dataesr/scientific-paragraphs-categorization huggingface dataset:
Several labs have provided data showing the interaction of integrin α5β1 or other αβ integrin heterodimers with different components of the cag-T4SS, especially CagL  [13, [34] [35] [36] [37] [38] [39] [40] [41] , but also CagA  [16] , CagI  [42]  and CagY  [14, 42]. Several previous studies suggested that integrins are required for CagA translocation. The major evidence for a functional role of β1 integrins as normalized to uninfected KatoIII cells. Statistics: Data were analyzed by Two-way ANOVA. As Post-Hoc Test a Tukey's multiple comparison test was performed. (ns: not significant; � P < 0. 05). B) KatoIII wild type and KatoIII CEACAM1/5/6 KO cells were infected with Hp P12[TEM-CagA] and corresponding mutant strains at an MOI of 60 for 2. 5 h, as indicated. Ratios of blue to green fluorescence of each sample were calculated and normalized to the mean of blue to green ratio of the negative controls.
Quantification of signals in Western Blots Western Blot data were quantified by densitometry using ImageJ. Band intensities of strainfree gel were normalized to the band intensity of KatoIII lane. CEACAM1, 5 and 6 expression was measured as area percent of the respective lane and normalized to the CEACAM1, 5 and 6 expression of KatoIII cells. Comparability between cell lines was achieved by standardizing each normalized CEACAM expression to the normalized loading controls.
This work was supported by the  Deutsche Forschungsgemeinschaft (DFG)   SFB914  Projects  B05  and  Z01  and  DFG HA2697/16-2 ,  DFG HA2697/18-1  to RH and  ANR-13-ISV3-0006-Sintesys  to LT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
, 2005). Barbervax Ò induces circulating antibodies which are ingested by the parasite when it feeds and which inhibit haemoglobinase activity in vitro  (Ekoja and Smith, 2010)  and probably in vivo. Because the gutmembrane antigens are not exposed to the host immune system during natural infection, Barbervax Ò relies on the induction of antibodies to ''hidden" antigens  (Knox et al. , 2003). Therefore, it is speculated that the Barbervax Ò proteins are not under selective pressure during natural infection, but whether vaccine-induced immunity influences levels of gene expression is currently unknown. The high level of genetic diversity observed in genomic datasets of H. contortus  (Laing et al. , 2013)  and other helminths underpins their capacity for adaptation and contributes to the evolution of drug resistance  (Gilleard and Redman, 2016).
Quantitative reverse transcription PCR (qRT-PCR) Total RNA was extracted from triplicate samples of five female worms from the same populations as the sequenced males. Total RNA (3 lg) was used per oligo(dT) cDNA synthesis (SuperScript Ò III First-Strand Synthesis System, ThermoFisher, UK, 18080051) with no-reverse transcriptase controls included for each sample. cDNA was diluted 1:100 for quantitative reverse transcription-PCR (qRT-PCR) and 1 ml added to each reaction. qRT-PCR was carried out following the Brilliant III Ultra Fast SYBR QPCR Master Mix protocol (Agilent Technologies, UK, 600882) and results analysed using MxPro qPCR Software, Version 4. 10. Gene expression was normalised to ama (HCOI01464300) and gpd (HCOI01760600)  (Lecova et al. , 2015). Primer sequences are listed in Supplementary Table  S2.
RNAseq data handling and differential expression analysis RNAseq data were mapped onto the reference genome using a gene index built with Bowtie2  (Langmead and Salzberg, 2012)  and TopHat v2. 1. 0 (Trapnell et al. , 2009)  with a maximal intron length of 50 Kbp and an inner mate distance of 30 bp that identified 48. 8% of the reads being mapped unambiguously to a gene feature. Counts of reads spanning annotated gene features were subsequently determined with HTSeq v0. 6. 0  (Anders et al. , 2015). To ensure our biological conclusions are not sensitive to details of the statistical methods used, we implemented two different analysis frameworks for the RNA-seq count data, using the DESeq2 v1. 12. 4 framework  (Love et al. , 2014)  and the voom function as implemented in the LIMMA package v3.
