dataesr/scientific-paragraphs-categorization huggingface dataset:
1 s, time steps = 1000, frequency steps = 250, Gaussian window shape, dynamic range = 60 dB) displaying the first 2500 Hz of the call, to determine the proportion of nonlinear phenomena relative to the full call duration. We then ran a custom-built script to batch process the remaining acoustic analyses  (Reby and McComb, 2003) , which contained two distinct procedures to characterise the F0 contour and modulation events, respectively. In particular, a band-pass filter (pass Hann band, from frequency = 40 Hz, to frequency = 2500 Hz, smoothing = 10 Hz) was firstly applied to each vocalisation to remove background noise produced by farm machinery and birds present in the maternity shed. The script procedure then involved extracting the F0 contour of each vocalisation ([Sound: To pitch (cc) command], time step = 0.
Statistical analyses Statistical analyses were performed using R Studio v. 1. 2. 1 335 (RStudio Team, 2020), an integrated development environment for R (R Core Team, 2020). For the vocal data, we used the 'lme4' package  (Bates et al. , 2015)  to carry out linear-mixed effects models (LMMs) with each vocal parameter included as the response variable. These models included the fixed effects of context (parturition or calf separation) and parity (primiparous or multiparous), and their two-way interaction. Since cattle calls are likely structured on a graded continuum  (Kiley, 1972) , the proportion of the call duration with the mouth open was included as a covariate in the model, as mouth configuration can influence F0-related parameters  (Sebe et al. , 2010). Additionally, to compensate for the variable duration of parturition amongst cows, time duration of both contexts was normalised to range between 0 and 1 with the time of each vocalisation included as a covariate.
Fixed effects included context (parturition or calf separation) and parity (primiparous or multiparous) along with their two-way interaction, and the covariate of normalised time. The random effect was cow ID to control for repeated measures. As tongue exposure was produced exclusively during parturition, no further statistical tests were applied to this behavioural parameter. To assess the significance of the fixed effects in both the vocal and behavioural datasets, we compared a full model including the fixed and random effects, to a null model, comprising the covariates and random effect for which we were controlling. Any non-significant interaction terms were dropped from the models, with models compared using Akaike's information criterion (AIC)  (Akaike, 1974) , with the lowest scoring AIC model selected.
Models were fitted with maximum likelihood estimation and likelihood ratio tests were used to confirm the significance of the full models. We used Tukey adjusted pairwise comparisons in the 'emmeans' package  (Lenth et al. , 2019)  to compare results of parturition and calf separation, and we report the estimated marginal means, along with their standard errors on the response scale. The main effect of context is reported in instances where the context by parity interaction was not significant. Further, we only report on fixed effects which were of relevance to our hypothesis, i. e. we do not report on the values of the covariates. For all models, a probability < 0. 05 was considered statistically significant, and a statistical trend was considered at 0. 05 < p < 0. 1.
Toxicokinetic analysis Following ingestion, the plasma concentration-time courses of BPS-d8 and BPSG-d8 showed three phases, a phase of appearance in plasma followed by a biexponential decrease in concentrations. The different rate constants for each of the three phases were determined by leastsquare fit adjustments of the following general function (Eq. (  1 )) to observed individual plasma concentration-time profiles of BPS-d8 and BPSG-d8 following oral administration of BPS-d8, by using "curve fitting" tool in Matlab. Apparent appearance and biphasic elimination phases were represented by: C(t) = Ae -αt + Be -βt + Ce -γt (Eq. (  1 )), where i) C (t) is the plasma concentration as a function of time; ii) A, B and C are the preexponential coefficients; iii) α, β and γ are the hybrid rate coefficients for the three phases.
Toxicokinetics of BPS in humans after oral exposure There are limited data on the toxicokinetics of BPS to date. This is the first study to document the toxicokinetics of BPS and BPSG specifically following dermal and oral exposure in volunteers within a same experimental framework, and complements the available oral kinetic data of  Oh et al. (2018)  and dermal data of  Liu and Martin (2019). Female volunteers of childbearing age were chosen for our study, given that the acquired data aimed to serve, in a next step, for the development of a human toxicokinetic model allowing reconstruction of absorbed doses from measurements of BPS and BPSG in the plasma and/or urine of vulnerable populations, such as pregnant women. Deuterated compound was administered (BPS-d8) to ensure that measured levels in plasma and urine were not partially due to a body burden resulting from environmental exposure to BPS  (Andra et al.
