dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analysis. The PCV, eosinophilia, FEC, body weight, and parasite burden variables were analyzed by using PROC MIXED of SAS (v. 9. 1, SAS Inst. Inc. , Cary, NC, USA, 2003) considering the challenges (challenges 1 and 2), the genetic status and their interactions as fixed effects. The FEC and eosinophilia variables were log transformed in order to normalize the variances. For all traits, the experimental unit was considered the kid and was included in the model as a random effect. Comparisons between means were tested by the least squares means procedure with adjustment for multiple comparisons (Tukey-Kramer). The results are presented after backtransformation. The data relative to the semiquantitative analysis of cell infiltration were analyzed by using PROC PROBIT of SAS considering the challenges and the genetic status.
Acknowledgments The authors want to give thanks to  H. Varo  and  L. Philibert  for their excellent technical assistance and  C. Barbier  and  F. Labirin  for care and handling of animals. This work was supported in part by  INRA  and by  La Région Guadeloupe. WC was supported by a doctoral fellowship from  Le Conseil Régional de la Guadeloupe. The authors are grateful to the Gardel team in charge of the goat flock:  R. Arquet ,  T. Kandassamy ,  W. Troupé ,  J. Gobardhan , and  S. -A. Matou.
Habitat characteristics The study site represents a gradient of elevation from north to south, corresponding to a similar gradient in human use of the landscape. As home ranges occupied very large and variable areas in the study site (lifetime home range size was on average 839. 506123. 84 [mean 6 SE] km 2 ), we described the landscape with a resolution of 1|1km 2 for every environmental layer (i. e. leading to an average of more than 800 pixels per lynx home range). We used the habitat typology based on the Global Land Cover 2000 database  [42]  to compute the proportion of forest and agricultural fields per square kilometre. Data on road density were obtained from the Norwegian Mapping Authority to define human accessibility. Paved and forest road densities were calculated as the total length of paved and forest roads (km) within each 1|1km 2 pixel, respectively.
This is then equivalent to logit(p i )~½b(x iS {x iL ) , where (x iS {x iL ) is a measure of thirdorder seasonal habitat selection, computed as the difference between home range composition and seasonal use. We can finally rewrite the last model as logit(p i )~½bm i , where m i ~xiS {x iL is the marginality (see above). As for the survival analysis, we proceeded in two steps, using first data collected during the lynx-hunting season only, and second, data all the year round. Again, at each step, we contrasted three different models that correspond to our predictions: 1) a null model with no habitat selection; 2) a model of seasonal habitat selection including environmental factors at the third selection order (P1b); 3) a model of habitat selection differing according to resource availability, including interactions terms between the seasonal use and the lifetime home range composition for each environmental factor (P2b).
Acknowledgments The data collection was conducted within the framework of Scandlynx, the  Scandinavian Lynx Project  (http://scandlynx. nina. no/). We thank many people for letting us work on their land, and all the people that have been involved in catching and tracking radio-collared lynx, often under harsh conditions. We warmly thank  Kamil Barton  ´for his great help in using the MuMIn package. We thank two anonymous referees for helpful comments on a previous draft of this paper. We are also most grateful to  Evelyn Merrill  for her constructive comments.
At various stages of the study, funding was provided by the  Norwegian Ministry of Defence  (www. regjeringen. no/nb/dep/fd. html), the  Norwegian Directorate for Nature Management  (www. dirnat. no), the  Research Council of Norway  (www. forskningsradet. no), the county governors' offices of Hedmark (www. fylkesmannen. no/Hedmark/), Akershus & Østfold  (www. fylkesmannen. no/Oslo-og-Akershus/) and Buskerud (www. fylkesmannen. no/Buskerud/)counties as well as the  Large Carnivore Management Boards  for regions 2 and 3 and the  Norwegian Institute for Nature Research  (www. nina. no). Mathieu Basille  was funded by a PhD grant from the  French Ministry of Research. All funding was provided based on detailed project descriptions submitted by the authors to the various funding mechanisms. Beyond this approval of the proposed study design and methodology, the funders had no input into the data collection, data analysis, interpretation of results, decision to publish, or preparation of this manuscript, with the exception of the occasional contribution to field work from game wardens of the  State Nature Inspectorate  (http://www.
