dataesr/scientific-paragraphs-categorization huggingface dataset:
The number, length distribution and the cumulative length of ROH regions (cROH) in each individual were then analysed. Six individuals presented unusual cROH, that is, four s. d. higher than the average of his/her population of origin, which was considered as evidence of recent inbreeding. As methods to infer genetic ancestry assume random mating among individuals, we excluded these six samples from subsequent analyses. Our final filtered data set thus included a total of 481 unrelated samples, that is, 260 unrelated samples studied here and 221 samples from previous studies  26, 29. Population structure and differentiation. To gain insight into the population structure of our samples, the unsupervised clustering algorithm Admixture  30  was used on our filtered data set of 481 unrelated individuals, for 310,883 SNPs, after pruning SNP pairs with r 2 40.
Our 289 samples genotyped for 930,134 SNPs were phased and missing data were imputed using SHAPEIT v. 2 (ref. 47), accounting for trios and duos. The genetic map was obtained from the HapMap phase 2 recombination map  66  , after interpolating by local linear regression the SNPs that were absent from the map. We specified a N e of 15,000 individuals (N e estimated from 10 expectation-maximization iterations was B16,000). The Monte Carlo Markov chain of fineSTRUCTURE was made of 10 million iterations as burn-in, 10 million iterations as runtime and with sampling every 1,000 iterations. Tree building was performed with default parameters (Supplementary Fig. 4 ). Inferred geographic location of Baka. To test the hypothesis that the Baka originate from the CAR, where they might have acquired their Ubangian language and formed a unique group with the Biaka, we considered the geographic location of the Baka unknown and deduced expected geographic distances between Baka and all other RHG populations from both the observed F ST values and the regression equation of the isolation-by-distance relationship among all RHG populations except the Baka (Supplementary Fig.
We then checked the consistency of the single-pulse model of admixture assumed by the program by calculating the distance between observed data and exponential fitted curves (that is, the mean-squared difference of observed and expected values), and by calculating the slope of a linear function relating the estimated time since admixture and d 0 , the first bin of genetic distance considered for time estimation. If admixture rates have fluctuated in time, the admixture LD decay curve will be composed of a series of curves with different decay rates  37  , and the time estimated by ALDER will depend on d 0. LD decay. We computed the r 2 LD statistic between every possible pair of SNPs in a 1-Mb sliding window using Haploview  67. The 25% of most highly admixed samples and the 10% presenting the highest cROH were discarded from the analysis.
2 (ref. 47), accounting for trios and duos. We then used the Markov Chain Monte Carlo method implemented in LDhat v. 2. 1 (ref. 50) to estimate the population recombination map. All autosomes-and the X chromosome in females and males separately-were explored by a sliding window of 2,000 SNPs, with an overlap of 500 SNPs between contiguous windows. Five million iterations were performed per window, 500,000 samples were removed as burn-in and sampling was done every 5,000 iterations. In overlapping segments, rate estimates from the last 250 SNPs of the 5 0 -region window and the first 250 SNPs from the 3 0 -region window were removed. We estimated the effective population sizes N e of Western RHG and AGR from the comparison of the genetic maps estimated here and the pedigreebased, sex-averaged, deCODE genetic map  51.
Demographic inference based on LD decay. We estimated LD decay as described above, but restricted our population sample to our two model populations: Baka Western RHG and Nzime/Nzebi Western AGR. To avoid any bias introduced by SNP ascertainment, we restricted this analysis to SNPs whose population frequency was higher than 5% in both populations. To determine the demographic models that best explain observed LD decay in Western RHG and AGR, we performed coalescent simulations using the program MaCS  68. We simulated two populations under an isolation-with-migration model, with sample sizes of 70 and 73 diploid individuals (Figs  4b  and 5 ) or 55 and 55 diploid individuals (Supplementary Fig. 15 ). The ancestral population size, the time of divergence and the migration rate between the two populations were sampled from posterior distributions of parameter estimates, obtained previously for the same populations using autosomal resequencing data  23.
Acknowledgements We thank  Serge Bahuchet ,  Gary Chen ,  Steve Gazal ,  Garrett Hellenthal ,  Simon Myers ,  Nick Patterson ,  Arti Tandon  and  Peter Underhill  for critical feedback and advice on different aspects of data analyses and interpretation. We also thank  Katarzyna Bryc  for sharing genotyping data of sub-Saharan Africans. We are particularly grateful to all the study participants for their generous contributions of DNA, and to the  Batwa Development Program  and the  Batwa Executive Council. This work was supported by the  Institut Pasteur , the  CNRS , a  CNRS 'MIE' (Maladies Infectieuses et Environnement) Grant , a  Foundation Simone & Cino del Duca Research Grant , and the  David and Lucile Packard Foundation  (Fellowship in Science and Engineering no. 2007-31754 ).
