dataesr/scientific-paragraphs-categorization huggingface dataset:
2016 (Mansouri et al. , 2018 (Mansouri et al. , 2020;; Wedebye et al. 2016 ) can be used to predict potency toward the estrogen and androgen receptors and help identify chemicals which may be potent agonist and thus excluded from the interim iTTC. The US EPA CompTox Chemicals Dashboard (https:// compt ox. epa. gov/ dashb oard/) and Danish QSAR Database (https:// qsar. food. dtu. dk/) contain QSAR models for the endocrine and androgen receptor. When in vitro bioactivity data (e. g. , ToxCast ™ data) are available for a chemical, they should be combined into predictive models as done in the Endocrine Disruptor Program (EDSP). These types of models are available in the US EPA CompTox Chemicals Dashboard  (Browne et al. 2015; Kleinstreuer et al. 2017; Mansouri et al. 2016 Mansouri et al. , 2020)).
Material and methods A European network was created by first developing a questionnaire and then sending it to laboratories and institutions in Europe, and the data gathered is presented and discussed. This entailed the creation of an email account (toxlabnetwork@hotmail. com) to communicate with the laboratories. The questionnaire was developed using SurveyMonkey® (https:// www. surve ymonk ey. com/) as a platform. Contact email addresses from potential laboratory candidates were obtained from different sources, including (i) Internet searching using combinations of keywords (i. e. laboratory, forensic, toxicology, wildlife, veterinary, Europe), (ii) contacting toxicology laboratories/ departments in European veterinary faculties, (iii) asking for known laboratories in different European countries to the members of the ERBFacility COST Action (COST CA16224) and (iv) personal knowledge.
Statistical analyses and cartography The seroprevalences of anti-HEV antibodies in pig sera samples were calculated by age groups, type of breeding system, year of collection and geographic areas. For each seroprevalence, the two-sided 95% CI F I G U R E 3 Phylogenetic tree of partial HEV ORF2 sequences. Phylogenetic tree with amplified HEV sequences in positive livers (purple dots). Partial ORF2 sequences were aligned using Muscle (MEGA X) with the reference sequences, for genotype 3 subtyping, published by Smith et al 2020  (Smith et al. , 2020). The 5 closest sequences were searched with the GenBank basic local alignment tool (BLAST). The tree with the highest log likelihood (-52384. 46) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches (1000 replicates).
The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Evolutionary analyses were conducted with MEGA X was calculated. Categorical variables were expressed as the number of cases (percentages). Frequencies were compared using the χ 2 test or Fisher's exact test (p <. 05). Odds ratios (ORs), including their 95% CIs, were calculated for the logistic regression models. The multivariate logistic regression analysis included variables that were related to outcome variables in the univariate analysis with a p value <. 2. The prevalence of HEV RNA in pig liver samples was calculated for the overall samples and among adults (pigs older than 12 months). All statistical analyses were performed using the R program (http://www. r-proje ct. org). The two maps (Figures  1  and 2 ) were built with the software Qgis.
Infection of HepaRG cells with HEV positive liver To determine if the presence of HEV RNA in liver samples corresponds to infectious virus, we tested the ability of two positive HEV livers from piglets (GenBank accession number OL504992 and OL504994) to induce an HEV replication in the human hepatic cell line HepaRG. These two liver samples were chosen for their high HEV RNA load (>4 e+08 HEV RNA copies/g) and were issued from piglets with (OL504994) or without (OL504992) anti-HEV antibodies. After sample preparation, HepaRG were infected and the presence of viral RNA was monitored in the supernatant by RT-qPCR for up to 56 days (Figure  4 ). From day 20 post-infection, an increase in viral RNA was detected in supernatant of both cultures and maintained for up to 56 days (Figure  4 ). Therefore, HEV RNA positive livers collected from piglets contain infectious HEV.
