", "activities", ",", "promoting", "systemic", "accumulation", "of", "pathogenesis-related", "proteins", "in", "TMV-", "inoculated", "tobacco", "there", "by", "producing", "antiviral", "activity", "."]], "ner": [[[0, 0, "Protein"], [6, 8, "Unicellular_organism"]], [[15, 16, "Multicellular_organism"], [26, 26, "Virus"], [29, 30, "Plant_region"]], [[91, 91, "Protein"], [83, 83, "Protein"], [50, 53, "Biochemical_process"], [55, 56, "Biochemical_process"], [64, 66, "Biochemical_process"], [61, 62, "Biochemical_process"], [70, 71, "Inorganic_compound_other"], [73, 73, "Inorganic_compound_other"], [96, 97, "Multicellular_organism"]], [[104, 104, "Protein"], [110, 111, "Plant_region"], [118, 126, "Biochemical_process"]], [[139, 140, "Multicellular_organism"]], [[164, 164, "Protein"], [166, 167, "Biochemical_process"]], [], [[212, 212, "Protein"], [194, 195, "Multicellular_organism"], [200, 201, "Plant_hormone"], [203, 203, "Plant_hormone"], [209, 209, "Plant_hormone"], [206, 207, "Plant_hormone"], [221, 221, "Plant_hormone"], [223, 223, "Plant_hormone"], [217, 217, "Multicellular_organism"], [239, 241, "Multicellular_organism"]]], "relations": [[[0, 0, 6, 8, "is-in"]], [[15, 16, 26, 26, "inhibits"], [26, 26, 29, 30, "interacts"]], [[50, 53, 96, 97, "is-in"], [55, 56, 96, 97, "is-in"], [61, 62, 96, 97, "is-in"], [64, 66, 96, 97, "is-in"], [70, 71, 96, 97, "is-in"], [73, 73, 96, 97, "is-in"]], [[104, 104, 118, 126, "activates"]], [], [[164, 164, 166, 167, "activates"]], [], [[212, 212, 221, 221, "activates"], [212, 212, 223, 223, "activates"]]]}
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{"doc_key": "PMID10707361_abstract", "dataset": "pickle", "sentences": [["In", "tobacco", ",", "two", "mitogen-activated", "protein", "(", "MAP", ")", "kinases", ",", "designated", "salicylic", "acid", "(SA)-induced", "protein", "kinase", "(", "SIPK", ")", "and", "wounding-induced", "protein", "kinase", "(", "WIPK", ")", "are", "activated", "in", "a", "disease", "resistance-specific", "manner", "following", "pathogen", "infection", "or", "elicitor", "treatment", "."], ["To", "investigate", "whether", "nitric", "oxide", "(", "NO", ")", ",", "SA", ",", "ethylene", ",", "or", "jasmonic", "acid", "(", "JA", ")", "are", "involved", "in", "this", "phenomenon", ",", "the", "ability", "of", "these", "defense", "signals", "to", "activate", "these", "kinases", "was", "assessed", "."], ["Both", "NO", "and", "SA", "activated", "SIPK", ";", "however", ",", "they", "did", "not", "activate", "WIPK", "."], ["Additional", "analyses", "with", "transgenic", "NahG", "tobacco", "revealed", "that", "SA", "is", "required", "for", "the", "NO-mediated", "induction", "of", "SIPK", "."], ["Neither", "JA", "nor", "ethylene", "activated", "SIPK", "or", "WIPK", "."], ["Thus", ",", "SIPK", "may", "function", "downstream", "of", "SA", "in", "the", "NO", "signaling", "pathway", "for", "defense", "responses", ",", "while", "the", "signals", "responsible", "for", "resistance-associated", "WIPK", "activation", "have", "yet", "to", "be", "determined", "."]], "ner": [[[1, 1, "Multicellular_organism"], [4, 9, "Protein"], [12, 16, "Protein"], [18, 18, "Protein"], [21, 23, "Protein"], [25, 25, "Protein"]], [[44, 45, "Inorganic_compound_other"], [47, 47, "Inorganic_compound_other"], [50, 50, "Plant_hormone"], [52, 52, "Plant_hormone"], [55, 56, "Plant_hormone"], [58, 58, "Plant_hormone"], [75, 75, "Protein"]], [[80, 80, "Inorganic_compound_other"], [82, 82, "Plant_hormone"], [84, 84, "Protein"], [92, 92, "Protein"]], [[97, 99, "Multicellular_organism"], [102, 102, "Plant_hormone"], [107, 108, "Biochemical_process"], [110, 110, "Protein"]], [[113, 113, "Plant_hormone"], [115, 115, "Plant_hormone"], [117, 117, "Protein"], [119, 119, "Protein"]], [[123, 123, "Protein"], [128, 128, "Plant_hormone"], [131, 133, "Biochemical_pathway"], [143, 145, "Biochemical_process"]]], "relations": [[[12, 16, 1, 1, "is-in"], [18, 18, 1, 1, "is-in"], [21, 23, 1, 1, "is-in"], [25, 25, 1, 1, "is-in"]], [], [[80, 80, 84, 84, "activates"], [82, 82, 84, 84, "activates"]], [[102, 102, 110, 110, "activates"], [107, 108, 110, 110, "activates"]], [], [[123, 123, 131, 133, "is-in"]]]}
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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": "PMID22994555_abstract", "dataset": "pickle", "sentences": [["WRKY", "proteins", "form", "a", "large", "family", "of", "plant", "transcription", "factors", "implicated", "in", "the", "modulation", "of", "numerous", "biological", "processes", ",", "such", "as", "growth", ",", "development", "and", "responses", "to", "various", "environmental", "stresses", "."], ["However", ",", "the", "roles", "of", "the", "majority", "WRKY", "family", "members", ",", "especially", "in", "non-model", "plants", ",", "remain", "poorly", "understood", "."], ["We", "identified", "CaWRKY40", "from", "pepper", "."], ["Transient", "expression", "in", "onion", "epidermal", "cells", "showed", "that", "CaWRKY40", "can", "be", "targeted", "to", "nuclei", "and", "activates", "expression", "of", "a", "W-box-containing", "reporter", "gene", "."], ["CaWRKY40", "transcripts