dataesr/scientific-paragraphs-categorization huggingface dataset:
The sex of the pigs was reported in 32 of 77 experiments with 18 of them using both male and female pigs, eight males only (two entire, one castrated and five not precise) and six experiments using only females. Housing conditions were scarcely recorded with only 10 experiments providing the type of floor. Housing temperature was not indicated, except in two instances. With respect to feeding, only nine experiments provided information on type of feed and/or feeding system. Amongst the experiments included in the database 78% were classified as intervention studies. This proportion of interventions largely differed between affected system and diseases: 39 of 40 experiments studying digestive diseases, 9 of 22 for the locomotory system and 12 of 13 for respiratory system. The nature of the intervention applied for the induction of production diseases in included studies varied within and across production diseases.
In a few experiments, affected groups were not subjected to an intervention but the control groups were given a protective intervention. The age of the animals varied according to the physiological stage during which the respective diseases occur. Sows were poorly represented in the database with only three experiments investigating occurrence of peptic ulcer, lameness and leg weakness. Pigs studied towards splay leg disease were newborn (0 to 8 h old), whereas animals affected by post-weaning diseases were weaned pigs (average of age 28 days at the beginning of the study). Colitis was studied across all stages; interventions to induce colitis were applied at various stages with 10 experiments comprising young piglets (intervention starting from day 6 after birth), and four and five studies comprising weaner and grower pigs, respectively.
Regarding the affected system studied, publication output and inclusion in the database were the greatest for digestive, the lowest for locomotor and intermediate for respiratory diseases. This order is not consistent with the reported economic impact of respiratory diseases with an estimated cost amounting to between 4 and 7 € per pig v. 3 to 5 € for enteric diseases  (Niemi et al. , 2016). Gaps evidenced in this work can also be directly linked to our methodological approach. Indeed, we included articles which fulfilled certain strict criteria, therefore limiting the number of studies that were included in the data set to 2. 9% of the total publications which characterise production diseases in pigs. The most significant factor for study exclusion was the partial presence of production diseases in the affected and control groups.
Acknowledgements This project has received funding from the  European Union Seventh Framework Programme  for research, technological development and demonstration under Grant Agreement No. 613574  (PROHEALTH). Preliminary results of this work have been published in Loisel F, Stravakakis S, Sakkas P, Kyriazakis I,  Stewart G, Le Floc 'h N, and Montagne L 2016. Identification of animal-based traits as indicators of production diseases in pigs. Proceedings of the  XVIth International Conference on Production Diseases in Farm Animals (ICPD) ,  Wageningen ,  Netherlands ,  Wageningen Academics Publishers. p 152 (poster).
Efficacy Outcome Clinical efficacy was evaluated in the same manner by vets during follow ups as the one used in the Orthopedics Department of VetAgro Sup upon inclusion. Whenever possible, the vet evaluating the dog was not the one who injected the dog. At the same time points, owners assessed their dog's global mobility before and after treatment based on a 4-stage scale by answering a single question: "Do you estimate that mobility is (1) significantly better-(2) slightly better-(3) not changed-(4) worse. " If dogs were re-injected at W24, they followed the same protocol for the additional months. Two years post-injection, dog's owners were asked to complete a survey to report any other OA-related treatments given plus the recurrence, degree, and persistence of lameness (Survey detailed in Supplementary Data 1).
Statistical Analysis Statistical analysis employed the GraphPad Prism 6. 0 program (GraphPad Software, USA). Changes in the clinical score over time were calculated using the non-parametric Friedman repeated measures ANOVA on a rank sum test. Post-hoc comparisons were made using a Dunn's test. Differences were considered significant for P ≤ 0. 05. Comparison of the clinical score evolution between more lame limbs group and less lame limbs group was conducted using two-way repeated measures ANOVA. A post-hoc comparison was obtained using Sidak's test. Baseline comparisons between hip and elbow on clinical scores, weight, age, were produced using the Mann-Whitney U-test. Categorical data (gender) were compared using Fisher's exact test.
