dataesr/scientific-paragraphs-categorization huggingface dataset:
Variation in behavior was calculated, pooling the different observations within periods (SEM, Table  6 ). The effect of group on geese behavior was tested within each of the 5 periods and also for all the 4 periods during which access to food was restricted. The data for feed intake were also pooled by period and analyzed including the effects of period (5 levels: period 1, 2, 3, 4, and 5), group (2 levels: C or M), and their interaction in the model. In this latter analysis, there was no effect of group nor interaction between periods and groups, thus these results were not reported here. Differences were treated as significant when P ≤ 0. 05.
Data collection Each farm was visited once by the same person, a student in the final year of veterinary school. During the visit, a faceto-face interview was conducted with one of the farmers from the farm, with the farmer answering a semi-structured questionnaire. This questionnaire had been pre-tested by the student on two farms before being used. Before beginning the interview, the farmers were shown pictures of DD lesions and other foot diseases to clarify what should be considered to be DD. Farmers' answers were recorded on a printed paper copy of the questionnaire (available upon request). The first part of the questionnaire collected data on the general characteristics of the herd (number and breed of milking cows, type of housing and milking parlour), livestock management (floor cleaning practices, grazing management, hoof care, purchase of dairy cows), and DD outbreaks in the dairy herd (DD detection methods, categories of cows affected, frequency and seasonality of DD outbreaks).
Farmers' adoption of digital dermatitis treatments Data analysis Data were entered by the student in an Excel spreadsheet (Microsoft Corp. , Redmont, WA, USA). They were managed and analysed using SAS R software version 9. 1. 3 (SAS Institute Inc. , Cary, NC, USA). A treatment protocol was deemed to have been adopted when a farmer, having tested one or more protocols on his herd, chose to continue using the protocol in question. Otherwise, it was deemed to have been abandoned. The answers to semi-open questions dealing with the motives for continuation (adoption) or discontinuation (abandonment) of a treatment protocol were coded by the first author, and closely related answers were grouped into the following six categories for statistical analysis: 'effectiveness', 'time  ', 'labour', 'cost', 'toxicity' and 'other'.
Sample description Of the 72 farmers who were visited, one had only beef cattle at the time of the interview and six had been treating DD for , 2 years. Finally, data from 65 farms were included in the analysis. Twenty-nine farms were in the West, 22 in the East, 7 in Normandy, 4 in the North, and 3 in the Southeast. Farmers milked a mean number of 76 cows (range from 35 to 150). The main characteristics of the farms are presented in Table  1. The farmers reported detecting DD in two ways: either they detected the disease once the lesions were established and caused lameness, or they actively looked for the presence of DD lesions. All of the farmers declared that the appearance of lameness enabled them to detect a cow infected with DD and for seven farmers (7/65 [11%]), this detection also could occur following the perception of a nauseating odour.
Polymerase chain reaction (PCR) amplification of snail ITS-2 was carried out with primers designed in a previous study  [11]  (forward: LT1 5′-TCGTCTGTGTGAGGGTCG-3′; reverse: ITS-2 Rixo R: 5′-TTCTATGCTTAAATTCAGGGG-3′), in 25 μl reaction tubes, as follows: 1 μl of snail DNA, 10 mM Tris-HCl pH 8. 3, 50 mM KCl, 2 mM MgCl 2 , 4 μg Bovine Serum Albumin (BSA; New England Biolabs, Inc. , UK), 0. 8 μM of each primer, 0. 2 mM dNTP and 0. 3 U Taq polymerase (Ampli Taq Gold, Applied Biosystems, USA). Separation, purification and sequencing of the PCR products was carried as described earlier  [21]. Sequences were edited with CLC Main Workbench (version 5. 6. 1), and compared with sequences available in GenBank (accessed in March 2013) [GenBank: AJ243017; AJ272051; AJ296271; AJ319620; AJ319621; AJ319622; AJ319623; AJ319624; FR797838; FR797839; FR797840; FR797841; FR797845; FR797846; FR797847; FR797848; HE577631; HE577632; HE577633; HE577634; HE577635; HE577636; HE577637; HE613327; JN614443; JN614444; JN614445; JN614446; JN614447; JN614448; JN614449], using Clustal W2 (EMBL-EBI) and the basic local alignment search (BLAST) tool (http:// blast.
