├── _config.yml ├── resources ├── CAPTag2ID.txt ├── OutTag2ID_fact.txt ├── OutTag2ID_condition.txt └── PosTag2ID.txt ├── requirments.txt ├── MIMO_service ├── client.py ├── model.py ├── filter.py └── mimo_server.py ├── load_pretrained_word_embeddings.py ├── model.py ├── data └── label │ ├── train_sort │ ├── label-15637280.txt │ ├── label-11985482.txt │ ├── label-15675505.txt │ ├── label-26117042.txt │ ├── label-15621307.txt │ ├── label-15647045.txt │ ├── label-11922914.txt │ ├── label-15969102.txt │ ├── label-15542189.txt │ ├── label-11953882.txt │ ├── label-26117043.txt │ ├── label-15663562.txt │ ├── label-26119656.txt │ ├── label-11922564.txt │ ├── label-23364796.txt │ ├── label-26124495.txt │ ├── label-26131289.txt │ ├── label-23111462.txt │ └── label-11895154.txt │ └── eval_sort │ ├── label-12064555.txt │ ├── label-23890451.txt │ ├── label-26118933.txt │ ├── label-11726654.txt │ ├── label-15498271.txt │ ├── label-15498306.txt │ ├── label-12027387.txt │ ├── label-26096460.txt │ ├── label-15472922.txt │ ├── label-11934839.txt │ ├── label-26133121.txt │ └── label-11991752.txt ├── README.md └── data_center.py /_config.yml: -------------------------------------------------------------------------------- 1 | theme: jekyll-theme-cayman -------------------------------------------------------------------------------- /resources/CAPTag2ID.txt: -------------------------------------------------------------------------------- 1 | O 0 2 | B-C 1 3 | I-C 2 4 | B-P 3 5 | I-P 4 6 | B-A 5 7 | I-A 6 -------------------------------------------------------------------------------- /resources/OutTag2ID_fact.txt: -------------------------------------------------------------------------------- 1 | O 0 2 | B-f1C 1 3 | B-f2P 2 4 | B-f3C 3 5 | B-f1A 4 6 | B-f3A 5 7 | I-f1C 6 8 | I-f2P 7 9 | I-f3C 8 10 | I-f1A 9 11 | I-f3A 10 -------------------------------------------------------------------------------- /resources/OutTag2ID_condition.txt: -------------------------------------------------------------------------------- 1 | O 0 2 | B-c1C 1 3 | B-c2P 2 4 | B-c3C 3 5 | B-c1A 4 6 | B-c3A 5 7 | I-c1C 6 8 | I-c2P 7 9 | I-c3C 8 10 | I-c1A 9 11 | I-c3A 10 -------------------------------------------------------------------------------- /requirments.txt: -------------------------------------------------------------------------------- 1 | requests 2 | torch==1.2.0 3 | gevent==1.4.0 4 | sklearn 5 | nltk 6 | spacy==2.1.8 7 | pytorch_pretrained_bert==0.6.2 8 | gensim 9 | flask 10 | -------------------------------------------------------------------------------- /resources/PosTag2ID.txt: -------------------------------------------------------------------------------- 1 | CC 0 2 | CD 1 3 | DT 2 4 | EX 3 5 | FW 4 6 | IN 5 7 | JJ 6 8 | JJR 7 9 | JJS 8 10 | LS 9 11 | MD 10 12 | NN 11 13 | NNS 12 14 | NNP 13 15 | NNPS 14 16 | PDT 15 17 | POS 16 18 | PRP 17 19 | PRP$ 18 20 | RB 19 21 | RBR 20 22 | RBS 21 23 | RP 22 24 | TO 23 25 | UH 24 26 | VB 25 27 | VBD 26 28 | VBG 27 29 | VBN 28 30 | VBP 29 31 | VBZ 30 32 | WDT 31 33 | WP 32 34 | WP$ 33 35 | WRB 34 36 | SYM 35 -------------------------------------------------------------------------------- /MIMO_service/client.py: -------------------------------------------------------------------------------- 1 | import requests 2 | import json 3 | 4 | text = {"text": 'Histone deacetylase inhibitor valproic acid (VPA) has been used to increase the reprogramming efficiency of induced pluripotent stem cell (iPSC) from somatic cells, yet the specific molecular mechanisms underlying this effect is unknown. Using an in vitro pre-mature senescence model, we found that VPA treatment increased cell proliferation and inhibited apoptosis through the suppression of the p16/p21 pathway.'} 5 | headers = {'Content-Type' : 'application/json'} 6 | req = requests.post('http://localhost:9997/mimo', data=json.dumps(text), headers=headers) 7 | 8 | if (req.status_code == 200): 9 | statements = json.loads(req.text) 10 | print(statements) 11 | else: 12 | print(req) 13 | print("Error! Status code :" + str(req.status_code)) 14 | 15 | # json.loads(requests.post('http://localhost:9997/mimo', data=json.dumps(text), headers={'Content-Type' : 'application/json'}).text) 16 | -------------------------------------------------------------------------------- /load_pretrained_word_embeddings.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import numpy as np 3 | import logging 4 | import torch 5 | import gensim 6 | 7 | logging.basicConfig(level = logging.DEBUG) 8 | 9 | class Glove: 10 | """ 11 | Stores pretrained word embeddings for GloVe. 12 | """ 13 | def __init__(self, WORDEMB_PATH, dim = 50): 14 | """ 15 | Load a GloVe pretrained embeddings model. 16 | WORDEMB_PATH - File Path from which to load the embeddings 17 | dim - Dimension of expected word embeddings. 18 | """ 19 | self.fn = WORDEMB_PATH+str(dim)+'d.txt' 20 | self.dim = dim 21 | logging.debug("Loading GloVe embeddings from: {} ...".format(self.fn)) 22 | self._load(self.fn) 23 | logging.debug("Done!") 24 | 25 | def _load(self, fn): 26 | """ 27 | Load glove embedding from a given filename 28 | """ 29 | self.word2vec_dict = dict() 30 | with open(fn, 'r') as fp: 31 | count = 0 32 | for line in fp: 33 | line_list = line.strip().split(' ') 34 | word = line_list[0] 35 | vector = [] 36 | for index in range(1, len(line_list)): 37 | vector.append(float(line_list[index])) 38 | vector = torch.FloatTensor(vector) 39 | self.word2vec_dict[word] = vector / torch.sum(vector) 40 | count += 1 41 | if (count % 100000) == 0: 42 | print(count, 'done.') 43 | 44 | vector = torch.randn(self.dim) 45 | self.word2vec_dict[''] = vector / torch.sum(vector) 46 | 47 | class Gensim(object): 48 | """docstring for Gensim""" 49 | def __init__(self, WORDEMB_PATH, dim = 50): 50 | super(Gensim, self).__init__() 51 | self.fn = WORDEMB_PATH 52 | self.dim = dim 53 | self.word2vec_dict = dict() 54 | logging.debug("loading word embeddings from: {} ...".format(self.fn)) 55 | wv_model = gensim.models.KeyedVectors.load_word2vec_format(self.fn, binary=True) 56 | for word in wv_model.vocab: 57 | self.word2vec_dict[word] = torch.tensor(wv_model.wv[word], dtype=torch.float32) 58 | assert len(self.word2vec_dict) == len(wv_model.vocab) 59 | vector = torch.randn(self.dim, dtype=torch.float32) 60 | self.word2vec_dict[''] = vector 61 | vector = torch.randn(self.dim, dtype=torch.float32) 62 | assert not '' in self.word2vec_dict 63 | self.word2vec_dict[''] = vector 64 | 65 | if __name__ == '__main__': 66 | Gensim('../preprocessing/pubmed-vectors=50.bin') 67 | -------------------------------------------------------------------------------- /model.py: -------------------------------------------------------------------------------- 1 | import torch.nn as nn 2 | 3 | class RNNModel(nn.Module): 4 | """Container module with an encoder, a recurrent module, and a decoder.""" 5 | 6 | def __init__(self, rnn_type, ntoken, ninp, nhid, nlayers, dropout=0.5, tie_weights=False): 7 | super(RNNModel, self).__init__() 8 | self.drop = nn.Dropout(dropout) 9 | self.encoder = nn.Embedding(ntoken, ninp) 10 | if rnn_type in ['LSTM', 'GRU']: 11 | self.rnn = getattr(nn, rnn_type)(ninp, nhid, nlayers, dropout=dropout) 12 | else: 13 | try: 14 | nonlinearity = {'RNN_TANH': 'tanh', 'RNN_RELU': 'relu'}[rnn_type] 15 | except KeyError: 16 | raise ValueError( """An invalid option for `--model` was supplied, 17 | options are ['LSTM', 'GRU', 'RNN_TANH' or 'RNN_RELU']""") 18 | self.rnn = nn.RNN(ninp, nhid, nlayers, nonlinearity=nonlinearity, dropout=dropout) 19 | self.decoder = nn.Linear(nhid, ntoken) 20 | 21 | # Optionally tie weights as in: 22 | # "Using the Output Embedding to Improve Language Models" (Press & Wolf 2016) 23 | # https://arxiv.org/abs/1608.05859 24 | # and 25 | # "Tying Word Vectors and Word Classifiers: A Loss Framework for Language Modeling" (Inan et al. 2016) 26 | # https://arxiv.org/abs/1611.01462 27 | if tie_weights: 28 | if nhid != ninp: 29 | raise ValueError('When using the tied flag, nhid must be equal to emsize') 30 | self.decoder.weight = self.encoder.weight 31 | 32 | self.init_weights() 33 | 34 | self.rnn_type = rnn_type 35 | self.nhid = nhid 36 | self.nlayers = nlayers 37 | 38 | def init_weights(self): 39 | initrange = 0.1 40 | self.encoder.weight.data.uniform_(-initrange, initrange) 41 | self.decoder.bias.data.zero_() 42 | self.decoder.weight.data.uniform_(-initrange, initrange) 43 | 44 | def forward(self, input, hidden): 45 | emb = self.drop(self.encoder(input)) 46 | output, hidden = self.rnn(emb, hidden) 47 | output = self.drop(output) 48 | #decoded = self.decoder(output.view(output.size(0)*output.size(1), output.size(2))) 49 | #return decoded.view(output.size(0), output.size(1), decoded.size(1)), hidden 50 | return output 51 | 52 | def init_hidden(self, bsz): 53 | weight = next(self.parameters()) 54 | if self.rnn_type == 'LSTM': 55 | return (weight.new_zeros(self.nlayers, bsz, self.nhid), 56 | weight.new_zeros(self.nlayers, bsz, self.nhid)) 57 | else: 58 | return weight.new_zeros(self.nlayers, bsz, self.nhid) 59 | -------------------------------------------------------------------------------- /MIMO_service/model.py: -------------------------------------------------------------------------------- 1 | import torch.nn as nn 2 | 3 | class RNNModel(nn.Module): 4 | """Container module with an encoder, a recurrent module, and a decoder.""" 5 | 6 | def __init__(self, rnn_type, ntoken, ninp, nhid, nlayers, dropout=0.5, tie_weights=False): 7 | super(RNNModel, self).__init__() 8 | self.drop = nn.Dropout(dropout) 9 | self.encoder = nn.Embedding(ntoken, ninp) 10 | if rnn_type in ['LSTM', 'GRU']: 11 | self.rnn = getattr(nn, rnn_type)(ninp, nhid, nlayers, dropout=dropout) 12 | else: 13 | try: 14 | nonlinearity = {'RNN_TANH': 'tanh', 'RNN_RELU': 'relu'}[rnn_type] 15 | except KeyError: 16 | raise ValueError( """An invalid option for `--model` was supplied, 17 | options are ['LSTM', 'GRU', 'RNN_TANH' or 'RNN_RELU']""") 18 | self.rnn = nn.RNN(ninp, nhid, nlayers, nonlinearity=nonlinearity, dropout=dropout) 19 | self.decoder = nn.Linear(nhid, ntoken) 20 | 21 | # Optionally tie weights as in: 22 | # "Using the Output Embedding to Improve Language Models" (Press & Wolf 2016) 23 | # https://arxiv.org/abs/1608.05859 24 | # and 25 | # "Tying Word Vectors and Word Classifiers: A Loss Framework for Language Modeling" (Inan et al. 2016) 26 | # https://arxiv.org/abs/1611.01462 27 | if tie_weights: 28 | if nhid != ninp: 29 | raise ValueError('When using the tied flag, nhid must be equal to emsize') 30 | self.decoder.weight = self.encoder.weight 31 | 32 | self.init_weights() 33 | 34 | self.rnn_type = rnn_type 35 | self.nhid = nhid 36 | self.nlayers = nlayers 37 | 38 | def init_weights(self): 39 | initrange = 0.1 40 | self.encoder.weight.data.uniform_(-initrange, initrange) 41 | self.decoder.bias.data.zero_() 42 | self.decoder.weight.data.uniform_(-initrange, initrange) 43 | 44 | def forward(self, input, hidden): 45 | emb = self.drop(self.encoder(input)) 46 | output, hidden = self.rnn(emb, hidden) 47 | output = self.drop(output) 48 | #decoded = self.decoder(output.view(output.size(0)*output.size(1), output.size(2))) 49 | #return decoded.view(output.size(0), output.size(1), decoded.size(1)), hidden 50 | return output 51 | 52 | def init_hidden(self, bsz): 53 | weight = next(self.parameters()) 54 | if self.rnn_type == 'LSTM': 55 | return (weight.new_zeros(self.nlayers, bsz, self.nhid), 56 | weight.new_zeros(self.nlayers, bsz, self.nhid)) 57 | else: 58 | return weight.new_zeros(self.nlayers, bsz, self.nhid) 59 | -------------------------------------------------------------------------------- /data/label/train_sort/label-15637280.txt: -------------------------------------------------------------------------------- 1 | # 15637280 requirement#0 of#1 voltage-gated#2 calcium#3 channel#4 beta4#5 subunit#6 for#7 t#8 lymphocyte#9 functions#10 .#11 2 | 3 | c1:[{voltage-gated_calcium_channel_beta4_subunit#2:requirement#0},for#7,t_lymphocyte_functions#8] 4 | stmt1 = c1 5 | 6 | # 15637280 calcium#0 is#1 known#2 to#3 play#4 vital#5 roles#6 in#7 diverse#8 physiological#9 processes#10 ,#11 and#12 it#13 is#14 known#15 that#16 voltage-gated#17 calcium#18 channels#19 mediate#20 calcium#21 influx#22 in#23 excitable#24 cells#25 .#26 7 | 8 | f1:[calcium#0,is_known_to_play#1,vital_roles#5] 9 | f2:[voltage-gated_calcium_channels#17,mediate#20,calcium_influx#21] 10 | c2:[vital_roles#5,in#7,diverse_physiological_processes#8] 11 | c3:[calcium_influx#21,in#23,excitable_cells#24] 12 | stmt2 = f1 f2 c2 c3 13 | 14 | # 15637280 however#0 ,#1 no#2 consensus#3 exists#4 on#5 the#6 molecular#7 identity#8 of#9 the#10 calcium#11 channels#12 present#13 in#14 nonexcitable#15 cells#16 such#17 as#18 t#19 lymphocytes#20 .#21 15 | 16 | f3:[consensus#3,exists_on#4,{calcium_channels_present#11:molecular_identity#7}] 17 | c4:[NIL,no#2,consensus#3] 18 | c5:[{calcium_channels_present#11:molecular_identity#7},in#14,nonexcitable_cells#15] 19 | c6:[{calcium_channels_present#11:molecular_identity#7},in#14,t_lymphocytes#19] 20 | stmt3 = f3 c4 c5 c6 21 | 22 | # 15637280 here#0 ,#1 we#2 demonstrate#3 that#4 t#5 lymphocytes#6 express#7 both#8 regulatory#9 beta4#10 and#11 poreforming#12 cav1#13 alpha1#14 subunits#15 of#16 cav#17 channels#18 .#19 23 | 24 | f4:[NIL,demonstrate_that#3,NIL] 25 | f5:[t_lymphocytes#5,express#7,regulatory_beta4#9] 26 | f6:[t_lymphocytes#5,express#7,{cav_channels#17:poreforming_cav1_alpha1_subunits#12}] 27 | stmt4 = f4 f5 f6 28 | 29 | # 15637280 cav#0 beta4-mutant#1 t#2 lymphocytes#3 fail#4 to#5 acquire#6 normal#7 functions#8 and#9 display#10 impairment#11 in#12 the#13 calcium#14 response#15 ,#16 activation#17 of#18 the#19 transcription#20 factor#21 nfat#22 ,#23 and#24 cytokine#25 production#26 .#27 30 | 31 | f7:[cav_beta4-mutant_t_lymphocytes#0,fail_to_acquire#4,normal_functions#7] 32 | f8:[cav_beta4-mutant_t_lymphocytes#0,display_impairment_in#10,calcium_response#14] 33 | f9:[cav_beta4-mutant_t_lymphocytes#0,display_impairment_in#10,{transcription_factor_nfat#20:activation#17}] 34 | f10:[cav_beta4-mutant_t_lymphocytes#0,display_impairment_in#10,cytokine_production#25] 35 | stmt5 = f7 f8 f9 f10 36 | 37 | # 15637280 although#0 cav1#1 channels#2 of#3 lymphocytes#4 retain#5 their#6 voltage#7 dependency#8 ,#9 t#10 cell#11 receptor#12 stimulation#13 dramatically#14 increases#15 channel#16 opening#17 ,#18 providing#19 a#20 new#21 mechanism#22 for#23 calcium#24 entry#25 in#26 lymphocytes#27 .#28 38 | 39 | f11:[{lymphocytes#4:cav1_channels#1},retain#5,{lymphocytes#4:voltage_dependency#7}] 40 | f12:[t_cell_receptor_stimulation#10,dramatically_increases#14,channel_opening#16] 41 | f13:[t_cell_receptor_stimulation#10,providing_a_new_mechanism_for#19,calcium_entry#24] 42 | c7:[calcium_entry#24,in#26,lymphocytes#27] 43 | stmt6 = f11 f12 f13 c7 44 | -------------------------------------------------------------------------------- /data/label/train_sort/label-11985482.txt: -------------------------------------------------------------------------------- 1 | # 11985482 the#0 role#1 of#2 immune#3 reconstitution#4 in#5 cytomegalovirus#6 infection#7 .#8 2 | 3 | c1:[{immune_reconstitution#3:role#1},in#5,cytomegalovirus_infection#6] 4 | stmt1 = c1 5 | 6 | # 11985482 cytomegalovirus#0 causes#1 high#2 morbidity#3 and#4 mortality#5 in#6 immunocompromised#7 patients#8 .#9 7 | 8 | f1:[cytomegalovirus#0,causes#1,high_morbidity#2] 9 | f2:[cytomegalovirus#0,causes#1,mortality#5] 10 | c2:[high_morbidity#2,in#6,immunocompromised_patients#7] 11 | c3:[mortality#5,in#6,immunocompromised_patients#7] 12 | stmt2 = f1 f2 c2 c3 13 | 14 | # 11985482 the#0 host#1 immune#2 response#3 to#4 cmv#5 comprises#6 specific#7 and#8 nonspecific#9 cellular#10 and#11 humoral#12 responses#13 ,#14 but#15 current#16 knowledge#17 supports#18 a#19 protective#20 role#21 only#22 for#23 cell-mediated#24 immune#25 responses#26 .#27 15 | 16 | f3:[host_immune_response#1,comprises#6,specific_and_nonspecific_cellular#7] 17 | f4:[host_immune_response#1,comprises#6,humoral_responses#12] 18 | f5:[current_knowledge#16,supports#18,protective_role#20] 19 | c4:[host_immune_response#1,to#4,cmv#5] 20 | c5:[current_knowledge#16,for#23,cell-mediated_immune_responses#24] 21 | stmt3 = f3 f4 f5 c4 c5 22 | 23 | # 11985482 although#0 complete#1 cmv#2 eradication#3 is#4 unusual#5 even#6 in#7 immunocompetent#8 hosts#9 ,#10 its#11 morbidity#12 can#13 be#14 limited#15 by#16 cmv-specific#17 cd8+#18 cytotoxic#19 lymphocytes#20 supported#21 by#22 cd4+-mediated#23 t#24 lymphocyte#25 helper#26 activity#27 .#28 24 | 25 | f6:[complete_cmv_eradication#1,is_unusual_even_in#4,immunocompetent_hosts#8] 26 | f7:[{complete_cmv_eradication#1:morbidity#12},can_be_limited_by#13,cmv-specific_cd8+_cytotoxic_lymphocytes#17] 27 | c6:[cmv-specific_cd8+_cytotoxic_lymphocytes#17,supported_by#21,cd4+-mediated_t_lymphocyte_helper_activity#23] 28 | stmt4 = f6 f7 c6 29 | 30 | # 11985482 in#0 patients#1 with#2 congenital#3 or#4 acquired#5 deficiencies#6 of#7 cell-mediated#8 immunity#9 ,#10 recovery#11 of#12 cd4+#13 lymphocyte#14 numbers#15 and/or#16 function#17 coincides#18 with#19 cessation#20 of#21 cmv-associated#22 morbidity#23 .#24 31 | 32 | f8:[{cd4+_lymphocyte_numbers_and/or_function#13:recovery#11},coincides_with#18,{cmv-associated_morbidity#22:cessation#20}] 33 | c7:[NIL,in#0,patients#1] 34 | c8:[patients#1,with#2,congenital#3] 35 | c9:[patients#1,acquired#5,{cell-mediated_immunity#8:deficiencies#6}] 36 | stmt5 = f8 c7 c8 c9 37 | 38 | # 11985482 however#0 ,#1 an#2 immunological#3 test#4 that#5 can#6 predict#7 protection#8 against#9 cmv#10 disease#11 across#12 different#13 types#14 of#15 high-risk#16 patients#17 is#18 not#19 yet#20 available#21 .#22 39 | 40 | f9:[immunological_test#3,is_not_yet_available#18,NIL] 41 | c10:[immunological_test#3,can_predict#6,protection#8] 42 | c11:[protection#8,against#9,cmv_disease#10] 43 | c12:[cmv_disease#10,across#12,{high-risk_patients#16:different_types#13}] 44 | stmt6 = f9 c10 c11 c12 45 | 46 | # 11985482 in#0 recent#1 years#2 ,#3 the#4 introduction#5 of#6 antivirals#7 active#8 against#9 cmv#10 has#11 improved#12 the#13 outcome#14 of#15 cmv#16 disease#17 .#18 47 | 48 | f10:[{antivirals_active#7:introduction#5},has_improved#11,{cmv_disease#16:outcome#14}] 49 | c13:[NIL,in#0,{NIL#-1:recent_years#1}] 50 | c14:[{antivirals_active#7:introduction#5},against#9,cmv#10] 51 | stmt7 = f10 c13 c14 52 | 53 | # 11985482 in#0 addition#1 ,#2 there#3 is#4 a#5 continuous#6 effort#7 to#8 develop#9 cmv-specific#10 immune-based#11 therapies#12 including#13 vaccines#14 and#15 immune#16 modulators#17 such#18 as#19 cytokines#20 ,#21 which#22 may#23 be#24 of#25 supplemental#26 benefit#27 in#28 the#29 control#30 of#31 cmv#32 disease#33 .#34 54 | 55 | f11:[{NIL#-1:effort#7},to_develop#8,cmv-specific_immune-based_therapies#10] 56 | f12:[immune_modulators#16,such_as#18,cytokines#20] 57 | c15:[cmv-specific_immune-based_therapies#10,including#13,vaccines#14] 58 | c16:[cmv-specific_immune-based_therapies#10,including#13,immune_modulators#16] 59 | c17:[immune_modulators#16,may_be_of_supplemental_benefit_in#23,{cmv_disease#32:control#30}] 60 | stmt8 = f11 f12 c15 c16 c17 61 | 62 | -------------------------------------------------------------------------------- /data/label/train_sort/label-15675505.txt: -------------------------------------------------------------------------------- 1 | # 15675505 hiv#0 and#1 children#2 ,#3 the#4 developing#5 immune#6 system#7 fights#8 back#9 .#10 2 | 3 | c1:[hiv#0,NIL#-1,NIL] 4 | c2:[children#2,NIL#-1,NIL] 5 | c3:[developing_immune_system_fights_back#5,NIL#-1,NIL] 6 | stmt1 = c1 c2 c3 7 | 8 | # 15675505 children#0 infected#1 with#2 hiv#3 display#4 great#5 variability#6 in#7 their#8 clinical#9 outcome#10 and#11 rate#12 of#13 progression#14 to#15 aids#16 .#17 9 | 10 | f1:[children#0,display#4,{clinical_outcome#9:great_variability#5}] 11 | f2:[children#0,display#4,{progression#14:rate#12}] 12 | c4:[children#0,infected_with#1,hiv#3] 13 | stmt2 = f1 f2 c4 14 | 15 | # 15675505 the#0 reasons#1 for#2 this#3 variability#4 are#5 largely#6 unknown#7 .#8 16 | 17 | f3:[{variability#4:reasons#1},are_largely_unknown#5,NIL] 18 | stmt3 = f3 19 | 20 | # 15675505 increasing#0 evidence#1 from#2 adult#3 studies#4 suggests#5 that#6 the#7 cellular#8 immune#9 response#10 is#11 a#12 critical#13 determinant#14 of#15 viral#16 containment#17 ,#18 and#19 likely#20 accounts#21 for#22 much#23 of#24 the#25 observed#26 variability#27 in#28 clinical#29 progression#30 .#31 21 | 22 | f4:[{adult_studies#3:increasing_evidence#0},suggests_that#5,NIL] 23 | f5:[cellular_immune_response#8,is#11,{viral_containment#16:critical_determinant#13}] 24 | f6:[cellular_immune_response#8,likely_accounts_for_much_of#20,observed_variability#26] 25 | c5:[observed_variability#26,in#28,clinical_progression#29] 26 | stmt4 = f4 f5 f6 c5 27 | 28 | # 15675505 detailed#0 studies#1 of#2 the#3 hiv-specific#4 immune#5 responses#6 generated#7 by#8 adults#9 with#10 long-term#11 nonprogressive#12 infection#13 have#14 revealed#15 elements#16 of#17 the#18 host#19 immune#20 response#21 that#22 correlate#23 with#24 effective#25 viral#26 control#27 .#28 29 | 30 | f7:[{hiv-specific_immune_responses#4:detailed_studies#0},have_revealed#14,{host_immune_response#19:elements#16}] 31 | c6:[{hiv-specific_immune_responses#4:detailed_studies#0},generated_by#7,adults_with_long-term_nonprogressive_infection#9] 32 | c7:[{host_immune_response#19:elements#16},correlate_with#23,effective_viral_control#25] 33 | stmt5 = f7 c6 c7 34 | 35 | # 15675505 however#0 ,#1 much#2 less#3 is#4 known#5 about#6 the#7 hiv-specific#8 immune#9 responses#10 generated#11 by#12 perinatally#13 infected#14 children#15 .#16 36 | 37 | f8:[NIL,much_less_is_known_about#2,hiv-specific_immune_responses#8] 38 | c8:[hiv-specific_immune_responses#8,generated_by#11,perinatally_infected_children#13] 39 | stmt6 = f8 c8 40 | 41 | # 15675505 recent#0 studies#1 have#2 revealed#3 that#4 elements#5 of#6 both#7 the#8 hiv-specific#9 cytotoxic#10 t#11 lymphocyte#12 response#13 and#14 the#15 t-helper#16 response#17 differ#18 between#19 adults#20 and#21 children#22 ,#23 and#24 these#25 differences#26 could#27 have#28 important#29 implications#30 for#31 the#32 ability#33 to#34 control#35 hiv#36 viraemia#37 .#38 42 | 43 | f9:[{NIL#-1:recent_studies#0},have_revealed_that#2,NIL] 44 | f10:[{hiv-specific_cytotoxic_t_lymphocyte_response#9:elements#5},differ_between#18,adults#20] 45 | f11:[{hiv-specific_cytotoxic_t_lymphocyte_response#9:elements#5},differ_between#18,children#22] 46 | f12:[{t-helper_response#16:elements#5},differ_between#18,adults#20] 47 | f13:[{t-helper_response#16:elements#5},differ_between#18,children#22] 48 | f14:[{NIL#-1:differences#26},could_have_important_implications_for#27,{NIL#-1:ability#33}] 49 | c9:[{NIL#-1:differences#26},to_control#34,hiv_viraemia#36] 50 | stmt7 = f9 f10 f11 f12 f13 f14 c9 51 | 52 | # 15675505 identification#0 of#1 the#2 precise#3 correlates#4 of#5 viral#6 containment#7 in#8 children#9 could#10 provide#11 important#12 insights#13 into#14 the#15 pathogenesis#16 of#17 vertical#18 infection#19 ,#20 and#21 will#22 greatly#23 assist#24 the#25 rational#26 design#27 of#28 hiv#29 vaccines#30 and#31 immunotherapies#32 .#33 53 | 54 | f15:[{NIL#-1:identification#0},could_provide_important_insights_into#10,{vertical_infection#18:pathogenesis#16}] 55 | f16:[{NIL#-1:identification#0},will_greatly_assist#22,{hiv_vaccines#29:rational_design#26}] 56 | f17:[{NIL#-1:identification#0},will_greatly_assist#22,{immunotherapies#32:rational_design#26}] 57 | c10:[{NIL#-1:identification#0},of#1,{viral_containment#6:precise_correlates#3}] 58 | c11:[{viral_containment#6:precise_correlates#3},in#8,children#9] 59 | stmt8 = f15 f16 f17 c10 c11 60 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | # Joint Extraction of Fact and Condition Tuples from Sceintific Text 3 | 4 | 5 | ## Introduction 6 | This repository contains source code for the EMNLP 2019 paper " "Multi-Input Multi-Output Sequence Labeling for Joint Extraction of Fact and Condition Tuples from Scientific Text" ([Paper](http://www.meng-jiang.com/pubs/mimo-emnlp19/mimo-emnlp19-paper.pdf)). 7 | 8 | ## Usage 9 | 10 | ### 1.Clone the Repository 11 | ```bash 12 | git clone https://github.com/twjiang/MIMO_CFE.git 13 | ``` 14 | ### 2.Download External Resources 15 | 16 | * The `dumped MIMO` can be found [here](https://www.dropbox.com/s/lc1bvoxc2wbut9t/dumped_models.pt?dl=0). 17 | 18 | * The `word embedding` we use can be found [here](https://www.dropbox.com/sh/6yx1l8euehgw12k/AAB9mWc3m8H7niuEF7NBYUdRa?dl=0). 19 | 20 | * The `pre-trained language model` we use can be found [here](https://www.dropbox.com/sh/q1kehix8q58sxmh/AADU35QFu1ZMuNQFTiEYWSxUa?dl=0). 21 | 22 | put these files into `./resources` folder 23 | ### 3.Install Requirements 24 | This repo is tested on Python 3.6, PyTorch 1.2.0 25 | 26 | Create Environment (Optional): Ideally, you should create an environment for the project. 27 | ```bash 28 | conda create -n mimo python=3.6 29 | 30 | conda activate mimo 31 | 32 | pip install -r requirments.txt 33 | ``` 34 | 35 | ### 4.Start a demo application 36 | ```bash 37 | cd MIMO_service 38 | 39 | python mimo_server.py #Start a MIMO service 40 | 41 | python client.py 42 | ``` 43 | 44 | The output of the demo is shown below. 45 | 46 | ```bash 47 | { 48 | 'statements': { 49 | 'stmt 1': { 50 | 'text': 'Histone deacetylase inhibitor valproic acid ( VPA ) has been used to increase the reprogramming efficiency of induced pluripotent stem cell ( iPSC ) from somatic cells , yet the specific molecular mechanisms underlying this effect is unknown .', 51 | 'fact tuples': [ 52 | ['Histone deacetylase inhibitor valproic acid', 'NIL', 'has been used to increase', 'induced pluripotent stem cell', 'reprogramming efficiency'], 53 | ['VPA', 'NIL', 'has been used to increase', 'induced pluripotent stem cell', 'reprogramming efficiency'], 54 | ['Histone deacetylase inhibitor valproic acid', 'NIL', 'has been used to increase', 'induced pluripotent stem cell', 'reprogramming'], 55 | ['specific molecular mechanisms', 'NIL', 'is unknown', 'NIL', 'NIL'] 56 | ], 57 | 'condition tuples': [ 58 | ['iPSC', 'reprogramming efficiency', 'from', 'somatic cells', 'NIL'], 59 | ['induced pluripotent stem cell', 'reprogramming efficiency', 'from', 'somatic cells', 'NIL'], 60 | ['specific molecular mechanisms', 'NIL', 'underlying', 'NIL', 'effect'] 61 | ], 62 | 'concept_indx': [0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 22, 25, 26, 30, 31, 32], 63 | 'attr_indx': [14, 15, 35], 64 | 'predicate_indx': [8, 9, 10, 11, 12, 24, 33, 36, 37] 65 | } 66 | } 67 | } 68 | 69 | ``` 70 | 71 | ### 5. Train Your Own MIMO 72 | 73 | example commands for pretrain: 74 | 75 | (all gates for LM, pretrain) 76 | ```bash 77 | python train.py --cuda --config 111000000 --model_name MIMO_BERT_LSTM --pretrain 78 | ``` 79 | 80 | 81 | (all gates for POS, pretrain) 82 | ```bash 83 | python train.py --cuda --config 000111000 --model_name MIMO_BERT_LSTM --pretrain 84 | ``` 85 | (all gates for LM and POS, pretrain) 86 | ```bash 87 | python train.py --cuda --config 111111000 --model_name MIMO_BERT_LSTM --pretrain 88 | ``` 89 | example commands with multi-output: 90 | 91 | (all gates for LM with multi-output) 92 | ```bash 93 | python train.py --cuda --config 111000000 --model_name MIMO_BERT_LSTM 94 | ``` 95 | 96 | 97 | (all gates for POS with multi-output) 98 | ```bash 99 | python train.py --cuda --config 000111000 --model_name MIMO_BERT_LSTM 100 | ``` 101 | (all gates for LM and POS, with multi-output) 102 | ```bash 103 | python train.py --cuda --config 111111000 --model_name MIMO_BERT_LSTM 104 | ``` 105 | 106 | 107 | ## Reference 108 | ``` 109 | @inproceedings{jiang-mimo, 110 | title = "Multi-Input Multi-Output Sequence Labeling for Joint Extraction of Fact and Condition Tuples from Scientific Text", 111 | author = "Jiang, Tianwen and Zhao, Tong and Qin, Bing and Liu, Ting and Chawla, Nitesh V and Jiang, Meng", 112 | booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing", 113 | month = nov, 114 | year = "2019", 115 | address = "Hong Kong, China", 116 | publisher = "Association for Computational Linguistics", 117 | } 118 | ``` 119 | 120 | -------------------------------------------------------------------------------- /data/label/train_sort/label-26117042.txt: -------------------------------------------------------------------------------- 1 | # 26117042 [#0 amplification#1 ex#2 vivo#3 and#4 cytocidal#5 activity#6 of#7 leukemia#8 tumor-associated#9 antigen-specific#10 cytotoxic#11 t#12 lymphocytes]#13 .#14 2 | 3 | c1:[{leukemia_tumor-associated_antigen-specific_cytotoxic_t_lymphocytes]#8:amplification_ex_vivo#1},NIL#-1,NIL] 4 | c2:[{leukemia_tumor-associated_antigen-specific_cytotoxic_t_lymphocytes]#8:cytocidal_activity#5},NIL#-1,NIL] 5 | stmt1 = c1 c2 6 | 7 | # 26117042 to#0 explore#1 the#2 feasibility#3 of#4 amplifying#5 the#6 leukemia#7 tumor#8 associated#9 antigens-specific#10 cytotoxic#11 t#12 lymphocytes#13 ex#14 vivo#15 and#16 to#17 evaluate#18 the#19 cytotoxicity#20 oftaa-ctl#21 .#22 8 | 9 | f1:[NIL,to_explore#0,feasibility#3] 10 | f2:[NIL,to_evaluate#17,cytotoxicity_oftaa-ctl#20] 11 | c3:[feasibility#3,amplifying#5,leukemia_tumor_associated_antigens-specific_cytotoxic_t_lymphocytes_ex_vivo#7] 12 | stmt2 = f1 f2 c3 13 | 14 | # 26117042 the#0 peripheral#1 blood#2 mononuclear#3 cells#4 were#5 enriched#6 by#7 density#8 gradient#9 centrifugtion#10 ,#11 taa-ctl#12 were#13 generated#14 by#15 stimulation#16 of#17 pbmnc#18 with#19 peptide-pulsed#20 dc#21 at#22 an#23 effector-to-target#24 ratio#25 of#26 10#27 ,#28 immunophenotype#29 of#30 taa-ctl#31 was#32 analyzed#33 by#34 flow#35 cytometry#36 ,#37 cytotoxicity#38 assay#39 was#40 used#41 to#42 evaluate#43 the#44 cytotoxic#45 activity#46 of#47 taa-ctl#48 against#49 peptide-pulsed#50 autologous#51 target#52 cells(pha-blasts)#53 .