dataesr/scientific-paragraphs-categorization huggingface dataset:
d-Statistical analysis The number of animals enrolled in this study was limited by the experimental facility capacity and the criteria retained for animal inclusion in each experimental group. More precisely, ewes had to be gestating with two fetuses and each experimental group was balanced by ewe's body score condition, live weight, age and parity. According to these criteria, 14 ewes were enrolled in each experimental group. Graphical representations and statistical analyses were performed using GraphPad Prism 9. 0. 2. The effect of Supplementation (C or SC) and Time factors and their interaction were evaluated using mixed model with repeated time and multiple comparisons with Sidak's adjustment. Colostrum qPCR data were log10 transformed before statistical analysis. For lamb serum analysis, a linear mixed model with repetitions was applied considering 3 factors: Time, Supplementation and Rearing mode (Art-or Mot-groups) and their interactions.
91 ± 39. 57 mg/l and 147. 38 ± 62. 92 mg/l in C and SC groups, respectively, p = 0. 042) and also 5 h after lambing (85. 39 ± 43. 53 mg/l and 130. 07 ± 53. 94 mg/l in C and SC groups, respectively, p = 0. 044). Concentration of 6'GSLN in SC group was about twice that measured in C group at the same time points (119 ± 40. 37 mg/l and 248. 47 ± 120. 09 mg/l in C and SC groups, respectively, p < 0. 001 at 0 h; 106. 26 ± 42. 59 mg/l and 180. 22 ± 70. 27 mg/l in C and SC groups, respectively at 5 h; p = 0. 009, Figure  7b ). After 12 hours, no differences between the groups were measured. The biosynthetic pathway for both Neu5Ac OS and Neu5Gc OS has been reconstructed from the nontargeted LC-MS data (Figure  8 ). A Neu5Ac residue is loaded onto a cytosine-monophosphate molecule (CMP) which can transfer the Neu5Ac to the 3' or 6' position of lactose or N-acetyllactosamine.
Acknowledgments: the authors would like to thank  Catherine Dhainaut  and  Raphaele Gresse  from  UMR MEDIS  and  Yu Jeaju  from  University of Guelph  for their skilled technical assistance;  Mickaël Bernard ,  Aline Cercy ,  Loic Gaillard ,  Bruno Viallard  and  Pierre Chirent  from  UE   Herbipôle  for their very valuable help in the animal experiment. Financial support: This research was partially funded by  Lallemand SAS.
Measures and Data Collection The sows were observed in gestation and farrowing pens and during transfers between rooms, the most convenient places and times for observations. Sow lameness was scored during the transfer between the service room and the gestation pen at W0 and W21 (Tb, beginning of gestation time), inside the gestation pen at W6 and W27 (Tm, mid-ges- The rubber mats (BioretAgri, Nort-sur-Erdre, France) were made of a foam underlayer for suppleness, and a rubber upper layer (thickness: 10 mm) (Supplementary file 1). The rubber layer was grooved to provide a non-slip surface and contained woven thread to improve durability. Mats were attached in pens' laying boxes using baseboards nailed to the partitions and threshold bars nailed to the slatted floor in the open part of the box.
Measures and Data Collection The sows were observed in gestation and farrowing pens and during transfers between rooms, the most convenient places and times for observations. Sow lameness was scored during the transfer between the service room and the gestation pen at W0 and W21 (Tb, beginning of gestation time), inside the gestation pen at W6 and W27 (Tm, mid-gestation) and during transfer between the gestation pen and the farrowing pen at W12 and W33 (Te, end of gestation) (Figure  1 ). Transfer corridors had a concrete floor. The sows were observed while they walked a distance of at least 15 m, except very lame sows, which were not forced to walk. Lameness was scored according to a four-category table based on the Welfare Quality protocol  [37]. Non-lame sows (0) were distinguished from slightly lame sows (1) who had difficulties walking but were still using all theirs legs.
A random component was introduced in the models accounting for the effects associated with a sow, within a pen, within a farm (nested effects). The Treatment × Cycle interaction was tested for all models and removed if non-significant (p > 0. 05). Risks of suffering from bursitis, leg injuries, scratches, and abnormal body condition (thin, fat) were modelled using a mixedeffect logistic regression model (binary response as affected vs. non-affected); the function glmer from the lme4 package  [40]  was used. Other measures related to lameness, claw defects and body cleanliness were categorized on a three-score scale (absence-mild-severe) according to score frequencies. The risks of suffering from mild and severe conditions were modelled using an ordinal regression based on a cumulative link mixed model (function clmm from the ordinal package [41]).
