dataesr/scientific-paragraphs-categorization huggingface dataset:
19 and 0. 51) in accordance with counterpart values found in literature  (Sellier and Monin, 1994; Ciobanu et al. , 2011). The heritability estimate for DL in the PB population was very high compared to published values that range from 0. 01 to 0. 30  (Ciobanu et al. , 2011). This could be because of the presence of the halothane gene that segregates in the Piétrain population. The halothane gene is a major gene known to have a detrimental effect on meat quality causing pale, soft and exudative meat of susceptible individuals  (Larzul et al. , 1997). Lesion traits showed moderate to low heritabilities (0. 07 to 0. 26). The moderate heritability of CL is in agreement with the previously estimated value by  Parois et al. (2015)  using the same dataset and with another study where carcass lesions were measured on farm after mixing  (Turner et al.
Accumulation of AN, SK and to some extent IN is the main cause for boar taint, that is an unpleasant odour found in pork meat when cooking  (Lundstrom et al. , 2009). In turn, ES is an indicator of sexual development  (Prunier et al. , 2013). Traits related to boar taint had a high (0. 37 to 0. 54 for AN, PB-CB respectively) and a moderate heritability (0. 13 to 0. 27 for SK, PB-CB respectively) and 0. 46 to 0. 07 for IN, PB-CB respectively. Heritability estimates obtained for AN, SK, IN and ES were of about the same magnitude as the previous study that used the same dataset  (Parois et al. , 2015). All the heritability estimates were within the range of values previously found in the literature except Additive and dominance genetic variances in pigs for IN in the PB where a high value was found compared to other studies (see revision made by  Parois et al.
Third, although the method above reflects the way in which a committee or project evaluator might arrive at a decision, it could be argued to involve some degree of subjective judgement so dendrograms were constructed following an average linkage method  19, 20  by using SPSS Statistics (PASW Statistics for Windows, Version 18. 0, Chicago: SPSS Inc. ). The average linkage method was applied to % scores in each of the categories for each scenario, and this allowed clustering of the data (i. e. scenarios).
Scenarios included in the survey were based on data derived from a non-systematic review of published works spanning from 1940 to 2014 that utilized cephalopods in studies including biochemistry, physiology, immunology, neuroscience, eco-toxicology, and behavioural sciences. The use of methods sections from published works publications was not considered practical for our aims because of: i. the need for extensive copyright clearance, ii. respondents recognising the original paper, and hence being influenced by the authorship, iii. the length of many methods sections would make the time required to complete the survey impractical. We are aware that the amount of information given in the scenarios is limited; however, the outcomes indicate that this was sufficient to reach a decision as overall scores in the "unable to decide" category were low.
We propose that if the cephalopod is able to hide from the predator and there is no physical or chemical contact with the predator then the procedure should be considered to be sub-threshold. However, if such studies are undertaken the actual severity should be monitored to provide objective data to support this prospective assessment. In cuttlefish, experimental induction of escape reactions (scenario 7) and investigation of agonistic social interactions in a small tank (scenario 18) were assessed as mild and moderate respectively. The latter is consistent with a classification of moderate severity for an agonistic social interaction study in O. vulgaris (scenario 16). Scenarios (19 and 37) describing a training paradigm of O. vulgaris involving brief electric shocks as negative reinforcements were assessed as moderate, but the scenario which additionally involved daily injections (scenario 37) was also assessed as moderate, although at the upper end of the score range.
Acknowledgements We thank all respondents and colleagues who provided comments in the pilot stage of the survey, particularly  Professor A. Olsson  (Portugal) and  Dr. J. Lenehan  ( Irish Republic ). This study was performed under the auspices of  COST Action FA1301 , benefited from its networking activities, and is considered a contribution to the  COST (European COoperation on Science and Technology) Action FA1301 "A network  for improvement of cephalopod welfare and husbandry in research, aquaculture and fisheries" (http://www. cephsinaction. org/). The authors wish to thank  Stefania Grella  for.
