dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments The authors thank  Françoise Thomas ,  Raphael Comte ,  Michel Lefebvre ,  Rachel Verdet  and  Sarah Poirot  from the PEGASE research unit for their help in the sample analysis, and  Josselin Delamarre  and  Patrice Roger  from the experimental unit for their technical assistance. This study was funded by  INRA  and the  French National Research Agency (L'Agence Nationale de la Recherche ,  ANP-09-BLAN-0083 ANDROPIG ). Proliferation plates were kindly processed by  Xénoblis (Saint-Grégoire, France ).
Note that we do not advocate use of the ITS2 sequence as an absolute criterion for species diagnosis, but only to prioritize crosses of a new isolate with known species. Indeed, ITS2 is polymorphic within some species and, conversely, some distinct biological species could potentially share identical ITS2 sequence. In sum, as pioneered in  [1] , we thus advocate the use of the ITS2 sequence barcode, and any other phylogenetically informative genes with widespread representation in sequence databases (e. g. those in  [1] ), to help prioritize crosses. Because of this utility, we strongly recommend that species naming articles include this molecular sequence information, or a reference to published work providing it, so as to ease future characterization of new isolates. As explained above, reliance on traditional fixed type specimens as a reference for the species name should be relaxed.
Therefore, we conclude that it is impossible to determine potential synonymy of fixed specimen with these new species. Below are the diagnostic features of each species to which we apply a name. For each species, we refer explicitely to publicly available data concerning cross results and their ribosomal SSU, LSU and ITS2 sequences from crosses that allow delineation as separate species and diagnosis of new isolates. Caenorhabditis portoensis Felix, Braendle & Cutter sp. nov. urn:lsid:zoobank. org:act:F473841A-9BDC-4FE1-B00B-20FC777489C4 = Caenorhabditis sp. 6 in  [1]  The type isolate by present designation is EG4788. The species is delineated and diagnosed by the positive result of the cross with the type isolate EG4788 in both cross directions, yielding highly fertile hybrid females and males that are interfertile and crossfertile with their parent strains.
MS/MS analysis of acetylated H3 In vivo modified histone H3 was digested either with trypsin or chymotrypsin and analyzed by nanoLC-MS as previously published  (Waldmann et al. , 2011). For both digests, STAGE tip-assisted sample purification was achieved essentially as described  (Rappsilber et al. , 2007). Desalted samples were subsequently analyzed using nanoflow (Agilent 1200 nanoLC, Germany) LC-MS/MS on a linear ion trap (LIT)-Orbitrap (LTQ-Orbitrap XL) mass spectrometer (ThermoFisher, Germany). Peptides were eluted with a linear gradient of 10-60% buffer B (80% ACN and 0. 5% acetic acid) at a flow rate of 250 nl/min over 40 or 60 min depending on the experiment. Data were acquired using a data-dependent 'top 5' method, dynamically choosing the five most abundant precursor ions from the survey scan (mass range 250-1650 Th) in order to isolate and fragment them in the LTQ.
All data were acquired in the profile mode and dynamic exclusion was defined by a list size of 500 features and exclusion duration of 30 s with a MMD of 10 ppm. Early expiration was disabled to decrease the resequencing of isotope clusters. The isolation window for the precursor ion selection was set to 2. 0 Th. Precursor ion charge state screening was enabled, and all unassigned charge states as well as singly charged ions were rejected. For the survey scan a target value of 10,00,000 (1000 ms maximal injection time) and a resolution of 60,000 at m/z 400 were set (with lock mass option enabled for the 445. 120024 ion), whereas the target value for the fragment ion spectra was limited to 10,000 ions (200 ms maximal injection time). The general mass spectrometric conditions were: spray voltage, 2.
3 kV; no sheath and auxiliary gas flow; ion transfer tube temperature, 150°C; collision gas pressure, 1. 3 mTorr; normalized collision energy using wide-band activation mode; 35% for MS 2. Ion selection thresholds were 500 or 1000 counts for MS 2 depending on the experiment. An activation q = 0. 25 and activation time of 30 ms was applied. MS data were processed into peak lists by DTASuperCharge 2. 0b1 (part of the MSQuant 2. 0b7 software environment  Mortensen et al. , 2010)  and searched with Mascot 2. 2 against the human International Protein Index protein database (IPI, version 3. 65) combined with frequently observed contaminants and concatenated with the reversed versions of all sequences. The MMD for monoisotopic precursor ions and MS/MS peaks were restricted to 5 ppm and 0. 8 Da, respectively.
