dataesr/scientific-paragraphs-categorization huggingface dataset:
Three factors of variation were successively analyzed in foals: 1) breed effect (pony vs saddlebred controls), 2) effect of increased fetal growth in ponies and 3) either restricted or increased fetal growth in saddlebred foals. Non repeated measures were analyzed using the coin plug-in for Rcmdr with the Mann-Whitney rank sum test for question 1 (P-P vs S-S) and 2 (P-D vs P-P) and with the Kruskal-Wallis test followed by the NDWD post-hoc test for question 3 (S-P vs S-S vs S-D)  [32]. Repeated measures were first analyzed using the F1 LD F1 model of the nparLD function to calculate an ANOVA-type statistic followed by paired comparison to answer the question of a group effect for each pair of groups  [32]. Data were then analyzed at each time point with the Mann-Whitney rank sum test for question 1 (P-P vs S-S) and 2 (P-D vs P-P) and with the Kruskal-Wallis test followed by the NDWD post-hoc test for question 3 (S-P vs S-S vs S-D).
Sexual dimorphism in control foals Data were analyzed for sexual dimorphism in 12 female vs 9 male control pony foals and in 16 vs 12 male control saddlebred foals. In both breeds, fillies and colts had similar gestational length and weight until 6 months of age. Saddlebred fillies had significantly higher IGF-1 concentrations on day 90 (p,0. 05) and higher T 3 concentrations on days 3 and 90 (p = 0,0. 05 for both) than saddlebred colts. In pony foals, significantly decreased T 4 levels were observed in pony fillies vs colts on day 180 (p,0. 05). There was a significant effect of the sex on fasting glucose in saddlebreds with increased concentrations in fillies vs colts on days 90 and 140 (p,0. 01). In contrast, fasting glucose in pony foals remained unaffected by the sex. No significant sex effect was found for IVGTT and clamps in either of the two breeds.
Acknowledgments The authors are grateful to  Joseph Bellonie ,  Philippe Barrie  `re,  Thierry Gascogne ,  Thierry Blard ,  Yvan Gaudeand Francois Stieau  for care and management of the mares and foals and for assistance during metabolic tests and Francoise Ternois and  Lionel Lardic  for management and assistance in the NEFA and insulin assays.
The device was chosen for its resistance to chewing or bites and its attractiveness (Courboulay, 2004;  Scott et al. , 2006). Each allowed simultaneous access of up to three pigs. Two devices were introduced in each pen and placed 50 cm apart in replacement of the fixed chains, without interfering with access to the feeder or the drinkers (Supplementary Figure  S1 ). The whole 9-h test period was videotaped. The pig interest in the devices was analysed at the pen level, using 5-min instantaneous scan sampling, defined by the investigative activity oriented towards the two devices by the experimental groups, including contacts such as sniffing, chewing or biting. Data were compiled per hour after the object introduction as percentage of pen activity dedicated to the object. Health criteria.
Feed intake SEF recording. After each visit to the SEF, the identity of the animal, the feeder entry and exit times, and the amount of feed consumed during the visit were stored (Labroue et al. , 1994). Data were analysed at three stages of the growing-finishing period, around 12, 17 and 22 weeks of age, for periods comprising 2 weeks before and 2 weeks after the day when health criteria were recorded, except for week 12, where only 1 week before was retained to ensure 1 week for pigs to get accustomed to the SEF. A 3 to 4-week period was retained to obtain accurate estimates of feeding patterns for the test  (Arthur et al. , 2008). The feed intake per visit and the feed intake, number of visits and visit durations per day were computed. A combined analysis of this data set with the feeding activity assessed from the video recordings was performed to evaluate if the video analysis of 24 h is representative of feeding activity over a longer period.
Statistical analysis Data on growth performance during the experimental period were submitted to a linear model including the line (two levels), sex (two levels) and batch (six levels) as fixed effects, and their interactions Y ijkl ¼ μ + line i + sex j + batch k + ðline i sex j Þ + ðline i batch k Þ + ðsex j batch k Þ + ε ijkl. A Pearson's χ 2 test was performed to compare time-budget items (8 d. f. ) and health criteria (within criteria, 2 d. f. ) between lines. Linear models were applied to the other traits to test line and sex effects (SAS software version 8; SAS Institute Inc. , Cary, NC, USA). For feeding patterns, the linear mixed model included the line, sex, batch and growth stage as fixed effects and all the two-way interactions and repeated animal as a random effect: Y ijklm ¼ μ + line i + sex j + batch k + stage l + ðline i sex j Þ + ðline i batch k Þ + ðsex j stage l Þ + ðsex j batch k Þ + ðbatch k stage l Þ + animal ijkm + ε ijklm.