Interest of the toxicokinetic data for the purpose of biomonitoring From a biomonitoring perspective, the data collected in this study will be used to develop a toxicokinetic model specific to BPS, which will allow dose reconstruction of BPS from plasma or urinary BPS and BPSG measurements in exposed individuals. Similar to BPA, the glucuronoconjugate of BPS is confirmed to be the main form of BPS excreted in urine and exhibited kinetics similar to the active unconjugated BPS moiety in humans with a short half-life. The rather short half-life of BPS-d8 and BPSG-d8 observed in our study following oral exposure suggests that steady-state equilibrium should be rapidly reached in individuals repeatedly exposed by ingestion, but there could be significant fluctuations in plasma and urinary concentrations for punctual BPS exposure through ingestion of contaminated food and drinks.
The data presented for MAFF (P103110), ATF5 (P119337) and JDP2 (P117582) are the results of 40 replicates as 10 probes for each mRNA were included on the Microarray Kit. Details are presented in Table  S1  (name and sequence of the probes, the corresponding gene name, the genbank accession number, the locus and the transcript variant). The MAF/c-MAF gene is not reported as this gene was slightly expressed in HT-29 cell line and hybridization results were not conclusive. Abbreviations: AP-1, Activator Protein-  Microarray-based identification of differentially expressed Activator Protein-1 family members in response to Helicobacter hepaticus CdtB in intestinal cells. The expression of genes was determined in HT-29 intestinal cells using the Human GE 4x44K v2 Microarray Kit (Agilent Technologies) after a 72 h transduction with lentiviral particles expressing the CdtB of H.
hepaticus strain 3B1 versus the tdTomato fluorescent protein (TFP). The relative expression of genes in response to CdtB is reported as a fold change versus the value for cells cultured with lentiviral particles expressing the TFP. The results are presented as the mean of four independent transduction experiments. The red discontinuous line shows the basal rate in cells expressing TFP. Statistical and bioinformatic analyses were performed as previously reported  [6]. Asterisks denote significant results. P1, P2, P3, and P4 represent the probe names of the corresponding gene used for mRNA quantification. The data presented for MAFF (P103110), ATF5 (P119337) and JDP2 (P117582) are the results of 40 replicates as 10 probes for each mRNA were included on the Microarray Kit. Details are presented in Table  S1  (name and sequence of the probes, the corresponding gene name, the genbank accession number, the locus and the transcript variant).
For this purpose, the image processing and analysis program "ImageJ" version 1. 49  [23]  was used to scan and analyze black and white images of transduced cells. (A) Nuclear surface was quantified by isolating the DAPI fluorescence for each nucleus by using the 'Threshold' function of ImageJ (v. 1. 52n, Madison, Wisconsin, WI, USA)  [23]. *** p < 0. 001, **** p < 0. 0001, ns: not significance. (B) γH2AX foci quantification was performed by measuring the pixel intensity with the "Threshold" function of ImageJ (v. 1. 52n)  [23]  using capture of fluorescent staining. **** p < 0. 0001, ns: not significance. were infected for 72 h with H. hepaticus and its corresponding ΔCDT mutant strain, as well as with lentiviruses allowing the constitutive expression of the control tdTomato fluorescent protein (TFP), the CdtB of H.
Reagents Monoclonal mouse anti-cortactin (clone 4F-11) and monoclonal rabbit anti-phospho-histone H2AX (Ser139) (clone 20E3) were purchased from Pierce (Rockford, IL, USA) and Cell Signaling (Danvers, MA, USA), respectively. Polyclonal rabbit anti-MAFB (NB600-266) was obtained from Novus Biologicals (Littleton, CO, USA). The MAFB primers (F-MAFB-P3220837 CGCCAAACCGCATAGAGAAC and R-MAFB-P3220837 ACCGTAATAATAAACCCAAACAAAGAC) were designed using the Primer Express software (version 3. 0. 1) package (Applied Biosystems, Carlsbad, CA, USA).
PCR amplification with subsequent Sanger sequencing of the targeted MAFB sequence was performed according the supplier's recommendations with external specific primers (5 -CTCAGCACTCCGTGTAGCTC-3 and 5 -ACGCTTGGTGATGATGGTGA-3 ). Sanger data were used to quantify Indels reflecting gene knock-out (KO) with the TIDE and ICE (Inference of CRISPR Edits) algorithms  [30, 31].
Statistical Analysis for Quantification Statistical analysis for transcriptomic analysis was performed as previously reported  [6]. Other statistical analyses were performed using GraphPad Prism version 5 (GraphPad software, San Diego, CA, USA). The results are presented as the mean ± standard deviation in one representative experiment (performed in triplicate) out of three experiments. The means were compared with a non-parametric test (one-way ANOVA, multiple comparison), and the Mann-Whitney-Wilcoxon test for comparison between two groups.