Microarray design, hybridization and analysis ChIP samples were hybridized to custom tiling microarrays  (Lienert et al. , 2011)  representing all wellannotated promoters and the complete chromosome 19 with an average probe spacing of 100 bp (NimbleGen Systems Inc. , Madison, WI). Sample labelling, hybridization and array scanning were performed according to the manufacturer's protocols using a MAUI hybridization station and a NimbleGen MS200 slide scanner in combination with NimbleScan software (NimbleGen Systems Inc. ). Further processing was done using R. For analysis raw fluorescent intensity values were used to calculate log2 of the bound/input ratios for each individual oligo. Subsequently, for comparison all arrays were normalized to a median log2 = 0 and scaled to have the same median absolute deviation using the 'LIMMA' R/Bioconductor package  (Smyth and Speed, 2003; Smyth, 2004).
Deep sequencing data and analysis H3K27ac and p300 ChIPseq data were taken from  Creyghton et al. (2010) , H3K4me1 data from  Stadler et al. (2011) , mRNA expression data from  Lienert et al. (2011). Raw data was downloaded from the NCBI Gene Expression Omnibus and the reads were mapped to the Mus musculus genome (mm9) and transcriptome (RefSeq, downloaded on 07/17/2009) as previously described  (Lienert et al. , 2011). For promoter analysis, mapped reads were counted in a 2-kb window centred around all transcription start sites without further normalization. Enhancers were classified according to the definitions previously reported  (Creyghton et al. , 2010). In brief, active enhancer regions required a significant enrichment for both, H3K4me1 and H3K27ac, while inactive enhancers were defined as regions containing only H3K4me1  (Creyghton et al.
Bound FlagHA-tagged H3s were eluted by boiling in Leammli buffer. Quantification was done using the ImageJ software and the ratio between specific H3K64ac and HA signals (loading control) was calculated. For Nap1 pull-down, His-tagged Nap1 was pre-incubated with different histone species in incubation buffer (10 mM Tris-HCl pH 8. 0, 100 mM NaCl, 100 ng/µl BSA, 0. 05% NP-40, 1 mM EDTA, 1 mM DTT, 5% glycerol) for 30 min at 30°C 300 RPM. Samples were then supplied with nickel beads (His-Select Nickel Affinity Gel, Sigma) and incubated for 4 hr on the wheel at 4°C. Bound material was washed with wash buffer (10 mM Tris-HCl pH 8, 250 mM NaCl, 0. 1% NP-40, 1 mM EDTA, 1 mM DTT, 5% glycerol) and elution was achieved by boiling the beads in Leammli buffer.
0 M. Reactions were left for at least 15 min to reach equilibrium, transferred to 96-well half-area black non-binding surface microplates (Corning, Corning NY) and AF488 fluorescence measured on a BMG Labtech FLUOstar Optima plate-reader using 488p and 520p excitation and emission filters, respectively. Titrations using DNA alone were performed and confirmed that NaCl-induced changes in qF of nucleosomes was due to nucleosome disruption and not solute-dependent effects on the fluorophore. Upper and lower plateaus for each titration were used to normalise the data on a scale from 1-0. The plateau values were calculated by fitting the raw data using the sigmoid function described below in Microcal Origin 8. 6 Software. Average titration curves were calculated from normalised data from three separate titrations (using different nucleosome reconstitutions) for unmodified and acetylated nucleosomes and fit again with the sigmoid function to determine the average NaCl concentration at which the normalised qF (qF norm ) is 0.
The reactions were stopped by the addition of 500 ng HindIII digested λ DNA and sucrose to 5% w/v and placing on ice. Products were resolved on 0. 2× TBE 5% native polyacrylamide gels run for 3 hr at 300 V at 4°C. Gels were imaged on an FLA-5100 fluorescence scanner. Band intensities were quantitated in AIDA software. Initial rates were obtained by fitting using the following equation in MicroCal Origin 7. 0 software and solving the derivative at zero time: ( ) 1 bx y a e - = - where, a describes the value of the asymptote of the curve and b the relative rate in terms of normalized fraction of nucleosomes repositioned per minute. The fraction is a normalised unitless value and so the units for the rate are just min -1.
