dataesr/scientific-paragraphs-categorization huggingface dataset:
This could be achieved by altering the conditions during the manufacturing process. For example, it is known that a pH of 1. 8-2. 2 in the reaction medium correlates with an increase in the quantity of ISM, whereas a higher pH results in a greater production of the blue isomer  (Berg, 1963; Tettey et al. , 1999). Thus, optimisation of the manufacturing process, and the strict adherence thereof, would be necessary to control the quantities of the byproducts. The data generated by this study will be very useful to improve the understanding of the efficacy and bioavailability or biotransformation of the commercial formulations of ISM and help to develop new drug compositions with optimal ratios for an improved trypanocidal and prophylactic effects. Laboratoire d'Excellence (LabEx) ParaFrap (French Parasitology Alliance for Health Care) ANR-11-LABX-0024.
Disease transmission, detection and control models We used the simulation model of FMD epizootics developed by Rautureau et al. [22]. This tool allows simulating realistic FMD epizootic dynamics in France, based upon actual data on French holdings (N = 390,565 including farms, markets, dealers and slaughterhouses) and on animal movements of cattle  [23]  and swine  [24]. The basic unit was the holding, consisting of at most three mono-specific animal batches: cattle, small ruminants and swine. Five individual exclusive health states were considered: exposed and susceptible (denoted S), infected but not infectious (denoted L), subclinically infectious (denoted I), clinically infectious (denoted J) and immune (denoted R). Inside a holding, we assumed that animals of a given species batch were exposed to three forces of infection: the within-batch force of infection, the between-batch force of infection and the environmental force of infection.
The latter two forces were based upon the within-batch force of infection, decreased according to species-specific biosecurity parameters, which represented the levels of separation between species in usual farm organization and management. Three modes of transmission between holdings were considered: live animal movements (inducing potentially nationwide epizootics), direct transmission by contacts between herds on pastures; and indirect transmission by contaminated vehicles, materials or fomites. Animal movements were simulated according to records stored in a national database. The health state of animals moved from one holding to another was assumed to be random. The direct between-herd force of infection was modelled as a fraction of the within-herd force of infection (decreased by a biosecurity parameter), whereas the indirect between-herd force of infection was modelled as a fraction of the within-herd environmental force of infection (also decreased by a biosecurity parameter).
In total, our analyses were thus conducted on 45 mating groups, for all of which courtship behavior was recorded. Only a small fraction (13%) of the animals in this study were tagged and as a result, individuals were counted several times over the season. Thus, to avoid pseudo-replication, we chose to work at the group level averaging time budgets over mating groups only. Indeed, no group was sampled twice within a given day, nor ibex twice within a given scan. Our data indicate that the different mating groups sampled never had the same composition of individuals and were thus, in effect, different statistical units.
Monitoring group social composition and/or the behavior of social conspecifics is an important component of ungulate social behavior  [48, 49]. For females, vigilance group-behavior might have increased with adult sex ratio because of higher sexual harassment in male-biased groups  [30, 50]. This suggestion is consistent with the fact that female group time-budget devoted to moving and agonistic behavior towards males (female PC2) also increased in male-biased mating groups. Although we recorded courtship behavior in all of the mating groups, we unfortunately have no data on female receptivity in this study. However, it is likely that in highly male-biased groups, female aggressiveness towards males reflected low female receptiveness. Alternately, sexually receptive females might have allocated less time to feeding and more time observing potential suitors when more males were present in the group  [50, 51].
Acknowledgments We are grateful to  Flurin Filli  and to  Park Rangers  for their support during this study. We wish to thank  Florian Zellweger  for his assistance in the field. We are grateful to  Pierre Bize  for his advice on statistics, and to  Stefano Grignolio  and  Nicolas Hanuise  for valuable comments on a previous draft of the paper. We are especially grateful to  Marco Festa-Bianchet  and two anonymous referees for enlightened suggestions on the paper, and to  Claire Saraux  for her important help with data analyses.
