dataesr/scientific-paragraphs-categorization huggingface dataset:
Counting of fluorescent colonies was performed using the Leica Application Suite software (Leica). The identification of colonies was confirmed by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) (Bruker Daltonics, Bremen, Germany) as previously described  65. Testing atmosphere conditions for culturing M. ulcerans. The first step consisted in the culture of M. ulcerans under different conditions. For each M. ulcerans strain, a 100 µL-volume of a 10 5 AFB/mL suspension corresponding to 10 4 AFB was cultured in triplicate onto Middlebrook 7H10 medium supplemented with 10% (v/v) OADC and 0. 5% (v/v) glycerol then, incubated at 30 °C under four different atmospheric conditions. The atmospheric growing conditions were artificially created by the use of sealed plastic pouch that can hold ten Middlebrook 7H10 medium poured in 55-mm diameter Petri dishes.
The 55-mm plates were incubated at 30 °C in microaerophilic atmosphere. Five days, ten days, fifteen days, twenty days and thirty days after inoculation, colonies were observed by a MZ-FLIII fluorescence microscope (Leica, Nanterre, France) equipped with a GFP filter and an ICA digital camera (Leica) to detect mycobacterial autofluorescence  64. Counting of fluorescent colonies was performed using the Leica Application Suite software (Leica)  64. Identification of colonies was confirmed by MALDI-TOF-MS as previously described  65, 67  and by rpoB gene sequence analysis  63.
Cultures and negative controls were examined at day 3, day 7 to appreciate the quality of the decontamination method and quality of the cultures. Colonies were counted at day 15 and day 30 using the Leica Application Suite software as described above. For the treatment of samples for seeding, water samples without and with plants debris were concentrated by centrifugation at 1,700 g for 15 min and the supernatants were removed. The resulting pellets from water without plant debris were suspended in PBS before decontamination. The resulting pellets from water with plant debris were suspended in PBS and mechanically disrupted with silica beads (0. 5 mm diameter) and the obtained suspensions were transferred into 50 mL Corning Falcon conical centrifuge tubes before decontamination. 500 mg aulacode feces added into 50 mL Corning Falcon conical centrifuge tubes containing 5 mL of PBS were mechanically disrupted with silica beads (0.
Acknowledgements The authors thank  Bernard Davoust ,  José Gómez Peñate ,  Augustin Kouakou-Adonis ,  Marcelin Assié ,  Sylvestre Dizoé ,  Djanwai B. Konan  and the  "Centre médico-social Walé" (Yamoussoukro)  for their kind cooperation; and  Olga Cusack  for editing the manuscript. This study was supported by  ANR Méditerranée Infection   10-IAHU-03.
1 ng/ml) serum testosterone concentrations and absence of penile spikes. Cat 1 was hit by a car and died 25 months PT. Not all periodic checks could be made owing to lack of owner compliance; as a consequence, for example, serum testosterone in the first week PT could be measured only on four cats. Also, not all clinical observations could be made independently by two different operators. All cats were in good health during the study and none showed any treatment-related side effects. Cat weight, post-GnRH serum testosterone concentrations, testicular size, presence of penile spikes, semen quality and reproductive behaviour during the study are shown in Tables  1 2 3. In 1/16 cats (cat 13) penile spikes never fully disappeared and testosterone always responded normally at every GnRH test, despite reproductive behaviour not being displayed for >1 year PT (400 days); therefore, this cat was considered as a non-respondent and its data were not included in the statistical analysis.
Histology and Fluorescence In situ Hybridization (FISH) At 96h post-infection lungs were inflated with 4% PFA and fixed overnight at 4˚C. Paraffinembedded tissue blocks were cut into 7 μm sections and stained with hematoxylin-eosin (HE). Images were acquired with the AxioScan. Z1 (Zeiss) using the Zeiss Zen2 software. FISH staining was performed as follows. Paraffin lung sections were deparaffinized, rehydrated in PBS and covered with a solution of lysozyme at 10 mg/ml in PBS during 30 min at 37˚C. Slides were then washed twice in PBS, preincubated 30 min at 42˚C in hybridization buffer (20 mM Tris-HCl [pH 8], 0. 9 M NaCl, 0. 01% SDS, 30% formamide) and incubated overnight at 55˚C in hybridization buffer containing 50 nM of the pan-bacteria probe Eub338-Alexa555 5 0 -GCTGCCTCCCGTAGGAGT-3  [30].