Data collection and analysis For stand structure analysis we selected all compartments which hosted pure silver fir stands with current age ranging from 80 to 145 years, according to the preceding management plans (Fig. 1 ). Forty-two 20 m radius circular plots (1256 m 2 ) were randomly distributed in these compartments. In each plot we recorded species and diameter at 1. 30 m (DBH) of all living trees with DBH > 2. 5 Fig. 1  -The Vallombrosa Forest. The area where gap analysis was carried out is outlined in black; black points show the 42 circular plots for stand structure analysis. cm; we also measured total height on a sample of trees (35 % of trees in each 5 cm DBH class). Fir trees belonging to the original planted stands (aged 80 to 145 years in the different plots) were identified during the survey and recorded separately, so as to obtain a picture of the fir plantation development as compared to other species spreading naturally into the stands.
2012 , Rugani et al. 2013 ) -and Airborne Laser Scanning data -useful for automatic gap detection over large areas  (Zhang 2008 , Barbati et al. 2009 ) -were not available in the study area, canopy gaps were monitored using multitemporal aerial remote sensing data. We used 1983 aerial photographs (flying height 750 m), and 1997 and 2007 digital orthophotos with 1 m and 0. 5 m pixel size, respectively. The 1983 images were scanned and orthorectified with 1 m pixel size (RMSE = 1 pixel) using the ORTHOEN-GINE software package (PCI Geomatics, Richmond Hill, Ontario, Canada). Because no information about the camera was available, the Rational Functions Model was used  (PCI 2001). To this purpose, a digital terrain model with a 5 m spatial resolution was created using contours extracted from topographic maps (1:10000) and ground control points were collected using the orthophotos as reference images.
Canopy openings ≥ 50 m 2 were considered gaps. Such threshold was chosen since 50 m 2 is the average crown projection area for fir trees in stands aged 100+ years in similar areas of the Apennines  (Travaglini et al. 2012). Gap margins were photointerpreted and digitized on-screen into a polygon layer on a GIS database. The following parameters were then calculated: number of gaps; total gap area; percent of total surveyed area covered by gaps (gap fraction); mean, standard deviation and maximum size of gaps for each survey year. We also examined the fate of the individual gaps, following the method proposed by  Kenderes et al. (2008) , i. e. , creation of new gaps, gap closure, dissection of gaps and merging of neighbouring gaps. Because stereopairs were available only for the 1983 aerial photographs, we could not use the height of the vegetation filling the gap as an indication of gap closure  (Runkle 1992 , Pedersen & Howard 2004).
Acknowledgments We wish to thank two anonymous reviewers for their helpful suggestions and comments on an early version of the manuscript. This study was partially supported by the  University of Florence ,  Fondi di ricerca di Ateneo 2010  " La rinaturalizzazione dei so-prassuoli di abete bianco di origine artificiale in seguito all ' applicazione del Piano di Gestione della Riserva Naturale di Vallombrosa (FI) " (Scientific coordinator:  Susanna Nocentini ).
109, P < 10 À5 ; Pse: 0. 064, P = 0. 015). The loss of H3K27me3 was also related to an average increase in expression of both duplicates (Permutation test: Sim, P < 10 À5 ; Yak, P < 10 À5 ; Pse, P < 10 À5 ). We examined expression patterns in newly duplicated genes using the Berkeley Drosophila Genome Project's in situ database  (Tomancak et al. 2002)  and found that such genes are enriched for tissuespecific expression (Fisher's exact test, P = 0. 0006). Since these recent duplicates generally lose H3K27me3, our results imply that such genes may acquire tissue specificity through DNA-binding trans-regulators. A notable exception to this pattern is the gene Zeus (FBgn0032089; also called Rcd-1r). Previously, Zeus has been shown to be a recent duplicate of CAF40 (FBgn0031047; also called Rcd-1), which has acquired an essential role in gonadal development  (Chen et al.
