dataesr/scientific-paragraphs-categorization huggingface dataset:
The PROC MIXED procedure implemented in the SAS software  [38]  was used to test for significant differences between R and N genotypic groups for each of the measured parasitological and haematological data. Usually encountered environmental effects were considered as fixed effects and the computed gEBV was fitted to the model as a covariate to account for the effect of the rest of the genome. For haematological parameters, basal value of the considered parameter (indexed by 0) was considered as covariate to account for potential interindividual variation before the beginning of the experiment. Normality of the cycle time (C T ) values distribution was checked using the Shapiro-Wilk test implemented in the R software  [39]. One outlier from the Ri group (sheep 12493, see Additional file 3), with C T values for house-keeping genes exceeding a ± three standard deviations range, was discarded from the AFM dataset.
Fold change in gene expression between considered groups was computed as 2 -ΔΔC T  [40]. Subsequently, a Wilcoxon test was applied to determine any significant difference between the compared groups. To account for multiple testing, a nominal p-value of 1% was considered for significance leading to less than one significant difference occurring by chance. An additional suggestive threshold was considered for nominal p-value below 5%. The complete data processing was performed using an in-house R script  [39].
This could be mediated by the stronger Th-2 response that seems to be mounted by R sheep after infection. Indeed, local IgA response limits worm fecundity in T. circumcincta infection  [9, 55]  and in H. contortus infection  [7]. More recent findings also support the relationship between T-cells number and worm female length  [56]. Additional investigations on the characterization of subpopulations of T-cells in allelic carriers of each type could bring additional insights. As well, histological examination of abomasal mucosa of extreme animals could also confirm the stronger Th-2 response by measuring the eosinophilic infiltration and the number of mast cells. Additional detrimental factors like an increase of lectins in mucus could not be demonstrated in this study. An additional meta-analysis of other parasite infection datasets gathered in the European 3SR project  [57]  is currently in process to confirm this region as a key player across multiple European breed, and eventually refine its location  [58].
Acknowledgements Staff of the Langlade and  La Sapinière  experimental units are acknowledged for the care and management of sheep. The authors are greatly in-debt to  S. C. Bishop  and  A. Legarra  for their fruitful comments and advice while analysing the dataset. Authors would also like to thank  L. Bodin ,  M. Lasalle  (Cryopic),  S. Coppin  and  V. Jacquiet  for their support during the experimental infection. Critical reviewing and constructive comments of this manuscript by anonymous reviewers,  A. Blanchard-Letort  and  R. Beech  were particularly appreciated. This project was funded by the European  3SR  project and  G. Sallé  was granted by the  INRA Animal Health and Animal Genetics departments.
We propose that there are statistical techniques which can be used to jointly analyse these diverse datasets and hence gain greater power. These are based on the concept of meta-analysis, a tool for aggregating information from multiple independent studies  (Cochran 1954; Fleiss 1993). The use of meta-analysis is becoming popular in GWA studies, because one can virtually collect data from tens of thousands of individuals, and this provides sufficient power to identify variants even with small effect sizes (de  Bakker et al. 2008; Zeggini & Ioannidis 2009). In humans, several large-scale meta-analyses have been performed for diseases including type 1 diabetes  (Barrett et al. 2009) , bipolar disorder  (Scott et al. 2009 ) and Crohn's disease  (Franke et al. 2010) , and these analyses have identified associations not revealed in the individual studies.
Meta-analysis studies have been also conducted in livestock, such as in cattle  (Khatkar et al. 2004 ) and pigs  (Switonski et al. 2010). Generally, these meta-analyses utilize public domain information on the trait/species considered and appropriately combine the output results to get overall p-values for each marker or QTL. We are in the fortunate position of having direct access to datasets comprising three different populations [Scottish Blackface (SBF), Sarda 9 Lacaune backcross (SAR) and Martinik Black-Belly 9 Romane backcross (MBR)], each of which has nematode resistance phenotypes as well as genotypes from the ovine 50k SNP chip. Therefore, instead of meta-analysis techniques combining published results, we were able to carry out a joint analysis considering the three populations together.