Paired-end sequencing was then performed on a NextSeq500 (Illumina). Quality was controlled using FastQC v0. 11. 3  (Wingett and Andrews, 2018). De novo assemblies were produced using SPAdes v3. 10. 1  (Bankevich et al. , 2012). Determination of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (DDH) A set of 69 Helicobacter species reference genomes was constructed based on75 strains from the CNRCH collection  (Ménard et al. , 2016)  (Supplementary Table  S1 ). Five strains were removed due to missing whole genome sequencing (WGS) (Helicobacter canadensis NCTC 13242, Helicobacter hepaticus Hh-2, Helicobacter mastomyrinus MIT 97-5574 and MIT 94-022, and Helicobacter nemestrinae ATCC 49396) and one for further identification (Helicobacter species CNRCH 2013/518). Accession numbers for each genome and genes are available on Supplementary Table  S2.
Genome Analyses All of the genomic sequences and associated information were stored in a web-based Bacterial Isolate Genomic Sequence database (BIGSdb 6  )  (Jolley and Maiden, 2010). The BLAST algorithm implemented in BIGSdb was used to perform gene-by-gene alignments on the three potential novel species and representative genomes from existing Helicobacter species. These analyses were run independently for each potential novel species using the list of all genes from this specific species as a reference list for the alignments. A phylogenetic tree based on gyrA was built from 72 nucleotide sequences from the three potential novel species and representative genomes  (Ménard et al. , 2016)  from existing Helicobacter species using Molecular Evolutionary Genetics Analysis (MEGA) X software  (Tamura et al.
95; Carl Zeiss Microscopy GmbH, Jena, Germany) and a high-resolution color camera (VCCFC60FR19CL, 4MP; CIS Corporation, Tokyo, Japan) available at the Experimental Histopathology Platform, US 005 UMS 3427-TBM CORE. The images were read using the Panoramic Viewer software version 1. 15. 4 (3DHISTECH, Ltd. ).
Clinical Data Strain CNRCH 2005/566H was isolated in 2005 from the feces of a 55-60-year old patient suffering from hepatocellular carcinoma and gastroenteritis at the Orléans Hospital, France. Strain 48519 was isolated in 2017 from the blood sample of a 25-35-year old patient, at Cochin Hospital in Paris, France. A bacteremia was detected following fever, shivers, abdominal pain, and nonbloody mucous diarrhea symptoms. Strain Cn23e was isolated in 2017 from a gastric biopsy obtained from a dog suffering from chronic gastritis hospitalized in the Aquivet Veterinary Clinic 7  (Eysines, France).
Taxonomy The two best ANI and DDH scores for each strain are indicated in Table  2. Supplementary Data are provided in Supplementary Table  S1. ANI analyses were performed to measure nucleotide-level genomic similarity among all pairs of previously selected genomes, including each potential novel species. It reveals that two of them, CNRCH 2005/566H and 48519, showed ANI percentages lower than the speciation threshold (95%)  (Klappenbach et al. , 2007)  when compared with genomes from the public database. More specifically, the closest species to CNRCH 2005/566H was H. valdiviensis with a non-significant ANI value of 84. 9%. Three of the closest species to 48519 belong to H. cinaedi species, with ANI values of 88. 8%, 89. 7% and 89. 7%. This is lower than the speciation threshold, suggesting the closeness of this strain with the H.
DISCUSSION Among the three isolates that were studied in the present article, two may correspond to two new Helicobacter species. The third one, strain Cn23e, is a new isolate of H. felis. The first species proposed in the present study is 'Helicobacter burdigaliensis sp. nov. ' 'Burdigaliensis' refers to the latin name of Bordeaux where the proposed type strain, CNRCH 2005/566H, was identified. This data has been submitted to GenBank under the accession number QXJG00000000. The version described in this paper is version QXJG00000000. 1. Raw reads are available at SRA under the accession number SRS3744858. The second species is 'Helicobacter labetoulli sp. nov. ' 'Labetoulli' refers to the family name of the microbiologist who isolated the proposed type strain 48519. Finally, strain Cn23e is a new member of the H.
SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: https://www. frontiersin. org/articles/10. 3389/fmicb. 2019. 02820/full#supplementary-material The DDH values were calculated using Genome-to-Genome Distance Calculator (v. 2. 1; http://ggdc. dsmz. de/distcalc2. php) formula 2 (isDDH estimates based on identities/HSP length). The Helicobacter species and accession numbers for each genome and genes used for the analyses are indicated on the second sheet of the Table. HSP, high-scoring segment pairs. TABLE  S2  | Strain list used in the study. WGS, 16S rRNA gene, and gyrA accession numbers are indicated. Similar accession numbers means that the nucleotide sequences of 16S rRNA and gyrA genes were extracted from Genbank annotation or with blastn command line tool (using WGS file as "subject" and the 16S rRNA or gyrA sequence from another strain as "query").
