dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analyses All statistical analyses were performed using R statistical software version 4. 2. 1 (R CORE TEAM, 2020). The package used for analysis was lme4 and p values were extracted with Laplace approximation. To estimate the means, we used the R package emmeans and the Tukey method to adjust the p-value estimates for multiple tests. The proportions in the data correspond to the time the observed rabbits spent performing a specific behaviour over the total time of observations for each location (pens or pastures). Data was not normally distributed. It followed a negative binomial distribution confirmed by the difference in µ and σ and the overdispersion of σ (evaluated with a chi-squared test). Data was then analyzed by fitting negative binomial GLMMs as follows: glmer. nb(y ∼ axb + c + d + (1|e)); where a is pasture size (2 levels: SP and LP) and b is genotype (2 levels: 1001 and PS119), both modelled as fixed effects (with their interaction used in the model), c is rabbit age (3 levels: 45, 69, and 71 days) and d is period of the day (3 levels: morning, afternoon, and early evening), set as co-variables.
Acknowledgements The authors thank  C. Trainini ,  M. Paccanelli ,  C. Lille-Larroucau ,  V. Helies ,  F. Benitez , and  F. Richard  for handling daily care of the animals. The authors also thank  O. Poireaud  for sewing the cloaks, and  V. Fillon  and  C. Dugué  for their help in dressing the rabbits. We also give special thanks to all the rabbits we worked with.
Data collection An interview guide was developed by the research team based mainly on the COM-B model (Supplementary material 1). It consisted of five open-ended questions investigating the different factors described previously, including knowledge about AMU and AMR and the regulation, attitudes toward the regulation, barriers and elements that facilitated changes in their practices, and perceived collateral impacts of the new regulation. Sociodemographic information was also collected to enable comparative analysis between subgroups. For producers, it consisted of the number of years of experience in dairy production, the number of lactating cows on their farms, cattle-housing methods (tie-stall barn vs. free-housing system), the region of their farm and gender of the participant. Veterinarians were required to indicate their number of years in practice, their gender, their type of practice, and the region of practice.
Data analysis All interviews were transcribed ad verbatim and all elements that would allow the identification of the participants were removed at this stage. Thematic analysis was performed using both a deductive and an inductive approach. A codebook was developed in two steps (Supplementary material 2). First, the COM-B model was used to define major categories of themes (capability, opportunity, and motivation) adapted to the context of the study. Second, transcripts were read by N. M. , and new codes were created and defined based on emerging themes using a deductive approach. These emerging themes were then classified as capability-opportunity-motivation or as collateral impacts. Codes' definitions were discussed until an agreement was reached between researchers (NM, CA). N. M. then coded all transcripts using the software NVivo 12.
Proliferation assay A 96-well plate was seeded with eACs (P2) at 2 × 10 4 cells/cm 2 in eAC amplification medium. After 16 h of culture in normoxia, cells were washed with PBS and 200 µL of treatments (corresponding to the conditions tested, i. e. , the control medium and the CMs differentially stored (Figure  1 ) or the CMs primed or not (Figure  7 )) were added to each well. The plate was placed at 37 °C in normoxia and monitored for 7 days with the live imaging IncuCyte ® technology (IncuCyte S3 microscope and IncuCyte 2021A software, Sartorius; Göttingen, Germany) to assess proliferation rate and cell morphology. Using ImageJ software (ImageJ 1. 35c, Wayne Rasband, National Institutes of Health, Bethesda, MD, United States), cells were counted on 3 representative areas of each picture taken after CM addition (200 µL/well) and after 48 h of treatment.
05, **p < 0. 01, ***p < 0. 005 significantly different from the control M3D condition. 10% FBS: chondrocyte amplification medium; used as positive control; A. U. : arbitrary unit; BM-MSCs: bone marrow-mesenchymal stromal cells; CM: conditioned medium; eACs: equine articular chondrocytes; FBS: fetal bovine serum; M3D: control medium with 2% FBS; P2: passage 2; P3: passage 3. system (Bio-Rad). All primer sequences are listed in Tables  1, 2. The results were normalized using the 2 -ΔΔCT method in Bio-Rad CFX Manager software. Each sample was normalized using two housekeeping genes, β-ACTIN and PPIA.
