dataesr/scientific-paragraphs-categorization huggingface dataset:
Further, OH/EH may also focus more on benefits of nature to human health. Also OH/EH should take into account more explicitly environmental factors, e. g. climate change effects on the emergence and incidence of infectious diseases and should more prominently take into account various chemical and physical environmental disturbances brought by human activities. It was in any case considered necessary for policy makers to develop clear criteria and indicators for application of OH/EH and related concepts, for the purpose of designing, selecting, financing and evaluating related projects. An important goal of the OH/EH approach should be to overcome ad hoc reactive actions responding to emerging public health challenges to build pro-active capacity and preparedness, being able to better foresee health risks scenarios thanks to knowledge compiled in integrated databases.
Funding The organization of the workshop was generously financed mainly by the  Belgian Biodiversity Platform (BBPF) ,  Belgian Federal Public Planning Service Science Policy (BELSPO)  and  Belgian Federal Public Service Health, Food Chain Safety and Environment -DG Environment  and with additional budgets from,  Veterinary and Agrochemical Research Centre (CODA-CERVA) ,  Institute of Tropical Medicine of Antwerp (ITM) ,  Royal Belgian Institute of Natural Sciences (RBINS)  ( CEBioS program :  Capacities for Biodiversity and Sustainable Development , funded by the  Belgian Directorate-General for Development Cooperation and Humanitarian Aid) ,  University of Liège, Faculty of Veterinary Medicine (ULg) ,  Scientific Institute of Public Health (WIV-ISP) ,  COST Action TD1404 (Network for Evaluation of One Health ), supported by  COST (European Cooperation in Science and Technology) ,  ComAcross  project (implemented by CIRAD and funded by  EU).
, 2015  for a detailed protocol). The apical plane of each blastomere (defined as the 2D plane containing the poles of the mitotic spindle which can separate most of the apical surface from the basolateral surface) was systematically extracted from 3D-rendered blastomeres using Imaris software following a specific protocol (see  Materials and methods and McDougall et al. , 2015)  for detailed protocols) and the position of the mitotic spindle in the extracted 2D plane was compared with the position of a mitotic spindle predicted by the computational model  (Minc et al. , 2011). 3D rendering and in silico isolation of each blastomere at interphase, prophase and metaphase revealed drastic cell shape changes during the cell cycle (Figure  3 ). Sphericity of each blastomere was determined using Imaris statistics (see Materials and methods) to estimate the complexity of polyhedral shape of in silico isolated blastomeres.
8 (normally displaying spindle rotation) shows that misoriented cell divisions are still predicted reliably by apical cell shape (Figure  6C ). Therefore the processes supporting spindle orientation in the long length of the cell in the apical plane are maintained in these embryos and misoriented cell divisions are probably due to altered cell shape in manipulated embryos. Since both PEM1 overexpression and DN-Tcf reduce cell cycle asynchrony  (Dumollard et al. , 2013)  we next sought to directly alter cell cycle duration to assess the impact cell cycle asynchrony has on the invariant cleavage pattern. unfertilized oocyte in Phallusia mammillata (Figure  7A , see also RNA-seq data in Aniseed database: http://www. aniseed. cnrs. fr/ with Gene Id: phmamm. CG. MTP2014. S423. g08568) where it is enriched in the vegetal cortex.
Manipulation of cell adhesion and apicobasal polarity and embryo compressions To remove cell adhesion, Phallusia zygotes stained with Cell Mask-Orange or expressing MAP7::GFP and PH::GFP (to image cell membranes and spindle poles) were cultured in Ca 2+ -free sea water (supplemented with 1 mM EDTA, as described in  Sardet et al. , 2011)  and imaged up to the 64 cell stage. Dominant active aPKC: Pm-aPKC (GenBank: AY987397. 1, Patalano et al. , 2006 ) was cut at K146 to remove the N-terminal regulatory domain of aPKC and tagged with Venus using our Gateway cloning system  (McDougall et al. , 2015; Roure et al. , 2007). Removal of the N-terminal regulatory domain of aPKC results in a constitutively active form (DA-aPKC). This construct can expand the apical domain of superficial cells at the expense of the basolateral domain in Xenopus embryos  (Sabherwal et al.