5 μM of each primer, and 2 μL of DNA template. Cycling parameters for the ITS region consisted of an initial nucleic acid denaturation at 95 °C for 5 min, followed by 35 cycles of 95 °C for 30 s, 56 °C for 1 min, and 72 °C for 1 min, with a final 7 min extension at 72 °C. Cycling parameters for the cox1 gene consisted of an initial nucleic acid denaturation at 94 °C for 5 min, followed by 35 cycles of 94 °C for 30 s, 52 °C for 1 min, and 72 °C for 1 min, with a final 7 min extension at 72 °C. PCR products were sequenced using the original PCR primers in a 3730xl DNA Analyzer system by GATC Biotech (Konstanz, Germany). Assembly and editing of contigs were performed with CodonCode Aligner v8. 0. 1 (CodonCode Corporation, Centerville, MA, USA). These data, together with previously published ITS and cox1 sequences available in the GenBank™ database (Table  1 ), were aligned using ProAlign v0.
, 2012) , respectively. For ML analyses, best-fit evolutionary models (GTR model with invariable sites (+I) and rate heterogeneity (+G) for the cox1 dataset, and GTR + G model for the ITS dataset) were selected using PartitionFinder v2. 1. 1  (Lanfear et al. , 2016) , with automatic arrest of bootstrap resampling to assess nodal support. For BI analyses, we invoked best-fit evolutionary models and partitioning schemes (i. e. , GTR + G for ITS, GTR + I + G for cox1 position one, F81 + I for cox1 position two, GTR + I + G for cox1 position three) using Parti-tionFinder v2. 1. 1  (Lanfear et al. , 2016). Each BI analysis was performed using two independent runs with four Markov Chain Monte Carlo (MCMC) chains and four million generations. MCMC chains were sampled every 4000 generations and the first 25% of the trees was discarded as burn-in.
9″N, 15°58′19. 1″W), a sampling site within LG_3. The ITS alignment excluded 314 of 1243 sites based on posterior probability filtering. ML analysis of the resulting ITS dataset (929 characters) yielded a single best-scoring tree strongly supporting monophyly of our West African Plagiorchis lineage (including isolates from M. huberti, A. niloticus, Crocidura sp. , and R. natalensis). ML bootstrap values and BI posterior probabilities yielded a highly resolved topology indicating two clades, one composed by Plagiorchis spp. infecting rodents, insectivores, and birds, while the other included parasites of bats (Fig. 2 ). In contrast, ML and BI analyses of the cox1 alignment (396 characters, no internal gaps) failed to resolve relationships between our West African lineage and other Plagiorchis taxa (Fig.
Discussion This study provides molecular data to characterise a previously undescribed Plagiorchis sp. and resolve its phylogenetic relationships within the genus. Sequencing of the ITS region proved to be useful for characterising Plagiorchis spp. (Tkach et al. , 2000; Boyce et al. , 2014) , while the simultaneous examination of rDNA and mtDNA loci is suitable for molecular prospecting and further hypothesis testing on species delimitation  (Nadler and Pérez-Ponce de León, 2011). Our findings revealed that Plagiorchis isolates from M. huberti, A. niloticus, and Crocidura sp. , represented the same evolutionary lineage. Furthermore, we recorded the occurrence of this parasite in one freshwater gastropod R. natalensis, which may act as a suitable first intermediate host in the region of Lake Guiers.
The phylogenetic analysis indicated that an unidentified Plagiorchis sp. found in the caddisfly genus Lepidostoma (GenBank™ KX160474) was most closely related to our West African lineage. However, the identity of this parasite specimen is not confirmed and is hypothesized to be Plagiorchis neomidis, a species described from the Eurasian water shrew (Neomys fodiens)  (Brendow, 1970) , according to its phylogenetic position in  Zikmundová et al. (2014). Within the same clade of our West African Plagiorchis sp. , the most closely related identified species were Plagiorchis maculosus, a parasite of insectivorous passerines and other birds (e. g. ,  Bušta, 1987) , and Plagiorchis elegans, a common parasite of rodents, various mammalian hosts, and birds of the Northern Hemisphere (e. g. ,  Boyce et al.
