diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1016123.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1016123.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d37509c75db30ed58f27095444d6bb99889286e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1016123.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10492485.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10492485.txt
new file mode 100644
index 0000000000000000000000000000000000000000..634294c2213594143663afdc9847900ca4c60fc9
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10492485.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10496597.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10496597.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f0dd9fb08befccc4b9a6b8cdac7052fc760f136
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10496597.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10618167.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10618167.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e38bde37aca579f3e6a30818d025247bbe26cbfc
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10618167.txt
@@ -0,0 +1,2 @@
+Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10645449.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10645449.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e775587891ae136e4a32ac2c6ae830ccaacdebb1
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10645449.txt
@@ -0,0 +1,6 @@
+Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10656819.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10656819.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e79022454b0e6b0161c42d13690bcaa19468cdaf
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10656819.txt
@@ -0,0 +1,2 @@
+Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10658649.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10658649.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c16f93500e6118440089760bc7b7374ee862d85
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10658649.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10665543.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10665543.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7be4de92f29f4b3929d14ebbb2e12a1989883bee
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10665543.txt
@@ -0,0 +1,2 @@
+Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10738994.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10738994.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1da4e7c68f673cd8f7bb0ebc3999bb7b74c73c7
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10738994.txt
@@ -0,0 +1,6 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10770276.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10770276.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74a9343f948d8787a80d1ddfdffa987a86ea7794
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10770276.txt
@@ -0,0 +1,2 @@
+Immune response to infection with Salmonella typhimurium in mice.
+Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10792385.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10792385.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7996602ca5e1b914333bf458cf47e1ea98da9c6b
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10792385.txt
@@ -0,0 +1,2 @@
+The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10796014.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10796014.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b21b5d2372de5ed5c15fb2850902d1aceab14a0
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-10796014.txt
@@ -0,0 +1,2 @@
+Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11162736.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11162736.txt
new file mode 100644
index 0000000000000000000000000000000000000000..230065d6701e0cf48a477066a87b672db12b31ca
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11162736.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11410343.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11410343.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc647eb8f176072b9bbccdbfed2a18cd19dde3de
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11410343.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11437594.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11437594.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e75bdc23c2f0f112880a789a3c5907b97c4a290e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11437594.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11551069.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11551069.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad7fdfcb617df2978260fee91642a1cfff24bfdd
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11551069.txt
@@ -0,0 +1,2 @@
+Cloning and expression analysis of Phytoplasma protein translocation genes.
+Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11989773.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11989773.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc5a9ab5a0754269f4a1ecafd4025757d2b4963d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-11989773.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12109661.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12109661.txt
new file mode 100644
index 0000000000000000000000000000000000000000..366bacff1bea9c406afacf21a7a48566ecc4cfd5
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12109661.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1214327.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1214327.txt
new file mode 100644
index 0000000000000000000000000000000000000000..581505118dc4953245cbaff6531f611496f11e9a
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1214327.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12417169.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12417169.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff76f0f788eee6802350c6cb88cb3b68c865ca9a
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12417169.txt
@@ -0,0 +1,2 @@
+Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12438382.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12438382.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62a242fbedfa16b18e68a9fce1dd9b8414705686
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12438382.txt
@@ -0,0 +1,2 @@
+Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12728302.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12728302.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04686bc34a04f3e00c19c6a65d2738bee9119a0f
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12728302.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12781527.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12781527.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b29ca59cb970e49466e03a8d184a754760f72fb1
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12781527.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12934822.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12934822.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c0d0127bfa1069bc8599a14ceb5510fedf05577
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12934822.txt
@@ -0,0 +1,2 @@
+Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12970344.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12970344.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17bcfbcffa02fb48b50084fe3dd3fd0ed03d486a
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-12970344.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1356998.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1356998.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8547c71aeea2f604a396215db77640964d80c5a0
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1356998.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14633026.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14633026.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8aed820331235b47f308d725e402abec1bdf62fd
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14633026.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14638480.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14638480.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e3698512f6579edc899fb830efa9e6f7b9476e7
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14638480.txt
@@ -0,0 +1,2 @@
+Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14645268.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14645268.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46538c62df74e7e0f86aa4d4644ea4f56f6a6689
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14645268.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14657131.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14657131.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8fdab5d810ca9fe0d113493153b7bdfb71ae445
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-14657131.txt
@@ -0,0 +1,2 @@
+Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15273106.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15273106.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa736498a093f6b9f6932a854ffed3ee4184b42a
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15273106.txt
@@ -0,0 +1,2 @@
+Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15293611.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15293611.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a3cfd469b1c48106a1856515b11f9930a4c1abe
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15293611.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15358511.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15358511.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1e6487ef839e3b81381d5915706b33ea661b461
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15358511.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15460321.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15460321.txt
new file mode 100644
index 0000000000000000000000000000000000000000..300dc1431f699041c389c7ccd47a11c2d8d6c80b
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15460321.txt
@@ -0,0 +1,2 @@
+Mycoplasma otitis in California calves.