", "are", "induced", "in", "pepper", "by", "Ralstonia", "solanacearum", "and", "heat", "shock", "."], ["To", "assess", "roles", "of", "CaWRKY40", "in", "plant", "stress", "responses", "we", "performed", "gain-", "and", "loss-of-function", "experiments", "."], ["Overexpression", "of", "CaWRKY40", "enhanced", "resistance", "to", "R.", "solanacearum", "and", "tolerance", "to", "heat", "shock", "in", "tobacco", "."], ["In", "contrast", ",", "silencing", "of", "CaWRKY40", "enhanced", "susceptibility", "to", "R.", "solanacearum", "and", "impaired", "thermotolerance", "in", "pepper", "."], ["Consistent", "with", "its", "role", "in", "multiple", "stress", "responses", ",", "we", "found", "CaWRKY40", "transcripts", "to", "be", "induced", "by", "signalling", "mechanisms", "mediated", "by", "the", "stress", "hormones", "salicylic", "acid", "(", "SA", ")", ",", "jasmonic", "acid", "(", "JA", ")", "and", "ethylene", "(", "ET", ")", "."], ["Overexpression", "of", "CaWRKY40", "in", "tobacco", "modified", "the", "expression", "of", "hypersensitive", "response", "(HR)-associated", "and", "pathogenesis-related", "genes", "."], ["Collectively", ",", "our", "results", "suggest", "that", "CaWRKY40", "orthologs", "are", "regulated", "by", "SA", ",", "JA", "and", "ET", "signalling", "and", "coordinate", "responses", "to", "R.", "solanacearum", "attacks", "and", "heat", "stress", "in", "pepper", "and", "tobacco", "."]], "ner": [[[0, 1, "Protein"]], [[38, 40, "Protein"]], [[53, 53, "Protein"], [55, 55, "Multicellular_organism"]], [[60, 62, "Cell"], [65, 65, "Protein"], [76, 78, "DNA"]], [[80, 81, "RNA"], [85, 85, "Multicellular_organism"], [87, 88, "Unicellular_organism"]], [[97, 97, "Protein"]], [[111, 111, "Protein"], [115, 116, "Unicellular_organism"], [123, 123, "Multicellular_organism"]], [[130, 130, "Protein"], [134, 135, "Unicellular_organism"], [140, 140, "Multicellular_organism"]], [[153, 154, "RNA"], [166, 167, "Plant_hormone"], [169, 169, "Plant_hormone"], [172, 173, "Plant_hormone"], [175, 175, "Plant_hormone"], [178, 178, "Plant_hormone"], [180, 180, "Plant_hormone"]], [[185, 185, "Protein"], [187, 187, "Multicellular_organism"], [192, 197, "DNA"]], [[205, 206, "DNA"], [210, 215, "Biochemical_process"], [220, 221, "Unicellular_organism"], [227, 227, "Multicellular_organism"], [229, 229, "Multicellular_organism"]]], "relations": [[], [], [[53, 53, 55, 55, "is-in"]], [[65, 65, 76, 78, "activates"]], [[80, 81, 85, 85, "is-in"], [87, 88, 80, 81, "activates"]], [], [[111, 111, 115, 116, "inhibits"], [111, 111, 123, 123, "is-in"]], [[130, 130, 140, 140, "is-in"]], [[166, 167, 153, 154, "interacts"], [153, 154, 169, 169, "interacts"], [153, 154, 172, 173, "interacts"], [153, 154, 175, 175, "interacts"], [153, 154, 178, 178, "interacts"], [153, 154, 180, 180, "interacts"]], [[185, 185, 192, 197, "interacts"]], [[205, 206, 210, 215, "interacts"], [205, 206, 220, 221, "interacts"], [205, 206, 227, 227, "is-in"], [205, 206, 229, 229, "is-in"]]]}
{"doc_key": "PMID24997625_abstract", "dataset": "pickle", "sentences": [["Arbuscular", "mycorrhizal", "(", "AM", ")", "symbioses", "are", "mutualistic", "associations", "between", "soil", "fungi", "and", "most", "vascular", "plants", "."], ["Modulation", "of", "the", "hormonal", "and", "transcriptional", "profiles", ",", "including", "changes", "related", "to", "defense", "signalling", ",", "has", "been", "reported", "in", "many", "host", "plants", "during", "AM", "symbioses", "."], ["These", "changes", "have", "been", "often", "related", "to", "the", "improved", "stress", "tolerance", "common", "in", "mycorrhizal", "plants", "."], ["However", ",", "results", "on", "the", "alterations", "in", "phytohormones", "content", "and", "their", "role", "on", "the", "symbiosis", "are", "controversial", "."], ["Here", ",", "an", "integrative", "analysis", "of", "the", "response", "of", "phylogenetically", "diverse", "plants", "(", "i.e.", ",", "tomato", ",", "soybean", ",", "and", "maize", ")", "to", "two", "mycorrhizal", "fungi", "-Funneliformis", "mosseae", "and", "Rhizophagus", "irregularis-", "was", "performed", "."], ["The", "analysis", "of", "the", "defense-related", "hormones", "salicylic", "acid", ",", "abscisic", "acid", ",", "and", "jasmonates", ",", "and", "the", "expression", "of", "marker", "genes", "of", "the", "pathways", "they", "regulate", ",", "revealed", "significant", "changes", "in", "the", "roots", "of", "mycorrhizal", "plants", "."], ["These", "changes", "depended", "on", "both", "the", "plant", "and", "the", "AM", "fungus", "(", "AMF", ")", "involved", "."], ["However", ",", "general", "trends", "can", "be", "identified", ":", "roots", "associated", "with", "the", "most", "effective", "colonizer", "R.", "irregularis", "showed", "fewer", "changes", "in", "these", "defense-related", "traits", ",", "while", "the", "colonization", "by", "F.", "mosseae", "led", "to", "significant", "modifications", "in", "all", "plants", "tested", "."], ["The", "up-regulation", "of", "the", "jasmonate", "pathway", "by", "F.", "mosseae", "was", "found", "to", "be", "highly", "conserved", "among", "the", "different", "plant", "species", ",", "suggesting", "an", "important", "role", "of", "jasmonates", "during", "this", "AM", "interaction", "."], ["Our", "study", "evidences", "a", "strong", "influence", "of", "the", "AMF", "genotype", "on", "the", "modulation", "of", "host", "defense", "signalling", ",", "and", "offers", "hints", "on", "the", "role", "of", "these", "changes", "in", "the", "symbiosis", "."]], "ner": [[[0, 