Unlike in elephants, the reported rhinoceroses' foot pathologies have long been known for being confined to soft tissues, such as chronic pododermatitis in Indian rhinoceros  [11, 13, 19] , while Figure  2. Distribution of bone pathologies in rhinoceroses' autopodium. Graphic numerical representation of the pathological bone sites (vertical axis) found in each autopodial element (horizontal axis). For podial elements (carpal and tarsal bones), the number of osteopathologies per bone was small and therefore we included the carpal (n = 7) and, respectively, tarsal (n = 8) joint as one unit. The data was collected from all four hind legs (''Hindleg'') and from all four front legs (''Frontleg''), therefore, for example, ''Ph I-DII'' of ''Hindleg'' represents the first phalanx of the second digit in all four hind legs.
Computed Tomographic Data Acquisition and Imaging Computed tomographic data was acquired from all eight distal limbs using a third-generation, 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 and 0. 5 mm acquisition slice thickness. The reconstruction protocol included both body-standard and bonehigh resolution algorithms with a reconstruction slice thickness/ slice interval of both 1/0. 8 mm and 0. 5/0. 25 mm. ViTREAH 2 version 4. 0 medical imaging software (Vital Images Inc. , Minnetonka, MN, USA) provided the tools for twodimensional (2D) and tri-dimensional (3D) analysis of CT images. We used volume-rendering software, simultaneous imaging of specific anatomical and pathological structures of interest using a combination of 2D orthogonal Multi-Planar Reconstructions (MPR) and 3D images; trim function with 3D and 2D segmentation to focus images on regions of interest, a wide variety of clinical viewing protocols, and fine adjustment of visualization parameters to enhance the diagnostic quality of the images.
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 three rhinoceroses combined. A P-value ,0.
For example, antibacterial activity of valnemulin containing dimethyl propane moiety is more effective than that of tiamulin in vitro as well in vivo  [21, 22]. Previous work in our group has led to the synthesis and analysis of antibacterial activity of 17 semisynthetic pleuromutilin derivatives bearing dimethyl propane moiety  [23]. Based on the bioactivity studies it was proposed that the antibacterial activity of these compounds is connected with the alkaline group at the end of side chain. As a part of our research work on the development of useful synthetic molecules, we have planned to introduce tertiary amine at the end of dimethyl propane moiety attached to the side chain at C-14 of pleuromutilin. Thus, the present study reports the synthesis, antibacterial studies, molecular docking of the synthesized compounds into 50S ribosomal subunit (PDB ID: 1XBP).
Antibacterial activity for all the synthesized compounds was evaluated against the above mentioned four bacterial strains. Oxford cup assay was carried out and the zones of inhibition for different concentrations of the synthetic compounds were measured. Data are reported as diameters of growth inhibition (mm) and the results are given in Table  2. Also pleuromutilin and tiamulin were used as reference drugs. Among all the pleuromutilin derivatives examined, compound 5b showed the highest antibacterial activities than the other  From MIC values and the zones of inhibition it was observed that replacement of the diethyl of tertiary amine (5b) with isopropyl (5a) or dipropyl (5c) resulted in lower antibacterial activities noticeably. While replacement of the piperidine of acetamide (5d) with pyrrolidine (5e) or morpholine (5f) resulted in lower antibacterial activities.
Molecular Docking Study In view of their biological activities and structural diversity, the synthesized compounds 5a-f were subjected to molecular docking study. A PTC ribosome model based on the X-ray structure of Deinococcus radiodurans in complex with tiamulin  [24]  was constructed that consists of all residues 30 A ˚from the PTC binding site. The docking experiments were performed with Homdock software in Chil 2 package  [25]. Dock binding affinities of those compounds were evaluated according to many parameters including: the binding free energies (DG b , kcal/mol), hydrogen bonding or other noncovalent molecular interaction, and RMSD values in comparison to the native co-crystallized ligand. The lowest binding free energies and the lowest RMSD values were considered as the best fitted ones  [26].