Ochrobactrum intermedium is considered as an emerging human environmental opportunistic pathogen with mild virulence. The distribution of isolates and sequences described in literature and databases showed frequent association with human beings and polluted environments. As population structures are related to bacterial lifestyles, we investigated by multi-locus approach the genetic structure of a population of 65 isolates representative of the known natural distribution of O. intermedium. The population was further surveyed for genome dynamics using pulsed-field gel electrophoresis and genomics. The population displayed a clonal epidemic structure with events of recombination that occurred mainly in clonal complexes. Concerning biogeography, clones were shared by human and environments and were both cosmopolitan and local.
O. intermedium life-style and habitat deciphered to construct a representative collection In order to learn about the habitat and lifestyle of O. intermedium, we undertook a literature review and we screened nucleotide databases in June 2013. We found thirty-nine publications presenting 115 strains or clones with confirmed affiliation to O. intermedium. In genetic databases, 56 sequences not associated with a publication matched with the reference sequences used for screening (Table  S2 ). One study reported the isolation of O. intermedium whereas the strains belonged to the later described species O. pseudintermedium (NR_043756) on the basis of 16S rRNA gene sequencing  [19]. Conversely, 13 strains or clones (Tables  S1  and S2 ) that actually belonged to O. intermedium were affiliated to other Ochrobactrum species, mainly to O.
anthropi. Misidentifications were especially linked to wrong nomenclature in databases. For instance, the partial 16S rRNA gene sequence of several collection strains (CCUG39736, LMG5446, LMG3306, CCUG1838, CCUG44770) are affiliated to the species O. anthropi although these strains were transferred to the species O. intermedium based on partial sequence of the recA gene  [20]. Similarly, partial 16S rRNA gene sequence of the type strain of O. intermedium CNS 2-75 ( = LMG3301 T ) (NR_026039) is affiliated to O. anthropi. The databanks survey showed the affiliation of 171 strains and clones from publications (n = 115) and from genetic databases (n = 56) to the species O. intermedium on the basis of partial sequence of the 16S rRNA and/or recA genes, sometimes completed by phenotypic data. Figure  1  shows their distribution in a wide range of habitats and lifestyles.
intermedium mainly on the basis of plant nodules formation  (Imran, 2010). Therefore, our database screening approach was not suitable for discriminating O. intermedium and O. ciceri. Metagenomic clones matching with the sequences of O. intermedium used for database screening were scarce considering the amount of metagenomic data currently deposited in databanks. Only 28 clones could be affiliated to O. intermedium/ O. ciceri. They were detected in 8 different environments, most of them being technological and polluted environments, such as metal degreasing systems  [21] , aerosols and fluids in metalworking industry  [22] , biofouling biofilms, petroleum reservoir, polychlorinated bephenyl (PCB) polluted soil and polyacrylamide (PAM)degrading consortium. Some clones were detected in velvetleaves seed and only one clone was found in the human skin microbiota (GQ115798)  [23].
The atypical 16S rDNA insertion was present in all CC68 strains, including O. ciceri (Tables  1  and 2 ). Outside the cosmopolitan CC68, only three singletons (ADV109, Toul55 and CCM7036) and a strain of the CC74 (ADV93) were positive for this insertion. Apart from O. intermedium, a database search showed the insertion to be found in Ochrobactrum daejeonense (HQ171203) and Ochrobactrum pituitosum (AM490609), and outside the genus Ochrobactrum, in Brucella strains isolated from frogs (HE608873 and HE603360), Rhizobium sp. (FM173842), Paenochrobactrum sp. (JF804769) and Phyllobacterium sp. (GQ183850). The sequences of the insertion were identical for strains belonging to Ochrobactrum and Brucella sp. but differed by 1 to 6 bp in the 3 other genera. S1  and S2. doi:10. 1371/journal. pone. 0083376.