6 joints, principally hips (5 hips #7;8;12;14;6 and 1 elbow #5) produced a worsened global clinical score. Median scores increased by 28% from 7. 2 at reinjection to 10. 7 the day after. Three (#7;8;12) of those 6 joints, all hips, had also presented a reaction after first injection. The elbow of dog #5 hadn't reacted for the first injection. Midterm assessment-Over the 6-month period following the initial injection, or repeats, no serious adverse events were reported either by the owners or by the vets. Long-Term Assessment AEs were monitored up to 2 years after initial injection. Nine dogs did not present again at investigation site. Clinical records collected from their vets did not report any AEs except for 3 dogs (#12;13; 17) for which data were lacking since they were lost to follow up.
Efficacy Taken together there was significant clinical improvement assessed by practitioners at all-time points after MSC treatment. A majority of owners attested to marked improvement as in other published studies  (8, 9). Interestingly, practitioner and owner evaluations were coherent at the mid-and end-point of the follow up (W12 and W24), strengthening analysis of our selected outcome variables. Despite the limited number of joints, sub analysis by joint (hip vs. elbow) is informative. In both cases, significant clinical improvement was shown at W12, while it was significant at W24 only for hips. Interestingly, after a second injection, clinical efficacy was restored up to W'24 in any joints. Our study did not include an objective measurement such as dynamic gait evaluation since different types of appendicular joints were evaluated and some dogs had bilateral OA, rendering data not comparable.
Procedure Data were collected between 30 April and 26 May 2015, during the breeding season of the common hamster. We first estimated the number of burrows that were active i. e. inhabited by an individual, indicated by the presence of faeces, recent feeding food and/or recent excavated soil and inactive i. e. no longer used, indicated by the vegetation at the entrance and the absence of pathways around it. As it was impossible to ascertain which entrances were linked to a burrow system, every single entrance was defined as a burrow  [28]. At the outset of the study, 685 burrows (194 active, 491 inactive) were detected. This number grew to 787 at the end of the study (208 active, 579 inactive). The spatial positions of these burrows were also recorded to evaluate whether their location was linked to the vicinity of trees or bushes and to the noise disturbances.
Behavioural data collection Overall, 66 focal periods (over a total of 156 hours of field work) were collected. After sex identification and the exclusion of poor-quality images, 54 focal periods remained. Video footage analysis was carried out according to the ethogram developed by  Ziomek et al. (2009)   [23] , which was completed with our observations (cf. Table  1  for description of behaviours). During the observations, all behaviours were precisely recorded and for rare ones, regrouped in the category "other" (cf. Table  1 ) in the following statistical analysis.
Not active Motionless (inactive or sleeping). https://doi. org/10. 1371/journal. pone. 0225347. t001 The dredge function of the "MuMIn" package was used to select the best-fitting models, based on corrected Akaike Information Criterion (AICc), delta AIC (ΔAIC) and the Akaike weight  [36]  (S1 Table ). Analyses on activity budget of individuals were then conducted: at each surface trip of a hamster, the time spent for each activity was measured, giving a ratio of the different activities per trip. These different activity ratios were then compared according to sex (male or female) and time of day (morning or evening). These analyses were performed on 31 adult individuals among 35, since it was impossible to determine the sex of four focal individuals from the data and videos. We ran generalized linear mixed model (GLMM) analyses using the "lme4" package  [37].
In each model, all VIF values were lower than 3. The dredge function of the "MuMIn" package was also used for model selection. We chose the model with the lowest AICc  [38]  which led us to exclude the time of day of the analysis (S2 Table ). Post-hoc tests were performed with the "emmeans" package  [39]  to investigate the results of interactions between qualitative variables. The same procedure was followed for vigilance behaviours analyses: at each surface trip of a hamster, the frequency of specific vigilance behaviours was measured, giving a ratio of specific vigilance behaviours on the total vigilance behaviours expressed during a surface trip. We compared the ratios of these different vigilance behaviours between type of vigilance behaviour (e. g. short-term freezing, long-term freezing, head-rearing or monitoring) and sex, and between type of vigilance and time of day.
