dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analyses on measures of parasitic community We removed the lungworm Varestrongylus from the dataset because the focus of the present study was on gastrointestinal nematodes. In order to control the representativeness of the data, we drew the accumulation curves for the ASV,and taxa with the "exact" method of the function "specaccum" of the package vegan  [53]. Instead of the exact read count per sample and items, we used the relative frequencies of reads. The read relative frequencies in samples were plotted with ggtree  [54]. After controlling for the year, the capture date, the epg and the number of L3 used for DNA extraction, we assessed the effects of age (i. e. , young < 1 year or adults) and sex (i. e. , males or females) on two proxies of diversity of gastrointestinal nematodes community: alpha (measure of community diversity within individual samples) and beta (measure of comparison of dissimilarity between each pair of samples).
Taxonomic and Community diversity Considering the whole dataset, we detetected 100 ASVs resolved across14 taxa of gastrointestinal nematodes (Table  1  and AppendixA2 ). ASVs were identi ed either at genus (38%), or species (62%) levels (Appendix A2). A total of 10 genera, including 11 species were identi ed and their phylogeny was consistent with previous knowledge on nematode taxonomy (Appendix A5). Sampling captured most of the taxa as the taxa-accumulation curves reach rapidly a plateau (Appendix A3). Procrustes analyses performed on ASV with taxa have tight correlations (p = 0. 001). Thus, we only show results at ASV taxonomic level, but results from taxa are available in Appendix A7-A9. According to the best models (Table  2 ; appendix A8), the taxonomic richness was higher in Trois Fontaines than in Chizé (estimate ± standard error, β = 0.
20 ± 0. 06, p = 0. 002). The Shannon index, which is more sensitive to rare species, included signi cant interactions between age and site, indicating a higher diversity in young than in adult roe deer in Trois Fontaines (β = 0. 26 ± 0. 13, p = 0. 038) (Fig. 3 ; Table  2 ). At the local scale of Chizé, no differences between the 3 sectors were detected for all alpha diversity indexes (Fig. 2 ). Fontaines, and a marked separation for young and adult roe deer in Trois Fontaines (Fig. 4 ). Locally in Chizé, the selected model for Bray-Curtis dissimilarity depended only on age (F 1,111 =6. 62, R²=0. 06, p = 0. 003). The most common species/genus in the entire dataset were Ostertagia leptospicularis, Trichostrongylus spp. and Spiculopteragia spiculoptera present in 139, 121, 120 samples of roe deer (93%, 81% and 81%, respectively) with a mean relative abundance among those samples of 44%, 29% and 17%, respectively (Fig.
contortus and B. trigonocephalum in this population. In Chizé and Trois Fontaines, we noted the presence of T. axei and O. venulosum, at low relative abundance, also considered as generalist species, and T. colubriformis (only in Chizé) and T. circumcincta, mostly parasitizing sheep and goats  [11, 63]. The identi cation of H. contortus and T. axei is at a "high con dence level' because these species were well represented in the nemabiome database and the three different methods of assignment provided the same species assignment. For B. trigonocephalum ASVs were only assigned at the moderate con dence level including a relatively low level of identity (92% over 283bp (query cover of 100%, e-value = 9e -110 ) to the best BLAST hit in Genebank (Appendix A2 ). To our knowledge, B. trigonocephalum and B.
phlebotomum are the only species among the Bunostomum genus which were identi ed in roe deer in Europe (e. g. ,  [61] ). These two species are highly divergent, and considering the low-level of intra-speci c variation observed within B. trigonocephalum [64], it is possible that the Bunostomum species identi ed in Trois Fontaines is apreviously unidenti ed, or cryptic, species closely related to B. trigonocephalum. For some ASVs, the taxonomic identi cation did not reach the species level, e. g. , Trichostrongylus spp. , Spiculopteragia spp. , or Ostertagia spp. This may be largely a due to the lack of reference sequence available for these species in the nemabiome database and ultimately in GenBank. This issue is accentuated when applying nemabiome metabarcoding to wildlife hosts than domestic livestock where parasite communites are better de ned.