Images analysis The number of Mikulicz cells was estimated from HE stained sections by manually segmenting region containing high number of Mikulicz cells in Zen Blue software (Zeiss). Regions containing Mikulicz cells within dense infiltrate of inflammatory cells were not included. Mikulicz cells-containing region was quantified as % area of the total lung area. The number of bacteria present in the tissue section was quantified from fluorescence images using the Fiji plugin TrackMate  [31]. Bacteria were defined as spots of 1. 5 μm after Laplace Gaussian fitting.
This work was supported by funding from the  European Union Seventh   Framework Programme Marie Curie Initial Training Networks  ( FP7-PEOPLE-2012-ITN ) for the project INBIONET (http://inbionet. eu/)under grant agreement  PITN-GA-2012-316682  (BC), from the  Fondation pour la Recherche Medicale (BC) , from the  Fundacao para countries a Ciência e a Tecnologia from  Portugal (ASA) , from the  French Government 's  Investissement d'Avenir program Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases " (grant  ANR-10-LABX-62-IBEID ), from  Infrastructure d'Avenir en Biologie et Sante"France Life Imaging" (grant   ANR-11-INBS-0006 ) and  France-BioImaging  supported by the  French National Research Agency  ( ANR-10-INBS-04 )". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Acknowledgements The study was funded by a grant from the  Belgium Institute of Tropical Medicine  through collaboration with the  University of Pretoria  and research funds from the  University of Pretoria. The authors wish to acknowledge the assistance of the  Mpumalanga Veterinary Services  and specifically the animal health technician  Gypsey Mathumbo , environmental monitor  Godfrey Tsela  and veterinarians  Drs Oupa Rikhotso  and  Bjorn Reininghaus. The  Hans Hoheisen Wildlife Research Station and Hluvukani Animal Clinic  and staff are acknowledged for their assistance in the study.
After a further resting time of at least 30 minutes, dogs were auscultated by a veterinary cardiologist (MM) and an echocardiographic assessment in lateral recumbency with a simultaneous lead II electrocardiogram (Vivid I, with 6S phased array probe, GE Healthcare, France) was performed in accordance with standard recommendations by another cardiologist (IB) to establish baseline values before sedation  [16]. Echocardiographic data were recorded by a single blinded third cardiologist (TR) for offline measurements. Measurements obtained from R-R interval over three consecutive cardiac cycles were averaged and compared to control values. Pulse rate was also registered independently every 5 minutes throughout. The echocardiography was always performed in the same order: 1) right parasternal window: right parasternal four-chamber long-axis view, right parasternal five-chamber long-axis view, right parasternal short-axis transventricular and transaortic view, and modified parasternal short-axis view, 2) subcostal view, 3) left parasternal window: left parasternal four-chamber long-axis view; left parasternal five-chamber long-axis view and a modified left parasternal short-axis view.
Mitral valve annulus velocities were measured from a left apical four-chamber view with Tissue Doppler Imaging (TDI). In order to measure the peak early diastolic lateral (E' lat ), the peak early diastolic septal (E' sept ), the peak late diastolic lateral (A' lat ) and the peak late diastolic septal (A' sept ) mitral valve annulus velocities the sample was placed successively on the septal and the lateral mitral valve annulus. The collected data were used to calculate the following ratios: E/A, E/E' lat , E/E' sept , E' lat /A' lat , E' sept /A' sept. Sedation. After completion of the echocardiography, dogs were allowed to rest for an hour and were then injected 4 mg kg -1 alfaxalone (Alfaxan, 10 mg ml -1 , Dechra-Jurox, UK) intramuscularly (IM). The drug was administered at two injection sites in the caudal lumbar muscle (T0), since the total volume exceeded 0.
Cardiopulmonary data The HR, respiratory rate (fR), oxyhemoglobin saturation (SpO 2 ), oscillometric non-invasive blood pressure (NIBP) and rectal temperature (T˚C) were monitored using a pre-calibrated monitor (Vetcare, B. Braun, Germany) at baseline and every five minutes after alfaxalone injection until the dog stood up. Arterial blood gas analyses were performed at T+5, T+20, and T+35.
