dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analysis Statistical analyses were performed to compare the values for BWG and pathophysiological measurements in the four experimental groups (using both T and NT controls as positive and negative indicators). For the parasitological parameters (namely EPG, worm counts and female worm fertility), the statistical analyses were restricted to the three infected groups (namely NT, CAR and S groups). The group treated with AH (T group), although FECs were also recorded in the same time intervals to ensure efficacy, was excluded from this analysis. In addition, the values of FECs, worm burden and fertility of females data were log 10 (X + 1) transformed before statistical analysis in order to normalize the distribution. Lastly, the analyses of worm fertility were restricted to H. contortus because of the patchy distribution and insufficient number of T.
colubriformis worms in many lambs of the different experimental groups. All analyses were performed by using SYSSTAT 9. 0 Software. AUC values for the EPGs of each animal were calculated using Graphpad Prism software for Windows (version 5. 01). AUC values were compared by using one-way analysis of variance (ANOVA) and post hoc comparisons with Bonferroni adjustment. For the worm counts (H. contortus, T. colubriformis and total number [total of both nematode species]), the differences in worm burden mean number and fertility were examined by using ANOVA after log (WN + 1) transformation of the data. Similarly, an ANOVA 2 was applied to examine the differences in egg count per female H. contortus worms taking into account the treatment and the individual animal. To compare the differences in body weight gains, ANOVA was performed on the BW rates calculated between D-7 and D63.
7% increase in live weight gain compared to the control ones. This last result confirmed previous ones obtained by comparing sainfoin and lucerne groups in ruminants  [44]. Two pathophysiological measurements were performed to evaluate the impact of carob pods and sainfoin hay on host resilience, in order to withstand the negative effects of GINs. They were respectively related to Haemonchus (PCV) and Trichostrongylus (serum inorganic phosphate) infections. Statistical differences in the mean PCV values were found throughout the assay with, overall, higher values in the S and T groups compared to the CAR and NT lambs. These results with sainfoin tend to confirm previous data suggesting positive effects of the consumption of tannin-containing legume forages on the resilience of animals  [25, 29].
Acknowledgements. This study was supported by funding from  Marie Curie Research Fellow  ( Healthy Hay  Project) and  COST-STSM-FA0805 -CAPARA -project. The authors also gratefully acknowledge funding from the  European Community  financial participation under the  Seventh Framework Programme for Research, Technological Development and Demonstration Activities , for the  Integrated  Project  LOWINPUTBREEDS FP7-CP-IP 222623. The views expressed in this publication are the sole responsibility of the author(s) and do not necessarily reflect the views of the  European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use which might be made of the information contained herein.
In addition to the 9 states reported in this study, Iowa has also had a recent detection of PorCoV HKU15 (3). Thus, PorCoV HKU15 has been detected in 10 of the 50 US states, and those 10 states mainly cluster in the midwestern United States  (Figure). As with data collected for porcine epidemic diarrhea outbreaks by the US National Animal Health Laboratory Network (http://www. nahln. org/default/), data collected on the geographic location and numbers of PorCoV HKU15 cases is also required to be reported weekly. Earlier reports support avian coronaviruses as the gene source for Deltacoronavirus spp. (1, 4). To confirm this, surveillance for PorCoV should be carried out among birds. Moreover, effective control strategies, including vaccine development, should be in place for prevention and control of infections caused by PorCoV HKU15.
Data from a cohort study were first used to characterize MDAs (IgG) kinetics in the early life of piglets (up to 14 weeks of age) and to estimate the distribution of the duration of passive immunity. A second dataset derived from a longitudinal study in 6 Spanish pig-herds  [23]  was then analyzed, accounting for previous estimates of MDAs waning time, to estimate forces of infection from herd-specific HEV prevalences.