Time-lapse and fluorescence microscopy Time-lapse imaging of Venus, GFP, mRfp1,Cherry and Tomato constructs was performed on a Zeiss Axiovert200 and a Zeiss Axiovert100 inverted microscopes set up for epifluorescence imaging. Sequential brightfield and fluorescence images were captured using a cooled CCD camera (Micromax, Sony Interline chip, Princeton Instruments, Trenton NJ) and data was collected using Meta-Morph software (Molecular Devices, Sunnyvale CA) essentially as described in  McDougall et al. (2014 McDougall et al. ( ), (2015)). Time series were reconstructed and analysed by MetaMorph and Image J (NIH, USA) software packages. 4D confocal imaging was performed on Leica CSLM SP2 through a long distance 40X (NA = 0. 8) objective to obtain 3D embryos over time (30-35 z-planes imaged every minute) that were manually segmented and 3D rendered using Imaris 3.
3D rendering and plane extraction using imaris software The complete protocol for 3D rendering of confocal stacks using Imaris (x64, version 7. 7. 2, Bitplane) is published in details in  McDougall et al. (2015)  and can be downloaded from http://www. biodev. obs-vlfr. fr/~dumollard/protocols/Segmentation-manuelle-Imaris-En. pdf. All cell contours were drawn manually on 2D-slices before 3D rendering and analysis by Imaris. Sphericity of the 3D shapes was calculated by Imaris software ('statistics' function) for each blastomere and compared to the sphericity of a spherical standard (an in vivo isolated blastomere at metaphase from a 2 cell stage which showed a sphericity of 0. 975 ± 0. 001, n = 4 cells). Sphericity was found to be significantly lower than spherical standard at the 4 cell stage (0.
Spindle position prediction using computational model Prediction of spindle position in 2D extracted planes was performed with MatLab using scripts which may be dowloaded at: http://www. minclab. fr/research/ (Minc et al. , 2011). This model postulates that MTs radiating from spindle poles reach the cell cortex and pull with forces that scale to MT length. The model assays all possible orientations in the 2D shape and computes the evolution of the torque with spindle orientation, which informs on the mechanical equilibrium corresponding to stable spindle orientation. To implement the model with the current study, the outline of the cells and the experimental positions of the spindle poles were drawn manually as inputs. The script returned the difference between the centers of observed and predicted spindles (computed as a 'centering deviation' in %) and the difference in angle orientation between predicted and observed spindles (computed as an 'orienting deviation' in degrees ( ˚)).
Acknowledgements We would like to thank the  ANR  ( ANR-12-BSV2-0005-02 ) and  ARC  (n  ˚SFI20111203776 ) for financial support. We would also like to thank  Hitoshi Yasuo  for helpful discussions and for providing WT bcatenin and DN-Tcf constructs. We thank  JO Irisson  (LOV,  UMR 7093 ,  CNRS ) for his help with the statistical analysis shown in Figure 4. Finally, we thank the members of  UMR7009  for their help and support.
1b ). Interestingly, ANO1 and miR-9 transcript levels were significantly inversely correlated in our cell line models (P = 0. 012; Pearson's correlation) (Fig. 1c ). This result was confirmed in primary human bronchial glandular cells (P < 0. 003; Pearson's correlation) and in fully differentiated bronchial cells from CF patients cultured in an air-liquid interface (ALI) (P < 0. 05; Pearson's correlation; see Supplementary Fig. 7a, b ). miR-9 regulates ANO1 expression and chloride activity. The increase in miR-9 expression in CF cells led us to hypothesize that ANO1 is a direct target of miR-9. We transfected non-CF cells (16HBE14o-) with a miR-9 mimic and verified the transfection efficiency by qRT-PCR and by using a SmartFlare probe (Supplementary Figs. 8  and 9 ). Additionally, we confirmed the specificity of the miR-9 mimic by quantifying the expression of other miRNAs (including miR-19a) by qRT-PCR (Supplementary Fig.
Methods Bioinformatics analysis of miRNA target genes. The role of miRNAs in the regulation of ANO1 expression was examined using a computational approach, which predicted the 3′UTR of ANO1 mRNA to contain various seed regions that are recognized by a variety of miRNAs. The putative miRNAs predicted for ANO1 mRNA were identified and compared using the online target prediction algorithms TargetScan (http://targetscan. org), Pictar (http://pictar. mdc-berlin. de), miRDB (http://mirdb. org/miRDB), and miRANDA (http://www. microrna. org). The NCBI and Ensembl genome browsers (http://www. ensembl. org/index. html) provided information on the human ANO1 transcript (NM_018043; ENST00000355303). The miRBase (http://www. mirbase. org) provided information on miR-9 (MI0000466). 15) and KM4 cell lines were a gift from Dr Caroline Norez (Poitiers-CNRS University, Poitiers, France).