Lameness Lameness was reported for 28% of the observations (663/2361), from a moderate state (17% of the observations) to a severe state on 39 occasions (2% of the observations, Figure  2 ). From the 495 sows observed for lameness scoring (no data available for 87 sows due to feasibility constraints), 256 were lame at least once (52%) and 7 sows exhibited severe lameness. The risk of suffering from mild or severe lameness increased during the gestation period: the odds ratio (OR) was 2. 1 (CI 95% [1. 6-2. 8]) when comparing Tm with Tb (p < 0. 001) and was 2. 5 ([1. 9-3. 3], p < 0. 001) when comparing Te with Tb (Figure  2 ). No effect of RM treatment was observed on the risk of suffering from lameness (RM vs. C, OR = 0. 50 [0. 13-2. 0], p = 0. 33). Animals 2021, 11, 3160 6 of  14 2). From the 495 sows observed for lameness scoring (no data available for 87 sows due to feasibility constraints), 256 were lame at least once (52%) and 7 sows exhibited severe lameness.
Acknowledgments: The authors thank the farmers and their staff for their kind hospitality. They thank  Claudie Guyomarc 'h from  Cooperl Arc Atlantique, Sylvia Turci from Aveltis, Jean-Vincent Bioret and Yannick Daubelcourt from BioretAgri and Christian Pellan from Socobati  for their participation in the study. They also thank  Christelle Fablet  and  Maëlys Brunon  from  ANSES  and  Yannick Ramonet  from the  Chambre Régionale d'Agriculture de Bretagne  for their scientific and technical support.
Statistical analyses At least four replicates per plant and per concentration were included in all experiments. The results on phenolic content are expressed as mean ± standard error of the mean (SEM). Anthelmintic data are expressed as the concentrations inhibiting 50% of larval exsheathment or egg hatching (IC 50 values, µg mL - 1 ) and 95% con dence intervals (CI). IC 50 values and 95% CI were obtained by Probit analysis, and signi cant differences among IC 50 values were detected using relative median potency estimates, using IBM SPSS Statistics v. 26. 0 software. Spearman correlations were calculated between the total avonoids, total phenols and the IC 50 values for LEIA on the 2 nematode species.
). Inula crithmoides, C. soldanella, M. marina, P. coronopus and L. monopetalum are halophyte plants included in the eHALOPH database[18]while others such as P. lentiscus, C. mariscus and C. maritima have recognized salt-tolerance despite not yet included in eHALOPH database. After collection, samples were taken to the laboratory, washed, frozen at -20ºC, freeze-dried (Lyoalfa 15) for three days, and grinded using a coffee and a ball miller (Retsch PM 100). Plant collection details, including collected organs, date, location and voucher number.
25%, p < 0. 05) (Table  5 , Figure  3 , online Supplementary Table  S3 ). The incidence rate of serious AEs (SAEs) was <1% in both groups. In the statin users group, one patient experienced diarrhea with disability after using the concomitant quadruple therapy. In the non-users cohort, three patients presented an SAE, all after the single capsule bismuth therapy. These events were: an episode of acute pancreatitis, a process of abdominal pain and vomiting, both requiring hospitalization, and a third event that was not explained in the database. The specific analysis evaluating effectiveness or safety of eradication therapies according to the different statins used (simvastatin, atorvastatin, rosuvastatin, and other statins) showed no differences, neither in the overall group nor when considering each therapy separately (online Supplementary Table  S4 ).
The sub-analysis performed specifically on each therapy revealed that the best mITT effectiveness result was achieved both with the single capsule bismuth and the bismuthamoxicillin-levofloxacin quadruple therapies (close to 90%; Figure  2 ). The presence of statins was significantly associated with higher effectiveness only in the single capsule bismuth treatment (OR = 2. 8; 95% CI: 1. 3-5. 7; p < 0. 05). No association between effectiveness and statin use was found within the remaining therapies (Table  8 ). of acute pancreatitis, a process of abdominal pain and vomiting, both requiring hospitalization, and a third event that was not explained in the database. The specific analysis evaluating effectiveness or safety of eradication therapies according to the different statins used (simvastatin, atorvastatin, rosuvastatin, and other statins) showed no differences, neither in the overall group nor when considering each therapy separately (online Supplementary Table  S4 ).