28. 21  (Law et al. , 2014)  in R v3. 3. 1 (R Core Team, 2016. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria). Genes found to be significantly differentially expressed (DE, adjusted P value <5%) by both voom and DESeq2 analyses were retained. A gene ontology (GO) enrichment analysis was performed using the TopGO package v2. 26. 0 (Alexa, A. , Rahnenfuhrer, J. , 2016. topGO: Enrichment Analysis for Gene Ontology; http://bioconductor. org/packages/release/bioc/html/topGO. html). Any adjusted P < 0. 05 was considered significant. Gene identifiers of the vaccine core components, namely MEP-3  (Smith et al. , 2000) , MEP-1,2,4, PEP-1  (Britton et al. , 1999)  and PEP-2  (Smith et al. , 2003)  as well as H11, were retrieved via a BLAST search of their nucleotide sequence against the H.
Transcriptional response of worms to host vaccination is dominated by higher expression of proteases and protease inhibitors We investigated any changes in H. contortus gene expression in worms surviving in vaccinated sheep relative to those surviving in controls. On average 11 million (S. D. of 1. 79 million) reads were available for each library (Supplementary Table  S1 ). In Principal component analysis (PCA) of the normalized RNA-seq read counts, the first two axes explained 53% of the total variation, 37% of which was resolved along the first axis that separated the experimental groups (Supplementary Fig. S1 ). Two pools of worms sampled from control sheep, C_4 and C_6, showed atypical behaviour that was resolved along the second PCA axis (Supplementary Fig. S1 ). These samples were discarded from the dataset for subsequent analyses, resulting in a comparison of six V samples and four C samples.
7 Â 10 À15 ), serine-type (P = 9. 6 Â 10 À8 ) and cysteine-type peptidase (P = 2. 8 Â 10 À10 ) GO terms (Supplementary Table  S5 ). This shift toward peptidase activity is also consistent with down-regulation of the gamma IFN-inducible lysosomal thiol reductase (GILT, HCOI02049600, Supplementary Table  S3 ), which is known to catalyse the reduction of cysteine proteases. Higher expression of two genes involved in the antimicrobial response, the Lys-8 encoding gene (HCOI00041100) associated with lysozyme formation, and the antimicrobial peptide theromacin coding gene (HCOI00456500), was also found in worms surviving in vaccinated animals. A proteinase inhibitor (HCOI01591500) and a prolyl-carboxypeptidase encoding gene (HCOI01624100) showing 99. 6% similarity with contortin 2 (Gen-Bank accession number CAM84574.
1, BLASTP, e-value = 0) also showed significantly greater expression in the V group (Supplementary Table  S3 ). To account for the suboptimal vaccinal response of sheep V_5, a differential expression analysis was also performed without this sample (Supplementary Table  S6 ). This produced a reduced list of only 13 DE genes due to a loss of power. However, the 12 most highly DE genes reported herein were also identified when using the reduced dataset, supporting the robustness of our analysis (Supplementary Table  S6 ).
Acknowledgements We thank  Stephen Doyle  for advice and comments on the manuscript and the biological services staff at  Moredun Research Institute, UK  for their expert animal care. JAC, NH, AM, AT and MB are supported by the  Wellcome Trust  via their core funding of the  Wellcome Trust Sanger Institute, UK , (grant  206194 ). JAC, NH, AT, MB, KM, RL, ED and CB are supported by  Biotechnology and Biological Sciences Research Council, UK , grant  BB/ M003949/1  (BUG), GS has received the support of the European.
bovis or S. haematobium genomes) in the SAM files. We were also willing to explore the introgression levels of the mitochondrial genome of these hybrid schistosomes. The scaffold 000439F contained the mitochondrial genome of S. bovis, and we also downloaded the S. haematobium mitochondrion genome from GenBank accession NC_008074  [92]. The two genomes were concatenated and used as reference to map the Corsican genome reads, again by restricting to best mapping location reads, and counting the proportion of reads aligned to each of the two organelle genomes. Similarity analysis between S. haematobium and S. bovis genomes The two species genomes were aligned with CACTUS  [93]  using the pre-release version msca_1508_Progressive_Cactus (https://github. com/glennhickey/progressiveCactus/releases).
Availability of data and material The Illumina datasets for the Corsican hybdrid strain are available in the SRA repository under submission number SUB4330327 (to be released upon publication). The S. bovis PacBio data are available under accession number ERS2549235. The Schistosoma bovis assembly SBOS_v1. 1 is available at ftp://ftp. sanger. ac. uk/pub/project/pathogens/Schistosoma/bovis/SBOS_v1. 1_pilon. fast a. Annotations are available as trackhub at http://ihpe. univperp. fr/IHPE_tracks/S. bovis/hub. txt.
