dataesr/scientific-paragraphs-categorization huggingface dataset:
1a ). The inverted case was observed for those repetitive DNA elements showing a negative correlation with GC content, instead. Little to no correlation with GC content was observed for microsatellites/SSRs and mirror repeats (Fig. 1a ). Next, we investigated the relation between the abovementioned repetitive elements and diverse histone modifications retrieved from publicly available databases (HeLa S3 cells, [ENCODE tier 2]). We computed the genome-wide Spearman's rho correlation coefficient between each DNA repetitive element and each given histone modification. Repetitive DNA elements scoring an (anti-)correlation with GC content also scored a strong (anti-)correlation with the majority of the histone modifications we tested. For example, Alu elements were abundant on genomic locations whose chromatin was decorated by typical active promoter (H3K4me3/2, H3K9ac, H3K27ac) or gene body (H3K36me3, H3K79me2) modifications.
The number of each repetitive DNA element copies, or the amount of a given genomic feature is counted in each 10 kb genomic interval. The correlation coefficient is calculated for comparison of repetitive DNA elements with GC content (a), histone modifications (from HeLa, ENCODE tier 2) or genic regions (b) and replication timing from Repli-Seq data (HeLa, ENCODE tier 2)  [31]  (c). Data are from > 290,000 genomic intervals. For each correlation, P < 2. 2 × 10 -16. In a, Topo(…): from left to right, topoisomerase I consensus sequences at decreasing GC content. Highlighted Alu and L1 repetitive elements are arbitrarily chosen to define chromatin compartments with opposing chromatin features, and are further investigated in FISH experiments. d Correlation matrix of histone modifications and replication timing in HeLa cells, for L1-rich (> 10 counts per genomic interval) L1-poor (> 1 count per genomic element) genomic regions centromeric chromatin, we established an immuno-FISH-based method.
S7. A large number of repetitive DNA elements can exist in at least two conformations: B and non-B forms. These structures-especially the latter-are involved in genome susceptibility to DNA damage  [28]. To investigate which non-B DNA structure was more likely to be formed by a given repetitive DNA element, we first retrieved the genomic distribution of six non-B DNA motifs (cruciform, slipped, triplex, G-quadruplex, Z-DNA and A-phased) from "non-B DB" (https ://nonb-abcc. ncifc rf. gov/)-a database for integrated annotation and analysis of non-B DNA forming motifs-and, next, we computed the number of such structures in 10 kbp genomic intervals. Then, we calculated the Spearman's correlation coefficient between the non-B forms and the previously investigated repetitive DNA elements (Additional file 1: Fig.
Next-generation sequencing (NGS) and data analysis γH2AX ChIP-Seq libraries were generated and processed as described in  [33]. The corresponding datasets are from  [33]  and can be found at the Gene Expression Omnibus database (GEO accession number: GSE60526). Briefly, reads were mapped to the human genome (University of California, Santa Cruz (UCSC) hg19 assembly, based on the National Center for Biotechnology Information (NCBI) build 37. 1) by means of SOAP2 software  [47] , allowing up to two mismatches for each 36 bp read. Data for genomic features were retrieved from publicly available databases (UCSC/non-B DB) (Table  1 ). Accession numbers for histone modification ChIP-Seq data are given in Table  2. Data that were originally generated in the hg18 assembly were transposed to hg19 using LiftOver (http:// genom e.
5 mm accuracy) and mass (in g, 0. 1 g accuracy) were recorded. The gender was determined based on the presence of a swollen cloaca and a large crest on the back in males  35. Body size was then categorized into three groups: small (40-55 mm), intermediate (55-70 mm), and large (above 70 mm), including large juveniles (sufficiently large to be marked, i. e. above 3 g). Local weather conditions were noted using standard meteorological indices provided by the Meteo France database (publitheque. meteo. fr). The selected metrics (mean daily temperature [°C] and rainfall [mm]) were recorded at the Marlieux meteorological station (46°02′N, 5°02′E), located 20 km from the study site on the same geological plateau, and they were computed to obtain monthly averages. For the overwintering period, we also included the number of frost days and the number of days with lying snow as indicators of weather conditions.