#54 15 | 16 | f3:[peripheral_blood_mononuclear_cells#1,were_enriched_by#5,density_gradient_centrifugtion#8] 17 | f4:[taa-ctl#12,were_generated_by#13,{pbmnc#18:stimulation#16}] 18 | f5:[{taa-ctl#31:immunophenotype#29},was_analyzed_by#32,flow_cytometry#35] 19 | f6:[cytotoxicity_assay#38,was_used_to_evaluate#40,{taa-ctl#48:cytotoxic_activity#45}] 20 | c4:[{pbmnc#18:stimulation#16},with#19,peptide-pulsed_dc#20] 21 | c5:[peptide-pulsed_dc#20,at#22,{effector-to-target_ratio#24:10#27}] 22 | c6:[{taa-ctl#48:cytotoxic_activity#45},against#49,peptide-pulsed_autologous_target_cells(pha-blasts)#50] 23 | stmt3 = f3 f4 f5 f6 c4 c5 c6 24 | 25 | # 26117042 taa-ctl#0 expanded#1 from#2 volunteer#3 showed#4 a#5 mean#6 expansion#7 of#8 3.81#9 !#10 1.61#11 ,#12 the#13 phenotyping#14 of#15 the#16 taa-ctl#17 was#18 predominantly#19 cd3(+)#20 ,#21 the#22 detection#23 of#24 intracellular#25 cytokines#26 after#27 stimulation#28 with#29 peptide#30 showed#31 that#32 the#33 secretion#34 rates#35 of#36 ifn-gamma#37 and#38 tnf-alpha#39 in#40 cd8(+)#41 taa-ctl#42 were#43 26 | 27 | f7:[taa-ctl#0,showed#4,{mean_expansion#6:3.81_!_1.61#9}] 28 | f8:[{taa-ctl#17:phenotyping#14},was_predominantly#18,cd3(+)#20] 29 | f9:[{intracellular_cytokines#25:detection#23},showed#31,NIL] 30 | f10:[{ifn-gamma#37:secretion_rates#34},were#43,NIL] 31 | f11:[{tnf-alpha#39:secretion_rates#34},were#43,NIL] 32 | c7:[taa-ctl#0,expanded_from#1,volunteer#3] 33 | c8:[{intracellular_cytokines#25:detection#23},after#27,stimulation#28] 34 | c9:[stimulation#28,with#29,peptide#30] 35 | c10:[{ifn-gamma#37:secretion_rates#34},in#40,cd8(+)_taa-ctl#41] 36 | c11:[{tnf-alpha#39:secretion_rates#34},in#40,cd8(+)_taa-ctl#41] 37 | stmt4 = f7 f8 f9 f10 f11 c7 c8 c9 c10 c11 38 | 39 | # 26117042 compared#0 with#1 the#2 cd8(+)#3 taa-ctl#4 group#5 ,#6 the#7 secretion#8 rates#9 of#10 ifn-gamma#11 and#12 tnf-alpha#13 were#14 40 | 41 | f12:[{ifn-gamma#11:secretion_rates#8},were#14,NIL] 42 | f13:[{tnf-alpha#13:secretion_rates#8},were#14,NIL] 43 | c12:[NIL,compared_with#0,cd8(+)_taa-ctl_group#3] 44 | stmt5 = f12 f13 c12 45 | 46 | # 26117042 the#0 secretions#1 of#2 ifn-gamma#3 and#4 tnf-alpha#5 in#6 ctl#7 were#8 both#9 significantly#10 lower#11 than#12 those#13 in#14 taa-ctl#15 ,#16 the#17 specific#18 killing#19 efficiency#20 of#21 the#22 taa-ctl#23 against#24 taa-pulesd#25 target#26 cells#27 were#28 .#29 47 | 48 | f14:[{ifn-gamma#3:secretions#1},were_both_significantly_lower_than_those_in#8,taa-ctl#15] 49 | f15:[{tnf-alpha#5:secretions#1},were_both_significantly_lower_than_those_in#8,taa-ctl#15] 50 | f16:[{taa-ctl#23:specific_killing_efficiency#18},were#28,NIL] 51 | c13:[{ifn-gamma#3:secretions#1},in#6,ctl#7] 52 | c14:[{tnf-alpha#5:secretions#1},in#6,ctl#7] 53 | c15:[{taa-ctl#23:specific_killing_efficiency#18},against#24,taa-pulesd_target_cells#25] 54 | stmt6 = f14 f15 f16 c13 c14 c15 55 | 56 | # 26117042 taa-ctl#0 can#1 be#2 successfully#3 induced#4 and#5 generated#6 ex#7 vivo#8 from#9 the#10 healthy#11 volunteer#12 peripheral#13 blood#14 ,#15 and#16 the#17 taa-ctl#18 possess#19 a#20 specific#21 killing#22 activity#23 .#24 57 | 58 | f17:[taa-ctl#0,can_be_successfully_induced#1,ex_vivo#7] 59 | f18:[taa-ctl#0,generated#6,ex_vivo#7] 60 | f19:[taa-ctl#18,possess#19,specific_killing_activity#21] 61 | c16:[ex_vivo#7,from#9,healthy_volunteer_peripheral_blood#11] 62 | stmt7 = f17 f18 f19 c16 63 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-12064555.txt: -------------------------------------------------------------------------------- 1 | # 12064555 association#0 of#1 low#2 job#3 control#4 with#5 a#6 decrease#7 in#8 memory#9 t#10 lymphocytes#11 in#12 japanese#13 middle-aged#14 male#15 workers#16 in#17 an#18 electric#19 power#20 plant#21 .#22 2 | 3 | c1:[{low_job_control#2:association#0},with#5,{memory_t_lymphocytes#9:decrease#7}] 4 | c2:[{memory_t_lymphocytes#9:decrease#7},in#12,japanese_middle-aged_male_workers#13] 5 | c3:[japanese_middle-aged_male_workers#13,in#17,electric_power_plant#19] 6 | stmt1 = c1 c2 c3 7 | 8 | # 12064555 to#0 clarify#1 the#2 relationship#3 between#4 perceived#5 job#6 stress#7 and#8 lymphocyte#9 subpopulations#10 ,#11 a#12 cross-sectional#13 study#14 was#15 conducted#16 in#17 231#18 male#19 electric#20 power#21 plant#22 workers#23 .#24 9 | 10 | f1:[NIL,to_clarify#0,{NIL#-1:relationship#3}] 11 | f2:[cross-sectional_study#13,was_conducted_in#15,231_male_electric_power_plant_workers#18] 12 | c4:[{NIL#-1:relationship#3},between#4,perceived_job_stress#5] 13 | c5:[{NIL#-1:relationship#3},between#4,lymphocyte_subpopulations#9] 14 | stmt2 = f1 f2 c4 c5 15 | 16 | # 12064555 job#0 stress#1 ,#2 i.e.#3 ,#4 job#5 control#6 ,#7 job#8 demands#9 ,#10 and#11 social#12 support#13 at#14 work#15 ,#16 was#17 assessed#18 by#19 means#20 of#21 the#22 japanese#23 version#24 of#25 the#26 job#27 content#28 questionnaire#29 .#30 17 | 18 | f3:[job_stress#0,i.e.#3,job_control#5] 19 | f4:[job_stress#0,i.e.#3,job_demands#8] 20 | f5:[job_stress#0,i.e.#3,social_support_at_work#12] 21 | f6:[job_stress#0,was_assessed_by_means_of#17,{job_content_questionnaire#27:japanese_version#23}] 22 | stmt3 = f3 f4 f5 f6 23 | 24 | # 12064555 blood#0 samples#1 were#2 taken#3 from#4 all#5 the#6 workers#7 ,#8 and#9 numbers#10 of#11 cd4+#12 t#13 lymphocyte#14 subpopulations#15 ,#16 total#17 cd4+#18 t#19 ,#20 t#21 lymphocytes#22 ,#23 cd16cd56+#24 natural#25 killer#26 cells#27 ,#28 total#29 lymphocytes#30 ,#31 and#32 white#33 blood#34 cells#35 were#36 determined#37 .#38 25 | 26 | f7:[blood_samples#0,were_taken_from#2,workers#7] 27 | f8:[{cd4+_t_lymphocyte_subpopulations#12:numbers#10},were_determined#36,NIL] 28 | f9:[{total_cd4+_t#17:numbers#10},were_determined#36,NIL] 29 | f10:[{t_lymphocytes#21:numbers#10},were_determined#36,NIL] 30 | f11:[{cd16cd56+_natural_killer_cells#24:numbers#10},were_determined#36,NIL] 31 | f12:[{total_lymphocytes#29:numbers#10},were_determined#36,NIL] 32 | f13:[{white_blood_cells#33:numbers#10},were_determined#36,NIL] 33 | stmt4 = f7 f8 f9 f10 f11 f12 f13 34 | 35 | # 12064555 after#0 controlling#1 for#2 age#3 ,#4 number#5 of#6 cigarettes#7 smoked#8 per#9 day#10 ,#11 alcohol#12 drinking#13 ,#14 frequency#15 of#16 regular#17 exercise#18 ,#19 job#20 demands#21 ,#22 and#23 social#24 support#25 at#26 work#27 by#28 the#29 partial#30 correlation#31 coefficients#32 ,#33 numbers#34 of#35 memory#36 t#37 ,#38 total#39 cd4+#40 t#41 ,#42 and#43 total#44 t#45 lymphocytes#46 were#47 positively#48 correlated#49 with#50 job#51 control#52 .#53 36 | 37 | f14:[{cigarettes_smoked_per_day#7:number#5},were_positively_correlated_with#47,job_control#51] 38 | f15:[{alcohol_drinking#12:number#5},were_positively_correlated_with#47,job_control#51] 39 | f16:[{regular_exercise#17:frequency#15},were_positively_correlated_with#47,job_control#51] 40 | f17:[{job_demands#20:number#5},were_positively_correlated_with#47,job_control#51] 41 | f18:[{social_support_at_work#24:number#5},were_positively_correlated_with#47,job_control#51] 42 | f19:[{memory_t#36:numbers#34},were_positively_correlated_with#47,job_control#51] 43 | f20:[{total_cd4+_t#39:numbers#34},were_positively_correlated_with#47,job_control#51] 44 | f21:[{total_t_lymphocytes#44:numbers#34},were_positively_correlated_with#47,job_control#51] 45 | c6:[NIL,after_controlling_for#0,{NIL#-1:age#3}] 46 | c7:[social_support_at_work#24,by#28,partial_correlation_coefficients#30] 47 | stmt5 = f14 f15 f16 f17 f18 f19 f20 f21 c6 c7 48 | 49 | # 12064555 neither#0 job#1 demands#2 nor#3 social#4 support#5 at#6 work#7 showed#8 significant#9 correlations#10 with#11 lymphocyte#12 subpopulations#13 .#14 50 | 51 | f22:[job_demands#1,showed_significant_correlations_with#8,{lymphocyte#12:subpopulations#13}] 52 | f23:[social_support#4,showed_significant_correlations_with#8,{lymphocyte#12:subpopulations#13}] 53 | c8:[NIL,neither#0,job_demands#1] 54 | c9:[NIL,nor#3,social_support#4] 55 | c10:[social_support#4,at#6,{NIL#-1:work#7}] 56 | stmt6 = f22 f23 c8 c9 c10 57 | 58 | # 12064555 it#0 is#1 suggested#2 that#3 lower#4 job#5 control#6 is#7 associated#8 with#9 a#10 decrease#11 in#12 the#13 number#14 of#15 cd4+#16 cd45ro+#17 t#18 lymphocytes#19 in#20 male#21 middle-aged#22 workers#23 .#24 59 | 60 | f24:[NIL,is_suggested_that#1,NIL] 61 | f25:[lower_job_control#4,is_associated_with#7,{NIL#-1:decrease#11}] 62 | c11:[{NIL#-1:decrease#11},in#12,{cd4+_cd45ro+_t_lymphocytes#16:number#14}] 63 | c12:[{cd4+_cd45ro+_t_lymphocytes#16:number#14},in#20,male_middle-aged_workers#21] 64 | stmt7 = f24 f25 c11 c12 65 | 66 | -------------------------------------------------------------------------------- /data/label/train_sort/label-15621307.txt: -------------------------------------------------------------------------------- 1 | # 15621307 equine#0 herpesvirus-1#1 infection#2 induces#3 ifn-gamma#4 production#5 by#6 equine#7 t#8 lymphocyte#9 subsets#10 .#11 2 | 3 | f1:[equine_herpesvirus-1_infection#0,induces#3,ifn-gamma_production#4] 4 | c1:[ifn-gamma_production#4,by#6,equine_t_lymphocyte_subsets#7] 5 | stmt1 = f1 c1 6 | 7 | # 15621307 a#0 commercial#1 bovine#2 ifn-gamma-specific#3 monoclonal#4 antibody#5 was#6 used#7 to#8 measure#9 antigen-specific#10 ifn-gamma#11 production#12 by#13 equine#14 lymphocytes#15 .#16 8 | 9 | f2:[commercial_bovine_ifn-gamma-specific_monoclonal_antibody#1,was_used_to_measure#6,antigen-specific_ifn-gamma_production#10] 10 | c2:[antigen-specific_ifn-gamma_production#10,by#13,equine_lymphocytes#14] 11 | stmt2 = f2 c2 12 | 13 | # 15621307 paired#0 pbmc#1 samples#2 were#3 collected#4 from#5 six#6 ponies#7 prior#8 to#9 and#10 10#11 days#12 after#13 challenge#14 infection#15 with#16 equine#17 herpesvirus-1#18 .#19 14 | 15 | f3:[paired_pbmc_samples#0,were_collected_from#3,{ponies#7:six#6}] 16 | c3:[{ponies#7:six#6},prior_to_and_10_days_after#8,challenge_infection#14] 17 | c4:[challenge_infection#14,with#16,equine_herpesvirus-1#17] 18 | stmt3 = f3 c3 c4 19 | 20 | # 15621307 each#0 sample#1 was#2 stimulated#3 in#4 vitro#5 with#6 ehv-1#7 ,#8 virus-free#9 medium#10 ,#11 or#12 pma#13 and#14 ionomycin#15 ,#16 and#17 labelled#18 with#19 monoclonal#20 antibodies#21 specific#22 for#23 various#24 equine#25 lymphocyte#26 subset#27 markers#28 .#29 21 | 22 | f4:[sample#1,was_stimulated#2,in_vitro#4] 23 | f5:[sample#1,labelled_with#18,monoclonal_antibodies#20] 24 | c5:[in_vitro#4,with#6,ehv-1#7] 25 | c6:[in_vitro#4,with#6,virus-free_medium#9] 26 | c7:[in_vitro#4,with#6,pma#13] 27 | c8:[in_vitro#4,with#6,ionomycin#15] 28 | c9:[monoclonal_antibodies#20,specific_for#22,various_equine_lymphocyte_subset_markers#24] 29 | stmt4 = f4 f5 c5 c6 c7 c8 c9 30 | 31 | # 15621307 following#0 fixation#1 ,#2 intracellular#3 ifn-gamma#4 was#5 detected#6 using#7 a#8 fitc-conjugated#9 bovine#10 ifn-gamma-specific#11 monoclonal#12 antibody#13 .#14 32 | 33 | f6:[intracellular_ifn-gamma#3,was_detected_using#5,fitc-conjugated_bovine_ifn-gamma-specific_monoclonal_antibody#9] 34 | c10:[NIL,following#0,fixation#1] 35 | stmt5 = f6 c10 36 | 37 | # 15621307 in#0 vitro#1 restimulation#2 of#3 pbmc#4 with#5 ehv-1#6 induced#7 ifn-gamma#8 production#9 by#10 a#11 significantly#12 higher#13 percentage#14 of#15 total#16 (cd5(+))#17 t#18 lymphocytes#19 ,#20 and#21 cd4(+)#22 and#23 cd8(+)#24 t#25 lymphocyte#26 subsets#27 among#28 post-ehv-1#29 infection#30 pbmc#31 samples#32 compared#33 to#34 pre-infection#35 samples#36 .#37 38 | 39 | f7:[{pbmc#4:in_vitro_restimulation#0},induced#7,ifn-gamma_production#8] 40 | c11:[{pbmc#4:in_vitro_restimulation#0},with#5,ehv-1#6] 41 | c12:[ifn-gamma_production#8,by_a_significantly_higher#10,{total_(cd5(+))_t_lymphocytes#16:percentage#14}] 42 | c13:[ifn-gamma_production#8,by_a_significantly_higher#10,{cd4(+)#22:percentage#14}] 43 | c14:[ifn-gamma_production#8,by_a_significantly_higher#10,{cd8(+)_t_lymphocyte_subsets#24:percentage#14}] 44 | c15:[{cd8(+)_t_lymphocyte_subsets#24:percentage#14},among#28,{post-ehv-1_infection_pbmc_samples#29:percentage#14}] 45 | c16:[{post-ehv-1_infection_pbmc_samples#29:percentage#14},compared_to#33,{post-ehv-1_infection_pbmc_samples#29:percentage#14}] 46 | stmt6 = f7 c11 c12 c13 c14 c15 c16 47 | 48 | # 15621307 this#0 response#1 was#2 associated#3 with#4 an#5 increase#6 in#7 virus-specific#8 ctl#9 activity#10 ,#11 a#12 critical#13 immune#14 effector#15 for#16 the#17 control#18 of#19 ehv-1#20 infection#21 and#22 disease#23 .#24 49 | 50 | f8:[{NIL#-1:response#1},was_associated_with#2,{virus-specific_ctl_activity#8:increase#6}] 51 | f9:[{NIL#-1:response#1},was_associated_with#2,critical_immune_effector#13] 52 | c17:[critical_immune_effector#13,for#16,{ehv-1_infection#20:control#18}] 53 | c18:[critical_immune_effector#13,for#16,{disease#23:control#18}] 54 | stmt7 = f8 f9 c17 c18 55 | 56 | # 15621307 no#0 significant#1 increase#2 in#3 ifn-gamma#4 production#5 by#6 b#7 lymphocytes#8 was#9 observed#10 .#11 57 | 58 | f10:[{ifn-gamma_production#4:significant_increase#1},was_observed#9,NIL] 59 | c19:[NIL,no#0,{ifn-gamma_production#4:significant_increase#1}] 60 | c20:[{ifn-gamma_production#4:significant_increase#1},by#6,b_lymphocytes#7] 61 | stmt8 = f10 c19 c20 62 | 63 | # 15621307 these#0 data#1 demonstrate#2 that#3 ehv-1#4 challenge#5 infection#6 of#7 ponies#8 results#9 in#10 increased#11 production#12 of#13 ifn-gamma#14 by#15 virus-specific#16 t#17 lymphocytes#18 ,#19 and#20 that#21 this#22 response#23 can#24 be#25 quantitated#26 using#27 flow#28 cytometry#29 .#30 64 | 65 | f11:[{NIL#-1:data#1},demonstrate_that#2,NIL] 66 | f12:[{ponies#8:ehv-1_challenge_infection#4},results_in#9,{ifn-gamma#14:increased_production#11}] 67 | c21:[{ifn-gamma#14:increased_production#11},by#15,virus-specific_t_lymphocytes#16] 68 | c22:[{NIL#-1:response#23},can_be_quantitated_using#24,flow_cytometry#28] 69 | stmt9 = f11 f12 c21 c22 70 | -------------------------------------------------------------------------------- /data/label/train_sort/label-15647045.txt: -------------------------------------------------------------------------------- 1 | # 15647045 age-#0 and#1 infection-related#2 maturation#3 of#4 the#5 nasal#6 immune#7 response#8 in#9 0-2-year-old#10 children#11 .#12 2 | 3 | c1:[{nasal_immune_response#6:age-#0},in#9,0-2-year-old_children#10] 4 | c2:[{nasal_immune_response#6:infection-related_maturation#2},in#9,0-2-year-old_children#10] 5 | stmt1 = c1 c2 6 | 7 | # 15647045 the#0 hygiene#1 hypothesis#2 suggests#3 that#4 exposure#5 to#6 micro-organisms#7 influences#8 development#9 of#10 the#11 immune#12 system#13 inchildren#14 .#15 8 | 9 | f1:[hygiene_hypothesis#1,suggests_that#3,NIL] 10 | f2:[{NIL#-1:exposure#5},influences#8,{immune_system_inchildren#12:development#9}] 11 | c3:[{NIL#-1:exposure#5},to#6,micro-organisms#7] 12 | stmt2 = f1 f2 c3 13 | 14 | # 15647045 in#0 this#1 study#2 ,#3 we#4 examined#5 nasal#6 immune#7 responses#8 in#9 the#10 first#11 2#12 years#13 of#14 life#15 in#16 relation#17 to#18 age#19 of#20 children#21 and#22 the#23 number#24 of#25 viral#26 infections#27 they#28 have#29 experienced#30 .#31 15 | 16 | f3:[NIL,examined#5,nasal_immune_responses#6] 17 | f4:[NIL,examined#5,{viral_infections#26:number#24}] 18 | c4:[NIL,in#0,{NIL#-1:study#2}] 19 | c5:[nasal_immune_responses#6,in#9,{life#15:first_2_years#11}] 20 | c6:[{life#15:first_2_years#11},in_relation_to#16,{children#21:age#19}] 21 | c7:[{viral_infections#26:number#24},they_have_experienced#28,NIL] 22 | stmt3 = f3 f4 c4 c5 c6 c7 23 | 24 | # 15647045 nasal#0 brushes#1 were#2 taken#3 during#4 rhinovirus-#5 or#6 respiratory#7 syncytial#8 virus#9 (rsv)-induced#10 upper#11 respiratory#12 tract#13 infections#14 ,#15 and#16 of#17 controls#18 .#19 25 | 26 | f5:[nasal_brushes#0,were_taken#2,NIL] 27 | c8:[NIL,during#4,rhinovirus-#5] 28 | c9:[NIL,during#4,respiratory_syncytial_virus_(rsv)-induced_upper_respiratory_tract_infections#7] 29 | stmt4 = f5 c8 c9 30 | 31 | # 15647045 the#0 number#1 of#2 macrophages#3 were#4 higher#5 during#6 urti#7 and#8 increased#9 with#10 age#11 .#12 32 | 33 | f6:[{macrophages#3:number#1},were_higher#4,NIL] 34 | c10:[{macrophages#3:number#1},increased_with#9,{NIL#-1:age#11}] 35 | c11:[NIL,during#6,urti#7] 36 | stmt5 = f6 c10 c11 37 | 38 | # 15647045 the#0 number#1 of#2 t#3 lymphocytes#4 increased#5 with#6 age#7 in#8 controls#9 and#10 were#11 higher#12 during#13 urti#14 at#15 all#16 ages#17 .#18 39 | 40 | f7:[{t_lymphocytes#3:number#1},increased_with#5,{NIL#-1:age#7}] 41 | f8:[{t_lymphocytes#3:number#1},were_higher#11,NIL] 42 | c12:[{NIL#-1:age#7},in#8,{NIL#-1:controls#9}] 43 | c13:[NIL,during#13,urti#14] 44 | c14:[urti#14,at#15,all_ages#16] 45 | stmt6 = f7 f8 c12 c13 c14 46 | 47 | # 15647045 we#0 found#1 an#2 age-related#3 decrease#4 in#5 the#6 number#7 of#8 interleukin#9 (il)-4-#10 and#11 il-10-positive#12 cells#13 in#14 controls#15 ,#16 while#17 the#18 number#19 of#20 il-12-positive#21 cells#22 remained#23 unchanged#24 .#25 48 | 49 | f9:[NIL,found#1,age-related_decrease#3] 50 | f10:[{il-12-positive_cells#21:number#19},remained_unchanged#23,NIL] 51 | c15:[age-related_decrease#3,in#5,{interleukin_(il)-4-#9:number#7}] 52 | c16:[age-related_decrease#3,in#5,{il-10-positive_cells#12:number#7}] 53 | c17:[{il-10-positive_cells#12:number#7},in#14,{controls#15:number#7}] 54 | stmt7 = f9 f10 c15 c16 c17 55 | 56 | # 15647045 changes#0 in#1 t#2 lymphocyte#3 and#4 il-4#5 cell#6 number#7 were#8 stronger#9 related#10 to#11 the#12 age#13 of#14 the#15 child#16 than#17 to#18 the#19 number#20 of#21 respiratory#22 infections#23 ,#24 while#25 the#26 opposite#27 was#28 true#29 formacrophages#30 .#31 57 | 58 | f11:[{t_lymphocyte#2:changes#0},were_stronger_related_to#8,{child#16:age#13}] 59 | f12:[{il-4_cell_number#5:changes#0},were_stronger_related_to#8,{child#16:age#13}] 60 | f13:[opposite#27,was#28,true_formacrophages#29] 61 | c18:[{child#16:age#13},than_to#17,{respiratory_infections#22:number#20}] 62 | stmt8 = f11 f12 f13 c18 63 | 64 | # 15647045 in#0 infants#1 ,#2 we#3 found#4 an#5 infection-#6 and#7 age-related#8 increase#9 respectively#10 for#11 nasal#12 macrophages#13 and#14 t#15 lymphocytes#16 during#17 urti#18 .#19 65 | 66 | f14:[NIL,found#4,infection-_and_age-related_increase#6] 67 | c19:[NIL,in#0,infants#1] 68 | c20:[infection-_and_age-related_increase#6,for#11,nasal_macrophages#12] 69 | c21:[infection-_and_age-related_increase#6,for#11,t_lymphocytes#15] 70 | c22:[NIL,during#17,urti#18] 71 | stmt9 = f14 c19 c20 c21 c22 72 | 73 | # 15647045 furthermore#0 ,#1 the#2 number#3 of#4 il-4-#5 and#6 il-10-positive#7 cells#8 decreased#9 with#10 age#11 .#12 74 | 75 | f15:[{il-4-#5:number#3},decreased_with#9,age#11] 76 | f16:[{il-10-positive_cells#7:number#3},decreased_with#9,age#11] 77 | stmt10 = f15 f16 78 | 79 | # 15647045 whether#0 this#1 maturation#2 reflects#3 a#4 natural#5 age-related#6 maturation#7 ,#8 the#9 degree#10 of#11 exposure#12 to#13 respiratory#14 infections#15 ,#16 or#17 possibly#18 both#19 ,#20 could#21 not#22 be#23 resolved#24 and#25 needs#26 further#27 study#28 .#29 80 | 81 | f17:[maturation#2,reflects#3,natural_age-related_maturation#5] 82 | f18:[{exposure_to_respiratory_infections#12:degree#10},could_not_be_resolved#21,NIL] 83 | f19:[{exposure_to_respiratory_infections#12:degree#10},needs#26,{NIL#-1:further_study#27}] 84 | stmt11 = f17 f18 f19 85 | -------------------------------------------------------------------------------- /data/label/train_sort/label-11922914.txt: -------------------------------------------------------------------------------- 1 | # 11922914 oxidant#0 stress#1 mechanism#2 of#3 homocysteine#4 potentiating#5 con#6 a-induced#7 proliferation#8 in#9 murine#10 splenic#11 t#12 lymphocytes#13 .#14 2 | 3 | c1:[{homocysteine#4:oxidant_stress_mechanism#0},potentiating#5,con_a-induced_proliferation#6] 4 | c2:[con_a-induced_proliferation#6,in#9,murine_splenic_t_lymphocytes#10] 5 | stmt1 = c1 c2 6 | 7 | # 11922914 an#0 elevated#1 plasma#2 homocysteine#3 level#4 is#5 considered#6 an#7 independent#8 risk#9 factor#10 for#11 atherosclerosis#12 .#13 8 | 9 | f1:[elevated_plasma_homocysteine_level#1,is_considered#5,{atherosclerosis#12:independent_risk_factor#8}] 10 | stmt2 = f1 11 | 12 | # 11922914 however#0 ,#1 the#2 mechanisms#3 by#4 which#5 hyperhomocysteinemia#6 induces#7 atherosclerosis#8 are#9 only#10 partially#11 understood#12 .#13 13 | 14 | f2:[mechanisms#3,are_only_partially_understood#9,NIL] 15 | f3:[hyperhomocysteinemia#6,induces#7,atherosclerosis#8] 16 | c3:[NIL,by#4,mechanisms#3] 17 | stmt3 = f2 f3 c3 18 | 19 | # 11922914 the#0 effect#1 of#2 hcy#3 on#4 t#5 lymphocyte#6 proliferation#7 and#8 its#9 mechanisms#10 were#11 examined#12 in#13 normal#14 and#15 hyperhomocysteinemia#16 apoe-knockoutmice#17 .#18 20 | 21 | f4:[{hcy#3:effect#1},were_examined_in#11,normal_and_hyperhomocysteinemia_apoe-knockoutmice#14] 22 | f5:[{hcy#3:mechanisms#10},were_examined_in#11,normal_and_hyperhomocysteinemia_apoe-knockoutmice#14] 23 | c4:[{hcy#3:effect#1},on#4,t_lymphocyte_proliferation#5] 24 | stmt4 = f4 f5 c4 25 | 26 | # 11922914 the#0 mouse#1 splenic#2 t-cells#3 were#4 treated#5 with#6 hcy#7 ,#8 related#9 compounds#10 and/or#11 antioxidants#12 in#13 the#14 presence#15 or#16 absence#17 of#18 concanavalin#19 a#20 .#21 27 | 28 | f6:[mouse_splenic_t-cells#1,were_treated_with#4,hcy#7] 29 | f7:[mouse_splenic_t-cells#1,were_treated_with#4,related_compounds#9] 30 | f8:[mouse_splenic_t-cells#1,were_treated_with#4,antioxidants#12] 31 | c5:[antioxidants#12,in#13,{concanavalin_a#19:presence#15}] 32 | c6:[antioxidants#12,in#13,{concanavalin_a#19:absence#17}] 33 | stmt5 = f6 f7 f8 c5 c6 34 | 35 | # 11922914 dna#0 synthesis#1 ,#2 cell#3 apoptosis#4 ,#5 interleukin-2#6 level#7 and#8 production#9 of#10 reactive#11 oxygen#12 species#13 weremeasured#14 .#15 36 | 37 | f9:[dna_synthesis#0,weremeasured#14,NIL] 38 | f10:[cell_apoptosis#3,weremeasured#14,NIL] 39 | f11:[interleukin-2_level#6,weremeasured#14,NIL] 40 | f12:[{reactive_oxygen_species#11:production#9},weremeasured#14,NIL] 41 | stmt6 = f9 f10 f11 f12 42 | 43 | # 11922914 hcy#0 and#1 related#2 compounds#3 with#4 thiol#5 ,#6 such#7 as#8 cysteine#9 and#10 glutathione#11 significantly#12 potentiated#13 con#14 a-induced#15 proliferation#16 and#17 partially#18 inhibited#19 apoptosis#20 in#21 t#22 lymphocytes#23 ,#24 but#25 it#26 had#27 no#28 direct#29 effect#30 on#31 resting#32 t#33 lymphocyte#34 .#35 44 | 45 | f13:[hcy#0,significantly_potentiated#12,con_a-induced_proliferation#14] 46 | f14:[hcy#0,partially_inhibited_apoptosis_in#18,t_lymphocytes#22] 47 | f15:[hcy#0,had_no#27,{NIL#-1:direct_effect#29}] 48 | f16:[related_compounds#2,significantly_potentiated#12,con_a-induced_proliferation#14] 49 | f17:[related_compounds#2,partially_inhibited_apoptosis_in#18,t_lymphocytes#22] 50 | f18:[related_compounds#2,had_no#27,{NIL#-1:direct_effect#29}] 51 | f19:[thiol#5,such_as#7,cysteine#9] 52 | f20:[thiol#5,such_as#7,glutathione#11] 53 | c7:[related_compounds#2,with#4,thiol#5] 54 | c8:[{NIL#-1:direct_effect#29},on_resting#31,t_lymphocyte#33] 55 | stmt7 = f13 f14 f15 f16 f17 f18 f19 f20 c7 c8 56 | 57 | # 11922914 apoe-knockout#0 mice#1 with#2 hyperhomocysteinemia#3 had#4 a#5 significant#6 promotion#7 of#8 t-cell#9 proliferation#10 in#11 response#12 to#13 con#14 a#15 .#16 58 | 59 | f21:[apoe-knockout_mice#0,had#4,{t-cell_proliferation#9:significant_promotion#6}] 60 | c9:[apoe-knockout_mice#0,with#2,hyperhomocysteinemia#3] 61 | c10:[{t-cell_proliferation#9:significant_promotion#6},in_response_to#11,con_a#14] 62 | stmt8 = f21 c9 c10 63 | 64 | # 11922914 hcy#0 also#1 increased#2 the#3 intracellular#4 ros#5 .#6 65 | 66 | f22:[hcy#0,increased#2,intracellular_ros#4] 67 | stmt9 = f22 68 | 69 | # 11922914 radical#0 scavengers#1 reduced#2 hcyeffect#3 .#4 70 | 71 | f23:[radical_scavengers#0,reduced#2,hcyeffect#3] 72 | stmt10 = f23 73 | 74 | # 11922914 these#0 data#1 indicate#2 that#3 ros#4 generated#5 by#6 thiol#7 of#8 hcy#9 auto-oxidation#10 are#11 involved#12 in#13 hcy#14 effect#15 on#16 con#17 a-induced#18 t#19 lymphocyte#20 proliferation#21 .#22 75 | 76 | f24:[{NIL#-1:data#1},indicate_that#2,NIL] 77 | f25:[ros#4,are_involved_in#11,{hcy#14:effect#15}] 78 | c11:[ros#4,generated_by#5,{hcy_auto-oxidation#9:thiol#7}] 79 | c12:[{hcy#14:effect#15},on#16,{con_a-induced_t_lymphocyte#17:proliferation#21}] 80 | stmt11 = f24 f25 c11 c12 81 | 82 | # 11922914 these#0 findings#1 suggest#2 a#3 novel#4 mechanism#5 may#6 be#7 involved#8 in#9 chronic#10 inflammatory#11 progression#12 of#13 atherosclerosis#14 with#15 hyperhomocysteinemia#16 .#17 83 | 84 | f26:[{NIL#-1:findings#1},suggest#2,NIL] 85 | f27:[novel_mechanism#4,may_be_involved_in#6,{atherosclerosis#14:chronic_inflammatory_progression#10}] 86 | c13:[{atherosclerosis#14:chronic_inflammatory_progression#10},with#15,hyperhomocysteinemia#16] 87 | stmt12 = f26 f27 c13 88 | 89 | -------------------------------------------------------------------------------- /data/label/train_sort/label-15969102.txt: -------------------------------------------------------------------------------- 1 | # 15969102 [#0 construction#1 of#2 human#3 mage-3#4 dna#5 vaccine#6 and#7 its#8 immune#9 effects#10 observed#11 in#12 vivo]#13 .#14 2 | 3 | c1:[{human_mage-3_dna_vaccine#3:construction#1},NIL#-1,NIL] 4 | c2:[{human_mage-3_dna_vaccine#3:immune_effects#9},observed_in#11,vivo]#13] 5 | stmt1 = c1 c2 6 | 7 | # 15969102 to#0 investigate#1 the#2 antitumor#3 immune#4 responses#5 induced#6 by#7 mage-3#8 dna#9 vaccine#10 ,#11 the#12 recombinant#13 mammalian#14 expression#15 plasmid#16 pcdna3.1/mage-3#17 was#18 constructed#19 by#20 ligating#21 mage-3#22 gene#23 ,#24 which#25 was#26 amplified#27 by#28 rt-pcr#29 ,#30 and#31 the#32 pcd-na3.1#33 +#34 vector#35 .#36 8 | 9 | f1:[NIL,to_investigate#0,antitumor_immune_responses#3] 10 | f2:[recombinant_mammalian_expression_plasmid_pcdna3.1/mage-3#13,was_constructed_by#18,ligating_mage-3_gene#21] 11 | c3:[antitumor_immune_responses#3,induced_by#6,mage-3_dna_vaccine#8] 12 | c4:[ligating_mage-3_gene#21,was_amplified_by#26,rt-pcr#29] 13 | c5:[ligating_mage-3_gene#21,was_amplified_by#26,pcd-na3.1_+_vector#33] 14 | stmt2 = f1 f2 c3 c4 c5 15 | 16 | # 15969102 the#0 recombinant#1 plasmids#2 were#3 transfected#4 into#5 b16#6 cells#7 by#8 liposome#9 ,#10 the#11 expression#12 of#13 mage-3#14 was#15 checked#16 by#17 rt-pcr#18 ,#19 immunocytochemistry#20 and#21 western#22 blot#23 .#24 17 | 18 | f3:[recombinant_plasmids#1,were_transfected_into#3,b16_cells#6] 19 | f4:[{mage-3#14:expression#12},was_checked_by#15,rt-pcr#18] 20 | f5:[{mage-3#14:expression#12},was_checked_by#15,immunocytochemistry#20] 21 | f6:[{mage-3#14:expression#12},was_checked_by#15,western_blot#22] 22 | c6:[b16_cells#6,by#8,liposome#9] 23 | stmt3 = f3 f4 f5 f6 c6 24 | 25 | # 15969102 then#0 ,#1 100#2 ug#3 recombinant#4 plasmids#5 were#6 injected#7 intramuscularly#8 per#9 c57bl/6#10 mouse#11 on#12 0#13 ,#14 10#15 and#16 20#17 days#18 ,#19 with#20 pcdna3.1#21 +#22 plasmid#23 and#24 pbs#25 as#26 controls#27 .#28 26 | 27 | f7:[{recombinant_plasmids#4:100_ug#2},were_injected_intramuscularly#6,c57bl/6_mouse#10] 28 | c7:[NIL,on#12,{NIL#-1:0#13}] 29 | c8:[NIL,on#12,{NIL#-1:10#15}] 30 | c9:[NIL,on#12,{NIL#-1:20_days#17}] 31 | c10:[pcdna3.1_+_plasmid#21,as#26,{NIL#-1:controls#27}] 32 | c11:[pbs#25,as#26,{NIL#-1:controls#27}] 33 | stmt4 = f7 c7 c8 c9 c10 c11 34 | 35 | # 15969102 splenocytes#0 ctls#1 ,#2 the#3 level#4 of#5 antibodies#6 against#7 mage-3#8 the#9 changes#10 of#11 the#12 t#13 lymphocyte#14 subsets#15 and#16 the#17 levels#18 of#19 cytokines#20 were#21 checked#22 after#23 3#24 times#25 immunization#26 .#27 36 | 37 | f8:[splenocytes_ctls#0,were_checked_after#21,3_times_immunization#24] 38 | f9:[{antibodies#6:level#4},were_checked_after#21,3_times_immunization#24] 39 | f10:[{t_lymphocyte_subsets#13:changes#10},were_checked_after#21,3_times_immunization#24] 40 | f11:[{cytokines#20:levels#18},were_checked_after#21,3_times_immunization#24] 41 | c12:[{antibodies#6:level#4},against#7,mage-3#8] 42 | stmt5 = f8 f9 f10 f11 c12 43 | 44 | # 15969102 as#0 a#1 result#2 ,#3 the#4 mice#5 immunized#6 with#7 pcdna3.1/mage-3#8 plasmid#9 can#10 produce#11 mage-3#12 specific#13 immune#14 response#15 .#16 45 | 46 | f12:[mice_immunized#5,can_produce#10,mage-3_specific_immune_response#12] 47 | c13:[NIL,as#0,{NIL#-1:result#2}] 48 | c14:[mice_immunized#5,with#7,pcdna3.1/mage-3_plasmid#8] 49 | stmt6 = f12 c13 c14 50 | 51 | # 15969102 the#0 ctls#1 kill#2 activities#3 against#4 b16/mage-3#5 cells#6 was#7 51.08#8 +/-#9 7.41%#10 ,#11 and#12 had#13 significant#14 difference#15 compared#16 with#17 that#18 of#19 pcdna3.1#20 +#21 group#22 and#23 pbs#24 group#25 .#26 52 | 53 | f13:[ctls_kill_activities#1,was#7,51.08_+/-_7.41%#8] 54 | f14:[ctls_kill_activities#1,had_significant_difference#13,NIL] 55 | c15:[ctls_kill_activities#1,against#4,b16/mage-3_cells#5] 56 | c16:[NIL,compared_with#16,pcdna3.1_+_group#20] 57 | c17:[NIL,compared_with#16,pbs_group#24] 58 | stmt7 = f13 f14 c15 c16 c17 59 | 60 | # 15969102 the#0 titre#1 of#2 antibody#3 against#4 mage-3#5 was#6 1#7 ,#8 while#9 controls#10 were#11 negtive#12 .#13 61 | 62 | f15:[{antibody#3:titre#1},was#6,{NIL#-1:1#7}] 63 | f16:[{NIL#-1:controls#10},were_negtive#11,NIL] 64 | c18:[{antibody#3:titre#1},against#4,mage-3#5] 65 | stmt8 = f15 f16 c18 66 | 67 | # 15969102 the#0 number#1 of#2 cd4#3 +#4 cd8#5 +#6 and#7 the#8 levels#9 of#10 ifn-gamma#11 il-2#12 increased#13 significantly#14 after#15 immunization#16 with#17 pcdna3.1/mage-3#18 plasmid#19 as#20 compared#21 with#22 those#23 of#24 control#25 groups#26 .#27 68 | 69 | f17:[{cd4_+_cd8_+#3:number#1},increased_significantly_after#13,immunization#16] 70 | f18:[{ifn-gamma_il-2#11:levels#9},increased_significantly_after#13,immunization#16] 71 | c19:[immunization#16,with#17,pcdna3.1/mage-3_plasmid#18] 72 | c20:[pcdna3.1/mage-3_plasmid#18,compared_with#21,control_groups#25] 73 | stmt9 = f17 f18 c19 c20 74 | 75 | # 15969102 it#0 is#1 concluded#2 that#3 the#4 pcdna3.1-mage-3#5 dna#6 vaccine#7 are#8 able#9 to#10 induce#11 both#12 cellular#13 and#14 humoral#15 immune#16 responses#17 in#18 vivo#19 .