ChIP-seq Strains were maintained at room temperature until collection at the white prepupa stage. ChIP-seq was carried out in duplicate using the standard modENCODE protocols. We mapped 36-bp reads to the appropriate reference genome using Bowtie (v. 0. 12. 7)  (Langmead et al. 2009). Caenorhabditis elegans H3K27me3 ChIP-seq data were generated as described in AP Boyle, CL Araya, C Brdlik, P Cayting, C Cheng, Y Cheng, K Gardner, L Hillier, J Janette,  L Jiang, et al. (in prep. ). Data from Negre et al. (  2011 ) are available under accession numbers GSE27111 and GSE23537.
Quantitative analysis We used BEDTools  (Quinlan and Hall 2010)  to count the number of reads occurring in either (1) the exons of each gene as determined by the reference annotation, or (2) regular sliding windows 1 kb in width  (Quinlan and Hall 2010). Genic H3K27me3 was normalized by the number of exons (see Supplemental Methods). We compared orthologous genes using the list of modENCODE orthologs, and we compared orthologous windows by using lift-Over to map windows between species.
Also  [11]  uses fluctuating initial conditions, here based on both Glauber Monte Carlo and Glasma initial conditions. Finally in  [12] , ideal hydrodynamical calculations are performed, starting from smooth Glauber model initial conditions. In the following, we will compare experimental data on identified particle production with our simulation results (referred to as EPOS3), and in addition to some other models, as there are QGSJET  [13] , AMPT  [14] , and EPOS LHC  [15]. The QGSJET model is also based on Gribov-Regge multiple scattering, but there is no fluid component. The main ingredients of the AMPT model are a partonic cascade and then a hadronic cascade, providing in this way some "collectivity". EPOS LHC is a tune (using LHC data) of EPOS1. 99. As all EPOS1 models, it contains flow, put in by hand, parametrizing the collective flow at freeze-out.
Finally, the approach discussed in this paper (EPOS3) contains a full viscous hydrodynamical simulation. So it is interesting to compare these four models, since they differ considerably concerning the implementation of flow, from full hydrodynamical flow in EPOS3 to no flow in QGSJET. The CMS collaboration published a detailed study  [1]  of the multiplicity dependence of (normalized) transverse momentum spectra in p-Pb scattering at 5. 02 TeV. The multiplicity (referred to as N track ) counts the number of charged particles in the range |η| < 2. 4. In fig. 2 , we compare experimental data  [1]     pendence: the spectra get somewhat harder with increasing multiplicity. The other models, AMPT, EPOS LHC, and EPOS3 are close to the data. In figs. 3, 4, we compare experimental data  [1]  for kaons and protons (black symbols) with the simulations.
02 TeV, for high multiplicity (red dashed-dotted lines, circles) and low multiplicity events (green solid lines, triangles), comparing data from ALICE  [2]  (symbols) and simulations from QGSJET, AMPT, EPOS LHC, and EPOS3 (lines). In all models, as in the data, there is little multiplicity dependence. However, the QGSJET model is considerably below the data, for both high and low multiplicity events. AMPT is slightly below, whereas EPOS LHC and EPOS3 do a reasonable job. Concerning the proton over pion ( p/π) ratio, fig. 6 , again QGSJET is way below the data, for both high and low multiplicity events, whereas the three other models show the trend correctly, but being slightly above the data. Most interesting are the lambdas over kaon (Λ/K s ) ratios, as shown in fig. 7 , because here a wider transverse momentum range is considered, showing a clear peak structure with a maximum around 2-3 GeV/c and a slightly more pronounced peak for the higher multiplicities.
5 microns or less  (PM 2. 5  ). This special issue of Geospatial Health came about because the use of remote sensing in conjunction with terrestrial meteorological data products was felt to be a novel area of spatio-temporal investigation where GnosisGIS could play a part. The growing availability of digital data for geospatial studies made possible by remote sensing and resources from influential national space agencies, such as the National Aeronautics Space Administration (NASA) in USA (http://www. nasa. gov/), the French national centre for space studies (Centre national d'études spatiales (CNES)  (Marechal et al. , 2008) , the European Space Agency (ESA) and the Japan Aerospace Exploration Agency (JAXA)  (Igarashi et al. , (2014)  has led to the establishment of a number of multi-disciplinary scientific teams interested in geospatial health applications.
