dataesr/scientific-paragraphs-categorization huggingface dataset:
Molecular analysis All sequences were automatically aligned using MUSCLE implemented in Geneious Pro version 5. 3. 4 [18]. Alignments were constructed separately for the nuclear (28S) and mitochondrial (COII) datasets using sequences available in GenBank to complete our dataset. Bayesian analyses were performed to infer phylogenetic relationships between flea species. First, the best-fitting model and associated parameters were selected by jModelTest  [19]  and phylogenies were constructed by Bayesian inference. Two sets of four MCMCMC (Metropolis Coupled Markov Chain Monte Carlo) chains incrementally-heated were run in MrBayes 3. 1. 2 [20]  for 20,000,000 generations. Trees and associated model parameters were sampled every 300 generations. The initial 2,000 trees were discarded as a conservative ''burn-in'' and the harmonic mean of the likelihood was calculated by combining the two independent runs.
Statistical analysis The data were entered into EPIData 3. 1 and analyzed with Epi info 6. 04 statistical software using the chi-squared or Fisher exact tests for observed frequencies. We used a p-value threshold of 0. 001. The effect of ''habitat'' on fleas' diversity was measured at two scales, host and sampling region, by using the flea percentage incidence index (PII: mammals parasitized by fleas of species A/ mammals caught (%)), the specific flea index (SFI: number of fleas of species A collected from host species Y/mammals of species Y parasitized by fleas of species A) and the total flea index (TFI: total fleas collected/total trapped mammals, i. e. mean number of fleas per trapped mammal)  [21]. The seasonality of flea diversity was tested by comparing PII on animals trapped at each site during the cool-dry versus hot-wet seasons.
Molecular analysis Sixty (28S) and seventy (COII) sequences were obtained from fleas sampled in Reunion Island. As all sequences of X. cheopis and X. brasiliensis were 100% identical, only a dozen sequences representative of each of those two species were included in the analyses. Few sequences from Genbank were added, including Parapsyllus longicornis used as an extra-group. Since no 28S or COII sequences were available on databases for X. brasiliensis, we sequenced three X. brasiliensis specimens sampled in Tanzania (KJ638557-59 in COII; KJ638585, 638589-90 in 28S: collectors Laudisoit A. , Makundi R. , Katakweba A. , S3u5899890 E35u2195600, 1994 m, 10/02/2009). Models selected.
Discussion The present investigation provides the first information on flea diversity and distribution on the five introduced small mammal species present on Reunion Island, where no data were available thus far. We describe the presence of three genera composed of four distinct cosmopolitan species, namely X. cheopis, X. brasiliensis, L. segnis and E. gallinacea. Morphological diagnosis of X. cheopis and X. brasiliensis was further confirmed by sequencing of 28S and COII markers: for X. cheopis, fleas sampled in Reunion Island showed 99% and 100% identity with sequences accessible in Genbank (i. e. EU336145. 1 and HM188404. 1 for 28S and COII sequences, respectively). As no sequences were currently available for X. brasiliensis on these 2 loci, we generated sequence data using specimens previously sampled in Tanzania and morphologically identified as X.
Acknowledgments The authors acknowledge  Yann Gomard  and  David Wilkinson  for technical help on molecular analysis,  Jean-Sebastien Dehecq  for providing Reunion Island maps and  Vincent Herbreteau  for critical comments on the manuscript. We also thank the  Direction de l'Environnement, de l'Amenagement et du Logement (DEAL Reunion)  for issuing permits, the  Office National des Forets (ONF)  and the  Parc National de La Reunion  who gave authorization for the trapping of Tenrec eucaudatus ( DIR/I/ 2013/008 ).
We predicted 32,273 high-confidence genes and a potential set of 44,966 protein-coding genes and checked these for codon usage (Supplementary Table  11 ). We found that 20,076 (ref. 6) protein-coding genes were functionally annotated and compared to other species (Supplementary Figs. 3 4 5 6 , Supplementary Tables  12  and 13 , and Supplementary Data Sets 1-6). The average gene had 5. 7 exons and coded for a 518-amino-acid protein. Multiple statistical analyses indicated a complex interplay between Copia transposable elements and stress-related genes. In addition, we sequenced the S. lycopersicum cv. M82 genome-the recurrent parent of the IL population-at approximately 44-fold coverage. We compared this sequence to the S. lycopersicum cv. Heinz genome  7  , identifying 1,338,510 variants, of which 1,188,524 were SNPs.
