dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments: We thank  Simona Normando  and  Paola Valsecchi  for contributing to both conceptualization and methodology of this study as well as for supervising V. B. We are also grateful to  Cesare Avesani Zaborra  and  Camillo Sandri  for supporting and making this study possible. In addition, we would like to thank the zookeepers of the carnivores for their support during the data collection and careful management of the study subjects.
Field survey and economic impact of diarrhoea As pathogens are not bound by national borders and trade between farms and breeding centres can be a vector for pathogens, including Cryptosporidium spp. , to spread far and wide, the European scale seemed more appropriate for the study. In order for the results of this study to be adapted to different kinds of farm model in each country, it was essential to recruit farms of different sizes and with different production systems. The data needed for the expertise were collected using a questionnaire from a network of pilot dairy farms facing or having faced cryptosporidiosis problems in northern Europe. Each farmer was surveyed individually, and the similar questionnaire completed in all 3 countries by the veterinarian in charge of the farm in Belgium and France, and by the livestock adviser in the Netherlands.
These data were provided by the farmer in the questionnaire. This direct loss was calculated for all breeders, whether they sold their calves or kept them for fattening. J o u r n a l P r e -p r o o f (B) Health expenditures. Health costs represent all expenses to manage calves ill with diarrhoea, i. e. veterinarian fees and medicine costs. Veterinarian costs included interventions, travel costs, flat-rate fees, self-tests etc. Medicine included oral rehydration solutions, perfusions, acidosis treatments, stomach-coating medication, antibiotics, halofuginone, probiotics, vitamins, and other medications used to fight diarrhoea. Each treatment cost was calculated by multiplying the price of the product by the number of doses used during the sick period for all the treated calves. Whenever a price was missing, it was approximated by an average calculated from the prices given by respondents from the same country, considering that tariffs in the agricultural sector are relatively homogeneous within the same region.
Risk factors outcomes and management practices effectiveness Among the specific measures proposed during the study, the most widely supported in Belgium were "Improving the time spent with dam after birth" chosen additionally by 4 farms, "The use of vaccines against E. coli or other vaccines" also by 4 farms and "Measure colostrum quality and only give good quality colostrum" tested by 5 farms. In the Netherlands, "Measure colostrum quality and only give good quality colostrum" has been chosen by 4 farms and "Improving the cleaning and disinfection" by 5 farms (Supplementary file S1). Data were not recorded for France. Original data collected about dairy farms and their cryptosporidiosis-related negative outcomes were looked for evidence about possible risk factors or protective practices (Supplementary file S2).
Plus, the dataset was small with only 10 calves tested per farm. The lack of data about experiences of individual calves, such as how much colostrum that individual calf had or its individual birth experience, etc. , prevented the practices dataset from being consistent or large enough to support an independent and robust epidemiological analysis to confidently link specific practices with individual outcomes. Thus, it is assumed that the results achieved are the result of several factors. Regarding improving the mortality results, two hypotheses could be formulated given what was observed during the study. First, the implementation of new Cryptosporidium spp. management practices may have played a large role in improving the situation on the farms  (Harp and Goff, 1998; Barrington et al. , 2002; Mee, 2008) , especially the colostrum management  (Carter et al.
Finally, while  Dianne et al. (2011)  found that acanthellae induced an increased use of refuges only in the presence of predator cues (fish scent),  Dianne et al. (2014)  found contradictorily that this protective manipulation in P. laevis was observed both in presence or absence of predatory cues, suggesting that the protective manipulation is not condition-dependent. However, again, no data is available on the entire ontogeny of the acanthella. In this study, we analyzed the behavioral changes induced by P. laevis in G. pulex, for the first time during the whole ontogeny of parasites. Two anti-predatory behaviors, namely the intensity of host refuge use and the host activity, were measured after experimental infections (as recommended by  Poulin & Maure, 2015)  and under two conditions: with or without predation cues.
Statistical analysis The survival of gammarids was analyzed using Cox regressions, where the effects of infection status (in a first analysis: unexposed vs exposed-uninfected vs exposed-infected individuals; in a second analysis: uninfected vs infected), water type (scented vs control) and their interaction were analyzed using the 'survival' R package (V 3. 2). Similar procedures were used in infected individuals only to test the effect of the number of parasites on survival. Scores for refuge use and activity rate were analyzed as repeated measures using the 'nparLD' R software package (V 2. 1), with the F2 LD F1 model. This function enables nonparametric analyses of rightcensored longitudinal data, allowing the decrease in sample size along time, due to individuals' death  (Noguchi et al.