#20 76 | 77 | f19:[NIL,it_is_concluded_that#0,NIL] 78 | f20:[pcdna3.1-mage-3_dna_vaccine#5,are_able_to_induce#8,cellular#13] 79 | f21:[pcdna3.1-mage-3_dna_vaccine#5,are_able_to_induce#8,humoral_immune_responses#15] 80 | c21:[humoral_immune_responses#15,in#18,vivo#19] 81 | stmt10 = f19 f20 f21 c21 82 | -------------------------------------------------------------------------------- /MIMO_service/filter.py: -------------------------------------------------------------------------------- 1 | from nltk import pos_tag 2 | 3 | def tuple_filter(query): 4 | 5 | def get_subject(tpl): 6 | return get_subject_concept(tpl), get_subject_attribute(tpl) 7 | 8 | def get_object(tpl): 9 | return get_object_concept(tpl), get_object_attribute(tpl) 10 | 11 | def get_object_concept(tpl): 12 | return tpl[3] 13 | 14 | def get_subject_concept(tpl): 15 | return tpl[0] 16 | 17 | def get_object_attribute(tpl): 18 | return tpl[4] 19 | 20 | def get_subject_attribute(tpl): 21 | return tpl[1] 22 | 23 | def get_relation(tpl): 24 | return tpl[2] 25 | 26 | 27 | def missing_relation(stmt): 28 | conditions = stmt['condition tuples'] 29 | facts = stmt['fact tuples'] 30 | for con_tpl in conditions: 31 | if get_relation(con_tpl) == 'NIL': 32 | stmt['condition tuples'].remove(con_tpl) 33 | for fac_tpl in facts: 34 | if get_relation(fac_tpl) == 'NIL': 35 | stmt['fact tuples'].remove(fac_tpl) 36 | return stmt 37 | 38 | def redundant_fact_conflict_with_condition(stmt): 39 | conditions = stmt['condition tuples'] 40 | facts = stmt['fact tuples'] 41 | for con_tpl in conditions: 42 | con_sub = get_subject_concept(con_tpl) # B -> C 43 | con_obj = get_object_concept(con_tpl) 44 | if con_obj == 'NIL' or con_sub == 'NIL': 45 | continue 46 | fac_tpl1, fac_tpl2 = None, None 47 | for tpl in facts: 48 | if con_sub == get_object_concept(tpl): 49 | fac_tpl1 = tpl # A -> B 50 | elif con_obj == get_object_concept(tpl): 51 | fac_tpl2 = tpl # A -> C 52 | 53 | if not fac_tpl1 or not fac_tpl2: 54 | continue 55 | 56 | if get_subject(fac_tpl1) == get_subject(fac_tpl2): 57 | stmt['fact tuples'].remove(fac_tpl2) 58 | 59 | return stmt 60 | 61 | 62 | def missing_concept(stmt): 63 | conditions = stmt['condition tuples'] 64 | facts = stmt['fact tuples'] 65 | for con_tpl in conditions: 66 | if get_object(con_tpl) == ('NIL', 'NIL')\ 67 | and get_subject(con_tpl) == ('NIL', 'NIL'): 68 | stmt['condition tuples'].remove(con_tpl) 69 | for fac_tpl in facts: 70 | if get_object(fac_tpl) == ('NIL', 'NIL') \ 71 | and get_subject(fac_tpl) == ('NIL', 'NIL'): 72 | stmt['fact tuples'].remove(fac_tpl) 73 | return stmt 74 | 75 | def redundant_condition_circle(stmt): 76 | 77 | conditions = stmt['condition tuples'] 78 | for con_tpl in conditions: 79 | con_sub = get_subject_concept(con_tpl) # B -> C 80 | con_obj = get_object_concept(con_tpl) 81 | if con_obj == 'NIL' or con_sub == 'NIL': 82 | continue 83 | con_tpl1, con_tpl2 = None, None 84 | for tpl in conditions: 85 | if con_sub == get_object_concept(tpl) and tpl != con_tpl: 86 | con_tpl1 = tpl # A -> B 87 | elif con_obj == get_object_concept(tpl) and tpl != con_tpl: 88 | con_tpl2 = tpl # A -> C 89 | 90 | if not con_tpl1 or not con_tpl2: 91 | continue 92 | 93 | if get_subject(con_tpl1) == get_subject(con_tpl2): 94 | relation = get_relation(con_tpl2).split() 95 | pos = pos_tag(relation) 96 | if pos[0][1] == 'IN': 97 | stmt['condition tuples'].remove(con_tpl2) 98 | 99 | return stmt 100 | 101 | query = missing_concept(query) 102 | query = missing_relation(query) 103 | query = redundant_condition_circle(query) 104 | query = redundant_fact_conflict_with_condition(query) 105 | 106 | return query 107 | 108 | 109 | 110 | # a = {'text': 'Here , we demonstrate that reprogramming with lentiviruses carrying the iPSC-inducing factors ( Oct4-Sox2-Klf4-cMyc , OSKM ) caused senescence in mouse fibroblasts , establishing a stress barrier for cell reprogramming .', 111 | # 'fact tuples': [['NIL', 'NIL', 'demonstrate that', 'NIL', 'NIL'], 112 | # ['reprogramming', 'NIL', 'caused', 'mouse fibroblasts', 'NIL'], 113 | # ['reprogramming', 'NIL', 'caused', 'senescence', 'NIL']], 114 | # 'condition tuples': [['reprogramming', 'NIL', 'with', 'iPSC-inducing factors', 'NIL'], 115 | # ['reprogramming', 'NIL', 'with', 'lentiviruses', 'NIL'], 116 | # ['lentiviruses', 'NIL', 'in', 'iPSC-inducing factors', 'NIL'], 117 | # ['lentiviruses', 'NIL', 'NIL', 'Oct4-Sox2-Klf4-cMyc', 'NIL'], 118 | # ['senescence', 'NIL', 'in', 'mouse fibroblasts', 'NIL']], 119 | # 'unit_indx': [[5, 20, 21, 5, 18, 28, 29, 25, 26, 5, 15, 5, 10, 11, 5, 7, 7, 15, 7, 13, 7, 10, 11, 5, 10, 11, 18, 20, 21, 28, 29], 120 | # [], [3, 4, 17, 17, 23, 23, 6, 6, 6, 8, 8, 8, 8, 19, 27]]} 121 | 122 | 123 | # print(tuple_filter(a)) -------------------------------------------------------------------------------- /data/label/eval_sort/label-23890451.txt: -------------------------------------------------------------------------------- 1 | # n1:[interferon_gamma_production,as,ifn-gamma_production] 2 | # n2:[jurkat_cells,as,jurkatcells] 3 | 4 | # h1:[various_mediators,contain,cytokines] 5 | # h2:[kb_cells,contain,lps-stimulated_kb_cells] 6 | 7 | # 23890451 Aggregatibacter#0 actinomycetemcomitans#1 lipopolysaccharide#2 stimulated#3 epithelial#4 cells#5 produce#6 interleukin-15#7 that#8 regulates#9 t#10 cell#11 activation#12 .#13 8 | 9 | f1:[aggregatibacter_actinomycetemcomitans_lipopolysaccharide_stimulated_epithelial_cells#0,produce#6,interleukin-15#7] 10 | c1:[interleukin-15#7,regulates#9,{t_cell#10:activation#12}] 11 | stmt1 = f1 c1 12 | 13 | # 23890451 Oral#0 epithelial#1 cells#2 act#3 not#4 only#5 as#6 mechanical#7 barriers#8 but#9 also#10 as#11 immunological#12 barriers#13 by#14 producing#15 various#16 mediators#17 such#18 as#19 cytokines#20 .#21 14 | 15 | f2:[oral_epithelial_cells#0,act_not_only_as#3,mechanical_barriers#7] 16 | f3:[oral_epithelial_cells#0,also_as#10,immunological_barriers#12] 17 | c2:[NIL,by_producing#14,various_mediators#16] 18 | c3:[NIL,by_producing#14,cytokines#20] 19 | stmt2 = f2 f3 c2 c3 20 | 21 | # 23890451 Since#0 ,#1 in#2 periodontal#3 disease#4 ,#5 limited#6 information#7 is#8 available#9 regarding#10 the#11 role#12 of#13 oral#14 epithelial#15 cell-derived#16 cytokines#17 on#18 T#19 cell#20 activation#21 ,#22 we#23 investigated#24 the#25 responses#26 of#27 human#28 T#29 cells#30 to#31 cytokines#32 in#33 KB#34 cells#35 that#36 had#37 been#38 stimulated#39 with#40 Aggregatibacter#41 actinomycetemcomitans#42 lipopolysaccharide(LPS)#43 .#44 22 | 23 | f4:[limited_information#6,is_available_regarding#8,{oral_epithelial_cell-derived_cytokines#14:role#12}] 24 | f5:[NIL,investigated#24,{human_t_cells#28:responses#26}] 25 | f6:[kb_cells#34,had_been_stimulated_with#37,aggregatibacter_actinomycetemcomitans_lipopolysaccharide(lps)#41] 26 | c4:[NIL,in#2,periodontal_disease#3] 27 | c5:[oral_epithelial_cell-derived_cytokines#14,on#18,t_cell_activation#19] 28 | c6:[cytokines#32,in#33,kb_cells#34] 29 | stmt3 = f4 f5 f6 c4 c5 c6 30 | 31 | # 23890451 To#0 evaluate#1 T#2 cell#3 activation#4 in#5 response#6 to#7 the#8 culture#9 supernatant#10 of#11 KB#12 cells#13 ,#14 we#15 examined#16 cell#17 proliferation#18 and#19 interferon#20 gamma#21 production#22 ,#23 which#24 is#25 closely#26 related#27 to#28 periodontal#29 disease#30 ,#31 in#32 Jurkat#33 cells#34 .#35 32 | 33 | f7:[NIL,to_evaluate#0,{t_cell#2:activation#4}] 34 | f8:[NIL,examined#16,cell_proliferation_and_interferon_gamma_production#17] 35 | c7:[{t_cell#2:activation#4},in_response_to#5,{kb_cells#12:culture_supernatant#9}] 36 | c8:[cell_proliferation_and_interferon_gamma_production#17,is_closely_related_to#25,periodontal_disease#29] 37 | c9:[NIL,in#32,jurkat_cells#33] 38 | stmt4 = f7 f8 c7 c8 c9 39 | 40 | # 23890451 Culture#0 supernatant#1 of#2 LPS-stimulated#3 KB#4 cells#5 enhanced#6 cell#7 proliferation#8 and#9 IFN-gamma#10 production#11 in#12 Jurkat#13 cells#14 .#15 41 | 42 | f9:[{lps-stimulated_kb_cells#3:culture_supernatant#0},enhanced#6,cell_proliferation#7] 43 | f10:[{lps-stimulated_kb_cells#3:culture_supernatant#0},enhanced#6,ifn-gamma_production#10] 44 | c10:[cell_proliferation#7,in#12,jurkat_cells#13] 45 | c11:[ifn-gamma_production#10,in#12,jurkat_cells#13] 46 | stmt5 = f9 f10 c10 c11 47 | 48 | # 23890451 To#0 determine#1 the#2 active#3 component#4 within#5 the#6 culture#7 supernatant#8 ,#9 the#10 production#11 of#12 epithelial#13 cell-derived#14 cytokines#15 ,#16 interleukin-12#17 ,#18 IL-15#19 and#20 IL-18#21 ,#22 in#23 LPS-stimulated#24 KB#25 cells#26 wasanalysed#27 .#28 49 | 50 | f11:[NIL,to_determine#0,active_component#3] 51 | f12:[{epithelial_cell-derived_cytokines#13:production#11},wasanalysed#27,NIL] 52 | f13:[{interleukin-12#17:production#11},wasanalysed#27,NIL] 53 | f14:[{il-15#19:production#11},wasanalysed#27,NIL] 54 | f15:[{il-18#21:production#11},wasanalysed#27,NIL] 55 | c12:[active_component#3,within#5,culture_supernatant#7] 56 | c13:[NIL,in#23,lps-stimulated_kb_cells#24] 57 | stmt6 = f11 f12 f13 f14 f15 c12 c13 58 | 59 | # 23890451 IL-15#0 ,#1 but#2 not#3 IL-18#4 ,#5 was#6 significantly#7 increased#8 in#9 the#10 culture#11 supernatant#12 of#13 LPS-stimulated#14 KB#15 cells#16 .#17 60 | 61 | f16:[il-15#0,was_significantly_increased#6,NIL#-1] 62 | c14:[il-15#0,in#9,{lps-stimulated_kb_cells#14:culture_supernatant#11}] 63 | c15:[NIL,not#3,il-18#4] 64 | stmt7 = f16 c14 c15 65 | 66 | # 23890451 Moreover#0 ,#1 additional#2 anti-IL-15#3 neutralizing#4 antibody#5 abolished#6 culture#7 supernatant-induced#8 IFN-gamma#9 expression#10 in#11 Jurkatcells#12 .#13 67 | 68 | f17:[additional_anti-IL-15_neutralizing_antibody#2,abolished#6,culture_supernatant-induced_ifn-gamma_expression#7] 69 | c16:[culture_supernatant-induced_ifn-gamma_expression#7,in#11,jurkatcells#12] 70 | stmt8 = f17 c16 71 | 72 | # 23890451 These#0 results#1 suggest#2 that#3 periodontal#4 pathogens#5 induce#6 the#7 production#8 of#9 IL-15#10 from#11 epithelial#12 cells#13 ,#14 and#15 leading#16 the#17 activation#18 of#19 T#20 cells#21 in#22 periodontal#23 lesions#24 .#25 73 | 74 | f18:[{NIL#-1:results#1},suggest_that#2,NIL] 75 | f19:[periodontal_pathogens#4,induce#6,{il-15#10:production#8}] 76 | f20:[periodontal_pathogens#4,leading#16,{t_cells#20:activation#18}] 77 | c17:[{il-15#10:production#8},from#11,epithelial_cells#12] 78 | c18:[{t_cells#20:activation#18},in#22,periodontal_lesions#23] 79 | stmt9 = f18 f19 f20 c17 c18 80 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-26118933.txt: -------------------------------------------------------------------------------- 1 | # 26118933 Immunization#0 of#1 sea#2 bream#3 juveniles#4 against#5 photobacterium#6 damselae#7 subsp.#8 piscicida#9 by#10 short#11 bath#12 ,#13 effect#14 on#15 some#16 pro-inflammatory#17 molecules#18 and#19 the#20 mx#21 gene#22 expression#23 .#24 2 | 3 | c1:[{sea_bream_juveniles#2:immunization#0},against#5,photobacterium_damselae_subsp._piscicida#6] 4 | c2:[{NIL#-1:effect#14},on#15,pro-inflammatory_molecules#17] 5 | c3:[{NIL#-1:effect#14},on#15,mx_gene_expression#21] 6 | stmt1 = c1 c2 c3 7 | 8 | # 26118933 Cytokines#0 are#1 a#2 family#3 of#4 proteins#5 derived#6 from#7 macrophages#8 ,#9 lymphocytes#10 ,#11 granulocytes#12 ,#13 mast#14 cells#15 and#16 epithelial#17 cells#18 and#19 can#20 be#21 divided#22 into#23 interferons#24 ,#25 Interleukins#26 and#27 Tumor#28 Necrosis#29 factors#30 among#31 others#32 .#33 9 | 10 | f1:[cytokines#0,are#1,{proteins#5:family#3}] 11 | f2:[cytokines#0,can_be_divided_into#20,interferons#24] 12 | f3:[cytokines#0,can_be_divided_into#20,interleukins#26] 13 | f4:[cytokines#0,can_be_divided_into#20,tumor_necrosis_factors#28] 14 | c4:[proteins#5,derived_from#6,macrophages#8] 15 | c5:[proteins#5,derived_from#6,lymphocytes#10] 16 | c6:[proteins#5,derived_from#6,granulocytes#12] 17 | c7:[proteins#5,derived_from#6,mast_cells#14] 18 | c8:[proteins#5,derived_from#6,epithelial_cells#17] 19 | c9:[tumor_necrosis_factors#28,among_others#31,NIL] 20 | stmt2 = f1 f2 f3 f4 c4 c5 c6 c7 c8 c9 21 | 22 | # 26118933 The#0 presence#1 of#2 cytokines#3 in#4 a#5 wide#6 number#7 of#8 fish#9 species#10 has#11 been#12 proved#13 and#14 several#15 molecules#16 types#17 have#18 been#19 already#20 cloned#21 and#22 sequenced#23 .#24 23 | 24 | f5:[{cytokines#3:presence#1},has_been_proved#11,NIL] 25 | f6:[molecules_types#16,have_been_already_cloned#18,NIL] 26 | f7:[molecules_types#16,sequenced#23,NIL] 27 | c10:[{cytokines#3:presence#1},in#4,fish_species#9] 28 | stmt3 = f5 f6 f7 c10 29 | 30 | # 26118933 In#0 this#1 work#2 some#3 proinflamatory#4 molecules#5 and#6 Mx#7 gene#8 were#9 detected#10 in#11 the#12 liver#13 of#14 vaccinated#15 sea#16 bream#17 juveniles#18 with#19 an#20 average#21 body#22 weight#23 of#24 5#25 g#26 .#27 31 | 32 | f8:[proinflamatory_molecules#4,were_detected_in#9,{vaccinated_sea_bream_juveniles#15:liver#13}] 33 | f9:[mx_gene#7,were_detected_in#9,{vaccinated_sea_bream_juveniles#15:liver#13}] 34 | c11:[average_body_weight#21,of#24,5_g#25] 35 | stmt4 = f8 f9 c11 36 | 37 | # 26118933 The#0 method#1 of#2 immunization#3 was#4 by#5 short#6 bath#7 and#8 three#9 different#10 bacterins#11 against#12 the#13 marine#14 pathogen#15 Photobacterium#16 damselae#17 subsp.#18 piscicida#19 were#20 designed#21 and#22 used#23 to#24 immunize#25 fish#26 .#27 38 | 39 | f10:[{immunization#3:method#1},was_by#4,short_bath#6] 40 | f11:[bacterins#11,were_designed#20,NIL] 41 | f12:[bacterins#11,used_to_immunize#23,fish#26] 42 | c12:[bacterins#11,against#12,marine_pathogen_photobacterium_damselae_subsp._piscicida#14] 43 | stmt5 = f10 f11 f12 c12 44 | 45 | # 26118933 Five#0 genes#1 encoding#2 for#3 five#4 different#5 molecules#6 were#7 analyzed#8 by#9 real#10 time#11 PCR#12 ,#13 IL-1#14 beta#15 ,#16 IL#17 Ir-2#18 ,#19 Cox-2#20 ,#21 Mx#22 and#23 TNFalpha#24 .#25 46 | 47 | f13:[genes#1,were_analyzed_by#7,real_time_pcr#10] 48 | f14:[genes#1,were_analyzed_by#7,il-1_beta#14] 49 | f15:[genes#1,were_analyzed_by#7,il_ir-2#17] 50 | f16:[genes#1,were_analyzed_by#7,cox-2#20] 51 | f17:[genes#1,were_analyzed_by#7,mx#22] 52 | f18:[genes#1,were_analyzed_by#7,tnfalpha#24] 53 | c13:[genes#1,encoding_for#2,molecules#6] 54 | stmt6 = f13 f14 f15 f16 f17 f18 c13 55 | 56 | # 26118933 Gene#0 expression#1 was#2 quantified#3 along#4 four#5 days#6 after#7 fish#8 immunization#9 and#10 results#11 were#12 compared#13 among#14 groups#15 .#16 57 | 58 | f19:[gene_expression#0,was_quantified_along#2,{NIL#-1:four_days#5}] 59 | c14:[fish_immunization#8,were_compared_among#12,groups#15] 60 | stmt7 = f19 c14 61 | 62 | # 26118933 Results#0 show#1 that#2 the#3 heat-inactivated#4 vaccine#5 stimulates#6 the#7 up-regulation#8 of#9 IL-1#10 beta#11 ,#12 IL#13 Ir-2#14 ,#15 Cox-2#16 and#17 TNFalpha#18 genes#19 whereas#20 the#21 UV-light#22 inactivated#23 vaccine#24 was#25 the#26 unique#27 vaccine#28 which#29 stimulates#30 the#31 expression#32 of#33 Mx#34 gene#35 .#36 63 | 64 | f20:[{NIL#-1:results#0},show_that#1,NIL] 65 | f21:[heat-inactivated_vaccine#4,stimulates#6,{il-1_beta#10:up-regulation#8}] 66 | f22:[heat-inactivated_vaccine#4,stimulates#6,{il_ir-2#13:up-regulation#8}] 67 | f23:[heat-inactivated_vaccine#4,stimulates#6,{cox-2#16:up-regulation#8}] 68 | f24:[heat-inactivated_vaccine#4,stimulates#6,{tnfalpha_genes#18:up-regulation#8}] 69 | f25:[uv-light_inactivated_vaccine#22,was#25,unique_vaccine#27] 70 | c15:[unique_vaccine#27,stimulates#30,{mx_gene#34:expression#32}] 71 | stmt8 = f20 f21 f22 f23 f24 f25 c15 72 | 73 | # 26118933 The#0 present#1 is#2 a#3 novel#4 study#5 that#6 shows#7 by#8 the#9 first#10 time#11 the#12 effect#13 of#14 the#15 inactivation#16 process#17 of#18 vaccines#19 on#20 the#21 expression#22 levels#23 of#24 genes#25 involved#26 in#27 the#28 defense#29 against#30 Photobacterium#31 damselae#32 subsp#33 piscicida#34 .#35 74 | 75 | f26:[{NIL#-1:novel_study#4},shows_by_the_first_time#7,{NIL#-1:effect#13}] 76 | c16:[{NIL#-1:effect#13},of#14,{vaccines#19:inactivation_process#16}] 77 | c17:[{vaccines#19:inactivation_process#16},on#20,{genes#25:expression_levels#22}] 78 | c18:[{genes#25:expression_levels#22},involved_in_defense_against#26,photobacterium_damselae_subsp_piscicida#31] 79 | stmt9 = f26 c16 c17 c18 80 | -------------------------------------------------------------------------------- /data/label/train_sort/label-15542189.txt: -------------------------------------------------------------------------------- 1 | # 15542189 cationic#0 microparticles#1 are#2 a#3 potent#4 delivery#5 system#6 for#7 a#8 hcv#9 dna#10 vaccine#11 .#12 2 | 3 | f1:[cationic_microparticles#0,are#2,potent_delivery_system#4] 4 | c1:[potent_delivery_system#4,for#7,hcv_dna_vaccine#9] 5 | stmt1 = f1 c1 6 | 7 | # 15542189 we#0 initially#1 evaluated#2 in#3 mice#4 the#5 ability#6 of#7 naked#8 dna#9 encoding#10 intracellular#11 forms#12 of#13 the#14 e1e2#15 envelope#16 proteins#17 from#18 hcv#19 to#20 induce#21 antibody#22 responses#23 and#24 compared#25 the#26 responses#27 induced#28 with#29 the#30 same#31 plasmid#32 adsorbed#33 onto#34 cationic#35 poly#36 microparticles#37 .#38 8 | 9 | f2:[NIL,evaluated#2,{naked_dna#8:ability#6}] 10 | f3:[NIL,to_induce#20,antibody_responses#22] 11 | f4:[NIL,compared#25,{NIL#-1:responses#27}] 12 | c2:[NIL,in#3,mice#4] 13 | c3:[{naked_dna#8:ability#6},encoding#10,{e1e2_envelope_proteins#15:intracellular_forms#11}] 14 | c4:[{e1e2_envelope_proteins#15:intracellular_forms#11},from#18,hcv#19] 15 | c5:[{NIL#-1:responses#27},induced_with#28,plasmid#32] 16 | c6:[plasmid#32,adsorbed_onto#33,cationic_poly_microparticles#35] 17 | stmt2 = f2 f3 f4 c2 c3 c4 c5 c6 18 | 19 | # 15542189 although#0 naked#1 dna#2 was#3 only#4 able#5 to#6 induce#7 detectable#8 responses#9 at#10 the#11 100#12 microg#13 dose#14 level#15 ,#16 making#17 this#18 approach#19 impractical#20 for#21 evaluation#22 in#23 larger#24 animals#25 ,#26 plg/dna#27 induced#28 detectable#29 responses#30 at#31 10#32 microg#33 .#34 20 | 21 | f5:[naked_dna#1,was_only_able_to_induce#3,detectable_responses#8] 22 | f6:[naked_dna#1,making_this_approach_impractical_for#17,{larger_animals#24:evaluation#22}] 23 | f7:[plg/dna#27,induced#28,detectable_responses#29] 24 | c7:[detectable_responses#8,at#10,100_microg_dose_level#12] 25 | c8:[detectable_responses#29,at#31,10_microg#32] 26 | stmt3 = f5 f6 f7 c7 c8 27 | 28 | # 15542189 in#0 addition#1 ,#2 the#3 plg/dna#4 microparticles#5 induced#6 significantly#7 enhanced#8 responses#9 to#10 naked#11 dna#12 when#13 compared#14 at#15 the#16 same#17 dose#18 level#19 .#20 29 | 30 | f8:[plg/dna_microparticles#4,induced_significantly_enhanced_responses_to#6,naked_dna#11] 31 | c9:[NIL,compared_at#14,same_dose_level#17] 32 | stmt4 = f8 c9 33 | 34 | # 15542189 remarkably#0 ,#1 plg/dna#2 induced#3 comparable#4 responses#5 to#6 recombinant#7 e1e2#8 protein#9 adjuvanted#10 with#11 the#12 emulsion#13 mf59#14 .#15 35 | 36 | f9:[plg/dna#2,induced_comparable_responses_to#3,recombinant_e1e2_protein#7] 37 | c10:[recombinant_e1e2_protein#7,adjuvanted_with#10,emulsion_mf59#13] 38 | stmt5 = f9 c10 39 | 40 | # 15542189 furthermore#0 ,#1 plg/dna#2 effectively#3 primed#4 for#5 a#6 booster#7 response#8 with#9 protein#10 immunization#11 ,#12 while#13 naked#14 dna#15 did#16 not#17 .#18 41 | 42 | f10:[plg/dna#2,effectively_primed_for#3,booster_response#7] 43 | f11:[naked_dna#14,did_not#16,NIL] 44 | c11:[booster_response#7,with#9,protein_immunization#10] 45 | stmt6 = f10 f11 c11 46 | 47 | # 15542189 therefore#0 ,#1 plg/dna#2 was#3 selected#4 for#5 further#6 evaluation#7 in#8 a#9 non-human#10 primate#11 model#12 .#13 48 | 49 | f12:[plg/dna#2,was_selected_for#3,{non-human_primate_model#10:evaluation#7}] 50 | stmt7 = f12 51 | 52 | # 15542189 in#0 a#1 study#2 in#3 rhesus#4 macaques#5 ,#6 plg/dna#7 induced#8 seroconversion#9 in#10 3/3#11 animals#12 following#13 three#14 immunizations#15 .#16 53 | 54 | f13:[plg/dna#7,induced#8,seroconversion#9] 55 | c12:[NIL,in#0,{rhesus_macaques#4:study#2}] 56 | c13:[seroconversion#9,in#10,{animals#12:3/3#11}] 57 | c14:[{animals#12:3/3#11},following#13,{immunizations#15:three#14}] 58 | stmt8 = f13 c12 c13 c14 59 | 60 | # 15542189 although#0 the#1 antibody#2 responses#3 appeared#4 lower#5 than#6 those#7 induced#8 with#9 recombinant#10 protein#11 adjuvanted#12 with#13 mf59#14 ,#15 following#16 a#17 fourth#18 dose#19 ,#20 plg/dna#21 and#22 protein#23 induced#24 comparable#25 responses#26 .#27 61 | 62 | f14:[antibody_responses#2,appeared_lower_than#4,those#7] 63 | f15:[antibody_responses#2,following#16,fourth_dose#18] 64 | f16:[plg/dna#21,induced#24,comparable_responses#25] 65 | f17:[protein#23,induced#24,comparable_responses#25] 66 | c15:[those#7,induced_with#8,recombinant_protein#10] 67 | c16:[recombinant_protein#10,adjuvanted_with#12,mf59#14] 68 | stmt9 = f14 f15 f16 f17 c15 c16 69 | 70 | # 15542189 however#0 ,#1 a#2 single#3 booster#4 dose#5 of#6 recombinant#7 protein#8 administered#9 to#10 the#11 animals#12 previously#13 immunized#14 with#15 plg/dna#16 induced#17 much#18 higher#19 responses#20 .#21 71 | 72 | f18:[{recombinant_protein#7:single_booster_dose#3},induced_much_higher_responses#17,NIL] 73 | c17:[{recombinant_protein#7:single_booster_dose#3},administered_to#9,animals#12] 74 | c18:[animals#12,previously_immunized_with#13,plg/dna#16] 75 | stmt10 = f18 c17 c18 76 | 77 | # 15542189 in#0 addition#1 ,#2 one#3 of#4 three#5 animals#6 immunized#7 with#8 plg/dna#9 showed#10 a#11 cytotoxic#12 t#13 lymphocyte#14 response#15 in#16 peripheral#17 blood#18 lymphocytes#19 .#20 78 | 79 | f19:[animals#6,showed#10,cytotoxic_t_lymphocyte_response#12] 80 | c19:[animals#6,immunized_with#7,plg/dna#9] 81 | c20:[cytotoxic_t_lymphocyte_response#12,in#16,peripheral_blood_lymphocytes#17] 82 | stmt11 = f19 c19 c20 83 | 84 | # 15542189 in#0 conclusion#1 ,#2 cationic#3 plg#4 microparticles#5 with#6 adsorbed#7 hcv#8 dna#9 generates#10 potent#11 immune#12 responses#13 .#14 85 | 86 | f20:[cationic_plg_microparticles#3,generates#10,potent_immune_responses#11] 87 | c21:[cationic_plg_microparticles#3,with#6,adsorbed_hcv_dna#7] 88 | stmt12 = f20 c21 89 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-11726654.txt: -------------------------------------------------------------------------------- 1 | # 11726654 nuclear#0 receptor#1 peroxisome#2 proliferator-activated#3 receptor#4 alpha#5 is#6 expressed#7 in#8 resting#9 murine#10 lymphocytes.#11 the#12 pparalpha#13 in#14 t#15 and#16 b#17 lymphocytes#18 is#19 both#20 transactivation#21 and#22 transrepression#23 competent#24 .#25 2 | 3 | f1:[nuclear_receptor_peroxisome_proliferator-activated_receptor_alpha#0,is_expressed_in#6,resting_murine_lymphocytes#9] 4 | f2:[pparalpha#13,is#19,transactivation#21] 5 | f3:[pparalpha#13,is#19,transrepression_competent#23] 6 | c1:[pparalpha#13,in#14,t#15] 7 | c2:[pparalpha#13,in#14,b_lymphocytes#17] 8 | stmt1 = f1 f2 f3 c1 c2 9 | 10 | # 11726654 peroxisome#0 proliferator-activated#1 receptors#2 are#3 transcription#4 factors#5 that#6 belong#7 to#8 the#9 nuclear#10 hormone#11 receptor#12 superfamily#13 .#14 11 | 12 | f4:[peroxisome_proliferator-activated_receptors#0,are#3,transcription_factors#4] 13 | c3:[transcription_factors#4,belong_to#7,nuclear_hormone_receptor_superfamily#10] 14 | stmt2 = f4 c3 15 | 16 | # 11726654 pparalpha#0 and#1 ppargamma#2 ligands#3 have#4 been#5 demonstrated#6 to#7 exert#8 anti-inflammatory#9 activities#10 in#11 macrophages#12 by#13 repressing#14 the#15 activities#16 of#17 several#18 transcription#19 factors#20 .#21 17 | 18 | f5:[pparalpha#0,been_demonstrated_to_exert#5,anti-inflammatory_activities#9] 19 | f6:[ppargamma_ligands#2,exert#8,anti-inflammatory_activities#9] 20 | c4:[anti-inflammatory_activities#9,in#11,macrophages#12] 21 | c5:[macrophages#12,by_repressing#13,{transcription_factors#19:activities#16}] 22 | stmt3 = f5 f6 c4 c5 23 | 24 | # 11726654 ppargamma#0 is#1 expressed#2 in#3 t#4 lymphocytes#5 and#6 may#7 play#8 a#9 role#10 in#11 cytokine#12 production#13 ,#14 cellular#15 proliferation#16 ,#17 and#18 susceptibility#19 to#20 apoptosis#21 .#22 25 | 26 | f7:[ppargamma#0,is_expressed_in#1,t_lymphocytes#4] 27 | f8:[ppargamma#0,may_play_a_role_in#7,cytokine_production#12] 28 | f9:[ppargamma#0,may_play_a_role_in#7,cellular_proliferation#15] 29 | f10:[ppargamma#0,may_play_a_role_in#7,susceptibility#19] 30 | c6:[susceptibility#19,to#20,apoptosis#21] 31 | stmt4 = f7 f8 f9 f10 c6 32 | 33 | # 11726654 herein#0 ,#1 we#2 demonstrate#3 that#4 t#5 and#6 b#7 lymphocytes#8 constitutively#9 express#10 pparalpha#11 .#12 34 | 35 | f11:[NIL,demonstrate_that#3,NIL] 36 | f12:[t#5,constitutively_express#9,pparalpha#11] 37 | f13:[b_lymphocytes#7,constitutively_express#9,pparalpha#11] 38 | stmt5 = f11 f12 f13 39 | 40 | # 11726654 pparalpha#0 represents#1 the#2 predominant#3 isoform#4 expressed#5 in#6 lymphocytes#7 ,#8 whereas#9 ppargamma#10 dominates#11 in#12 all#13 cell#14 types#15 of#16 the#17 myeloid#18 lineage#19 .#20 41 | 42 | f14:[pparalpha#0,represents#1,predominant_isoform#3] 43 | f15:[ppargamma#10,dominates_in#11,{myeloid_lineage#18:cell_types#14}] 44 | c7:[predominant_isoform#3,expressed_in#5,lymphocytes#7] 45 | stmt6 = f14 f15 c7 46 | 47 | # 11726654 pparalpha#0 expression#1 was#2 down-regulated#3 following#4 t-cell#5 activation#6 while#7 ppargamma#8 expression#9 increased#10 under#11 the#12 same#13 activating#14 conditions#15 .#16 48 | 49 | f16:[pparalpha_expression#0,was_down-regulated_following#2,t-cell_activation#5] 50 | f17:[ppargamma_expression#8,increased_under_the_same#10,activating_conditions#14] 51 | stmt7 = f16 f17 52 | 53 | # 11726654 pparalpha#0 expression#1 in#2 t#3 cells#4 may#5 be#6 regulated#7 by#8 microenvironmental#9 factors#10 ,#11 because#12 peyer#13 's#14 patch#15 t#16 cells#17 expressed#18 far#19 greater#20 levels#21 of#22 pparalpha#23 than#24 t#25 cells#26 isolated#27 from#28 peripheral#29 lymphoid#30 organs#31 .#32 54 | 55 | f18:[pparalpha_expression#0,may_be_regulated_by#5,microenvironmental_factors#9] 56 | f19:[{peyer#13:patch_t_cells#15},expressed#18,{pparalpha#23:far_greater_levels#19}] 57 | c8:[pparalpha_expression#0,in#2,t_cells#3] 58 | c9:[{pparalpha#23:far_greater_levels#19},than#24,t_cells#25] 59 | c10:[t_cells#25,isolated_from#27,peripheral_lymphoid_organs#29] 60 | stmt8 = f18 f19 c8 c9 c10 61 | 62 | # 11726654 exposure#0 to#1 specific#2 ligand#3 determined#4 that#5 pparalpha#6 in#7 lymphocytes#8 can#9 effectively#10 transactivate#11 a#12 peroxisome#13 proliferator#14 response#15 element#16 reporter#17 construct#18 .#19 63 | 64 | f20:[{NIL#-1:exposure#0},determined_that#4,NIL] 65 | f21:[pparalpha#6,can_effectively_transactivate#9,peroxisome_proliferator_response_element_reporter_construct#13] 66 | c11:[{NIL#-1:exposure#0},to#1,specific_ligand#2] 67 | c12:[pparalpha#6,in#7,lymphocytes#8] 68 | stmt9 = f20 f21 c11 c12 69 | 70 | # 11726654 pparalpha#0 's#1 ability#2 to#3 regulate#4 endogenous#5 genes#6 ,#7 however#8 ,#9 required#10 treatment#11 with#12 histone#13 deacetylase#14 inhibitors#15 .#16 71 | 72 | f22:[{pparalpha#0:ability#2},required_treatment_with#10,histone_deacetylase_inhibitors#13] 73 | c13:[{pparalpha#0:ability#2},to_regulate#3,endogenous_genes#5] 74 | stmt10 = f22 c13 75 | 76 | # 11726654 finally#0 ,#1 ligand#2 activation#3 of#4 lymphocyte#5 pparalpha#6 antagonized#7 nf-kappab#8 .#9 77 | 78 | f23:[{lymphocyte_pparalpha#5:ligand_activation#2},antagonized#7,nf-kappab#8] 79 | stmt11 = f23 80 | 81 | # 11726654 our#0 observation#1 that#2 a#3 functional#4 pparalpha#5 exists#6 within#7 t#8 cells#9 and#10 b#11 lymphocytes#12 suggests#13 an#14 expanding#15 role#16 for#17 this#18 nuclear#19 receptor#20 in#21 cells#22 of#23 the#24 immune#25 system#26 .#27 82 | 83 | f24:[{NIL#-1:observation#1},suggests_an_expanding_role_for#13,nuclear_receptor#19] 84 | f25:[functional_pparalpha#4,exists_within#6,t_cells#8] 85 | f26:[functional_pparalpha#4,exists_within#6,b_lymphocytes#11] 86 | c14:[nuclear_receptor#19,in#21,{immune_system#25:cells#22}] 87 | stmt12 = f24 f25 f26 c14 88 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-15498271.txt: -------------------------------------------------------------------------------- 1 | # 15498271 [#0 the#1 significance#2 of#3 cell#4 cycle#5 distribution#6 and#7 expression#8 of#9 cell#10 cycle#11 regulatory#12 proteins#13 in#14 t#15 lymphocytes#16 in#17 patients#18 with#19 acute#20 asthma#21 attack]#22 .#23 2 | 3 | c1:[{cell_cycle_distribution#4:significance#2},in#14,t_lymphocytes#15] 4 | c2:[{cell_cycle_regulatory_proteins#10:expression#8},in#14,t_lymphocytes#15] 5 | c3:[t_lymphocytes#15,in#17,patients#18] 6 | c4:[patients#18,with#19,acute_asthma_attack]#20] 7 | stmt1 = c1 c2 c3 c4 8 | 9 | # 15498271 to#0 explore#1 the#2 molecular#3 regulatory#4 mechanisms#5 of#6 excessive#7 t#8 lymphocyte#9 activation#10 and#11 proliferation#12 in#13 patients#14 with#15 asthma#16 attack#17 by#18 studying#19 the#20 cell#21 cycle#22 distribution#23 and#24 the#25 expression#26 of#27 cell#28 cycle#29 regulatory#30 proteins#31 in#32 peripheral#33 blood#34 tlymphocytes#35 .#36 10 | 11 | f1:[NIL,to_explore#0,{excessive_t_lymphocyte_activation#7:molecular_regulatory_mechanisms#3}] 12 | f2:[NIL,to_explore#0,proliferation#12] 13 | c5:[proliferation#12,in#13,patients#14] 14 | c6:[proliferation#12,with#15,asthma#16] 15 | c7:[asthma#16,attack_by_studying#17,{cell_cycle_regulatory_proteins#28:cell_cycle_distribution#21}] 16 | c8:[asthma#16,attack_by_studying#17,{cell_cycle_regulatory_proteins#28:expression#26}] 17 | c9:[{cell_cycle_regulatory_proteins#28:expression#26},in#32,peripheral_blood_tlymphocytes#33] 18 | stmt2 = f1 f2 c5 c6 c7 c8 c9 19 | 20 | # 15498271 dna#0 of#1 t#2 lymphocytes#3 from#4 30#5 patients#6 with#7 asthma#8 attack#9 and#10 20#11 normal#12 subjects#13 was#14 stained#15 with#16 propidium#17 iodide#18 ,#19 and#20 the#21 cell#22 cycle#23 distribution#24 was#25 analyzed#26 by#27 flow#28 cytometry#29 .#30 21 | 22 | f3:[{t_lymphocytes#2:dna#0},was_stained_with#14,propidium_iodide#17] 23 | f4:[cell_cycle_distribution#22,was_analyzed_by#25,flow_cytometry#28] 24 | c10:[{t_lymphocytes#2:dna#0},from#4,{patients#6:30#5}] 25 | c11:[{patients#6:30#5},with#7,asthma_attack#8] 26 | c12:[{patients#6:30#5},with#7,normal_subjects#12] 27 | stmt3 = f3 f4 c10 c11 c12 28 | 29 | # 15498271 by#0 indirect#1 immunofluorescence#2 ,#3 the#4 expressions#5 of#6 p27kipl#7 ,#8 cyclin#9 e#10 ,#11 cyclin#12 a#13 ,#14 and#15 cyclin#16 b#17 in#18 t#19 lymphocytes#20 were#21 measured#22 by#23 flow#24 cytometry#25 .#26 30 | 31 | f5:[NIL,by#0,indirect_immunofluorescence#1] 32 | f6:[{p27kipl#7:expressions#5},were_measured_by#21,flow_cytometry#24] 33 | f7:[{cyclin_e#9:expressions#5},were_measured_by#21,flow_cytometry#24] 34 | f8:[{cyclin_a#12:expressions#5},were_measured_by#21,flow_cytometry#24] 35 | f9:[{cyclin_b#16:expressions#5},were_measured_by#21,flow_cytometry#24] 36 | c13:[{p27kipl#7:expressions#5},in#18,t_lymphocytes#19] 37 | c14:[{cyclin_e#9:expressions#5},in#18,t_lymphocytes#19] 38 | c15:[{cyclin_a#12:expressions#5},in#18,t_lymphocytes#19] 39 | c16:[{cyclin_b#16:expressions#5},in#18,t_lymphocytes#19] 40 | stmt4 = f5 f6 f7 f8 f9 c13 c14 c15 c16 41 | 42 | # 15498271 the#0 difference#1 between#2 patients#3 with#4 asthma#5 attack#6 and#7 normal#8 subjects#9 wasanalyzed#10 .