dataesr/scientific-paragraphs-categorization huggingface dataset:
Genome-Wide Association Study (GWAS) DNAs were genotyped on the Illumina 173k SNV Canine HD array at CNG (Evry, France) and on the Affymetrix Axiom Canine Genotyping Array Set A and B 1. 1M SNV array at Affymetrix, Inc. (Santa Clara, USA). We used mixed linear model analyses, taking into account population structure and kinship (Eigenstrat -GenABEL 1. 8)  52  , removing SNV with a minor allele frequency under 0. 01. Pvalue corrected for inflation factor λ were used and the threshold for genome-wide significance for each association analysis was defined based on 500 permutations. For imputation, the Beagle software  53 [version 4. 1]  was used to impute the Illumina 20k SNV and Illumina 170k SNV arrays to the Affymetrix 712k SNV array format, as well as to input 21,614 variants identified from the capture and targeted sequencing of 16 dogs.
1200 ng of these purified libraries were then hybridized to the SureSelect oligo probe capture library for 72 hr. After hybridization, washing, and elution, the eluted fraction was PCR-amplified with 9 cycles, purified and quantified by QPCR. Based on this quantification, an equimolar pool was performed then quantified again by QPCR. Finally, the pool was sequenced on an Illumina HiSeq 2000 as paired-end 75b reads. Image analysis and determination of the bases were made using Illumina RTA software version 1. 12. 4. 2 with default settings. The bioinformatic analyses of sequencing data were based on the Illumina pipeline (CASAVA1. 8. 2). CASAVA performs alignment of a sequencing run to a reference genome (canFam3), calls the SNVs based on the allele calls and read depth, and detects variants (SNVs and Indels).
Methylation analyses Methylation analyses were performed on 12 histiocytic sarcoma cell lines, including one commercial cell line (DH82; ATTC, CRL-10389; RRID:CVCL_2018) and eleven cell lines developed in the team from HS affected dog fresh tissues. These eleven cell lines are available on request. Cells were cultivated in a complete RPMI medium containing RMPI 1640 GlutaMAX supplemented medium (Gibco. life technologies) with 10% of Fetal Bovine Serum (HyClone, GE Healthcare, Life Sciences, Logan, UT) and 0. 025% of Primocin (InvivoGen, Toulouse France) at 37 C in a humidified 5% CO2 incubator. All cell lines were tested for mycoplasma with MycoAlertTM Plus kit (Lonza, Rockland, ME) and were mycoplasma-free cells. The SNVs of CFA5 and CFA2 were sequenced by Sanger sequencing as previously described  10  with the following primers: CFA2_29716535-F : GGTGTACTTTCGGGTCCAAC, CFA2_29716535-R :CCCTGTCATTCGATGTCCTT, CFA5_30489203-30489217_F : CCTGAGTGAGTGGAATGAGGA, CFA5_30489203-30489217_R : CTTCCTGCGACCTGCTGT) in absence and or (CFA2_29716242-29716795_FM: TAGGTGTTGGGTTTATATTGTTAGG, CFA2_29716242-29716795_RM: CTTCCTGCGACCTGCTGT, CFA5_30488738-30489339_FM : TAGGTGTTGGGTTTATATTGTTAGG CFA5_30488738-30489339_RM) in presence of bisulfite conversion (EZ DNA Methylation-Gold Kit, Ozyme, St Cyrl'école, France).
sample collection performed through the French Cani-DNA BRC was funded by the CRB-Anim infrastructure ANR-11-INBS-0003 in the frame of the 'Investing for the Future Program (PIA1). Last, donations from Bernese Mountain dogs Associations were kindly offered by the French AFBS, the Italian SIBB and the German DCBS. BMD GWAS results for HS with 172 cases and 154 controls (GWAS_1_HS_BMD). A) Quantile-Quantile plot displaying a genomic inflation λ of 1. 000005, indicating no residual inflation. B) Manhattan plot displaying the statistical results from the GWAS. This analysis pointed out three loci (arrows) on chromosome 5 (CFA5: 30496048, pcorrected = 6. 36 x 10 -5 ), on chromosome 11 (CFA11: 41161441, pcorrected = 4. 85 x 10 -7 ) and on chromosome 20 (CFA20:30922308, pcorrected = 2. 52 x 10 -5 ).
