dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis The responses for the mouse/rat strain were reviewed by two persons: In mice, the 129 substrains were subsumed under "129", C57BL/6J and C57BL/6N under "C57BL/6", and ICR and CD-1 under "CD-1". In rats, Holtzman and Sprague Dawley were subsumed under "Sprague Dawley". For genetically modified animals, the background strain was extracted. If strains were on a mixed genetic background, "mixed background" was indicated. If responses appeared not to be plausible or free text-responses had to be clustered, the answers were corrected and the corrected responses were used for further analysis. All original and corrected responses can be found in S6 Data. SPSS (IBM Corp. Released 2020. IBM SPSS Statistics for Windows, Version 27. 0. Armonk, NY: IBM Corp) was used for the linear regression analysis and for creating the figures.
Since the animals are usually handled when cages are changed, the effects listed above may not only be due to a novel environment but can also be associated with the handling techniques used  [18, 93]. Since habituation times are rarely reported, we refrained from extracting the time the animals were allowed to acclimatize to the respective HCM. Instead, data on the duration of measurement using the HCM techniques was collected. HCM techniques were mainly applied for short-term periods (i. e. , 1-28 days). The number of techniques being applied for intermediate length periods (i. e. , 4-12 weeks) slightly increased over time in the years between 2011 and 2020, however, 2-7 days remained the most frequent duration of measurement. Only in rare cases, HCM techniques were applied for long-term periods (i.
Funding VV is supported by  Jane and Aatos Erkko Foundation. PK, PM, AJ, BL, CTR, LL, and KH were funded by the  Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)  under Germany's  Excellence Strategy -EXC 2002/1  " Science of Intelligence "project number  390523135. The  Vienna BioCenter Core Facilities  ( VBCF) Preclinical Phenotyping Facility  acknowledges funding from the  Austrian Federal Ministry of Education, Science & Research ; and the  City of Vienna.
Animal management The dataset originated from an experiment that was carried out in the experimental farm of the Chambre Régionale d'Agriculture de Bretagne (Saint-Nicolas-du-Pélem, France) and was fully described previously  (Quesnel et al. , 2019). From insemination until day 105 of gestation, sows were housed in two different systems. The conventional group-housing system was on a concrete slatted floor and offered 2. 4 m 2 of space per gestating sow, while the enriched group-housing system was on deep straw and offered more space per sow (3. 5 m 2 ). In each system, sows were transferred into identical farrowing rooms on a slatted floor at 105 days of gestation. Sows were confined in individual crates during the whole lactation, those were located in individual pens provided with a heating lamp.
Data collection All live-born piglets (279 females and 225 males) were subjected to measurements of farrowing and morphological traits, and a subset of these piglets (6-7 piglets per litter, distributed throughout the farrowing progress, n = 203) was also submitted to blood sampling for further physiological analyses. Blood samples (3 mL) were collected in heparinised (10 IU of heparin/mL) tubes from the umbilical cord at birth. They were immediately centrifuged for 10 min at 2 600g at 4 °C to obtain plasma. Birth order and time of birth of each piglet (stillborn and born alive) were recorded during farrowing supervision. Farrowing traits included birth order, birth interval (interval from birth of the piglet to that of the previous one) and cumulative birth interval (interval from birth of the piglet to that of the first piglet of the litter).
10) but was influenced by sex, with female piglets having a 45% lower risk of dying than males (odds ratio = 0. 55, P = 0. 020). This variable, however, might be biased by the fact that one male within litter was euthanised for tissue sampling and removed from the dataset  (Quesnel et al. , 2019). The risk of dying decreased when colostrum birth weight, or rectal temperature at 1 h increased (P < 0. 001). The multivariable analysis was performed only on traits available for all piglets (n = 504). It did not include piglet physiological traits because the number of piglets submitted to blood sampling was too small to observe significant relationships (only 25 dead piglets vs 178 surviving). Variables kept in the multivariable model were colostrum intake, rectal temperature at 1 h, litter heterogeneity and number of piglets born alive.