A total number of 1474 environmental samples, biomaterial from patients with EVI and exposed persons were analyzed via molecular-genetic methods. Reconstruction of genetic affinity was performed using Bayesian modeling. Circulation of Russian and foreign EV strains was registered in the Russian Far East and Siberia. The most epidemiologically significant strains were as follows -Coxsackie В-4, В-5, ЕСНО-6, 9, 30. During the last four years Coxsackie А, mostly Coxsackie А-6 was also identified. The breakouts of Coxsackie А-6infection were registered in children's ensembles in the Amur, Sakhalin and Khabarovsk Regions. Most EV had a genetic relation to reference sequences obtained from the GenBank database. This indicates the possibility of importation of EVI from different countries. Epidemiological investigations confirmed that some cases were imported.
The death rate from influenza in the world is 0. 01-0. 2%, increasing in children under 2 years and those over 65 years of age, as well as in the development of pneumonia, as complications. We conducted a clinical and laboratory analysis of cases of influenza infection in the epidemic season 2017/18 in adult patients hospitalized in the Botkin Clinical Infectious Diseases Hospital. 423 medical charts were reviewed, with confirmed influenza infection by PCR. The analysis of the obtained results was carried out using the statistical package SPSS 17. 0RU for Windows. The etiological composition was presented by influenza A viruses -56%, 25% of them H1N1, H3N2 -64%, undifferentiated influenza A viruses -9%, influenza A+B -2%, and influenza B viruses -44%, 85% of them Yamagata, Victoria -0. 7% and 14.
lignieresii in both tissues tested with 99. 4% DNA similarity to the type strain of the species (strain NCTC 4189 T , GenBank accession number AY170215, https://www. ncbi. nlm. nih. gov/genbank/). The 2 strains sequenced using purulent material from a cutaneous nodule and mammary lymph node from the cows in the herd showed 99. 4% DNA similarity, indicating that the infection in the herd was not related to a single clone (strain MH426972 T and MH426973 T , GenBank accession number BankIt2120127 and BankIt2120132, respectively).
Background: Canine brucellosis, due to Brucella canis, is a worldwide zoonosis that remains endemic in South America, including Brazil. Implementation of powerful whole-genome sequencing approaches allowed exploring the Brucella genus considered as monomorphic, with, to date, more than 500 genomes available in public databases. Nevertheless, with under-representation of B. canis genomes -only twenty complete or draft genomes-, lack of knowledge about this species is still considerable. This report describes a comparative genomics-based phylogeographic investigation of 53 B. canis strains, including 28 isolates paired-end sequenced in this work. Results: Obtained results allow identifying a SNP panel species-specific to B. canis of 1086 nucleotides. In addition, high-resolution analyses assess the epidemiological relationship between worldwide isolates.
Our findings show worldwide strains are distributed among 2 distinct lineages. One of them seems to be specific to South American strains, including Brazil. B. canis South American strains may be identified by a SNP panel of 15 nucleotides, whereas a 22 SNP panel is sufficient to define contamination origin from Brazil. These results lead to the proposal of a possible spread route for dog brucellosis through South America. Additionally, whole-genome analyses highlight the remarkable genomic stability of B. canis strains over time and the sustainability of the infection in São Paulo over 12 year-period. Conclusions: Significant increase of B. canis genomes available in public databases provides new insights into B. canis infection in South America, including Brazil, as well as in the world, and also offers new perspectives for the Brucella genus largo sensu.
Nevertheless, lack of knowledge about B. canis is still considerable. Indeed, although more than 500 Brucella genomes are available on public databases, B. canis is poorly represented with only 20 complete and draft genomes available  [20] [21] [22] [23] [24] [25]. The purpose of this work was a comparative genomics-based phylogeographic investigation of 27 worldwide B. canis field strains, with a focus on Brazil, in order to improve knowledge about B. canis epidemiology in the world, and especially in South America.
To discard misassemblies, raw sequencing reads were trimmed using Trimmomatic-0. 36 (phred33, minimum 50 bp length). Chimeric genomes from databases have been generated by merging both chromosomes 1 and 2 to compare complete and draft genomes. To homogenize data, sets of sequencing pseudo-reads were created in silico on contigs from public databases using ART program with a 250 bp length and a 50-fold depth  [28]. The mapping step of short read datasets on FASTQ format from this study as well as from pseudo-reads generated with ART was realized using BWA algorithm implemented in BioNumerics 7. 6. 1 (Applied Maths, Belgium) with 90% sequence similarity against the Rm6-66 B. canis reference genome (CP007758. 1, CP007759. 1). A set of SNPs was determined for each genome sequencing data respect to the Rm6-66 genome, using the BioNumerics whole genome SNP (wgSNP) module.