, 2014). Therefore, our results supported two divergent lineages within the Plagiorchis genus, one of which appears restricted to chiropterans as definitive hosts. Bats, rodents, and insectivores may have acquired the ancestors of their modern Plagiorchis spp. from birds  (Tkach et al. , 2000) , and the phylogenetic structure we observed may be the result of the ancient evolutionary histories and ecological differences between these mammalian orders. Nevertheless, our understanding of the genus Plagiorchis is poor and molecular data for further comparisons are lacking; this is evidenced by the scarce phylogenetic resolution for P. muris, the only species within the rodent clade for which human infections have been documented  (Asada et al. , 1962; Hong et al. , 1996). However, the trees generated from the cox1 dataset partially supported isolates of P.
Acknowledgements This work was supported by the  Royal Veterinary College  and the  Zoonoses and Emerging Livestock Systems (ZELS)  initiative including the  Department for International Development, Biotechnology and Biological Sciences Research Council, Economic and Social Sciences Research Council, Medical Research Council ,  Natural Environment Research Council , and  Defence Science and Technology Laboratory  (grant numbers  BB/L018985/1  and  BB/N503563/1 ). Chelsea L. Wood was supported by a  Sloan Research Fellowship  from the  Alfred P. Sloan Foundation  and the  Michigan Society of Fellows  at the  University of Michigan. We are grateful to  Boubacar Bâ ,  Alassane Ndiaye ,  Alima Thiam , and  Cheikh Thiam  for their outstanding support during fieldwork, and to the  Senegalese communities  involved in the project for their hospitality.
We thank  Fiona Allan ,  Bonnie Webster , the  Schistosomiasis Collection at the Natural History Museum (SCAN) , and The Upstream Alliance partnership for the donation of trematode cercariae. Finally, we acknowledge the immense contribution made by all the wild animals trapped and sacrificed during this study. Fig. 3. Phylogenetic relationships among Plagiorchis spp. inferred by  Maximum Likelihood  (A) and  Bayesian Inference (B)  analyses of the cytochrome c oxidase subunit 1 gene data. The taxon Fasciola hepatica (GenBank™  AP017707 ) was used as outgroup. Nodal support ≥ 80% from likelihood bootstrap replicates and Bayesian posterior probabilities is indicated with an asterisk.
Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated. In the entire dataset, 180 ROH islands were identified, whilst 100 islands were breed specific, all other overlapped in 36 genomic regions with at least one ROH island of another breed.
The majority of the horses (Haflinger, Noriker, Lipizzan, Posavina, Bosnian Mountain Horse, Gidran and Shagya Arabian) were selected in order to represent the genealogical population structure (sire lines and mare families) of the respective breeds based on pedigree information. For Akhal Teke, French Trotter and Selle Francais, the horses were chosen to be unrelated within two generations. In the Exmoor Pony sample only horses with four generation long pedigrees were included and closely related individuals (full sibs) were excluded. For Lipizzan, Noriker, Posavina and Bosnian Mountain Horse SNP data were available from previous studies  [17, 18, 20]. The samples for Lipizzan, Shagya Arabian, Akhal Teke, Haflinger and Noriker were discussed and approved by the institutional Commission for Ethics and Animal Welfare, University of Veterinary Medicine, Vienna, protocol number: ETK-06/05/2015.
The distribution of ROH segments across the genome was visualized using the R-package detectROHs (www. r-project. org). Putative ROH islands were determined based on overlapping homozygous regions, shared by more than 50% of studied horses within each breed  [12]. ROH islands which occurred only in one single breed were defined as "breed-specific" or "private". Resulting ROH islands were checked for overlaps between breeds, whereas no threshold for the minimal overlapping length size was applied. Further statistical analyses, graphical representations and data preparation were performed using the software package SAS v. 9. 1  [33]. In order to provide a general overview, we plotted all chromosomes and illustrated length and position of ROH islands with boxes and pinpointed location of genes as vertical lines with either: (a) known functions, (b) associated with phenotypes in horses, (c) highlighted in selection signature studies, (d) with singular occurrence in ROH islands, and (e) genes, highlighted by GO analysis.