As shown in Table  S1  and Figure  4 , all the six compounds are found to bind with the same hydrogen bondings formed between the hydroxyl group of eight-membered ring and residue of G-2484, and between the ester of side chain and residue of G-2044. Moreover, a cation-p interaction formed between tertiary amine of 5b and A-2045 play an important role in increasing the binding affinity. The geometry of the interaction further, confirming that cation-p interactions are strongest when the cation is situated perpendicular to the plane of atoms  [27]. We presume that the conformation of 5b make its tertiary amine perpendicular to the purine ring of A-2045. Although compounds 5c-f also bear a tertiary amine at the terminal of side chain, no cation-p interaction is found by PoseView, a software tool that can automatically create twodimensional diagrams of complexes with known 3D structure according to the docking results  [28].
Molecular modeling The crystal structure of 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin (PDB ID: 1XBP)  [24]  was used for all simulations with Homdock software in Chil 2 package  [25]  combining of a Graph based molecular alignment (GMA) tool and a Monte-Carlo/Simulated Annealing (MC/SA) algorithm based docking (GlamDock) tool. Molecular docking was performed with Homdock software in Chil2 package  [25] , which introduced a similarity based docking. In this study, tiamulin was the template for flexible molecular alignment, and the interaction was optimized by GlamDock according to the Chil 2 Score scoring function based on Chem-Score with smooth, improved potential. All the compounds were prepared with Avogadro software  [30] , including 5000 steps Steepest Descent and 1000 steps Conjugate Gradients geometry optimization based on MMFF94 force field.
The structure was refined with SHELXL program  [32]  by full-matrix least-squares techniques on F 2. The non-hydrogen atoms were refined anisotropically, and hydrogen atoms were determined with theoretical calculations. A full-matrix least-squares refinement gave the final R = 0. 0373, wR = 0. 0869 (w = 1/[s 2 (F o 2 )+(0. 0348P) 2 +0. 2946P], where P = (F o 2 +2Fc 2 )/3), S = 1. 039, (Dr) max = 0. 229, and (Dr) min = 20. 212 e/A ˚3 (see Table  S3 ). PLATON 1. 17  [33]  was used for molecular representations and SHELXL  [32]  was used for packing diagrams.
Mice and cells Six weeks old female C57Bl/6 and BALB/c mice from Jackson Laboratory were used. INSERM guidelines have been followed regarding animal experimentation (authorization No. 02875 for mouse experimentation). Animals were killed by cervical dislocation at appropriate times. Cells were isolated from lymphoid organs (spleen and lymph nodes) of infected and non-infected mice using a mix of type I collagenase (Sigma) and DNAse I (Sigma-Aldrich). Isolated cells were stimulated by CD3 antibody for 4 h at 37°C in the presence of BD Golgi Stop (BD Biosciences). The expression of molecular markers, intracellular cytokines and Granzyme B was then evaluated by flow cytometry. Five mice were used for each infection and the representative data is shown. All experiments were carried out at least 3 independent times.
Flow cytometry Antibodies used for flow cytometry included PerCP-Cy5. 5-CD4, Alexa700-CD8, Pacific blue-CD5, FITC-CD25, PE-CD127, PerCP-Cy5. 5-CD27, Alexa700-CD44, PE-Cy7-CD4, FITC-NK1. 1 (all from eBiosciences). The Aqua Dead Cell Stain (Invitrogen) was used to stain the dead cells. CD4 and CD8 T cells were fixed and permeabilized with Fixation/ Permeabilization buffers (eBiosciences) following manufacturer's protocol. PE-Cy7-IFN-γ (eBiosciences) and APC-Granzyme B (Invitrogen) antibodies were used for the intracellular labeling of lymphocytes. Isotype matched controls were used appropriately. At least 100,000 events were collected on flow cytometry Canto II (BDBiosciences). Flow cytometry data was analyzed by FlowJo software.