In Phase 3, the number of coded chemicals was increased to 29 as part of the validation process. All results were sent to ECVAM for decoding and evaluation according to specific pre-determined criteria. Results demonstrated an excellent specificity such that    (Fautz et al. , 2012). Of the 29 chemicals tested, only 8 chemicals were classified as carcinogens with a suggested genotoxic mode of action and 21 were non-carcinogens. Therefore, the current dataset is biased towards non-carcinogens with the total number of carcinogens in the dataset considered too low to draw a final conclusion about the sensitivity of the RSMN assay. More coded compounds will be tested in the next project phase with a focus on carcinogens. During the testing, it was noted that a couple of compounds precipitated, which was not considered in the initial criteria, but should be included in future evaluations.
Acknowledgements This work was funded by the  Cosmetics Europe. The '' 3D skin model '' project received input from ECVAM. Work by Covance and TNO was co-funded by  ECVAM and UK NC3Rs. We would like to thank  David Kirkland  and  Paul Fowler  for their dedicated contributions to the '' False Positives '' project. We would also like to thank  Marilyn Aardema  for her role in the  RSMN  project and  Raffaella Corvi  for her help with steering the program.
Abbreviations: ITS, internal transcribed spacer The GenBank/EMBL/DDBJ accession number for the ITS sequence of the isolate determined in this study is LN651080. of the internal transcribed spacer 1 (ITS1)-5. 8S-ITS2 region of the rDNA gene  (Alvarez et al. , 2010). A BLAST (http:// www. ncbi. nlm. nih. gov/BLAST) search revealed 99 % identity (565/568 bp) with the type strain of F. nubica CBC 269. 64. Antifungal susceptibility was determined by the broth microdilution EUCAST method [Subcommittee on Antifungal Susceptibility Testing (AFST) of the ESCMID European Committee for Antimicrobial Susceptibility Testing (EUCAST), 2008], which was applied with some modifications. MICs for echinocandins (caspofungin, micafungin and anidulafungin) were high (0. 25 mg l 21 ), but they were considerably lower for amphotericin B (0.
ACKNOWLEDGMENTS We acknowledge the RAS Legge Regionale 7 agosto 2007, (n) 7, bando 2010 Bando 2010-2011, for funding bioanthropological investigations. We thank  Warwick Medical School  for funding laboratory and bioinformatics work. We thank  Jackie Chan  for storage of samples,  Oliver Smith  for supplying a drill and for advice on library preparation,  Robin Allaby  for providing access to the ancient-DNA laboratory, and  Nick Loman  for advice on phylogenetic placement. We thank the  Brucella Group Sequencing Project ,  Broad Institute of Harvard and MIT , for making prepublication genomes available. R. B. , B. B. , and M. J. P. designed the research; M. M. , R. B. , V. G. , P. B. , and G. L. K. performed the research;  G. L. K. , M. J. S. , and M. J. P. analyzed the data; and M. J. P.
Data analysis The first five parameters were the number of surviving snails at week 4 p. e. , their shell height at week 8, their life span, the time between the onset of the experiment and the first egglaying, and the length of this oviposition period. The total number of eggs laid by each surviving snail during the experiment, the quantity of egg masses, the number of eggs per mass, and that of eggs per snail and per day were also taken into account. In order to specify potential relationships between the egg-laying period and cercarial shedding in the CS snails, the date of the first cercarial shedding and the length of the patent period were also considered. Individual values recorded for the shell height of snails, their life span, the time between the onset of the experiment and the first egg-laying, the length of this oviposition period, and the numbers of egg masses and eggs were averaged and standard deviations were calculated taking into account the snail group or subgroup.
Parameters studied and data analysis The first two parameters were snail survival at day 30 p. e. and the prevalence of F. hepatica infection (calculated in relation to the number of snails surviving at day 30 p. e. ). In the first experiment, prevalence took into account the numbers of snails with immature rediae only, cercariae-containing rediae, or with free cercariae. In the second experiment, prevalence was calculated using the numbers of cercariae-shedding (CS) and NCS snails. For each parameter, the differences were analyzed using a χ 2 test. In the second experiment, shell growth of CS and NCS snails during the experiment (calculated using the difference between shell heights at exposure and at snail death), length of the prepatent and patent periods, and the number of shed cercariae were also considered.
Nevertheless, position of H. meleagridis, as related to Tritrichomonas foetus could be seen in glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and enolase trees which was concordant with phylogenetic studies on parabasalid microorganisms  [2, [17] [18] [19] [20]. In the present investigation genetic heterogeneity of H. meleagridis isolates was investigated by comparing phylogenetic data of partial 18S rRNA, alpha-actinin1 and rpb1 gene sequences. Additionally, ITS1-5. 8S rRNA-ITS2 sequences from different clonal cultures of H. meleagridis were analyzed to clarify the presence of sequence variants within the same isolate. Results of the analyses and applicability of each locus for sub-typing purposes are discussed.