Parameters were estimated using MLE and the SAEM algorithm for the analysis of hierarchical nonlinear mixed-effects models  [25]. Individual antibody kinetics were derived from the individual empirical parameter estimates. Subjects with antibody levels below the cut-off value of the ELISA test were considered seronegative (HEV ELISA 4. 0v, MP Diagnostics,Illkirch,France,  [26] ). Different distributions were tested to model the time to immunity waning (Weibull, lognormal and gamma distributions). Distribution parameters were estimated using the maximum likelihood method and model selection was based on the AIC values. A nonparametric bootstrap procedure was used to determine the 95% confidence intervals for the parameter estimates and thus measure their accuracy. One thousand bootstrap replicates were generated by resampling individual profiles for each dataset.
Application to Hepatitis E virus transmission in pigs No data were specifically collected for the present analysis. Data were available from previous field studies which were described in references  [23]  and  [28]. Passive immunity duration. Serological data, used to estimate the duration of PI, were derived from a longitudinal epidemiological study on HEV prevalence in France  [28]  by monitoring 120 piglets, from 3 consecutive batches in one herd known to be infected by HEV, from birth to 14 weeks of age. Ten sows were chosen at random from this herd and from each followed batch. One week post-farrowing, 4 piglets born to the selected sows were chosen at random and ear-tagged. At the same time, blood samples were collected from the sows to determine their serological status with regard to HEV infection.
ð4Þ Analyses were performed according to the manufacturer's instructions except that 10 ml of sera were used. Samples were considered positive when the OD450 value of the sample was above the cut-off value (Co = mean of the negative control + 0. 300). Impact of passive immunity on transmission. The forces of infection in the presence and absence of PI were estimated from data provided by Casas et al. [23]  because these data had shown evidence of early infections occurring in young piglets in the presence of residual maternal antibodies. Briefly, 6 farrow-to-finish Spanish swine herds of similar size (100-300 productive sows) and known to be infected by HEV were included in the study. In each farm, 20 piglets from 6 previously selected sows, were randomly selected and ear-tagged and serial blood samples were collected at 3, 7, 13, and 18 weeks.
Data from a longitudinal survey in France were used to characterize the kinetics of maternally-derived antibodies in 120 piglets. The serological titers of piglets at 1 week of age were highly correlated with those of the dam, thus supporting previous observations  [37, 38]. The duration of PI was modeled by a gamma distribution with a mean duration of 45. 6 days  [41. 4; 50. 4]. Although the duration was slightly shorter than in several epidemiological studies (8-9 weeks of age)  [19, 37, 38] , because of the gamma distribution, the probability of remaining passively immune fell below 0. 1 by 60 days of age, as in these previous studies. In a recent study, the transmission parameters for hepatitis E virus in pigs were estimated from field data and the effectiveness of different hypothetical control strategies (early life vaccination and delayed vaccination around 10 weeks of age) was evaluated  [18].
Moreover, only 20 piglets in each herd were sampled to establish the herd-specific seroprevalence profiles, which might have led to considerable uncertainty, especially if prevalence was low. These considerations are supported by the good concordance between the estimates and the data from 7 weeks of age onwards. In herd 2, the prevalence increased slowly, continuously and exponentially. Indeed the cumulative prevalence observed at slaughter age was about 50%. As the level of PI was similar to that of the other herds, this difference reflects a low infection pressure which might be due to differences in husbandry practices and herd structure. In models with a single force of infection, the inverse of the force of infection corresponds to the average age at infection  [41]. However, this relationship cannot be applied to the full model due to the interplay between piglet serological status and the differential forces of infection.
This study was funded by the  French Research Agency (ANR)  as part of the  research project called ''HEVECODYN''  ( ANR-10-CESA-0010 ; http://www. agence-nationale-recherche. fr/en/anr-funded-project/?tx_lwmsuivibilan_pi2[CODE] =  ANR-10-CESA-0010 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data collection In-depth interviews were conducted by the same person at the participants' location of choice (office or home) from October to December 2012. At the beginning of the interview, the aim and background of the study were recalled, as was the confidentiality of the interview. These issues were presented in a document that was given to each participant. In accordance with  [18] , participants were again asked to provide verbal informed consent prior to the interview. It was made clear that by agreeing to be interviewed, they were agreeing to be part of the study. All participants agreed to the interview being recorded. Interviews lasted between 50 and 105 minutes. Through open-ended questions, the interviewer asked the farmer or veterinarian to talk about their knowledge of abortive diseases, their perception of this issue, and the difficulties and barriers to participating in the surveillance system (Table  1 ).