Relative quantification was performed by densitometric analysis using MultiGauge software (Fujifilm, Courbevoie, France). See Supplementary Fig. 22  for gel source data. Migration assays. Migration assays were performed using specific wound assay chambers (Ibidi ® ; Biovalley, Marne La Vallée, France) that provide uniform wounds between two monolayers. CFBE41o-cells (3. 5 × 10 4 ) were seeded in Ibidi silicone culture-inserts and were incubated at 37 °C with 5% CO 2. After 24 h, the cells were transfected with a miR-9 mimic, negative control (Life Technologies, Saint Aubin, France), or ANO1 TSB/LNA control (Exiqon). The culture inserts were removed after 48 h, leaving a cell-free gap (or wound) for cell colonization. For hAECB, wounds were generated using a tip soaked in liquid nitrogen. Wound closure was observed for 4 h under an Axiovert 200 microscope in a chamber maintained at 37 °C with 5% CO 2.
Mean migration rates during wound closure were assessed in three areas of the gap. At each time point and in each field, five lengths were measured using the AxioVision Rel software (Zeiss, Marly-Le-Roi, France). ANO1 chloride channel activity assay. ANO1 channel activity was assessed by I -quenching of halide-sensitive YFP-H148Q/I152L protein (Thermo Fischer Scientific). The probe was transfected into the cells, and after 48 h of culture, conductance was stimulated with UTP (10 µM). I -solution (140 mM) was added, and the fluorescence was recorded using a plate reader as previously described  39. The initial I -influx rate upon addition of each solution was computed from changes in YFP fluorescence data using non-linear regression. For quantitative analysis, the slope for fluorescence quenching, which correlates to the level of chloride conductance (I -uptake), was determined using linear regression.
The rate of change (ΔF/min) was then calculated. Microinjection experiments. CF cells were seeded on glass-bottom Ibidi dishes 24 h after transfection with the YFP-H148Q/I152L protein construct, and ANO1 TSB or control TSB were microinjected using a Xenowork micromanipulator and digital microinjector (Sutter Instrument, CA, USA). To discriminate the different transfections, ANO1 TSB was microinjected with Dextran Texas Red neutral (Thermo Fischer Scientific). Four hours after microinjection, the cells were injected with I - using a microperfusion system (Valvelink; Automate Scientific, CA, USA) and observed under an Axiovert 200 microscope (63 × objective lens, Zeiss). The fluorescence was quantified with the ImageJ software (US National Institutes of Health, ML, USA). Mucus clearance assay.
Thirty days after transfection of hAECB cells with ANO1 TSB or control TSB, FluoSpheres Carboxylate-Modified Microspheres, 1. 0 µm, yellow-green fluorescent (505/515) (Thermo Fisher Scientific) diluted in culture medium (1/50) were added to the apical face of the cultures. Movement of the beads was recorded under an Axiovert 200 microscope (Zeiss). Fluorescence images were collected every 3 ms and composed into a time-lapse image series using Axiovision software (version 4. 6). Animal experiments. All experiments were approved and conducted in accordance with our Institutional Animal Care and Use Department (approval 20150511145844v3 of the Ethical Committee for Laboratory Animal Care Charles Darwin France). For all the experiments, we used 8-week-old male 129-Cftr tm1Eur CF model mice homozygous for the F508del mutation in the 129/FVB outbred background (F508del-CFTR) and their wild-type littermates obtained from CDTA-CNRS (Orléans, France).
Acknowledgements We thank  O. Bregerie  and coworkers of the  Animal Research Facility of the Pitié-Salpétrière-UPMC Université Paris 06, France. We thank  Dr D. C. Gruenert  for providing the 16HBE14o-and CFBE41o-cells and  Dr C. Norez  for providing MLE-15 cells. This research was funded in part by grants from  Inserm ,  UPMC-Paris 06 , the non-profit organization Vaincre la mucoviscidose, and the  Legs Poix-Chancellerie des Universités, Paris. F. S. received a Ph. D. grant from  Vaincre la Mucoviscidose. M. R. received a Ph. D. grant from the  Émergence-UPMC   2010 research program.