Discussion In the present study, piglet physiological traits were assessed immediately after birth by collecting umbilical blood, before suckling and before any manipulation of the piglet. The umbilical cord contains two arteries and a vein, and blood samples were most often collected from the vein whose wall is thinner. However, it cannot be excluded that some samples of blood were collected from an artery. This is not an issue since we demonstrated high correlations between arterial and venous concentrations of metabolites or hormones (R 2 > 0. 96 for glucose, fructose, albumin and lactate, R 2 = 0. 86 for cortisol, unpublished data from Liaubet et al. ).
Acknowledgements The authors thank the participants of the experiment  C. Calvar ,  B. Le Bris  and the staff of Crécom (CRAB, France),  F. Robert  and  T. Pinard  from  Deltavit CCPA group , and the technical staff of  UMR1348   PEGASE  ( S. Tacher ,  S. Daré ,  N. Bonhomme ,  C. Tréfeu ,  R. Comte ,  F. Thomas ,  F. Mayeur ,  M. Lefebvre ).
The EFSA also provides a guidance document on how the literature review should be conducted including the search, selection of relevant data, and its presentation in the dossier  (EFSA, 2011). The literature review will only likely yield additional vertebrate data when an active substance is up for renewal, as new active substances will not have vertebrate data outside of the regulatory databases at the time of submission. Knowledge collection solutions such as ECOTOXicology Knowledgebase (initially developed by the USEPA in the 1980s) and adverse outcome pathways  (Ankley et al. , 2010; Delrue et al. , 2016; discussed in detail in a companion paper, Rattner et al. , forthcoming)  also serve to support more robust risk assessments. The latest version of ECOTOX Knowledgebase (Ver. 5, www. epa.
g. , rat, poultry). Generally, no quantification of internal exposure or dose. Extensive data available on responses of existing animal models to a wide range of chemicals and contaminants. Little or no investigation of underlying mechanisms of toxicity that could potentially be used as biomarkers in field studies. Clinical chemistry parameters and mammalian toxicity data are conducted as part of the human health assessment. Chronic studies only have three groups plus a control, which is not well suited to benchmark dose models. Validity criteria for a regulatory acceptable study are clearly defined. Rarely have sufficient data for species sensitivity distributions or geometric mean across species. Controlled design can establish cause-effect relationships. Absence of testing protocols for air-breathing amphibians and reptiles necessitates extrapolation of data from fish, birds, and mammals.
Ethical Statement The and with the Declaration of Helsinki (6th revision). The European GDPR (General Data Protection Regulation) was fully applied, and all participants were informed of the subject of the study, of the protocol for processing personal data, video recordings and of their rights of withdrawal. For all participant, access to experiments was conditional on an explicit, free, informed and written consent to participate, obtained by signing themselves or signature from their legal guardians. Data were all collected and analyzed anonymously. This study involved 2 different riding centres, centre 1 located in North-East part of France where observations were performed between February and March 2019 and centre 2 located on the east coast of Ireland where experiments were performed between April and May 2019.
Climate and temperature were the same in both centres (mean Nancy = 6. 1 • C; mean Dublin = 6. 3 • C) at the time of testing. The proportion of each activity was between 7% and 86% of equine assisted activities (EAI), mean ± SE = 40. 5 ± 5. 1% of the total amount of working hours per week. EAI activities consisted mostly in grooming, groundwork, lunging, and riding. It involved persons with disabilities such as motor disabilities, visual, hearing, or cognitive impairments, crippling diseases, or other health diseases linked to psychosocial risks or social problems (e. g. , jail, dropping out of school). Information on management practices were obtained through a questionnaire filled by riding centre managers. We found no effect of the riding centre on tactile reactivity (see results), thus individual data of horses were pooled between centres.
Data and Statistical Analyses All statistics were performed using R 3. 6. 2 software (The R foundation for statistical computing, http://www. R-project. org/, accessed on 1 January 2020, Vienna, Austria)  [49]. The significance level was set at 0. 05. Descriptive statistics are reported as means and standard error of mean (SEM). As the data were not normally distributed, we used nonparametric statistical tests  [50]. The following data were used to characterize horses' tactile reactivity: (1) Total reactivity: sum of all responses, up to a maximum of 24 (4 filaments tested on both sides on 3 areas of the body). (2) The reactivity by filament size: the sum of the responses for each size of filaments tested. Since data were similar for thin (0. 008 g and 0. 002 g) or thick (1 g and 300 g) filaments, respectively, we used these categories for statistical analyses.