5, "Biochemical_process"]], [[40, 41, "Biochemical_process"]], [], [[66, 66, "Plant_hormone"]], [[92, 92, "Multicellular_organism"], [94, 94, "Multicellular_organism"], [97, 97, "Multicellular_organism"]], [[117, 118, "Plant_hormone"], [120, 121, "Plant_hormone"], [124, 124, "Plant_hormone"]], [], [[179, 180, "Multicellular_organism"], [193, 194, "Multicellular_organism"]], [[208, 209, "Biochemical_pathway"], [211, 212, "Multicellular_organism"], [230, 230, "Plant_hormone"], [233, 234, "Biochemical_process"]], []], "relations": [[], [], [], [], [], [], [], [], [[211, 212, 208, 209, "activates"], [230, 230, 233, 234, "interacts"]], []]}
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{"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"]]]}
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{"doc_key": "PMID31083282_abstract", "dataset": "pickle", "sentences": [["Petal", "color", ",", "size", ",", "and", "morphology", "play", "important", "roles", "in", "protecting", "other", "floral", "organs", ",", "attracting", "pollinators", ",", "and", "facilitating", "sexual", "reproduction", "in", "plants", "."], ["In", "a", "previous", "study", ",", "we", "obtained", "a", "petal", "degeneration", "mutant", "(", "pdm", ")", "from", "the", "'", "FT", "'", "doubled", "haploid", "line", "of", "Chinese", "cabbage", "and", "found", "that", "the", "candidate", "gene", "for", "pdm", ",", "Bra040093", ",", "encodes", "the", "enzyme", "acyl-CoA", "oxidase1", "."], ["In", "this", "study", ",", "we", "sought", "to", "examine", "the", "gene", "networks", "regulating", "petal", "development", "in", "pdm", "plants", "."], ["We", "show", "that", "the", "mRNA", "and", "protein", "expression", "of", "Bra040093", ",", "which", "is", "involved", "in", "the", "jasmonic", "acid", "(", "JA", ")", "biosynthetic", "pathway", ",", "were", "significantly", "lower", "in", "the", "petals", "of", "pdm", "plants", "than", "in", "those", "of", "'", "FT", "'", "plants", "."], ["Similarly", ",", "the", "JA", "and", "methyl", "jasmonate", "(", "MeJA", ")", "contents", "of", "petals", "were", "significantly", "lower", "in", "pdm", "plants", "than", "in", "'", "FT", "'", "plants", "and", "we", "found", "that", "exogenous", "application", "of", "these", "hormones", "to", "the", "inflorescences", "of", "pdm", "plants", "restored", "the", "'", "FT", "'", "phenotype", "."], ["Comparative", "analyses", "of", "the", "transcriptomes", "of", "'", "FT", "'", ",", "pdm", "and", "pdm", "+", "JA", "(", "pJA", ")", "plants", "revealed", "10,160", "differentially", "expressed", "genes", "(", "DEGs", ")", "with", "consistent", "expression", "tendencies", "in", "'", "FT", "'", "vs.", "pdm", "and", "pJA", "vs.", "pdm", "comparisons", "."], ["Among", "these", "DEGs", ",", "we", "identified", "69", "DEGs", "related", "to", "floral", "organ", "development", ",", "11", "of", "which", "are", "involved", "in", "petal", "development", "regulated", "by", "JA", "."], ["On", "the", "basis", "of", "qRT-PCR", "verification", ",", "we", "propose", "regulatory", "pathways", "whereby", "JA", "may", "mediate", "petal", "development", "in", "the", "pdm", "mutant", "."], ["We", "demonstrate", "that", "mutation", "of", "Bra040093", "in", "pdm", "plants", "leads", "to", "reduced", "JA", "levels", "and", "that", "this", "in", "turn", "promotes", "changes", "in", "the", "expression", "of", "genes", "that", "are", "expressed", "in", "response", "to", "JA", ",", "ultimately", "resulting", "in", "petal", "degeneration", "."], ["These", "findings", "thus", "indicate", "that", "JA", "is", "associated", "with", "petal", "development", "in", "Chinese", "cabbage", "."], ["These", "results", "enhance", "our", "knowledge", "on", "the", "molecular", "mechanisms", "underlying", "petal", "development", "and", "lay", "the", "foundations", "for", "further", "elucidation", "of", "the", "mechanisms", "associated", "with", "floral", "organ", "development", "in", "Chinese", "cabbage", "."]], "ner": [[], [[34, 36, "Multicellular_organism"], [38, 38, "Multicellular_organism"], [42, 47, "Multicellular_organism"], [49, 50, "Multicellular_organism"], [58, 58, "Multicellular_organism"], [60, 60, "DNA"], [65, 66, "Protein"]], [[83, 84, "Multicellular_organism"]], [[95, 95, "DNA"], [102, 108, "Biochemical_pathway"], [117, 118, "Multicellular_organism"], [123, 126, "Multicellular_organism"]], [[131, 131, "Plant_hormone"], [133, 134, "Plant_hormone"], [136, 136, "Plant_hormone"], [145, 146, "Multicellular_organism"], [149, 152, "Multicellular_organism"], [166, 167, "Multicellular_organism"]], [[181, 193, "Multicellular_organism"], [208, 208, "Multicellular_organism"], [211, 211, "Multicellular_organism"], [213, 213, "Multicellular_organism"], [215, 215, "Multicellular_organism"]], [[242, 242, "Plant_hormone"]], [[256, 256, "Plant_hormone"], [263, 264, "Multicellular_organism"]], [[271, 271, "DNA"], [273, 274, "Multicellular_organism"], [278, 278, "Plant_hormone"], [298, 298, "Plant_hormone"]], [[311, 311, "Plant_hormone"], [318, 319, "Multicellular_organism"]], [[349, 350, "Multicellular_organism"]]], "relations": [[], [[60, 60, 65, 66, "produces"]], [], [[95, 95, 102, 108, "is-in"]], [], [], [], [[256, 256, 263, 264, "is-in"]], [[271, 271, 273, 274, "is-in"], [271, 271, 278, 278, "interacts"]], [[311, 311, 318, 319, "is-in"]], []]}