No significant difference was observed in E velocity, E/A, EDT, V pulm max, A velocity, E'sept/A'sept, IVRT and E/IVRT. A local false discovery rate was also calculated using 24 variables (excluding the ratios as composite variables) with a cut-off of 0. 01 and obtained the same three variables (EDV, E'sept, and V Ao max) that were significantly different with the Bonferroni correction. Mild tricuspid regurgitation was present in all dogs. The peak velocity of the TR could be measured in all dogs but one after sedation because the flow profile was poorly defined in that dog. Mild pulmonary regurgitation was present in 6 dogs at baseline and in 8 dogs after sedation. None of the recorded maximum velocities were indicative of systolic and/or diastolic pulmonary hypertension according to previously published data (> 2.
[20]  was chosen to evaluate sedation in our patients. Taking into account posture, appearance, interactive behaviour, restrainability, response to noise and general attitude, this subjective score was made to be as discriminating as possible. We expanded the existing score to include the response to shoulder touch, as used in a sedation score by Smith et al. [26]. It should be noted that the sedation scores obtained after IM injection have a great individual variability. This is evident from the wide range of each data (Table  1  and Fig   In our study, times of sedation were similar to those observed by Tamura et al. [10]  after alfaxalone 5 mg kg -1 IM (VFMT: 28 ± 10 minutes vs 26 ± 18 minutes; HLT: 31 ± 8 minutes vs 37 ± 28 minutes, DecT 42 ± 14 minutes vs 36 ± 28 minutes, respectively), except for UST (48 ± 12 minutes vs 84 ± 31 minutes, respectively) and RecT (16 ± 8 minutes vs 34 ± 8 minutes, respectively).
Acknowledgments We would like to thank  Dr. Mehdi Midoun  and SCIL for lending us the echocardiograph and  Dechra and Jurox  for providing us with alfaxalone and for their financial support. We would like to thank  Dr. Benoit Rannou  from the  biochemistry department of Vetagro-Sup  for sponsoring the pre-operative blood work and  Mr. Guillaume Noel  from the  Institut Claude.
Before loading into the GC autosampler a mix of a series of eight alkanes (chain lengths: C10-C36) was included. Analyses were performed by injecting 1 mL in splitless mode at 230°C (injector temperature). The chromatographic separation was performed in helium as a gas-carrier at 1 mL min -1 in the constant flow mode and using a temperature ramp ranging from 80 to 330°C between minute 2 and 18, followed by 6 min at 330°C. Ionization was made by electron impact at 70 eV and the MS acquisition rate was 20 spectra s -1 over a m/z range 80-500. Peak identity was established by comparison of the fragmentation pattern with available MS databases (NIST), using a match cut-off criterion of 700/1000 and retention time using the alkane series as retention standards. The integration of peaks was performed using the LECO Pegasus (Garges-lès-Gonesse, France) software.
Pairs of primers for each targets genes were designed using the Roche Real Time ready (UPL probes) configurator tool. Expression stability of reference genes was assayed using GeNorm software application, which allows selecting the two most stable housekeeping genes, GAPDH and PGK1, in our model. For each gene, quantitative RT-PCR was performed in triplicate. Data from target genes were normalized with two selected reference genes. Data were analyzed using the ∆Ct method  (Pfaffl, 2001)  after validation of each triplicate (i. e. elimination of outliers from triplicate with a standard deviation above 0. 3). We examined the impact of DDT and PMT on the expression of selected genes: genes of the estrogen pathway (ESR1, CYP1A1, CYP2A2, CYP2A1, HSD17B2), lipid, sugar metabolisms (PCK, CPT1A1, HMGSC2, ACSS2, HSPA5), hepatic metabolism (PXR, CAR, CYP2B1, CYP3A1, CYP2B3, CYP2D1, ESD, CES3), inflammatory response (IL1A, IL1B, IL6, TNF, TGFB3), and oxidative stress (NFE2L2, GCLC, GCLM, GPX2, GSS, GSTA2, SOD1, SOD2).