Streptavidin-phycoerythrin was then added to each well, incubated for 30 min at RT and the plate was washed three times before adding sheath fluid. Following the manufacturer's instructions, measurements were performed with the Luminex ® MAGPIX ® CCD imager (Luminex Corp. ; Texas, United States) and processed with Luminex ® xPONENT software. A null value corresponds to a measurement value lower than the detection threshold, specific to each cytokine.
Statistical analysis Each experiment was repeated at least three times with different MSC and eAC strains. The Shapiro, Wilk test was used to test the normal distribution of the data. Significance of the results was tested using the Mann-Whitney test. To compare more than two groups we used the Kruskal-Wallis and the Dunn's tests. The GraphPad Prism 8 software (GraphPad Software Inc. ; San Diego, CA, United States) was used to process data and assemble graphs. A p-value ≤0. 05 was considered significant.
IFN-γ priming led to a drastic 100-and 1000-fold higher concentrations of CXL10 and IFN-γ, respectively, in the primed CM compared with the unprimed control CM3D condition. Finally, we checked if priming with IL1-β increases the BMP2 concentration in the medium, as observed at the mRNA level (Figure  5 ). Unfortunately, the BMP2 levels remained too low to be detected with an enzyme-linked immunosorbent assay (ELISA) (data not shown). Overall, the priming did not decrease the concentration of the pro-inflammatory cytokines studied, and even increased the concentration of the cytokines used for MSC priming. Priming does not significantly modulate CM pro-proliferative capacities eAC relative confluence was assessed based on cell counts after 48 h of culture in the presence of CMs (Figure  7 ).
Then, sponges were harvested, washed twice with PBS and stored at -80 °C. Total proteins were extracted using a dedicated buffer supplemented with protease inhibitors and western blots were run to evaluate protein levels, as shown in the representative images. The D0 condition corresponds to eACs cultured in monolayer until P2. Experiments were repeated with different strains of eACs and BM-MSCs (n = 5). The densitometry of each band was measured thanks to the Image Lab software (Biorad). The relative values (relative to GAPDH) are indicated below each blot. BM-MSCs: bone marrow-mesenchymal stromal cells; CM: conditioned medium; eACs: equine articular chondrocytes; M3D: control medium with 2% FBS; P2: passage 2; P3: passage 3. OA-related inflammation  (Hunter and Bierma-Zeinstra, 2019). Recent research has demonstrated the potency of these cytokines to trigger MSC activation  (Colombini et al.
Then, sponges were harvested, washed twice with PBS and stored at -80 °C. Total proteins were extracted using a dedicated buffer supplemented with protease inhibitors and western blots were run to evaluate protein levels, as shown in the representative images. The D0 condition corresponds to eACs cultured in monolayer until P2. Experiments were repeated with different strains of eACs and BM-MSCs (n = 3). The densitometry of each band was measured thanks to the Image Lab software (Biorad). The relative values (relative to GAPDH) are indicated below each blot. BM-MSCs: bone marrow-mesenchymal stromal cells; CM: conditioned medium; eACs: equine articular chondrocytes; M3D: control medium with 2% FBS; P2: passage 2; P3: passage 3. histocompatibility complex I (MHC-I). Here, we tested only the common immunomodulation-associated markers, some of which were not detected by RT-qPCR, which can easily be attributed to their low gene expression.
Experiments were repeated with different strains of eACs and BM-MSCs (n = 5). The densitometry of each band was measured thanks to the Image Lab software (Biorad). The relative values (relative to GAPDH) are indicated below each blot. BM-MSCs: bone marrow-mesenchymal stromal cells; CM: conditioned medium; eACs: equine articular chondrocytes; M3D: control medium with 2% FBS; P2: passage 2; P3: passage 3.
The D0 condition corresponds to eACs cultured in monolayer until P2. Experiments were repeated with different strains of eACs and BM-MSCs (n = 3). The densitometry of each band was measured thanks to the Image Lab software (Biorad). The relative values (relative to GAPDH) are indicated below each blot. BM-MSCs: bone marrow-mesenchymal stromal cells; CM: conditioned medium; eACs: equine articular chondrocytes; M3D: control medium with 2% FBS; P2: passage 2; P3: passage 3.
