dataesr/scientific-paragraphs-categorization huggingface dataset:
Adults receiving HB immunization had significantly increased odds ratios (OR) for MS (OR 5. 2; CI 1. 9-20) in comparison with an age-, sex-, and vaccine yearmatched unexposed tetanus-containing vaccine group  [11]. A Hernan's paper, based on a case-control study in the United Kingdom within the General Practice Research Database (GPRD), found an increased risk (OR 3. 1; CI 1. 5-6. 3) of MS within the 3 years following HB immunization  [12]. In the same way, a French study on demyelination in childhood  [13]  showed that Engerix B Ò vaccine administration was associated with an increased trend of confirmed MS after 3 years (OR 2. 77; CI 1. 23-6. 24). On these grounds, we compared temporal HB vaccine dose distribution and MS occurrence in the French population, using the official data collected by the French pharmacovigilance system (ANSM) and the national health insurance (CNAM).
ANSM data analysis Since the beginning of practicing HB vaccination in France until December 31, 2010, ANSM has registered 1,650 demyelinating diseases including 1,418 MS. These data are available online on the Web site of ANSM in the French national commission for pharmacovigilance of September 27, 2011  [15]. When you draw a distribution curve of MS reported each year to ANSM in the aftermath of a vaccine injection, we see that this distribution is neither linear nor regular, far from it (Fig. 2 ). There is a huge peak of reported MS culminating in the years 1995 (229 reports) and 1996 (246 reports). This peak of post-vaccine neurological disorders during the period 1994-1998 corresponds, with an interval of one year, to the beginning of the campaign and intense promotion of the HB vaccination in France (culminating in the year 1995 with about 23 million vaccine doses sold).
00106 for Xt and 0. 02491 for Xt ? 1) on the number of reported MS at t ? 2 years (Yt ? 2), i. e. , 2 years later. But we cannot say whether the number of vaccines sold in year t ? 2 (Xt ? 2) has a significant influence (p = 0. 07014). Graphically, this relation is also the model that best fits the peak of reported MS to ANSM. It is difficult to adjust the MS data after year 2002. There is then a notable difference between the theoretical series (models) and the actual series. This can be explained by the fact that the number of vaccinations mentioned by ANSM became less precise figures, rounded and approximate. In addition, since 1999, the immunization target has been focused on young children. Adult vaccination has become uncommon, reserved only for high-risk groups. Finally, the number of MS reported to pharmacovigilance has arguably become more and more underestimated over the years.
This is a strong signal that requires further epidemiological studies. The positive and statistically significant correlation between HB vaccine exposure and reported MS incidence is consistently observed in different places, circumstances, and times (criterion 2). First, this result is consistent with the Hernan's casecontrol study  [12]  that found in the British population an increased risk of MS (OR 3. 1; CI 1. 5-6. 3) in the 3 years following HB vaccination. Moreover, in this same study, the risk was greater when the last immunization took place within the second or third years before first symptoms of MS (OR 4. 1; CI 1. 3-13. 6). The results of the case-control study by Geier  [11]  in USA are also consistent with the French pharmacovigilance data. There is a very significant change in the risk of developing MS after HB vaccine in adults in the VAERS database (OR 5.
Acknowledgments The author thanks  Mr. A. Sesbou  ¨e ( Department of Statistics, Caen University, France ) a lot for his statistical interpretation. He also gratefully acknowledges  Pr. C. Exley  ( Bioinorganic Chemistry Laboratory, Keele University, Staffordshire, UK ) and Pr. R. K. Gherardi  ( Department of Pathology, Creteil University Hospital, France ) for their judicious rewriting.
5 mag). Dwarf systems are of particular interest in the study of the effects of the environment on galaxy evolution since they are fragile objects easily perturbed just because of their shallow potential well (e. g. Boselli & Gavazzi 2014 ). The paper is structured as follows: in section 2 we describe the dataset used in this analysis, while in section 3 we explain the different techniques used to identify Virgo cluster members. The UV luminosity function is derived in section 4 and analysed in the framework of galaxy evolution in rich environments in section 5.
Acknowledgements. We thank the anonymous referee for constructive comments that helped improving the quality of the manuscript. This research has been financed by the  French ANR  grant VIRAGE and the  French national program  PNCG. We wish to thank the  GALEX Time Allocation Committee  for the generous allocation of time devoted to this project. LC acknowledges financial support from the  Australian Research Council  ( DP130100664 ). This research has made use of the NASA/IPAC Extragalactic Database (NED) which is operated by the  Jet Propulsion Laboratory, California Institute of Technology , under contract with the  National Aeronautics and Space Administration and of the GOLDMine database  (http://goldmine. mib. infn. it/)(Gavazzi et al. 2003). GALEX (Galaxy Evolution Explorer) is a NASA Small Explorer, launched in 2003 April.