Survey of genome dynamics in O. intermedium The genomic DNA of strains was analysed by PFGE after macro-restriction with the endonuclease SpeI. The 65 strains showed 58 pulsotypes and nearly 80% (51/65) of strains had a unique pulsotype, indicating the global non-redondancy of the collection (Fig. 5 ). Seven pairs of strains displaying identical ST shared a pulsotype. Among them, two pairs of strains were isolated from the same patients (ADV67/ADV69 in ST90 and ADV127/ ADV126 in ST86). Two other pairs (CIP105839-CIP105840 in ST96 and LMG3306-LMG18956 in ST74) consisted of strains isolated from the same environmental habitat or body site, in the same country but no data on the link between these strains was available from bacterial collections. The three remaining pairs of strains appeared epidemiologically unrelated: LMG5426 and RT148-2 in ST68 were isolated from human urine (UK, before 1983) and water lake (France 2010), respectively; strains ADV101/ RT148-1P in ST70 and RT172/RT190-1 in ST76 were respectively isolated from distinct environmental habitats at different dates.
The sizes and sequences were determined from the complete sequence of strain LMG3301 T (PRJNA55963) for these two fragments. They corresponded to fragments of 206 and 289 kbp, respectively present on the large and the small chromosome of the bipartite genome of LMG3301 T. The chromosome size of the two strains was compared by PFGE after macrorestriction with the intronic enzyme I-CeuI. Each of the two chromosomes were cut in  two parts by hydrolysis in the 23S rRNA genes. The I-CeuI fragments could be placed on each chromosomes by reference to the complete sequence of strain LMG3301 T. The fragments corresponding to the small chromosomes had the same size, suggesting that the 289-kbp fragment was not deleted but that chromosomal rearrangement occurred in strain ADV147 (data not show). In contrast, a decrease in size consistent with the loss of a fragment of approximately 200 kbp was observed for the large I-CeuI fragment (2.
36 Mbp for LMG3301 T ) of the large chromosome of strain ADV147 without increase in size of the other I-CeuI fragment (240 kb). These results suggested that a genomic deletion occurred during the evolution of this clone. The DNA G+C content of the deleted fragment (59. 07%) was similar to the DNA G+C content of the O. intermedium LMG3301 T genome (57. 7%). The deleted fragment corresponded to positions 1734814 to 1941167 of the complete sequence of strain LMG3301 T (PRJNA55963) and contained 206 genes. The entire genomic fragment with 206 genes was syntenic in the genome of O. intermedium strain M86, the other strain of O. intermedium with completely sequenced genome  [26]. We considered that these 206 genes were potentially deleted in strain ADV147, even if sporadic translocation of some genes on other genomic contigs could not be excluded.
The lack of data about Ochrobactrum reservoir is mainly due to rare environmental investigations when clinical cases are described but also to difficulties for species identification in the genus. The database survey performed in this study showed that strains of O. intermedium/O. ciceri were affiliated to O. anthropi in 7. 6% of cases including recent publications probably because this species remains the only representative of the genus in several identification system databases. Consequently, the role of O. intermedium in human infection remains probably underestimated, as previously suggested  [16]. Despite the increasing number of infections due to O. intermedium, clones affiliated to this species were not found in human microbiotae  [30] , except one sequence from normal skin microbiota  [23].
Moreover, environmental metagenomics detected scarce O. intermedium clones, mainly in polluted or technological environments. Finally, the databanks survey suggests that O. intermedium is mostly found in hospitalized patients and in environments modified by human activities suggesting that this minority bacterium is selected by human practices involving the use of xenobiotics such as medicine, agriculture and industry. O. intermedium displayed a high level of resistance to several antimicrobial agents, notably to beta lactam antibiotics  [16, 31] , which represent the most commonly prescribed antimicrobial agents, and antibiotic resistance is frequently associated with resistance to environmental xenobiotics  [32, 33]. Altogether, the niche of O. intermedium could be described as a human-associated technological niche.
Bibliography and BLAST research strategy The literature search was conducted in March 2013 using Pubmed and the keywords ''Ochrobactrum intermedium'', crossreferences were also considered. When sequence accession numbers were reported in a publication, the affiliation of the sequence(s) to the species O. intermedium has been verified. Selection of other O. intermedium sequences deposited in databases was performed using the nearly complete 16S rRNA gene of O. intermedium strains LMG3301 T (AM490623), CCUG44770 (AM114410), LMG18956 (AJ242582), CCUG39736 (AM114408), CCM7036 (AM490631) and of O. ciceri strain Ca-34 T (DQ647056) using the Megablast program optimized for highly similar sequences for Genbank  [57]  and the Simrank program for Greengene  [58]  databases. The sequences having a similarity level of at least 99% with those of previous strains were selected.