Data and statistical analyses In experimental infections, survival rate at day 30 PE and the prevalence of F. hepatica infection in relation to the number of surviving snails at day 30 PE were determined. The following characteristics were recorded: mean and total number of spontaneously emerged cercariae from cercariae-shedding (CS) snails; first day of cercarial shedding; mean number of metacercariae obtained from snails where no cercarial shedding (NCS) was observed until dissection; and shell size at the end of the experiment. All statistical analyses were performed using GraphPad Prism 5. 02 (GraphPad Software, USA). Analysis of variance (ANOVA) was applied to assess differences between mean sizes of infected snails, exposed but uninfected snails, and the snails from the negative control group.
Monitoring of F. hepatica infection of snails collected in the field A total of 668 snails determined as L. palustris [GenBank: KC248373; KC248374; KC905167] from all three sampling sites (Norrköping, Linköping and Kristianstad) during 2011-2012 were examined for liver fluke DNA by PCR. Only one L. palustris collected on the beef farm in Linköping was F. hepatica positive. The species identity of ) PCR products (ITS-2) were obtained according to our described ITS-2 gene amplification method (from the left side); five others (cox-1) were obtained according to the previously used PCR protocol with primers for mitochondrial cytochromoxidase 1  [23]. this positive specimen was confirmed by morphology and ITS-2 sequencing [GenBank: KC248374]. All L. fuscus snails (n = 130) were negative.
Acknowledgements This study was supported by the  Swedish Foundation for Agricultural Research  (contract No. H1050003 ), the 7th framework programme of the  EU (GLOWORM , Project  FP7-KBBE-2012-288975 ) and the  Charles University in Prague  ( UNCE 204017 ,  PRVOUK P41 ,  SVV 267210/2013 ). We thank  Annie Engström  and  Sofia Sollenberg (BVF, SLU, Uppsala)  for their help with DNA isolation and sequencing, and help during experimental infections of snails. We are grateful for cooperation with the  Swedish Animal Health Service  (namely  Katarina Gustafsson ,  Ulrika König ,  Virpi Welling  and  Helen B. Averpil ). The authors thank  David A. Morrison  for revising the English text.
Acknowledgments The authors would like to thank  Guy Duchamp ,  Fabrice Reigner , and their staff ( INRA Nouzilly, France ) for allowing the use of the animals and facilities. The authors would also like to thank  Aurelie Holtz ,  Jean-Marie Yvon , and  Anne-Marie Mounier  for their assistance in data collection, and  Laura Szymanski  for having checked the quality of the English language of our manuscript.
MST analysis Sequences of the whole intergenic spacers were extracted from the reference M. abscessus CIP104536 T (ATCC19977) genome (GenBank accession CU458896. 1) using the perl script software and a total of 8 spacers with a 200-700-bp sequence size were further used in analysis. For each of these 8 spacers, specific PCR primers were designed using Primer3 software v 0. 4. 0 (http://frodo. wi. mit. edu/primer3) and tested in silico for specificity using BLAST software (http://www. ncbi. nlm. nih. gov). The PCR conditions were first optimized using DNA extracted from the reference M. abscessus, "M. bolletii" and "M. massiliense" isolates before analysis of DNA extracted from the 17 clinical isolates (Table  1 ). The PCR amplifications were performed in a 50 μl PCR mixture containing 5 μl 10x buffer (Qiagen, Courtaboeuf, France), 200 mM each dNTP, 1.
42; Technelysium Pty Ltd), aligned using Clustal W (MEGA 5 software) and compared with the reference M. abscessus ATCC 19977 sequences (GenBank accession CU458896. 1). For MST and MLSA discrimination power was calculated using the Hunter-Gaston Index  [31] : DI ¼ 1 À 1 N N À 1 ð Þ X 8 j¼1 n j n j À 1 À Á ! where D is the numerical index of discrimination, N is the total number of isolates in the sample population, s is the total number of different types and nj is the number of isolates belonging to the jth type.
Results and discussion rpoB identification and rpoB tree The identification of M. abscessus CIP104536 T , M. abscessus DSMZ44567, M. bolletii CIP108541 T and M. massiliense CIP108297 T was confirmed by partial rpoB sequencing. The sequences were deposited in the GenBank database (GenBank accession: KC352778 -KC352795). Isolates P1, P2. 1, P2. 2, P2. 3, P2. 4, P2. 5, P3. 1, P3. 2, P4, P5, P6, P7 and P8 exhibited 99% rpoB sequence similarity with M. abscessus ATCC19977 T and were identified as M. abscessus. Isolates P9 and P10 exhibited 99% rpoB sequence similarity with "M. bolletii" CIP108541 T and were identified as "M. bolletii" whereas isolate P11 exhibited 99% rpoB sequence similarity with "M. massiliense" CIP108297 T and was identified as "M. massiliense". A total of 23 M. abscessus sequenced genomes were identified as M.