, 2015). In the present study, pig livers and serum samples were collected during four successive seasons, covering two of the four slaughterhouses of the island. Pigs randomly selected were mostly (90%) older than 12  (1096/1238) with an age-related increase (47. 6% before 6 months of age, 84% after 6 months of age, and 89. 5% after 12 months of age). These results are in agreement with our previous observations in 2013, where 88% of Corsican pigs had anti-HEV antibodies (182/206), with similar differences between young and adult animals (42% vs. 93%)  (Jori et al. , 2016). This result underlines the stable enzootic presence of HEV in pigs in Corsica for several years and provides new data on HEV seroprevalence in pigs older than 12 months of age, raised in extensive free-range farms. Overall HEV seroprevalence in Corsican pigs is high (>80%) but we observed an impact of the pig breeding systems on HEV seroprevalence.
since it reflects the diversity of full-length HEV genomes. All sequences obtained (GenBank accession numbers OL504991 through OL504994) are of genotype 3. Sequences were aligned using Muscle (MEGA X) with reference sequences for genotype 3 subtyping published by Smith et al. (2020). Screening for high sequence identity was performed using the GenBank basic local alignment search tool (BLAST) to identify the 5 best hits. The evolutionary history was inferred by using the Maximum Likelihood method and Tamura-Nei model. The tree with the highest log likelihood(-5,238,446) is shown in Figure3. The percentage of trees in which the associated taxa clustered together is shown next to the branches (1000 replicates). Initial tree(s) for the heuristic search were obtained automatically by applying Neighbour-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value.
over 12 months in 2017 (Genbank accession number OL504991) and the 3 others from the 2-to 3-month-young piglets, from the same TA B L E 1 Age distribution of pigs included for liver and serum during the four seasons of collect in 2019 (GenBank accession number OL504992 to OL504994). All sequences belong to HEV genotype 3 (HEV-3). Using reference sequences for HEV-3 subtyping, one sequence is assigned to HEV-3c (OL504991) and the 3 others (OL504992 to OL504994) to HEV-3f (Figure3). These last 3 have more that 99% identity in nucleotides between each other and belong to animals living in the same farm. For each sequence, the 5 best hits were searched using the BLAST tool in GenBank. All sequences clustered with Corsican sequences previously published (Figure3). The sequence OL504991 (HEV-3c) has more than 98% identity in nucleotides with other swine HEV sequences from Corsica (MK234019, MK234081, MK234074, MK234003) isolated in 2017 and one wild boar sequence from Corsica (KT334188) isolated in 2009 (Figure3).
ACKNOWLEDGEMENTS We are grateful to  Margot Penru ,  Antonin Demange ,  Elise Jeannière  and  Anne-Solène de Joybert  for their technical assistance in experimental procedures. We wish to thank Anses for the constant support of HEV research, within the  Animal Health Laboratory  and the  UMR Virology. Authors are grateful to the  Collectivité de Corse  who funded this study through two regional projects: NOVPATH (New forms of organization for Pathosystems management) and  VHE (Hepatitis E virus)  projects.
Experimental Design A generalized randomized block design was used to evaluate the impact of repeated indomethacin intramuscular injections on the development of leaky gut in male Holstein calves. A power analysis was conducted to calculate the number of replicates per treatment based on reported data for plasma lactulose concentration in an indomethacin challenge study conducted in sheep  (Minuti et al. , 2013) , with a standard error of the mean of 3. 6 μg/mL, an expected difference of 20 μg/ mL between treatments, an α level of 0. 05, and a power (1 -β) of 0. 8. Based on the power analysis, a total of 18 singlet (n = 6/treatment) naturally delivered Holstein bull calves were enrolled in the study. Animals were distributed across 2 periods consisting of 21 d of adaptation followed by the start of the challenge on d 21 when they started receiving either saline or sequential indomethacin (Sigma-Aldrich) intramuscular injections in the neck every 12 h for 48 h.
Cytokine and Acute Phase Protein Quantification Plasma cytokine concentrations were measured in duplicate using a commercially available multiplex immunoassay kit [MILLIPLEX Bovine Cytokine/Chemokine kit (BCYT1-33 K; EMD Millipore Sigma] according to the manufacturer's instructions. Plasma samples were diluted 1:2 with the provided assay buffer, and a standard provided with the kit was serially diluted 6 times and included in each plate run. Antibodies to bovine IFN-γ, IL-6, IL-8, IL-10, chemokine ligand 2 (CCL2), and CCL4 were used. The median fluorescent intensity of each well was obtained using the Luminex 200 (Bio-Rad), and data were processed using the Milliplex Analyst software. Concentrations were determined using the 5-parameter logistic regression fitting model. Serum amyloid A (SAA) concentration in plasma was measured using an enzyme immune assay (Tri-Delta Diagnostics Inc.