Further investigation showed that around half of the candidate stress-related genes had extensive polymorphisms in the regions upstream of their initiation codons. These sequence polymorphisms (a-d) The expression of genes related to cutin biosynthesis (a) and wax biosynthesis (b) and of genes putatively (c) or known to be (d) associated with the formation of cuticular aromatic components was analyzed using quantitative PCR to validate data from RNA sequencing experiments and biochemical analysis. Statistical analysis was performed using a two-tailed t test. *P < 0. 05, **P < 0. 01, ***P < 0. 001. Gene expression shown is relative to that for actin (Solyc05g054480). Error bars, s. e. m. ; four biological replicates, each with three technical replicates. Underlined genes are those characterized by large differences in expression between S.
lycopersicum-specific Copia-like elements (Supplementary Note). This differential distribution of Gypsy and Copia-like elements, along with their association with stress responsiveness, suggests that, at least in some instances, LTR-RTs may exert a potential role in the regulation of gene expression. Such a role was proposed decades ago  23  , and some evidence of a role for transposable elements in the modulation of proximal gene expression has accumulated  [24] [25] [26]. Our S. pennellii data set thus provide grounds, in future investigations, to assess the hypothesis that, in specific gene neighborhoods, Copia-like elements might represent 'conditional' regulatory sequences co-opted by the host genome upon exposure to different environmental stresses. S. pennellii has additionally been widely documented to show phenotypes divergent from S.
Methods and any associated references are available in the online version of the paper. Accession codes. The S. pennellii (LA716) raw data have been deposited with the European Bioinformatics Institute (EBI) under project number PRJEB5809. The genome sequence is available from the European Nucleotide Archive (ENA) under accessions HG975439-HG975452. The S. lycopersicum cv. M82 raw data have been deposited at the EBI under project number PRJEB6302. The genome sequence is available from the ENA under accessions HG975512-HG975525. Note: Any Supplementary Information and Source Data files are available in the online version of the paper.
ACKNOWLEDGMENTS We gratefully acknowledge the support of the  Max Planck Society  in the form of an exceptional grant to cover the costs of sequencing the tomato species. In addition, work in the laboratories of D. Z. and A. R. F. was funded in the framework of  Deutsche Israeli  Project  FE 552/12-1 , which is administered by the Deutsche VOLUME 46 | NUMBER 9 | SEPTEMBER 2014  Nature GeNetics Forschungsgemeinschaft. B. U. and M. E. B. acknowledge the support of the  Bundesministerium für Bildung und Forschung (BMBF) -funded primary database FKZ 0315961. B. A. thanks the  Deutsche Forschungsgemeinschaft International Research Training Groups (IRTG)   1525. F. S. acknowledges the support of the  CRA Young Investigator Program. Work in the laboratory of F. C. was funded by  INTA ,  Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)  and  Agencia Nacional de Promoción Científica y Tecnológica (ANPCYPT)  grants.
Work in the laboratories of N. S. and J. N. M. was funded by  NSF  grant  IOS-0820854. J. R. was supported by the  US National Science Foundation  ( Plant Genome Program ;  DBI-0606595  and  DBI-1313887 ) and by  Agriculture and Food Research Initiative  competitive grant  2011-04197  from the  USDA National Institute of Food and Agriculture. Work in the laboratories of J. G. and Z. F. was additionally supported by  US National Science Foundation Plant Genome Program  grants  DBI-0820612  and  IOS-0923312. A. B. would like to thank  Y. Brotman  for preparing the Pseudomonas syringae-infected S. pennellii samples.
Quantification was carried out by real time quantitative RT-PCR using the Power SYBR Green RNA-to-CT one step kit (Applied Biosystem). Total RNA was extracted from cultured cells using TRIzol (Invitrogen) according to the manufacturer's instructions. Polyadenylated RNAs were reverse transcribed using the Superscript III kit (Invitrogen) and oligo dT primers (Promega) according to the manufacturer's recommendation. Quantification was carried out by real time quantitative PCR using the Fast SYBR green master mix (Invitrogen). All PCR reactions were done in triplicate. Specificity of the PCR reactions was assessed by analysis of melting curves for each data point. Values were normalized against the Aedes aegypti ribosomal protein S7 gene. Following real-time quantitative PCR assays, analysis of relative expression of Ago-1, Ago-2 and S7 was performed according to the 2 2DDCt method  [36].