Samples were rinsed twice in PB, once in PBS, once in H 2 O and embedded in ProLongGold (Invitrogen) for analysis with a confocal Leica SP5X microscope. For cytotoxicity assay, Raw macrophages were seeded onto coverslips and incubated with heat-killed B. abortus 2308 at an MOI of 100 for 4 h. Macrophages were rinsed twice with PBS. CD4 + or CD8 + effector cells isolated as described above were added at an effector:macrophage ratio of 5:1 and cells were incubated for another 4 h before fixation. Antibodies used for immunofluorescence staining were anti-CD8-Alexa488, anti-CD4-Alexa647, anti-F4/80 (all from Biolegend) and anti-rat-DyLight549 (Abcam). Cells' nuclei were visualized by embedding samples into Prolong Gold (Invitrogen) containing DAPI. Coverslips were analysed at a Leica SP5X confocal microscope and images processed using the corresponding software LAS AF Lite.
31 U/ml). This mixture was incubated at 37°Celsius (37°C) for 2 h. Analysis of DNA base composition was performed on an Instrumentation Consommable Service (ICS; Toulouse, France) chromatograph equipped with a UV Spectra Focus 3-D at room temperature using a C18-phenyl-nucleosyl column (250 × 3. 4 mm). Elution was carried out with 6. 5 mM H 2 PO 4 (NH 4 ), pH 3. 95, and 4% (v/v) methanol at a flow rate of 1 ml/min. Eluates were monitored at 254 nm. Standard bases (dC, dT, dG, dA) (100 mg/ml) and m5dC (10 mg/ml) were obtained from Sigma Chemical and used for quantification, after sequential injection into the high-performance liquid chromatography (HPLC) system. The surface under the curve adjusted to the known concentration of each base was used with computer aided software (Pic3, ICS, France) to quantify the bases.
Methods Data for this article were entirely assessed from previously published work and no information that could identify individual patients is provided. Therefore, written consent and institutional ethical review are not required for this review. The PRISMA checklist and flow diagram  [21]  are available as supporting information (Diagram S1, Checklist S1). Several medical databases (MEDLINE, ScienceDirect, Scopus) and the ''African Neurology Database of the Institute of Neuroepidemiology and Tropical Neurology of the University of Limoges'' (http://www-ient. unilim. fr/) were screened by use of the key words ''onchocerciasis'' AND ''epilepsy''. Other sources, such as commercial search engines or unpublished congress proceedings, were searched with no specified limits, and reference lists of retrieved articles and reviews were screened for further records of relevance (Latest search:  May 23, 2012).
When within this restricted sample indicators giving information on infection intensity, namely nodule palpation and microfilarial density in untreated patients, were taken into consideration, again a significant result was found. In their overall constellation these results corroborate the hypothesis that epilepsy in endemic areas is caused by a disease process induced by infection with O. volvulus, especially in patients with severe infection. Cochrane's Q chi-squared tests and the I 2 statistics  [24, 25]. The latter describes the percentage of total variation across studies that is due to heterogeneity rather than chance. Analyses were performed using the metan procedure  [26]  available in the Stata software (StataCorp, TX). In order to discuss factors that might have influenced the results, information on the characteristics of each study site was also collected, and in some cases, the authors were directly contacted to get data not available in the publications.
Result of the literature search An overall number of 290 entries were found in the medical databases by use of the keywords ''onchocerciasis'' AND ''epilepsy'', corresponding to a number of 210 distinct records after duplicates were removed. Out of these records, 16 articles, medical theses and abstracts representing 11 studies were found to include a control group for the investigation of a relationship between onchocerciasis and epilepsy  [18, 20, [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42]. Two records, each representing an additional eligible study  [43, 44] , and one unpublished congress abstract  [45]  containing relevant information about one of the above-mentioned studies were identified in other sources.
Discussion In a search for comparative studies on the relationship between onchocerciasis and epilepsy published until to date, we identified a total number of 13 studies of which 11 studies presented data of  The article by Kabore et al. [33]  reports data from only 5 of the 12 villages for which data are given in reference  [34]  and  [35]. e Patients without skin microfilariae but having experienced a reaction to ivermectin treatment within 1 year were also considered infected. f Results of eye examinations were reported in this study but are not considered in the present analysis. doi:10. 1371/journal. pntd. 0002147. t001 Table  2. Case-control studies on the onchocerciasis-epilepsy relationship: study areas characteristics and odds ratios (OR). [ qualitative skin biopsies for the diagnosis of onchocerciasis amenable to combined analysis.