Additionally, as repeated collinearity between environmental predictors usually prevents the inclusion of multiple weather variables in models, we also opted to use the NAO index as an integrator variable. This can be correlated to local indices to get an idea of the significance of NAO variations on a local scale  36. The NAO values were provided by the open-access database from the Climatic Research Unit, University of East Anglia (crudata. uea. ac. uk/ cru/data/nao). Hypotheses concerning recapture probability. Before building capture-recapture models based on the data from the long-term monitoring study, we performed a goodness-of-fit test using the U-CARE program  37. We tested both the full dataset and a subset containing only adults, as juveniles were included only in the analysis of survival (not of recruitment).
Modeling recruitment. Because we were only interested in adult recruitment, capture-recapture histories of juveniles were eliminated from the dataset. We extended Pradel's seniority model  43  to estimate recruitment while including transience; the model calculates the probability of not being in the system the year before, i. e. of being 'recruited' during the current year. For this purpose, we reversed the capture histories in order to use the survival models  41  in the multi-event context. This led to the consideration of three states (transient, resident, and not yet recruited) and two events (not captured and captured). As with the survival model, the transient/resident state was updated in the initial state of departure step (SF2: Transience). The recruitment probability was then updated (SF2: Recruitment).
Concerning events, an individual could be recaptured with probability p, or not recaptured with probability 1-p (SF2: Events). This parameterization was implemented with E-SURGE software  39. Analyses were carried out following the same procedure used for survival. First, through a backward stepwise selection from the most general model, δ(SEX + T) r(SEX + T) p(SEX + T), we tested the hypotheses that adult transience, recruitment and recapture could vary according to gender and between years. We first fixed the structure of the recapture component of the model, then the transience component, and finally tested hypotheses on recruitment. Once the structure of the best-fit model was ascertained, the relationship of each weather covariate with recruitment was tested individually, and its explanatory power quantified with ANODEV.
Acknowledgements We thank three anonymous referees for their useful comments on previous versions of the manuscript. A. W. received a grant from the  École Normale Supérieure in Lyon. The research program is supported by the  Institut Universitaire de France (IUF). The Pierre Vérots Foundation made the long-term monitoring possible by allowing access to a protected natural area without intensive agriculture. The foundation assisted in pond construction and the maintenance of the surrounding meadows, as well as providing technical support for newt collection. It also provided access to a well-equipped laboratory, making it possible to mark and measure the newts on site, thus reducing stress to the animals. We would especially like to thank  Benoît Castanier ,  Jean-Philippe Rabatel  and  Charles Granat  for their valuable assistance, and the  Rhône-Alpes regional government  for providing funding for the marking equipment.
Methodology The study was approved by the Charles Sturt University Ethics in the Human Research Committee (Ethics approval number: 2006/042) and followed the Helsinki protocol. All participants provided written informed consent to take part in this study. Data for this study were obtained from a total of 256 participants (female:male, 157:99) attending the Charles Sturt University rural health screening clinic. Inclusion and exclusion criteria were kept to a minimum to reflect routine patient presentation to general practice in a rural population. Exclusion criteria were CVD, kidney disease, any evidence of acute inflammation, and any evidence of depressive illness. All participants were assessed for waist circumference (WC), BP, and body mass index (BMI). Fasting blood glucose (FBG), hemoglobin A1c (HbA1c), lipid profiles including TC, triglycerides (TG), HDL-C, low-density lipoprotein cholesterol (LDL-C), TC/HDL-C ratio, and d-dimer were performed by the local National Association of Testing Authorities accredited pathology laboratory.
com TM (Jomar Pty Ltd, Melbourne, Australia). All inflammatory markers utilized the same analytical principle. Standards and samples are bound to the specific antibody pre-coated on a microplate. A biotin-conjugated anti-human biomarker antibody was added which binds to human biomarker captured by the antibody. After addition of streptavidin-HRP and substrate solution, color development was measured according to the assay protocol. Plasma C5a was determined using Human C5a Platinum ELISA TM (eBioscience, Affymetrix, San Diego, CA, USA). All ELISA measurements conducted on the inflammatory, oxidative stress biomarkers were carried out with a Thermo Scientific Multiskan FC TM (Thermo Fisher Scientific, Waltham, MA, USA). Data analysis for the ELISA analysis utilized 4-parameter logistic curve fit software.