#11 43 | 44 | f10:[{NIL#-1:difference#1},wasanalyzed#10,NIL] 45 | c17:[{NIL#-1:difference#1},between#2,patients#3] 46 | c18:[{NIL#-1:difference#1},between#2,normal_subjects#8] 47 | c19:[patients#3,with#4,asthma_attack#5] 48 | stmt5 = f10 c17 c18 c19 49 | 50 | # 15498271 the#0 percentage#1 of#2 t#3 lymphocytes#4 in#5 the#6 s#7 phase#8 and#9 s#10 +#11 g(2)#12 /#13 m#14 phase#15 was#16 51 | 52 | f11:[{t_lymphocytes#3:percentage#1},was#16,NIL] 53 | c20:[{t_lymphocytes#3:percentage#1},in#5,s_phase#7] 54 | c21:[{t_lymphocytes#3:percentage#1},in#5,s_+_g(2)_/_m_phase#10] 55 | stmt6 = f11 c20 c21 56 | 57 | # 15498271 the#0 percentage#1 of#2 t#3 lymphocytes#4 in#5 the#6 g(0)#7 /#8 g(1)#9 phase#10 in#11 the#12 asthma#13 group#14 was#15 58 | 59 | f12:[{t_lymphocytes#3:percentage#1},was#15,NIL] 60 | c22:[{t_lymphocytes#3:percentage#1},in#5,g(0)_/_g(1)_phase#7] 61 | c23:[g(0)_/_g(1)_phase#7,in#11,asthma_group#13] 62 | stmt7 = f12 c22 c23 63 | 64 | # 15498271 the#0 expression#1 of#2 p27kipl#3 in#4 t#5 lymphocytes#6 of#7 the#8 asthma#9 group#10 65 | 66 | c24:[{p27kipl#3:expression#1},in#4,{asthma_group#9:t_lymphocytes#5}] 67 | stmt8 = c24 68 | 69 | # 15498271 the#0 expression#1 of#2 cyclin#3 e#4 ,#5 cyclin#6 a#7 ,#8 and#9 cyclin#10 b#11 in#12 t#13 lymphocytes#14 of#15 the#16 asthma#17 group#18 [#19 (25#20 +/-#21 24)%#22 ,#23 .#24 70 | 71 | c25:[{cyclin_e#3:expression#1},in#12,{asthma_group#17:t_lymphocytes#13}] 72 | c26:[{cyclin_a#6:expression#1},in#12,{asthma_group#17:t_lymphocytes#13}] 73 | c27:[{cyclin_b#10:expression#1},in#12,{asthma_group#17:t_lymphocytes#13}] 74 | stmt9 = c25 c26 c27 75 | 76 | # 15498271 the#0 abnormal#1 expression#2 of#3 ccrp#4 in#5 t#6 lymphocytes#7 was#8 related#9 to#10 the#11 excessive#12 activation#13 and#14 proliferation#15 of#16 t#17 lymphocytes#18 in#19 patients#20 with#21 asthma#22 attack#23 .#24 77 | 78 | f13:[{ccrp#4:abnormal_expression#1},was_related_to_#8,{t_lymphocytes#17:excessive_activation#12}] 79 | f14:[{ccrp#4:abnormal_expression#1},was_related_to_#8,{t_lymphocytes#17:proliferation#15}] 80 | c28:[{ccrp#4:abnormal_expression#1},in#5,t_lymphocytes#6] 81 | c29:[{t_lymphocytes#17:excessive_activation#12},in#19,patients#20] 82 | c30:[{t_lymphocytes#17:proliferation#15},in#19,patients#20] 83 | c31:[patients#20,with#21,asthma_attack#22] 84 | stmt10 = f13 f14 c28 c29 c30 c31 85 | 86 | # 15498271 a#0 new#1 approach#2 to#3 asthma#4 therapy#5 may#6 be#7 developed#8 with#9 ccrp#10 as#11 a#12 regulatory#13 target#14 .#15 87 | 88 | f15:[new_approach#1,may_be_developed#6,ccrp#10] 89 | c32:[new_approach#1,to#3,asthma_therapy#4] 90 | c33:[ccrp#10,as#11,regulatory_target#13] 91 | stmt11 = f15 c32 c33 92 | -------------------------------------------------------------------------------- /data/label/train_sort/label-11953882.txt: -------------------------------------------------------------------------------- 1 | # 11953882 cimetidine#0 modulates#1 the#2 antigen#3 presenting#4 capacity#5 of#6 dendritic#7 cells#8 from#9 colorectal#10 cancer#11 patients#12 .#13 2 | 3 | f1:[cimetidine#0,modulates#1,antigen#3] 4 | f2:[cimetidine#0,presenting#4,{dendritic_cells#7:capacity#5}] 5 | c1:[{dendritic_cells#7:capacity#5},from#9,colorectal_cancer_patients#10] 6 | stmt1 = f1 f2 c1 7 | 8 | # 11953882 cimetidine#0 ,#1 a#2 h(2)#3 receptor#4 antagonist#5 ,#6 has#7 been#8 reported#9 to#10 improve#11 survival#12 in#13 gastrointestinal#14 cancer#15 patients#16 .#17 9 | 10 | f3:[cimetidine#0,NIL#-1,h(2)_receptor_antagonist#3] 11 | f4:[cimetidine#0,has_been_reported_to_improve#7,{gastrointestinal_cancer_patients#14:survival#12}] 12 | f5:[h(2)_receptor_antagonist#3,has_been_reported_to_improve#7,{gastrointestinal_cancer_patients#14:survival#12}] 13 | stmt2 = f3 f4 f5 14 | 15 | # 11953882 these#0 effects#1 have#2 largely#3 been#4 attributed#5 to#6 the#7 enhancing#8 effects#9 of#10 cimetidine#11 on#12 the#13 host#14 's#15 antitumour#16 cell-mediated#17 immune#18 response#19 ,#20 such#21 as#22 inhibition#23 of#24 suppressor#25 t#26 lymphocyte#27 activity#28 ,#29 stimulation#30 of#31 natural#32 killer#33 cell#34 activity#35 and#36 increase#37 of#38 interleukin-2#39 production#40 from#41 helper#42 t#43 lymphocytes#44 .#45 16 | 17 | f6:[{NIL#-1:effects#1},have_largely_been_attributed_to#2,{cimetidine#11:enhancing_effects#8}] 18 | f7:[{NIL#-1:effects#1},such_as#21,{suppressor_t_lymphocyte_activity#25:inhibition#23}] 19 | f8:[{NIL#-1:effects#1},such_as#21,{natural_killer_cell_activity#32:stimulation#30}] 20 | f9:[{NIL#-1:effects#1},such_as#21,{interleukin-2_production#39:increase#37}] 21 | c2:[{cimetidine#11:enhancing_effects#8},on#12,{host#14:antitumour_cell-mediated_immune_response#16}] 22 | c3:[{interleukin-2_production#39:increase#37},from#41,helper_t_lymphocytes#42] 23 | stmt3 = f6 f7 f8 f9 c2 c3 24 | 25 | # 11953882 we#0 conducted#1 an#2 in#3 vitro#4 study#5 on#6 the#7 effects#8 of#9 cimetidine#10 on#11 differentiation#12 and#13 antigen#14 presenting#15 capacity#16 of#17 monocyte-derived#18 dendritic#19 cells#20 from#21 advanced#22 colorectal#23 cancer#24 patients#25 and#26 normal#27 controls#28 .#29 26 | 27 | f10:[NIL,conducted#1,in_vitro_study#3] 28 | c4:[in_vitro_study#3,on#6,{cimetidine#10:effects#8}] 29 | c5:[{cimetidine#10:effects#8},on#11,{monocyte-derived_dendritic_cells#18:differentiation#12}] 30 | c6:[{cimetidine#10:effects#8},on#11,{monocyte-derived_dendritic_cells#18:antigen_presenting_capacity#14}] 31 | c7:[{monocyte-derived_dendritic_cells#18:antigen_presenting_capacity#14},from#21,advanced_colorectal_cancer_patients#22] 32 | c8:[{monocyte-derived_dendritic_cells#18:antigen_presenting_capacity#14},from#21,normal_controls#27] 33 | stmt4 = f10 c4 c5 c6 c7 c8 34 | 35 | # 11953882 as#0 a#1 result#2 ,#3 an#4 investigation#5 of#6 expression#7 of#8 surface#9 molecules#10 associated#11 with#12 dendritic#13 cells#14 by#15 flow#16 cytometric#17 analyses#18 showed#19 that#20 cimetidine#21 had#22 no#23 enhancing#24 effect#25 on#26 differentiation#27 of#28 dendritic#29 cells#30 from#31 cancer#32 patients#33 and#34 normal#35 controls#36 .#37 36 | 37 | f11:[{NIL#-1:investigation#5},showed_that#19,flow_cytometric_analyses#16] 38 | f12:[cimetidine#21,had_no_enhancing_effect_on#22,{dendritic_cells#29:differentiation#27}] 39 | c9:[NIL,as#0,{NIL#-1:result#2}] 40 | c10:[{NIL#-1:investigation#5},by#15,flow_cytometric_analyses#16] 41 | c11:[{surface_molecules#9:expression#7},associated_with#11,dendritic_cells#13] 42 | c12:[{dendritic_cells#29:differentiation#27},from#31,cancer_patients#32] 43 | c13:[{dendritic_cells#29:differentiation#27},from#31,normal_controls#35] 44 | stmt5 = f11 f12 c9 c10 c11 c12 c13 45 | 46 | # 11953882 an#0 investigation#1 of#2 [(3)h]thymidine#3 incorporation#4 by#5 allogeneic#6 mixed#7 lymphocyte#8 reactions#9 revealed#10 that#11 cimetidine#12 increased#13 the#14 antigen#15 presenting#16 capacity#17 of#18 dendritic#19 cells#20 from#21 both#22 materials#23 .#24 47 | 48 | f13:[{[(3)h]thymidine_incorporation#3:investigation#1},revealed_that#10,NIL] 49 | f14:[cimetidine#12,increased#13,{dendritic_cells#19:antigen_presenting_capacity#15}] 50 | c14:[{[(3)h]thymidine_incorporation#3:investigation#1},by#5,allogeneic_mixed_lymphocyte_reactions#6] 51 | c15:[{dendritic_cells#19:antigen_presenting_capacity#15},from#21,materials#23] 52 | stmt6 = f13 f14 c14 c15 53 | 54 | # 11953882 moreover#0 ,#1 a#2 higher#3 antigen#4 presenting#5 capacity#6 was#7 observed#8 in#9 advanced#10 cancer#11 patients#12 compared#13 to#14 normal#15 controls#16 .#17 55 | 56 | f15:[higher_antigen_presenting_capacity#3,was_observed_in#7,advanced_cancer_patients#10] 57 | c16:[advanced_cancer_patients#10,compared_to#13,normal_controls#15] 58 | stmt7 = f15 c16 59 | 60 | # 11953882 these#0 effects#1 might#2 be#3 mediated#4 via#5 specific#6 action#7 of#8 cimetidine#9 and#10 not#11 via#12 h(2)#13 receptors#14 because#15 famotidine#16 did#17 not#18 show#19 similar#20 effects#21 .#22 61 | 62 | f16:[{NIL#-1:effects#1},might_be_mediated_via#2,{cimetidine#9:specific_action#6}] 63 | f17:[{NIL#-1:effects#1},not_via#11,h(2)_receptors#13] 64 | f18:[famotidine#16,did_not_show#17,{NIL#-1:similar_effects#20}] 65 | stmt8 = f16 f17 f18 66 | 67 | # 11953882 our#0 results#1 suggest#2 that#3 cimetidine#4 may#5 enhance#6 the#7 host#8 's#9 antitumour#10 cell-mediated#11 immunity#12 by#13 improving#14 the#15 suppressed#16 dendritic#17 cells#18 function#19 of#20 advanced#21 cancer#22 patients#23 .#24 68 | 69 | f19:[{NIL#-1:results#1},suggest_that#2,NIL] 70 | f20:[cimetidine#4,may_enhance#5,{host#8:antitumour_cell-mediated_immunity#10}] 71 | c17:[NIL,by_improving#13,{advanced_cancer_patients#21:suppressed_dendritic_cells_function#16}] 72 | stmt9 = f19 f20 c17 73 | 74 | -------------------------------------------------------------------------------- /data/label/train_sort/label-26117043.txt: -------------------------------------------------------------------------------- 1 | # 26117043 [#0 Effect#1 of#2 sAHA#3 on#4 maturation#5 of#6 dendritic#7 cells#8 and#9 its#10 mechanism]#11 .#12 2 | 3 | c1:[{saha#3:effect#1},on#4,{dendritic_cells#7:maturation#5}] 4 | c2:[{saha#3:mechanism]#11},NIL#-1,NIL] 5 | stmt1 = c1 c2 6 | 7 | # 26117043 To#0 investigate#1 the#2 effect#3 of#4 SAHA#5 on#6 the#7 maturation#8 of#9 human#10 dendritic#11 cells#12 and#13 to#14 explore#15 its#16 underlyingmechanism#17 .#18 8 | 9 | f1:[NIL,to_investigate#0,{saha#5:effect#3}] 10 | f2:[NIL,to_explore#14,{saha#5:underlyingmechanism#17}] 11 | c3:[{saha#5:effect#3},on#6,{human_dendritic_cells#10:maturation#8}] 12 | stmt2 = f1 f2 c3 13 | 14 | # 26117043 Peripheral#0 blood#1 mononuclear#2 cells#3 were#4 isolated#5 from#6 human#7 peripheral#8 blood#9 and#10 cultured#11 in#12 RPMI#13 1640#14 medium#15 with#16 100#17 ng/ml#18 rhGM-CSF#19 and#20 500#21 U/ml#22 rhIL-4#23 .#24 15 | 16 | f3:[peripheral_blood_mononuclear_cells#0,were_isolated_from#4,human_peripheral_blood#7] 17 | f4:[peripheral_blood_mononuclear_cells#0,cultured_in#11,rpmi_1640_medium#13] 18 | c4:[rpmi_1640_medium#13,with#16,{rhgm-csf#19:100_ng/ml#17}] 19 | c5:[rpmi_1640_medium#13,with#16,{rhil-4#23:500_u/ml#21}] 20 | stmt3 = f3 f4 c4 c5 21 | 22 | # 26117043 In#0 the#1 LPS#2 induced#3 maturation#4 process#5 ,#6 dendritic#7 cells#8 treated#9 with#10 or#11 without#12 SAHA#13 were#14 used#15 as#16 test#17 group#18 ,#19 and#20 dendritic#21 cells#22 treated#23 without#24 LPS#25 or#26 SAHA#27 were#28 used#29 as#30 control#31 group#32 .#33 23 | 24 | f5:[dendritic_cells#7,were_used_as#14,test_group#17] 25 | f6:[dendritic_cells#21,were_used_as#28,control_group#31] 26 | c6:[NIL,in#0,lps_induced_maturation_process#2] 27 | c7:[dendritic_cells#7,treated_with_or_without#9,saha#13] 28 | c8:[dendritic_cells#21,treated_without#23,lps#25] 29 | c9:[dendritic_cells#21,treated_without#23,saha#27] 30 | stmt4 = f5 f6 c6 c7 c8 c9 31 | 32 | # 26117043 DC#0 was#1 observed#2 under#3 inverted#4 microscope#5 .#6 33 | 34 | f7:[dc#0,was_observed_under#1,inverted_microscope#4] 35 | stmt5 = f7 36 | 37 | # 26117043 Flow#0 cytometer#1 was#2 used#3 to#4 detect#5 the#6 surface#7 antigen#8 molecules#9 expressed#10 by#11 DC#12 .#13 38 | 39 | f8:[flow_cytometer#0,was_used_to_detect#2,surface_antigen_molecules#7] 40 | c10:[surface_antigen_molecules#7,expressed_by#10,dc#12] 41 | stmt6 = f8 c10 42 | 43 | # 26117043 The#0 mixed#1 lymphocyte#2 culture#3 was#4 used#5 to#6 observe#7 the#8 allogeneic#9 lymphocyte#10 stimulation#11 .#12 44 | 45 | f9:[mixed_lymphocyte_culture#1,was_used_to_observe#4,allogeneic_lymphocyte_stimulation#9] 46 | stmt7 = f9 47 | 48 | # 26117043 The#0 NF-kappaB#1 signaling#2 pathway#3 was#4 detected#5 by#6 electrophoretic#7 mobility#8 shift#9 assay(EMSA)#10 .#11 49 | 50 | f10:[nf-kappab_signaling_pathway#1,was_detected_by#4,electrophoretic_mobility_shift_assay(emsa)#7] 51 | stmt8 = f10 52 | 53 | # 26117043 the#0 saha#1 could#2 effectively#3 suppress#4 the#5 maturation#6 of#7 dc#8 induced#9 by#10 lps#11 ,#12 the#13 dc#14 treated#15 with#16 saha+lps#17 had#18 immature#19 morphological#20 characteristics#21 ,#22 the#23 expression#24 of#25 cd80#26 ,#27 cd83#28 and#29 hla-dr#30 in#31 saha+lps#32 group#33 and#34 control#35 group#36 were#37 significantly#38 down-regulated#39 as#40 compared#41 with#42 single#43 lps#44 group#45 ,#46 the#47 ability#48 of#49 dc#50 to#51 stimulate#52 the#53 proliferation#54 of#55 allogeneic#56 t#57 lymphocytes#58 in#59 saha+lps#60 group#61 and#62 control#63 group#64 was#65 significantly#66 weaker#67 than#68 that#69 in#70 single#71 lps#72 group#73 ,#74 emsa#75 results#76 showed#77 that#78 nf-kappab#79 activity#80 decreased#81 after#82 saha#83 and#84 lps#85 treatment#86 and#87 was#88 significantly#89 lower#90 than#91 that#92 of#93 single#94 lpsgroup#95 .#96 54 | 55 | f11:[saha#1,could_effectively_suppress#2,{dc#8:maturation#6}] 56 | f12:[dc#14,had#18,immature_morphological_characteristics#19] 57 | f13:[{cd80#26:expression#24},were_significantly_down-regulated#37,NIL] 58 | f14:[{cd83#28:expression#24},were_significantly_down-regulated#37,NIL] 59 | f15:[{hla-dr#30:expression#24},were_significantly_down-regulated#37,NIL] 60 | f16:[{dc#50:ability#48},was_significantly_weaker_than_that_in#65,single_lps_group#71] 61 | f17:[nf-kappab_activity#79,decreased_after#81,saha#83] 62 | f18:[nf-kappab_activity#79,decreased_after#81,lps_treatment#85] 63 | f19:[nf-kappab_activity#79,was_significantly_lower_than_that_in#88,single_lpsgroup#94] 64 | c11:[{dc#8:maturation#6},induced_by#9,lps#11] 65 | c12:[dc#14,treated_with#15,saha+lps#17] 66 | c13:[{cd80#26:expression#24},in#31,saha+lps_group#32] 67 | c14:[{cd80#26:expression#24},in#31,control_group#35] 68 | c15:[{cd83#28:expression#24},in#31,saha+lps_group#32] 69 | c16:[{cd83#28:expression#24},in#31,control_group#35] 70 | c17:[{hla-dr#30:expression#24},in#31,saha+lps_group#32] 71 | c18:[{hla-dr#30:expression#24},in#31,control_group#35] 72 | c19:[saha+lps_group#32,compared_with#41,single_lps_group#43] 73 | c20:[control_group#35,compared_with#41,single_lps_group#43] 74 | c21:[{dc#50:ability#48},to_stimulate#51,{allogeneic_t_lymphocytes#56:proliferation#54}] 75 | c22:[{allogeneic_t_lymphocytes#56:proliferation#54},in#59,saha+lps_group#60] 76 | c23:[{allogeneic_t_lymphocytes#56:proliferation#54},in#59,control_group#63] 77 | stmt9 = f11 f12 f13 f14 f15 f16 f17 f18 f19 c11 c12 c13 c14 c15 c16 c17 c18 c19 c20 c21 c22 c23 78 | 79 | # 26117043 saha#0 can#1 effectively#2 suppress#3 dc#4 maturation#5 induced#6 by#7 lps#8 and#9 also#10 weaken#11 the#12 ability#13 to#14 stimulate#15 allogeneic#16 t#17 lymphocyte#18 .#19 80 | 81 | f20:[saha#0,can_effectively_suppress#1,dc_maturation#4] 82 | f21:[saha#0,weaken_ability_to_stimulate#11,allogeneic_t_lymphocyte#16] 83 | c24:[dc_maturation#4,induced_by#6,lps#8] 84 | stmt10 = f20 f21 c24 85 | 86 | # 26117043 nf-kappab#0 signaling#1 pathway#2 is#3 involved#4 in#5 regulating#6 dc#7 maturation#8 .#9 87 | 88 | f22:[nf-kappab_signaling_pathway#0,is_involved_in#3,regulating_dc_maturation#6] 89 | stmt11 = f22 90 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-15498306.txt: -------------------------------------------------------------------------------- 1 | # 15498306 [#0 effects#1 of#2 escharectomy#3 during#4 burn#5 shock#6 stage#7 on#8 the#9 mrna#10 expression#11 of#12 ifn-gamma#13 and#14 il-4#15 in#16 spleen#17 t#18 lymphocytes#19 in#20 rats#21 after#22 thermal#23 injury]#24 .#25 2 | 3 | c1:[{escharectomy#3:effects#1},during#4,burn_shock_stage#5] 4 | c2:[burn_shock_stage#5,on#8,{ifn-gamma#13:mrna_expression#10}] 5 | c3:[burn_shock_stage#5,on#8,spleen_t_lymphocytes#17] 6 | c4:[spleen_t_lymphocytes#17,in#20,rats#21] 7 | c5:[rats#21,after#22,thermal_injury]#23] 8 | stmt1 = c1 c2 c3 c4 c5 9 | 10 | # 15498306 to#0 determine#1 the#2 serum#3 level#4 and#5 mrna#6 expression#7 of#8 type-1/type-2#9 cytokines#10 of#11 t#12 lymphocytes#13 in#14 spleens#15 of#16 rats#17 after#18 thermal#19 injury#20 and#21 to#22 investigate#23 the#24 effects#25 of#26 escharectomy#27 during#28 burn#29 shock#30 stage#31 on#32 ifn-gamma#33 andil-4#34 .#35 11 | 12 | f1:[NIL,to_determine#0,{type-1/type-2_cytokines_of_t_lymphocytes#9:serum_level#3}] 13 | f2:[NIL,to_determine#0,{type-1/type-2_cytokines_of_t_lymphocytes#9:mrna_expression#6}] 14 | f3:[NIL,to_investigate#22,{escharectomy#27:effects#25}] 15 | c6:[{type-1/type-2_cytokines_of_t_lymphocytes#9:serum_level#3},in#14,{rats#17:spleens#15}] 16 | c7:[{type-1/type-2_cytokines_of_t_lymphocytes#9:mrna_expression#6},in#14,{rats#17:spleens#15}] 17 | c8:[{rats#17:spleens#15},after#18,thermal_injury#19] 18 | c9:[{escharectomy#27:effects#25},during#28,burn_shock_stage#29] 19 | c10:[burn_shock_stage#29,on#32,ifn-gamma_andil-4#33] 20 | stmt2 = f1 f2 f3 c6 c7 c8 c9 c10 21 | 22 | # 15498306 one#0 hundred#1 and#2 sixty#3 male#4 wistar#5 rats#6 were#7 randomized#8 into#9 four#10 groups#11 .#12 23 | 24 | f4:[{male_wistar_rats#4:one_hundred_and_sixty#0},were_randomized_into#7,{groups#11:four#10}] 25 | stmt3 = f4 26 | 27 | # 15498306 in#0 group#1 a#2 ,#3 animals#4 were#5 not#6 subjected#7 to#8 escharectomy#9 .#10 28 | 29 | f5:[animals#4,were_not_subjected_to#5,escharectomy#9] 30 | c11:[NIL,in#0,group_a#1] 31 | stmt4 = f5 c11 32 | 33 | # 15498306 in#0 groups#1 b#2 ,#3 c#4 and#5 d#6 ,#7 escharectomy#8 and#9 skin#10 allograft#11 were#12 performed#13 at#14 8#15 ,#16 24#17 ,#18 96#19 hours#20 postburn#21 respectively#22 .#23 34 | 35 | f6:[escharectomy#8,were_performed_at#12,postburn#21] 36 | f7:[skin_allograft#10,were_performed_at#12,postburn#21] 37 | c12:[NIL,in#0,groups_b#1] 38 | c13:[NIL,in#0,c#4] 39 | c14:[NIL,in#0,d#6] 40 | stmt5 = f6 f7 c12 c13 c14 41 | 42 | # 15498306 at#0 4#1 ,#2 12#3 ,#4 24#5 ,#6 48#7 ,#8 96#9 ,#10 120#11 and#12 168#13 hours#14 pb#15 ,#16 animals#17 were#18 killed#19 and#20 blood#21 and#22 spleens#23 samples#24 were#25 harvested#26 .#27 43 | 44 | f8:[animals#17,were_killed#18,NIL] 45 | f9:[blood#21,were_harvested#25,NIL] 46 | f10:[spleens_samples#23,were_harvested#25,NIL] 47 | c15:[NIL,at#0,{NIL#-1:4#1}] 48 | c16:[NIL,at#0,{NIL#-1:12#3}] 49 | c17:[NIL,at#0,{NIL#-1:24#5}] 50 | c18:[NIL,at#0,{NIL#-1:48#7}] 51 | c19:[NIL,at#0,{NIL#-1:96#9}] 52 | c20:[NIL,at#0,{NIL#-1:120#11}] 53 | c21:[NIL,at#0,{NIL#-1:168_hours_pb#13}] 54 | stmt6 = f8 f9 f10 c15 c16 c17 c18 c19 c20 c21 55 | 56 | # 15498306 elisa#0 was#1 applied#2 to#3 determine#4 the#5 concentration#6 of#7 ifn-gamma#8 and#9 il-4#10 in#11 serum#12 .#13 57 | 58 | f11:[elisa#0,was_applied_to#1,{ifn-gamma#8:concentration#6}] 59 | f12:[elisa#0,was_applied_to#1,{il-4_in_serum#10:concentration#6}] 60 | stmt7 = f11 f12 61 | 62 | # 15498306 the#0 expression#1 pattern#2 of#3 ifn-gamma#4 and#5 il-4#6 were#7 observed#8 at#9 mrna#10 level#11 in#12 t#13 lymphocytes#14 isolated#15 from#16 spleen#17 byrt-pcr#18 .#19 63 | 64 | f13:[{ifn-gamma#4:expression_pattern#1},were_observed_at#7,mrna_level#10] 65 | c22:[mrna_level#10,in#12,t_lymphocytes#13] 66 | c23:[t_lymphocytes#13,isolated_from#15,spleen_byrt-pcr#17] 67 | stmt8 = f13 c22 c23 68 | 69 | # 15498306 the#0 serum#1 level#2 of#3 ifn-gamma#4 and#5 il-4#6 rose#7 rapidly#8 and#9 significantly#10 after#11 scald#12 injury#13 ,#14 expression#15 of#16 ifn-gamma#17 and#18 il-4#19 mrna#20 in#21 rats'#22 t#23 lymphocyte#24 were#25 also#26 up-regulated#27 spontaneously#28 .#29 70 | 71 | f14:[{ifn-gamma#4:serum_level#1},rose_rapidly_and_significantly#7,NIL] 72 | f15:[{il-4#6:serum_level#1},rose_rapidly_and_significantly#7,NIL] 73 | f16:[{ifn-gamma#17:expression#15},were_also_up-regulated_spontaneously#25,NIL] 74 | f17:[{il-4_mrna#19:expression#15},were_also_up-regulated_spontaneously#25,NIL] 75 | c24:[NIL,after#11,scald_injury#12] 76 | c25:[{ifn-gamma#17:expression#15},in#21,rats'_t_lymphocyte#22] 77 | c26:[{il-4_mrna#19:expression#15},in#21,rats'_t_lymphocyte#22] 78 | stmt9 = f14 f15 f16 f17 c24 c25 c26 79 | 80 | # 15498306 the#0 serum#1 level#2 of#3 ifn-gamma#4 and#5 its#6 mrna#7 expression#8 began#9 to#10 rise#11 within#12 4#13 hours#14 pb#15 ,#16 peaking#17 at#18 24#19 hours#20 pb#21 .#22 81 | 82 | f18:[{ifn-gamma#4:serum_level#1},began_to_rise#9,NIL] 83 | f19:[{ifn-gamma#4:serum_level#1},peaking_at#17,{pb#21:24_hours#19}] 84 | f20:[{ifn-gamma#4:mrna_expression#7},began_to_rise#9,NIL] 85 | c27:[NIL,within#12,{pb#15:4_hours#13}] 86 | stmt10 = f18 f19 f20 c27 87 | 88 | # 15498306 whereas#0 il-4#1 and#2 its#3 mrna#4 expression#5 showed#6 a#7 persistent#8 elevation#9 .#10 89 | 90 | f21:[{il-4#1:mrna_expression#4},showed#6,persistent_elevation#8] 91 | f22:[il-4#1,showed#6,persistent_elevation#8] 92 | stmt11 = f21 f22 93 | 94 | # 15498306 thereby#0 leading#1 to#2 a#3 dominant#4 tendency#5 of#6 th2#7 cytokine#8 response#9 on#10 7#11 d#12 pb#13 .#14 95 | 96 | f23:[NIL,thereby_leading_to#0,{th2_cytokine_response#7:dominant_tendency#4}] 97 | c28:[{th2_cytokine_response#7:dominant_tendency#4},on#10,{pb#13:7_d#11}] 98 | stmt12 = f23 c28 99 | 100 | # 15498306 in#0 group#1 a#2 all#3 above#4 parameters#5 revealed#6 most#7 obvious#8 changes#9 compared#10 with#11 controls#12 ,#13 then#14 ranked#15 in#16 group#17 d#18 ,#19 b#20 andc#21 .#22 101 | 102 | f24:[parameters#5,revealed#6,obvious_changes#8] 103 | f25:[parameters#5,ranked_in#15,group_d#17] 104 | f26:[parameters#5,ranked_in#15,b_andc#20] 105 | c29:[NIL,in#0,group_a#1] 106 | stmt13 = f24 f25 f26 c29 107 | 108 | # 15498306 escharectomy#0 during#1 burn#2 shock#3 stage#4 is#5 helpful#6 to#7 decrease#8 the#9 harmful#10 over#11 expression#12 of#13 th2-type#14 lymphocyte#15 after#16 severe#17 thermal#18 injury#19 .#20 109 | 110 | f27:[escharectomy#0,is_helpful_to_decrease#5,{th2-type_lymphocyte#14:harmful_over_expression#10}] 111 | c30:[escharectomy#0,during#1,burn_shock_stage#2] 112 | c31:[{th2-type_lymphocyte#14:harmful_over_expression#10},after#16,severe_thermal_injury#17] 113 | stmt14 = f27 c30 c31 114 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-12027387.txt: -------------------------------------------------------------------------------- 1 | # 12027387 calcium#0 influx#1 into#2 dendrites#3 of#4 the#5 leech#6 retzius#7 neuron#8 evoked#9 by#10 5-hydroxytryptamine#11 .#12 2 | 3 | c1:[calcium_influx#0,into#2,{leech_retzius_neuron#6:dendrites#3}] 4 | c2:[{leech_retzius_neuron#6:dendrites#3},evoked_by#9,5-hydroxytryptamine#11] 5 | stmt1 = c1 c2 6 | 7 | # 12027387 5-hydroxytryptamine#0 is#1 a#2 ubiquitous#3 neurotransmitter#4 and#5 neuromodulator#6 that#7 affects#8 neural#9 circuits#10 and#11 behaviours#12 in#13 vertebrates#14 and#15 invertebrates#16 .#17 8 | 9 | f1:[5-hydroxytryptamine#0,is#1,ubiquitous_neurotransmitter#3] 10 | f2:[5-hydroxytryptamine#0,is#1,neuromodulator#6] 11 | c3:[neuromodulator#6,affects#8,neural_circuits#9] 12 | c4:[neuromodulator#6,affects#8,behaviours#12] 13 | c5:[behaviours#12,in#13,vertebrates#14] 14 | c6:[behaviours#12,in#13,invertebrates#16] 15 | stmt2 = f1 f2 c3 c4 c5 c6 16 | 17 | # 12027387 in#0 the#1 present#2 study#3 ,#4 we#5 have#6 investigated#7 5-ht-induced#8 ca(2+)#9 transients#10 in#11 subcellular#12 compartments#13 of#14 retzius#15 neurons#16 in#17 the#18 leech#19 central#20 nervous#21 system#22 using#23 confocal#24 laser#25 scanning#26 microscopy#27 ,#28 and#29 studied#30 the#31 effect#32 of#33 5-ht#34 on#35 the#36 electrical#37 coupling#38 between#39 the#40 retzius#41 neurons#42 .#43 18 | 19 | f3:[NIL,have_investigated#6,5-ht-induced_ca(2+)_transients#8] 20 | f4:[NIL,studied#30,{5-ht#34:effect#32}] 21 | c7:[NIL,in#0,{NIL#-1:present_study#2}] 22 | c8:[5-ht-induced_ca(2+)_transients#8,in#11,{retzius_neurons#15:subcellular_compartments#12}] 23 | c9:[5-ht-induced_ca(2+)_transients#8,in#17,leech_central_nervous_system#19] 24 | c10:[leech_central_nervous_system#19,using#23,confocal_laser_scanning_microscopy#24] 25 | c11:[{5-ht#34:effect#32},on#35,electrical_coupling#37] 26 | c12:[electrical_coupling#37,between#39,retzius_neurons#41] 27 | stmt3 = f3 f4 c7 c8 c9 c10 c11 c12 28 | 29 | # 12027387 bath#0 application#1 of#2 5-ht#3 induced#4 a#5 ca(2+)#6 transient#7 in#8 axon#9 ,#10 dendrites#11 and#12 cell#13 body#14 of#15 the#16 retzius#17 neuron#18 .#19 30 | 31 | f5:[{5-ht#3:bath_application#0},induced#4,ca(2+)_transient#6] 32 | f6:[{5-ht#3:bath_application#0},induced#4,dendrites#11] 33 | f7:[{5-ht#3:bath_application#0},induced#4,{retzius_neuron#17:cell_body#13}] 34 | c13:[ca(2+)_transient#6,in#8,axon#9] 35 | stmt4 = f5 f6 f7 c13 36 | 37 | # 12027387 this#0 ca(2+)#1 transient#2 was#3 significantly#4 faster#5 and#6 larger#7 in#8 dendrites#9 than#10 in#11 axon#12 and#13 cell#14 body#15 ,#16 and#17 was#18 half-maximal#19 at#20 a#21 5-ht#22 concentration#23 of#24 5-12mm#25 .#26 38 | 39 | f8:[ca(2+)_transient#1,was_significantly_faster_and_larger_in#3,dendrites#9] 40 | f9:[ca(2+)_transient#1,was_half-maximal_at#18,{5-ht_concentration#22:5-12mm#25}] 41 | c14:[dendrites#9,than#10,axon#12] 42 | c15:[dendrites#9,than#10,cell_body#14] 43 | stmt5 = f8 f9 c14 c15 44 | 45 | # 12027387 the#0 ca(2+)#1 transient#2 was#3 suppressed#4 in#5 the#6 absence#7 of#8 extracellular#9 ca(2+)#10 and#11 by#12 methysergide#13 ,#14 a#15 non-specific#16 antagonist#17 of#18 metabotropic#19 5-ht#20 receptors#21 ,#22 and#23 was#24 strongly#25 reduced#26 by#27 bath#28 application#29 of#30 the#31 ca(2+)#32 channel#33 blocker#34 co(2+)#35 .#36 46 | 47 | f10:[ca(2+)_transient#1,was_suppressed_in#3,{extracellular_ca(2+)#9:absence#7}] 48 | f11:[ca(2+)_transient#1,was_strongly_reduced_by#24,{ca(2+)_channel_blocker_co(2+)#32:bath_application#28}] 49 | f12:[methysergide#13,NIL#-1,{metabotropic_5-ht_receptors#19:non-specific_antagonist#16}] 50 | c16:[ca(2+)_transient#1,by#12,methysergide#13] 51 | stmt6 = f10 f11 f12 c16 52 | 53 | # 12027387 injection#0 of#1 the#2 non-hydrolysable#3 gtp#4 analogue#5 gtpgammas#6 increased#7 and#8 prolonged#9 the#10 dendritic#11 5-ht-induced#12 ca(2+)#13 transient#14 .#15 54 | 55 | f13:[{non-hydrolysable_gtp_analogue_gtpgammas#3:injection#0},increased#7,dendritic_5-ht-induced_ca(2+)_transient#11] 56 | f14:[{non-hydrolysable_gtp_analogue_gtpgammas#3:injection#0},prolonged#9,dendritic_5-ht-induced_ca(2+)_transient#11] 57 | stmt7 = f13 f14 58 | 59 | # 12027387 the#0 non-selective#1 protein#2 kinase#3 inhibitor#4 h7#5 and#6 the#7 adenylate#8 cyclase#9 inhibitor#10 sq22536#11 did#12 not#13 affect#14 the#15 ca(2+)#16 transient#17 ,#18 and#19 the#20 membrane-permeable#21 camp#22 analogue#23 dibutyryl-camp#24 did#25 not#26 mimic#27 the#28 effect#29 of#30 5-ht#31 application#32 .#33 60 | 61 | f15:[non-selective_protein_kinase_inhibitor_h7#1,did_not_affect#12,ca(2+)_transient#16] 62 | f16:[adenylate_cyclase_inhibitor_sq22536#8,did_not_affect#12,ca(2+)_transient#16] 63 | f17:[membrane-permeable_camp_analogue_dibutyryl-camp#21,did_not_mimic#25,{5-ht_application#31:effect#29}] 64 | stmt8 = f15 f16 f17 65 | 66 | # 12027387 5-ht#0 reduced#1 the#2 apparent#3 electrical#4 coupling#5 between#6 the#7 two#8 retzius#9 neurons#10 ,#11 whereas#12 suppression#13 of#14 the#15 ca(2+)#16 influx#17 by#18 removal#19 of#20 external#21 ca(2+)#22 improved#23 the#24 transmission#25 of#26 action#27 potentials#28 at#29 the#30 electrical#31 synapses#32 which#33 are#34 located#35 between#36 the#37 dendrites#38 of#39 the#40 adjacent#41 retzius#42 neurons#43 .#44 67 | 68 | f18:[5-ht#0,reduced#1,apparent_electrical_coupling#3] 69 | f19:[{ca(2+)_influx#16:suppression#13},improved#23,{action_potentials#27:transmission#25}] 70 | c17:[apparent_electrical_coupling#3,between#6,retzius_neurons#9] 71 | c18:[{ca(2+)_influx#16:suppression#13},by#18,{external_ca(2+)#21:removal#19}] 72 | c19:[{action_potentials#27:transmission#25},at#29,electrical_synapses#31] 73 | c20:[electrical_synapses#31,are_located_between#34,{adjacent_retzius_neurons#41:dendrites#38}] 74 | stmt9 = f18 f19 c17 c18 c19 c20 75 | 76 | # 12027387 the#0 results#1 indicate#2 that#3 5-ht#4 induces#5 a#6 ca(2+)#7 influx#8 through#9 calcium#10 channels#11 located#12 primarily#13 in#14 the#15 dendrites#16 ,#17 and#18 presumably#19 activated#20 by#21 a#22 g#23 protein-coupled#24 5-ht#25 receptor#26 .#27 77 | 78 | f20:[{NIL#-1:results#1},indicate_that#2,NIL] 79 | f21:[5-ht#4,induces#5,ca(2+)_influx#7] 80 | c21:[ca(2+)_influx#7,through#9,calcium_channels#10] 81 | c22:[calcium_channels#10,located_primarily_in#12,dendrites#16] 82 | c23:[calcium_channels#10,presumably_activated_by#19,g_protein-coupled_5-ht_receptor#23] 83 | stmt10 = f20 f21 c21 c22 c23 84 | 85 | # 12027387 the#0 dendritic#1 ca(2+)#2 increase#3 appears#4 to#5 modulate#6 the#7 excitability#8 of#9 ,#10 and#11 the#12 synchronization#13 between#14 ,#15 the#16 two#17 retzius#18 neurons#19 .#20 86 | 87 | f22:[dendritic_ca(2+)_increase#1,appears_to_modulate#4,{NIL#-1:excitability#8}] 88 | f23:[dendritic_ca(2+)_increase#1,appears_to_modulate#4,synchronization#13] 89 | c24:[synchronization#13,between#14,{retzius_neurons#18:two#17}] 90 | stmt11 = f22 f23 c24 91 | 92 | -------------------------------------------------------------------------------- /data/label/train_sort/label-15663562.txt: -------------------------------------------------------------------------------- 1 | # 15663562 biological#0 effects#1 of#2 montelukast#3 ,#4 a#5 cysteinyl-leukotriene#6 receptor-antagonist#7 ,#8 on#9 t#10 lymphocytes#11 .#12 2 | 3 | f1:[{montelukast#3:biological_effects#0},NIL#-1,cysteinyl-leukotriene_receptor-antagonist#6] 4 | c1:[{montelukast#3:biological_effects#0},on#9,t_lymphocytes#10] 5 | stmt1 = f1 c1 6 | 7 | # 15663562 montelukast#0 ,#1 a#2 cysteinyl-leukotriene#3 receptor#4 antagonist#5 ,#6 has#7 anti-inflammatory#8 activity#9 in#10 the#11 treatment#12 of#13 allergic#14 diseases#15 .#16 8 | 9 | f2:[montelukast#0,NIL#-1,cysteinyl-leukotriene_receptor_antagonist#3] 10 | f3:[montelukast#0,has#7,anti-inflammatory_activity#8] 11 | c2:[anti-inflammatory_activity#8,in#10,{allergic_diseases#14:treatment#12}] 12 | stmt2 = f2 f3 c2 13 | 14 | # 15663562 if#0 this#1 effect#2 is#3 due#4 only#5 to#6 blocking#7 leukotrienes#8 or#9 also#10 owing#11 to#12 inhibiting#13 proliferation#14 and#15 survival#16 of#17 inflammatory#18 cells#19 ,#20 is#21 actuallyunknown#22 .