Geographic and demographic data This study was carried out in rural areas of Cameroon (figure  1 ). The present study was performed on a large population of Bantus and Pygmies, living in remote rural villages or settlements of the rain forest area of South and East Cameroon. Study populations were sequentially sampled over different time periods. Samples from the South were mostly collected from 1994 through 2000. A complementary series was collected from 2006 through 2010. Samples from the Centre and the East areas were collected from 2004 through 2010. Populations and collection procedures have been previously described  [51, 52]  and comprise diverse Bantu groups from the three study areas and two Pygmy groups. The Baka Pygmies, by far the most important Pygmy group in Cameroon is found in Eastern and Southern Cameroon.
The Bakolas are the second most important group and have their settlements exclusively in the Southern part of the country and the Bedzams are the less numerically important and less accessible. This group was not included in the current work. A systematic approach for the enrolment was carried out in all reachable villages and settlements, scattered alongside roads and tracks across the forest. A standardized questionnaire was used to collect personal demographic data. Collected data included the name, age, sex, location, ethnicity, family links. A 5 to 10 ml whole blood sample was collected in EDTA K2 vacuum tubes, from all consenting individuals meeting the inclusion criteria. Plasma and buffy-coat were obtained 48 to 72 hours after sampling and kept frozen at 280uC. A simple clinical examination was performed when requested by participants in the study.
KSHV molecular analysis and phylogenetic analyses Conditions and procedures for DNA extraction from blood buffy coats in all positive plasmas on BC3 serological assays, as well as amplification method have been previously described  [37]. Amplified products for 29 samples were directly sequenced and phylogenetic analyses were conducted. All new sequences are deposited in GenBank under accession numbers: JX290272 (O350805), JX290273 (Mezi5), JX290274 (AKO107), JX290275 (Lobak80), JX290276 (Mezi1), JX290277 (Ako381), JX290278 (BAD54), JX290279 (BAD84), JX290280 (BAD230), JX290281 (BAD337), JX290282 (CHAS59), JX290283 (CHAS80), JX290284 (Lobak42), JX290285 (lozi5), JX290286 (Lozi6), JX290287 (MEBAK55), JX290288 (MEZI8), JX290289 (MEZI11), JX290290 (O290107), JX290291 (AKO205), JX290292 (O300153), JX290293 (O300186), JX290294 (O300189), JX290295 (O300137), JX290296 (O300227), JX290297 (O300237), JX290298 (O300265), JX290299 (O300275), JX290300 (O323101).
Phylogenetic relationships between the 27 unique new KSHV/HHV-8 sequences. The phylogenetic tree includes the 29 new 633 bp KSHV K1 consensus sequences and worldwide A to E sub-types prototypes from healthy persons and KS patients. Amplification was done with primers K1AG75s: GACCTTGTTGGACATCCCGTACAATC, K1AG1200as: AGGCCATGCTGTAAGTAGCACGGTT for the outter fragment and VR1s: ATCCTTGCCAAYATCCTGGTATTGBAA and VR2 as1: AGTACCAMTCCACTGGTTGYGTAT for the inner fragment. Amplified products for 29 samples were directly sequenced. Once the sequences obtained, a multiple sequence alignment was performed with the DAMBE program (v. 4. 2. 13) on the basis of a previous amino acid alignment created from the original sequences. The final alignment was submitted to the Modeltest program (v. 3. 6) to select the best evolutionary model, according to the Akaike Information Criterion, to apply for the phylogenetic analyses.
The phylogeny was derived by both the neighbor-joining (NJ) and maximum parsimony (MP) method, performed in the PAUP program (v. 4. 0b10) (Sinauer Associates, Sunderland, MA, USA) and the reliability of the inferred tree was evaluated by bootstrap analysis on 1000 replicates. New A5 sequences are shown in bulk red and B sequences are in bulk blue. The tree is drawn to scale with 0. 1 nucleotide replacements per site. doi:10. 1371/journal. pntd. 0002851. g003 populations and an ancient speciation. In contrast, the African sequences from the A5 paraphyletic group are closely related to viruses found mostly in populations, which form the A1-4 subgroup. The origin of the A5 group is thus quite intriguing. We first envisioned that the A5 clade could have emerged upon recombination, and would therefore form an intermediate group.