Gene silencing efficiency was then tested. 500 ng dsRNA (Ago-2 specific or FFLuc specific as a control) was injected into mosquitoes 48 h prior to infectious blood-meal (CHIKV at 10 7 PFU/ml). Ago-2 expression (relative to S7 expression) in midguts or heads of injected mosquitoes was determined by real-time quantitative PCR at time points indicated (1, 2, 3, 4 and 7 days pi). The S7 gene was chosen as a control housekeeping gene due to its stability in infected and non-infected conditions [data not shown]. Mosquitoes were analyzed at days 0, 1, 2, 3, 4 and 7 pi. Injection of Ago-2 specific dsRNA strongly decreased the expression of Ago-2 in midguts (Fig. 4A : ranging from 80% silencing at day 2 to 70% silencing at day 7) and heads (Fig. 4C : ranging from 68% at day 2 to 50% at day 7) compared to the controls (FFLuc specific dsRNA dsFFLuc, PBS or non-injected mosquitoes).
To determine the effect of gene silencing on viral dissemination, the number of viral particles in heads was also determined. At day 4 pi, heads of mosquitoes injected with Ago-2specific dsRNA contained significantly more infectious viral particles (10 3. 1 610 2. 3 ) (Fig. 4D ) than controls (Kruskall-Wallis test: p,0. 05). This effect was transitory as at day 7 pi, viral loads remained similar when compared to other treatments. Taken together the in vitro and in vivo data imply a control of virus replication by the exogenous RNAi pathway with the virus being unable or not efficiently able to avoid this antiviral response.
This work was funded by the  Institut Pasteur (ACIP  grant  A-10-2009 ) (ABF),  UK Medical Research Council (AK) ,  Netherlands Organisation for Scientific Research NWO (Rubicon fellowship) (ES) ,  Ministry of Higher Education Malaysia fellowship (SM) , the  EU  7-th Framework  ICRES  project and by the  European Union  through the  European Regional Development Fund  via the  Center of Excellence in Chemical Biology (AM), the ''Fondation Odette and Jean Duranton de Magny'' (EM) , the '' Fondation de France: Fonds Inckermann'' (CAG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
ncbi. nlm. nih. gov/genomes/static/Pipeline. html). Using this automated pipeline, we identified 3,943 predicted coding sequences; out of them, 3,825 had a functional assignment. It also predicted 65 pseudogenes, 3 rRNAs, and 45 tRNAs. Comparison with available M. bovis BCG genomes indicates that the clinical isolate is related to BCG Tokyo and BCG Russia. Nonsynonymous mutations were identified in genes known to be involved in the development of resistant forms of the M. tuberculosis complex. The availability of this genome will allow comparative genomic analysis with other M. bovis BCG daughter strains and might provide insights into the emergence of MDR clinical strains of M. bovis BCG. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no.
Rap1 ChIP-on-chip Rap1 ChIP experiments (duplicates) were performed with anti-Rap1 antibodies kindly provided by David Shore (University of Geneva). Rap1 ChIP and input DNA samples were hybridized to Nimblegen S. cerevisiae high density tiling arrays that were designed by us in collaboration with Frederic Devaux (Ecole Normale de Paris) and Nimblegen to cover the entire genome. They contain 50 nt-long oligonucleotides separated by ,15 ntlong gaps. The chip covers both strands of S. cerevisiae genome. Hybridizations and data analysis were performed by Nimblegen (Roche NimbleGen). Rap1 peaks were visualized with the signalMap software (Nimblegen) or with the Integrative Genomics Viewer (Broad Institute). The genome-wide Rap1 binding profiles were consistent with the recent published studies  [55].
Acknowledgments We are grateful to  A. Bianchi ,  D. Sinclair ,  B. Johnson  for sharing yeast strains, plasmids, and results, and  Bertrand Llorente  and  Eric Gilson  for helpful discussions and advices. We thank  Pierre-Marie Dehe  for his contribution to the Rap1 ChIP experiments,  David Shore  for providing the Rap1 antibody, and  Ghislain Bidaut  for his help with Bioinformatics.
Questions asked were based on literature reports suggesting that the targeted young people felt invulnerable to chlamydia infection, did not compare themselves with people who get infected, and had no time or interest in participating  [6, 7] , experienced barriers such as lack of knowledge, worries, and lack of guidance  [8] , were afraid of doing it wrong, found the procedure unpleasant, were afraid of the consequences of a possible positive outcome, and expressed fear of negative reactions from a partner and others  [9] [10] [11]. Furthermore, three single category implicit association tasks (scIAT)  [12]  were included to identify impulsive reactions towards chlamydia in terms of annoyance, threat, and reassurance. All data were gathered without giving any information in advance about chlamydia or chlamydia testing.