Other Materials and Methods The other materials and methods used in this study were previously reported. They include transcriptomic analysis using the Human GE 4x44K v2 Microarray Kit (Agilent Technologies, Les Ulis, France) with subsequent statistics  [6] , reagents and antibodies  [5, 15] , cell lines and Helicobacter strains  [5, 6, 15] , construction of lentivirus plasmids with cdtB sequences  [5, 7] , lentivirus production  [5] , coculture and transduction experiments  [5, 6] , RT-qPCR  [5, 15] , and immunofluorescence with subsequent image analysis (wide field and confocal imaging)  [5, 6, 15]. The sequence of the cdtB of H. hepaticus strain 3B1 fused at its 3 end to three repeats of the human influenza hemagglutinin (HA) epitope and that of its corresponding mutated cdtB sequence (A→T transversion at nucleotide 794  [5] ) are available in the GenBank database under the accession numbers KT590046 and KT590047, respectively.
Asterisks denote significant results. P1, P2, P3, and P4 represent the probe names of the corresponding gene used for mRNA quantification. The data presented for MAFF (P103110), ATF5 (P119337) and JDP2 (P117582) are the results of 40 replicates as 10 probes for each mRNA were included on the Microarray Kit. Details are presented in TableS1(name and sequence of the probes, the corresponding gene name, the genbank accession number, the locus and the transcript variant). The MAF/c-MAF gene is not reported as this gene was slightly expressed in HT-29 cell line and hybridization results were not conclusive. Abbreviations: AP-1, Activator Protein-1, ATF, Activating Transcription Factor; BATF, Basic Leucine Zipper ATF-Like Transcription Factor; CAMP, Responsive Element Modulator; CREB, CAMP Responsive Element Binding Protein; FOS-L1/FRA-1, FOS Like 1; FOS-L2/FRA-2, FOS Like 2; JDP2, JUN Dimerization Protein 2; NRL, Neural Retina Leucine Zipper; TFP, tdTomato fluorescent protein.
The data presented for RND3 transcript are the results of 40 replicates as 10 probes for each mRNA were included on the Microarray Kit. Details are presented in TableS2(name and sequence of the probes, the corresponding gene name, the genbank accession number, the locus and the transcript variant). Abbreviations: BAMBI, Bone Morphogenetic Protein and Activin Membrane Bound Inhibitor; CD55, CD55 Molecule, Decay Accelerating Factor for Complement (Cromer Blood Group); CLU, Clusterin; CXCL10, C-X-C Motif Chemokine Ligand 10; GRHL3, Grainyhead Like Transcription Factor 3; MYB, MYB Proto-Oncogene, Transcription Factor; MYO5A, Myosin Heavy Chain 12; PRDM1, Beta-Interferon Gene Positive-Regulatory Domain I Binding; RBP4, Retinol Binding Protein 4; RND3, Rho-Related GTP-Binding Protein RHOE; TFP, tdTomato fluorescent protein.
CdtB in intestinal epithelial cells. The expression of genes was determined in HT-29 intestinal cells using the Human GE 4x44K v2 Microarray Kit (Agilent Technologies) after a 72 h transduction with lentiviral particles expressing the CdtB of H. hepaticus strain 3B1 versus the tdTomato fluorescent protein (TFP). The relative expression of genes in response to CdtB is reported as a fold change versus the value for cells cultured with lentiviral particles expressing the TFP. The results are presented as the mean of four independent transduction experiments. The discontinuous line shows the basal rate in cells expressing the TFP. Asterisks denote significant results. P1 and P2 represent the probe names (P3342081 and P350451) used for PRDM1 mRNA quantification. The data presented for RND3 transcript are the results of 40 replicates as 10 probes for each mRNA were included on the Microarray Kit.
Acknowledgments:  Christelle Péré-Védrenne  is the recipient of a predoctoral fellowship from the  Ligue Nationale Contre le Cancer. Lentivirus productions were performed at the " Vectorologie lentivirale" service platform of the Federative Research Structure "TransBioMed"  of the  University of Bordeaux (Bordeaux, France). Confocal microscopy was performed in the  Bordeaux Imaging Center , a service unit of the  CNRS-INSERM  and the  University of Bordeaux , member of the national infrastructure France BioImaging. We are grateful to  Véronique Guyonnet-Duperat  and  Nathalie Dugot-Senant  for technical assistance in confocal imaging.
