dataesr/scientific-paragraphs-categorization huggingface dataset:
These data are consistent with our previous results obtained at day-3 p. i. , showing an important role of TLR2 and TLR4 in the mouse defense and clearance of Leptospira  [10] , and further suggest that the extent of fibrosis is not directly proportional to bacterial excretion, reflecting the renal bacterial loads. To evaluate whether Leptospira infection, and subsequent renal colonization and fibrosis could be deleterious to renal function, the level of serum creatinine, used as a marker of renal function, was measured in the serum of mice at day-90 p. i. Interestingly, the infected WT mice did not show any statistically significant elevation of the serum creatinine when compared to naı ¨ve WT mice (Fig. 4D ). In contrast, all TLRko mice presented a slight but significant elevation of the serum creatinine levels compared to those of WT mice and corresponding naı ¨ve TLRko mice (Fig.
Immunofluorescence images at low magnification were obtained by wide-field microscopy using a Leica DMI 6000B microscope and, afterwards, acquired images were deconvolved using the AutoQuant X 3 software (Media Cybernetics Inc. , Rockville, MD, USA). For high-magnification images, acquisitions were done using a Leica TCS SP2 AOBS confocal laser scanning imaging system (Leica Microsystems AG, Nanterre, France). The specificity of the immunoreactions was verified by omitting the primary antibodies. Quantification of Nkx2. 1-positive cells immunoreactive for cleaved caspase-3. High-magnification images were acquired in the cortex of E15 brain slices by confocal microscopy and saved in a TIFF format. Images were subsequently opened in the Metamorph software and a grid was affixed on the image defining three regions of interest (ROIs).
The emitted fluorescence was collected at 510 nm and the ratio of the two signals calculated using Metamorph software (Roper Scientific, Evry, France). Data were exported to the biostatistics software Prism (GraphPad Inc. , San Diego, CA, USA), which was used to compute the maximal fluorescence intensity and the area under the curve. Quantification of densities of Gad67-GFP cells and primary neuritis. For measurement of Gad67-GFP and GABAergic cell density, images were acquired and saved in TIFF format with a confocal laser scanning microscope (Noran Instruments, Middleton, WI, USA) using INTERVISION software (Noran Instruments). Images were subsequently opened in Mercator software and ROIs were drawn. Afterwards, a counting frame was defined within the ROI and a threshold was set in order to differentiate GFP-positive and GABApositive cells from the background.
Z-stack series of images were later deconvolved using AutoQuant X 3 deconvolution software and loaded into IMARIS imaging software (Bitplane, Zurich, Switzerland) for 3D reconstruction. The Filament Tracer function was used to assign and classify spines, yielding spine density and spine categories (stubby, filopodial or mushroom-shaped). Quantification was done on three slices per animals and three animals per group were analyzed. In particular, for a given slice, two ROIs were defined, two to three dendrites were quantified per ROI and the total number of quantified neuritis was fixed at 40 per group. Determination of cortical GABA content. At P45, control and ketamine-exposed animals were killed by decapitation. The brains were quickly removed, the cortex were dissected on ice and homogenized by sonication at high frequency (70 Hz) for 4 s using a VibraCell Sonicator (Sonics and Materials, Newtwon, CT, USA) in ice-cold perchloric acid (0.
6 V versus a Ag/AgCl reference electrode. The mobile phase consisted of Na 2 HPO 4 (0. 1 M), methanol (240 g/l) and Na 2 EDTA (0. 15 mM) (pH 5. 5), filtered through 0. 45-mm filters (Millipore) and delivered by a pump (Spectrasystem P1000XR, Thermo Fisher Scientific, San Jose, CA, USA) at a flow rate of 0. 3 ml/min. Samples (20 ml) were then injected into the HPLC system by means of an automatic device (AS 300; Spectra Physics, Santa Clara, CA, USA). Chromatograms were recorded and integrated using PC integration Azur software (Datalys, Le Touvet, France). Glutamate concentration assay. The glutamate concentrations from P45 cortex extracts were quantified following the instructions provided within the glutamate assay kit. In practice, several dilutions of cortex extracts from control and ketamine-exposed animals were incubated with 100 ml of assay buffer in a 96-well plate.