Acknowledgments We thank veterinarians who provided anatomopathologic diagnoses, especially  Olivier Albaric  and  Laetitia Dorso  ( Laboniris, Oniris, Ecole Nationale Vétérinaire de Nantes, France ) as well as  Marie-Odile SEMIN  ( LAPV, Amboise, France ),  Caroline Laprie  ( Vet-Histo, Marseille, France ),  Marie Lagadic  ( Idexx Alfort, France ) and  Frédérique Degorce-Rubiale  ( LAPVSO, Toulouse, France ). We thank the veterinarians for providing us with clinical data and samples, as well as dog owners, breeders and breed clubs, especially the  French club AFBS, European clubs , the  American club BMDCA , the  IWG International Working Group (for Bernese Mountain Dogs ) and the  US Berner garde foundation , especially  Pat Long  for her dedicated trust and follow-up of our work. We also warmly thank  Clotilde de Brito ,  Laetitia Lagoutte ,  Annabelle Garand ,  Anne Sophie Guillory ,  Melanie Rault  and  Ronan Ulve  ( IGDR, Rennes, France ) for their help to sample collection and  Stéphane Dréano  ( IGDR, Rennes, France ) for Sanger sequencing and the Biogenouest bioinformatic platform.
Acknowledgements The authors want to thank  Cindy Louvet  and  Nathalie Arancibia  for all aspects concerning the maintenance of the life-cycle of S. mansoni in B. glabrata. We thank all team members for their advice and helpful discussions. Also, the authors thank  Josie Harris  for revising the English writing of this paper. Paradev company is also warmly thanked for its technical support. The spectroscopic experiments have been performed using the Biodiversity and  Biotechnologies Marines  ( Bio2Mar , http://bio2m ar. obsba nyuls. fr/fr/index. html)facilities at the  University of Perpignan via Domitia.
Assessment of the horse's locomotion and the movements of the rider's spine during the riding session The data recorded on 24 out of the 30 horse-rider dyads could be analysed. Three inertial measurement units (IMUs; APDM, USA) were located on the dyad: one on the horse's sternum, one on the rider's fifth lumbar vertebra (L5) and one on the rider's sternum (ST; Figure  1 ). These positions were chosen because they were close to both horse' and rider's centre of gravity, and because the attachment of the IMU to the girth ensured its stability  [55]. This first part of the riding session lasted 2. 8 ± 0. 1 (mean ± SEM) minutes. Fast gaits such as trot and canter were preferred to walk to maximize the chances of observing the impact of a compromised welfare state assessed in loose boxes on the horse's locomotion and the movements of the rider's spine, due to the greater physical effort this required of the horses.
Acknowledgements This project was funded by the  IFCE and the "Fonds Eperon". This funding source has no role in the study design, data collection and analyses or in the preparation and submission of the manuscript. The authors are very grateful to the staff of the  French Horse and Riding Institute  and  INRAE (Nouzilly, France) , and especially to  Marc-André Morin. We would like to thank the  Springer Nature Author Services team  and  Sue Edrich  from  Interconnect  for correcting the English manuscript.
Data From 1993 to 2019, 50955 standard radiographs of extended hindlimbs submitted by breeders or owners were evaluated independently by the same examiner (XXX) for HD assessment. All the data were computerized and recorded in a single electronic database to allow further analysis. For the present study, and for each selected breed, the incidence of each of the 5 scoring classes (Table  1 ) was extracted from the database for each year covered in this retrospective study. Breeds were excluded if the single panelist changed before the end (2019) of the study period, or if the total number of radiographs read per breed was insufficient (i. e. <200).
These results must be interpreted with caution since the evaluation of coxo-femoral joint status is not mandatory for breeding in France  [7]. In a 1993-2002 survey  [24] , it was demonstrated that in France, only 2 to 19% of the dogs were screened for HD. Although the number of screened dogs has increased since this period, it is likely that, depending on the breed, a small fraction of all breeding dogs undergo a hip radiograph. Moreover, there is an unknown proportion of veterinarian (or owner) prescreening of the radiographs with obvious hip dysplasia, leading to the lack of presentation of the "worst" radiographs for official screening. Therefore, our data reflect only those dogs whose owners and breeders submitted radiographs for analysis. This proportion varies from 20 to 40% in Switzerland  [25].