Acknowledgements We thank  A Izzo  and all members of  RS laboratory. We are grateful to  H Neumann  and  R Margueron  for providing expression plasmids and helpful advices. We acknowledge  C Beisel  and  I Nissen  for handling samples,  M Stadler ,  D Gaidatzis ,  L Burger  and  R Ivanek  for providing a computational framework for data analysis. We are grateful to  P Eberling  for peptide synthesis.
Empirical Covariates of HA Diversity We analyzed available AIV sequence data from GenBank for 11 HA subtypes from 1976-2013 (see Materials and Methods as well as Text S1, section S2) and developed a set of covariates reflecting specific predictions of the competing hypotheses. We sought to place these covariates on an equal footing and simultaneously to assess the contribution of each to HA diversity using a statistical model. Ordinary linear regression with a large number of covariates (of the same order as the number of observations) results in variance inflation, low statistical power, and issues of statistical identifiability  [18]. We therefore adopted a regularized regression method, known as elastic-net regression  [19] , that solves this problem using a shrinkage estimator to trade off a small amount of bias for substantial reductions in the variance of estimated parameters.
Phylogenetic Analyses For the phylogenetic analyses presented in Figure  1 , we focused on the HA gene for 10 subtypes sampled from wild bird species in North America between 1976 and 2001. We restricted our attention to this period because of the availability of parallel subtype-specific AIV prevalence data. For the remaining phylogenetic analyses (such as those presented in Table  1  and Figure  5 ), we examined sequence data from 1976-2013 from North America (United States and Canada) for avian, swine, and equine subtypes (Figures  S2, S3 , S4, S5, S6 and Table  S1 ). For human influenza viruses, we considered only sequences from Memphis, Tennessee, in order to use a comparable number of sequences. Data for avian subtypes are available from the Dryad Digital Repository (http:// dx. doi.
org/10. 5061/dryad. dryad. 8ct18 [56] ). Phylogenetic trees have been computed using the software BEAST  [57]  assuming a strict molecular clock  [58] , a site heterogeneity that is gamma distributed, a HKY substitution model, and a Bayesian Skyline Plot (BSP) with 10 groups  [59]. The number of replicates was adjusted to maximize effective sample size; 5 millions replicates were used for burn-in.
Experimental Protocol for Determining Environmental Durability Data on environmental durability for each subtype come from experimental data  [38]. For each virus subtype, infective virions were diluted 1:100 in water samples. The inoculated water samples were then divided into 3. 0 ml aliquots in 5. 0 ml polystyrene tubes and placed in incubators set to the appropriate treatment temperature. For each virus temperature trial, the viral inoculated water was sampled at the time of viral inoculation and at a second time point postinoculation. Titrations at all time points were performed in duplicate. The second postinoculation time point varied with each trial and was determined based on prior estimates of the time required for the titer of the virus in the water sample to be reduced by at least 1 log10 TCID50/ml  [33, 35].
Approval notices for trapping and investigation of rodents were given by the Ministry of Health Council of Medical Sciences, National Ethics Committee for Health Research (NHCHR) Lao PDR, number 51/NECHR, and by the Ethical Committee of Mahidol University, Bangkok, Thailand, number 0517. 1116/661. Cambodia has no ethics committee overseeing animal experimentation. The ANR-SEST (Agence Nationale pour la Recherche, Sante-Environnement et Sante-Travail) program on rodent-born diseases in Southeast Asia, which provided part of the funding for this project, has been approved by the Managing Directors from both the Asian and French research institutes. In addition, regional approval was obtained from the regional Head of Veterinary Service (Herault, France), for the sampling and killing of rodents and the harvesting of their tissues (approval no.
borgpetersenii and L. interrogans, have different habitat requirements, which supposes different modes of transmission. Lastly, in Southeast Asia, the risk of leptospiral transmission to humans is not solely limited to wetlands and rice paddy fields, but is also linked to forested areas, and activities such as the hunting and/or preparation of rodents for consumption. Leptospira species, strains and genetic diversity PCR detection of Leptospira. Real-time polymerase chain reaction (RT-PCR) targeting lipL32 and bactin genes were performed on rodent kidney DNA, extracted with Bio Basic EZ-10 96 Well Plate genomic DNA isolation kit for animals and the Qiagen DNeasy Blood & Tissue Kit. Following alignment of bactin gene sequences of Asian rodents  [20] , the bactin primers (forward: 59-CCA TGA AAC TAC ATT CAA TTC CA-39; reverse: 59-TTC TGC ATC CTG TCA GCA A-39) and probe (59-AGA CCT CTA TGC CAA CAC AGT GCT G-39) were designed using the highly conserved fifth exon sequence along with the Probe Design software for Light Cycler LC480 (Roche).