Approximately 200 ng of the resulting peptides were analysed by nanoLC-MS/MS using a nanoElute (Bruker Daltonik GmbH, Bremen, Germany) coupled with a TimsTOF Pro mass spectrometer (Bruker) using PASEF acquisition mode as previously described  [13]. Peptide and protein identification were performed using the Mascot (Mascot server v2. 6. 2; http://www. matrixscience. com) database search engine and its automatic decoy database search to calculate a false discovery rate (FDR). MS/MS spectra were queried against the sequence of the Eat(A)v_LSAP-resistance protein, the E. coli SwissProt proteins (23,230 sequences, 2023_02 release) and a common proteomic contaminant database from the Max Planck Institute of Biochemistry, Martinsried (247 sequences). Mass tolerance for MS and MS/MS was set at 15 ppm and 0.
05 Da. The enzyme selectivity was set to full trypsin with one miscleavage allowed. Protein modifications were fixed carbamidomethylation of cysteines, variable oxidation of methionine. Identification results from Mascot (. dat files) were imported into the Proline Studio software (v2. 2. 0)  [14]  that was then used for validation as previously described  [15]. Identified peptides were validated with a peptide rank of 1 and filtered based on Mascot score values to obtain a false discovery rate (FDR) of 1% at the PSM level.
ATPase characterization Determination of the ATPase activity of the purified ABC-F proteins was performed using the Malachite Green assay kit. The reaction mixture contained 2 μM protein, 500 μM ATP in 40 μL. Reactions were started when ATP was added, and hydrolysis reactions were incubated at 37 • C for 30 min. After this period, the samples were diluted 1:1 in water, and the reactions were stopped by adding 20 μL of the working reagent (supplied with the kit). The generated amounts of inorganic phosphate were determined by comparing the absorbance at 620 nm with a standard phosphate curve. Bovine serum albumin (BSA) was used as a negative control. The data reported are averages of triplicate samples analysed with GraphPad Prism software. Statistical analysis was performed with unpaired t-tests, with a P-value ≤0.
Funding F. D. was funded by a doctoral grant from the  University of Rennes. This work was supported by the  Fondation pour la Recherche Médicale  (Equipe FRM EQU202203014663). Protim Core Facility was supported by structural grants from  Biogenouest ,  Infrastructures en Biologie Santé et Agronomie (IBiSA) , and the  Conseil Régional de Bretagne.
How? A comprehensive exploration of nuclear receptor-driven effects will be carried out using stably transfected cell lines, expanding on the on-going pre-validation of transient cell lines already in Horizon-2020 EURION cluster of projects. Specific compounds In each Task there are two Activities, and in each activity different projects. The task/activity described in this document is T5. 2/A5. 2. 1 and its primary focus is on human health, with environmental health being covered by Task 5. 2. 2. will be selected from the PARC priority list (BPA alternatives), the EURION cluster, or data gaps identified by EU agencies such as ECHA and EFSA. The assessed substances include major metabolites and breakdown molecules, allowing further MoA exploration, as well as adverse outcome pathway (AOP) and read-across development.
Worm collection procedures Unless stated otherwise, worms were harvested from Welsh ponies maintained in INRAE facilities. Infected ponies were given pyrantel pamoate (6. 6 mg/kg liveweight, Strongid ® , Zoetis, Malakoff, France) per os and faecal matter was harvested between 18 and 24 h after treatment to collect individual male worms. Upon collection, worms were bathed in PBS 1x to remove faecal debris, placed in microcentrifuge tubes left on ice for no more than 15 min before being put at -80C. For Hi-C data production, 70 worms were used and collected following the same procedure. In that case however, worms had their head cut for genotyping while their body was flash frozen. Transcriptomic data were generated from whole worms. These worms were picked from faecal matter collected 18h after pyrantel treatment, briefly bathed in 1x PBS, placed in a microcentrifuge tube and flash frozen in liquid nitrogen.