Since majority of isolates grouped to the cluster 1, it was broadly represented throughout Europe. In contrary, cluster 2 was predominantly found in France with the exception of a single isolate from Austria (Table  S1 ). Two sequences, detected in 3 samples from 2 different flocks, were shown specific to H. meleagridis according to the BLAST search. However, more detailed analysis demonstrated only 92. 6-94. 8% identity to H. meleagridis sequences. The sequence identities to the related protozoan species P. wenrichi and D. fragilis were 89. 3% to 89. 5% and 88. 1 to 90. 5%, respectively. The fact that these sequence types formed a separate cluster in the phylogenetic tree (Figure  1 ) and that their sequence identities were lower when compared to other H. melagridis isolates, indicated the detection of another species whose sequences are currently not available in the database.
Furthermore, in two turkey flocks only T. gallinarum was detected, with one flock showing clinical signs of histomonosis and the other not (Table  1 ). The flock with clinical signs was analyzed as a single sample containing a pool of caeca from five birds, which possibly contributed to over dilution of H. meleagridis and resulted in the unsuccessful detection of this protozoan. Therefore, in order to pinpoint the agent that caused pathogenicity, a microorganism should be isolated and its virulence determined in infection experiments. The degree of heterogeneity of H. meleagridis isolates belonging to a single genotype differed depending on the analyzed genetic locus. The analysis of 18S rRNA sequences demonstrated a clear genetic diversity of H. meleagridis isolates within each genotype. Interestingly, even though data on genetic diversity of D.
Alpha-actinin1 locus showed the lowest sequence diversity with clear sequence variations present only when representatives of two genotypes were analyzed. These features clearly argue against the use of this locus as a marker for subtyping H. meleagridis isolates. Analysis of 18S rRNA locus identified two sequences of an unknown species related to H. meleagridis, D. fragilis and P. wenrichi, which formed a separate cluster in phylogenetic analysis. Histomonas-specific PCRs amplifying a-actinin1 and rpb1 sequences were negative; therefore no further sequences were obtained. The identity of this species is unknown, as matching sequence data are not available in the database. All analyzed samples, except the clonal cultures, were not cultured and so it was not possible to inspect the morphology of this protozoan.
Furthermore, it was never reported whether the method is reproducible when different sequencing companies or machines are used to generate chromatograms. It was only reported that identical C-profiles were obtained by several independent analyses of a sample within the same laboratory  [24]. The obvious drawback stems from the fact that the method is not standardized and the ''in-silico'' support, as database and software for the analysis, is not developed. Therefore at the moment it seems that C-profiling, if at all, could only be used as a sub-typing method within a laboratory. Conclusively, by analyzing different genetic loci the present study demonstrated for the first time the separation H. meleagridis isolates into two genotypes. Genotype 1 seemed to be broadly represented in Europe, whereas genotype 2 was rare.
8S rRNA-ITS2 amplicons, which were cloned to TOPO vector (TOPO TA Cloning Kit for Sequencing, Invitrogen, Life Technologies, Austria) prior to sequencing. Fluorescence-based sequencing of three to five clones was performed by LGC Genomics GmbH (Berlin, Germany) using M13 primers. All sequences were deposited to the EMBL database [EMBL: HG008073-HG008105, HG008107-HG008112].
Sequence analyses Assembly and analyses of sequences, the nucleotide and amino acid alignments were performed with Acccelrys Gene, version 2. 5 (Accelrys, San Diego, CA), Lasergene (DNASTAR Inc. ) and ClustalX v2. 1  [26]  software. Primer binding sites were excluded from sequences used in the analyses. Phylogenetic analysis of 18S rDNA (aprox. 544bp), a-actinin1 (819bp) and rpb1 (759bp and 1242bp) nucleotide sequences were performed with the aid of PHYLIP package version 3. 68  [27]  using distance and maximum likelihood methods. For all PHYLIP applications default settings were used if not otherwise specified. Bootstrap re-sampling analyses of 1000 replicates for distance trees and 100 replicates for maximum likelihood trees were performed with the SEQBOOT program to prove the stability of the trees.