For example, there is just a single ITS-2 reference sequence for Trichostrongylus capricola in comparison to 299 ITS-2 reference sequences for Haemonchus contortus in the nemabiome database (see also Aivelo and Medlar 2018 for the SILVA database). The potential presence of cryptic species and/ or hybrids of closely-related species [65], may futher complicate accurate species assignation. Consequently, the generation of reference sequences from morphologically validated parasites should continue to be a research priority for scienti c community as a whole. Ashworthius sidemi was not detected in Trois Fontaines, although it has previously been isolated from bodies during winter in this study area  [16, 66]. This may be due to the hypobiosis in this species [67] or to the fact that during winter, females contained only non-embryonated eggs  [68].
Declarations Figures Figure 1 Sampling sites in two regions of France, where roe deer were captured. In Trois Fontaines, habitat is homogeneous with rich coppices, while in Chizé, 3 sectors with different habitat types and quality are observed (grey color gradient). N corresponds to sampling size within each site. Figure 2 Egg count, number of L3 and read relative frequencies of gastrointestinal nematodes at taxa level. Each taxon is de ned by one color. The data are split based on site location (Chizé or Trois Fontaines), age (young or adult roe deer) and sex (F: females and M: males). In addition, Samples from Chizé are subdivided according to the 3 different sectors: sector 1: "rich coppices", sector 2: "medium coppices", sector 3: "poor beech stand".
Acknowledgments The authors warmly thank all the professionals from the  O ce Français de la Biodiversité  and all the trainees for data collection. This project was founded by  Results Driven Agriculture Research  (RDAR; grant number  2017R021R ),  University of Calgary , the  O ce Français de la Biodiversité , the  NSERC-CREATE (Canada) Host Parasite Interactions (HPI)  graduate training program and  VetAgro Sup -Pôle d'Expertise Vétérinaire et Agronomique des Animaux Sauvages  (EVAAS ; http://evaas. vetagro-sup. fr/;.
Focal Sows Behaviors were recorded for 10 randomly selected focal sows per pen (40 sows in total). The list of sows' identification numbers was randomized in the 2016 Excel software (Microsoft Corporation, Redmond, WA) and the first 10 sows in each pen were selected for behavioral observations. Each of the selected focal sows were scored for lameness based on a previously described protocol (Performance Zinpro Swine Locomotion Scoring, Feet First Scoring System, Zinpro Performance Minerals) where sows were scored between 0 and 3. Any sow scoring above 2. 5 (defined as: "Lameness is involved in one or more limbs. The sow exhibits compensatory behaviors such as dipping her head or arching her back") was not considered for behavioral observations and the next sow on the randomly generated list was evaluated.
Data Collection Eight cameras (two per pen) were installed on the ceiling or walls surrounding pens. Cameras captured video footage for a total of nine days including day 0 (baseline) before enrichment was added. Video footage of the pens was recorded daily from 0800 until 1500, when the lights were on in the gestation room and when farm staff were less likely to be in the room for morning and late afternoon checks. To obtain estimates of time budgets  (Whalin et al. , 2016) , four observers recorded behaviors for each of the focal sows every 15 min between day 0 and day 8, yielding 29 observations per sow per day (261 total behavior scans per sow over the study period). Training of observers was considered sufficient after at least 90% agreement between observers for 120 scans. Table  2  presents the ethogram of behaviors recorded for this study.
Time Budget Data from the behavioral scans were used to construct a time budget for the following behaviors: standing inactive, lying inactive, walking, exploring, enrichment use, sham chewing, sitting, agonistic behaviors, and other. Agonistic behaviors, including vulva biting, knocking over, levering, biting, mounting, chasing, disturbing, and displacing, were aggregated into a single behavior for analysis. All other behaviors, including scratching, elimination, human interaction, positive or neutral social interactions, were aggregated due to low frequencies of observation. For each behavior outcome, daily pen means were calculated by summing the number of observations that sows were recorded performing that behavior outcome and dividing by the number of complete observations, resulting in a single daily non-Bernoulli binomial value per pen.
