dataesr/scientific-paragraphs-categorization huggingface dataset:
Stained cross-sections were then analyzed by image analysis with two home-made programs developed by our team using Visilog 6. 7 Professional Software (Noesis, Gif-sur-Yvette, France): Perimysium Analyzer to study perimysium, and Endomysium Fibre Analyzer to study endomysium, previously described  (Dubost et al. , 2013a). About perimysium study, each stained muscle section (1. 5 × 1. 5 cm) was scanned entirely in transmission mode using an EPSON (Levallois Perret, France) Expression 10000XL PRO A3 scanner (resolution of 2400 dpi, corresponding to a spatial resolution of 10. 58 µm/pixel). For endomysium, stained sections were visualized in bright field mode with an Olympus BX51 microscope (Olympus, Tokyo, Japan) using a 10 × objective (NA = 0. 3). Five images were acquired randomly from the stained sections of 1.
5 × 1. 5 cm (the same as used for perimysium study) with a DP-72 colour camera and Cell-D image acquisition software (Olympus Soft Imaging Solutions, Münster, Germany). The resolution was 1360 × 1024 pixels, representing an 879 × 662 µm field of view. The resulting spatial resolution was 0. 65 µm/pixel. Perimysium, area (percentage of the total image) and number of branch points per cm² were determined. Only area of endomysium (percentage of the total image) was determined. Collagen and CL measurements Total and insoluble collagen were determined according to the procedures of  Woessner (1961)  and  Hill (1966) , previously described and updated by  Listrat et al. (Listrat et al. , 1999; Dubost, Micol, Lethias and Listrat Listrat and Hocquette, 2004). Both for total and insoluble collagen, each sample was weighed and measured in triplicate and data were expressed in milligrams of collagen per gram of dry matter (mg/g DM), using the factor 7.
14 as ratio corresponding to the mean hydroxyproline content of the collagen present in intramuscular CT. About CLs measurement, 1 ml of acid hydrolysate (in HCl 6 N) from total collagen was centrifuged at 16 000 × g for 5 min at +4°C. Then 600 µl of 6 N NaOH and 600 µl of 1 M Tris were added to 600 µl of acid supernatant. Final pH was adjusted between 7 and 8 with a few microliters of 6 N HCl or NaOH. Pyridinoline CLs were determined by the enzymelinked immunoassay Metra Pyd EIA kit (Quidel Corporation, San Diego, USA) according to the manufacturer. Previous assays had indicated no interfering effect of the 1/10 diluted muscle extract on the pyridinoline CL determination (data not shown). Results were expressed in nanomolar of pyridinoline per gram of dry matter (nM pyr/g DM) and in millimolar of pyridinoline per mole of collagen (mM pyr/M collagen) (assuming that collagen had a molecular weight of 300 000 Da)  (Etherington and Sims, 1981).
Anti-decorin was from Developmental Studies Hybridoma Bank, and anti-collagen XIV and anti-tenascin-X have been characterized by  Lethias et al. (1993)  and  Lethias et al. (2001) , respectively. Membranes were washed 2 × for 10 min in T-TBS 1 × and hybridized with the second antibody associated with horseradish peroxidase for chemiluminescence detection (IgG sheep anti-mouse, NA931; Amersham, GE Health Care, Vélizy Villacoublay, France) diluted to 1/5000. Bands corresponding to the studied molecules were quantified under Image Quant software. Each band was normalized by the mix of the samples deposited on each gel. Quantities of decorin, tenascin-X and collagen XIV were expressed in arbitrary units (AU) or per milligram of total collagen or per microgram PGs in DM. Meat quality evaluation About Warner-Bratzler shear force measurement, LT muscle cuts (3 cm thick pieces parallel as possible to the muscle fibres long axis) were grilled up to an internal temperature of 55°C and BF muscle cuts were cooked in a water bath (hermetically sealed in plastic bags) for 1 h to an internal temperature of 70°C.
Statistical analyses Structural (perimysium and endomysium characteristics), biochemical (total collagen and its CLs, total PGs, decorin, tenascin-X and collagen XIV) data and the proportions of decorin, tenascin-X and collagen XIV to total collagen or PGs were submitted to ANOVA. We calculated these proportions Muscle ECM molecules and sensory beef qualities to determine if for the same quantity of collagen or PGs, the proportion of decorin, tenascin-X and collagen XIV was constant. All results were presented as LS means with appropriate SEM and the level of significance. Differences between the two muscles were claimed significant for P < 0. 05. The model included also breed effect. The breed effect and the interactions between muscle and breed were not significant, then only muscle effect was presented in this paper.