For analyses with nucleotide sequences, distance matrices were calculated by using DNADIST application with the Kimura 2-parameter model and translation/transversion ratio of 2. 0. Maximum likelihood analysis was performed by using DNAMLK application. The final phenogram was produced by DNAMLK where the tree obtained by CONSENSE was implemented as user tree. The graphical output was generated using DRAWGRAM program. Phylogenetic analysis of ITS1-5. 8S rRNA-ITS2 region was performed using MegAlign application of Lasergene software (DNASTAR Inc. ) with default settings.
, 2011). β-Lactoglobulin known for its allergenic potential is lacking in camel whey  (Elagamy et al. , 2009) , whereas α-lactalbumin (α-LA; SwissProt accession number P00710) constitutes the main component (2. 2 g L -1 of milk; El  Hatmi et al. , 2006). An advantage of α-LA may be its beneficial role in the antioxidant system of the neonate  (Lien, 2003). The bovine α-LA  (Sadat et al. , 2011)  and the camel α-LA  (Salami et al. , 2009; 2010)  are a source of free radical-scavenging peptides. Therefore, attention is being focused on producing α-LA-enriched formulae because α-LA might have an ability to attenuate oxidative stress occurring in inflammatory bowel disease after oral administration (IBD;  Rezaie et al. , 2007). The protein or its peptides generated by gastrointestinal digestion might act directly on the inflammatory site in the gut without passing through the intestinal barrier.
Fractionation of CWP by Ä KTA-FPLC chromatography After separation of the CWP, the chromatographic fractions were analyzed by SDS-PAGE electrophoresis (Figure  1 ). Fraction F1 mainly contained the major soluble protein of camel whey i. e. α-LA and camel serum albumin (CSA). As expected, these proteins were not adsorbed onto the cation-exchanger due to their acidic isoelectric points (pHi). The theoretical pHis are 5. 01 and 5. 60 for the camel α-LA and bovine serum albumin (SwissProt accession number P02769), respectively (the CSA sequence is not available in the databank). The fractions F2 and F3 mainly contained heavy chains H45 and H42 of IgG2 and IgG3, respectively, these IgGs being devoided of light chains  (Lauwereys et al. , 1998; Daley-Bauer et al. , 2010)  whereas IgG1, which consisted of both heavy chains H55 and light chains L30 was recovered in fraction F4.
Acknowledgments The authors would like to thank the  Ministère des Affaires Etrangères (France)  for supporting  Dr. Halima El Hatmi 's stay (SSHN grants) in  URAFPA (Université de Lorraine, France) laboratory  and the  MESR for (Ministère de  l'enseignement supérier et de la recherche scientifique) for financing this research and  Z. Hafeez  ( URAFPA, Université de Lorraine ) for manuscript corrections.
A pathology resident from Québec spent 6 weeks in France and Switzerland to develop the contents and build the module on an e-learning Moodle platform under the supervision of two dermatopathologists. The learning module contains text, interactive clinical cases, tests with feedback, virtual slides, images and clinical photographs. For that module, the virtual slides are decentralized in 2 universities (Bordeaux and Paris 7). Each university is responsible of its own slide scanning, image storage and online display with virtual slide viewers. Results: The module on inflammatory skin pathology includes more than 50 web pages with French original content, tests and clinical cases, links to over 45 virtual images and more than 50 microscopic and clinical photographs. The whole learning module is being revised by four dermatopathologists and two senior pathologists.
Method The French national university network includes teachers from 19 universities across France. This network was used as a starting point for the international project. The national e-learning platform is hosted by PRES Sorbonne Paris Cité http://moodle. sorbonne-paris-cite. fr and is based on the free software modular object-oriented dynamic learning environment (Moodle). One of the first steps of the international project was to build an e-learning module intended for interns and residents in pathology. The first international fellowship was attributed to a pathology resident (EP) from Québec who spent 6 weeks in France and Switzerland to develop the contents and build the module with financial support obtained from CFQCU http://www. cfqcu. org/. This first module, created under the supervision of two dermatopathologists (BV, MB), focuses on inflammatory skin pathology.