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{"doc_key": "PMID12060229_abstract", "dataset": "pickle", "sentences": [["Herbivore", "attacks", "induce", "leaves", "to", "emit", "a", "specific", "blend", "of", "volatiles", "."], ["Here", "we", "show", "that", "exposure", "to", "Tetranychus", "urticae-induced", "volatiles", ",", "as", "well", "as", "T.", "urticae", "infestation", "and", "artificial", "wounding", ",", "activates", "the", "transcription", "of", "the", "genes", "involved", "in", "the", "biosynthesis", "of", "ethylene", "[", "S-adenosylmethionine", "(", "SAM", ")", "synthetase", "and", "1-aminocyclopropane-1-carboxylic", "acid", "oxidase", "]", "and", "a", "gene", "involved", "in", "the", "biosynthesis", "of", "polyamines", "from", "SAM", "(", "SAM", "decarboxylase", ")", "in", "lima", "bean", "leaves", "."], ["Moreover", ",", "exposure", "of", "leaves", "to", "any", "one", "of", "the", "seven", "major", "chemical", "components", "of", "T.", "urticae-induced", "volatiles", "also", "induces", "expression", "of", "these", "genes", "."], ["Furthermore", ",", "we", "found", "that", ",", "when", "lima", "bean", "plants", "were", "exposed", "to", "T.", "urticae-induced", "volatiles", ",", "they", "emitted", "ethylene", "."], ["Lima", "bean", "plants", "infested", "by", "T.", "urticae", "and", "artificially", "wounded", "plants", "also", "emitted", "ethylene", "."], ["Endogenous", "polyamine", "levels", "were", "not", "increased", "in", "the", "exposed", "leaves", "or", "the", "infested", "leaves", ",", "suggesting", "that", "polyamine", "production", "from", "SAM", "was", "only", "slightly", "promoted", "at", "the", "metabolic", "levels", "present", "in", "the", "leaves", "."], ["We", "found", "that", "jasmonate", "(", "JA", ")", "accumulated", "in", "leaves", "exposed", "to", "T.", "urticae-induced", "volatiles", ",", "and", "that", "both", "JA", "and", "salicylate", "(", "SA", ")", "accumulated", "in", "leaves", "infested", "by", "T.", "urticae", "."], ["These", "findings", ",", "as", "well", "as", "results", "of", "pharmacological", "analyses", ",", "suggest", "that", ",", "in", "leaves", "exposed", "to", "T.", "urticae-induced", "volatiles", ",", "ethylene", "biosynthesis", "might", "be", "regulated", "by", "pathways", "involving", "JA", "and", "the", "ethylene", "positive", "feedback", "loop", "."], ["They", "also", "suggest", "that", "ethylene", "biosynthesis", "might", "be", "regulated", "by", "signaling", "pathways", "involving", "JA", ",", "SA", "and", "ethylene", "in", "T.", "urticae-infested", "leaves", "."]], "ner": [[], [[18, 20, "Organic_compound_other"], [25, 26, "Multicellular_organism"], [43, 43, "Plant_hormone"], [45, 49, "DNA"], [51, 53, "DNA"], [63, 63, "Organic_compound_other"], [65, 65, "Organic_compound_other"], [67, 68, "DNA"], [71, 73, "Plant_region"]], [[90, 92, "Organic_compound_other"]], [[107, 109, "Multicellular_organism"], [113, 115, "Organic_compound_other"], [119, 119, "Plant_hormone"]], [[121, 123, "Multicellular_organism"], [126, 127, "Multicellular_organism"], [134, 134, "Plant_hormone"]], [[137, 137, "Organic_compound_other"], [153, 154, "Biochemical_process"], [156, 156, "Organic_compound_other"]], [[173, 173, "Plant_hormone"], [175, 175, "Plant_hormone"], [182, 184, "Organic_compound_other"], [189, 189, "Plant_hormone"], [191, 191, "Plant_hormone"], [193, 193, "Plant_hormone"], [200, 201, "Multicellular_organism"]], [[221, 223, "Organic_compound_other"], [225, 226, "Biochemical_pathway"], [233, 233, "Plant_hormone"], [236, 239, "Biochemical_process"]], [[245, 246, "Biochemical_pathway"], [254, 254, "Plant_hormone"], [256, 256, "Plant_hormone"], [258, 258, "Plant_hormone"], [260, 262, "Plant_region"]]], "relations": [[], [[18, 20, 45, 49, "activates"], [18, 20, 51, 53, "activates"], [25, 26, 45, 49, "activates"], [25, 26, 51, 53, "activates"], [18, 20, 67, 68, "activates"], [25, 26, 67, 68, "activates"], [65, 65, 63, 63, "produces"], [67, 68, 63, 63, "produces"], [45, 49, 71, 73, "is-in"], [51, 53, 71, 73, "is-in"], [67, 68, 71, 73, "is-in"]], [], [[113, 115, 119, 119, "activates"]], [[121, 123, 134, 134, "produces"], [126, 127, 134, 134, "activates"]], [], [[182, 184, 173, 173, "activates"], [182, 184, 175, 175, "activates"], [200, 201, 189, 189, "activates"], [200, 201, 191, 191, "activates"], [200, 201, 193, 193, "activates"]], [[221, 223, 225, 226, "interacts"], [225, 226, 233, 233, "interacts"], [225, 226, 236, 239, "interacts"], [221, 223, 233, 233, "interacts"]], [[245, 246, 254, 254, "interacts"], [245, 246, 256, 256, "interacts"], [245, 246, 258, 258, "interacts"], [245, 246, 260, 262, "is-in"]]]}