This study was financially supported by: The  Institut Pasteur ; and through the  Investissement d'Avenir as part of a Laboratoire d'Excellence (LabEx) French research program :  Integrative Biology of Emerging Infectious Diseases (IBEID). Fundings were also received from the  Service de Cooperation et de l'Action Culturelle (SCAC) Yaounde , the  Institut National du Cancer (INCa) , and the  Association Virus Cancer Prevention. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Material and Methods The material studied herein was collected thanks to numerous summer field and washing campaigns, in which the authors took part. The excavations in the CBFC were carried out according to the authorization issued by the Direccion General de Patrimonio Historico de la Comunidad de Madrid. All necessary permits were obtained for the described study, which complied with all relevant regulations. We have received permission from the Universite Ćlaude Bernard-Lyon 1 (Villeurbanne, France) for the loan of the The systematic revision presented below is based on the examination of specimens and casts of the MNCN and FSL collections and data from the literature. We examined dental material of the following taxa: -Rotundomys sp. nov. from Batallones (see below); -Rotundomys montisrotundi from Montredon (Herault, France) and Rotundomys cf.
The occlusal measurements (greatest length and greatest width; Table  1 ) of the teeth of Rotundomys from Batallones have been obtained with a Nikon digital counter CM-6S measuring device. The calculations of the statistical descriptives and Analyses of Variance (ANOVA) have been carried out with a standard software (SPSS Statistics version 18. 0, SPSS Inc. , Chicago, IL, USA). Tests on normality and homogeneity of variance have been performed with this software before the Analyses of the Variance. The relative reduction in the length of the third molars was calculated using the (mean Length of M1)/(mean Length of M3) and (mean Length m1)/(mean Length m3) ratios, which is a classic method for evaluating the degree of reduction of the third molars  [3]. For Rotundomys samples whose variance was known, the standard error of the ratio (SER) was calculated using the Delta approximation (sensu Ratio technique in SPSS)  [3].
Acknowledgments For sharing data on the French material, we sincerely thank  J. -P. Aguilar  (UniversiteMontpellier 2, Montpellier). P. Mein  ( UniversiteClaude Bernard-Lyon 1, Villeurbanne ) kindly lent material of Rotundomys kept in his institution. L. Viriot ( E ´cole Normale Superieure de Lyon, Lyon ),  L. J. Flynn  ( Harvard University, Cambridge, MA ), and an anonymous reviewer enhanced this work through careful, critical reading.
Pathogen-Host Interaction and Secondary Metabolite Genes/Clusters Genes potentially involved in host-pathogen interactions were identified using local BLASTp (E value cutoff of e À20 ) against the PHI-base curated database (www. phi-base. org, last accessed December 19, 2014;  Winnenberg et al. 2008). Potential clusters of secondary metabolite genes were identified using the online SMURF tool (jcvi. org/smurf, last accessed December 19, 2014;  Khaldi et al. 2010).
Sequencing of the Mating-Type Locus from Additional Strains In order to complete the mating-type analysis of strains related to H327, the entire mating-type locus was sequenced using the combinations of primers listed in supplementary table  S2 , Supplementary Material online, from the following strains: O. ulmi Q412T (MAT1-1), O. novo-ulmi subsp. americana VA (MAT1-1), O. novo-ulmi subsp. americana MH75 (MAT1-2), O. novo-ulmi subsp. novo-ulmi CKT11 (MAT1-2), O. himal-ulmi HP25 (MAT1-1), and O. himal-ulmi HP30 (MAT1-2). PCR reaction volumes and cycling conditions were as above, except the extension time for initial long-PCRs to generate the entire locus (~8-10 kb) was 10 min. PCR products were then Sangersequenced as above and complete mating-type loci sequences were deposited in GenBank: KF961042-KF961047.
The raw RNA-seq data were submitted to the NCBI Sequence Read Archive under accession SRP047075. The approximately 28 million raw reads (supplementary table  S3 , Supplementary Material online) were filtered/quality-controlled using FastQC v0. 11. 2 (www. bioinformatics. babraham. ac. uk/projects/fastqc/, last accessed December 19, 2014) and Prinseq v0. 20. 4 (prinseq. sourceforge. net/, last accessed December 19, 2014) as follows: Adaptors and poly-A/T tails (>10 nt) were trimmed; sequences with greater than 20% Ns, less than 20 nt in length and exact duplicates were removed completely. We then used both Newbler v2. 8 (GS de novo Assembler; Roche) and TopHat v2. 0. 10 (ccb. jhu. edu/software/tophat/index. shtml, last accessed December 19, 2014;  Kim et al. 2013 ) aligners to control for individual software variability in mapping quality.