Finally, to ensure that ovulation has occurred, blood should be taken one to three weeks after the last observed mating to measure blood progesterone. In case of an anovulatory cycle, the value will remain basal  [17]. In case of confirmed anovulatory cycle, induction of ovulation can be tried during the next cycle; even though in cats, there is no standardized protocol for induction of ovulation at the time of natural mating. Preliminary data in our department have shown that a series of 5 vaginal stimulations at 30 minutes interval on females at the peak of oestrus induced ovulation in 8/11 queens (unpublished results). This is preferable, since hormonal stimulation can cause side effects. In one study, induction of ovulation with hCG lead to disruption of oviductal embryo transport and development, probably due to abnormal endocrine environment  [18] , although successful ovulation was induced in queens in nonbreeding season by administration of eCG and hCG before embryo transfer in the study of the team of Tsutsui  [19].
Teratozoospermia Teratozoospermia is a common phenomenon in felids (both wild and domestic cat)  [50]. The threshold for teratozoospermia in cats has been established at less than 40% of normal spermatozoa in the sample  [51]. One study showed that teratozoospermic spermatozoa possessed worse motility parameters, compromised ability to capacitate and undergo the acrosome reaction, abnormal chromatin integrity and lower expression of phospholipase C Zeta  [52]. Importantly, even apparently normal spermatozoa from teratozoospermic males were impaired  [51]. In none of these studies in vivo fertility was evaluated and it is known that teratozoospermic tomcats can be fertile. In one study  [53] , 11 teratozoospermic cats with known breeding records were all fertile. Unpublished data from our laboratory showed that 6 out of 20 ejaculates from ten fertile pedigree cats (four cats collected more than once) were classified as teratozoospermic.
, 2020b; Kulichevskaya et al. , 2020a; Kulichevskaya et al. , 2020b; Rivas-Marin et al. , 2020b; Rivas-Marin et al. , 2020c; Salbreiter et al. , 2020; Sandargo et al. , 2020; Schubert et al. , 2020; Wang et al. , 2020; Wiegand et al. , 2020). Hence, enormous work remains to be done to improve their culture and their isolation, in view of the enormity of 16S rRNA genes sequenced deposited in GenBank but have never yet been isolated in pure culture (uncultured Planctomycetes) up to the present day (see review  Wiegand et al. , 2018  for more details) because, the true knowledge of bacterial taxonomy, physiology, and pathogenicity has long time based only on the isolation of the strain in pure culture and presents several challenges for clinical microbiologists. Also, for decades, most of the Planctomycetes studies have focused only on their diversity, distribution, and relative temporal or permanent abundance in diverse habitats  (Stackebrandt et al.
review  (Wiegand et al. , 2018)  and the 64 new species isolated in this year from various habitats  (Wiegand et al. , 2020). Most genera cited above are represented by only one or two species. The cultured strains are not at all representative of the great diversity and ubiquity that has been revealed by molecular microbial ecology techniques  (Kirkpatrick et al. , 2006; Penton et al. , 2006; Hamersley et al. , 2007; Schmid et al. , 2007; Pizzetti et al. , 2011b; Pollet et al. , 2011; Fuchsman et al. , 2012; Ivanova and Dedysh, 2012). Indeed, recent study revealed that on the 8. 312 operational taxonomic units (OTUs) defined by a 99% identity threshold (full length 16S rRNA (SILVA SSU Ref NR99 database (release 128 from 07-09-2016)  (Quast et al. , 2013) , only 0. 6% of the known planctomycetal diversity on OTU level is covered by axenic cultures  (Wiegand et al.
SUBJECTS AND HOUSING Our study comprised two groups of capuchin monkeys (Sapajus libidinosus) under the care of the Wildlife Rescue Center (CETAS) of Cabedelo, in the state of Paraiba, Brazil. Group A contained nine adult individuals (six males and three females), and Group B contained six individuals, four adults (two males and two females), and two juveniles (one male and one female). Only 12 adult individuals, out of the 15 animals initially available, were included in the analyses. Data from the two juveniles were not collected, and one adult female from Group B was housed individually after enclosure change and was therefore excluded from our analysis. The environment provided to both groups was similar: barren, non-enriched enclosures of equal size (4. 60 m x 3. 15 m x 2. 40 m), with concrete floor and barred walls allowing an outside view, and limited presence of humans (only caretakers and researchers had contact with these animals).
BASELINE DATA COLLECTION Behavioral and physiological baseline data of adult individuals were collected three workdays per week, over two months before group enclosure change. The collection of data followed the same procedure as  (Ferreira et al. , 2018) : 'focal animal' method  (Altmann, 1974) , with two 10-minute sessions, one in the morning and one in the afternoon, per individual and records at every 30-second intervals, totaling 40 daily behavioral records (states) per animal. In this study we focused only in BPIS. The BPIS were divided into two types: states (behavior lasting more than 5s: "Pacing", "Selfgrooming", and "Crouching/self-clasp/huddle") and events (behavior lasting less than 5s: "Head twirl", "Pirouette", and "Self-scratching"). Four BPIS could be described as either states or events, depending on their duration ("Boucing/rocking", "Ingestion/Manipulation of urine, feces, and sperm", "Masturbation/auto-erotic", and "Sexual Display to humans", see full BPIS ethogram in Tables 1).