After purification, a small fraction of the indexed DNA was used to determine by qPCR the number of PCR cycles necessary for optimal amplification. Based on this result, we performed 6 cycles of PCR amplification on the remaining indexed DNA. The size distribution of the resulting library was monitored using a Fragment Analyzer with the High Sensitivity NGS kit (Agilent Technologies, Santa Clara, CA, USA) and the library was quantified using microfluorimetry (Qubit dsDNA HS kit, Thermofischer scientific). The library was denatured with NaOH, neutralised with Tris-HCl, and diluted to 300 pM. Clustering and sequencing were performed on a NovaSeq 6000 (Illumina, San Diego, CA, USA) using the paired end 150 nt protocol on 1 lane of a flow cell SP. Image analyses and base calling were performed using the Miniseq Control Software and the Real-Time Analysis component (Illumina).
Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2. 20. 0. 422). The quality of the raw data was assessed using FastQC v0. 11. 9 (http://www. bioinformatics. babraham. ac. uk/projects/fastqc/) from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). FastqScreen  (Wingett and Andrews 2018 ) was used to identify potential contamination.
2 software (Uliano-Silva et al. 2022), feeding quality filtered HiFi reads and the C. nassatus reference mitogenome  (Gao et al. 2017 ) as a backbone. The final mitogenome sequence was subsequently added to the assembly fasta file. We also identified and removed the chimeric hifiasm assembled mitochondrion sequence (38 Kbp in length, matched to scaffold 57 with the minimap2 software  (Li 2018). Repeat elements were identified using RepeatMasker (Tarailo-Graovac and Chen 2009) v4. 0. 7, Dust  (Morgulis et al. 2006 ) v1. 0. 0 and TRF  (Benson 1999)  v4. 09. To locate repeat regions, the C. elegans libraries and a C. nassatus-specific de novo repeat library built with RepeatModeler  (Flynn et al. 2020) v1. 0. 11 were fed to RepeatMasker (Tarailo-Graovac and Chen 2009). Bedtools v2. 26. 0 was used to aggregate repeated regions identified with the three tools and to soft mask the genome.
Gene models were built from RNAseq data generated from male and female samples. RNAseq reads were mapped onto the masked genome (repeatMasker v4. 0. 7) using the HiSat2  (Zhang et al. 2021 )software to produce hints subsequently used for protein to genome alignment with exonerate. Ab initio gene structures were subsequently estimated with the BRAKER  (Hoff et al. 2019 ) pipeline relying on both RNAseq data and available proteomes for other clade V species (Ancylostoma ceylanicum, Haemonchus contortus, Caenorhabditis elegans, C. inopinata, C. remanei, C. tropicalis) and more phylogenetically distant species (Brugia malayi and Onchocerca volvulus for clade III, and Trichuris muris for clade I parasitic nematodes). These gene predictions were fed to MAKER  (Campbell et al. 2014 ) for final gene model prediction.
Comparative genomic analyses Ortholog groups were identified using the Orthofinder software v2. 5. 4 (Emms and Kelly 2019), considering the subset of the most complete nematode genomes (N50 above 10 Mbp) present in WormBaseParasite v. 17 and annotated with RNAseq data, including clade V parasitic (Haemonchus contortus) and free-living species (C. briggsae, C. elegans, C. inopinata, C. nigoni, C. remanei, C. tropicalis and Pristionchus pacificus), clade IV plant (Bursaphelenchus xylophylus, Heterodera glycines) and animal parasites (Strongyloides ratti), filarial species (Brugia malayi, Onchocerca volvulus) and Trichuris muris as a clade I representative. Because of the close phylogenetic relationship with ancylostomatidae, the Ancylostoma ceylanicum proteome was also considered. The species tree was built using the iTOL software  (Letunic and Bork 2021).
Gene family evolution was performed with the CAFE v3 software  (Han et al. 2013). Differential transcriptomic response of male and female C. nassatus after exposure to pyrantel RNA-seq reads were mapped with the Salmon software v1. 4  (Patro et al. 2017)  with correction for GC-content, sequence-specific and position biases and the validateMappings option. Pseudo-counts were imported with the tximport package v1. 18. 0 and differential gene expression was estimated with the DESeq2 v1. 30. 1 package  (Love et al. 2014). Out of the 22,568 expressed genes, 12,569 with at least ten counts in five replicates were considered for analysis. Female worm gene counts displayed a bimodal distribution. The cut-off splitting the two underlying distributions was determined with the peakPick package v0. 11.