Human interaction recorded when focal sow is observed <1 meter from human. Other behaviors "Other" All other behaviors, or behavior cannot be clearly defined Unknown 1 "Other" Sow is not visible on camera/occluded and behavior cannot be determined or the camera has malfunctioned 1 For observations in which a sow was occluded or not visible on camera, or camera malfunctioned, observations were removed and excluded from analysis. Data were analyzed using logistic regression models with binomial error distributions and logit link functions using the glmmTMB function of the glmmTMB package  (Brooks et al. , 2017)  in RStudio (version 1. 3. 1073, R Core Team). Models were built for each behavior outcome with a covariate for baseline measures, fixed factors of treatment (2 levels: control and enrichment), day (4 levels: day 1-day 4), the treatment and day interaction, period (2 levels; period 1: day 1-4 and period 2: day 5-8), and order in which pens received the enrichment (2 levels: first or second).
Pen within treatment (8 levels) was a random subject intercept and the weight statement included the total number of complete observations. The baseline covariate was removed if the corresponding Wald Chi-square test had p > 0. 05. Baseline covariates were included to analyze behaviors of exploring, sham chewing, standing inactive, and walking. The model for the analysis of enrichment interaction included only the fixed factors of order and day, and the random subject intercept was pen (4 levels). Furthermore, a subset of the full dataset was used that only included data for when the enrichment was present in the pen. The weighted arithmetic mean was used to determine means and 90% CIs for baseline behaviors.
| Data analyses Statistical analysis was performed using a dedicated statistical software package (JASP, Version 0. 14. 1, University of Amsterdam). Continuous and ordinal data were summarised by mean and standard deviation or by the median and range, as appropriate. Categorical F I G U R E 1 Ultrasonographic images of the iliac wing. Cranial and medial is to the left. A, Craniocaudal ultrasonographic image of the iliac wing obtained with a transcutaneous approach. Note the localised irregular bone surface consistent with acute incomplete fatigue fracture of the caudal margin of the ilium (arrow). B, Lateromedial ultrasonographic image of the iliac wing obtained with a transcutaneous approach. Note the complete and displaced fracture of the iliac wing with the lateral part displaced proximally (arrow).
This concept is widely recognised in human sports medicine and the need for training adaptation to sand has been highlighted. 47  previously reported, muscles play an essential role in fatigue fractures because the most important forces are created by muscle A predisposition of females for pelvis fractures has been previously reported in some studies because of sex-related differences in bone shape. 4, 28, 48 According to other studies, females (67%) were overrepresented in this study based on data available on the FEI database, where over the study period, geldings and males (n = 328) were overrepresented in the UAE compared to females (n = 132). 49  contrast with our second hypothesis, the number of seasons did not affect the type of pelvic injury. Overall, 48% of bone stress injuries Horses with asymmetry of bone landmarks were more likely to have bone-stress injuries and/or fatigue fractures of the tuber ischiadicum compared to horses without.
Data analysis In addition to health observations of females and kittens, and anatomic pathology evaluations of females and kittens that died or were euthanized, breeding parameters were analyzed to assess any interference of the novel formulation. Breeding parameters included success of mating and gestation, length of gestation, abortion rate, number of live/dead kittens at birth, number of kittens born with abnormalities, weight of kittens 1 week after birth and at weaning and growth during lactation, proportion of male and female kittens, and proportion of kittens born alive and weaned. Breeding parameters, statistical analyses, and results are described in Table  1.
We performed factorial discriminant analysis to statistically discriminate the five days around surgery (D-6, D1, D3, D5, and D13), as described by de Boyer des  Roches et al. (2017). We performed the analysis using all behavioural, physiological (i. e. inflammation, HPA, oxidative stress), and production performance measures. To interpret the discriminant components (axes) of the factorial discriminant analysis, we focused on variables with an absolute value of correlation with an axis >0. 4. We estimated the performance of the final predictive model with the current dataset by performing leave-one-out cross-validation, which calculates the probability of each animal being accurately classified for the correct day around surgery. This multiparametric analytical approach enabled us to calculate the probability of each cow belonging to each day.
