diff --git a/.gitignore b/.gitignore index 7b829ec7858ac542d09b369d49277eed61cee8d8..eb351eb32c3cf253392b84eb829fbd4f16513aad 100644 --- a/.gitignore +++ b/.gitignore @@ -27,6 +27,31 @@ corpora/genbank/mapped_habitats.txt corpora/genbank/mapped_taxids.txt corpora/genbank/taxids.txt corpora/genbank/test-3.2.txt +corpora/*/batches/*/adb/ +corpora/*/batches/*/alvisnlp.log +corpora/*/batches/*/anaphora.txt +corpora/*/batches/*/bacteria.txt +corpora/*/batches/*/dependencies.txt +corpora/*/batches/*/doc-mesh.txt +corpora/*/batches/*/geo.txt +corpora/*/batches/*/habitats.txt +corpora/*/batches/*/index-food/ +corpora/*/batches/*/index/ +corpora/*/batches/*/microorganisms-short.txt +corpora/*/batches/*/microorganisms.txt +corpora/*/batches/*/phenotype-relations.txt +corpora/*/batches/*/phenotypes.txt +corpora/*/batches/*/relations.txt +corpora/*/batches/*/sentences.txt +corpora/*/batches/*/success.txt +corpora/*/batches/*/taxa.txt +corpora/*/batches/*/uses-relations.txt +corpora/*/batches/*/uses.txt +corpora/*/batches/*/words.txt +corpora/*/batches/*/yatea-var/ +corpora/*/batches/*/yatea/ +corpora/BioNLP-OST-2019/batches/*/a2/ +corpora/BioNLP-OST-2019/batches/*/predictions.zip corpora/*/batch/*/adb/ corpora/*/batch/*/alvisnlp.log corpora/*/batch/*/anaphora.txt @@ -56,14 +81,20 @@ corpora/BioNLP-OST-2019/batch/*/eval.json corpora/BioNLP-OST-2019/batch/*/predictions.zip corpora/microbes-2019/*.full.txt corpora/microbes-2019/index/ +corpora/BioNLP-OST-2019/batches/*/eval.json +corpora/BioNLP-OST-2019/batches/*/eval.txt +corpora/BioNLP-OST-2019/batches/*/errors.csv .snakemake/ ancillaries/extended-microorganisms-taxonomy +ancillaries/BioNLP-OST+EnovFood-Habitat.obo ancillaries/BioNLP-OST+EnovFood-Habitat.json ancillaries/BioNLP-OST+EnovFood-Habitat.paths ancillaries/BioNLP-OST+EnovFood-Habitat.tomap +ancillaries/BioNLP-OST+EnovFood-Phenotype.obo ancillaries/BioNLP-OST+EnovFood-Phenotype.json ancillaries/BioNLP-OST+EnovFood-Phenotype.paths ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap +ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo ancillaries/NCBI_common_names ancillaries/NCBI_taxa_ontobiotope.txt ancillaries/Use_V2.json diff --git a/config/config.yaml b/config/config.yaml index c7350860b35633cd69cd10305d5103b3c58c452a..31afd6904d19dc970a65dbb1e4263fc7de2fe4c7 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -84,3 +84,6 @@ OLD_RESULT_FOLDER: "corpora/florilege/compare/old" ## put new *.full.txt in this folder NEW_RESULT_FOLDER: "corpora/florilege/compare/new" + +## Location of the previous corpora/BioNLP-OST-2019/batches +PREV_BB_BATCHES: prev-BB-batches/ diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json deleted file mode 100644 index 7f67a6c7847c9ab341236ecde64dfbe77bcfab00..0000000000000000000000000000000000000000 --- a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json +++ /dev/null @@ -1,185 +0,0 @@ -{ - "evaluation": { - "submission-id": 19531, - "global-evaluations": [{ - "name": "Standard pairing", - "scorings": [{ - "name": "Standard scoring", - "measures": [ - { - "name": "mean-references", - "value": 0.32943585572615347 - }, - { - "name": "Predictions", - "value": 518 - }, - { - "name": "False Negatives", - "value": 290 - } - ] - }] - }] - }, - "messages": [ - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-10770276.a2", - "lineno": 34, - "level": "SERIOUS", - "body": "referent dsm:44495 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-12417169.a2", - "lineno": 53, - "level": "SERIOUS", - "body": "referent dsm:40778 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2", - "lineno": 51, - "level": "SERIOUS", - "body": "referent dsm:11729 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2", - "lineno": 53, - "level": "SERIOUS", - "body": "referent dsm:11729 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2", - "lineno": 54, - "level": "SERIOUS", - "body": "referent dsm:11729 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15460321.a2", - "lineno": 31, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15460321.a2", - "lineno": 46, - "level": "SERIOUS", - "body": "referent 2770636 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-21511409.a2", - "lineno": 33, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-21511409.a2", - "lineno": 39, - "level": "SERIOUS", - "body": "referent OBT:003719 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-21511409.a2", - "lineno": 43, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25046729.a2", - "lineno": 50, - "level": "SERIOUS", - "body": "referent dsm:3300 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-2617654.a2", - "lineno": 31, - "level": "SERIOUS", - "body": "referent OBT:004147 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-2617654.a2", - "lineno": 32, - "level": "SERIOUS", - "body": "referent OBT:003836 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-3015879.a2", - "lineno": 29, - "level": "SERIOUS", - "body": "referent dsm:4887 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-3015879.a2", - "lineno": 32, - "level": "SERIOUS", - "body": "referent dsm:3879 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2", - "lineno": 69, - "level": "SERIOUS", - "body": "referent dsm:11729 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2", - "lineno": 71, - "level": "SERIOUS", - "body": "referent dsm:11729 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2", - "lineno": 76, - "level": "SERIOUS", - "body": "referent dsm:4475 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-24010601-001.a2", - "lineno": 24, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-24010601-010.a2", - "lineno": 34, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-25064656-012.a2", - "lineno": 60, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-25064656-015.a2", - "lineno": 30, - "level": "SERIOUS", - "body": "referent dsm:661 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-25955289-003.a2", - "lineno": 17, - "level": "SERIOUS", - "body": "referent OBT:004138 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-26187841-001.a2", - "lineno": 18, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-26187841-001.a2", - "lineno": 19, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-26187841-002.a2", - "lineno": 11, - "level": "SERIOUS", - "body": "referent OBT:003761 is not in the vocabulary" - } - ], - "highest-message-level": "SERIOUS", - "success": false -} \ No newline at end of file diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/batch.xml b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/batch.xml similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/batch.xml rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/batch.xml diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10618167.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10618167.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10618167.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10618167.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10645449.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10645449.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10645449.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10645449.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10656819.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10656819.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10656819.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10656819.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10665543.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10665543.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10665543.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10665543.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10770276.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10770276.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10770276.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10770276.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10792385.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10792385.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10792385.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10792385.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10796014.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10796014.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10796014.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-10796014.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-11551069.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-11551069.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-11551069.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-11551069.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12417169.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12417169.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12417169.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12417169.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12438382.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12438382.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12438382.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12438382.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12934822.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12934822.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-12934822.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.txt rename to 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a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-001.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-001.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-002.txt similarity index 100% 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--git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-004.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-004.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-004.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-004.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-005.a1 similarity index 100% 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a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-006.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-006.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-007.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-007.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-007.txt similarity index 100% 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--git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-009.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-009.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-009.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-009.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-010.a1 similarity index 100% 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a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-011.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-011.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-012.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-012.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-012.txt similarity index 100% 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--git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-014.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-014.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-014.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-014.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-015.a1 similarity index 100% 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a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-016.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-016.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-017.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-017.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-017.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25064656-017.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-000.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-000.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-001.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-001.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-002.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-002.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-003.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-003.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-003.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-25955289-003.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-000.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-000.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-001.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-001.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-002.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.txt rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_test/bionlp-st/BB-kb+ner-F-26187841-002.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/batch.xml b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/batch.xml similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/batch.xml rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/batch.xml diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1016123.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1016123.a1 new file mode 100644 index 0000000000000000000000000000000000000000..8e0270020a4af788625956dbc3ac374d3465c70f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1016123.a1 @@ -0,0 +1,2 @@ +T1 Title 0 141 An evaluation of selective broths based on the bi-selenite ion and on hypertonic strontium chloride in Salmonellae detection in egg products. +T2 Paragraph 142 579 Of the 104 isolations of Salmonella sp. from egg pulp, 97 were obtained from strontium chloride M broth, 42 from strontium selenite broth and 57 from strontium selenite A broth. The results suggest that the first medium may be used more successfully than bi-selenite based media for enrichment and subsequent detection of salmonellae in egg products; however, the growth of S. pullorum was not satisfactory in strontium chloride M broth. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1016123.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1016123.txt new file mode 100644 index 0000000000000000000000000000000000000000..25b30eb5ff510340e40d12761b416ff8ec915b86 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1016123.txt @@ -0,0 +1,3 @@ +An evaluation of selective broths based on the bi-selenite ion and on hypertonic strontium chloride in Salmonellae detection in egg products. +Of the 104 isolations of Salmonella sp. from egg pulp, 97 were obtained from strontium chloride M broth, 42 from strontium selenite broth and 57 from strontium selenite A broth. The results suggest that the first medium may be used more successfully than bi-selenite based media for enrichment and subsequent detection of salmonellae in egg products; however, the growth of S. pullorum was not satisfactory in strontium chloride M broth. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10492485.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10492485.a1 new file mode 100644 index 0000000000000000000000000000000000000000..d848eb1f510d9c6d7eb301460351ba89b3239dac --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10492485.a1 @@ -0,0 +1,2 @@ +T1 Title 0 93 Application of ozone for enhancing the microbiological safety and quality of foods: a review. +T2 Paragraph 94 1854 Ozone (O3) is a strong antimicrobial agent with numerous potential applications in the food industry. High reactivity, penetrability, and spontaneous decomposition to a nontoxic product (i.e., O2) make ozone a viable disinfectant for ensuring the microbiological safety of food products. Ozone has been used for decades in many countries and recently, the generally recognized as safe (GRAS) status of this gas has been reaffirmed in the United States. Ozone, in the gaseous or aqueous phases, is effective against the majority of microorganisms tested by numerous research groups. Relatively low concentrations of ozone and short contact time are sufficient to inactivate bacteria, molds, yeasts, parasites, and viruses. However, rates of inactivation are greater in ozone demand-free systems than when the medium contains oxidizable organic substances. Susceptibility of microorganisms to ozone also varies with the physiological state of the culture, pH of the medium, temperature, humidity, and presence of additives (e.g., acids, surfactants, and sugars). Ozone applications in the food industry are mostly related to decontamination of product surface and water treatment. Ozone has been used with mixed success to inactivate contaminant microflora on meat, poultry, eggs, fish, fruits, vegetables, and dry foods. The gas also is useful in detoxification and elimination of mycotoxins and pesticide residues from some agricultural products. Excessive use of ozone, however, may cause oxidation of some ingredients on food surface. This usually results in discoloration and deterioration of food flavor. Additional research is needed to elucidate the kinetics and mechanisms of microbial inactivation by ozone and to optimize its use in food applications. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10492485.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10492485.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc450e286e2b3c28ad7be74615213b5119889289 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10492485.txt @@ -0,0 +1,3 @@ +Application of ozone for enhancing the microbiological safety and quality of foods: a review. +Ozone (O3) is a strong antimicrobial agent with numerous potential applications in the food industry. High reactivity, penetrability, and spontaneous decomposition to a nontoxic product (i.e., O2) make ozone a viable disinfectant for ensuring the microbiological safety of food products. Ozone has been used for decades in many countries and recently, the generally recognized as safe (GRAS) status of this gas has been reaffirmed in the United States. Ozone, in the gaseous or aqueous phases, is effective against the majority of microorganisms tested by numerous research groups. Relatively low concentrations of ozone and short contact time are sufficient to inactivate bacteria, molds, yeasts, parasites, and viruses. However, rates of inactivation are greater in ozone demand-free systems than when the medium contains oxidizable organic substances. Susceptibility of microorganisms to ozone also varies with the physiological state of the culture, pH of the medium, temperature, humidity, and presence of additives (e.g., acids, surfactants, and sugars). Ozone applications in the food industry are mostly related to decontamination of product surface and water treatment. Ozone has been used with mixed success to inactivate contaminant microflora on meat, poultry, eggs, fish, fruits, vegetables, and dry foods. The gas also is useful in detoxification and elimination of mycotoxins and pesticide residues from some agricultural products. Excessive use of ozone, however, may cause oxidation of some ingredients on food surface. This usually results in discoloration and deterioration of food flavor. Additional research is needed to elucidate the kinetics and mechanisms of microbial inactivation by ozone and to optimize its use in food applications. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10496597.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10496597.a1 new file mode 100644 index 0000000000000000000000000000000000000000..04eeb6f1fb4a07bb5db9c0987aee30e3d6d46736 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10496597.a1 @@ -0,0 +1,2 @@ +T1 Title 0 137 The differential diagnosis of early gastric mucosa-associated lymphoma: polymerase chain reaction and paraffin section immunophenotyping. +T2 Paragraph 138 2048 The distinction between benign florid lymphoid hyperplasia and low-grade gastric mucosal-associated lymphoid tissue (MALT) lymphoma may be a challenge. The presence of monoclonal B cells in Helicobacter pylori-chronic active gastritis has suggested that polymerase chain reaction (PCR) data should be viewed with caution. We investigated the reliability of PCR versus immunophenotyping in diagnosing early gastric MALT lymphoma. We studied 1511 biopsies from eight patients with high-grade primary gastric lymphoma, 25 with low-grade MALT lymphoma, 32 with atypical lymphoid infiltrates, and 39 with Helicobacter pylori-chronic active gastritis. Paraffin sections from all cases were stained with antibodies to CD20, CD3, AE1/AE3, kappa and lambda. PCR was performed on paraffin sections using the primer set VH-FR3/J(H). Using histopathology as the gold standard in diagnosis, we confirmed monoclonality in 22 of 25 MALT lymphomas (88%); a clonal band was found in 38% (15 of 39) of patients with chronic active gastritis. An immunophenotype pattern with predominance of CD20-positive cells in lymphocytic infiltrates was associated with monoclonality in 92% of cases. The presence of an enlarged irregular mantle zone was found in both monoclonal and polyclonal areas. An equal prevalence of B and T cells in lymphocytic infiltrates was associated with a polyclonal pattern in 24 of 31 cases (77%). Immunostaining of sIg (kappa and lambda) was difficult in paraffin sections and convincing proof of monoclonality was not obtained. Lymphoepithelial lesions were infrequent in gastric biopsies and their presence was highlighted with keratin stains. Because monoclonal B cells are observed in Helicobacter pylori-associated gastritis, the correct interpretation of clonality by PCR remains unclear. Paraffin section IHC using CD20 and CD3 is especially useful to confirm the diagnosis of gastric MALT lymphoma. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10496597.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10496597.txt new file mode 100644 index 0000000000000000000000000000000000000000..cff06a920903d6255a5956ab6e9174f991d551bc --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10496597.txt @@ -0,0 +1,3 @@ +The differential diagnosis of early gastric mucosa-associated lymphoma: polymerase chain reaction and paraffin section immunophenotyping. +The distinction between benign florid lymphoid hyperplasia and low-grade gastric mucosal-associated lymphoid tissue (MALT) lymphoma may be a challenge. The presence of monoclonal B cells in Helicobacter pylori-chronic active gastritis has suggested that polymerase chain reaction (PCR) data should be viewed with caution. We investigated the reliability of PCR versus immunophenotyping in diagnosing early gastric MALT lymphoma. We studied 1511 biopsies from eight patients with high-grade primary gastric lymphoma, 25 with low-grade MALT lymphoma, 32 with atypical lymphoid infiltrates, and 39 with Helicobacter pylori-chronic active gastritis. Paraffin sections from all cases were stained with antibodies to CD20, CD3, AE1/AE3, kappa and lambda. PCR was performed on paraffin sections using the primer set VH-FR3/J(H). Using histopathology as the gold standard in diagnosis, we confirmed monoclonality in 22 of 25 MALT lymphomas (88%); a clonal band was found in 38% (15 of 39) of patients with chronic active gastritis. An immunophenotype pattern with predominance of CD20-positive cells in lymphocytic infiltrates was associated with monoclonality in 92% of cases. The presence of an enlarged irregular mantle zone was found in both monoclonal and polyclonal areas. An equal prevalence of B and T cells in lymphocytic infiltrates was associated with a polyclonal pattern in 24 of 31 cases (77%). Immunostaining of sIg (kappa and lambda) was difficult in paraffin sections and convincing proof of monoclonality was not obtained. Lymphoepithelial lesions were infrequent in gastric biopsies and their presence was highlighted with keratin stains. Because monoclonal B cells are observed in Helicobacter pylori-associated gastritis, the correct interpretation of clonality by PCR remains unclear. Paraffin section IHC using CD20 and CD3 is especially useful to confirm the diagnosis of gastric MALT lymphoma. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10658649.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10658649.a1 new file mode 100644 index 0000000000000000000000000000000000000000..61630681e1e68cd472f0d1337e0e22d182f85629 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10658649.a1 @@ -0,0 +1,2 @@ +T1 Title 0 108 Identification of a novel glycoprotein-binding activity in Streptococcus pyogenes regulated by the mga gene. +T2 Paragraph 109 1148 The interaction between Streptococcus pyogenes and the host cell surface is not completely understood. Characterization of the adhesion mechanisms of the bacterium to the host cell surface is needed in order to develop new vaccines and anti-adhesion drugs. The presence of glycoprotein-binding activities among streptococcal strains was investigated. An activity binding to thyroglobulin, fetuin, asialofetuin and mucin but not non-glycosylated proteins was found to be present in the majority of the S. pyogenes strains studied. Cross-inhibition experiments suggested that the glycoproteins share a common structure recognized by the bacteria. The glycoprotein-binding activity was found to be proteinaceous, tightly attached to the bacterial surface and it also mediated the adherence of bacteria to solid surfaces coated with glycoproteins. The activity was found by transposon mutagenesis and complementation to be regulated by the multiple-gene regulator Mga, which has been implicated as a regulator of S. pyogenes virulence factors. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10658649.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10658649.txt new file mode 100644 index 0000000000000000000000000000000000000000..928f8b8c01b0739c7dff02409ad4ba895a2c5889 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10658649.txt @@ -0,0 +1,3 @@ +Identification of a novel glycoprotein-binding activity in Streptococcus pyogenes regulated by the mga gene. +The interaction between Streptococcus pyogenes and the host cell surface is not completely understood. Characterization of the adhesion mechanisms of the bacterium to the host cell surface is needed in order to develop new vaccines and anti-adhesion drugs. The presence of glycoprotein-binding activities among streptococcal strains was investigated. An activity binding to thyroglobulin, fetuin, asialofetuin and mucin but not non-glycosylated proteins was found to be present in the majority of the S. pyogenes strains studied. Cross-inhibition experiments suggested that the glycoproteins share a common structure recognized by the bacteria. The glycoprotein-binding activity was found to be proteinaceous, tightly attached to the bacterial surface and it also mediated the adherence of bacteria to solid surfaces coated with glycoproteins. The activity was found by transposon mutagenesis and complementation to be regulated by the multiple-gene regulator Mga, which has been implicated as a regulator of S. pyogenes virulence factors. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10738994.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10738994.a1 new file mode 100644 index 0000000000000000000000000000000000000000..0e1c49bec6b1c06eb5de542f28c4d1ebc420588f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10738994.a1 @@ -0,0 +1,6 @@ +T1 Title 0 188 Genotyping by restriction endonuclease analysis compared to phenotyping by antibiogram for typing methicillin-resistant Staphylococcus aureus strains colonizing patients in a nursing home. +T2 Paragraph 189 545 To assist in defining patterns of methicillin-resistant Staphylococcus aureus (MRSA) colonization in a skilled nursing facility (SNF), we compared genotyping by field-inversion gel electrophoresis (FIGE) restriction endonuclease digestion analysis (REA) with phenotyping by antibiogram for defining strain relatedness among MRSA isolates from SNF patients. +T3 Paragraph 546 632 Prospective screening culture surveillance for MRSA among patients in a community SNF. +T4 Paragraph 633 877 Nares and stool swab cultures were obtained from newly admitted patients and from all patients quarterly. MRSA were isolated by oxacillin screening agar. Antibiograms were determined by the disk-diffusion method, and genotyping was by FIGE REA. +T5 Paragraph 878 1159 It was shown that, among isolates with the same genotypes, many had different antibiograms; among isolates with the same antibiograms, many had different genotypes; and the discriminatory indices for isolates of MRSA by FIGE REA and by antibiogram were 0.56 and 0.78, respectively. +T6 Paragraph 1160 1632 Our study demonstrated that, in patients from one SNF, genotyping by FIGE REA identified two prevalent REA DNA types, but with variability of antibiogram patterns within each DNA type; the antibiogram also identified prevalent patterns with variability of REA DNA type within each antibiogram pattern. The discriminatory index of antibiograms alone, or of genotypes alone as determined by FIGE REA, was poor for strains of MRSA isolated from the SNF patients in our study. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10738994.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10738994.txt new file mode 100644 index 0000000000000000000000000000000000000000..764b1c16449e4a710dc0cb8c1132749a8e6c1783 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-10738994.txt @@ -0,0 +1,7 @@ +Genotyping by restriction endonuclease analysis compared to phenotyping by antibiogram for typing methicillin-resistant Staphylococcus aureus strains colonizing patients in a nursing home. +To assist in defining patterns of methicillin-resistant Staphylococcus aureus (MRSA) colonization in a skilled nursing facility (SNF), we compared genotyping by field-inversion gel electrophoresis (FIGE) restriction endonuclease digestion analysis (REA) with phenotyping by antibiogram for defining strain relatedness among MRSA isolates from SNF patients. +Prospective screening culture surveillance for MRSA among patients in a community SNF. +Nares and stool swab cultures were obtained from newly admitted patients and from all patients quarterly. MRSA were isolated by oxacillin screening agar. Antibiograms were determined by the disk-diffusion method, and genotyping was by FIGE REA. +It was shown that, among isolates with the same genotypes, many had different antibiograms; among isolates with the same antibiograms, many had different genotypes; and the discriminatory indices for isolates of MRSA by FIGE REA and by antibiogram were 0.56 and 0.78, respectively. +Our study demonstrated that, in patients from one SNF, genotyping by FIGE REA identified two prevalent REA DNA types, but with variability of antibiogram patterns within each DNA type; the antibiogram also identified prevalent patterns with variability of REA DNA type within each antibiogram pattern. The discriminatory index of antibiograms alone, or of genotypes alone as determined by FIGE REA, was poor for strains of MRSA isolated from the SNF patients in our study. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11162736.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11162736.a1 new file mode 100644 index 0000000000000000000000000000000000000000..020c7a523c8b05813801165eb5c1e8206e453351 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11162736.a1 @@ -0,0 +1,2 @@ +T1 Title 0 86 A new purification method for overproduced proteins sensitive to endogenous proteases. +T2 Paragraph 87 1379 Proteolysisis a major problem in purification of overproduced proteins for structural studies. We developed a new method to avoid proteolysis of the products even in cases where popular protease inhibitors do not work effectively. When we cloned FlgF, a flagellar rod protein, from Salmonella typhimurium and overproduced it in Escherichia coli, FlgF was highly susceptible to cleavage by endogenous proteases after cell disruption even in the presence of various protease inhibitors. However, FlgF was not digested when the cells were disrupted in the presence of urea, which allowed us to develop the following new purification procedure. After cell disruption in the presence of urea and removal of the cell debris, the supernatant was passed through tandem-connected cation- and anion-exchange columns. Proteases were trapped in the cation-exchange column, and protease-free FlgF was eluted from the disconnected anion-exchange column. This gave a stable full-length product suitable for crystallization trials. The key procedures are cell disruption in the presence of urea and linked ion-exchange chromatography to quickly remove proteases as well as urea. This fast and simple method can be applied to purification of other overproduced proteins that are very sensitive to proteolysis. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11162736.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11162736.txt new file mode 100644 index 0000000000000000000000000000000000000000..fecf5b3fd66b3931aed9e13444381eafd74f4bda --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11162736.txt @@ -0,0 +1,3 @@ +A new purification method for overproduced proteins sensitive to endogenous proteases. +Proteolysisis a major problem in purification of overproduced proteins for structural studies. We developed a new method to avoid proteolysis of the products even in cases where popular protease inhibitors do not work effectively. When we cloned FlgF, a flagellar rod protein, from Salmonella typhimurium and overproduced it in Escherichia coli, FlgF was highly susceptible to cleavage by endogenous proteases after cell disruption even in the presence of various protease inhibitors. However, FlgF was not digested when the cells were disrupted in the presence of urea, which allowed us to develop the following new purification procedure. After cell disruption in the presence of urea and removal of the cell debris, the supernatant was passed through tandem-connected cation- and anion-exchange columns. Proteases were trapped in the cation-exchange column, and protease-free FlgF was eluted from the disconnected anion-exchange column. This gave a stable full-length product suitable for crystallization trials. The key procedures are cell disruption in the presence of urea and linked ion-exchange chromatography to quickly remove proteases as well as urea. This fast and simple method can be applied to purification of other overproduced proteins that are very sensitive to proteolysis. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11410343.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11410343.a1 new file mode 100644 index 0000000000000000000000000000000000000000..795401bff25bac63431216d8cab1bbdb57579fcd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11410343.a1 @@ -0,0 +1,2 @@ +T1 Title 0 99 Effects of 2,2',5,5'-tetrachlorobiphenyl and biphenyl on cell membranes of Ralstonia eutropha H850. +T2 Paragraph 100 1308 The effects of 2,2',5,5'-tetrachlorobiphenyl (TeCB), a PCB congener, and biphenyl on the cytoplasmic membranes of Ralstonia eutropha H850 were investigated by measuring fluorescence polarization using 1,6-diphenyl-1,3,5-hexatriene (DPH) as the probe, and determining the cellular fatty acid compositions. TeCB significantly affected the membrane of R. eutropha H850 cells grown on fructose by decreasing DPH fluorescence polarization. In contrast, the membrane of cells grown on biphenyl showed a considerably less significant effect of TeCB on membrane polarization than in fructose-grown cells. An increase in the ratio of total saturated to unsaturated fatty acids in cells grown on biphenyl suggested less of a fluidizing effect of TeCB on membranes in those cells. When biphenyl-grown cells were transferred back to a fructose medium, they required 25 generations for the membrane polarization and fatty acid compositions of these cells to revert back to those of the initial fructose-grown cells. The re-adaptation to a change in temperature required only five generations to return to normal. These results show that biphenyl affects cells in more ways than simply fluidizing the cytoplasmic membrane. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11410343.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11410343.txt new file mode 100644 index 0000000000000000000000000000000000000000..a8bfee90b2b0800870397c91364e8fed9bfab326 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11410343.txt @@ -0,0 +1,3 @@ +Effects of 2,2',5,5'-tetrachlorobiphenyl and biphenyl on cell membranes of Ralstonia eutropha H850. +The effects of 2,2',5,5'-tetrachlorobiphenyl (TeCB), a PCB congener, and biphenyl on the cytoplasmic membranes of Ralstonia eutropha H850 were investigated by measuring fluorescence polarization using 1,6-diphenyl-1,3,5-hexatriene (DPH) as the probe, and determining the cellular fatty acid compositions. TeCB significantly affected the membrane of R. eutropha H850 cells grown on fructose by decreasing DPH fluorescence polarization. In contrast, the membrane of cells grown on biphenyl showed a considerably less significant effect of TeCB on membrane polarization than in fructose-grown cells. An increase in the ratio of total saturated to unsaturated fatty acids in cells grown on biphenyl suggested less of a fluidizing effect of TeCB on membranes in those cells. When biphenyl-grown cells were transferred back to a fructose medium, they required 25 generations for the membrane polarization and fatty acid compositions of these cells to revert back to those of the initial fructose-grown cells. The re-adaptation to a change in temperature required only five generations to return to normal. These results show that biphenyl affects cells in more ways than simply fluidizing the cytoplasmic membrane. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11437594.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11437594.a1 new file mode 100644 index 0000000000000000000000000000000000000000..12cdf3af5d6042091093877f432dec7d3beac2d0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11437594.a1 @@ -0,0 +1,2 @@ +T1 Title 0 85 Optimization of the production of Chondrus crispus hexose oxidase in Pichia pastoris. +T2 Paragraph 86 1277 Hexose oxidase (D-hexose:O(2)-oxidoreductase, EC 1.1.3.5, HOX) normally found in the red alga Chondrus crispus was produced heterologously in different host systems. Full-length HOX polypeptide was produced in Escherichia coli, but no HOX activity could be detected. In contrast, active HOX could be produced in the methylotrophic yeast Pichia pastoris. Several growth physiological and genetic approaches for optimization of hexose oxidase production in P. pastoris were investigated. Our results indicate that specific growth conditions are essential in order to produce active HOX with the correct conformation. Furthermore, HOX seems to be activated by proteolytic cleavage of the full-length polypeptide chain into two fragments, which remain physically associated. Attempts to direct HOX to the extracellular compartment using the widely used secretion signals from Saccharomyces cerevisiae invertase or alpha-mating factor failed. However, we show in this study that HOX is transported out of P. pastoris via a hitherto unknown mechanism and that it is possible to enhance this secretion by mutagenesis from below the detection limit to at least 250 mg extracellular enzyme per liter. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11437594.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11437594.txt new file mode 100644 index 0000000000000000000000000000000000000000..3242f318ea4f19ae5524f6734aded9a386cd7fdc --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11437594.txt @@ -0,0 +1,3 @@ +Optimization of the production of Chondrus crispus hexose oxidase in Pichia pastoris. +Hexose oxidase (D-hexose:O(2)-oxidoreductase, EC 1.1.3.5, HOX) normally found in the red alga Chondrus crispus was produced heterologously in different host systems. Full-length HOX polypeptide was produced in Escherichia coli, but no HOX activity could be detected. In contrast, active HOX could be produced in the methylotrophic yeast Pichia pastoris. Several growth physiological and genetic approaches for optimization of hexose oxidase production in P. pastoris were investigated. Our results indicate that specific growth conditions are essential in order to produce active HOX with the correct conformation. Furthermore, HOX seems to be activated by proteolytic cleavage of the full-length polypeptide chain into two fragments, which remain physically associated. Attempts to direct HOX to the extracellular compartment using the widely used secretion signals from Saccharomyces cerevisiae invertase or alpha-mating factor failed. However, we show in this study that HOX is transported out of P. pastoris via a hitherto unknown mechanism and that it is possible to enhance this secretion by mutagenesis from below the detection limit to at least 250 mg extracellular enzyme per liter. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11989773.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11989773.a1 new file mode 100644 index 0000000000000000000000000000000000000000..8457dea1456a8925030cc6bdbe1d9266f0678b25 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11989773.a1 @@ -0,0 +1,2 @@ +T1 Title 0 135 Evaluation of two commercial methods for the detection of Listeria sp. and Listeria monocytogenes in a chicken nugget processing plant. +T2 Paragraph 136 1243 This study measures the detection performances of two rapid test systems (Listeria Rapid Test Clearview and Bax system) for the screening of Listeria sp. and Listeria monocytogenes, respectively. A total of 413 samples from different sources (product from (i) different stages of processing, (ii) different environments, and (iii) different food handlers), collected from a chicken nugget processing plant, were analysed by both rapid methods and a cultural method consisting of pre-enrichment, enrichment, and isolation onto selective agars (PALCAM, LPM, and HCLA). Overall, results showed an excellent correlation between data obtained using Clearview and the cultural method, with Clearview presenting an efficiency of 99%. Bax showed a lower correlation using the cultural method, with an efficiency of 71.1%. The type of sample did not affect the efficiency of Clearview, which varied from 98.1% for product samples to 100% for environmental and food handler samples, while for Bax it had a marked influence. Efficiency of Bax varied from as high as 100% for food handlers to 37.9% for product samples. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11989773.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11989773.txt new file mode 100644 index 0000000000000000000000000000000000000000..23c0948ee732e7547393cfb196cc47948e9be24c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-11989773.txt @@ -0,0 +1,3 @@ +Evaluation of two commercial methods for the detection of Listeria sp. and Listeria monocytogenes in a chicken nugget processing plant. +This study measures the detection performances of two rapid test systems (Listeria Rapid Test Clearview and Bax system) for the screening of Listeria sp. and Listeria monocytogenes, respectively. A total of 413 samples from different sources (product from (i) different stages of processing, (ii) different environments, and (iii) different food handlers), collected from a chicken nugget processing plant, were analysed by both rapid methods and a cultural method consisting of pre-enrichment, enrichment, and isolation onto selective agars (PALCAM, LPM, and HCLA). Overall, results showed an excellent correlation between data obtained using Clearview and the cultural method, with Clearview presenting an efficiency of 99%. Bax showed a lower correlation using the cultural method, with an efficiency of 71.1%. The type of sample did not affect the efficiency of Clearview, which varied from 98.1% for product samples to 100% for environmental and food handler samples, while for Bax it had a marked influence. Efficiency of Bax varied from as high as 100% for food handlers to 37.9% for product samples. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12109661.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12109661.a1 new file mode 100644 index 0000000000000000000000000000000000000000..7f4c7a07fc09313f530822116fd34528385f0753 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12109661.a1 @@ -0,0 +1,2 @@ +T1 Title 0 110 Long-term Helicobacter pylori infection and the development of atrophic gastritis and gastric cancer in Japan. +T2 Paragraph 111 1577 The incidence of gastric cancer and the prevalence of Helicobacter pylori are high in Japan, so it is an important issue whether long-term H. pylori infection leads to chronic atrophic gastritis, considered one of the precursors of gastric cancer. We have reported that the grade of atrophy was higher in H. pylori-positive subjects than in H. pylori-negative subjects. It has also been reported that the atrophy of gastric mucosa increased in H. pylori-infected monkeys compared with control monkeys in a 5-year follow-up study. Most H. pylori infections occur in children, and atrophy of the gastric mucosa progresses during aging. Long-term data show that H. pylori infection can lead to gastric atrophy and may play an important role in the development of gastric cancer. Interestingly, there was no difference in the prevalence of H. pylori between patients with chronic gastritis and gastric cancer in Japan, but the prevalence of H. pylori in young Japanese gastric cancer patients was significantly higher than in the control group. These data clearly show that H. pylori infection is one of the risk factors of gastric cancer in young Japanese people, There is no answer to whether curing H. pylori infection can reverse the atrophy of the gastric mucosa and decrease the risk of gastric cancer development. To clarify this issue, an intervention study must be done. A large clinical trial called the Japanese Intervention Trial of H. pylori is in progress. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12109661.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12109661.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e430185309732e6e1837af8895889a74b7a43b3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12109661.txt @@ -0,0 +1,3 @@ +Long-term Helicobacter pylori infection and the development of atrophic gastritis and gastric cancer in Japan. +The incidence of gastric cancer and the prevalence of Helicobacter pylori are high in Japan, so it is an important issue whether long-term H. pylori infection leads to chronic atrophic gastritis, considered one of the precursors of gastric cancer. We have reported that the grade of atrophy was higher in H. pylori-positive subjects than in H. pylori-negative subjects. It has also been reported that the atrophy of gastric mucosa increased in H. pylori-infected monkeys compared with control monkeys in a 5-year follow-up study. Most H. pylori infections occur in children, and atrophy of the gastric mucosa progresses during aging. Long-term data show that H. pylori infection can lead to gastric atrophy and may play an important role in the development of gastric cancer. Interestingly, there was no difference in the prevalence of H. pylori between patients with chronic gastritis and gastric cancer in Japan, but the prevalence of H. pylori in young Japanese gastric cancer patients was significantly higher than in the control group. These data clearly show that H. pylori infection is one of the risk factors of gastric cancer in young Japanese people, There is no answer to whether curing H. pylori infection can reverse the atrophy of the gastric mucosa and decrease the risk of gastric cancer development. To clarify this issue, an intervention study must be done. A large clinical trial called the Japanese Intervention Trial of H. pylori is in progress. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1214327.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1214327.a1 new file mode 100644 index 0000000000000000000000000000000000000000..19bd7dd1c211899ca88d77224661191494cfb955 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1214327.a1 @@ -0,0 +1,2 @@ +T1 Title 0 99 Serotypes of Vibrio parahaemolyticus from clinical and environmental sources in Togo (West Africa). +T2 Paragraph 100 723 Serological analysis of O and K antigens was performed on 343 strains of Vibro parahaemolyticus isolated from clinical and environmental sources in Togo. Only two strains were not typable by the available O antisera. K untypable strains were found in 4.8% of isolates from gastroenteritis patients, in 11% from healthy carriers, and in 47% and 46% of isolates, respectively, from water and fish samples. Thirteen serotypes identified in Togo are not considered in the Japanese antigenic scheme. The suitability of the Japanese typing scheme for geographic areas outside of Japan is discussed and its extension is suggested. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1214327.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1214327.txt new file mode 100644 index 0000000000000000000000000000000000000000..58a1dfeebd95a553b3ec7aabf124b1e101546847 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1214327.txt @@ -0,0 +1,3 @@ +Serotypes of Vibrio parahaemolyticus from clinical and environmental sources in Togo (West Africa). +Serological analysis of O and K antigens was performed on 343 strains of Vibro parahaemolyticus isolated from clinical and environmental sources in Togo. Only two strains were not typable by the available O antisera. K untypable strains were found in 4.8% of isolates from gastroenteritis patients, in 11% from healthy carriers, and in 47% and 46% of isolates, respectively, from water and fish samples. Thirteen serotypes identified in Togo are not considered in the Japanese antigenic scheme. The suitability of the Japanese typing scheme for geographic areas outside of Japan is discussed and its extension is suggested. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12728302.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12728302.a1 new file mode 100644 index 0000000000000000000000000000000000000000..9be353292c92848522594382c54441a3c1dde724 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12728302.a1 @@ -0,0 +1,2 @@ +T1 Title 0 123 Heat-shock response and its contribution to thermotolerance of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31. +T2 Paragraph 124 1248 Compared to Escherichia coli, the nitrogen-fixing soil cyanobacterium Anabaena sp. strain L-31 exhibited significantly superior abilities to survive prolonged and continuous heat stress and recover therefrom. Temperature upshift induced the synthesis of heat-shock proteins of similar molecular mass in the two microbes. However, in Anabaena sp. strain L-31 the heat-shock proteins (particularly the GroEL proteins) were synthesised throughout the stress period, were much more stable and accumulated during heat stress. In contrast, in E. coli the heat-shock proteins were transiently synthesised, quickly turned over and did not accumulate. Nitrogenase activity of Anabaena cells of sp. strain L-31 continuously exposed to heat stress for 7 days rapidly recovered from thermal injury, although growth recovery was delayed. Exposure of E. coli cells to >4.5 h of heat stress resulted in a complete loss of viability and the ability to recover. Marked differences in the synthesis, stability and accumulation of heat-shock proteins appear to distinguish these bacteria in their thermotolerance and recovery from heat stress. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12728302.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12728302.txt new file mode 100644 index 0000000000000000000000000000000000000000..25dd09dd03a0f84f649a21a47a90c8265983bf21 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12728302.txt @@ -0,0 +1,3 @@ +Heat-shock response and its contribution to thermotolerance of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31. +Compared to Escherichia coli, the nitrogen-fixing soil cyanobacterium Anabaena sp. strain L-31 exhibited significantly superior abilities to survive prolonged and continuous heat stress and recover therefrom. Temperature upshift induced the synthesis of heat-shock proteins of similar molecular mass in the two microbes. However, in Anabaena sp. strain L-31 the heat-shock proteins (particularly the GroEL proteins) were synthesised throughout the stress period, were much more stable and accumulated during heat stress. In contrast, in E. coli the heat-shock proteins were transiently synthesised, quickly turned over and did not accumulate. Nitrogenase activity of Anabaena cells of sp. strain L-31 continuously exposed to heat stress for 7 days rapidly recovered from thermal injury, although growth recovery was delayed. Exposure of E. coli cells to >4.5 h of heat stress resulted in a complete loss of viability and the ability to recover. Marked differences in the synthesis, stability and accumulation of heat-shock proteins appear to distinguish these bacteria in their thermotolerance and recovery from heat stress. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12781527.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12781527.a1 new file mode 100644 index 0000000000000000000000000000000000000000..9312994dcfd0721b414e887bf8debd9e13e9e33f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12781527.a1 @@ -0,0 +1,2 @@ +T1 Title 0 59 Campylobacter--a tale of two protein glycosylation systems. +T2 Paragraph 60 926 Post-translational glycosylation is a universal modification of proteins in eukarya, archaea and bacteria. Two recent publications describe the first confirmed report of a bacterial N-linked glycosylation pathway in the human gastrointestinal pathogen Campylobacter jejuni. In addition, an O-linked glycosylation pathway has been identified and characterized in C. jejuni and the related species Campylobacter coli. Both pathways have similarity to the respective N- and O-linked glycosylation processes in eukaryotes. In bacteria, homologues of the genes in both pathways are found in other organisms, the complex glycans linked to the glycoproteins share common biosynthetic precursors and these modifications could play similar biological roles. Thus, Campylobacter provides a unique model system for the elucidation and exploitation of glycoprotein biosynthesis. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12781527.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12781527.txt new file mode 100644 index 0000000000000000000000000000000000000000..e22e7b7211d7b3b45402b6f1f7f203a0542aa846 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12781527.txt @@ -0,0 +1,3 @@ +Campylobacter--a tale of two protein glycosylation systems. +Post-translational glycosylation is a universal modification of proteins in eukarya, archaea and bacteria. Two recent publications describe the first confirmed report of a bacterial N-linked glycosylation pathway in the human gastrointestinal pathogen Campylobacter jejuni. In addition, an O-linked glycosylation pathway has been identified and characterized in C. jejuni and the related species Campylobacter coli. Both pathways have similarity to the respective N- and O-linked glycosylation processes in eukaryotes. In bacteria, homologues of the genes in both pathways are found in other organisms, the complex glycans linked to the glycoproteins share common biosynthetic precursors and these modifications could play similar biological roles. Thus, Campylobacter provides a unique model system for the elucidation and exploitation of glycoprotein biosynthesis. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12970344.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12970344.a1 new file mode 100644 index 0000000000000000000000000000000000000000..421ba6bb510874bac56366e6c44e05e04afefd66 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12970344.a1 @@ -0,0 +1,2 @@ +T1 Title 0 54 The three-dimensional structures of two beta-agarases. +T2 Paragraph 55 1756 Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12970344.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12970344.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba5ec372d2d3094952f242afa15a626eae0638a4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-12970344.txt @@ -0,0 +1,3 @@ +The three-dimensional structures of two beta-agarases. +Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1356998.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1356998.a1 new file mode 100644 index 0000000000000000000000000000000000000000..3082aa3342237a253ad0bbdf9c37ae7e71cbd545 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1356998.a1 @@ -0,0 +1,2 @@ +T1 Title 0 89 Human and tick spotted fever group Rickettsia isolates from Israel: a genotypic analysis. +T2 Paragraph 90 1386 The genomes of spotted fever group rickettsiae isolated in different geographical areas of Israel (two from ticks and four from humans, obtained over a span of 20 years) were studied by polymerase chain reaction (PCR) and restriction endonuclease fragment length polymorphism (RFLP) analysis. The human isolates were obtained from patients suffering from rickettsial disease of different degrees of severity. The PCR products obtained with five pairs of oligonucleotide primers (two primer sets derived from the 190-kDa polypeptide gene and three from the 120-kDa polypeptide gene) and cleaved with restriction endonucleases were used to study the Israeli isolates and reference Rickettsia conorii isolates. Subtle differences between the PCR-RFLP patterns of Israeli isolates and the two R. conorii reference strains (Moroccan and no. 7) were seen when the PCR products derived from the 190-kDa gene-derived primer sets were digested. All of the Israeli isolates were identical by RFLP analysis using all of the primer sets. This study showed that the Israeli spotted fever group isolates (from both ticks and humans) were genetically homogeneous by the criteria used in this study, despite the time and location differences in their original isolation, and different as a group from R. conorii. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1356998.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1356998.txt new file mode 100644 index 0000000000000000000000000000000000000000..c8746569c067e21a1cbee16c14caac4570ab0471 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-1356998.txt @@ -0,0 +1,3 @@ +Human and tick spotted fever group Rickettsia isolates from Israel: a genotypic analysis. +The genomes of spotted fever group rickettsiae isolated in different geographical areas of Israel (two from ticks and four from humans, obtained over a span of 20 years) were studied by polymerase chain reaction (PCR) and restriction endonuclease fragment length polymorphism (RFLP) analysis. The human isolates were obtained from patients suffering from rickettsial disease of different degrees of severity. The PCR products obtained with five pairs of oligonucleotide primers (two primer sets derived from the 190-kDa polypeptide gene and three from the 120-kDa polypeptide gene) and cleaved with restriction endonucleases were used to study the Israeli isolates and reference Rickettsia conorii isolates. Subtle differences between the PCR-RFLP patterns of Israeli isolates and the two R. conorii reference strains (Moroccan and no. 7) were seen when the PCR products derived from the 190-kDa gene-derived primer sets were digested. All of the Israeli isolates were identical by RFLP analysis using all of the primer sets. This study showed that the Israeli spotted fever group isolates (from both ticks and humans) were genetically homogeneous by the criteria used in this study, despite the time and location differences in their original isolation, and different as a group from R. conorii. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14633026.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14633026.a1 new file mode 100644 index 0000000000000000000000000000000000000000..c723e3433505e331fc8286081b5679eb3a5c6362 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14633026.a1 @@ -0,0 +1,5 @@ +T1 Title 0 109 Characterization of a mosquitocidal Bacillus thuringiensis serovar sotto strain isolated from Okinawa, Japan. +T2 Paragraph 110 307 To characterize the mosquitocidal activity of parasporal inclusions of the Bacillus thuringiensis serovar sotto strain 96-OK-85-24, for comparison with two well-characterized mosquitocidal strains. +T3 Paragraph 308 628 The strain 96-OK-85-24 significantly differed from the existing mosquitocidal B. thuringiensis strains in: (1) lacking the larvicidal activity against Culex pipiens molestus and haemolytic activity, and (2) SDS-PAGE profiles, immunological properties and N-terminal amino acid sequences of parasporal inclusion proteins. +T4 Paragraph 629 764 It is clear from the results that the strain 96-OK-85-24 synthesizes a novel mosquitocidal Cry protein with a unique toxicity spectrum. +T5 Paragraph 765 937 This is the first report of the occurrence of a mosquitocidal B. thuringiensis strain with an unusual toxicity spectrum, lacking the activity against the culicine mosquito. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14633026.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14633026.txt new file mode 100644 index 0000000000000000000000000000000000000000..05f290d635bf9c71ca3874f40dce94d9db589c22 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14633026.txt @@ -0,0 +1,6 @@ +Characterization of a mosquitocidal Bacillus thuringiensis serovar sotto strain isolated from Okinawa, Japan. +To characterize the mosquitocidal activity of parasporal inclusions of the Bacillus thuringiensis serovar sotto strain 96-OK-85-24, for comparison with two well-characterized mosquitocidal strains. +The strain 96-OK-85-24 significantly differed from the existing mosquitocidal B. thuringiensis strains in: (1) lacking the larvicidal activity against Culex pipiens molestus and haemolytic activity, and (2) SDS-PAGE profiles, immunological properties and N-terminal amino acid sequences of parasporal inclusion proteins. +It is clear from the results that the strain 96-OK-85-24 synthesizes a novel mosquitocidal Cry protein with a unique toxicity spectrum. +This is the first report of the occurrence of a mosquitocidal B. thuringiensis strain with an unusual toxicity spectrum, lacking the activity against the culicine mosquito. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14645268.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14645268.a1 new file mode 100644 index 0000000000000000000000000000000000000000..3d69b262755a077567db7d4774418f41263fd0b3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14645268.a1 @@ -0,0 +1,2 @@ +T1 Title 0 96 XopC and XopJ, two novel type III effector proteins from Xanthomonas campestris pv. vesicatoria. +T2 Paragraph 97 1660 Pathogenicity of the gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria depends on a type III secretion (TTS) system which translocates bacterial effector proteins into the plant cell. Previous transcriptome analysis identified a genome-wide regulon of putative virulence genes that are coexpressed with the TTS system. In this study, we characterized two of these genes, xopC and xopJ. Both genes encode Xanthomonas outer proteins (Xops) that were shown to be secreted by the TTS system. In addition, type III-dependent translocation of both proteins into the plant cell was demonstrated using the AvrBs3 effector domain as a reporter. XopJ belongs to the AvrRxv/YopJ family of effector proteins from plant and animal pathogenic bacteria. By contrast, XopC does not share significant homology to proteins in the database. Sequence analysis revealed that the xopC locus contains several features that are reminiscent of pathogenicity islands. Interestingly, the xopC region is flanked by 62-bp inverted repeats that are also associated with members of the Xanthomonas avrBs3 effector family. Besides xopC, a second gene of the locus, designated hpaJ, was shown to be coexpressed with the TTS system. hpaJ encodes a protein with similarity to transglycosylases and to the Pseudomonas syringae pv. maculicola protein HopPmaG. HpaJ secretion and translocation by the X. campestris pv. vesicatoria TTS system was not detectable, which is consistent with its predicted Sec signal and a putative function as transglycosylase in the bacterial periplasm. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14645268.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14645268.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1b7bff09ec03b86fb1d04509d685149727ca45d --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-14645268.txt @@ -0,0 +1,3 @@ +XopC and XopJ, two novel type III effector proteins from Xanthomonas campestris pv. vesicatoria. +Pathogenicity of the gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria depends on a type III secretion (TTS) system which translocates bacterial effector proteins into the plant cell. Previous transcriptome analysis identified a genome-wide regulon of putative virulence genes that are coexpressed with the TTS system. In this study, we characterized two of these genes, xopC and xopJ. Both genes encode Xanthomonas outer proteins (Xops) that were shown to be secreted by the TTS system. In addition, type III-dependent translocation of both proteins into the plant cell was demonstrated using the AvrBs3 effector domain as a reporter. XopJ belongs to the AvrRxv/YopJ family of effector proteins from plant and animal pathogenic bacteria. By contrast, XopC does not share significant homology to proteins in the database. Sequence analysis revealed that the xopC locus contains several features that are reminiscent of pathogenicity islands. Interestingly, the xopC region is flanked by 62-bp inverted repeats that are also associated with members of the Xanthomonas avrBs3 effector family. Besides xopC, a second gene of the locus, designated hpaJ, was shown to be coexpressed with the TTS system. hpaJ encodes a protein with similarity to transglycosylases and to the Pseudomonas syringae pv. maculicola protein HopPmaG. HpaJ secretion and translocation by the X. campestris pv. vesicatoria TTS system was not detectable, which is consistent with its predicted Sec signal and a putative function as transglycosylase in the bacterial periplasm. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15293611.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15293611.a1 new file mode 100644 index 0000000000000000000000000000000000000000..150b6dbeb48554026befb29329b3ec1378a8109f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15293611.a1 @@ -0,0 +1,2 @@ +T1 Title 0 87 Clonal strains of Pseudomonas aeruginosa in paediatric and adult cystic fibrosis units. +T2 Paragraph 88 1551 Despite recent reports of clonal strains of Pseudomonas aeruginosa in cystic fibrosis (CF) units, the need for routine microbiological surveillance remains contentious. Sputum was collected prospectively from productive patients attending the regional paediatric and adult CF units in Brisbane, Australia. All P. aeruginosa isolates were typed using pulsed-field gel electrophoresis. Spirometry, anthropometrics, hospitalisations and antibiotic sensitivity data were recorded. The first 100 sputum samples (first 50 patients at each clinic) harboured 163 isolates of P. aeruginosa. A total of 39 patients shared a common strain (pulsotype 2), 20 patients shared a strain with at least one other patient and 41 patients harboured unique strains. Eight patients shared a strain identical to a previously reported Australian transmissible strain (pulsotype 1). Compared with the unique strain group, patients harbouring pulsotype 2 were younger and had poorer lung function. Treatment requirements were similar in these two groups, as were the rates of multiresistance. In conclusion, 59% of patients harboured a clonal strain, supporting the need for routine microbiological surveillance. In contrast to previously described clonal strains, the dominant pulsotype was indistinguishable from nonclonal strains with respect to both colonial morphology and multiresistance. The clinical significance of clonal strains remains uncertain and requires longitudinal study. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15293611.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15293611.txt new file mode 100644 index 0000000000000000000000000000000000000000..ec529b16f2153b81c2a684918feb27cf96c238a6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15293611.txt @@ -0,0 +1,3 @@ +Clonal strains of Pseudomonas aeruginosa in paediatric and adult cystic fibrosis units. +Despite recent reports of clonal strains of Pseudomonas aeruginosa in cystic fibrosis (CF) units, the need for routine microbiological surveillance remains contentious. Sputum was collected prospectively from productive patients attending the regional paediatric and adult CF units in Brisbane, Australia. All P. aeruginosa isolates were typed using pulsed-field gel electrophoresis. Spirometry, anthropometrics, hospitalisations and antibiotic sensitivity data were recorded. The first 100 sputum samples (first 50 patients at each clinic) harboured 163 isolates of P. aeruginosa. A total of 39 patients shared a common strain (pulsotype 2), 20 patients shared a strain with at least one other patient and 41 patients harboured unique strains. Eight patients shared a strain identical to a previously reported Australian transmissible strain (pulsotype 1). Compared with the unique strain group, patients harbouring pulsotype 2 were younger and had poorer lung function. Treatment requirements were similar in these two groups, as were the rates of multiresistance. In conclusion, 59% of patients harboured a clonal strain, supporting the need for routine microbiological surveillance. In contrast to previously described clonal strains, the dominant pulsotype was indistinguishable from nonclonal strains with respect to both colonial morphology and multiresistance. The clinical significance of clonal strains remains uncertain and requires longitudinal study. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15358511.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15358511.a1 new file mode 100644 index 0000000000000000000000000000000000000000..5ad175e388e4ded2164f3f45e3dd603fba3bb2a3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15358511.a1 @@ -0,0 +1,2 @@ +T1 Title 0 189 Attachment of Escherichia coli O157:H7 grown in tryptic soy broth and nutrient broth to apple and lettuce surfaces as related to cell hydrophobicity, surface charge, and capsule production. +T2 Paragraph 190 1044 This study investigated the effect of growth in tryptic soy broth (TSB) and nutrient broth (NB) on the ability Escherichia coli O157:H7 to attach to lettuce and apple surfaces. In addition, cell surface hydrophobicity, charge and capsule production were determined on cells grown in these media. Cells grown in NB attached less to lettuce and apple surfaces than did those grown in TSB. TSB, but not NB, supported capsule production by E. coli O157:H7. Cells grown in TSB were more hydrophilic than those grown in NB. No difference was found in the electrokinetic properties of cells grown in these media. Electrostatic and hydrophobic interactions and surface proteins did not appear to play an important role in the attachment of E. coli O157:H7 to these surfaces. Of the factors studied, only capsule production was associated with attachment ability. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15358511.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15358511.txt new file mode 100644 index 0000000000000000000000000000000000000000..c45c0e1edfbb0e55d3d91dbed1add48ad54812fd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15358511.txt @@ -0,0 +1,3 @@ +Attachment of Escherichia coli O157:H7 grown in tryptic soy broth and nutrient broth to apple and lettuce surfaces as related to cell hydrophobicity, surface charge, and capsule production. +This study investigated the effect of growth in tryptic soy broth (TSB) and nutrient broth (NB) on the ability Escherichia coli O157:H7 to attach to lettuce and apple surfaces. In addition, cell surface hydrophobicity, charge and capsule production were determined on cells grown in these media. Cells grown in NB attached less to lettuce and apple surfaces than did those grown in TSB. TSB, but not NB, supported capsule production by E. coli O157:H7. Cells grown in TSB were more hydrophilic than those grown in NB. No difference was found in the electrokinetic properties of cells grown in these media. Electrostatic and hydrophobic interactions and surface proteins did not appear to play an important role in the attachment of E. coli O157:H7 to these surfaces. Of the factors studied, only capsule production was associated with attachment ability. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15618837.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15618837.a1 new file mode 100644 index 0000000000000000000000000000000000000000..fbd77f10dc790ea99ac8759dd69f86eb51417e2e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15618837.a1 @@ -0,0 +1,5 @@ +T1 Title 0 129 Recurrence of Helicobacter pylori infection 1 year after successful treatment: prospective cohort study in the Republic of Yemen. +T2 Paragraph 130 311 To investigate the prevalence of Helicobacter pylori infection in dyspeptic patients in the Republic of Yemen and the recurrence rate 1 year after apparently successful eradication. +T3 Paragraph 312 798 A total of 275 patients with chronic dyspepsia seen in one clinic were enrolled. Gastric biopsies were obtained at endoscopy and H. pylori infection was diagnosed using the rapid urease test. Patients with H. pylori infection were given either clarithromycin or metronidazole-based triple therapy. Six weeks later H. pylori status was assessed using the C-urea breath test (C-UBT). Those who were negative for H. pylori had a further C-UBT after 1 year to establish the recurrence rate. +T4 Paragraph 799 1360 The prevalence of H. pylori infection at entry to the study was 82.2% [95% confidence interval (CI) 78-87%]. The overall eradication rate 6 weeks after treatment was 49.1% (95% CI 42.6-55.6%) by intention-to-treat analysis, and 60% (95% CI 53-67%) by per-protocol analysis. Recurrence rate of H. pylori infection at 1 year was 34% (95% CI 14-45%) and the only predictor of recurrence was an excess delta C-UBT value less than 3.5 per million but equal to or greater than 2.5 per million at 6 weeks after treatment (odds ratio 2.28; 95% CI 1.17-4.44; P = 0.028). +T5 Paragraph 1361 1744 The prevalence of H. pylori infection in dyspeptic patients in Yemen is very high, the eradication rate with standard triple therapy was unsatisfactory probably because of widespread bacterial resistance due to unrestricted antibiotic use. The recurrence rate of infection at 1 year was high, as a result of recrudescence of incompletely eradicated organisms rather than reinfection. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15618837.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15618837.txt new file mode 100644 index 0000000000000000000000000000000000000000..5a32d3b97deff3814cf3d68d9a8119933e90a72b --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-15618837.txt @@ -0,0 +1,6 @@ +Recurrence of Helicobacter pylori infection 1 year after successful treatment: prospective cohort study in the Republic of Yemen. +To investigate the prevalence of Helicobacter pylori infection in dyspeptic patients in the Republic of Yemen and the recurrence rate 1 year after apparently successful eradication. +A total of 275 patients with chronic dyspepsia seen in one clinic were enrolled. Gastric biopsies were obtained at endoscopy and H. pylori infection was diagnosed using the rapid urease test. Patients with H. pylori infection were given either clarithromycin or metronidazole-based triple therapy. Six weeks later H. pylori status was assessed using the C-urea breath test (C-UBT). Those who were negative for H. pylori had a further C-UBT after 1 year to establish the recurrence rate. +The prevalence of H. pylori infection at entry to the study was 82.2% [95% confidence interval (CI) 78-87%]. The overall eradication rate 6 weeks after treatment was 49.1% (95% CI 42.6-55.6%) by intention-to-treat analysis, and 60% (95% CI 53-67%) by per-protocol analysis. Recurrence rate of H. pylori infection at 1 year was 34% (95% CI 14-45%) and the only predictor of recurrence was an excess delta C-UBT value less than 3.5 per million but equal to or greater than 2.5 per million at 6 weeks after treatment (odds ratio 2.28; 95% CI 1.17-4.44; P = 0.028). +The prevalence of H. pylori infection in dyspeptic patients in Yemen is very high, the eradication rate with standard triple therapy was unsatisfactory probably because of widespread bacterial resistance due to unrestricted antibiotic use. The recurrence rate of infection at 1 year was high, as a result of recrudescence of incompletely eradicated organisms rather than reinfection. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16263187.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16263187.a1 new file mode 100644 index 0000000000000000000000000000000000000000..7c9d4eafd821cbe594049841fe14e60a1678e025 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16263187.a1 @@ -0,0 +1,2 @@ +T1 Title 0 135 Ability of Lactobacillus gasseri K 7 to inhibit Escherichia coli adhesion in vitro on Caco-2 cells and ex vivo on pigs' jejunal tissue. +T2 Paragraph 136 1930 The ability of Lactobacillus (Lb.) gasseri K 7 to inhibit adhesion of Escherichia coli O8:K88 to intestinal mucosa was studied on cultured Caco-2 cells and ex vivo on pigs' small intestinal tissue. Lactobacilli were added simultaneously with E. coli, before E. coli and after E. coli for competition, exclusion and displacement assays. The concentration of lactobacilli on fully differentiated Caco-2 cells was 4.5+/-0.3 x 10(8) cfu/well, while the concentration of E. coli varied from 1.5 x 10(6) to 4.3 x 10(8) cfu/well. The number of E. coli adhered to Caco-2 monolayer (cfu/well) was lineary correlated (R(2)=0.97) to the concentration of added cells. In the assay simulating exclusion, E. coli adhesion was reduced by Lb. gasseri K 7 strain by 0.1 to 0.6 log cfu/well. The binding of E. coli was inhibited even more when incubated simultaneously with lactobacilli, particularly at the lowest concentration of E. coli (ratio E. coli/lactobacilli 1:248), where five-times reduction (or 0.7 log) was observed. When adhesion to tissue derived from pigs' jejunum was tested, concentration of E. coli was constant (6.9+/-0.14 x 10(7) cfu/ml), while the concentration of Lb. gasseri K 7 was 5.9 x 10(7) and 1.3 x 10(7) cfu/ml in two independent experiments, respectively. The adhesion of E. coli and Lb. gasseri K 7 cells to jejunal mucosa was similar (1.0+/-0.17 x 10(6) and 1.54+/-0.10 x 10(6) cfu/cm(2)) when the concentrations of single strains in suspensions were approximately the same. No significant competition, exclusion or displacement of E. coli by lactobacilli was observed on jejunal tissue. In conclusion, Lb. gasseri K 7 was found to be effective in reducing E. coli adhesion to Caco-2 enterocytes, but it was not able to do so in ex vivo conditions tested for pig jejunal tissue. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16263187.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16263187.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ab0389d1e5667664070d840050f79ddae97a38f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16263187.txt @@ -0,0 +1,3 @@ +Ability of Lactobacillus gasseri K 7 to inhibit Escherichia coli adhesion in vitro on Caco-2 cells and ex vivo on pigs' jejunal tissue. +The ability of Lactobacillus (Lb.) gasseri K 7 to inhibit adhesion of Escherichia coli O8:K88 to intestinal mucosa was studied on cultured Caco-2 cells and ex vivo on pigs' small intestinal tissue. Lactobacilli were added simultaneously with E. coli, before E. coli and after E. coli for competition, exclusion and displacement assays. The concentration of lactobacilli on fully differentiated Caco-2 cells was 4.5+/-0.3 x 10(8) cfu/well, while the concentration of E. coli varied from 1.5 x 10(6) to 4.3 x 10(8) cfu/well. The number of E. coli adhered to Caco-2 monolayer (cfu/well) was lineary correlated (R(2)=0.97) to the concentration of added cells. In the assay simulating exclusion, E. coli adhesion was reduced by Lb. gasseri K 7 strain by 0.1 to 0.6 log cfu/well. The binding of E. coli was inhibited even more when incubated simultaneously with lactobacilli, particularly at the lowest concentration of E. coli (ratio E. coli/lactobacilli 1:248), where five-times reduction (or 0.7 log) was observed. When adhesion to tissue derived from pigs' jejunum was tested, concentration of E. coli was constant (6.9+/-0.14 x 10(7) cfu/ml), while the concentration of Lb. gasseri K 7 was 5.9 x 10(7) and 1.3 x 10(7) cfu/ml in two independent experiments, respectively. The adhesion of E. coli and Lb. gasseri K 7 cells to jejunal mucosa was similar (1.0+/-0.17 x 10(6) and 1.54+/-0.10 x 10(6) cfu/cm(2)) when the concentrations of single strains in suspensions were approximately the same. No significant competition, exclusion or displacement of E. coli by lactobacilli was observed on jejunal tissue. In conclusion, Lb. gasseri K 7 was found to be effective in reducing E. coli adhesion to Caco-2 enterocytes, but it was not able to do so in ex vivo conditions tested for pig jejunal tissue. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16273411.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16273411.a1 new file mode 100644 index 0000000000000000000000000000000000000000..19b6a3b32cfaaa2f2566f19fe6a48323f7f097cb --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16273411.a1 @@ -0,0 +1,2 @@ +T1 Title 0 140 Early pregnancy loss and neonatal deaths associated with Klebsiella pneumonia infection: a mini review of possible occupational health risk. +T2 Paragraph 141 711 Recurrent pregnancy loss is a disease of grave psychological and economic concern. The etiology in the vast majority of the cases is unknown or at best poorly understood. Although Klebsiella pneumonia infections have been reported in humans and animals during pregnancy, there is hardly any information to indicate whether or not these infections may be responsible for early pregnancy loss. We present a review of literature and report for the first time in humans, Klebsiella pneumonia infection in placenta of a 38-year-old secondary recurrent aborter (parity 2 + 3). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16273411.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16273411.txt new file mode 100644 index 0000000000000000000000000000000000000000..31d2864abee7eb12f96fa3c5c6923e0822a5bc51 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16273411.txt @@ -0,0 +1,3 @@ +Early pregnancy loss and neonatal deaths associated with Klebsiella pneumonia infection: a mini review of possible occupational health risk. +Recurrent pregnancy loss is a disease of grave psychological and economic concern. The etiology in the vast majority of the cases is unknown or at best poorly understood. Although Klebsiella pneumonia infections have been reported in humans and animals during pregnancy, there is hardly any information to indicate whether or not these infections may be responsible for early pregnancy loss. We present a review of literature and report for the first time in humans, Klebsiella pneumonia infection in placenta of a 38-year-old secondary recurrent aborter (parity 2 + 3). + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16432479.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16432479.a1 new file mode 100644 index 0000000000000000000000000000000000000000..de2991e57e7aeedef483f91706a9c1e15e390905 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16432479.a1 @@ -0,0 +1,4 @@ +T1 Title 0 131 Challenges in the control of gonorrhea in South America and the Caribbean: monitoring the development of resistance to antibiotics. +T2 Paragraph 132 387 : The objective of this study was to ascertain the antimicrobial susceptibility of Neisseria gonorrhoeae isolates from 6 South American and 13 Caribbean countries participating in the Gonococcal Antimicrobial Surveillance Program (GASP) from 1990 to 1999. +T3 Paragraph 388 683 : A GASP network of laboratories was launched in the Americas and the Caribbean during the 1990s. Standardized methods and interpretative criteria were established for the isolation of N. gonorrhoeae, strain identification, and determination, and quality control of antimicrobial susceptibility. +T4 Paragraph 684 1551 : Two countries (Argentina and Uruguay) maintained continuous surveillance during the study period. Some countries gathered data periodically and several others were unable to initiate antimicrobial surveillance as a result of lack of resources. The percentage of penicillin-resistant N. gonorrhoeae isolated in the region over the decade varied considerably (1.0-11.9% carried chromosomal resistance and 17.9-38.8% produced beta-lactamase) with an overall trend to declining numbers of penicillin-resistant isolates. For tetracycline, 7.4% to 36.3% carried chromosomal resistance, whereas 12.0% to 27.4% carried plasmid-mediated resistance. There were no reports of ciprofloxacin-resistant isolates, although N. gonorrhoeae with decreased susceptibility to ciprofloxacin and azithromycin as well as spectinomycin-resistant isolates were identified in some countries. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16432479.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16432479.txt new file mode 100644 index 0000000000000000000000000000000000000000..598dbbbb09e4166b655fdbe9c1258927a2e1d3fd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16432479.txt @@ -0,0 +1,5 @@ +Challenges in the control of gonorrhea in South America and the Caribbean: monitoring the development of resistance to antibiotics. +: The objective of this study was to ascertain the antimicrobial susceptibility of Neisseria gonorrhoeae isolates from 6 South American and 13 Caribbean countries participating in the Gonococcal Antimicrobial Surveillance Program (GASP) from 1990 to 1999. +: A GASP network of laboratories was launched in the Americas and the Caribbean during the 1990s. Standardized methods and interpretative criteria were established for the isolation of N. gonorrhoeae, strain identification, and determination, and quality control of antimicrobial susceptibility. +: Two countries (Argentina and Uruguay) maintained continuous surveillance during the study period. Some countries gathered data periodically and several others were unable to initiate antimicrobial surveillance as a result of lack of resources. The percentage of penicillin-resistant N. gonorrhoeae isolated in the region over the decade varied considerably (1.0-11.9% carried chromosomal resistance and 17.9-38.8% produced beta-lactamase) with an overall trend to declining numbers of penicillin-resistant isolates. For tetracycline, 7.4% to 36.3% carried chromosomal resistance, whereas 12.0% to 27.4% carried plasmid-mediated resistance. There were no reports of ciprofloxacin-resistant isolates, although N. gonorrhoeae with decreased susceptibility to ciprofloxacin and azithromycin as well as spectinomycin-resistant isolates were identified in some countries. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16436701.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16436701.a1 new file mode 100644 index 0000000000000000000000000000000000000000..8fd2feb3bc5200c451df8ff288476d7a388f61bb --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16436701.a1 @@ -0,0 +1,2 @@ +T1 Title 0 91 Antibacterial properties of dermaseptin S4 derivatives under extreme incubation conditions. +T2 Paragraph 92 1342 Antibacterial properties of the frog-derived peptide dermaseptin S4 and a series of synthetic derivatives against the food pathogen Escherichia coli O157:H7 were investigated under extreme incubation conditions. The 28-mer analog K4K20S4 (P28) displayed an MIC of 8 microM and rapid bactericidal kinetics under standard culture conditions. Potent bactericidal properties were maintained at high salt concentrations, under acidic or basic conditions, and at extreme temperatures. The N-terminal 14-mer sequence (P14) displayed higher potency (MIC, 4 microM) but only within a narrow range of incubation conditions, pointing to the importance of the C-terminal domain of P28. The potency range was reextended upon conjugation of aminododecanoic acid to P14. The resulting lipopeptide was even more potent (MIC, 2 microM) and affected bacterial viability under most of the conditions tested, including in commercial apple juice. The mechanistic implications of peptides' hydrophobicity, charge, structure, and binding to an idealized membrane were probed and are discussed here. Collectively, the data indicate interest in simple peptide-based compounds for design of antimicrobials that affect pathogens under a variable range of incubation conditions. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16436701.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16436701.txt new file mode 100644 index 0000000000000000000000000000000000000000..f41fb9465c80058ca151182cda3ac33e3d453e01 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16436701.txt @@ -0,0 +1,3 @@ +Antibacterial properties of dermaseptin S4 derivatives under extreme incubation conditions. +Antibacterial properties of the frog-derived peptide dermaseptin S4 and a series of synthetic derivatives against the food pathogen Escherichia coli O157:H7 were investigated under extreme incubation conditions. The 28-mer analog K4K20S4 (P28) displayed an MIC of 8 microM and rapid bactericidal kinetics under standard culture conditions. Potent bactericidal properties were maintained at high salt concentrations, under acidic or basic conditions, and at extreme temperatures. The N-terminal 14-mer sequence (P14) displayed higher potency (MIC, 4 microM) but only within a narrow range of incubation conditions, pointing to the importance of the C-terminal domain of P28. The potency range was reextended upon conjugation of aminododecanoic acid to P14. The resulting lipopeptide was even more potent (MIC, 2 microM) and affected bacterial viability under most of the conditions tested, including in commercial apple juice. The mechanistic implications of peptides' hydrophobicity, charge, structure, and binding to an idealized membrane were probed and are discussed here. Collectively, the data indicate interest in simple peptide-based compounds for design of antimicrobials that affect pathogens under a variable range of incubation conditions. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16458564.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16458564.a1 new file mode 100644 index 0000000000000000000000000000000000000000..ef922524253ed0784fabbd880e9b4c1981ec7595 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16458564.a1 @@ -0,0 +1,5 @@ +T1 Title 0 68 Etiology and epidemiology of diarrhea in children in Hanoi, Vietnam. +T2 Paragraph 69 272 This paper provides a preliminary picture of diarrhea with regards to etiology, clinical symptoms, and some related epidemiologic factors in children less than five years of age living in Hanoi, Vietnam. +T3 Paragraph 273 586 The study population included 587 children with diarrhea and 249 age-matched healthy controls. The identification of pathogens was carried out by the conventional methods in combination with ELISA, immunoseparation, and PCR. The antibiotic susceptibility was determined by MIC following the NCCLS recommendations. +T4 Paragraph 587 2024 Of those with diarrhea, 40.9% were less than one year old and 71.0% were less than two years old. A potential pathogen was identified in 67.3% of children with diarrhea. They were group A rotavirus, diarrheagenic Escherichia coli, Shigella spp, and enterotoxigenic Bacteroides fragilis, with prevalences of 46.7%, 22.5%, 4.7%, and 7.3%, respectively. No Salmonella spp or Vibrio cholerae were isolated. Rotavirus and diarrheagenic E. coli were predominant in children less than two years of age, while Shigella spp, and enterotoxigenic B. fragilis were mostly seen in the older children. Diarrheagenic E. coli and Shigella spp showed high prevalence of resistance to ampicillin, chloramphenicol, and to trimethoprim/sulfamethoxazole. Children attending the hospitals had fever (43.6%), vomiting (53.8%), and dehydration (82.6%). Watery stool was predominant with a prevalence of 66.4%, followed by mucous stool (21.0%). The mean episodes of stools per day was seven, ranging from two to 23 episodes. Before attending hospitals, 162/587 (27.6%) children had been given antibiotics. Overall, more children got diarrhea in (i) poor families; (ii) families where piped water and a latrine were lacking; (iii) families where mothers washed their hands less often before feeding the children; (iv) families where mothers had a low level of education; (v) families where information on health and sanitation less often reached their households. +T5 Paragraph 2025 2431 Group A rotavirus, diarrheagenic Escherichia coli, Shigella spp, and enterotoxigenic Bacteroides fragilis play an important role in causing diarrhea in children in Hanoi, Vietnam. Epidemiological factors such as lack of fresh water supply, unhygienic septic tank, low family income, lack of health information, and low educational level of parents could contribute to the morbidity of diarrhea in children. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16458564.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16458564.txt new file mode 100644 index 0000000000000000000000000000000000000000..20213d8d2d66dacba7bc188b9e082b1c7f6e7481 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16458564.txt @@ -0,0 +1,6 @@ +Etiology and epidemiology of diarrhea in children in Hanoi, Vietnam. +This paper provides a preliminary picture of diarrhea with regards to etiology, clinical symptoms, and some related epidemiologic factors in children less than five years of age living in Hanoi, Vietnam. +The study population included 587 children with diarrhea and 249 age-matched healthy controls. The identification of pathogens was carried out by the conventional methods in combination with ELISA, immunoseparation, and PCR. The antibiotic susceptibility was determined by MIC following the NCCLS recommendations. +Of those with diarrhea, 40.9% were less than one year old and 71.0% were less than two years old. A potential pathogen was identified in 67.3% of children with diarrhea. They were group A rotavirus, diarrheagenic Escherichia coli, Shigella spp, and enterotoxigenic Bacteroides fragilis, with prevalences of 46.7%, 22.5%, 4.7%, and 7.3%, respectively. No Salmonella spp or Vibrio cholerae were isolated. Rotavirus and diarrheagenic E. coli were predominant in children less than two years of age, while Shigella spp, and enterotoxigenic B. fragilis were mostly seen in the older children. Diarrheagenic E. coli and Shigella spp showed high prevalence of resistance to ampicillin, chloramphenicol, and to trimethoprim/sulfamethoxazole. Children attending the hospitals had fever (43.6%), vomiting (53.8%), and dehydration (82.6%). Watery stool was predominant with a prevalence of 66.4%, followed by mucous stool (21.0%). The mean episodes of stools per day was seven, ranging from two to 23 episodes. Before attending hospitals, 162/587 (27.6%) children had been given antibiotics. Overall, more children got diarrhea in (i) poor families; (ii) families where piped water and a latrine were lacking; (iii) families where mothers washed their hands less often before feeding the children; (iv) families where mothers had a low level of education; (v) families where information on health and sanitation less often reached their households. +Group A rotavirus, diarrheagenic Escherichia coli, Shigella spp, and enterotoxigenic Bacteroides fragilis play an important role in causing diarrhea in children in Hanoi, Vietnam. Epidemiological factors such as lack of fresh water supply, unhygienic septic tank, low family income, lack of health information, and low educational level of parents could contribute to the morbidity of diarrhea in children. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16514151.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16514151.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e0bdd899baa67a97d39515b9687825bf78a26bb7 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16514151.a1 @@ -0,0 +1,2 @@ +T1 Title 0 75 Hg(II) sequestration and protection by the MerR metal-binding domain (MBD). +T2 Paragraph 76 1411 MerR, the metalloregulator of the bacterial mercury resistance (mer) operon, binds Hg(II) with high affinity. To study the mechanism of metal-induced activation, a small protein was previously engineered embodying in a single polypeptide the metal-binding domain (MBD) ordinarily formed between two monomers of MerR. Here the physiological and biochemical properties of MBD expressed on the cell surface or in the cytosol were examined, to better understand the environments in which specific metal binding can occur with this small derivative. Over 20 000 surface copies of MBD were expressed per Escherichia coli cell, with metal stoichiometries of approximately 1.0 Hg(II) per MBD monomer. Cells expressing MBD on their surface in rich medium bound 6.1-fold more Hg(II) than those not expressing MBD. Although in nature cells use the entire mer operon to detoxify mercury, it was interesting to note that cells expressing only MBD survived Hg(II) challenge and recovered more quickly than cells without MBD. Cell-surface-expressed MBD bound Hg(II) preferentially even in the presence of a 22-fold molar excess of Zn(II) and when exposed to equimolar Cd(II) in addition. MBD expressed in the cystosol also afforded improved survival from Hg(II) exposure for E. coli and for the completely unrelated bacterium Deinococcus radiodurans. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16514151.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16514151.txt new file mode 100644 index 0000000000000000000000000000000000000000..8ec76367edf14652b707bf2ad01ea54558143f8f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16514151.txt @@ -0,0 +1,3 @@ +Hg(II) sequestration and protection by the MerR metal-binding domain (MBD). +MerR, the metalloregulator of the bacterial mercury resistance (mer) operon, binds Hg(II) with high affinity. To study the mechanism of metal-induced activation, a small protein was previously engineered embodying in a single polypeptide the metal-binding domain (MBD) ordinarily formed between two monomers of MerR. Here the physiological and biochemical properties of MBD expressed on the cell surface or in the cytosol were examined, to better understand the environments in which specific metal binding can occur with this small derivative. Over 20 000 surface copies of MBD were expressed per Escherichia coli cell, with metal stoichiometries of approximately 1.0 Hg(II) per MBD monomer. Cells expressing MBD on their surface in rich medium bound 6.1-fold more Hg(II) than those not expressing MBD. Although in nature cells use the entire mer operon to detoxify mercury, it was interesting to note that cells expressing only MBD survived Hg(II) challenge and recovered more quickly than cells without MBD. Cell-surface-expressed MBD bound Hg(II) preferentially even in the presence of a 22-fold molar excess of Zn(II) and when exposed to equimolar Cd(II) in addition. MBD expressed in the cystosol also afforded improved survival from Hg(II) exposure for E. coli and for the completely unrelated bacterium Deinococcus radiodurans. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16990433.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16990433.a1 new file mode 100644 index 0000000000000000000000000000000000000000..33079854d8b75b521902f2a1c539a705b84ae95d --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16990433.a1 @@ -0,0 +1,2 @@ +T1 Title 0 136 An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. +T2 Paragraph 137 1580 Several pathogenic strains of Escherichia coli exploit type III secretion to inject "effector proteins" into human cells, which then subvert eukaryotic cell biology to the bacterium's advantage. We have exploited bioinformatics and experimental approaches to establish that the effector repertoire in the Sakai strain of enterohemorrhagic E. coli (EHEC) O157:H7 is much larger than previously thought. Homology searches led to the identification of >60 putative effector genes. Thirteen of these were judged to be likely pseudogenes, whereas 49 were judged to be potentially functional. In total, 39 proteins were confirmed experimentally as effectors: 31 through proteomics and 28 through translocation assays. At the protein level, the EHEC effector sequences fall into >20 families. The largest family, the NleG family, contains 14 members in the Sakai strain alone. EHEC also harbors functional homologs of effectors from plant pathogens (HopPtoH, HopW, AvrA) and from Shigella (OspD, OspE, OspG), and two additional members of the Map/IpgB family. Genes encoding proven or predicted effectors occur in >20 exchangeable effector loci scattered throughout the chromosome. Crucially, the majority of functional effector genes are encoded by nine exchangeable effector loci that lie within lambdoid prophages. Thus, type III secretion in E. coli is linked to a vast phage "metagenome," acting as a crucible for the evolution of pathogenicity. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16990433.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16990433.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c9cbcd1f5e21e413b2fe70c35ae8e03aa2a0433 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-16990433.txt @@ -0,0 +1,3 @@ +An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. +Several pathogenic strains of Escherichia coli exploit type III secretion to inject "effector proteins" into human cells, which then subvert eukaryotic cell biology to the bacterium's advantage. We have exploited bioinformatics and experimental approaches to establish that the effector repertoire in the Sakai strain of enterohemorrhagic E. coli (EHEC) O157:H7 is much larger than previously thought. Homology searches led to the identification of >60 putative effector genes. Thirteen of these were judged to be likely pseudogenes, whereas 49 were judged to be potentially functional. In total, 39 proteins were confirmed experimentally as effectors: 31 through proteomics and 28 through translocation assays. At the protein level, the EHEC effector sequences fall into >20 families. The largest family, the NleG family, contains 14 members in the Sakai strain alone. EHEC also harbors functional homologs of effectors from plant pathogens (HopPtoH, HopW, AvrA) and from Shigella (OspD, OspE, OspG), and two additional members of the Map/IpgB family. Genes encoding proven or predicted effectors occur in >20 exchangeable effector loci scattered throughout the chromosome. Crucially, the majority of functional effector genes are encoded by nine exchangeable effector loci that lie within lambdoid prophages. Thus, type III secretion in E. coli is linked to a vast phage "metagenome," acting as a crucible for the evolution of pathogenicity. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17237163.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17237163.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e43aaa5f45bf3bb74f3bf4c7241ce03ce2dfa626 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17237163.a1 @@ -0,0 +1,2 @@ +T1 Title 0 86 Quorum-sensing regulation of adhesion in Serratia marcescens MG1 is surface dependent. +T2 Paragraph 87 1888 Serratia marcescens is an opportunistic pathogen and a major cause of ocular infections. In previous studies of S. marcescens MG1, we showed that biofilm maturation and sloughing were regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). Because of the importance of adhesion in initiating biofilm formation and infection, the primary goal of this study was to determine whether QS is important in adhesion to both abiotic and biotic surfaces, as assessed by determining the degree of attachment to hydrophilic tissue culture plates and human corneal epithelial (HCE) cells. Our results demonstrate that while adhesion to the abiotic surface was AHL regulated, adhesion to the HCE cell biotic surface was not. Type I fimbriae were identified as the critical adhesin for non-QS-mediated attachment to the biotic HCE cell surface but played no role in adhesion to the abiotic surface. While we were not able to identify a single QS-regulated adhesin essential for attachment to the abiotic surface, four AHL-regulated genes involved in adhesion to the abiotic surface were identified. Interestingly, two of these genes, bsmA and bsmB, were also shown to be involved in adhesion to the biotic surface in a non-QS-controlled fashion. Therefore, the expression of these two genes appears to be cocontrolled by regulators other than the QS system for mediation of attachment to HCE cells. We also found that QS in S. marcescens regulates other potential cell surface adhesins, including exopolysaccharide and the outer membrane protein OmpX. We concluded that S. marcescens MG1 utilizes different regulatory systems and adhesins in attachment to biotic and abiotic surfaces and that QS is a main regulatory pathway in adhesion to an abiotic surface but not in adhesion to a biotic surface. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17237163.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17237163.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb1ff26a514b3f270e0cd750de58c7ea0284baf9 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17237163.txt @@ -0,0 +1,3 @@ +Quorum-sensing regulation of adhesion in Serratia marcescens MG1 is surface dependent. +Serratia marcescens is an opportunistic pathogen and a major cause of ocular infections. In previous studies of S. marcescens MG1, we showed that biofilm maturation and sloughing were regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). Because of the importance of adhesion in initiating biofilm formation and infection, the primary goal of this study was to determine whether QS is important in adhesion to both abiotic and biotic surfaces, as assessed by determining the degree of attachment to hydrophilic tissue culture plates and human corneal epithelial (HCE) cells. Our results demonstrate that while adhesion to the abiotic surface was AHL regulated, adhesion to the HCE cell biotic surface was not. Type I fimbriae were identified as the critical adhesin for non-QS-mediated attachment to the biotic HCE cell surface but played no role in adhesion to the abiotic surface. While we were not able to identify a single QS-regulated adhesin essential for attachment to the abiotic surface, four AHL-regulated genes involved in adhesion to the abiotic surface were identified. Interestingly, two of these genes, bsmA and bsmB, were also shown to be involved in adhesion to the biotic surface in a non-QS-controlled fashion. Therefore, the expression of these two genes appears to be cocontrolled by regulators other than the QS system for mediation of attachment to HCE cells. We also found that QS in S. marcescens regulates other potential cell surface adhesins, including exopolysaccharide and the outer membrane protein OmpX. We concluded that S. marcescens MG1 utilizes different regulatory systems and adhesins in attachment to biotic and abiotic surfaces and that QS is a main regulatory pathway in adhesion to an abiotic surface but not in adhesion to a biotic surface. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17687514.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17687514.a1 new file mode 100644 index 0000000000000000000000000000000000000000..bd9bb0c4e8e5e2f77aedc7801817278336418def --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17687514.a1 @@ -0,0 +1,2 @@ +T1 Title 0 130 Unveiling molecular mechanisms of bacterial surface proteins: Streptococcus pneumoniae as a model organism for structural studies. +T2 Paragraph 131 1204 Bacteria present a variety of molecules either on their surface or in a cell-free form. These molecules take part in numerous processes in the interactions with their host, with its tissues and other molecules. These molecules are essential to bacterial pathogenesis either during colonization or the spread/invasion stages, and most are virulence factors. This review is focused on such molecules using Streptococcus pneumoniae, a Gram-positive bacterium, as an example. Selected surface proteins are introduced, their structure described, and, whenever available, their mechanisms of function on an atomic level are explained. Such mechanisms for hyaluronate lyase, pneumococcal surface protein A, pneumolysin, histidine-triad and fibronectin-binding proteins are discussed. Elucidation of molecular mechanisms of virulence factors is essential for the understanding of bacteria and their functional properties. Structural biology appears pivotal for these studies, as structural and mechanistic insights facilitate rational approach to the development of new treatments. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17687514.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17687514.txt new file mode 100644 index 0000000000000000000000000000000000000000..ee4e62e4ee6ab42418a473f5b7d0cffbeaacb584 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-17687514.txt @@ -0,0 +1,3 @@ +Unveiling molecular mechanisms of bacterial surface proteins: Streptococcus pneumoniae as a model organism for structural studies. +Bacteria present a variety of molecules either on their surface or in a cell-free form. These molecules take part in numerous processes in the interactions with their host, with its tissues and other molecules. These molecules are essential to bacterial pathogenesis either during colonization or the spread/invasion stages, and most are virulence factors. This review is focused on such molecules using Streptococcus pneumoniae, a Gram-positive bacterium, as an example. Selected surface proteins are introduced, their structure described, and, whenever available, their mechanisms of function on an atomic level are explained. Such mechanisms for hyaluronate lyase, pneumococcal surface protein A, pneumolysin, histidine-triad and fibronectin-binding proteins are discussed. Elucidation of molecular mechanisms of virulence factors is essential for the understanding of bacteria and their functional properties. Structural biology appears pivotal for these studies, as structural and mechanistic insights facilitate rational approach to the development of new treatments. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18094887.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18094887.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e1c43158dfa445d03e86b627bb94ead8e0656b80 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18094887.a1 @@ -0,0 +1,2 @@ +T1 Title 0 69 Rickettsia infection in five areas of the state of São Paulo, Brazil. +T2 Paragraph 70 1458 This study investigated rickettsial infection in animals, humans, ticks, and fleas collected in five areas of the state of São Paulo. Eight flea species (Adoratopsylla antiquorum antiquorum, Ctenocephalides felis felis, Polygenis atopus, Polygenis rimatus, Polygenis roberti roberti, Polygenis tripus, Rhopalopsyllus lugubris, and Rhopalopsyllus lutzi lutzi), and five tick species (Amblyomma aureolatum, Amblyomma cajennense, Amblyomma dubitatum, Ixodes loricatus, and Rhipicephalus sanguineus) were collected from dogs, cats, and opossums. Rickettsia felis was the only rickettsia found infecting fleas, whereas Rickettsia bellii was the only agent infecting ticks, but no animal or human blood was shown to contain rickettsial DNA. Testing animal and human sera by indirect immunofluorescence assay against four rickettsia antigens (R. rickettsii, R. parkeri, R. felis, and R. bellii), some opossum, dog, horse, and human sera reacted to R. rickettsii with titers at least four-fold higher than to the other three rickettsial antigens. These sera were considered to have a predominant antibody response to R. rickettsii. Using the same criteria, opossum, dog, and horse sera showed predominant antibody response to R. parkeri or a very closely related genotype. Our serological results suggest that both R. rickettsii and R. parkeri infected animals and/or humans in the studied areas. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18094887.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18094887.txt new file mode 100644 index 0000000000000000000000000000000000000000..334d4ab11053f0041b8f2667d022cb3c46e83e12 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18094887.txt @@ -0,0 +1,3 @@ +Rickettsia infection in five areas of the state of São Paulo, Brazil. +This study investigated rickettsial infection in animals, humans, ticks, and fleas collected in five areas of the state of São Paulo. Eight flea species (Adoratopsylla antiquorum antiquorum, Ctenocephalides felis felis, Polygenis atopus, Polygenis rimatus, Polygenis roberti roberti, Polygenis tripus, Rhopalopsyllus lugubris, and Rhopalopsyllus lutzi lutzi), and five tick species (Amblyomma aureolatum, Amblyomma cajennense, Amblyomma dubitatum, Ixodes loricatus, and Rhipicephalus sanguineus) were collected from dogs, cats, and opossums. Rickettsia felis was the only rickettsia found infecting fleas, whereas Rickettsia bellii was the only agent infecting ticks, but no animal or human blood was shown to contain rickettsial DNA. Testing animal and human sera by indirect immunofluorescence assay against four rickettsia antigens (R. rickettsii, R. parkeri, R. felis, and R. bellii), some opossum, dog, horse, and human sera reacted to R. rickettsii with titers at least four-fold higher than to the other three rickettsial antigens. These sera were considered to have a predominant antibody response to R. rickettsii. Using the same criteria, opossum, dog, and horse sera showed predominant antibody response to R. parkeri or a very closely related genotype. Our serological results suggest that both R. rickettsii and R. parkeri infected animals and/or humans in the studied areas. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18687046.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18687046.a1 new file mode 100644 index 0000000000000000000000000000000000000000..b76b00110e4d429755933b55e9f859a0e535e8d2 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18687046.a1 @@ -0,0 +1,5 @@ +T1 Title 0 125 Impact of intracranial pressure monitor prophylaxis on central nervous system infections and bacterial multi-drug resistance. +T2 Paragraph 126 586 Routine intracranial pressure monitor (ICP) prophylaxis is not practiced at our institution. Nevertheless, some patients receive de facto prophylaxis as a result of the use of antibiotics for injuries such as open or facial fractures. We tested the hypothesis that prophylactic antibiotics do not reduce the incidence of central nervous system (CNS) infections but instead are associated with the acquisition of multi-drug resistant (MDR) bacterial infections. +T3 Paragraph 587 1634 Patients admitted to the trauma intensive care unit (TICU) from January, 2001 through December, 2004 with blunt, non-operative traumatic brain injury who were managed solely with an ICP monitor were identified from our trauma registry and divided into two groups: (1) Those receiving no antibiotics prior to or during ICP monitoring (NONE; n = 71); and (2) those already receiving antibiotics at the time of ICP monitor insertion (PRO; n = 84). Groups were stratified on the basis of age, Injury Severity Score (ISS), Glasgow Coma Scale (GCS) Score, base excess (BE), ICP days, transfusions in 24 h, ICU days, ventilator days, head Abbreviated Injury Score (AIS), and chest AIS. The study groups did not differ with respect to age, ISS, GCS, BE, ICP days, 24-h transfusions, ICU days, ventilator days, head AIS, or length of stay. In all, 183 patients were identified, of whom 28 died within seven days and were excluded from the analysis. All patients were followed until discharge for both CNS infections and subsequent infectious complications. +T4 Paragraph 1635 2119 Only two patients, both in the PRO group, developed CNS infection. Both infectious complications (0.7 vs 1.4 per patient; p < 0.05) and infections secondary to MDR pathogens (0.03 vs. 0.33 per patient; p < 0.01) were significantly more common in the PRO group. Twenty-nine percent of the ventilator-associated pneumonias and 33% of the blood stream infections in the PRO group were MDR, whereas only two blood stream infections in the NONE group (4% of the total infections) were MDR. +T5 Paragraph 2120 2346 The routine use of prophylactic antibiotics for ICP monitor insertion is not warranted. This practice does not reduce the CNS infection rate and is associated with more MDR pathogens in any subsequent infectious complications. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18687046.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18687046.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab1ccdbe7589ae4b7497589c6d301629b98eb4fe --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18687046.txt @@ -0,0 +1,6 @@ +Impact of intracranial pressure monitor prophylaxis on central nervous system infections and bacterial multi-drug resistance. +Routine intracranial pressure monitor (ICP) prophylaxis is not practiced at our institution. Nevertheless, some patients receive de facto prophylaxis as a result of the use of antibiotics for injuries such as open or facial fractures. We tested the hypothesis that prophylactic antibiotics do not reduce the incidence of central nervous system (CNS) infections but instead are associated with the acquisition of multi-drug resistant (MDR) bacterial infections. +Patients admitted to the trauma intensive care unit (TICU) from January, 2001 through December, 2004 with blunt, non-operative traumatic brain injury who were managed solely with an ICP monitor were identified from our trauma registry and divided into two groups: (1) Those receiving no antibiotics prior to or during ICP monitoring (NONE; n = 71); and (2) those already receiving antibiotics at the time of ICP monitor insertion (PRO; n = 84). Groups were stratified on the basis of age, Injury Severity Score (ISS), Glasgow Coma Scale (GCS) Score, base excess (BE), ICP days, transfusions in 24 h, ICU days, ventilator days, head Abbreviated Injury Score (AIS), and chest AIS. The study groups did not differ with respect to age, ISS, GCS, BE, ICP days, 24-h transfusions, ICU days, ventilator days, head AIS, or length of stay. In all, 183 patients were identified, of whom 28 died within seven days and were excluded from the analysis. All patients were followed until discharge for both CNS infections and subsequent infectious complications. +Only two patients, both in the PRO group, developed CNS infection. Both infectious complications (0.7 vs 1.4 per patient; p < 0.05) and infections secondary to MDR pathogens (0.03 vs. 0.33 per patient; p < 0.01) were significantly more common in the PRO group. Twenty-nine percent of the ventilator-associated pneumonias and 33% of the blood stream infections in the PRO group were MDR, whereas only two blood stream infections in the NONE group (4% of the total infections) were MDR. +The routine use of prophylactic antibiotics for ICP monitor insertion is not warranted. This practice does not reduce the CNS infection rate and is associated with more MDR pathogens in any subsequent infectious complications. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18694716.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18694716.a1 new file mode 100644 index 0000000000000000000000000000000000000000..67ae61842bc8ca029c99db846f7c66a777bdca49 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18694716.a1 @@ -0,0 +1,2 @@ +T1 Title 0 95 Quantitative metabolome analysis using liquid chromatography-high-resolution mass spectrometry. +T2 Paragraph 96 1409 In this report, we introduce a liquid chromatography single-mass spectrometry method for metabolome quantification, using the LTQ Orbitrap high-resolution mass spectrometer. Analytes were separated with hydrophilic interaction liquid chromatography. At a working resolution of 30,000 (at m/z 400), the limit of detection varied from 50 fmol to 5 pmol for 25 metabolites tested. In terms of metabolite concentration, the linearity was about 2 to 3 orders of magnitude for most compounds (R(2)>0.99). To determine the accuracy of the system in complex sample matrices, the isotope dilution method was evaluated from mixtures of pure compounds and uniformly 13C-labeled cell extracts. With the application of this method, quantification was possible within single runs even when the pool sizes of individual metabolites varied from 0.13 to 55.6 microM. As a case study, intracellular concentrations of central metabolites were determined for Methylobacterium extorquens AM1 during growth on two different carbon sources, methanol and succinate. Reproducible results from technical and biological repetitions were obtained that revealed significant variations of intracellular metabolite pool sizes, depending on the carbon source. The LTQ Obitrap offers new perspectives and strategies for metabolome quantification. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18694716.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18694716.txt new file mode 100644 index 0000000000000000000000000000000000000000..8add4104daf385eabd2a972d3e5a6361f8c589b5 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18694716.txt @@ -0,0 +1,3 @@ +Quantitative metabolome analysis using liquid chromatography-high-resolution mass spectrometry. +In this report, we introduce a liquid chromatography single-mass spectrometry method for metabolome quantification, using the LTQ Orbitrap high-resolution mass spectrometer. Analytes were separated with hydrophilic interaction liquid chromatography. At a working resolution of 30,000 (at m/z 400), the limit of detection varied from 50 fmol to 5 pmol for 25 metabolites tested. In terms of metabolite concentration, the linearity was about 2 to 3 orders of magnitude for most compounds (R(2)>0.99). To determine the accuracy of the system in complex sample matrices, the isotope dilution method was evaluated from mixtures of pure compounds and uniformly 13C-labeled cell extracts. With the application of this method, quantification was possible within single runs even when the pool sizes of individual metabolites varied from 0.13 to 55.6 microM. As a case study, intracellular concentrations of central metabolites were determined for Methylobacterium extorquens AM1 during growth on two different carbon sources, methanol and succinate. Reproducible results from technical and biological repetitions were obtained that revealed significant variations of intracellular metabolite pool sizes, depending on the carbon source. The LTQ Obitrap offers new perspectives and strategies for metabolome quantification. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18789156.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18789156.a1 new file mode 100644 index 0000000000000000000000000000000000000000..84390d901c608e9d4debf4067d96e5893d5f594e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18789156.a1 @@ -0,0 +1,4 @@ +T1 Title 0 173 A novel receptor - ligand pathway for entry of Francisella tularensis in monocyte-like THP-1 cells: interaction between surface nucleolin and bacterial elongation factor Tu. +T2 Paragraph 174 689 Francisella tularensis, the causative agent of tularemia, is one of the most infectious human bacterial pathogens. It is phagocytosed by immune cells, such as monocytes and macrophages. The precise mechanisms that initiate bacterial uptake have not yet been elucidated. Participation of C3, CR3, class A scavenger receptors and mannose receptor in bacterial uptake have been already reported. However, contribution of an additional, as-yet-unidentified receptor for F. tularensis internalization has been suggested. +T3 Paragraph 690 1808 We show here that cell-surface expressed nucleolin is a receptor for Francisella tularensis Live Vaccine Strain (LVS) and promotes LVS binding and infection of human monocyte-like THP-1 cells. The HB-19 pseudopeptide that binds specifically carboxy-terminal RGG domain of nucleolin inhibits LVS binding and infection of monocyte-like THP-1 cells. In a pull-down assay, elongation factor Tu (EF-Tu), a GTP-binding protein involved in protein translation, usually found in cytoplasm, was recovered among LVS bacterial membrane proteins bound on RGG domain of nucleolin. A specific polyclonal murine antibody was raised against recombinant LVS EF-Tu. By fluorescence and electron microscopy experiments, we found that a fraction of EF-Tu could be detected at the bacterial surface. Anti-EF-Tu antibodies reduced LVS binding to monocyte-like THP-1 cells and impaired infection, even in absence of complement and complement receptors. Interaction between EF-Tu and nucleolin was illustrated by two different pull-down assays using recombinant EF-Tu proteins and either RGG domain of nucleolin or cell solubilized nucleolin. +T4 Paragraph 1809 2536 Altogether, our results demonstrate that the interaction between surface nucleolin and its bacterial ligand EF-Tu plays an important role in Francisella tularensis adhesion and entry process and may therefore facilitate invasion of host tissues. Since phagosomal escape and intra-cytosolic multiplication of LVS in infected monocytes are very similar to those of human pathogenic F. tularensis ssp tularensis, the mechanism of entry into monocyte-like THP-1 cells, involving interaction between EF-Tu and nucleolin, might be similar in the two subspecies. Thus, the use of either nucleolin-specific pseudopeptide HB-19 or recombinant EF-Tu could provide attractive therapeutic approaches for modulating F. tularensis infection. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18789156.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18789156.txt new file mode 100644 index 0000000000000000000000000000000000000000..cbaad2de68c07772ee9296da00a42b9e94ceddcc --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18789156.txt @@ -0,0 +1,5 @@ +A novel receptor - ligand pathway for entry of Francisella tularensis in monocyte-like THP-1 cells: interaction between surface nucleolin and bacterial elongation factor Tu. +Francisella tularensis, the causative agent of tularemia, is one of the most infectious human bacterial pathogens. It is phagocytosed by immune cells, such as monocytes and macrophages. The precise mechanisms that initiate bacterial uptake have not yet been elucidated. Participation of C3, CR3, class A scavenger receptors and mannose receptor in bacterial uptake have been already reported. However, contribution of an additional, as-yet-unidentified receptor for F. tularensis internalization has been suggested. +We show here that cell-surface expressed nucleolin is a receptor for Francisella tularensis Live Vaccine Strain (LVS) and promotes LVS binding and infection of human monocyte-like THP-1 cells. The HB-19 pseudopeptide that binds specifically carboxy-terminal RGG domain of nucleolin inhibits LVS binding and infection of monocyte-like THP-1 cells. In a pull-down assay, elongation factor Tu (EF-Tu), a GTP-binding protein involved in protein translation, usually found in cytoplasm, was recovered among LVS bacterial membrane proteins bound on RGG domain of nucleolin. A specific polyclonal murine antibody was raised against recombinant LVS EF-Tu. By fluorescence and electron microscopy experiments, we found that a fraction of EF-Tu could be detected at the bacterial surface. Anti-EF-Tu antibodies reduced LVS binding to monocyte-like THP-1 cells and impaired infection, even in absence of complement and complement receptors. Interaction between EF-Tu and nucleolin was illustrated by two different pull-down assays using recombinant EF-Tu proteins and either RGG domain of nucleolin or cell solubilized nucleolin. +Altogether, our results demonstrate that the interaction between surface nucleolin and its bacterial ligand EF-Tu plays an important role in Francisella tularensis adhesion and entry process and may therefore facilitate invasion of host tissues. Since phagosomal escape and intra-cytosolic multiplication of LVS in infected monocytes are very similar to those of human pathogenic F. tularensis ssp tularensis, the mechanism of entry into monocyte-like THP-1 cells, involving interaction between EF-Tu and nucleolin, might be similar in the two subspecies. Thus, the use of either nucleolin-specific pseudopeptide HB-19 or recombinant EF-Tu could provide attractive therapeutic approaches for modulating F. tularensis infection. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18845825.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18845825.a1 new file mode 100644 index 0000000000000000000000000000000000000000..40b008e4c35e2dd761eb9c92e9cf6d094fbad1ce --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18845825.a1 @@ -0,0 +1,2 @@ +T1 Title 0 116 High genetic diversity of nontypeable Haemophilus influenzae isolates from two children attending a day care center. +T2 Paragraph 117 471 Twenty-one nontypeable Haemophilus influenzae (NTHi) isolates from the throats of two healthy children were genotyped by multilocus sequence typing. Nine unique sequence types (STs) were identified. These STs were scattered throughout the phylogenetic tree of reported NTHi STs, demonstrating the high level of NTHi diversity found in colonized children. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18845825.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18845825.txt new file mode 100644 index 0000000000000000000000000000000000000000..4beae679b887ccc6666e7bc50b922e19ec607c8a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-18845825.txt @@ -0,0 +1,3 @@ +High genetic diversity of nontypeable Haemophilus influenzae isolates from two children attending a day care center. +Twenty-one nontypeable Haemophilus influenzae (NTHi) isolates from the throats of two healthy children were genotyped by multilocus sequence typing. Nine unique sequence types (STs) were identified. These STs were scattered throughout the phylogenetic tree of reported NTHi STs, demonstrating the high level of NTHi diversity found in colonized children. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19004249.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19004249.a1 new file mode 100644 index 0000000000000000000000000000000000000000..93a8d5a120d43aeb93333efb42294f6fe727fcbd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19004249.a1 @@ -0,0 +1,2 @@ +T1 Title 0 91 Evaluation of antibacterial activity of synthetic aliphatic and aromatic monoacylglycerols. +T2 Paragraph 92 618 The antibacterial activity of synthetic aliphatic and aromatic monoacylglycerols (MAGs) was studied against two human pathogens: Staphylococcus aureus and Escherichia coli. The active compounds inhibited selectively S. aureus. The most active compounds amongst them were those with medium size aliphatic chain and aromatic MAGs with electron withdrawing substituents at the aryl ring. The introduction of one or two-carbon spacer between the aryl ring and the carboxylic function did not influence antibacterial effectiveness. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19004249.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19004249.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b902dacfe6b9aa8da9c2869f38a51b40302dfc4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19004249.txt @@ -0,0 +1,3 @@ +Evaluation of antibacterial activity of synthetic aliphatic and aromatic monoacylglycerols. +The antibacterial activity of synthetic aliphatic and aromatic monoacylglycerols (MAGs) was studied against two human pathogens: Staphylococcus aureus and Escherichia coli. The active compounds inhibited selectively S. aureus. The most active compounds amongst them were those with medium size aliphatic chain and aromatic MAGs with electron withdrawing substituents at the aryl ring. The introduction of one or two-carbon spacer between the aryl ring and the carboxylic function did not influence antibacterial effectiveness. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19049879.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19049879.a1 new file mode 100644 index 0000000000000000000000000000000000000000..cc77b3e3b9a3aebd6f44081cb6d121232e23547e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19049879.a1 @@ -0,0 +1,2 @@ +T1 Title 0 88 Molecular cloning and expression of MyD88 in large yellow croaker, Pseudosciaena crocea. +T2 Paragraph 89 1466 Myeloid differentiation factor 88 (MyD88) is an adaptor protein involved in the interleukin-1 receptor and Toll-like receptor-induced activation of nuclear factor-kappaB (NF-kappaB). In this report, the full-length cDNA of MyD88 was cloned from the large yellow croaker, Pseudosciaena crocea. It was of 1574 bp, including a 5'-terminal untranslated region (UTR) of 89 bp, a 3'-terminal UTR of 621bp and an open reading frame (ORF) of 864 bp encoding a polypeptide of 287 amino acids. It contained a typical death domain at the N-terminal and a conservative Toll/IL-1R (TIR) domain structure at the C-terminal. The quantitative real-time reverse transcription PCR analysis revealed a broad expression of MyD88 with the highest expression in the spleen and the weakest expression in the muscle. The expression of MyD88 after challenge with formalin-inactivated Gram-negative bacterium Vibrio parahaemolyticus was tested in blood, spleen and liver. It suggested that the highest expression was in the spleen (p<0.05) with 1.9 times (at 48 h) as much as that in the control and the lowest expression of MyD88 was in the liver (p<0.05) with 0.29 times (at 3h) of that in the control. These results indicated that as a universal key adaptor in the Toll-like receptor pathway in mammals, MyD88 might play an important role in large yellow croaker defense against pathogenic infection. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19049879.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19049879.txt new file mode 100644 index 0000000000000000000000000000000000000000..25e106aff4260023e4b38549123c12adb7da48f1 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19049879.txt @@ -0,0 +1,3 @@ +Molecular cloning and expression of MyD88 in large yellow croaker, Pseudosciaena crocea. +Myeloid differentiation factor 88 (MyD88) is an adaptor protein involved in the interleukin-1 receptor and Toll-like receptor-induced activation of nuclear factor-kappaB (NF-kappaB). In this report, the full-length cDNA of MyD88 was cloned from the large yellow croaker, Pseudosciaena crocea. It was of 1574 bp, including a 5'-terminal untranslated region (UTR) of 89 bp, a 3'-terminal UTR of 621bp and an open reading frame (ORF) of 864 bp encoding a polypeptide of 287 amino acids. It contained a typical death domain at the N-terminal and a conservative Toll/IL-1R (TIR) domain structure at the C-terminal. The quantitative real-time reverse transcription PCR analysis revealed a broad expression of MyD88 with the highest expression in the spleen and the weakest expression in the muscle. The expression of MyD88 after challenge with formalin-inactivated Gram-negative bacterium Vibrio parahaemolyticus was tested in blood, spleen and liver. It suggested that the highest expression was in the spleen (p<0.05) with 1.9 times (at 48 h) as much as that in the control and the lowest expression of MyD88 was in the liver (p<0.05) with 0.29 times (at 3h) of that in the control. These results indicated that as a universal key adaptor in the Toll-like receptor pathway in mammals, MyD88 might play an important role in large yellow croaker defense against pathogenic infection. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19075662.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19075662.a1 new file mode 100644 index 0000000000000000000000000000000000000000..d2ada706474140acff46f83a41208c4cde66b4b0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19075662.a1 @@ -0,0 +1,2 @@ +T1 Title 0 52 Prevention and treatment of Staphylococcus biofilms. +T2 Paragraph 53 866 Staphylococcus growth on medical devices represents a common occurrence that can lead to serious illness and death. Biomaterial-associated infection, mostly caused by Staphylococcus epidermidis and Staphylococcus aureus, is fairly complicated by the organism' development of a biofilm, which provides a microenvironment that protects from attack by the host immune system and antibiotics. In this review we present recent insights regarding S. aureus and S. epidermidis structural and functional factors that are effective in biofilm development and describe the regulation of their expression. On the basis of the knowledge gained, we also present the potential and limits of current biochemical and biophysical strategies aimed at preventing biofilm formation or at the treatment of established mature biofilms. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19075662.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19075662.txt new file mode 100644 index 0000000000000000000000000000000000000000..f4d04b1dc21722cbd6ff578cb8b2b8cc0fd47d24 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19075662.txt @@ -0,0 +1,3 @@ +Prevention and treatment of Staphylococcus biofilms. +Staphylococcus growth on medical devices represents a common occurrence that can lead to serious illness and death. Biomaterial-associated infection, mostly caused by Staphylococcus epidermidis and Staphylococcus aureus, is fairly complicated by the organism' development of a biofilm, which provides a microenvironment that protects from attack by the host immune system and antibiotics. In this review we present recent insights regarding S. aureus and S. epidermidis structural and functional factors that are effective in biofilm development and describe the regulation of their expression. On the basis of the knowledge gained, we also present the potential and limits of current biochemical and biophysical strategies aimed at preventing biofilm formation or at the treatment of established mature biofilms. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19099664.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19099664.a1 new file mode 100644 index 0000000000000000000000000000000000000000..20ead49dfaf44d8695b2a8943439efa45de48ae3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19099664.a1 @@ -0,0 +1,2 @@ +T1 Title 0 100 [Changes of pathogens and susceptibility to antibiotics in hematology ward from years 2001 to 2005]. +T2 Paragraph 101 1277 The purpose of this study was to determine the changes of pathogens in hematological ward and susceptibility of patients received chemotherapy to antibiotics. The pathogens were taken from blood, urine and sputum of patients who accepted chemotherapy from years 2001 to 2005, then were isolated and identified. The susceptibility test was performed by disk diffusion method. The results showed that the total of 418 strains were detected. Gram-negative bacteria were the most common of nosocomial infection. Pseudomonas aeruginosa, Enterobacter cloacae, E. coli account for the most of Gram negative- bacteria infection and most resistant to broad-spectrum penicillin, Acinetobacter baumannii showed a trend of increase. The ratios of gram positive bacteria and fungi were increased slowly, mainly as Enterococcus and Candida. Enterococcus is the most common cause of Gram-positive bacterial infection. Vancomycin resistance did not occur. It is concluded that Gram-negative bacteria are main cause of nosocomial infection in patients with hematological malignancies. Gram positive bacteria and fungi had been more frequent. Strains resistant to antimicrobial agents increase. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19099664.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19099664.txt new file mode 100644 index 0000000000000000000000000000000000000000..78cc10cd7a3e1632c4d9998857f1c5cc744a4baf --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19099664.txt @@ -0,0 +1,3 @@ +[Changes of pathogens and susceptibility to antibiotics in hematology ward from years 2001 to 2005]. +The purpose of this study was to determine the changes of pathogens in hematological ward and susceptibility of patients received chemotherapy to antibiotics. The pathogens were taken from blood, urine and sputum of patients who accepted chemotherapy from years 2001 to 2005, then were isolated and identified. The susceptibility test was performed by disk diffusion method. The results showed that the total of 418 strains were detected. Gram-negative bacteria were the most common of nosocomial infection. Pseudomonas aeruginosa, Enterobacter cloacae, E. coli account for the most of Gram negative- bacteria infection and most resistant to broad-spectrum penicillin, Acinetobacter baumannii showed a trend of increase. The ratios of gram positive bacteria and fungi were increased slowly, mainly as Enterococcus and Candida. Enterococcus is the most common cause of Gram-positive bacterial infection. Vancomycin resistance did not occur. It is concluded that Gram-negative bacteria are main cause of nosocomial infection in patients with hematological malignancies. Gram positive bacteria and fungi had been more frequent. Strains resistant to antimicrobial agents increase. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19175621.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19175621.a1 new file mode 100644 index 0000000000000000000000000000000000000000..ece8e527172067a697bb75d07748eda1b1dcce28 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19175621.a1 @@ -0,0 +1,2 @@ +T1 Title 0 159 Occurrence of extended-spectrum beta-lactamase-producing Salmonella enterica in northern Spain with evidence of CTX-M-9 clonal spread among animals and humans. +T2 Paragraph 160 1017 Among the 1233 Salmonella enterica isolates obtained in two Spanish hospitals, five isolates (0.4%) (serovars: Virchow, four; Livingstone, one) had the phenotype of an extended-spectrum beta-lactamase (ESBL) producer. The genetic characterization of the ESBL of S. enterica Livingstone revealed a bla(SHV-2) gene. The bla(CTX-M-10) gene in a phage-related genetic environment was found in one S. enterica Virchow isolate, and the bla(CTX-M-9) gene within the In60 integron was found in the three remaining Virchow isolates. These three isolates presented indistinguishable or closely related pulsed-field gel electrophoresis patterns among themselves and also as compared with the two other bla(CTX-M-9)-containing isolates previously obtained from animals. ESBL production is an emerging mechanism of resistance in S. enterica in the two studied hospitals. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19175621.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19175621.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab256aa3dc4341bf1b8b8c29a7f4fb24b13763f1 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19175621.txt @@ -0,0 +1,3 @@ +Occurrence of extended-spectrum beta-lactamase-producing Salmonella enterica in northern Spain with evidence of CTX-M-9 clonal spread among animals and humans. +Among the 1233 Salmonella enterica isolates obtained in two Spanish hospitals, five isolates (0.4%) (serovars: Virchow, four; Livingstone, one) had the phenotype of an extended-spectrum beta-lactamase (ESBL) producer. The genetic characterization of the ESBL of S. enterica Livingstone revealed a bla(SHV-2) gene. The bla(CTX-M-10) gene in a phage-related genetic environment was found in one S. enterica Virchow isolate, and the bla(CTX-M-9) gene within the In60 integron was found in the three remaining Virchow isolates. These three isolates presented indistinguishable or closely related pulsed-field gel electrophoresis patterns among themselves and also as compared with the two other bla(CTX-M-9)-containing isolates previously obtained from animals. ESBL production is an emerging mechanism of resistance in S. enterica in the two studied hospitals. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19339076.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19339076.a1 new file mode 100644 index 0000000000000000000000000000000000000000..bf32fe867f4a1e90f2ba973ac60ba7d1536be361 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19339076.a1 @@ -0,0 +1,2 @@ +T1 Title 0 132 Bile resistance in Lactococcus lactis strains varies with cellular fatty acid composition: analysis by using different growth media. +T2 Paragraph 133 2382 Bile resistance is one of the basic characteristics of probiotic bacteria. The aim of this study was to investigate the characteristics of bile resistance in lactococci by studying the relationship between bile resistance and cellular fatty acid composition in lactococcci grown on different media. We determined the bile resistance of 14 strains in lactose-free M17 medium supplemented with either glucose only (GM17) or lactose only (LM17). Gas chromatographic analyses of free lipids extracted from the tested strains were used for determining their fatty acid composition. A correlation analysis of all strains grown in both media revealed significant positive correlations between bile resistance and relative contents of hexadecanoic acid and octadecenoic acid, and negative correlations between bile resistance and relative contents of hexadecenoic acid and C-19 cyclopropane fatty acid. It is also a fact that the fatty acids associated with bile resistance depended on species, strain, and/or growth medium. In L. lactis subsp. cremoris strains grown in GM17 medium, the bile-resistant strains had significantly more octadecenoic acid than the bile-sensitive strains. In LM17 medium, bile-resistant strains had significantly more octadecenoic acid and significantly less C-19 cyclopropane fatty acid than the bile-sensitive strains. In L. lactis subsp. lactis strains, bile resistances of some of the tested strains were altered by growth medium. Some strains were resistant to bile in GM17 medium but sensitive to bile in LM17 medium. Some strains were resistant in both media tested. The strains grown in GM17 medium had significantly more hexadecanoic acid and octadecenoic acid, and significantly less tetradecanoic acid, octadecadienoic acid and C-19 cyclopropane fatty acid than the strains grown in LM17 medium. In conclusion, the fatty acid compositions of the bile-resistant lactococci differed from those of the bile-sensitive ones. More importantly, our data suggest that altering their fatty acid composition (i.e. increased hexadecanoic acid and octadecenoic acid and decreased hexadecenoic acid and C-19 cyclopropane fatty acid) by changing growth conditions may be a useful way to enhance their bile resistance in lactococci. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19339076.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19339076.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8fb7fc5e094673c299a36b7f65f92afc775e127 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19339076.txt @@ -0,0 +1,3 @@ +Bile resistance in Lactococcus lactis strains varies with cellular fatty acid composition: analysis by using different growth media. +Bile resistance is one of the basic characteristics of probiotic bacteria. The aim of this study was to investigate the characteristics of bile resistance in lactococci by studying the relationship between bile resistance and cellular fatty acid composition in lactococcci grown on different media. We determined the bile resistance of 14 strains in lactose-free M17 medium supplemented with either glucose only (GM17) or lactose only (LM17). Gas chromatographic analyses of free lipids extracted from the tested strains were used for determining their fatty acid composition. A correlation analysis of all strains grown in both media revealed significant positive correlations between bile resistance and relative contents of hexadecanoic acid and octadecenoic acid, and negative correlations between bile resistance and relative contents of hexadecenoic acid and C-19 cyclopropane fatty acid. It is also a fact that the fatty acids associated with bile resistance depended on species, strain, and/or growth medium. In L. lactis subsp. cremoris strains grown in GM17 medium, the bile-resistant strains had significantly more octadecenoic acid than the bile-sensitive strains. In LM17 medium, bile-resistant strains had significantly more octadecenoic acid and significantly less C-19 cyclopropane fatty acid than the bile-sensitive strains. In L. lactis subsp. lactis strains, bile resistances of some of the tested strains were altered by growth medium. Some strains were resistant to bile in GM17 medium but sensitive to bile in LM17 medium. Some strains were resistant in both media tested. The strains grown in GM17 medium had significantly more hexadecanoic acid and octadecenoic acid, and significantly less tetradecanoic acid, octadecadienoic acid and C-19 cyclopropane fatty acid than the strains grown in LM17 medium. In conclusion, the fatty acid compositions of the bile-resistant lactococci differed from those of the bile-sensitive ones. More importantly, our data suggest that altering their fatty acid composition (i.e. increased hexadecanoic acid and octadecenoic acid and decreased hexadecenoic acid and C-19 cyclopropane fatty acid) by changing growth conditions may be a useful way to enhance their bile resistance in lactococci. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19396518.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19396518.a1 new file mode 100644 index 0000000000000000000000000000000000000000..1acad77c8dc0faf52edc42a75c45ff668840b5ba --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19396518.a1 @@ -0,0 +1,2 @@ +T1 Title 0 104 Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR. +T2 Paragraph 105 1735 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. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19396518.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19396518.txt new file mode 100644 index 0000000000000000000000000000000000000000..1fe9bd0cc005116ffef11c0b7125f865a3077b3b --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19396518.txt @@ -0,0 +1,3 @@ +Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR. +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. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19501788.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19501788.a1 new file mode 100644 index 0000000000000000000000000000000000000000..1e0bf61dde0a0f5f6c030f95a53a5b2d72d155ef --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19501788.a1 @@ -0,0 +1,2 @@ +T1 Title 0 123 Construction of an attenuated Pseudomonas fluorescens strain and evaluation of its potential as a cross-protective vaccine. +T2 Paragraph 124 1683 Ferric uptake regulator (Fur) is a global transcription regulator that is ubiquitous to Gram-negative bacteria and regulates diverse biological processes, including iron uptake, cellular metabolism, stress response, and production of virulence determinants. As a result, for many pathogenic bacteria, Fur plays a crucial role in the course of infection and disease development. In this study, the fur gene was cloned from a pathogenic Pseudomonas fluorescens strain, TSS, isolated from diseased Japanese flounder cultured in a local farm. TSS Fur can partially complement the defective phenotype of an Escherichia coli fur mutant. A TSS fur null mutant, TFM, was constructed. Compared to TSS, TFM exhibits reduced growth ability, aberrant production of outer membrane proteins, decreased resistance against host serum bactericidal activity, impaired ability to disseminate in host blood and tissues, and drastic attenuation in overall bacterial virulence in a Japanese flounder infection model. When used as a live vaccine administered via the injection, immersion, and oral routes, TFM affords high levels of protection upon Japanese flounder against not only P. fluorescens infection but also Aeromonas hydrophila infection. Furthermore, a plasmid, pJAQ, was constructed, which expresses the coding element of the Vibrio harveyi antigen AgaV-DegQ. TFM harboring pJAQ can secret AgaV-DegQ into the extracellular milieu. Vaccination of Japanese flounder with live TFM/pJAQ elicited strong immunoprotection against both V. harveyi and A. hydrophila infections. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19501788.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19501788.txt new file mode 100644 index 0000000000000000000000000000000000000000..101f49bda8f44cc3f2989d279c4bd3b01020ec46 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19501788.txt @@ -0,0 +1,3 @@ +Construction of an attenuated Pseudomonas fluorescens strain and evaluation of its potential as a cross-protective vaccine. +Ferric uptake regulator (Fur) is a global transcription regulator that is ubiquitous to Gram-negative bacteria and regulates diverse biological processes, including iron uptake, cellular metabolism, stress response, and production of virulence determinants. As a result, for many pathogenic bacteria, Fur plays a crucial role in the course of infection and disease development. In this study, the fur gene was cloned from a pathogenic Pseudomonas fluorescens strain, TSS, isolated from diseased Japanese flounder cultured in a local farm. TSS Fur can partially complement the defective phenotype of an Escherichia coli fur mutant. A TSS fur null mutant, TFM, was constructed. Compared to TSS, TFM exhibits reduced growth ability, aberrant production of outer membrane proteins, decreased resistance against host serum bactericidal activity, impaired ability to disseminate in host blood and tissues, and drastic attenuation in overall bacterial virulence in a Japanese flounder infection model. When used as a live vaccine administered via the injection, immersion, and oral routes, TFM affords high levels of protection upon Japanese flounder against not only P. fluorescens infection but also Aeromonas hydrophila infection. Furthermore, a plasmid, pJAQ, was constructed, which expresses the coding element of the Vibrio harveyi antigen AgaV-DegQ. TFM harboring pJAQ can secret AgaV-DegQ into the extracellular milieu. Vaccination of Japanese flounder with live TFM/pJAQ elicited strong immunoprotection against both V. harveyi and A. hydrophila infections. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19552770.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19552770.a1 new file mode 100644 index 0000000000000000000000000000000000000000..c0b99335fe07fdd91c6ca574ef8044dd5c823978 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19552770.a1 @@ -0,0 +1,5 @@ +T1 Title 0 73 Prevalence of thermotolerant Campylobacter in partridges (Perdix perdix). +T2 Paragraph 74 206 To estimate the prevalence of thermotolerant Campylobacter spp. in commercially reared partridges (Perdix perdix) in southern Italy. +T3 Paragraph 207 1018 Cloacal swabs of partridges (n = 240), equally distributed between male and female birds, from a game bird farm located in the Southern Italy were examined for the prevalence of thermotolerant Campylobacter spp. The samples were processed in order to detect thermotolerant Campylobacter spp. by culture methods. The positive samples were then confirmed by multiplex polymerase chain reaction. Thermotolerant Campylobacter spp. were isolated from 118 (49.2%) of the 240 cloacal swabs examined. As proved by PCR, 100% of the strains were identified as Campylobacter coli (118/118), and 15 (12.7%) out of the 118 positive samples were also positive for Campylobacter jejuni. In contrast, Campylobacter lari was not identified. Adult partridges showed a significantly higher prevalence (P < 0.05) than younger ones. +T4 Paragraph 1019 1177 These results reinforce the assumption that game birds may be considered as potential carriers of Campylobacter spp. for human being and other animal species. +T5 Paragraph 1178 1379 Although an earlier 1986 publication described the prevalence of Campylobacter coli in commercially reared partridges, this is the first report to confirm the species of Campylobacter using a PCR test. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19552770.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19552770.txt new file mode 100644 index 0000000000000000000000000000000000000000..d0609923ffef677845d1dcbdac22cba167eb55cd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19552770.txt @@ -0,0 +1,6 @@ +Prevalence of thermotolerant Campylobacter in partridges (Perdix perdix). +To estimate the prevalence of thermotolerant Campylobacter spp. in commercially reared partridges (Perdix perdix) in southern Italy. +Cloacal swabs of partridges (n = 240), equally distributed between male and female birds, from a game bird farm located in the Southern Italy were examined for the prevalence of thermotolerant Campylobacter spp. The samples were processed in order to detect thermotolerant Campylobacter spp. by culture methods. The positive samples were then confirmed by multiplex polymerase chain reaction. Thermotolerant Campylobacter spp. were isolated from 118 (49.2%) of the 240 cloacal swabs examined. As proved by PCR, 100% of the strains were identified as Campylobacter coli (118/118), and 15 (12.7%) out of the 118 positive samples were also positive for Campylobacter jejuni. In contrast, Campylobacter lari was not identified. Adult partridges showed a significantly higher prevalence (P < 0.05) than younger ones. +These results reinforce the assumption that game birds may be considered as potential carriers of Campylobacter spp. for human being and other animal species. +Although an earlier 1986 publication described the prevalence of Campylobacter coli in commercially reared partridges, this is the first report to confirm the species of Campylobacter using a PCR test. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19621381.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19621381.a1 new file mode 100644 index 0000000000000000000000000000000000000000..90ee8ea5f1724663a90da6dde6cd856dd5150ef1 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19621381.a1 @@ -0,0 +1,2 @@ +T1 Title 0 99 A general strategy for the bacterial expression of amyloidogenic peptides using BCL-XL-1/2 fusions. +T2 Paragraph 100 1436 Biophysical studies on amyloidogenic and aggregation-prone peptides often require large quantities of material. However, solid-phase synthesis, handling, and purification of peptides often present challenges on these scales. Recombinant expression is an attractive alternative because of its low cost, the ability to isotopically label the peptides, and access to sequences exceeding approximately 50 residues. However, expression systems that seek to solubilize amyloidogenic peptides suffer from low yields, difficult optimizations, and isolation challenges. We present a general strategy for expressing and isolating amyloidogenic peptides in Escherichia coli by fusion to a polypeptide that drives the expression of attached peptides into bacterial inclusion bodies. This scheme minimizes toxicity during bacterial growth and enables the processing and handling of the peptides in denaturing solutions. Immobilized metal affinity chromatography, reverse phase HPLC, and cyanogen bromide cleavage are used to isolate the peptide, followed by further reverse phase HPLC, which yields milligram quantities of the purified peptide. We demonstrate that driving the peptides into inclusion bodies using fusion to BCL-XL-1/2 is a general strategy for their expression and isolation, as exemplified by the production of 11 peptides species. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19621381.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19621381.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d4a8fb46143ab6b0d117d658024f385c3fc2cad --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19621381.txt @@ -0,0 +1,3 @@ +A general strategy for the bacterial expression of amyloidogenic peptides using BCL-XL-1/2 fusions. +Biophysical studies on amyloidogenic and aggregation-prone peptides often require large quantities of material. However, solid-phase synthesis, handling, and purification of peptides often present challenges on these scales. Recombinant expression is an attractive alternative because of its low cost, the ability to isotopically label the peptides, and access to sequences exceeding approximately 50 residues. However, expression systems that seek to solubilize amyloidogenic peptides suffer from low yields, difficult optimizations, and isolation challenges. We present a general strategy for expressing and isolating amyloidogenic peptides in Escherichia coli by fusion to a polypeptide that drives the expression of attached peptides into bacterial inclusion bodies. This scheme minimizes toxicity during bacterial growth and enables the processing and handling of the peptides in denaturing solutions. Immobilized metal affinity chromatography, reverse phase HPLC, and cyanogen bromide cleavage are used to isolate the peptide, followed by further reverse phase HPLC, which yields milligram quantities of the purified peptide. We demonstrate that driving the peptides into inclusion bodies using fusion to BCL-XL-1/2 is a general strategy for their expression and isolation, as exemplified by the production of 11 peptides species. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19622846.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19622846.a1 new file mode 100644 index 0000000000000000000000000000000000000000..b45d8d4027a978a469c461d4e282099a409df23f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19622846.a1 @@ -0,0 +1,2 @@ +T1 Title 0 94 Detection of Staphylococcus aureus including MRSA on environmental surfaces in a jail setting. +T2 Paragraph 95 964 We examined jail environmental surfaces to explore whether they might serve as reservoirs of viable methicillin-resistant Staphylococcus aureus (MRSA). We swabbed 132 surfaces, inoculated primary and secondary mannitol salts and oxacillin-resistant screening agar, and used API tests to identify S. aureus and E-tests to determine methicillin/oxacillin resistance. We recovered S. aureus from 10 (7.6%) surfaces; eight (6.1%) isolates were MRSA. We ran pulsed-field gel electrophoresis on six resistant isolates and observed three patterns, one of which was identical to that identified in a previous study of inmates' nasal specimens. Finding MRSA-contaminated surfaces on a variety of environmental surfaces in the absence of an overt outbreak emphasizes that correctional facilities should have protocols for environmental cleaning as a component of MRSA prevention. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19622846.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19622846.txt new file mode 100644 index 0000000000000000000000000000000000000000..faf4e1f15ddf7c15ea68819a8f0b9bce915fee3f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-19622846.txt @@ -0,0 +1,3 @@ +Detection of Staphylococcus aureus including MRSA on environmental surfaces in a jail setting. +We examined jail environmental surfaces to explore whether they might serve as reservoirs of viable methicillin-resistant Staphylococcus aureus (MRSA). We swabbed 132 surfaces, inoculated primary and secondary mannitol salts and oxacillin-resistant screening agar, and used API tests to identify S. aureus and E-tests to determine methicillin/oxacillin resistance. We recovered S. aureus from 10 (7.6%) surfaces; eight (6.1%) isolates were MRSA. We ran pulsed-field gel electrophoresis on six resistant isolates and observed three patterns, one of which was identical to that identified in a previous study of inmates' nasal specimens. Finding MRSA-contaminated surfaces on a variety of environmental surfaces in the absence of an overt outbreak emphasizes that correctional facilities should have protocols for environmental cleaning as a component of MRSA prevention. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20005916.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20005916.a1 new file mode 100644 index 0000000000000000000000000000000000000000..60da296cee085fddd04d0044a03655fccf74c6e9 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20005916.a1 @@ -0,0 +1,2 @@ +T1 Title 0 98 Usage of signaling in neurodegeneration and regeneration of peripheral nerves by leprosy bacteria. +T2 Paragraph 99 2262 Multiple signaling pathways play key regulatory roles during the development of peripheral nervous system (PNS) and also in neuroregeneration process following nerve degeneration. Schwann cells, the glial cells of the PNS, by interacting with neuronal (axonal) ligands, mainly neuregulins via receptor tyrosine kinase (RTK) complex, ErbB2/ErbB3, initiate intracellular signaling pathways to drive proliferation and differentiation of Schwann cells, both during development and the process of regeneration and re-myelination after nerve injury. One of the major signaling kinases, extracellular signal-regulated kinase-1/2 (ERK1/2), that is also a downstream signaling pathway of neuregulin-ErbB2/ErbB3 activation, has been identified as a key regulator of Schwann cell proliferation, differentiation, demyelination and nerve regeneration. Recent studies have provided evidence that the bacterium that causes human leprosy, Mycobacterium leprae that has a unique capacity to invade Schwann cells of the adult PNS, utilizes the neuregulin-ErbB2/ErbB3 associated signaling network to the bacterial advantage. M. leprae directly bind to ErbB2 on myelinated Schwann cells and activate the RTK by a novel route that bypasses the classical neuregulin/growth factor-induced ErbB2-ErbB3 heterodimerization, and subsequently induce downstream the canonical Erk1/2 signaling, leading to myelin breakdown and subsequent axonal damage. This initial injury provides a survival advantage for M. leprae as it induces de-differentiation and generates myelin-free cells, which are highly susceptible to M. leprae invasion and promote bacterial survival. Once invaded M. leprae activate Erk1/2 via a non-canonical pathway and subsequently increase the cell proliferation and maintain the infected cells in de-differentiated state, thereby preventing remyelination. Therefore, by subverting major RTKs and signaling pathways in adult Schwann cells M. leprae appear to propagate the bacterial niche and maintain survival within the PNS. These studies may also provide new insights into our understanding of signaling mechanisms involve in both neurodegeneration and neuroregeneration. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20005916.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20005916.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0ff2234d4f371b420a39d673da44a1c9f8f9acb --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20005916.txt @@ -0,0 +1,3 @@ +Usage of signaling in neurodegeneration and regeneration of peripheral nerves by leprosy bacteria. +Multiple signaling pathways play key regulatory roles during the development of peripheral nervous system (PNS) and also in neuroregeneration process following nerve degeneration. Schwann cells, the glial cells of the PNS, by interacting with neuronal (axonal) ligands, mainly neuregulins via receptor tyrosine kinase (RTK) complex, ErbB2/ErbB3, initiate intracellular signaling pathways to drive proliferation and differentiation of Schwann cells, both during development and the process of regeneration and re-myelination after nerve injury. One of the major signaling kinases, extracellular signal-regulated kinase-1/2 (ERK1/2), that is also a downstream signaling pathway of neuregulin-ErbB2/ErbB3 activation, has been identified as a key regulator of Schwann cell proliferation, differentiation, demyelination and nerve regeneration. Recent studies have provided evidence that the bacterium that causes human leprosy, Mycobacterium leprae that has a unique capacity to invade Schwann cells of the adult PNS, utilizes the neuregulin-ErbB2/ErbB3 associated signaling network to the bacterial advantage. M. leprae directly bind to ErbB2 on myelinated Schwann cells and activate the RTK by a novel route that bypasses the classical neuregulin/growth factor-induced ErbB2-ErbB3 heterodimerization, and subsequently induce downstream the canonical Erk1/2 signaling, leading to myelin breakdown and subsequent axonal damage. This initial injury provides a survival advantage for M. leprae as it induces de-differentiation and generates myelin-free cells, which are highly susceptible to M. leprae invasion and promote bacterial survival. Once invaded M. leprae activate Erk1/2 via a non-canonical pathway and subsequently increase the cell proliferation and maintain the infected cells in de-differentiated state, thereby preventing remyelination. Therefore, by subverting major RTKs and signaling pathways in adult Schwann cells M. leprae appear to propagate the bacterial niche and maintain survival within the PNS. These studies may also provide new insights into our understanding of signaling mechanisms involve in both neurodegeneration and neuroregeneration. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20073421.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20073421.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e1e435be7ac94ecd4f19ca5ca0839c2209fb4447 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20073421.a1 @@ -0,0 +1,5 @@ +T1 Title 0 139 The effect of interferon-gamma and lipopolysaccharide on the growth of Francisella tularensis LVS in murine macrophage-like cell line J774. +T2 Paragraph 140 263 Francisella tularensis, a causative agent of human tularemia, displaying the ability to proliferate inside the human cells. +T3 Paragraph 264 440 To evaluate the growth potential of F. tularensis LVS strain in macrophage-like cell line J774 modulated by recombinant interferon gamma and E. coli derived lipopolysaccharide. +T4 Paragraph 441 712 Stimulation of J774 cells either by interferon-gamma or lipopolysaccharide alone, or especially in combination before infection F. tularensis, revealed protective effects. Higher concentrations of stimulating agents were needed to inhibit ongoing F. tularensis infection. +T5 Paragraph 713 853 Stimulation of J774 cell line by combination of interferon-gamma with lipopolysaccharide inhibits the intracellular growth of F. tularensis. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20073421.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20073421.txt new file mode 100644 index 0000000000000000000000000000000000000000..eace22001460181043e1d66f6b25d2a0b4941f38 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20073421.txt @@ -0,0 +1,6 @@ +The effect of interferon-gamma and lipopolysaccharide on the growth of Francisella tularensis LVS in murine macrophage-like cell line J774. +Francisella tularensis, a causative agent of human tularemia, displaying the ability to proliferate inside the human cells. +To evaluate the growth potential of F. tularensis LVS strain in macrophage-like cell line J774 modulated by recombinant interferon gamma and E. coli derived lipopolysaccharide. +Stimulation of J774 cells either by interferon-gamma or lipopolysaccharide alone, or especially in combination before infection F. tularensis, revealed protective effects. Higher concentrations of stimulating agents were needed to inhibit ongoing F. tularensis infection. +Stimulation of J774 cell line by combination of interferon-gamma with lipopolysaccharide inhibits the intracellular growth of F. tularensis. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20148898.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20148898.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e1aaab2e87b8e2fecee5f9f1f39cb4d2b5604d98 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20148898.a1 @@ -0,0 +1,2 @@ +T1 Title 0 122 The presence of professional phagocytes dictates the number of host cells targeted for Yop translocation during infection. +T2 Paragraph 123 1600 Type III secretion systems deliver effector proteins from Gram-negative bacterial pathogens into host cells, where they disarm host defences, allowing the pathogens to establish infection. Although Yersinia pseudotuberculosis delivers its effector proteins, called Yops, into numerous cell types grown in culture, we show that during infection Y. pseudotuberculosis selectively targets Yops to professional phagocytes in Peyer's patches, mesenteric lymph nodes and spleen, although it colocalizes with B and T cells as well as professional phagocytes. Strikingly, in the absence of neutrophils, the number of cells with translocated Yops was significantly reduced although the bacterial loads were similar, indicating that Y. pseudotuberculosis did not arbitrarily deliver Yops to the available cells. Using isolated splenocytes, selective binding and selective targeting to professional phagocytes when bacteria were limiting was also observed, indicating that tissue architecture was not required for the tropism for professional phagocytes. In isolated splenocytes, YadA and Invasin increased the number of all cells types with translocated Yops, but professional phagocytes were still preferentially translocated with Yops in the absence of these adhesins. Together these results indicate that Y. pseudotuberculosis discriminates among cells it encounters during infection and selectively delivers Yops to phagocytes while refraining from translocation to other cell types. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20148898.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20148898.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba5327405dfaa0a3f8bdcfbc8d10fe02e0484506 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20148898.txt @@ -0,0 +1,3 @@ +The presence of professional phagocytes dictates the number of host cells targeted for Yop translocation during infection. +Type III secretion systems deliver effector proteins from Gram-negative bacterial pathogens into host cells, where they disarm host defences, allowing the pathogens to establish infection. Although Yersinia pseudotuberculosis delivers its effector proteins, called Yops, into numerous cell types grown in culture, we show that during infection Y. pseudotuberculosis selectively targets Yops to professional phagocytes in Peyer's patches, mesenteric lymph nodes and spleen, although it colocalizes with B and T cells as well as professional phagocytes. Strikingly, in the absence of neutrophils, the number of cells with translocated Yops was significantly reduced although the bacterial loads were similar, indicating that Y. pseudotuberculosis did not arbitrarily deliver Yops to the available cells. Using isolated splenocytes, selective binding and selective targeting to professional phagocytes when bacteria were limiting was also observed, indicating that tissue architecture was not required for the tropism for professional phagocytes. In isolated splenocytes, YadA and Invasin increased the number of all cells types with translocated Yops, but professional phagocytes were still preferentially translocated with Yops in the absence of these adhesins. Together these results indicate that Y. pseudotuberculosis discriminates among cells it encounters during infection and selectively delivers Yops to phagocytes while refraining from translocation to other cell types. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20174624.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20174624.a1 new file mode 100644 index 0000000000000000000000000000000000000000..02a36f8e6e4478df0544842949235be610dc9343 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20174624.a1 @@ -0,0 +1,4 @@ +T1 Title 0 143 Neutrophils are resistant to Yersinia YopJ/P-induced apoptosis and are protected from ROS-mediated cell death by the type III secretion system. +T2 Paragraph 144 664 The human innate immune system relies on the coordinated activity of macrophages and polymorphonuclear leukocytes (neutrophils or PMNs) for defense against bacterial pathogens. Yersinia spp. subvert the innate immune response to cause disease in humans. In particular, the Yersinia outer protein YopJ (Y. pestis and Y. pseudotuberculosis) and YopP (Y. enterocolitica) rapidly induce apoptosis in murine macrophages and dendritic cells. However, the effects of Yersinia Yop J/P on neutrophil fate are not clearly defined. +T3 Paragraph 665 1672 In this study, we utilized wild-type and mutant strains of Yersinia to test the contribution of YopJ and YopP on induction of apoptosis in human monocyte-derived macrophages (HMDM) and neutrophils. Whereas YopJ and YopP similarly induced apoptosis in HMDMs, interaction of human neutrophils with virulence plasmid-containing Yersinia did not result in PMN caspase activation, release of LDH, or loss of membrane integrity greater than PMN controls. In contrast, interaction of human PMNs with the virulence plasmid-deficient Y. pestis strain KIM6 resulted in increased surface exposure of phosphatidylserine (PS) and cell death. PMN reactive oxygen species (ROS) production was inhibited in a virulence plasmid-dependent but YopJ/YopP-independent manner. Following phagocytic interaction with Y. pestis strain KIM6, inhibition of PMN ROS production with diphenyleneiodonium chloride resulted in a reduction of PMN cell death similar to that induced by the virulence plasmid-containing strain Y. pestis KIM5. +T4 Paragraph 1673 2071 Our findings showed that Yersinia YopJ and/or YopP did not induce pronounced apoptosis in human neutrophils. Furthermore, robust PMN ROS production in response to virulence plasmid-deficient Yersinia was associated with increased PMN cell death, suggesting that Yersinia inhibition of PMN ROS production plays a role in evasion of the human innate immune response in part by limiting PMN apoptosis. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20174624.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20174624.txt new file mode 100644 index 0000000000000000000000000000000000000000..7163e37fea756d4db5bcc22e0bac2b0c1824a6e5 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20174624.txt @@ -0,0 +1,5 @@ +Neutrophils are resistant to Yersinia YopJ/P-induced apoptosis and are protected from ROS-mediated cell death by the type III secretion system. +The human innate immune system relies on the coordinated activity of macrophages and polymorphonuclear leukocytes (neutrophils or PMNs) for defense against bacterial pathogens. Yersinia spp. subvert the innate immune response to cause disease in humans. In particular, the Yersinia outer protein YopJ (Y. pestis and Y. pseudotuberculosis) and YopP (Y. enterocolitica) rapidly induce apoptosis in murine macrophages and dendritic cells. However, the effects of Yersinia Yop J/P on neutrophil fate are not clearly defined. +In this study, we utilized wild-type and mutant strains of Yersinia to test the contribution of YopJ and YopP on induction of apoptosis in human monocyte-derived macrophages (HMDM) and neutrophils. Whereas YopJ and YopP similarly induced apoptosis in HMDMs, interaction of human neutrophils with virulence plasmid-containing Yersinia did not result in PMN caspase activation, release of LDH, or loss of membrane integrity greater than PMN controls. In contrast, interaction of human PMNs with the virulence plasmid-deficient Y. pestis strain KIM6 resulted in increased surface exposure of phosphatidylserine (PS) and cell death. PMN reactive oxygen species (ROS) production was inhibited in a virulence plasmid-dependent but YopJ/YopP-independent manner. Following phagocytic interaction with Y. pestis strain KIM6, inhibition of PMN ROS production with diphenyleneiodonium chloride resulted in a reduction of PMN cell death similar to that induced by the virulence plasmid-containing strain Y. pestis KIM5. +Our findings showed that Yersinia YopJ and/or YopP did not induce pronounced apoptosis in human neutrophils. Furthermore, robust PMN ROS production in response to virulence plasmid-deficient Yersinia was associated with increased PMN cell death, suggesting that Yersinia inhibition of PMN ROS production plays a role in evasion of the human innate immune response in part by limiting PMN apoptosis. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20580604.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20580604.a1 new file mode 100644 index 0000000000000000000000000000000000000000..3830902955074b394aad95a7a0c25330d82bfede --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20580604.a1 @@ -0,0 +1,2 @@ +T1 Title 0 212 Effects of a probiotic fermented milk beverage containing Lactobacillus casei strain Shirota on defecation frequency, intestinal microbiota, and the intestinal environment of healthy individuals with soft stools. +T2 Paragraph 213 1814 The effects of drinking a fermented milk beverage that contains Lactobacillus casei strain Shirota (LcS) at 40 billion bacterial cells/bottle for 4 weeks (probiotics, 1 bottle/day) on defecation frequency, intestinal microbiota and the intestinal environment of healthy individuals with soft stools were evaluated. Thirty-four healthy adults who had soft stools were randomised into 2 groups, and the effects of a regular 4-week intake of probiotics were evaluated by a placebo-controlled, double-blind, parallel-group comparative design. Defecation frequency significantly decreased after the 4-week intake period compared with before the probiotic treatment. The stool quality significantly improved (hardened) compared to the placebo. Also, the water content of the stools was lower in the probiotic group than in the placebo group. Live LcS was recovered at 6.9 ± 1.3 and 7.2 ± 0.8 log(10) CFU per 1g of stool after 2 and 4 weeks, respectively, of probiotic treatment. The number of bifidobacteria in the stools also increased significantly compared with the level before starting the probiotics. The organic acid levels (total, acetic acid, propionic acid, and butyric acid) significantly increased compared with the level before intake in both the probiotic and placebo groups, but they returned to the original levels after the end of the intake period. These results suggest that probiotic fermented milk beverage has an intestine-conditioning effect by improving the frequency of defecation and stool quality and increasing the intrinsic bifidobacteria in healthy individuals with soft stool. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20580604.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20580604.txt new file mode 100644 index 0000000000000000000000000000000000000000..63618d930544147a33ed0b753aa76af793f8035c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-20580604.txt @@ -0,0 +1,3 @@ +Effects of a probiotic fermented milk beverage containing Lactobacillus casei strain Shirota on defecation frequency, intestinal microbiota, and the intestinal environment of healthy individuals with soft stools. +The effects of drinking a fermented milk beverage that contains Lactobacillus casei strain Shirota (LcS) at 40 billion bacterial cells/bottle for 4 weeks (probiotics, 1 bottle/day) on defecation frequency, intestinal microbiota and the intestinal environment of healthy individuals with soft stools were evaluated. Thirty-four healthy adults who had soft stools were randomised into 2 groups, and the effects of a regular 4-week intake of probiotics were evaluated by a placebo-controlled, double-blind, parallel-group comparative design. Defecation frequency significantly decreased after the 4-week intake period compared with before the probiotic treatment. The stool quality significantly improved (hardened) compared to the placebo. Also, the water content of the stools was lower in the probiotic group than in the placebo group. Live LcS was recovered at 6.9 ± 1.3 and 7.2 ± 0.8 log(10) CFU per 1g of stool after 2 and 4 weeks, respectively, of probiotic treatment. The number of bifidobacteria in the stools also increased significantly compared with the level before starting the probiotics. The organic acid levels (total, acetic acid, propionic acid, and butyric acid) significantly increased compared with the level before intake in both the probiotic and placebo groups, but they returned to the original levels after the end of the intake period. These results suggest that probiotic fermented milk beverage has an intestine-conditioning effect by improving the frequency of defecation and stool quality and increasing the intrinsic bifidobacteria in healthy individuals with soft stool. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21270066.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21270066.a1 new file mode 100644 index 0000000000000000000000000000000000000000..49cf4825b9ad87d5862cab9c20c4c7d270b8bc81 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21270066.a1 @@ -0,0 +1,2 @@ +T1 Title 0 94 Lymphogranuloma venereum presenting as perianal ulceration: an emerging clinical presentation? +T2 Paragraph 95 1145 An outbreak of lymphogranuloma venereum (LGV) infection has been recognised in the UK since 2004, predominantly affecting HIV-positive men who have sex with men (MSM). Patients typically present with proctitis symptoms. The prevalence of rectal LGV in MSM attending sexually transmitted infection clinics in London is estimated at 1%. Health Protection Agency surveillance has shown a decrease in anorectal manifestations despite little demographic change. Two cases of HIV-infected patients presenting with isolated perianal ulcer disease are reported here. Both cases were confirmed to have rectal Chlamydia trachomatis-specific DNA of an LGV associated serovar. As presentations of LGV diversify, further education and surveillance are needed in order to reduce transmission and prevent long-term complications. A strong argument already exists for the incorporation of chlamydia nucleic acid amplification tests in the management of MSM with proctitis; this paper provides evidence that this should be extended to MSM with perianal ulcer disease. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21270066.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21270066.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0e9543fd8e5664942c54ab02d648efb685110c5 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21270066.txt @@ -0,0 +1,3 @@ +Lymphogranuloma venereum presenting as perianal ulceration: an emerging clinical presentation? +An outbreak of lymphogranuloma venereum (LGV) infection has been recognised in the UK since 2004, predominantly affecting HIV-positive men who have sex with men (MSM). Patients typically present with proctitis symptoms. The prevalence of rectal LGV in MSM attending sexually transmitted infection clinics in London is estimated at 1%. Health Protection Agency surveillance has shown a decrease in anorectal manifestations despite little demographic change. Two cases of HIV-infected patients presenting with isolated perianal ulcer disease are reported here. Both cases were confirmed to have rectal Chlamydia trachomatis-specific DNA of an LGV associated serovar. As presentations of LGV diversify, further education and surveillance are needed in order to reduce transmission and prevent long-term complications. A strong argument already exists for the incorporation of chlamydia nucleic acid amplification tests in the management of MSM with proctitis; this paper provides evidence that this should be extended to MSM with perianal ulcer disease. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21498521.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21498521.a1 new file mode 100644 index 0000000000000000000000000000000000000000..ac7eb1f1e8de056f2fa19f3724ce68b375af5a71 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21498521.a1 @@ -0,0 +1,2 @@ +T1 Title 0 105 The lipid A from Vibrio fischeri lipopolysaccharide: a unique structure bearing a phosphoglycerol moiety. +T2 Paragraph 106 1786 Vibrio fischeri, a bioluminescent marine bacterium, exists in an exclusive symbiotic relationship with the Hawaiian bobtail squid, Euprymna scolopes, whose light organ it colonizes. Previously, it has been shown that the lipopolysaccharide (LPS) or free lipid A of V. fischeri can trigger morphological changes in the juvenile squid's light organ that occur upon colonization. To investigate the structural features that might be responsible for this phenomenon, the lipid A from V. fischeri ES114 LPS was isolated and characterized by multistage mass spectrometry (MS(n)). A microheterogeneous mixture of mono- and diphosphorylated diglucosamine disaccharides was observed with variable states of acylation ranging from tetra- to octaacylated forms. All lipid A species, however, contained a set of conserved primary acyl chains consisting of an N-linked C14:0(3-OH) at the 2-position, an unusual N-linked C14:1(3-OH) at the 2'-position, and two O-linked C12:0(3-OH) fatty acids at the 3- and 3'-positions. The fatty acids found in secondary acylation were considerably more variable, with either a C12:0 or C16:1 at the 2-position, C14:0 or C14:0(3-OH) at the 2'-position, and C12:0 or no substituent at the 3'-position. Most surprising was the presence of an unusual set of modifications at the secondary acylation site of the 3-position consisting of phosphoglycerol (GroP), lysophosphatidic acid (GroP bearing C12:0, C16:0, or C16:1), or phosphatidic acid (GroP bearing either C16:0 + C12:0 or C16:0 + C16:1). Given their unusual nature, it is possible that these features of the V. fischeri lipid A may underlie the ability of E. scolopes to recognize its symbiotic partner. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21498521.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21498521.txt new file mode 100644 index 0000000000000000000000000000000000000000..1942145c208920045883012b5b457451499b68e1 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21498521.txt @@ -0,0 +1,3 @@ +The lipid A from Vibrio fischeri lipopolysaccharide: a unique structure bearing a phosphoglycerol moiety. +Vibrio fischeri, a bioluminescent marine bacterium, exists in an exclusive symbiotic relationship with the Hawaiian bobtail squid, Euprymna scolopes, whose light organ it colonizes. Previously, it has been shown that the lipopolysaccharide (LPS) or free lipid A of V. fischeri can trigger morphological changes in the juvenile squid's light organ that occur upon colonization. To investigate the structural features that might be responsible for this phenomenon, the lipid A from V. fischeri ES114 LPS was isolated and characterized by multistage mass spectrometry (MS(n)). A microheterogeneous mixture of mono- and diphosphorylated diglucosamine disaccharides was observed with variable states of acylation ranging from tetra- to octaacylated forms. All lipid A species, however, contained a set of conserved primary acyl chains consisting of an N-linked C14:0(3-OH) at the 2-position, an unusual N-linked C14:1(3-OH) at the 2'-position, and two O-linked C12:0(3-OH) fatty acids at the 3- and 3'-positions. The fatty acids found in secondary acylation were considerably more variable, with either a C12:0 or C16:1 at the 2-position, C14:0 or C14:0(3-OH) at the 2'-position, and C12:0 or no substituent at the 3'-position. Most surprising was the presence of an unusual set of modifications at the secondary acylation site of the 3-position consisting of phosphoglycerol (GroP), lysophosphatidic acid (GroP bearing C12:0, C16:0, or C16:1), or phosphatidic acid (GroP bearing either C16:0 + C12:0 or C16:0 + C16:1). Given their unusual nature, it is possible that these features of the V. fischeri lipid A may underlie the ability of E. scolopes to recognize its symbiotic partner. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21543877.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21543877.a1 new file mode 100644 index 0000000000000000000000000000000000000000..eabb5c60192049ad721ed1c8b65536e8175395b0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21543877.a1 @@ -0,0 +1,2 @@ +T1 Title 0 135 Cloning, expression, purification, crystallization and X-ray crystallographic analysis of Rv3168 from Mycobacterium tuberculosis H37Rv. +T2 Paragraph 136 1163 Tuberculosis is a widespread and deadly infectious disease, with one third of the human population already being infected. Aminoglycoside antibiotics have become less effective in recent years owing to antibiotic resistance, which arises primarily through enzymatic modification of the antibiotics. The gene product Rv3168, a putative aminoglycoside phosphotransferase (APH), from Mycobacterium tuberculosis was crystallized using the sitting-drop vapour-diffusion method in the presence of 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.0 and 20% PEG 3000 at 295 K. X-ray diffraction data were collected to a maximum resolution of 1.67 Å on a synchrotron beamline. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.74, b = 62.37, c = 103.61 Å. With one molecule per asymmetric unit, the crystal volume per unit protein weight (V(M)) is 2.91 Å(3) Da(-1). The structure was solved by the single-wavelength anomalous dispersion method and refinement of the selenomethionine structure is in progress. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21543877.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21543877.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ff08211455cf7b1f106e72a875ea0126513e267 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21543877.txt @@ -0,0 +1,3 @@ +Cloning, expression, purification, crystallization and X-ray crystallographic analysis of Rv3168 from Mycobacterium tuberculosis H37Rv. +Tuberculosis is a widespread and deadly infectious disease, with one third of the human population already being infected. Aminoglycoside antibiotics have become less effective in recent years owing to antibiotic resistance, which arises primarily through enzymatic modification of the antibiotics. The gene product Rv3168, a putative aminoglycoside phosphotransferase (APH), from Mycobacterium tuberculosis was crystallized using the sitting-drop vapour-diffusion method in the presence of 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.0 and 20% PEG 3000 at 295 K. X-ray diffraction data were collected to a maximum resolution of 1.67 Å on a synchrotron beamline. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.74, b = 62.37, c = 103.61 Å. With one molecule per asymmetric unit, the crystal volume per unit protein weight (V(M)) is 2.91 Å(3) Da(-1). The structure was solved by the single-wavelength anomalous dispersion method and refinement of the selenomethionine structure is in progress. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21695078.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21695078.a1 new file mode 100644 index 0000000000000000000000000000000000000000..3b33bcf236ce176bd7b3218c16bf8bc364c3fafe --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21695078.a1 @@ -0,0 +1,2 @@ +T1 Title 0 99 Enhanced virulence of Chlamydia muridarum respiratory infections in the absence of TLR2 activation. +T2 Paragraph 100 1061 Chlamydia trachomatis is a common sexually transmitted pathogen and is associated with infant pneumonia. Data from the female mouse model of genital tract chlamydia infection suggests a requirement for TLR2-dependent signaling in the induction of inflammation and oviduct pathology. We hypothesized that the role of TLR2 in moderating mucosal inflammation is site specific. In order to investigate this, we infected mice via the intranasal route with C. muridarum and observed that in the absence of TLR2 activation, mice had more severe disease, higher lung cytokine levels, and an exaggerated influx of neutrophils and T-cells into the lungs. This could not be explained by impaired bacterial clearance as TLR2-deficient mice cleared the infection similar to controls. These data suggest that TLR2 has an anti-inflammatory function in the lung during Chlamydia infection, and that the role of TLR2 in mucosal inflammation varies at different mucosal surfaces. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21695078.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21695078.txt new file mode 100644 index 0000000000000000000000000000000000000000..9243cf2ab479722ce7d11b2a3b95ed62323e0e31 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21695078.txt @@ -0,0 +1,3 @@ +Enhanced virulence of Chlamydia muridarum respiratory infections in the absence of TLR2 activation. +Chlamydia trachomatis is a common sexually transmitted pathogen and is associated with infant pneumonia. Data from the female mouse model of genital tract chlamydia infection suggests a requirement for TLR2-dependent signaling in the induction of inflammation and oviduct pathology. We hypothesized that the role of TLR2 in moderating mucosal inflammation is site specific. In order to investigate this, we infected mice via the intranasal route with C. muridarum and observed that in the absence of TLR2 activation, mice had more severe disease, higher lung cytokine levels, and an exaggerated influx of neutrophils and T-cells into the lungs. This could not be explained by impaired bacterial clearance as TLR2-deficient mice cleared the infection similar to controls. These data suggest that TLR2 has an anti-inflammatory function in the lung during Chlamydia infection, and that the role of TLR2 in mucosal inflammation varies at different mucosal surfaces. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21894542.