The D0 condition corresponds to eACs cultured in monolayer until P2. Experiments were repeated with different strains of eACs and BM-MSCs (n = 5). The densitometry of each band was measured thanks to the Image Lab software (Biorad). The relative values (relative to GAPDH) are indicated below each blot. BM-MSCs: bone marrow-mesenchymal stromal cells; CM: conditioned medium; eACs: equine articular chondrocytes; M3D: control medium with 2% FBS; P2: passage 2; P3: passage 3.
Intervention study design An intervention study was conducted in 20 farrow-to-finish French pig farms with the aim to assess the effectiveness of Tailor-Made Health Plans (TMHP). Figure  1  provides a synthetic overview of the study design. The intervention in each farm was based on the collection of a set of data during an initial farm visit, leading to the formulation of recommendations by veterinarians at the end of the visit. Collected data were: i) results of a systematic biosecurity audit, ii) description of management practices not related to biosecurity (including other measures promoting health than biosecurity, feeding, housing and reproduction), iii) observed clinical signs at every physiological stage, iv) past records of health disorders, v) antimicrobial purchases during the previous year and vi) records of technical performances during the previous year.
A TMHP was a set of tailor-made recommendations formulated by the veterinarian, at the farm scale aiming at improving pig health. Three visits were included in a prospective longitudinal study to initiate and follow-up the TMHP: i) visit 1 was performed to describe the initial farm context by collecting data then to formulate recommendations, ii) visit 2 was performed to assess compliance with recommendations formulated at visit 1, iii) visit 3 was performed to collect the same data as at the visit 1 and carry out an update on compliance. After the visit 3, the opinion of the farm's veterinarian was asked with regard to the evolution of the health situation in the farm. Standardized indicators were calculated for health, technical performances and antimicrobial use. Indicators were estimated at visits 1 and 3 to assess possible evolutions.
Technical performances Technical performance data were collected from farm records. Data were collected for i) the year preceding the intervention and ii) the on-going year period. The the average daily gain (ADG) and the feed conversion ratio (FCR) in the wean-to-finish period, the mortality rate in post-weaning and fattening units, and the number of piglets weaned/sow/year (PWSY) were selected to cover the whole production cycle.
DDDvet were only considered to describe the evolution of health disorders when antimicrobials were administrated to animals for the identified health disorders 4: Definition of improved, statu quo, deteriorated: see Table  2  5: Indicator was not considered to assess tailor-made health plan effectiveness because its evolution was not biologically linked to the targeted health disorder evolution. In particular, DDDvet were only selected to assess effectiveness when there was an initial antimicrobial use to cure the targeted health disorder 6: NA = Not Available. Indicators were selected to assess effectiveness but observations could not be performed during visits or data could not be provided by farmers and/or veterinarians 7: NS = No scoring since indicators were not avaible or presented no room for improvement at the first visit.
Materials and Methods Data from 325 separate host-parasite combinations were analysed, drawn from published studies, as well as additional data held by the authors on natural, tracer, and experimental studies (Table  1 ). Datasets measured the intensity of parasite infection, either through faecal egg counts or post mortem worm counts. The average size of the host group sampled was 29 (range 9-123), and all but 24 of the groups included at least 20 individuals. Host systems consisted of sheep, goats, cattle, and saiga antelopes (Saiga tatarica) in Kazakhstan; sheep in Poland, France, and Morocco; goats in France and Martinique; cattle in Argentina, Brazil, and New Zealand; and roe deer (Capreolus capreolus) in France. Parasites were all from the superfamily Trichostrongyloidea in Clade V of Blaxter's molecular phylogeny  [30] , with the exception of Trichuris capreoli in Clade I.