This work was supported by the  National Institutes of Health   R01  grants  AR050087  and  AR055655  (to MVR). CM received funding from the  People Program  ( Marie Curie Actions ) of the European Union's  Seventh Framework Program  (FP7/2007-2013) registered under the  Research Executive Agency  grant agreement  no300388. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Whereas this approach can be applied in any clinical field, as a case of outstanding importance and great concern for zoological institutions, we selected foot bone pathologies in captive rhinoceroses to demonstrate the manifold applications of the method. Several advances were achieved, endowing the wildlife clinician with all-important tools: prototype DR exposure protocols and a modus operandi for foot positioning, advancing both traditional projections and, for the first-time, species-related radiographic views; assessment of radiographic diagnostic value for the whole foot and, in premiere, for each autopodial bone; together with additional insights into radiographic appearance of bone anatomy and pathology with a unique, simultaneous CT-DR correlation. Based on its main advantages in availing a wide range of keystone data in wildlife imaging from a limited number of examined subjects and combining advantages of CT as the golden standard method for bone diseases' diagnostic with DR's clinical feasibility under field conditions, synchronized CT-DR presents a new perspective on wildlife's health management.
Computed tomographic data acquisition and imaging Computed tomographic data was acquired from all ten distal limbs using a high-resolution, 128-slice scanner (Aquilion CX, Toshiba Medical Systems Cooperation, Tochigi, Japan). Settings for the CT helical scan protocol were: 120 kV, 100-300 mA, 0. 6 s rotation time, helical pitch HP 41. 0 and 0. 5 mm acquisition slice thickness. Reconstruction protocols included two soft tissue reconstructions (body-standard and body-sharp) and a highresolution reconstruction algorithm for bones. The reconstruction slice thickness/slice interval of both was set to 1/0. 8 mm and 0. 5/ 0. 25 mm. Vitrea workstation with ViTREA 2 version 4. 0 medical diagnostic software (Vital Images Inc. , Minnetonka, MN, USA) provided the tools for two-dimensional (2D) and three-dimensional (3D) processing and analysis of the CT images.
Synchronized computed tomography and digital radiography Fully rendered volumetric (3D) CT images were acquired from all ten feet. Based on a predefined sectional plane of the object, synchronized X-ray projections were calculated and generated by applying specialized software tools on the image console. For each foot, eight 3D CT images (45u apart) equivalent to eight standard radiographic views were generated. In order to simulate DR views, the acquired CT datasets were used to generate renderings from 8 different viewing directions for each foot. Thus, each 3D CT image was transformed into a synchronized digital radiographic image (Synch DR), in total eighty Synch DR images for all ten feet (Fig. 1 ). The standardized nomenclature for radiographic projections in veterinary medicine was used  [37, 38].
Statistical analysis Statistical analysis was performed using PASW Statistics 18 (formerly SPSS, IBM Inc. , Chicago, IL). The Chi-square goodness-of-fit exact test was used to test whether the observed proportions for categorical variables differ from the hypothesized equal distribution. Rhinoceros 1 suffered from epidermoid carcinoma on the only limb available from this animal. As this tumor may have been the cause for at least some of the osteopathologies found in this foot and thus may have biased the statistical analysis, we have also analyzed our data after excluding this animal. Results indicate no biasing effect of rhinoceros 1 as none of the comparisons changed in a way that alter our findings (data not shown). Results are therefore shown for all four rhinoceroses combined. A P-value ,0.
Tools offered by synchronized computed tomography and digital radiography The main advantage of Synch CT-DR is its capability to provide a wide range of keystone data in wildlife imaging from a limited number of examined subjects. Additionally, it combines the advantages of CT as the golden standard method for bone diseases' diagnostic with DR's clinical feasibility under field conditions. Several advances were achieved from this pioneering approach, providing the wildlife clinician with all-important tools: a) Prototype digital radiographic exposure protocols and a modus operandi for foot positioning, advancing both traditional projections and first-time, species-related radiographic views; b) Radiographic diagnostic value for the whole foot and, in premiere, for each autopodial bone; c) Additional insights into radiographic appearance of bone anatomy and pathology with a unique CT-DR correlation.