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21894542.a1 new file mode 100644 index 0000000000000000000000000000000000000000..0a0286f8db536bc6203fdb1c0e74097064588238 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21894542.a1 @@ -0,0 +1,2 @@ +T1 Title 0 41 Iron transport in the genus Marinobacter. +T2 Paragraph 42 1335 Marinobacter belong to the class of Gammaproteobacteria and these motile, halophilic or halotolerent bacteria are widely distributed throughout the world's oceans having been isolated from a wide variety of marine environments. They have also been identified as members of the bacterial flora associated with other marine organisms. Here, using a combination of natural products chemistry and genomic analysis, we assess the nature of the siderophores produced by this genus and their potential relationship to phylogeny and lifestyle/ecological niche of this diverse group of organisms. Our analysis shows a wide level of diversity in siderophore based iron uptake systems among this genus with three general strategies: (1) production and utilization of native siderophores in addition to utilization of a variety of exogenous ones, (2) production and utilization of native siderophores only, (3) lack of siderophore production but utilization of exogenous ones. They all share the presence of at least one siderophore-independent iron uptake ABC transport systems of the FbpABC iron metal type and lack the ability for direct transport of ferrous iron. Siderophore production and utilization can be correlated with phylogeny and thus it forms a type of chemotaxonomic marker for this genus. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21894542.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21894542.txt new file mode 100644 index 0000000000000000000000000000000000000000..ce7c340073998c7a3507e5c88464e51a9fbaa1b0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21894542.txt @@ -0,0 +1,3 @@ +Iron transport in the genus Marinobacter. +Marinobacter belong to the class of Gammaproteobacteria and these motile, halophilic or halotolerent bacteria are widely distributed throughout the world's oceans having been isolated from a wide variety of marine environments. They have also been identified as members of the bacterial flora associated with other marine organisms. Here, using a combination of natural products chemistry and genomic analysis, we assess the nature of the siderophores produced by this genus and their potential relationship to phylogeny and lifestyle/ecological niche of this diverse group of organisms. Our analysis shows a wide level of diversity in siderophore based iron uptake systems among this genus with three general strategies: (1) production and utilization of native siderophores in addition to utilization of a variety of exogenous ones, (2) production and utilization of native siderophores only, (3) lack of siderophore production but utilization of exogenous ones. They all share the presence of at least one siderophore-independent iron uptake ABC transport systems of the FbpABC iron metal type and lack the ability for direct transport of ferrous iron. Siderophore production and utilization can be correlated with phylogeny and thus it forms a type of chemotaxonomic marker for this genus. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21917915.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21917915.a1 new file mode 100644 index 0000000000000000000000000000000000000000..73ebdde8f84d42fff0798471d18a7168b015df5f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21917915.a1 @@ -0,0 +1,2 @@ +T1 Title 0 92 Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH. +T2 Paragraph 93 1013 Pathogens must steal iron from their hosts to establish infection. In mammals, hemoglobin (Hb) represents the largest reservoir of iron, and pathogens express Hb-binding proteins to access this source. Here, we show how one of the commonest and most significant human pathogens, Staphylococcus aureus, captures Hb as the first step of an iron-scavenging pathway. The x-ray crystal structure of Hb bound to a domain from the Isd (iron-regulated surface determinant) protein, IsdH, is the first structure of a Hb capture complex to be determined. Surface mutations in Hb that reduce binding to the Hb-receptor limit the capacity of S. aureus to utilize Hb as an iron source, suggesting that Hb sequence is a factor in host susceptibility to infection. The demonstration that pathogens make highly specific recognition complexes with Hb raises the possibility of developing inhibitors of Hb binding as antibacterial agents. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21917915.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21917915.txt new file mode 100644 index 0000000000000000000000000000000000000000..cd652f552fb316fdd9ddda62a6ff1d4347048b71 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21917915.txt @@ -0,0 +1,3 @@ +Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH. +Pathogens must steal iron from their hosts to establish infection. In mammals, hemoglobin (Hb) represents the largest reservoir of iron, and pathogens express Hb-binding proteins to access this source. Here, we show how one of the commonest and most significant human pathogens, Staphylococcus aureus, captures Hb as the first step of an iron-scavenging pathway. The x-ray crystal structure of Hb bound to a domain from the Isd (iron-regulated surface determinant) protein, IsdH, is the first structure of a Hb capture complex to be determined. Surface mutations in Hb that reduce binding to the Hb-receptor limit the capacity of S. aureus to utilize Hb as an iron source, suggesting that Hb sequence is a factor in host susceptibility to infection. The demonstration that pathogens make highly specific recognition complexes with Hb raises the possibility of developing inhibitors of Hb binding as antibacterial agents. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21924022.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21924022.a1 new file mode 100644 index 0000000000000000000000000000000000000000..bac17145bf2b78f86587ebf0477db73c6cf46eae --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21924022.a1 @@ -0,0 +1,5 @@ +T1 Title 0 87 [Value of protein array in the diagnosis of Helicobactor pylori infection in children]. +T2 Paragraph 88 237 To study the value of multiple Helicobacter pylori (H.pylori) antibody detection by protein array in the diagnosis of H.pylori infection in children. +T3 Paragraph 238 740 Biopsy specimens obtained by gastroscopy from 120 children with digestive system symptoms were detected by rapid urease test (RUT) and modified Giemsa staining. Positivity in both RUT and Giemsa staining was the "gold criterion" of H.pylori infection. Serum samples of these patients were obtained and the antibodies against cytotoxin associated gene A protein (CagA), vacuolating toxin A (VacA), urease, heat shock protein 60 (Hsp60) and RdxA (nitroreductase) were detected by protein array technique. +T4 Paragraph 741 1559 H.pylori infection was identified according to the "gold criterion" in 60 children. Compared with the "gold criterion", the goodness of fit and the coefficient of contingency in the diagnosis of H.pylori infection of the following four groups antibody detection were all statistically significant (P<0.001): anti-Ure antibody alone, anti-Ure antibody combined with anti-CagA antibody, anti-Ure antibody combined with anti-VacA antibody and anti-Ure antibody combined with anti-CagA and anti-VacA antibody. The sensitivity, specificity and accuracy of the detection of anti-Ure antibody combined with anti-CagA antibody for the diagnosis of H.pylori infection were 81.7%, 91.7% and 86.7%, respectively. The antibody detection showed a high positive predictive value (90.7%) and a high negative predictive value (83.3%). +T5 Paragraph 1560 1732 The antibody detection by protein array, especially the detection of anti-Ure antibody combined with anti-CagA antibody, is valuable in the diagnosis of H.pylori infection. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21924022.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21924022.txt new file mode 100644 index 0000000000000000000000000000000000000000..d69971ca6ffec9d0e1e56574dadda6d3bff73e9c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-21924022.txt @@ -0,0 +1,6 @@ +[Value of protein array in the diagnosis of Helicobactor pylori infection in children]. +To study the value of multiple Helicobacter pylori (H.pylori) antibody detection by protein array in the diagnosis of H.pylori infection in children. +Biopsy specimens obtained by gastroscopy from 120 children with digestive system symptoms were detected by rapid urease test (RUT) and modified Giemsa staining. Positivity in both RUT and Giemsa staining was the "gold criterion" of H.pylori infection. Serum samples of these patients were obtained and the antibodies against cytotoxin associated gene A protein (CagA), vacuolating toxin A (VacA), urease, heat shock protein 60 (Hsp60) and RdxA (nitroreductase) were detected by protein array technique. +H.pylori infection was identified according to the "gold criterion" in 60 children. Compared with the "gold criterion", the goodness of fit and the coefficient of contingency in the diagnosis of H.pylori infection of the following four groups antibody detection were all statistically significant (P<0.001): anti-Ure antibody alone, anti-Ure antibody combined with anti-CagA antibody, anti-Ure antibody combined with anti-VacA antibody and anti-Ure antibody combined with anti-CagA and anti-VacA antibody. The sensitivity, specificity and accuracy of the detection of anti-Ure antibody combined with anti-CagA antibody for the diagnosis of H.pylori infection were 81.7%, 91.7% and 86.7%, respectively. The antibody detection showed a high positive predictive value (90.7%) and a high negative predictive value (83.3%). +The antibody detection by protein array, especially the detection of anti-Ure antibody combined with anti-CagA antibody, is valuable in the diagnosis of H.pylori infection. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-22834551.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-22834551.a1 new file mode 100644 index 0000000000000000000000000000000000000000..39069ba6d89f6e0d014b50b22050e34a9ca8d7d6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-22834551.a1 @@ -0,0 +1,2 @@ +T1 Title 0 180 The effect of Artemisia annua on broiler performance, on intestinal microbiota and on the course of a Clostridium perfringens infection applying a necrotic enteritis disease model. +T2 Paragraph 181 1772 The aerial parts of the plant Artemisia annua contain essential oils having antimicrobial properties against Clostridium perfringens Type A, the causal agent for necrotic enteritis in broilers. In two experiments, the influence of increasing dietary concentrations of dried A. annua leaves (0, 5, 10 and 20 g/kg) and n-hexane extract from fresh A. annua leaves (0, 125, 250 and 500 mg/kg) on broiler performance was investigated. Dried plant material decreased feed intake and body weight in a dose-dependent manner, and 10 and 20 g/kg diet tended to improve the feed conversion ratio. The n-hexane extract also reduced feed intake, but broiler weight tended to decrease only at the highest dietary concentration. The feed conversion ratio tended to improve when birds received 250 and 500 mg/kg n-hexane extract. In a third experiment, a necrotic enteritis disease model was applied to investigate the effect of the dietary addition of dried A. annua leaves (10 g/kg on top) or n-hexane extract of A. annua (250 mg/kg) on the severity of the disease in broilers. The addition of n-hexane extract reduced the intestinal C. perfringens numbers and the severity of the disease-related small intestinal lesions. Over the infection period from day 17 to day 27, birds supplemented with the n-hexane extract gained more weight than both the challenged control birds and birds receiving dried plant material. The results indicate that n-hexane extracts derived from A. annua can modulate the course of necrotic enteritis and compensate to a certain extent for the disease-associated weight losses. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-22834551.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-22834551.txt new file mode 100644 index 0000000000000000000000000000000000000000..c43386bb1d6f7ce74840dc8c398c00357783ade6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-22834551.txt @@ -0,0 +1,3 @@ +The effect of Artemisia annua on broiler performance, on intestinal microbiota and on the course of a Clostridium perfringens infection applying a necrotic enteritis disease model. +The aerial parts of the plant Artemisia annua contain essential oils having antimicrobial properties against Clostridium perfringens Type A, the causal agent for necrotic enteritis in broilers. In two experiments, the influence of increasing dietary concentrations of dried A. annua leaves (0, 5, 10 and 20 g/kg) and n-hexane extract from fresh A. annua leaves (0, 125, 250 and 500 mg/kg) on broiler performance was investigated. Dried plant material decreased feed intake and body weight in a dose-dependent manner, and 10 and 20 g/kg diet tended to improve the feed conversion ratio. The n-hexane extract also reduced feed intake, but broiler weight tended to decrease only at the highest dietary concentration. The feed conversion ratio tended to improve when birds received 250 and 500 mg/kg n-hexane extract. In a third experiment, a necrotic enteritis disease model was applied to investigate the effect of the dietary addition of dried A. annua leaves (10 g/kg on top) or n-hexane extract of A. annua (250 mg/kg) on the severity of the disease in broilers. The addition of n-hexane extract reduced the intestinal C. perfringens numbers and the severity of the disease-related small intestinal lesions. Over the infection period from day 17 to day 27, birds supplemented with the n-hexane extract gained more weight than both the challenged control birds and birds receiving dried plant material. The results indicate that n-hexane extracts derived from A. annua can modulate the course of necrotic enteritis and compensate to a certain extent for the disease-associated weight losses. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23702192.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23702192.a1 new file mode 100644 index 0000000000000000000000000000000000000000..a087893e1e48e182e9943948fc66da9e9d486d86 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23702192.a1 @@ -0,0 +1,5 @@ +T1 Title 0 99 Clinical factors associated with development of severe-complicated Clostridium difficile infection. +T2 Paragraph 100 379 Clostridium difficile infection (CDI) can cause life-threatening complications. Severe-complicated CDI is characterized by hypotension, shock, sepsis, ileus, megacolon, and colon perforation. We created a model to identify clinical factors associated with severe-complicated CDI. +T3 Paragraph 380 1316 We analyzed data from 1446 inpatient cases of CDI (48.6% female; median age, 62.5 years; range, 0.1-103.7 years) at the Mayo Clinic from June 28, 2007, to June 25, 2010. Patients with severe-complicated CDI (n = 487) were identified as those who required admission to the intensive care unit or colectomy, or died, within 30 days of CDI diagnosis. Logistic regression models were used to identify variables that were independently associated with the occurrence of severe-complicated CDI in 2 cohorts. One cohort comprised all hospitalized patients; the other comprised a subset of these inpatients who were residents of Olmsted County, Minnesota to assess the association of comorbid conditions with the development of severe-complicated infection in a population-based cohort. The linear combinations of variables identified by using logistic regression models provided scores to predict the risk of developing severe-complicated CDI. +T4 Paragraph 1317 1758 In a multivariable model that included all inpatients, increasing age, leukocyte count >15 × 10(9)/L, increase in serum level of creatinine >1.5-fold from baseline, and use of proton pump inhibitors or narcotic medications were independently associated with severe-complicated CDI. In the secondary analysis, which included only patients from Olmsted County, comorbid conditions were not significantly associated with severe-complicated CDI. +T5 Paragraph 1759 2080 Older age, high numbers of leukocytes in blood samples, an increased serum level of creatinine, gastric acid suppression, and use of narcotic medications were independently associated with development of severe-complicated CDI in hospitalized patients. Early aggressive monitoring and intervention could improve outcomes. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23702192.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23702192.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f3950a11fee168f1cfccea54c8c93e8025ed20a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23702192.txt @@ -0,0 +1,6 @@ +Clinical factors associated with development of severe-complicated Clostridium difficile infection. +Clostridium difficile infection (CDI) can cause life-threatening complications. Severe-complicated CDI is characterized by hypotension, shock, sepsis, ileus, megacolon, and colon perforation. We created a model to identify clinical factors associated with severe-complicated CDI. +We analyzed data from 1446 inpatient cases of CDI (48.6% female; median age, 62.5 years; range, 0.1-103.7 years) at the Mayo Clinic from June 28, 2007, to June 25, 2010. Patients with severe-complicated CDI (n = 487) were identified as those who required admission to the intensive care unit or colectomy, or died, within 30 days of CDI diagnosis. Logistic regression models were used to identify variables that were independently associated with the occurrence of severe-complicated CDI in 2 cohorts. One cohort comprised all hospitalized patients; the other comprised a subset of these inpatients who were residents of Olmsted County, Minnesota to assess the association of comorbid conditions with the development of severe-complicated infection in a population-based cohort. The linear combinations of variables identified by using logistic regression models provided scores to predict the risk of developing severe-complicated CDI. +In a multivariable model that included all inpatients, increasing age, leukocyte count >15 × 10(9)/L, increase in serum level of creatinine >1.5-fold from baseline, and use of proton pump inhibitors or narcotic medications were independently associated with severe-complicated CDI. In the secondary analysis, which included only patients from Olmsted County, comorbid conditions were not significantly associated with severe-complicated CDI. +Older age, high numbers of leukocytes in blood samples, an increased serum level of creatinine, gastric acid suppression, and use of narcotic medications were independently associated with development of severe-complicated CDI in hospitalized patients. Early aggressive monitoring and intervention could improve outcomes. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23704121.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23704121.a1 new file mode 100644 index 0000000000000000000000000000000000000000..4c14450ffaf72eb843f5eda0b2ffd3c5b7512080 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23704121.a1 @@ -0,0 +1,5 @@ +T1 Title 0 52 Is fidaxomicin worth the cost? An economic analysis. +T2 Paragraph 53 309 In May 2011, the Food and Drug Administration approved fidaxomicin for the treatment of Clostridium difficile infection (CDI). It has been found to be noninferior to vancomycin; however, its cost-effectiveness for the treatment of CDI remains undetermined. +T3 Paragraph 310 603 We developed a decision analytic simulation model to determine the economic value of fidaxomicin for CDI treatment from the third-party payer perspective. We looked at CDI treatment in these 3 cases: (1) no fidaxomicin, (2) only fidaxomicin, and (3) fidaxomicin based on strain typing results. +T4 Paragraph 604 1244 The incremental cost-effectiveness ratio for fidaxomicin based on screening given current conditions was >$43.7 million per quality-adjusted life-year and using only fidaxomicin was dominated (ie, more costly and less effective) by the other 2 treatment strategies explored. The fidaxomicin strategy tended to remain dominated, even at lower costs. With approximately 50% of CDI due to the NAP1/BI/027 strain, a course of fidaxomicin would need to cost ≤$150 to be cost-effective in the treatment of all CDI cases and between $160 and $400 to be cost-effective for those with a non-NAP1/BI/027 strain (ie, treatment based on strain typing). +T5 Paragraph 1245 1528 Given the current cost and NAP1/BI/027 accounting for approximately 50% of isolates, using fidaxomicin as a first-line treatment for CDI is not cost-effective. However, typing and treatment with fidaxomicin based on strain may be more promising depending on the costs of fidaxomicin. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23704121.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23704121.txt new file mode 100644 index 0000000000000000000000000000000000000000..fdeda0d6bff7591eb555baf4b1ef23e0618ab885 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23704121.txt @@ -0,0 +1,6 @@ +Is fidaxomicin worth the cost? An economic analysis. +In May 2011, the Food and Drug Administration approved fidaxomicin for the treatment of Clostridium difficile infection (CDI). It has been found to be noninferior to vancomycin; however, its cost-effectiveness for the treatment of CDI remains undetermined. +We developed a decision analytic simulation model to determine the economic value of fidaxomicin for CDI treatment from the third-party payer perspective. We looked at CDI treatment in these 3 cases: (1) no fidaxomicin, (2) only fidaxomicin, and (3) fidaxomicin based on strain typing results. +The incremental cost-effectiveness ratio for fidaxomicin based on screening given current conditions was >$43.7 million per quality-adjusted life-year and using only fidaxomicin was dominated (ie, more costly and less effective) by the other 2 treatment strategies explored. The fidaxomicin strategy tended to remain dominated, even at lower costs. With approximately 50% of CDI due to the NAP1/BI/027 strain, a course of fidaxomicin would need to cost ≤$150 to be cost-effective in the treatment of all CDI cases and between $160 and $400 to be cost-effective for those with a non-NAP1/BI/027 strain (ie, treatment based on strain typing). +Given the current cost and NAP1/BI/027 accounting for approximately 50% of isolates, using fidaxomicin as a first-line treatment for CDI is not cost-effective. However, typing and treatment with fidaxomicin based on strain may be more promising depending on the costs of fidaxomicin. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23855904.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23855904.a1 new file mode 100644 index 0000000000000000000000000000000000000000..b77359240b6b90b814c4e4c4280d9704e5dac1be --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23855904.a1 @@ -0,0 +1,4 @@ +T1 Title 0 159 Widespread acquisition of antimicrobial resistance among Campylobacter isolates from UK retail poultry and evidence for clonal expansion of resistant lineages. +T2 Paragraph 160 837 Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimicrobial susceptibility of isolates from a UK-wide survey of Campylobacter in retail poultry in 2001 and 2004-5 was investigated. The occurrence of phenotypes resistant to tetracycline, quinolones (ciprofloxacin and naladixic acid), erythromycin, chloramphenicol and aminoglycosides was quantified. This was compared with a phylogeny for these isolates based upon Multi Locus Sequence Typing (MLST) to investigate the pattern of antimicrobial resistance acquisition. +T3 Paragraph 838 1292 Antimicrobial resistance was present in all lineage clusters, but statistical testing showed a non-random distribution. Erythromycin resistance was associated with Campylobacter coli. For all antimicrobials tested, resistant isolates were distributed among relatively distant lineages indicative of widespread acquisition. There was also evidence of clustering of resistance phenotypes within lineages; indicative of local expansion of resistant strains. +T4 Paragraph 1293 1795 These results are consistent with the widespread acquisition of antimicrobial resistance among chicken associated Campylobacter isolates, either through mutation or horizontal gene transfer, and the expansion of these lineages as a proportion of the population. As Campylobacter are not known to multiply outside of the host and long-term carriage in humans is extremely infrequent in industrialized countries, the most likely location for the proliferation of resistant lineages is in farmed chickens. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23855904.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23855904.txt new file mode 100644 index 0000000000000000000000000000000000000000..d857e1d95e9bf3dbe992f00679c0d27642989836 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23855904.txt @@ -0,0 +1,5 @@ +Widespread acquisition of antimicrobial resistance among Campylobacter isolates from UK retail poultry and evidence for clonal expansion of resistant lineages. +Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimicrobial susceptibility of isolates from a UK-wide survey of Campylobacter in retail poultry in 2001 and 2004-5 was investigated. The occurrence of phenotypes resistant to tetracycline, quinolones (ciprofloxacin and naladixic acid), erythromycin, chloramphenicol and aminoglycosides was quantified. This was compared with a phylogeny for these isolates based upon Multi Locus Sequence Typing (MLST) to investigate the pattern of antimicrobial resistance acquisition. +Antimicrobial resistance was present in all lineage clusters, but statistical testing showed a non-random distribution. Erythromycin resistance was associated with Campylobacter coli. For all antimicrobials tested, resistant isolates were distributed among relatively distant lineages indicative of widespread acquisition. There was also evidence of clustering of resistance phenotypes within lineages; indicative of local expansion of resistant strains. +These results are consistent with the widespread acquisition of antimicrobial resistance among chicken associated Campylobacter isolates, either through mutation or horizontal gene transfer, and the expansion of these lineages as a proportion of the population. As Campylobacter are not known to multiply outside of the host and long-term carriage in humans is extremely infrequent in industrialized countries, the most likely location for the proliferation of resistant lineages is in farmed chickens. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23902156.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23902156.a1 new file mode 100644 index 0000000000000000000000000000000000000000..aceb2b8242c77f7f326bf33125c5a15492c7efd5 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23902156.a1 @@ -0,0 +1,2 @@ +T1 Title 0 90 Isolation, expression and characterization of a minor allergen from Penicillium crustosum. +T2 Paragraph 91 1393 A ribosomal P1 protein, Pen b 26 from Penicillium brevicompactum, was previously identified as a major allergen. A homolog protein was isolated and characterized from Penicillium crustosum which is not known to be allergenic mold. A cDNA library of P. crustosum was constructed and screened using a probe based on the DNA sequence of Pen b 26. A positive clone was isolated, expressed in Escherichia coli, purified and characterized by comparing its immunological and physical properties to Pen b 26. It was designated as Pen cr 26 and had a 321 nt ORF corresponding to 107 amino acids with a MW of 11 kDa. Pen cr 26 had strong sequence homology to Pen b 26 (92% for nucleotides and 86% for amino acids) and its physical and predicted structural properties were similar to the latter. The level of expression of Pen cr 26 was much lower than that of Pen b 26 in the same expression vector. Both proteins were recognized equally well by the IgG class specific antibodies, but Pen cr 26 was poorly recognized by Penicillium-sensitive atopic sera (IgE), suggesting striking antigenic difference in IgE epitopes, i.e., 87% were positive for Pen b 26 while only 23% were positive for Pen cr 26. The allergenicity of Pen cr 26 seems to be minor in nature and it could be a hypoallergenic variant of Pen b 26. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23902156.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23902156.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e6d416d3b4722e47c8739a9cf514987eb27281d --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23902156.txt @@ -0,0 +1,3 @@ +Isolation, expression and characterization of a minor allergen from Penicillium crustosum. +A ribosomal P1 protein, Pen b 26 from Penicillium brevicompactum, was previously identified as a major allergen. A homolog protein was isolated and characterized from Penicillium crustosum which is not known to be allergenic mold. A cDNA library of P. crustosum was constructed and screened using a probe based on the DNA sequence of Pen b 26. A positive clone was isolated, expressed in Escherichia coli, purified and characterized by comparing its immunological and physical properties to Pen b 26. It was designated as Pen cr 26 and had a 321 nt ORF corresponding to 107 amino acids with a MW of 11 kDa. Pen cr 26 had strong sequence homology to Pen b 26 (92% for nucleotides and 86% for amino acids) and its physical and predicted structural properties were similar to the latter. The level of expression of Pen cr 26 was much lower than that of Pen b 26 in the same expression vector. Both proteins were recognized equally well by the IgG class specific antibodies, but Pen cr 26 was poorly recognized by Penicillium-sensitive atopic sera (IgE), suggesting striking antigenic difference in IgE epitopes, i.e., 87% were positive for Pen b 26 while only 23% were positive for Pen cr 26. The allergenicity of Pen cr 26 seems to be minor in nature and it could be a hypoallergenic variant of Pen b 26. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23908036.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23908036.a1 new file mode 100644 index 0000000000000000000000000000000000000000..4953e52f66d84da0debb16c3281de32c9e6ddf35 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23908036.a1 @@ -0,0 +1,2 @@ +T1 Title 0 102 Preliminary X-ray crystallographic analysis of β-carbonic anhydrase psCA3 from Pseudomonas aeruginosa. +T2 Paragraph 103 1458 Pseudomonas aeruginosa is a Gram-negative bacterium that causes life-threatening infections in susceptible individuals and is resistant to most clinically available antimicrobials. Genomic and proteomic studies have identified three genes, pa0102, pa2053 and pa4676, in P. aeruginosa PAO1 encoding three functional β-carbonic anhydrases (β-CAs): psCA1, psCA2 and psCA3, respectively. These β-CAs could serve as novel antimicrobial drug targets for this pathogen. X-ray crystallographic structural studies have been initiated to characterize the structure and function of these proteins. This communication describes the production of two crystal forms (A and B) of β-CA psCA3. Form A diffracted to a resolution of 2.9 Å; it belonged to space group P212121, with unit-cell parameters a = 81.9, b = 84.9, c = 124.2 Å, and had a calculated Matthews coefficient of 2.23 ų Da⁻¹ assuming four molecules in the crystallographic asymmetric unit. Form B diffracted to a resolution of 3.0 Å; it belonged to space group P21212, with unit-cell parameters a = 69.9, b = 77.7, c = 88.5 Å, and had a calculated Matthews coefficient of 2.48 ų Da⁻¹ assuming two molecules in the crystallographic asymmetric unit. Preliminary molecular-replacement solutions have been determined with the PHENIX AutoMR wizard and refinement of both crystal forms is currently in progress. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23908036.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23908036.txt new file mode 100644 index 0000000000000000000000000000000000000000..b6bd1240adddecaca747a2426370e07c0eb01e9a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-23908036.txt @@ -0,0 +1,3 @@ +Preliminary X-ray crystallographic analysis of β-carbonic anhydrase psCA3 from Pseudomonas aeruginosa. +Pseudomonas aeruginosa is a Gram-negative bacterium that causes life-threatening infections in susceptible individuals and is resistant to most clinically available antimicrobials. Genomic and proteomic studies have identified three genes, pa0102, pa2053 and pa4676, in P. aeruginosa PAO1 encoding three functional β-carbonic anhydrases (β-CAs): psCA1, psCA2 and psCA3, respectively. These β-CAs could serve as novel antimicrobial drug targets for this pathogen. X-ray crystallographic structural studies have been initiated to characterize the structure and function of these proteins. This communication describes the production of two crystal forms (A and B) of β-CA psCA3. Form A diffracted to a resolution of 2.9 Å; it belonged to space group P212121, with unit-cell parameters a = 81.9, b = 84.9, c = 124.2 Å, and had a calculated Matthews coefficient of 2.23 ų Da⁻¹ assuming four molecules in the crystallographic asymmetric unit. Form B diffracted to a resolution of 3.0 Å; it belonged to space group P21212, with unit-cell parameters a = 69.9, b = 77.7, c = 88.5 Å, and had a calculated Matthews coefficient of 2.48 ų Da⁻¹ assuming two molecules in the crystallographic asymmetric unit. Preliminary molecular-replacement solutions have been determined with the PHENIX AutoMR wizard and refinement of both crystal forms is currently in progress. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24198224.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24198224.a1 new file mode 100644 index 0000000000000000000000000000000000000000..75f3097b7e0265c2682fd3c51914b8409696ba7f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24198224.a1 @@ -0,0 +1,5 @@ +T1 Title 0 86 A large outbreak of Salmonella Paratyphi A infection among israeli travelers to Nepal. +T2 Paragraph 87 312 In Asia, Salmonella Paratyphi A is an emerging infection, and travelers are increasingly at risk. During October 2009-November 2009, an outbreak in S. Paratyphi A infection was noted in Israeli travelers returning from Nepal. +T3 Paragraph 313 540 An outbreak investigation included a standardized exposure questionnaire admitted to all patients and medical chart abstraction. Isolates were tested for antimicrobial susceptibility and pulsed-field gel electrophoresis (PFGE). +T4 Paragraph 541 1173 During 1 October 2009-30 November 2009, 37 Israeli travelers returning from Nepal were diagnosed with S. Paratyphi A bacteremia. All 37 case isolates had an identical pattern on PFGE, and all were nalidixic acid resistant. Only 1 food venue was frequented by all the outbreak cases, with the largest number of exposures occurring around the Jewish New Year. All patients recovered without complications. Time to defervescence in 17 patients treated with ceftriaxone and azithromycin combination was 3.2 days (± 1.7), whereas in 13 cases treated with ceftriaxone monotherapy, the time to defervescence was 6.6 days (± 1.8; P < .001). +T5 Paragraph 1174 1406 A point-source, "Paratyphoid Mary"-like outbreak was identified among Israeli travelers to Nepal. Combination Ceftriaxone-Azithromycin therapy may provide a therapeutic advantage over monotherapy, and merits further clinical trials. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24198224.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24198224.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b349651e06baaf24ce933bbfcab8055d6991cd3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24198224.txt @@ -0,0 +1,6 @@ +A large outbreak of Salmonella Paratyphi A infection among israeli travelers to Nepal. +In Asia, Salmonella Paratyphi A is an emerging infection, and travelers are increasingly at risk. During October 2009-November 2009, an outbreak in S. Paratyphi A infection was noted in Israeli travelers returning from Nepal. +An outbreak investigation included a standardized exposure questionnaire admitted to all patients and medical chart abstraction. Isolates were tested for antimicrobial susceptibility and pulsed-field gel electrophoresis (PFGE). +During 1 October 2009-30 November 2009, 37 Israeli travelers returning from Nepal were diagnosed with S. Paratyphi A bacteremia. All 37 case isolates had an identical pattern on PFGE, and all were nalidixic acid resistant. Only 1 food venue was frequented by all the outbreak cases, with the largest number of exposures occurring around the Jewish New Year. All patients recovered without complications. Time to defervescence in 17 patients treated with ceftriaxone and azithromycin combination was 3.2 days (± 1.7), whereas in 13 cases treated with ceftriaxone monotherapy, the time to defervescence was 6.6 days (± 1.8; P < .001). +A point-source, "Paratyphoid Mary"-like outbreak was identified among Israeli travelers to Nepal. Combination Ceftriaxone-Azithromycin therapy may provide a therapeutic advantage over monotherapy, and merits further clinical trials. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24251551.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24251551.a1 new file mode 100644 index 0000000000000000000000000000000000000000..a95acf603f48c75f856a9c12394a94b26574d3f0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24251551.a1 @@ -0,0 +1,2 @@ +T1 Title 0 100 Structure of MurNAc 6-phosphate hydrolase (MurQ) from Haemophilus influenzae with a bound inhibitor. +T2 Paragraph 101 1870 The breakdown and recycling of peptidoglycan, an essential polymeric cell structure, occur in a number of bacterial species. A key enzyme in the recycling pathway of one of the components of the peptidoglycan layer, N-acetylmuramic acid (MurNAc), is MurNAc 6-phosphate hydrolase (MurQ). This enzyme catalyzes the cofactor-independent cleavage of a relatively nonlabile ether bond and presents an interesting target for mechanistic studies. Open chain product and substrate analogues were synthesized and tested as competitive inhibitors (K(is) values of 1.1 ± 0.3 and 0.23 ± 0.02 mM, respectively) of the MurNAc 6P hydrolase from Escherichia coli (MurQ-EC). To identify the roles of active site residues that are important for catalysis, the substrate analogue was cocrystallized with the MurNAc 6P hydrolase from Haemophilus influenzae (MurQ-HI) that was amenable to crystallographic studies. The cocrystal structure of MurQ-HI with the substrate analogue showed that Glu89 was located in the proximity of both the C2 atom and the oxygen at the C3 position of the bound inhibitor and that no other potential acid/base residue that could act as an active site acid/base was located in the vicinity. The conserved residues Glu120 and Lys239 were found within hydrogen bonding distance of the C5 hydroxyl group and C6 phosphate group, suggesting that they play a role in substrate binding and ring opening. Combining these results with previous biochemical data, we propose a one-base mechanism of action in which Glu89 functions to both deprotonate at the C2 position and assist in the departure of the lactyl ether at the C3 position. This same residue would serve to deprotonate the incoming water and reprotonate the enolate in the second half of the catalytic cycle. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24251551.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24251551.txt new file mode 100644 index 0000000000000000000000000000000000000000..77a18910cd1bb748360efbe6a1b9867cc54b91f1 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24251551.txt @@ -0,0 +1,3 @@ +Structure of MurNAc 6-phosphate hydrolase (MurQ) from Haemophilus influenzae with a bound inhibitor. +The breakdown and recycling of peptidoglycan, an essential polymeric cell structure, occur in a number of bacterial species. A key enzyme in the recycling pathway of one of the components of the peptidoglycan layer, N-acetylmuramic acid (MurNAc), is MurNAc 6-phosphate hydrolase (MurQ). This enzyme catalyzes the cofactor-independent cleavage of a relatively nonlabile ether bond and presents an interesting target for mechanistic studies. Open chain product and substrate analogues were synthesized and tested as competitive inhibitors (K(is) values of 1.1 ± 0.3 and 0.23 ± 0.02 mM, respectively) of the MurNAc 6P hydrolase from Escherichia coli (MurQ-EC). To identify the roles of active site residues that are important for catalysis, the substrate analogue was cocrystallized with the MurNAc 6P hydrolase from Haemophilus influenzae (MurQ-HI) that was amenable to crystallographic studies. The cocrystal structure of MurQ-HI with the substrate analogue showed that Glu89 was located in the proximity of both the C2 atom and the oxygen at the C3 position of the bound inhibitor and that no other potential acid/base residue that could act as an active site acid/base was located in the vicinity. The conserved residues Glu120 and Lys239 were found within hydrogen bonding distance of the C5 hydroxyl group and C6 phosphate group, suggesting that they play a role in substrate binding and ring opening. Combining these results with previous biochemical data, we propose a one-base mechanism of action in which Glu89 functions to both deprotonate at the C2 position and assist in the departure of the lactyl ether at the C3 position. This same residue would serve to deprotonate the incoming water and reprotonate the enolate in the second half of the catalytic cycle. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24361838.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24361838.a1 new file mode 100644 index 0000000000000000000000000000000000000000..bd37843978ea99058ab450c54aa6a0821f428f2c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24361838.a1 @@ -0,0 +1,2 @@ +T1 Title 0 114 Evaluation of a lytic bacteriophage, Φ st1, for biocontrol of Salmonella enterica serovar Typhimurium in chickens. +T2 Paragraph 115 2050 In this study, a Salmonella Typhimurium lytic bacteriophage, Φ st1, which was isolated from chicken faecal material, was evaluated as a candidate for biocontrol of Salmonella in chickens. The morphology of Φ st1 showed strong resemblance to members of the Siphoviridae family. Φ st1 was observed to be a DNA phage with an estimated genome size of 121 kbp. It was found to be able to infect S. Typhimurium and S. Hadar, with a stronger lytic activity against the former. Subsequent characterisation of Φ st1 against S. Typhimurium showed that Φ st1 has a latent period of 40 min with an average burst size of 22 particles per infective centre. Approximately 86.1% of the phage adsorbed to the host cells within the initial 5 min of infection. At the optimum multiplicity of infection (MOI) (0.1), the highest reduction rate of S. Typhimurium (6.6 log₁₀ CFU/ml) and increment in phage titre (3.8 log₁₀ PFU/ml) was observed. Φ st1 produced adsorption rates of 88.4-92.2% at pH7-9 and demonstrated the highest bacteria reduction (6.6 log₁₀ CFU/ml) at pH9. Φ st1 also showed an insignificant different (P>0.05) reduction rate of host cells at 37 °C (6.4 log₁₀ CFU/ml) and 42 °C (6.0 log₁₀ CFU/ml). The in vivo study using Φ st1 showed that intracloacal inoculation of ~10¹² PFU/ml of the phage in the chickens challenged with ~10¹⁰ CFU/ml of S. Typhimurium was able to reduce (P<0.05) the S. Typhimurium more rapidly than the untreated group. The Salmonella count reduced to 2.9 log₁₀ CFU/ml within 6h of post-challenge and S. Typhimurium was not detected at and after 24h of post-challenge. Reduction of Salmonella count in visceral organs was also observed at 6h post-challenge. Approximately 1.6 log₁₀ FU/ml Φ st1 was found to persist in the caecal wall of the chicks at 72 h of post-challenge. The present study indicated that Φ st1 may serve as a potential biocontrol agent to reduce the Salmonella count in caecal content of chickens. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24361838.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24361838.txt new file mode 100644 index 0000000000000000000000000000000000000000..21423b920ba49376b09b453b17e96c358a3e472a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24361838.txt @@ -0,0 +1,3 @@ +Evaluation of a lytic bacteriophage, Φ st1, for biocontrol of Salmonella enterica serovar Typhimurium in chickens. +In this study, a Salmonella Typhimurium lytic bacteriophage, Φ st1, which was isolated from chicken faecal material, was evaluated as a candidate for biocontrol of Salmonella in chickens. The morphology of Φ st1 showed strong resemblance to members of the Siphoviridae family. Φ st1 was observed to be a DNA phage with an estimated genome size of 121 kbp. It was found to be able to infect S. Typhimurium and S. Hadar, with a stronger lytic activity against the former. Subsequent characterisation of Φ st1 against S. Typhimurium showed that Φ st1 has a latent period of 40 min with an average burst size of 22 particles per infective centre. Approximately 86.1% of the phage adsorbed to the host cells within the initial 5 min of infection. At the optimum multiplicity of infection (MOI) (0.1), the highest reduction rate of S. Typhimurium (6.6 log₁₀ CFU/ml) and increment in phage titre (3.8 log₁₀ PFU/ml) was observed. Φ st1 produced adsorption rates of 88.4-92.2% at pH7-9 and demonstrated the highest bacteria reduction (6.6 log₁₀ CFU/ml) at pH9. Φ st1 also showed an insignificant different (P>0.05) reduction rate of host cells at 37 °C (6.4 log₁₀ CFU/ml) and 42 °C (6.0 log₁₀ CFU/ml). The in vivo study using Φ st1 showed that intracloacal inoculation of ~10¹² PFU/ml of the phage in the chickens challenged with ~10¹⁰ CFU/ml of S. Typhimurium was able to reduce (P<0.05) the S. Typhimurium more rapidly than the untreated group. The Salmonella count reduced to 2.9 log₁₀ CFU/ml within 6h of post-challenge and S. Typhimurium was not detected at and after 24h of post-challenge. Reduction of Salmonella count in visceral organs was also observed at 6h post-challenge. Approximately 1.6 log₁₀ FU/ml Φ st1 was found to persist in the caecal wall of the chicks at 72 h of post-challenge. The present study indicated that Φ st1 may serve as a potential biocontrol agent to reduce the Salmonella count in caecal content of chickens. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24678646.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24678646.a1 new file mode 100644 index 0000000000000000000000000000000000000000..2c3bd71a013c3c2c780c8b884de4d4eeec6bb930 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24678646.a1 @@ -0,0 +1,5 @@ +T1 Title 0 153 Natural history of colonization with methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE): a systematic review. +T2 Paragraph 154 443 No published systematic reviews have assessed the natural history of colonization with methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococcus (VRE). Time to clearance of colonization has important implications for patient care and infection control policy. +T3 Paragraph 444 653 We performed parallel searches in OVID Medline for studies that reported the time to documented clearance of MRSA and VRE colonization in the absence of treatment, published between January 1990 and July 2012. +T4 Paragraph 654 1897 For MRSA, we screened 982 articles, identified 16 eligible studies (13 observational studies and 3 randomized controlled trials), for a total of 1,804 non-duplicated subjects. For VRE, we screened 284 articles, identified 13 eligible studies (12 observational studies and 1 randomized controlled trial), for a total of 1,936 non-duplicated subjects. Studies reported varying definitions of clearance of colonization; no study reported time of initial colonization. Studies varied in the frequency of sampling, assays used for sampling, and follow-up period. The median duration of total follow-up was 38 weeks for MRSA and 25 weeks for VRE. Based on pooled analyses, the model-estimated median time to clearance was 88 weeks after documented colonization for MRSA-colonized patients and 26 weeks for VRE-colonized patients. In a secondary analysis, clearance rates for MRSA and VRE were compared by restricting the duration of follow-up for the MRSA studies to the maximum observed time point for VRE studies (43 weeks). With this restriction, the model-fitted median time to documented clearance for MRSA would occur at 41 weeks after documented colonization, demonstrating the sensitivity of the pooled estimate to length of study follow-up. +T5 Paragraph 1898 2508 Few available studies report the natural history of MRSA and VRE colonization. Lack of a consistent definition of clearance, uncertainty regarding the time of initial colonization, variation in frequency of sampling for persistent colonization, assays employed and variation in duration of follow-up are limitations of the existing published literature. The heterogeneity of study characteristics limits interpretation of pooled estimates of time to clearance, however, studies included in this review suggest an increase in documented clearance over time, a result which is sensitive to duration of follow-up. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24678646.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24678646.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e06be1e42b7fe2319c4c4b058473a74ebdfca72 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24678646.txt @@ -0,0 +1,6 @@ +Natural history of colonization with methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE): a systematic review. +No published systematic reviews have assessed the natural history of colonization with methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococcus (VRE). Time to clearance of colonization has important implications for patient care and infection control policy. +We performed parallel searches in OVID Medline for studies that reported the time to documented clearance of MRSA and VRE colonization in the absence of treatment, published between January 1990 and July 2012. +For MRSA, we screened 982 articles, identified 16 eligible studies (13 observational studies and 3 randomized controlled trials), for a total of 1,804 non-duplicated subjects. For VRE, we screened 284 articles, identified 13 eligible studies (12 observational studies and 1 randomized controlled trial), for a total of 1,936 non-duplicated subjects. Studies reported varying definitions of clearance of colonization; no study reported time of initial colonization. Studies varied in the frequency of sampling, assays used for sampling, and follow-up period. The median duration of total follow-up was 38 weeks for MRSA and 25 weeks for VRE. Based on pooled analyses, the model-estimated median time to clearance was 88 weeks after documented colonization for MRSA-colonized patients and 26 weeks for VRE-colonized patients. In a secondary analysis, clearance rates for MRSA and VRE were compared by restricting the duration of follow-up for the MRSA studies to the maximum observed time point for VRE studies (43 weeks). With this restriction, the model-fitted median time to documented clearance for MRSA would occur at 41 weeks after documented colonization, demonstrating the sensitivity of the pooled estimate to length of study follow-up. +Few available studies report the natural history of MRSA and VRE colonization. Lack of a consistent definition of clearance, uncertainty regarding the time of initial colonization, variation in frequency of sampling for persistent colonization, assays employed and variation in duration of follow-up are limitations of the existing published literature. The heterogeneity of study characteristics limits interpretation of pooled estimates of time to clearance, however, studies included in this review suggest an increase in documented clearance over time, a result which is sensitive to duration of follow-up. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24831788.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24831788.a1 new file mode 100644 index 0000000000000000000000000000000000000000..ea6b850778d1f257008853069f98d80772e23a40 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24831788.a1 @@ -0,0 +1,2 @@ +T1 Title 0 144 Evaluation of impermeant, DNA-binding dye fluorescence as a real-time readout of eukaryotic cell toxicity in a high throughput screening format. +T2 Paragraph 145 1457 Interpretation of high throughput screening (HTS) data in cell-based assays may be confounded by cytotoxic properties of screening compounds. Therefore, assessing cell toxicity in real time during the HTS process itself would be highly advantageous. Here, we investigate the potential of putatively impermeant, fluorescent, DNA-binding dyes to give cell toxicity readout during HTS. Amongst 19 DNA-binding dyes examined, three classes were identified that were (1) permeant, (2) cytotoxic, or (3) neither permeant nor cytotoxic during 3-day incubation with a macrophage cell line. In the last class, four dyes (SYTOX Green, CellTox Green, GelGreen, and EvaGreen) gave highly robust cytotoxicity data in 384-well screening plates. As proof of principle, successful combination with a luminescence-based assay in HTS format was demonstrated. Here, both intracellular growth of Legionella pneumophila (luminescence) and host cell viability (SYTOX Green exclusion) were assayed in the same screening well. Incorporation of membrane-impermeant, DNA-binding, fluorescent dyes in HTS assays should prove useful by allowing evaluation of cytotoxicity in real time, eliminating reagent addition steps and effort associated with endpoint cell viability analysis, and reducing the need for follow-up cytotoxicity screening. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24831788.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24831788.txt new file mode 100644 index 0000000000000000000000000000000000000000..6620a9c3aa7f0424f35642148a16e0fda9b8c54b --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24831788.txt @@ -0,0 +1,3 @@ +Evaluation of impermeant, DNA-binding dye fluorescence as a real-time readout of eukaryotic cell toxicity in a high throughput screening format. +Interpretation of high throughput screening (HTS) data in cell-based assays may be confounded by cytotoxic properties of screening compounds. Therefore, assessing cell toxicity in real time during the HTS process itself would be highly advantageous. Here, we investigate the potential of putatively impermeant, fluorescent, DNA-binding dyes to give cell toxicity readout during HTS. Amongst 19 DNA-binding dyes examined, three classes were identified that were (1) permeant, (2) cytotoxic, or (3) neither permeant nor cytotoxic during 3-day incubation with a macrophage cell line. In the last class, four dyes (SYTOX Green, CellTox Green, GelGreen, and EvaGreen) gave highly robust cytotoxicity data in 384-well screening plates. As proof of principle, successful combination with a luminescence-based assay in HTS format was demonstrated. Here, both intracellular growth of Legionella pneumophila (luminescence) and host cell viability (SYTOX Green exclusion) were assayed in the same screening well. Incorporation of membrane-impermeant, DNA-binding, fluorescent dyes in HTS assays should prove useful by allowing evaluation of cytotoxicity in real time, eliminating reagent addition steps and effort associated with endpoint cell viability analysis, and reducing the need for follow-up cytotoxicity screening. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24874563.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24874563.a1 new file mode 100644 index 0000000000000000000000000000000000000000..3e60e62dca3e99404ec608a0e1cb1f3129351bde --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24874563.a1 @@ -0,0 +1,2 @@ +T1 Title 0 45 Methylocella: a gourmand among methanotrophs. +T2 Paragraph 46 346 A recent article in Nature describes the ability of Methylocella silvestris to grow simultaneously on methane and longer chain alkanes, something never before observed in the microbial world. It adds to a growing list of unique metabolic traits that distinguish Methylocella from any other bacterium. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24874563.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24874563.txt new file mode 100644 index 0000000000000000000000000000000000000000..618cd23187384b5024e6737c570af67986ea1f0d --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-24874563.txt @@ -0,0 +1,3 @@ +Methylocella: a gourmand among methanotrophs. +A recent article in Nature describes the ability of Methylocella silvestris to grow simultaneously on methane and longer chain alkanes, something never before observed in the microbial world. It adds to a growing list of unique metabolic traits that distinguish Methylocella from any other bacterium. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25098305.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25098305.a1 new file mode 100644 index 0000000000000000000000000000000000000000..87d00dcf4753e7ec9113157130597e98e74463f8 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25098305.a1 @@ -0,0 +1,2 @@ +T1 Title 0 135 Surveillance for upper respiratory tract disease and Mycoplasma in free-ranging gopher tortoises (Gopherus polyphemus) in Georgia, USA. +T2 Paragraph 136 1742 Abstract Upper respiratory tract disease (URTD) in the gopher tortoise (Gopherus polyphemus) is highly contagious and has been implicated in the reduction of populations throughout the range. With the exception of a few limited studies, the prevalence of URTD in Georgia, USA tortoise populations is poorly known. We found that exposure to Mycoplasma agassizii and Mycoplasma testudineum, associated with URTD, varied geographically among 11 Georgia tortoise populations. The prevalence of antibodies to M. agassizii in individual populations was either very low (0-3%, n=7 populations) or very high (96-100%, n=4 populations), whereas there was variation in the prevalence of antibodies to M. testudineum among populations (20-61%, n=10) with only one site being negative. Five sites had tortoises with antibodies to both pathogens, and these were the only sites where we observed tortoises with clinical signs consistent with URTD. We did not find tortoises with clinical signs of URTD at sites with tortoises with antibodies only to M. testudineum, which provides evidence that this organism may be of limited pathogenicity for gopher tortoises. Collectively, these data indicate that both M. agassizii and M. testudineum are present in Georgia populations of gopher tortoises and that clinical disease is apparent in populations where both pathogens are present. Additional research is needed to better understand the role of these two pathogens, and other potential pathogens, in the overall health of tortoise populations, especially if future conservation efforts involve translocation of tortoises. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25098305.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25098305.txt new file mode 100644 index 0000000000000000000000000000000000000000..b151c475c0fc2353dc4ce2588027cb19395e066f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25098305.txt @@ -0,0 +1,3 @@ +Surveillance for upper respiratory tract disease and Mycoplasma in free-ranging gopher tortoises (Gopherus polyphemus) in Georgia, USA. +Abstract Upper respiratory tract disease (URTD) in the gopher tortoise (Gopherus polyphemus) is highly contagious and has been implicated in the reduction of populations throughout the range. With the exception of a few limited studies, the prevalence of URTD in Georgia, USA tortoise populations is poorly known. We found that exposure to Mycoplasma agassizii and Mycoplasma testudineum, associated with URTD, varied geographically among 11 Georgia tortoise populations. The prevalence of antibodies to M. agassizii in individual populations was either very low (0-3%, n=7 populations) or very high (96-100%, n=4 populations), whereas there was variation in the prevalence of antibodies to M. testudineum among populations (20-61%, n=10) with only one site being negative. Five sites had tortoises with antibodies to both pathogens, and these were the only sites where we observed tortoises with clinical signs consistent with URTD. We did not find tortoises with clinical signs of URTD at sites with tortoises with antibodies only to M. testudineum, which provides evidence that this organism may be of limited pathogenicity for gopher tortoises. Collectively, these data indicate that both M. agassizii and M. testudineum are present in Georgia populations of gopher tortoises and that clinical disease is apparent in populations where both pathogens are present. Additional research is needed to better understand the role of these two pathogens, and other potential pathogens, in the overall health of tortoise populations, especially if future conservation efforts involve translocation of tortoises. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25114119.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25114119.a1 new file mode 100644 index 0000000000000000000000000000000000000000..55374b43d6fe496714b0f02620716e9a7f8a7ac5 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25114119.a1 @@ -0,0 +1,2 @@ +T1 Title 0 199 Characterization of a lipopolysaccharide-targeted monoclonal antibody and its variable fragments as candidates for prophylaxis against the obligate intracellular bacterial pathogen Coxiella burnetii. +T2 Paragraph 200 1966 Our previous study demonstrated that treatment of Coxiella burnetii with the phase I lipopolysaccharide (PI-LPS)-targeted monoclonal antibody (MAb) 1E4 significantly inhibited C. burnetii infection in mice, suggesting that 1E4 is a protective MAb. To determine whether passive transfer of antibodies (Abs) can provide protection against C. burnetii natural infection, we examined if passive transfer of 1E4 would protect SCID mice against C. burnetii aerosol infection. The results indicated that 1E4 conferred significant protection against aerosolized C. burnetii, suggesting that 1E4 may be useful for preventing C. burnetii natural infection. To further understand the mechanisms of 1E4-mediated protection and to test the possibility of using humanized 1E4 to prevent C. burnetii infection, we examined whether the Fab fragment of 1E4 (Fab1E4), a recombinant murine single-chain variable fragment (muscFv1E4), and a humanized single-chain variable fragment (huscFv1E4) retained the ability of 1E4 to inhibit C. burnetii infection. The results indicated that Fab1E4, muscFv1E4, and huscFv1E4 were able to inhibit C. burnetii infection in mice but that their ability to inhibit C. burnetii infection was lower than that of 1E4. In addition, treatment of C. burnetii with Fab1E4, muscFv1E4, or huscFv1E4 can block C. burnetii infection of macrophages. Interestingly, treatment of C. burnetii with huscFv1E4 can significantly reduce C. burnetii infectivity in human macrophages. This report provides the first evidence to demonstrate that the humanized variable fragments of an LPS-specific MAb can neutralize C. burnetii infection and appears to be a promising step toward the potential use of a humanized MAb as emergency prophylaxis against C. burnetii exposure. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25114119.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25114119.txt new file mode 100644 index 0000000000000000000000000000000000000000..95270a119600343cc1314882003146cd0d87a942 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25114119.txt @@ -0,0 +1,3 @@ +Characterization of a lipopolysaccharide-targeted monoclonal antibody and its variable fragments as candidates for prophylaxis against the obligate intracellular bacterial pathogen Coxiella burnetii. +Our previous study demonstrated that treatment of Coxiella burnetii with the phase I lipopolysaccharide (PI-LPS)-targeted monoclonal antibody (MAb) 1E4 significantly inhibited C. burnetii infection in mice, suggesting that 1E4 is a protective MAb. To determine whether passive transfer of antibodies (Abs) can provide protection against C. burnetii natural infection, we examined if passive transfer of 1E4 would protect SCID mice against C. burnetii aerosol infection. The results indicated that 1E4 conferred significant protection against aerosolized C. burnetii, suggesting that 1E4 may be useful for preventing C. burnetii natural infection. To further understand the mechanisms of 1E4-mediated protection and to test the possibility of using humanized 1E4 to prevent C. burnetii infection, we examined whether the Fab fragment of 1E4 (Fab1E4), a recombinant murine single-chain variable fragment (muscFv1E4), and a humanized single-chain variable fragment (huscFv1E4) retained the ability of 1E4 to inhibit C. burnetii infection. The results indicated that Fab1E4, muscFv1E4, and huscFv1E4 were able to inhibit C. burnetii infection in mice but that their ability to inhibit C. burnetii infection was lower than that of 1E4. In addition, treatment of C. burnetii with Fab1E4, muscFv1E4, or huscFv1E4 can block C. burnetii infection of macrophages. Interestingly, treatment of C. burnetii with huscFv1E4 can significantly reduce C. burnetii infectivity in human macrophages. This report provides the first evidence to demonstrate that the humanized variable fragments of an LPS-specific MAb can neutralize C. burnetii infection and appears to be a promising step toward the potential use of a humanized MAb as emergency prophylaxis against C. burnetii exposure. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25204345.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25204345.a1 new file mode 100644 index 0000000000000000000000000000000000000000..bddf875f208bfa9f23f430d67d1cb0bfffac5cc5 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25204345.a1 @@ -0,0 +1,2 @@ +T1 Title 0 113 Association of mutation patterns in GyrA and ParC genes with quinolone resistance levels in lactic acid bacteria. +T2 Paragraph 114 1553 The quinolone resistance of 19 lactic acid bacterial strains belonging to the genera Enterococcus and Lactobacillus isolated from the natural fermented koumiss and yoghurt were investigated. The objective of this study was to determine the quinolone resistance levels and to explore the association of the resistance with the mutation patterns in gyrA and parC genes, as is currently recommended by the Food and Agriculture Organization/World Health Organization Joint Expert Committee in Guidelines for Evaluation of Probiotics in Food for probiotic lactic acid bacteria drug resistance in 2001. The Oxford Cup method and double-tube dilution method were used to determine the quinolone resistance levels of the isolated strains. Generally, all of the 19 strains showed resistance towards norfloxacin and ciprofloxacin when the Oxford cup method was used, whereas the incidence was lower (to norfloxacin 89.5% and to ciprofloxacin 68.4%) when minimum inhibitory concentration breakpoints (CLSI M100-S23) were tested. Furthermore, gene sequencing was conducted on gyrA and parC of topoisomerase II of these isolated strains. The genetic basis for quinolone resistance may be closely related to mutations in gyrA genes as there were 10 mutation sites in amino-acid sequences encoded by gyrA genes in 10 quinolone resistance strains and 14 mutation sites in Enterococcus durans HZ28, whereas no typical mutations were detected in parC genes. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25204345.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25204345.txt new file mode 100644 index 0000000000000000000000000000000000000000..cb10289d320be45f1fd1ace025cae69665d512f4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25204345.txt @@ -0,0 +1,3 @@ +Association of mutation patterns in GyrA and ParC genes with quinolone resistance levels in lactic acid bacteria. +The quinolone resistance of 19 lactic acid bacterial strains belonging to the genera Enterococcus and Lactobacillus isolated from the natural fermented koumiss and yoghurt were investigated. The objective of this study was to determine the quinolone resistance levels and to explore the association of the resistance with the mutation patterns in gyrA and parC genes, as is currently recommended by the Food and Agriculture Organization/World Health Organization Joint Expert Committee in Guidelines for Evaluation of Probiotics in Food for probiotic lactic acid bacteria drug resistance in 2001. The Oxford Cup method and double-tube dilution method were used to determine the quinolone resistance levels of the isolated strains. Generally, all of the 19 strains showed resistance towards norfloxacin and ciprofloxacin when the Oxford cup method was used, whereas the incidence was lower (to norfloxacin 89.5% and to ciprofloxacin 68.4%) when minimum inhibitory concentration breakpoints (CLSI M100-S23) were tested. Furthermore, gene sequencing was conducted on gyrA and parC of topoisomerase II of these isolated strains. The genetic basis for quinolone resistance may be closely related to mutations in gyrA genes as there were 10 mutation sites in amino-acid sequences encoded by gyrA genes in 10 quinolone resistance strains and 14 mutation sites in Enterococcus durans HZ28, whereas no typical mutations were detected in parC genes. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25562320.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25562320.a1 new file mode 100644 index 0000000000000000000000000000000000000000..a40ac492280152f8143845f9029f3bb4d2b7e80b --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25562320.a1 @@ -0,0 +1,2 @@ +T1 Title 0 103 Annexin1 regulates DC efferocytosis and cross-presentation during Mycobacterium tuberculosis infection. +T2 Paragraph 104 1185 The phagocytosis of apoptotic cells and associated vesicles (efferocytosis) by DCs is an important mechanism for both self tolerance and host defense. Although some of the engulfment ligands involved in efferocytosis have been identified and studied in vitro, the contributions of these ligands in vivo remain ill defined. Here, we determined that during Mycobacterium tuberculosis (Mtb) infection, the engulfment ligand annexin1 is an important mediator in DC cross-presentation that increases efferocytosis in DCs and intrinsically enhances the capacity of the DC antigen-presenting machinery. Annexin1-deficient mice were highly susceptible to Mtb infection and showed an impaired Mtb antigen-specific CD8+ T cell response. Importantly, annexin1 expression was greatly downregulated in Mtb-infected human blood monocyte-derived DCs, indicating that reduction of annexin1 is a critical mechanism for immune evasion by Mtb. Collectively, these data indicate that annexin1 is essential in immunity to Mtb infection and mediates the power of DC efferocytosis and cross-presentation. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25562320.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25562320.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe93ae2e376a7f24520b7dede51c533d1c689ef4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25562320.txt @@ -0,0 +1,3 @@ +Annexin1 regulates DC efferocytosis and cross-presentation during Mycobacterium tuberculosis infection. +The phagocytosis of apoptotic cells and associated vesicles (efferocytosis) by DCs is an important mechanism for both self tolerance and host defense. Although some of the engulfment ligands involved in efferocytosis have been identified and studied in vitro, the contributions of these ligands in vivo remain ill defined. Here, we determined that during Mycobacterium tuberculosis (Mtb) infection, the engulfment ligand annexin1 is an important mediator in DC cross-presentation that increases efferocytosis in DCs and intrinsically enhances the capacity of the DC antigen-presenting machinery. Annexin1-deficient mice were highly susceptible to Mtb infection and showed an impaired Mtb antigen-specific CD8+ T cell response. Importantly, annexin1 expression was greatly downregulated in Mtb-infected human blood monocyte-derived DCs, indicating that reduction of annexin1 is a critical mechanism for immune evasion by Mtb. Collectively, these data indicate that annexin1 is essential in immunity to Mtb infection and mediates the power of DC efferocytosis and cross-presentation. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25634638.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25634638.a1 new file mode 100644 index 0000000000000000000000000000000000000000..46af639ee7ff0a1106818c5eeef7c8ffdbc88ea2 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25634638.a1 @@ -0,0 +1,2 @@ +T1 Title 0 99 Real-time monitoring of hydrogen cyanide (HCN) and ammonia (NH₃) emitted by Pseudomonas aeruginosa. +T2 Paragraph 100 1302 We present the real-time monitoring of hydrogen cyanide (HCN) production from Pseudomonas aeruginosa (P. aeruginosa) strains in vitro, using laser-based photoacoustic spectroscopy. Simultaneously, the production of ammonia (NH3) was measured, and the influence of different factors (e.g. the medium, temperature and antibiotics treatment) was assessed. Both reference strains and clinical isolates of patients with CF were studied, and compared to other pathogens commonly present in lungs/airways of CF patients. Hydrogen cyanide production starts to rise as soon as P. aeruginosa bacteria reach the stationary phase ((9.0-9.5) × 10(9) colony forming units, CFUs), up to concentrations of 14.5 microliters per hour (µl h(-1)). Different strains of P. aeruginosa produced HCN to varying degrees, and addition of tobramycin strongly reduced HCN production within 2 h from application. Burkholderia cepacia also produced HCN (up to 0.35µl h(-1) in 9.0  ×  10(9) CFU) while other pathogens (Aspergillus fumigatus, Stenotrophomonas maltophilia, Mycobacterium abscessus) did not produce detectable levels. Our study reveals for the first time a broad overview of the dynamics of the HCN production in vitro. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25634638.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25634638.txt new file mode 100644 index 0000000000000000000000000000000000000000..c114676015317d2543ebc289112cf8d712ca3a61 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-25634638.txt @@ -0,0 +1,3 @@ +Real-time monitoring of hydrogen cyanide (HCN) and ammonia (NH₃) emitted by Pseudomonas aeruginosa. +We present the real-time monitoring of hydrogen cyanide (HCN) production from Pseudomonas aeruginosa (P. aeruginosa) strains in vitro, using laser-based photoacoustic spectroscopy. Simultaneously, the production of ammonia (NH3) was measured, and the influence of different factors (e.g. the medium, temperature and antibiotics treatment) was assessed. Both reference strains and clinical isolates of patients with CF were studied, and compared to other pathogens commonly present in lungs/airways of CF patients. Hydrogen cyanide production starts to rise as soon as P. aeruginosa bacteria reach the stationary phase ((9.0-9.5) × 10(9) colony forming units, CFUs), up to concentrations of 14.5 microliters per hour (µl h(-1)). Different strains of P. aeruginosa produced HCN to varying degrees, and addition of tobramycin strongly reduced HCN production within 2 h from application. Burkholderia cepacia also produced HCN (up to 0.35µl h(-1) in 9.0  ×  10(9) CFU) while other pathogens (Aspergillus fumigatus, Stenotrophomonas maltophilia, Mycobacterium abscessus) did not produce detectable levels. Our study reveals for the first time a broad overview of the dynamics of the HCN production in vitro. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-2696427.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-2696427.a1 new file mode 100644 index 0000000000000000000000000000000000000000..62cb9fbc9f62ab4c9fffe8d9355d3ee291f54c48 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-2696427.a1 @@ -0,0 +1,2 @@ +T1 Title 0 72 Presence of the fish pathogen Vibrio salmonicida in fish farm sediments. +T2 Paragraph 73 920 The persistence of the fish pathogen Vibrio salmonicida in fish farm sediments was studied by use of fluorescent-antibody techniques. The specificities of the monoclonal antibodies and polyclonal rabbit serum used in the study were tested against a number of Vibrio strains, including 4 isolates from intestinal tracts of healthy fish and 98 isolates from sediments. V. salmonicida was detected in sediment samples from diseased farms several months after an outbreak of the disease. The bacterium was also detected in a sediment sample from a disease-free fish farm. No V. salmonicida could be detected in sediments not influenced by fish farming. The number of positive samples was generally higher with application of rabbit serum as opposed to use of monoclonal antibodies, indicating that the rabbit serum may cross-react with other bacteria. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-2696427.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-2696427.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd33df05717eaec44f49de2e0902e50c6bfcab10 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-2696427.txt @@ -0,0 +1,3 @@ +Presence of the fish pathogen Vibrio salmonicida in fish farm sediments. +The persistence of the fish pathogen Vibrio salmonicida in fish farm sediments was studied by use of fluorescent-antibody techniques. The specificities of the monoclonal antibodies and polyclonal rabbit serum used in the study were tested against a number of Vibrio strains, including 4 isolates from intestinal tracts of healthy fish and 98 isolates from sediments. V. salmonicida was detected in sediment samples from diseased farms several months after an outbreak of the disease. The bacterium was also detected in a sediment sample from a disease-free fish farm. No V. salmonicida could be detected in sediments not influenced by fish farming. The number of positive samples was generally higher with application of rabbit serum as opposed to use of monoclonal antibodies, indicating that the rabbit serum may cross-react with other bacteria. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3074181.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3074181.a1 new file mode 100644 index 0000000000000000000000000000000000000000..99e62707e25fa5fa9d483d827c274ec7d5cd7968 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3074181.a1 @@ -0,0 +1,2 @@ +T1 Title 0 202 [Experimental and clinical studies of flomoxef in the field of obstetrics and gynecology. Representative Committee Members of the Research Team for Infections in the Field of Obstetrics and Gynecology]. +T2 Paragraph 203 1977 Flomoxef (FMOX) has a broad antibacterial spectrum against Gram-positive and Gram-negative bacteria; especially its potent antibacterial activity against Staphylococcus aureus is a significant advantage that may not be found with other cephem compounds. In our determination of its antibacterial potency against various clinical isolates obtained from clinical materials (amniotic fluid, intrauterine secretions, exudates of the pelvic dead space) of patients with various infections, we obtained results representing specific features of this drug. From the results, the drug may be expected to produce an excellent effect in the treatment of various infections. Our study on drug concentrations in body fluids and genital tissues demonstrated a good transfer of this drug into various tissues; in every tissue examined, the drug administered by the usual method in the usual dose yielded a concentration exceeding MIC for principal pathogens, thus promising a good clinical response. Indeed a high clinical efficacy rate of 90.1% (good to very good responses) was obtained in a clinical trial involving 222 cases. Administration of the drug in 2 g quantity daily produced a high response rate of 92.8%. It was especially noteworthy that a good response was obtained in 30 of 32 cases (93.8%) in which other cephem compounds had failed. In evaluation of the bacteriological effect, furthermore, the drug showed an excellent rate of bacterial elimination. In conclusion, this drug is expected to be greatly useful in the light of its good transfer into genital tissues and its strong antibacterial activities against Gram-positive cocci, Gram-negative bacteria and anaerobes as well as against multiple bacterial infections predominating among women with genital infections. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3074181.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3074181.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd818fccd64c7a77e55428286c39656c2bb01295 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3074181.txt @@ -0,0 +1,3 @@ +[Experimental and clinical studies of flomoxef in the field of obstetrics and gynecology. Representative Committee Members of the Research Team for Infections in the Field of Obstetrics and Gynecology]. +Flomoxef (FMOX) has a broad antibacterial spectrum against Gram-positive and Gram-negative bacteria; especially its potent antibacterial activity against Staphylococcus aureus is a significant advantage that may not be found with other cephem compounds. In our determination of its antibacterial potency against various clinical isolates obtained from clinical materials (amniotic fluid, intrauterine secretions, exudates of the pelvic dead space) of patients with various infections, we obtained results representing specific features of this drug. From the results, the drug may be expected to produce an excellent effect in the treatment of various infections. Our study on drug concentrations in body fluids and genital tissues demonstrated a good transfer of this drug into various tissues; in every tissue examined, the drug administered by the usual method in the usual dose yielded a concentration exceeding MIC for principal pathogens, thus promising a good clinical response. Indeed a high clinical efficacy rate of 90.1% (good to very good responses) was obtained in a clinical trial involving 222 cases. Administration of the drug in 2 g quantity daily produced a high response rate of 92.8%. It was especially noteworthy that a good response was obtained in 30 of 32 cases (93.8%) in which other cephem compounds had failed. In evaluation of the bacteriological effect, furthermore, the drug showed an excellent rate of bacterial elimination. In conclusion, this drug is expected to be greatly useful in the light of its good transfer into genital tissues and its strong antibacterial activities against Gram-positive cocci, Gram-negative bacteria and anaerobes as well as against multiple bacterial infections predominating among women with genital infections. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-351567.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-351567.a1 new file mode 100644 index 0000000000000000000000000000000000000000..4984d76b50c231e7e48e08c7b3abab8637b9a0d1 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-351567.a1 @@ -0,0 +1,2 @@ +T1 Title 0 72 A cell-free system for the replication fo bacteriophage M-13 duplex DNA. +T2 Paragraph 73 1055 Cell-free extracts from M-13 am5 infected Escherichia coli cells which are highly concentrated on cellophane membrane disks replicate efficiently endogenous M-13 duplex DNA. If the reaction is carried out in the presence of bromodeoxyuridine triphosphate, the majority of the label is found in two classes of hybrid DNA molecules in which either the viral or the complementary strand is newly synthesized. A minor portion of the label is incorporated into fully synthetic duplex DNA. DNA synthesis requires ATP and is inhibited by nalidixic acid, novobiocin, and arabinosylnucleoside triphosphates. Rifampicin blocks preferentially the synthesis of molecules with labeled complementary strands. A similar effect is observed upon addition of the helix-destabilising M-13 gene V protein. In contrast, addition of E. coli helix-destabilising protein (Eco HD-protein) stimulates the synthesis of both types of hybrid DNA molecules as well as the formation of fully synthetic duplex DNA. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-351567.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-351567.txt new file mode 100644 index 0000000000000000000000000000000000000000..e098b8972de65b4f95119b420c49bba797b6a90b --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-351567.txt @@ -0,0 +1,3 @@ +A cell-free system for the replication fo bacteriophage M-13 duplex DNA. +Cell-free extracts from M-13 am5 infected Escherichia coli cells which are highly concentrated on cellophane membrane disks replicate efficiently endogenous M-13 duplex DNA. If the reaction is carried out in the presence of bromodeoxyuridine triphosphate, the majority of the label is found in two classes of hybrid DNA molecules in which either the viral or the complementary strand is newly synthesized. A minor portion of the label is incorporated into fully synthetic duplex DNA. DNA synthesis requires ATP and is inhibited by nalidixic acid, novobiocin, and arabinosylnucleoside triphosphates. Rifampicin blocks preferentially the synthesis of molecules with labeled complementary strands. A similar effect is observed upon addition of the helix-destabilising M-13 gene V protein. In contrast, addition of E. coli helix-destabilising protein (Eco HD-protein) stimulates the synthesis of both types of hybrid DNA molecules as well as the formation of fully synthetic duplex DNA. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3544198.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3544198.a1 new file mode 100644 index 0000000000000000000000000000000000000000..def36cbe660f882df233d10408e0b35ce5a9b9d4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3544198.a1 @@ -0,0 +1,2 @@ +T1 Title 0 102 Methods for the detection of a specific Mycobacterium leprae antigen in the urine of leprosy patients. +T2 Paragraph 103 733 Two methods for detecting the phenolic glycolipid, PGL-1, a Mycobacterium leprae-specific molecule, in the urine of leprosy patients are described. Both methods rely on the 100-fold preconcentration of the urine, which can be accomplished by a single-step ultrafiltration procedure. The equivalent of approximately 2.5 micrograms of PGL-1/ml was detected in the urine of LL patients with an inhibition ELISA. The second method, a direct dot-blot assay on nitrocellulose paper, was much simpler and more sensitive. As little as 3 ng of antigen was detected by the dot-blot technique. PGL-1 was detected in the urine of LL patients. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3544198.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3544198.txt new file mode 100644 index 0000000000000000000000000000000000000000..3bcd1aa02d0f3ee6bd5af97e58869c3652b786bf --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-3544198.txt @@ -0,0 +1,3 @@ +Methods for the detection of a specific Mycobacterium leprae antigen in the urine of leprosy patients. +Two methods for detecting the phenolic glycolipid, PGL-1, a Mycobacterium leprae-specific molecule, in the urine of leprosy patients are described. Both methods rely on the 100-fold preconcentration of the urine, which can be accomplished by a single-step ultrafiltration procedure. The equivalent of approximately 2.5 micrograms of PGL-1/ml was detected in the urine of LL patients with an inhibition ELISA. The second method, a direct dot-blot assay on nitrocellulose paper, was much simpler and more sensitive. As little as 3 ng of antigen was detected by the dot-blot technique. PGL-1 was detected in the urine of LL patients. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4105033.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4105033.a1 new file mode 100644 index 0000000000000000000000000000000000000000..58d361348ec986683c80c41b6ebb16b5795cc8d4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4105033.a1 @@ -0,0 +1,2 @@ +T1 Title 0 81 Interactions of alkaline phosphatase and the cell wall of Pseudomonas aeruginosa. +T2 Paragraph 82 1469 Spheroplasts prepared by lysozyme treatment of cells of Pseudomonas aeruginosa, suspended in 20% sucrose or 0.2 m MgCl(2), were examined in detail. Preparation of spheroplasts in the presence of 0.2 m Mg(2+) released periplasmic alkaline phosphatase, whereas preparation in the presence of 20% sucrose did not, even though untreated cells released phosphatase when suspended in sucrose in the absence of lysozyme. Biochemical characterizations of the sucrose-lysozyme preparations indicated that lysozyme mediated a reassociation of the released phosphatase with the spheroplasts. In addition, the enzyme released from whole cells suspended in 20% sucrose (which represents 20 to 40% of the cell-bound phosphatase) reassociates with the cells in the presence of lysozyme. Electron microscopic examinations of various preparations revealed that phosphatase released in sucrose reassociated with the external cell wall layers in the presence of lysozyme, that sucrose-lysozyme prepared spheroplasts did not dissociate phosphatase which remained in the periplasm of sucrose-washed cells, and that phosphatase was never observed to be associated with the cytoplasmic membrane. A model to account for the binding of P. aeruginosa alkaline phosphatase to the internal portion of the tripartite layer of the cell wall rather than to the cytoplasmic membrane or peptidoglycan layer is presented. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4105033.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4105033.txt new file mode 100644 index 0000000000000000000000000000000000000000..036aced54fdad44a823443da6271c0374e0bf731 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4105033.txt @@ -0,0 +1,3 @@ +Interactions of alkaline phosphatase and the cell wall of Pseudomonas aeruginosa. +Spheroplasts prepared by lysozyme treatment of cells of Pseudomonas aeruginosa, suspended in 20% sucrose or 0.2 m MgCl(2), were examined in detail. Preparation of spheroplasts in the presence of 0.2 m Mg(2+) released periplasmic alkaline phosphatase, whereas preparation in the presence of 20% sucrose did not, even though untreated cells released phosphatase when suspended in sucrose in the absence of lysozyme. Biochemical characterizations of the sucrose-lysozyme preparations indicated that lysozyme mediated a reassociation of the released phosphatase with the spheroplasts. In addition, the enzyme released from whole cells suspended in 20% sucrose (which represents 20 to 40% of the cell-bound phosphatase) reassociates with the cells in the presence of lysozyme. Electron microscopic examinations of various preparations revealed that phosphatase released in sucrose reassociated with the external cell wall layers in the presence of lysozyme, that sucrose-lysozyme prepared spheroplasts did not dissociate phosphatase which remained in the periplasm of sucrose-washed cells, and that phosphatase was never observed to be associated with the cytoplasmic membrane. A model to account for the binding of P. aeruginosa alkaline phosphatase to the internal portion of the tripartite layer of the cell wall rather than to the cytoplasmic membrane or peptidoglycan layer is presented. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4328756.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4328756.a1 new file mode 100644 index 0000000000000000000000000000000000000000..09792f8316c2335b471b734f09ad431c8c82291f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4328756.a1 @@ -0,0 +1,2 @@ +T1 Title 0 59 Biochemistry of Coxiella burnetii: Embden-Meyerhof pathway. +T2 Paragraph 60 896 Purified preparations of Coxiella burnetii were examined for enzymes of the glycolytic pathway. Glucose-phosphate isomerase, fructose-1,6-diphosphatase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, and pyruvate kinase were shown to be present in C. burnetii extracts. Heat-killed C. burnetii purified with normal yolk sacs demonstrated no activity after disruption. Aldolase was shown to be of the class II type by complete inhibition of activity in the presence of 8 x 10(-3)m ethylenediaminetetraacetic acid. The host enzyme activity (normal and infected yolk sacs) was not affected by the same treatment. When cellulose acetate electrophoresis was performed on the extracts, aldolase from both normal and infected yolk sacs exhibited five isozyme bands, whereas aldolase from the C. burnetii extract appeared as a single band. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4328756.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4328756.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f8283e5905beafc1a61cc6673ab6f3886368d83 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4328756.txt @@ -0,0 +1,3 @@ +Biochemistry of Coxiella burnetii: Embden-Meyerhof pathway. +Purified preparations of Coxiella burnetii were examined for enzymes of the glycolytic pathway. Glucose-phosphate isomerase, fructose-1,6-diphosphatase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, and pyruvate kinase were shown to be present in C. burnetii extracts. Heat-killed C. burnetii purified with normal yolk sacs demonstrated no activity after disruption. Aldolase was shown to be of the class II type by complete inhibition of activity in the presence of 8 x 10(-3)m ethylenediaminetetraacetic acid. The host enzyme activity (normal and infected yolk sacs) was not affected by the same treatment. When cellulose acetate electrophoresis was performed on the extracts, aldolase from both normal and infected yolk sacs exhibited five isozyme bands, whereas aldolase from the C. burnetii extract appeared as a single band. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4329237.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4329237.a1 new file mode 100644 index 0000000000000000000000000000000000000000..431fd06170942fa683cf63441782af30bea04ac6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4329237.a1 @@ -0,0 +1 @@ +T1 Title 0 183 The in vitro assay of tuberculin hypersensitivity in Macaca mulatta sensitized with bacille Calmette Guerin cell wall vaccine and-or infected with virulent Mycobacterium tuberculosis. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4329237.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4329237.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f73010dc61169f18a29cdef9805b3818fb8c1ec --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-4329237.txt @@ -0,0 +1,2 @@ +The in vitro assay of tuberculin hypersensitivity in Macaca mulatta sensitized with bacille Calmette Guerin cell wall vaccine and-or infected with virulent Mycobacterium tuberculosis. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-448557.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-448557.a1 new file mode 100644 index 0000000000000000000000000000000000000000..6ba860be7a7a1eb78d4df039f26563062a3de28e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-448557.a1 @@ -0,0 +1,2 @@ +T1 Title 0 80 The etiologic and epidemiologic spectrum of bronchiolitis in pediatric practice. +T2 Paragraph 81 1213 To develop a broad understanding of the causes and patterns of occurrence of wheezing associated respiratory infections, we analyzed data from an 11-year study of acute lower respiratory illness in a pediatric practice. Although half of the WARI occurred in children less than 2 years of age, wheezing continued to be observed in 19% of children greater than 9 years of age who had lower respiratory illness. Males experienced LRI 1.25 times more often than did females; the relative risk of males for WARI was 1.35. A nonbacterial pathogen was recovered from 21% of patients with WARI; respiratory syncytial virus, parainfluenza virus types 1 and 3, adenoviruses, and Mycoplasma pneumoniae accounted for 81% of the isolates. Patient age influenced the pattern of recovery of these agents. The most common cause of WARI in children under 5 years of age was RSV whereas Mycoplasma pneumoniae was the most frequent isolate from school age children with wheezing illness. The data expand our understanding of the causes of WARI and are useful to diagnosticians and to researchers interested in the control of lower respiratory disease. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-448557.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-448557.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae59a150186220777127200cc3740608c4c4ea53 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-448557.txt @@ -0,0 +1,3 @@ +The etiologic and epidemiologic spectrum of bronchiolitis in pediatric practice. +To develop a broad understanding of the causes and patterns of occurrence of wheezing associated respiratory infections, we analyzed data from an 11-year study of acute lower respiratory illness in a pediatric practice. Although half of the WARI occurred in children less than 2 years of age, wheezing continued to be observed in 19% of children greater than 9 years of age who had lower respiratory illness. Males experienced LRI 1.25 times more often than did females; the relative risk of males for WARI was 1.35. A nonbacterial pathogen was recovered from 21% of patients with WARI; respiratory syncytial virus, parainfluenza virus types 1 and 3, adenoviruses, and Mycoplasma pneumoniae accounted for 81% of the isolates. Patient age influenced the pattern of recovery of these agents. The most common cause of WARI in children under 5 years of age was RSV whereas Mycoplasma pneumoniae was the most frequent isolate from school age children with wheezing illness. The data expand our understanding of the causes of WARI and are useful to diagnosticians and to researchers interested in the control of lower respiratory disease. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-460951.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-460951.a1 new file mode 100644 index 0000000000000000000000000000000000000000..f37c79a1c4238be10c9421db76ebcd899cf104ff --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-460951.a1 @@ -0,0 +1,2 @@ +T1 Title 0 66 Atypical mycobacteria causing non-pulmonary disease in Queensland. +T2 Paragraph 67 564 During the period 1971--7, the Tuberculosis Reference Laboratory in Queensland dealt with 52 isolates of atypical mycobacteria made from non-pulmonary sites under circumstances suggesting complicity in disease. Twenty-four isolates belonging to the MAIS complex were associated with lymph node infections in children. Twelve isolates belonged to the M. fortuitum-chelonei complex; most were from superficial abscesses. Five cases of M. marinum infection and 8 of M. ulcerans disease were detected. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-460951.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-460951.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b55073a9b4126e8370d1cdc17efe337ffdf9897 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-460951.txt @@ -0,0 +1,3 @@ +Atypical mycobacteria causing non-pulmonary disease in Queensland. +During the period 1971--7, the Tuberculosis Reference Laboratory in Queensland dealt with 52 isolates of atypical mycobacteria made from non-pulmonary sites under circumstances suggesting complicity in disease. Twenty-four isolates belonging to the MAIS complex were associated with lymph node infections in children. Twelve isolates belonged to the M. fortuitum-chelonei complex; most were from superficial abscesses. Five cases of M. marinum infection and 8 of M. ulcerans disease were detected. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-47483.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-47483.a1 new file mode 100644 index 0000000000000000000000000000000000000000..0cd11eef065e99f43c4c65f096814fbcc007dfe0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-47483.a1 @@ -0,0 +1,2 @@ +T1 Title 0 134 Ampicillin-resistant Haemophilus influenzae type B possessing a TEM-type beta-lactamase but little permeability barrier to ampicillin. +T2 Paragraph 135 1070 Ampicillin-resistant Haemophilus influenzae type B have been reported only during the past year. Five clinical isolates from the U.S. and Germany all had the TEM-type beta-lactamase which is known to be transferred widely among other gram-negative bacilli. Unlike those bacilli, however, the H. influenzae cell had very little barrier to entry of penicillins. This greater permeability of the H. influenzae cell to penicillins appeared to reduce the protective effect of its beta-lactamase, in that acquisition of the TEM-type beta-lactamase increased levels of resistance to penicillins much less for individual cells of H. influenzae than for those of Escherichia coli. Large inocula of either species appeared highly resistant. The unusually low level of resistance of individual cells of H. influenzae containing the TEM-type beta-lactamase may have delayed their emergence or recognition, and has unresolved clinical implications. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-47483.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-47483.txt new file mode 100644 index 0000000000000000000000000000000000000000..962d1ba39ed8e93cb856bc329034b1dd081fab1e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-47483.txt @@ -0,0 +1,3 @@ +Ampicillin-resistant Haemophilus influenzae type B possessing a TEM-type beta-lactamase but little permeability barrier to ampicillin. +Ampicillin-resistant Haemophilus influenzae type B have been reported only during the past year. Five clinical isolates from the U.S. and Germany all had the TEM-type beta-lactamase which is known to be transferred widely among other gram-negative bacilli. Unlike those bacilli, however, the H. influenzae cell had very little barrier to entry of penicillins. This greater permeability of the H. influenzae cell to penicillins appeared to reduce the protective effect of its beta-lactamase, in that acquisition of the TEM-type beta-lactamase increased levels of resistance to penicillins much less for individual cells of H. influenzae than for those of Escherichia coli. Large inocula of either species appeared highly resistant. The unusually low level of resistance of individual cells of H. influenzae containing the TEM-type beta-lactamase may have delayed their emergence or recognition, and has unresolved clinical implications. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-5526468.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-5526468.a1 new file mode 100644 index 0000000000000000000000000000000000000000..4543269d0520dc41afbe4bb062b1b7ea65c39d60 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-5526468.a1 @@ -0,0 +1 @@ +T1 Title 0 84 Vibrio fetus human infection--isolation from a subacute bacterial endocarditis case. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-5526468.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-5526468.txt new file mode 100644 index 0000000000000000000000000000000000000000..5bec0120973c38e95ca86a9a91cfa07d56d1d6de --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-5526468.txt @@ -0,0 +1,2 @@ +Vibrio fetus human infection--isolation from a subacute bacterial endocarditis case. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-607884.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-607884.a1 new file mode 100644 index 0000000000000000000000000000000000000000..6a93efa6cbbfda87855ad08b4b6e8a683808017a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-607884.a1 @@ -0,0 +1 @@ +T1 Title 0 104 [The infections from "Serratia" in the Hospital S. Camillo De Lellis of Roma (Italy) (author's transl)]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-607884.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-607884.txt new file mode 100644 index 0000000000000000000000000000000000000000..ff653f175594516ffaace0e05b4fb97622e9df76 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-607884.txt @@ -0,0 +1,2 @@ +[The infections from "Serratia" in the Hospital S. Camillo De Lellis of Roma (Italy) (author's transl)]. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6107735.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6107735.a1 new file mode 100644 index 0000000000000000000000000000000000000000..acfce2e15774c9d1d753fd796e735bfc5e96e790 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6107735.a1 @@ -0,0 +1,2 @@ +T1 Title 0 55 Recurrence of Pelecypod-associated cholera in Sardinia. +T2 Paragraph 56 934 From Oct. 30 to Nov. 7, 1979, 10 people in the Sardinian province of Cagliari had onset of bacteriologically confirmed cholera. Two symptom-free excretors of Vibrio cholerae O:1 were detected in household contacts of the patients. There were no deaths. All but 1 of the 12 people with V. cholerae O:1 infection gave a history of recent consumption of marine bivalves known locally as arselle (pelecypods). Triplicate matched neighbourhood controls for each of the first 7 cases identified were also interviewed; none had recently eaten arselle. V. cholerae O:1 was also recovered from samples of water and bivalves obtained from a lagoon on the outskirts of the city of Cagliari. Arselle had also been implicated as the vehicle of transmission in 1973 in the last outbreak of cholera in Sardinia. It seems unlikely that cholera transmission had persisted locally in the interim. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6107735.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6107735.txt new file mode 100644 index 0000000000000000000000000000000000000000..73a1d21f2e9909c56490f057f6ad29eec34917e3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6107735.txt @@ -0,0 +1,3 @@ +Recurrence of Pelecypod-associated cholera in Sardinia. +From Oct. 30 to Nov. 7, 1979, 10 people in the Sardinian province of Cagliari had onset of bacteriologically confirmed cholera. Two symptom-free excretors of Vibrio cholerae O:1 were detected in household contacts of the patients. There were no deaths. All but 1 of the 12 people with V. cholerae O:1 infection gave a history of recent consumption of marine bivalves known locally as arselle (pelecypods). Triplicate matched neighbourhood controls for each of the first 7 cases identified were also interviewed; none had recently eaten arselle. V. cholerae O:1 was also recovered from samples of water and bivalves obtained from a lagoon on the outskirts of the city of Cagliari. Arselle had also been implicated as the vehicle of transmission in 1973 in the last outbreak of cholera in Sardinia. It seems unlikely that cholera transmission had persisted locally in the interim. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6143890.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6143890.a1 new file mode 100644 index 0000000000000000000000000000000000000000..36f81f6a34f60807f26ce645c294666cd9b0aa43 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6143890.a1 @@ -0,0 +1 @@ +T1 Title 0 107 Rapid detection with monoclonal antibodies of Chlamydia trachomatis in urethral smears and urine sediments. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6143890.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6143890.txt new file mode 100644 index 0000000000000000000000000000000000000000..02be44f5337a0c44cdbe3dc23122959c3a983c56 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6143890.txt @@ -0,0 +1,2 @@ +Rapid detection with monoclonal antibodies of Chlamydia trachomatis in urethral smears and urine sediments. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6631408.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6631408.a1 new file mode 100644 index 0000000000000000000000000000000000000000..f968a062f07d5cdde8e13264e967a97b16d5225e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6631408.a1 @@ -0,0 +1,2 @@ +T1 Title 0 152 Amino acid requirements of strains of Chlamydia trachomatis and C. psittaci growing in McCoy cells: relationship with clinical syndrome and host origin. +T2 Paragraph 153 1309 The effects of omission of individual amino acids from growth medium on the multiplication of a range of Chlamydia trachomatis and C. psittaci strains in cycloheximide-treated McCoy cells have been assessed. Differences in requirements were revealed which for C. trachomatis strains correlated with clinical syndrome and for C. psittaci with host origin. All 11 strains of C. trachomatis examined showed a requirement for addition of histidine to the medium; this was not shown by any of four C. psittaci strains. Among the strains of C. trachomatis, three from cases of trachoma, representing serotypes A, B and C, showed a distinctive requirement for the addition of tryptophan to the medium, whilst six strains of oculogenital origin, representing serotypes D-I, exhibited no requirement for tryptophan or methionine; a lymphogranuloma venereum and a 'fast variant' strain both showed a requirement for methionine. Of the four C. psittaci strains from different hosts, three showed distinct patterns of amino acid requirements. All chlamydiae required the addition of valine to medium and the majority required leucine, phenylalanine and also glutamine. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6631408.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6631408.txt new file mode 100644 index 0000000000000000000000000000000000000000..11296913bb01272b4113e09d83492f490e2bee16 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-6631408.txt @@ -0,0 +1,3 @@ +Amino acid requirements of strains of Chlamydia trachomatis and C. psittaci growing in McCoy cells: relationship with clinical syndrome and host origin. +The effects of omission of individual amino acids from growth medium on the multiplication of a range of Chlamydia trachomatis and C. psittaci strains in cycloheximide-treated McCoy cells have been assessed. Differences in requirements were revealed which for C. trachomatis strains correlated with clinical syndrome and for C. psittaci with host origin. All 11 strains of C. trachomatis examined showed a requirement for addition of histidine to the medium; this was not shown by any of four C. psittaci strains. Among the strains of C. trachomatis, three from cases of trachoma, representing serotypes A, B and C, showed a distinctive requirement for the addition of tryptophan to the medium, whilst six strains of oculogenital origin, representing serotypes D-I, exhibited no requirement for tryptophan or methionine; a lymphogranuloma venereum and a 'fast variant' strain both showed a requirement for methionine. Of the four C. psittaci strains from different hosts, three showed distinct patterns of amino acid requirements. All chlamydiae required the addition of valine to medium and the majority required leucine, phenylalanine and also glutamine. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8347510.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8347510.a1 new file mode 100644 index 0000000000000000000000000000000000000000..473e3f535a08c1995377e205f863ad977391a4fb --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8347510.a1 @@ -0,0 +1,2 @@ +T1 Title 0 111 Arhodomonas aquaeolei gen. nov., sp. nov., an aerobic, halophilic bacterium isolated from a subterranean brine. +T2 Paragraph 112 1288 Arhodomonas aquaeolei gen. nov., sp. nov., isolated from a petroleum reservoir production fluid, is described. The single isolate was an obligately halophilic, aerobic, gram-negative, oval rod-shaped bacterium that was actively motile by means of a single polar flagellum. It was catalase and oxidase positive. The isolate had a specific requirement for NaCl; growth occurred at NaCl concentrations between 6 and 20%, and optimal growth occurred in the presence of 15% NaCl. This species metabolized primarily organic acids and required biotin for growth. The name Arhodomonas is proposed for the new genus, which was placed in the gamma subclass of the Proteobacteria on the basis of the results of a 16S rRNA sequence analysis. Although A. aquaeolei is most closely related to purple sulfur bacteria (the genera Ectothiorhodospira and Chromatium), it is not a phototrophic microorganism, which is consistent with its isolation from a subterranean environment. The major components of its cellular fatty acids were C16:0, C18:1, C19:0, C16:1, and C18:0 acids. The DNA base composition of the type strain is 67 mol% G+C. The type and only strain is strain HA-1 (= ATCC 49307). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8347510.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8347510.txt new file mode 100644 index 0000000000000000000000000000000000000000..b175d3bb59ba623f5226c82da2e78eb09578f3a0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8347510.txt @@ -0,0 +1,3 @@ +Arhodomonas aquaeolei gen. nov., sp. nov., an aerobic, halophilic bacterium isolated from a subterranean brine. +Arhodomonas aquaeolei gen. nov., sp. nov., isolated from a petroleum reservoir production fluid, is described. The single isolate was an obligately halophilic, aerobic, gram-negative, oval rod-shaped bacterium that was actively motile by means of a single polar flagellum. It was catalase and oxidase positive. The isolate had a specific requirement for NaCl; growth occurred at NaCl concentrations between 6 and 20%, and optimal growth occurred in the presence of 15% NaCl. This species metabolized primarily organic acids and required biotin for growth. The name Arhodomonas is proposed for the new genus, which was placed in the gamma subclass of the Proteobacteria on the basis of the results of a 16S rRNA sequence analysis. Although A. aquaeolei is most closely related to purple sulfur bacteria (the genera Ectothiorhodospira and Chromatium), it is not a phototrophic microorganism, which is consistent with its isolation from a subterranean environment. The major components of its cellular fatty acids were C16:0, C18:1, C19:0, C16:1, and C18:0 acids. The DNA base composition of the type strain is 67 mol% G+C. The type and only strain is strain HA-1 (= ATCC 49307). + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8358765.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8358765.a1 new file mode 100644 index 0000000000000000000000000000000000000000..d873c62c0759234b6aa74efd9b73f01338808f65 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8358765.a1 @@ -0,0 +1,2 @@ +T1 Title 0 92 [The effect of omeprazole on healing of duodenal ulcers, Helicobacter pylori and gastritis]. +T2 Paragraph 93 1196 Losec (omeprazole) Astra Co. is a blocker of the proton pump of the parietal cell. It inhibits basal and stimulated HCl secretion. It is used for treatment of gastroduodenal ulcers, reflux oesophagitis and Zollinger Ellison's syndrome. In a group of 17 patients with duodenal ulcers the authors investigated the effect of omeprazole on (1) healing of duodenal ulcers and bulbitis after 2-4 weeks of therapy, (2) elimination of Helicobacter pylori in the antrum, (3) chronic antral gastritis. Ad 1. After two weeks of treatment the authors found that 5 of 17 chronic duodenal ulcers were healed in the remainder substantial regression was found. Four-week treatment led to healing of 16 from a total of 17 ulcers (P < 0.001), i. e. 94%. In subjects with ulcers and bulbitis (12 patients) the ulcer healed in 11 instances, in 7 patients residual bulbitis persisted. Ad 2. H. pylori was detected before treatment in 16 of 17 patients, after treatment only in 5 (P < 0.001). Ad 3. Chronic gastritis was recorded before treatment in all patients. Treatment reduced its activity and the presence of H. pylori. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8358765.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8358765.txt new file mode 100644 index 0000000000000000000000000000000000000000..5da94f4551eb0e4ffcefffc2ce6ede0c4b1f2b55 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8358765.txt @@ -0,0 +1,3 @@ +[The effect of omeprazole on healing of duodenal ulcers, Helicobacter pylori and gastritis]. +Losec (omeprazole) Astra Co. is a blocker of the proton pump of the parietal cell. It inhibits basal and stimulated HCl secretion. It is used for treatment of gastroduodenal ulcers, reflux oesophagitis and Zollinger Ellison's syndrome. In a group of 17 patients with duodenal ulcers the authors investigated the effect of omeprazole on (1) healing of duodenal ulcers and bulbitis after 2-4 weeks of therapy, (2) elimination of Helicobacter pylori in the antrum, (3) chronic antral gastritis. Ad 1. After two weeks of treatment the authors found that 5 of 17 chronic duodenal ulcers were healed in the remainder substantial regression was found. Four-week treatment led to healing of 16 from a total of 17 ulcers (P < 0.001), i. e. 94%. In subjects with ulcers and bulbitis (12 patients) the ulcer healed in 11 instances, in 7 patients residual bulbitis persisted. Ad 2. H. pylori was detected before treatment in 16 of 17 patients, after treatment only in 5 (P < 0.001). Ad 3. Chronic gastritis was recorded before treatment in all patients. Treatment reduced its activity and the presence of H. pylori. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8532424.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8532424.a1 new file mode 100644 index 0000000000000000000000000000000000000000..a1c75abf3fd32acfff1ffedcdbabf5511293751f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8532424.a1 @@ -0,0 +1,2 @@ +T1 Title 0 63 Respiratory carriage of Kingella kingae among healthy children. +T2 Paragraph 64 1552 The role of Kingella kingae as an invasive pathogen of young children is being increasingly recognized, but the niche of the organism in the respiratory tract and its prevalence in the normal flora of children remain unknown. To investigate these two aspects throat and nasopharyngeal cultures were obtained every 2 weeks from two cohorts of children, ages 6 to 42 months on enrollment, attending a day-care center in southern Israel. To determine the age-related prevalence of K. kingae, throat cultures were obtained from children ages 6 months to 14 years hospitalized for elective surgery who had not received antibiotics during the previous 30 days and from healthy infants younger than 6 months attending a well-baby-care clinic for routine vaccinations. During an 11-month follow-up 109 of 624 (27.5%) throat cultures but none of the nasopharyngeal cultures obtained from 48 day-care center attendees grew K. kingae. The monthly prevalence of K. kingae ranged from 6.1 to 34.6% with December and April peaks. Overall 35 of 48 (72.9%) children had at least one positive culture for the organism. Among the 27 children who had > or = 2 positive cultures, continuous and intermittent patterns of carriage were observed. None of the colonized children experienced an invasive K. kingae infection. The prevalence of pharyngeal carriage among surgical patients was 8.0%, and the organism was not isolated from any of the infants younger than 6 months attending the well-baby-care clinic. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8532424.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8532424.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ed565d725884788485064b8d76e7eaa2006d999 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8532424.txt @@ -0,0 +1,3 @@ +Respiratory carriage of Kingella kingae among healthy children. +The role of Kingella kingae as an invasive pathogen of young children is being increasingly recognized, but the niche of the organism in the respiratory tract and its prevalence in the normal flora of children remain unknown. To investigate these two aspects throat and nasopharyngeal cultures were obtained every 2 weeks from two cohorts of children, ages 6 to 42 months on enrollment, attending a day-care center in southern Israel. To determine the age-related prevalence of K. kingae, throat cultures were obtained from children ages 6 months to 14 years hospitalized for elective surgery who had not received antibiotics during the previous 30 days and from healthy infants younger than 6 months attending a well-baby-care clinic for routine vaccinations. During an 11-month follow-up 109 of 624 (27.5%) throat cultures but none of the nasopharyngeal cultures obtained from 48 day-care center attendees grew K. kingae. The monthly prevalence of K. kingae ranged from 6.1 to 34.6% with December and April peaks. Overall 35 of 48 (72.9%) children had at least one positive culture for the organism. Among the 27 children who had > or = 2 positive cultures, continuous and intermittent patterns of carriage were observed. None of the colonized children experienced an invasive K. kingae infection. The prevalence of pharyngeal carriage among surgical patients was 8.0%, and the organism was not isolated from any of the infants younger than 6 months attending the well-baby-care clinic. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8559802.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8559802.a1 new file mode 100644 index 0000000000000000000000000000000000000000..7be25667f27430e6040ce7fb63c96f71009c67f3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8559802.a1 @@ -0,0 +1,2 @@ +T1 Title 0 94 Construction of a cloning vector from a naturally occurring plasmid of Salmonella typhimurium. +T2 Paragraph 95 986 A naturally occurring plasmid isolated from a drug-resistant strain of Salmonella typhimurium (993) has been used to construct a plasmid vector for cloning in a wild strain of Salmonella. The strain (993) contains at least two plasmids. The smaller plasmid (9 kb) contains an ampicillin-resistant marker, while the larger one (25 kb) is cryptic. Physical mapping of the 9-kb plasmid and construction of a 3.5-kb derivative have been carried out. This plasmid has been used for cloning in a restriction+modification+strain of S. typhimurium using a conventional calcium chloride method. It exhibited better efficiency of transformation than other commonly used plasmids such as pBR322 or its derivatives and transformants were found to be stable in the absence of antibiotic selection. The vector is compatible with pBR322 and can be used to study the expression of cloned genes in minicells. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8559802.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8559802.txt new file mode 100644 index 0000000000000000000000000000000000000000..c5c0ffc0bde9c1b15ab4718f3bc7079ae74fa5ed --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8559802.txt @@ -0,0 +1,3 @@ +Construction of a cloning vector from a naturally occurring plasmid of Salmonella typhimurium. +A naturally occurring plasmid isolated from a drug-resistant strain of Salmonella typhimurium (993) has been used to construct a plasmid vector for cloning in a wild strain of Salmonella. The strain (993) contains at least two plasmids. The smaller plasmid (9 kb) contains an ampicillin-resistant marker, while the larger one (25 kb) is cryptic. Physical mapping of the 9-kb plasmid and construction of a 3.5-kb derivative have been carried out. This plasmid has been used for cloning in a restriction+modification+strain of S. typhimurium using a conventional calcium chloride method. It exhibited better efficiency of transformation than other commonly used plasmids such as pBR322 or its derivatives and transformants were found to be stable in the absence of antibiotic selection. The vector is compatible with pBR322 and can be used to study the expression of cloned genes in minicells. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8607503.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8607503.a1 new file mode 100644 index 0000000000000000000000000000000000000000..c4491b383507f3cdaf7cc4f55d82146def988978 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8607503.a1 @@ -0,0 +1,5 @@ +T1 Title 0 107 Non-O1 Vibrio cholerae bacteremia in patients with cirrhosis: 5-yr experience from a single medical center. +T2 Paragraph 108 300 To assess the clinical features and susceptibility of cirrhotic patients to non-O1 Vibrio cholerae bacteremia and to provide our therapeutic experiences in this rare and high lethal infection. +T3 Paragraph 301 547 Twenty-eight blood culture isolates of non-O1 V. cholerae were identified by our clinical microbiology laboratory between July 1989 and June 1994. Patients with underlying cirrhosis and the aforementioned bacteremia were retrospectively reviewed. +T4 Paragraph 548 1414 Twenty-one cirrhotic patients (16 male, five female; mean age, 50.9 yr; range 28-67 yr) were identified and classified as Child B (6 cases) and Child C (15 cases). Bacteremic episodes occurred most often from March to September. Seafood ingestion (seven cases) and seawater exposure (two cases) were risk factors, but nosocomial infections were also noted in six cases. Presenting symptoms and signs included ascites (95.2%), fever (81%), abdominal pain (52.4%), diarrhea (33.3%), and cellulitis with bullae formation (19%). Concurrent spontaneous bacterial peritonitis was determined in 10 cases, seven with positive ascites cultures. Antibiotic therapy (either cephalothin with gentamicin or ceftriaxone alone) cured most of the bacteremic episodes. The overall case-fatality rate was 23.8%, but 75% of the deaths were observed in patients with skin manifestation. +T5 Paragraph 1415 1668 Patients with decompensated cirrhosis are susceptible to non-O1 V. cholerae bacteremia and should not ingest raw seafood or expose skin wounds to salt water. A high index of suspicion and early administration of antibiotics may lower the mortality rate. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8607503.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8607503.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9b51264c602992f2efe876aa435c550859c430b --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8607503.txt @@ -0,0 +1,6 @@ +Non-O1 Vibrio cholerae bacteremia in patients with cirrhosis: 5-yr experience from a single medical center. +To assess the clinical features and susceptibility of cirrhotic patients to non-O1 Vibrio cholerae bacteremia and to provide our therapeutic experiences in this rare and high lethal infection. +Twenty-eight blood culture isolates of non-O1 V. cholerae were identified by our clinical microbiology laboratory between July 1989 and June 1994. Patients with underlying cirrhosis and the aforementioned bacteremia were retrospectively reviewed. +Twenty-one cirrhotic patients (16 male, five female; mean age, 50.9 yr; range 28-67 yr) were identified and classified as Child B (6 cases) and Child C (15 cases). Bacteremic episodes occurred most often from March to September. Seafood ingestion (seven cases) and seawater exposure (two cases) were risk factors, but nosocomial infections were also noted in six cases. Presenting symptoms and signs included ascites (95.2%), fever (81%), abdominal pain (52.4%), diarrhea (33.3%), and cellulitis with bullae formation (19%). Concurrent spontaneous bacterial peritonitis was determined in 10 cases, seven with positive ascites cultures. Antibiotic therapy (either cephalothin with gentamicin or ceftriaxone alone) cured most of the bacteremic episodes. The overall case-fatality rate was 23.8%, but 75% of the deaths were observed in patients with skin manifestation. +Patients with decompensated cirrhosis are susceptible to non-O1 V. cholerae bacteremia and should not ingest raw seafood or expose skin wounds to salt water. A high index of suspicion and early administration of antibiotics may lower the mortality rate. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8703935.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8703935.a1 new file mode 100644 index 0000000000000000000000000000000000000000..9abeacae28420d89eb009edd7f2126f5535c78ce --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8703935.a1 @@ -0,0 +1,2 @@ +T1 Title 0 174 NMR analysis of site-specific ligand binding in oligomeric proteins. Dynamic studies on the interaction of riboflavin synthase with trifluoromethyl-substituted intermediates. +T2 Paragraph 175 1645 The binding of small ligands to symmetrical oligomeric proteins may lead to a number of different partially ligated intermediates but should finally yield a symmetrical fully ligated enzyme/ligand complex. In the case of the trimeric protein, riboflavin synthase, some ligands form an unexpected protein/ligand complex, even in the presence of a large excess of ligand. Three different bound forms were observed by 19F NMR spectroscopy, and Scatchard-type analysis suggested binding sites of similar affinities. NOESY analysis of the kinetic network revealed that the three bound states exchange with free ligand, but not with each other, thus suggesting that the trimeric enzyme could be asymmetrical. This information permits appropriate precautions to be taken during X-ray structure analysis of riboflavin synthase, which is in progress. Quantitative analysis of the NOESY spectra yielded different rate constants for the different binding sites. For comparison, the monomeric lumazine protein was investigated as an example of a case with simple two-site exchange. For such systems, all kinetic parameters including kon and the dissociation constant can be determined from the NOESY spectrum. The data show that NMR spectroscopy can produce qualitative and quantitative information in cases of nonequivalent binding sites in oligomeric proteins if isolated NMR signals of the different forms can be observed. The technique is not limited to 19F as reporter nucleus. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8703935.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8703935.txt new file mode 100644 index 0000000000000000000000000000000000000000..4255da75a16c7aa12681af3dbd9dc3fdfc156bbc --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8703935.txt @@ -0,0 +1,3 @@ +NMR analysis of site-specific ligand binding in oligomeric proteins. Dynamic studies on the interaction of riboflavin synthase with trifluoromethyl-substituted intermediates. +The binding of small ligands to symmetrical oligomeric proteins may lead to a number of different partially ligated intermediates but should finally yield a symmetrical fully ligated enzyme/ligand complex. In the case of the trimeric protein, riboflavin synthase, some ligands form an unexpected protein/ligand complex, even in the presence of a large excess of ligand. Three different bound forms were observed by 19F NMR spectroscopy, and Scatchard-type analysis suggested binding sites of similar affinities. NOESY analysis of the kinetic network revealed that the three bound states exchange with free ligand, but not with each other, thus suggesting that the trimeric enzyme could be asymmetrical. This information permits appropriate precautions to be taken during X-ray structure analysis of riboflavin synthase, which is in progress. Quantitative analysis of the NOESY spectra yielded different rate constants for the different binding sites. For comparison, the monomeric lumazine protein was investigated as an example of a case with simple two-site exchange. For such systems, all kinetic parameters including kon and the dissociation constant can be determined from the NOESY spectrum. The data show that NMR spectroscopy can produce qualitative and quantitative information in cases of nonequivalent binding sites in oligomeric proteins if isolated NMR signals of the different forms can be observed. The technique is not limited to 19F as reporter nucleus. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8997164.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8997164.a1 new file mode 100644 index 0000000000000000000000000000000000000000..58fa265192bf3d4041d8514836b0ba1a2b54be38 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8997164.a1 @@ -0,0 +1,2 @@ +T1 Title 0 59 Gamma/delta T lymphocytes in the BCG granulomatous lesions. +T2 Paragraph 60 1098 Recent studies in man and animal models have demonstrated that TCR-gamma delta-bearing T cells (gamma delta T cells) are activated by mycobacteria and accumulate in the sites of mycobacterial infection. Although the function of gamma delta T cells remains unclear, some data suggest a potential role for these cells in the granulomatous immune response. To address the presence of gamma delta T cells within the BCG granulomas, we have characterized the TCR phenotype of T-lymphocytes present in the BCG granulomatous lesion immunohistochemically using a monoclonal antibody to TCR delta 1 and others. Fairly large numbers of gamma delta T cells were located at the periphery of the BCG granulomas without necrosis and most of them also expressed CD8. However, gamma delta T cells were rarely present in the granulomas with central caseous necrosis, calcification and fibrotic changes. With these results, it might be speculated that the CD8+ gamma delta T lymphocytes participate in the BCG granuloma formation mainly in the early stage. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8997164.