Reference MLSA analysis Fragments for the expected size were amplified and sequenced for the five MLSA genes. The sequences were deposited in the GenBank database (GenBank accession: KC352742 -KC352759, KC352760 -KC352777, KC352796 -KC352813, KC352814 -KC352831, KC352832 -KC352849). Concatenation of the five sequences yielded a total of 19 different types, including 9 types for 37 M. abscessus organisms, four types for 4 "M. bolletii" organisms and M. abscessus M139 and five types for 27 "M. massiliense" organisms. The Hunter-Gaston Index for MLSA was of 0. 903. The MLSA tree based on the five gene concatened sequences showed three principal clusters, i. e. a M. abscessus cluster, a "M. bolletii" cluster and a "M. massiliense" cluster (Figure  1b ). Latter cluster comprised of five sub-clusters with "M.
MST analysis Analysis of the reference M. abscessus ATCC 19977 complete genome sequence yielded 3538 intergenic spacers with > 300 spacers were 200-700 bp in length. Successful PCR sequencing was achieved for 8 spacers in all the isolates studied; the sequences were deposited in the GenBank database (GenBank accession: KC352850 -KC352890). In M. abscessus isolates, including the 37 sequenced genomes, the spacer sequence variability was generated by one to 12 single nucleotide polymorphisms (SNPs) (spacers n°1 and n°8), one to 18 SNPs and one to two nucleotide deletions (spacer n°2), one to two SNPs (spacers n°3 and n°7) and nucleotide insertion (spacers n°2 and n°5). In "M. bolletii" isolates, the spacer sequence polymorphisms were generated by one SNP for spacer n°1, two SNPs and one deletion for spacer n°2, two SNPs for spacer n°3 and nine SNPs for spacer n°7.
Acknowledgments IBK was financially supported by the  Oeuvre Antituberculeuse des Bouches du Rhône. MS was financially supported by  Infectiopole Sud Foundation. Author details 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) ,  UMR CNRS 7278 ,  IRD 198 ,  INSERM 1095. Faculté de médecine ,  27 ,  Boulevard Jean Moulin-Cedex 5, Marseille, France. 2 Laboratoire de Microbiologie et d'Immunologie ,  UR02/SP13 ,  CHU Farhat Hached Sousse, Tunisie, France. Received: 7 March 2012 Accepted: 20 December 2012 Published: 7 January 2013.
05 × 10 8 CFU/spleen for wild type versus 6. 5 × 10 7 CFU/spleen for the btpAbtpB mutant). To better study the role of BtpB in brucellosis in vivo, we inoculated wild type BALB/c mice i. p. and enumerated the bacterial load at 30, 60, 90, and 130 days post-infection. No significant differences in bacterial CFU counts between the wild type Brucella and the btp mutants were observed at different stages of the infection (30, 60, 90, and 130 days). Data at 60 days post-infection is shown as an example (Figure  6B ). We then performed histological examination of spleens obtained from wild type BALB/c mice infected with the btpA, btpB, btpAbtpB mutants or the wild type B. abortus strains to quantify granuloma formation, which usually reflects the host's ability to develop a protective immune response.
FLOW CYTOMETRY OF INFECTED CELLS BMDCs were harvested 8 h or 24 h after infection and stained for 20 min at 4 • C with anti CD11c APC-Cy7, anti CD40 Alexa 647, anti CD80 Pe-Cy5, anti CD86 FITC and anti MHC class II PE (all purchased at BioLegend). Cells were then washed once in 1% FCS in PBS and once in PBS. Cells were fixed for 20 min in 3% PFA at room temperature. At least 100,000 CD11c+ events were collected on flow cytometry using a FACS Canto II (Becton Dickinson) and analysis was done on FlowJo software (TreeStar).