Gene Ontology Analysis The equine Ensembl database EquCab2 was used to identify genes located in ROH islands, available at www. ensembl. org. For the determination of gene ontology (GO) terms and KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways of identified annotated genes, the open source database for annotation, visualization and integrated discovery (DAVID) v6. 8 package  [34]  was used. For the GO analysis the equine annotation file as background and a significance threshold of p < 0. 05, correcting for multiple testing applying Bonferroni-Holm test, were chosen.
Genotype Frequencies of Genes Involved in Coat Color and Body Size In six breeds of the dataset, coat color represents an explicit breeding objective. In the Gidran and Haflinger, chestnut coat color is fixed. The desired color for the Exmoor Pony is brown combined with mealy areas around the eyes, muzzle, elbow and flanks. Lipizzan horses have been selected for their gray color for 150 years and the frequency of gray phenotypes reaches up to 98% [18] and the breeding program of the Noriker horse is based upon the selection for six different coat colors (bay, black, chestnut, leopard, roan and tobiano). We identified a ROH island containing MC1R, responsible for chestnut coat color, in the Gidran (1. 1 Mb length), Haflinger (2. 2 Mb length) and the Purebred Arabian (2. 1 Mb length) samples.
ECA3 and ECA11 were common ROH island hotspots in nearly all breeds of our dataset, except for French Trotter and Selle Francais, harboring genes involved in coat color (ECA3: MC1R), size (ECA3: LCORL/NCAPG, ECA11: LASP1), NER pathway (ECA3: UVSSA), embryonic skeletal morphogenesis (ECA11: HOXB-cluster) and coat texture (ECA11: KRT-complex). Recently, Gurgul et al. [7]  identified ECA11 as a major selection signature hotspot in six Polish horse breeds with a similar type composition (two draught horse breeds, two autochthonous/primitive breeds, one oriental and one Warmblood horse breed). The authors focused on diversifying selection signatures by grouping the breeds into different major horse type categories (light, primitive and draught type). Based upon this grouping they detected a strong signal between draught and primitive breeds on ECA11 within the LASP1 locus associated with body size  [35] , a region which overlapped with a ROH island  (23.
-Rolbing (Rol) group (one group composition): the group was composed of 11 individuals, namely two castrated males (2yo), two young females (1yo) and seven young males (1yo). Its composition did not change during the study. Data were scored by two observers located two to ten meters from the animals. The two observers were always within one meter of each other. One observed and communicated the behaviours to the other, who recorded the data. This allowed behaviours to be confirmed by two observers. Cattle were already habituated to human presence and were not disturbed by the observations, which were made once a week over a six-hour period between 9am and 5pm. The groups were not observed during rainy or snowy days or during the weekends. Sampling frequency for each group composition is given in Table  2.
e. Social network analysis Social network analysis (SNA) is an increasingly widespread tool for the study of sociality and its dynamic  (Croft et al. , 2008; Farine and Whitehead, 2015; Pinter-Wollman et al. , 2013; Sueur et al. , 2011a). Indeed, social relationships can evolve over time because of changes in the social strategies of group members, and the arrival or departure of individuals through births, deaths, migrations or transfers. Specific tools were developed in SNA to analyse these changes and their causes  (Borgeaud et al. , 2017 (Borgeaud et al. , , 2016;; Boucherie et al. , 2017; Pasquaretta et al. , 2016). SNA has also been recognised as a reliable tool for animal welfare and conservation  (Koene and Ipema, 2014; Snijders et al. , 2017; Sueur and Pelé, 2015). During data analysis, the matrices of spatial associations obtained per observation day were added together for each group composition.
These three matrices were calculated for each group composition and correlated to the dyadic spatial association matrices for each group composition. The 'CombinePValue' package in R 3. 24 was used to combine the p-value of all group compositions and obtain global statistics. The goal here was to test whether vectors of p-values are significant when combined and to confirm or negate the possible effect of a given socio-demographic factor at the population level. ii. How does a change of group composition or enclosure affect dyadic spatial associations? A Mantel test with 1 000 permutations in SocProg 2. 6 was used to correlate the dyadic association matrices after a change (transfers or enclosure change). Only individuals that were present in the two adjacent matrices for each matrix (ex: Rob1-Rob2, Rob2-Rob3, Stu1-Stu2, etc.