+A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15612668.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15612668.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c3bdcc33f5ca44cdb73eb99865fbce130f1f5a9
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15612668.txt
@@ -0,0 +1,5 @@
+Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15618837.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15618837.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f48e36e04a608e7301ae5f9878f521ef97f3407
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15618837.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15626953.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15626953.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6194f93c9634f17f28a116375de1e43eed191e75
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-15626953.txt
@@ -0,0 +1,2 @@
+Haemophilus influenzae: a significant pathogen in acute otitis media.
+Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16263187.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16263187.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0b3cc89d57cd6873613f18e2af0f2562f0379ea
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16263187.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16273411.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16273411.txt
new file mode 100644
index 0000000000000000000000000000000000000000..672e63e79f413d43c63f84b129937cd8c1177f0d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16273411.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16432479.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16432479.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33a07b3965da19326a3143c35ddece47c18c288e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16432479.txt
@@ -0,0 +1,4 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16436701.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16436701.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ab2ece92e9d4d334cc6560cc0dfc8ea7f337a58
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16436701.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16458564.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16458564.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4710c0d52e027c83f0774bec761af90c0c50b1df
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16458564.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1649682.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1649682.txt
new file mode 100644
index 0000000000000000000000000000000000000000..745cd47dc87bc058b7f6c6923034368010324a91
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-1649682.txt
@@ -0,0 +1,2 @@
+[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16510930.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16510930.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86bc40fc15defb73995e62eab301553c8911507c
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16510930.txt
@@ -0,0 +1,2 @@
+[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16514151.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16514151.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e229c51ed8b147e56c18a5bbe663dca29ffdf589
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16514151.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16728960.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16728960.txt
new file mode 100644
index 0000000000000000000000000000000000000000..285cfc49d4224bb42ef0d588ff5df1d98b8ac57f
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16728960.txt
@@ -0,0 +1,2 @@
+Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16990433.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16990433.txt
new file mode 100644
index 0000000000000000000000000000000000000000..428736780bdffad1ad3a0ee6b35dbb5d348e43ff
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-16990433.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17237163.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17237163.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82140e862e2ae729bfa471221b330e2fc2900bc1
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17237163.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17261513.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17261513.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ace33bf9058c255ccf736dd92b52085663b25d5e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17261513.txt
@@ -0,0 +1,2 @@
+Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17687514.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17687514.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3fed904c1c8b3ca596545dd3fb537d48e01bb46
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-17687514.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18094887.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18094887.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1af0e7ed4676bf44395e94ddd6d6a075fdf4b227
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18094887.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18687046.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18687046.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6aadfe43d0d2b0e00c9b95b79c9c5d9b6dcd91fe
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18687046.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18694716.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18694716.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d384cdbb1ce9a4678b69ec15fcf1e570bc7920f3
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18694716.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18789156.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18789156.txt
new file mode 100644
index 0000000000000000000000000000000000000000..828d21960bc927b85865b27e0693ebe83d434abe
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18789156.txt
@@ -0,0 +1,4 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18845825.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18845825.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3d4b706605bd56b94fb4c5a5efcceb379ab80a8
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-18845825.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19004249.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19004249.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b02d5edb1f4dc5f3d938bc575bb91bcbbe2380e8
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19004249.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19049879.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19049879.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6803a8d3b02cd127d0bcd7e97d4fa3fd15f33cc3
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19049879.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19075662.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19075662.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7f714555582afb8920cfe18a47fc3ab09f95e19
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19075662.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19099664.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19099664.txt
new file mode 100644
index 0000000000000000000000000000000000000000..464dbe292f412bf2aad05d73c4a3c5f728893e8d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19099664.txt
@@ -0,0 +1,2 @@
+[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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19175621.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19175621.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7501d71052d9dffc2710ec0b6a32bfacf90dba57
