dataesr/scientific-paragraphs-categorization huggingface dataset:
Overall Study Design and Participating Farms The present assessments are based on data collected during visits to 74 organic pig farms, representing three different husbandry systems, IN (34 farms), POUT (28 farms), and OUT (12 farms), in eight European countries (Austria, Czech Republic, Denmark, France, Germany, Italy, Switzerland, and the United Kingdom) during 2012 and 2013 (see Supplementary Materials). In each country, all assessments were carried out by one trained observer. All observers attended a common training course to standardize assessments. The different husbandry systems were defined as described in Table  1. There can be at least one production stage (dry sows, lactating sows, group suckling, weaned piglets, or finishing pigs) outside while the rest is housed, or pigs spending part of the year outside and the rest indoors (seasonal housing).
Recruitment was also based on the type of husbandry system, as the objective was to compare the three different organic pig systems. As this study investigated the environmental impact of pork production from piglet production until slaughter, production chains from farrowing to finishing (PC) were the statistical unit. This comprised 64 PCs (24 IN, 30 POUT, 10 OUT), which were either farrow-to-finish farms (15 IN, 24 POUT, 9 OUT) or which were formed of co-operating farrowing-only and fattening-only farms (6, 6, and 1 IN, POUT and OUT PCs, respectively). Additionally, for three other PCs (IN), data from the co-operating farm was not available during the study, and the average of the other farms was then used for the missing part of the PC. For each individual PC, environmental impact categories were calculated as outlined below, with pairs of farrowing-only and fattening-only farms being treated as farrow-to-finish farms.
The nitrogen (N)-related part of feeds' EP was calculated by multiplying typical quantities of N applied in manure and commercial fertilizers on organic farms in Austria with typical NO 3 -N leaching factors identified in  [37]. For P-losses from feed production, it was assumed that, on average, a surplus of 5% over plant requirements (according to yield) was applied and lost. The GWP of the rarely used components, fishmeal and fish oil, originate from  [38]. The GWP, AP, and EP for monocalcium phosphate and mineral premixes are based on the Danish LCA food database  [39]. The total feed consumption per animal, including bought-in-feedstuffs, was calculated from farm-specific data (based on daily consumption per animal, feed conversion rate, duration of the periods, average daily gains, etc.
Statistical Data Analysis All statistical analyses were performed with each individual PC as the statistical unit in SAS 9. 2 and 9. 3 (SAS-Institute, Cary, North Carolina, USA, 2008). Non-parametric Kruskal-Wallis tests were used for comparisons between husbandry systems. When significant effects (p < 0. 05) were revealed in global tests, pairwise comparisons were performed using the Wilcoxon Two-Sample (Rank sum) test. p-Values were adjusted for multiple comparisons using Bonferroni correction. Additionally, to investigate associations between the environmental impact categories of AP, EP, and GWP and farm characteristics, Spearman rank correlations were calculated. Only those characteristics were included which were not directly considered in the LCA calculation, except for piglets weaned per sow per year [n, 1 yr mean] and carcass weight [kg, 1 yr mean].
Since AP, EP, and GWP did not significantly correlate with each other, they were subjected to a hierarchical cluster analysis using the average linkage method. Values were standardized using the procedure, STDIZE, in SAS using the mean as a location measure and the sample standard deviation as a scale measure. For this analysis, five outliers (2 IN, 2 POUT, 1 OUT) were excluded, as identified from boxplots, resulting in 59 PCs being included in the final cluster analysis. The number of clusters was based on R-Squared (SAS-Institute, 2008), Pseudo F, and Pseudo t2 statistics. Additionally, the average distance between the clusters was graphically checked in a dendrogram.
In general, most of our results are within the ranges reported in the literature, e. g. , as provided in a review of six comparable LCA studies of pork products  [4]  (Table  12 ). The authors also found a large variation, especially regarding acidification and eutrophication potential. Our results are particularly comparable to results reported by  [15] , who used a similar methodology and system boundaries for an evaluation of 15 pig farming systems from five European countries. For each pig farming system, data from five to 10 farms were obtained from surveys, and systems were categorized into conventional, adapted conventional, traditional, and organic. Feed production contributed less to EP in organic systems than in the others  [15]. In the present study, the results regarding EP (medians ranging from 20.