So far, the immediate relation between epilepsy and intensity of infection with O. volvulus has been adequately investigated at only one occasion  [29]. This study found a significantly higher mf count in dermal biopsies of patients with epilepsy if compared to pair-matched controls without epilepsy when examined prior to ivermectin treatment. Another study reported quantitative results from an area where annual mass treatment had been implemented prior to the investigation  [30]. However, after five treatment rounds in this Table  3. Results of studies utilizing supplementary methods for assessment of O. volvulus infection (serology, polymerase chain reaction, circulating antigen). Numbers of persons examined differed slightly between reports from this study. Data for skin snip results alone are presented as given in reference  [37] , and for skin snip and skin PCR results combined as given in reference  [36].
Conclusions This is, to our knowledge, the first time that a noninvasive measure of cortisol (i. e. without potential bias due to sampling procedure) was performed in addition to plasma cortisol analysis in order to investigate the relationship between stereotypic behaviours and adrenocortical activity in horses. The present data do not show a significant relationship between stereotypic behaviours and both pC and fCM concentrations in two large and very different groups of domestic horses kept in suboptimal conditions and already known to experience poor welfare states. This appears to be a general trend, as neither oral nor motor stereotypic behaviours predicted glucocorticoids levels. Cortisol measures therefore do not seem to indicate that stereotypic horses cope better, at least in terms of adrenocortical activity.
Study 2 Observations were made by a single observer (HB) every day during 46 days using instantaneous scan sampling. Twice a day (once in the morning before feeding and once in the evening after feeding), the observer walked through along the stalls and noted the behaviour of each of the mares at the instantaneous time of her passage. The time budget for each behaviour was determined as the recorded number of each behaviour divided by the total recorded number of scans in each horse. Previous observations and preliminary observations indicated that two such scans are enough to identify stereotypic animals, especially over a longer time period as was the case in this study  [5]. Although we recorded all behavioural patterns in both studies, presented data are limited to stereotypic behaviours.
Data and statistical analyses Behavioural data collected were frequencies (per min, as the total time of observation was less than one hour) of oral and motor stereotypic behaviours (study 1) and number of scans performing a stereotypic behaviour (study 2). Only one out of the 58 horses displayed an oral stereotypic behaviour (in addition to its motor stereotypic behaviours), therefore the distinction between oral and motor stereotypic behaviours was not relevant in study 2. Physiological data collected were plasma cortisol (pC, ng/mL, study 1) and/or faecal cortisol metabolites (fCM, ng/g, studies 1 and 2). Cortisol levels after a day's work and after a day's rest were positively correlated (Spearman correlation tests: plasma r s = 0. 56, fCM r s = 0. 44 to 0. 69, N = 55, P = 0. 001 in all cases) and no significant difference could be detected between sampling time periods (plasma: Wilcoxon test: Z = 0.
62, P = 0. 51, N = 55; fCM: Friedman test (55, 2) = 4. 8, P = 0. 09). Data were therefore averaged between sampling time periods, either for plasma and fCM. Descriptive statistics are median values (Med), followed by 1 st (Q1) and 3 rd (Q3) quartiles, range. Analyses were conducted in JMP 9. 0. 2. (SAS Institute Inc. , Cary, NC, USA) (accepted P level = 0. 05, two tailed tests). Horses were a posteriori binary classified for the analyses as "being stereotypic" (i. e. observed at least once performing an oral and/or a motor stereotypic behaviour shown in Table  1 ) or "non-stereotypic" (i. e. never observed performing a stereotypic behaviour). Relationships between cortisol levels (plasma cortisol or fCM concentrations) and being stereotypic or not were analysed using general linear models (GLMs), controlling for age, frequencies of oral and motor stereotypic behaviours (both type of stereotypic behaviours were considered separately as they can have different aetiologies), and other factors where appropriate, i.