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19175621.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19339076.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19339076.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02e84e7e018a2738acdb04a2698c8fbc929ba11d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19339076.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19396518.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19396518.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc93cb5946a1b17f083eb3c6740783c805834886
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19396518.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19494280.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19494280.txt
new file mode 100644
index 0000000000000000000000000000000000000000..acaec4a41175abb8d471ac72b68a04a6424a7713
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19494280.txt
@@ -0,0 +1,2 @@
+Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19501788.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19501788.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5faf6d76a24f70ea337ff8780a1088c267edb8fc
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19501788.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19552770.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19552770.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14fc86f13b2e2106fbc6a078b388124b522933af
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19552770.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19621381.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19621381.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a0f99de6cf7150cdbb4095b40b332435ec75296
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19621381.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19622846.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19622846.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfb2bf0390ec50d539b08235270939175b54ed50
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19622846.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19656787.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19656787.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e291156f51a09019615bb890d7558399e049cf6
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19656787.txt
@@ -0,0 +1,2 @@
+Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20005916.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20005916.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1613542c234b2141663620dfdcb47c9b185328be
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20005916.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20073421.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20073421.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54da5bf808a39fdf10f5cc23293309bc6fb49b15
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20073421.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20148898.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20148898.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba8b62aa746430af15c2913b7dde6288071f1b64
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20148898.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20174624.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20174624.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b080720a4ac1fab2ba529cc54432e82735e5557
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20174624.txt
@@ -0,0 +1,4 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20400104.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20400104.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12d0c12e9838563002e4530073f4e52687a3fcf5
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20400104.txt
@@ -0,0 +1,5 @@
+Microbiota in pediatric inflammatory bowel disease.
+To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20580604.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20580604.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d25f48665763ba030d8041a155258293e219e28c
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20580604.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20672296.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20672296.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e08d30ee2b0db478a200de6cfc9bf36e0a1810f
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20672296.txt
@@ -0,0 +1,2 @@
+An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21148810.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21148810.txt
new file mode 100644
index 0000000000000000000000000000000000000000..592e04b368ce10495a746ef1c7c4ae7dff31954b
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21148810.txt
@@ -0,0 +1,2 @@
+TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21270066.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21270066.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9627628089e6bbf41e2bdf98afe0e09c39352fe
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21270066.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21476570.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21476570.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3a5a8d6358fdc24ec92c543540beaf893a2de64
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21476570.txt
@@ -0,0 +1,2 @@
+Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21498521.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21498521.txt
new file mode 100644
index 0000000000000000000000000000000000000000..017de59b7b4e6ebd6546e05da71f350fcde4f9b6
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21498521.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21511409.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21511409.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4fec4294d4b2d0d699415f25d20cbe1c64666626
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21511409.txt
@@ -0,0 +1,2 @@
+Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21543877.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21543877.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e93932cfe72eb5ee876696862b986cb7d0376076
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21543877.txt
@@ -0,0 +1,2 @@
+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 Ã… 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 Ã…. With one molecule per asymmetric unit, the crystal volume per unit protein weight (V(M)) is 2.91 Ã…(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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21695078.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21695078.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b13c95d0037c191bb3517c517c5c082986e682ca
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21695078.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21894542.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21894542.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97e3af098993f98050b50a0bd1b5166bf2042dfd
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21894542.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21917915.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21917915.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed31c4c20e3a611fd2ab216c908549195972e85e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21917915.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21924022.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21924022.txt
new file mode 100644
index 0000000000000000000000000000000000000000..637d8758458268c00555e56c1b5f22645d35e5bc
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21924022.txt
@@ -0,0 +1,5 @@
+[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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21989983.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21989983.txt
new file mode 100644
index 0000000000000000000000000000000000000000..958f662a4bea32d82f0cebca2f0bb952a414b912
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21989983.txt
@@ -0,0 +1,2 @@
+Insights into Acinetobacter baumannii pathogenicity.
+Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22203552.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22203552.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af1fc60d37087570d18add9b3f4e5cd8340fe5be
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22203552.txt
@@ -0,0 +1,2 @@
+Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22537874.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22537874.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b868e1e4430770cf98b3e471272e663fc74ca9b2
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22537874.txt
@@ -0,0 +1,2 @@
+Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22834551.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22834551.txt
new file mode 100644
index 0000000000000000000000000000000000000000..36226cc5ad8a57e940c2860e3dbac1bbb526d350
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-22834551.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23645023.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23645023.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ef1de48ea9e84692e47e52f9587efee7b8146f6
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23645023.txt
@@ -0,0 +1,2 @@
+Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23702192.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23702192.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ff742c3b5d5c04d03c99ee997506721c1ddb214
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23702192.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23704121.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23704121.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ed2b8bba2d8b430cb0431194fb6e4f3e51d2f5d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23704121.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23855904.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23855904.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a31de981c99ed836f1ebe10103e01f43ff02f12
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23855904.txt
@@ -0,0 +1,4 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23902156.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23902156.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a7f0d4b7b0b96d76ad58ad83700925c43a3a43b
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23902156.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23908036.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23908036.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ead1387baf18ddbfd30af067753f99202e7a4b4
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-23908036.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24198224.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24198224.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d563cc084d3f18c946db9973cc24328fbd6310bf
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24198224.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24251551.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24251551.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3371bdb2c39657e14560e9c3df2757518061ff1
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24251551.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24361838.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24361838.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c36e1c475b7a7820212a19afacd57ae46cc67e1d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24361838.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24389148.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24389148.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5427937d38e300ec2cddf564a14690fbfa81baa
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24389148.txt
@@ -0,0 +1,2 @@
+Molecular determinants for a cardiovascular collapse in anthrax.
+Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24584903.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24584903.txt
new file mode 100644
index 0000000000000000000000000000000000000000..205836fa4498c024dd8229a00f37515017f28402
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24584903.txt
@@ -0,0 +1,2 @@
+On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24678646.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24678646.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e1958a1236de0075debdac88ab6b73dda77480d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24678646.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24739626.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24739626.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ef09cb9e2bf7b39302677021100eb89c449588e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24739626.txt
@@ -0,0 +1,2 @@
+Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24794581.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24794581.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad60d720ed7d125f35fca8c52173f1ce1439d01b
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24794581.txt
@@ -0,0 +1,2 @@
+The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24831788.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24831788.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bf49f252ba779de58d49dd1cbb79879ff81f6fb
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24831788.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24865686.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24865686.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e46797d9c43ee68318244652d35951e62e63b63
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24865686.txt
@@ -0,0 +1,2 @@
+Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24874563.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24874563.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e8ee9b2a2d4b488a3079f500a0f767e5f1135cf
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-24874563.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25046729.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25046729.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6cd1d513bfa337d3cf7567a4d9d52bd84277c37
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25046729.txt
@@ -0,0 +1,2 @@
+Wolbachia endosymbionts and human disease control.
+Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25098305.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25098305.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c95f4362ef31eb49d5246cfb3862a1143740adcd
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25098305.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25114119.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25114119.txt
new file mode 100644
index 0000000000000000000000000000000000000000..392f867b9369b1370f11c6999f96e84bff09ee1c
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25114119.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25179651.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25179651.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2953a0fc9dc810276cbb73236e816587497e9242
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25179651.txt
@@ -0,0 +1,6 @@
+Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25204345.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25204345.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26c09e22b48546790235c1fa635bc6d0bdf4ef7d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25204345.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25562320.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25562320.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdf053678ca2a77dabf89f37d840e3627a053355
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25562320.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25607366.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25607366.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae5d4e3570db3a08d3d269f5bb542187fb4350e3
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25607366.txt
@@ -0,0 +1,2 @@
+Biocontainment of genetically modified organisms by synthetic protein design.
+Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25634638.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25634638.txt
new file mode 100644
index 0000000000000000000000000000000000000000..109d750ea12d02bf48a21c8f332a676cc3113c69
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25634638.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25644009.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25644009.txt
new file mode 100644
index 0000000000000000000000000000000000000000..25adcf6f3fb0048778d9d484ed6091ca4545530c
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-25644009.txt
@@ -0,0 +1,2 @@
+Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors. 
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-26155675.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-26155675.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b736f6447821bd0d906272624c75f2f434d7432e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-26155675.txt
@@ -0,0 +1,2 @@
+Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-2617654.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-2617654.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78037147c18571830adc3960096cdd2ff96c081f
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-2617654.txt
@@ -0,0 +1,2 @@
+Carriage of Haemophilus influenzae in healthy Gambian children.