Pooled western blot data from the two muscles, for decorin, tenascin-X and collagen XIV expressed in AU were submitted to Pearson's correlation analysis, respectively, with structural and biochemical parameters of CT. It was possible to pool data from the two muscles, because both populations were evenly distributed homogeneously. ANOVA and Pearson's correlations were achieved using XLSTAT-Pro 2012. 3. 01. The REG procedure of SAS (1990, SAS Institute Inc. ; Cary, NC, USA) was used to study the explained variance and regression coefficients of decorin, tenascin-X and collagen XIV relative abundance on beef quality traits from pooled data of the two muscles. In addition, to verify if the ratios of decorin, tenascin-X and collagen XIV to total collagen or PGs could explain quality parameters, Pearson's correlations were achieved on pooled data of the two muscles.
Acknowledgements The authors thank the staff of  Experimental Unit (UERT) of INRA (Theix)  for animal management, slaughtering and  Warner-Bratzler  shear force measurements, the staff of  Amuvi (Animal, Muscle, Viande ) team for muscle sampling and  Arnaud Delavaud  for western blot contribution. The authors also thank the staff and panellists of  Experimental Unit of INRA (Le Magneraud ) for sensory evaluation.
Materials and Methods Stimulus acquisition and preparation. Howl vocalisations and bark-howls were selected from a database of recordings collected since 2012 from captive dingoes housed in two sanctuaries: Colong Station and Secret Creek Reserve, New South Wales, described elsewhere  27. A total of 141 calls from nine dingoes were selected. To prevent any potential confounding effect of differences in social relationships between exemplar and test dingoes, all exemplar dingoes were initially unknown to the test animals (they were maintained in sanctuaries different from the one where we conducted the tests). Instead, we experimentally created 'familiar' conspecifics by broadcasting their howl vocalisations (hereafter termed 'familiarization howl series') to the test dingoes during familiarization trials performed for two days before starting the test trials (Table  2 ).
Trial durations were 10-30 min. Behavioural measures. Behavioural responses were scored from the videos using VideoPad 3. 34 (NCH Software) and the experimenter E1 was blind to the treatment condition. We recorded three behavioural responses: 1) number of looks, 2) approach toward the speaker (i. e. positive phonotaxis) and 3) vigilance behaviours including 'watching' and 'focused'. We recorded the number of looks for a given trial by scoring whether dingoes looked toward the speaker for each of the five calls of the test series. When the focal individual's head was not clearly visible, we coded the response as missing for that call (7% of 360 observations). For each trial, we scored the presence/absence of approach behaviours, defined as a movement that decreased the distance between the focal individual and the speaker and exhibited during stimulus presentation.
Acknowledgements We thank  Lyn Watson  and the staff at  Dingo Discovery and Research Centre  for their help and support during the experiment. We are also grateful to Amanda and  Gavin McDowell  from  Colong Station , and  Trevor Evans  from  Secret Creek Reserve , for permission to record their animals. This research was funded by the  Hermon Slade Foundation  project grant # 9201300442 ,  Macquarie University  and the  CNRS. The funding bodies had no involvement in the conception of the study, data collection, analysis or interpretation.
The analysis was performed with 67 hepatitis E virus (HEV) complete genomes or complete coding sequences available in the GenBank database and representative of each genotype. The sequence size varies between 6543 and 7318 nt in length, and they were aligned using Clustal W. The bootstraps were obtained from 1000 replicates and values over 70% are indicated at the genotype level. The initial tree was obtained by applying the Neighbour-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. The tree is drawn to scale, with branch lengths proportional to the number of substitutions per site. Evolutionary analyses were conducted using Molecular Evolutionary Genetics Analysis (Version 6. 0). The Orthohepevirus species taxon name is added at the junction of the last common ancestor for each species.
HEV Phylogeny To date, 240 complete genomes are available in Genbank (NCBI database), compared to 49 complete genomes available in 2006, with more than 120 sequences of HEV-3. The use of full-length sequences has improved the phylogeny and classification of HEV, but trees generated previously, using shorter sequences from selected genomic regions (partial-ORF1 or partial-ORF2), show similar structures than those generated with full genomes  [35]. Within genotypes, a high diversity can be observed requiring further classification into subtypes or clade/group and subclade/subgroup (genotype 3, Figure  2 )  [35] [36] [37]. Thus, a methodology was recently proposed to standardise HEV subtyping. Using this method, subtypes can be redefined when novel full-sequences are added (Figure  2 )  [38].