Once mapped, TopHat output BAM files and a GTF of the "final model" CDS from above were fed into the Artemis genome browser and annotation tool (www. sanger. ac. uk/resources/software/artemis/, last accessed  December 19, 2014; Carver et al. 2012)  for manual correction of the entire gene set. In the case of alternatively spliced transcripts, the most common variant (or longest if similar frequencies) for any one gene was selected for the final gene set. The final validated gene, transcript, and protein sets are available as supplementary datafiles S1-S3, Supplementary Material online.
clavigera, followed by 36% in other close Sordariomycetes, 5% in other Pezizomycotina, and surprisingly few (439 = 5%) orphans (ORFs with no known homologs-actually only 181 once the Ophiostoma/Sporothrix sister species are readded) (fig. 2  and supplementary figs. S1 and S2, Supplementary Material online). The proteins were confirmed through our RNA-seq analysis which adopted a redundant approach to read-mapping by employing Newbler and TopHat aligners (see Materials and Methods) to account for software variability in mapping quality. In our case, TopHat achieved superior performance and showed that 99% (8,521/8,640) of the final gene models could be detected with at least one read (supplementary table  S3 , Supplementary Material online). Nearly 90% of genes were also covered by at least 20 reads which, given our average read length of 96 nt and the average mature transcript length of 1,665 nt, essentially correspond to 1-fold coverage along the entire length of the average gene.
This gene is therefore quite divergent from the other "true" MAT1-2-1 genes; however, Conserved Database Domain and Pfam searches confirmed significant hits to the MATA_HMG-box domain (e À32 to cd01389 and e À21 to PF00505, respectively), hallmark of the MAT1-2-1 proteins  (Debuchy and Turgeon 2006; Martin et al. 2010). We propose to label this new, divergent mating-type 2 allele MAT1-2-1 H327. Curiously, we have also been able to find homologs of this new allele in other sequenced Sordariomycete genomes (fig. 7 ): O. ulmi W9 (3582_g), G. clavigera kw1407 (CMQ_1586), Podospora anserina S mat+(Pa_6_4110), Fusarium verticillioides MRC8560 (FVEG_4822), and Magnaporthe orzyae 70-15 (MGG_3959). The existence of both potentially functional mating-types in the heterothallic H327 is interesting as a recent study on the heterothallic O.
7. -Mating-type idiomorph in the O. novo-ulmi H327 genome compared with other Sordariomycetes. For each fungus, an example of a mating-type 1 strain (to the left) and a mating-type 2 strain (to the right) are given. Where possible, fully sequenced genomes were used as the examples and they are indicated by red strain names. For simplicity, sizes are roughly relative to final protein sizes (small 500 aa, medium = 500-1,000 aa, large ! 1,000 aa), not gene lengths, and variable intergenic spaces are ignored. Individual gene names are given for those from completely sequenced genomes (according to the respective projects' nomenclatures-see publications or genome browser websites), otherwise GenBank nucleotide accession numbers are given. The whole locus (between conserved regions upstream and downstream of the MAT genes) was sequenced in all cases except O.
; 10 À4 E value cutoff) against GenBank nr (ftp://ftp. ncbi. nlm. nih. gov/blast/db, last accessed December 19, 2014), UniProt Knowledgebase and UniProt Swiss-Prot (www. uniprot. org, last accessed December 19, 2014) to achieve a manually verified consensus label for each CDS. Other manual protein domain verifications were conducted using Pfam (pfam. sanger. ac. uk, last accessed December 19, 2014). General functional (ontology) analyses (and statistics) were conducted with an online version of BLAST2GO Pro (www. blast2go. com, last accessed December 19, 2014) by importing the top ten hits from the above BLASTp analyses for each CDS (generated in XML format). Assignment of KEGG ontology was conducted using the KEGG Automatic Annotation Server (www. genome. jp/tools/kaas/, last accessed December 19, 2014; Moriya et al.
Acknowledgments The authors thank  Mialy Rabemanantsoa , our colleagues at the  IBIS/UniversiteLaval Plate-forme d'Analyses Genomiques  and the  McGill University/Genome Quebec Innovation Centre  for technical assistance. They thank  Fabienne Malagnac  ( CNRS/UniversiteParis-Sud ) for discussions on RIP/RID,  David Nelson  ( University of Tennessee HSC ) for manual verification/naming of CYP450s,  Marilou Desharnais  ( UniversiteLaval ) for production of figure 1, and two anonymous reviewers for constructive comments. This work was funded by the  Natural Sciences and Engineering Research Council of Canada  (grant  105519 ) and  Fonds de Recherche du Quebec-Nature et Technologies  (grant  2012-PR-146155 ).