Populations Three populations were used for the analysis. As shown in the principal component plot of SNP chip markers reported in Figure  S1 , the three populations are genetically very distant and hence can be considered to be unrelated. The SBF population comprised 752 F2 and double backcross lambs from two lines selected for carcass lean content from the same foundation population, bred from 10 sires (half-sib family size = 11-146). More details on the data structure are given in  Riggio et al. (2013). The SAR population consisted of 2371 ewes, derived from 927 backcross Sarda 9 Lacaune ewes subsequently crossed to purebred Sarda rams. A detailed description of the animals is given in  Sechi et al. (2009). The MBR population consisted of 1000 backcross lambs, obtained from mating Martinik Black-Belly 9 Romane F1 rams with purebred Romane ewes.
Genotype data Animals were genotyped using the 50k SNP chip. The SNP genotype data were subjected to quality control (QC) measures, specific for each population (see Data S1). Furthermore, markers on the sex chromosome were removed from the analysis. After QC, 42 841 SNPs were available for the SBF population, 44 859 for the SAR and 42 469 for the MBR. Out of these SNPs, 38 991 were in common among the three populations and therefore used for further analyses. Positions of SNP markers were obtained from the Sheep Genome browser v2. 0 (http://www. livestockgenomics. csiro. au/sheep/).
Statistical analyses Analyses were performed using the regional heritability mapping (RHM) approach  (Nagamine et al. 2012) , in which each chromosome (OAR) is divided into windows of a predefined number of SNPs, and the variance attributable to each window estimated. In our case, the window size was 100 adjacent SNPs, and the window was shifted every 50 SNPs. Initially, the analyses were performed using only the Strongyles data. Subsequently, a second analysis was performed substituting the Nematodirus FEC data for the Strongyles data in the SBF population, to test whether common QTL regions across populations could be detected when combining data from very different nematode species. A mixed model was used for the analysis, with residual and additive genetic (both regional genomic and whole genomic) effects fitted as random.
Discussion Analysis of our three genetically distant sheep populations, with contrasting experimental protocols for phenotype collection, identified regions affecting FEC not previously revealed in the individual studies, demonstrating the power of meta-analysis over single analyses. However, in this study, we also showed that results can be affected by the methodology used (RHM with either whole or n-1 G matrix) and the trait definition (only Stongyles or combination of Strongyles and Nematodirus). For example, when analysing our Stongyles data with RHM, using the whole G matrix, the only significant regions were identified on OAR4 and 20. These same regions were confirmed in the other two analyses with RHM (i. e. Strongyles data with n-1 G matrix and data combining Nematodirus and Strongyles with n-1 G matrix), with these analyses also identifying other regions significant at both genome-wide and suggestive level.
Our results highlight the utility of using the RHM approach, which allowed us to combine the three datasets and simultaneously account for the population substructure. We achieved this by assuming no genomic covariance between the populations, and employing n-1 G matrices. Furthermore, this approach can detect different types of QTL architecture from LA or LD methods, as it does not necessarily require a large difference between contrasting loci/ haplotypes in the same population. This approach allows identification of regions that, as a whole, contain variation which is associated with the phenotype. Therefore, a combination of small effects in the same region can also give a significant result. This may include mutations in different linkage phases with SNPs in different populations, or even different mutations in the same or different genes in the same region, affecting the outcome phenotype in the different populations.
e. h 2 w ¼ 0:01 À 0:03), suggesting that nematode resistance is a complex trait for which many variants contribute. This is in agreement with  Kemper et al. (2011)  and  Lee et al. (2011) , who reported that there is no single mechanism of nematode resistance in sheep. Lee et al. (2011) , however, also highlighted that the complex heterogeneity of results can be due to differences in environmental conditions, nutritional status of the animals, geographical locations and the large variety of gastrointestinal nematode parasites. However, this diversity is found in our combined dataset, and despite this diversity, significant regions were still found. Nagamine et al. (2012)  have reported that if a single SNP is in complete association with the causative variant (i. e. r 2 = 1), then the standard single SNP-based association analysis should be the most powerful ana-lytical approach.