Fine mapping and identification of a causal mutation associated with mastitis To fine map the most significant QTLs on OAR3 QTL in Lacaune  (Rupp et al. , 2015)  and OAR20 in Churra  (Gutiérrez-Gil et al. , 2018)  ewes, authors subsequently used whole genome sequencing of three animals: a QTL sire and two of his sons with extreme phenotypes. Among candidate causal mutations, Gutiérrez-Gil et al. (  2018 ) detected 13 variants distributed across seven immune-related genes predicted to cause an effect on protein function. The nominated genes were: PKHD1, NOTCH4, AGER, MOG and three genes orthologous to the human MHC: ENSOARG00000009395 (HLA-C, Homo sapiens), EN-SOARG00000015002 (HLA-B, Homo sapiens) and EN-SOARG00000018075 (BoLA, Bos taurus, orthologous to human HLA-A). For the OAR3 region,  Rupp al.
Interestingly,  Banos et al. (2017)  used crossed information from QTL detection and several public and in house datasets to propose 14 candidate genes for mastitis. This was based on the assumption that genes contributing to mastitis resistance are likely to be expressed both in the mammary gland and in immune tissues and differentially expressed in sheep bone marrow-derived macrophages in response to lipopolysaccharide administration. This analysis was completed with the study of 1 kb upstream regions of the Transcription Factor Binding Sites different in dairy and meat breeds. Further studies are required to confirm the functional impact of the candidate polymorphisms.
, 2006; Marie-Etancelin et al. , 2006)  has been added. Following the cattle initiative in the 1980s  (Heringstad et al. , 2000) , in several dairy sheep populations, milk somatic cell counting has been considered as a proxy for mastitis and included that in recording schemes and breeding objectives. Thus, somatic cell counting recording has been implemented in several breeds in France (Lacaune, Manech), Italy (Sarda) and Spain (Churra, Manchega, and Laxta)  (Carta et al. , 2009). Repeated cell counting data can be routinely recorded as part of milk recording. However, the recording cost per animal, relative to the potential income, is prohibitive for many traits other than production. Therefore, simplified schemes have been developed, with only 2-4 test days per lactation period or with sampling only in ewes in their first or/ and second parity  (Rupp et al.
Acknowledgments Claire Oget acknowledges the support of the  Agence Nationale de la Recherche  ( ANR ) for her scholarship (Project  Reidsocs, ID :  ANR-16-CE20-0010 ). The authors are grateful to the  H2020  project ' SMAll RuminanTs breeding for Efficiency and Resilience ' (SMARTER, https:// cordis. europa. eu/project/rcn/215954_fr. html) for the support.
| Statistical analysis Objective clinical response to treatment and clinical relapse were the primary end points, evaluated according to the VCOG Response Evaluation Criteria for Peripheral Nodal Lymphoma in Dogs v1. 0. 56 Continuous data was expressed as median and range, and categorical data as frequencies and percentages. Serum TK1 activity was compared among subsets of dogs using a Mann-Whitney rank-sum test or Kruskal-Wallis 1-way analysis of variance on ranks as appropriate. Evaluation of correlation between sTK1 activity and plasma LDH activity was performed using a Pearson correlation coefficient. A receiver operating characteristic (ROC) curve was used to determine the area under the curve (AUC) and select the optimum cutoff value that maximized the Youden's J statistic (sensitivity + specificity -1) for sensitivity and specificity reporting.
ACKNOWLEDGMENTS This study was presented as an oral research abstract at the 20th ESVONC congress,  Gran Canaria ,  2018. This study was conducted by  Oncovet Clinical Research (OCR)  as part of a collaborative research project between  OCR and Biovica International. The authors are grateful to  Anaïs Quérard ,  Virginie Coste ,  Spela Bavcar , and  Alisdair Boag  for their assistance and contributions throughout the study.
Primers and probes. The primers and probes used to detect the tox gene and rpoB genes for C. diphtheriae and C. ulcerans/C. pseudotuberculosis species identification were as described by De Zoysa et al. (21). For this study we introduced a conserved fragment of the 16S rRNA gene instead of the fragment of gfp gene (28) as the internal process control (IPC). The two primers and probe (u-16S) used to detect the 16S rRNA gene were designed with the software LC probe design2 (Roche). 16S rRNA sequences of known pathogenic or commensal species of the respiratory tract were aligned and a final selection of primers and probe was accomplished according to their universality (Figure  S1 ). The sequences of primers and probes are given in Table  2. Reference end-point PCR method for tox gene detection.