Differential gene expression was applied to both gene populations, i. e. those with a median count below or above the identified cut-off. In any case, genes showing an absolute fold change above 2 and an adjusted P-value below 1% were deemed significant. Gene Ontology enrichment was run using the topGO package v2. 42 (Alexa 2016) and processed with the GeneTonic package  (Marini et al. 2021). GO terms with P-value below 1% were considered as significant. To gain additional functional insights, one-to-one orthologs of the differentially expressed genes in C. elegans were considered for tissue or phenotype enrichment using the wormbase enrichment tool (considering a qvalue cut-off of 1%). To investigate differences between male and female worms that would not be associated with the presence of egg in female utero, the subset of DE genes with one-to-one ortholog in C.
Pyrantel-resistant worms were exposed to pyrantel embonate to first confirm their resistance potential (Strongid ® , 6. 6 mg/kg, Zoetis, France) 14 days after treatment, and finally recovered 24 hours after ivermectin treatment (Eqvalan pate, 200 µg/kg, Boehringer Ingelheim animal health, France). Pyrantel sensitivity (measured as a Faecal Egg Count Reduction coefficient) was estimated using the eggCounts package  (Wang et al. 2018)  for the Normandy isolates, while previously published data were used for the reference  (Boisseau et al. 2023 ) and American isolates  (Scare et al. 2018). For every population, single male worms were considered and genotyped for the ITS-2 and COI barcodes  (Courtot et al. 2023)  to ascertain their identity. DNA was extracted using the same salting-out protocol as before, quantified using a Qubit apparatus, and pooled together with an equi-molar contribution of each individual worm to the pool.
Image analyses and base calling were performed using the Miniseq Control Software and the Real-Time Analysis component (Illumina). Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2. 20. 0. 422). The quality of the raw data was assessed using FastQC (v0. 11. 9) from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). FastqScreen was used to identify potential contamination. Pool-sequencing data processing and SNP calling After adapter trimming using cutadapt v. 3. 4, genomic data were mapped onto the reference using bwa-mem2 v2. 2, retaining properly mapped reads with quality phred score above 20 with samtools v1. 9. Duplicate reads were identified and filtered using Picard v. 2. 20. 7 (Anon 2019) and indel realignment was applied using GATK v3.
Investigation of genome-wide diversity and pyrantel resistance architecture Nucleotide diversity and Tajima's D statistics were estimated for 100-Kbp sliding windows with npstats v2. 8 from the high quality SNP set provided as a bed file. Investigation of genome-wide diversity was subsequently performed on the set of SNPs shared across old and modern populations after filtering for sites with minimum coverage below 15, maximum coverage above 400 and minor allele frequency below 5% with the poolfstat package v2. 0. 0  (Gautier et al. 2022). Private variants were selected from the set of unfiltered autosomal SNPs, isolating markers with a minimal depth of coverage of 10 in every pool but absent in all but the focal isolate. Reference allele frequencies were binned by 10% MAF for plotting. Population connectivity was investigated using a principal component analysis applied to folded allele frequencies using the pcadapt  (Luu et al.
2017 ) R package v4. 3. 3 and the set of filtered SNPs (n = 1,346,424). Genetic differentiation (FST) and admixture statistics (f3 and f4) were estimated using the "anova" method of the poolfstat v2. 0. 0  (Gautier et al. 2022 ). To isolate genomic regions associated with pyrantel susceptibility, we regressed allele frequencies upon scaled population pyrantel efficacy while accounting for population genomic relatedness using the Baypass software v2. 2  (Gautier 2015). The modern population SNP set was filtered using the poolfstat  (Gautier et al. 2022 ) R package to retain sites with a pool coverage between 10 and 400, a minimal MAF of 5% and 4 reads to support an allele leaving 8,365,939 and 1,049,048 SNPs on the autosomes and X chromosome respectively. The analysis was run on 15 pseudo-replicates of 557,727 to 557,732 autosomal SNPs (69,936 to 69,936 for the X chromosome) and averaged from six independent runs (-npilot 15 -pilotlength 500 -burnin 2500).