Select your title and keywords wisely Title and keywords have the potential to significantly impact the chances of getting picked up when searched, read, cited and included in systematic reviews that synthesise evidence on an issue. 8 ournals, search engines, and indexing and abstracting services classify papers using keywords. An accurate list of keywords will therefore ensure correct indexing and help showcase the research to attract interested groups. It is best to select keywords from a list of key terms/phrases that are used repeatedly in the text and preferably not repeated in the title or abstract. It is recommended to use the Medical Subject Headings (MeSH) tool to choose keywords. MeSH is a comprehensive, controlled vocabulary for the purpose of indexing journal articles and books for the MED-LINE database (US National Library of Medicine ® , Bethesda, MD, USA).
Make your articles open access 0] [11]  Publishing in an open access journal will make the paper available to all readers free of charge. Effective dissemination of evidence is important in bridging the gap between research and policy. In this paper, we list 10 approaches for improving the visibility of research findings, which in turn will hopefully contribute towards changes in policy. Current approaches include using social media (Facebook, Twitter, LinkedIn); sharing podcasts and other research outputs such as conference papers, posters, presentations, reports, protocols, preprint copy and research data (figshare, Zenodo, Slideshare, Scribd); and using personal blogs and unique author identifiers (ORCID, ResearcherID). Researchers and funders could consider drawing up a systematic plan for dissemination of research during the stage of protocol development.
Sharing research outputs other than the manuscript In addition to published articles, preprints, conference papers and posters, presentations, reports, working papers, protocols, preprint copy, research data and videos are all evidence of your research activity. By making them all publicly accessible you can increase visibility, preserve your output and make it available for future use. Slideshare (LinkedIn Corp, Mountain View, CA, USA) and Scribd (Scribd Inc, San Francisco, CA, USA), while not exclusive to the research community, are useful for sharing presentations and keynotes and providing basic usage statistics. F1000 Research (Science Navigation Group, London, UK) is an option for researchers in the life sciences that allows free deposit of research posters and presentations. Publishing research data in Data Dryad (Dryan, Durham, NC, USA) or via multi-purpose services such as figshare (London, UK) (http://figshare.
Dissemination of research findings 13 of their impact. They allow authors to showcase their publications by creating links to full texts and including additional information such as a short title, a lay language explanation, an impact statement and links to additional related content, such as underlying data, code, video, slides, or other elements. In addition, it offers a streamlined process for sharing your content via social media and allows you to monitor the results of that activity through the number of tweets, posts, visits, downloads and views, and a score generated by Altmetric. com. Google Scholar is by far the most widely used bibliographical tool for scholarly publications. Create an account in Google Scholar and go to 'My citation'. The profile shows your list of publications in Google Scholar, with basic metrics.
Les approches actuelles incluent le recours aux réseaux sociaux (Facebook, Twitter, LinkedIn), le partage de podcasts et d'autres résultats de recherche comme des documents de conférences, des affiches, des présentations, des rapports, des protocoles, des photocopies, des données de recherche (figshare, Zenodo, Slideshare, Scribd), l'utilisation d'un blog personnel et un identifiant unique de l'auteur (ORCID, ResearcherID). Les chercheurs et les financeurs pourraient envisager d'ébaucher un plan systématique de dissémination de la recherche dès l'élaboration du protocole.
In a recent study, the International Sheep Genomics Consortium (ISGC)  (Kijas et al. , 2012)  compiled a dataset of DNA samples from 74 populations of sheep from around the world genotyped for approximately 50 000 SNP markers: the SheepHapMap dataset. Analyses of this dataset showed both clear geographical structure of breeds and strong admixture among breeds. In Western Europe, geographical structure was clear with several population groups identified that corresponded to their area of origin: Italian, Iberian, Swiss, British and Northern European groups  (Kijas et al. , 2012). Only one French sheep population, the Lacaune breed, was included in this study. It clustered in the Iberian group, consistent with its origin from the south-western region of France. Besides the Lacaune breed, France harbours many other different sheep breeds across the country and because of its geographical position, France borders many of the geographic areas associated with western European sheep population groups of the SheepHapMap dataset.