+1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-2696427.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-2696427.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc4f8a0cc0252a8facd163fb60cff0a582736ba3
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-2696427.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3015879.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3015879.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6f6c12d83fcd8687ffe78e73c26b7e409088605
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3015879.txt
@@ -0,0 +1,2 @@
+Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3074181.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3074181.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6e51fe684b2ad17838d3d3fa67e9af58da0ef46
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3074181.txt
@@ -0,0 +1,2 @@
+[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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-351567.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-351567.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dbd73dffe008762c868a1024db27e75c79392898
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-351567.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3516874.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3516874.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e37713622ab4f20444a0342371d94173048a472
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3516874.txt
@@ -0,0 +1,2 @@
+Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3544198.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3544198.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca16a69035f3b8fbf4b6d3b507e250023b72f2f6
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-3544198.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4105033.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4105033.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd418ed765efc33f6985a9a66781e67a188b9d73
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4105033.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4328756.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4328756.txt
new file mode 100644
index 0000000000000000000000000000000000000000..510321cc626e6f646fff4bd44a2122e83fd9e755
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4328756.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4329237.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4329237.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fab2becf06b9b6f961a613b386418e501de94eb5
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-4329237.txt
@@ -0,0 +1 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-448557.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-448557.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d0fd1741d02d4fbaf1d68029c4e4960f1fd84dd
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-448557.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-460951.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-460951.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56f16c42eab8ebab88c358357c4268b8ba8feda4
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-460951.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-47483.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-47483.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ee2101c213b45b60ab270a80125e0408f7142ab
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-47483.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-5526468.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-5526468.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b63f4bb18a1cbb567f3df8c4da37e5c3f3dfbb25
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-5526468.txt
@@ -0,0 +1 @@
+Vibrio fetus human infection--isolation from a subacute bacterial endocarditis case.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-607884.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-607884.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb814e45ff8b7ba58127b94c176a6816af6106e8
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-607884.txt
@@ -0,0 +1 @@
+[The infections from "Serratia" in the Hospital S. Camillo De Lellis of Roma (Italy) (author's transl)].
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6107735.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6107735.txt
new file mode 100644
index 0000000000000000000000000000000000000000..685c651841c6727efc6048ff25f922bb60b6a986
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6107735.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6143890.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6143890.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52fe061d4270bfe200479f7303264bd3edcaeb1b
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6143890.txt
@@ -0,0 +1 @@
+Rapid detection with monoclonal antibodies of Chlamydia trachomatis in urethral smears and urine sediments.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6631408.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6631408.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47f6a4a159a92f01c38516facdaaee76e4ac8226
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-6631408.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-7867953.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-7867953.txt
new file mode 100644
index 0000000000000000000000000000000000000000..961521763cabec8202f5b517540ee15ceab95a0f
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-7867953.txt
@@ -0,0 +1,2 @@
+Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-7876637.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-7876637.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d032309b89e7ca67da7c566ccc63a31ef18835e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-7876637.txt
@@ -0,0 +1 @@
+The spread of Vibrio cholerae O139 in India.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-817056.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-817056.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04d40c5fac0de5f6e7324d2e246502784338fa41
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-817056.txt
@@ -0,0 +1,2 @@
+Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8347510.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8347510.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd0539479e34eaf5c21fe633bb07a455cada64a0
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8347510.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8358765.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8358765.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7885204de86bfd6d9d587c42f8a104d74d92d4e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8358765.txt
@@ -0,0 +1,2 @@
+[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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8406892.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8406892.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1b5fccf031dcd3c88c0fc1828208815e9203bef
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8406892.txt
@@ -0,0 +1,2 @@
+Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8532424.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8532424.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dd9b26a8d7a3e62953d080ba9148893fb851941
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8532424.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8559802.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8559802.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca70d2b2147fbff0d151dab47148586cb5174926
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8559802.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8607503.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8607503.txt
new file mode 100644
index 0000000000000000000000000000000000000000..134e9e1e3456031250792a4f1d5226858fc8a003
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8607503.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8698477.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8698477.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9307a04362eb4d0349b411daeb539daaad35c7f
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8698477.txt
@@ -0,0 +1,2 @@
+Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8703935.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8703935.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46471a90c191607fc0d2f1dcfd13400c45a7bbf6
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8703935.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8997164.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8997164.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b456e2f60396f665ad50ca32003399ed975ae31
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8997164.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9231420.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9231420.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9713b9e80c80904e75bfa672f85dfcf478c39fad
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9231420.txt
@@ -0,0 +1,2 @@
+Neuraminidase (sialidase) activity of Haemophilus parasuis.
+Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9255900.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9255900.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3bca703694ef1bcbfb4c2e8aeb96d12bee3ecd3b
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9255900.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9521147.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9521147.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2be862de6e201f4eb49229e264168119e5c4e637
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9521147.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9526514.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9526514.txt
new file mode 100644
index 0000000000000000000000000000000000000000..daf5e495a088263138deb302a034d478bd88b488
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9526514.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9535771.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9535771.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f518b461038c62062dfb2594d9907e4002c28979
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9535771.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9553794.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9553794.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1d5e37cd42d1ae817a1280f2e9ac279bae3f633
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9553794.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9562874.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9562874.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3d732d3f963c86a4e61c31aee88b158352489ff
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9562874.txt
@@ -0,0 +1,2 @@
+Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9564489.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9564489.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3308462c5b0ba9740216dd449a4d38167d9fe13e
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9564489.txt
@@ -0,0 +1 @@
+Gingivomandibular infection due to Mycobacterium kansasii in a patient with AIDS.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9575437.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9575437.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a5ce93a7a85ee0bd9b869d2aa2be8ad97ec9362
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9575437.txt
@@ -0,0 +1,2 @@
+[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9643457.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9643457.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c855301abbb235ff5bc2fbf2dd9de2660b73ce85
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9643457.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9666962.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9666962.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63dc8b05d7f6dd5575bb3a7a6f01b216411ba00f
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9666962.txt
@@ -0,0 +1,6 @@
+Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+Experimental murine tuberculosis.
+To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
diff --git a/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9693738.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9693738.txt
new file mode 100644
index 0000000000000000000000000000000000000000..952859a89899a60a954b90cdc8ad5ee77185e2fd
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9693738.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9745160.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9745160.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cadc3dfcf04c092367d0dbe9d59740b347ba5949
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9745160.txt
@@ -0,0 +1,5 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9798026.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9798026.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23dda421577fec8927763351669ec29f36b69c2d
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9798026.txt
@@ -0,0 +1,2 @@
+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/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9864452.txt b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9864452.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e4a76d55e51c717c1ccfa303c19489736aaa123
--- /dev/null
+++ b/BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-9864452.txt
@@ -0,0 +1,2 @@
+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/ner-taxa.plan b/ner-taxa.plan
new file mode 100644
index 0000000000000000000000000000000000000000..6268a1e919650e6a31ae17f018f11aec3ac0ed03
--- /dev/null
+++ b/ner-taxa.plan
@@ -0,0 +1,70 @@
+<alvisnlp-plan id="ner-taxa">
+  <param name="taxaDict">
+    <alias module="dict" param="dictFile"/>
+  </param>
+
+  <param name="compiledDict">
+    <alias module="dict" param="trieSource"/>
+  </param>
+
+  <param name="sectionFilter">
+    <alias module="dict" param="sectionFilter"/>
+  </param>
+
+  <dict class="TabularProjector">
+    <targetLayerName>ambiguousTaxa</targetLayerName>
+    <!--<dictFile>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt</dictFile>-->
+    <trieSource>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.trie</trieSource>
+    <matchStartCaseInsensitive/>
+    <valueFeatures>,taxid,canonical-name,path,pos,rank,species-taxid,species-name</valueFeatures>
+    <constantAnnotationFeatures>source=NCBI</constantAnnotationFeatures>
+  </dict>
+
+  <disambiguate>
+    <not-ambiguous class="Action">
+      <target>documents.sections.layer:ambiguousTaxa</target>
+      <action>$[not span:ambiguousTaxa].(add:taxa|remove:ambiguousTaxa|set:feat:disambiguation("not-ambiguous"))</action>
+      <addToLayer/>
+      <removeFromLayer/>
+      <setFeatures/>
+    </not-ambiguous>
+
+    <disambiguate-coreferences class="Action">
+      <target>documents.sections.layer:ambiguousTaxa</target>
+      <action>$[(section.nav:sections-before.layer:taxa|before:taxa)[@taxid == target.@taxid]].
