bionlp-ost-19-BB-rel-train  

BB-rel@ldeleger:BB-rel-19396518 JSONTXT

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Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T1 0-104 Title denotes Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR.
T3 35-44 Phenotype denotes pathogens
T2 105-1735 Paragraph denotes We aimed to detect causative pathogens in cerebrospinal fluid (CSF) collected from patients diagnosed with bacterial meningitis by real-time polymerase chain reaction (PCR). In addition to Streptococcus pneumoniae, Haemophilus influenzae, and Mycoplasma pneumoniae described previously, five other pathogens, Neisseria meningitidis, Escherichia coli, Streptococcus agalactiae, Staphylococcus aureus, and Listeria monocytogenes, were targeted, based on a large-scale surveillance in Japan. Results in CSF from neonates and children (n=150), and from adults (n=18) analyzed by real-time PCR with molecular beacon probes were compared with those of conventional culturing. The total time from DNA extraction from CSF to PCR analysis was 1.5 h. The limit of detection for these pathogens ranged from 5 copies to 28 copies per tube. Nonspecific positive reactions were not recognized for 37 microorganisms in clinical isolates as a negative control. The pathogens were detected in 72.0% of the samples by real-time PCR, but in only 48.2% by culture, although the microorganisms were completely concordant. With the real-time PCR, the detection rate of H. influenzae from CSF was high, at 45.2%, followed by S. pneumoniae (21.4%), S. agalactiae (2.4%), E. coli (1.8%), L. monocytogenes (0.6%), and M. pneumoniae (0.6%). The detection rate with PCR was significantly better than that with cultures in patients with antibiotic administration (chi2=18.3182; P=0.0000). In conclusion, detection with real-time PCR is useful for rapidly identifying the causative pathogens of meningitis and for examining the clinical course of chemotherapy.
T4 134-143 Phenotype denotes pathogens
T5 147-166 Habitat denotes cerebrospinal fluid
T6 168-171 Habitat denotes CSF
T7 188-232 Habitat denotes patients diagnosed with bacterial meningitis
T8 294-318 Microorganism denotes Streptococcus pneumoniae
E1 294-318 Lives_In denotes Streptococcus pneumoniae
E2 294-318 Exhibits denotes Streptococcus pneumoniae
T9 320-342 Microorganism denotes Haemophilus influenzae
E3 320-342 Lives_In denotes Haemophilus influenzae
E4 320-342 Exhibits denotes Haemophilus influenzae
T10 348-369 Microorganism denotes Mycoplasma pneumoniae
E5 348-369 Lives_In denotes Mycoplasma pneumoniae
E6 348-369 Exhibits denotes Mycoplasma pneumoniae
T11 403-412 Phenotype denotes pathogens
T12 414-436 Microorganism denotes Neisseria meningitidis
E7 414-436 Lives_In denotes Neisseria meningitidis
E8 414-436 Exhibits denotes Neisseria meningitidis
T13 438-454 Microorganism denotes Escherichia coli
E9 438-454 Lives_In denotes Escherichia coli
E10 438-454 Exhibits denotes Escherichia coli
T14 456-480 Microorganism denotes Streptococcus agalactiae
E11 456-480 Lives_In denotes Streptococcus agalactiae
E12 456-480 Exhibits denotes Streptococcus agalactiae
T15 482-503 Microorganism denotes Staphylococcus aureus
E13 482-503 Lives_In denotes Staphylococcus aureus
E14 482-503 Exhibits denotes Staphylococcus aureus
T16 509-531 Microorganism denotes Listeria monocytogenes
E15 509-531 Lives_In denotes Listeria monocytogenes
E16 509-531 Exhibits denotes Listeria monocytogenes
T17 587-592 Geographical denotes Japan
T19-0 605-608 _FRAGMENT denotes CSF
T18 605-635 Habitat denotes CSF from neonates and children
T20 614-622 Habitat denotes neonates
T21 627-635 Habitat denotes children
T19-1 649-660 Habitat denotes from adults
T22 654-660 Habitat denotes adults
T23 815-818 Habitat denotes CSF
T24 879-888 Phenotype denotes pathogens
T25 1009-1017 Habitat denotes clinical
T26 1054-1063 Phenotype denotes pathogens
T27 1252-1265 Microorganism denotes H. influenzae
E17 1252-1265 Lives_In denotes H. influenzae
E18 1252-1265 Lives_In denotes H. influenzae
T28 1271-1274 Habitat denotes CSF