#23 15 | 16 | f4:[{NIL#-1:effect#2},is_due_only_to#3,blocking_leukotrienes#7] 17 | f5:[{NIL#-1:effect#2},owing_to#11,{inflammatory_cells#18:inhibiting_proliferation#13}] 18 | f6:[{NIL#-1:effect#2},owing_to#11,{inflammatory_cells#18:survival#16}] 19 | f7:[NIL,is_actuallyunknown#21,NIL] 20 | stmt3 = f4 f5 f6 f7 21 | 22 | # 15663562 testing#0 the#1 hypothesis#2 that#3 mnt#4 could#5 influence#6 t#7 lymphocyte#8 functional#9 behaviour#10 invitro#11 .#12 23 | 24 | f8:[NIL,testing_the_hypothesis_that#0,NIL] 25 | f9:[mnt#4,could_influence#5,t_lymphocyte_functional_behaviour_invitro#7] 26 | stmt4 = f8 f9 27 | 28 | # 15663562 normal#0 t#1 lymphocytes#2 were#3 analysed#4 for#5 surface#6 expression#7 of#8 cys-ltr(1)#9 and#10 cys-ltr(2)#11 by#12 means#13 of#14 monoclonal#15 antibodies#16 ,#17 in#18 the#19 resting#20 state#21 and#22 after#23 activation#24 with#25 t#26 helper#27 type#28 2#29 cytokine#30 or#31 t#32 cell#33 receptor#34 stimulation#35 .#36 29 | 30 | f10:[normal_t_lymphocytes#0,were_analysed_for#3,{cys-ltr(1)#9:surface_expression#6}] 31 | f11:[normal_t_lymphocytes#0,were_analysed_for#3,{cys-ltr(2)#11:surface_expression#6}] 32 | c3:[{cys-ltr(2)#11:surface_expression#6},by_means_of#12,monoclonal_antibodies#15] 33 | c4:[NIL,in#18,resting_state#20] 34 | c5:[NIL,after#23,activation#24] 35 | c6:[activation#24,with#25,t_helper_type_2_cytokine#26] 36 | c7:[activation#24,with#25,t_cell_receptor_stimulation#32] 37 | stmt5 = f10 f11 c3 c4 c5 c6 c7 38 | 39 | # 15663562 proliferative#0 activity#1 ,#2 as#3 well#4 as#5 il-4#6 andifn-gamma#7 production#8 ,#9 were#10 simultaneously#11 determined#12 in#13 samples#14 exposed#15 to#16 molar#17 concentrations#18 of#19 mnt#20 from#21 10(-8)#22 to#23 10(-5)#24 .#25 40 | 41 | f12:[proliferative_activity#0,were_simultaneously_determined_in#10,{NIL#-1:samples#14}] 42 | f13:[il-4_andifn-gamma_production#6,were_simultaneously_determined_in#10,samples#14] 43 | c8:[{NIL#-1:samples#14},exposed_to#15,{mnt_from_10(-8)_to_10(-5)#20:molar_concentrations#17}] 44 | stmt6 = f12 f13 c8 45 | 46 | # 15663562 programmed#0 cell#1 death#2 in#3 cultured#4 samples#5 was#6 evaluated#7 by#8 means#9 of#10 propidium#11 iodide#12 and#13 fluorescein#14 isothiocyanate-conjugated#15 anti-annexin#16 v#17 mab#18 staining#19 .#20 47 | 48 | f14:[programmed_cell_death#0,was_evaluated_by_means_of#6,propidium_iodide#11] 49 | f15:[programmed_cell_death#0,was_evaluated_by_means_of#6,fluorescein_isothiocyanate-conjugated_anti-annexin_v_mab_staining#14] 50 | c9:[programmed_cell_death#0,in#3,cultured_samples#4] 51 | stmt7 = f14 f15 c9 52 | 53 | # 15663562 the#0 complementary#1 dna#2 microarray#3 technique#4 was#5 adopted#6 to#7 identify#8 gene#9 products#10 involved#11 in#12 apoptosisinduction#13 .#14 54 | 55 | f16:[complementary_dna_microarray_technique#1,was_adopted_to_identify#5,gene_products#9] 56 | c10:[gene_products#9,involved_in#11,apoptosisinduction#13] 57 | stmt8 = f16 c10 58 | 59 | # 15663562 resting#0 t#1 cells#2 expressed#3 low#4 levels#5 of#6 cys-ltr#7 .#8 60 | 61 | f17:[NIL,resting#0,t_cells#1] 62 | c11:[t_cells#1,expressed#3,{cys-ltr#7:low_levels#4}] 63 | stmt9 = f17 c11 64 | 65 | # 15663562 upon#0 anti-cd3#1 mab#2 activation#3 ,#4 a#5 progressive#6 increase#7 in#8 cys-ltr(1)#9 and#10 -ltr(2)#11 expression#12 was#13 observed#14 .#15 66 | 67 | f18:[{cys-ltr(1)_and_-ltr(2)_expression#9:progressive_increase#6},was_observed#13,NIL] 68 | c12:[NIL,upon#0,anti-cd3_mab_activation#1] 69 | stmt10 = f18 c12 70 | 71 | # 15663562 exposure#0 to#1 mnt#2 reduced#3 proliferative#4 response#5 to#6 tcr#7 engagement#8 ,#9 increased#10 ifn-gamma#11 production#12 and#13 led#14 to#15 apoptosis#16 at#17 minimal#18 concentrations#19 of#20 10(-6)#21 m#22 .#23 72 | 73 | f19:[{NIL#-1:exposure#0},reduced#3,{tcr_engagement#7:proliferative_response#4}] 74 | f20:[{NIL#-1:exposure#0},increased#10,ifn-gamma_production#11] 75 | f21:[{NIL#-1:exposure#0},led_to#14,apoptosis#16] 76 | c13:[{NIL#-1:exposure#0},to#1,mnt#2] 77 | c14:[apoptosis#16,at#17,{10(-6)_m#21:minimal_concentrations#18}] 78 | stmt11 = f19 f20 f21 c13 c14 79 | 80 | # 15663562 a#0 progressive#1 loss#2 in#3 bad#4 and#5 b#6 cell#7 lymphoma/leukaemia-2#8 activities#9 ,#10 and#11 an#12 increase#13 in#14 the#15 expression#16 of#17 cd27#18 ,#19 traf3#20 ,#21 trail#22 ,#23 p53#24 and#25 fas#26 genes#27 were#28 alsoobserved#29 .#30 81 | 82 | f22:[{bad_and_b_cell_lymphoma/leukaemia-2_activities#4:progressive_loss#1},were_alsoobserved#28,NIL] 83 | f23:[{NIL#-1:increase#13},were_alsoobserved#28,NIL] 84 | c15:[{NIL#-1:increase#13},in#14,{cd27#18:expression#16}] 85 | c16:[{NIL#-1:increase#13},in#14,{traf3#20:expression#16}] 86 | c17:[{NIL#-1:increase#13},in#14,{trail#22:expression#16}] 87 | c18:[{NIL#-1:increase#13},in#14,{p53#24:expression#16}] 88 | c19:[{NIL#-1:increase#13},in#14,{fas_genes#26:expression#16}] 89 | stmt12 = f22 f23 c15 c16 c17 c18 c19 90 | 91 | # 15663562 biological#0 effects#1 of#2 mnt#3 delineate#4 a#5 complex#6 picture#7 of#8 gene#9 activation#10 and#11 repression#12 ,#13 probably#14 induced#15 by#16 cys-ltr#17 blockade#18 .#19 92 | 93 | f24:[{mnt#3:biological_effects#0},delineate#4,{gene_activation#9:complex_picture#6}] 94 | c20:[{mnt#3:biological_effects#0},delineate#4,{repression#12:complex_picture#6}] 95 | c21:[NIL,probably_induced_by#14,cys-ltr_blockade#17] 96 | stmt13 = f24 c20 c21 97 | 98 | # 15663562 the#0 induction#1 of#2 apoptosis#3 in#4 allergen-specific#5 t#6 cell#7 population#8 ,#9 as#10 a#11 final#12 result#13 ,#14 appears#15 fundamental#16 in#17 the#18 treatment#19 of#20 asthma#21 .#22 99 | 100 | f25:[{apoptosis#3:induction#1},appears_fundamental_in#15,{asthma#21:treatment#19}] 101 | c22:[{apoptosis#3:induction#1},in#4,allergen-specific_t_cell_population#5] 102 | stmt14 = f25 c22 103 | 104 | -------------------------------------------------------------------------------- /data/label/train_sort/label-26119656.txt: -------------------------------------------------------------------------------- 1 | # 26119656 The#0 neutrophil#1 function#2 and#3 lymphocyte#4 profile#5 of#6 milk#7 from#8 bovine#9 mammary#10 glands#11 infected#12 with#13 streptococcus#14 dysgalactiae#15 .#16 2 | 3 | c1:[{milk#7:neutrophil_function#1},from#8,bovine_mammary_glands#9] 4 | c2:[{milk#7:lymphocyte_profile#4},from#8,bovine_mammary_glands#9] 5 | c3:[bovine_mammary_glands#9,infected_with#12,streptococcus_dysgalactiae#14] 6 | stmt1 = c1 c2 c3 7 | 8 | # 26119656 Streptococcus#0 dysgalactiae#1 is#2 a#3 bacterium#4 that#5 accounts#6 for#7 a#8 notable#9 proportion#10 of#11 both#12 clinical#13 and#14 subclinical#15 intramammary#16 infections#17 .#18 9 | 10 | f1:[streptococcus_dysgalactiae#0,is#2,bacterium#4] 11 | c4:[bacterium#4,accounts_for#6,{clinical#13:notable_proportion#9}] 12 | c5:[bacterium#4,accounts_for#6,{subclinical_intramammary_infections#15:notable_proportion#9}] 13 | stmt2 = f1 c4 c5 14 | 15 | # 26119656 Thus#0 ,#1 the#2 present#3 study#4 explores#5 the#6 function#7 of#8 milk#9 neutrophils#10 and#11 the#12 lymphocyte#13 profile#14 in#15 mammary#16 glands#17 naturally#18 infected#19 with#20 Streptococcus#21 dysgalactiae#22 .#23 16 | 17 | f2:[{NIL#-1:present_study#3},explores#5,{milk_neutrophils#9:function#7}] 18 | f3:[{NIL#-1:present_study#3},explores#5,{lymphocyte_profile#13:function#7}] 19 | c6:[{milk_neutrophils#9:function#7},in#15,mammary_glands#16] 20 | c7:[{lymphocyte_profile#13:function#7},in#15,mammary_glands#16] 21 | c8:[mammary_glands#16,naturally_infected_with#18,streptococcus_dysgalactiae#21] 22 | stmt3 = f2 f3 c6 c7 c8 23 | 24 | # 26119656 Here#0 ,#1 we#2 used#3 32#4 culture-negative#5 control#6 quarters#7 from#8 eight#9 clinically#10 healthy#11 dairy#12 cows#13 with#14 low#15 somatic#16 cell#17 counts#18 and#19 13#20 S.#21 dysgalactiae-infected#22 quarters#23 from#24 six#25 dairy#26 cows#27 .#28 25 | 26 | f4:[NIL,used#3,culture-negative_control_quarters#5] 27 | f5:[NIL,used#3,s._dysgalactiae-infected_quarters#21] 28 | c9:[culture-negative_control_quarters#5,from#8,{clinically_healthy_dairy_cows#10:eight#9}] 29 | c10:[{clinically_healthy_dairy_cows#10:eight#9},with#14,low_somatic_cell_counts#15] 30 | c11:[s._dysgalactiae-infected_quarters#21,from#24,dairy_cows#26] 31 | stmt4 = f4 f5 c9 c10 c11 32 | 33 | # 26119656 Using#0 flow#1 cytometry#2 ,#3 we#4 evaluated#5 the#6 percentage#7 of#8 milk#9 monocytes/macrophages#10 and#11 neutrophils#12 ,#13 expression#14 of#15 CD62L#16 ,#17 CD11b#18 and#19 CD44#20 by#21 milk#22 neutrophils#23 ,#24 the#25 levels#26 of#27 intracellular#28 reactive#29 oxygen#30 species#31 production#32 and#33 phagocytosis#34 of#35 Staphylococcus#36 aureus#37 by#38 milk#39 neutrophils#40 ,#41 and#42 neutrophil#43 viability#44 .#45 34 | 35 | f6:[NIL,evaluated#5,{milk_monocytes/macrophages#9:percentage#7}] 36 | f7:[NIL,evaluated#5,{neutrophils#12:percentage#7}] 37 | f8:[NIL,evaluated#5,{cd62l#16:expression#14}] 38 | f9:[NIL,evaluated#5,{cd11b#18:expression#14}] 39 | f10:[NIL,evaluated#5,{cd44#20:expression#14}] 40 | f11:[NIL,evaluated#5,{intracellular_reactive_oxygen_species_production#28:levels#26}] 41 | f12:[NIL,evaluated#5,{staphylococcus_aureus#36:phagocytosis#34}] 42 | f13:[NIL,evaluated#5,neutrophil_viability#43] 43 | c12:[NIL,using#0,flow_cytometry#1] 44 | c13:[{cd62l#16:expression#14},by#21,milk_neutrophils#22] 45 | c14:[{cd11b#18:expression#14},by#21,milk_neutrophils#22] 46 | c15:[{cd44#20:expression#14},by#21,milk_neutrophils#22] 47 | c16:[{staphylococcus_aureus#36:phagocytosis#34},by#38,milk_neutrophils#39] 48 | stmt5 = f6 f7 f8 f9 f10 f11 f12 f13 c12 c13 c14 c15 c16 49 | 50 | # 26119656 Furthermore#0 ,#1 the#2 percentages#3 of#4 B#5 cell#6 and#7 T#8 lymphocyte#9 subsets#10 ,#11 and#12 the#13 expression#14 of#15 CD25#16 by#17 T#18 milk#19 lymphocytes#20 and#21 T#22 CD4+#23 milk#24 cells#25 were#26 also#27 assessed#28 by#29 flow#30 cytometry#31 using#32 monoclonal#33 antibodies#34 .#35 51 | 52 | f14:[{b_cell#5:percentages#3},were_also_assessed_by#26,flow_cytometry#30] 53 | f15:[{t_lymphocyte_subsets#8:percentages#3},were_also_assessed_by#26,flow_cytometry#30] 54 | f16:[{cd25#16:expression#14},were_also_assessed_by#26,flow_cytometry#30] 55 | f17:[{t_cd4+_milk_cells#22:expression#14},were_also_assessed_by#26,flow_cytometry#30] 56 | c17:[{cd25#16:expression#14},by#17,t_milk_lymphocytes#18] 57 | c18:[flow_cytometry#30,using#32,monoclonal_antibodies#33] 58 | stmt6 = f14 f15 f16 f17 c17 c18 59 | 60 | # 26119656 The#0 present#1 study#2 showed#3 a#4 higher#5 SCC#6 and#7 percentage#8 of#9 milk#10 neutrophils#11 ,#12 and#13 a#14 decrease#15 in#16 the#17 percentage#18 of#19 milk#20 monocytes/macrophages#21 from#22 S.#23 dysgalactiae-infected#24 quarters#25 when#26 compared#27 to#28 uninfected#29 ones#30 .#31 61 | 62 | f18:[NIL,showed#3,{milk_neutrophils#10:higher_scc#5}] 63 | f19:[NIL,showed#3,{milk_neutrophils#10:percentage#8}] 64 | f20:[NIL,showed#3,{NIL#-1:decrease#15}] 65 | c19:[{NIL#-1:decrease#15},in#16,{milk_monocytes/macrophages#20:percentage#18}] 66 | c20:[{milk_monocytes/macrophages#20:percentage#18},from#22,s._dysgalactiae-infected_quarters#23] 67 | c21:[NIL,compared_to#27,{NIL#-1:uninfected_ones#29}] 68 | stmt7 = f18 f19 f20 c19 c20 c21 69 | 70 | # 26119656 We#0 also#1 observed#2 a#3 higher#4 expression#5 of#6 CD11b#7 by#8 milk#9 neutrophils#10 and#11 a#12 tendency#13 toward#14 a#15 decrease#16 in#17 neutrophil#18 apoptosis#19 rate#20 in#21 S.#22 dysgalactiae-infected#23 quarters#24 .#25 71 | 72 | f21:[NIL,observed#2,{cd11b#7:higher_expression#4}] 73 | f22:[NIL,observed#2,{NIL#-1:tendency#13}] 74 | c22:[{cd11b#7:higher_expression#4},by#8,milk_neutrophils#9] 75 | c23:[{NIL#-1:tendency#13},toward#14,{neutrophil_apoptosis_rate#18:decrease#16}] 76 | c24:[{neutrophil_apoptosis_rate#18:decrease#16},in#21,s._dysgalactiae-infected_quarters#22] 77 | stmt8 = f21 f22 c22 c23 c24 78 | 79 | # 26119656 In#0 addition#1 ,#2 the#3 S.#4 dysgalactiae-infected#5 quarters#6 had#7 higher#8 percentages#9 of#10 milk#11 T#12 cells#13 and#14 their#15 subset#16 CD3+CD8+CD4-#17 cells#18 .#19 80 | 81 | f23:[s._dysgalactiae-infected_quarters#4,had#7,{milk_t_cells#11:higher_percentages#8}] 82 | f24:[s._dysgalactiae-infected_quarters#4,had#7,{cd3+cd8+cd4-_cells#17:higher_percentages#8}] 83 | stmt9 = f23 f24 84 | 85 | # 26119656 Overall#0 ,#1 the#2 present#3 study#4 provided#5 new#6 insights#7 into#8 S.#9 dysgalactiae#10 IMIs#11 ,#12 including#13 distinct#14 lymphocyte#15 profiles#16 ,#17 and#18 a#19 tendency#20 toward#21 an#22 inhibition#23 of#24 apoptosis#25 in#26 milk#27 neutrophils#28 .#29 86 | 87 | f25:[{NIL#-1:present_study#3},provided#5,{s._dysgalactiae_imis#9:new_insights#6}] 88 | f26:[{NIL#-1:present_study#3},provided#5,{NIL#-1:tendency#20}] 89 | c25:[{s._dysgalactiae_imis#9:new_insights#6},including#13,distinct_lymphocyte_profiles#14] 90 | c26:[{NIL#-1:tendency#20},toward#21,{apoptosis#25:inhibition#23}] 91 | c27:[{apoptosis#25:inhibition#23},in#26,milk_neutrophils#27] 92 | stmt10 = f25 f26 c25 c26 c27 93 | -------------------------------------------------------------------------------- /data/label/train_sort/label-11922564.txt: -------------------------------------------------------------------------------- 1 | # 11922564 synergistic#0 inhibitory#1 effect#2 of#3 cyclosporin#4 a#5 and#6 vitamin#7 d#8 derivatives#9 on#10 t-lymphocyte#11 proliferation#12 in#13 active#14 ulcerative#15 colitis#16 .#17 2 | 3 | c1:[{cyclosporin_a#4:synergistic_inhibitory_effect#0},on#10,t-lymphocyte_proliferation#11] 4 | c2:[{vitamin_d_derivatives#7:synergistic_inhibitory_effect#0},on#10,t-lymphocyte_proliferation#11] 5 | c3:[t-lymphocyte_proliferation#11,in#13,active_ulcerative_colitis#14] 6 | stmt1 = c1 c2 c3 7 | 8 | # 11922564 1@25-dihydroxyvitamin#0 d3#1 [#2 1@25(oh)2d3#3 ]#4 ,#5 the#6 hormonal#7 active#8 form#9 of#10 vitamin#11 d3#12 ,#13 could#14 represent#15 a#16 potentially#17 therapeutic#18 agent#19 in#20 autoimmune#21 diseases#22 .#23 9 | 10 | f1:[1@25-dihydroxyvitamin_d3_[_1@25(oh)2d3_]#0,NIL#-1,{vitamin_d3#11:hormonal_active_form#7}] 11 | f2:[1@25-dihydroxyvitamin_d3_[_1@25(oh)2d3_]#0,could_represent#14,therapeutic_agent#18] 12 | c4:[therapeutic_agent#18,in#20,autoimmune_diseases#21] 13 | stmt2 = f1 f2 c4 14 | 15 | # 11922564 cyclosporin#0 a#1 shows#2 immunoregulatory#3 properties#4 ,#5 which#6 ,#7 in#8 many#9 respects#10 ,#11 seem#12 to#13 be#14 similar#15 to#16 those#17 of#18 1@25(oh)2d3#19 .#20 16 | 17 | f3:[cyclosporin_a#0,shows#2,immunoregulatory_properties#3] 18 | c5:[immunoregulatory_properties#3,seem_to_be_similar_to#12,1@25(oh)2d3#19] 19 | stmt3 = f3 c5 20 | 21 | # 11922564 our#0 aim#1 was#2 to#3 investigate#4 the#5 possible#6 synergistic#7 effect#8 exerted#9 by#10 csa#11 in#12 combination#13 with#14 1@25(oh)2d3#15 or#16 its#17 nonhypercalcemic#18 analogues#19 ,#20 eb#21 1089#22 and#23 kh#24 1060#25 ,#26 on#27 the#28 proliferative#29 response#30 of#31 t#32 lymphocytes#33 obtained#34 from#35 active#36 ulcerative#37 colitispatients#38 .#39 22 | 23 | f4:[{NIL#-1:aim#1},was_to_investigate#2,possible_synergistic_effect#6] 24 | c6:[possible_synergistic_effect#6,exerted_by#9,csa#11] 25 | c7:[csa#11,in_combination_with#12,{1@25(oh)2d3#15:nonhypercalcemic_analogues#18}] 26 | c8:[csa#11,in_combination_with#12,eb_1089#21] 27 | c9:[csa#11,in_combination_with#12,kh_1060#24] 28 | c10:[NIL,on#27,{t_lymphocytes#32:proliferative_response#29}] 29 | c11:[{t_lymphocytes#32:proliferative_response#29},obtained_from#34,active_ulcerative_colitispatients#36] 30 | stmt4 = f4 c6 c7 c8 c9 c10 c11 31 | 32 | # 11922564 the#0 t#1 lymphocyte-enriched#2 population#3 was#4 treated#5 with#6 phytohemagglutinin#7 and#8 csa#9 alone#10 or#11 in#12 association#13 with#14 1@25(oh)2d3#15 or#16 eb#17 1089#18 or#19 kh#20 1060#21 .#22 33 | 34 | f5:[t_lymphocyte-enriched_population#1,was_treated_with#4,phytohemagglutinin#7] 35 | f6:[t_lymphocyte-enriched_population#1,was_treated_with#4,csa#9] 36 | c12:[csa#9,alone_or_in_association_with#10,1@25(oh)2d3#15] 37 | c13:[csa#9,alone_or_in_association_with#10,eb_1089#17] 38 | c14:[csa#9,alone_or_in_association_with#10,kh_1060#20] 39 | stmt5 = f5 f6 c12 c13 c14 40 | 41 | # 11922564 cell#0 proliferation#1 was#2 determined#3 by#4 [3h]thymidine#5 incorporation#6 and#7 analyzed#8 on#9 day#10 5#11 ofculture#12 .#13 42 | 43 | f7:[cell_proliferation#0,was_determined_by#2,[3h]thymidine_incorporation#5] 44 | f8:[cell_proliferation#0,analyzed_on#8,day_5_ofculture#10] 45 | stmt6 = f7 f8 46 | 47 | # 11922564 after#0 incubation#1 with#2 csa#3 ,#4 t#5 lymphocyte#6 proliferation#7 was#8 significantly#9 inhibited#10 in#11 comparison#12 with#13 the#14 vehicle-treated#15 cultures#16 .#17 48 | 49 | f9:[t_lymphocyte_proliferation#5,was_significantly_inhibited#8,NIL] 50 | c15:[NIL,after_incubation_with#0,csa#3] 51 | c16:[t_lymphocyte_proliferation#5,in_comparison_with#11,vehicle-treated_cultures#15] 52 | stmt7 = f9 c15 c16 53 | 54 | # 11922564 however#0 ,#1 t#2 lymphocytes#3 from#4 ulcerative#5 colitis#6 patients#7 were#8 significantly#9 more#10 sensitive#11 to#12 csa#13 than#14 those#15 from#16 healthy#17 controls#18 .#19 55 | 56 | f10:[t_lymphocytes#2,were_significantly_more_sensitive_to#8,csa#13] 57 | c17:[t_lymphocytes#2,from#4,ulcerative_colitis_patients#5] 58 | c18:[csa#13,than_those_from#14,healthy_controls#17] 59 | stmt8 = f10 c17 c18 60 | 61 | # 11922564 the#0 inhibition#1 in#2 t#3 lymphocyte#4 proliferation#5 ,#6 after#7 treatment#8 of#9 the#10 cultures#11 with#12 csa#13 associated#14 with#15 either#16 1@25(oh)2d3#17 or#18 eb#19 1089#20 or#21 kh#22 1060#23 ,#24 was#25 synergistic#26 at#27 well-definedconcentrations#28 .#29 62 | 63 | f11:[{t_lymphocyte_proliferation#3:inhibition#1},was_synergistic_at#25,well-definedconcentrations#28] 64 | c19:[NIL,after#7,{cultures#11:treatment#8}] 65 | c20:[{cultures#11:treatment#8},with#12,csa#13] 66 | c21:[csa#13,associated_with#14,1@25(oh)2d3#17] 67 | c22:[csa#13,associated_with#14,eb_1089#19] 68 | c23:[csa#13,associated_with#14,kh_1060#22] 69 | stmt9 = f11 c19 c20 c21 c22 c23 70 | 71 | # 11922564 taking#0 into#1 account#2 the#3 lowest#4 csa#5 dose#6 ,#7 the#8 highest#9 synergistic#10 inhibition#11 in#12 the#13 proliferation#14 of#15 t#16 lymphocytes#17 prepared#18 from#19 ulcerative#20 colitis#21 patients#22 was#23 found#24 combining#25 csa#26 and#27 10#28 nm#29 of#30 1@25(oh)2d3#31 or#32 10#33 nm#34 of#35 eb#36 1089#37 or#38 kh#39 1060#40 at#41 the#42 three#43 concentrations#44 .#45 72 | 73 | f12:[highest_synergistic_inhibition#9,was_found_combining#23,csa#26] 74 | f13:[highest_synergistic_inhibition#9,was_found_combining#23,{1@25(oh)2d3#31:10_nm#28}] 75 | f14:[highest_synergistic_inhibition#9,was_found_combining#23,{eb_1089#36:10_nm#33}] 76 | f15:[highest_synergistic_inhibition#9,was_found_combining#23,{kh_1060#39:10_nm#33}] 77 | c24:[NIL,taking_into_account#0,lowest_csa_dose#4] 78 | c25:[highest_synergistic_inhibition#9,in#12,{t_lymphocytes#16:proliferation#14}] 79 | c26:[{t_lymphocytes#16:proliferation#14},prepared_from#18,ulcerative_colitis_patients#20] 80 | c27:[csa#26,at#41,{concentrations#44:three#43}] 81 | c28:[{1@25(oh)2d3#31:10_nm#28},at#41,{concentrations#44:three#43}] 82 | c29:[{eb_1089#36:10_nm#33},at#41,{concentrations#44:three#43}] 83 | c30:[{kh_1060#39:10_nm#33},at#41,{concentrations#44:three#43}] 84 | stmt10 = f12 f13 f14 f15 c24 c25 c26 c27 c28 c29 c30 85 | 86 | # 11922564 the#0 results#1 obtained#2 ,#3 associating#4 the#5 lowest#6 csa#7 dose#8 and#9 the#10 lowest#11 kh#12 1060#13 concentration#14 ,#15 may#16 suggest#17 an#18 alternative#19 therapeutic#20 approach#21 in#22 these#23 patients#24 ,#25 reducing#26 the#27 dose#28 ,#29 and#30 consequently#31 the#32 toxicity#33 ,#34 of#35 csa#36 .#37 87 | 88 | f16:[{NIL#-1:results#1},may_suggest#16,alternative_therapeutic_approach#19] 89 | f17:[{NIL#-1:results#1},reducing#26,{csa#36:dose#28}] 90 | f18:[{NIL#-1:results#1},reducing#26,{csa#36:toxicity#33}] 91 | c31:[{NIL#-1:results#1},obtained#2,NIL] 92 | c32:[{NIL#-1:results#1},associating#4,lowest_csa_dose#6] 93 | c33:[{NIL#-1:results#1},associating#4,lowest_kh_1060_concentration#11] 94 | c34:[alternative_therapeutic_approach#19,in#22,patients#24] 95 | stmt11 = f16 f17 f18 c31 c32 c33 c34 96 | 97 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-26096460.txt: -------------------------------------------------------------------------------- 1 | # n1:[trpv5,as,calcium_channels_trpv5] 2 | # n2:[trpv6,as,trpv6_channels] 3 | # n3:[trpv5/v6,as,calcium_channels_trpv5/v6] 4 | # n4:[trpv5/v6,as,trpv5/v6_channels] 5 | # n5:[jurkat_t_cells,as,human_leukemia_jurkat_t_cells] 6 | # n6:[jurkat_t_cells,as,jurkat_cells] 7 | 8 | # h1:[different_cell_types,contain,lymphocytes] 9 | # h2:[lymphocytes,contain,t_lymphocyte] 10 | # h3:[external_stimuli,contain,low-ph_stressor] 11 | # h4:[external_stimuli,contain,high-ph_stressor] 12 | # h5:[extracellular_ph,contain,extracellular_acidic_ph] 13 | # h6:[trpv5/v6,contain,trpv5] 14 | # h7:[trpv5/v6,contain,trpv6] 15 | # h8:[early_endocytosis_marker,contain,eea1] 16 | 17 | # 26096460 trpv5/v6#0 channels#1 mediate#2 ca(2+)#3 influx#4 in#5 jurkat#6 t#7 cells#8 under#9 the#10 control#11 of#12 extracellular#13 ph#14 .#15 18 | 19 | f1:[trpv5/v6_channels#0,mediate#2,ca(2+)_influx#3] 20 | c1:[ca(2+)_influx#3,in#5,jurkat_t_cells#6] 21 | c2:[jurkat_t_cells#6,under#9,{extracellular_ph#13:control#11}] 22 | stmt1 = f1 c1 c2 23 | 24 | # 26096460 regulation#0 of#1 cytoplasmic#2 free#3 calcium#4 concentration#5 [#6 ca(2+)#7 ]i#8 is#9 a#10 key#11 factor#12 for#13 the#14 maintenance#15 of#16 cellular#17 homeostasis#18 in#19 different#20 cell#21 types#22 ,#23 including#24 lymphocytes#25 .#26 25 | 26 | f2:[{cytoplasmic_free_calcium_concentration#2:regulation#0},is_a_key_factor_for#9,{cellular_homeostasis#17:maintenance#15}] 27 | c3:[{cellular_homeostasis#17:maintenance#15},in#19,lymphocytes#25] 28 | stmt2 = f2 c3 29 | 30 | # 26096460 during#0 t#1 lymphocyte#2 activation#3 as#4 well#5 as#6 production#7 of#8 cytokines#9 ,#10 sustained#11 ca(2+)#12 influx#13 is#14 essential#15 ,#16 however#17 it#18 remains#19 unclear#20 how#21 this#22 influx#23 is#24 regulated#25 .#26 31 | 32 | f3:[sustained_ca(2+)_influx#11,is_essential#14,NIL] 33 | c4:[NIL,during#0,t_lymphocyte_activation#1] 34 | c5:[NIL,during#0,{cytokines#9:production#7}] 35 | stmt3 = f3 c4 c5 36 | 37 | # 26096460 previously#0 ,#1 we#2 reported#3 the#4 expression#5 and#6 functional#7 activity#8 of#9 calcium#10 channels#11 trpv5#12 and#13 trpv6#14 in#15 human#16 leukemia#17 jurkat#18 t#19 cells#20 .#21 38 | 39 | f4:[NIL,reported#3,{calcium_channels_trpv5#10:expression#5}] 40 | f5:[NIL,reported#3,{calcium_channels_trpv5#10:functional_activity#7}] 41 | f6:[NIL,reported#3,{trpv6#14:expression#5}] 42 | f7:[NIL,reported#3,{trpv6#14:functional_activity#7}] 43 | c6:[calcium_channels_trpv5#10,in#15,human_leukemia_jurkat_t_cells#16] 44 | c7:[trpv6#14,in#15,human_leukemia_jurkat_t_cells#16] 45 | stmt4 = f4 f5 f6 f7 c6 c7 46 | 47 | # 26096460 in#0 this#1 study#2 ,#3 using#4 single#5 channel#6 recordings#7 ,#8 we#9 found#10 that#11 activity#12 of#13 calcium#14 channels#15 trpv5/v6#16 in#17 jurkat#18 t#19 cells#20 is#21 subject#22 to#23 strong#24 control#25 of#26 external#27 stimuli#28 such#29 as#30 a#31 low-#32 or#33 high-ph#34 stressor#35 .#36 48 | 49 | f8:[NIL,found_that#10,NIL] 50 | f9:[{calcium_channels_trpv5/v6#14:activity#12},is_subject_to#21,{external_stimuli#27:strong_control#24}] 51 | f10:[{calcium_channels_trpv5/v6#14:activity#12},is_subject_to#21,{low-_or_high-ph_stressor#32:strong_control#24}] 52 | c8:[NIL,in#0,{NIL#-1:study#2}] 53 | c9:[NIL,using#4,single_channel_recordings#5] 54 | c10:[{calcium_channels_trpv5/v6#14:activity#12},in#17,jurkat_t_cells#18] 55 | stmt5 = f8 f9 f10 c8 c9 c10 56 | 57 | # 26096460 we#0 showed#1 that#2 extracellular#3 acidic#4 ph#5 reduces#6 the#7 activity#8 of#9 trpv5/v6#10 channels#11 ,#12 whereas#13 alkaline#14 ph#15 increases#16 the#17 activity#18 of#19 trpv5/v6#20 channels#21 in#22 jurkat#23 t#24 cells#25 .#26 58 | 59 | f11:[NIL,showed_that#1,NIL] 60 | f12:[extracellular_acidic_ph#3,reduces#6,{trpv5/v6_channels#10:activity#8}] 61 | f13:[alkaline_ph#14,increases#16,{trpv5/v6_channels#20:activity#18}] 62 | c11:[{trpv5/v6_channels#20:activity#18},in#22,jurkat_t_cells#23] 63 | stmt6 = f11 f12 f13 c11 64 | 65 | # 26096460 using#0 calcium#1 imaging#2 ,#3 we#4 found#5 that#6 ca(2+)#7 influx#8 in#9 jurkat#10 t#11 cells#12 displayed#13 sensitivity#14 to#15 extracellular#16 ph#17 ,#18 similar#19 to#20 that#21 shown#22 for#23 the#24 calcium#25 channels#26 trpv5/v6#27 .#28 66 | 67 | f14:[NIL,found_that#5,NIL] 68 | f15:[ca(2+)_influx#7,displayed_sensitivity_to#13,extracellular_ph#16] 69 | c12:[NIL,using#0,calcium_imaging#1] 70 | c13:[ca(2+)_influx#7,in#9,jurkat_t_cells#10] 71 | c14:[NIL,similar_to_that_shown_for#19,calcium_channels_trpv5/v6#25] 72 | stmt7 = f14 f15 c12 c13 c14 73 | 74 | # 26096460 double#0 immunostaining#1 of#2 jurkat#3 cells#4 revealed#5 that#6 trpv5#7 and#8 trpv6#9 channels#10 colocalize#11 with#12 clathrin#13 and#14 the#15 early#16 endocytosis#17 marker#18 ,#19 eea1#20 .#21 75 | 76 | f16:[trpv5#7,colocalize_with#11,clathrin#13] 77 | f17:[trpv5#7,colocalize_with#11,early_endocytosis_marker#16] 78 | f18:[trpv5#7,colocalize_with#11,eea1#20] 79 | f19:[trpv6_channels#9,colocalize_with#11,clathrin#13] 80 | f20:[trpv6_channels#9,colocalize_with#11,early_endocytosis_marker#16] 81 | f21:[trpv6_channels#9,colocalize_with#11,eea1#20] 82 | c15:[{jurkat_cells#3:double_immunostaining#0},revealed_that#5,NIL#-1] 83 | stmt8 = f16 f17 f18 f19 f20 f21 c15 84 | 85 | # 26096460 moreover#0 ,#1 we#2 demonstrated#3 that#4 a#5 specific#6 inhibitor#7 of#8 clathrin-dependent#9 endocytosis#10 ,#11 dynasore#12 ,#13 blocked#14 trpv5/v6#15 activity#16 and#17 ca(2+)#18 influx#19 into#20 jurkat#21 cells#22 .#23 86 | 87 | f22:[NIL,demonstrated_that#3,NIL] 88 | f23:[{clathrin-dependent_endocytosis#9:specific_inhibitor#6},blocked#14,{trpv5/v6#15:activity#16}] 89 | f24:[{clathrin-dependent_endocytosis#9:specific_inhibitor#6},blocked#14,ca(2+)_influx#18] 90 | f25:[dynasore#12,blocked#14,{trpv5/v6#15:activity#16}] 91 | f26:[dynasore#12,blocked#14,ca(2+)_influx#18] 92 | c16:[{trpv5/v6#15:activity#16},into#20,jurkat_cells#21] 93 | c17:[ca(2+)_influx#18,into#20,jurkat_cells#21] 94 | stmt9 = f22 f23 f24 f25 f26 c16 c17 95 | 96 | # 26096460 overall#0 ,#1 our#2 findings#3 indicate#4 that#5 strong#6 environmental#7 cues#8 may#9 affect#10 the#11 intracellular#12 calcium#13 level#14 in#15 jurkat#16 cells#17 by#18 influencing#19 the#20 traffic#21 of#22 trpv5/v6#23 channels#24 in#25 lymphocytes#26 .#27 97 | 98 | f27:[{NIL#-1:findings#3},indicate_that#4,NIL] 99 | f28:[strong_environmental_cues#6,may_affect#9,intracellular_calcium_level#12] 100 | c18:[intracellular_calcium_level#12,in#15,jurkat_cells#16] 101 | c19:[NIL,by_influencing#18,{trpv5/v6_channels#23:traffic#21}] 102 | c20:[{trpv5/v6_channels#23:traffic#21},in#25,lymphocytes#26] 103 | stmt10 = f27 f28 c18 c19 c20 104 | 105 | #26096460 this#0 article#1 is#2 protected#3 by#4 copyright#5 .#6 106 | 107 | f29:[article#1,is_protected_by#2,copyright#5] 108 | stmt11 = f29 109 | 110 | #26096460 all#0 rights#1 reserved#2 .#3 111 | 112 | c21:[{NIL#-1:rights#1},reserved#2,NIL] 113 | stmt12 = c21 114 | -------------------------------------------------------------------------------- /data/label/train_sort/label-23364796.txt: -------------------------------------------------------------------------------- 1 | # h1:[mitochondrial_membrane_integrity,contain,heat_shock_proteins] 2 | # h2:[mitochondrial_membrane_integrity,contain,prohibitin] 3 | # h3:[mitochondrial_membrane_integrity,contain,nucleophosmin] 4 | # h4:[nf-kappab-dependent_anti-apoptotic_proteins,contain,bcl2] 5 | # h5:[nf-kappab-dependent_anti-apoptotic_proteins,contain,c-flips] 6 | # h6:[nf-kappab-dependent_anti-apoptotic_proteins,contain,xiap] 7 | # h7:[nf-kappab-dependent_anti-apoptotic_proteins,contain,c-iap2] 8 | # h8:[second_exon,contain,nf-kappab-related_motif_eskkkve] 9 | 10 | # 23364796 The#0 presence#1 of#2 hIV-1#3 tat#4 protein#5 second#6 exon#7 delays#8 fas#9 protein-mediated#10 apoptosis#11 in#12 cD4+#13 t#14 lymphocytes#15 ,#16 a#17 potential#18 mechanism#19 for#20 persistent#21 viral#22 production#23 .#24 11 | 12 | f1:[{hiv-1_tat_protein_second_exon#3:presence#1},delays#8,fas_protein-mediated_apoptosis#9] 13 | f2:[{hiv-1_tat_protein_second_exon#3:presence#1},delays#8,{persistent_viral_production#21:potential_mechanism#18}] 14 | c1:[fas_protein-mediated_apoptosis#9,in#12,cd4+_t_lymphocytes#13] 15 | stmt1 = f1 f2 c1 16 | 17 | # 23364796 HIV-1#0 replication#1 is#2 efficiently#3 controlled#4 by#5 the#6 regulator#7 protein#8 Tat#9 and#10 codified#11 by#12 two#13 exons#14 ,#15 although#16 the#17 first#18 exon#19 is#20 sufficient#21 for#22 this#23 process#24 .#25 18 | 19 | f3:[hiv-1_replication#0,is_efficiently_controlled_by#2,regulator_protein_tat#7] 20 | f4:[hiv-1_replication#0,codified_by#11,two_exons#13] 21 | f5:[first_exon#18,is_sufficient_for#20,{NIL#-1:process#24}] 22 | stmt2 = f3 f4 f5 23 | 24 | # 23364796 Tat#0 can#1 be#2 released#3 to#4 the#5 extracellular#6 medium#7 ,#8 acting#9 asa#10 soluble#11 pro-apoptotic#12 factor#13 in#14 neighboring#15 cells#16 .#17 25 | 26 | f6:[tat#0,be_released_to#2,extracellular_medium#6] 27 | f7:[tat#0,acting_asa#9,soluble_pro-apoptotic_factor#11] 28 | c2:[soluble_pro-apoptotic_factor#11,in#14,neighboring_cells#15] 29 | stmt3 = f6 f7 c2 30 | 31 | # 23364796 However#0 ,#1 HIV-1-infected#2 CD4(+)#3 T#4 lymphocytes#5 show#6 a#7 higher#8 resistance#9 to#10 apoptosis#11 .#12 32 | 33 | f8:[hiv-1-infected_cd4(+)_t_lymphocytes#2,show_a_higher_resistance_to#6,apoptosis#11] 34 | stmt4 = f8 35 | 36 | # 23364796 We#0 observed#1 that#2 the#3 intracellular#4 expression#5 of#6 Tat#7 delayed#8 FasL-mediated#9 apoptosis#10 in#11 both#12 peripheral#13 blood#14 lymphocytes#15 and#16 Jurkat#17 cells#18 ,#19 as#20 it#21 is#22 an#23 essential#24 pathway#25 to#26 control#27 T#28 cell#29 homeostasis#30 during#31 immune#32 activation#33 .