TGF-B1 is important in the regulation of immune responses and plays, together with IL-10, a central role in minimizing pathology and enhancing tissue repair during helminth infections  (Belkaid et al. 2006). Significantly positive correlation of TGF-B1 levels with adult worm count and FEC have been reported in the abomasal mucosa by  Gossner et al. (2012)  in progeny of the SBF sheep in this study. At present, there appear to be no obvious candidate genes within the other regions identified as significant, using either the UCSC genome browser (http:// genome. ucsc. edu/) or the CSIRO sheep genome browser (http://www. livestockgenomics. csiro. au/cgibin/gbrowse/oarv3. 1/). In summary, this study has been successful in detecting QTL for nematode resistance, combining data from three genetically distant sheep populations, identifying associations not previously revealed in the individual studies and therefore confirming the power of meta-analysis over single-experiment analyses.
Acknowledgements The authors would like to thank  Dr. Christopher Pooley  for his help drawing the Figures. These results are obtained through the  EC- funded  FP7  Project  3SR-245140. French SNP data were funded by the  SHEEP-SNPQTL ANR  project. Funding from the  Regional Government of Sardinia  contributed to the collection of Sardinian SNP and phenotype data. We also wish to acknowledge funding contributions from the  BBSRC   Institute Strategic Programme Grant  at  The Roslin Institute  and the  Scottish Government's Strategic Partnership for Animal Science Excellence (SPASE) initiative.
e. , too little or too much attention). Moreover, learning was influenced by attention which was highly visible at the end of the training where the more attentive horses (which were FR horses) had also better learning performances. Since the present study was based on an earlier dataset it was not possible to gather data on longer training periods. The increasing pattern of differences between both groups until clear differences on days 4 and/or 5 suggests that it would be worth in further studies to study longer time periods. Moreover, the trends of differences appeared clearly from day 3 and 4 on which may be a crucial step in training. In another training study,  Sankey et al. (2010b)  had shown that horses have anticipations on the quality of training sessions from day 3 on. Actually, the main difference between both procedures was the homogeneity of responses of FR horses as compared to GR horses.
ACKNOWLEDGMENTS The authors wish to thank  Professor Jaworski  and the staff at the  research Station for Ecological Agriculture and Preservation of Animal Breeding, Popielno, Poland , where the study was performed. The authors are grateful to  R. Ha  for statistical advise and  A. Cloarec  for correcting the English of this manuscript. The authors thank  C. Coye ,  C. Fureix ,  D. Kremers ,  C. Lesimple ,  A. Maille , and  H. Thieltges  for helpful discussions. The authors thank the  COST of the "Haras Nationaux" and the "Région Bretagne " for financial support.
On the reverse side of the media, S. brevicaulis gradually turned from honey-colored to brown. Microscope examination showed septate, hyaline hyphae and chains of round to ovoid, finely to coarsely rough spores with a distinctly truncate base  [1, 5, 6]. The diagnosis was confirmed by double strand sequencing of the ITS (internal transcribed spacer) region of the ribosomal DNA (primers ITS1/ITS4). The aligned sequence was compared to the GenBank and CBS databases. Antifungal susceptibility testing of the isolate by the Etest s method showed the fungus to have MICs (minimum inhibitory concentrations) above 32 μg/ml for all of the antifungal drugs tested: amphotericin B, voriconazole, posaconazole, itraconazole and caspofungin. The patient was discharged the day after the intervention on December 22nd 2012 (Day 70), without antifungal treatment.
Behavioural tests 6. 1. Reactivity to a motionless observer: short-term effects on time-budget. One week after the end of the URNS procedure (URNS+1), the experimenter, dressed in green (all quail saw the experimenter in that outfit for the same amount of time during the whole experiment), sat 1. 50 m in front of the battery. Then, the quail's behaviour was monitored by scan sampling for 1 hour in each room alternatively, between 8:30 and 12:30. Behaviours were noted every 2 minutes, yielding 30 scan data for each subject. The behavioural items as above were recorded (see 2. 5. Activity budget) and also vigilance (head and body stretched) and fear posture (low posture with head near to the ground and below the body) which could be displayed in reaction to frightening stimuli. 6. 2. Reactivity to a motionless observer: long-term effects on time budget.