ACKNOWLEDGMENTS We are grateful to  R. Tsolis  for the pFLAG-TEM1,  L. O'Neill  for the pACT2 vector encoding human MyD88-Gal4 activation domain (AD) fusion and  R. Jerala  for the MD2 plasmid. This work was supported by the  Agence National Recherche (ANR BruTir) , the  Centre National de la Recherche Scientifique , the  Institut National de la Santé et de la Recherche Médicale  and the  Aix-Marseille Université. Matthieu Terwagne  held a Ph. D. fellowship from the  Fonds National de la Recherche Scientifique  and his work was supported by an  ARC  convention from the  French-Speaking Community of Belgium  ( N • 08/13-015 ). Paul Roger Claude Imbert held a Ph. D. fellowship from FINOVI and TLSL was funded by the  ANR  grant CELLPATH, awarded under the  ERA-NET PathoGenoMics scheme. Diego José Comerci  and  María Ines Marchesini  are members of the  Scientific Research Career  from  Consejo Nacional de Investigaciones Científicas y Técnicas  ( CONICET, Argentina );  Claudia Karina Herrmann  is a Ph.
Database collection and collagen determination We used an updated database since 2007  (Schreurs et al. , 2008) , which was created to compile experiments conducted at the Herbivore Research Unit (INRA) in France and to allow the investigation of the effects of animal factors such as muscle, gender, breed and DOM on muscle characteristics, usually associated with beef quality. Detailed description of the muscle characteristics included in the database can be found in a study by  Schreurs et al. (2008). The collagen sub-database comprised 22 experiments with 1165 and 1145 measurements of total and insoluble collagen, respectively (Table  1 ). DOM of each animal at slaughter was included in the database. It a priori helps to compare individuals on a physiological basis  (Robelin, 1986). DOM is an index of development of each animal and it accounts for differences between earlyand late-maturing genders and breeds in the study.
DOM was calculated as the proportion of mature BW achieved when the muscle sample was taken. One unique mature BW was defined for each gender (bull, steer and cow) in each breed  (Schreurs et al. , 2008). This results in possible DOMs. 1, as individuals could have a higher BW than the mature one. Collagen characteristics included in the database were contents of total collagen (mg of OH-proline/mg) and insoluble collagen (mg of OH-proline/mg) in dry muscle. Muscle sampling and collagen determination procedures were standardised in the laboratory to minimise the sources of intra-and inter-assay variability  (Listrat and Hocquette, 2004). Muscle weighing ,100 g was frozen and homogenised in a household cutter, then lyophilised for 48 h and then pulverised in a horizontal blade mill. Insoluble collagen content was determined on muscle powder rehydrated for 1 h and heated in a water bath at 758C for 1 h to remove possible effects of temperature on collagen solubility.
Muscles considered were the Longissimus thoracis, the Semitendinosus and the Triceps brachii in bulls, steers and cows. Breed effect was studied in interaction with DOM as the predictive continuous variable separately for each muscle, with separate analyses for bulls and cows. To make comparisons between breeds, data were classified according to two categories: beef breeds grouping Charolais and Limousin and non-beef breeds grouping Aubrac, Holstein and Salers  (Schreurs et al. , 2010). Gender effect (bull v. steer) was studied separately in Longissimus, Semitendinosus and Triceps brachii muscles in Charolais males. Data were plotted for each muscle, gender and breed successively against age, weight and DOM as potential continuous predictor variables. Means of treatments within experiment were also plotted and connected to highlight the intra-study relationship as suggested by  Sauvant et al.
(2008). Finally, DOM was chosen as the best continuous predictive variable because it is more synthetic, data were more evenly distributed among DOMs and it allows for comparisons between early-and late-maturing breeds with different frame sizes at maturity. Data were analysed using mixed models (Proc mixed, v 9. 1. 3. SAS Institute Inc. , Cary, NC, USA) with restricted maximum likelihood estimation to obtain the variance components. The degrees of freedom used for testing were corrected with the Satterthwaite correction to account for possible unequal number of observations  (Kaps and Lamberson, 2009). Each analysis investigated the effect of the continuous predictive variable DOM and the qualitative factor (t) being muscle, breed or gender, with model (1) when investigating muscle effect and with model (2) when investigating breed or gender effect.