8 29. 8 41. 7 41. 0 ~36 Number of chromosomes 8 7 7 7 7 %GC genome 50. 1 53. 4 51. 6 48. 3 52. 0 %GC transcripts 57. 0 60. 5 56. 0 54. 0 55. 9 %GC exons 57. 9 nr 57. 3 54. 6 nr Protein-coding genes 8,640 8,314 11,043 9,733 10,545 Percent coding 45. 3 45. 8 46. 4 48. 0 44. 8 Gene density 1 per 3. 7 kb 1 per 3. 5 kb 1 per 3. 8 kb 1 per 4. 2 kb 1 per 3. 4 kb Mean intergenic distance (bp) 1,842 1,466 2,041 2,297 nr Mean gene length (bp) 1,786 1,641 1,754 2,023 nr Mean protein length 555 aa 545 aa 481 aa 486 aa 496 aa Percent genes with introns 59. 0 77. 2 84. 8 91. 6 nr Mean number of introns/gene 1. 77 1. 86 nr 1. 7 1. 27 Mean intron length (bp) 114 70 a Nr 134 79 tRNA genes 254 nr 341 415 361 5 S rRNA genes 43 nr 46 79 87 NOTE. -Statistics were compiled from the original genome publications, with modifications as per the most current assemblies available in public databases: For Grosmannia, a Only the median intron length, and not mean, was reported/available.
NOTE. -BLASTp, Protein BLAST at NCBI (blast. ncbi. nlm. nih. gov, last accessed December 19, 2014); BLAST2GO, Blast to Gene Ontology (GO) (www. blast2go. com, last accessed December 19, 2014); CAZy, Carbohydrate-Active Enzyme Database (www. cazy. org, last accessed December 19, 2014; manual annotation by B. Henrissat); CYP Homepage, Cytochrome P450 Homepage (drnelson. uthsc. edu/CytochromeP450. html, last accessed December 19, 2014; manual annotation by DR Nelson); KEGG Mapper, Kyoto Encyclopedia of Genes and Genomes Mapper (www. genome. jp/kegg/ mapper. html, last accessed December 19, 2014); MEROPS Peptidase Database (merops. sanger. ac. uk, last accessed December 19, 2014); PHI-base, Pathogen-Host Interactions Database (www. phi-base. org, last accessed December 19, 2014); SignalP, Signal Peptide Cleavage Site Predictor (www.
Molecular identification The two COI sequences we obtained from two individuals were identical. They were compared to the only available COI sequences of a member of the genus Platydemus in GenBank (Platydemus manokwari; Accession number: AF178320. 1). The p-distance between our new sequence and the GenBank sequence of Platydemus manokwari was 4%. Although this is not mentioned in the GenBank record, we know that this specimen was collected in Australia by one of us (LW). The population from which the GenBank example of Platydemus manokwari (AF178320. 1) was taken had previously been confirmed histologically (by LW from lot LW1065) as P. manokwari and voucher specimens lodged in the Queensland Museum (Registration numbers GL4724, whole specimen in alcohol, and GL4725, 126 slides).
Molecular identification The p-distance between our two sequences and the GenBank sequence of Platydemus manokwari was 4%. This genetic distance roughly corresponds to the genetic distances generally found between closely related species or distant populations within a single species. Alvarez-Presas et al. (  2012 ) studied variation of COI in species belonging to the same family as Platydemus manokwari, i. e. , the Geoplanidae. In this study of the European species Microplana terrestris (Muller, 1774), specimens were studied from two localities, East and West of Northern Spain. Variation ranged from 0% to 3% within the western localities, and from 0% to 1. 6% in the eastern localities; West and East presented a difference of 2. 4% to 4%. The between-species difference (M. terrestris vs M.
ACKNOWLEDGEMENTS The authors are grateful to  Gerard Peaucellier  and  Mrs J. Vivant  for providing information on terrestrial flatworms in France, to  David Bellwood in Townsville, Queensland  for his observations on the feeding response of domestic bantams to P. manokwari, to  Gilianne Brodie ,  School of Biological and Chemical Sciences, University of the South Pacific, Fiji , for her papers on the occurrence of Platydemus manokwari at Rotuma, to  Archie Murchie ,  Agri-Food and Biosciences Institute, Belfast, Northern Ireland , for information and advice on current plant sanitation practices, standards and legislation for the Invasive Alien Species Arthurdendyus triangulatus, to  Nicolas Puillandre  ( MNHN, Paris ) for help with the sequences, to  Pierre Lozouet  ( MNHN, Paris ) who identified the prey snail.