Limitations of the Method and Uncertainties The present study used primary data from a non-representative sample of farms instead of modelled data based on assumptions. Therefore, sensitivity analyses, which are used for specific scenarios, were not applied here. Besides the influence of the PC-specific characteristics, LCA results depend on underlying methodological assumptions (e. g. , emission factors for different floor types, allocation approach  [49] ). The degree of uncertainty for estimates revealed from these assumptions might vary between PCs, and estimates may therefore not be fully appropriate for the diverse husbandry systems in organic pig farming. A Monte Carlo analysis for the calculation of uncertainties of primary data as well as emission factors, describing the uncertainty areas of GWP, AP, and EP results, was not applied in the present study.
Zebrafish Embryo Infections The various M. abscessus strains expressing tdTomato were prepared, injected and monitored according to protocols reported previously  (Bernut et al. , 2015). In brief, infections were performed by microinjection of bacterial suspensions (≈2 nL containing 150-200 bacteria) intravenously in dechorionated and anesthetized 30 hpf embryos. The size of the inoculum was verified a posteriori by injecting 2 nL of each bacterial suspension in sterile PBS T and plating on 7H10 OADC. For kill kinetics, infected larvae were transferred into 12 well plates (3 embryos/well) and incubated at 28. 5 • C. Survival curves were drawn by counting dead embryos every day for up to 13 days. To analyze abscess size induced by different strains of M. abscessus, the largest abscess in each infected fish was first marked off on scale-set microscope images of whole embryos using the polygon selection tool of the Fiji software.
abscessus R virulence  (Bernut et al. , 2014) , were observed in liquid cultures of mmpS4::pUX3 as for mmpL4a::pUX1 and M. abscessus R, but not for M. abscessus S (Figure  3C ). Several tests employing acetamide as supplement were then performed in order to induce MmpS4-MmpL4a-MmpL4b expression and GPL production both in broth and on solid agar culture. However, stable high-level GPL production supporting S phenotypes was not fully achieved, despite testing various acetamide concentrations and medium compositions (data not shown). In addition to colony morphology and bacterial aggregation phenotypes, GPL profiles of cultures were also assessed by TLC. As shown in Figure  3D , the mmpS4::pUX3 strain still produced low levels of GPL compared to the S progenitor (approximately 30% of S levels), even in the absence of inducer.
75, 10% increase not included). Feed (commercial pellets for rabbits with (weeks 1 to 4) or without (week 5) antibiotics, as detailed in Piles et al. [7] ) was distributed once a day in a 3-place feeder. Water was available ad libitum (one nipple drinker per cage). Individual body weights (BW) were recorded at weaning and weekly after weaning. Average daily gain (g/d) for each week was calculated as the change in BW from the beginning to the end of the week divided by the number of days elapsed (7 ± 1 d). On the weighing day, information regarding the animal health status was also recorded. Groups with animals showing disease symptoms (not caused by antagonist behaviors) or groups who suffered death events during the week were discarded from the analyses. The final dataset comprised 11,255 ADG records from 3096 individuals born in 1106 litters.
The choice of the "best" animals was based on their estimated breeding values (EBV) that were calculated according to the genetic evaluation strategies described below. Each selected male was randomly mated to four of the selected females, avoiding individuals from the same sire family. The population and phenotypes were generated to match the previously described experimental data design. Individuals in each generation were assigned to groups of eight animals, with each group originating from four fullsib families and each family contributing two progeny. Individual phenotypes (5 records per animal, corresponding to 5 weeks of fattening) were constructed according to a multiple trait model that considered ADG as a different trait for each week. Average daily gain of each animal was computed for each week as the sum of: a week effect, the animal's direct genetic effect for the corresponding week, the indirect genetic effects of the seven other pen mates for the corresponding week, a week-specific group effect, and a pseudo-permanent effect (correlated within animal): y im w j = µ i w j + DGE i w j + k∈K i IGE k w j + g m w j + p i w j , (= Eq.