The recording apparatus was connected to a computer to process the data. Horizontal locomotor activity (the number of infrared beams crossed) and vertical locomotor activity (the number of infrared beams broken up to a height of 9 cm) were measured during six consecutive 30-min periods. In addition, video tracking using ANY-maze software (Stoelting, Wood Dale, IL, USA) was also performed to illustrate quantitative data acquired with the actimeter. Statistical analysis. Statistical tests were run using the biostatistics software Prism (GraphPad Inc. ). To analyze the effects of ketamine on caspase-3 activity, statistical analyses were used to compare the ketamine-treated ipsilateral side versus the control contralateral side using the Wilcoxon signed-rank test. To analyze the effects of ketamine on mitochondrial integrity, cell density, primary neurite and spine numbers, Nkx2.
1-cleaved caspase 3 co-labeled cells, GABA and glutamate concentrations, western blot data and calcimetry, statistical analyses were used to compare ketamine-treated versus control conditions using the Mann-Whitney U-test. Locomotor activity was analyzed by two-way ANOVA (time/treatment) followed by Bonferroni's post test. For the distribution of spine subtypes, a w 2 -test was used.
Genotyping DNA extraction from mycobacteria isolates and high-throughput spoligotyping on Luminex 100 (Luminex Corp. , TX) were performed as previously described  [16, 17]. The obtained data were compared with those of the international databases SpolDB4. 0  [18]  and http://www. Mbovis. org [19]. The new spoligo-Human and cattle isolates were also genotyped by PCR amplification of 26 MIRU-VNTR loci: ETR A, B, C, D, E; QUB-11a, 11b,  26, 4156, 3232; MIRU 2, 10, 16, 20, 23, 24, 26, 27, 39, 40 and Mtub 04, 21, 29, 30, 34, 39 [20, 21]. We used multiplex PCR and capillary electrophoresis-based sequencers (ABI 3730-XL), as previously described  [22]. PCR fragment sizing and assignment of the different MIRU-VNTR alleles were done using Genemapper, version 4. 0 (PE Applied Biosystems). The results for each of the 26 loci were combined into 26-digit allelic profiles  [22].
bovis circulates between Burkina Faso and its neighbouring countries and ii) M. bovis is transmitted mainly between cattle, but also between cattle and humans, and potentially between humans. This study stresses the need to develop an efficient strategy to control M. bovis transmission, but also the difficulty to implement control measures because of the complex epidemiology of bovine tuberculosis in Burkina Faso. new SB numbers (spoligotype codes) were assigned accordingly. types were submitted to the http://www. Mbovis. org database, and.
Genetic characterization Spoligotyping confirmed species identification for all 33 M. bovis isolates. Among the 12 spoligotype signatures obtained (Table  2 ), only five (SB1398, SB0300, SB0857, SB0944, SB1439) were already described in the http://www. Mbovis. org database. M. bovis isolate (Fig. 1  and Table  2 ). By MIRU-VNTR typing, only one (human sample h7, spoligotype = SB2284, pattern P4) of the 33 isolates could not be genotyped. MIRU-VNTR typing produced 24 distinct patterns (Fig. 1  and Table  2 ). Fifteen isolates (46. 9%) were grouped in seven clusters and the other 17 isolates (53. 1%) had a specific pattern each. Moreover analysis of the 26 MIRU-VNTR loci, showed that nine loci were monomorphic in the 32 M. bovis strains analysed (see Table  3 ), indicating the presence of moderate polymorphism.