Seven weeks after the end of the URNS procedure (URNS+7), all females were moved to larger individual cages in the same room (no visual contact between females). Inside the room, the position of control and treated quail's cages was balanced between rows and lines. The standing experimenter dressed in green scanned the cages, moving between each row of cages (17 rows of 2 or 3 cages). Behaviours were noted for 6 hours, every 8 minutes, yielding 40 scan data for each quail, between 8:30 and 14:30. The same behavioural items as above were recorded. As these cages were larger than the battery cages, the position of the quail (head and feet) was noted in addition (rear, middle, and front of the cage). 6. 3. Habituation to the experimenter presenting a mealworm. After the end of the URNS procedure, all quail were given mealworms in a small opaque trough placed inside their cage, for three consecutive days to habituate them to this food type.
Statistical analysis Normality and homoscedasticity of the residuals were verified for growth and activity budget data. Frequency for each behaviour (number of occurrence of a given behaviour/total number of scans) were extracted from scan samplings (activity budget and reaction to the experimenter). Growth and activity budget behaviours were analysed using mixed models (URNS 6 time) and with individuals as a random factor. Feeding data were arcsine root transformed to achieve a normal distribution of the residuals. Interactions between weeks and URNS were analysed with posthoc Tukey HSD tests. Because of minor health problems (diarrhea), body weight data were missing for two control quail which were thus removed for growth analyses. Other behavioural data residuals (short and long-term effects on time budgets, habituation to the experimenter presenting a mealworm) did not fit a normal distribution, thus non-parametric statistics were used.
For each parameter, Mann-Whitney U-tests compared treated and control quail. When a test was repeated, data were compared with Friedman tests conducted within each group. Data are presented as means 6 standard error of the mean (SEM). Moreover, the numbers of quail that displayed and that did not display a given behaviour (e. g. adopting a fear posture or approaching the experimenter) were compared with G-tests, and with a Fisher test when samples were small. These data are presented as the number of quail that expressed the behaviour divided by the total number of quail for each group, in percent. All tests were performed using Statistica (Statsoft, Inc. ) and R softwares. The significance level was set at P#0. 05 (two-tailed) and tendencies were considered up to P,0. 10.
PCR amplification and DNA sequencing The DNA amplification by Polymerase Chain Reaction (PCR) was conducted with primers designed from COI sequences of A. cantonensis (subgenus Parastrongylus) (GenBank accession number GQ398121), as Ac-COI Forward 5'GTTCTAATCATAAGGATATTG3' and Ac-COI Reverse 5'CAAACAAACAAACTCATATG3'. PCR amplicons were approximately 500 bp in length. 50 µL of each PCR reaction was composed of the 1xKAPA TaqReadyMix DNA Polymerase (1U KAPA Taq Polymerase, 1. 5 mM MgCl2 and KAPA Taq Polymerase Buffer), 0. 25 µM of each primer, and 1 µL of DNA template. Amplification conditions were initially heated at 94 °C for 3 min, followed by 34 amplification cycles, consisting of denaturation at 95 °C for 30 sec, annealing at 53 °C for 30 sec and elongation 72 °C for 1 min and final extension at 72 °C for 5 min.
PCR products were run into 1. 0 % agarose gel and visualized on UV-transilluminator. Each PCR amplicons was sequenced using the 2 amplification primers on an ABI's 3730XL DNA Analyzers and BigDye Terminator at AITBIOTECH Pte Ltd (Singapore). GenBank as follows: A. vasorum GQ982777, GQ982875, GQ982835, GQ982858, GQ982785, GQ982876, GQ982734; A. cantonensis (subgenus Parastrongylus) GQ398121, NC013065; P. tenuis EF173723; M. pudendotectus NC013 813; M. salmi NC013815; and S. mekongi AF217449.