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{"doc_key": "PMID25885025_abstract", "dataset": "pickle", "sentences": [["BACKGROUND", ":", "Jasmonic", "acid", "(", "JA", ")", "and", "methyl", "jasmonate", "(", "MeJA", ")", "regulate", "plant", "development", ",", "resistance", "to", "stress", ",", "and", "insect", "attack", "by", "inducing", "specific", "gene", "expression", "."], ["However", ",", "little", "is", "known", "about", "the", "mechanism", "of", "plant", "defense", "against", "herbivore", "attack", "at", "a", "protein", "level", "."], ["Using", "a", "high-resolution", "2-D", "gel", ",", "we", "identified", "62", "MeJA-responsive", "proteins", "and", "measured", "protein", "expression", "level", "changes", "."], ["RESULTS", ":", "Among", "these", "62", "proteins", ",", "43", "proteins", "levels", "were", "increased", "while", "11", "proteins", "were", "decreased", "."], ["We", "also", "found", "eight", "proteins", "uniquely", "expressed", "in", "response", "to", "MeJA", "treatment", "."], ["Data", "are", "available", "via", "ProteomeXchange", "with", "identifier", "PXD001793", "."], ["The", "proteins", "identified", "in", "this", "study", "have", "important", "biological", "functions", "including", "photosynthesis", "and", "energy", "related", "proteins", "(", "38.4", "%", ")", ",", "protein", "folding", ",", "degradation", "and", "regulated", "proteins", "(", "15.0", "%", ")", ",", "stress", "and", "defense", "regulated", "proteins", "(", "11.7", "%", ")", ",", "and", "redox-responsive", "proteins", "(", "8.3", "%", ")", "."], ["The", "expression", "levels", "of", "four", "important", "genes", "were", "determined", "by", "qRT-PCR", "analysis", "."], ["The", "expression", "levels", "of", "these", "proteins", "did", "not", "correlate", "well", "with", "their", "translation", "levels", "."], ["To", "test", "the", "defense", "functions", "of", "the", "differentially", "expressed", "proteins", ",", "expression", "vectors", "of", "four", "protein", "coding", "genes", "were", "constructed", "to", "express", "in-fusion", "proteins", "in", "E.", "coli", "."], ["The", "expressed", "proteins", "were", "used", "to", "feed", "Ostrinia", "furnacalis", ",", "the", "Asian", "corn", "borer", "(", "ACB", ")", "."], ["Our", "results", "demonstrated", "that", "the", "recombinant", "proteins", "of", "pathogenesis-related", "protein", "1", "(", "PR1", ")", "and", "thioredoxin", "M-type", ",", "chloroplastic", "precursor", "(", "TRXM", ")", "showed", "the", "significant", "inhibition", "on", "the", "development", "of", "larvae", "and", "pupae", "."], ["CONCLUSIONS", ":", "We", "found", "MeJA", "could", "not", "only", "induce", "plant", "defense", "mechanisms", "to", "insects", ",", "it", "also", "enhanced", "toxic", "protein", "production", "that", "potentially", "can", "be", "used", "for", "bio-control", "of", "ACB", "."]], "ner": [[[2, 3, "Plant_hormone"], [8, 9, "Plant_hormone"], [11, 11, "Plant_hormone"], [5, 5, "Plant_hormone"]], [], [[58, 59, "Protein"]], [], [[95, 95, "Plant_hormone"]], [], [[151, 152, "Protein"]], [], [], [[211, 212, "Unicellular_organism"]], [[221, 222, "Multicellular_organism"], [225, 227, "Multicellular_organism"], [229, 229, "Multicellular_organism"]], [[240, 242, "Protein"], [244, 244, "Protein"], [247, 248, "Protein"], [253, 253, "Protein"]], [[271, 271, "Plant_hormone"], [296, 296, "Multicellular_organism"]]], "relations": [[], [], [], [], [], [], [], [], [], [], [], [], []]}
{"doc_key": "PMID29187153_abstract", "dataset": "pickle", "sentences": [["BACKGROUND", ":", "Plants", "respond", "to", "various", "stress", "stimuli", "by", "activating", "an", "enhanced", "broad-spectrum", "defensive", "ability", "."], ["The", "development", "of", "novel", "resistance", "inducers", "represents", "an", "attractive", ",", "alternative", "crop", "protection", "strategy", "."], ["In", "this", "regard", ",", "hexanoic", "acid", "(", "Hxa", ",", "a", "chemical", "elicitor", ")", "and", "azelaic", "acid", "(", "Aza", ",", "a", "natural", "signaling", "compound", ")", "have", "been", "proposed", "as", "inducers", "of", "plant", "defense", ",", "by", "means", "of", "a", "priming", "mechanism", "."], ["Here", ",", "we", "investigated", "both", "the", "mode", "of", "action", "and", "the", "complementarity", "of", "Aza", "and", "Hxa", "as", "priming", "agents", "in", "Nicotiana", "tabacum", "cells", "in", "support", "of", "enhanced", "defense", "."], ["RESULTS", ":", "Metabolomic", "analyses", "identified", "signatory", "biomarkers", "involved", "in", "the", "establishment", "of", "a", "pre-conditioned", "state", "following", "Aza", "and", "Hxa", "treatment", "."], ["Both", "inducers", "affected", "the", "metabolomes", "in", "a", "similar", "manner", "and", "generated", "common", "biomarkers", ":", "caffeoylputrescine", "glycoside", ",", "cis-5-caffeoylquinic", "acid", ",", "feruloylglycoside", ",", "feruloyl-3-methoxytyramine", "glycoside", "and", "feruloyl-3-methoxytyramine", "conjugate", "."], ["Subsequently", ",", "quantitative", "real", "time-PCR", "was", "used", "to", "investigate", "the", "expression", "of", "inducible", "defense", "response", "genes", ":", "phenylalanine", "ammonia", "lyase", ",", "hydroxycinnamoyl", "CoA", "quinate", "transferase", "and", "hydroxycinnamoyl", "transferase", "to", "monitor", "activation", "of", "the", "early", "phenylpropanoid", "pathway", "and", "chlorogenic", "acids", "metabolism", ",", "while", "ethylene", "response", "element-binding", "protein", ",", "small", "sar1", "GTPase", ",", "heat", "shock", "protein", "90", ",", "RAR1", ",", "SGT1", ",", "non-expressor", "of", "PR", "genes", "1", "and", "thioredoxin", "were", "analyzed", "to", "report", "on", "signal", "transduction", "events", "."], ["Pathogenesis-related", "protein", "1a", "and", "defensin", "were", "quantified", "to", "investigate", "the", "activation", "of", "defenses", "regulated", "by", "salicylic", "acid", "and", "jasmonic", "acid", "respectively", "."], ["The", "qPCR", "results", "revealed", "differential", "expression", "kinetics", "and", ",", "in", "general", "(", "except", "for", "NPR1", ",", "Thionin", "and", "PR1a", ")", ",", "the", "relative", "gene", "expression", "ratios", "observed", "in", "the", "Hxa-treated", "cells", "were", "significantly", "greater", "than", "the", "expression", "observed", "in", "the", "cells", "treated", "with", "Aza", "."], ["CONCLUSIONS", ":", "The", "results", "indicate", "that", "Aza", "and", "Hxa", "have", "a", "similar", "priming", "effect", "through", "activation", "of", "genes", "involved", "in", "the", "establishment", "of", "systemic", "acquired", "resistance", ",", "associated", "with", "enhanced", "synthesis", "of", "hydroxycinnamic", "acids", "and", "related", "conjugates", "."]], "ner": [[], [], [[35, 36, "Organic_compound_other"], [38, 38, "Organic_compound_other"], [45, 46, "Organic_compound_other"], [48, 48, "Organic_compound_other"]], [[84, 84, "Organic_compound_other"], [86, 86, "Organic_compound_other"], [91, 93, "Cell"]], [[116, 116, "Organic_compound_other"], [118, 118, "Organic_compound_other"]], [[135, 136, "Organic_compound_other"], [138, 139, "Organic_compound_other"], [141, 141, "Organic_compound_other"], [143, 144, "Organic_compound_other"], [146, 147, "Organic_compound_other"]], [[166, 168, "DNA"], [170, 173, "DNA"], [175, 176, "DNA"], [182, 184, "Biochemical_pathway"], [186, 188, "Biochemical_process"], [191, 194, "DNA"], [196, 198, "DNA"], [200, 203, "DNA"], [205, 205, "DNA"], [207, 207, "DNA"], [209, 213, "DNA"], [215, 215, "DNA"]], [[225, 227, "Protein"], [229, 229, "Protein"], [240, 241, "Plant_hormone"], [243, 244, "Plant_hormone"]], [[261, 261, "DNA"], [263, 263, "DNA"], [265, 265, "DNA"], [290, 290, "Organic_compound_other"]], [[298, 298, "Organic_compound_other"], [300, 300, "Organic_compound_other"], [315, 317, "Biochemical_process"], [324, 325, "Organic_compound_other"]]], "relations": [[], [], [], [], [], [], [], [], [], [[298, 298, 315, 317, "interacts"], [300, 300, 315, 317, "interacts"], [298, 298, 324, 325, "activates"], [300, 300, 324, 325, "activates"]]]}
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{"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": "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"]]]}
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{"doc_key": "PMID12754834_abstract", "dataset": "pickle", "sentences": [["The", "effects", "of", "phytohormones", "(", "abscisic", "acid", ",", "gibberelic", "acid", ",", "and", "jasmonic", "acid", ")", "and", "ambiol", "(", "a", "synthetic", "growth", "regulator", ")", "on", "processes", "of", "H+", "transport", "across", "the", "plasmalemma", "were", "studied", "in", "membrane", "vesicles", "isolated", "from", "the", "parenchyma", "of", "potato", "(", "Solanum", "tuberosum", "L.", ")", "tubers", "."], ["Phytohormones", "and", "ambiol", "were", "tested", "either", "individually", "or", "in", "combinations", "."], ["Each", "of", "the", "substances", "tested", "changed", "the", "initial", "rate", "of", "H+", "uptake", "by", "the", "vesicles", "."], ["Two", "signaling", "substances", "added", "to", "the", "incubation", "medium", "simultaneously", "modified", "the", "activity", "of", "each", "other", "."], ["It", "is", "suggested", "that", "the", "interaction", "of", "a", "signaling", "substance", "with", "components", "of", "the", "plasmalemma", "alters", "the", "responses", "of", "the", "membrane", "to", "other", "signaling", "molecules", "."]], "ner": [[[3, 3, "Plant_hormone"], [5, 6, "Plant_hormone"], [8, 9, "Plant_hormone"], [12, 13, "Plant_hormone"], [16, 16, "Organic_compound_other"], [26, 27, "Biochemical_process"], [41, 47, "Plant_region"]], [[49, 49, "Plant_hormone"], [51, 51, "Organic_compound_other"]], [[70, 71, "Biochemical_process"]], [], []], "relations": [[], [], [], [], []]}