Statistical analysis was performed with SPSS V20 (IBM Corporation, Armonk, NY, USA). To determine if there were significant differences in biomarker levels between the different groups for non-normally distributed data, the non-parametric Kruskal-Wallis test for multiple groups was applied followed by the Mann-Whitney U-test as a post hoc test. Anthropometric data were analyzed using ANOVA followed by the Fisher's least significant difference post hoc test. A p-value ≤0. 05 was considered significant. Results in Tables 1-3 are expressed as mean ± 1 SD.
Document review The aim of the document review was to describe the Cameroon policy context and content, identify existing policies and gaps therein and understand the policy development processes and implementation status. We focused on policy documents on tobacco use prevention and control (including acts and laws, strategic plans, guidelines and government directives), relevant documents on tobacco use and reviews and case studies of successful policy formulation and implementation at national level. All documents review was done between mid-2014 to the end of 2015 in which we selected related sectors based on their expected role in tobacco use policy formulation and implementation. We looked for laws, presidential decisions, ministerial orders, circulars, recommendations and guidelines, action plans, articles, government structures, research institutions, NGOs and associations of civil society reports from both online databases and in physical space.
An initial screening of all the selected tobacco policy documents was performed by the primary investigator (CMT). This was followed by a second review by a secondary investigator (CRB) after which documents not relating to the WHO "best buy" interventions were eliminated. We extracted data from retrieved documents and entered them into a Microsoft Excel database by these variables: authors, document title, date of publication, publisher/journal title, source, tobacco policy element addressed, summary of document type and objective, summary of key document analysis findings related to "best buy" interventions.
We repeated these steps for all identified policies. We used different interview guides for policy-makers and policy implementers. The policy makers' interview guide focused primarily on the context, process and actors of formulation. Whereas for the implementer's interview guide, we focused more on the process and actors of the implementation. We limited our interviews to actors of national policies formulated only in the last 10 years both because of our focus on formulation and to reduce possible recall bias and availability of actors for policies implemented more than 10 years ago. During interviews, we collected data on: (1) the policy context, including the political and historical context, social and economic factors, the health system, and technological factors; (2) the policy content, including risk factors addressed in the policy, the rationale for the policy, the objectives of the policy, the actors in the policy, other interventions mentioned, and mechanisms of actualizing the policy; (3) policy formulation and implementation processes; and (4) actors in the policy formulation and implementation as well as facilitating and hindering factors in their involvement.
Data management Using the Walt and Gilson framework  [16] , we developed a comprehensive codebook to guide coding of documents, interviews, and community observation reports. Codes identified the content, context, and process of tobacco prevention and control "best buy" interventions categories as well as the individual, group, and organization actors involved. We conducted data collection and analyses concurrently. We prepare a data analyses plan and compiled all datasets including the spreadsheets of policies, transcripts and field notes from interviews, and notes from observations. We cleaned data by reading through the transcripts to identify incomplete sections, typographical errors, formatting errors and clarifying the use of idioms, metaphors and slang language. Notes were inserted where explanations were required before the data was uploaded into NVivo10 software  [18]  for coding and analysis.
Data analyses We analyzed qualitative data using a content analysis approach. Researchers conducted content analysis using the NVivo10 software applying a pre-determined coding frame based on Walt and Gilson's framework. The software assisted researchers in labeling sections of text with content areas and key themes, from which we performed a thematic analyses  [19]. We sorted codes into categories depending on how the different codes were thematically related and linked. We also integrated data across data sources by examining areas of consistency and inconsistency among findings.