Strengths and Limitations The strength of this study is that actual behavior was measured, while the weakness is that there was only observational data and no data on how people processed the information or on possible changes in the determinants of behavior. It is, however, difficult to imagine how a mass media letter could be improved differently to reach a substantial larger number of young people participating in the screening. It is obvious that the approach to invite the target population via a general letter does not lead to sufficient participation rates for chlamydia screening.
Acknowledgments We would like to acknowledge the  Chlamydia Screening Implementation (CSI)  project group:  JEAM van Bergen, IVF van den Broek, EEHG Brouwers, JSA Fennema ,  HM Götz ,  CJPA Hoebe ,  RH Koekenbier ,  ELM Op de Coul, LL Pars , and  SM van Ravesteijn. Financial support was provided by  ZonMw.
Transport and magnetotransport properties The electrical resistivity (ρ) as a function of temperature is shown in Fig. 8 (a) for CMW and CMN samples. The experimental data were obtained from room temperature down to 110 K and 100 K for CMW and CMN, respectively; below this temperature the resistance was out of range in our experimental set-up. At RT the values of resistivity are 33 and 9 Ω cm for CMW and CMN respectively. In both cases the resistivity increases diminishing the temperature, showing a semiconducting-like or thermally activated behaviour. In the inset of Fig. 8 (a) a plot of ln(ρ) vs. T À 1 clearly shows a linear behaviour. This can be associated with a thermally-activated electronic conduction mechanism (ρ¼ρ 0 exp (E g /kT)). From the linear fit, the obtained activation energies (E g ) are 0.
Conclusions The synthesis and crystal structure of two new manganesebased double perovskite oxides Ca 3 Mn 2 B″O 9 with B″ ¼ W and Nb have been reported by first time from XRPD and NPD. The initial refinements by XRPD indicate a maximum cationic order between Mn and W and a high degree of disorder between Mn and Nb, confirmed by NPD. For CMN the analysis of difference-Fourier allowed selecting the correct structural model in the P2 1 /n space group. The same symmetry is obtained for Ca 3 Mn 2 WO 9. The main difference in these samples is the oxidation states of manganese cations. CMW contain Mn 3 þ while CMN includes a mixed-valence between Mn 3 þ and Mn 4 þ. The amount of each oxidation state was confirmed by thermogravimetric analysis. From the sequential neutron diffraction data in CMW the expected contraction of the cell parameters is observed, without change of the octahedral size.
Acknowledgements C. A. L. and M. E. S. thanks a  CONICET  fellowship. J. C. P. thanks  CONICET  (Project  PIP 2008-01360 ),  SECyT-UNSL  (Project  7707  and Project  2-1612 ). R. D. S. acknowledges financial support of  ANPCYT  (Project  PICT 2011-0752 ) and  SEPCyT-UNCu  ( 06/C389 ). J. C. P. and R. D. S are member of  CONICET. J. A. A. acknowledges the financial support of the  Spanish Ministry of Education  to the project  MAT2010-16404. We are grateful to I. L. L. for making all facilities available.
Whole genome phylogeny, comparative genomics, and core genome analysis A phylogenetic tree based on the currently available complete streptococcal genome sequences was constructed using the EDGAR software  [23]. On this tree, S. gallolyticus, S. macedonicus, S. pasteurianus, as well as S. infantarius Figure  1  The circular map of the genome of Streptococcus macedonicus ACA-DC 198. Genomic features appearing from the periphery to the centre of the map: 1. Forward CDSs (red); 2. Reverse CDSs (blue); 3. Putative pseudogenes (cyan); 4. rRNA genes (orange); 5. tRNA genes (green); 6. % GC plot; 7. GC skew. formed a single, monophyletic branch, providing strong evidence for the taxonomic integrity of the SBSEC (Additional file 1: Figure  S1 ). Subsequently, full chromosome alignments were performed using progressiveMAUVE  [24].
Interestingly, the inclusion of the S. infantarius genome in the MAUVE analysis resulted in an increased number of LCBs with a decreased average length. As the level of sequence conservation of individual LCBs among the four species remains relatively high, this observation suggests that specific genome structure reorganization events occurred specifically in S. infantarius (Figure  2B ). Analysis with the EDGAR software revealed a core genome of only 1,372 orthologous genes based on the sequence and the current annotation of S. gallolyticus, S. pasteurianus and S. macedonicus (Figure  3A , Additional file 2: Table  S1 )  [23]. Once more, inclusion of S. infantarius increased the diversity, resulting in reduction of the core genome by more than 100 genes among the four species (Figure  3B , Additional file 3: Table  S2 ).