The tree was inferred using the Maximum Likelihood method based on the Tamura-Nei model. The analysis involved the 75 most representative HEV-3 complete sequences/cds available on the GenBank database and aligned using the clustal W method. The bootstraps were obtained from 1000 replicates and values >70% are indicated. The initial tree was obtained by applying the Neighbour-Joining method to a matrix of pairwise distances estimated using the MCL approach. The tree is drawn to scale, with branch lengths proportional to the number of substitutions per site. Evolutionary analyses were conducted using Molecular Evolutionary Genetics Analysis (Version 6. 0). Cluster names from the classification proposed by Lu et al. , Vina-Rodrigues et al. and Smith et al. (letters a to j and ra cluster) are indicated in the table on the right side of the tree  [35, 38, 39]  and by Mirazo et al.
Genotypes 1 and 2 These two human genotypes are genetically close with almost 76% nt identity. HEV-1 is well described and divided into six subtypes (1a to 1f) while HEV-2 is less documented and divided into 2 subtypes (2a and 2b) (Figure  1 )  [38]. Strains belonging to genotype 1 share 88. 53% to 94. 05% nt identity and are found mainly in Asia, Africa and Mexico  [40]. Genotype 2 strains were isolated in Central America (Mexico) and Africa (Tchad, Nigeria)  [39, [41] [42] [43]. Genotype 3 HEV-3 is the best described and documented genotype in Genbank. Most sequences originate from humans, pigs and wild boars (Figure  2 ). HEV-3 is divided into 10 subtypes (a to j) and two clades (3abchij and 3efg)  [35, 36, 38, 44, 45]  (Figure  2 ), sharing 78. 74% to 82. 46% nt identity. HEV-3 includes some unassigned strains  [38]  and rabbit HEV for which genotyping it is still under consideration.
The annual numbers of publications on mutation discoveries have more than doubled in the last decade compared with the early 2000s when only linkage maps were available. Today, well-annotated genome assemblies and SNP chips are available as screening tools for genome-wide association studies  (Nicholas and Hobbs, 2013). In the Online Mendelian Inheritance in Animals (OMIA) database, where update lists of scientifically described Mendelian traits in non-laboratory species can be found, the number of entries for horses is much lower than that for other species, particularly dogs. As shown in Table  1 , the number of Mendelian traits that has been described in horses until August 2015 is about six times smaller than in dogs and five times smaller than in cattle. Furthermore, coat color genetics make up a relatively larger part in horses (24.
Introduction Nocardioides massiliensis strain GD13 T (= DSM 28216 = CSUR P894) is the type strain of N. massiliensis sp. nov. This bacterium was isolated from the human faeces of a 62-year-old man admitted to intensive care for a Guillain-Barré syndrome as part of an effort called culturomics to cultivate all bacterial species from the human gut  [1, 2]. The current taxonomic classification of prokaryotes is based on a combination of phenotypic and genotypic characteristics  [3, 4] , which includes 16S rRNA gene phylogeny, G+C content and DNA-DNA hybridization. Although these tools are considered the reference standard, they have several drawbacks  [5, 6]. As a result of the declining cost of sequencing, the number of sequenced bacterial genomes has rapidly grown; to date, almost 40 000 bacterial genomes have been sequenced (GOLD Database, https://gold.
Organism Information and Classification A stool sample was collected from a 62-year-old man admitted to the intensive care unit of Hôpital Nord, Marseille, France, in March 2012  [2]. The study was approved by the ethics committee of the Institut Fédératif de Recherche IFR48 (Faculty of Medicine, Marseille, France), under agreement 09-002. At the time of sampling, the patient had received a 10-day course of imipenem (3 g per day). The faecal specimen was preserved at -80°C after collection. Strain GD13 T (Table  1 ) was isolated in March 2012 by cultivation on PVX agar (bioMérieux, Marcy l'Étoile, France) in an aerobic atmosphere at 28°C after 14 days of incubation. Strain GD13 T exhibited a 98. 07% 16S rRNA sequence identity with N. mesophilus (GenBank accession no. EF466117), the phylogenetically closest bacterial species with a validly published name (Figure  1 ).