Materials and Methods The "European Registry on H. pylori Management" (Hp-EuReg) is an international (30 countries), multicenter (>300 investigators), prospective, non-interventional registry that was started in 2013 and was promoted by the European Helicobacter and Microbiota Study Group (www. helicobacter. org, accessed on 6 August 2021). The Hp-EuReg protocol was approved by the Ethics Committee of La Princesa University Hospital (Madrid, Spain)  [29]  and was prospectively registered at ClinicalTrials. gov under the code NCT02328131. The study protocol conforms to the ethical guidelines of the 1975 Declaration of Helsinki as reflected in the approval of the institution's human research committee. Written, informed consent was obtained from each patient included in the study. Criteria for country selection, national coordinators, and gastroenterologist recruiting investigators are shown in the protocol publication.
Variables The e-CRF registered 290 variables containing information about a patient's demographics, comorbidity, indication and method of diagnosis, previous eradication regimens prescribed (if any), current treatment, and data on effectiveness, safety, and compliance. The variable treatment length was assessed using three categories, corresponding to the most frequent treatment durations: 7, 10, and 14 days. Similarly, PPI data were standardized using PPI acid inhibition potency as defined by Kirchheiner  [42]  and Graham  [32] , and classified as low, standard and high dose PPIs (online Supplementary File S2). Eradication was confirmed with at least one of the following diagnostic methods: urea breath test, stool antigen test and/or histology.
S. haematobium v2 (Egyptian strain [18]) The mean similarity of these shared sequences was 95. 9% compared to ~99% and ~90% for commonly used phylogenetic markers such as ITS and cox1, respectively. The mean similarity between S. haematobium mitochondria (GenBank accession number DQ157222. 2) and S. bovis mitochondria (Contig 00439F of our assembly) was 82. 1%. Besides being of fundamental interest for the evolutionary biology of the parasite, this finding could also have immediate consequences for parasite control. One of the few phenotypic features that are of relevance for infection success and for which the genetic basis is known is resistance to Oxamniquine (OXA). In S. mansoni the mutations that confer resistance occur in the SmSULT-OR gene (Smp_089320), encoding a sulfotransferase that is required for drug activation, are p.
Schistosoma bovis genome assembly and annotation PacBio reads were assembled using the Hierarchical Genome Assembly Process (HGAP4) de novo assembly analysis application, followed by polishing with Pilon using consensus PacBio reads and illumina short reads. Gene prediction was carried out with AUGUSTUS 3. 3. 1. No new training was performed for our data but the parameter set "schistosoma2" of the AUGUS-TUS distribution was used. RepeatMasker 4. 0. 7 and RepeatScout 1. 0. 5 were used for repeat prediction and masking. RNAseq data from male and female adult worms was employed as external hints. This RNA-seq data was aligned with STAR version 020201. The Benchmarking Universal Single-Copy Orthologs (BUSCO) version 3. 0. 2 [19]  was used in-genome mode and with the metazoa_odb9 dataset to assess genome assembly and annotation completeness.
fr/IHPE_tracks/S. bovi/hub. txt. Funding: CG and RA were supported by the  Wellcome Trust  [grant number  107475/Z/15/Z ], and  Deutsche Forschungsgemeinschaft Fellowship   BU 2685/5-1. MB was supported by the  Wellcome Trust  [grant number  098051 ]. SMC was funded by  Health Research  Project No. PI16/00520 ,  Plan Estatal de Investigacion Cientı ´fica y Tecnica y de Innovacion, ISCIII-MINECO, Madrid, Spain ;  Red de Investigacion de Centros de Enfermedades Tropicales -RICET  (Project No. RD16/0027/0023  of the  PN de I+D+I, ISCIII-RETICS) ,  Ministry of Health and Consumption, Madrid, Spain. JB, ET, OR were funded by the  French National Research Agency   ANR  project  HySWARM   ANR-18-CE35-0001. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Calculations and statistical analyses Statistical analyses were conducted using SPSS software (IBM Corp. , Version 21. 0, New York, USA). Quantitative PCR data (rDNA copies/mg DM) and taxa abundances (sequences) were tested for normality using the Shapiro-Wilk test and data were log10 transformed to achieve a normal distribution. Data were analysed based on a repeated measures mixed -effects (residual maximum likelihood) as follows: Y ijkl ¼ Ë c þ I i þ T j þ I Â T ð Þ ij þ G k þ A G ð Þ l þ e ijkl where Y ijkl is the dependent, continuous variable, μ is the overall population of the mean, I i is the fixed effect of the inoculation (i = CTL vs AUT vs RFF vs RFC), T j is the fixed effect of the sampling time or age (j = 5 vs 7 vs 9 weeks), (I × A) ij is the interaction term, G k is the random effect of the pen considered as a block (j = 1 to 5), A(G) l is the random effect of the animal nested to the pen (l = 1 to 80 for qPCR and 1 to 32 for sequencing data) and e ijkl is the residual error.