[33]  (40. 4 g/d). Because of the limited amount of food, the ADG of restricted animals was lower than that of animals fed ad libitum from the same population of rabbits  [7]. In addition, there was an effect of feeding restriction on the growth pattern, with the deceleration phase and the inflexion point of the growth curve being delayed. Because animals were raised in collective cages, we included indirect genetic effects in the model to account for the competition between individuals to access feed. In a previous analysis of the same dataset that did not consider the longitudinal characteristics of the data, Piles et al. [7]  confirmed that indirect genetic effects play an important role in ADG under restricted feeding. The significance of IGE was also confirmed in our study when the longitudinal characteristics of the data were accounted for by the likelihood ratio test that compared the SAD model with and without IGE.
Using a larger dataset is one approach to overcome this problem  [52]. Across the replicates that converged, the bias in estimates of the variance components and the correlations between weeks were moderate, which indicates that the SAD model was able to estimate the different variance components. Nonetheless, it should be noted that the indirect genetic variances tended to be overestimated, while the group variances were slightly underestimated, which confirms the difficulties (but not the impossibility) of separating IGE from group effects. Thus, in practice, when applying such a complex model, it is highly recommended to inspect closely the average information matrix to determine whether the data structure supports the fitted model. We proposed three selection scenarios. All scenarios used the SAD model to compute TEBV and took the longitudinality of the data and the possibility that ADG corresponds to different traits at different time points into account.
Geographic and climatic data The mean altitude of each municipality was obtained by considering that of its main city and was determined using the Carte-de-France website (http://www. cartesfrance. fr). As the mean altitude of these municipalities ranged from 160 to 570 m, we have used four categories of altitude (<300 m, 300-400 m, 401-500 m, and >500 m) to classify individual values provided by the study of several parameters. The other two variables were the mean annual rainfall and the mean annual temperature recorded in the 200 municipalities of Haute Vienne between 1971 and 2000. The latter data came from maps published by Météo France  (Météo France, 2016). Five categories were used for mean annual rainfall (<900 mm, 900-1000 mm, 1001-1100 mm, 1101-1200 mm, and >1200 mm), whereas five other categories (<9.
Normality of these last values was analysed using Shapiro-Wilk normality test  (Shapiro and Wilk, 1965). As the distributions of these values were not normal, the Kruskal-Wallis test was used to establish levels of significance. We have also used the pgirmess r package  (Siegel and Castellan, 1988)  as a posthoc test to do pairwise multiple comparisons. The different analyses were performed using the R 3. 3. 0 software (R Core Team, 2016).
Acknowledgements. The authors gratefully thank  M. Abrous ,  D. Bouix-Busson ,  B. Didier  and  C. Vareille-Morel  for providing their data on the snail populations they have investigated in the Haute Vienne department during their studies. They are also grateful to several PharmD students:  C. Apostoloff ,  L. Farge ,  C. Granet ,  D. Guichard ,  F. Guy ,  C. Lacourarie ,  S. Nauche ,  L. Vareille  and  F. Xuereb , for their assistance in the field.
Statistical analysis of results All data were analysed using R version 3. 1. 0 (R Core Team, 2013). α was set at 0. 05. Comparison of targeted selective treatment and whole-group treatment sub-groups within each group. Average pre- and post-treatment ADWG as well as parasitological and clinical parameters measured at housing were compared between TST and WT sub-groups in each group using a Mann-Whitney test. Assessment of the treatment effect according to the level of exposure to gastrointestinal nematodes and to the level of abomasal damage. To validate the TST strategy taking into account the different exposure and abomasal damage classes, the evaluation of the treatment effect on posttreatment ADWG was done through a stratified analysis based on the level of exposure and on the level of abomasal damage.
The random effect α j and the residual ε ij were assumed to be normally distributed with mean 0 and variance σ 2 α and σ 2 ε respectively. Residuals and predicted values were plotted to evaluate their heteroscedasticity and their normality. The P values for the fixed effects were calculated for the t-test based on Satterthwaite's approximation for denominator degrees of freedom and the P values for the random effects were based on likelihood ratio test according to the package lmerTest of R (SAS Technical Report  R-101, 1978).
Comparison of growth and parasitological and clinical parameters between groups and between sub-groups The mean values for post-treatment ADWG and parasitological and clinical parameters at housing according to groups are presented in Table  2. A wide range of post-treatment ADWG was observed between the groups (from 336 g/day for G10 to 1 210 g/d for G18). Within groups, no significant difference in terms of pre-treatment ADWG was observed between TST and WT sub-groups (data not shown). Furthermore, the posttreatment ADWG differences were not significant between WT and TST sub-groups except for G19 (+131 g/day for WT subgroup) and G20 (-159 g/day for WT sub-group) (Figure  2a ). At housing, the mean Ostertagia ODR levels varied from 0. 3 to 1. 7, the mean pepsinogen level ranged from 1. 3 to 4.