BPIS events were quantified in 'all occurrences', that is, every event of selected behaviors was recorded within the 10 min focal sampling. (Table  1 about here)  All occurrences of agonistic behaviors between all individuals (focal and/or non-focal individuals), and the identity of participants, were recorded in order to calculate the dominance hierarchy for each group. The daily observation started 30 minutes after the meal to avoid biased data for food-related behavior, from 08:00 to 17:00, approximately. The total time of behavioral collection was of 78 hours in Group A and 19 hours in Group B (Mean Group A: 8. 6 hours/individual; Mean Group B: 6. 3 hours/individual). In a previous experiment  (Ferreira et al. , 2018) , to determine captive capuchin monkey personality axes, behavioral data on 12 genus normative behaviors (GNB, see the full GNB ethogram in Table  S1  in the supplementary material) from 25 captive capuchin individuals (including the two groups that were submitted to enclosure change) were analyzed through a principal component analysis (PCA), generating four components labeled 'Feeding', 'Sociability', 'Exploration', and 'Activity' (see Table  S2  in the supplementary material for the PCA structure matrix, its components and the explained variance).
Each individual received a score within each component (regression method). The scores for our 12 relocated individuals were subsequently used for enclosure change analyses (see Data analysis section). The fecal collection was conducted opportunistically (morning and afternoon) at least three times per week, during the behavioral observation. After seeing the defecation and identifying the individual, the researcher entered the enclosure and collected the fecal samples within two hours after defecation. The feces were packed in Eppendorf tubes and identified by the name of the animal, time of defecation, time of collection, and date. Samples were frozen at -5 °C within two hours after defecation until analyses  (Ferreira et al. , 2018). In total, 246 samples of feces from 12 adult monkeys were collected (average of 20.
ENCLOSURE CHANGE DATA COLLECTION Due to enclosure renovation, the groups were relocated to new enclosures within the same facility on January 16, 2016, between 6:30 and 7:30 am. Individuals were captured one by one by a caretaker using a net and were immediately released into the new enclosures (less than 30 m apart). These new enclosures were of the same size for both groups (4. 65m x 2. 30m x 2. 63m) and, similar to the previous enclosure, they were barren and non-enriched. The behavioral observation was performed over the next 14 days (with the exception of the third day post-enclosure change, which was excluded due to heavy rain) in the new enclosure, and similarly to the first period, the adult animals were observed 10 minutes in the morning and 10 minutes in the afternoon. As the time to peak FGM excretion after a stressful incident can vary 1.
(Table  2 about here)  The dyadic events of agonism were used to calculate the dominance hierarchy using the SOCPROG 2. 4 software  (Whitehead, 2008) , and the dominance index used was the MDS (Modified David's Score)  (De Vries et al. , 2006). Individual FGM values were compiled into four indices to analyze the impact on stress physiology: median, mean, maximum, and minimum  (Ferreira et al. , 2018). All outliers (values more than three interquartile ranges) within each variable were excluded in order to obtain a more reliable database. According to previous literature on animal enclosure change and capuchin monkeys FGM analyses  (Cinque et al. , 2017; Mendonça-Furtado et al. , 2017; Watson et al. , 2005) , the FGM repeated measures were assessed in four different periods, named baseline (before enclosure change), day 1, week 1 (from day 2 to day 7) and week 2 (from day 8 to day 14) after the enclosure change.
ACKNOWLEDGEMENTS We thank the  CETAS Cabedelo  for permission to work within their facilities and for all logistical support during data collection. VHBF was supported by a postgraduate scholarship from the  Brazilian National Council for Scientific and Technological Development -CNPQ  -during this research ( 133216/2015-2 ). This research was funded by  CNPq Universal  ( 4403041-2014-8 ) and  Fundação Grupo Boticário  ( 0973-2013. 1 ) to RGF.