Statistical analyses and Biomarker identification A C C E P T E D M A N U S C R I P T The multivariate data analysis was performed with the SIMCA-P 13. 0 software (Umetrics AB, Umea, Sweden). The supervised OPLS-DA was carried out to discover best discriminators between the groups. Metabolites that best discriminate treated group from control samples were identified using loadings along axis 1 (discriminating) and the variable importance for the projection (VIP). All other statistical tests (Mann and Witney test, Student t-tests, hierarchical clustering and two-way ANOVA) were performed using MeV 4. 9 open source software  (Saeed et al. , 2003). The metabolites with significant changes in the groups (P < 0. 05) were selected as biomarkers. The pathways analysis of potential biomarkers was performed with MetaboAnalyst 3.
On the one hand, in the absence of exhaustive datasets, this method depends heavily on the farms selected for observation and is not sensitive to the contextual market situation. On the other hand, the proposed approach might help farmers decide how to adapt their management practices to market changes because health standards account for input and output prices. For a given livestock system (P FTP,h,t = 0 = 30% for instance), Optimal_P FPT changed depending on the labour costs (Tables  2  and 3 ) and the prices of products (S4 Fig). The use of observational methods (and not economic optimisation reasoning) to define health standards might not allow for reactions to agricultural price volatility, which is an increasing tendency in a liberalised economy. P mortality and P morbidity were not highly sensitive to changes in labour cost or product price.
Segregation between the sexes or related to age and/or reproductive status is common in many animal taxa, particularly in dimorphic species. The causes of this segregation remain difficult to disentangle, despite numerous attempts. This is probably due to the difficulty of obtaining sufficient data on animal behaviour (e. g. habitat use, activity budgets) and group composition (age/sex and reproductive status) during the various phases of the species' reproductive cycle. Based on an intensive long-term monitoring of a Mediterranean mouflon, Ovis gmelini musimon x Ovis sp. , population, we concurrently assessed five hypotheses for segregation linked to forage selection (FSH), reproductive strategy (RSH), social preference (SPH), activity budget (ABH) and weather sensitivity (WSH). We found marked segregation between most age/sex classes.
, 2016; Aublet, Festa-Bianchet, Bergero, & Bassano, 2009; Conradt et al. , 2000; Garnick, Di Stefano, Elgar, & Coulson, 2014; Shrestha et al. , 2014). To tease apart the relative contribution of habitat, social and climatic factors for explaining segregation, we analysed a large data set composed of more than 7800 spatially explicit observations of groups of the polygynous, dimorphic Mediterranean mouflon, Ovis gmelini musimon x Ovis sp. , in the south of  France, between 1994 and 2014. We combined this data set with detailed information on the activity states of each individual recorded from almost 3000 scan observations of these groups, between 1996 and 1997. We first assessed the temporal patterns of segregation in relation to sex, age and reproductive status of females. We then investigated the degree to which differential habitat use and weather conditions drive this pattern.
<H2>Observational data A total of 7880 individuals/groups of mouflon were observed over the year during two periods: 1994-1996 (period 1; N = 3783;  Cransac et al. , 1998; Martinetto, Cugnasse, & Gilbert, 1998)  and 2002-2014 (period 2; N = 4097). Data were collected during repeated foot surveys along predefined footpaths and from fixed points, covering the study site. Observations were performed during daytime, from sunrise to sunset, with an observation peak during the 2 h following sunrise and the 2 h before sunset. Mouflon were observed at a distance (50-1000 m) using binoculars and spotting scopes (x10-60). For each observation, the group size, its composition in terms of age/sex classes (see below) and its location were recorded. We considered an individual or a group of individuals at >50 m from other mouflon as separate groups.
<H3>Differences in activity budget as a driver of segregation Finally, we computed the synchronization coefficient developed by  Conradt (1998a)  on our activity data recorded in 1996-1997. We considered individuals that were eating, moving and vigilant as active. The synchronization coefficient ranges from 0 (no synchronization of activity within groups) to 1 (complete synchronization). This coefficient was computed with data recorded from March to November for (1) females only, adult males only and mixed groups; (2) groups of males, considering all groups composed of males of similar age class (i. e. groups of adults, of young adults and of yearling males) and groups composed of males of different age classes. We computed synchrony also for (3) groups of females with lambs (i. e. groups with Nlambs≥ Nfemales), females without lambs and mixed (i.