Leptospirosis is an important but neglected disease. Because of the lack of data, the global impact of this disease is unknown. Estimated leptospirosis incidence ranges from 0. 1 to 1/100 000/ year in temperate countries to over than 100/100 000/year during epidemics outbreaks in tropical areas. Between 300,000 and 500,000 severe cases are estimated to occur each year. More than 50% of severe cases may cause death  (Bharti et al. 2003; Lau et al. 2010). More recently, a study based on a systematic review of published morbidity and mortality studies and databases estimated, using modelling, that there were annually 1. 03 million cases (95% CI 434,000-1,750,000) and 58,900 deaths (95%  CI 23, 900)  due to leptospirosis worldwide  (Costa et al. 2015). The highest median annual incidence of leptospirosis is in Africa, standing at 95.
| Statistical analyses The prevalence was calculated as the number of animals with positive serum devised by the total number of animals studied in each group. Prevalence rates were compared between species, location and sex using Chi 2 when the number of observation was sufficient, or the Fisher exact test when it was not. Analysis of variance (ANOVA) was used to evaluate associations between positivity to leptospiral antibodies and age. Odds ratios (OR), 95% confidence interval (CI) and p values were calculated separately for each variable. A p value ≤. 05 was considered significant. All statistical tests were carried out using the Epi Info Software (7. 1. 3. 0 version, CDC Atlanta, USA).
| RE SULTS Of the 545 human blood samples tested, 42 (7. 7% [CI 95 :5. 5 to 9. 9]) were found to be positive to one or more serovars when a cut off of 1:100 was applied (Data S1 and S2). Leptospiral prevalence according to respective location was shown in Figure  2. The prevalence rate was not significantly different between the two villages: 6. 4% Dielmo (17/266) and 9% Ndiop (25/279). Among the 42 human positive samples there is no significant difference (p >. 5; OR: 0. 88 [0. 44-1. 75]) between female (22/301) and male villagers (20/244). Correlation was found between seroprevalence and age (p <. 01). Positive individuals were older  (27. 9 ± 20).
This study was supported by the Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, the National Research Agency under the program « Investissementsd'avenir », reference ANR-10-IAHU-03, the Région Provence-Alpes-Côte d'Azur and European funding FEDER PRIMI. AUTH O R CO NTR I B UTI O N S BD, OM, CS and DR designed the study; BD, PS, JPD, GD, HB and OM collected the samples; AK conducted the laboratory analysis; AK, F I G U R E 5 Distribution of animal hosts by serogroup. Each histogram stands for the percent contribution of each host on the total positive hosts for the whole given serogroup. All serogroups were considered on a basis of a similar scale.
Primary production assessment We used the Normalised Difference Vegetation Index (NDVI) as a proxy for vegetation productivity and phenology in Fontalba and Costabona (for review, see  [52] ). We worked with MOD13Q1 NDVI data extracted from the MODIS repository (Moderate Resolution Imaging Spectroradiometer) provided by NASA  [53]. NDVI time series were calculated for Costabona and Fontalba for the period from January 2009 to December 2012 with 16 day composites at a spatial resolution of 250 m. NDVI pixels (146 pixels for Fontalba and 86 for Costabona) that fell within the boundaries of the study area shape files were extracted and an average of these pixel values was calculated.
Statistical analysis Firstly, differences in vegetation availability between the two study areas were checked using a permutational multivariate analysis of variance (PERMANOVA). This resemblance-based permutation method allows a geometric partitioning of variation across a distribution-free multivariate dataset using distance matrices  [54]. PERMANOVA is widely used in ecology to compare communities across ecological gradients  [55]. In our case, the multivariate response variable was the percentage of the total count of the five plant groups (NLW, LW, Gr, NLF and LF), whereas the study area (Fontalba vs Costabona) was our fixed categorical factor. Manhattan dissimilarity index was used, as it had the highest rank-order similarity with gradient separation in our community matrix. Seasonal changes in the diet composition of chamois, in terms of plant use, were described performing the same PERMANOVA approach using the five plant groups as response variables.
Acknowledgments We would like to thank  Jordi Xifra  and all the game keepers from the  Cos d'Agents Rurals of the National Game Reserve of Freser-Setcases  for their support during the Pyrenean chamois population monitoring. We also thank  Dr. Anne Loison  and an anonymous reviewer for their valuable comments on the manuscript. This study is the fruit of the research partnership programme " Approche Integree de la Demographie des Populations d'Isard " between the  Office de la Chasse et de la Faune Sauvage (ONCFS)  and the  Servei d'Ecopatologia de la Fauna Salvatge (SEFaS).