Sequence alignment and phylogenetic analysis The electropherogram of each sequence was examined for sequence accuracy by BioEdit program version 7. 0  (Hall, 1999). The DNA sequences of COI were aligned by CLUSTAL X  (Thompson, 1997). All gap sites in the sequences were removed from the alignment. Phylogram was constructed from COI sequences by neighbour-joining (NJ) method by estimating 1000 replications with p-distance in MEGA 5  (Tamura et al. , 2011).
Acknowledgements This study was supported by  French   ANR 11 CPEL 002 , project  BiodivHealthSEA, Local impacts and perceptions of global changes: Biodiversity, health and zoonoses in Southeast Asia  (www. biodivhealthsea. org)and the  French ANR Biodiversity   ANR 07 BDIV 012 , project  CERoPath, Community Ecology of Rodents  and their Pathogens in a changing environment (www. ceropath. org). A. Ribas was partially supported by  2014-SGR-1241  from the  Catalan Government.
Data collection and statistical analyses Qualitative and quantitative analyses of interview questionnaire responses from dog owners were used to determine how well owners perceived the body condition of their dog, the usefulness of the BCS chart and which aspects of the chart should be improved. Statistical analyses were conducted using computer software (StatsDirect, version 2. 6. 8, StatsDirect Ltd). Since questionnaire responses comprised categorical data, non-parametric methods were chosen. The prevalence of misperception was calculated as the proportion of owners who incorrectly assessed their dog's body condition. For this, the investigator's assessment of canine body condition was assumed to be the 'gold standard'. Fisher's exact test was used to examine the relationship between the misperception of owners of dogs that attracted conflicting investigatorclassified scores (i.
Acknowledgements A. J. G. 's readership is financially supported by  Royal Canin. This research received no specific grant from any funding agency, commercial or not-for-profit sectors. A. J. G. 's academic position at the  University of Liverpool  is financially supported by  Royal Canin. V. B. is an employee of  Royal Canin. The study was based upon a project conducted by R. C. E. -J. , as part of the requirements for the  Bioveterinary Science B. Sc. (Hons) degree at the University of Liverpool. A. J. G. and L. C. P. proposed the research question; S. L. H. trained R. C. E. -J. in body condition scoring and assisted with recruitment of cases; R. C. E. -J. executed the study and analysed the data, under supervision of L. C. P. and A. J. G. ; A. J. G. produced the first draft of the manuscript, which was subsequently edited by R.
All adult patients with reliable medical charts and meeting these criteria were included. Outpatients or patients with incomplete medical records, and patients with samples growing Actinomyces sp without a related focus of infection or with a superficial infection were excluded (Figure  1 ). For each patient, demographic characteristics, underlying diseases, clinical and radiological manifestations, microbiological results, and treatment and outcome data were collected retrospectively and reviewed. Statistical analyses were done with Epi Info 3. 5. 1. Means were compared with a Mann-Whitney test. Qualitative variables were compared with a Fisher's exact test.
Study patients As shown in Figure  1 , 97 patients were screened for actinomycosis by pathology or bacteriology. Data were missing for 30 of them (mostly outpatients). Of the remaining 67 medical records that were examined, the clinician did not retain the diagnosis of infection due to actinomycosis in 19. These cases were systematic cultures of vaginal tract samples from the gynecology ward, or of bronchoalveolar lavage samples from pulmonary transplanted patients. Forty-eight patients met the criteria for actinomycosis, but 15 were considered to have focal and superficial infections and were finally excluded. The remaining 33 patients were considered to have an invasive actinomycosis and represented the study population (Table  1 ).
Data were expressed as eggs per gram of faeces (EPG). Individual blood samples were taken fortnightly (D0, D14, D28 and D42) during the trial. Blood was taken by venipuncture of the jugular vein and collected in heparin and heparinfree tubes. The first tubes were used to measure Packed Cell Volume (PCV) according to the microhaematocrit method. Serum was collected from heparin-free tubes, separated and frozen to determine inorganic phosphate values using a photometric assay  [34]. On D63 (end of the assay), only lamb males were slaughtered (8 animals per group) and the female lambs were drenched with albendazole at the commercial recommended dose (15 mg/Kg) and returned to the flock. After necropsy, total adult worm burdens and fertility of female worms for the two nematode species (H. contortus and T.