Histomorphology. The fixed intestinal tissues were embedded in paraffin and subsequently processed onto glass slides and stained with hematoxylin and eosin (Animal Health Laboratory, Pathobiology Department, University of Guelph). Images were captured using a Leica ICC50W microscope at ×40 magnification, connected to the Leica Airlab app (Leica Microsystems). Measurements were performed using ImageJ software (ImageJ 1. 46r, National Institutes of Health). For each segment, 20 intact villi, crypt attached to the submucosa, or both were selected and measured per calf. The measurements included villus height (from the tip of the villus to the villus-crypt interface), villus width (at mid-villus height), crypt depth (from the villus-crypt interface to the muscularis mucosa), and crypt width (the opening between villi at the villus-crypt interface level).
Statistical Analysis The experiment was conducted as a randomized complete block design, with period used as a blocking factor and calf nested within treatment as the experimental unit. Data were analyzed using a generalized linear mixed-effect model, with repeated measures over experimental hour (SAS version 9. 4, SAS Institute Inc. ). The model included the fixed effects of treatment, hour, and treatment × hour interaction, and the random effect of calf nested within treatment. The covariance structure with the lowest Akaike's information criterion was selected for each variable. We used the first-order autoregressive structure for equally spaced measurements or spatial power for unequally spaced measurements. When an interaction of treatment by time was detected as significant, a partitioned analysis of the treatment least squares means was performed.
For data collected at single time points, the same generalized linear mixed-effect model without repeated measures was used. The Kenward-Roger method was used to calculate the approximate denominator degrees of freedom for the F tests in the statistical models. Continuous data were examined for normal distribution of residuals after fitting the statistical models using the Shapiro-Wilk test and homogeneity of variance by plotting residuals against predicted values. Nonnormally distributed data were subjected to Box-Cox transformation using the TRANS-REG procedure of SAS to achieve normality before analyses. Statistical significance was considered at P ≤ 0. 05, and a tendency was considered at 0. 05 < P ≤ 0. 10.
ACKNOWLEDGMENTS The authors gratefully acknowledge the staff of the Ponsonby Research station ( University of Guelph, Guelph, ON, Canada ) for their assistance with the animal experiment, and  Jaeju Yu  for his assistance with laboratory analysis ( Department of Animal Biosciences, University of Guelph, Guelph, Canada ). This study was supported by funding from  Lallemand Health Solutions (Mirabel, QC) , the  Saskatoon Colostrum Co. Ltd. (Saskatoon, SK, Canada) , and the  Natural Sciences and Engineering Research Council of Canada (Ottawa, ON). The authors have not stated any conflicts of interest.
If an animal entered and exited the field using a different edge this was not recorded, however, observational data suggest that primate crop foraging events rarely occurred where all individuals involved did not use the crop-bushveld edge (personal observation, L. Findlay). After the fence was erected, cameras were placed using the same set up in the neighbouring field A A12 (all fields now inside the electric fence) from 3 October -7 November 2014, during which time tomatoes were present. Camera traps collected information on the frequency with which wildlife visited the fields with and without an electric fence present. These sites were both equidistant from the original provisioning site, which ensured baboons visited the area, and far enough apart for each site to be out of view from the other.
Both sites were baited each morning with approximately 7 kg of butternut squash for 20 days, from 10 August -4 September 2014. For the first 10 days, one of three rubber snakes were placed on top of the bait at site A (Figure  3 ), while site B contained just the bait. For the last 10 days, the rubber snake was placed on top of the bait at site B, but not site A. Data collection occurred via one camera trap placed at each baiting station, with the species visiting the bait and duration of their stay recorded. A life-sized leopard model was concealed within a second hide (Figure  4 ), approximately 35 m east from the bait station. A pulley system was constructed so that the observer could pull a string to drop the door of the hide, thus revealing the leopard model. The site was baited each afternoon at approximately 2 pm with a variety of available crops, including watermelon and corn.