Overall Fit to Taylor's Power Law Across the whole dataset, log M was positively correlated with log V (r 2 = 0. 821, p < 0. 001). Linear regression of log V on log M was highly significant (MS regression 941. 215, MS residual 0. 633, F 1,323 = 1486. 04, p < 0. 001), with estimated coefficients a = 0. 781 (95% confidence intervals 0. 609-0. 952) and b = 1. 683 (1. 597-1. 769). Model fit to the entire data set is shown in Figure  1. ANCOVA using all the factors in Table  1  revealed that only host sex (F 2,274 = 3. 811, p = 0. 023) and frequency of treatment (F 2,274 = 36. 678, p < 0. 001) significantly affected regression slope b. However, both factors were confounded with host species. Hence, free-ranging wildlife, and sheep in Kazakhstan were not treated, whereas other hosts were treated and goats especially frequently, while the most intensively treated groups tended to be of mixed sex, which was allocated a third sex category.
, 2008 [40] ). While the previous work cited above described statistical distributions of parasites in animal populations, including grazing ruminant livestock, there have been only very limited attempts to model this distribution across multiple host populations or to relate observed patterns to unifying theories, such as fluctuation scaling. The a priori expectation was that acquired immunity would have a dominant effect, tending to stabilise host-parasite interactions and decrease levels of aggregation, although the analysis was conducted independently of this assumption. With only cross-sectional data available, the effect of immune-mediated regulation of parasite burdens was initially assessed by comparing the slope of Taylor's power relationship between Nematodirus worm burdens and faecal egg counts.
Animals 2023 , 13 Figure 1. 2023131 Figure 1. Regression of log10 (variance) on log10 (mean parasite abundance) for the entire dataset (n = 325 groups). Solid line: regression equation (log V = 0. 781 + 1. 683 log M); dashed line: log V = log M. Open circles: faecal egg counts; filled circles: post mortem worm counts.
Dataset The performance and pedigree information used in this study are from the French national database. Data from first (L1) and second (L2) lactation test-day records on Montbeliarde cows were selected from five French regions (Franche-Comté, Rhône-Alpes, Auvergne, Bretagne and Pays-de-Loire) over a period of four years (August 2016 to June 2020). Six phenotypes were analyzed: milk yield (MY), fat content (FC), protein content (PC), fat yield (FY), protein yield (PY), and somatic cell score (SCS). SCS was obtained as a log-transformation of somatic cell concentration (SCS = log2(SCC/100,000) + 3)  [17]. All the phenotypes were monthly recorded. Only animals with known parents, and age at calving between 23 and 42 months at first parity and between 35 and 60 months at second parity were considered.
Records on lactations that lasted less than 120 days were removed, as well as all test-day records after 305 days in milk (DIM). Data from herd-year-parity (HY) combinations with less than five cows and herd-test-day-parity (HTD) combinations with less than three records were discarded. Finally, about 25 and 30% of herds were randomly sampled in L1 and L2, respectively, which resulted in a reduced dataset that was more computationally tractable for REML variance components estimation. The final data on first parity comprised 446,717 test-day records from 55,650 cows, and the final data on second parity comprised 457,516 test-day records from 58,229 cows. The pedigree of these animals was traced back to three generations. After trimming, the L1 and L2 pedigree files included 132,562 and 143,008 animals, respectively.
Statistics on raw data are in Table  1. The meteorological SAFRAN data provided by the French national meteorological agency (Météo-France) included daily estimates of various indicators for each of the 9892 8 × 8-km 2 squares covering the whole French territory. The use of modeled data instead of observed data was proposed by Mbuthia et al. [18]. These daily estimates are the result from a model developed for meteorological forecasting that uses local recordings that are obtained continuously over a wide network of meteorological stations. The meteorological variables used in this study were average daily temperature and relative humidity. The daily meteorological data assigned to each herd (geographically identified by its zipcode) were weighted averages of the values at each of the 8 × 8-km 2 squares that covered the location, with the weights equal to the proportion of the surface of the village in each square.
Several factors may explain the lower THI thresholds observed in our study compared to those commonly reported for high-producing dairy cows. First, many of the studies on high-producing dairy cows concern animals that are raised in indoor farming systems, sometimes in barns equipped with cooling systems, which mitigate the effect of high outdoor temperatures  [28, 32]. French Montbeliarde cows are kept outdoors during the spring and summer, and thus are more exposed to warmer temperatures and extreme heat waves, without any mitigation. Second, many studies on the effect of heat stress on high-producing dairy cows are performed in countries with a warmer climate than France and with THI that have higher values than those observed in France for our datasets. For example, in the climate data for some studies, the minimum THI observed was of ~ 50 in Italy  [26]  and in the United States  [33] , a value close to our observed THI threshold for several traits.