The entire glycobiome of the SBSEC members was further analyzed based on the data available in the CAZy database (Additional file 4: Table  S3 )  [26]. Important differences in the distribution of enzymes among the SBSEC members were observed for all CAZy categories including glycoside hydrolases (GHs), glycosyl tranferases, polysaccharide lyases, carbohydrate esterases and carbohydrate-binding modules (CBMs). Streptococcus macedonicus and Streptococcus infantarius had the smallest glycobiome within the SBSEC. The two strains had only 24 and 23 GHs, while the rest SBSEC members had more than 40. Given that most of these GHs are potentially involved in plant and dietary carbohydrate catabolism (e. g. GH1, GH3, GH13, GH36 etc. )  [27] , it could be hypothesized that S. macedonicus and S. infantarius have a diminished necessity for such enzymes in their ecological niche.
Sequence analysis of Sinf_1513 and Sinf_1683, also annotated as hemolysin genes, was not supportive of a hemolysin protein product (data not shown). Apart from hemolysins, a putative exfoliative toxin B (Sinf_0933) and a macrophage infectivity potentiator protein (Sinf_0931) are present in the S. infantarius genome  [20]. Similar genes can be found in S. thermophilus strains but not in the other SBSEC species and in our opinion functional analysis is required to verify these annotations. In order to expand our investigation for putative pathogenicity traits, we screened the genomes of S. macedonicus and its related SBSEC species using the VFDB (virulence factors database)  [55]  and the genes determined to encode putative VFs during this analysis are presented in Additional file 11: Table  S7.
V. , Sint-Martens-Latem, Belgium). Final corrections and quality assessment of the annotation were performed with the GenePRIMP pipeline  [21]. GenePRIMP was also used for the identification of putative pseudogenes. The circular map of the S. macedonicus genome was generated by the DNAPlotter software  [75]. Comparative genomics of Streptococcus macedonicus ACA-DC 198 against related members of the SBSEC The complete genome sequence of S. macedonicus was compared to those of S. gallolyticus strains UCN34, ATCC 43143 and ATCC BAA-2069, S. pasteurianus ATCC 43144 and S. infantarius CJ18 using a variety of tools. In order to visualize conserved genomic regions or chromosomal rearrangements, whole genome sequence alignments were performed by progressiveMAUVE  [24]. Estimation of the differential gene content of the genomes, as well as whole genome phylogeny of streptococci was carried out within the EDGAR software framework  [23].
Statistics Qualitative variables were described as number (percentages) and quantitative variables as median (1st and 3rd quartiles). We built a two levels hierarchical logistic mixed model for qualitative outcomes as interruption of dialysis session and linear mixed model for quantitative outcomes. Level one represented the dialysis sessions as fixed effect and level two the patient as random effect. Results are expressed in Odd Ratio and regression coefficient with their 95% confidence interval (with intermittent saline flushes as the reference method). All tests were bilateral and statistical significance was stated to 5%. Data management was performed with SAS 9. 2 (SAS Institute, Cary, NC) and hierarchical models building used MLwiN v2. 0.
Acknowledgments The authors thank the participating patients,  Dr Soraya Soulimane ,  Mr Patrick Vaillant ,  Caroline Quintin  ( Unitede Recherche Clinique, Paris Nord ) for their implementation and monitoring of the study,  Priscilla Armoogum  for statistical analyses, the nurses of Necker dialysis unit for their unvaluable help in this study,  Pr Gru  ¨nfeld and  Pr Lesavre  for their support.
This work was supported by a research grant from the  Departement ala Recherche Clinique et au Developpement, Assistance Publique-Hopitaux de Paris , which was also the sponsor of the study ( CRC 05 032 ), and  AURA (Association pour l'Utilisation du Rein Artificiel ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Description of the numerical tool The great advantage of a numerical tool is the ease to vary the test parameters as compared to experiments. In recent years, increasing capabilities of computers and development of more and more precise physical models have enabled the CFD code to become a reliable engineering tool. The computational tool used for the present work is PHOENICS by CHAM  [6]. It is a multi-purpose Computational Fluid Dynamics (CFD) software package which is applicable to steady or unsteady, one-, two-or three-dimensional, turbulent or laminar, multi-phase, compressible or incompressible flows using Cartesian, cylindrical-polar or curvilinear coordinates. The code is based on a finite-volume approach and includes models, enabling the simulation of a wide range of situations. In the present work, calculations were performed using an iterative integration procedure of the finite volume equations.