T29 1307-1320 Microorganism denotes S. pneumoniae
E19 1307-1320 Lives_In denotes S. pneumoniae
E20 1307-1320 Lives_In denotes S. pneumoniae
T30 1330-1343 Microorganism denotes S. agalactiae
E21 1330-1343 Lives_In denotes S. agalactiae
E22 1330-1343 Lives_In denotes S. agalactiae
T31 1352-1359 Microorganism denotes E. coli
E23 1352-1359 Lives_In denotes E. coli
E24 1352-1359 Lives_In denotes E. coli
T32 1368-1384 Microorganism denotes L. monocytogenes
E25 1368-1384 Lives_In denotes L. monocytogenes
E26 1368-1384 Lives_In denotes L. monocytogenes
T33 1397-1410 Microorganism denotes M. pneumoniae
E27 1397-1410 Lives_In denotes M. pneumoniae
E28 1397-1410 Lives_In denotes M. pneumoniae
T34 1499-1538 Habitat denotes patients with antibiotic administration
T35 1657-1666 Phenotype denotes pathogens
C-T19-0 T19-1 T19-0 _lexicallyChainedTo from adults,CSF
R1 E1 T8 Microorganism Streptococcus pneumoniae,Streptococcus pneumoniae
R10 E5 T17 Location Mycoplasma pneumoniae,Japan
R11 E6 T10 Microorganism Mycoplasma pneumoniae,Mycoplasma pneumoniae
R12 E6 T11 Property Mycoplasma pneumoniae,pathogens
R13 E7 T12 Microorganism Neisseria meningitidis,Neisseria meningitidis
R14 E7 T17 Location Neisseria meningitidis,Japan
R15 E8 T12 Microorganism Neisseria meningitidis,Neisseria meningitidis
R16 E8 T11 Property Neisseria meningitidis,pathogens
R17 E9 T13 Microorganism Escherichia coli,Escherichia coli
R18 E9 T17 Location Escherichia coli,Japan
R19 E10 T13 Microorganism Escherichia coli,Escherichia coli
R2 E1 T17 Location Streptococcus pneumoniae,Japan
R20 E10 T11 Property Escherichia coli,pathogens
R21 E11 T14 Microorganism Streptococcus agalactiae,Streptococcus agalactiae
R22 E11 T17 Location Streptococcus agalactiae,Japan
R23 E12 T14 Microorganism Streptococcus agalactiae,Streptococcus agalactiae
R24 E12 T11 Property Streptococcus agalactiae,pathogens
R25 E13 T15 Microorganism Staphylococcus aureus,Staphylococcus aureus
R26 E13 T17 Location Staphylococcus aureus,Japan
R27 E14 T15 Microorganism Staphylococcus aureus,Staphylococcus aureus
R28 E14 T11 Property Staphylococcus aureus,pathogens
R29 E15 T16 Microorganism Listeria monocytogenes,Listeria monocytogenes
R3 E2 T8 Microorganism Streptococcus pneumoniae,Streptococcus pneumoniae
R30 E15 T17 Location Listeria monocytogenes,Japan
R31 E16 T16 Microorganism Listeria monocytogenes,Listeria monocytogenes
R32 E16 T11 Property Listeria monocytogenes,pathogens
R33 E17 T27 Microorganism H. influenzae,H. influenzae
R34 E17 T28 Location H. influenzae,CSF
R35 E18 T27 Microorganism H. influenzae,H. influenzae
R36 E18 T34 Location H. influenzae,patients with antibiotic administration
R37 E19 T29 Microorganism S. pneumoniae,S. pneumoniae
R38 E19 T28 Location S. pneumoniae,CSF
R39 E20 T29 Microorganism S. pneumoniae,S. pneumoniae
R4 E2 T11 Property Streptococcus pneumoniae,pathogens
R40 E20 T34 Location S. pneumoniae,patients with antibiotic administration
R41 E21 T30 Microorganism S. agalactiae,S. agalactiae
R42 E21 T34 Location S. agalactiae,patients with antibiotic administration
R43 E22 T30 Microorganism S. agalactiae,S. agalactiae
R44 E22 T28 Location S. agalactiae,CSF
R45 E23 T31 Microorganism E. coli,E. coli
R46 E23 T28 Location E. coli,CSF
R47 E24 T31 Microorganism E. coli,E. coli
R48 E24 T34 Location E. coli,patients with antibiotic administration
R49 E25 T32 Microorganism L. monocytogenes,L. monocytogenes
R5 E3 T9 Microorganism Haemophilus influenzae,Haemophilus influenzae
R50 E25 T28 Location L. monocytogenes,CSF
R51 E26 T32 Microorganism L. monocytogenes,L. monocytogenes
R52 E26 T34 Location L. monocytogenes,patients with antibiotic administration
R53 E27 T33 Microorganism M. pneumoniae,M. pneumoniae
R54 E27 T28 Location M. pneumoniae,CSF
R55 E28 T33 Microorganism M. pneumoniae,M. pneumoniae
R56 E28 T34 Location M. pneumoniae,patients with antibiotic administration
R6 E3 T17 Location Haemophilus influenzae,Japan
R7 E4 T9 Microorganism Haemophilus influenzae,Haemophilus influenzae
R8 E4 T11 Property Haemophilus influenzae,pathogens
R9 E5 T10 Microorganism Mycoplasma pneumoniae,Mycoplasma pneumoniae