PFGE bands above 100 kbp were measured with the Mesurim software (http:// pedagogie. ac-amiens. fr/svt/info/logiciels/Mesurim2/Telecharge. htm). The bands were scored as present  (1)  or absent (0) in a binary table, a tolerance of 2% in band position was applied. PFGE patterns were compared by calculation of the Dice correlation coefficient with the FAMD software (http://www. famd. me. uk/) and were clustered into a dendrogram by the unweighted pair group method with the arithmetic average clustering technique.
Gene amplification and sequencing Genomic DNA was obtained using the MasterPure TM DNA purification kit (EpiCentre). Seven genes (dnaK, recA, rpoB, trpE, aroC, omp25 and gap) were amplified using primers and PCR conditions previously described for MLST scheme of O. anthropi  [37]. PCR products and molecular weight marker (phage phiX DNA digested with HaeIII, New England Biolabs) were separated in 1. 5% (w/v) agarose gels in 0. 5X TBE buffer. Amplification products were sequenced in both directions using forward and reverse sequencing primers  [37]  on an ABI 3730xl automatic sequencer (Cogenics, France). The sequences were deposited to GenBank database with accession numbers KF825086 to KF825540 and KF866307 to KF866369. The primer ins1 was used in association with the universal primer 1492r for specific detection of rrs copies carrying a 46-bp atypical insertion previously described  [9].
Phylogeny and decomposition analysis Gene sequences were codon-aligned using ClustalX after translation with TRANSLATE (http://www. expasy. org). The size of the codon-aligned sequences used for further analyses is indicated in Table  3. Phylogenetic analyses were performed for each of the seven gene sequences and for the manually concatenated sequence. Evolutionary distance was analyzed using Phylip package v3. 66  [59]  by Neighbor-Joining after distance matrix construction using DNADIST (F84 as substitution model). Bootstrap values were calculated using SEQBOOT and CON-SENSE after 1000 reiterations. Maximum-likelihood (ML) analysis was performed using phylogenetic analyses available at http:// www. phylogeny. fr [60]. The general time-reversible (GTR) model plus gamma distribution and invariant sites was used as a substitution model.
ML bootstrap support was computed after 100 reiterations. The sequences of O. anthropi ATCC49188 T (PRJNA58921) and/or Rhizobium rhizogenes (PRJNA58269) were included in phylogenetic analyses in order to place an artificial tree root. Along with the phylogenetic reconstruction, we performed a network reconstruction on concatenated data using the Neighbornet algorithm available in Splitstree4 software  [61].
Multi Locus Sequence Typing (MLST) and multilocus genetics For each locus, each different allele was assigned to a different arbitrary number using a nonredundant database program available at http://linux. mlst. net/nrdb/nrdb. htm. The combination of allele numbers for each isolate defined the sequence type (ST). A Minimum Spanning (MS) tree was constructed using Prim's algorithm to determine the links among STs (http://www. pubmlst. org). Clonal complexes (CC) included STs that differed by 1 or 2 alleles. The singleton STs corresponded to STs differing from every other ST at 3 or more of the 7 loci. The LIAN v3. 5 program  [62]  was used to calculate the standardized I A (sI A ) and to test the null hypothesis of linkage disequilibrium as well as to determine mean genetic diversity (H) and genetic diversity at each locus (h).
Acknowledgments We are particularly indebted to the microbiology lab team of the Montpellier academic hospital for providing clinical isolates. We also thank  Corentine Alauzet ,  Christine Seconds  and  Anne Gouby  for providing additional clinical isolates,  Sylvie Pages  for her help in isolating nematode-associated strains,  Jean-Luc Jeannot  for isolation of environmental strains and  Helene Marion  for technical assistance.
Data French birth registration forms for draft horses include, since 1998, a score to record the conditions of foaling. In this study, we focused on the main breeds: Breton (B), Comtois (C), Percheron (P) and a fourth category designated Ardennais (A) including Ardennais, Auxois, Trait du Nord breeds between which the genetic distance is very small and that can mate together  (Leroy et al. , 2009). Only pure bred births from 1998 to 2010 were considered. Scores for FE were assigned by the breeder: 'without help', 'easy', 'difficult' and 'intervention of the veterinarian'. It was found to be difficult, both for breeders and during data analysis, to clearly distinguish between 'without help' and 'easy'. The data for these two categories were therefore grouped during analysis and we used three ordered categories: 1 = 'without help or easy', 2 = 'difficult', 3 = 'intervention of the veterinarian'.