Results The total tactile reactivity (i. e. , total number of reactions for all tests and including all body areas and filament range) showed high individual variations ranging from 0 to 24 (9. 93 ± 0. 81). More precisely, there were clear differences according to the horses' usual working activity: EAI horses showed a higher reactivity (14. 5 ± (2) The reactivity by filament size: the sum of the responses for each size of filaments tested. Since data were similar for thin (0. 008 g and 0. 002 g) or thick (1 g and 300 g) filaments, respectively, we used these categories for statistical analyses. (3) Reactivity per side of the body: the sum of the responses on the left and right sides of the body (areas and filaments pooled), respectively. (4) Reactivity by body area: the sum of the responses recorded for each body area tested (sides and filaments pooled).
Data Recording and Analyses Participants' behaviours during the grooming session were analysed from the video footages. In order to have a fine description of the time spent grooming each body area, data analysis was performed using continuous focal sampling  [54] ) by the same experimenter (MS). Given the shortness of the grooming sessions and related low data sampling, we analysed further the data by considering two main "classical" areas  [55] : (1) forehand (head, mane, neck, wither, shoulder, forelimbs); (2) hindquarters (back, flank, croup, hind limbs). The number of grooming stops (i. e. , breaking contact between the brush and the horse's body) was measured and a brushing fragmentation index was calculated: number of brushing stops divided by the total duration of brushing time during the test.
The number of grooming stops (i. e. , breaking contact between the brush and the horse's body) was measured and a brushing fragmentation index was calculated: number of brushing stops divided by the total duration of brushing time during the test. All statistics were performed using R 3. 6. 2 software  [49]. The significance level was set at 0. 05. Descriptive statistics are reported as means and standard error of the mean. As data were not normally distributed, we used non-parametric statistical tests  [50]. Mann-Whitney U tests were used to compare the time spent grooming each body area and the brushing fragmentation between participants with or without disorder. Friedman and Wilcoxon signed rank tests were used to compare the time spent grooming the two main areas (forehand and hindquarters).
The national and autonomous community levels take a political-administrative approach with legislative implications, while the operations at the provincial and county levels are sanctioning-advisory through direct contact with farmers in their public offices or on farm visits. For the purposes of the study, government veterinarians were considered to be the key informants. This is partly due to their knowledge and experience  (36, 37) , but also enabled the researchers to collect quality data in a short amount of time (38). Key informants were identified through an initial exploration of all structural and organizational levels of the government services according to the territoriality of Spain to ensure that the key informants offered a good representation of all these different levels. Government veterinarians with knowledge and experience of biosecurity on livestock farms and who were known to be willing to participate in the study were contacted and recruited through purposive sampling.
Data collection Data was collected during the COVID-19 pandemic. Europe had one of the highest rates of positive cases in the world from early 2020 until early 2021, and Spain established containment policies, with a significant restriction of mobility between and within its territories  (39, 40). Hence the data was collected by means of remote interviews via an online conference program, as in other fields of study  (41, 42) , which also offered advantages in terms of less displacement in the field and more flexibility in participants' schedules (43). The remote interviews were conducted and recorded between 19 March 2020 and 19 October 2020. They were conducted by SM, who was at the time a PhD candidate and had conducted similar studies on dairy cattle farms with farmers and veterinarians  (18, 19, 32).
Data analysis The interviews were analyzed through content analysis using the qualitative ATLAS. ti software. The approach proposed by Elo and Kyngas (45) and Elo et al. (46)  was considered. As biosecurity was being explored through a limited number of participants, a mainly deductive logic was used  (47). The transcriptions were read for a general understanding of their content, and then established codes (i. e. , deductive approach) were created along with their meaning units (Table  2 ), which are sections of text that are related to the objective of the study. Each meaning unit was coded according to its content in the established codes, but emerging codes (i. e. , inductive approach) were also created as the texts were analyzed. Finally, all codes were compared, and similar codes were grouped and labeled into categories.