, Plymouth, UK). Log10transformed data were analyzed by non-parametric PERMANOVA after 999 random permutations of residuals under the reduced model using the Monte Carlo test  [67]. When a significant factor was found in the PERMANOVA, pair-wise comparisons were performed using the same software and settings (999 permutations) to elucidate differences between treatments. Principal Coordinate analysis (PCoA) were performed to illustrate the impact of the treatments on the overall microbial community structure and tripod vectors were included to describe the direction and intensity of the most discriminant OTUs (Spearman's correlation > 0. 55). Given that three different nutritional situations were studied, Distance-Based Redundancy Analyses were performed to illustrate the relationship between the community structure of the rumen microbiota and metadata (32 variables reported in Suppl.
| Data Data on goat Capra aegagrus hircus movement were collected at the Bauges Mountain (Massif des Bauges, 45. 61°N, 6. 19°E) of the French Alps, using triaxial accelerometers and magnetometers (Wildbytes Technologies http://www. wildb ytete chnol ogies. com/) contained in Daily Diary tags  (Wilson et al. , 2008) , combined with Gipsy5 GPS tags (TechnoSmArtTracking Systems http://www. techn osmart. eu) inside custom-built 3D printed ABS plastic housings attached to commercial nylon collars (Fearing Lifestyles). Accelerometer data were collected at a frequency of 20 Hz, magnetometer at 8 Hz, and temperature at 2 Hz. GPS locations were collected every 15 min. The data were dead-reckoned at 1 Hz  (Bidder et al. , 2015)  with the Framework4 software  (Walker et al. , 2015)  to reconstruct paths of locations over time.
Overall, seven trajectories were reconstructed from the data, each of which was 1-week long. The goats tended to spend most of their time in a central area (radius ~70 m) which contains a pen and nearby salt licks. We define the centre of this area as the central point for the purposes of this manuscript. As well as locational data, we also use data on the terrain and elevation. The terrain consists of areas of scree biotope  (Devillers et al. , 1991) , which we term rocky terrain, as well as woodland and grassland. Elevation recordings were found using Google's Elevation API (https://devel opers. google. com/maps/docum entat ion/ javas cript/ eleva tion) at a resolution of 1 m.
| Non-constant step-times To apply tiSSA to the paths inferred using the Turning-Points algorithm, we use a uniform distribution for the headings and gamma distributions for the step-times and step-lengths. In other words, we define where k 1 and θ 1 are, respectively, the shape and scale parameters of the gamma distribution fitted to the step-times, and k 2 and θ 2 are the best fit shape and scale parameters (respectively) for the probability density function g (r)  2 ( l | ). (We also show that the same k 2 and θ 2 are the best fit shape and scale parameters for a gamma distribution of step-speeds in Appendix S2, which can ease inference of these parameters). We use the superscript (r) to represent functions and coefficients used for non-constant step-time data.
| Constant step-times To perform iSSA on the regularly subsampled paths, and thus compare it with tiSSA plus the Turning-Points Algorithm, we define the sampling kernel as follows  (Avgar et al. , 2016). where k 3 and θ 3 are the shape and scale parameters from the gamma distribution fitted to the step-lengths. Note the difference between Equations 6 and 8: in the latter, no step-time distribution is required. The superscript (c) refers to any function or coefficient used with constant step-time data. We use the same covariates as the Base Model above, but instead of correcting for the step-time ( (r) 6 ) and step-speed ( (r) 7 ) and the natural logarithm of each ( (r)  8 and (r) 9 ), as we do for non-constant step-time data, we instead only correct for the step-length (c)   10 and its natural logarithm ( (c).