#34 37 | 38 | f9:[NIL,observed_that#1,NIL] 39 | f10:[{tat#7:intracellular_expression#4},delayed#8,fasl-mediated_apoptosis#9] 40 | f11:[{tat#7:intracellular_expression#4},is_essential_pathway_to_control#22,t_cell_homeostasis#28] 41 | c3:[fasl-mediated_apoptosis#9,in#11,peripheral_blood_lymphocytes#13] 42 | c4:[fasl-mediated_apoptosis#9,in#11,jurkat_cells#17] 43 | c5:[t_cell_homeostasis#28,during#31,immune_activation#32] 44 | stmt5 = f9 f10 f11 c3 c4 c5 45 | 46 | # 23364796 Jurkat-Tat#0 cells#1 showed#2 impairment#3 in#4 the#5 activation#6 of#7 caspase-8#8 ,#9 deficient#10 release#11 of#12 mitochondrial#13 cytochrome#14 c#15 ,#16 and#17 delayed#18 activation#19 of#20 both#21 caspase-9#22 and#23 -3#24 .#25 47 | 48 | f12:[jurkat-tat_cells#0,showed_impairment_in#2,{caspase-8#8:activation#6}] 49 | f13:[jurkat-tat_cells#0,showed_impairment_in#2,{mitochondrial_cytochrome_c#13:deficient_release#10}] 50 | f14:[jurkat-tat_cells#0,showed_impairment_in#2,{caspase-9#22:delayed_activation#18}] 51 | f15:[jurkat-tat_cells#0,showed_impairment_in#2,{-3#24:delayed_activation#18}] 52 | stmt6 = f12 f13 f14 f15 53 | 54 | # 23364796 This#0 protection#1 was#2 due#3 to#4 a#5 profound#6 deregulation#7 of#8 proteins#9 that#10 stabilized#11 the#12 mitochondrial#13 membrane#14 integrity#15 ,#16 such#17 as#18 heat#19 shock#20 proteins#21 ,#22 prohibitin#23 ,#24 or#25 nucleophosmin#26 ,#27 as#28 well#29 as#30 to#31 the#32 up-regulation#33 of#34 NF-kappaB-dependent#35 anti-apoptotic#36 proteins#37 ,#38 such#39 as#40 BCL2#41 ,#42 c-FLIPS#43 ,#44 XIAP#45 ,#46 and#47 C-IAP2#48 .#49 55 | 56 | f16:[protection#1,was_due_to#2,{proteins#9:profound_deregulation#6}] 57 | f17:[protection#1,as_well_as_to#28,{nf-kappab-dependent_anti-apoptotic_proteins#35:up-regulation#33}] 58 | f18:[protection#1,as_well_as_to#28,bcl2#41] 59 | f19:[protection#1,as_well_as_to#28,c-flips#43] 60 | f20:[protection#1,as_well_as_to#28,xiap#45] 61 | f21:[protection#1,as_well_as_to#28,c-iap2#48] 62 | c6:[proteins#9,stabilized#11,mitochondrial_membrane_integrity#13] 63 | c7:[proteins#9,stabilized#11,heat_shock_proteins#19] 64 | c8:[proteins#9,stabilized#11,prohibitin#23] 65 | c9:[proteins#9,stabilized#11,nucleophosmin#26] 66 | stmt7 = f16 f17 f18 f19 f20 f21 c6 c7 c8 c9 67 | 68 | # 23364796 These#0 effects#1 were#2 observed#3 in#4 Jurkat#5 expressing#6 full-length#7 Tat#8 but#9 not#10 in#11 Jurkat#12 expressing#13 the#14 first#15 exon#16 of#17 Tat#18 ,#19 proving#20 that#21 the#22 second#23 exon#24 ,#25 and#26 particularly#27 the#28 NF-kappaB-related#29 motif#30 ESKKKVE#31 ,#32 was#33 necessary#34 for#35 Tat-mediated#36 protection#37 against#38 FasL#39 apoptosis#40 .#41 69 | 70 | f22:[{NIL#-1:effects#1},were_observed_in#2,jurkat#5] 71 | f23:[{NIL#-1:effects#1},not_in#10,jurkat#12] 72 | f24:[second_exon#23,was_necessary_for#33,tat-mediated_protection#36] 73 | f25:[nf-kappab-related_motif_eskkkve#29,was_necessary_for#33,tat-mediated_protection#36] 74 | c10:[jurkat#5,expressing#6,full-length_tat#7] 75 | c11:[jurkat#12,expressing#6,{tat#18:first_exon#15}] 76 | c12:[tat-mediated_protection#36,against#38,fasl_apoptosis#39] 77 | stmt8 = f22 f23 f24 f25 c10 c11 c12 78 | 79 | # 23364796 Accordingly#0 ,#1 the#2 protection#3 exerted#4 by#5 Tat#6 was#7 independent#8 of#9 its#10 function#11 as#12 a#13 regulator#14 of#15 both#16 viral#17 transcription#18 and#19 elongation#20 .#21 80 | 81 | f26:[protection#3,was_independent_of#7,{protection#3:function#11}] 82 | f27:[protection#3,as#12,{viral_transcription#17:regulator#14}] 83 | f28:[protection#3,as#12,{elongation#20:regulator#14}] 84 | c13:[protection#3,exerted_by#4,tat#6] 85 | stmt9 = f26 f27 f28 c13 86 | 87 | # 23364796 Moreover#0 ,#1 these#2 data#3 proved#4 that#5 HIV-1#6 could#7 have#8 developed#9 strategies#10 to#11 delay#12 FasL-mediated#13 apoptosis#14 in#15 infected#16 CD4(+)#17 T#18 lymphocytes#19 through#20 the#21 expression#22 of#23 Tat#24 ,#25 thus#26 favoring#27 the#28 persistent#29 replication#30 of#31 HIV-1#32 in#33 infected#34 T#35 cells#36 .#37 88 | 89 | f29:[{NIL#-1:data#3},proved_that#4,NIL] 90 | f30:[hiv-1#6,could_have_developed_strategies_to_delay#7,fasl-mediated_apoptosis#13] 91 | f31:[hiv-1#6,favoring#27,{hiv-1#32:persistent_replication#29}] 92 | c14:[fasl-mediated_apoptosis#13,in#15,infected_cd4(+)_t_lymphocytes#16] 93 | c15:[infected_cd4(+)_t_lymphocytes#16,through#20,{tat#24:expression#22}] 94 | c16:[{hiv-1#32:persistent_replication#29},in#33,infected_t_cells#34] 95 | stmt10 = f29 f30 f31 c14 c15 c16 96 | -------------------------------------------------------------------------------- /data/label/train_sort/label-26124495.txt: -------------------------------------------------------------------------------- 1 | # 26124495 Live#0 cell#1 evaluation#2 of#3 granzyme#4 delivery#5 and#6 death#7 receptor#8 signaling#9 in#10 tumor#11 cells#12 targeted#13 by#14 human#15 natural#16 killer#17 cells#18 .#19 2 | 3 | c1:[{granzyme_delivery#4:live_cell_evaluation#0},in#10,tumor_cells#11] 4 | c2:[{death_receptor_signaling#7:live_cell_evaluation#0},in#10,tumor_cells#11] 5 | c3:[tumor_cells#11,targeted_by#13,human_natural_killer_cells#15] 6 | stmt1 = c1 c2 c3 7 | 8 | # 26124495 Growing#0 interest#1 in#2 natural#3 killer#4 cell-based#5 therapy#6 for#7 treating#8 human#9 cancer#10 has#11 made#12 it#13 imperative#14 to#15 develop#16 new#17 tools#18 to#19 measure#20 early#21 events#22 in#23 cell#24 death#25 .#26 9 | 10 | f1:[{natural_killer_cell-based_therapy#3:growing_interest#0},has_made_it_imperative_to_develop#11,{NIL#-1:new_tools#17}] 11 | c4:[{natural_killer_cell-based_therapy#3:growing_interest#0},for_treating#7,human_cancer#9] 12 | c5:[{NIL#-1:new_tools#17},to_measure#19,{cell_death#24:early_events#21}] 13 | stmt2 = f1 c4 c5 14 | 15 | # 26124495 We#0 recently#1 demonstrated#2 that#3 protease-cleavable#4 luciferase#5 biosensors#6 detect#7 granzyme#8 B#9 and#10 pro-apoptotic#11 caspase#12 activation#13 within#14 minutes#15 of#16 target#17 cell#18 recognition#19 by#20 murine#21 cytotoxic#22 lymphocytes#23 .#24 16 | 17 | f2:[NIL,recently_demonstrated_that#1,NIL] 18 | f3:[protease-cleavable_luciferase_biosensors#4,detect#7,granzyme_b#8] 19 | f4:[protease-cleavable_luciferase_biosensors#4,detect#7,pro-apoptotic_caspase_activation#11] 20 | c6:[pro-apoptotic_caspase_activation#11,within#14,target_cell_recognition#17] 21 | c7:[target_cell_recognition#17,by#20,murine_cytotoxic_lymphocytes#21] 22 | stmt3 = f2 f3 f4 c6 c7 23 | 24 | # 26124495 Here#0 ,#1 we#2 report#3 successful#4 adaptation#5 of#6 the#7 biosensor#8 technology#9 to#10 assess#11 perforin-dependent#12 and#13 independent#14 induction#15 of#16 death#17 pathways#18 in#19 tumor#20 cells#21 recognized#22 by#23 human#24 natural#25 killer#26 cell#27 lines#28 and#29 primary#30 cells#31 .#32 25 | 26 | f5:[NIL,report#3,{biosensor_technology#8:successful_adaptation#4}] 27 | f6:[NIL,to_assess#10,{death_pathways#17:perforin-dependent#12}] 28 | f7:[NIL,to_assess#10,{death_pathways#17:independent_induction#14}] 29 | c8:[{death_pathways#17:perforin-dependent#12},in#19,tumor_cells#20] 30 | c9:[{death_pathways#17:perforin-dependent#12},recognized_by#22,human_natural_killer_cell_lines#24] 31 | c10:[{death_pathways#17:perforin-dependent#12},recognized_by#22,primary_cells#30] 32 | c11:[{death_pathways#17:independent_induction#14},in#19,tumor_cells#20] 33 | c12:[{death_pathways#17:independent_induction#14},recognized_by#22,primary_cells#30] 34 | stmt4 = f5 f6 f7 c8 c9 c10 c11 c12 35 | 36 | # 26124495 Cell-cell#0 signaling#1 via#2 both#3 Fc#4 receptors#5 and#6 NK#7 activating#8 receptors#9 led#10 to#11 measurable#12 luciferase#13 signal#14 within#15 15#16 minutes#17 .#18 37 | 38 | f8:[cell-cell_signaling#0,led_to#10,measurable_luciferase_signal#12] 39 | c13:[cell-cell_signaling#0,via#2,fc_receptors#4] 40 | c14:[cell-cell_signaling#0,via#2,nk_activating_receptors#7] 41 | c15:[measurable_luciferase_signal#12,within#15,{NIL#-1:15_minutes#16}] 42 | stmt5 = f8 c13 c14 c15 43 | 44 | # 26124495 In#0 addition#1 to#2 the#3 previously#4 described#5 aspartase-cleavable#6 biosensors#7 ,#8 we#9 report#10 development#11 of#12 granzyme#13 A#14 and#15 granzyme#16 K#17 biosensors#18 ,#19 for#20 which#21 no#22 other#23 functional#24 reporters#25 are#26 available#27 .#28 45 | 46 | f9:[NIL,report#10,{granzyme_a#13:development#11}] 47 | f10:[NIL,report#10,{granzyme_k_biosensors#16:development#11}] 48 | f11:[functional_reporters#24,are_available#26,NIL] 49 | c16:[NIL,in_addition_to#0,aspartase-cleavable_biosensors#6] 50 | c17:[NIL,no_other#22,functional_reporters#24] 51 | stmt6 = f9 f10 f11 c16 c17 52 | 53 | # 26124495 The#0 strength#1 of#2 signaling#3 for#4 granzyme#5 biosensors#6 was#7 dependent#8 upon#9 perforin#10 expression#11 in#12 IL-2-activated#13 NK#14 effectors#15 .#16 54 | 55 | f12:[{signaling_for_granzyme_biosensors#3:strength#1},was_dependent_upon#7,perforin_expression#10] 56 | c18:[perforin_expression#10,in#12,il-2-activated_nk_effectors#13] 57 | stmt7 = f12 c18 58 | 59 | # 26124495 Perforin-independent#0 induction#1 of#2 apoptotic#3 caspases#4 was#5 mediated#6 by#7 death#8 receptor#9 ligation#10 and#11 was#12 detectable#13 after#14 45#15 minutes#16 of#17 conjugation#18 .#19 60 | 61 | f13:[{apoptotic_caspases#3:perforin-independent_induction#0},was_mediated_by#5,death_receptor_ligation#8] 62 | f14:[{apoptotic_caspases#3:perforin-independent_induction#0},was_detectable_after#12,{conjugation#18:45_minutes#15}] 63 | stmt8 = f13 f14 64 | 65 | # 26124495 Evidence#0 of#1 both#2 FasL#3 and#4 TRAIL-mediated#5 signaling#6 was#7 seen#8 following#9 engagement#10 of#11 Jurkat#12 cells#13 by#14 perforin-deficient#15 human#16 cytotoxic#17 lymphocytes#18 .#19 66 | 67 | f15:[{fasl#3:evidence#0},was_seen_following#7,{jurkat#12:engagement#10}] 68 | f16:[{trail-mediated_signaling#5:evidence#0},was_seen_following#7,{jurkat#12:engagement#10}] 69 | c19:[{jurkat#12:engagement#10},by#14,perforin-deficient_human_cytotoxic_lymphocytes#15] 70 | stmt9 = f15 f16 c19 71 | 72 | # 26124495 Although#0 K562#1 cells#2 have#3 been#4 reported#5 to#6 be#7 insensitive#8 to#9 TRAIL#10 ,#11 robust#12 activation#13 of#14 pro-apoptotic#15 caspases#16 by#17 NK#18 cell-derived#19 TRAIL#20 was#21 detectable#22 in#23 K562#24 cells#25 .#26 73 | 74 | f17:[k562_cells#1,be_insensitive_to#7,trail#10] 75 | f18:[{pro-apoptotic_caspases#15:robust_activation#12},was_detectable_in#21,k562_cells#1] 76 | c20:[{pro-apoptotic_caspases#15:robust_activation#12},by#17,nk_cell-derived_trail#18] 77 | stmt10 = f17 f18 c20 78 | 79 | # 26124495 These#0 studies#1 highlight#2 the#3 sensitivity#4 of#5 protease-cleaved#6 luciferase#7 biosensors#8 to#9 measure#10 previously#11 undetectable#12 events#13 in#14 live#15 cells#16 in#17 real#18 time#19 .#20 80 | 81 | f19:[{NIL#-1:studies#1},highlight#2,{protease-cleaved_luciferase_biosensors#6:sensitivity#4}] 82 | f20:[{NIL#-1:studies#1},to_measure#9,undetectable_events#12] 83 | c21:[undetectable_events#12,in#14,live_cells#15] 84 | c22:[live_cells#15,in#17,real_time#18] 85 | stmt11 = f19 f20 c21 c22 86 | 87 | # 26124495 Further#0 development#1 of#2 caspase#3 and#4 granzyme#5 biosensors#6 will#7 allow#8 interrogation#9 of#10 additional#11 features#12 of#13 granzyme#14 activity#15 in#16 live#17 cells#18 including#19 localization#20 ,#21 timing#22 ,#23 and#24 specificity#25 .#26 88 | 89 | f21:[{caspase#3:development#1},will_allow#7,{additional_features_of_granzyme_activity#11:interrogation#9}] 90 | f22:[{granzyme_biosensors#5:development#1},will_allow#7,{additional_features_of_granzyme_activity#11:interrogation#9}] 91 | f23:[live_cells#17,including#19,localization#20] 92 | f24:[live_cells#17,including#19,timing#22] 93 | f25:[live_cells#17,including#19,specificity#25] 94 | c23:[{additional_features_of_granzyme_activity#11:interrogation#9},in#16,live_cells#17] 95 | stmt12 = f21 f22 f23 f24 f25 c23 96 | -------------------------------------------------------------------------------- /data/label/train_sort/label-26131289.txt: -------------------------------------------------------------------------------- 1 | # 26131289 Comparison#0 of#1 peripheral#2 blood#3 t#4 lymphocyte#5 immune#6 function#7 among#8 venous#9 thromboembolism#10 patients#11 with#12 and#13 without#14 infection#15 and#16 patients#17 with#18 simple#19 infection#20 .#21 2 | 3 | c1:[{peripheral_blood_t_lymphocyte_immune_function#2:comparison#0},among#8,venous_thromboembolism_patients#9] 4 | c2:[{peripheral_blood_t_lymphocyte_immune_function#2:comparison#0},among#8,patients#17] 5 | c3:[venous_thromboembolism_patients#9,with_and_without#12,infection#15] 6 | c4:[patients#17,with#18,simple_infection#19] 7 | stmt1 = c1 c2 c3 c4 8 | 9 | # 26131289 To#0 investigate#1 the#2 differences#3 of#4 T#5 lymphocyte#6 subgroups#7 and#8 high-sensitivity#9 C#10 reactive#11 protein#12 levels#13 among#14 patients#15 with#16 venous#17 thromboembolism#18 ,#19 VTE#20 patients#21 with#22 infection#23 ,#24 simple#25 infection#26 patients#27 and#28 the#29 normal#30 controls.289#31 patients#32 were#33 enrolled#34 in#35 this#36 study#37 and#38 divided#39 into#40 control#41 group#42 ,#43 VTE#44 group#45 ,#46 VTE#47 with#48 infection#49 group#50 and#51 simple#52 infectiongroup#53 .#54 10 | 11 | f1:[NIL,to_investigate#0,{t_lymphocyte_subgroups#5:differences#3}] 12 | f2:[NIL,to_investigate#0,{high-sensitivity_c_reactive_protein_levels#9:differences#3}] 13 | f3:[{t_lymphocyte_subgroups#5:differences#3},among#14,patients#15] 14 | f4:[{high-sensitivity_c_reactive_protein_levels#9:differences#3},among#14,patients#15] 15 | f5:[vte_patients#20,were_enrolled_in#33,{NIL#-1:this_study#36}] 16 | f6:[vte_patients#20,divided_into#39,control_group#41] 17 | f7:[vte_patients#20,divided_into#39,vte_group#44] 18 | f8:[vte_patients#20,divided_into#39,vte_with_infection_group#47] 19 | f9:[vte_patients#20,divided_into#39,simple_infectiongroup#52] 20 | f10:[simple_infection_patients#25,were_enrolled_in#33,{NIL#-1:this_study#36}] 21 | f11:[simple_infection_patients#25,divided_into#39,control_group#41] 22 | f12:[simple_infection_patients#25,divided_into#39,vte_group#44] 23 | f13:[simple_infection_patients#25,divided_into#39,vte_with_infection_group#47] 24 | f14:[simple_infection_patients#25,divided_into#39,simple_infectiongroup#52] 25 | f15:[normal_controls.289_patients#30,were_enrolled_in#33,{NIL#-1:this_study#36}] 26 | f16:[normal_controls.289_patients#30,divided_into#39,control_group#41] 27 | f17:[normal_controls.289_patients#30,divided_into#39,vte_group#44] 28 | f18:[normal_controls.289_patients#30,divided_into#39,simple_infectiongroup#52] 29 | c5:[patients#15,with#16,venous_thromboembolism#17] 30 | c6:[vte_patients#20,with#22,infection#23] 31 | stmt2 = f1 f2 f3 f4 f5 f6 f7 f8 f9 f10 f11 f12 f13 f14 f15 f16 f17 f18 c5 c6 32 | 33 | # 26131289 Compared#0 with#1 the#2 control#3 group#4 ,#5 the#6 serum#7 levels#8 of#9 CD3(+)#10 ,#11 CD4(+)#12 ,#13 CD8(+)#14 T#15 lymphocytes#16 significantly#17 decreased#18 and#19 CD4(+)#20 /#21 CD8(+)#22 ratio#23 significantly#24 increased#25 in#26 simple#27 infection#28 group#29 ,#30 CD3(+)#31 and#32 CD8(+)#33 T#34 lymphocytes#35 significantly#36 decreased#37 and#38 CD4(+)#39 /#40 CD8(+)#41 ratio#42 significantly#43 increased#44 in#45 VTE#46 and#47 VTE#48 with#49 infection#50 group#51 ,#52 the#53 proportion#54 of#55 declined#56 CD3(+)#57 and#58 CD8(+)#59 T#60 lymphocytes#61 increased#62 ,#63 and#64 the#65 proportion#66 of#67 increased#68 CD4(+)#69 /#70 CD8(+)#71 ratio#72 statistically#73 elevated#74 in#75 three#76 disease#77 groups#78 .#79 34 | 35 | f19:[{cd3(+)#10:serum_levels#7},significantly_decreased#17,NIL] 36 | f20:[{cd4(+)#12:serum_levels#7},significantly_decreased#17,NIL] 37 | f21:[{cd8(+)_t_lymphocytes#14:serum_levels#7},significantly_decreased#17,NIL] 38 | f22:[cd4(+)_/_cd8(+)_ratio#20,significantly_increased_in#24,simple_infection_group#27] 39 | f23:[cd3(+)#31,significantly_decreased#36,NIL] 40 | f24:[cd8(+)_t_lymphocytes#33,significantly_decreased#36,NIL] 41 | f25:[cd4(+)_/_cd8(+)_ratio#39,significantly_increased_in#43,vte#46] 42 | f26:[cd4(+)_/_cd8(+)_ratio#39,significantly_increased_in#43,vte_with_infection_group#48] 43 | f27:[{declined_cd3(+)#56:proportion#54},increased#62,NIL] 44 | f28:[{cd8(+)_t_lymphocytes#59:proportion#54},increased#62,NIL] 45 | f29:[{increased_cd4(+)_/_cd8(+)_ratio#68:proportion#66},statistically_elevated_in#73,three_disease_groups#76] 46 | c7:[NIL,compared_with#0,control_group#3] 47 | stmt3 = f19 f20 f21 f22 f23 f24 f25 f26 f27 f28 f29 c7 48 | 49 | # 26131289 As#0 an#1 important#2 inflammatory#3 factor#4 ,#5 all#6 HsCRP#7 levels#8 in#9 three#10 disease#11 groups#12 significantly#13 increased#14 when#15 compared#16 with#17 the#18 controlgroup#19 .#20 50 | 51 | f30:[hscrp_levels#7,significantly_increased#13,NIL] 52 | c8:[NIL,as#0,inflammatory_factor#3] 53 | c9:[hscrp_levels#7,in#9,{disease_groups#11:three#10}] 54 | c10:[{disease_groups#11:three#10},compared_with#16,controlgroup#19] 55 | stmt4 = f30 c8 c9 c10 56 | 57 | # 26131289 Immune#0 dysfunction#1 exists#2 in#3 both#4 of#5 VTE#6 and#7 infection#8 patients#9 ,#10 while#11 VTE#12 patients#13 tend#14 to#15 be#16 accompanied#17 with#18 infections#19 .#20 58 | 59 | f31:[immune_dysfunction#0,exists_in#2,vte#6] 60 | f32:[immune_dysfunction#0,exists_in#2,infection_patients#8] 61 | f33:[vte_patients#12,tend_to_be_accompanied_with#14,infections#19] 62 | stmt5 = f31 f32 f33 63 | 64 | # 26131289 The#0 changes#1 of#2 T#3 lymphocyte#4 subgroups#5 in#6 VTE#7 patients#8 ,#9 who#10 were#11 independent#12 from#13 infection#14 ,#15 could#16 cause#17 T#18 lymphocyte#19 immune#20 dysfunction#21 ,#22 suggesting#23 that#24 there#25 were#26 abnormalities#27 of#28 T#29 lymphocyte#30 immune#31 function#32 in#33 VTE#34 itself#35 .#36 65 | 66 | f34:[{t_lymphocyte_subgroups#3:changes#1},could_cause#16,t_lymphocyte_immune_dysfunction#18] 67 | f35:[{t_lymphocyte_subgroups#3:changes#1},suggesting#23,{t_lymphocyte_immune_function#29:abnormalities#27}] 68 | f36:[{t_lymphocyte_immune_function#29:abnormalities#27},in#33,vte#34] 69 | c11:[{t_lymphocyte_subgroups#3:changes#1},in#6,vte_patients#7] 70 | c12:[vte_patients#7,were_independent_from#11,infection#14] 71 | stmt6 = f34 f35 f36 c11 c12 72 | 73 | # 26131289 The#0 overall#1 T#2 lymphocyte#3 functions#4 of#5 recognizing#6 antigens#7 and#8 transducing#9 activation#10 signals#11 decline#12 in#13 VTE#14 patients#15 .#16 74 | 75 | f37:[{t_lymphocyte#2:functions#4},decline_in#12,vte_patients#14] 76 | c13:[{t_lymphocyte#2:functions#4},recognizing#6,antigens#7] 77 | c14:[{t_lymphocyte#2:functions#4},transducing#9,activation_signals#10] 78 | stmt7 = f37 c13 c14 79 | 80 | # 26131289 Besides#0 ,#1 the#2 function#3 of#4 T#5 lymphocyte#6 of#7 directly#8 killing#9 virus#10 microbes#11 declines#12 significantly#13 and#14 the#15 inflammatory#16 mechanisms#17 are#18 involved#19 in#20 the#21 occurrence#22 and#23 development#24 of#25 venous#26 thrombosis#27 .#28 81 | 82 | f38:[{t_lymphocyte#5:function#3},declines_significantly#12,NIL] 83 | f39:[inflammatory_mechanisms#16,are_involved_in#18,{venous_thrombosis#26:occurrence#22}] 84 | f40:[inflammatory_mechanisms#16,are_involved_in#18,{venous_thrombosis#26:development#24}] 85 | c15:[{t_lymphocyte#5:function#3},directly_killing#8,virus_microbes#10] 86 | stmt8 = f38 f39 f40 c15 87 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-15472922.txt: -------------------------------------------------------------------------------- 1 | # 15472922 cytokine#0 secretion#1 from#2 mononuclear#3 cells#4 cultured#5 in#6 vitro#7 with#8 starch-based#9 polymers#10 and#11 poly-l-lactide#12 .#13 2 | 3 | c1:[cytokine_secretion#0,from#2,mononuclear_cells_cultured_in_vitro#3] 4 | c2:[mononuclear_cells_cultured_in_vitro#3,with#8,starch-based_polymers#9] 5 | c3:[mononuclear_cells_cultured_in_vitro#3,with#8,poly-l-lactide#12] 6 | stmt1 = c1 c2 c3 7 | 8 | # 15472922 the#0 cytokine#1 network#2 is#3 one#4 of#5 the#6 major#7 controlling#8 systems#9 of#10 the#11 inflammatory#12 process#13 ,#14 driving#15 the#16 magnitude#17 and#18 duration#19 of#20 the#21 host#22 response#23 against#24 invading#25 microorganisms#26 ,#27 foreign#28 materials#29 ,#30 or#31 altered#32 internal#33 stimuli#34 .#35 9 | 10 | f1:[cytokine_network#1,is_one_of#3,{inflammatory_process#12:major_controlling_systems#7}] 11 | f2:[cytokine_network#1,driving#15,{host_response#22:magnitude#17}] 12 | f3:[cytokine_network#1,driving#15,{host_response#22:duration#19}] 13 | c4:[{host_response#22:magnitude#17},against#24,invading_microorganisms#25] 14 | c5:[{host_response#22:magnitude#17},against#24,foreign_materials#28] 15 | c6:[{host_response#22:magnitude#17},against#24,altered_internal_stimuli#32] 16 | c7:[{host_response#22:duration#19},against#24,invading_microorganisms#25] 17 | c8:[{host_response#22:duration#19},against#24,foreign_materials#28] 18 | c9:[{host_response#22:duration#19},against#24,altered_internal_stimuli#32] 19 | stmt2 = f1 f2 f3 c4 c5 c6 c7 c8 c9 20 | 21 | # 15472922 pro-#0 and#1 antiinflammatory#2 cytokines#3 were#4 quantified#5 after#6 in#7 vitro#8 culture#9 of#10 a#11 mixed#12 population#13 of#14 monocytes/macrophages#15 and#16 lymphocytes#17 with#18 biodegradable#19 polymers#20 .#21 22 | 23 | f4:[pro-#0,were_quantified_after_in#4,{mixed_population_of_monocytes/macrophages#12:vitro_culture#8}] 24 | f5:[pro-#0,were_quantified_after_in#4,{lymphocytes#17:vitro_culture#8}] 25 | c10:[{mixed_population_of_monocytes/macrophages#12:vitro_culture#8},with#18,biodegradable_polymers#19] 26 | c11:[{lymphocytes#17:vitro_culture#8},with#18,biodegradable_polymers#19] 27 | stmt3 = f4 f5 c10 c11 28 | 29 | # 15472922 different#0 blends#1 of#2 starch-based#3 polymers#4 and#5 their#6 composites#7 filled#8 with#9 hydroxyapatite#10 were#11 studied#12 and#13 compared#14 with#15 poly-l-lactide#16 .#17 30 | 31 | f6:[{starch-based_polymers#3:different_blends#0},were_studied_and_compared_with#11,poly-l-lactide#16] 32 | f7:[{starch-based_polymers#3:composites#7},were_studied_and_compared_with#11,poly-l-lactide#16] 33 | c12:[{starch-based_polymers#3:composites#7},filled_with#8,hydroxyapatite#10] 34 | stmt4 = f6 f7 c12 35 | 36 | # 15472922 interleukin#0 (il)-1beta#1 ,#2 il-6#3 ,#4 and#5 tumour#6 necrosis#7 factor-alpha#8 were#9 investigated#10 as#11 the#12 markers#13 of#14 immunological#15 reactivity#16 because#17 they#18 are#19 known#20 to#21 act#22 at#23 the#24 early#25 stages#26 of#27 injury/invasion#28 .#29 37 | 38 | f8:[interleukin_(il)-1beta#0,were_investigated_as#9,{immunological_reactivity#15:markers#13}] 39 | f9:[interleukin_(il)-1beta#0,are_known_to_act_at#19,{injury/invasion#28:early_stages#25}] 40 | f10:[il-6#3,were_investigated_as#9,{immunological_reactivity#15:markers#13}] 41 | f11:[il-6#3,are_known_to_act_at#19,{injury/invasion#28:early_stages#25}] 42 | f12:[tumour_necrosis_factor-alpha#6,were_investigated_as#9,{immunological_reactivity#15:markers#13}] 43 | f13:[tumour_necrosis_factor-alpha#6,are_known_to_act_at#19,{injury/invasion#28:early_stages#25}] 44 | stmt5 = f8 f9 f10 f11 f12 f13 45 | 46 | # 15472922 interferon-gamma#0 ,#1 recognized#2 as#3 a#4 proinflammatory#5 cytokine#6 ,#7 although#8 not#9 present#10 during#11 early#12 responses#13 was#14 also#15 investigated#16 .#17 47 | 48 | f14:[interferon-gamma#0,not_present_during#9,early_responses#12] 49 | f15:[interferon-gamma#0,was_also_investigated#14,NIL] 50 | c13:[interferon-gamma#0,recognized_as#2,proinflammatory_cytokine#5] 51 | stmt6 = f14 f15 c13 52 | 53 | # 15472922 contrarily#0 ,#1 il-4#2 derived#3 from#4 t#5 lymphocytes#6 ,#7 was#8 investigated#9 because#10 it#11 is#12 an#13 immunoregulator#14 that#15 counteracts#16 some#17 aspects#18 of#19 inflammation#20 .#21 54 | 55 | f16:[il-4#2,was_investigated#8,NIL] 56 | f17:[il-4#2,is#12,immunoregulator#14] 57 | c14:[il-4#2,derived_from#3,t_lymphocytes#5] 58 | c15:[immunoregulator#14,counteracts#16,{inflammation#20:aspects#18}] 59 | stmt7 = f16 f17 c14 c15 60 | 61 | # 15472922 t#0 lymphocyte#1 activation#2 was#3 also#4 determined#5 by#6 quantifying#7 il-2#8 .#9 62 | 63 | f18:[t_lymphocyte_activation#0,was_also_determined_by_quantifying#3,il-2#8] 64 | stmt8 = f18 65 | 66 | # 15472922 the#0 results#1 support#2 the#3 hypothesis#4 that#5 different#6 biodegradable#7 polymers#8 can#9 affect#10 mononuclear#11 cell#12 activation#13 and#14 the#15 production#16 of#17 several#18 cytokines#19 associated#20 with#21 the#22 inflammatory#23 process#24 .#25 67 | 68 | f19:[{NIL#-1:results#1},support_the_hypothesis_that#2,NIL] 69 | f20:[biodegradable_polymers#7,can_affect#9,mononuclear_cell_activation#11] 70 | f21:[biodegradable_polymers#7,can_affect#9,{cytokines#19:production#16}] 71 | c16:[{cytokines#19:production#16},associated_with#20,inflammatory_process#23] 72 | stmt9 = f19 f20 f21 c16 73 | 74 | # 15472922 no#0 il-2#1 or#2 interferon-gamma#3 was#4 found#5 in#6 the#7 culture#8 supernatants#9 after#10 3#11 ,#12 7#13 ,#14 and#15 14#16 days#17 in#18 the#19 presence#20 of#21 any#22 of#23 the#24 materials#25 .#26 75 | 76 | f22:[il-2#1,was_found_in#4,culture_supernatants#8] 77 | f23:[interferon-gamma#3,was_found_in#4,culture_supernatants#8] 78 | c17:[NIL,no#0,il-2#1] 79 | c18:[NIL,no#0,interferon-gamma#3] 80 | c19:[culture_supernatants#8,after#10,{NIL#-1:3#11}] 81 | c20:[culture_supernatants#8,after#10,{NIL#-1:7#13}] 82 | c21:[culture_supernatants#8,after#10,{NIL#-1:14_days#16}] 83 | c22:[{NIL#-1:14_days#16},in#18,{materials#25:presence#20}] 84 | stmt10 = f22 f23 c17 c18 c19 c20 c21 c22 85 | 86 | # 15472922 il-6#0 was#1 detected#2 in#3 the#4 highest#5 amounts#6 ,#7 for#8 all#9 the#10 conditions#11 ,#12 followed#13 by#14 tumour#15 necrosis#16 factor-alpha#17 .#18 87 | 88 | f24:[il-6#0,was_detected_in#1,{NIL#-1:highest_amounts#5}] 89 | c23:[il-6#0,followed_by#13,tumour_necrosis_factor-alpha#15] 90 | stmt11 = f24 c23 91 | 92 | # 15472922 il-1beta#0 was#1 produced#2 in#3 very#4 low#5 amounts#6 ,#7 being#8 undetectable#9 with#10 some#11 of#12 the#13 starch-based#14 materials#15 .#16 93 | 94 | f25:[il-1beta#0,was_produced_in#1,{NIL#-1:very_low_amounts#4}] 95 | f26:[il-1beta#0,being_undetectable_with#8,starch-based_materials#14] 96 | stmt12 = f25 f26 97 | 98 | # 15472922 il-4#0 was#1 the#2 only#3 cytokine#4 that#5 did#6 not#7 demonstrate#8 any#9 significant#10 difference#11 within#12 this#13 group#14 of#15 materials#16 .#17 99 | 100 | f27:[il-4#0,was#1,cytokine#4] 101 | c24:[cytokine#4,did_not_demonstrate_any#6,{NIL#-1:significant_difference#10}] 102 | c25:[{NIL#-1:significant_difference#10},within#12,materials#16] 103 | stmt13 = f27 c24 c25 104 | 105 | # 15472922 starch-based#0 polymers#1 and#2 composites#3 induced#4 lower#5 production#6 of#7 proinflammatory#8 cytokines#9 in#10 comparison#11 to#12 poly-l-lactide#13 .#14 106 | 107 | f28:[starch-based_polymers#0,induced#4,{proinflammatory_cytokines#8:lower_production#5}] 108 | c26:[{proinflammatory_cytokines#8:lower_production#5},in_comparison_to#10,poly-l-lactide#13] 109 | stmt14 = f28 c26 110 | -------------------------------------------------------------------------------- /data/label/train_sort/label-23111462.txt: -------------------------------------------------------------------------------- 1 | # n1:[trpv5,as,transient_receptor_potential_vanilloid_channels_trpv5] 2 | # n2:[jurkat_t_cells,as,jurkat_leukemia_t_cells] 3 | # n3:[lymphocytes,as,lymphocyte] 4 | # n4:[trpv5/v6,as,transient_receptor_potential_vanilloid_5_and_6] 5 | # n5:[jurkat_t_cells,as,jurkat_cells] 6 | 7 | # h1:[lymphocytes,contain,human_lymphocytes] 8 | # h2:[human_lymphocytes,contain,human_blood_lymphocytes] 9 | # h3:[ca(2+)-selective_members,contain,trps] 10 | # h4:[ca(2+)-selective_members,contain,ca(2+)_channels] 11 | # h5:[ca(2+)-selective_members,contain,transient_receptor_potential_vanilloid_5_and_6] 12 | 13 | # 23111462 expression#0 of#1 transient#2 receptor#3 potential#4 vanilloid#5 channels#6 trpv5#7 and#8 trpv6#9 in#10 human#11 blood#12 lymphocytes#13 and#14 jurkat#15 leukemia#16 t#17 cells#18 .#19 14 | 15 | c1:[{transient_receptor_potential_vanilloid_channels_trpv5#2:expression#0},in#10,human_blood_lymphocytes#11] 16 | c2:[{transient_receptor_potential_vanilloid_channels_trpv5#2:expression#0},in#10,jurkat_leukemia_t_cells#15] 17 | c3:[{trpv6#9:expression#0},in#10,human_blood_lymphocytes#11] 18 | c4:[{trpv6#9:expression#0},in#10,jurkat_leukemia_t_cells#15] 19 | stmt1 = c1 c2 c3 c4 20 | 21 | # 23111462 regulation#0 of#1 ca(2+)#2 entry#3 is#4 a#5 key#6 process#7 for#8 lymphocyte#9 activation#10 ,#11 cytokine#12 synthesis#13 and#14 proliferation#15 .#16 22 | 23 | f1:[{ca(2+)_entry#2:regulation#0},is_a_key_process_for#4,lymphocyte_activation#9] 24 | f2:[{ca(2+)_entry#2:regulation#0},is_a_key_process_for#4,cytokine_synthesis#12] 25 | f3:[{ca(2+)_entry#2:regulation#0},is_a_key_process_for#4,proliferation#15] 26 | stmt2 = f1 f2 f3 27 | 28 | # 23111462 several#0 members#1 of#2 the#3 transient#4 receptor#5 potential#6 channel#7 family#8 can#9 contribute#10 to#11 changes#12 in#13 [ca(2+)](in)#14 ,#15 however#16 ,#17 the#18 properties#19 and#20 expression#21 levels#22 of#23 these#24 channels#25 in#26 human#27 lymphocytes#28 continue#29 to#30 be#31 elusive#32 .#33 29 | 30 | f4:[{transient_receptor_potential_channel_family#4:members#1},can_contribute_to#9,{[ca(2+)](in)#14:changes#12}] 31 | f5:[{channels#25:properties#19},continue_to_be_elusive#29,NIL] 32 | f6:[{channels#25:expression_levels#21},continue_to_be_elusive#29,NIL] 33 | c5:[{channels#25:properties#19},in#26,human_lymphocytes#27] 34 | c6:[{channels#25:expression_levels#21},in#26,human_lymphocytes#27] 35 | stmt3 = f4 f5 f6 c5 c6 36 | 37 | # 23111462 here#0 ,#1 we#2 established#3 and#4 compared#5 the#6 expression#7 of#8 the#9 most#10 ca(2+)-selective#11 members#12 of#13 the#14 trps#15 ,#16 ca(2+)#17 channels#18 transient#19 receptor#20 potential#21 vanilloid#22 5#23 and#24 6#25 ,#26 in#27 human#28 blood#29 lymphocytes#30 and#31 leukemia#32 jurkat#33 t#34 cells#35 .#36 38 | 39 | f7:[NIL,established#3,{ca(2+)-selective_members#11:expression#7}] 40 | f8:[NIL,established#3,{ca(2+)_channels_transient_receptor_potential_vanilloid_5#17:expression#7}] 41 | f9:[NIL,established#3,{6#25:expression#7}] 42 | f10:[NIL,compared#5,{ca(2+)-selective_members#11:expression#7}] 43 | f11:[NIL,compared#5,{ca(2+)_channels_transient_receptor_potential_vanilloid_5#17:expression#7}] 44 | f12:[NIL,compared#5,{6#25:expression#7}] 45 | c7:[NIL,in#27,human_blood_lymphocytes#28] 46 | c8:[NIL,in#27,leukemia_jurkat_t_cells#32] 47 | stmt4 = f7 f8 f9 f10 f11 f12 c7 c8 48 | 49 | # 23111462 we#0 found#1 that#2 trpv6#3 and#4 trpv5#5 mrnas#6 are#7 expressed#8 in#9 both#10 jurkat#11 cells#12 and#13 quiescent#14 hbls#15 ,#16 however#17 ,#18 the#19 levels#20 of#21 mrnas#22 were#23 significantly#24 higher#25 in#26 malignant#27 cells#28 than#29 in#30 quiescent#31 lymphocytes#32 .