ACPD  ACPD ACPD ACPD ACPD ACPD ACPD ACPD ACPD ACPD ACPD Acknowledgements. This work is financially supported by grants from the  National Key Project of Basic Research  ( 2011CB403401&2014CB441201 ), the  Project  ( 41005086 ,  41275167 & 41130104 ) supported by  NSFC , the  Strategic Priority Research Program  of the  Chinese Academy of Sciences  (Grant No. XDA05100301 ),  CAMS Basis Research Project  ( 2012Y02 & 2013Z007 ). Cimel master calibration of CARSNET was performed at the  AERONET-EUROPE calibration center (LOA and AEMET-Tenerife ), supported by  ACTRIS  ( European Union   Seventh Framework Program  ( FP7/2007-2013)  under grant agreement no. 262254. ACPD ACPD ACPD ACPD ACPD ACPD ACPD ACPD ACPD ACPD.
In silico analysis We used CRISPR sequencing data from a previous study, which included 18 strains and two genomes (Ty2 and CT18, GenBank accession nos. AE014613 and AL627276, respectively) of S. enterica serotype Typhi and 12 strains and two genomes (ATCC 9150 and AKU_12601, GenBank accession nos. CP000026 and FM200053, respectively) of S. enterica serotype Paratyphi A  [15]. A new genome (P-stx-12, GenBank accession no. CP003278) of serotype Typhi was also analyzed.
Serotype-specific PCRs The PCR specific for S. enterica serotype Typhi was carried out with forward primer TY-F (59-ACGTAGACTCATCCTC-GACC-39 corresponding to region 2928811-2928830 of S. enterica serotype Typhi strain Ty2; GenBank accession no. NC_004631), binding 206 bp upstream from CRISPR2, and the reverse primer TY-R (59-GCGTGTAGCAGTATTCACCA-39 corresponding to region 2929055-2929036 of strain Ty2), binding to the DR-EntB0var1 spacer junction of CRISPR2. The PCR specific for S. enterica serotype Paratyphi A was carried out with forward primer PA-F (59-ACGGGTTGCTGTAAT-GATGC-39 corresponding to region 2889276-2889295 of S. enterica serotype Paratyphi A strain ATCC 9150; GenBank accession no. NC_006511), binding 293 bp upstream from CRISPR1, and the reverse primer PA-R (59-GCATCATCGCG-.
Thus, for 100% specificity to be achieved with this approach, several targets must be incorporated into the PCR assay. A new approach for identifying targets on the basis of genome comparison analysis has recently been described. However, the complete Salmonella genomes available cannot really be considered representative of the entire genus (39 complete genomes online, covering only 25 serotypes from the. 2,500 described when this work was begun in 2011). Moreover, only three assembled genomes of serotypes Typhi (Ty2, CT18, and P-stx-12) and two of Paratyphi A (ATCC 9150 and AKU_1260) are available online. Seventeen 454 shotgun-sequenced serotype Typhi strains representing various genetic lineages  [24]  have been deposited in wholegenome sequence databases since 2008, but have rarely been used for the selection of serotype-specific targets  [13].
General paradigms of species extinction risk are urgently needed as global habitat loss and rapid climate change threaten Earth with what could be its sixth mass extinction. Using the stony coral Lophelia pertusa as a model organism with the potential for wide larval dispersal, we investigated how the global ocean conveyor drove an unprecedented post-glacial range expansion in Earth's largest biome, the deep sea. We compiled a unique ocean-scale dataset of published radiocarbon and uranium-series dates of fossil corals, the sedimentary protactinium-thorium record of Atlantic meridional overturning circulation (AMOC) strength, authigenic neodymium and lead isotopic ratios of circulation pathways, and coral biogeography, and integrated new Bayesian estimates of historic gene flow. Our compilation shows how the export of Southern Ocean and Mediterranean waters after the Younger Dryas 11.
The validity of each dispersal pathway was examined on a region-by-region basis relative to published coral biogeographic and genetic patterns and new estimates of historic gene flow. Consolidating recent community and population data along these pathways with palaeoceanographic patterns was vital to reconstructing coral history: understanding Lophelia biogeography and genetic patterns allowed us to infer migration pathways that were historically and are currently important to buffering extinction risk by promoting dispersal between habitats in the deep sea.