Animals and samples Twenty dairy herds from different regions of Sfax (Tunisia) that experienced reproductive disorders (mainly abortions) from October 2010 to May 2012 were included in this study. Informations on individual animal such as age, sex and abortion history were recorded separately on sample data sheets. Herd sizes ranged from 20 to 1500 cows, knowing that all cows studied in this work are the descendents of pure Holsteins from the national production. All these dairy cows were vaccinated against foot and mouth disease (FMD) during national immunization campaigns. The majority of included cows were kept on limited pastures or tethered on a pasture. Seventy percent of the herds possessed small ruminants, and only twenty percent reported having bought new cattle. In dairy herds, nutrient requirements may not be the same depending on the animal's age and stage of production.
Detection of the amplification product and sequencing Ten ml of each PCR product were electrophoresed in agarose gel, stained with ethidium bromide and observed under UV illumination. The fragments at correct size were excised and further purified for sequencing. Briefly, DNA was extracted using the QIAquick Gel extraction Kit (Qiagen, Courtaboeuf, France), was then subjected to cycle sequencing using the BigDye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems) and processed by the ABI 3100 Genetic Analyzer. The obtained sequences were compared with the sequences available in GenBank by using the BLAST server from the NCBI website (http://www. ncbi. nlm. nih. gov/BLAST).
Statistical analysis The association of abortion with positive results for different agents by real-time PCR and frequencies of positive results between vaginal and milk samples were assessed using the Fisher's exact test. The correlation between real-time PCR and the serological test (RBPT) for Brucella cases was assessed using Kruskal-Wallis test (nonparametric test). In all tests, a p value,0. 05 was considered to be statistically significant. We decided to use a one-sided p value as all the evidence points to the directionality of this relationship only going one way. All tests were conducted using the Graph-Pad Prism 5 statistical package (Graph-Pad Software, San Diego, CA, USA).
Samples showing Ct values above 43 were considered as negative. Interestingly, the mean Ct-value of samples negative for Brucella was significantly lower than that of samples with a strong reactivity, which is lower than that of samples with a weak reactivity (p,0. 0001) (Fig. 1 ). In conventional gel PCR, all positive samples by real-time PCR produced amplicon of 63 bp when resolved on an agarose gel (Figs. S1B, S2A ). All of them were identified as B. abortus based on speciesspecific PCR  [30]. To confirm that positive samples were due to the presence of B. abortus DNA, PCR products were sequenced and analyzed using the BLAST web interface (http://blast. ncbi. nlm. nih. gov/Blast. cgi). The amplicons of these positive samples were found to be 100% identical to the B. abortus gene in the database.
Detection of L. monocytogenes L. monocytogenes DNA was detected in 7/150 (4. 66%) vaginal swab samples all obtained from the 150 cows that suffered of an abortion (OR = 6. 74, 95% CI [0. 37-119. 9], p value = 0. 08) (Table  3 ). Only 3/150 (2%) milk samples were found to be positive (Table  3 ). These cases originated from different herds in different regions of Sfax. All control samples remained negative by real-time PCR. The real-time PCR melt curve data identified one peak with a melting temperature of 87uC for all samples (Fig. S4A, S4B ). In conventional gel PCR, all samples positive by real-time PCR produced amplicon of 63 bp when resolved on an agarose gel 3% (Fig. S4A, S4B ). To confirm that positive samples were due to the presence of L. monocytogenes DNA, PCR products were sequenced and analyzed using the BLAST web interface (http:// blast.