An overall descriptive analysis of the responses of 339 participants is presented; results by country or breed are also mentioned. The data collected covers 11 countries and 32 breeds, with unequal representation by breed and country. Preserving genetic diversity is the main motivation stated by the stakeholders surveyed, followed by the economic activities associated with LB. The animals are raised purebred in small (median size: nine sows) and quite recent farms(median existence: 7 years); their selection is based mainly on phenotypic features(breed standards, number and quality of the teats). Participants expressed interest in selection, particularly for reproductive traits, but there are many barriers to the implementation of breeding programmes. Most of them expressed concern about the sustainability of LB, especially for economic reasons.
Concerns about compliance with health regulations and fears of infection by pathogens came next. Stakeholders expected support from public authorities, especially to improve productivity and to protect the use of breed names. Novel precision livestock farming technologies such as computer vision systems are pivotal for phenotyping novel traits on a large scale, as behaviour and robustness are becoming increasingly important in pig breeding goals. This study aimed to expand pig weighing with automated activity levels using DeepLabCut TM , an automated video-analysis system. These activity data were validated with manual recordings of pig activity. Finally, data were related to pedigree information to estimate heritabilities and genetic correlations. The dataset consisted of 7428 recordings for 1556 finishing pigs (Piétrain sire Â crossbred dam) with biweekly recordings of the same pig.
Statistical analysis Normality of distribution of continuous variables was evaluated using the Shapiro-Wilk W test. Categorical variables were summarized using number and percent of observations in each category. Comparison of prevalence between groups was performed with Yates' X 2 test. All data were then gathered for comparative analysis of sample sites and methods. Comparison between sample sites (TW, BAL P , BAL L , BAL R ) and between methods (culture vs. cytology) was assessed using the McNemar Test with continuity correction. Agreement between sample sites and methods was assessed with Cohen's kappa coe cient (κ). Values of P <. 05 were considered statistically signi cant.
Acknowledgments We acknowledge all the technical staff at UEPR: especially  Patrick Touanel  and  Marie-Hélène Lohat , who largely participated in handling the piglets. We thank  Eric Siroux  who helped building the acoustic chamber at the beginning of the experiment,  Remi Resmond  for great discussions about statistics and  Bliss Elizabeth Bagnato-Conlin  for their carefully proof reading of the manuscript. All the authors acknowledge  Camille Noûs , affirming the collective and open character of the creation and dissemination of knowledge (Cogitamus Laboratory https://www. cogitamus. fr/indexen. html). This project is part of the  SoundWel  project in the framework of the  Anihwa Eranet and  funded by  ANR 30001199.
A major effort was made by Vineer et al. , who created an open database summarising 535 AR surveys in 22 countries to represent the most up to date situation on the prevalence of AR in sheep, goats and cattle in Europe  [13]. Knowing where the parasites are can underpin regionally targeted control measures. In this context, Hendrickx et al. used historical data to compare species distribution models detecting "hot spots" of the lancet fluke Dicrocoelium dendriticum  [5]. They concluded that an even spatial distribution of the input data is more important than the actual sample size, hence the importance of correcting for sample biases when data originally collected for other purposes are used. The study of Untersweg et al. found reduced anthelmintic efficacy against different parasite species in a majority of examined sheep flocks in Austria and flags the rise of Haemonchus contortus infections in areas where they were previously rarely encountered  [16].
We have shown that HEV-3f replication is slow in HepaRG cells, reaches a plateau around day 90 post-infection and is then maintained for several months without clearance of the virus  (34). Expression of 84 to 168 genes involved in the IFN response was quantified using customized quantitative PCR (qPCR) arrays in these 2 models. Analysis of these data have shown that expression of 12 and 25 ISGs was up-regulated during HEV infection in swine liver and HepaRG, respectively. The expression level of five of these genes, CXCL10, IFIT2, MX2, OASL and OAS2, was up-regulated in both species. The expression of IFI16 was also found to be up-regulated in swine liver tissues. This study contributes to the identification of putative host factors that could play a role in the control of HEV infection and need to be further investigated.