Leptospira species and strain identification. Leptospira species were identified by sequencing rrs genes and subsequent BLAST searches using the GenBank database (http://www. ncbi. nlm. nih. gov/BLAST). Strain characterization below the species level, was performed using both secY gene  [26, 27, 28, 29]  and MLVA analyses  [25]. secY genotypes were compared to the MLST database of Nalam et al. [29] , which contains data from 271 isolates from different geographical areas, as well as sequences found in the NCBI database. MLVA patterns were compared to the National Reference Center (NRC) database for Leptospirosis (Institut Pasteur, Paris, France), which contains more than one hundred genotypes of Leptospira isolates. Phylogenetic analyses of secY were performed with the Neighbour-Joining method using Kimura 2-parameters distance with Seaview software v.
4. 2. 12  [30]  and visualized in FigTree v1. 3. 1 (http://tree. bio. ed. ac. uk/). Nodal supports were determined using the bootstrap approach (1000 replicates). Statistical analyses. We investigated the effects of host species, sex, maturity (young vs adult) and environmentally-linked variables (habitat and locality) on the infection status of individual rodents. Statistical logistic regressions were performed with the R statistical platform using the package MuMIn v. 1. 7. 2  [31]  and lme4  [32]. Model selection was performed using Akaike's Information Criterion (AIC)  [33, 34]. The model with the lowest AIC value was viewed as the most parsimonious, i. e. the model which explains the majority of variance with the fewest parameters  [33]. The significance of each explanatory variable was tested using Wald tests based on z values.
borgpetersenii (n = 36), L. interrogans (n = 25), L. kirschneri (n = 2) and L. weilli (n = 1). The amplification of secY was successful in 31 of the 64 samples positive for Leptospira, including 20 L. borgpetersenii and 11 L. interrogans. No amplification could be detected for L. kirschneri and L. weilli. Lack of amplification was probably due to low levels of Leptospira DNA in the samples. The alignment of the 549-bp secY fragments distinguished a total of eight distinct alleles (GenBank accession numbers: KF770694-KF770731), including two alleles for L. borgpetersenii (A and B) and six for L. interrogans (C to H). There was no clear association between secY-identified strains and either locality or rodent species (Figure  2  and Text S1). MLVA positively identified 15 of the 25 tested samples, which were positive for L.
Statistical analyses of our dataset revealed that males were clearly more susceptible to Leptospira infections than females, consistent with many reports on vertebrate infections  [43]. Differing infection rates observed due to sex might result from endocrine-immune interactions. Androgens have immunosuppressive effects, explaining the reduced efficiency of the male immune system and its association with higher infection rates. Moreover, steroid hormones alter rodent behavior which then influences susceptibility to infection. Males of most mammals are more aggressive than females, more likely to disperse, and have larger home ranges with more intense foraging activities; all these behaviors cause increased pathogen exposure. Additionally, rodent susceptibility to Leptospira infection did not significantly vary across rodent species.
Acknowledgments The authors wish to thank CERoPath Project team (drivers and students) for sample collection, with a special mention to  Hul Vibol ,  Kim Aun  and  Kim Blasdell in Cambodia ,  Kittipong Chaisiri  in Thailand, and  Kone  and  Bouneuang Douangboupha  in Lao PDR. We also thank the technicians from the  National Reference Center for Leptospirosis (Sylvie Bremont ,  Annie Landier  and  Farida Zinini ) for molecular typing of DNA extracts.