This is especially true of groups whose members come from different orientations and training and whose work are on very diverse health issues. A key aim of this special issue is to establish communication and collaboration linkages between ISPRS WG VIII/2 and GnosisGIS, so that the mutual interests of both scientific bodies can be further developed. Six papers in this special issue emanate from ISPRS. The lead paper by  Lary et al. (2014)  describes the development of a unique global air quality surveillance system based on satellite data generated by the moderate resolution imaging spectroradiometer (MODIS) (http://modis. gsfc. nasa. gov/), while  Liss et al. , (2014)  propose an updated global climate classification system made possible by advances in remote sensing technology. Both of these papers offer striking new ways to view the Earth system in relation to public health.
jpl. nasa. gov/mission/), 40 years of Landsat legacy data, vividly presented as a slide show available at http:// www. oosa. unvienna. org/pdf/pres/copuos2012/panel-01. pdf and, perhaps most crucially, the sub-meter resolution environmental data now available from  Worldview-2 and Worldview-3 (De Roeck et al. , 2014). Add to this the elective value-added potential of low-altitude sensors on drone airborne vehicles as a source of very high resolution data collection within a user-set agenda  (Capolupo et al. , 2014). Future NASA satellite and international space station missions such as HyspIRI (http://hyspiri. jpl. nasa. gov/) will provide further enhanced capability to map vector-borne and other environmentally sensitive diseases based on global hyperspectral visible and multispectral thermal data products (60 m 2 , 5day thermal and 19-day hyperspectral repeat intervals) that will enable structural and functional classification of ecosystems and the measurement of key environmental parameters (temperature, soil moisture).
Further confirmation for the effect of PARP inhibition on BUBR1 levels was established by the use of a different PARP inhibitor, olaparib, that induced BUBR1 down-regulation in U87MG but not in LN229 cells (figure  S4C ). Furthermore, silencing PTEN in LN229 cells also results in BUBR1 decrease after PARP inhibition (figure  2B ) while introduction of PTEN in U87MG cells delayed BUBR1 loss (figure  2B ). In addition, in silico analysis using the database Array Express of U87MG cells transduced with wild type PTEN showed a statistically significant decrease in BUB1B expression (the gene for BUBR1) in PTEN transduced cells as well as in the gene coding for the SAC-related factor (and BUBR1 associated protein) AURKB (-2,62 and -3. 31 fold decrease respectively). In order to approach the clinical relevance of these variations in BUBR1 levels as function of PTEN we used two available datasets: Oncomine and Array Express from EMBO-EBI.
Cell Cycle Assay Cell cycle was analysed by flow cytometry  [42]. Cells were plated in 6 wells at a density of 1. 5 x 10 5 cells. After the treatments, cells were trypsinized, washed with PBS, permeabilized with 70% ice cold ethanol, washed again with PBS and incubated with propidium iodide and 100 μg/ml RNAase A (Ribonuclease A from bovine pancreas R6513-10MG Sigma-Aldrich, St Louis, USA) for 20 min. When GFP population was examined, cell fixation before permeabilization was required, as previously described by Lamm et al  [42]. Cells were analysed on a FACScan using CellQuest software, and cell cycle was determined using FlowJo software. In the case of PTEN overexpression, GFP population was gated in order to analyze cell cycle in a 100% transfected population.
24 hours later, cells were transfected with 4 μg SceI plasmid per well using JetPRIME TM (Polyplus transfection, Illkirch, France) according to the manufacturer's protocol. 24 hours after the transfection, cells were treated with PJ34 hours during 48 hours. Finally, cells were trypsinized and percentage of GFP expressing cells was measured by flow cytometry on a FACScan. Frequency of recombination events was calculated as mean percentage of GFP positive cells transfected with SceI divided by mean percentage of GFP positive cells transfected with pEGFP. Results were represented through Kolmogorov-Smirnov adjust using CellQuest software. Additionally, homologous recombination was indirectly evaluated by the number of cells with rad51 foci to get the fraction of γH2AX positive cells bearing Rad51 foci.
Sodium Chloride solution/60% DMSO was used as vehicle. In order to develop in vivo bioluminiscence measurement, mice were injected intraperitoneally with D-luciferin solution dissolved in phosphate-buffered saline at a dose of 150 mg/kg body weight. After 5 minutes, the animals anesthetized in the dark chamber using 3% isoflurane in air at 1. 5 L/min and O2 at 0. 2 L/min/mouse, and animals were imaged in a chamber connected to a camera (IVIS, Xenogen, Alameda, CA). The quantification of light emission was performed in photons/second/cm 2 /steradian using Living Image 2. 6. 1 software (Xenogen). Tumour growth was monitored at 0, 2, 8, 15 and 21 days by in vivo imaging and bioluminiscence measurement. After 21 days, mice were sacrificed, and brains were dissected and placed in Petri dishes with D-luciferin solution at a dose of 20μg/ml.