Data were missing about foaling difficulty on the registration forms in 21% to 30% of cases, but without any particular distribution depending on the region, maternal age, sex of foal or sires. Cases of observed dystocia were excluded if the sex of the foal was missing (1%). Unfortunately the scores for these excluded observations were high with 31% of the births recorded as 'difficult', instead of 3% to 7% in the data retained for analysis. But as the sex ratio remained close to 50% in the analysed data, we expected the estimates not to be biased for the effects included in the model. SBs were defined as foals that were born dead and never showed a detectable heartbeat. The characteristics of the data sets are provided in Table  1. All available pedigree data for mares and foals were used in the analysis.
Discussion The data included in the present study were sufficiently consistent and unselected to be used for genetic analysis. We failed to understand the causes of environmental improvement for FE for B and P with time (year effect) and change of the interpretation of scoring with time cannot be entirely excluded. In the same way, differences observed for SB in the four first years without improvement from then on, may be due to the way that observations are recorded (choice between SB and early mortality of a live foal). The estimates Figure  2  Effect of maternal age (in years) and parity on liability of foaling ease, expressed relative to parity 2 to 3 of mares aged 5 to 9 for the four breeds. Genetics of dystocia and stillbirths in draft horses of environmental effects obtained here show the importance of maternal age and parity.
diphtheriae database (http://pubmlst. org/cdiphtheriae/) and only provisional because there is presently no MLST scheme for C. ulcerans. Nevertheless, this result strongly suggests that transmission of C. ulcerans tox+ occurred from a stray cat. Few studies have described toxigenic C. ulcerans in domestic cats  [8] [9] [10]. Transmission from animal to human or from a common unknown source of infection cannot be formally ruled out as several recent studies have mentioned C. ulcerans carriage in different mammalian species  [11, 12].
To ensure that relevant clinical information is archived in the national EV surveillance database, the IDED sends a letter with a standardised questionnaire regarding information on the clinical symptoms (including information on acute flaccid paralysis) and a reminder to send stool for virus characterisation directly to the doctors/departments in charge of the EV-positive patients. Completed questionnaires are returned and data entered in the database by the IDED, SSI. To ensure completeness of clinical data information for this paper, we have contacted relevant hospital departments and asked for relevant information on all EV71 cases where clinical information was missing.
French national surveillance programme on listeriosis and therefore has some limitations. As no information on clinical symptoms was available, we considered neonates with L. monocytogenes isolated exclusively from surface swabs as possible listeriosis cases although they may not actually have been infected. Moreover, we have no information on the long-term sequelae in the newborn. The MONALISA study (Multicentric Observational National Analysis of LISteriosis and ListeriA; http://clinicaltrials. gov/show/ NCT01520597), a prospective study on listeriosis, will present detailed clinical, biological and microbiological data of all incident cases of listeriosis in France from the end of November 2009 until 2013, including pregnancy-related cases, and provide extensive information on the prognosis of newborns.
Acknowledgements The authors are grateful to  Daniel Lévy-Bruhl ,  Beatrice Pangon ,  Constance Lebas ,  Juan Vinas ,  Mireille Billet ,  Catherine Vogeleisen ,  Agnes Giraud ,  Florence Collemare ,  Lyderic Aubert ,  Christiane Bruel ,  Celine Legout  and  Jourdain de Muizon.
The sequence identifiers for the sequences obtained in this study are made up of a two figure prefix to denote the year of sample collection, followed by our internal sample number. Subgenotype C reference sequences were downloaded from GenBank (EV71 C1 accession number: DQ341360; EV71 C2: AF136379; EV71 C3: DQ341355; EV71 C4a: EU913466; EV71 C4b: EU547500; EV71 C5: EU527983). EV71 subgenotypes A (EV71A: ETU22521) and B (B1: AB482183; B2: ETU22522; B3: EU364841; B4: DQ341365; B5: DQ341362) were included to root the tree. Previously identified European C4 strains were also included in the analysis. The scale bar represents the number of nucleotide substitutions per site. D Girard (delphine. gd@gmail.