#33 50 | 51 | 52 | f13:[NIL,found_that#1,NIL] 53 | f14:[trpv6#3,are_expressed_in#7,jurkat_cells#11] 54 | f15:[trpv6#3,are_expressed_in#7,quiescent_hbls#14] 55 | f16:[trpv5_mrnas#5,are_expressed_in#7,jurkat_cells#11] 56 | f17:[trpv5_mrnas#5,are_expressed_in#7,quiescent_hbls#14] 57 | f18:[{mrnas#22:levels#20},were_significantly_higher_in#23,malignant_cells#27] 58 | c9:[NIL,than_in#29,quiescent_lymphocytes#31] 59 | stmt5 = f13 f14 f15 f16 f17 f18 c9 60 | 61 | # 23111462 western#0 blot#1 analysis#2 showed#3 trpv5/v6#4 proteins#5 in#6 jurkat#7 t#8 cells#9 and#10 trpv5#11 protein#12 in#13 quiescent#14 hbls#15 .#16 62 | 63 | f19:[western_blot_analysis#0,showed#3,trpv5/v6_proteins#4] 64 | f20:[western_blot_analysis#0,showed#3,trpv5_protein#11] 65 | c10:[trpv5/v6_proteins#4,in#6,jurkat_t_cells#7] 66 | c11:[trpv5_protein#11,in#13,quiescent_hbls#14] 67 | stmt6 = f19 f20 c10 c11 68 | 69 | # 23111462 however#0 ,#1 the#2 expression#3 of#4 trpv6#5 protein#6 was#7 switched#8 off#9 in#10 quiescent#11 hbls#12 and#13 turned#14 on#15 after#16 mitogen#17 stimulation#18 of#19 the#20 cells#21 with#22 phytohemagglutinin#23 .#24 70 | 71 | f21:[{trpv6_protein#5:expression#3},was_switched_off_in#7,quiescent_hbls#11] 72 | f22:[{trpv6_protein#5:expression#3},turned_on_after#14,{cells_with_phytohemagglutinin#21:mitogen_stimulation#17}] 73 | stmt7 = f21 f22 74 | 75 | # 23111462 inwardly#0 directed#1 monovalent#2 currents#3 that#4 displayed#5 characteristics#6 of#7 trpv5/v6#8 currents#9 were#10 recorded#11 in#12 both#13 jurkat#14 cells#15 and#16 normal#17 hbls#18 .#19 76 | 77 | f23:[inwardly_directed_monovalent_currents#0,were_recorded_in#10,jurkat_cells#14] 78 | f24:[inwardly_directed_monovalent_currents#0,were_recorded_in#10,normal_hbls#17] 79 | c12:[inwardly_directed_monovalent_currents#0,displayed#5,{trpv5/v6_currents#8:characteristics#6}] 80 | stmt8 = f23 f24 c12 81 | 82 | # 23111462 in#0 outside-out#1 patch-clamp#2 studies#3 ,#4 currents#5 were#6 reduced#7 by#8 ruthenium#9 red#10 ,#11 a#12 nonspecific#13 inhibitor#14 of#15 trpv5/v6#16 channels#17 .#18 83 | 84 | f25:[currents#5,were_reduced_by#6,ruthenium_red#9] 85 | f26:[currents#5,were_reduced_by#6,{trpv5/v6_channels#16:nonspecific_inhibitor#13}] 86 | c13:[NIL,in#0,outside-out_patch-clamp_studies#1] 87 | stmt9 = f25 f26 c13 88 | 89 | # 23111462 in#0 addition#1 ,#2 ruthenium#3 red#4 downregulated#5 cell-cycle#6 progression#7 in#8 both#9 activated#10 hbls#11 and#12 jurkat#13 cells#14 .#15 90 | 91 | f27:[ruthenium_red#3,downregulated#5,cell-cycle_progression#6] 92 | c14:[cell-cycle_progression#6,in#8,activated_hbls#10] 93 | c15:[cell-cycle_progression#6,in#8,jurkat_cells#13] 94 | stmt10 = f27 c14 c15 95 | 96 | # 23111462 thus#0 ,#1 we#2 identified#3 trpv5#4 and#5 trpv6#6 calcium#7 channels#8 ,#9 which#10 can#11 be#12 considered#13 new#14 candidates#15 for#16 ca(2+)#17 entry#18 into#19 human#20 lymphocytes#21 .#22 97 | 98 | f28:[NIL,identified#3,trpv5#4] 99 | f29:[NIL,identified#3,trpv6_calcium_channels#6] 100 | c16:[trpv5#4,can_be_considered#11,{ca(2+)_entry#17:new_candidates#14}] 101 | c17:[trpv6_calcium_channels#6,can_be_considered#11,{ca(2+)_entry#17:new_candidates#14}] 102 | c18:[{ca(2+)_entry#17:new_candidates#14},into#19,human_lymphocytes#20] 103 | stmt11 = f28 f29 c16 c17 c18 104 | 105 | # 23111462 the#0 correlation#1 between#2 expression#3 of#4 trpv6#5 channels#6 and#7 the#8 proliferative#9 status#10 of#11 lymphocytes#12 suggests#13 that#14 trpv6#15 may#16 be#17 involved#18 in#19 the#20 physiological#21 and/or#22 pathological#23 proliferation#24 of#25 lymphocytes#26 .#27 106 | 107 | f30:[trpv6#15,may_be_involved_in#16,{lymphocytes#26:physiological_and/or_pathological_proliferation#21}] 108 | c19:[{NIL#-1:correlation#1},between#2,{trpv6_channels#5:expression#3}] 109 | c20:[{NIL#-1:correlation#1},between#2,{lymphocytes#12:proliferative_status#9}] 110 | stmt12 = f30 c19 c20 111 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-11934839.txt: -------------------------------------------------------------------------------- 1 | # 11934839 ppar#0 activators#1 as#2 antiinflammatory#3 mediators#4 in#5 human#6 t#7 lymphocytes#8 ,#9 implications#10 for#11 atherosclerosis#12 and#13 transplantation-associated#14 arteriosclerosis#15 .#16 2 | 3 | c1:[ppar_activators#0,as#2,antiinflammatory_mediators#3] 4 | c2:[ppar_activators#0,in#5,human_t_lymphocytes#6] 5 | c3:[implications#10,for#11,atherosclerosis#12] 6 | c4:[implications#10,for#11,transplantation-associated_arteriosclerosis#14] 7 | stmt1 = c1 c2 c3 c4 8 | 9 | # 11934839 activation#0 of#1 t#2 lymphocytes#3 and#4 their#5 ensuing#6 elaboration#7 of#8 proinflammatory#9 cytokines#10 ,#11 such#12 as#13 interferon#14 (ifn)-gamma#15 ,#16 represent#17 a#18 critical#19 step#20 in#21 atherogenesis#22 and#23 arteriosclerosis#24 .#25 10 | 11 | f1:[{t_lymphocytes#2:activation#0},represent#17,{atherogenesis#22:critical_step#19}] 12 | f2:[{t_lymphocytes#2:activation#0},represent#17,{arteriosclerosis#24:critical_step#19}] 13 | f3:[{proinflammatory_cytokines#9:ensuing_elaboration#6},represent#17,{atherogenesis#22:critical_step#19}] 14 | f4:[{proinflammatory_cytokines#9:ensuing_elaboration#6},represent#17,{arteriosclerosis#24:critical_step#19}] 15 | f5:[interferon_(ifn)-gamma#14,represent#17,{atherogenesis#22:critical_step#19}] 16 | f6:[interferon_(ifn)-gamma#14,represent#17,{arteriosclerosis#24:critical_step#19}] 17 | c5:[{proinflammatory_cytokines#9:ensuing_elaboration#6},such_as#12,interferon_(ifn)-gamma#14] 18 | stmt2 = f1 f2 f3 f4 f5 f6 c5 19 | 20 | # 11934839 ifngamma#0 pathways#1 also#2 appear#3 integral#4 to#5 the#6 development#7 of#8 transplantation-associated#9 arteriosclerosis#10 ,#11 limiting#12 long-term#13 cardiac#14 allograft#15 survival#16 .#17 21 | 22 | f7:[ifngamma_pathways#0,also_appear_integral_to#2,{transplantation-associated_arteriosclerosis#9:development#7}] 23 | c6:[NIL,limiting#12,long-term_cardiac_allograft_survival#13] 24 | stmt3 = f7 c6 25 | 26 | # 11934839 although#0 disruption#1 of#2 these#3 ifngamma#4 signaling#5 pathways#6 limits#7 atherosclerosis#8 and#9 tx-aa#10 in#11 animals#12 ,#13 little#14 is#15 known#16 about#17 inhibitory#18 regulation#19 of#20 proinflammatory#21 cytokine#22 production#23 in#24 humans#25 .#26 27 | 28 | f8:[{ifngamma_signaling_pathways#4:disruption#1},limits#7,atherosclerosis#8] 29 | f9:[{ifngamma_signaling_pathways#4:disruption#1},limits#7,tx-aa#10] 30 | f10:[NIL,little_is_known_about#14,{proinflammatory_cytokine_production#21:inhibitory_regulation#18}] 31 | c7:[atherosclerosis#8,in#11,animals#12] 32 | c8:[tx-aa#10,in#11,animals#12] 33 | c9:[{proinflammatory_cytokine_production#21:inhibitory_regulation#18},in#24,humans#25] 34 | stmt4 = f8 f9 f10 c7 c8 c9 35 | 36 | # 11934839 the#0 present#1 study#2 investigated#3 whether#4 activators#5 of#6 peroxisome#7 proliferator-activated#8 receptor#9 (ppar)alpha#10 and#11 ppargamma#12 ,#13 with#14 their#15 known#16 antiinflammatory#17 effects#18 ,#19 might#20 regulate#21 the#22 expression#23 of#24 proinflammatory#25 cytokines#26 in#27 human#28 cd4-positive#29 t#30 cells#31 .#32 37 | 38 | f11:[{NIL#-1:present_study#1},investigated_whether#3,NIL] 39 | f12:[{peroxisome_proliferator-activated_receptor_(ppar)alpha#7:activators#5},might_regulate#20,{proinflammatory_cytokines#25:expression#23}] 40 | f13:[{ppargamma#12:activators#5},might_regulate#20,{proinflammatory_cytokines#25:expression#23}] 41 | c10:[{peroxisome_proliferator-activated_receptor_(ppar)alpha#7:activators#5},with#14,antiinflammatory_effects#17] 42 | c11:[{ppargamma#12:activators#5},with#14,antiinflammatory_effects#17] 43 | c12:[{proinflammatory_cytokines#25:expression#23},in#27,human_cd4-positive_t_cells#28] 44 | stmt5 = f11 f12 f13 c10 c11 c12 45 | 46 | # 11934839 isolated#0 human#1 cd4-positive#2 t#3 cells#4 express#5 pparalpha#6 and#7 ppargamma#8 mrna#9 and#10 protein#11 .#12 47 | 48 | f14:[isolated_human_cd4-positive_t_cells#0,express#5,pparalpha#6] 49 | f15:[isolated_human_cd4-positive_t_cells#0,express#5,ppargamma_mrna#8] 50 | f16:[isolated_human_cd4-positive_t_cells#0,express#5,protein#11] 51 | stmt6 = f14 f15 f16 52 | 53 | # 11934839 activation#0 of#1 cd4-positive#2 t#3 cells#4 by#5 anti-cd3#6 monoclonal#7 antibodies#8 significantly#9 increased#10 ifngamma#11 protein#12 secretion#13 from#14 0#15 to#16 504+/-168#17 pg/ml#18 ,#19 as#20 determined#21 by#22 elisa#23 .#24 54 | 55 | f17:[{cd4-positive_t_cells#2:activation#0},significantly_increased#9,ifngamma_protein_secretion#11] 56 | c13:[{cd4-positive_t_cells#2:activation#0},by#5,anti-cd3_monoclonal_antibodies#6] 57 | c14:[ifngamma_protein_secretion#11,from#14,0_to_504+/-168_pg/ml#15] 58 | c15:[NIL,as_determined_by#20,elisa#23] 59 | stmt7 = f17 c13 c14 c15 60 | 61 | # 11934839 pretreatment#0 of#1 cells#2 with#3 well-established#4 pparalpha#5 or#6 ppargamma#7 activators#8 reduced#9 anti-cd3-induced#10 ifngamma#11 secretion#12 in#13 a#14 concentration-dependent#15 manner#16 .#17 62 | 63 | f18:[{cells#2:pretreatment#0},reduced#9,anti-cd3-induced_ifngamma_secretion#10] 64 | c16:[{cells#2:pretreatment#0},with#3,well-established_pparalpha#4] 65 | c17:[{cells#2:pretreatment#0},with#3,ppargamma_activators#7] 66 | c18:[anti-cd3-induced_ifngamma_secretion#10,in#13,concentration-dependent_manner#15] 67 | stmt8 = f18 c16 c17 c18 68 | 69 | # 11934839 ppar#0 activators#1 also#2 inhibited#3 tnfalpha#4 and#5 interleukin-2#6 protein#7 expression#8 .#9 70 | 71 | f19:[ppar_activators#0,inhibited#3,tnfalpha#4] 72 | f20:[ppar_activators#0,inhibited#3,interleukin-2_protein_expression#6] 73 | stmt9 = f19 f20 74 | 75 | # 11934839 in#0 addition#1 ,#2 ppar#3 activators#4 markedly#5 reduced#6 cytokine#7 mrna#8 expression#9 in#10 these#11 cells#12 .#13 76 | 77 | f21:[ppar_activators#3,markedly_reduced#5,cytokine_mrna_expression#7] 78 | c19:[cytokine_mrna_expression#7,in#10,cells#12] 79 | stmt10 = f21 c19 80 | 81 | # 11934839 such#0 antiinflammatory#1 actions#2 were#3 also#4 evident#5 in#6 cell-cell#7 interactions#8 with#9 medium#10 conditioned#11 by#12 ppar#13 activator-treated#14 t#15 cells#16 attenuating#17 human#18 monocyte#19 cd64#20 expression#21 and#22 human#23 endothelial#24 cell#25 major#26 histocompatibility#27 complex#28 class#29 ii#30 induction#31 .#32 82 | 83 | f22:[antiinflammatory_actions#1,were_also_evident_in#3,cell-cell_interactions#7] 84 | c20:[medium#10,conditioned_by#11,ppar_activator-treated_t_cells_attenuating_human_monocyte_cd64_expression#13] 85 | c21:[medium#10,conditioned_by#11,human_endothelial_cell_major_histocompatibility_complex_class_ii_induction#23] 86 | stmt11 = f22 c20 c21 87 | 88 | # 11934839 thus#0 ,#1 activation#2 of#3 pparalpha#4 and#5 ppargamma#6 in#7 human#8 cd4-positive#9 t#10 cells#11 limits#12 the#13 expression#14 of#15 proinflammatory#16 cytokines#17 ,#18 such#19 as#20 ifngamma#21 ,#22 yielding#23 potential#24 therapeutic#25 benefits#26 in#27 pathological#28 processes#29 ,#30 such#31 as#32 atherosclerosis#33 and#34 tx-aa#35 .#36 89 | 90 | f23:[{pparalpha#4:activation#2},limits#12,{proinflammatory_cytokines#16:expression#14}] 91 | f24:[{pparalpha#4:activation#2},yielding#23,potential_therapeutic_benefits#24] 92 | f25:[{ppargamma#6:activation#2},limits#12,{proinflammatory_cytokines#16:expression#14}] 93 | f26:[{ppargamma#6:activation#2},yielding#23,potential_therapeutic_benefits#24] 94 | f27:[{proinflammatory_cytokines#16:expression#14},such_as#19,ifngamma#21] 95 | f28:[potential_therapeutic_benefits#24,such_as#31,atherosclerosis#33] 96 | f29:[potential_therapeutic_benefits#24,such_as#31,tx-aa#35] 97 | c22:[{pparalpha#4:activation#2},in#7,human_cd4-positive_t_cells#8] 98 | c23:[{ppargamma#6:activation#2},in#7,human_cd4-positive_t_cells#8] 99 | c24:[potential_therapeutic_benefits#24,in#27,pathological_processes#28] 100 | stmt12 = f23 f24 f25 f26 f27 f28 f29 c22 c23 c24 101 | -------------------------------------------------------------------------------- /data/label/train_sort/label-11895154.txt: -------------------------------------------------------------------------------- 1 | # 11895154 fatty#0 acids#1 and#2 lymphocyte#3 functions#4 .#5 2 | 3 | c1:[fatty_acids#0,NIL#-1,NIL] 4 | c2:[lymphocyte_functions#3,NIL#-1,NIL] 5 | stmt1 = c1 c2 6 | 7 | # 11895154 the#0 immune#1 system#2 acts#3 to#4 protect#5 the#6 host#7 against#8 pathogenic#9 invaders#10 .#11 8 | 9 | f1:[immune_system#1,acts_to_protect#3,host#7] 10 | f2:[immune_system#1,against#8,pathogenic_invaders#9] 11 | stmt2 = f1 f2 12 | 13 | # 11895154 however#0 ,#1 components#2 of#3 the#4 immune#5 system#6 can#7 become#8 dysregulated#9 such#10 that#11 their#12 activities#13 are#14 directed#15 against#16 host#17 tissues#18 ,#19 so#20 causing#21 damage#22 .#23 14 | 15 | f3:[{components#2:activities#13},are_directed_against#14,host_tissues#17] 16 | f4:[{components#2:activities#13},causing#21,damage#22] 17 | f5:[{immune_system#5:components#2},can_become_dysregulated#7,NIL] 18 | stmt3 = f3 f4 f5 19 | 20 | # 11895154 lymphocytes#0 are#1 involved#2 in#3 both#4 the#5 beneficial#6 and#7 detrimental#8 effects#9 of#10 the#11 immune#12 system#13 .#14 21 | 22 | f6:[lymphocytes#0,are_involved_in#1,{immune_system#12:beneficial_and_detrimental_effects#6}] 23 | stmt4 = f6 24 | 25 | # 11895154 both#0 the#1 level#2 of#3 fat#4 and#5 the#6 types#7 of#8 fatty#9 acid#10 present#11 in#12 the#13 diet#14 can#15 affect#16 lymphocyte#17 functions#18 .#19 26 | 27 | f7:[{fat#4:level#2},can_affect#15,lymphocyte_functions#17] 28 | f8:[{fatty_acid#9:types#7},can_affect#15,lymphocyte_functions#17] 29 | c3:[{fat#4:level#2},present_in#11,diet#14] 30 | c4:[{fatty_acid#9:types#7},present_in#11,diet#14] 31 | stmt5 = f7 f8 c3 c4 32 | 33 | # 11895154 the#0 fatty#1 acid#2 composition#3 of#4 lymphocytes#5 ,#6 and#7 other#8 immune#9 cells#10 ,#11 is#12 altered#13 according#14 to#15 the#16 fatty#17 acid#18 composition#19 of#20 the#21 diet#22 and#23 this#24 alters#25 the#26 capacity#27 of#28 those#29 cells#30 to#31 produce#32 eicosanoids#33 ,#34 such#35 as#36 prostaglandin#37 e2#38 ,#39 which#40 are#41 involved#42 in#43 immunoregulation#44 .#45 34 | 35 | f9:[{lymphocytes#5:fatty_acid_composition#1},is_altered_according_to#12,{diet#22:fatty_acid_composition#17}] 36 | f10:[immune_cells#9,is_altered_according_to#12,{diet#22:fatty_acid_composition#17}] 37 | f11:[NIL,alters#25,{cells#30:capacity#27}] 38 | f12:[NIL,to_produce#31,eicosanoids#33] 39 | f13:[eicosanoids#33,such_as#35,prostaglandin_e2#37] 40 | c5:[eicosanoids#33,are_involved_in#41,immunoregulation#44] 41 | stmt6 = f9 f10 f11 f12 f13 c5 42 | 43 | # 11895154 a#0 high#1 fat#2 diet#3 can#4 impair#5 lymphocyte#6 function#7 .#8 44 | 45 | f14:[high_fat_diet#1,can_impair#4,lymphocyte_function#6] 46 | stmt7 = f14 47 | 48 | # 11895154 cell#0 culture#1 and#2 animal#3 feeding#4 studies#5 indicate#6 that#7 oleic#8 ,#9 linoleic#10 ,#11 conjugated#12 linoleic#13 ,#14 gamma-linolenic#15 ,#16 dihomo-gamma-linolenic#17 ,#18 arachidonic#19 ,#20 alpha-linolenic#21 ,#22 eicosapentaenoic#23 and#24 docosahexaenoic#25 acids#26 can#27 all#28 influence#29 lymphocyte#30 proliferation#31 ,#32 the#33 production#34 of#35 cytokines#36 by#37 lymphocytes#38 ,#39 and#40 natural#41 killer#42 cell#43 activity#44 .#45 49 | 50 | f15:[cell_culture#0,indicate_that#6,NIL] 51 | f16:[animal_feeding_studies#3,indicate_that#6,NIL] 52 | f17:[oleic#8,influence#29,lymphocyte_proliferation#30] 53 | f18:[oleic#8,influence#29,{cytokines#36:production#34}] 54 | f19:[oleic#8,influence#29,natural_killer_cell_activity#41] 55 | f20:[linoleic#10,influence#29,lymphocyte_proliferation#30] 56 | f21:[linoleic#10,influence#29,{cytokines#36:production#34}] 57 | f22:[linoleic#10,influence#29,natural_killer_cell_activity#41] 58 | f23:[conjugated_linoleic#12,influence#29,lymphocyte_proliferation#30] 59 | f24:[conjugated_linoleic#12,influence#29,{cytokines#36:production#34}] 60 | f25:[conjugated_linoleic#12,influence#29,natural_killer_cell_activity#41] 61 | f26:[gamma-linolenic#15,influence#29,lymphocyte_proliferation#30] 62 | f27:[gamma-linolenic#15,influence#29,{cytokines#36:production#34}] 63 | f28:[gamma-linolenic#15,influence#29,natural_killer_cell_activity#41] 64 | f29:[dihomo-gamma-linolenic#17,influence#29,lymphocyte_proliferation#30] 65 | f30:[dihomo-gamma-linolenic#17,influence#29,{cytokines#36:production#34}] 66 | f31:[dihomo-gamma-linolenic#17,influence#29,natural_killer_cell_activity#41] 67 | f32:[arachidonic#19,influence#29,lymphocyte_proliferation#30] 68 | f33:[arachidonic#19,influence#29,{cytokines#36:production#34}] 69 | f34:[arachidonic#19,influence#29,natural_killer_cell_activity#41] 70 | f35:[alpha-linolenic#21,influence#29,lymphocyte_proliferation#30] 71 | f36:[alpha-linolenic#21,influence#29,{cytokines#36:production#34}] 72 | f37:[alpha-linolenic#21,influence#29,natural_killer_cell_activity#41] 73 | f38:[eicosapentaenoic#23,influence#29,lymphocyte_proliferation#30] 74 | f39:[eicosapentaenoic#23,influence#29,{cytokines#36:production#34}] 75 | f40:[eicosapentaenoic#23,influence#29,natural_killer_cell_activity#41] 76 | f41:[docosahexaenoic_acids#25,influence#29,lymphocyte_proliferation#30] 77 | f42:[docosahexaenoic_acids#25,influence#29,{cytokines#36:production#34}] 78 | f43:[docosahexaenoic_acids#25,influence#29,natural_killer_cell_activity#41] 79 | c6:[{cytokines#36:production#34},by#37,lymphocytes#38] 80 | stmt8 = f15 f16 f17 f18 f19 f20 f21 f22 f23 f24 f25 f26 f27 f28 f29 f30 f31 f32 f33 f34 f35 f36 f37 f38 f39 f40 f41 f42 f43 c6 81 | 82 | # 11895154 high#0 intakes#1 of#2 some#3 of#4 these#5 fatty#6 acids#7 are#8 necessary#9 to#10 induce#11 these#12 effects#13 .#14 83 | 84 | f44:[{fatty_acids#6:high_intakes#0},are_necessary_to_induce#8,{NIL#-1:effects#13}] 85 | stmt9 = f44 86 | 87 | # 11895154 among#0 these#1 fatty#2 acids#3 the#4 long#5 chain#6 n-3#7 fatty#8 acids#9 ,#10 especially#11 eicosapentaenoic#12 acid#13 ,#14 appear#15 to#16 be#17 the#18 most#19 potent#20 when#21 included#22 in#23 the#24 human#25 diet#26 .#27 88 | 89 | f45:[long_chain_n-3_fatty_acids#5,appear_to_be_the_most_potent#15,NIL] 90 | f46:[eicosapentaenoic_acid#12,appear_to_be_the_most_potent#15,NIL] 91 | c7:[NIL,among#0,fatty_acids#2] 92 | c8:[eicosapentaenoic_acid#12,included_in#22,human_diet#25] 93 | stmt10 = f45 f46 c7 c8 94 | 95 | # 11895154 although#0 not#1 all#2 studies#3 agree#4 ,#5 it#6 appears#7 that#8 fish#9 oil#10 ,#11 which#12 contains#13 eicosapentaenoic#14 acid#15 ,#16 down#17 regulates#18 the#19 t-helper#20 1-type#21 response#22 which#23 is#24 associated#25 with#26 chronic#27 inflammatory#28 disease#29 .#30 96 | 97 | f47:[{NIL#-1:studies#3},appears_that#7,NIL] 98 | f48:[fish_oil#9,down_regulates#17,t-helper_1-type_response#20] 99 | c9:[fish_oil#9,contains#13,eicosapentaenoic_acid#14] 100 | c10:[t-helper_1-type_response#20,is_associated_with#24,chronic_inflammatory_disease#27] 101 | stmt11 = f47 f48 c9 c10 102 | 103 | # 11895154 there#0 is#1 evidence#2 for#3 beneficial#4 effects#5 of#6 fish#7 oil#8 in#9 such#10 diseases#11 ,#12 this#13 evidence#14 is#15 strongest#16 for#17 rheumatoid#18 arthritis#19 .#20 104 | 105 | f49:[{NIL#-1:evidence#14},is_strongest_for#15,{rheumatoid_arthritis#18:beneficial_effects#4}] 106 | c11:[{NIL#-1:evidence#2},for#3,{fish_oil#7:beneficial_effects#4}] 107 | c12:[{fish_oil#7:beneficial_effects#4},in#9,{diseases#11:beneficial_effects#4}] 108 | stmt12 = f49 c11 c12 109 | 110 | # 11895154 since#0 n-3#1 fatty#2 acids#3 also#4 antagonise#5 the#6 production#7 of#8 inflammatory#9 eicosanoid#10 mediators#11 from#12 arachidonic#13 acid#14 ,#15 there#16 is#17 potential#18 for#19 benefit#20 in#21 asthma#22 and#23 related#24 diseases#25 .#26 111 | 112 | f50:[n-3_fatty_acids#1,antagonise#5,{inflammatory_eicosanoid_mediators#9:production#7}] 113 | f51:[NIL,is_potential_for_benefit_in#17,asthma#22] 114 | f52:[NIL,is_potential_for_benefit_in#17,related_diseases#24] 115 | c13:[{inflammatory_eicosanoid_mediators#9:production#7},from#12,arachidonic_acid#13] 116 | stmt13 = f50 f51 f52 c13 117 | 118 | # 11895154 recent#0 evidence#1 indicates#2 that#3 fish#4 oil#5 may#6 be#7 of#8 benefit#9 in#10 some#11 asthmatics#12 but#13 not#14 others#15 .#16 119 | 120 | f53:[{NIL#-1:recent_evidence#0},indicates_that#2,NIL] 121 | f54:[fish_oil#4,may_be_of_benefit_in#6,asthmatics#12] 122 | stmt14 = f53 f54 123 | 124 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-26133121.txt: -------------------------------------------------------------------------------- 1 | # 26133121 An#0 act#1 of#2 balance#3 between#4 adaptive#5 and#6 maladaptive#7 immunity#8 in#9 depression#10 ,#11 a#12 role#13 for#14 t#15 lymphocytes#16 .#17 2 | 3 | c1:[{balance#3:act#1},between#4,adaptive#5] 4 | c2:[{balance#3:act#1},between#4,maladaptive_immunity#7] 5 | c3:[{balance#3:act#1},a_role_for#12,t_lymphocytes#15] 6 | c4:[maladaptive_immunity#7,in#9,depression#10] 7 | stmt1 = c1 c2 c3 c4 8 | 9 | # 26133121 Historically#0 the#1 monoaminergic#2 neurotransmitter#3 system#4 ,#5 in#6 particular#7 the#8 serotonergic#9 system#10 ,#11 was#12 seen#13 as#14 being#15 responsible#16 for#17 the#18 pathophysiology#19 of#20 major#21 depressive#22 disorder#23 .#24 10 | 11 | f1:[monoaminergic_neurotransmitter_system#2,was_seen_as_being_responsible_for#12,{major_depressive_disorder#21:pathophysiology#19}] 12 | f2:[serotonergic_system#9,was_seen_as_being_responsible_for#12,{major_depressive_disorder#21:pathophysiology#19}] 13 | stmt2 = f1 f2 14 | 15 | # 26133121 With#0 the#1 advent#2 of#3 psychoneuroimmunology#4 an#5 important#6 role#7 of#8 the#9 immune#10 system#11 in#12 the#13 interface#14 between#15 the#16 central#17 nervous#18 systems#19 and#20 peripheral#21 organ#22 systems#23 has#24 emerged#25 .#26 16 | 17 | f3:[{immune_system#10:important_role#6},has_emerged#24,NIL] 18 | c5:[NIL,with#0,{psychoneuroimmunology#4:advent#2}] 19 | c6:[{immune_system#10:important_role#6},in#12,interface#14] 20 | c7:[interface#14,between#15,central_nervous_systems#17] 21 | c8:[interface#14,between#15,peripheral_organ_systems#21] 22 | stmt3 = f3 c5 c6 c7 c8 23 | 24 | # 26133121 In#0 addition#1 to#2 the#3 well-characterised#4 neurobiological#5 activities#6 of#7 cytokines#8 ,#9 T#10 cell#11 function#12 in#13 the#14 context#15 of#16 depression#17 has#18 been#19 neglected#20 so#21 far#22 .#23 25 | 26 | f4:[t_cell_function#10,has_been_neglected#18,NIL] 27 | c9:[NIL,in_addition_to#0,{cytokines#8:well-characterised_neurobiological_activities#4}] 28 | c10:[t_cell_function#10,in#13,{depression#17:context#15}] 29 | stmt4 = f4 c9 c10 30 | 31 | # 26133121 In#0 this#1 review#2 we#3 will#4 investigate#5 the#6 biological#7 roles#8 of#9 T#10 cells#11 in#12 depression#13 .#14 32 | 33 | f5:[NIL,will_investigate#4,{t_cells#10:biological_roles#7}] 34 | c11:[NIL,in#0,{NIL#-1:review#2}] 35 | c12:[{t_cells#10:biological_roles#7},in#12,depression#13] 36 | stmt5 = f5 c11 c12 37 | 38 | #26133121 Originally#0 it#1 was#2 thought#3 that#4 the#5 adaptive#6 immune#7 arm#8 including#9 T#10 lymphocytes#11 was#12 excluded#13 from#14 the#15 CNS#16 .#17 39 | 40 | f6:[NIL,it_was_thought_that#1,NIL] 41 | f7:[adaptive_immune_arm#6,was_excluded_from#12,cns#16] 42 | c13:[adaptive_immune_arm#6,including#9,t_lymphocytes#10] 43 | stmt6 = f6 f7 c13 44 | 45 | # 26133121 It#0 is#1 now#2 clear#3 that#4 peripheral#5 naive#6 T#7 cells#8 not#9 only#10 carry#11 out#12 continuous#13 surveillance#14 within#15 the#16 brain#17 but#18 also#19 maintain#20 neural#21 plasticity#22 .#23 46 | 47 | f8:[NIL,it_is_now_clear_that#0,NIL] 48 | f9:[peripheral_naive_t_cells#5,not_only_carry_out#9,continuous_surveillance#13] 49 | f10:[peripheral_naive_t_cells#5,also_maintain#19,neural_plasticity#21] 50 | c14:[continuous_surveillance#13,within#15,brain#17] 51 | stmt7 = f8 f9 f10 c14 52 | 53 | # 26133121 Furthermore#0 animal#1 studies#2 demonstrate#3 that#4 regulatory#5 T#6 lymphocytes#7 can#8 provide#9 protection#10 against#11 maladaptive#12 behavioural#13 responses#14 associated#15 with#16 depression#17 .#18 54 | 55 | f11:[animal_studies#1,demonstrate_that#3,NIL] 56 | f12:[regulatory_t_lymphocytes#5,can_provide#8,{NIL#-1:protection#10}] 57 | c15:[{NIL#-1:protection#10},against#11,maladaptive_behavioural_responses#12] 58 | c16:[maladaptive_behavioural_responses#12,associated_with#15,depression#17] 59 | stmt8 = f11 f12 c15 c16 60 | 61 | # 26133121 Psychogenic#0 stress#1 as#2 a#3 major#4 inducer#5 of#6 depression#7 can#8 lead#9 to#10 transient#11 trafficking#12 of#13 T#14 lymphocytes#15 into#16 the#17 brain#18 stimulating#19 the#20 secretion#21 of#22 certain#23 neurotrophic#24 factors#25 and#26 cytokines#27 .#28 62 | 63 | f13:[psychogenic_stress#0,can_lead_to#8,{t_lymphocytes#14:transient_trafficking#11}] 64 | c17:[psychogenic_stress#0,as#2,{depression#7:major_inducer#4}] 65 | c18:[{t_lymphocytes#14:transient_trafficking#11},into#16,{certain_neurotrophic_factors#23:brain_stimulating_the_secretion#18}] 66 | c19:[{t_lymphocytes#14:transient_trafficking#11},into#16,{cytokines#27:brain_stimulating_the_secretion#18}] 67 | stmt9 = f13 c17 c18 c19 68 | 69 | # 26133121 The#0 separate#1 and#2 combined#3 mechanism#4 of#5 CD4#6 and#7 CD8#8 T#9 cell#10 activation#11 is#12 likely#13 to#14 determine#15 the#16 response#17 pattern#18 of#19 CNS#20 specific#21 neurokines#22 and#23 neurotrophins#24 .#25 70 | 71 | f14:[{cd4#6:separate_and_combined_mechanism#1},is_likely_to_determine#12,{cns_specific_neurokines#20:response_pattern#17}] 72 | f15:[{cd4#6:separate_and_combined_mechanism#1},is_likely_to_determine#12,{neurotrophins#24:response_pattern#17}] 73 | f16:[{cd8_t_cell_activation#8:separate_and_combined_mechanism#1},is_likely_to_determine#12,{cns_specific_neurokines#20:response_pattern#17}] 74 | f17:[{cd8_t_cell_activation#8:separate_and_combined_mechanism#1},is_likely_to_determine#12,{neurotrophins#24:response_pattern#17}] 75 | stmt10 = f14 f15 f16 f17 76 | 77 | # 26133121 Under#0 chronic#1 stress-induced#2 neuroinflammatory#3 conditions#4 associated#5 with#6 depression#7 ,#8 T#9 cell#10 responses#11 may#12 become#13 maladaptive#14 and#15 can#16 be#17 involved#18 in#19 neurodegeneration#20 .#21 78 | 79 | f18:[t_cell_responses#9,may_become_maladaptive#12,NIL] 80 | f19:[t_cell_responses#9,can_be_involved_in#16,neurodegeneration#20] 81 | c20:[chronic_stress-induced_neuroinflammatory_conditions#1,associated_with#5,depression#7] 82 | stmt11 = f18 f19 c20 83 | 84 | # 26133121 Additionally#0 ,#1 intracellular#2 adhesion#3 and#4 MHC#5 molecule#6 expression#7 as#8 well#9 as#10 glucocorticoid#11 receptor#12 expression#13 within#14 the#15 brain#16 may#17 play#18 a#19 role#20 in#21 determining#22 T#23 lymphocyte#24 functionality#25 in#26 depression#27 .#28 85 | 86 | f20:[intracellular_adhesion#2,may_play#17,{NIL#-1:role#20}] 87 | f21:[mhc_molecule_expression#5,may_play#17,{NIL#-1:role#20}] 88 | f22:[glucocorticoid_receptor_expression#11,may_play#17,{NIL#-1:role#20}] 89 | c21:[intracellular_adhesion#2,within#14,brain#16] 90 | c22:[mhc_molecule_expression#5,within#14,brain#16] 91 | c23:[glucocorticoid_receptor_expression#11,within#14,brain#16] 92 | c24:[{NIL#-1:role#20},determining#22,t_lymphocyte_functionality#23] 93 | c25:[t_lymphocyte_functionality#23,in#26,depression#27] 94 | stmt12 = f20 f21 f22 c21 c22 c23 c24 c25 95 | 96 | # 26133121 Taken#0 together#1 ,#2 T#3 lymphocyte#4 mechanisms#5 ,#6 which#7 confer#8 susceptibility#9 or#10 resilience#11 to#12 MDD#13 ,#14 are#15 not#16 yet#17 fully#18 understood#19 .#20 97 | 98 | f23:[t_lymphocyte_mechanisms#3,are_not_yet_fully_understood#15,NIL] 99 | c26:[t_lymphocyte_mechanisms#3,confer_susceptibility_or_resilience_to#8,mdd#13] 100 | stmt13 = f23 c26 101 | 102 | # 26133121 Further#0 insight#1 into#2 the#3 cellular#4 and#5 molecular#6 mechanisms#7 which#8 balance#9 the#10 adaptive#11 and#12 maladaptive#13 roles#14 of#15 T#16 lymphocytes#17 may#18 provide#19 a#20 better#21 understanding#22 of#23 both#24 the#25 neuro-#26 degenerative#27 and#28 -regenerative#29 repair#30 functions#31 as#32 present#33 within#34 the#35 neuroimmune#36 network#37 during#38 depression#39 .#40 103 | 104 | f24:[{cellular_and_molecular_mechanisms#4:further_insight#0},may_provide#18,{neuro-_degenerative#26:better_understanding#21}] 105 | f25:[{cellular_and_molecular_mechanisms#4:further_insight#0},may_provide#18,{-regenerative_repair_functions#29:better_understanding#21}] 106 | c27:[{cellular_and_molecular_mechanisms#4:further_insight#0},balance#9,{t_lymphocytes#16:adaptive#11}] 107 | c28:[{cellular_and_molecular_mechanisms#4:further_insight#0},balance#9,{t_lymphocytes#16:maladaptive_roles#13}] 108 | c29:[neuro-_degenerative#26,as_present_within#32,neuroimmune_network#36] 109 | c30:[-regenerative_repair_functions#29,as_present_within#32,neuroimmune_network#36] 110 | c31:[NIL,during#38,depression#39] 111 | stmt14 = f24 f25 c27 c28 c29 c30 c31 112 | 113 | # 26133121 Furthermore#0 T#1 cells#2 may#3 be#4 important#5 players#6 in#7 restoration#8 of#9 normal#10 behaviour#11 and#12 immune#13 cell#14 homeostasis#15 in#16 depression#17 .#18 114 | 115 | f26:[t_cells#1,may_be#3,{NIL#-1:important_players#5}] 116 | c32:[{NIL#-1:important_players#5},in#7,{normal_behaviour#10:restoration#8}] 117 | c33:[{NIL#-1:important_players#5},in#7,immune_cell_homeostasis#13] 118 | c34:[immune_cell_homeostasis#13,in#16,depression#17] 119 | stmt15 = f26 c32 c33 c34 120 | -------------------------------------------------------------------------------- /data/label/eval_sort/label-11991752.txt: -------------------------------------------------------------------------------- 1 | # 11991752 significant#0 antitumor#1 effects#2 obtained#3 by#4 autologous#5 tumor#6 cell#7 vaccine#8 engineered#9 to#10 secrete#11 interleukin#12 (il)-12#13 and#14 il-18#15 by#16 means#17 of#18 the#19 ebv/lipoplex#20 .#21 2 | 3 | c1:[significant_antitumor_effects#0,obtained_by#3,autologous_tumor_cell_vaccine#5] 4 | c2:[autologous_tumor_cell_vaccine#5,engineered_to#9,secrete_interleukin_(il)-12#11] 5 | c3:[autologous_tumor_cell_vaccine#5,engineered_to#9,il-18#15] 6 | c4:[NIL,by_means_of#16,ebv/lipoplex#20] 7 | stmt1 = c1 c2 c3 c4 8 | 9 | # 11991752 the#0 ebv/lipoplex#1 is#2 a#3 nonviral#4 gene#5 delivery#6 system#7 composed#8 of#9 a#10 cationic#11 lipid#12 and#13 epstein-barr#14 virus#15 (ebv)-based#16 plasmid#17 vector#18 that#19 carries#20 the#21 ebv#22 orip#23 and#24 ebv#25 nuclear#26 antigen#27 1#28 gene#29 .