No observations occurred between 12:30 PM and 2 PM. Data was collected using the focal animal sampling  (Altmann, 1974). We defined a sample as a continuous observation of one individual and a session as a sequence of six samples, one for each elephant. Each sample lasted 15 min and one to three sessions were performed per observation day. Before each session, the sampling order was defined thanks to a simulator of random lists. A total of 92 samples were collected, with 14-17 samples per individual. In the afternoon some elephants had access to the cement-flooring outdoor area, and the conditions of observation were not comparable to the usual conditions. Hence, we skipped the observation of individuals outdoor, which explains the variable number of collected samples per individual. During the observation of an elephant, behaviours involving the trunk were scored continuously as occurrences, and the type of activity (e.
Data analysis As described in the literature, feeding was the main activity of the elephants. They spent 72. 7% ± 5. 8% (mean ± S. D. ) of their time feeding and feeding behaviours corresponded to 77. 9% ± 4. 7% of all the occurrences of behaviours collected. The repertoire of feeding behaviours encompassed 19 different behaviours. We collected 15,234 occurrences but seven behaviours were rarely (<4 occurrences) or never observed during the sampling period. Consequently, they were not considered in the analyses. In a first step, we tried to establish a link between the different behaviours and the type of food item manipulated. The six different types of food items were: hay, vegetables, apples, and branches (three sizes). Branches were distributed into three different classes (named b1-b3 thereafter) according to their diameter estimated by eye: b1 < 5 mm; 1 cm < b2 < 2 cm; b3 > 2 cm.
For each individual we calculated the number of occurrences of each feeding behaviour according to each type of food. Hay was permanently available to the elephants contrary to the other food items and was over-represented in our data set. To avoid this bias we transformed the number of occurrences of the behaviours into the proportion of occurrences, calculated for each food item and each animal. We obtained a table with 10 columns/behaviours and 36 rows (six individuals × six types of food items, N = 36). This data set was submitted to a normed Principal Component Analysis (PCA) to detect links between behaviours considered as variables and food items considered as individuals. We then compared the distribution of the coordinates of the 'individuals' on the first component axis to test whether different foods items differed.
A nonparametric ANOVA with General Scores and a Monte Carlo procedure was performed, followed by paired comparisons between each type of food items using a Fisher Pitman test for paired samples (pairing by individuals). Because multiple comparisons were made, the probabilities were corrected using a Holm-Bonferroni procedure  (Holm, 1979)  and P' (the corrected P) is presented. Hay was always available to the elephants and most of our data were collected when elephants were manipulating and eating hay (62. 2% ± 7. 9% of feeding occurrences). The inter-individual differences were tested in comparing the behaviour of the animals when feeding on hay. Because the total number of occurrences varied greatly between animals and samples of a given individual we used the proportions to compare the animals.
ACKNOWLEDGEMENTS We gratefully thank the  ZooParc of Beauval  who owns the elephants and welcomed our project. Experiments were conducted with the help of the keepers under the direction of  Yann Ménager. All our thanks go to him and  Nathan Durand ,  Amaury Boutier ,  Matthieu Villemain ,  Matthieu Fromet ,  Mathieu Hysbergue ,  Mégane Marron  and  Clément Langles.
freudenreichii CIRM-BIA 129. The database search parameters were specified as follows: trypsin cleavage was used and the peptide mass tolerance was set at 10 ppm for MS and 0. 05 Da for MS/MS. Methionine oxidation was selected as a variable modification. For each peptide identified, a minimum e-value of 0. 05 was considered to be a prerequisite for validation. A minimum of two peptides per protein was imposed, resulting in a false discovery rate (FDR) of 0. 15% for protein identification. Proteomic data were further analyzed and visualized using Python libraries Pandas, NumPy, Matplotlib, and Seaborn. Functional annotations and Clusters of Orthologous Groups (COGs) were obtained using the eggNOG-mapper v2 web tool  (Huerta-Cepas et al. , 2017 , 2019) , while proteins and gene data were retrieved from NCBI and Uniprot  (Bateman, 2019).
Prediction of Protein-Protein Interactions In order to screen for potential biological functions of EVs, the prediction of interactions between EV proteins and human proteins was carried out. The reference human proteome was retrieved from Uniprot (UP000005640) and contained 74,788 protein sequences. For the first method of prediction, EVs and human proteins were submitted to the InterSPPI web server  (Lian et al. , 2019) , a machine-learning-based predictor. For the second method of prediction, a interologbased approach was used  (Folador et al. , 2014) , establishing homology relationships with the interactions described in the String and Intact databases  (Kerrien et al. , 2012; Szklarczyk et al. , 2017). The resulting interactions were filtered according to the prediction scores (intersppi: minimum score of 0.