{"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": "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.", " ", "annua", "."], ["AaGSW1", "exhibited", "similar", "expression", "patterns", "to", "the", "trichome-specific", "genes", "of", "the", "artemisinin", "biosynthetic", "pathway", "and", "AP2/ERF", "transcription", "factor", "AaORA", "."], ["A", "β-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.", " ", "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.", " ", "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": "PMID32244290_abstract", "dataset": "pickle", "sentences": [["The", "necrotrophic", "fungus", "Botrytis", "cinerea", "causes", "devastating", "pre-", "and", "post-harvest", "yield", "losses", "in", "grapevine", "(", "Vitis", "vinifera", "L.", ")", "."], ["Although", "B.", "cinerea", "has", "been", "well-studied", "in", "different", "plant", "species", ",", "there", "is", "limited", "information", "related", "to", "the", "resistance", "and", "susceptibility", "mechanisms", "of", "Vitis", "genotypes", "against", "B.", "cinerea", "infection", "."], ["In", "the", "present", "study", ",", "leaves", "and", "berries", "of", "twenty", "four", "grape", "genotypes", "were", "evaluated", "against", "B.", "cinerea", "infection", "."], ["According", "to", "the", "results", ",", "one", "genotype", "(", "Ju", "mei", "gui", ")", "was", "highly", "resistant", "(", "HR", ")", ",", "one", "genotype", "(", "Kyoho", ")", "was", "resistant", "(", "R", ")", ",", "eight", "genotypes", "were", "susceptible", "(", "S", ")", ",", "and", "fourteen", "genotypes", "were", "highly", "susceptible", "(", "HS", ")", "against", "infection", "of", "B.", "cinerea", "in", "leaves", "."], ["Whereas", "in", "the", "case", "of", "B.", "cinerea", "infection", "in", "grape", "berry", ",", "three", "genotypes", "were", "found", "to", "be", "highly", "resistant", ",", "three", "resistant", ",", "eleven", "genotypes", "susceptible", ",", "and", "seven", "were", "highly", "susceptible", "."], ["To", "further", "explore", "the", "mechanism", "of", "disease", "resistance", "in", "grapevine", ",", "we", "evaluated", "\"", "Ju", "mei", "gui", "\"", "and", "\"", "Summer", "black", "\"", "in", "terms", "of", "B.", "cinerea", "progression", ",", "reactive", "oxygen", "species", "reactions", ",", "jasmonic", "acid", "contents", ",", "and", "the", "activities", "of", "antioxidant", "enzymes", "in", "leaf", "and", "fruit", "."], ["We", "surmise", "that", "the", "resistance", "of", "\"", "Ju", "mei", "gui", "\"", "is", "due", "to", "seized", "fungal", "growth", ",", "minor", "reactive", "oxygen", "species", "(", "ROS", ")", "production", ",", "elevated", "antioxidant", "enzyme", "activity", ",", "and", "more", "jasmonic", "acid", "(", "JA", ")", "contents", "."], ["This", "study", "provides", "insights", "into", "the", "resistance", "and", "susceptibility", "mechanism", "of", "Vitis", "genotypes", "against", "B.", "cinerea", "."], ["This", "will", "help", "for", "the", "selection", "of", "appropriate", "germplasm", "to", "explore", "the", "molecular", "basis", "of", "disease", "resistance", "mechanisms", "in", "grapevine", "."]], "ner": [[[3, 4, "Multicellular_organism"], [13, 13, "Multicellular_organism"], [15, 17, "Multicellular_organism"]], [[21, 22, "Multicellular_organism"], [43, 44, "Multicellular_organism"], [46, 48, "Biochemical_process"]], [[61, 62, "Multicellular_organism"], [66, 68, "Biochemical_process"]], [[78, 80, "Multicellular_organism"], [92, 92, "Multicellular_organism"], [120, 121, "Multicellular_organism"]], [[130, 132, "Biochemical_process"], [134, 135, "Plant_region"]], [[168, 168, "Multicellular_organism"], [173, 175, "Multicellular_organism"], [179, 180, "Multicellular_organism"], [185, 187, "Biochemical_process"], [189, 192, "Biochemical_process"], [194, 195, "Plant_hormone"]], [[216, 218, "Multicellular_organism"], [228, 234, "Biochemical_process"], [237, 239, "Biochemical_process"], [243, 244, "Plant_hormone"], [246, 246, "Plant_hormone"]], [[261, 262, "Multicellular_organism"], [264, 265, "Multicellular_organism"]], [[286, 286, "Multicellular_organism"]]], "relations": [[[3, 4, 13, 13, "inhibits"], [3, 4, 15, 17, "inhibits"]], [], [], [[78, 80, 120, 121, "inhibits"], [92, 92, 120, 121, "inhibits"]], [[130, 132, 134, 135, "is-in"]], [], [[216, 218, 237, 239, "activates"], [216, 218, 243, 244, "activates"], [216, 218, 246, 246, "activates"]], [], []]}
{"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", "α-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", "α-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", "α-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", "α-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", "α-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": "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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{"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"]]]}