+      (add:taxa|remove:ambiguousTaxa|span:ambiguousTaxa.remove:ambiguousTaxa|set:feat:disambiguation("coreference"))</action>
+      <addToLayer/>
+      <removeFromLayer/>
+      <setFeatures/>
+    </disambiguate-coreferences>
+
+    <disambiguate-coreference-more-general class="Action">
+      <target>documents.sections.layer:ambiguousTaxa</target>
+      <action>$[(section.nav:sections-before.layer:taxa|before:taxa)[@path ^= target.@path and @rank == "genus"]].
+      (add:taxa|remove:ambiguousTaxa|span:ambiguousTaxa.remove:ambiguousTaxa|set:feat:disambiguation("is-general"))</action>
+      <addToLayer/>
+      <removeFromLayer/>
+      <setFeatures/>
+    </disambiguate-coreference-more-general>
+
+    <disambiguate-coreferences-more-specific class="Action">
+      <target>documents.sections.layer:ambiguousTaxa</target>
+      <action>$[(section.nav:sections-before.layer:taxa|before:taxa) as gen.$[target.@path ^= @path and not target.span:ambiguousTaxa[@path ^= gen.@path]]].
+      (add:taxa|remove:ambiguousTaxa|span:ambiguousTaxa.remove:ambiguousTaxa|set:feat:disambiguation("is-specific"))</action>
+      <addToLayer/>
+      <removeFromLayer/>
+      <setFeatures/>
+    </disambiguate-coreferences-more-specific>
+
+    <remove-disambiguated class="Action">
+      <target>documents.sections.layer:ambiguousTaxa</target>
+      <action>$[span:taxa].remove:ambiguousTaxa</action>
+      <removeFromLayer/>
+    </remove-disambiguated>
+
+    <report-ambiguous class="Action">
+      <target>documents.sections.layer:ambiguousTaxa</target>
+      <action>module:log("Ambiguous taxon in " ^ section.document.@id ^ "/" ^ section.@name ^ " at " ^ start ^ "-" ^ end ^ ": " ^ @form ^ " -> " ^ @taxid ^ " (" ^ @canonical-name ^ ")")</action>
+    </report-ambiguous>
+  </disambiguate>
+</alvisnlp-plan>
diff --git a/select-taxa.plan b/select-taxa.plan
new file mode 100644
index 0000000000000000000000000000000000000000..3e054bc62d4bbbd23683b3d86bb5cadc294d674a
--- /dev/null
+++ b/select-taxa.plan
@@ -0,0 +1,35 @@
+<alvisnlp-plan id="select-taxa">
+
+  <param name="list">
+    <alias module="taxids" param="mappingFile"/>
+  </param>
+
+  <param name="name">
+    <alias module="name" param="featureValue"/>
+    <alias module="overlaps" param="layerName"/>
+  </param>
+
+  <name class="SetFeature">
+    <target>$</target>
+    <featureName>select-taxa-name</featureName>
+  </name>
+
+  <taxids class="FileMapper">
+    <target>documents.sections.layer:taxa</target>
+    <form>@taxid</form>
+    <targetFeatures>selected-taxa</targetFeatures>
+  </taxids>
+    
+  <layer class="Action">
+    <target>documents.sections.layer:taxa[@select-taxa]</target>
+    <action>
+      setlayer:add(corpus.@select-taxa-name)
+      | set:feat(corpus.@select-taxa-name, corpus.@select-taxa-name)
+      | set:remove-feature:selected-taxa
+    </action>
+    <addToLayer/>
+    <setFeatures/>
+  </layer>
+
+  <ovrelaps class="RemoveOverlaps"/>
+</alvisnlp-plan>
diff --git a/test.plan b/test.plan
new file mode 100644
index 0000000000000000000000000000000000000000..3605013442f9e95cd5d86cb1500e9aece5e3485a
--- /dev/null
+++ b/test.plan
@@ -0,0 +1,11 @@
+<alvisnlp-plan id="test">
+  <read class="TextFileReader">
+    <sourcePath recursive="true">BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-8347510.txt</sourcePath>
+    <baseNameId/>
+  </read>
+  
+  <ner-taxa href="ner-taxa.plan">
+    <taxaDict>output/taxa+id_full.txt</taxaDict>
+    <compiledDict>output/taxa+id_full.trie</compiledDict>
+  </ner-taxa>
+</alvisnlp-plan>
\ No newline at end of file