Acknowledgements This analysis began during the  Trans-Atlantic Coral Ecosystem Study  (http://www. lophelia. org/traces)sponsored by the  European Commission   FP6  project  TRACES  ( MOIF-CT-2006-040018  to JMR) with additional funding from the  British Consulate-General Boston ,  Canadian Department of Fisheries and Oceans , the  NOAA Undersea Research Center , the  University of North Carolina Wilmington Center for Marine Science , the  U. S. Geological Survey, Environmental Defence, Oceana , the  South Atlantic Fishery Management Council , the  U. K. Natural Environment Research Council , the  Scottish Association for Marine Science  and the  Marine Conservation Institute. This paper is a contribution towards the  European Commission   FP7 projects HERMIONE  (Grant  226354 ) and EPOCA (Grant  211384 ), the  UK Ocean Acidification programme (NERC  Grant  NE/H017305/1 ), and the  Deutsche Forschungsgemeinschaft DFG -project  WACOM.
ulcerans to describe the virulence mechanisms of this bacterial species. In fact, little knowledge is available regarding the C. ulcerans virulence factors associated with infectious conditions  (11)  and the pathogen-host interaction process. To date, only three genomes for this species have been entered into the National Center for Biotechnology Information (NCBI) database  (7, 8). Two of these lineages were considered to be nontoxigenic because they lack the DT gene. The FRC58 lineage of C. ulcerans examined in the present study was isolated from the secretions of an 86-year-old patient with bronchitis who was hospitalized at the Hospital Center of Troyes (France). The genome of this bacterial species was sequenced using the Ion Torrent PGM system, using a fragment library. The sequencing process generated 6,686,040 reads (~2 gigabases), which represents a coverage of 800ϫ.
The reads were assembled de novo using the CLC Genomics Workbench. This assembly produced a total of 241 contigs with an N 50 contig length of 113 kb; the longest contig is 419 kb, and the shortest contig is 201 bp. The contigs were annotated using Rapid Annotations using Subsystems Technology (12), and 2,503 coding sequences (CDSs), 10 rRNAs, and 61 tRNAs were identified. The GϩC content of the examined genome is 53. 23%. The complete C. ulcerans FRC58 genome was obtained, with a total of 2,609,412 bp. Nucleotide sequence accession numbers. The C. ulcerans FRC58 draft genome sequence has been deposited in GenBank under the accession no. AYTI00000000. The version described in this paper is version AYTI01000000.
ACKNOWLEDGMENTS This work was part of the  Paraense Network of Genomics and proteomics (Rede Paraense de Genômica e Proteômica) , supported by the  Paraense Amazonia Foundation (Fundação Amazônia Paraense [FAPESPA]) , the  Amazon Center of Excellence in Genomics of Microorganisms (Núcleo Amazônico de Excelência em Genômica de Microorganismos)-Centers of Excellence Support Program (Programa de Apoio a Núcleo de Excelência) Pronex/CNPq/FAPESPA , the  National Program for Academic Coopera-.
The interaction map was generated using STRING  [123]  and default settings (Medium confidence of 0. 4 and 4 criteria for linkage: co-expression, experimental evidences, existing databases and text mining). The proteins names used in this network are listed in Tables  1  and 2. For immunoblotting, the monoclonal antibodies against VCL and FHL3 were from Sigma. The anti-mouse IgG-HRP, anti-rabbit IgG-HRP, anti-SRL and anti-β-actin (ACTB) were from Santa-Cruz biotechnology (Heidelberg, Germany). The polyclonal antibodies against GPD1, MYOZ1, ANXA1, ANXA5, GSTO1, HSPB5, HSPC3, ALDH2, NDUFS2, UQCRFS1, ENO3, HSPA1A and VCP were purchased from Euromedex (Genetex, Souffelweyersheim, France).