Vervet visits were video recorded. Recordings were started when vervets were seen moving towards the bait station and finished when all vervets had left the bait site and two minutes had passed without any individuals returning. Videos were coded to provide information on the frequency and duration of visits. Baseline data were collected for seven days, during which time the leopard was not revealed, followed by a 29-day experimental phase, from 31 August -8 October 2018. During this period, the pulley system was used to reveal the leopard when vervets were observed foraging on the bait. The leopard was usually revealed once a day when vervets were present, although on five days the leopard was not revealed due to the pulley system malfunctioning. camera trap placed at each bait station, and included when baboons visited the bait and duration of their stay.
Data Analyses For each deterrent method we quantified the number of days a baboon or vervet group visited the sites, as well as the duration of time spent at each site during these visits. We used a Wilcoxon rank-sum test to compare the frequency of baboon and/or vervet visits before and after the electric fence was erected. One visit included any number of the same species present at the site and 30 minutes had to pass with no sightings of this species for the next sighting to be counted as a separate visit. We also used Wilcoxon rank-sum tests to compare the duration of foraging at the bait site between the two phases of the rubber snake, leopard model, bioacoustic sounds, human sounds, and bee sounds. Durations were calculated from the time the first animal was sighted until the time the last animal of the same species was sighted; the time the last animal seen being when no other member of this species was sighted for a further 30 minutes.
COI and ITS-2 primer design We aimed to define a 450-bp amplicon within the 650-bp fragment of the cytochrome c oxidase subunit I (COI) locus previously described  (Bredtmann et al. , 2019; Louro et al. , 2021). This would leave at most 50 bp overlap, thereby allowing sequencing error correction and better amplicon resolution  (Edgar and Flyvbjerg, 2015). For this, the mitochondrial sequences of 18 Cylicocyclus auriculatus; NC_046711: Cylicocyclus ashworthi). These sequences were aligned with Muscle v. 3. 8. 21  (Edgar, 2004). Subsequently, this alignment was used to quantify sequence heterozygosity for 450-bp sliding windows using a custom python script (supplementary file S1). The consensus sequence of the region with the highest diversity, i. e. best discriminant across species, was isolated to design primers with the Primer3 blast web-based interface  (Untergasser et al.
In every case, denoising was run using the pseudo-pool option and chimera detection relied on the consensus mode. Taxonomic assignment was subsequently performed using a sequence composition approach using the IDTAXA algorithm  (Murali et al. , 2018)  as implemented in the DECIPHER R package v. 2. 18. 1 with minimal bootstrap support of 50%. This last step relied on the curated ITS-2 rDNA database for nematodes  (Workentine et al. , 2020) , last accessed on February 3rd 2022.
Analytical pipelines for community structure inference using the COI amplicon For the COI barcode, we built a custom COI barcode sequence database for Cyathostominae and Strongylidae species collected from Genbank, BOLD database using the Primerminer package v. 0. 18  (Elbrecht and Leese, 2017b ) and concatenated into a single fasta file. Sequences were subsequently edited to remove elephant Cyathostominae species (Quilonia sp, Murshidia sp, Kilonia sp, and Milulima sp) using the seqtk v. 1. 3 subseq option (https://github. com/lh3/seqtk). Some entry names (n = 18) consisted of an accession number that was manually backtransformed to the corresponding species name. Duplicate entries were removed with the rmdup option of the seqkit software v. 0. 16. 0  (Shen et al. , 2016)  and sequences were dereplicated using the usearch v11.
0. 667 -fastx_uniques option  (Edgar, 2010). To reduce the database complexity and promote primary alignment, the most representative sequences were further determined using the usearch -cluster_smallmem option, considering two identity thresholds of 97 and 99%. Amplicon analysis relied on a mapping approach to the custom COI sequence database implemented using the minimap2 software v. 2-2. 11 (Li, 2018)  as described elsewhere  (Ji et al. , 2020). First, paired-end reads were merged into amplicon sequences using the usearch software v11. 0. 667 and the -fastq_mergepair option  (Edgar, 2010). Merged amplicon sequences were subsequently mapped onto the COI sequence database using the minimap2 short read mode (-ax sr)  (Li, 2018). Mapping stringency was varied to select the most appropriate combinations using k-mer sizes of 10, 13, and 15 (default), window sizes w of 8, 9 or 10 (default), and varying mismatch penalty values (B = 1, 2, 3 or the default values 4).