Genetic-by-THI interactions We estimated the trajectory of genetic parameters of production and SCS traits along the THI gradient in Montbeliarde dairy cattle using random regressions and Legendre polynomials. Ravagnolo and Misztal  [35]  proposed a broken line model to estimate the change in response for MY with THI. Because of the assumption of the presence of a neutral zone with no effect of THI (plateau) followed by a linear decay, the broken line model does not fit our data for which a negative effect of low THI is also found. Moreover, this model requires the estimation of identical thresholds marking the onset of heat stress. However, applying an identical threshold to all the animals, assumes the absence of individual variability in the onset of heat stress, which is contrary to the findings of several authors  [33, 36] , and could bias the slopes of individual production loss  [37].
Some general conclusions can be drawn: the beginning of the lactation differs substantially from the later lactation periods; the intermediate period of the lactation is the most representative of the whole lactation, with the highest correlations with any other time period; and the correlation between the beginning and the end of the lactation can be rather low, nonetheless still positive. Therefore, we chose to account for the two gradients in the random regression model, on DIM and on THI. This choice corresponds to the model which fits best our objective to evaluate the genetic-by-environment interactions, although this model is computationally very demanding and limits the size of the analyzed dataset. Nevertheless, this model was relevant, since the estimates of heritability varied considerably with DIM (0.
It is important to note that these increases were observed for high THI, i. e. above 72 (78 for FY), which are very rare THI values in our dataset. Moreover, Aguilar et al. [41]  and Ravagnolo and Misztal  [35]  used the broken line model with a THI threshold fixed at 72 for all cows, which does not allow to estimate variations in heritability below this threshold. Since our dataset contained few performances recorded for THI values higher than 70, the decrease in heritability observed in our study needs to be confirmed. Among the results for SCS, Bohlouli et al. [19] , Hammami et al. [42]  and Santana et al. [22]  reported heritability estimates for German, Belgian and multiparous Brazilian Holstein cows, respectively, which increased as THI increased, in agreement with our results. This increase in heritabilities may be explained by the increase in SCS with THI which may favor the expression of genetic variability.
[28]  estimated genetic correlations ranging from 0. 85 to 0. 96 for milk, fat and protein yields and SCS also in agreement with our results. However, due to a higher prevalence of warm temperature conditions encountered in their dataset, these authors highlighted that genetic-by-THI interactions can be much stronger (with estimates of genetic correlations ranging from 0. 24 to 0. 86 between extreme temperatures, -1 vs. 34 °C, depending on the model), especially for fat and protein contents and SCS. In many studies, MY was not the best trait to identify variability in response to heat stress with genotype  [28, 42, 45]. Among all the traits studied here, PY and SCS in L2 are those with the largest genetic-by-THI interactions. Within-trait and DIM, the permanent environmental correlations between adjacent and between distant THI were also high [minimum estimates of permanent environmental correlations at DIM = 150d were 0.
OBJECTIVE: We assessed the combined and relative strengths of the two mechanisms by developing a metabolic approach (French uplands context). METHODS: We used recently published equations to model the infection cost of gastrointestinal nematodes in metabolizable energy (ME), and crude protein (CP). By comparing infection levels in mixed and monospecific grazing, we quantified the gains of PD in ME and CP. We also used feed value tables to assess the gains in ME and CP resulting from FNS sheep diet improvement. We interpreted these gains in light of ME and CP requirements of lambs. We applied this approach to the dataset of a mixed-grazing experiment, involving sheep monospecific grazing and mixed sheep/cattle grazing, without veterinary treatment. We also applied it to a generic situation where we studied the relative gains in ME and CP, along gradients of increasing strength of PD and FNS.
Metabolic assessments of FNS and PD gains In Section 2. 2, we present the equations used to conduct our metabolic assessment. Their application to our experimental dataset and according to the generic approach is presented in Sections 2. 3 and 2. 4. The equations does not consider interactions between FNS and PD, as none were observed in our experiment  (Joly et al. , 2022). PD and FNS equations are thus independent.