Policy context The introduction of the tobacco control discussions to the political agenda of Cameroon was influenced by both global context and local factors. High tobacco consumption and its effects were global concerns that led to international coalition towards tobacco control. In 2003, the FCTC was developed and ratified by Cameroon in 2006. The adoption of this convention motivated the formulation of various policies in Cameroon such as health warnings on tobacco products and creation of smoke-free zones. With regard to the local context; the formulation of tobacco control policies was driven by epidemiological data on tobacco use. Most decisions in Cameroon are based on its adverse effects on humans with an emphasis on the problem of smoking/delinquency among youths and particularly in school settings.
Four capture sites were structures (trees, caves, cistern and Mayan ruins) known to be inhabited by vampire bats. Other sites (n ¼ 6) included capture near livestock corrals or chicken coops where bat bites had been recently reported. We quantified livestock abundance as the total biomass of mammalian livestock (cattle, pigs) and poultry (chickens) rstb. royalsocietypublishing. org Phil. Trans. R. Soc. B 373: 20170089 (hereafter livestock biomass) within a 5 km radius of each site using the 2014 Gridded Livestock of the World (GLW) database of modelled livestock abundance estimates  [44]  and average species mass (kilogram) from the AnAge Database  [45]. GLW data were provided at a 1 km resolution and were processed and assigned to sites (figure  1e ; electronic supplementary material, table  S1 ) using the raster package in R  [49].
CMA estimates how much of a direct relationship between two variables (i. e. outcome model) is mediated indirectly through a third variable (i. e. mediator model)  [77]. The mediator model was given as a GLMM for the immune PC1 with livestock biomass and isotopic distance from livestock as predictors. For the outcome models, we fitted two GLMMs with both provisioning covariates and the immunity PC1 to reduced datasets (n ¼ 119 for Bartonella and n ¼ 116 for haemoplasmas) to accommodate missing values. We performed CMA with 5000 Monte Carlo draws using the mediation package to estimate the proportion of the relationship between provisioning covariates and infection mediated through the immunity PC1  [78] ; only bat ID was included as a random effect in GLMMs for the CMA owing to repeated measures and as the mediation package cannot support multilevel models.
Funding. D. J. B. was supported by a  National Science Foundation Graduate Research Fellowship, ARCS Foundation Award ,  Sigma Xi ,  Animal Behavior Society, Bat Conservation International, American Society of Mammalogists, Odum School of Ecology ,  UGA Graduate School ,  UGA Latin American and Caribbean Studies Institute ,  UGA Biomedical and Health Sciences Institute, Explorer's Club  and  NSF   Doctoral Dissertation Improvement Grant  ( DEB-1601052 ); fieldwork was also supported by  NSF   DEB-1020966. G. A. C. was supported by the  Leibniz Institute for Zoo and Wildlife Research. A. B. B. was supported by an  NSF   Graduate Research Fellowship , the  American Society of Mammalogists  and a  UGA   Global Programs International Travel Award. KJN was funded by  NSF   DEB-1518611. Fieldwork by N.
B. S. was supported by the  American Museum of Natural History Taxonomic Mammalogy Fund. A. T. G. was supported by the  USDA   National Rabies Management Program. S. A. acknowledges support from  NSF   DEB-1518611 , and D. G. S. was supported by a  Sir Henry Dale Fellowship , jointly funded by the  Wellcome Trust and Royal Society  ( 102507/Z/13/Z ).
4 Figure 1. 41 Figure 1. Vampire bat sampling sites in Peru and Belize (a), where shading and colour strip represent the log biomass (kilogram) of cows, pigs, and chickens from the GLW and AnAge databases [44,45]. Fine-scale patterns in livestock biomass are shown in (b) Loreto, (c) Amazonas and Cajamarca and (d) Belize; site coordinates are jittered to reduce overlap. (e) Quarter-root-transformed livestock biomass within 5 km of each capture location. Colours correspond to sampling region: green, Loreto; purple, Amazonas and Cajamarca; blue, Belize.
e. plant water relations) and dry matter accumulation (i. e. carbon allocation at the leaf level)  (Turner 1981; Jolly et al. 2014). There is therefore a need for robust and longterm LFMC datasets to improve our understanding of LFMC variations and refine our predictions. In 1996, the French organization in charge of protection of the Mediterranean forest (DPFM 1 ) initiated the systematic measurement of LFMC to improve its operational fire danger rating system during the fire season. Weekly measurements have been performed in various sites and shrub species over the fire-prone French Mediterranean. This operational network, called the "Reseau Hydrique" (what could be translated as "hydric network") has been operated by the National Forest Service (Office National des Forêts (ONF)) since then.