Regularly subsampled paths at low frequencies tend to give both imprecise and inaccurate results whereas those at high frequencies tend to give precise but inaccurate results. This general trend follows for both the simulated and empirical datasets we used. Being a direct generalisation of iSSA, and therefore SSA, our method can, in principle, be used to examine any of the behavioural processes affecting movement that have been demonstrated in the existing literature on step selection. These include attraction to areas of higher quality food  (Merkle et al. , 2016) , avoidance of or attraction to linear features  (Dickie et al. , 2019) , avoidance of prey  (Latombe et al. , 2014)  or competitors  (Vanak et al. , 2013) , territorial interactions  (Potts, Mokross, & Lewis, 2014) , effects of anthropogenic disturbances  (Ladle et al.
Population pharmacokinetics Pharmacokinetic modeling was carried out using commercially available software  (MONOLIX® version 2018R2, Lixoft, Antony, France). A nonlinear mixed effects (NLME) approach was used to generate Pop PK parameter estimates , the interindividual variability Ω and the residual variability 2. One-two-and three-compartment models were evaluated to identify the model that best described the dataset. Model selection was carried out according to different criteria: (i) visual inspection of different diagnostic plot (i. e. visual predictive check, residual plot…), (ii) precision of the estimated parameters, (iii) correct estimation of the information fisher matrix and (iv) values of the objective function (i. e. Likelihood ratio test, LRT; Akaike information criterion, AIC and Bayesian Information Criterion, BIC).
None of the goodness-of-fit plots showed a systematic bias or trend. The intraindividual variability was around 6 %, which is small enough to expect precise Bayesian estimations. The robustness of the results was strengthened by the inclusion of a varied population of dogs both by their demographical characteristics and by their renal status. Indeed, dogs' weights ranged from 3. 9 kg to 46 kg. The values of creatinine and urea varied respectively from 0. 67 to 14. 4 mg/dL and from 16 to 181. 4 mg/dL. Finally, female, male and female neutered dogs were included in the study allowing to study a sex-effect. Furthermore, the Pop PK parameters' estimates were consistent with the data published in our previous work  (Pocar et al. , 2019)  and this supports the reliability of our Pop PK model. Covariate analysis was performed to identify the influence of various baseline characteristics on the PK of iohexol.
Patients were investigated in a hospital setting, according to good clinical practices. Written informed consent for the endoscopic and diagnostic procedures was obtained from patients or their parents/legal guardians and kept in their medical records. The study was carried out in care structures, which have a CNIL correspondent who ensures data compliance. No extra biopsy sampling or additional endoscopies were required, and all samples were anonymized. This is a retrospective study therefore non-interventional study. Furthermore, in France no declaration to the CNIL is needed if more than 1000 patients are included.
Statistical Analysis The online software VassarStats (Richard Lowry) was used for data analysis. Frequencies of categorical variables were calculated, and Fisher's exact test, chi-square test or Student t test was used to determine differences between groups. Statistical significance was set at p < 0. 05. H. pylori positivity rates were significantly higher in adults than children (p < 0. 001), but rates did not differ by sex or age within each group. With the in-house qPCR confirmed by the glmM PCR as the reference, culture showed a sensitivity and specificity of 74. 4% and 100%, respectively. When considering only high-bacterial-load biopsies (i. e. , qPCR Ct < 30), the sensitivity of culture increased to 93. 4%. Most biopsies (105/131, 80. 1%) with a false negative culture had low bacterial load (i.
Different side effects after the use of DIA were observed including ataxia, unpredictable behavioural effects, decreased reflexes or cardiopulmonary effects like decrease of blood pressure  (Shini, 2000). As the sedative effect can also be abused for doping purposes  (Jaussaud & Courtot, 1990) , DIA is prohibited under the rules of different equine sports jurisdictions. Thus, the analysis of DIA is part of the routine testing scheme of horse doping laboratories. According to the anti-doping rules of the International Federation of Horseracing Authorities (IFHA), DIA is classified as a prohibited substance, that is not permitted during competition (International Agreement on Breeding, Racing and Wagering, Article 6a) (International Federation of Horseracing Authorities, 2020). The '2020 Equine Prohibited Substance List' of the Fédération Equestre Internationale (FEI) classifies DIA as a prohibited controlled medication (The Official FEI Equine Prohibited Substances Database of the Fédération Equestre Internationale, 2020).