Synthesis and model development The results of the meta-analysis clarify fairly the effects of muscle, breed and DOM together on total and insoluble collagen contents in young bulls, cows and steers. However, the accuracy of some of the models, according to R 2 , was low. Thus, another type of modelling will be recommended for the purpose of prediction. Our findings are helpful for further model development because they rely on a database consistent in terms of sampling size and site and in terms of cooking temperature. In this sense, together with results from the literature, they allowed us to draw the main biological hypotheses of a future dynamic model of total and insoluble collagen contents in bovine muscle. We propose a diagram for this model, relying on the formalism of Forrester compartmental models  (Radzicki and Taylor, 2008) , widely encountered in pharmacokinetics and in dynamic modelling of the processes occurring at the animal, metabolism or organ level or in the field (Figure  4 ).
Conclusions Total and insoluble collagen contents were differently affected by the muscle, type of breed (beef v. non-beef) and DOM in bulls, cows and steers. The interactions observed among factors could be linked to differences in precocity between muscles and types of breeds, which were already discussed in the literature. The present meta-analyses, relying on a consistent database in terms of sampling and cooking methodologies, clarify to some extent the impact of these animal factors. The resulting conceptual model constitutes a good basement for a dynamic mechanistic model that would account for animal factors through the biological hypotheses on the dynamics of collagen synthesis and cross-linking, but also for management factors through the link to a dynamic growth model.
Statistical analysis For cats included in the evaluation of efficacy, effectiveness was calculated by comparing post-treatment geometric mean flea counts with baseline data collected at the time of the clinic visit before the first treatment. Further analysis on the log-transformed (flea count+1) data used a repeated measures mixed effects linear model with treatment group, time, time by treatment group and household type (single cat and multiple cats) as fixed effects in the model. A non-inferiority analysis was performed by calculating the reduction in flea count for each treatment group using back-transformed least squares (LS) means with the following formula: Reduction ð%Þ ¼ Geometric mean visit 1 À Geometric mean visit 3 Geometric mean visit 1 Â 100 In order to declare the non-inferiority of spinosad in relation to selamectin, the evaluation required the following conditions to be met: (1) a statistically significant (P<0.
Administration of tablets to cats has traditionally been seen as challenging, often requiring restraint of the animal and can be associated with reduced owner compliance  (Thombre 2004 ). The data from the field study show that over a third of cats freely accepted the flavoured spinosad tablet or ate it with food and acceptance by free choice increased when the tablets were offered in the cat's home environment, although some owners and clinic staff elected to administer the tablet by pilling and did not use any other method. Overall acceptance of the tablets was recorded as >98 per cent, indicating that owners successfully chose an administration method that was most appropriate to themselves and their cat. There are several advantages to orally administered products, including that efficacy is not affected by bathing or shampooing and there is no active ingredient present on the surface of the animal that could potentially be transferred to the owner or to children.
Factor Analyses Wild-and captive-born populations were analysed separately as the aim of the study was to investigate the differential presence of atypical profiles among both populations. As data were not normally distributed, they were submitted to multifactorial correspondence analyses (MCA; SPAD ß 7. 4, Coheris) that uses chi-square criterion to assess differences and similarities between frequencies of qualitative variables. Active variables are placed in a multidimensional cloud in which two items are at a short distance if they show similar proportions in the same individuals and conversely they are distant if expressed by different individuals. The same process is then repeated with individuals. Two individuals are close if they share similar behavioural profiles. Both clouds are then displayed together by projection onto planes, defined by factors.
Data analysis Kolmogorov-Smirnov tests determined whether the data were normally distributed. In the hens, all the morpho-physiological and behavioral measures were analyzed using one-way analysis of variance (ANOVA) for repeated measures (treatment 6 time). When required, PLSD Fisher post-hoc tests were performed. The relative proportions of egg components (yolk and eggshell) were determined and analyzed using multivariate analysis of variance (MANOVA). If Wilks' Lambda tests showed a significant multivariate effect, individual one-way ANOVAs were performed for each dependent variable. Yolk hormone concentrations were analyzed using a MANOVA and individual one-way ANOVAs. Hatching success and the number of hatchlings obtaining the maximum morphological quality score were tested using a Chisquare test.
Acknowledgments All birds were maintained at the  Experimental Unit PEAT of INRA (Nouzilly, France). We are grateful to all the members of the experimental unit and particularly JM Brigant and  H Rigoreau  for providing care to the birds. We thank  I Bouvarel  and  P Lescoat  for early discussions on the protocol. We are grateful to MH Pinard who kindly accepted that we used the line of hens. We thank  Charline Parenteau  for hormonal assays and  Paul Constantin  for blood samples collection. Our manuscript was proofread for English content by  Editage.