Visualization of proteins and image analysis 2DGE were fixed overnight in a solution containing 30% (v/v) ethanol and 2% (v/v) orthophosphoric acid, washed twice for 30 min in 2% (v/v) orthophosphoric acid and then transferred to a solution containing 18% (v/v) ethanol, 2% (v/v) orthophosphoric acid and 15% (v/v) ammonium sulphate for 30 min. The gels were stained for 72 h with 0. 06% (w/v) Coomassie Blue G-250 added to this last solution. Gels were scanned using the ImageScanner and LabScan-v. 5 software (Amersham Bioscience) and protein spots were analyzed and matched between all gels using Progenesis SameSpot software (Non Linear Dynamics, Newcastle upon Tyne, UK). Age effect was evaluated for normalized volumes of 2DGE spots using an unpaired Student's t test procedure with significance set at P <0.
Eight microliters of each peptide sample were loaded on a C18 pre-column (300-μm inner diameter × 5 mm; Dionex) at 20 μl/min in 5% acetonitrile, 0. 05% trifluoroacetic acid. After 6 min of desalting, the pre-column was switched on line with the analytical C18 column (75-μm inner diameter × 15 cm; PepMap C18, Dionex) equilibrated in 96% solvent A (0. 5% formic acid) and 4% solvent B (80% acetonitrile, 0. 5% formic acid). Peptides were eluted using a 4-50% gradient of solvent B during 30 min at a 300 nl/min flow rate. The eluate was electrosprayed into the mass spectrometer through a nano-electrospray ion source. The LTQ-Velos was operated in a CID top 10 mode (1 full scan MS and the 10 major peaks in the full scan are selected for MS/MS). The Mascot Daemon software (version 2. 3. 2; Matrix Science, London, UK) was used to perform database searches, using the Thermo Proteome Discoverer v1.
3 with default parameters to generate peak lists. For protein identification, the UniP Human database (2012/11, 86675 seq) was used. Peptide mass tolerance was set to 1. 5 Da and fragment mass tolerance was set to 0. 8 Da. Two missed cleavages were allowed, and variable modifications were methionine oxidation and carbamidomethylation of cysteine. Identification results were imported and filtered by Proteome Discoverer. Protein identification was validated when at least three unique peptides originating from one protein showed significant identification Mascot scores (P <0. 05) with False Discovery Rate (FDR < 5%) automatically calculated by Proteome Discoverer. When redundancy occurs, Proteome Discover uses principles of parsimony to give unambiguous identification of an isoform of a protein.
This was not possible for only 2 spots (LIS spots 1210 and 755), for which we indicate the two isoforms in Table  2. In the present study we considered that proteins validated for the entire number of spots analysed were really present on the basis of Mascot score, percentage of sequence coverage of the entire protein, peptide spectrum matches, unique peptides related to each protein isoform/member, and MW agreements. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium  [122]  via the PRIDE partner repository with the dataset identifier PXD001527.
Acknowledgements This work was partly funded by the  European Union   Collaborative Project MyoAge  ( EC Fp7 CT-223576 ) and by the  Fondation Caisse d'Epargne Rhone-Alpes  ( CERA Sarcopenie n°30 ). MG was supported by a postgraduate fellowship from  Région Auvergne  and  Fonds Européens de Développement Régional (FEDER ,  n°23000422 ), and LT by a postdoctoral fellowship from  Région Auvergne  and  FEDER  ( n°35380 T2a 2011 Prenusa ). The authors wish to gratefully acknowledge  Professor Philippe Courpron  for his constant support and his central role in initiating and developing this work. The authors thank the  Fondation pour l'Université de Lyon  for assistance with obtaining reagents.