Hence, French sheep populations are likely to harbour a large part of European sheep diversity in a relatively small geographical region, offering a powerful model for the study of adaptation. Several studies have identified signatures of selection in sheep: signatures associated with pigmentation  (Garcia-Gamez et al. , 2011) , fat deposition  (Moradi et al. , 2012) , milk yield  (Moioli et al. , 2013) , adaptations to climate  (Lv et al. , 2014)  and resistance to parasites  (McRae et al. , 2014). There have also been studies looking at a number of breeds: a study which included only American breeds of sheep  (Zhang et al. , 2013)  and two studies including sheep populations from around the world  (Kijas et al. , 2012; Fariello et al. , 2014). These worldwide studies, which both used data from the ISGC SheepHapMap data set, detected signatures containing genes or QTLs associated with pigmentation, morphology, muscling, milk production and wool quality.
Studying data sets with many different breeds also allows the study of diversity in selection, the different mutations and genes selected on to reach the same phenotype (ie. colour, muscling etc. ). All of these studies however, relied on medium density genotyping using about 50 000 SNP markers. This limits the precision of localization of candidate genes underlying selection signatures as well as the identification of potential haplotypes carrying causal mutations. The present study aims to enhance our understanding of adaptation in sheep by providing and analyzing a large data set of high density genotyping (around 600 000 SNP markers) in 542 samples from 27 French sheep populations. Our analyses of the genetic structure in this dataset identify clearly two main origins of breeds and show how these breeds complement the SheepHapMap.
CC-BY-ND 4. 0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 25, 2017. ; https://doi. org/10. 1101/103010 doi: bioRxiv preprint 5 dataset. Then, in what is the first selection scan based on high-density genotyping in sheep, our results show clear evidence for adaptive introgression between groups along with allelic heterogeneity at some adaptive loci. Finally, we confirm this heterogeneity by re-sequencing a known coat colour gene (MC1R) in three populations presenting evidence for selection at this locus, and pinpoint a set of new potential causal mutations for coat colour phenotypes in sheep.
French sheep data A total of 691 French sheep were genotyped for 653 305 autosomal SNPs (Ovine Infinium® HD SNP BeadChip) with 27 sheep breeds being represented in this study. Breed names and their short forms are listed in Table  1. In each breed genotyped animals were chosen so as to be as unrelated as possible based on pedigree records. DNA samples from this study came from various French flocks. Blood sampling was not performed specifically for this study. Blood samples were taken from commercial farms. Animals did not belong to any experimental design but were sampled by veterinarians and/or under veterinarian supervision for routine veterinary care. A test for Hardy Weinberg Equilibrium (HWE) was calculated for each SNP within each breed using PLINK  (Purcell and Chang, 2015)  and SNPs not is HWE (False discovery rate (FDR) 5% calculated with R package qvalue  (Storey, 2015) ) in one or more breeds were removed.
Population structure of French sheep Three methods were used to study population structure in French sheep from SNP genotypes: A principal components analysis to visualize patterns in relationships between individuals using PLINK  (Purcell and Chang, 2015) ; A model based approach to estimate individual ancestry coefficients, using the software sNMF  (Frichot et al. , 2014) ; A model based approach to infer populations splits and mixtures using the software treemix  (Pickrell and Pritchard, 2012). For sNMF, the optimal number of ancestral populations (K) was the one that had the lowest cross entropy criterion (Supplementary Figure  1 )  (Frichot et al. , 2014). For treemix, only the 498 651 SNPs genotyped in both Asian Mouflon and French sheep were included. The number of migration events included in the population tree was chosen based on the comparison of the fraction of the variance in relatedness between populations that is accounted for by the model, as explained in the software documentation (Supplementary Figure  2 ).
Population structure of European sheep Shared markers between the French sheep breeds and the SheepHapMap subset of breeds, 39 976 SNPs, were used to estimate individual ancestry coefficients using sNMF  (Frichot et al. , 2014). The same Iranian Asian Mouflon sheep were included in the analysis to root the population tree when estimating population splits and mixtures using treemix  (Pickrell and Pritchard, 2012)  where allele frequencies from 30 Iranian Asian Mouflon sheep from the NEXTGEN project were included to root the population tree. For the combination of our dataset with the SheepHapMap dataset, a total of 38 596 SNPs common to the French sheep, SheepHapMap subset and Asian Mouflon sheep were used in the analyses.