Acknowledgements The authors warmly thank the people involved in the network of experiment units of  INRA (Installation Expérimentale de Production Laitière ,  UMR 1348 ,  J. Lassalas ;  Unité Expérimentale ,  UE 0326 ,  F. Launay ;  Installation Expérimentale de l'unité SAD-ASTER ,  UR 55 ,  C. Mignolet ;  Unité Expérimentale UEMA ,  UE 1296 ,  P. D'Hour ) and of chambres d'agriculture (Trévarez:  G. Trou ; Derval:  B. Le Danois ; Trinottières:  D. Plouzin ) and the farmers from  Groupement des Agriculteurs Biologistes in Loire-Atlantique and Morbihan  for their huge contribution to this work. Special thanks are also due to  F. Leray  and  E. Blandin  (Oniris). This study was funded by the metaprogram GISA STREP (INRA) and by the  Ecologically Intensive Agriculture Chair (Chaire AEI) (Agrial, Terrena, Triskalia ,  Agrocampus Ouest ,  ESA, Oniris).
Olfactory extracellular recordings. Electroantennogram bioassays were performed using an EAG system (Syntech, Kirchzarten, Germany) consisting of an EAG probe containing pre-amplifier (Type PRG-2), a data acquisition interface board (Type IDAC-2), and a stimulus air controller (Type CS-55). Based on a previous protocol  19  , the antennae of each individual S. cicatricosus were excised and mounted between two metal electrodes in an antenna holder using small droplets of conductive gel (Spectra 360, Parker Laboratories, Fairfield, NJ, USA) and placed under a constant stream of humidified air (flow of 500 ml min -1 ). A Syntech PC-based signal processing system was used to amplify and process the EAG signals. The signals were further analysed using EAG 2000 software (Syntech, Kirchzarten, Germany).
05). Furthermore, the lowest observed effect concentration (LOEC) was determined by an ANOVA design using General Linear Models (GLM). Normality was examined using a Kolmogorov-Smirnov test (P > 0. 05 in all cases). Multiple post hoc comparisons between treatment groups against the control group were made using Dunnet's tests (EAG test: mean of treatment < mean of control). The software STATISTICA v8. 0 (StatSoft Inc, Tulsa, Oklahoma, USA) was used for these statistical analyses. For the pre-lethal test (ataxia), we calculated the total ingestion of each ML until irreversible paralysis of each individual, normalising it by fresh body weight (µg ML g -1 individual). In these analyses, we used individual data (not replicated data). Data sets for each ML were fitted to a three parameter inhibitor vs.
Acknowledgements We thank the staff of  Doñana Biological Reserve (DBR-ICTS ) and  Doñana National Park , especially  D. Paz, M. D. Cobo ,  F. Ibáñez , and  P. Bayón  for logistic facilities for the field work. Financial support was provided by the project  CGL2015-68207-R  of the  Secretaría de Estado de Investigación-Ministerio de Economía y Competitividad.
Specimen processing and culture method RGM medium was prepared at Freeman Hospital Microbiology Department (Newcastle upon Tyne, UK) as previously described by Preece et al. and transported to Saint-Luc University Hospital. Without concentration or prior decontamination step, 100 µl of diluted sputum sample (1:1 with Sputasol, Oxoid Microbiological Products) was inoculated onto RGM medium, and incubated at 35 °C in air. Growth was recorded once a week during 42 days. In parallel, these samples were inoculated into a Mycobacterial Growth Indicator Tube (MGIT™, Becton Dickinson, USA) after in-house 15 min decontamination protocol using N-acetyl-L-cysteine-sodium hydroxide solution (NALC(0. 5%)-NaOH (4%)). Auramine O smear was performed for all specimens and on all positive cultures. After inactivation and extraction steps, identification of NTM was confirmed using the Microflex LT MALDI-TOF MS and MBT Compass software using the standard reference library-Mycobacterium (Bruker Daltonics, Bremen, Germany).