Microarray hybridization and data analysis Labeled cRNA was prepared according to Affymetrix protocols and hybridized to Mouse Genome 430A 2. 0 arrays (Affymetrix Ltd. , High Wycombe, UK). The hybridization was performed with 30 mg cRNA for VCaP and Ep156T xenografts, and for intact, sham bones. Double the amount of cRNA was used for the C4-2B xenografts in order to correct for the high human RNA content in these xenografts. Three replicates were performed for all experimental groups except sham-operated bones and Ep156T xenografts, which were done in duplicates. Quality control of the microarray data was performed using RReportGenerator  [92]  and confirmed that all arrays used in the study were of good and consistent quality. Raw data are available on GEO (GSE22813). We computed statistical significance using the standard moderated t-test approach of the limma package  [93]  and computed local false discovery rates (FDR)  [94]  to adjust statistical significance to multiple-testing.
Reverse transcription quantitative PCR (RT-qPCR) RNA was reverse transcribed with M-MLV-RT (Promega, Wallisellen, Switzerland) and random primers (Roche Diagnostics, Rotkreuz, Switzerland) in the presence of a RNase inhibitor (Promega). mRNA expression was measured by RT-qPCR using ABI Prism Sequence Detection Systems (Applied Biosystems, Rotkreuz, Switzerland). The mouse and human specific gene expression assays are listed in the S1 File. RNA expression data were analyzed with two-tailed, unpaired t-test using GraphPad Prism version 6. 0 (GraphPad Software Inc. , La Jolla, USA).
Identification of key biological processes The OB-BMST and Core OB-BMST common to VCaP and C4-2B (''common'' OB-BMST/Core OB-BMST) were analyzed for enriched gene ontology (GO) terms (DAVID 6. 7; FDR,0. 5) and functional protein networks (STRING, 9. 05; confidence score50. 4). The interaction partners highlighted by the STRING analysis were assigned to biological processes according to BioGPS platform (http://biogps. org/). The upstream regulators of the ''common'' OB-BMST and Core OB-BMST were predicted by using default options of the Ingenuity Pathway Analysis software. Genes of the ''common'' Core OB-BMST were analyzed for the overrepresentation of sequence motifs in their promoters within 2-kilobases of the transcription start site. Enrichment was calculated against a matched number of randomly selected genes and represented as p values versus this random set and also as an enrichment factor, which is the frequency of the transcription factor binding motif within the gene cluster versus its frequency within the background gene set as previously reported  [14].
We report transcription factor motif using enrichment factors of 1. 2-1. 5 and p values ,10E-05. The motif database used for this analysis is supplied by TRANSFAC  [96]. Results were further validated using the accessible web-based tool called GeneCodis (http://genecodis. cnb. csic. es/) [97]. G  and H ) and in primary PCa (I and J). Normal bone and hematopoietic marrow (A) are lacking POSTN immunoreactivity. In contrast, in PCa (C) and MCa (E) bone metastases, myofibroblasts surrounding areas of cancer cell growth are POSTN-positive. OBs, osteocytes, OCs and cancer cells are negative. Normal prostate (G) is devoid of POSTN immunoreactivity both in the stroma and epithelial compartment. In contrast, in PCa (I) strong POSTN immunoreactivity is found in myofibroblasts over the entire tumor stroma, while cancer cells are negative.
Acknowledgments We would like to thank  Irena Klima  and  Ursula Gerber  for their excellent technical assistance. We are grateful to  Dr. Guido Jenster  and  Dr. Arno van Leenders ,  Erasmus Medical Center ,  Rotterdam , the  Netherlands , for providing us with sections of clinical specimens of bone metastases. We also thank  Dr. Ilaria Malanchi ,  Cancer Research UK ,  London Research Institute, London, United Kingdom , for helpful discussions.
This work was supported by grants from the  European Commission  ( CANCURE-2006-020970  and  FP7 Marie Curie ITN PRO-NEST-238278 ) and from the  Swiss National Foundation  ( 3100A0-116237 ). B. C. O ¨. received funding from the  OncoSuisse MD/PhD Scholarship  ( 323630-128865/1 ). Part of the costs for the microarray hybridization was supported by the  Department of Clinical Research, University of Bern , Switzerland. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.