Nucleotide sequence accession numbers Raw sequencing data of five representative strains of this whole-genome sequencing project (PRJEB22763) have been deposited in the European Nucleotide Archive (ENA) (http://www. ebi. ac. uk/ena/data/view/PRJEB22763) under accession numbers ERR2136545, ERR2136546, ERR2136547, ERR2136548 and ERR2136549 (Additional file 1: Table  S1 ).
Results All isolates investigated in this study were confirmed as B. canis by phenotypic and molecular (Suis-Ladder) approaches (data not shown). A total of 27 B. canis field strains, as well as the B. canis reference strain Rm6-66, were characterized by paired-end WGS. After applying different filters, a maximum likelihood tree (Fig. 1 ) was generated from 53 B. canis complete genomes and rooted with the reference strain B. melitensis biovar 1 16 M. A 0. 25% homoplasia was considered. Bootstrap values supported strong confidence for each branch (mean: 97. 43%; intervals 63-100%). A total of 7327 chromosomal SNPs were identified, including 1086 nucleotides specific to B. canis. The B. canis investigated strains were distributed into two distinct clades (Fig. 1 ). The first clade, named here lineage 1 (n = 26), was mainly composed of strains isolated in Europe, Asia and USA, including the reference strain.
North America Seven strains from North America (USA) were included in this study. Surprisingly, the great majority (n = 6) clustered into lineage 1 (Fig. 1 ), and only one strain -2,009,013,648-  [25]  isolated from Arizona in 2009 belonged to lineage 2, including all South and Central American strains (Fig. 1 ). Interestingly, Arizona shares common boundaries with Mexico. Regarding closeness of both strains, results suggest a same cross-border contamination origin. Within lineage 1, the distribution of USA strains was heterogeneous since strains belonged to distinct sub-clusters -e. g. strains 2,010,009,751 and 2,009,004,498 respectively isolated from Massachusetts in 2010 and from Louisiana in 2009  [25]  were 140 SNP distant between each other-. Although almost 40 B. canis raw sequencing data have recently been added to NCBI SRA (PRJNA369091), faced with lack of information and metadata poorly filled, only 4 of these strains have been included in this study.
Discussion To improve understanding of the genetic diversity of B. canis, we genotyped 27 worldwide B. canis field isolates by performing whole genome SNP analysis. Indeed, this approach is able to infer the relationships among worldwide B. canis isolates. Comparative genomic analysis of 53 dog and human B. canis strains was performed. Robustness of the wgSNP method applied in this study was assessed by sequencing data comparison of 2 isolates from ANSES collection (Additional file 1: Table  S1 ), independently sequenced in this study and previously by the Broad Institute center. Thus, C280 and SVA10 strains showed a strictly identical genome, as well as A590 and 96-7258 genomes harbored only one SNP difference. These results highlighted in vitro genomic stability of B. canis genomes despite successive cultural steps susceptible to induce several mutational events.
The potential of whole-genome sequencing leads to propose a possible spread route for dog brucellosis through South America. Indeed, our findings suggested the presence of B. canis in South America probably might be resulted from an introduction from USA and/ or from Mexico (Fig. 1 ) to Colombia (maximum distance of 84, 85 and 87 SNPs respectively with Chile, Brazil and Argentina), followed by spread to Brazil, Argentina and Chile (Fig. 2 ). On the current state of available genome dataset -Argentina, Chile and Brazil are part of a polytomic branch (Fig. 1 )-, it is difficult to hypothesize into the details this second evolving step of the B. canis infection through South America. Indeed, a largest dataset of representative strains of these countries is required to propose a strongest hypothesis.
Conclusions This report describes a comparative genomics-based phylogeographic investigation of B. canis field strains isolated from Brazil. Results obtained allow assessing the epidemiological relationship between worldwide strains and hypothesizing a possible spread route for dog brucellosis through South America. In addition, whole genome analyses highlight the remarkable genomic stability of B. canis strains over time and the sustainability of the infection in São Paulo. Significant increase of B. canis genomes available in public databases, resulting from this work, provides new insights not only into B. canis infection in South America, including Brazil, as well in the world, but also offers new perspectives for the Brucella genus largo sensu.