0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and clustered onto a flow-cell on the Illumina NovaSeq instrument according to manufacturer's instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (. bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2. 20 software. One mis-match was allowed for index sequence identification. Data were analysed using a similar framework as that applied to the sex-specific differential transcriptomic analysis using pseudo-mapping and performing differential analysis with the DESeq2 package  (Love et al. 2014).
nassatus genome size relative to that of A. ceylanicum  (Schwarz et al. 2015)  and H. contortus  (Doyle et al. 2020). Of note, another HOG under rapid expansion (HOG0000865, +10 genes, P = 7. 4246e-06, table  S3 ) contained five genes harbouring Phlebovirus glycoprotein G2 fusion domain (PF07245), a feature of endogenous viral elements recently described in the A. ceylanicum genome  (Merchant et al. 2022 ). Among the 27 genes assigned to this HOG, six had EggNOGG homology to A. ceylanicum EVEs (Y032_0203g1846 and Y032_0070g451 proteins) with protein similarity ranging from 39. 7 to 58. 1% and a coverage of 91. 4%. Active transcription was found for nine members of this HOG (Fig. S5 ), including four homologs of the A. ceylanicum EVEs (CNASG00027320, CNASG00122160, CNASG00189380, CNASG00213220) whereby the CNASG00189380:Acey_s0070.
The last century affected allele frequencies over known anthelmintic drug targets The genome-wide diversity of C. nassatus populations was investigated from nine populations sampled across five countries (Fig  2a ), including an older population sampled from Egypt at the end of the XIXth century. The windowed depth of coverage was 38. 6x on average (Fig  2b ) but lower in the older sample and in the Hi-C derived dataset from the reference population (18x in both cases). Despite DNA fragmentation of the old sample, the data yielded an even representation of the whole genome (Fig. S6 ) and did not show evidence of strong degradation (Fig. S7 ). Cylicocyclus nassatus genetic diversity was high as illustrated by the 23,384,719 autosomal Single Nucleotide Polymorphisms identified or their average genome-wide nucleotide diversity estimates ranging from 6.
Funding This project was funded by the  French  horse and horse  riding institute (IFCE)  and the  Fonds Éperon. MGX and Get-PlaGe (doi:10. 17180/ nvxj-533) acknowledge financial support from  France Génomique National infrastructure , funded as part of " Investissement d'Avenir" program  managed by  Agence Nationale pour la Recherche  (contract  ANR-10-INBS-09 ). ".
Ethical statement Diphtheria is a notifiable disease in France. Phenotypic and genotypic analyses of bacterial isolates were carried out within the framework of the mandate given to the National Reference Center for Corynebacteria of the Diphtheriae Complex by the Ministry of Health (Public Health France). All French bacteriological samples and associated clinical data are collected, coded, shipped, managed and analysed according to the French National Reference Center protocols that received approval by French supervisory ethics authority (CNIL, n°1474671).
Material and methods Data were collected via face-to-face interviews with farmers on organic mixed livestock farms in seven European countries (see Sample description below) between autumn 2018 and spring 2019. With the help of organic associations and agricultural consultants, we contacted farmers with more than one livestock species or livestock category (e. g. , dairy and beef cattle). Further inclusion criteria were that each animal branch contributed at least 10 % of the farm income (thereby excluding farms with a small number of one animal species, e. g. , for their own consumption) and that the farmers were willing to participate in the approximately 3-h interview. In some countries, farmers received monetary compensation for their participation. As OMLF are not registered in any of the participating countries  (Ulukan et al.
This complex data collection allowed the calculation of a number of indicators as described in  Ulukan et al. (2021) , e. g. , the proportion of work peaks per year or the ability of farmers to manage their farm resources for production (e. g. , feed autonomy). In total, we interviewed 128 farmers who usually performed (part of) the daily farm work. Out of this sample, 100 farmers provided a rating of work satisfaction, whereas only 84 farmers provided a qualitative explanation for their rating and who were therefore included in further qualitative analysis. For the analysis of quantitative data, responses from up to 102 farmers were included after data validation (e. g. , number of offspring consistent with the number of mothers, amount of products sold consistent with the number of animals  (Ulukan et al.