P1 and P2 represent the probe names (P3342081 and P350451) used for PRDM1 mRNA quantification. The data presented for RND3 transcript are the results of 40 replicates as 10 probes for each mRNA were included on the Microarray Kit. Details are presented in TableS2(name and sequence of the probes, the corresponding gene name, the genbank accession number, the locus and the transcript variant). Abbreviations: BAMBI, Bone Morphogenetic Protein and Activin Membrane Bound Inhibitor; CD55, CD55 Molecule, Decay Accelerating Factor for Complement (Cromer Blood Group); CLU, Clusterin; CXCL10, C-X-C Motif Chemokine Ligand 10; GRHL3, Grainyhead Like Transcription Factor 3; MYB, MYB Proto-Oncogene, Transcription Factor; MYO5A, Myosin Heavy Chain 12; PRDM1, Beta-Interferon Gene Positive-Regulatory Domain I Binding; RBP4, Retinol Binding Protein 4; RND3, Rho-Related GTP-Binding Protein RHOE; TFP, tdTomato fluorescent protein.
Details are presented in TableS2(name and sequence of the probes, the corresponding gene name, the genbank accession number, the locus and the transcript variant). * p < 0. 05 versus non-infected cells or TFP. Abbreviations: CdtB, CdtB of H. hepaticus strain 3B1; CdtB H265L, H. hepaticus CdtB with the mutation His/Leu at residue 265 involved in catalytic activity; ∆CDT, CDT isogenic mutant of H. hepaticus strain 3B1; NI, non-infected; TFP, tdTomato fluorescent protein; WT, H. hepaticus strain 3B1 (CCUG 44777) = wild type strain. Figure 3. Microarray-based identification of differentially expressed MAFB target genes in response to Helicobacter hepaticus Abbreviations: BAMBI, Bone Morphogenetic Protein and Activin Membrane Bound Inhibitor; CD55, CD55 Molecule, Decay Accelerating Factor for Complement (Cromer Blood Group); CLU, Clusterin; CXCL10, C-X-C Motif Chemokine Ligand 10; GRHL3, Grainyhead Like Transcription Factor 3; MYB, MYB Proto-Oncogene, Transcription Factor; MYO5A, Myosin Heavy Chain 12; PRDM1, Beta-Interferon Gene Positive-Regulatory Domain I Binding; RBP4, Retinol Binding Protein 4; RND3, Rho-Related GTP-Binding Protein RHOE; TFP, tdTomato fluorescent protein.
TableS2(name and sequence of the probes, the corresponding gene name, the genbank accession number, the locus and the transcript variant). Abbreviations: BAMBI, Bone Morphogenetic Protein and Activin Membrane Bound Inhibitor; CD55, CD55 Molecule, Decay Accelerating Factor for Complement (Cromer Blood Group); CLU, Clusterin; CXCL10, C-X-C Motif Chemokine Ligand 10; GRHL3, Grainyhead Like Transcription Factor 3; MYB, MYB Proto-Oncogene, Transcription Factor; MYO5A, Myosin Heavy Chain 12; PRDM1, Beta-Interferon Gene Positive-Regulatory Domain I Binding; RBP4, Retinol Binding Protein 4; RND3, Rho-Related GTP-Binding Protein RHOE; TFP, tdTomato fluorescent protein.
Animals and inclusion criteria This retrospective study included 180 cats with invasive mammary carcinomas, which have been previously described. 36 Female cats were eligible for inclusion if they had an invasive mammary carcinoma, if they were treated solely by surgery, and if follow-up was available for at least 2 years post-mastectomy. Owners' written consent was obtained prior to inclusion. Approval was obtained from the local animal welfare and ethics committee ''Comite´d'Ethique en Recherche clinique et e´pide´miologique Ve´te´rinaire d'Oniris'' (CERVO), of the Nantes Atlantic College of Veterinary Medicine, Food Science and Engineering (Oniris, France). Recorded epidemiologic and clinical data included age at diagnosis, breed, medical and reproductive history, the location of the mammary carcinoma, and clinical stage according to the modified World Health Organization staging system,  37, 38  as previously described.
Statistical analyses Statistical analyses were conducted using the MedCalc Ò statistical software (Ostend, Belgium). Chi-squared tests (for discontinuous variables) and one-way analyses of variance (for continuous variables) were used to compare the clinicopathologic characteristics of Tregenriched and Treg-poor FMCs. The Kaplan-Meier method and log-rank tests were used in univariate survival analyses, and Cox proportional hazard models for multivariate survival analyses. The results are reported using the hazard ratio (HR), its 95% confidence interval (95% CI), and the p-value of each covariate. The prognostic cutoffs for Treg numbers were determined by receiver operating characteristic curve analysis calculated for 2-year cancer-specific survival. A p-value of \0. 05 was considered significant.