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8997164.txt new file mode 100644 index 0000000000000000000000000000000000000000..e35788e0b53c878776657cec553c2f5963790713 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-8997164.txt @@ -0,0 +1,3 @@ +Gamma/delta T lymphocytes in the BCG granulomatous lesions. +Recent studies in man and animal models have demonstrated that TCR-gamma delta-bearing T cells (gamma delta T cells) are activated by mycobacteria and accumulate in the sites of mycobacterial infection. Although the function of gamma delta T cells remains unclear, some data suggest a potential role for these cells in the granulomatous immune response. To address the presence of gamma delta T cells within the BCG granulomas, we have characterized the TCR phenotype of T-lymphocytes present in the BCG granulomatous lesion immunohistochemically using a monoclonal antibody to TCR delta 1 and others. Fairly large numbers of gamma delta T cells were located at the periphery of the BCG granulomas without necrosis and most of them also expressed CD8. However, gamma delta T cells were rarely present in the granulomas with central caseous necrosis, calcification and fibrotic changes. With these results, it might be speculated that the CD8+ gamma delta T lymphocytes participate in the BCG granuloma formation mainly in the early stage. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9255900.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9255900.a1 new file mode 100644 index 0000000000000000000000000000000000000000..37332980f32a61bc1ec6f936fc203577348baddb --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9255900.a1 @@ -0,0 +1,2 @@ +T1 Title 0 64 Isolation of Helicobacter pullorum from patients with enteritis. +T2 Paragraph 65 473 Helicobacter pullorum, recently described as sp. nov., is commonly isolated from asymptomatic poultry. Two cases of human enteritis associated with H. pullorum, one of them in an immunocompromised patient, are reported. Problems in the correct species identification by means of phenotypic and genotypic methods are discussed and for the first time a fatty acid pattern of Helicobacter pullorum is presented. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9255900.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9255900.txt new file mode 100644 index 0000000000000000000000000000000000000000..1107d8b747e24388be06a8720abde729b6253c5e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9255900.txt @@ -0,0 +1,3 @@ +Isolation of Helicobacter pullorum from patients with enteritis. +Helicobacter pullorum, recently described as sp. nov., is commonly isolated from asymptomatic poultry. Two cases of human enteritis associated with H. pullorum, one of them in an immunocompromised patient, are reported. Problems in the correct species identification by means of phenotypic and genotypic methods are discussed and for the first time a fatty acid pattern of Helicobacter pullorum is presented. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9521147.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9521147.a1 new file mode 100644 index 0000000000000000000000000000000000000000..0d63254df2e978c66f9f0ff736edb2d4c58f9c36 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9521147.a1 @@ -0,0 +1,2 @@ +T1 Title 0 174 Lipopolysaccharide from nonvirulent Ara+ Burkholderia pseudomallei isolates is immunologically indistinguishable from lipopolysaccharide from virulent Ara- clinical isolates. +T2 Paragraph 175 1742 Different lines of evidence suggest that a discrepancy between the distribution of Burkholderia (Pseudomonas) pseudomallei in the environment and the distribution of the disease melioidosis is attributable, at least in part, to phenotypic differences between clinical and some environmental isolates. Two antigenically and biochemically distinct biotypes have been described, only one of which is virulent. In this study, lipopolysaccharides (LPSs) were extracted by the proteinase K digestion method from a total of 214 B. pseudomallei isolates, and their immunoreactivities with sera from patients with different clinical spectra and with other infections were evaluated. With the exception of4 isolates from a total of 214 tested, the sodium dodecyl sulfate-polyacrylamide gel electrophoresis silver-staining profiles of the LPSs from the two biotypes showed identical ladder patterns that were typical for smooth LPSs from other gram-negative bacteria. The 210 isolates with typical LPS patterns (119 Ara- clinical, 13 Ara- soil, 70 Ara+ soil, and 8 reference National Type Culture Collection strains) also exhibited similar immunoblot profiles against pooled sera from patients with melioidosis and hyperimmune mouse sera. Concordant findings were noted in the indirect enzyme-linked immunosorbent assay with Ara- and Ara+ LPSs to coat the microtiter plates. The LPSs of the different B. pseudomallei biotypes appear antigenically indistinguishable. It is, therefore, unlikely that this component is related to the virulence and pathogenicity of B. pseudomallei. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9521147.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9521147.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c757190746dbc2207819ca64e6c8b039d2ee148 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9521147.txt @@ -0,0 +1,3 @@ +Lipopolysaccharide from nonvirulent Ara+ Burkholderia pseudomallei isolates is immunologically indistinguishable from lipopolysaccharide from virulent Ara- clinical isolates. +Different lines of evidence suggest that a discrepancy between the distribution of Burkholderia (Pseudomonas) pseudomallei in the environment and the distribution of the disease melioidosis is attributable, at least in part, to phenotypic differences between clinical and some environmental isolates. Two antigenically and biochemically distinct biotypes have been described, only one of which is virulent. In this study, lipopolysaccharides (LPSs) were extracted by the proteinase K digestion method from a total of 214 B. pseudomallei isolates, and their immunoreactivities with sera from patients with different clinical spectra and with other infections were evaluated. With the exception of4 isolates from a total of 214 tested, the sodium dodecyl sulfate-polyacrylamide gel electrophoresis silver-staining profiles of the LPSs from the two biotypes showed identical ladder patterns that were typical for smooth LPSs from other gram-negative bacteria. The 210 isolates with typical LPS patterns (119 Ara- clinical, 13 Ara- soil, 70 Ara+ soil, and 8 reference National Type Culture Collection strains) also exhibited similar immunoblot profiles against pooled sera from patients with melioidosis and hyperimmune mouse sera. Concordant findings were noted in the indirect enzyme-linked immunosorbent assay with Ara- and Ara+ LPSs to coat the microtiter plates. The LPSs of the different B. pseudomallei biotypes appear antigenically indistinguishable. It is, therefore, unlikely that this component is related to the virulence and pathogenicity of B. pseudomallei. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9526514.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9526514.a1 new file mode 100644 index 0000000000000000000000000000000000000000..53715d7c793ef226cf267d4f1cdcc5a82510e9f9 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9526514.a1 @@ -0,0 +1,2 @@ +T1 Title 0 128 A putative rolB gene homologue of the Agrobacterium rhizogenes TR-DNA has different morphogenetic activity in tobacco than rolB. +T2 Paragraph 129 1214 Agrobacterium rhizogenes strains of the agropine type harbor on their Ri-plasmid two T-DNAs, a left TL-DNA and a right TR-DNA. The rolB gene of the TL-DNA is the major factor in the pathogenesis of the hairy-root disease and its constitutive expression interfere profoundly with plant morphogenesis. We have tested whether the expression of its sequence related putative homologue from the TR-DNA (rolBTR) may cause also bacterial virulence or affect plant development. Unlike rolB, rolBTR is unable to induce root formation on tobacco leaf discs. Tobacco plants expressing a chimeric 35S::rolBTR gene have reduced stature, off-shoots at the stem base and bent and wrinkled leaves with epinastic growth. 14 N-terminal amino acids which are absent in the rolB protein are indispensable to rolBTR protein activity. The characteristic tyrosine phosphatase super family motif CX5R is absent in the rolBTR protein. For rolB this motif is possibly functionally relevant. We conclude that the rolBTR gene product has morphogenic activity but is not a functional homologue of the rolB protein. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9526514.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9526514.txt new file mode 100644 index 0000000000000000000000000000000000000000..a53183d68777b30cb9dee0d22d6ee6590702ccf6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9526514.txt @@ -0,0 +1,3 @@ +A putative rolB gene homologue of the Agrobacterium rhizogenes TR-DNA has different morphogenetic activity in tobacco than rolB. +Agrobacterium rhizogenes strains of the agropine type harbor on their Ri-plasmid two T-DNAs, a left TL-DNA and a right TR-DNA. The rolB gene of the TL-DNA is the major factor in the pathogenesis of the hairy-root disease and its constitutive expression interfere profoundly with plant morphogenesis. We have tested whether the expression of its sequence related putative homologue from the TR-DNA (rolBTR) may cause also bacterial virulence or affect plant development. Unlike rolB, rolBTR is unable to induce root formation on tobacco leaf discs. Tobacco plants expressing a chimeric 35S::rolBTR gene have reduced stature, off-shoots at the stem base and bent and wrinkled leaves with epinastic growth. 14 N-terminal amino acids which are absent in the rolB protein are indispensable to rolBTR protein activity. The characteristic tyrosine phosphatase super family motif CX5R is absent in the rolBTR protein. For rolB this motif is possibly functionally relevant. We conclude that the rolBTR gene product has morphogenic activity but is not a functional homologue of the rolB protein. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9535771.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9535771.a1 new file mode 100644 index 0000000000000000000000000000000000000000..3c753afaa3c8815d17310070d240cc5950a0615a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9535771.a1 @@ -0,0 +1,2 @@ +T1 Title 0 103 Order of fusions between bacterial and mammalian proteins can determine solubility in Escherichia coli. +T2 Paragraph 104 1049 We made fusions between Escherichia coli maltose-binding protein (MBP) and the mammalian aspartic proteinases pepsinogen or procathepsin D. When MBP was at the N-terminus, the fusions were soluble in E. coli. When the order was reversed, the chimeric proteins formed inclusion bodies. The data suggest that the solubility of fusion proteins is controlled by whether the protein domains emerging first from the ribosome normally fold into soluble or insoluble states. The soluble MBP-aspartic proteinase fusions were stable but proteolytically inactive. MBP-pepsinogen, however, was efficiently renatured from 8 M urea in vitro, suggesting that the E. coli cytoplasm does not support folding of the mammalian partner protein to the native state. Thus, inclusion body formation may be the consequence, rather than the cause, of non-native folding in vivo, and in E. coli soluble proteins may fold into states different from those reached in vitro. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9535771.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9535771.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd532b7dc1daf503c76bebfea38429bb36f00832 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9535771.txt @@ -0,0 +1,3 @@ +Order of fusions between bacterial and mammalian proteins can determine solubility in Escherichia coli. +We made fusions between Escherichia coli maltose-binding protein (MBP) and the mammalian aspartic proteinases pepsinogen or procathepsin D. When MBP was at the N-terminus, the fusions were soluble in E. coli. When the order was reversed, the chimeric proteins formed inclusion bodies. The data suggest that the solubility of fusion proteins is controlled by whether the protein domains emerging first from the ribosome normally fold into soluble or insoluble states. The soluble MBP-aspartic proteinase fusions were stable but proteolytically inactive. MBP-pepsinogen, however, was efficiently renatured from 8 M urea in vitro, suggesting that the E. coli cytoplasm does not support folding of the mammalian partner protein to the native state. Thus, inclusion body formation may be the consequence, rather than the cause, of non-native folding in vivo, and in E. coli soluble proteins may fold into states different from those reached in vitro. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9553794.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9553794.a1 new file mode 100644 index 0000000000000000000000000000000000000000..a2e70d6def889167ef43a38e3225e89924ae3757 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9553794.a1 @@ -0,0 +1,2 @@ +T1 Title 0 146 Evaluation of the role of Carnobacterium piscicola in spoilage of vacuum- and modified-atmosphere-packed cold-smoked salmon stored at 5 degrees C. +T2 Paragraph 147 2138 The microflora on spoiled cold-smoked salmon often consists of a mixture of lactic acid bacteria (LAB) and Gram-negative bacteria. To elucidate the role of the different groups, a storage trial was carried out in which nisin and CO2 were used for the selective inhibition of the two bacterial groups. The shelf-life of vacuum-packed cold-smoked salmon, recorded by sensory evaluation, was four weeks at 5 degrees C and the microflora was composed of LAB (10(6)-10(7) cfu/g) with an associate Gram-negative flora in varying levels (10(5)-10(7) cfu/g). The addition of nisin and/or a CO2-atmosphere increased the shelf-life to five or six weeks and limited the level of LAB to about 10(4)-10(6), 10(3)-10(6) and 10(2)-10(4) cfu/g, respectively. CO2-atmosphere +/- nisin inhibited the growth of Gram-negative bacteria, whereas nisin had no effect on these in vacuum packages. The Gram-negative flora on vacuum-packed salmon was dominated by a Vibrio sp., resembling V. marinus, Enterobacteriaceae (Enterobacter agglomerans, Serratia liquefaciens and Rahnella aquatilis) and occasionally Aeromonas hydrophila. Irrespective of the addition of nisin and/or CO2-atmosphere, the LAB microflora was dominated by Carnobacterium piscicola, which was found to account for 87% of the 255 LAB isolates characterized. Whole-cell-protein patterns analysed by SDS-PAGE confirmed the Carnobacterium species identification. The spoilage potential of C. piscicola isolates was further studied by inoculation of approx. 10(6) cfu/g in cold-smoked salmon stored at 5 degrees C. The salmon did not spoil within 4 weeks of storage in vacuum- or CO2-atmosphere, and it is concluded that despite high levels (> 10(7) cfu/g) of C. piscicola, sensory rejection was caused by autolytic changes. This was supported by the development of soft texture and sour, rancid and bitter off-flavours at the point of spoilage, irrespective of the length of shelf-life and low or high total counts of LAB and Gram-negative bacteria. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9553794.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9553794.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f5caf9fc1f519a84cfa9c09c6e1b1e3aef20a17 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9553794.txt @@ -0,0 +1,3 @@ +Evaluation of the role of Carnobacterium piscicola in spoilage of vacuum- and modified-atmosphere-packed cold-smoked salmon stored at 5 degrees C. +The microflora on spoiled cold-smoked salmon often consists of a mixture of lactic acid bacteria (LAB) and Gram-negative bacteria. To elucidate the role of the different groups, a storage trial was carried out in which nisin and CO2 were used for the selective inhibition of the two bacterial groups. The shelf-life of vacuum-packed cold-smoked salmon, recorded by sensory evaluation, was four weeks at 5 degrees C and the microflora was composed of LAB (10(6)-10(7) cfu/g) with an associate Gram-negative flora in varying levels (10(5)-10(7) cfu/g). The addition of nisin and/or a CO2-atmosphere increased the shelf-life to five or six weeks and limited the level of LAB to about 10(4)-10(6), 10(3)-10(6) and 10(2)-10(4) cfu/g, respectively. CO2-atmosphere +/- nisin inhibited the growth of Gram-negative bacteria, whereas nisin had no effect on these in vacuum packages. The Gram-negative flora on vacuum-packed salmon was dominated by a Vibrio sp., resembling V. marinus, Enterobacteriaceae (Enterobacter agglomerans, Serratia liquefaciens and Rahnella aquatilis) and occasionally Aeromonas hydrophila. Irrespective of the addition of nisin and/or CO2-atmosphere, the LAB microflora was dominated by Carnobacterium piscicola, which was found to account for 87% of the 255 LAB isolates characterized. Whole-cell-protein patterns analysed by SDS-PAGE confirmed the Carnobacterium species identification. The spoilage potential of C. piscicola isolates was further studied by inoculation of approx. 10(6) cfu/g in cold-smoked salmon stored at 5 degrees C. The salmon did not spoil within 4 weeks of storage in vacuum- or CO2-atmosphere, and it is concluded that despite high levels (> 10(7) cfu/g) of C. piscicola, sensory rejection was caused by autolytic changes. This was supported by the development of soft texture and sour, rancid and bitter off-flavours at the point of spoilage, irrespective of the length of shelf-life and low or high total counts of LAB and Gram-negative bacteria. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9564489.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9564489.a1 new file mode 100644 index 0000000000000000000000000000000000000000..04cf34825851846f6a76569843471bf23e6ebd6d --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9564489.a1 @@ -0,0 +1 @@ +T1 Title 0 81 Gingivomandibular infection due to Mycobacterium kansasii in a patient with AIDS. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9564489.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9564489.txt new file mode 100644 index 0000000000000000000000000000000000000000..504b9059ac1a1034ddadd2a35ede0eb2bc97d150 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9564489.txt @@ -0,0 +1,2 @@ +Gingivomandibular infection due to Mycobacterium kansasii in a patient with AIDS. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9643457.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9643457.a1 new file mode 100644 index 0000000000000000000000000000000000000000..cdf70ac50a00dbbf9c8dde1315cee4a5c408a3b3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9643457.a1 @@ -0,0 +1,2 @@ +T1 Title 0 142 Flow cytometric measurement of neutrophil alkaline phosphatase before and during initiation of an induced Escherichia coli mastitis in cattle. +T2 Paragraph 143 1541 In 12 healthy cows, neutrophil alkaline phosphatase (NAP) activity was measured by flow cytometer before and during an experimentally induced Escherichia coli mastitis, to study the role and increase of NAP in Gram-negative bacterial infections. Percentage of neutrophils containing alkaline phosphatase and intensity of NAP activity were measured. Preinfection percentage of neutrophils with enzyme activity varied between 64.0% and 84.4% and the intensity of enzyme activity was low in all cows. After induction of infection, percentage of neutrophils with enzyme activity showed a significant decrease on day 1 followed by an significant increase on day 3. NAP intensity increased significantly on the second and third day after infection. This increase of intensity was significantly, positively correlated with the severity of infection. From this study we may conclude that variation in susceptibility to E. coli mastitis could not be explained by preinfection NAP levels. The post-infection increase of NAP activity, that was found following an induced infection was more a result of increased enzyme intensity per neutrophil, then from an increase of percentage neutrophils with enzyme activity. Furthermore, a strong correlation was found between NAP intensity and severity of inflammation. There was evidence that the more severely diseased animals showed stronger NAP intensity increase. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9643457.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9643457.txt new file mode 100644 index 0000000000000000000000000000000000000000..85125479a973588bbe83da6b9458174598a06139 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9643457.txt @@ -0,0 +1,3 @@ +Flow cytometric measurement of neutrophil alkaline phosphatase before and during initiation of an induced Escherichia coli mastitis in cattle. +In 12 healthy cows, neutrophil alkaline phosphatase (NAP) activity was measured by flow cytometer before and during an experimentally induced Escherichia coli mastitis, to study the role and increase of NAP in Gram-negative bacterial infections. Percentage of neutrophils containing alkaline phosphatase and intensity of NAP activity were measured. Preinfection percentage of neutrophils with enzyme activity varied between 64.0% and 84.4% and the intensity of enzyme activity was low in all cows. After induction of infection, percentage of neutrophils with enzyme activity showed a significant decrease on day 1 followed by an significant increase on day 3. NAP intensity increased significantly on the second and third day after infection. This increase of intensity was significantly, positively correlated with the severity of infection. From this study we may conclude that variation in susceptibility to E. coli mastitis could not be explained by preinfection NAP levels. The post-infection increase of NAP activity, that was found following an induced infection was more a result of increased enzyme intensity per neutrophil, then from an increase of percentage neutrophils with enzyme activity. Furthermore, a strong correlation was found between NAP intensity and severity of inflammation. There was evidence that the more severely diseased animals showed stronger NAP intensity increase. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9693738.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9693738.a1 new file mode 100644 index 0000000000000000000000000000000000000000..67b9a434bc092094fc938b18bb93863b1372f099 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9693738.a1 @@ -0,0 +1,2 @@ +T1 Title 0 89 Maintenance energy requirement: what is required for stasis survival of Escherichia coli? +T2 Paragraph 90 941 Little is known about how the energy of maintenance is generated in a cell supporting its persistence solely on endogenous carbon material, and what this energy is used for. However, it is clear that the endogenous metabolism of Escherichia coli cells held in the absence of exogenous carbon includes de novo protein synthesis, and that this synthesis is required for the maintenance of the growth-arrested cell. Recent findings suggest that several genes/proteins responding to carbon starvation are themselves involved in reorganizing and modulating catabolic flux, while others form an integral part of a defense system aimed at avoiding the damaging effects of ongoing respiratory activity. A significant fraction of the energy of maintenance is suggested to be required to prevent the denaturation and spontaneous aging of proteins during stasis. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9693738.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9693738.txt new file mode 100644 index 0000000000000000000000000000000000000000..eee1e4d9a74c01e87bfbe85479cc6fe54d8c9200 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9693738.txt @@ -0,0 +1,3 @@ +Maintenance energy requirement: what is required for stasis survival of Escherichia coli? +Little is known about how the energy of maintenance is generated in a cell supporting its persistence solely on endogenous carbon material, and what this energy is used for. However, it is clear that the endogenous metabolism of Escherichia coli cells held in the absence of exogenous carbon includes de novo protein synthesis, and that this synthesis is required for the maintenance of the growth-arrested cell. Recent findings suggest that several genes/proteins responding to carbon starvation are themselves involved in reorganizing and modulating catabolic flux, while others form an integral part of a defense system aimed at avoiding the damaging effects of ongoing respiratory activity. A significant fraction of the energy of maintenance is suggested to be required to prevent the denaturation and spontaneous aging of proteins during stasis. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9745160.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9745160.a1 new file mode 100644 index 0000000000000000000000000000000000000000..1631ad8b6bc926132f5831a05a8cc9f4022fe9ee --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9745160.a1 @@ -0,0 +1,5 @@ +T1 Title 0 109 New one-week, low-dose triple therapy for the treatment of duodenal ulcer with Helicobacter pylori infection. +T2 Paragraph 110 656 Antimicrobial therapy is the recommended treatment for duodenal ulcer associated with Helicobacter pylori infection. The eradication of bismuth-based triple therapy with bismuth subcitrate, metronidazole and amoxicillin is limited by low compliance, drug resistance and side-effects. Two-week proton pump inhibitor (PPI)-based triple therapy has a higher eradication rate but is costly. This study was designed to compare the efficacy, patient compliance and cost of short-term PPI-based triple therapy with those of bismuth-based triple therapy. +T3 Paragraph 657 1547 Ninety patients with active duodenal ulcer disease and H pylori infection, proven with the 13C-urea breath test and CLO test (Campylobacter-like organism test) were treated randomly in three therapeutic groups: Group A, DeNol 120 mg, amoxicillin 500 mg and metronidazole 250 mg four times a day orally for 14 days; Group B, omeprazole 20 mg plus clarithromycin 500 mg twice a day and amoxicillin 500 mg four times a day for 14 days; Group C, omeprazole 20 mg, clarithromycin 250 mg and metronidazole 500 mg twice a day for seven days. Nizatidine 150 mg twice a day was given continuously following the end of anti-H pylori therapy for each group. Two months later, endoscopy, the CLO test and 13C-urea breath test were repeated to assess the eradication rate of H pylori and the ulcer-healing rate. Drug tolerance was evaluated by patients themselves by daily recording of any side-effects. +T4 Paragraph 1548 2241 Eighty-four patients completed the entire course of therapy and evaluation for H pylori infection. The H pylori eradication rates in Groups A, B and C were 75% (21/28), 93% (26/28) and 89% (25/28), respectively (p = 0.466). The ulcer healing rate was 86% (24/28) in Group A and 89% (25/28) in Groups B and C (p = 0.764). A total of 74 patients (88%) were free from symptoms at the end of the triple therapy. Symptom relief was faster in patients with PPI-based triple therapy (Groups B and C) (days 3 and 4) than for patients with bismuth-based triple therapy (day 5). The cost of Group C therapy was lower than that for Groups A and B. There were no major side-effects in any of the patients. +T5 Paragraph 2242 2579 One-week triple therapy with omeprazole, clarithromycin and metronidazole is highly effected for the eradication of H pylori. A therapeutic regime of one week's duration with lower cost, good compliance and mild side-effects may offer a good choice for treatment of duodenal ulcer associated with H pylori infection in clinical practice. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9745160.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9745160.txt new file mode 100644 index 0000000000000000000000000000000000000000..ce7c0e53fb0b8198ee57a261dad9650f3364a7a8 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9745160.txt @@ -0,0 +1,6 @@ +New one-week, low-dose triple therapy for the treatment of duodenal ulcer with Helicobacter pylori infection. +Antimicrobial therapy is the recommended treatment for duodenal ulcer associated with Helicobacter pylori infection. The eradication of bismuth-based triple therapy with bismuth subcitrate, metronidazole and amoxicillin is limited by low compliance, drug resistance and side-effects. Two-week proton pump inhibitor (PPI)-based triple therapy has a higher eradication rate but is costly. This study was designed to compare the efficacy, patient compliance and cost of short-term PPI-based triple therapy with those of bismuth-based triple therapy. +Ninety patients with active duodenal ulcer disease and H pylori infection, proven with the 13C-urea breath test and CLO test (Campylobacter-like organism test) were treated randomly in three therapeutic groups: Group A, DeNol 120 mg, amoxicillin 500 mg and metronidazole 250 mg four times a day orally for 14 days; Group B, omeprazole 20 mg plus clarithromycin 500 mg twice a day and amoxicillin 500 mg four times a day for 14 days; Group C, omeprazole 20 mg, clarithromycin 250 mg and metronidazole 500 mg twice a day for seven days. Nizatidine 150 mg twice a day was given continuously following the end of anti-H pylori therapy for each group. Two months later, endoscopy, the CLO test and 13C-urea breath test were repeated to assess the eradication rate of H pylori and the ulcer-healing rate. Drug tolerance was evaluated by patients themselves by daily recording of any side-effects. +Eighty-four patients completed the entire course of therapy and evaluation for H pylori infection. The H pylori eradication rates in Groups A, B and C were 75% (21/28), 93% (26/28) and 89% (25/28), respectively (p = 0.466). The ulcer healing rate was 86% (24/28) in Group A and 89% (25/28) in Groups B and C (p = 0.764). A total of 74 patients (88%) were free from symptoms at the end of the triple therapy. Symptom relief was faster in patients with PPI-based triple therapy (Groups B and C) (days 3 and 4) than for patients with bismuth-based triple therapy (day 5). The cost of Group C therapy was lower than that for Groups A and B. There were no major side-effects in any of the patients. +One-week triple therapy with omeprazole, clarithromycin and metronidazole is highly effected for the eradication of H pylori. A therapeutic regime of one week's duration with lower cost, good compliance and mild side-effects may offer a good choice for treatment of duodenal ulcer associated with H pylori infection in clinical practice. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9798026.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9798026.a1 new file mode 100644 index 0000000000000000000000000000000000000000..d407f11353b9dfe635e4c2db0558840b03024a79 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9798026.a1 @@ -0,0 +1,2 @@ +T1 Title 0 159 Previous infection with Helicobacter pylori is the primary determinant of spontaneous gastric hypoacidity in human immunodeficiency virus-infected outpatients. +T2 Paragraph 160 1282 To investigate the incidence and demographics of gastric hypoacidity among persons infected with human immunodeficiency virus (HIV), 146 asymptomatic subjects were evaluated with use of a radiotelemetry device (Heidelberg capsule). Gastric hypoacidity (minimum gastric pH of > or = 3) occurred in 24 subjects (17%). Demographic characteristics, CD4 cell counts, and Helicobacter pylori serological status were evaluated for an association with gastric pH. Subjects with hypoacidity were more likely to have positive H. pylori serology than were subjects without hypoacidity (15 of 24 vs. 23 of 74, respectively; P = .004). Multivariate analysis indicated that a positive H. pylori serology was the most significant predictor of hypoacidity, accounting for an increase in gastric pH of 39%. A history of injection drug use, heterosexual transmission of HIV, and male gender were also associated with an elevated gastric pH. CD4 cell counts did not contribute to predictions of gastric pH. A history of H. pylori infection is relatively common in HIV-positive black and Hispanic populations and is a predictor of gastric pH. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9798026.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9798026.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1ec8b75e53c933d8f1e13e6e01b630dd8b62189 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9798026.txt @@ -0,0 +1,3 @@ +Previous infection with Helicobacter pylori is the primary determinant of spontaneous gastric hypoacidity in human immunodeficiency virus-infected outpatients. +To investigate the incidence and demographics of gastric hypoacidity among persons infected with human immunodeficiency virus (HIV), 146 asymptomatic subjects were evaluated with use of a radiotelemetry device (Heidelberg capsule). Gastric hypoacidity (minimum gastric pH of > or = 3) occurred in 24 subjects (17%). Demographic characteristics, CD4 cell counts, and Helicobacter pylori serological status were evaluated for an association with gastric pH. Subjects with hypoacidity were more likely to have positive H. pylori serology than were subjects without hypoacidity (15 of 24 vs. 23 of 74, respectively; P = .004). Multivariate analysis indicated that a positive H. pylori serology was the most significant predictor of hypoacidity, accounting for an increase in gastric pH of 39%. A history of injection drug use, heterosexual transmission of HIV, and male gender were also associated with an elevated gastric pH. CD4 cell counts did not contribute to predictions of gastric pH. A history of H. pylori infection is relatively common in HIV-positive black and Hispanic populations and is a predictor of gastric pH. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9864452.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9864452.a1 new file mode 100644 index 0000000000000000000000000000000000000000..c49e6744773ce0df57023f378884c6e401d10872 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9864452.a1 @@ -0,0 +1,2 @@ +T1 Title 0 89 Isolation and properties of extracellular alkaline phosphatase from Bacillus intermedius. +T2 Paragraph 90 956 Alkaline phosphatase (APase) was isolated from the culture liquid of the streptomycin-resistant strain of Bacillus intermedius S3-19 and purified as a homogeneous preparation by ion-exchange chromatography and FPLC. Electrophoresis and gel-filtration revealed that the active enzyme is a monomer with molecular weight of 46-47 kD. The enzyme possessed phosphomonoesterase and phosphodiesterase activities with maximal levels at pH 9.5 and 55 degreesC and was stable until 60 degreesC at pH 8.0-10.0. The isolated APase exhibits a broad specificity towards a wide variety of substrates. The effect of divalent metal ions and other reagents on its catalytic activities was studied. It was concluded that alkaline phosphatase of B. intermedius is similar to the secreted alkaline phosphatases from other Bacillus species in its physicochemical and catalytic properties. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9864452.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9864452.txt new file mode 100644 index 0000000000000000000000000000000000000000..c2970a6c08910bd679f6a0ef6bb2fdc986254d47 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-9864452.txt @@ -0,0 +1,3 @@ +Isolation and properties of extracellular alkaline phosphatase from Bacillus intermedius. +Alkaline phosphatase (APase) was isolated from the culture liquid of the streptomycin-resistant strain of Bacillus intermedius S3-19 and purified as a homogeneous preparation by ion-exchange chromatography and FPLC. Electrophoresis and gel-filtration revealed that the active enzyme is a monomer with molecular weight of 46-47 kD. The enzyme possessed phosphomonoesterase and phosphodiesterase activities with maximal levels at pH 9.5 and 55 degreesC and was stable until 60 degreesC at pH 8.0-10.0. The isolated APase exhibits a broad specificity towards a wide variety of substrates. The effect of divalent metal ions and other reagents on its catalytic activities was studied. It was concluded that alkaline phosphatase of B. intermedius is similar to the secreted alkaline phosphatases from other Bacillus species in its physicochemical and catalytic properties. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..4fe1fb1cf9d080a9840afd02150fce70da1e538f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-000.txt @@ -0,0 +1,2 @@ +In semi-hard cheeses, like Gouda or Cheddar, degradation of protein +into amino acids and subsequent conversion of amino acids by Lactococcus sp. and/or Lactobacillus sp. is crucial for flavour development (Smit et al. 2000; Visser 1993). Other examples of microorganisms involved in the formation of very diverse flavours in dairy products are Propionibacterium sp. in Maasdammer and Swiss-type cheeses (Sarkar and Misra 1995), Streptococcus sp., Lb. bulgaricus spp. and Bifidobacterium sp. in (health-promoting) yoghurts (Nosova et al. 2000; Zourari et al. 1992; Hugenholtz et al. 2000), and Arthrobacter, Brevibacterium and Corynebacterium sp. in surface-ripened cheeses (Bockelmann and Hoppe Seyler 2001). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..5245eb154671fe3530a29bc590f95b1409f460fa --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-001.txt @@ -0,0 +1,2 @@ +A number of transaminases with different substrate specificities +have been described (Engels et al. 2000; Yvon et al. 1998). These enzymes are reported for several Lactococcus lactis, Lactobacillus, Streptococcus and Propionibacterium species (Engels et al. 2000; Hansen et al. 2001; Thierry et al. 2002). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-002.txt new file mode 100644 index 0000000000000000000000000000000000000000..19291ff70597eb5e0edea489c2c8de76bbc0a818 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-002.txt @@ -0,0 +1,4 @@ +Corynebacterium ammoniagenes B1506 and Lactococcus lactis + B1157 were able to produce considerable amounts of 3-methylbutanal and +3-methylbutanol, while all other strains tested, including those closely + related to the two above, lacked this ability. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-003.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-003.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-003.txt new file mode 100644 index 0000000000000000000000000000000000000000..7f3ba223b74ae20209d7ab511c71ace56623065f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-003.txt @@ -0,0 +1,8 @@ +First, the activity of branched-chain transaminase was measured by +incubating CFE with leucine and an excess of the co-substrate, +α-ketoglutarate. The transaminase activity was found to be present in +all microorganisms tested (Fig. 3A). The highest variation was observed in the Lactobacillus genus. L. lactis spp. and Streptococcus thermophilus + showed the highest specific transaminase activity towards leucine and +therefore potentially produce the highest concentrations of +α-ketoisocaproic acid, which is the substrate for the formation of +3-methylbutanal. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-004.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-004.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-004.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-004.txt new file mode 100644 index 0000000000000000000000000000000000000000..cf4e4fe25d3700678e8565a5922cc8bd1989ead0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-004.txt @@ -0,0 +1 @@ +In most anaerobic strains belonging to the genera Lactococcus, Lactobacillus, Streptococcus and Leuconostoc, specific hydroxy acid dehydrogenase activity was found to be 5- to 10-fold higher than the transaminase activity.The decarboxylation of α-ketoisocaproic acid leads to the formation of 3-methylbutanal (Fig. 1). This decarboxylase activity was found in only two of the strains tested (B1157 and B1506) (Fig. 3C). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-005.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-005.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-005.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-005.txt new file mode 100644 index 0000000000000000000000000000000000000000..8168638e9e263951e64e5ef7e81f0ff6b67c5816 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-005.txt @@ -0,0 +1,3 @@ +In line with this, L. lactis subsp. cremoris B697, a strain with a high hydroxy acid dehydrogenase activity compared to the transaminase activity (Fig. 3A, B), did not produce detectable amounts of 3-methylbutanal. Interestingly, L. lactis subsp. cremoris strain B1157, a strain reported to produce high levels of 3-methylbutanal (Ayad et al. 1999, 2000), + has transaminase and hydroxy acid dehydrogenase activities +approximately similar to those of strain B697. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-006.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-006.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-006.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-006.txt new file mode 100644 index 0000000000000000000000000000000000000000..97ea8115df18d3032ba3a6a9d9e6b744e503d5a6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-006.txt @@ -0,0 +1,5 @@ +Nevertheless, only two strains were found to be able to produce + 3-methylbutanal or the reduced aldehyde, 3-methylbutanol. This +3-methylbutanal production clearly correlated with the presence or +absence of decarboxylase activity. Again the difference between L. lactis B1157 and B697 is illustrative (Fig. 3), + with B1157 being decarboxylase-positive and B697 negative. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-007.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-007.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-007.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-007.txt new file mode 100644 index 0000000000000000000000000000000000000000..f9477a417ea3b77692d6d73749d96888a352464d --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-14624315-007.txt @@ -0,0 +1,5 @@ +This could also be seen from the data: in L. lactis subsp. cremoris B1157 about 80% of the flavour formed in the incubation experiment was 3-methylbutanal, while for C. ammoniagenes B1506 this percentage was about 20% (data not shown).Taken + together, our results indicate that various strains and species used in + the dairy industry vary significantly in the enzyme activities involved + in the conversion of the amino acid leucine into flavour components +like 3-methylbutanal. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa84ab5d1996643655216b720c3561642f2b0111 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-000.txt @@ -0,0 +1,18 @@ +In + the dairy industry, exopolysaccharides (EPS) contribute to improving +the texture and viscosity of cheese and yoghurt and also receive +increasing attention because of their beneficial properties for health. +For lactic acid bacteria, the production of EPS is well studied. +However, for dairy propionibacteria the biosynthesis of EPS is poorly +documented. A polysaccharide synthase-encoding gene was identified in +the genome of Propionibacterium freudenreichii subsp. shermanii TL 34 (CIP 103027). This gene best aligns with Tts, the polysaccharide synthase gene of Streptococcus pneumoniae + type 37 that is responsible for the production of a β-glucan capsular +polysaccharide. PCR amplification showed the presence of an internal +fragment of this gene in twelve strains of P. freudenreichii subsp. shermanii + with a ropy phenotype in YEL+ medium. The gene sequence is highly +conserved, as less than 1% of nucleotides differed among the 10 strains +containing the complete gtf gene. The same primers failed to detect the gene in Propionibacterium acidipropionici strain TL 47, which is known to excrete exopolysaccharides in milk. The presence of (1→3, 1→2)-β-d-glucan capsule was demonstrated for 7 out of 12 strains by agglutination with a S. pneumoniae-type + 37-specific antiserum. The presence of mRNA corresponding to the gene +was detected by RT-PCR in three strains at both exponential and +stationary growth phases. This work represents the first identification +of a polysaccharide synthase gene of P. freudenreichii, and further studies will be undertaken to elucidate the role of capsular EPS. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..37d13c8b1375c6da5da83754b0994b7e1e1f26e5 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-18524407-001.txt @@ -0,0 +1,7 @@ +Dairy + propionibacteria have been shown to be able to produce EPS, although +the biosynthesis mechanism involved is poorly documented. Recently, the +structure of excreted EPS by P. freudenreichii subsp. shermanii was studied by NMR, showing a homopolysaccharide with the structure [→3)[β-d-Glcp-(1→2)]-β-d-Glcp-(1→] ( Nordmark et al., 2005). + To date, no data are available concerning the genes responsible for EPS + biosynthesis by propionibacteria. In this work, 20% of the tested +strains of P. freudenreichii subsp. shermanii, including the sequenced type strain TL 34 ( Meurice et al., 2004), were identified as “ropy-producing”, suggesting the production of EPS. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..7259889bfac48e5dc060321bd26f0fed0f2ffb65 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-000.txt @@ -0,0 +1,7 @@ +Bands showing different intensity and identified as Staphylococcus, Micrococcus, Psychrobacter, Enterococcus and Brevibacterium + species were detected on the surface of cheeses. The cluster analysis +showed that Gorgonzola, Taleggio and Formaggio di Fossa cheeses present +high similarity in their surface bacterial composition while major +differences in the DGGE profiles were observed in Scimudin and Casera. +The molecular taxonomical identification among the Gram positive +isolates, reveals the presence of the following bacterial genera: Staphylococcus, Micrococcus, Macrococcus, Enterococcus, Lactobacillus, Carnobacterium, Leuconostoc, Brevibacterium, Corynebacterium, Brochothrix, Bacillus. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..0fadf361ca2d16ab306c6accbb1cb08769207e81 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-001.txt @@ -0,0 +1,5 @@ +In addition, the +production of growth factors by yeasts appears to promote the +development of a Gram positive, catalase positive, salt-tolerant +microbial communities composed mainly of coagulase-negative cocci (CNC) +and coryneform bacteria, belonging to genera such as Staphylococcus, Micrococcus, Brevibacterium, and Arthrobacter ( Bockelmann, 1999, Bockelmann et al., 1997, Corsetti et al., 2001, Eliskases-Lechner and Ginzinger, 1995a, Eliskases-Lechner and Ginzinger, 1995b and Valdés-Stauber et al., 1997) diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-002.txt new file mode 100644 index 0000000000000000000000000000000000000000..f060cbd74b2aef754486a480be08ab269f47ae42 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-002.txt @@ -0,0 +1 @@ +Contamination of some varieties of soft smear cheeses with Listeria monocytogenes is an important problem for the consumer's health, leading to industrial substantial financial losses ( Cocolin et al., 2009, de Cesare et al., 2007, Lomonaco et al., 2009 and Rudolf and Scherer, 2001). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-003.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-003.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-003.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c7d1e245700683885eecbdba1e721dc2f7f6bd4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-003.txt @@ -0,0 +1,3 @@ +DGGE bands (a, b, e, g, h, i) corresponding to Psychrobacter species were evident in Formaggio di Fossa, Gorgonzola, Taleggio and Scimudin. DGGE band “d” identified as Staphylococcus equorum was present in all cheese profiles, with the most intense signal in Casera. Micrococcus luteus (band “l”) was detected in all samples except for Casera cheese, while the band for S. vitulinus (band “c”) was only evident in Scimudin. A faint DNA band of Lactobacillus delbrueckii (band “f”) could be detected in Casera and Gorgonzola cheeses, as well as faint Streptococcus thermophilus band (“k”) in the Casera and Formaggio di Fossa samples. Enterococcus faecium + band (band “j”) was detected in Casera cheese, and showed less +intensity in Formaggio di Fossa and Scimudin cheeses. DGGE bands of Brevibacterium casei (bands “n”) and B. linens (band “m”) could only be observed in Casera cheese surface. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-004.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-004.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-004.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-004.txt new file mode 100644 index 0000000000000000000000000000000000000000..13fea4a2a451a86edf8c07515739df10038a7055 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-004.txt @@ -0,0 +1,6 @@ +Bacterial enumeration revealed +the presence of a large community of Staphylococcus and micrococci-corynebacteria groups on the cheese surfaces. Although E. faecium DNA was present in Formaggio di Fossa, no presumptive enterococci were found on Enterococcus + selective agar (SB), though they were detected in different amounts in +Casera, Taleggio, Gorgonzola and Scimudin cheeses. Lactobacilli were +also detected using Rogosa agar in all cheese surfaces in a range of 104–106 CFU/cm2. The counts obtained on Pseudomonas agar were high in Gorgonzola, Scimudin and Taleggio surfaces (108 CFU/cm2), while in Casera samples the Pseudomonas values were three log units lower, and were absent (< 100) in Formaggio di Fossa.Table 3. + Results of the enumeration of the bacterial groups on cheese surfaces by plating. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-005.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-005.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-005.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-005.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0bfba5b3a0e5b95cc75a1cc4a3c6626a5aa4c24 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-005.txt @@ -0,0 +1,4 @@ +When V3 region of 16S rRNA gene +motility from the isolates was compared with those of the reference +strains on DGGE gels, several Staphylococcus were identified, mainly S. saprophyticus, S. equorum, S. vitulinus and S. caprae species. E. faecalis, E. faecium, B. linens, Corynebacterium flavescens were also frequently isolated. M. luteus + was only isolated from Scimudin cheese. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-006.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-006.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-006.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-006.txt new file mode 100644 index 0000000000000000000000000000000000000000..439c08d84da0bbab930ba019ac30867c699b5aa2 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-006.txt @@ -0,0 +1,12 @@ +S. saprophyticus strains analysed ( Fig. 2A), + at a similarity level of 60%; (i) Cluster 1 (S of 65%) containing two +strains from Taleggio and Scimudin cheeses, (ii) Cluster 2 (S of 78%) +only contained strains from Gorgonzola cheese, (iii) Cluster 3 (S of +65%) included ten strains, of which 4 were isolated from Taleggio and +Casera cheeses, and one each from Scimudin and Gorgonzola, and (iv) +Cluster 4 (S of 80%) including three strains, of which one was from +Taleggio and two from Scimudin cheeses. The cluster analysis of 23S. equorum strains ( Fig. 2B) + shows two main clusters (i) Cluster 1 (S of 84%) containing strains +from Taleggio (4), Scimudin (6), Casera (5) and Gorgonzola (1) cheeses +and (ii) Cluster 2 (S of 87%) including 4 strains from Gorgonzola, 2 +from Scimudin and only one from Taleggio. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-007.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-007.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-007.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-007.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f7df2a08c36c032946d95c88dbb63e26964ebb9 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-007.txt @@ -0,0 +1,5 @@ +Despite + the different production technologies and geographical origin, the +surface microbiota of Formaggio di Fossa, Gorgonzola and Taleggio +cheeses share common features. Common DGGE bands originated by P. celer, P. aquimaris, P. glacincolaus, S. equorum, and M. luteus + were identified. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-008.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-008.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-008.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-008.txt new file mode 100644 index 0000000000000000000000000000000000000000..738195f2b4f9f4bf8b582fec293b3f3313036cab --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-008.txt @@ -0,0 +1,3 @@ +The culture independent analysis of +the white mould rind, Scimudin cheese, revealed as major bands M. luteus and P. glacincolaus and the presence of S. vitulinus. DGGE analysis of Casera Valtellina, a cheese characterized by low water activity of the rind, showed a surface composed by S. equorum, B. linens and B. casei + as the main bacterial species. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-009.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-009.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-009.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-009.txt new file mode 100644 index 0000000000000000000000000000000000000000..611e07b6b08dcb8cb3193b7ce220fc321d1007e7 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-009.txt @@ -0,0 +1,4 @@ +B. linens + was only isolated from the Casera, Gorgonzola and Scimudin cheese +surfaces, confirming the more recent information that this species is +not the most important bacterium on smear cheeses. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-010.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-010.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-010.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-010.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae34b24413ec44487076bc3b7b54ac1b3764e6bf --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-010.txt @@ -0,0 +1 @@ +With regard to the Corynebacterium species, C. casei and C. variabilis were those more commonly isolated from the cheese rinds ( Brennan et al., 2002, Mounier et al., 2005 and Rea et al., 2007). C. flavescens was only found on the rind of Gorgonzola and Scimudin cheeses. This species was also isolated by Brennan et al. (2002) on the surface of Gobbeen cheese, though only once during the ripening. C. flavescens produced a yellow pigment and together with C. casei, C. variabile, and C. ammoniagenes are considered dairy species ( Denis and Irlinger, 2008). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-011.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-011.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-011.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-011.txt new file mode 100644 index 0000000000000000000000000000000000000000..18ffc850e2237c0352de02e0059a92f570665fd7 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-011.txt @@ -0,0 +1,9 @@ +Regarding the lactic acid bacterial group (LAB), Lactobacillus was seen to be present in different numbers depending of the cheese surface. Dolci et al. (2009) detected Lactobacillus counts of 105–107 CFU/cm2 on Fontina cheese surface after 90 days of ripening and Cocolin et al. (2009) + reported that lactococci and lactobacilli, dominated the microbial +ecology of Gorgonzola rind. Our results showed that the species L. curvatus for example was only isolated from Taleggio rind and L. brevis + was isolated from the surface of Gorgonzola and Scimudin cheeses. In +particular most of the surface isolates from Formaggio di Fossa cheese +were identified as L. acidipiscis, a Gram positive rod, +microaerophilic, able to grow in 10–12% (w/v) NaCl. This species +originally isolated from fermented fish, and characterized by Tanasupawat et al. (2000), was recently reported to be present in Greek cheese (Asteri et al., 2009). Enteroccocci were present in larger numbers on Scimudin (107 CFU/cm2) and Gorgonzola (105 CFU/cm2) surfaces than on Fontina rind (104 CFU/cm2) as reported by Dolci et al. (2009) while Cocolin et al. (2009) obtained diverse enterococci counts, with variation between 103–108 CFU/g + within the 18 samples of Gorgonzola rinds analyzed. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-012.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-012.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-012.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-012.txt new file mode 100644 index 0000000000000000000000000000000000000000..934cc077eac496cb7529985b479b344aa82bfce4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-012.txt @@ -0,0 +1,3 @@ +Deetae et al. (2009) reported that Gram negative bacteria including Microbacterium foliorum, Psychrobacter sp. and Proteus vulgaris, + showed a strong potential for producing aroma compounds with pronounced + “cheese” notes such as volatile sulphur compounds. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-013.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-013.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-013.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-013.txt new file mode 100644 index 0000000000000000000000000000000000000000..11593b66b5c5c8ed5ba0d05b53fb64914300a22b --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-013.txt @@ -0,0 +1,2 @@ +In addition, +several authors reported that Pseudomonas, and other Gram-negative bacteria such as Halomonas and members of the Enterobacteriaceae family may be very common on the cheese surface ( Chaves-Lopez et al., 2006, Deetae et al., 2009, Larpin, 2006, Morales et al., 2003, Mounier et al., 2005 and Rea et al., 2007). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-014.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-014.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-014.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-014.txt new file mode 100644 index 0000000000000000000000000000000000000000..0cd6f7ef59d0f2d81989b2552fcceab4a7267ac4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-014.txt @@ -0,0 +1,3 @@ +An example of this fact is the +presence of Psychrobacter DNA on the surface of Formaggio di +Fossa cheese. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-015.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-015.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-015.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-015.txt new file mode 100644 index 0000000000000000000000000000000000000000..085bd1b59383a5a10177d3fe959f5e4d98121a03 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-20167385-015.txt @@ -0,0 +1,3 @@ +Also bands detected by DGGE were originating from S. thermophilus and L. delbrueckii, + bacteria involved in the primary stage of cheese fermentation, but not +found among the analysed isolates. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..9852c7bce8cd701811ccb24ff77f2995e58f6d50 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-000.txt @@ -0,0 +1 @@ +Ecological and aromatic impact of two Gram-negative bacteria (Psychrobacter celer and Hafnia alvei) inoculated as part of the whole microbial community of an experimental smear soft cheese diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..22ee0d831e609168745757cce149047613d0e3e6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-001.txt @@ -0,0 +1,10 @@ +Results showed that P. celer was able to successfully implant +itself in cheese, regardless of its inoculation level. However, when it +was inoculated at a high level, the bacterial biodiversity was +drastically lowered from day 25 to the end of ripening. Overall, the +presence of P. celer led to the higher production of volatile +aroma compounds such as aldehydes, ketones and sulfur compounds. +Regardless of its inoculation level, H. alvei barely affected +the growth of the bacterial community and was subdominant at the end of +ripening. It influenced total volatile aroma compound production with +volatile sulfur compounds being the most abundant. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-002.txt new file mode 100644 index 0000000000000000000000000000000000000000..16a64a5ccafcea26a4ed8b674a1b4a298bb374b4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-002.txt @@ -0,0 +1,8 @@ +During milk coagulation, lactic acid bacteria such as Lactococcus lactis acidify curd by metabolizing the lactose into lactate. Then, at the beginning of the ripening process, acid-tolerant yeasts (Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces sp. and Yarrowia lipolytica) dominate the surface and metabolize lactate ( Corsetti et al., 2001, Mounier et al., 2005 and Larpin et al., 2006). + This utilization leads to the deacidification of the cheese surface, +allowing the development of less acid-tolerant, aerobic or facultative +anaerobic, catalase-positive, halo-tolerant Gram-positive bacteria. +Bacteria such as Brevibacterium aurantiacum, Corynebacterium, Arthrobacter and Staphylococcus spp. + are the most common species found on the cheese surface and play a role + during the ripening step in terms of aroma compounds and color +development of smear surface-ripened cheese ( Corsetti et al., 2001, Brennan et al., 2002, Rea et al., 2007, Goerges et al., 2008 and Mounier et al., 2005). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-003.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-003.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-003.txt new file mode 100644 index 0000000000000000000000000000000000000000..83e377ccf059bcc8b7e922383250ca7c8781be7d --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-003.txt @@ -0,0 +1 @@ +They sometimes constitute more than 40% of the bacterial microbiota of some smear cheese surfaces ( Maoz et al., 2003, Mounier et al., 2005, Mounier et al., 2009 and Larpin-Laborde et al., 2011). The most common genera are Psychrobacter that includes psychrotrophic species, Halomonas, frequently isolated from marine environments, and Hafnia, of which some strains are commercialized and inoculated during cheese-making ( Mounier et al., 2005, Mounier et al., 2009 and Rea et al., 2007). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-004.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-004.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-004.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-004.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a3438c9cc940c030c07dad2d911c925c9738185 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-004.txt @@ -0,0 +1,10 @@ +Gram-negative + bacteria are known to constitute an enzymatic reservoir because they +possess proteolytic enzymes that degrade casein and peptides, leading to + the production of free amino acids in cheese and accelerating ripening (Chaves-Lopez et al., 2006, Morales et al., 2003 and Corsetti et al., 1998). Morales et al. (2005) showed that some species of Pseudomonas + spp. of dairy origin can produce a large variety of volatile compounds +such as alcohols or esters and, consequently, may have a negative effect + on the organoleptic characteristics of cheeses. Other bacteria +belonging of the Enterobacteriaceae family such as Hafnia alvei are able to produce flavor compounds ( Morales et al., 2004) but may also lead to stronger proteolysis, thus modifying the final texture of the cheese (Morales et al., 2003). A strain of Psychrobacter sp., isolated from cheese, was inoculated with a yeast at a high concentration in model cheese ( Deetae et al., 2009a). + This strain produced a large quantity of volatile aroma compounds and, +more particularly, sulfur compounds. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-005.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-005.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-005.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-005.txt new file mode 100644 index 0000000000000000000000000000000000000000..87431da96d0ee71e3d88b00ae2de927b4a7b094c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-005.txt @@ -0,0 +1,9 @@ +The strain studied, Proteus vulgaris + 1 M10, produced high concentrations of flavor compounds, +particularly branched-chain alcohols, during the ripening process in a +model cheese. However, this strain has also been shown to exhibit some +potential risks for human health (Coton et al., 2012) even if no sanitary problems have been linked to the presence of this species as of this time.The objective of this study was to determine the capacity of colonization of two Gram-negative bacteria, Psychrobacter celer and H. alvei, + and their impact on the growth of other microbial populations and on +aroma compound production at the surface of experimental smear soft +cheese. These bacteria were isolated from cheeses and chosen on the +basis of their low potential sanitary risk evaluated in the study of Coton et al. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-006.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-006.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-006.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-006.txt new file mode 100644 index 0000000000000000000000000000000000000000..cb8bc138a99233643c4160b05fbd848812a1c939 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-006.txt @@ -0,0 +1,10 @@ +The strain S3 + and its protease-negative variant S3-, assigned to Lactococcus lactis sp. lactis, was used for cheese-making. The 11 microorganisms that composed the model community included seven bacteria — Lactobacillus casei FH1, Arthrobacter arilaitensis Re117, Corynebacterium casei Mu120, C. flavescens Mu128, C. variabile Mu129, Staphylococcus xylosus Com1 and S. equorum Mu2 — and four yeasts — D. hansenii DH68, G. candidum GC129, Y. lipolytica CI35 and K. lactis + KL65. This composition is representative of the diversity of smear soft + cheese. The microorganisms were originally isolated from Munster except + for Re117 (Reblochon), Com1 (unknown) and FH1 (St. Nectaire). The +Gram-negative bacteria studied, P. celer 91 and H. alvei + 2 920, isolated from Livarot and Munster cheese, respectively, were +chosen from a large cheese bacteria collection for their low level of +sanitary risk (sensitivity to 24 antibiotics, no production of biogenic +amines in synthetic media and no growth under anaerobic condition and at + 37 °C) (Coton et al., 2012). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-007.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-007.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-007.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-007.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ae8a7aa6cd9aac74a316420a76cb471ac8af725 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-007.txt @@ -0,0 +1,5 @@ +Growth + of two Gram-negative bacteria during ripening had no effect on the +growth of the yeasts studied (data not shown). All yeast communities, +with or without Gram-negative bacteria, reached viable cell numbers +above 7.9–8.0 log10 cfu/g after 5 days of ripening. D. hansenii followed by G. candidum dominated the cheese surface on day 5 with 7.6 log10 cfu/g and 7.1 log10 cfu/g, respectively. After day 5, G. candidum levels remained close to 7.8 log10 cfu/g while the D. hansenii population decreased by 1.0 to 1.5 log10 cfu/g between day 15 and day 35. Y. lipolytica levels slightly increased after day 5 and reached a maximum after 35 days with counts of 7.5 log10 cfu/g. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-008.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-008.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-008.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-008.txt new file mode 100644 index 0000000000000000000000000000000000000000..1881b1537e4332546455a1ce18823dc259358901 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-008.txt @@ -0,0 +1,4 @@ +At day 5, in the two +cheese ecosystems, C. flavescens dominated the cheese surface +with 6.4 log10 cfu/g. However, from day 15 to day 35, distribution of +bacterial species between the cheese without H. alvei (T) and the cheese with H. alvei (HA2) was different. In the absence of H. alvei, A. arilaitensis dominated the cheese surface with counts of 9.3 log10 cfu/g at day 35. With H. alvei in the cheese ecosystem, the maximal population of A. arilaitensis was 7.4 log10 cfu/g at day 35. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-009.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-009.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-009.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-009.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d36516c24188d43c6e3b721cad21f23f02658dd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-009.txt @@ -0,0 +1,2 @@ +When +inoculated at 2 log10 cfu/g, P. celer reached counts of 8.5 log10 cfu/g at the end of ripening and had a major effect on the counts and distributions of C. variabile/C. casei ( Table 1, T and PC2). These bacterial strains were not detected in the presence of P. celer in the cheese ecosystem. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-010.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-010.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-010.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-010.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a04bac80244eee5c56717f55210ac570a4c8a34 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-010.txt @@ -0,0 +1 @@ +In contrast, A. arilaitensis dominated the cheese surface microbiota with counts of 9.3 log10 cfu/g (85% of the total bacterial counts) when P. celer was not inoculated in the cheese. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-011.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-011.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-011.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-011.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f73d1f428012b8d26b24e3e24de94f475fe3a5a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-011.txt @@ -0,0 +1,8 @@ +The community containing H. alvei + (inoculated at a low or high level) produced the largest quantity of +aroma compounds – between 13 and 15 mg/kg of total aroma compounds – + primarily corresponding to sulfur compounds [methanethiol, dimethyl +disulfide (DMDS) and dimethyl trisulfide (DMTS)]. The overall production + of aroma compounds was enhanced when P. celer was inoculated at a high level: 8.1 mg/kg versus 4.5 mg/kg in the community without P. celer. + Mainly aldehydes (3-methylbutanal), ketones (2-heptanone, 2-nonanone, +2-pentanone) and sulfur compounds (DMDS) were produced ( Table 2). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-012.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-012.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-012.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-012.txt new file mode 100644 index 0000000000000000000000000000000000000000..a27158283555a3d1b201b5825e6889fb2779f34c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-012.txt @@ -0,0 +1,3 @@ +On the other hand, methylthiobutyrate, methyl ester octanoic acid, +benzeneacetaldehyde and 3-heptanone were only found in the community +with P. celer. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-013.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-013.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-013.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-013.txt new file mode 100644 index 0000000000000000000000000000000000000000..966017e6495d7ef0947c1e74a90ec2141dbc2836 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-013.txt @@ -0,0 +1 @@ +Psychrobacter sp. and Hafnia sp. are frequently detected in milk or smear cheeses ( Mayr et al., 2004, Hantsis-Zacharov and Halpern, 2007, Mounier et al., 2009, Abriouel et al., 2008 and Fontana et al., 2010). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-014.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-014.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-014.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-014.txt new file mode 100644 index 0000000000000000000000000000000000000000..b767ebbcb687778c1368b0c4540ef66bc16793a9 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-014.txt @@ -0,0 +1 @@ +In this paper, we show the colonization of P. celer and H. alvei in a complex cheese community for the first time and the contribution of these species to the flavor properties of the cheeses. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-015.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-015.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-015.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-015.txt new file mode 100644 index 0000000000000000000000000000000000000000..d4a4308af88805f9efe7abd887b4bcd7bf0ef5b3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-015.txt @@ -0,0 +1,3 @@ +D. hansenii, G. candidum, Y. lipolytica and A. arilaitensis + were dominant on the cheese surface at day 35 of ripening. These yeasts + were also the dominant species in Munster and Livarot cheeses ( Larpin et al., 2006), and it was previously shown that two French red-smear soft cheeses were largely dominated by A. arilaitensis ( Feurer et al., 2004). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/batch.xml b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-016.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/batch.xml rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-016.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-016.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-016.txt new file mode 100644 index 0000000000000000000000000000000000000000..929243daba4ed8805f02c423a05e08f21fee60f0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-016.txt @@ -0,0 +1,2 @@ +Consequently, the inoculation level of P. celer had an impact +on the production of volatile aroma compounds. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-017.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-017.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-017.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-017.txt new file mode 100644 index 0000000000000000000000000000000000000000..655a077178ee470ce46a2e58f0924217f190f26a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-017.txt @@ -0,0 +1,4 @@ +The +most abundant aroma compounds produced during cheese ripening in the +presence of P. celer were branched-chain aldehydes such as +3-methyl butanal and ketones. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-018.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-018.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-018.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-018.txt new file mode 100644 index 0000000000000000000000000000000000000000..973d592e4e2d0e66f1b3f8cbfe8904b664494859 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-018.txt @@ -0,0 +1,5 @@ +These branch-chain aldehydes and alcohols are +associated with fruity tastes and are considered to be potent odorants +in Camembert ( Curioni and Bosset, 2002). The production of 3-methylbutanal and 3-methylbutanol has already been reported in P. phenylpyruvica in a cured meat model system ( Moller et al., 1998), and in Psychrobacter sp. in a model cheese ( Deetae et al., 2009a). When P. celer + was present in cheeses, 2-pentanone, 2-heptanone and 2-nonanone were +produced in greater quantities than in the control cheeses. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-019.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-019.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-019.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-019.txt new file mode 100644 index 0000000000000000000000000000000000000000..aba51bdaac1943b8cb2e3759da26506e6ecb4d91 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-019.txt @@ -0,0 +1,3 @@ +It is possible that P. celer was able to degrade acids with a lipase activity. No information is available on the lipolytic system of this species.H. alvei + was able to successfully establish itself in the community at the +beginning of ripening, regardless of the inoculation level. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-020.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-020.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-020.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-020.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a28d094902e75c90706c813e1d7057c93b956da --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-020.txt @@ -0,0 +1 @@ +However, some recent studies have reported the presence of H. alvei at the end of ripening of Livarot cheese ( Mounier et al., 2009) and a Spanish farmhouse cheese, but in small counts of approximately 105 ufc/g (Abriouel et al., 2008). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-021.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-021.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-021.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-021.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf1b49e78caf97f6135877d28d6709c1279a6e81 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-021.txt @@ -0,0 +1 @@ +C. variabile/C. casei were also detected in a Gubbeen cheese and were dominant among bacterial species ( Mounier et al., 2005). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-022.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-022.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-022.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-022.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c7633635b45702887b4c7593dd11df2be7062c6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-022.txt @@ -0,0 +1,5 @@ +The presence of H. alvei + in the cheese community, regardless of its inoculation level, had a +significant effect on the volatile compound content of cheeses with a +higher production of total volatile compounds, mainly volatile sulfur +compounds (VSC). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-023.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-023.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-023.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-023.txt new file mode 100644 index 0000000000000000000000000000000000000000..e87c307d5ebb5d9a434ca2ea7c3e1aa6cb96fb69 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-22177851-023.txt @@ -0,0 +1,8 @@ +In our cheese model, +methanethiol, DMDS, DMTS and DMS should significantly contribute to +flavor because of their very low perception thresholds and their garlic +or very ripe cheese notes ( Sablé and Cottenceau, 1999). The high capacity of H. alvei + to produce VSC is probably the result of its high capacity to convert +methionine or cysteine into aroma compounds with a transamination or +deamination activity. It was previously shown that VSC (methanethiol, +DMDS, DMTS) were produced by H. alvei but grown on beef models ( Dainty et al., 1989). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..a811aec33ac437c39feeddfcd9fc4afeaff48643 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-000.txt @@ -0,0 +1,12 @@ +For + studying the microbiota of four Danish surface-ripened cheeses produced + at three farmhouses and one industrial dairy, both a culture-dependent +and culture-independent approach were used. After dereplication of the +initial set of 433 isolates by (GTG)5-PCR fingerprinting, 217 bacterial +and 25 yeast isolates were identified by sequencing of the 16S rRNA gene + or the D1/D2 domain of the 26S rRNA gene, respectively. At the end of +ripening, the cheese core microbiota of the farmhouse cheeses consisted +of the mesophilic lactic acid bacteria (LAB) starter cultures Lactococcus lactis subsp. lactis and Leuconostoc mesenteorides as well as non-starter LAB including different Lactobacillus spp. The cheese from the industrial dairy was almost exclusively dominated by Lb. paracasei. The surface bacterial microbiota of all four cheeses were dominated by Corynebacterium spp. and/or Brachybacterium spp. Brevibacterium spp. was found to be subdominant compared to other bacteria on the farmhouse cheeses, and no Brevibacterium spp. was found on the cheese from the industrial dairy, even though B. linens was used as surface-ripening culture. Moreover, Gram-negative bacteria identified as Alcalignes faecalis and Proteus vulgaris + were found on one of the farmhouse cheeses. The surface yeast +microbiota consisted primarily of one dominating species for each +cheese. For the farmhouse cheeses, the dominant yeast species were Yarrowia lipolytica, Geotrichum spp. and Debaryomyces hansenii, respectively, and for the cheese from the industrial dairy, D. hansenii was the dominant yeast species. Additionally, denaturing gradient gel electrophoresis (DGGE) analysis revealed that Streptococcus thermophilus was present in the farmhouse raw milk cheese analysed in this study. Furthermore, DGGE bands corresponding to Vagococcus carniphilus, Psychrobacter spp. and Lb. curvatus on the cheese surfaces indicated that these bacterial species may play a role in cheese ripening. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1477ff528a9925dc9ab69e9bdeb6f895cfdcaaf --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-001.txt @@ -0,0 +1,6 @@ +Cheeses + harbour a complex microbiota characterised by a succession of different + microorganisms during milk coagulation and ripening [24]. During cheese ripening, lactic acid bacteria (LAB) starter cultures (e.g., mesophilic Lactocococcus lactis or thermophilic Streptococcus thermophilus) metabolise residual lactose and citrate to different aroma compounds [17]. + Later, LAB starter numbers decrease with cell death and their +subsequent lysis results in release of intracellular peptidases involved + in proteolysis of peptides to free amino acids [8, 31, 54]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-002.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c63cfa39b0a67c4f22462a1b41ea1cf2824ff84 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-002.txt @@ -0,0 +1,13 @@ +During the initial ripening period, yeasts (primarily Debaryomyces hansenii for semi-soft cheeses and additionally Geotrichum candidum for soft cheeses) and coagulase-negative staphylococci (Staphylococcus equorum) are present [3, 21, 26]. Generally, D. hansenii + and staphylococci on cheese surface are assumed to originate from the +cheese brine, which often is not changed or pasteurised between salting +of different batches [2, 3, 42]. For D. hansenii, Petersen et al. [46] showed that the dominating D. hansenii + strain on cheeses of the Danish Danbo type did not originate from the +added ripening culture, but from the dairy housemicrobiota present in +the ripening room. D. hansenii is important during +cheese ripening as it assimilates lactate and produces alkaline +metabolites such as ammonia thereby increasing pH of the cheese surface [23, 46], which enables the growth of the less acid tolerant bacterial microbiota, primarily Gram-positive coryneforms (Brevibacterium spp., Corynebacterium spp. and Microbacterium spp.) [4]. In addition, subpopulations of bacteria such as Gram-positive Marinilactibacillus spp. and Gram-negative Halomonas spp., Vibrio spp. and Proteus spp., and bacteria of the Enterobacteriaceae family have been reported to occur on cheese surfaces [14, 15, 25, 34, 35, 41, 50]. + The presence of Gram-negative bacteria was first hypothesised to be +indicative of hygienic problems. However, more recent results have shown + that they produce important cheese flavour compounds and thus might +contribute positively to the cheese ripening process [11]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-003.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-003.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-003.txt new file mode 100644 index 0000000000000000000000000000000000000000..d54efd2411d7c4e0f1fa9bcb9626cf54f13284cc --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-003.txt @@ -0,0 +1,6 @@ +The cheeses +from dairies A and C were primarily dominated by the LAB starter +cultures Leuconostoc mesenteroides and Lactococcus lactis subsp. lactis (Table 3). Furthermore, the cheeses from dairies A and C were dominated by the non-starter lactic acid bacteria (NSLAB) Lactobacillus paracasei, and for the cheese from dairy A, a minor group consisting of the NSLAB Lb. parabuchneri + was found. The interior bacterial isolates from the cheeses from +dairies B and D were primarily dominated by NSLAB. The cheese from dairy + B was dominated by a range of NSLAB including Lb. brevis, Lb. oligofermentans and Lb. farminis, whereas the cheese from dairy D was exclusively dominated by the NSLAB Lb. paracasei. Additionally, minor groups of the LAB starter cultures Lc. lactis subsp. lactis and Lc. lactis subsp. cremoris were found on the cheeses from dairies B and D, respectively. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-004.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-004.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-004.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-004.txt new file mode 100644 index 0000000000000000000000000000000000000000..75803b7bd1ba175330e3c7bcf8a363a2a939c7a2 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-004.txt @@ -0,0 +1,8 @@ +Most species were Gram-positive Actinobacteria with Corynebacterium casei and/or C. variabile as the predominant (Table 4). Additionally, the cheese from dairy A was dominated by high of numbers of Brachybacterium alimentarum. Various Brevibacterium species were found on the cheeses from the farmhouses (dairies A, B and C). B. permense was found on the cheese from dairy A, B. linens was found on the cheese from dairy B and B. aurantiacum was found on the cheese from dairy C. Brevibacterium + spp. could not be isolated on the cheese from dairy D. Furthermore, a +number of coagulase negative staphylococci were found, i.e., Staphylococcus saprophyticus on the cheeses from dairies B and D, and Staph. equorum on the cheeses from dairies C and D. Finally, a number of Gram-negative bacteria species including Proteus vulgaris and Alcaligenes faecalis was found on the cheese from dairy C.Figure 3 + shows the grouping of the surface yeast microbiota. The yeast surface +microbiota on the three farmhouse cheeses consisted of two to four +groups, whereas the cheese produced at the industrial dairy (dairy D) +consisted of only one single group. The cheese from dairy A was equally +dominated by Yarrowia lipolytica and Scopulariopsis brevicaulis. The yeast microbiota on cheese from dairy B was primarily dominated by Geotrichum spp., however, Kluyveromyces marxianus and Debaryomyces hansenii were additionally found in minor amounts. The cheese from dairy C was dominated by D. hansenii followed by a minor group of Geothrichum spp. Finally, the cheese from dairy D was entirely dominated by D. hansenii. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-005.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-005.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-005.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-005.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae786c590c76e91341110e33bac2575a22325ddc --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-005.txt @@ -0,0 +1,8 @@ +Culture + dependent isolation followed by genotypic identifications was basically + confirmed by the culture-independent method, DGGE (Fig. 4). Additionally, in the sample from the interior of the cheese from dairy A, DGGE band with strong intensity was identified as Streptococcus thermophilus. Furthermore, DGGE bands with strong intensities from the cheese surface samples were found to represent Vagococcus carniphilus (the cheeses from dairies A, B and D), Psychrobacter spp. (the cheeses from dairies A and C) and Lb. curvatus + (the cheese from dairy B) indicating that these bacterial species may +play a role in cheese ripening, even though they were not found by the +culture dependent approach. Unfortunately, several major DGGE bands in +the samples from the cheese surface could not be successfully +identified. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-006.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-006.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-006.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-006.txt new file mode 100644 index 0000000000000000000000000000000000000000..07c7d3dfcb7da00281b15f3951ebd792bb9d3e6c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-006.txt @@ -0,0 +1,5 @@ +Most significantly, the DGGE analysis +found that Streptococcus thermophilus is present in raw milk +cheese from dairy A, even though this thermophilic lactic acid bacterium + was not included in the mesophilic LAB starter culture used for +production of the raw milk cheese from dairy A. No culturable Str. thermophilus isolates was isolated from GM17 agar incubated at 37 °C (data not shown). In the study by Masoud et al. [38], Str. thermophilus was similarly detected by DGGE analysis without being added as part of the LAB starter culture. However, Masoud et al. [38] excluded that Str. thermophilus originates from the raw milk, as it was not identified in the DGGE profile of the raw milk. Even though the source of Str. thermophilus remains unknown, it is likely that Str. thermophilus may play an important role in milk acidification and cheese ripening as previously reported [36, 47, 48]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-007.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-007.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-007.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-007.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f99c9154e4fbeb9c73baeaa9a14e99ce968b75c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-007.txt @@ -0,0 +1,6 @@ +A difference in autolysis can be seen between the two subspecies of Lactococcus lactis. Lactococcus lactis subsp. lactis survives better in cheese than Lc. lactis subsp. cremoris [8]. + This fact even though not examined in the present study suggests that +the level of autolysis of the latter is the highest and thus explains +why Lc. lactis subsp. cremoris was generally +not found in the cheeses at the end of ripening, even though it was +added as a part of the primary LAB starter culture. Contrary, the NSLAB Lactobacillus paracasei was found in three out of four cheeses. This confirms the findings by Antonsson et al. [1], who found Lb. paracasei to be the main NSLAB in several Danbo cheeses. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-008.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-008.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-008.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-008.txt new file mode 100644 index 0000000000000000000000000000000000000000..d86d1a49bb827a07b4c21f573368507f4f464388 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-008.txt @@ -0,0 +1,2 @@ +These observations were confirmed in the present study as Brevibacterium linens was found to be subdominant compared to other bacteria on the farmhouse cheeses, and no Brevibacterium + spp. was found on the cheese from the industrial dairy. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-009.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-009.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-009.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-009.txt new file mode 100644 index 0000000000000000000000000000000000000000..067e44373fe5a18fdf3689e14f54181c5024ea2f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-009.txt @@ -0,0 +1,6 @@ +.B. linens was usually reported to be the most important bacterial species associated with cheese surfaces [13, 28, 49]. In the present study, various Brevibacterium spp. were found on the cheeses from the farmhouses (dairies A, B and C). B. linens and B. aurantiacum, + found on the cheeses from dairies B and C, respectively, have been used + for a long time as ripening cultures by the dairy industry [16], whereas the soil bacteria B. permense found on the cheese from dairy A, to our knowledge, has not previously been found on cheese.Several studies have now shown that Corynebacterium spp. is the most dominant bacterial species on surface-ripened cheeses [3, 6, 34]. C. casei and/or C. variabile + were found in the present study to be the predominant bacterial species + on the surfaces of the four cheeses and thus potentially important +during cheese ripening. These data confirm that strains of Corynebacterium spp. are candidates as ripening cultures for production of surface-ripened cheeses. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-010.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-010.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-010.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-010.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd720c97a2c3d12a60da99a9fd32d8ba76364fa6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-010.txt @@ -0,0 +1,7 @@ +In the present study, a significant Gram-negative bacterial microbiota consisting of Proteus vulgaris and Alcaligenes faecalis was found on cheese from dairy C. A previous study has focused on P. vulgaris as cheese ripening culture [11]. P. vulgaris + was found to produce important flavour notes including aldehydes and +acids, but influenced other surface-ripening cultures negatively. A. faecalis, which is found in soil, water, and environments in association with humans and generally considered non-pathogenic [19], has also previously been found on Livarot cheese [30].The present study confirms the presence of the marine bacteria Marinilactibacillus psychrotolerans + on cheese as this species was found on the surface of cheese D. Both +French and German cheeses have previously been reported to contain M. psychrotolerans [14, 34]. It was suggested that M. psychrotolerans + is transferred to the cheeses from the marine environments via sea +salt. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-011.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-011.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-011.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-011.txt new file mode 100644 index 0000000000000000000000000000000000000000..de3bb2552a4832bc4b990bba1dcb87e6f1f333f7 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-011.txt @@ -0,0 +1,4 @@ +The present study confirms that Debaryomyces hansenii and Geotrichum spp. are the dominating yeast species on surface-ripened cheeses. D. hansenii was found to be the dominating yeast species on the cheeses from dairies C and D, whereas Geotrichum spp. was found to dominate on the cheese from dairy B. On the cheese from dairy A, Yarrowia lipolytica was the dominating yeast species. Y. lipolytica + is a naturally developing yeast species on cheese surfaces, and has in +some cases been shown to rapidly outnumber other yeast species including + D. hansenii and Geotrichum spp. [33]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-012.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-012.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-012.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-012.txt new file mode 100644 index 0000000000000000000000000000000000000000..68516ae1f076fb43956a4d4425b43e8a1084d89e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-012.txt @@ -0,0 +1,5 @@ +Finally, the filamentous fungus Scopulariopsis brevicaulis was found in a high number on cheese A. S. brevicaulis has previously been found in Danish cheese [52], + and has been subject to spoilage of cheeses due to its high proteolytic + activity resulting in ammonia production and its production of +arsenical compounds, e.g., diethylarsine, which has a very +characteristic garlic-like odour [5]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-013.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-013.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-013.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-013.txt new file mode 100644 index 0000000000000000000000000000000000000000..326080ab443caa73329ea89aa83757c0fb38982a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23224222-013.txt @@ -0,0 +1,5 @@ +Culture +dependent identifications were basically confirmed by the culture +independent method DGGE, even though the latter technique proved the +presence of additional cultures including Str. thermophilus in cheese interiors as well as Vagococcus carniphilus, Psychrobacter spp. and Lb. curvatus + on cheese surfaces. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23290227-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23290227-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23290227-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23290227-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..b02700f33ce7baf670189f0a6c4734ae8779dfa5 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-23290227-000.txt @@ -0,0 +1,7 @@ +The Hafnia strains slightly reduced counts of Enterococcus faecalis (~− 0.5 log from day 1) and promoted Lactobacillus plantarum + growth (+ 0.2 to 0.5 log from day 8) in cheese. They produced +small amounts of putrescine (~ 1.3 mmol/kg) and cadaverine +(~ 0.9 mmol/kg) in cheese after 28 days, and did not +affect levels of volatile aroma compounds. Further work on H. alvei strain B16 showed that E. coli O26:H11, inoculated at 2 log CFU/ml, was inhibited by H. alvei + B16 inoculated at 6 log CFU/ml and not at +4.5 log CFU/ml. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..380ca625e561d22a414e976870a1afb18bd59c32 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-000.txt @@ -0,0 +1,4 @@ +For + most uninoculated microbial groups, their function in the context of +the community or in the production of cheese is largely unexplored. For +example, we identified two bacterial genera, Yaniella and Nocardiopsis, that have never been reported in food microbial ecosystems. We also find that halotolerant γ-Proteobacteria such as Vibrio, Halomonas, and Pseudoalteromonas that are typically associated with marine environments ( Holmström and Kjelleberg, 1999 and Reen et al., 2006) are widespread in cheese communities (Figure 2). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..670cee640075af954020718a173c8ddd4f9f4f5c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-001.txt @@ -0,0 +1 @@ +The fungus Galactomyces and four genera of Proteobacteria, both found in high abundance on moist bloomy rinds ( Figure S2C), are positively correlated with moisture (Figure 3D), whereas several other fungal and bacterial taxa (Scopulariopsis, Aspergillus, Actinobacteria, and Staphylococcus), which are abundant on dry natural rinds ( Figure S2C), are negatively associated with moisture (Figure 3D). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-002.txt new file mode 100644 index 0000000000000000000000000000000000000000..bebcae6735f22dafd5002fa0c08525fae9d17980 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-002.txt @@ -0,0 +1 @@ +Three mgl sequences with high similarity to the marine bacterium Pseudoalteromonas haloplanktis were recovered from three cheese metagenomes (highlighted in gray box). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-003.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-003.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-003.txt new file mode 100644 index 0000000000000000000000000000000000000000..42b6ff6c513fe8bfcc912e4adcef497a9ab80123 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-003.txt @@ -0,0 +1 @@ +However, to date, a cheese-associated mgl gene has only been identified in Brevibacterium linens ( Amarita et al., 2004, Monnet et al., 2010 and Schröder et al., 2011). Our metagenomic sequencing uncovered previously undescribed mgl sequences with high sequence similarity to various γ-Proteobacteria in cheeses from both Europe and North America ( Table S4B). Several of these previously undescribed mgl sequences belonged to Pseudoalteromonas spp. ( Figures 4C and S4B). We mapped metagenomic reads from three cheeses in which Pseudoalteromonas was abundant to the reference genome of Pseudoalteromonas haloplanktis (99.5% pairwise identity, Table S4C). Additionally, Pseudoalteromonas is known to have many cold-adapted enzymes that function in the polar seawater where this bacterium typically grows ( Médigue et al., 2005). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-004.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-004.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-004.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-004.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b06d07c2275bfabb1422d92ffc1d9dfc2a74f7f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-004.txt @@ -0,0 +1,6 @@ +From our metagenomic reads, we identified +homologs of a previously characterized secreted cold-adapted lipase and +protease ( de Pascale et al., 2008 and de Pascale et al., 2010) (Table S4C), + which could contribute to lipolysis and proteolysis and subsequent +flavor formation in cheeses. Collectively, these metagenomic insights +into the potential function of Pseudoalteromonas suggest that this and other uninoculated yet abundant microbes could play key roles in cheese rind microbial communities. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-005.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-005.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-005.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-005.txt new file mode 100644 index 0000000000000000000000000000000000000000..9de27f555b87e9f4064a4ca82517b3e28c4700ab --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25036636-005.txt @@ -0,0 +1,9 @@ +Intensive sampling of three batches of cheese over a + 63-day aging period demonstrates that patterns of succession are highly + reproducible (Figures 7A and 7B). At the first time point, the community consisted primarily of Proteobacteria, the bacterium Leuconostoc, and the yeast Candida, which can be found at low levels in raw milk ( Quigley et al., 2013). Whereas Candida persisted in the fungal portion of the community, the Proteobacteria were succeeded by Staphylococcus within the first 7 days. As the rinds matured, bacterial taxa Brevibacterium and Brachybacterium and fungal taxa Penicillium and Scopulariopsis + emerged consistently as a significant fraction of the community (on +average, >1% in mature cheeses). Principal coordinate analysis shows a + reproducible trajectory of all three communities over time ( Figure 7B), + with the most rapid changes in composition occurring at early time +points, which is consistent with previous observations of primary +succession ( Fierer et al., 2012 and Shade et al., 2013). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..da250bfe0f4d2b6877f6a6eeaea1e62641016b06 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-000.txt @@ -0,0 +1,6 @@ +Our + study provides data, which combined with publicly available genome +references, represents the most expansive catalog to date of +cheese-associated bacteria. Using this extended dairy catalog, we +revealed the presence in traditional cheese of dominant microorganisms +not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..aafdc672cf296c6bd013537b5450d109627c31af --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-001.txt @@ -0,0 +1 @@ +Several species, such as Corynebacterium casei, Microbacterium gubbeenense, Arthrobacter arilaitensis, Arthrobacter bergerei, Agrococcus casei, Mycetocola reblochoni and Vibrio casei appear to be endemic in the cheese habitat and the environment of cheese manufacturing [14–17]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-002.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-002.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-002.txt new file mode 100644 index 0000000000000000000000000000000000000000..99ca371d1ff9606555e5fcaae7df06bd6643c0b1 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-002.txt @@ -0,0 +1,6 @@ +In a first + example, we compared the genomic sequences of the four Arthrobacter strains isolated from cheese to that of 15 environmental isolates. Most bacteria of the genus Arthrobacter are isolated from environments such as soil, where they are considered to be ubiquitous [41]. + Interestingly, the four cheese strains share several properties that +may be linked to adaptation to the cheese habitat, such as a cluster of +five genes involved in the catabolism of D-galactonate, as already +described in Arthrobacter arilaitensis Re117 [20]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-003.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-003.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-003.txt new file mode 100644 index 0000000000000000000000000000000000000000..b359b0a3791ff1b05f64af1091ebd93ea5c7c305 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-003.txt @@ -0,0 +1,6 @@ +As a second example, we compared the genomes of two strains of Streptococcus infantarius + isolated from Western African fermented milks, sequenced in this work +(3AG and 11FA), with those of the type strain isolated from infant feces + (ATCC BAA-102), and of strain CJ18, isolated from Eastern African +fermented milk. The four strains contain each 1900–2000 genes and share +1567 genes. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-004.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-004.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-004.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-004.txt new file mode 100644 index 0000000000000000000000000000000000000000..c760f6e46f78e0f055b14a1b3e35d674199e4858 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-004.txt @@ -0,0 +1,4 @@ +Further study of the gene content of the two Western African Streptococcus infantarius + strains showed that these strains had acquired the ability to ferment +lactose through the LacZS system, as previously described for Eastern +African strain CJ18 [42]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-005.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-005.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-005.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-005.txt new file mode 100644 index 0000000000000000000000000000000000000000..8bb6315052a72c65776a351faba505cbc634964a --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-005.txt @@ -0,0 +1,3 @@ +Most prevalent microorganisms detected by metagenomic sequencing of three cheese surface samples +In the smear-ripened cheese E, the Arthrobacter arilaitensis GMPA29 reference genome was the most represented, as it corresponded to 19.8% of the total good quality reads, followed by Psychrobacter immobilis PG1 and Vibrio litoralis + B4, with 8.5 and 5.2% of the reads, respectively. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-006.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-006.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-006.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-006.txt new file mode 100644 index 0000000000000000000000000000000000000000..851b72df4daad5b1ea5d608154067565a0ddbba0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-006.txt @@ -0,0 +1,8 @@ +The reference strain Psychrobacter immobilis + PG1 was isolated from the dairy plant that produces the smear-ripened +cheese E, but two years earlier. The high proportion of perfect matches +with reference strain PG1 may thus be explained by the presence of an +offspring of this strain in cheese E. Many reads were also assigned to +the genomes of the yeasts Geotrichum candidum CLIB 918 and Debaryomyces hansenii CBS767.In the second smear-ripened cheese (cheese L), Pseudoalteromonas haloplanktis TAC125, Halomonas sp. 1 M45 and Psychrobacter celer + 91 were the three dominant reference bacteria, with 17.0%, 10.5% and +1.7% of the good quality matches, respectively. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-007.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-007.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-007.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-007.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8f3f0a94fc45c74a18fb669f94763343fa3dddf --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-007.txt @@ -0,0 +1,7 @@ +These data suggest that +the Halomonas strains present in the cheese sample are almost +identical to the reference strain. However, even though the reference +strain 1 M45 has also been isolated from a smear-ripened cheese of +the same protected designation of origin, it originated from another +manufacturing plant. More than fifty thousand reads were assigned to Providencia heimbachae + GR4. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-008.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-008.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-008.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-008.txt new file mode 100644 index 0000000000000000000000000000000000000000..50bef4f324ff4879ab72c28fd79f383b5095d439 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-008.txt @@ -0,0 +1,8 @@ +Surprisingly, more than 80 thousand +reads (~1% of the total good quality reads in cheese L) mapped to the Penicillium camemberti + FM 013 genome, with 97.7% of perfect match reads, even though this +species is not known to occur in smear-ripened cheeses. One may +hypothesize that this could result from cross-contamination due to the +manufacturing of mould-ripened cheese in the same plant.The surface of the blue-veined cheese G was dominated by a strain close to Arthrobacter bergerei Ca106 (18.6% of the reads, 99.2% perfect match reads). Like for the two other cheeses, Psychrobacter + species seem to be present in this cheese. Cheese G was probably +manufactured with a thermophilic lactic starter culture, since Streptococcus thermophilus and Lactobacillus delbrueckii species were the dominant lactic acid bacteria, in contrast to the two other cheeses, in which Lactococcus lactis was the dominant lactic acid bacterium. Strains related to other reference strains sequenced in the present study, such as Psychrobacter aquimaris, Brachybacterium tyrofermentans, Corynebacterium ammoniagenes, Brevibacterium antiquum, Microbacterium gubbeenense, Brochothrix thermosphacta and Marinilactibacillus psychrotolerans, were also present in the cheeses (>80% perfect match reads, see Additional file 14: Table S8). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-009.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-009.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-009.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-009.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bab340eb1e8f5d19e6c1dd70fc43c8029225d4c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-009.txt @@ -0,0 +1,6 @@ +As all the DNA present in the cheese +samples is sequenced, the high throughput sequencing may detect any type + of DNA (bacteria, archaea, eukaryotes and viruses), provided that +adequate references are used. Eukaryotes, such as Geotrichum candidum, Debaryomyces hansenii, and Penicillium roqueforti, + were found, which was not surprising, as these fungi are frequently +used in cheesemaking. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-010.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-010.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-010.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-010.txt new file mode 100644 index 0000000000000000000000000000000000000000..cac38391cd1f7e95198b1115795c313f6a0f7978 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-010.txt @@ -0,0 +1,6 @@ +High throughput sequencing allows higher resolution +quantitation and we have shown that we can recover even fairly minor +taxonomi groups, such as the Leuconostoc genus (see Additional file 14: Table S8), known to be part of the minority population in cheeses [48]. However, additional experiments may be needed to validate the identification and quantitation of low abundance populations.Presence + or absence of complete set of genes or of specific genes, and their +level of sequence homology allows also confirming characteristics of +particular strains. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-011.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-011.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-011.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-011.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e63ba4ac24449cdcb9799c0a661d4538af3ad9f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-25496341-011.txt @@ -0,0 +1,2 @@ +Several +of the corresponding microorganisms, such as Pseudoalteromonas, Halomonas, Vibrio, Marinilactibacillus and Psychrobacter are Gram-negative bacteria which had been previously detected in such cheeses[1, 2, 9, 12, 13, 28, 49–53], and also in a recent large amplicon sequencing study of the microbial composition of 137 different cheese rinds [33]. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-000.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-000.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..f108b41033c7e741aef767172b88d3c279297105 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-000.txt @@ -0,0 +1,5 @@ +Strains of Lactococcus lactis, +Lactococcus garvieae, Leuconostoc pseudomesenteroides, Leuconostoc +citreum, Lactobacillus sp, Carnobacterium mobile, Enterococcus faecalis, + Enterococcus faecium, Macrococcus caseolyticus and Hafnia alvei reduced STEC O26:H11 counts by 1.4–2.5 log cfu g−1 + and to a lesser extent STEC O157:H7 counts in pasteurized milk cheeses. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-001.a1 similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.a1 rename to corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-001.a1 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f76a8d7d569e3f760ed175b905f64b5ff4dca05 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-001.txt @@ -0,0 +1,4 @@ +The association of H. alvei, Lactobacillus plantarum and Lc. lactis + was the most inhibitory: after inoculation of this consortium into +milk, STEC O26:H11 and O157:H7, inoculated at +2 log cfu ml−1, were reduced by up to 3 log cfu g−1 in ripened cheese. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-002.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-002.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc275b5ff8881954a230246e7d50e4e29cbd9070 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-002.txt @@ -0,0 +1 @@ +Ln. pseudomesenteroides (M7), Ln. citreum (M2), Lb. plantarum (FH3), M. caseolyticus (RP8) have also been described as inhibiting Listeria monocytogenes ( Callon et al., 2011). Delbes-Paus et al. (2013) described a strain of H. alvei that can inhibit STEC O26:H11 in an uncooked pressed model cheese. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-003.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-003.txt new file mode 100644 index 0000000000000000000000000000000000000000..387746dd5addbd784cff2ca83f38914078614d92 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-003.txt @@ -0,0 +1,2 @@ +Cheeses with consortium (A) (composed of Lb. plantarum (FH3)+ H. alvei (B16)+ Lc. lactis (D5.3)) had higher levels of dextran-producing Leuconostoc, Lactococcus, Lactobacillus (due to the inoculation) and non-Pseudomonas Gram negative bacteria. They had lower counts of other non-inoculated groups such as Pseudomonas, + Gram positive catalase positive bacteria and yeasts. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-004.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-004.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-004.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-004.txt new file mode 100644 index 0000000000000000000000000000000000000000..644385021fcc0c41948b486416744da7a70af2c0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-26678131-004.txt @@ -0,0 +1,4 @@ +The cheese +inoculated with H. alvei (B16) alone was clearly different + from other cheeses, being associated with dairy product, salty and +butter aroma and a granular texture. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-000.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-000.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-000.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-000.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0733e7f36acd10946ed0b9134f0215ef12bd016 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-000.txt @@ -0,0 +1 @@ +The production of exopolysaccharides by LAB has been correlated to specific gene clusters tagged as eps or cps, located, as in Streptococcus thermophilus or Lactobacillus plantarum, mainly on the bacterial chromosome (Stingele et al. 1996; De Vuyst and Degeest 1999; Siezen et al. 2010) or in species such as Lactococcus lactis and Pediococcus damnsosus predominantly on plasmids (Van Kranenburg et al. 1997, 1999b). Remus et al. (2012) identified four cps genes clusters in the chromosome of L. plantarum WCFS1, which are associated with surface polysaccharide production. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-001.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-001.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac00b0dd9054f3b3d2fb6d1263df351a698faa43 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-001.txt @@ -0,0 +1,5 @@ +Several models of EPS assembly have been proposed for L. lactis (Kleerebezem et al. 1999; Laws et al. 2001), Streptococcus pneumoniae (Bentley et al. 2006), and Lactobacillus rhamnosus (Lebeer et al. 2009). + However, in addition to the “flippase-like” route, it could be +possible, in LAB, another route involving ABC transporters, although the + export-polymerization pathway for EPS production in LAB has not yet +been demonstrated. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-002.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-002.txt new file mode 100644 index 0000000000000000000000000000000000000000..7710ee9884417eb1b1e3eb655887c4ef312cdfa0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-002.txt @@ -0,0 +1 @@ +To date, among LAB, the yield of heteropolysaccharides is quite variable (Tsuda 2013); one of the largest EPS producers is L. rhamnosus RW-9595M (2775 mg/L) (Macedo et al. 2002) and Lactobacillus kefiranofaciens WT-2B (2500 mg/L) (Maeda et al. 2004a) followed by L. lactis subsp. cremoris (80–600 mg/L), S. thermophilus (50–350 mg/L), Lactobacillus delbrueckii subsp. bulgaricus (60–150 mg/L), Lactobacillus casei (50–60 mg/L) (Cerning 1995), and L. plantarum (140 mg/L) (Tsuda and Miyamoto 2010). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-003.a1 b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-003.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-003.txt b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-003.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd7403e594a07b5af42dede28a6a8416b43f5335 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner_train+dev/bionlp-st/BB-kb+ner-F-27020288-003.txt @@ -0,0 +1,3 @@ +For instance, Stack et al. (2010) reported that β-glucan produced by P. parvulus confers to Lactobacillus paracasei + higher survival during gastrointestinal passage or technological +process conditions. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json deleted file mode 100644 index 1f20b175ac96f4aebb00e5b7f001935375265e84..0000000000000000000000000000000000000000 --- a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json +++ /dev/null @@ -1,6847 +0,0 @@ -{ - "evaluation": { - "submission-id": 19532, - "global-evaluations": [ - { - "name": "Standard pairing", - "scorings": [ - { - "name": "Standard scoring", - "measures": [ - { - "name": "SER", - "value": 0.6627659574468086 - }, - { - "name": "ISER", - "value": 0.6014075495841331 - }, - { - "name": "Mismatches", - "value": 230.10181078209246 - }, - { - "name": "Matches", - "value": 1017.898189217908 - }, - { - "name": "Insertions", - "value": 384 - }, - { - "name": "Deletions", - 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a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_test/bionlp-st/BB-norm+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_test/bionlp-st/BB-norm+ner-F-26187841-001.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_test/bionlp-st/BB-norm+ner-F-26187841-001.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.txt rename to corpora/BioNLP-OST-2019/batches/BB19-norm+ner_test/bionlp-st/BB-norm+ner-F-26187841-001.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_test/bionlp-st/BB-norm+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_test/bionlp-st/BB-norm+ner-F-26187841-002.a1 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_test/bionlp-st/BB-norm+ner-F-26187841-002.txt similarity index 100% rename from corpora/BioNLP-OST-2019/batches/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.txt rename to corpora/BioNLP-OST-2019/batches/BB19-norm+ner_test/bionlp-st/BB-norm+ner-F-26187841-002.txt diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/batch.xml b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/batch.xml new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1016123.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1016123.a1 new file mode 100644 index 0000000000000000000000000000000000000000..8e0270020a4af788625956dbc3ac374d3465c70f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1016123.a1 @@ -0,0 +1,2 @@ +T1 Title 0 141 An evaluation of selective broths based on the bi-selenite ion and on hypertonic strontium chloride in Salmonellae detection in egg products. +T2 Paragraph 142 579 Of the 104 isolations of Salmonella sp. from egg pulp, 97 were obtained from strontium chloride M broth, 42 from strontium selenite broth and 57 from strontium selenite A broth. The results suggest that the first medium may be used more successfully than bi-selenite based media for enrichment and subsequent detection of salmonellae in egg products; however, the growth of S. pullorum was not satisfactory in strontium chloride M broth. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1016123.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1016123.txt new file mode 100644 index 0000000000000000000000000000000000000000..25b30eb5ff510340e40d12761b416ff8ec915b86 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1016123.txt @@ -0,0 +1,3 @@ +An evaluation of selective broths based on the bi-selenite ion and on hypertonic strontium chloride in Salmonellae detection in egg products. +Of the 104 isolations of Salmonella sp. from egg pulp, 97 were obtained from strontium chloride M broth, 42 from strontium selenite broth and 57 from strontium selenite A broth. The results suggest that the first medium may be used more successfully than bi-selenite based media for enrichment and subsequent detection of salmonellae in egg products; however, the growth of S. pullorum was not satisfactory in strontium chloride M broth. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10492485.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10492485.a1 new file mode 100644 index 0000000000000000000000000000000000000000..d848eb1f510d9c6d7eb301460351ba89b3239dac --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10492485.a1 @@ -0,0 +1,2 @@ +T1 Title 0 93 Application of ozone for enhancing the microbiological safety and quality of foods: a review. +T2 Paragraph 94 1854 Ozone (O3) is a strong antimicrobial agent with numerous potential applications in the food industry. High reactivity, penetrability, and spontaneous decomposition to a nontoxic product (i.e., O2) make ozone a viable disinfectant for ensuring the microbiological safety of food products. Ozone has been used for decades in many countries and recently, the generally recognized as safe (GRAS) status of this gas has been reaffirmed in the United States. Ozone, in the gaseous or aqueous phases, is effective against the majority of microorganisms tested by numerous research groups. Relatively low concentrations of ozone and short contact time are sufficient to inactivate bacteria, molds, yeasts, parasites, and viruses. However, rates of inactivation are greater in ozone demand-free systems than when the medium contains oxidizable organic substances. Susceptibility of microorganisms to ozone also varies with the physiological state of the culture, pH of the medium, temperature, humidity, and presence of additives (e.g., acids, surfactants, and sugars). Ozone applications in the food industry are mostly related to decontamination of product surface and water treatment. Ozone has been used with mixed success to inactivate contaminant microflora on meat, poultry, eggs, fish, fruits, vegetables, and dry foods. The gas also is useful in detoxification and elimination of mycotoxins and pesticide residues from some agricultural products. Excessive use of ozone, however, may cause oxidation of some ingredients on food surface. This usually results in discoloration and deterioration of food flavor. Additional research is needed to elucidate the kinetics and mechanisms of microbial inactivation by ozone and to optimize its use in food applications. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10492485.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10492485.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc450e286e2b3c28ad7be74615213b5119889289 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10492485.txt @@ -0,0 +1,3 @@ +Application of ozone for enhancing the microbiological safety and quality of foods: a review. +Ozone (O3) is a strong antimicrobial agent with numerous potential applications in the food industry. High reactivity, penetrability, and spontaneous decomposition to a nontoxic product (i.e., O2) make ozone a viable disinfectant for ensuring the microbiological safety of food products. Ozone has been used for decades in many countries and recently, the generally recognized as safe (GRAS) status of this gas has been reaffirmed in the United States. Ozone, in the gaseous or aqueous phases, is effective against the majority of microorganisms tested by numerous research groups. Relatively low concentrations of ozone and short contact time are sufficient to inactivate bacteria, molds, yeasts, parasites, and viruses. However, rates of inactivation are greater in ozone demand-free systems than when the medium contains oxidizable organic substances. Susceptibility of microorganisms to ozone also varies with the physiological state of the culture, pH of the medium, temperature, humidity, and presence of additives (e.g., acids, surfactants, and sugars). Ozone applications in the food industry are mostly related to decontamination of product surface and water treatment. Ozone has been used with mixed success to inactivate contaminant microflora on meat, poultry, eggs, fish, fruits, vegetables, and dry foods. The gas also is useful in detoxification and elimination of mycotoxins and pesticide residues from some agricultural products. Excessive use of ozone, however, may cause oxidation of some ingredients on food surface. This usually results in discoloration and deterioration of food flavor. Additional research is needed to elucidate the kinetics and mechanisms of microbial inactivation by ozone and to optimize its use in food applications. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10496597.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10496597.a1 new file mode 100644 index 0000000000000000000000000000000000000000..04eeb6f1fb4a07bb5db9c0987aee30e3d6d46736 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10496597.a1 @@ -0,0 +1,2 @@ +T1 Title 0 137 The differential diagnosis of early gastric mucosa-associated lymphoma: polymerase chain reaction and paraffin section immunophenotyping. +T2 Paragraph 138 2048 The distinction between benign florid lymphoid hyperplasia and low-grade gastric mucosal-associated lymphoid tissue (MALT) lymphoma may be a challenge. The presence of monoclonal B cells in Helicobacter pylori-chronic active gastritis has suggested that polymerase chain reaction (PCR) data should be viewed with caution. We investigated the reliability of PCR versus immunophenotyping in diagnosing early gastric MALT lymphoma. We studied 1511 biopsies from eight patients with high-grade primary gastric lymphoma, 25 with low-grade MALT lymphoma, 32 with atypical lymphoid infiltrates, and 39 with Helicobacter pylori-chronic active gastritis. Paraffin sections from all cases were stained with antibodies to CD20, CD3, AE1/AE3, kappa and lambda. PCR was performed on paraffin sections using the primer set VH-FR3/J(H). Using histopathology as the gold standard in diagnosis, we confirmed monoclonality in 22 of 25 MALT lymphomas (88%); a clonal band was found in 38% (15 of 39) of patients with chronic active gastritis. An immunophenotype pattern with predominance of CD20-positive cells in lymphocytic infiltrates was associated with monoclonality in 92% of cases. The presence of an enlarged irregular mantle zone was found in both monoclonal and polyclonal areas. An equal prevalence of B and T cells in lymphocytic infiltrates was associated with a polyclonal pattern in 24 of 31 cases (77%). Immunostaining of sIg (kappa and lambda) was difficult in paraffin sections and convincing proof of monoclonality was not obtained. Lymphoepithelial lesions were infrequent in gastric biopsies and their presence was highlighted with keratin stains. Because monoclonal B cells are observed in Helicobacter pylori-associated gastritis, the correct interpretation of clonality by PCR remains unclear. Paraffin section IHC using CD20 and CD3 is especially useful to confirm the diagnosis of gastric MALT lymphoma. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10496597.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10496597.txt new file mode 100644 index 0000000000000000000000000000000000000000..cff06a920903d6255a5956ab6e9174f991d551bc --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10496597.txt @@ -0,0 +1,3 @@ +The differential diagnosis of early gastric mucosa-associated lymphoma: polymerase chain reaction and paraffin section immunophenotyping. +The distinction between benign florid lymphoid hyperplasia and low-grade gastric mucosal-associated lymphoid tissue (MALT) lymphoma may be a challenge. The presence of monoclonal B cells in Helicobacter pylori-chronic active gastritis has suggested that polymerase chain reaction (PCR) data should be viewed with caution. We investigated the reliability of PCR versus immunophenotyping in diagnosing early gastric MALT lymphoma. We studied 1511 biopsies from eight patients with high-grade primary gastric lymphoma, 25 with low-grade MALT lymphoma, 32 with atypical lymphoid infiltrates, and 39 with Helicobacter pylori-chronic active gastritis. Paraffin sections from all cases were stained with antibodies to CD20, CD3, AE1/AE3, kappa and lambda. PCR was performed on paraffin sections using the primer set VH-FR3/J(H). Using histopathology as the gold standard in diagnosis, we confirmed monoclonality in 22 of 25 MALT lymphomas (88%); a clonal band was found in 38% (15 of 39) of patients with chronic active gastritis. An immunophenotype pattern with predominance of CD20-positive cells in lymphocytic infiltrates was associated with monoclonality in 92% of cases. The presence of an enlarged irregular mantle zone was found in both monoclonal and polyclonal areas. An equal prevalence of B and T cells in lymphocytic infiltrates was associated with a polyclonal pattern in 24 of 31 cases (77%). Immunostaining of sIg (kappa and lambda) was difficult in paraffin sections and convincing proof of monoclonality was not obtained. Lymphoepithelial lesions were infrequent in gastric biopsies and their presence was highlighted with keratin stains. Because monoclonal B cells are observed in Helicobacter pylori-associated gastritis, the correct interpretation of clonality by PCR remains unclear. Paraffin section IHC using CD20 and CD3 is especially useful to confirm the diagnosis of gastric MALT lymphoma. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10658649.