This work was supported by the  ANR   ANR-11-CEPL-002-01   BioDivHealth SEA (Local impacts  and perceptions of global changes: health, biodiversity and zoonoses in Southeast Asia), the  Institut Pasteur , the  French Institute for Public Health Surveillance (InVS)  and the  French National Institute for Agricultural Research (INRA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
7 [10] [11] [12]  GARD is a voluntary alliance of organizations, institutions, and agencies working towards a common vision to improve global lung health according to local needs. GARD aims to develop a standard way of obtaining relevant data on CRD and risk factors, encourage countries to implement CRD prevention policies and to make recommendations of simple and affordable strategies for CRD management. 7 he rationale of this study was to investigate the prevalence of COPD in patients with respiratory symptoms, as well as the prevalence of bronchial asthma (BA), allergic rhinitis (AR), and chronic bronchitis (CB) in the overall Russian population. The frequency of major risk factors for CRD was also evaluated in the same study population.
Methods This was a cross-sectional population-based epidemiological study conducted in 2010-2011 across 12 regions (Figure  S1 ) of the Russian Federation. The aim of the study was to recruit 250 adult ($18 years) respondents in each major Russian city. As a general procedure, the administrative districts of each region participating in the study were selected based on a stratified random cluster sampling procedure. This stratification ensured appropriate weighted representation of each district's target population in the study sample. The most current census data from the entire region and from each district were collected from official sources in order to proportionally stipulate the number of participants in each district. In a second stage, streets from each previous selected district were also selected by applying a two-step stratified random cluster sampling procedure with a standard random number generator (Microsoft Excel 2010; Microsoft Corporation, Redmond, WA, USA).
Statistical analysis The primary study endpoint was to establish prevalence of COPD, BA, and AR in accordance with the current diagnostics standards in the representative population. Using a twotailed binomial test with a significance level of 5%, the study was designed to have 80% power to establish prevalence for each disease under study with the significance level not less than 1% on each side. The calculation of the sample size was made using Stata 12 package (sampsi) (StataCorp LP, College Station, TX, USA). The target sample size of 7,164 respondents was determined using the following assumptions: • Binomial distribution of the prevalence • The maximum prevalence for each study indication according to literature was 20% • Maximum acceptable one-sided error for prevalence determination was 5%, which was a 1% one-sided error for a maximum prevalence of 20% • Two-sided type 1 error of 5%, which was the risk to incorrectly accept the false null hypothesis of nonequivalence of sample prevalence and estimated population prevalence • An 80% probability to detect non-equivalence of the sample prevalence and the estimated population prevalence in case of true non-equivalence • A 10% probability that patients did not show up for the functional testing at the investigational site after the completion of the questionnaire.
Prevalence of COPD based on spirometry Spirometry data was recorded in 16% (251) of the total study sample in patients with suspected CRD. This information was based on both historical and newly performed spirometry data collected as part of the study. A post-bronchodilator test was performed in 94. 4% of these subjects. Subjects with a post-bronchodilator test had a significantly reduced vital capacity and FEV 1 when compared to the total population who had spirometry, and also had a significantly higher age (P,0. 001). The prevalence of COPD in patients with respiratory symptoms, or risk factors, was 21. 8% (95% CI: 19. 5%-24. 5%). By extrapolation, the prevalence of symptomatic COPD in the total study population was 15. 3%.
Discussion The GARD study was the first cross-sectional populationbased epidemiological study among a representative sample, using a standardized methodology and validated questionnaire, to evaluate the prevalence of respiratory diseases in several regions of the Russian Federation. Partial use of data collected from previously completed GARD questionnaires from 2009-2010 was approved by the study steering committee. The GARD questionnaire has been used in several studies and has been shown to be an accurate and reliable diagnostic tool. 17, 18 he prevalence of respiratory symptoms in the population sampled was found to be high. The percentage of patients with asthma related symptoms was 25. 7%, AR 18. 2% and CB 8. 6%. Based on spirometry-confirmed diagnosis, 21. 8% of respondents with respiratory symptoms had COPD, and, by extrapolations, 15.
Acknowledgments The authors wish to acknowledge  Diana Jones of Cambrian Clinical Associates Ltd  for the development of the first draft of the manuscript, editorial suggestions to draft versions of this paper, assembling tables and figures, collating author comments, and referencing. This assistance was funded by  GlaxoSmithKline. The study was supported from the grant provided by  GlaxoSmithKline Russia  to the contract-research organization " Worldwide Clinical Trials". Worldwide Clinical Trials  has conducted the study and assisted in developing the study protocol to investigators. This study was supported by  ZAO GlaxoSmithKline Trading Ltd.