ACKNOWLEDGEMENTS We acknowledge  Abelardo López-Rivas  and  Tania Sánchez  ( CABIMER, CSIC, Sevilla ) for helpful discussions, and  Eva Mª Galán Moya  ( Hôpital Cochin, INSERM-CNRS, Paris ) for her advices for primary cells lines experiments set up and helpful discussions. Joan Seoane  ( Hospital Vall d'Hebron, Barcelona ) for providing LN229 cells,  Guillermo Velasco  ( Complutense University, Madrid ) for providing U118MG and SW1783 cells and  Professor Yasuhiro Matsumura  ( National Cancer Center Hospital East, Kashiwanoha, Kashiwa City, Japan ), for his kindness in providing the cells U87MG luciferase. We also acknowledge  Salvador Guerrero  and  Jose Luis Luque  for excellent technical assistance. JMM has been funded by a predoctoral fellowship by the programme  FPU ,  Spanish Ministery of Economy and Competitiveness.
Chronic Dietary Exposure The exposure estimate to be used in the safety assessment of the candidate substance is the Added Portions Exposure Technique (APET) approach defined in the EFSA scientific opinion "Guidance on the data required for the risk assessment of flavourings to be used in or on foods"  6. The chronic APET will be calculated both for adults and children and the highest value among these will be used as the exposure estimate to be compared to the Threshold of Toxicological Concern (TTC) value in the Procedure. The highest chronic exposure is 231 µg/kg body weight (bw)/day derived from the scenario of a 15 kg three year old child consuming one portion of category 14. 1 (Non-alcoholic ("soft") beverages) and one portion of category 12. 5 (Soups and broths). This intake will result in a chronic APET 7  of 3465 μg/child per day (231 μg/kg bw per day for a 15 kg child) (for calculation of the chronic APET, see Appendix C).
Mammals and fleas' molecular diagnosis The morphological diagnosis of Rattus spp. was confirmed by molecular data through sequencing of cytB locus from 15 randomly selected animals morphologically identified as R. rattus or R. norvegicus. Briefly, DNA was prepared from 20 mg of kidney tissue as previously described  [15]  and used as a template with L14723 and H15915 primers set, following a previously described PCR protocol  [14]. For molecular diagnosis of fleas, DNA was prepared as follows: fleas were dried individually and subsequently crushed with a TissueLyser (Qiagen, Valencia, CA) using 3 mm tungsten beads and cetyl trimethyl ammonium bromide 2%; DNA was further.
Author Summary Fleas are blood-feeding parasites involved in the transmission of several arthropod borne pathogens. Rat-fleas (Xenopsylla spp. ) are known vectors of bubonic plague together with other human diseases receiving less attention such as murine typhus. This latter disease was recorded for the first time in 2011 on Reunion Island where seven human cases were further confirmed within the following year. The outbreak motivated a large survey of fleas, as these insects of major veterinary and medical importance have never been investigated on this oceanic island. We collected fleas on almost 1000 small wild mammals trapped on two altitudinal transects along the humid eastern and dry western sides of the island. Our data reveal the presence of four cosmopolitan flea species and shows an astonishing distribution pattern: 81% of all collected fleas were sampled on the western transect while not a single rat-flea was sampled on the eastern humid side of the island.
Interestingly, this distribution did at least in part overlay the map of murine typhus human cases. These data stimulate the need for a diagnosis of pathogens in natural flea populations together with a comprehensive distribution map of fleas, allowing a risk assessment of flea-borne diseases in humans. extracted following a previously described procedure  [16]. Both nuclear and mitochondrial loci were sequenced by amplifying 28S ribosomal RNA (28S rRNA gene) and cytochrome oxidase II (COII) encoding gene using 28S A/28S rD7b1 and COII F-leu/ COII R-lys primer pairs, that produce 1473-bp and 770-bp PCR fragments respectively  [17]. Amplicons were sequenced on both strands by Genoscreen (Lille, France) using the same PCR primers, and sequences were edited using Geneious Pro  [18]. All sequences used in this study were deposited in Genbank and are accessible under accession numbers KJ638526 to KJ638590.