Acknowledgements The authors thank  Dr Me´lanie Pohu ,  Dr Floriane Morio , and  Dr Clotilde de Brito , who helped in collecting the clinical and follow-up data, as well as the veterinary pathologists  Dr Jean-Loı¨c Le Net ,  Dr Virginie The´au ,  Dr Pierre Lagourette ,  Dr Olivier Albaric , and  Dr Sophie Labrut  who performed the initial diagnoses of FMCs, and the technicians in histopathology,  Mr Bernard Fernandez ,  Mrs Florence Lezin , and  Mrs Catherine Gue´reaud  who made the slides. The authors are very grateful to  Prof. Dominique Fanuel  (DVM), for critical review of this work. Finally, the authors thank the referring veterinarians and the owners of the cats included in this study, who gave us the clinical and follow-up data.
Funding The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by the  French National Cancer Institute (INCa, Institut National du Cancer)  with a grant for translational research (grant number  INCa-DHOS 2010 ) (M. C. ); by a grant for PhD students from the  Ministry of Education and Higher Education of Lebanon  (E. D. ); and by  Roche Diagnostics GmbH, Germany , which provided financial and technical support for the immunohistochemical characterization of the carcinomas. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
GENOMIC DATA. MPM genomic general data. A total of 44 whole genome sequences (annotated as M. marinum (n = 33), M. ulcerans (n = 7), Mycobacterium liflandii (n = 1), Mycobacterium pseudoshottsii (n = 2) and one unnamed Mycobacterium sp. 012931 were retrieved from the Pubmed assembly databases using M. marinum and MPM as keywords. Taken together, these genomes, consisting of 260 million bases, exhibited a GC% varying between 62. 3% for M. ulcerans subsp. shinshuensis strain ATCC 33728 (AP017635. 1), 63. 4% for M. ulcerans CSURP9951 and 65. 2-65. 7% for the 42 remaining isolates (Supplementary Fig. S1 ). Whole genome sequence analysis. Average nucleotide identity (ANI) analysis revealed using MORPHEUS (Versatile matrix visualisation and analysis software) delineated two large clusters and several small clusters, the M.
ECOLOGY AND PHENOTYPIC CHARACTERISTICS. Geography and Hosts. The pan-genomic analysis carried out on the 44 genomes used in this study separated 24 M. marinum genomes, forming group (1) and 20 MPMs genomes forming group  (2). We reviewed the geographical and ecological origins and type of mycolactone for each of the 44 isolates here studied, using the NCBI database and the PATRIC web site. Thus, of the 24 genomes of M. marinum isolates, 16 isolates regrouped on the taxon (1. 1) were isolated from the USA, the United Kingdom, Israel, Sweden, and an unspecified European country (10, 3, 1, 1) genomes, respectively. The unique M. marinum strain Davis1 forming taxon (1. 2) was isolated from a human sample from the USA. The taxon (1. 3) groups two strains, M. marinum MB2 isolated from fish from Thailand, and M.
CONCLUSIONS This study highlighted the profound bias in genome datasets: all the currently named M. ulcerans isolates were made from clinical sources, evidently obscuring the probable genomic diversity of environmental M. ulcerans and underlying the absolute necessity to boost the culture-based evaluation of environments, while none of the 24 M. marinum isolates here investigated were made from the environment. Despite this limitation, our study was able to firmly delineate a group of isolates as M. ulcerans and a group of isolates as M. marinum. In between, nine isolates were here tentatively named M. marinum, M. ulcerans and M. guyanensis sp. nov. ; a temporary classification aimed to stimulate contributing researchers in the field. We report clearcut characteristics for the laboratory identification of these two species.
METHODS Whole genome sequence retrieval and analysis. In order to retrieve the MPM genome sequences, we consulted the Assembly (https://www. ncbi. nlm. nih. gov/assembly/) and EBI (https://www. ebi. ac. uk/genomes/) databases using the keyword "Mycobacterium" in April 2020. Seven genomes of M. ulcerans and one genome of M. marinum strains from different geographical origin were then sequenced in our laboratory using MiSeq platform (Illumina, Inc. , San Diego, CA, USA). All these genomes were assembled using SPAdes software version 3. 5. 0 [61]  and annotated using Prokka version 1. 12  [62]. The selected genomes were then analysed using different comparative genomics tools such as ANI, DHH, Roary and SNP-distance. Identity cards. NCBI/PubMed, Google Scholar were used to perform a literature review as well as the Web of Science website, using the following keywords "Buruli ulcer", "Mycobacterium ulcerans" "M.