0 software (Bruker) and analysed by standard pattern matching (with default parameter settings) against the main spectra of 7379 bacteria, including 48 spectra from two Nocardioides species. It corresponded to the Bruker database combined with our own database constantly incremented with new species. The method of identification included the m/z from 3000 to 15 000 Da. For every spectrum, a maximum of 100 peaks were compared with spectra in the database. The resulting score enabled the identification or not of tested species: a score of 2 with a validly published species enabled identification at the species level, a score of 1. 7 but <2 enabled identification at the genus level and a score of <1. 7 did not enable any identification. No significant MALDI-TOF score was obtained for strain GD13 T against the Bruker database and against our own database, suggesting that our isolate was not a member of a known species.
Genome Sequencing Information Genome project history Nocardioides massiliensis GD13 T was selected for sequencing on the basis of its phenotypic differences, phylogenetic position and 16S rRNA sequence similarity to other members of the genus Nocardioides. It was part of a culturomics study aimed at isolating all bacterial species from the human digestive flora from patients treated with broad-spectrum antibiotics. It is the first sequenced genome of N. massiliensis sp. nov. The GenBank Bioproject number is PRJEB1962 and consists of 839 large contigs. Table  3  shows the project information and its association with minimum information about a genome sequence (MIGS) 2. 0 compliance  [47].
Automated cluster generation and sequencing run was performed in a single 39-hour run at a 2 × 250 bp read length. Total mate paired run information of 3. 2 Gb was obtained from a 690K/mm 2 density with 95. 4% (13 264 000 clusters) of the clusters passing QC filters. Within this pooled run, the index representation for Nocardioides massiliensis was determined to be 8. 12%. From this genome sequencing process, the 1 027 586 produced Illumina paired end reads of N. massiliensis were filtered according to the read qualities. The reads obtained from both applications were trimmed and the optimal assembly was obtained through the CLC genomics wb4 software with 839 contigs which generated a genome size of 4. 00 Mb. - - + + + Urease - NA - NA NA - α-Galactosidase - - - - - - β-Galactosidase - - - + - + β-Glucuronidase - - - - - w α-Glucosidase + + - + - + β-Glucosidase + + - + - + Esterase + - + + - + Esterase lipase + - - + + Naphthol-AS-BI-phosphohydrolase + NA + + w - N-acetyl-β-glucosaminidase - - - - - - α-Mannosidase - - - - - - α-Fucosidase - - - - - - Leucine arylamidase + + + + + + Valine arylamidase - - - - - - Cystine arylamidase - - - + - - α-Chymotrypsin - - - - - - Trypsin - - - - - + Utilization of: 5-Keto-gluconate - NA NA NA NA + D-Xylose - - + N A - - D-Fructose - - - NA - - D-Glucose - - + N A - + D-Mannose - - + N A - -.
Genome annotation and comparison Open reading frames (ORFs) were predicted using Prodigal  [48]  with default parameters, but the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank database  [49]  and the Clusters of Orthologous Groups (COGs) database using BLASTP. The tRNAScanSE tool  [50]  was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer  [51]  and BLASTN against the GenBank database. Lipoprotein signal peptides and the number of transmembrane helices were predicted using SignalP  [52]  and TMHMM  [53]  respectively. ORFans were identified if their BLASTP E value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E value of 1e-05.
Such parameter thresholds have already been used in previous works to define ORFans. For the genomic comparison, we compared the genome sequence of N. massiliensis strain GD13 T (GenBank accession no. CCXJ00000000) with those of Nocardioides alkalitolerans strain DSM 16699 (GenBank accession no. AUFN00000000), Nocardioides halotolerans strain DSM 19273 (AUGT00000000), Nocardioides insulae strain DSM 17944 (AUGU00000000) and Aeromicrobium massiliense strain JC14 T (CAHG00000000). To estimate the nucleotide sequence similarity at the genome level between N. massiliensis and other members of the family Nocardioidaceae, we determined the average genomic identity of orthologous gene sequences (AGIOS) parameter using the MAGi (Marseille Average genomic identity) software as follows: orthologous proteins were detected using the Proteinortho software (version 1.