To date, the "Reseau Hydrique" produced a dataset that includes 584 "Sites × Years", on 24 species, with 7 to 20 measurement dates per year. In addition, rainfall amounts during the fire season have been recorded since 2009 on some sites. The raw dataset is currently available on demand via the Reseau Hydrique website 2 but, in its current form, cannot be easily used for scientific purposes for several reasons: (i) the database is not referenced (i. e. does not have a DOI); (ii) information is in French only; (iii) the labels and names of sampling sites and species names are not always consistent; (iv) outliers, duplications and inconsistencies in LFMC data 1 Délégation à la Protection de la Forêt Méditerranéenne 2 www. reseau-hydrique. org.
Handling Editor: Marianne Peiffer Key message We present a dataset of weekly live fuel moisture content (LFMC) time series over the summer season for 584 sites × years for several woody species in the French Mediterranean area. This database can be used to develop fire danger models and remote sensing products as well as to understand the physiological drivers of LFMC. Dataset access is at https://doi. org/10. 5281/zenodo. 162978. Associated metadata is available at https://agroenvgeo. data. inra. fr/geonetwork/srv/eng/catalog. search#/metadata/184ff098-eae2-44e1-9b8b-2e25a456c9a6. Contribution of the co-authors N. Martin-StPaul and F. Pimont are the co-first authors. NM, FP, JL, JR, ER designed the study and the analysis. FP performed the uncertainty analysis. NM wrote the manuscript with inputs from all authors.
Electronic supplementary material The online version of this article (https://doi. org/10. 1007/s13595-018-0729-3) contains supplementary material, which is available to authorized users. have not been corrected; (v) measurement uncertainties (confidence levels) are not provided. Here, we describe a revised version of the "Reseau Hydrique" dataset. The database was cleaned up and robust estimations of LFMC uncertainties were computed. Metadata description and accessibility are also provided.
Site and species description In each French administrative unit (called "départements") of the fire-prone Mediterranean area, between one and three sampling sites were selected according to the climatic heterogeneity and the averaged levels of fire hazard observed in the surrounding areas (Fig. 1a , Table  1 ). Since 1996, measurements have been carried out over 50 sites among which 35 are geolocalized. There are currently 30 active measurement sites in the region (Fig. 1a , Table  1 ). All sites are located on a south-exposed slope and include a shrubby layer, possibly associated with a sparse tree layer. The site labels are "DmSn" where m is the "département" number and n, the site number within a "département". In the refactored database presented below, site identifiers are unique and static (contrary to the operational database).
Data from non-geolocalized (NG) sites are labelled "DmSNGn" with m the "département" index number and n the site index number within a "département". The different sites cover a wide range of summer water availability (Fig. 1b ), expressed as the yearly average ratio between rainfall and evapotranspiration during the fire season (June to September). We estimated both quantities with the SAFRAN climatic dataset, which provides daily climatic variables on an 8-km grid over France  (Vidal et al. 2010 ). In the network, one to three shrub species are sampled in each site. They are selected among the dominant species. When species show both shrub and tree habits, only shrubby individuals are sampled.
LFMC and rainfall measurements Apical and lateral shoots of branches fully exposed to the sun are sampled from different individuals of a given species within plots on the order of 1000 m 2 representative of the surrounding landscape. Sampled individuals were chosen to be representative of the average status of each species. Samples were used to fill five 0. 35 l-aluminium containers sealed with paper tape, corresponding to an overall fresh mass on the order of 50 to 75 g. Once at the laboratory, samples were weighed fresh, oven dried at 60 °C during 24 h and weighed dry. The sampling operations take place at ca. 12:00 UT. Fuel moisture content is computed and released on fresh mass basis by the ONF. In the refactored database, values are provided in dry mass (see supplementary S1 for conversion).