| Skin histology and integrity It has been shown that the integrity of skin explants using MTT and lactate dehydrogenase can be maintained for up to 72 hours  (Jacques, Perdu, Dorio, et al. , 2010; Jacques, Perdu, Duplan, et al. , 2010). Likewise, we confirmed that the integrity of non-treated skin explants were maintenance of skin integrity over 24 hours (human) and 48 hours (pig) using histological analysis. Skin samples were fixed in Bouin's liquid, embedded in paraffin, cut into 5 μm sections and stained with hematoxylin and eosin  (Rijnkels, Whiteley, & Beijersbergen van Henegouwen, 2001). Morphological examinations were carried out using a Nikon eclipse E600 microscope equipped with a Dxm1200 digital camera. Images were collected at 50× magnification using Lucia G version 4. 82 software.
| Statistical analysis The data were analyzed using Graphpad Prism 7 (Graphpad Software, San Diego, CA, USA). Results were expressed as mean ± SEM. For comparison between pig (n = 3 or 4) and human skin (n = 4), data were analyzed using the non-parametric Mann-Whitney U-test. P < 0. 05 was regarded as statistically significant. 3 | RESULTS.
ACKNOWLEDGEMENTS We would like to thank  Sandrine Bruel  at the  MeX team in Toxalim department of INRA (Toulouse, France ) for their help and expertise. HRMS analyses were achieved in the MetaToul-AXIOM platform, which is part of the  French national infrastructure for metabolomics and fluxomics: Metabo-HUB (MetaboHUB- ANR-11-INBS-0010 ). We would also like to thank  Pr Grolleau , head of plastic surgery service in Rangueil hospital (Toulouse) and  Dr Vasse , head of plastic surgery service in L' Union clinic (Toulouse)  for the supply of human skin from cosmetic surgery. We would also like to thank  Mr Zaidi  and his team from  Arcadie Sud-ouest in Montauban, France , for the supply of pig skin. This work was sponsored by  Cosmetics Europe.
An average of 3,306 coding DNA sequences (CDS) were predicted. The genome sequences of 5 B. canis isolates from South America and Europe reported here are a valuable source of information for studying epidemiology of this underestimated infection. Data availability. This whole-genome sequencing project (PRJEB22763) has been deposited in the European Nucleotide Archive (ENA) under the accession numbers UFQW00000000 (UFQW01000001 to UFQW01000033) (strain 09-369-776-1), UEXJ01000000 (UEXJ01000001 to UEXJ01000024) (strain 10469), UEXH01000000 (UEXH01000001 to UEXH01000026) (strain 96-9626), UEXI01000000 (UEXI01000001 to UEXI01000025) (strain 07-2859-6071), and UEXG01000000 (UEXG01000001 to UEXG01000029) (strain 07-2859-6070). The versions described in this paper are the first versions.
ACKNOWLEDGMENTS A. F. V. was supported by the  FAPESP  ( 2014/00889-0 ) and  CAPES  ( 88887. 117958/2016-00 ) programs. The research work was supported by the  UE  project  Bru-EPIDIA  ( 291815-FP7/ERANET/ANIHWA ) and the  European Union Reference Laboratory for Brucellosis.
However, the nonreinnervated horse in the present study had an unstable left arytenoid even though laser ventriculocordectomy had been performed. The main limitations of this study include the lack of a control group and follow-up assessment beyond 12 months. A sham-operated group of horses would allow to better assess the benefit of a successful reinnervation as observed in our client-owned horses and especially to differentiate the impact of the laser ventriculocordectomy to the success of the technique on arytenoid abduction during exercise. However, this was not possible with client-owned horses and would have necessitated experimental animals. Objective performance data in the follow-up period was not obtained as these horses had a heterogenic performance levels. A more homogenic and larger group of horses (especially racehorses) would allow more objective analysis.
Acknowledgements The authors would like to thank the owners and the referring veterinarians that made this study possible and special thanks goes to the former ECVSresidents of  F. Rossignol ,  Dr Antoine Lechartier  and  Dr Amelie Vitte  for their help with the study execution. Furthermore, the authors acknowledge the entire team of the CIRALE, especially  Dr Dagmar Trachsel  and  Ms Marie Martin  for her help with the treadmill tests.