Detection of Salmonella spp. Salmonella DNA was detected in 5 (3. 33%) milk samples all obtained from the 150 cows that suffered of an abortion (OR = 4. 87, 95% CI [0. 26-89. 5], p value = 0. 1658) (Table  3 ). No salmonella DNA was detected in vaginal swab samples (OR = 0. 08, 95% CI [0-1. 6], p value = 0. 0302) (Table  3 ). These cases were collected from the same herd located in the southern region of Sfax. The real-time PCR melt curve data identified one peak with a melting temperature of 76uC for all samples (Fig. S5A ). In conventional gel PCR, all positive samples by real-time PCR produced amplicon of 243 bp when resolved on an agarose gel 1. 5% (Fig. S5B ). To confirm that positive samples were due to the presence of Salmonella spp. DNA, PCR products were sequenced and analyzed using the BLAST web interface (http://blast.
4%), soya bean husks (5%), sugar cane molasses, pomace, vitamin and mineral premix. 20°C using a fixed voltage of 2500 V. Then, ~2. 5 ng/µl of denatured purified PCR product were applied per well and electrophoresed for 15 h at 45°C using a fixed voltage of 2500 V on an 4300 DNA Analyzer (LI-COR Biosciences, Lincoln, USA). The data were analysed using the 1D-Scan software (ScienceTec)  (Ranjard et al. , 2003).
Statistical analysis The DNA extraction data were processed by ANOVA using the MIXED procedure of SAS v9 (SAS Institute Inc. , Cary, NC, USA). The statistical model included DNA extraction method, gut segment and gut segment × DNA extraction method. Effects of individual animals were considered as random variables. Effects were regarded as statistically different at P < 0. 05. ARISA statistical analyses were carried out using R version 2. 9. 2 (http://www. r-project. org). Data obtained from the 1D-Scan software were converted into a table summarizing the band presence (i. e. peak) and intensity (i. e. area of peak) using the PrepRISA program  (Ranjard et al. , 2001). One hundred bands were integrated for each ARISA profile with 2 bp resolution to ensure a robust analysis  (Ranjard et al. , 2003).
According to this, the samples were plotted on the factorial map according to their scores on the first two principle components. The third principle component was not represented on the figure to limit the number of data. Differences between gut segments, DNA extraction methods and gut segment × DNA extraction method were tested by a Monte-Carlo permutation test (1000 permutations). All these analyses were performed with the R software using the ADE-4 package  (Thioulouse and Dray, 2007).
Moreover, these authors did not give any data about the DNA yield obtained by their protocol. Additionally, McOrist et al. (2002)  who used the  Boom et al. (1990)  method to extract DNA from human faecal samples did not provide any data about the DNA yield. The  Yu and Morrison (2004)  method had the better DNA yield, suggesting a higher efficiency of cell disruption, DNA precipitation and elution. According to  Salonen et al. (2010) , DNA yield alone may be an unreliable measure for extraction efficiency and should be complemented by other parameters, such as DNA purity and bacterial diversity. Therefore, in this study, DNA purity was assessed spectrophotometrically. The  Yu and Morrison (2004)  method yielded more pure DNA extract compared with  Boom et al. (1990). No difference was observed between ARISA profiles whatever the DNA extraction method, suggesting that neither method induced bias in DNA bacterial community extraction.
Statistical methods Data collected at the individual trial sites were pooled and analyzed descriptively and statistically. Nonparametric statistical tests were used to perform comparisons between groups. All qualitative data (qualitative oocyst excretion, incidence and prevalence of diarrhoea) were tested with Fisher's exact test. The quantitative data (quantitative oocyst excretion, body weight, age) were tested with the Mann-Whitney test. Growth performance was analyzed by calculating weight gain between the end of the study period (SD78) and the day of treatment (SD1). A multiple linear regression model with mixed effect was used to compare average daily gain between groups. Effects were considered significant at an error level of 5% (p = 0. 05) or lower.
Acknowledgements The authors thank  Magali Melon  and  Jean-Loïc Martin , from  Elanco France , for their support during the study. Samplings and clinical examination were performed by local French practitioners, faecal oocysts count and species identification were tested by  Laboratoire Vétérinaire Départemental de l'Ariège, rue de Las Escoumes , 09008  FOIX CDIS (France).