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10658649.a1 new file mode 100644 index 0000000000000000000000000000000000000000..61630681e1e68cd472f0d1337e0e22d182f85629 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10658649.a1 @@ -0,0 +1,2 @@ +T1 Title 0 108 Identification of a novel glycoprotein-binding activity in Streptococcus pyogenes regulated by the mga gene. +T2 Paragraph 109 1148 The interaction between Streptococcus pyogenes and the host cell surface is not completely understood. Characterization of the adhesion mechanisms of the bacterium to the host cell surface is needed in order to develop new vaccines and anti-adhesion drugs. The presence of glycoprotein-binding activities among streptococcal strains was investigated. An activity binding to thyroglobulin, fetuin, asialofetuin and mucin but not non-glycosylated proteins was found to be present in the majority of the S. pyogenes strains studied. Cross-inhibition experiments suggested that the glycoproteins share a common structure recognized by the bacteria. The glycoprotein-binding activity was found to be proteinaceous, tightly attached to the bacterial surface and it also mediated the adherence of bacteria to solid surfaces coated with glycoproteins. The activity was found by transposon mutagenesis and complementation to be regulated by the multiple-gene regulator Mga, which has been implicated as a regulator of S. pyogenes virulence factors. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10658649.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10658649.txt new file mode 100644 index 0000000000000000000000000000000000000000..928f8b8c01b0739c7dff02409ad4ba895a2c5889 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10658649.txt @@ -0,0 +1,3 @@ +Identification of a novel glycoprotein-binding activity in Streptococcus pyogenes regulated by the mga gene. +The interaction between Streptococcus pyogenes and the host cell surface is not completely understood. Characterization of the adhesion mechanisms of the bacterium to the host cell surface is needed in order to develop new vaccines and anti-adhesion drugs. The presence of glycoprotein-binding activities among streptococcal strains was investigated. An activity binding to thyroglobulin, fetuin, asialofetuin and mucin but not non-glycosylated proteins was found to be present in the majority of the S. pyogenes strains studied. Cross-inhibition experiments suggested that the glycoproteins share a common structure recognized by the bacteria. The glycoprotein-binding activity was found to be proteinaceous, tightly attached to the bacterial surface and it also mediated the adherence of bacteria to solid surfaces coated with glycoproteins. The activity was found by transposon mutagenesis and complementation to be regulated by the multiple-gene regulator Mga, which has been implicated as a regulator of S. pyogenes virulence factors. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10738994.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10738994.a1 new file mode 100644 index 0000000000000000000000000000000000000000..0e1c49bec6b1c06eb5de542f28c4d1ebc420588f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10738994.a1 @@ -0,0 +1,6 @@ +T1 Title 0 188 Genotyping by restriction endonuclease analysis compared to phenotyping by antibiogram for typing methicillin-resistant Staphylococcus aureus strains colonizing patients in a nursing home. +T2 Paragraph 189 545 To assist in defining patterns of methicillin-resistant Staphylococcus aureus (MRSA) colonization in a skilled nursing facility (SNF), we compared genotyping by field-inversion gel electrophoresis (FIGE) restriction endonuclease digestion analysis (REA) with phenotyping by antibiogram for defining strain relatedness among MRSA isolates from SNF patients. +T3 Paragraph 546 632 Prospective screening culture surveillance for MRSA among patients in a community SNF. +T4 Paragraph 633 877 Nares and stool swab cultures were obtained from newly admitted patients and from all patients quarterly. MRSA were isolated by oxacillin screening agar. Antibiograms were determined by the disk-diffusion method, and genotyping was by FIGE REA. +T5 Paragraph 878 1159 It was shown that, among isolates with the same genotypes, many had different antibiograms; among isolates with the same antibiograms, many had different genotypes; and the discriminatory indices for isolates of MRSA by FIGE REA and by antibiogram were 0.56 and 0.78, respectively. +T6 Paragraph 1160 1632 Our study demonstrated that, in patients from one SNF, genotyping by FIGE REA identified two prevalent REA DNA types, but with variability of antibiogram patterns within each DNA type; the antibiogram also identified prevalent patterns with variability of REA DNA type within each antibiogram pattern. The discriminatory index of antibiograms alone, or of genotypes alone as determined by FIGE REA, was poor for strains of MRSA isolated from the SNF patients in our study. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10738994.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10738994.txt new file mode 100644 index 0000000000000000000000000000000000000000..764b1c16449e4a710dc0cb8c1132749a8e6c1783 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-10738994.txt @@ -0,0 +1,7 @@ +Genotyping by restriction endonuclease analysis compared to phenotyping by antibiogram for typing methicillin-resistant Staphylococcus aureus strains colonizing patients in a nursing home. +To assist in defining patterns of methicillin-resistant Staphylococcus aureus (MRSA) colonization in a skilled nursing facility (SNF), we compared genotyping by field-inversion gel electrophoresis (FIGE) restriction endonuclease digestion analysis (REA) with phenotyping by antibiogram for defining strain relatedness among MRSA isolates from SNF patients. +Prospective screening culture surveillance for MRSA among patients in a community SNF. +Nares and stool swab cultures were obtained from newly admitted patients and from all patients quarterly. MRSA were isolated by oxacillin screening agar. Antibiograms were determined by the disk-diffusion method, and genotyping was by FIGE REA. +It was shown that, among isolates with the same genotypes, many had different antibiograms; among isolates with the same antibiograms, many had different genotypes; and the discriminatory indices for isolates of MRSA by FIGE REA and by antibiogram were 0.56 and 0.78, respectively. +Our study demonstrated that, in patients from one SNF, genotyping by FIGE REA identified two prevalent REA DNA types, but with variability of antibiogram patterns within each DNA type; the antibiogram also identified prevalent patterns with variability of REA DNA type within each antibiogram pattern. The discriminatory index of antibiograms alone, or of genotypes alone as determined by FIGE REA, was poor for strains of MRSA isolated from the SNF patients in our study. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11162736.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11162736.a1 new file mode 100644 index 0000000000000000000000000000000000000000..020c7a523c8b05813801165eb5c1e8206e453351 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11162736.a1 @@ -0,0 +1,2 @@ +T1 Title 0 86 A new purification method for overproduced proteins sensitive to endogenous proteases. +T2 Paragraph 87 1379 Proteolysisis a major problem in purification of overproduced proteins for structural studies. We developed a new method to avoid proteolysis of the products even in cases where popular protease inhibitors do not work effectively. When we cloned FlgF, a flagellar rod protein, from Salmonella typhimurium and overproduced it in Escherichia coli, FlgF was highly susceptible to cleavage by endogenous proteases after cell disruption even in the presence of various protease inhibitors. However, FlgF was not digested when the cells were disrupted in the presence of urea, which allowed us to develop the following new purification procedure. After cell disruption in the presence of urea and removal of the cell debris, the supernatant was passed through tandem-connected cation- and anion-exchange columns. Proteases were trapped in the cation-exchange column, and protease-free FlgF was eluted from the disconnected anion-exchange column. This gave a stable full-length product suitable for crystallization trials. The key procedures are cell disruption in the presence of urea and linked ion-exchange chromatography to quickly remove proteases as well as urea. This fast and simple method can be applied to purification of other overproduced proteins that are very sensitive to proteolysis. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11162736.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11162736.txt new file mode 100644 index 0000000000000000000000000000000000000000..fecf5b3fd66b3931aed9e13444381eafd74f4bda --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11162736.txt @@ -0,0 +1,3 @@ +A new purification method for overproduced proteins sensitive to endogenous proteases. +Proteolysisis a major problem in purification of overproduced proteins for structural studies. We developed a new method to avoid proteolysis of the products even in cases where popular protease inhibitors do not work effectively. When we cloned FlgF, a flagellar rod protein, from Salmonella typhimurium and overproduced it in Escherichia coli, FlgF was highly susceptible to cleavage by endogenous proteases after cell disruption even in the presence of various protease inhibitors. However, FlgF was not digested when the cells were disrupted in the presence of urea, which allowed us to develop the following new purification procedure. After cell disruption in the presence of urea and removal of the cell debris, the supernatant was passed through tandem-connected cation- and anion-exchange columns. Proteases were trapped in the cation-exchange column, and protease-free FlgF was eluted from the disconnected anion-exchange column. This gave a stable full-length product suitable for crystallization trials. The key procedures are cell disruption in the presence of urea and linked ion-exchange chromatography to quickly remove proteases as well as urea. This fast and simple method can be applied to purification of other overproduced proteins that are very sensitive to proteolysis. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11410343.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11410343.a1 new file mode 100644 index 0000000000000000000000000000000000000000..795401bff25bac63431216d8cab1bbdb57579fcd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11410343.a1 @@ -0,0 +1,2 @@ +T1 Title 0 99 Effects of 2,2',5,5'-tetrachlorobiphenyl and biphenyl on cell membranes of Ralstonia eutropha H850. +T2 Paragraph 100 1308 The effects of 2,2',5,5'-tetrachlorobiphenyl (TeCB), a PCB congener, and biphenyl on the cytoplasmic membranes of Ralstonia eutropha H850 were investigated by measuring fluorescence polarization using 1,6-diphenyl-1,3,5-hexatriene (DPH) as the probe, and determining the cellular fatty acid compositions. TeCB significantly affected the membrane of R. eutropha H850 cells grown on fructose by decreasing DPH fluorescence polarization. In contrast, the membrane of cells grown on biphenyl showed a considerably less significant effect of TeCB on membrane polarization than in fructose-grown cells. An increase in the ratio of total saturated to unsaturated fatty acids in cells grown on biphenyl suggested less of a fluidizing effect of TeCB on membranes in those cells. When biphenyl-grown cells were transferred back to a fructose medium, they required 25 generations for the membrane polarization and fatty acid compositions of these cells to revert back to those of the initial fructose-grown cells. The re-adaptation to a change in temperature required only five generations to return to normal. These results show that biphenyl affects cells in more ways than simply fluidizing the cytoplasmic membrane. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11410343.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11410343.txt new file mode 100644 index 0000000000000000000000000000000000000000..a8bfee90b2b0800870397c91364e8fed9bfab326 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11410343.txt @@ -0,0 +1,3 @@ +Effects of 2,2',5,5'-tetrachlorobiphenyl and biphenyl on cell membranes of Ralstonia eutropha H850. +The effects of 2,2',5,5'-tetrachlorobiphenyl (TeCB), a PCB congener, and biphenyl on the cytoplasmic membranes of Ralstonia eutropha H850 were investigated by measuring fluorescence polarization using 1,6-diphenyl-1,3,5-hexatriene (DPH) as the probe, and determining the cellular fatty acid compositions. TeCB significantly affected the membrane of R. eutropha H850 cells grown on fructose by decreasing DPH fluorescence polarization. In contrast, the membrane of cells grown on biphenyl showed a considerably less significant effect of TeCB on membrane polarization than in fructose-grown cells. An increase in the ratio of total saturated to unsaturated fatty acids in cells grown on biphenyl suggested less of a fluidizing effect of TeCB on membranes in those cells. When biphenyl-grown cells were transferred back to a fructose medium, they required 25 generations for the membrane polarization and fatty acid compositions of these cells to revert back to those of the initial fructose-grown cells. The re-adaptation to a change in temperature required only five generations to return to normal. These results show that biphenyl affects cells in more ways than simply fluidizing the cytoplasmic membrane. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11437594.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11437594.a1 new file mode 100644 index 0000000000000000000000000000000000000000..12cdf3af5d6042091093877f432dec7d3beac2d0 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11437594.a1 @@ -0,0 +1,2 @@ +T1 Title 0 85 Optimization of the production of Chondrus crispus hexose oxidase in Pichia pastoris. +T2 Paragraph 86 1277 Hexose oxidase (D-hexose:O(2)-oxidoreductase, EC 1.1.3.5, HOX) normally found in the red alga Chondrus crispus was produced heterologously in different host systems. Full-length HOX polypeptide was produced in Escherichia coli, but no HOX activity could be detected. In contrast, active HOX could be produced in the methylotrophic yeast Pichia pastoris. Several growth physiological and genetic approaches for optimization of hexose oxidase production in P. pastoris were investigated. Our results indicate that specific growth conditions are essential in order to produce active HOX with the correct conformation. Furthermore, HOX seems to be activated by proteolytic cleavage of the full-length polypeptide chain into two fragments, which remain physically associated. Attempts to direct HOX to the extracellular compartment using the widely used secretion signals from Saccharomyces cerevisiae invertase or alpha-mating factor failed. However, we show in this study that HOX is transported out of P. pastoris via a hitherto unknown mechanism and that it is possible to enhance this secretion by mutagenesis from below the detection limit to at least 250 mg extracellular enzyme per liter. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11437594.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11437594.txt new file mode 100644 index 0000000000000000000000000000000000000000..3242f318ea4f19ae5524f6734aded9a386cd7fdc --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11437594.txt @@ -0,0 +1,3 @@ +Optimization of the production of Chondrus crispus hexose oxidase in Pichia pastoris. +Hexose oxidase (D-hexose:O(2)-oxidoreductase, EC 1.1.3.5, HOX) normally found in the red alga Chondrus crispus was produced heterologously in different host systems. Full-length HOX polypeptide was produced in Escherichia coli, but no HOX activity could be detected. In contrast, active HOX could be produced in the methylotrophic yeast Pichia pastoris. Several growth physiological and genetic approaches for optimization of hexose oxidase production in P. pastoris were investigated. Our results indicate that specific growth conditions are essential in order to produce active HOX with the correct conformation. Furthermore, HOX seems to be activated by proteolytic cleavage of the full-length polypeptide chain into two fragments, which remain physically associated. Attempts to direct HOX to the extracellular compartment using the widely used secretion signals from Saccharomyces cerevisiae invertase or alpha-mating factor failed. However, we show in this study that HOX is transported out of P. pastoris via a hitherto unknown mechanism and that it is possible to enhance this secretion by mutagenesis from below the detection limit to at least 250 mg extracellular enzyme per liter. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11989773.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11989773.a1 new file mode 100644 index 0000000000000000000000000000000000000000..8457dea1456a8925030cc6bdbe1d9266f0678b25 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11989773.a1 @@ -0,0 +1,2 @@ +T1 Title 0 135 Evaluation of two commercial methods for the detection of Listeria sp. and Listeria monocytogenes in a chicken nugget processing plant. +T2 Paragraph 136 1243 This study measures the detection performances of two rapid test systems (Listeria Rapid Test Clearview and Bax system) for the screening of Listeria sp. and Listeria monocytogenes, respectively. A total of 413 samples from different sources (product from (i) different stages of processing, (ii) different environments, and (iii) different food handlers), collected from a chicken nugget processing plant, were analysed by both rapid methods and a cultural method consisting of pre-enrichment, enrichment, and isolation onto selective agars (PALCAM, LPM, and HCLA). Overall, results showed an excellent correlation between data obtained using Clearview and the cultural method, with Clearview presenting an efficiency of 99%. Bax showed a lower correlation using the cultural method, with an efficiency of 71.1%. The type of sample did not affect the efficiency of Clearview, which varied from 98.1% for product samples to 100% for environmental and food handler samples, while for Bax it had a marked influence. Efficiency of Bax varied from as high as 100% for food handlers to 37.9% for product samples. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11989773.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11989773.txt new file mode 100644 index 0000000000000000000000000000000000000000..23c0948ee732e7547393cfb196cc47948e9be24c --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-11989773.txt @@ -0,0 +1,3 @@ +Evaluation of two commercial methods for the detection of Listeria sp. and Listeria monocytogenes in a chicken nugget processing plant. +This study measures the detection performances of two rapid test systems (Listeria Rapid Test Clearview and Bax system) for the screening of Listeria sp. and Listeria monocytogenes, respectively. A total of 413 samples from different sources (product from (i) different stages of processing, (ii) different environments, and (iii) different food handlers), collected from a chicken nugget processing plant, were analysed by both rapid methods and a cultural method consisting of pre-enrichment, enrichment, and isolation onto selective agars (PALCAM, LPM, and HCLA). Overall, results showed an excellent correlation between data obtained using Clearview and the cultural method, with Clearview presenting an efficiency of 99%. Bax showed a lower correlation using the cultural method, with an efficiency of 71.1%. The type of sample did not affect the efficiency of Clearview, which varied from 98.1% for product samples to 100% for environmental and food handler samples, while for Bax it had a marked influence. Efficiency of Bax varied from as high as 100% for food handlers to 37.9% for product samples. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12109661.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12109661.a1 new file mode 100644 index 0000000000000000000000000000000000000000..7f4c7a07fc09313f530822116fd34528385f0753 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12109661.a1 @@ -0,0 +1,2 @@ +T1 Title 0 110 Long-term Helicobacter pylori infection and the development of atrophic gastritis and gastric cancer in Japan. +T2 Paragraph 111 1577 The incidence of gastric cancer and the prevalence of Helicobacter pylori are high in Japan, so it is an important issue whether long-term H. pylori infection leads to chronic atrophic gastritis, considered one of the precursors of gastric cancer. We have reported that the grade of atrophy was higher in H. pylori-positive subjects than in H. pylori-negative subjects. It has also been reported that the atrophy of gastric mucosa increased in H. pylori-infected monkeys compared with control monkeys in a 5-year follow-up study. Most H. pylori infections occur in children, and atrophy of the gastric mucosa progresses during aging. Long-term data show that H. pylori infection can lead to gastric atrophy and may play an important role in the development of gastric cancer. Interestingly, there was no difference in the prevalence of H. pylori between patients with chronic gastritis and gastric cancer in Japan, but the prevalence of H. pylori in young Japanese gastric cancer patients was significantly higher than in the control group. These data clearly show that H. pylori infection is one of the risk factors of gastric cancer in young Japanese people, There is no answer to whether curing H. pylori infection can reverse the atrophy of the gastric mucosa and decrease the risk of gastric cancer development. To clarify this issue, an intervention study must be done. A large clinical trial called the Japanese Intervention Trial of H. pylori is in progress. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12109661.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12109661.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e430185309732e6e1837af8895889a74b7a43b3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12109661.txt @@ -0,0 +1,3 @@ +Long-term Helicobacter pylori infection and the development of atrophic gastritis and gastric cancer in Japan. +The incidence of gastric cancer and the prevalence of Helicobacter pylori are high in Japan, so it is an important issue whether long-term H. pylori infection leads to chronic atrophic gastritis, considered one of the precursors of gastric cancer. We have reported that the grade of atrophy was higher in H. pylori-positive subjects than in H. pylori-negative subjects. It has also been reported that the atrophy of gastric mucosa increased in H. pylori-infected monkeys compared with control monkeys in a 5-year follow-up study. Most H. pylori infections occur in children, and atrophy of the gastric mucosa progresses during aging. Long-term data show that H. pylori infection can lead to gastric atrophy and may play an important role in the development of gastric cancer. Interestingly, there was no difference in the prevalence of H. pylori between patients with chronic gastritis and gastric cancer in Japan, but the prevalence of H. pylori in young Japanese gastric cancer patients was significantly higher than in the control group. These data clearly show that H. pylori infection is one of the risk factors of gastric cancer in young Japanese people, There is no answer to whether curing H. pylori infection can reverse the atrophy of the gastric mucosa and decrease the risk of gastric cancer development. To clarify this issue, an intervention study must be done. A large clinical trial called the Japanese Intervention Trial of H. pylori is in progress. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1214327.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1214327.a1 new file mode 100644 index 0000000000000000000000000000000000000000..19bd7dd1c211899ca88d77224661191494cfb955 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1214327.a1 @@ -0,0 +1,2 @@ +T1 Title 0 99 Serotypes of Vibrio parahaemolyticus from clinical and environmental sources in Togo (West Africa). +T2 Paragraph 100 723 Serological analysis of O and K antigens was performed on 343 strains of Vibro parahaemolyticus isolated from clinical and environmental sources in Togo. Only two strains were not typable by the available O antisera. K untypable strains were found in 4.8% of isolates from gastroenteritis patients, in 11% from healthy carriers, and in 47% and 46% of isolates, respectively, from water and fish samples. Thirteen serotypes identified in Togo are not considered in the Japanese antigenic scheme. The suitability of the Japanese typing scheme for geographic areas outside of Japan is discussed and its extension is suggested. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1214327.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1214327.txt new file mode 100644 index 0000000000000000000000000000000000000000..58a1dfeebd95a553b3ec7aabf124b1e101546847 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1214327.txt @@ -0,0 +1,3 @@ +Serotypes of Vibrio parahaemolyticus from clinical and environmental sources in Togo (West Africa). +Serological analysis of O and K antigens was performed on 343 strains of Vibro parahaemolyticus isolated from clinical and environmental sources in Togo. Only two strains were not typable by the available O antisera. K untypable strains were found in 4.8% of isolates from gastroenteritis patients, in 11% from healthy carriers, and in 47% and 46% of isolates, respectively, from water and fish samples. Thirteen serotypes identified in Togo are not considered in the Japanese antigenic scheme. The suitability of the Japanese typing scheme for geographic areas outside of Japan is discussed and its extension is suggested. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12728302.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12728302.a1 new file mode 100644 index 0000000000000000000000000000000000000000..9be353292c92848522594382c54441a3c1dde724 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12728302.a1 @@ -0,0 +1,2 @@ +T1 Title 0 123 Heat-shock response and its contribution to thermotolerance of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31. +T2 Paragraph 124 1248 Compared to Escherichia coli, the nitrogen-fixing soil cyanobacterium Anabaena sp. strain L-31 exhibited significantly superior abilities to survive prolonged and continuous heat stress and recover therefrom. Temperature upshift induced the synthesis of heat-shock proteins of similar molecular mass in the two microbes. However, in Anabaena sp. strain L-31 the heat-shock proteins (particularly the GroEL proteins) were synthesised throughout the stress period, were much more stable and accumulated during heat stress. In contrast, in E. coli the heat-shock proteins were transiently synthesised, quickly turned over and did not accumulate. Nitrogenase activity of Anabaena cells of sp. strain L-31 continuously exposed to heat stress for 7 days rapidly recovered from thermal injury, although growth recovery was delayed. Exposure of E. coli cells to >4.5 h of heat stress resulted in a complete loss of viability and the ability to recover. Marked differences in the synthesis, stability and accumulation of heat-shock proteins appear to distinguish these bacteria in their thermotolerance and recovery from heat stress. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12728302.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12728302.txt new file mode 100644 index 0000000000000000000000000000000000000000..25dd09dd03a0f84f649a21a47a90c8265983bf21 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12728302.txt @@ -0,0 +1,3 @@ +Heat-shock response and its contribution to thermotolerance of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31. +Compared to Escherichia coli, the nitrogen-fixing soil cyanobacterium Anabaena sp. strain L-31 exhibited significantly superior abilities to survive prolonged and continuous heat stress and recover therefrom. Temperature upshift induced the synthesis of heat-shock proteins of similar molecular mass in the two microbes. However, in Anabaena sp. strain L-31 the heat-shock proteins (particularly the GroEL proteins) were synthesised throughout the stress period, were much more stable and accumulated during heat stress. In contrast, in E. coli the heat-shock proteins were transiently synthesised, quickly turned over and did not accumulate. Nitrogenase activity of Anabaena cells of sp. strain L-31 continuously exposed to heat stress for 7 days rapidly recovered from thermal injury, although growth recovery was delayed. Exposure of E. coli cells to >4.5 h of heat stress resulted in a complete loss of viability and the ability to recover. Marked differences in the synthesis, stability and accumulation of heat-shock proteins appear to distinguish these bacteria in their thermotolerance and recovery from heat stress. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12781527.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12781527.a1 new file mode 100644 index 0000000000000000000000000000000000000000..9312994dcfd0721b414e887bf8debd9e13e9e33f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12781527.a1 @@ -0,0 +1,2 @@ +T1 Title 0 59 Campylobacter--a tale of two protein glycosylation systems. +T2 Paragraph 60 926 Post-translational glycosylation is a universal modification of proteins in eukarya, archaea and bacteria. Two recent publications describe the first confirmed report of a bacterial N-linked glycosylation pathway in the human gastrointestinal pathogen Campylobacter jejuni. In addition, an O-linked glycosylation pathway has been identified and characterized in C. jejuni and the related species Campylobacter coli. Both pathways have similarity to the respective N- and O-linked glycosylation processes in eukaryotes. In bacteria, homologues of the genes in both pathways are found in other organisms, the complex glycans linked to the glycoproteins share common biosynthetic precursors and these modifications could play similar biological roles. Thus, Campylobacter provides a unique model system for the elucidation and exploitation of glycoprotein biosynthesis. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12781527.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12781527.txt new file mode 100644 index 0000000000000000000000000000000000000000..e22e7b7211d7b3b45402b6f1f7f203a0542aa846 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12781527.txt @@ -0,0 +1,3 @@ +Campylobacter--a tale of two protein glycosylation systems. +Post-translational glycosylation is a universal modification of proteins in eukarya, archaea and bacteria. Two recent publications describe the first confirmed report of a bacterial N-linked glycosylation pathway in the human gastrointestinal pathogen Campylobacter jejuni. In addition, an O-linked glycosylation pathway has been identified and characterized in C. jejuni and the related species Campylobacter coli. Both pathways have similarity to the respective N- and O-linked glycosylation processes in eukaryotes. In bacteria, homologues of the genes in both pathways are found in other organisms, the complex glycans linked to the glycoproteins share common biosynthetic precursors and these modifications could play similar biological roles. Thus, Campylobacter provides a unique model system for the elucidation and exploitation of glycoprotein biosynthesis. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12970344.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12970344.a1 new file mode 100644 index 0000000000000000000000000000000000000000..421ba6bb510874bac56366e6c44e05e04afefd66 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12970344.a1 @@ -0,0 +1,2 @@ +T1 Title 0 54 The three-dimensional structures of two beta-agarases. +T2 Paragraph 55 1756 Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12970344.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12970344.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba5ec372d2d3094952f242afa15a626eae0638a4 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-12970344.txt @@ -0,0 +1,3 @@ +The three-dimensional structures of two beta-agarases. +Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1356998.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1356998.a1 new file mode 100644 index 0000000000000000000000000000000000000000..3082aa3342237a253ad0bbdf9c37ae7e71cbd545 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1356998.a1 @@ -0,0 +1,2 @@ +T1 Title 0 89 Human and tick spotted fever group Rickettsia isolates from Israel: a genotypic analysis. +T2 Paragraph 90 1386 The genomes of spotted fever group rickettsiae isolated in different geographical areas of Israel (two from ticks and four from humans, obtained over a span of 20 years) were studied by polymerase chain reaction (PCR) and restriction endonuclease fragment length polymorphism (RFLP) analysis. The human isolates were obtained from patients suffering from rickettsial disease of different degrees of severity. The PCR products obtained with five pairs of oligonucleotide primers (two primer sets derived from the 190-kDa polypeptide gene and three from the 120-kDa polypeptide gene) and cleaved with restriction endonucleases were used to study the Israeli isolates and reference Rickettsia conorii isolates. Subtle differences between the PCR-RFLP patterns of Israeli isolates and the two R. conorii reference strains (Moroccan and no. 7) were seen when the PCR products derived from the 190-kDa gene-derived primer sets were digested. All of the Israeli isolates were identical by RFLP analysis using all of the primer sets. This study showed that the Israeli spotted fever group isolates (from both ticks and humans) were genetically homogeneous by the criteria used in this study, despite the time and location differences in their original isolation, and different as a group from R. conorii. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1356998.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1356998.txt new file mode 100644 index 0000000000000000000000000000000000000000..c8746569c067e21a1cbee16c14caac4570ab0471 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-1356998.txt @@ -0,0 +1,3 @@ +Human and tick spotted fever group Rickettsia isolates from Israel: a genotypic analysis. +The genomes of spotted fever group rickettsiae isolated in different geographical areas of Israel (two from ticks and four from humans, obtained over a span of 20 years) were studied by polymerase chain reaction (PCR) and restriction endonuclease fragment length polymorphism (RFLP) analysis. The human isolates were obtained from patients suffering from rickettsial disease of different degrees of severity. The PCR products obtained with five pairs of oligonucleotide primers (two primer sets derived from the 190-kDa polypeptide gene and three from the 120-kDa polypeptide gene) and cleaved with restriction endonucleases were used to study the Israeli isolates and reference Rickettsia conorii isolates. Subtle differences between the PCR-RFLP patterns of Israeli isolates and the two R. conorii reference strains (Moroccan and no. 7) were seen when the PCR products derived from the 190-kDa gene-derived primer sets were digested. All of the Israeli isolates were identical by RFLP analysis using all of the primer sets. This study showed that the Israeli spotted fever group isolates (from both ticks and humans) were genetically homogeneous by the criteria used in this study, despite the time and location differences in their original isolation, and different as a group from R. conorii. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14633026.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14633026.a1 new file mode 100644 index 0000000000000000000000000000000000000000..c723e3433505e331fc8286081b5679eb3a5c6362 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14633026.a1 @@ -0,0 +1,5 @@ +T1 Title 0 109 Characterization of a mosquitocidal Bacillus thuringiensis serovar sotto strain isolated from Okinawa, Japan. +T2 Paragraph 110 307 To characterize the mosquitocidal activity of parasporal inclusions of the Bacillus thuringiensis serovar sotto strain 96-OK-85-24, for comparison with two well-characterized mosquitocidal strains. +T3 Paragraph 308 628 The strain 96-OK-85-24 significantly differed from the existing mosquitocidal B. thuringiensis strains in: (1) lacking the larvicidal activity against Culex pipiens molestus and haemolytic activity, and (2) SDS-PAGE profiles, immunological properties and N-terminal amino acid sequences of parasporal inclusion proteins. +T4 Paragraph 629 764 It is clear from the results that the strain 96-OK-85-24 synthesizes a novel mosquitocidal Cry protein with a unique toxicity spectrum. +T5 Paragraph 765 937 This is the first report of the occurrence of a mosquitocidal B. thuringiensis strain with an unusual toxicity spectrum, lacking the activity against the culicine mosquito. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14633026.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14633026.txt new file mode 100644 index 0000000000000000000000000000000000000000..05f290d635bf9c71ca3874f40dce94d9db589c22 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14633026.txt @@ -0,0 +1,6 @@ +Characterization of a mosquitocidal Bacillus thuringiensis serovar sotto strain isolated from Okinawa, Japan. +To characterize the mosquitocidal activity of parasporal inclusions of the Bacillus thuringiensis serovar sotto strain 96-OK-85-24, for comparison with two well-characterized mosquitocidal strains. +The strain 96-OK-85-24 significantly differed from the existing mosquitocidal B. thuringiensis strains in: (1) lacking the larvicidal activity against Culex pipiens molestus and haemolytic activity, and (2) SDS-PAGE profiles, immunological properties and N-terminal amino acid sequences of parasporal inclusion proteins. +It is clear from the results that the strain 96-OK-85-24 synthesizes a novel mosquitocidal Cry protein with a unique toxicity spectrum. +This is the first report of the occurrence of a mosquitocidal B. thuringiensis strain with an unusual toxicity spectrum, lacking the activity against the culicine mosquito. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14645268.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14645268.a1 new file mode 100644 index 0000000000000000000000000000000000000000..3d69b262755a077567db7d4774418f41263fd0b3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14645268.a1 @@ -0,0 +1,2 @@ +T1 Title 0 96 XopC and XopJ, two novel type III effector proteins from Xanthomonas campestris pv. vesicatoria. +T2 Paragraph 97 1660 Pathogenicity of the gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria depends on a type III secretion (TTS) system which translocates bacterial effector proteins into the plant cell. Previous transcriptome analysis identified a genome-wide regulon of putative virulence genes that are coexpressed with the TTS system. In this study, we characterized two of these genes, xopC and xopJ. Both genes encode Xanthomonas outer proteins (Xops) that were shown to be secreted by the TTS system. In addition, type III-dependent translocation of both proteins into the plant cell was demonstrated using the AvrBs3 effector domain as a reporter. XopJ belongs to the AvrRxv/YopJ family of effector proteins from plant and animal pathogenic bacteria. By contrast, XopC does not share significant homology to proteins in the database. Sequence analysis revealed that the xopC locus contains several features that are reminiscent of pathogenicity islands. Interestingly, the xopC region is flanked by 62-bp inverted repeats that are also associated with members of the Xanthomonas avrBs3 effector family. Besides xopC, a second gene of the locus, designated hpaJ, was shown to be coexpressed with the TTS system. hpaJ encodes a protein with similarity to transglycosylases and to the Pseudomonas syringae pv. maculicola protein HopPmaG. HpaJ secretion and translocation by the X. campestris pv. vesicatoria TTS system was not detectable, which is consistent with its predicted Sec signal and a putative function as transglycosylase in the bacterial periplasm. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14645268.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14645268.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1b7bff09ec03b86fb1d04509d685149727ca45d --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-14645268.txt @@ -0,0 +1,3 @@ +XopC and XopJ, two novel type III effector proteins from Xanthomonas campestris pv. vesicatoria. +Pathogenicity of the gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria depends on a type III secretion (TTS) system which translocates bacterial effector proteins into the plant cell. Previous transcriptome analysis identified a genome-wide regulon of putative virulence genes that are coexpressed with the TTS system. In this study, we characterized two of these genes, xopC and xopJ. Both genes encode Xanthomonas outer proteins (Xops) that were shown to be secreted by the TTS system. In addition, type III-dependent translocation of both proteins into the plant cell was demonstrated using the AvrBs3 effector domain as a reporter. XopJ belongs to the AvrRxv/YopJ family of effector proteins from plant and animal pathogenic bacteria. By contrast, XopC does not share significant homology to proteins in the database. Sequence analysis revealed that the xopC locus contains several features that are reminiscent of pathogenicity islands. Interestingly, the xopC region is flanked by 62-bp inverted repeats that are also associated with members of the Xanthomonas avrBs3 effector family. Besides xopC, a second gene of the locus, designated hpaJ, was shown to be coexpressed with the TTS system. hpaJ encodes a protein with similarity to transglycosylases and to the Pseudomonas syringae pv. maculicola protein HopPmaG. HpaJ secretion and translocation by the X. campestris pv. vesicatoria TTS system was not detectable, which is consistent with its predicted Sec signal and a putative function as transglycosylase in the bacterial periplasm. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15293611.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15293611.a1 new file mode 100644 index 0000000000000000000000000000000000000000..150b6dbeb48554026befb29329b3ec1378a8109f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15293611.a1 @@ -0,0 +1,2 @@ +T1 Title 0 87 Clonal strains of Pseudomonas aeruginosa in paediatric and adult cystic fibrosis units. +T2 Paragraph 88 1551 Despite recent reports of clonal strains of Pseudomonas aeruginosa in cystic fibrosis (CF) units, the need for routine microbiological surveillance remains contentious. Sputum was collected prospectively from productive patients attending the regional paediatric and adult CF units in Brisbane, Australia. All P. aeruginosa isolates were typed using pulsed-field gel electrophoresis. Spirometry, anthropometrics, hospitalisations and antibiotic sensitivity data were recorded. The first 100 sputum samples (first 50 patients at each clinic) harboured 163 isolates of P. aeruginosa. A total of 39 patients shared a common strain (pulsotype 2), 20 patients shared a strain with at least one other patient and 41 patients harboured unique strains. Eight patients shared a strain identical to a previously reported Australian transmissible strain (pulsotype 1). Compared with the unique strain group, patients harbouring pulsotype 2 were younger and had poorer lung function. Treatment requirements were similar in these two groups, as were the rates of multiresistance. In conclusion, 59% of patients harboured a clonal strain, supporting the need for routine microbiological surveillance. In contrast to previously described clonal strains, the dominant pulsotype was indistinguishable from nonclonal strains with respect to both colonial morphology and multiresistance. The clinical significance of clonal strains remains uncertain and requires longitudinal study. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15293611.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15293611.txt new file mode 100644 index 0000000000000000000000000000000000000000..ec529b16f2153b81c2a684918feb27cf96c238a6 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15293611.txt @@ -0,0 +1,3 @@ +Clonal strains of Pseudomonas aeruginosa in paediatric and adult cystic fibrosis units. +Despite recent reports of clonal strains of Pseudomonas aeruginosa in cystic fibrosis (CF) units, the need for routine microbiological surveillance remains contentious. Sputum was collected prospectively from productive patients attending the regional paediatric and adult CF units in Brisbane, Australia. All P. aeruginosa isolates were typed using pulsed-field gel electrophoresis. Spirometry, anthropometrics, hospitalisations and antibiotic sensitivity data were recorded. The first 100 sputum samples (first 50 patients at each clinic) harboured 163 isolates of P. aeruginosa. A total of 39 patients shared a common strain (pulsotype 2), 20 patients shared a strain with at least one other patient and 41 patients harboured unique strains. Eight patients shared a strain identical to a previously reported Australian transmissible strain (pulsotype 1). Compared with the unique strain group, patients harbouring pulsotype 2 were younger and had poorer lung function. Treatment requirements were similar in these two groups, as were the rates of multiresistance. In conclusion, 59% of patients harboured a clonal strain, supporting the need for routine microbiological surveillance. In contrast to previously described clonal strains, the dominant pulsotype was indistinguishable from nonclonal strains with respect to both colonial morphology and multiresistance. The clinical significance of clonal strains remains uncertain and requires longitudinal study. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15358511.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15358511.a1 new file mode 100644 index 0000000000000000000000000000000000000000..5ad175e388e4ded2164f3f45e3dd603fba3bb2a3 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15358511.a1 @@ -0,0 +1,2 @@ +T1 Title 0 189 Attachment of Escherichia coli O157:H7 grown in tryptic soy broth and nutrient broth to apple and lettuce surfaces as related to cell hydrophobicity, surface charge, and capsule production. +T2 Paragraph 190 1044 This study investigated the effect of growth in tryptic soy broth (TSB) and nutrient broth (NB) on the ability Escherichia coli O157:H7 to attach to lettuce and apple surfaces. In addition, cell surface hydrophobicity, charge and capsule production were determined on cells grown in these media. Cells grown in NB attached less to lettuce and apple surfaces than did those grown in TSB. TSB, but not NB, supported capsule production by E. coli O157:H7. Cells grown in TSB were more hydrophilic than those grown in NB. No difference was found in the electrokinetic properties of cells grown in these media. Electrostatic and hydrophobic interactions and surface proteins did not appear to play an important role in the attachment of E. coli O157:H7 to these surfaces. Of the factors studied, only capsule production was associated with attachment ability. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15358511.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15358511.txt new file mode 100644 index 0000000000000000000000000000000000000000..c45c0e1edfbb0e55d3d91dbed1add48ad54812fd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15358511.txt @@ -0,0 +1,3 @@ +Attachment of Escherichia coli O157:H7 grown in tryptic soy broth and nutrient broth to apple and lettuce surfaces as related to cell hydrophobicity, surface charge, and capsule production. +This study investigated the effect of growth in tryptic soy broth (TSB) and nutrient broth (NB) on the ability Escherichia coli O157:H7 to attach to lettuce and apple surfaces. In addition, cell surface hydrophobicity, charge and capsule production were determined on cells grown in these media. Cells grown in NB attached less to lettuce and apple surfaces than did those grown in TSB. TSB, but not NB, supported capsule production by E. coli O157:H7. Cells grown in TSB were more hydrophilic than those grown in NB. No difference was found in the electrokinetic properties of cells grown in these media. Electrostatic and hydrophobic interactions and surface proteins did not appear to play an important role in the attachment of E. coli O157:H7 to these surfaces. Of the factors studied, only capsule production was associated with attachment ability. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15618837.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15618837.a1 new file mode 100644 index 0000000000000000000000000000000000000000..fbd77f10dc790ea99ac8759dd69f86eb51417e2e --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15618837.a1 @@ -0,0 +1,5 @@ +T1 Title 0 129 Recurrence of Helicobacter pylori infection 1 year after successful treatment: prospective cohort study in the Republic of Yemen. +T2 Paragraph 130 311 To investigate the prevalence of Helicobacter pylori infection in dyspeptic patients in the Republic of Yemen and the recurrence rate 1 year after apparently successful eradication. +T3 Paragraph 312 798 A total of 275 patients with chronic dyspepsia seen in one clinic were enrolled. Gastric biopsies were obtained at endoscopy and H. pylori infection was diagnosed using the rapid urease test. Patients with H. pylori infection were given either clarithromycin or metronidazole-based triple therapy. Six weeks later H. pylori status was assessed using the C-urea breath test (C-UBT). Those who were negative for H. pylori had a further C-UBT after 1 year to establish the recurrence rate. +T4 Paragraph 799 1360 The prevalence of H. pylori infection at entry to the study was 82.2% [95% confidence interval (CI) 78-87%]. The overall eradication rate 6 weeks after treatment was 49.1% (95% CI 42.6-55.6%) by intention-to-treat analysis, and 60% (95% CI 53-67%) by per-protocol analysis. Recurrence rate of H. pylori infection at 1 year was 34% (95% CI 14-45%) and the only predictor of recurrence was an excess delta C-UBT value less than 3.5 per million but equal to or greater than 2.5 per million at 6 weeks after treatment (odds ratio 2.28; 95% CI 1.17-4.44; P = 0.028). +T5 Paragraph 1361 1744 The prevalence of H. pylori infection in dyspeptic patients in Yemen is very high, the eradication rate with standard triple therapy was unsatisfactory probably because of widespread bacterial resistance due to unrestricted antibiotic use. The recurrence rate of infection at 1 year was high, as a result of recrudescence of incompletely eradicated organisms rather than reinfection. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15618837.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15618837.txt new file mode 100644 index 0000000000000000000000000000000000000000..5a32d3b97deff3814cf3d68d9a8119933e90a72b --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-15618837.txt @@ -0,0 +1,6 @@ +Recurrence of Helicobacter pylori infection 1 year after successful treatment: prospective cohort study in the Republic of Yemen. +To investigate the prevalence of Helicobacter pylori infection in dyspeptic patients in the Republic of Yemen and the recurrence rate 1 year after apparently successful eradication. +A total of 275 patients with chronic dyspepsia seen in one clinic were enrolled. Gastric biopsies were obtained at endoscopy and H. pylori infection was diagnosed using the rapid urease test. Patients with H. pylori infection were given either clarithromycin or metronidazole-based triple therapy. Six weeks later H. pylori status was assessed using the C-urea breath test (C-UBT). Those who were negative for H. pylori had a further C-UBT after 1 year to establish the recurrence rate. +The prevalence of H. pylori infection at entry to the study was 82.2% [95% confidence interval (CI) 78-87%]. The overall eradication rate 6 weeks after treatment was 49.1% (95% CI 42.6-55.6%) by intention-to-treat analysis, and 60% (95% CI 53-67%) by per-protocol analysis. Recurrence rate of H. pylori infection at 1 year was 34% (95% CI 14-45%) and the only predictor of recurrence was an excess delta C-UBT value less than 3.5 per million but equal to or greater than 2.5 per million at 6 weeks after treatment (odds ratio 2.28; 95% CI 1.17-4.44; P = 0.028). +The prevalence of H. pylori infection in dyspeptic patients in Yemen is very high, the eradication rate with standard triple therapy was unsatisfactory probably because of widespread bacterial resistance due to unrestricted antibiotic use. The recurrence rate of infection at 1 year was high, as a result of recrudescence of incompletely eradicated organisms rather than reinfection. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16263187.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16263187.a1 new file mode 100644 index 0000000000000000000000000000000000000000..7c9d4eafd821cbe594049841fe14e60a1678e025 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16263187.a1 @@ -0,0 +1,2 @@ +T1 Title 0 135 Ability of Lactobacillus gasseri K 7 to inhibit Escherichia coli adhesion in vitro on Caco-2 cells and ex vivo on pigs' jejunal tissue. +T2 Paragraph 136 1930 The ability of Lactobacillus (Lb.) gasseri K 7 to inhibit adhesion of Escherichia coli O8:K88 to intestinal mucosa was studied on cultured Caco-2 cells and ex vivo on pigs' small intestinal tissue. Lactobacilli were added simultaneously with E. coli, before E. coli and after E. coli for competition, exclusion and displacement assays. The concentration of lactobacilli on fully differentiated Caco-2 cells was 4.5+/-0.3 x 10(8) cfu/well, while the concentration of E. coli varied from 1.5 x 10(6) to 4.3 x 10(8) cfu/well. The number of E. coli adhered to Caco-2 monolayer (cfu/well) was lineary correlated (R(2)=0.97) to the concentration of added cells. In the assay simulating exclusion, E. coli adhesion was reduced by Lb. gasseri K 7 strain by 0.1 to 0.6 log cfu/well. The binding of E. coli was inhibited even more when incubated simultaneously with lactobacilli, particularly at the lowest concentration of E. coli (ratio E. coli/lactobacilli 1:248), where five-times reduction (or 0.7 log) was observed. When adhesion to tissue derived from pigs' jejunum was tested, concentration of E. coli was constant (6.9+/-0.14 x 10(7) cfu/ml), while the concentration of Lb. gasseri K 7 was 5.9 x 10(7) and 1.3 x 10(7) cfu/ml in two independent experiments, respectively. The adhesion of E. coli and Lb. gasseri K 7 cells to jejunal mucosa was similar (1.0+/-0.17 x 10(6) and 1.54+/-0.10 x 10(6) cfu/cm(2)) when the concentrations of single strains in suspensions were approximately the same. No significant competition, exclusion or displacement of E. coli by lactobacilli was observed on jejunal tissue. In conclusion, Lb. gasseri K 7 was found to be effective in reducing E. coli adhesion to Caco-2 enterocytes, but it was not able to do so in ex vivo conditions tested for pig jejunal tissue. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16263187.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16263187.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ab0389d1e5667664070d840050f79ddae97a38f --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16263187.txt @@ -0,0 +1,3 @@ +Ability of Lactobacillus gasseri K 7 to inhibit Escherichia coli adhesion in vitro on Caco-2 cells and ex vivo on pigs' jejunal tissue. +The ability of Lactobacillus (Lb.) gasseri K 7 to inhibit adhesion of Escherichia coli O8:K88 to intestinal mucosa was studied on cultured Caco-2 cells and ex vivo on pigs' small intestinal tissue. Lactobacilli were added simultaneously with E. coli, before E. coli and after E. coli for competition, exclusion and displacement assays. The concentration of lactobacilli on fully differentiated Caco-2 cells was 4.5+/-0.3 x 10(8) cfu/well, while the concentration of E. coli varied from 1.5 x 10(6) to 4.3 x 10(8) cfu/well. The number of E. coli adhered to Caco-2 monolayer (cfu/well) was lineary correlated (R(2)=0.97) to the concentration of added cells. In the assay simulating exclusion, E. coli adhesion was reduced by Lb. gasseri K 7 strain by 0.1 to 0.6 log cfu/well. The binding of E. coli was inhibited even more when incubated simultaneously with lactobacilli, particularly at the lowest concentration of E. coli (ratio E. coli/lactobacilli 1:248), where five-times reduction (or 0.7 log) was observed. When adhesion to tissue derived from pigs' jejunum was tested, concentration of E. coli was constant (6.9+/-0.14 x 10(7) cfu/ml), while the concentration of Lb. gasseri K 7 was 5.9 x 10(7) and 1.3 x 10(7) cfu/ml in two independent experiments, respectively. The adhesion of E. coli and Lb. gasseri K 7 cells to jejunal mucosa was similar (1.0+/-0.17 x 10(6) and 1.54+/-0.10 x 10(6) cfu/cm(2)) when the concentrations of single strains in suspensions were approximately the same. No significant competition, exclusion or displacement of E. coli by lactobacilli was observed on jejunal tissue. In conclusion, Lb. gasseri K 7 was found to be effective in reducing E. coli adhesion to Caco-2 enterocytes, but it was not able to do so in ex vivo conditions tested for pig jejunal tissue. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16273411.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16273411.a1 new file mode 100644 index 0000000000000000000000000000000000000000..19b6a3b32cfaaa2f2566f19fe6a48323f7f097cb --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16273411.a1 @@ -0,0 +1,2 @@ +T1 Title 0 140 Early pregnancy loss and neonatal deaths associated with Klebsiella pneumonia infection: a mini review of possible occupational health risk. +T2 Paragraph 141 711 Recurrent pregnancy loss is a disease of grave psychological and economic concern. The etiology in the vast majority of the cases is unknown or at best poorly understood. Although Klebsiella pneumonia infections have been reported in humans and animals during pregnancy, there is hardly any information to indicate whether or not these infections may be responsible for early pregnancy loss. We present a review of literature and report for the first time in humans, Klebsiella pneumonia infection in placenta of a 38-year-old secondary recurrent aborter (parity 2 + 3). diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16273411.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16273411.txt new file mode 100644 index 0000000000000000000000000000000000000000..31d2864abee7eb12f96fa3c5c6923e0822a5bc51 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16273411.txt @@ -0,0 +1,3 @@ +Early pregnancy loss and neonatal deaths associated with Klebsiella pneumonia infection: a mini review of possible occupational health risk. +Recurrent pregnancy loss is a disease of grave psychological and economic concern. The etiology in the vast majority of the cases is unknown or at best poorly understood. Although Klebsiella pneumonia infections have been reported in humans and animals during pregnancy, there is hardly any information to indicate whether or not these infections may be responsible for early pregnancy loss. We present a review of literature and report for the first time in humans, Klebsiella pneumonia infection in placenta of a 38-year-old secondary recurrent aborter (parity 2 + 3). + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16432479.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16432479.a1 new file mode 100644 index 0000000000000000000000000000000000000000..de2991e57e7aeedef483f91706a9c1e15e390905 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16432479.a1 @@ -0,0 +1,4 @@ +T1 Title 0 131 Challenges in the control of gonorrhea in South America and the Caribbean: monitoring the development of resistance to antibiotics. +T2 Paragraph 132 387 : The objective of this study was to ascertain the antimicrobial susceptibility of Neisseria gonorrhoeae isolates from 6 South American and 13 Caribbean countries participating in the Gonococcal Antimicrobial Surveillance Program (GASP) from 1990 to 1999. +T3 Paragraph 388 683 : A GASP network of laboratories was launched in the Americas and the Caribbean during the 1990s. Standardized methods and interpretative criteria were established for the isolation of N. gonorrhoeae, strain identification, and determination, and quality control of antimicrobial susceptibility. +T4 Paragraph 684 1551 : Two countries (Argentina and Uruguay) maintained continuous surveillance during the study period. Some countries gathered data periodically and several others were unable to initiate antimicrobial surveillance as a result of lack of resources. The percentage of penicillin-resistant N. gonorrhoeae isolated in the region over the decade varied considerably (1.0-11.9% carried chromosomal resistance and 17.9-38.8% produced beta-lactamase) with an overall trend to declining numbers of penicillin-resistant isolates. For tetracycline, 7.4% to 36.3% carried chromosomal resistance, whereas 12.0% to 27.4% carried plasmid-mediated resistance. There were no reports of ciprofloxacin-resistant isolates, although N. gonorrhoeae with decreased susceptibility to ciprofloxacin and azithromycin as well as spectinomycin-resistant isolates were identified in some countries. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16432479.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16432479.txt new file mode 100644 index 0000000000000000000000000000000000000000..598dbbbb09e4166b655fdbe9c1258927a2e1d3fd --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16432479.txt @@ -0,0 +1,5 @@ +Challenges in the control of gonorrhea in South America and the Caribbean: monitoring the development of resistance to antibiotics. +: The objective of this study was to ascertain the antimicrobial susceptibility of Neisseria gonorrhoeae isolates from 6 South American and 13 Caribbean countries participating in the Gonococcal Antimicrobial Surveillance Program (GASP) from 1990 to 1999. +: A GASP network of laboratories was launched in the Americas and the Caribbean during the 1990s. Standardized methods and interpretative criteria were established for the isolation of N. gonorrhoeae, strain identification, and determination, and quality control of antimicrobial susceptibility. +: Two countries (Argentina and Uruguay) maintained continuous surveillance during the study period. Some countries gathered data periodically and several others were unable to initiate antimicrobial surveillance as a result of lack of resources. The percentage of penicillin-resistant N. gonorrhoeae isolated in the region over the decade varied considerably (1.0-11.9% carried chromosomal resistance and 17.9-38.8% produced beta-lactamase) with an overall trend to declining numbers of penicillin-resistant isolates. For tetracycline, 7.4% to 36.3% carried chromosomal resistance, whereas 12.0% to 27.4% carried plasmid-mediated resistance. There were no reports of ciprofloxacin-resistant isolates, although N. gonorrhoeae with decreased susceptibility to ciprofloxacin and azithromycin as well as spectinomycin-resistant isolates were identified in some countries. + diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16436701.a1 b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16436701.a1 new file mode 100644 index 0000000000000000000000000000000000000000..8fd2feb3bc5200c451df8ff288476d7a388f61bb --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16436701.a1 @@ -0,0 +1,2 @@ +T1 Title 0 91 Antibacterial properties of dermaseptin S4 derivatives under extreme incubation conditions. +T2 Paragraph 92 1342 Antibacterial properties of the frog-derived peptide dermaseptin S4 and a series of synthetic derivatives against the food pathogen Escherichia coli O157:H7 were investigated under extreme incubation conditions. The 28-mer analog K4K20S4 (P28) displayed an MIC of 8 microM and rapid bactericidal kinetics under standard culture conditions. Potent bactericidal properties were maintained at high salt concentrations, under acidic or basic conditions, and at extreme temperatures. The N-terminal 14-mer sequence (P14) displayed higher potency (MIC, 4 microM) but only within a narrow range of incubation conditions, pointing to the importance of the C-terminal domain of P28. The potency range was reextended upon conjugation of aminododecanoic acid to P14. The resulting lipopeptide was even more potent (MIC, 2 microM) and affected bacterial viability under most of the conditions tested, including in commercial apple juice. The mechanistic implications of peptides' hydrophobicity, charge, structure, and binding to an idealized membrane were probed and are discussed here. Collectively, the data indicate interest in simple peptide-based compounds for design of antimicrobials that affect pathogens under a variable range of incubation conditions. diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16436701.txt b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16436701.txt new file mode 100644 index 0000000000000000000000000000000000000000..f41fb9465c80058ca151182cda3ac33e3d453e01 --- /dev/null +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner_train+dev/bionlp-st/BB-norm+ner-16436701.txt @@ -0,0 +1,3 @@ +Antibacterial properties of dermaseptin S4 derivatives under extreme incubation conditions. +Antibacterial properties of the frog-derived peptide dermaseptin S4 and a series of synthetic derivatives against the food pathogen Escherichia coli O157:H7 were investigated under extreme incubation conditions. The 28-mer analog K4K20S4 (P28) displayed an MIC of 8 microM and rapid bactericidal kinetics under standard culture conditions. Potent bactericidal properties were maintained at high salt concentrations, under acidic or basic conditions, and at extreme temperatures. The N-terminal 14-mer sequence (P14) displayed higher potency (MIC, 4 microM) but only within a narrow range of incubation conditions, pointing to the importance of the C-terminal domain of P28. The potency range was reextended upon conjugation of aminododecanoic acid to P14. The resulting lipopeptide was even more potent (MIC, 2 microM) and affected bacterial viability under most of the conditions tested, including in commercial apple juice. The mechanistic implications of peptides' hydrophobicity, charge, structure, and binding to an i