Acknowledgements We thank the staff of the experimental unit for providing technical assistance during the experiments and  Dr Heliez  ( Clinique Vétérinaire des Faluns, Saint Grégoire, France ). We also thank  Agnès Thomas ,  Anne-Sophie Bage ,  Eric Delval ,  Stéphane Andanson , and  Christine Ravel  for providing assistance with the laboratory analyses, and  Metaform Langues  and  Michael Corson  for providing editorial support.
Starting date of the monitoring period Duration in days June 24 th 2020 8 July 8 th 2020 7 July 22 nd 2020 9 August 5 th 2020 10 August 19 th 2020 7 September 2 nd 2020 7 September 22 nd 2020 6 using feed experiments on pigs (https://anr. fr/Project-ANR-17-CE27-0002). This experiment lasted 15 weeks to observe a possible effect of diets on pig mandibles and imposed several constraints (age of the animal, duration of the experiment, housing of the animals in individual crates to quantify individual feed intake and refusal). These constraints were an opportunity to study the behavior and assess the welfare of slaughter pigs individually over a long period of time. 1. Pigs were fed a conventional diet supplemented with sugar cane. Sugar cane stalks were provided ad libitum, and grounded in 20 cm medium-sized cut pieces just before the distribution.
Ambient Temperature Room temperature and relative humidity were monitored every 10 min, all along the experiment using a stand-alone USB data logger (EL-USB-2+; DATAQ Instruments, Inc. , Akron, OH). The temperature sensor and the crates were located in the same room. Average temperature and humidity are available in Figure  1. Temperature was generally below 30 • C before 10:00 and after 16:00. Temperatures were highest between 12:00 and 14:00. It  increased until 13:00 and then started decreasing for the rest of the day. Humidity follows the opposite pattern: it was highest in the morning, decreased until 13:00 and then increased for the rest of the day. The minimal and maximal temperatures recorded were 24. 5 • C and 37 • C. The minimal and maximal humidity recorded were 45% and 95. 5%.
Statistical Analysis All the statistical analyzes were performed with Matlab 2020a. To compare the posture distribution of the two breeds, we used the Wilcoxon rank sum test between two independent samples, with 5% significance level. For a given posture, a sample was the daily proportion of time spent in this posture over the monitoring period. The daily proportion of time spent in a posture was compiled for all animals of the same breed. As the animals were video-recorded during 54 days, for a given posture, a sample had 3 × 54 = 162 elements. The null hypothesis of the statistical test was that the two samples had the same mean. Or in other words, that the two breeds spent an equal time in a given posture. The null hypothesis was rejected when the p-value is under 0. 05. One Wilcoxon rank sum test was performed for each posture, i.
They are generally raised indoor, with relatively constant light exposure and access to electricity and network. In addition, they are raised in relatively small areas, reducing the number of cameras to be used. Compared to embedded technology, such as accelerometers, image analysis allows to monitor pigs behavior without human intervention on pigs, which can be difficult. In this article, we showed that stateof-the-art CNNs can be used almost directly to track and estimate the postures of an animal. This is particularly convenient because the CNNs that we used (i. e. resNet50 as a feature extractor for Yolo and GoogleNet to predict posture) were pre-trained on a large amount of images (several millions using ImageNet) and only a small amount of parameters needed to be tuned to obtain a good accuracy on a specific dataset.
As a consequence, only thousands of images have to be manually labeled to re-train the CNNs. However, the trained CNNs are most likely not suitable for other environments, such as group-housed pigs. Indeed, the experimental setup was particular, with a centered top view of the scene and with only one animal in the camera field of view. More variability in the training dataset would be needed to train a generic CNNs that could work for most studies on pig behavior. In our study, we used computer-based analysis of images to investigate the behavioral response to HS of two contrasted breeds. The European LW breed has been selected for lean growth for several decades in optimal growing conditions, i. e. in buildings controlled for temperature and under temperate climate. The Caribbean CR breed has been submitted to little genetic selection and is characterized by high fat deposition and good adaptation to harsh environmental conditions  (Rinaldo et al.
