BB-norm@ldeleger:BB-norm-19396518 JSONTXT

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bionlp-ost-19-BB-norm-train

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

Id Subject Object Predicate Lexical cue NCBI_Taxonomy OntoBiotope
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 OBT:000375
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 OBT:002806
T5 147-166 Habitat denotes cerebrospinal fluid OBT:000550
T6 168-171 Habitat denotes CSF OBT:000550
T7 188-232 Habitat denotes patients diagnosed with bacterial meningitis OBT:003269
T8 294-318 Microorganism denotes Streptococcus pneumoniae 1313
T9 320-342 Microorganism denotes Haemophilus influenzae 727
T10 348-369 Microorganism denotes Mycoplasma pneumoniae 2104
T11 403-412 Phenotype denotes pathogens OBT:002806
T12 414-436 Microorganism denotes Neisseria meningitidis 487
T13 438-454 Microorganism denotes Escherichia coli 562
T14 456-480 Microorganism denotes Streptococcus agalactiae 1311
T15 482-503 Microorganism denotes Staphylococcus aureus 1280
T16 509-531 Microorganism denotes Listeria monocytogenes 1639
T17 605-635 Habitat denotes CSF from neonates and children OBT:000550
T18-0 605-608 _FRAGMENT denotes CSF OBT:000550
T18-1 649-660 Habitat denotes from adults
T19 614-622 Habitat denotes neonates OBT:003453|OBT:003269
T20 627-635 Habitat denotes children OBT:003188|OBT:003269
T21 654-660 Habitat denotes adults OBT:003245|OBT:003269
T22 815-818 Habitat denotes CSF OBT:000550
T23 879-888 Phenotype denotes pathogens OBT:002806
T24 1009-1017 Habitat denotes clinical OBT:003220
T25 1054-1063 Phenotype denotes pathogens OBT:002806
T26 1252-1265 Microorganism denotes H. influenzae 727
T27 1271-1274 Habitat denotes CSF OBT:000550
T28 1307-1320 Microorganism denotes S. pneumoniae 1313
T29 1330-1343 Microorganism denotes S. agalactiae 1311
T30 1352-1359 Microorganism denotes E. coli 562
T31 1368-1384 Microorganism denotes L. monocytogenes 1639
T32 1397-1410 Microorganism denotes M. pneumoniae 1313
T33 1499-1538 Habitat denotes patients with antibiotic administration OBT:003269
T34 1657-1666 Phenotype denotes pathogens OBT:002806
C-T18-0 T18-1 T18-0 _lexicallyChainedTo from adults,CSF