Acknowledgments We are grateful to all the professionals from the  Institut National de la Recherche Agronomique  (N. Cransac), the  Office National de la Chasse et de la Faune Sauvage  ( K. Martinetto ,  E. Marty ,  C. Itty ,  J. Duhayer ) and all the trainees for data collection. We also warmly thank  Marina Tronchot  for providing the vegetation map and  Météo France  for providing the weather data. Thanks to two anonymous referees for their useful and relevant comments allowing us to improve the manuscript.
Investigation of the possible impact of a univariate outcome variable in risk factor analyses is needed. In order to assess this impact, multivariate statistical methods have to be applied to analyze different outcome variables simultaneously, while at the same time investigating multiple risk factors for all of these outcomes. Therefore, the objectives of this study were (1) to identify possible influences on plumage condition and (2) to analyze and discuss possible advantages of the use of plumage conditions of different body parts as outcome variables in a multiblock redundancy analysis for assessing these influences. Results were compared with whole body plumage scores as an outcome variable, using data collected from a German project on farms keeping laying hens in aviaries. To illustrate the challenges encountered in the interpretation of the findings, different possible influences on the plumage condition of laying hens for all body parts (including the head) were considered.
Data Collection and Management To ensure consistency in data collection, standard operating procedures were determined for the health and behavior assessments and the measurements of hygienic conditions of the air and housing equipment. Data on general farm management  (light program, feed, hygiene, personnel, etc. )  and animal/flock characteristics (e. g. , breed) were collected by trained observers in personal interviews with farm managers or owners (i. e. , decision makers) using a standardized questionnaire. Data on housing conditions were measured or scored by trained assessors during farm visits. Productivity data were collected by an economics expert in personal meetings after the end of the laying period. The data collection sheets comprised more than 1,000 items in total. All of the data collection sheets were pilot tested on 6 farms and then were modified to their final forms.
Data were collected according to farm, hen house, and flock, the last representing the experimental unit. Additionally, plumage damage was assessed in 100 hens per flock. Inter-observer agreement was assessed and assured using the exclusion test, which is based on kappa coefficients  (Ruddat et al. , 2014). All of the data were kept in a Structured Query Language database, except the economic data, which were digitized in Microsoft Excel TM , Redmond, WA. The plumage of 6 different body parts (neck, back, breast, vent, wing, and tail) was scored according to the Here, a dichotomous score was chosen, with 0 indicating a head with complete plumage and 1 representing damaged feathers, nude parts, or a completely nude head. More detailed scoring was considered difficult due to the relatively small feathered area of the head.
Feed efficiency was calculated as the gain-to-feed (G : F) ratio (kilogram BW per kilogram of feed consumed). Growth performance calculated during Period 1 and Period 2, blood metabolites and immune variables measured at each sampling time, and the overall score values of pulmonary were analysed with a linear mixed model (PROC MIXED procedure, SAS software; SAS Institute Inc. , Version 9. 4, Cary, NC, USA). The statistical analyses were carried out separately for each period. The model included the effect of the hygiene conditions (poor or good), line (LRFI or HRFI), replicate (one or two) and sex (male or female) as main effects, and all significant two-way interactions with the pair as a random effect. The experimental unit was the pair of pigs for testing line effects, and the pig to test the hygiene effect and the corresponding interactions.
General observations Data of total of 157 pigs were finally kept for the statistical analysis. One animal died from acute diarrhoea soon after the beginning of the experiment (good-HRFI group). Two animals were euthanised, one for a rectal prolapse (poor-HRFI group) and one due to an unexplained weight loss (good-LRFI group). In poor conditions, five animals had feed spillage behaviours and therefore they were removed from the analysis of feed consumption and feed efficiency. During Period 1, the following clinical signs were recorded at least once: sneezing and coughing (16 pigs in poor conditions and eight in good conditions); anaemia (one pig in poor conditions, treated with vitamin K), hyperthermia (one pig in good conditions, treated with flunixin), umbilical hernia (one pig in good conditions), lameness (two pigs in good conditions, treated with flunixin).
Acknowledgements This study has received funding from the  European Union 's  Seventh Framework Programme  for research, technological development and demonstration under grant agreement No. 613574  ( PROHEALTH  project). The authors are grateful to the staff of the laboratory and experimental pig facilities from  INRA UMR PEGASE and GenESI as well as M. Hassouna (UMR SAS Rennes)  and  S. Lagadec  ( CRAB Rennes ). A. C. was funded by  INRA Phase division, Region Bretagne  and PROHEALTH.