Funding The PhD researcher was supported by  FAPESP  ( 2014/00889-0 ) and  CAPES  ( 88887. 117958/2016-00 )programs. Research work was supported by the  UE  project  Bru-EPIDIA  ( 291815-FP7/ERANET/ANIHWA ). The funding agencies were not involved in the design of the study, collection, analysis, and interpretation of data and in writing the manuscript.
Availability of data and materials Most of the data generated during this study are included in this article and supplementary information files and available in the NCBI Genome database (https://www. ncbi. nlm. nih. gov/genome/?term=Brucella+canis) or PATRIC database (https://www. patricbrc. org/view/Taxonomy/ 234#view_tab=genomes). Datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
Genetic variability Genetic variability per locus, isolate, population and overall loci, was assessed by computing: (i) the mean number of alleles per locus (Na); (ii) effective number of alleles (Ne); (iii) proportion of polymorphic loci (%Pl); (iv) observed heterozygosity (Ho); and (v) unbiased expected heterozygosity (He) under Hardy-Weinberg expectations (HWE). All values were assessed using Genepop v. 4. 3 software  [16]. The deviation of genotypic frequencies from panmixia was evaluated according to HWE. The accordance to panmixia (as null hypothesis), for each locus per isolate, was evaluated by Fis using the exact test (nominal level P < 0. 05)  [17, 18]  by Genepop v. 4. 3 (settings for Markov chain parameters: dememorization = 1000, batches = 100 and Markov chain Monte Carlo iterations per batch = 5000).
ACKNOWLEDGMENTS This work was financed by a grant from the  BPI-France/ISI   Ulvans  project (n • :  I1110001W ) to  Amadéite company, Bréhan (France) , a project certified by  Pôle Mer Bretagne. The authors would like to acknowledge  Michael Theron , head of the biology department  UBO , the  ORPHY team (Christine Moisan, Christelle Goanvec)  for their support and the lipidocean plateform ( Fabienne Guerard ,  Philippe Soudant ,  Fabienne Legrand ) for its help in analyzing lipids.
Data collection In a first step, we searched the study area for patches, which numbered 30. We then calculated the unobstructed area around each patch, which represents the overall area from the center of the patch to the surrounding mounds (higher than 20 cm, i. e. , capable of hiding an ambushing cat from a rabbit, even in an upright posture, and of hiding a rabbit from a cat, unless the rabbit was in an upright posture), following procedure detailed in  [25]. In a second step, we selected the 7 patches with the largest unobstructed area (thereafter referred to as "open" patches) and the 7 patches with the smallest unobstructed area (thereafter referred to as "closed" patches) and deployed a camera-trap (Reconyx PC 900 or PC 950) in those patches from the 29th November 2016 to the 13th January 2017.
Camera traps have been used previously for fine-scale behavioral studies of prey facing risk (e. g. ,  [36, 37] ). For each patch type, one camera did not take any picture (malfunction or destruction by an animal) and one ran out of batteries before the 13th January (i. e. , on the 20th December and 4th January) but their data were included in the analyses when relevant (see below). Camera traps were set up to take one picture per hour (thereafter referred to as "time lapse" setting) as well as 10 pictures (1 per second) each time an animal's movement triggered the motion detector (including at night) with no quiet period (thereafter referred to as "motion detector" setting) (i. e. , similar design as in  [37] ). We used pictures from the time lapse setting to investigate variability in patches frequentation and pictures from the motion detector setting to study variability in rabbit behavior.
5 m/s and 4. 4 m/s in closed and open habitats respectively; LR = 40. 04, df = 1, p < 0. 001). For the main analyses (29th November 2016-13th January 2017), climate data were available from the meteorological station of Port-aux-Français research station, located about 15 km away from the study area. Finally, to later confirm that camera-trap data could correctly estimate rabbit frequentation of patches, we removed all fecal pellets from patches at the beginning of the study, and counted the number of pellets at the end. Focusing on patches with complete recording (n = 10), the number of time lapse pictures with a rabbit was strongly related to the total number of pellets collected at the end of the session (r = 0. 92, LR = 66. 60, df = 1, p < 0. 001). Pellet quantity has been proved to be a reliable method to assess rabbit abundance in other systems  [6, 38].