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{"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": "PMID24961571_abstract", "dataset": "pickle", "sentences": [["Oxophytodienoate", "reductases", "(", "OPRs", ")", "are", "a", "small", "group", "of", "flavin-dependent", "oxidoreductases", "in", "plants", "."], ["In", "this", "study", ",", "a", "new", "member", "of", "the", "OPR", "gene", "family", "(", "HvOPR2", ")", "was", "cloned", "from", "barley", "(", "Hordeum", "vulgare", "L.", ")", "using", "reverse", "transcription", "polymerase", "chain", "reaction", "(", "RT-PCR", ")", "."], ["The", "full-length", "cDNA", "of", "HvOPR2", "was", "1,206", "bp", "with", "an", "open", "reading", "frame", "of", "1,101", "bp", ",", "encoding", "a", "366", "amino", "acids", "long", "polypeptide", "with", "a", "predicted", "molecular", "weight", "of", "40.52", "and", "a", "theoretical", "isoelectric", "point", "of", "6.21", "."], ["The", "corresponding", "genomic", "clone", "of", "HvOPR2", "was", "isolated", "using", "the", "PCR", "amplification", "technique", "and", "was", "found", "to", "consist", "of", "five", "exons", "and", "four", "introns", "."], ["Bioinformatic", "analysis", "revealed", "that", "the", "deduced", "HvOPR2", "has", "a", "considerable", "homology", "with", "other", "plant", "OPRs", "and", "possessed", "the", "flavin", "oxidoreductase/NADH", "oxidase", "substrate-binding", "domain", "."], ["Phylogenetic", "analysis", "showed", "that", "HvOPR2", "codes", "for", "the", "OPR", "of", "subgroup", "I", ",", "which", "contains", "enzymes", "that", "are", "not", "required", "for", "jasmonic", "acid", "biosynthesis", "."], ["Time-course", "transcriptional", "profiling", "of", "HvOPR2", "was", "analyzed", "in", "response", "to", "a", "variety", "of", "abiotic", "stresses", "and", "hormonal", "treatments", "by", "semi-quantitative", "RT-PCR", "."], ["The", "HvOPR2", "gene", "was", "induced", "in", "response", "to", "drought", ",", "hydrogen", "peroxide", ",", "and", "wounding", "."], ["Moreover", ",", "the", "corresponding", "mRNA", "transcripts", "were", "increased", "in", "response", "to", "jasmonic", "acid", "and", "salicylic", "acid", ",", "but", "not", "in", "response", "to", "abscisic", "acid", "."], ["These", "results", "strongly", "suggested", "a", "role", "for", "HvOPR2", "in", "barley", "defense/response", "to", "abiotic", "stresses", "and", "signaling", "molecules", "."]], "ner": [[[0, 1, "Protein"], [3, 3, "Protein"], [10, 11, "Protein"]], [[24, 26, "DNA"], [28, 28, "DNA"], [35, 37, "Multicellular_organism"], [33, 33, "Multicellular_organism"]], [[53, 53, "DNA"]], [[93, 93, "DNA"]], [[119, 119, "DNA"], [131, 135, "Protein"], [126, 127, "DNA"]], [[141, 141, "DNA"], [145, 145, "Protein"], [158, 160, "Biochemical_pathway"]], [[166, 166, "DNA"]], [[185, 186, "DNA"], [194, 195, "Inorganic_compound_other"]], [[211, 212, "Plant_hormone"], [214, 215, "Plant_hormone"], [222, 223, "Plant_hormone"]], [[232, 232, "DNA"], [234, 235, "Biochemical_process"]]], "relations": [[], [[28, 28, 33, 33, "is-in"], [24, 26, 33, 33, "is-in"], [28, 28, 35, 37, "is-in"], [24, 26, 35, 37, "is-in"]], [], [], [[131, 135, 119, 119, "is-in"]], [[141, 141, 145, 145, "produces"]], [], [[194, 195, 185, 186, "activates"]], [], [[232, 232, 234, 235, "is-in"]]]}
{"doc_key": "PMID17174363_abstract", "dataset": "pickle", "sentences": [["The", "oxidative", "deamination", "of", "N-methylputrescine", "is", "an", "essential", "step", "in", "both", "pyridine", "and", "tropane", "alkaloid", "biosynthesis", "."], ["Reverse", "genetic", "approaches", "have", "not", "resulted", "in", "the", "cloning", "of", "a", "methylputrescine", "oxidase", "gene", "(", "MPO", ")", "."], ["However", ",", "we", "have", "used", "a", "homology-based", "approach", "to", "clone", "a", "full-length", "tobacco", "MPO1", "cDNA", "."], ["The", "MPO1", "gene", "is", "part", "of", "a", "small", "multigene", "family", "comprised", "of", "approximately", "six", "members", "."], ["MPO1-like", "transcript", "levels", "increased", "in", "roots", "that", "were", "either", "deprived", "of", "auxin", "or", "treated", "with", "methyl", "jasmonic", "acid", "."], ["Similar", "to", "other", "known", "nicotine", "biosynthetic", "genes", "in", "domesticated", "tobacco", ",", "MPO1-like", "mRNA", "levels", "were", "lower", "in", "roots", "with", "the", "mutant", "a", "and", "b", "alleles", "."], ["The", "MPO1", "protein", "was", "expressed", "in", "bacteria", "as", "a", "recombinant", "Thioredoxin-His(6)-MPO1", "fusion", "protein", "."], ["The", "recombinant", "MPO1", "protein", "utilized", "N-methylputrescine", "more", "efficiently", "than", "other", "diamines", "."], ["Therefore", ",", "the", "kinetic", "properties", "of", "the", "MPO1", "enzyme", "may", "play", "an", "important", "role", "in", "determining", "the", "pyridine", "alkaloid", "profiles", "observed", "in", "tobacco", "roots", "."]], "ner": [[[4, 4, "Protein"], [11, 15, "Biochemical_pathway"]], [[28, 30, "DNA"], [32, 32, "DNA"]], [[47, 48, "DNA"]], [[52, 53, "DNA"]], [[67, 68, "RNA"], [78, 78, "Plant_hormone"], [82, 84, "Plant_hormone"]], [[97, 98, "RNA"], [90, 92, "DNA"], [94, 95, "Multicellular_organism"]], [[113, 114, "Protein"], [121, 124, "Protein"]], [[131, 131, "Protein"], [127, 129, "Protein"], [136, 136, "Organic_compound_other"]], [[145, 146, "Protein"], [155, 156, "Organic_compound_other"], [160, 161, "Plant_region"]]], "relations": [[[4, 4, 11, 15, "is-in"]], [], [], [], [[82, 84, 67, 68, "activates"]], [[90, 92, 94, 95, "is-in"]], [], [[127, 129, 131, 131, "interacts"], [136, 136, 127, 129, "interacts"]], [[155, 156, 160, 161, "is-in"]]]}