Acknowledgements The Moodle website is hosted by  PRES Sorbonne Paris Cité , and financial supports for hardware have been obtained from UNF3S http://www. unf3s. org/ and  PRES Sorbonne Paris Cité. E. P. developed the contents and build the module with the financial support obtained from CFQCU http://www. cfqcu. org/. The dermatologists who kindly give us clinical pictures of cases ( Services de dermatologie du CHU de Bordeaux :  Prs M. S. Doutre ,  M. Beylot-Barry ,  A. Taieb  and  Services de dermatologie, Hopital St Louis :  Pr Martine Bagot  and  Dr Antoine Petit ) Publication of this supplement has been funded by 12th  European Congress on Digital Pathology. This article has been published as part of Diagnostic Pathology Volume 9 Supplement 1, 2014: Selected articles from the 12th European Congress on Digital Pathology.
All Oxyurida thus far investigated have a haplodiploid mode of reproduction: Unfertilized eggs give rise to haploid males and fertilized eggs always produce diploid females  [18]. There is currently no evidence showing a reversal of this mode of reproduction in any taxa of the Nemata or other groups of organisms that manifest a haplodiploid mode of reproduction; this list includes, but is not restricted to, the Hymenoptera (ants, wasps, honey bees), Homoptera, and some mites (Acari: Mesostigmata). Data available from the phylogenetic databases of the Nemata, and the groups mentioned above, show clearly that once a species has made the transition from a diploid to a haplodiploid mode of reproduction, reversal back to a diploid system of sexual recombination is unlikely. We therefore interpret haplodiploidy in the Nemata as an ancient life-history character that probably originated simultaneously with the speciation event that gave rise to the Oxyurida  [13].
Acknowledgements Financial support for field and laboratory work in Brazil was provided by:  CNPq  ( Conselho Nacional de Desenvolvimento Científico e Tecnológico)  and  FAPERJ (Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro ). Thanks to  Angie Fox  for preparing some figures and to  Jason Head  for advice on the manuscript. Work in the  Harold W. Manter Laboratory of Parasitology at the University of Nebraska-Lincoln  was supported through grants from the  United States National Science Foundation  (NSF) including:  DBI-1127386  and  DEB-0717214  to SLG.
DNA manipulations and sequence analyses Plasmid and genomic DNA were isolated with Qiaprep Miniprep (Qiagen GmbH, Hilden, Germany) and Ultraclean Microbial DNA Isolation Kit (MoBio Laboratories, Carlsbad, CA, USA), respectively. When needed, DNA was also purified from agarose gels using a Qiack Gel extraction kit (Qiagen). DNA sequencing was performed by the dideoxy method at the Sequencing Unit of Centro de Investigación Médica Aplicada (CIMA, Universidad de Navarra, Spain), and primers were synthesized by Sigma-Aldrich Ltd. Searches for DNA and protein homologies were carried out using the Kyoto Encyclopedia of Genes and Genomes  [21] , EMBL-European Bioinformatics Institute server  [22]  and National Center for Biotechnology Information (NCBI) database  [23]. Proposed structure of the Brucella core LPS as described by Kubler-Kielb  [8].
Construction of B. ovis LPS mutants Several ORF encoding putative glycosyltransferases have been shown to be involved in the biosynthesis of the core of B. abortus LPS: wadA (formerly named wa**, BAB1_0639,  [17, 18] ), wadB (BAB1_0351,  [6, 7] ) and wadC (BAB1_1522,  [5, 6] ). We searched for orthologues of these glycosyltransferases in the B. ovis strain ATCC25840 genome sequence and we identified three ORF: BOV_0614 for wadA, BOV_0337 for wadB and BOV_1453 for wadC, with 99. 4%, 99. 9% and 100% DNA sequence identity, respectively. Non-polar mutant and sibling revertant strains were obtained for each target gene from B. ovis PA strain as described in the Materials and methods section. PCR amplification and sequencing of the target loci in the genome of the mutants confirmed inactivation of the respective genes (data not shown).
Acknowledgements This work was funded by  Ministerio de Economía y Competitividad of Spain  (reference project  AGL2011-30453-C04 ) and  Fundación para la Investigación Médica Aplicada (FIMA). Financial support to PS-L from  Ministerio de Economía y Competitividad of Spain  (reference  BES-2009-015656 ), AZ-B from  Universidad Pública de Navarra , and  BSR  from  CSIC  and  European Social Fund (Programa JAE-Doc)  are also gratefully acknowledged.