Statistical analyses Statistical analyses were run with R v. 4. 0. 2 (R Core Team, 2016). Community compositional data were imported and handled with the phyloseq package v1-34. 0 (McMurdie and Holmes, 2013). Abundance data (read count for the ITS-2 rDNA region, or scaled read depth for COI) were aggregated at the species level using the taxglom() function of the phyloseq package v1-34. 0 and converted to relative abundances for further analysis. These data were used to compare the predictive ability of each barcode and pipeline in a first comparison. After the best bioinformatics parameters were identified for each barcode, the ASV count tables were further filtered to remove putative contaminants or spurious signals representing either less than 100 reads per base pair for the COI barcode or 40 reads for the ITS-2 rDNA barcodes.
, 2021). Alpha diversity was estimated using the Shannon and Simpson's indices using the estimate_richness() function of the phyloseq package  (McMurdie and Holmes, 2013). To compare between conditions and barcodes, the difference between the mock community expected and observed alpha diversity values was further considered. The divergence between the inferred community species composition and the true mock community composition was estimated from a between-community distance matrix based on species presence/absence (Jaccard distance) or species relative abundances (Bray-Curtis dissimilarity) using the vegdist() function of the vegan package  (Oksanen et al. , 2017). Differences in nemabiome between sample types were visualized with a non-metric multidimensional scaling (NMDS) with two dimensions using Jaccard and Bray-Curtis dissimilarity.
These analyses were applied to every available data within each barcode. These variables were subsequently compared between the ITS-2 and COI barcodes using the best bioinformatic pipeline and across every community available for each barcode. Replicability was estimated from the two mock communities with five species, available for both barcodes (Table  1 ) and the contribution of species and replicate run effects were determined using the same AICbased procedure. To estimate amplification efficiencies, the threshold cycle (Ct) values were regressed upon the log10-transformed DNA concentration for each species and barcode. The PCR efficiency was subsequently derived as: ‫ܧ‬ , ൌ 10 ି భ ഁ,ೕ , where ‫ܧ‬ , is the efficiency, and ߚ݅, ݆ stands for the regression slope of species i and barcode j.
The considered life stage has limited effect on the inference of community composition Nemabiome data were generated from six horses for three life stages (eggs, infective larvae and adult worms collected after pyrantel treatment). The total number of species present in this population remains unknown to date. The COI barcode retrieved 12 species, of which C. radiatus was not found with the ITS-2 barcode. This latter barcode allowed the retrieval of 13 species and four additional amplicon sequence variants that were assigned at the genus level only (Figure  3 ). ITS-2 data also recovered C. leptostomum and Craterostomum acuticaudatum that were not found with the COI marker (Figure  3 ). The Shannon index showed no significant variation across the considered life-stages for both barcodes (P = 0.
2021 ). This study aimed to produce amplicons suitable for merging of read pairs, i. e. with a total length lower than 500 bp. To compensate for the diversity found across species over that region, primer sequences were degenerated and a 5-cycle at lower temperature pre-amplification was applied to compensate for suboptimal priming  (Kwok et al. , 1994)  while subsequent mapping stringency was lowered to promote read mapping against the reference sequence database. As can be expected, this strategy yielded a poor correlation between input DNA and quantified reads. Specifically, the PCR amplification efficiency showed significant variation across species with suboptimal amplification for C. calicatus and C. longibursatus species. Additional factors such as the type of DNA polymerase could also affect the results and warrant further investigations  (Nichols et al.
, 2018). The designed COI barcode did not outperform the ITS-2 rDNA region in terms of species detection or Jaccard-based (species presence or absence) diversity estimates. In this respect, inclusion of C. coronatus in mock communities may have yielded less favourable results for the ITS-2 rDNA barcode as this species entertains close phylogenetic relationship with C. calicatus  (Bredtmann et al. , 2019). While the described approach was suboptimal, other strategies targeting the mitochondrial genome could still be applied  (Ji et al. , 2020; Liu et al. , 2016). First, bulk shotgun sequencing of cyathostomin populations could be used for mapping against a reference database of mitogenomes as applied to arthropods  (Ji et al. , 2020). This strategy improved the correlation between species input DNA and the number of mapped reads  (Ji et al.