BmR SM strain is characterized by a mutation of the glycosyltransferase-encoding gene wbkE To identify the mutation(s) responsible for the rough phenotype in BmR SM , its genome was sequenced and compared with that of B. microti CCM4915 T , accessible in the NCBI database. Out of 48 variants, 28 were assigned to SNV (Single Nucleotide Variants) and 20 to InDel (Insertion/Deletion) variants. Scrutiny of the variants resulted in retaining of 3 SNV and 4 InDels, fulfilling all the following criteria: (1) located within open reading frames or in the immediate upstream vicinity, (2) causing amino acids substitutions, frameshift-or stop-mutations in the corresponding genes, (3) not located in pseudogenes, and (4) representing the most prevalent variant according to the number of sequencing reads (≥ 90%) with respect to the reference sequence (Supplementary Table  S1 ).
Acknowledgments We thank  Pascale Bouhours  and  Magali Abrantes  for technical assistance in solution and media preparation,  Julien Ogier  and  Margot Bichon  in constructing plasmids in E. coli,  Dr. Anthony Boureux  and the  Bio2M bioinformatics  and biomarkers platform of the  CHU Montpellier  for support in bioinformatics analysis. The authors are grateful to  Dr. Véronique Jubier-Maurin  (IRIM, Montpellier) for helpful discussions. This work was supported by grants from the  German Federal Institute for Risk Assessment  ( n°1329-562 ) and from the  Spanish INIA  ( n°RTA2017-00083-00-00 ). LF and JdlG were recipients of a doctoral fellowship from the foundation  Infectiopôle Sud , JdlG also of a doctoral fellowship from the  Conacyt/Mexico , and AO received an International mobility support ( Muse Explore ) from the  I-SITE Montpellier University of Excellence  ( MUSE ) for visiting DDB laboratory.
Statistical analysis Statistical analysis was performed with the GraphPad Prism 6. 0 program i. Baseline comparisons between groups (MSC1 and MSC2) for age, clinical scores, and radiographic scores were performed using the Mann-Whitney U test. Categorical data (gender) were compared using Fisher's exact test and limb affected (front versus hind limb) was compared using a χ2 test. The clinical and radiographic scores of horses from each group and from both groups combined at different time points (M1, M2 and M6), were compared to baseline (M0) using the non-parametric Friedman repeated measures ANOVA on a rank sum test. Post hoc comparisons were then performed using a Dunn's test. Clinical scores were compared between groups (MSC1 and MSC2) using a 2-way ANOVA corrected by Sidak's test. Radiographic scores were compared between groups using Wilcoxon's matched pairs test.
Few equine MSC studies have been performed in a blinded fashion, which introduces a high risk of bias when subjective clinical outcome parameters are used, like lameness grading and scoring of flexion test responses. Different methodologies to implement blindness can be used. In a study performed by Broeckx et al. , the practitioner evaluating clinical outcome was different to the one administering the treatment  [32]. In agreement with investigation sites in our study, this method was considered difficult to implement and masking of the injectate was chosen instead. The assessment of horses' return to athletic performance was based on public performance databases (letrot. com; francegalop. com; ffe. com) rather than relying on owners' assessment. Owner-detected adverse effects to MSC injection were recorded in 18% of the horses in our study, three horses after the first injection and one horse after the second injection.
Our study had some limitations inherent to equine multicenter clinical field trials. An increasing number of investigational centers induces variability in clinical assessment and uneven data collection. Objective lameness evaluation was only feasible in a limited number of patients due to limited availability of the Lameness locator equipment j. Not all horses were evaluated after intra-articular analgesia of the MPJ to confirm the presence of intra-articular pain associated with osteoarthritis. Even so, we feel that the combination of perineural analgesia, a positive flexion test and imaging findings can be conclusive for a diagnosis of osteoarthritis, even without the benefit of a recorded response to intra-articular analgesia  [1]. Drugs selected for prophylactic treatment for prevention of adverse injection effects varied between operators.