Availability of In Vitro DNT Data The data from the EFSA-funded project can be found in the report  [28]  and on the link to that report ( https://efsa. onlinelibrary. wiley. com/doi/10. 2903/sp. efsa. 2020. EN-1938;  see "supporting information file: efs31938e-sup-0001-Annex-A. xlsx"). When it is complete, the data from the US EPA laboratory will be made available through the US EPA's CompTox Chemicals Dashboard ( https://comptox. epa. gov/dashboard/chemical_lists/TOXCAST), but this is not expected to be available to the public before mid-2021. Finally, although separate from this project, the National Toxicology Program at the US National Institute for Environmental Health Sciences maintains a DNT-related database (DNT DIVER, https://sandbox. ntp. niehs. nih. gov/neurotox/) that houses data from several of these assays as well as zebrafish behavioral assays.
Adverse Outcome Pathways The AOP conceptual framework describes a sequence of measurable key events (KEs) which are expected to be triggered by the activation of a molecular initiating event, MIE. This cascade of KEs finally results in an adverse outcome (AO)  [46, 47]  of regulatory relevance. The adverse outcome pathway (AOP) concept would therefore facilitate the application of mechanistic knowledge to regulatory decisions. The AOPs also represent the ideal tool to identify experimental data gaps or lack of knowledge in the pathophysiological process. Indeed, the regulatory acceptance of NAMs, and particularly of DNT mechanistic endpoints which currently lack specific guidance, needs a strong biological rationale. The understanding of the pathological pathways leading from functional in vitro endpoints to behavioral changes at organism level appears particularly challenging.
AOPs will assist in structuring the available information in terms of MIE, KEs and AO, and in the identification of missing data and/or in the design of testing strategies. One relevant consideration is that the endpoints measured in the DNT-IVB, in the AOP conceptual framework, represent KEs and not MIEs. However, more downstream KEs, closer to the AO, are expected to be more comprehensive in terms of coverage of potentially relevant pathways and the expected propagation of effects within the AOP to higher levels of organization may be more certain and consequently regulatory relevant. It is therefore important to establish the amount of data to be gathered in an AOPinformed IATA, still based on problem formulation. More uncertainty can be an acceptable condition for screening and prioritization of a large number of chemicals.
This might be less acceptable for, e. g. , single chemical risk assessments. In this case, the DNT-IVB will be part of the mechanistic evidence influencing the overall WoE for the postulated AOP. The use of a prototype chemical stressor can be therefore an option to inform on the most probable MIE. Mapping the available DNT-IVB data in the AOP wiki ( https://aopkb. oecd. org/ and https://aopwiki. org/) enables the generation of DNT AOP networks and provides evidence that the DNT-IVB is indeed testing the fundamental neurodevelopment KEs in an AOP network  [12]. This greatly facilitates the use of the DNT-IVB data for overall WoE in the IATA case studies, and the identification of missing data and/or design of testing strategies in accordance with the IATA iterative process. This approach will be described in the guidance through the case studies.
Life Cycle Assessment The LCA was performed for each pig, considering all the impacts associated with feed production, animal housing, and manure management (as described by 6). We based our analysis on the CML 2001 (baseline) method version 3. 02 as implemented in SimaPro software version 8. 05 (PRé Consultants) and added the category land occupation from CML 2001 (all categories) version 2. 04. Thus, we considered the potential impacts of pig production on CC (kg CO 2 -eq), EU (g PO 4 -eq), AC (g SO 2 -eq), and LO (m 2 • year). The CC was calculated according to the 100-year global warming potential factors in kilograms CO 2 -eq. Impacts were calculated at the farm gate, and the functional unit considered was 1 kg of BW gain over the fattening period.
Statistical Analysis The LCA calculation model was implemented using SAS software (SAS Inst. Inc. , Cary, NC). Performance and environmental impacts were subjected to variance analysis using GLM procedure with feeding strategy as main effect. Pearson correlations for each feeding strategy were calculated between performance and environmental impacts data using CORR procedure, and pigs were ranked according to their CC impact, considering the feeding strategy and using the RANK procedure. All analyses were conducted using SAS software version 9. 1 (SAS Inst. Inc. , Cary, NC). All the data used in the statistical analysis are available in the INRAE data repository  (10).