Growth occurred aerobically between 25 and 37°C. Cells exhibit catalase activity but are oxidase negative. Positive reactions are observed for esterase (C4), esterase lipase (C8), acid phosphatase, alkaline phosphatase, leucine arylamidase, naphthol-AS-BI-phosphohydrolase, α-glucosidase, β-glucosidase, arginine arylamidase, proline arylamidase, esculin The G+C content of the genome is 71. 0%. The 16S rRNA and whole-genome sequence of N. massiliensis strain GD13 T are deposited in EMBL-EBI under the accession numbers HF952922 and CCXJ00000000 respectively. The type strain GD13 T (= CSUR P894 = DSM 28216) was isolated from the faecal flora of a 62-year-old man admitted to intensive care in Marseille, France, for Guillain-Barré syndrome who had received 10 days of broad-spectrum antibiotics.
76 Nucleotide transport and metabolism H 126 3. 04 Coenzyme transport and metabolism I 268 6. 48 Lipid transport and metabolism P 213 5. 15 Inorganic ion transport and metabolism Q 178 4. 30 Secondary metabolites biosynthesis, transport and catabolism R 460 11. 13 General function prediction only S 190 4. 59 Function unknown - 1396 33. 4 Not in COGs COGS, Clusters of Orthologous Groups database. 54 New Microbes and New Infections, Volume 10 Number C, March 2016 NMNI New Microbes and New Infections © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases, NMNI, 10, 47-57 This is an open access article under the CC BY-NC-ND license (http://creativecommons. org/licenses/by-nc-nd/4. 0/).
For managers, having access to scientific evidence on the efficacy of conservation interventions is essential to formulating and enacting sound conservation policies  [4, 65]. Open access journals and online databases, such as ConservationEvidence. com, narrow the gap between science and conservation management by making systematic reviews of evidence readily available. Despite their success, these reviews are still in their infancy for many important conservation areas  [66] , including many of the questions within this list. Therefore, by including a systematic review as part of the dedicated research proposal or grant that tackles a question from this list, researchers can increase the likelihood that findings in their field will be adopted in management policy. Such efforts will be instrumental in developing novel, effective, and costefficient conservation and wildlife management actions that both researchers and practitioners will be eager to pursue together (see the 50 Outstanding Questions listed in the previous sections).
Photographs from 12 dogs were included, with 3 dorsal and 3 nonstandardised photographs from each dog. Again, the investigator ensured that they represented a range of breeds (corgi, Cavalier King Charles spaniel [CKCS], crossbred, JRT, Labrador retriever  [4] , Lhasa apso, and Yorkshire terrier  [2] ), sexes (8 neutered male, 4 female), BCS scores (median 7, range 5-9), coat lengths (3 short, 6 medium, 3 long), coat colours (3 dark, 1 mid, 4 mixed, 4 light), and stages of weight loss (7 pre-weight-loss, 5 post-weight loss). Dorsal and non-standardised photographs were separately coded using the random number generator function of a computer software programme (Stats Direct version 2. 6. 8),.
Statistical analysis Study data are available in the supplemental material (see Additional file 1). Data are expressed as median (range) except where indicated. Statistical analyses were performed with computer software (Stats Direct version 2. 6. 8), and the level of significance was set at P < 0. 05 for two-sided analyses. For continuous data (e. g. age, A:T ratio and body fat percentage), the Shapiro-Wilk test was first used to assess whether or not data were normally distributed, and parametric and non-parametric tests were then used as appropriate. The association between A:T ratio and body fat mass was determined with Spearman's rank correlation, whilst grouped linear regression was used to determine the effect of various factors (e. g. breed group, sex, coat length, coat colour) on this association.
Whilst such an assessment would not replace the use of conventional BCS performed by an experienced operator, it would arguably be better than relying on BCS measurements from owners or other lay people. Owner scores are unreliable demonstrating a systematic tendency to under-estimate condition  [7]  whether or not training has been provided  [8]. If an online tool for assessing vBCS were to be developed, it could be used to advise owners on the likely body condition of their dog, and also to provide cautious guidance as to what action they should take. For instance, owners of dogs that were categorised as ideal weight Results are expressed as median (range). The columns represent data for the three methods indirect body condition scoring (BCS) using photographs. vBCS measured : BCS based upon abdominal width to thoracic width ratio measured from a dorsal photograph; vBCS subjective : BCS semi-quantitatively assessed from a non-standardised photograph using visual descriptors; vBCS adjusted : a refinement of vBCS measured , whereby the A:T ratio was first used to estimate BS, but the observer could then modify after examining standardised dorsal and lateral photographs and applying visual BCS descriptors.