#30 10 | 11 | f1:[ebv/lipoplex#1,is#2,nonviral_gene_delivery_system#4] 12 | c5:[nonviral_gene_delivery_system#4,composed_of#8,cationic_lipid#11] 13 | c6:[nonviral_gene_delivery_system#4,composed_of#8,epstein-barr_virus_(ebv)-based_plasmid_vector#14] 14 | c7:[epstein-barr_virus_(ebv)-based_plasmid_vector#14,carries#20,ebv_orip#22] 15 | c8:[epstein-barr_virus_(ebv)-based_plasmid_vector#14,carries#20,ebv_nuclear_antigen_1_gene#25] 16 | stmt2 = f1 c5 c6 c7 c8 17 | 18 | # 11991752 because#0 the#1 ebna1#2 supports#3 retention#4 ,#5 nuclear#6 localization#7 ,#8 and#9 transcriptional#10 upregulation#11 of#12 the#13 orip-bearing#14 plasmid#15 ,#16 cells#17 transfected#18 with#19 the#20 ebv/lipoplex#21 express#22 the#23 transgene#24 at#25 a#26 very#27 high#28 level#29 .#30 19 | 20 | f2:[ebna1#2,supports#3,retention#4] 21 | f3:[ebna1#2,supports#3,nuclear_localization#6] 22 | f4:[ebna1#2,supports#3,{orip-bearing_plasmid#14:transcriptional_upregulation#10}] 23 | f5:[cells#17,express#22,transgene#24] 24 | c9:[cells#17,transfected_with#18,ebv/lipoplex#21] 25 | c10:[transgene#24,at#25,very_high_level#27] 26 | stmt3 = f2 f3 f4 f5 c9 c10 27 | 28 | # 11991752 we#0 hypothesized#1 that#2 tumor#3 cells#4 genetically#5 manipulated#6 with#7 the#8 ebv/lipoplex#9 may#10 be#11 used#12 as#13 a#14 tumor#15 vaccine#16 without#17 drug#18 selection#19 ,#20 strongly#21 contributing#22 to#23 immunotherapy#24 of#25 patients#26 with#27 malignancies#28 .#29 29 | 30 | f6:[NIL,hypothesized_that#1,NIL] 31 | f7:[tumor_cells#3,may_be_used_as#10,tumor_vaccine#15] 32 | f8:[tumor_cells#3,strongly_contributing_to#21,{patients#26:immunotherapy#24}] 33 | c11:[tumor_cells#3,genetically_manipulated_with#5,ebv/lipoplex#9] 34 | c12:[tumor_vaccine#15,without#17,drug_selection#18] 35 | c13:[{patients#26:immunotherapy#24},with#27,malignancies#28] 36 | stmt4 = f6 f7 f8 c11 c12 c13 37 | 38 | # 11991752 the#0 cytokines#1 interleukin#2 (il)-12#3 and#4 il-18#5 exert#6 a#7 variety#8 of#9 immune-regulatory#10 functions#11 including#12 interferon#13 (ifn)-gamma#14 production#15 and#16 cytotoxic#17 t#18 lymphocyte#19 and#20 natural#21 killer#22 activation#23 .#24 39 | 40 | f9:[cytokines_interleukin#1,exert#6,immune-regulatory_functions#10] 41 | f10:[(il)-12#3,exert#6,immune-regulatory_functions#10] 42 | f11:[il-18#5,exert#6,immune-regulatory_functions#10] 43 | c14:[immune-regulatory_functions#10,including#12,{interferon_(ifn)-gamma#13:production#15}] 44 | c15:[immune-regulatory_functions#10,including#12,cytotoxic_t_lymphocyte#17] 45 | c16:[immune-regulatory_functions#10,including#12,{natural_killer#21:activation#23}] 46 | stmt5 = f9 f10 f11 c14 c15 c16 47 | 48 | # 11991752 here#0 ,#1 we#2 investigated#3 the#4 possible#5 therapeutic#6 effects#7 of#8 an#9 autologous#10 tumor#11 cell#12 vaccine#13 in#14 the#15 b16#16 melanoma#17 model#18 .#19 49 | 50 | f12:[NIL,investigated#3,{autologous_tumor_cell_vaccine#10:possible_therapeutic_effects#5}] 51 | c17:[{autologous_tumor_cell_vaccine#10:possible_therapeutic_effects#5},in#14,b16_melanoma_model#16] 52 | stmt6 = f12 c17 53 | 54 | # 11991752 the#0 vaccine#1 was#2 engineered#3 to#4 secrete#5 il-12#6 and#7 il-18#8 by#9 means#10 of#11 the#12 ebv/lipoplex#13 .#14 55 | 56 | f13:[vaccine#1,was_engineered_to#2,secrete_il-12#5] 57 | f14:[vaccine#1,was_engineered_to#2,il-18#8] 58 | c18:[il-18#8,by_means_of#9,ebv/lipoplex#13] 59 | stmt7 = f13 f14 c18 60 | 61 | # 11991752 b16#0 cells#1 were#2 subcutaneously#3 implanted#4 into#5 syngenic#6 mice#7 followed#8 by#9 repetitive#10 immunization#11 with#12 irradiated#13 b16#14 cells#15 that#16 had#17 been#18 transfected#19 3#20 days#21 earlier#22 by#23 tfl2-3#24 ,#25 a#26 novel#27 cationic#28 lipid#29 ,#30 with#31 ebv-plasmid#32 vectors#33 encoding#34 il-12#35 and/or#36 il-18#37 genes#38 .#39 62 | 63 | f15:[b16_cells#0,were_subcutaneously_implanted_into#2,syngenic_mice#6] 64 | f16:[tfl2-3#24,NIL#-1,novel_cationic_lipid#27] 65 | c19:[syngenic_mice#6,followed_by#8,repetitive_immunization#10] 66 | c20:[repetitive_immunization#10,with#12,irradiated_b16_cells#13] 67 | c21:[irradiated_b16_cells#13,had_been_transfected_3_days_earlier_by#17,tfl2-3#24] 68 | c22:[tfl2-3#24,with#31,ebv-plasmid_vectors#32] 69 | c23:[tfl2-3#24,encoding#34,il-12#35] 70 | c24:[tfl2-3#24,encoding#34,il-18_genes#37] 71 | stmt8 = f15 f16 c19 c20 c21 c22 c23 c24 72 | 73 | # 11991752 the#0 mice#1 vaccinated#2 with#3 b16/mil-12#4 underwent#5 strong#6 tumor#7 suppression#8 accompanied#9 by#10 a#11 high#12 ifn-gamma#13 production#14 .#15 74 | 75 | f17:[mice#1,underwent#5,strong_tumor_suppression#6] 76 | c25:[mice#1,vaccinated_with#2,b16/mil-12#4] 77 | c26:[strong_tumor_suppression#6,accompanied_by#9,{high_ifn-gamma#12:production#14}] 78 | stmt9 = f17 c25 c26 79 | 80 | # 11991752 both#0 ctl#1 and#2 nk#3 activities#4 were#5 significantly#6 elevated#7 in#8 these#9 mice#10 .#11 81 | 82 | f18:[{ctl#1:activities#4},were_significantly_elevated_in#5,mice#10] 83 | f19:[{nk#3:activities#4},were_significantly_elevated_in#5,mice#10] 84 | stmt10 = f18 f19 85 | 86 | # 11991752 when#0 the#1 tumor#2 cell#3 vaccine#4 was#5 prepared#6 by#7 means#8 of#9 conventional#10 plasmid#11 vectors#12 combined#13 with#14 the#15 same#16 cationic#17 lipid#18 ,#19 the#20 therapeutic#21 outcome#22 was#23 not#24 as#25 good#26 ,#27 suggesting#28 the#29 superiority#30 of#31 the#32 ebv-based#33 plasmid#34 in#35 engineering#36 these#37 types#38 of#39 tumor#40 vaccines#41 .#42 87 | 88 | f20:[therapeutic_outcome#21,was_not_as_good#23,NIL] 89 | f21:[therapeutic_outcome#21,suggesting#28,NIL] 90 | f22:[{ebv-based_plasmid#33:superiority#30},engineering#36,tumor_vaccines#40] 91 | c27:[tumor_cell_vaccine#2,was_prepared_by_means_of#5,conventional_plasmid_vectors#10] 92 | c28:[conventional_plasmid_vectors#10,combined_with#13,same_cationic_lipid#16] 93 | stmt11 = f20 f21 f22 c27 c28 94 | 95 | # 11991752 vaccination#0 with#1 b16/mil-18#2 was#3 not#4 effective#5 in#6 suppressing#7 tumors#8 ,#9 whereas#10 b16/mil-12+mil-18#11 showed#12 comparable#13 antitumor#14 therapeutic#15 validity#16 as#17 b16/mil-12#18 did#19 .#20 96 | 97 | f23:[vaccination#0,was_not_effective_in_suppressing#3,tumors#8] 98 | f24:[{b16/mil-12+mil-18#11:antitumor_therapeutic_validity#14},showed#12,antitumor_therapeutic_validity#14] 99 | c29:[vaccination#0,with#1,b16/mil-18#2] 100 | c30:[antitumor_therapeutic_validity#14,as_b16/mil-12_did#17,NIL] 101 | stmt12 = f23 f24 c29 c30 102 | 103 | # 11991752 when#0 ifn-gamma#1 mutant#2 mice#3 were#4 treated#5 ,#6 b16/mil-12#7 vaccine#8 did#9 not#10 show#11 any#12 therapeutic#13 activity#14 ,#15 suggesting#16 the#17 necessity#18 of#19 ifn-gamma#20 in#21 the#22 anti-melanoma#23 immune#24 responses#25 .#26 104 | 105 | f25:[b16/mil-12_vaccine#7,did_not_show#9,therapeutic_activity#13] 106 | f26:[{ifn-gamma#20:necessity#18},in#21,anti-melanoma_immune_responses#23] 107 | c31:[ifn-gamma_mutant_mice#1,were_treated#4,NIL] 108 | stmt13 = f25 f26 c31 109 | 110 | # 11991752 in#0 contrast#1 ,#2 the#3 antitumor#4 effect#5 was#6 not#7 affected#8 by#9 nk#10 depletion#11 in#12 mice#13 that#14 received#15 repetitive#16 injections#17 with#18 anti-asialo#19 gm1#20 antibody#21 .#22 111 | 112 | f27:[antitumor_effect#4,was_not_affected_by#6,{nk#10:depletion#11}] 113 | c32:[{nk#10:depletion#11},in#12,mice#13] 114 | c33:[mice#13,received#15,repetitive_injections#16] 115 | c34:[repetitive_injections#16,with#18,anti-asialo_gm1_antibody#19] 116 | stmt14 = f27 c32 c33 c34 117 | 118 | # 11991752 furthermore#0 ,#1 vaccination#2 with#3 b16/mil-12#4 significantly#5 suppressed#6 pulmonary#7 metastases#8 in#9 mice#10 that#11 had#12 been#13 intravenously#14 injected#15 with#16 parental#17 b16#18 .#19 119 | 120 | f28:[vaccination#2,significantly_suppressed#5,pulmonary_metastases#7] 121 | c35:[vaccination#2,with#3,b16/mil-12#4] 122 | c36:[pulmonary_metastases#7,in#9,mice#10] 123 | c37:[mice#10,had_been_intravenously_injected_with#12,parental_b16#17] 124 | stmt15 = f28 c35 c36 c37 125 | 126 | # 11991752 our#0 results#1 suggest#2 that#3 the#4 ebv/lipoplex#5 is#6 quite#7 useful#8 in#9 generating#10 an#11 autologous#12 tumor#13 cell#14 vaccine#15 and#16 that#17 il-12#18 is#19 an#20 important#21 component#22 of#23 the#24 vaccine#25 .#26 127 | 128 | f29:[{NIL#-1:results#1},suggest_that#2,NIL] 129 | f30:[ebv/lipoplex#5,is_quite_useful_in_generating#6,autologous_tumor_cell_vaccine#12] 130 | f31:[il-12#18,is#19,{vaccine#25:important_component#21}] 131 | stmt16 = f29 f30 f31 132 | 133 | -------------------------------------------------------------------------------- /MIMO_service/mimo_server.py: -------------------------------------------------------------------------------- 1 | import sys, os, io 2 | sys.path.append('../') 3 | os.environ[" CUDA_VISIBLE_DEVICES"]="1" 4 | 5 | import random 6 | import json 7 | import torch 8 | import argparse 9 | import struct 10 | import math 11 | import itertools 12 | import copy 13 | import re 14 | import time 15 | import warnings 16 | import gevent.pywsgi 17 | 18 | warnings.filterwarnings('ignore') 19 | 20 | if sys.version_info[0] == 2: 21 | import cPickle as pickle 22 | else: 23 | import pickle 24 | 25 | import numpy as np 26 | import torch.nn as nn 27 | import torch.nn.functional as F 28 | import torch.optim as optim 29 | import torch.autograd as autograd 30 | 31 | from torch.autograd import Variable 32 | from sklearn.utils import shuffle 33 | from nltk.tokenize import sent_tokenize, word_tokenize 34 | from nltk import pos_tag 35 | from spacy.lemmatizer import Lemmatizer 36 | from spacy.lang.en import LEMMA_INDEX, LEMMA_EXC, LEMMA_RULES 37 | from pytorch_pretrained_bert import BertTokenizer, BertModel 38 | from collections import defaultdict as ddict 39 | from collections import Counter 40 | from collections import OrderedDict 41 | 42 | from utils import * 43 | from MIMO import * 44 | from data_center import * 45 | from filter import * 46 | 47 | from flask import Flask, request 48 | from flask import render_template 49 | import json, argparse 50 | app = Flask(__name__) 51 | 52 | clusters = dict() 53 | 54 | parser = argparse.ArgumentParser(description='Implement of SISO, SIMO, MISO, MIMO for Conditional Statement Extraction') 55 | 56 | # Model parameters. 57 | parser.add_argument('--data', type=str, default='./data/stmts-eval-sort.tsv', 58 | help='location of the evaluation set') 59 | parser.add_argument('--output', type=str, default='./predicts/tuples.txt', 60 | help='location of the saved results') 61 | parser.add_argument('--seed', type=int, default=160824, 62 | help='random seed') 63 | parser.add_argument('--cuda', action='store_true', 64 | help='use CUDA') 65 | parser.add_argument('--debug', action='store_true') 66 | parser.add_argument('--local', action='store_true') 67 | parser.add_argument('--wv', action='store_true') 68 | parser.add_argument('--port', type=int, default='9997') 69 | args = parser.parse_args() 70 | 71 | if torch.cuda.is_available(): 72 | if not args.cuda: 73 | print("WARNING: You have a CUDA device, so you should probably run with --cuda") 74 | else: 75 | device_id = torch.cuda.current_device() 76 | print('using device', device_id, torch.cuda.get_device_name(device_id)) 77 | 78 | device = torch.device("cuda" if args.cuda else "cpu") 79 | print('DEVICE:', device) 80 | 81 | def device_model(dumped_models): 82 | models, tokenizer, LM_model, LM_corpus, mimo_extractor_fact, mimo_extractor_cond, multi_head, multi_head_two = dumped_models 83 | for model in models: 84 | model.to(device) 85 | model.device = device 86 | model.model_LSTM_decoder.device = device 87 | LM_model.to(device) 88 | mimo_extractor_fact.to(device) 89 | mimo_extractor_cond.to(device) 90 | multi_head.to(device) 91 | multi_head_two.to(device) 92 | dumped_models = [models, tokenizer, LM_model, LM_corpus, mimo_extractor_fact, mimo_extractor_cond, multi_head, multi_head_two] 93 | return dumped_models 94 | 95 | def getEmbeddings(phr_list): 96 | embed_list = [] 97 | for phr in phr_list: 98 | if phr in wv_model.vocab: 99 | embed_list.append(wv_model.word_vec(phr)) 100 | # else: 101 | # vec = np.zeros(50, np.float32) 102 | # wrds = word_tokenize(phr) 103 | # for wrd in wrds: 104 | # if wrd in wv_model.vocab: 105 | # vec += wv_model.word_vec(wrd) 106 | # else: vec += np.random.randn(50) 107 | # embed_list.append(vec / len(wrds)) 108 | else: 109 | vecs = [] 110 | wrds = word_tokenize(phr) 111 | for wrd in wrds: 112 | if wrd in wv_model.vocab: 113 | vecs.append(wv_model.word_vec(wrd)) 114 | else: vecs.append(np.random.randn(50)) 115 | vec = np.max(np.asarray(vecs), axis=0) 116 | embed_list.append(vec) 117 | 118 | embs = np.array(embed_list) 119 | embs = embs/np.expand_dims(np.linalg.norm(embs,ord=2,axis=1), 1) 120 | return embs 121 | 122 | def CFE_Data_Transform(text): 123 | dataCenter.WPC_Data_Transform(text) 124 | DATA = dataCenter.get_data_to_predict() 125 | CFE_list = run_mimo(dumped_models, dataCenter, DATA, device=device) 126 | 127 | statements = {} 128 | stmts_tagging = [[] for i in range(len(CFE_list))] 129 | stmt_id = 1 130 | for CFE in CFE_list: 131 | sentence = CFE[0] 132 | index = int(CFE[3].stmt_id.split('stmt ')[-1])-1 133 | facts, conds = CFE[1:3] 134 | concpet_indx = [] 135 | attr_indx = [] 136 | predicate_indx = [] 137 | if len(facts) == 0 and len(conds) == 0: 138 | stmt_id += 1 139 | stmts_tagging[index] = [sentence, concpet_indx, attr_indx, predicate_indx] 140 | continue 141 | fact_tuples = [] 142 | for fact in facts: 143 | fact_tuples.append([x[0].replace('_', ' ') if x!='NIL' else 'NIL' for x in fact]) 144 | assert len(fact) == 5 145 | for i in range(len(fact)): 146 | unit = fact[i] 147 | if i in [0, 3]: 148 | concpet_indx.extend(list(range(unit[1], unit[2])) if unit!='NIL' else []) 149 | if i in [1, 4]: 150 | attr_indx.extend(list(range(unit[1], unit[2])) if unit!='NIL' else []) 151 | if i == 2: 152 | predicate_indx.extend(list(range(unit[1], unit[2])) if unit!='NIL' else []) 153 | # c1, a1, r, c3, a3 = fact_tuples[-1] 154 | cond_tuples = [] 155 | for cond in conds: 156 | cond_tuples.append([x[0].replace('_', ' ') if x!= 'NIL' else 'NIL' for x in cond]) 157 | assert len(cond) == 5 158 | for i in range(len(cond)): 159 | unit = cond[i] 160 | if i in [0, 3]: 161 | concpet_indx.extend(list(range(unit[1], unit[2])) if unit!='NIL' else []) 162 | if i in [1, 4]: 163 | attr_indx.extend(list(range(unit[1], unit[2])) if unit!='NIL' else []) 164 | if i == 2: 165 | predicate_indx.extend(list(range(unit[1], unit[2])) if unit!='NIL' else []) 166 | # c1, a1, r, c3, a3 = cond_tuples[-1] 167 | 168 | concpet_indx = sorted(list(set(concpet_indx))) 169 | attr_indx = sorted(list(set(attr_indx))) 170 | predicate_indx = sorted(list(set(predicate_indx))) 171 | _statement = {'text': ' '.join(sentence), 'fact tuples': fact_tuples, 'condition tuples': cond_tuples, 'concept_indx': concpet_indx, 'attr_indx': attr_indx, 'predicate_indx': predicate_indx} 172 | 173 | _statement = tuple_filter(_statement) 174 | 175 | statements[CFE[3].stmt_id] = _statement 176 | stmt_id += 1 177 | stmts_tagging[index] = [sentence, concpet_indx, attr_indx, predicate_indx] 178 | 179 | return statements, stmts_tagging 180 | 181 | def get_nice_tuple(_tuple): 182 | _subject = _tuple[0] 183 | relation = _tuple[2] 184 | _object = _tuple[3] 185 | if _tuple[1] != 'NIL' and _tuple[1] != 'nil': 186 | _subject = f'{{{_subject}: {_tuple[1]}}}' 187 | if _tuple[4] != 'NIL' and _tuple[4] != 'nil': 188 | _object = f'{{{_object}: {_tuple[4]}}}' 189 | 190 | nice_form = f'({_subject}, {relation}, {_object})' 191 | nice_form = nice_form.replace("'", "`").replace('"', '``') 192 | return nice_form 193 | 194 | def run_search(text): 195 | statements, stmts_tagging = CFE_Data_Transform(text) 196 | 197 | return statements, stmts_tagging 198 | 199 | @app.route('/', methods=['GET', 'POST']) 200 | def home(): 201 | return render_template('index.html') 202 | 203 | @app.route('/mimo', methods=['GET', 'POST']) 204 | def mimo(): 205 | if request.method == 'POST': 206 | start_time = time.time() 207 | text = request.get_json()['text'] 208 | 209 | statements, stmts_tagging = run_search(text) 210 | print('Searching elapse: ', time.time() - start_time) 211 | 212 | return json.dumps({'statements': statements}) 213 | else: 214 | return 'Error! in mimo' 215 | 216 | 217 | def debug(): 218 | text = 'Histone deacetylase inhibitor valproic acid (VPA) has been used to increase the reprogramming efficiency of induced pluripotent stem cell (iPSC) from somatic cells, yet the specific molecular mechanisms underlying this effect is unknown. Here, we demonstrate that reprogramming with lentiviruses carrying the iPSC-inducing factors (Oct4-Sox2-Klf4-cMyc, OSKM) caused senescence in mouse fibroblasts, establishing a stress barrier for cell reprogramming. Administration of VPA protected cells from reprogramming-induced senescent stress. Using an in vitro pre-mature senescence model, we found that VPA treatment increased cell proliferation and inhibited apoptosis through the suppression of the p16/p21 pathway. In addition, VPA also inhibited the G2/M phase blockage derived from the senescence stress. These findings highlight the role of VPA in breaking the cell senescence barrier required for the induction of pluripotency.' 219 | 220 | print('================================================================') 221 | print(text) 222 | 223 | statements, stmts_tagging = run_search(text) 224 | print(statements) 225 | 226 | if __name__ == "__main__": 227 | random.seed(args.seed) 228 | np.random.seed(args.seed) 229 | torch.manual_seed(args.seed) 230 | torch.cuda.manual_seed_all(args.seed) 231 | 232 | # dataCenter = DataCenter(None, args.data) 233 | # DATA = dataCenter.get_data_to_predict() 234 | dataCenter = DataCenter() 235 | print('loading models') 236 | dumped_models = device_model(torch.load('../resources/dumped_models.pt', map_location=device)) 237 | print('done.') 238 | 239 | print('loading word2vector models') 240 | if args.wv: 241 | wv_model = gensim.models.KeyedVectors.load_word2vec_format('./word2vector/glove.6B.50d_word2vec.txt', binary=False) 242 | threshold = 0.8 243 | else: 244 | wv_model = gensim.models.KeyedVectors.load_word2vec_format('../resources/pubmed-vectors=50.bin', binary=True) 245 | # pickle.dump(wv_model, open('./word2vector/pubmed-wv_model.pkl','wb')) 246 | # wv_model = pickle.load(open('./word2vector/pubmed-wv_model.pkl','rb')) 247 | threshold = 0.8 248 | 249 | print('done.') 250 | 251 | if args.debug: 252 | debug() 253 | else: 254 | print("MIMO Server Running") 255 | app.run(host='127.0.0.1', port=args.port) 256 | # app_server = gevent.pywsgi.WSGIServer(('127.0.0.1', args.port), app) 257 | # app_server.serve_forever() 258 | -------------------------------------------------------------------------------- /data_center.py: -------------------------------------------------------------------------------- 1 | import sys, os, io 2 | import random 3 | import torch 4 | import logging 5 | import argparse 6 | 7 | class Instance(object): 8 | """docstring for Instance""" 9 | def __init__(self, paper_id, stmt_id, multi_input, multi_output): 10 | super(Instance, self).__init__() 11 | 12 | self.paper_id = paper_id 13 | self.stmt_id = stmt_id 14 | self.multi_input = multi_input 15 | self.multi_output = multi_output 16 | 17 | self.SENTENCE = None 18 | self.POSTAG = None 19 | self.CAP = None 20 | self.LM_SENTENCE = None 21 | self.OUT = None 22 | 23 | class DataCenter(object): 24 | """docstring for Instance""" 25 | def __init__(self, train_file, eval_file): 26 | super(DataCenter, self).__init__() 27 | 28 | self.POS2ID, self.ID2POS = self.getTag2ID('./resources/PosTag2ID.txt') 29 | self.CAP2ID, self.ID2CAP = self.getTag2ID('./resources/CAPTag2ID.txt') 30 | 31 | self.Tag2ID_fact, self.ID2Tag_fact = self.getTag2ID('./resources/OutTag2ID_fact.txt') 32 | self.Tag2ID_condition, self.ID2Tag_condition = self.getTag2ID('./resources/OutTag2ID_condition.txt') 33 | 34 | self.Tag2Num = dict() 35 | 36 | self.TRAIN_SENTENCEs = [] 37 | self.TRAIN_POSTAGs = [] 38 | self.TRAIN_CAPs = [] 39 | self.TRAIN_OUTs = [] 40 | 41 | self.ex_TRAIN_SENTENCEs = [] 42 | self.ex_TRAIN_POSTAGs = [] 43 | self.ex_TRAIN_CAPs = [] 44 | self.ex_TRAIN_OUTs = [] 45 | 46 | self.EVAL_SENTENCEs = [] 47 | self.EVAL_POSTAGs = [] 48 | self.EVAL_CAPs = [] 49 | self.EVAL_OUTs = [] 50 | 51 | self.max_outpus = 0 52 | 53 | self.instance_TRAIN = [] 54 | self.instance_EVAL = [] 55 | self.instance_ex_TRAIN = [] 56 | 57 | self.paper_id_set_TRAIN = set() 58 | self.paper_id_set_EVAL = set() 59 | self.paper_id_set_ex_TRAIN = set() 60 | 61 | self.loading_dataset(train_file, eval_file) 62 | 63 | def getTag2ID(self, fileName): 64 | tag2ID = dict() 65 | ID2Tag = dict() 66 | with open(fileName, 'r') as f: 67 | for line in f: 68 | tag, _id = line.strip().split(' ') 69 | tag2ID[tag] = int(_id) 70 | ID2Tag[int(_id)] = tag 71 | return tag2ID, ID2Tag 72 | 73 | def _add_instance(self, dataset_type, paper_id, stmt_id, multi_input, multi_output, attr_tuple): 74 | if len(multi_input) == 0: 75 | return 76 | 77 | SENTENCEs, POSTAGs, CAPs, OUTs = attr_tuple 78 | instance = Instance(paper_id, stmt_id, multi_input, multi_output) 79 | senLen = len(instance.multi_input[0][-1]) 80 | # print(instance.multi_input[0][-1]) 81 | for _input in instance.multi_input: 82 | seq_name = _input[0] 83 | seq = _input[1] 84 | if seq_name == 'WORD': 85 | sentence = [] 86 | for word in seq: 87 | sentence.append(word.lower()) 88 | assert len(sentence) == senLen 89 | SENTENCEs.append(sentence) 90 | instance.SENTENCE = seq 91 | # formatted_anno_file.write('WORD:\t'+'\t'.join(sentence)+'\n') 92 | elif seq_name == 'POSTAG': 93 | assert len(seq) == senLen 94 | POSTAGs.append(seq) 95 | instance.POSTAG = seq 96 | # formatted_anno_file.write('POSTAG:\t'+'\t'.join(seq)+'\n') 97 | else: 98 | assert len(seq) == senLen 99 | CAPs.append(seq) 100 | instance.CAP = seq 101 | # formatted_anno_file.write('CAP:\t'+'\t'.join(seq)+'\n') 102 | 103 | # print 'OUT:' 104 | facts_out = [self.Tag2ID_fact['O']] * senLen 105 | conditions_out = [self.Tag2ID_condition['O']] * senLen 106 | 107 | predicate_fact = dict() 108 | predicate_cond = dict() 109 | for _output in instance.multi_output: 110 | key = _output[0] 111 | seq = _output[1] 112 | if key.startswith('f'): 113 | if 'B-f2P' in seq: 114 | p_index = seq.index('B-f2P') 115 | if p_index not in predicate_fact: 116 | predicate_fact[p_index] = [] 117 | predicate_fact[p_index].append([self.Tag2ID_fact[tag] for tag in seq]) 118 | # print('F_G: ', seq) 119 | else: 120 | if -1 not in predicate_fact: 121 | predicate_fact[-1] = [] 122 | # print('F_G: ', seq) 123 | predicate_fact[-1].append([self.Tag2ID_fact[tag] for tag in seq]) 124 | else: 125 | if 'B-c2P' in seq: 126 | p_index = seq.index('B-c2P') 127 | if p_index not in predicate_cond: 128 | predicate_cond[p_index] = [] 129 | # print('C_G: ', seq) 130 | predicate_cond[p_index].append([self.Tag2ID_condition[tag] for tag in seq]) 131 | else: 132 | if -1 not in predicate_cond: 133 | predicate_cond[-1] = [] 134 | # print('C_G: ', seq) 135 | predicate_cond[-1].append([self.Tag2ID_condition[tag] for tag in seq]) 136 | 137 | for index in range(len(seq)): 138 | tag = seq[index] 139 | # print tag, 140 | if key.startswith('f'): 141 | if tag != 'O': 142 | facts_out[index] = self.Tag2ID_fact[tag] 143 | else: 144 | if tag != 'O': 145 | conditions_out[index] = self.Tag2ID_condition[tag] 146 | 147 | for index in range(len(facts_out)): 148 | tag_id_fact = facts_out[index] 149 | tag_id_condition = conditions_out[index] 150 | if dataset_type == 'TRAIN': 151 | self.count_tag(self.ID2Tag_fact[tag_id_fact]) 152 | self.count_tag(self.ID2Tag_condition[tag_id_condition]) 153 | 154 | multi_facts = [facts_out, ] 155 | multi_conds = [conditions_out, ] 156 | # print([self.ID2Tag_fact[tag_id] for tag_id in facts_out]) 157 | # print([self.ID2Tag_condition[tag_id] for tag_id in conditions_out]) 158 | # print(predicate_fact.keys()) 159 | for p_index in sorted(predicate_fact): 160 | facts_out = [self.Tag2ID_fact['O']] * senLen 161 | for seq in predicate_fact[p_index]: 162 | for index in range(len(seq)): 163 | tag_id = seq[index] 164 | if tag_id != 0: 165 | facts_out[index] = tag_id 166 | # print([self.ID2Tag_fact[tag_id] for tag_id in facts_out]) 167 | multi_facts.append(facts_out) 168 | for p_index in sorted(predicate_cond): 169 | conds_out = [self.Tag2ID_condition['O']] * senLen 170 | for seq in predicate_cond[p_index]: 171 | for index in range(len(seq)): 172 | tag_id = seq[index] 173 | if tag_id != 0: 174 | conds_out[index] = tag_id 175 | # print([self.ID2Tag_condition[tag_id] for tag_id in conds_out]) 176 | multi_conds.append(conds_out) 177 | # print('===========================================================') 178 | assert len(facts_out) == len(conditions_out) == senLen 179 | 180 | # print(multi_facts) 181 | # print(multi_conds) 182 | outs = [multi_facts, multi_conds] 183 | OUTs.append(outs) 184 | instance.OUT = outs 185 | 186 | assert len(SENTENCEs) == len(POSTAGs) ==len(CAPs) == len(OUTs) 187 | if len(SENTENCEs) % 10000 == 0: 188 | print(len(SENTENCEs), 'done') 189 | 190 | instance_list = getattr(self, 'instance_'+dataset_type) 191 | instance_list.append(instance) 192 | 193 | def count_tag(self, tag): 194 | if tag not in self.Tag2Num: 195 | self.Tag2Num[tag] = 0 196 | self.Tag2Num[tag] += 1 197 | 198 | def _loading_dataset(self, dataset_type, dataFile): 199 | 200 | SENTENCEs = getattr(self, dataset_type+'_SENTENCEs') 201 | POSTAGs = getattr(self, dataset_type+'_POSTAGs') 202 | CAPs = getattr(self, dataset_type+'_CAPs') 203 | OUTs = getattr(self, dataset_type+'_OUTs') 204 | instance_list = getattr(self, 'instance_'+dataset_type) 205 | 206 | del SENTENCEs[:] 207 | del POSTAGs[:] 208 | del CAPs[:] 209 | del OUTs[:] 210 | del instance_list[:] 211 | 212 | attr_tuple = (SENTENCEs, POSTAGs, CAPs, OUTs) 213 | 214 | logging.debug('loading '+dataset_type+' data from '+dataFile) 215 | 216 | paper_id_set = getattr(self, 'paper_id_set_'+dataset_type) 217 | paper_id = 'none' 218 | stmt_id = '0' 219 | multi_input = [] 220 | multi_output = [] 221 | previous = False 222 | 223 | # formatted_anno_file = open(dataFile.replace('.tsv', '_formatted.tsv'), 'w') 224 | 225 | with open(dataFile, 'r') as fd: 226 | for line in fd: 227 | if line.startswith('=====') or line.startswith('#'): 228 | # conclude the previous instance 229 | if previous: 230 | self._add_instance(dataset_type, paper_id, stmt_id, multi_input, multi_output, attr_tuple) 231 | 232 | # start a new instance 233 | if not line.startswith('====='): 234 | continue 235 | paper_id = line.strip().split('===== ')[-1].split(' stmt')[0] 236 | paper_id_set.add(paper_id) 237 | stmt_id = line.split('stmt')[-1].split(' =====')[0] 238 | # logging.debug('doing the paper '+paper_id+', stmt '+stmt_id) 239 | multi_input = [] 240 | multi_output = [] 241 | previous = True 242 | # formatted_anno_file.write(line) 243 | continue 244 | line_list = line.strip('\n').split('\t') 245 | seq_name = line_list[0] 246 | seq = line_list[1:] 247 | if seq_name in ['WORD', 'POSTAG', 'CAP']: 248 | multi_input.append((seq_name, seq)) 249 | else: 250 | multi_output.append((seq_name, seq)) 251 | 252 | # formatted_anno_file.close() 253 | 254 | instance_list = getattr(self, 'instance_'+dataset_type) 255 | 256 | print(len(SENTENCEs), len(POSTAGs), len(CAPs)) 257 | 258 | print('done.') 259 | 260 | # def loading_dataset(self, trainFile, validFile, testFile): 261 | def loading_dataset(self, trainFile, evalFile, exTrainFile=None): 262 | 263 | if trainFile != None: 264 | self._loading_dataset('TRAIN', trainFile) 265 | 266 | if evalFile != None: 267 | self._loading_dataset('EVAL', evalFile) 268 | 269 | if exTrainFile != None: 270 | self._loading_dataset('ex_TRAIN', exTrainFile) 271 | 272 | def get_evaluation(self, valid_prop, dataset_type='EVAL'): 273 | 274 | VALID_SENTENCEs = [] 275 | VALID_POSTAGs = [] 276 | VALID_CAPs = [] 277 | VALID_OUTs = [] 278 | VALID_instances = [] 279 | 280 | TEST_SENTENCEs = [] 281 | TEST_POSTAGs = [] 282 | TEST_CAPs = [] 283 | TEST_OUTs = [] 284 | TEST_instances = [] 285 | 286 | SENTENCEs = getattr(self, dataset_type+'_SENTENCEs') 287 | POSTAGs = getattr(self, dataset_type+'_POSTAGs') 288 | CAPs = getattr(self, dataset_type+'_CAPs') 289 | OUTs = getattr(self, dataset_type+'_OUTs') 290 | instance_list = getattr(self, 'instance_'+dataset_type) 291 | 292 | #print range(len(self.EVAL_SENTENCEs)) 293 | id_list = random.sample(range(len(SENTENCEs)), int(len(SENTENCEs)*valid_prop)) 294 | #print id_list 295 | for index in range(len(SENTENCEs)): 296 | if index not in id_list: 297 | TEST_SENTENCEs.append(SENTENCEs[index]) 298 | TEST_POSTAGs.append(POSTAGs[index]) 299 | TEST_CAPs.append(CAPs[index]) 300 | TEST_OUTs.append(OUTs[index]) 301 | TEST_instances.append(instance_list[index]) 302 | else: 303 | VALID_SENTENCEs.append(SENTENCEs[index]) 304 | VALID_POSTAGs.append(POSTAGs[index]) 305 | VALID_CAPs.append(CAPs[index]) 306 | VALID_OUTs.append(OUTs[index]) 307 | VALID_instances.append(instance_list[index]) 308 | 309 | VALID_DATA = (VALID_SENTENCEs, VALID_POSTAGs, VALID_CAPs, VALID_OUTs, VALID_instances) 310 | 311 | TEST_DATA = (TEST_SENTENCEs, TEST_POSTAGs, TEST_CAPs, TEST_OUTs, TEST_instances) 312 | 313 | return VALID_DATA, TEST_DATA 314 | 315 | def get_trainning_data(self, is_semi=False): 316 | SENTENCEs = getattr(self, 'TRAIN_SENTENCEs') 317 | POSTAGs = getattr(self, 'TRAIN_POSTAGs') 318 | CAPs = getattr(self, 'TRAIN_CAPs') 319 | OUTs = getattr(self, 'TRAIN_OUTs') 320 | if is_semi: 321 | ex_SENTENCEs = getattr(self, 'ex_TRAIN_SENTENCEs') 322 | ex_POSTAGs = getattr(self, 'ex_TRAIN_POSTAGs') 323 | ex_CAPs = getattr(self, 'ex_TRAIN_CAPs') 324 | ex_OUTs = getattr(self, 'ex_TRAIN_OUTs') 325 | SENTENCEs.extend(ex_SENTENCEs) 326 | POSTAGs.extend(ex_POSTAGs) 327 | CAPs.extend(ex_CAPs) 328 | OUTs.extend(ex_OUTs) 329 | print(len(SENTENCEs), len(POSTAGs), len(CAPs), len(OUTs)) 330 | return SENTENCEs, POSTAGs, CAPs, OUTs 331 | --------------------------------------------------------------------------------