Virus inoculation of HepaRG cells A HEV-3f strain originating from a French patient suffering from acute autochthonous hepatitis E was used and has been described previously (GenBank under accession number JN906974)  (34, 36). Supernatant from the 6 th passage of the virus in HepaRG cells was used in this study to perform all the infections in HepaRG cells. HepaRG cells were differentiated in 6-well plates as described above. Two days before infection, differentiation medium was replaced by proliferation medium. Cells were infected overnight with an HEV inoculum diluted in proliferation medium to a final volume of 1ml at a multiplicity of infection (MOI) of 10 or 100 genome equivalent (GE)/cell. The viral suspension was then removed and cells were washed three times in PBS before adding 2 ml of proliferation medium.
Pig liver samples Samples were collected in a previous study  (37). This experimental protocol was validated by the ethics committee (ComEth number 12-043) of the National Veterinary School of Alfort, the French Agency for Food, Environmental and Occupational Health & Safety, and University Paris 12 and has obtained formal approval (notice number 09/10/12-9). HEV-3c (GenBank accession number JQ953664) and HEV-3f (GenBank accession number JQ953666) viral suspensions were generated using fecal samples from infected pigs. Eight-week-old specific pathogen free Large-White piglets were infected intravenously with 10 6 copies of HEV RNA or mock-infected with PBS  (37). At the peak of excretion (8 days post-infection), liver tissues were snapfrozen in liquid nitrogen. Samples from 2 control pigs, 3 pigs infected with HEV-3c and 3 pigs infected with HEV-3f were available and analyzed in this study.
01 database  (40). For pig liver samples, a customized RT 2 Profiler PCR array (CLAS34508, Qiagen) was designed to study the expression of 89 porcine genes involved in the IFN response. Data were analyzed using the RT 2 Profiler PCR Arrays & Assays Data Analysis software (Qiagen) and normalized using the housekeeping genes selected above. Fold change was calculated by using the DDCT method (  41 ). An arbitrary cut-off of 2 was applied to determine significant differences.
Immunostaining and fluorescent microscopy Cells were seeded onto a 15μ-24-well IBIDI plate (Clinisciences). After infection, cells were fixed with 4% paraformaldehyde in PBS. Cells were then permeabilized with 0. 2% Triton X-100 in PBS and incubated in blocking buffer (0. 5% BSA in PBS). Anti-ORF2 antibody (mouse, 1/500 dilution, 1E6, Millipore) was then added for 1h at room temperature. Cells were then washed several times in PBS and incubated with a DyLight ™ 488 anti-mouse secondary antibody (Thermo Scientific). After several washes in PBS, cell nuclei were stained with 4,6diamidine-2-phenylindole dihydrochloride (DAPI) (Sigma-Aldrich). Microscopy was carried out with an Axio observer Z1 fluorescent microscope (Zeiss) and images were acquired using the Zen 2012 software.
Statistical analyses For the PCR array data, the p-values were determined by the RT 2 Profiler PCR Arrays & Assays Data Analysis software (Qiagen) and calculations were based on a Student's t-test of the replicate 2 -DCT. For the qPCR and CXCL10 ELISA experiments, an unpaired t-test with Welch's correction was used to analyze the data using GraphPad Prism version 9. 2. 0. The statistical analysis on the qPCR data was performed using the DCt values.
Quantification of HEV RNA in these samples is shown in Supplementary Table  1C. A PCR array was designed to study the expression of additional ISGs that were found to be differentially expressed in hepatic cells following IFN stimulation according to the interferome v2. 01 database  (40). The expression of a total of 168 ISGs were analyzed, among which 74 are orthologues of genes analyzed in the swine PCR arrays described above. The expression of 25 ISGs (BATF2, CMPK2, CXCL9, CXCL10, EPSTI1, ETV7, HERC6, IFI27, IFI44, IFI6, IFIT1, IFIT2, IFIT3, IFITM1, ISG15, LAMP3, MX1, MX2, OAS1, OAS2, OAS3, OASL, PRIC285, RSAD2, XAF1) was found to be significantly upregulated and 2 IFN-regulated genes (CRP and NOS2) downregulated in HepaRG cells infected with HEV-3f out of the 168 genes analyzed (Figure  4 ; Supplementary Table  4 ).