dataesr/scientific-paragraphs-categorization huggingface dataset:
X-Ray diffraction study To analyze the structural properties of our samples, we carried out XRD analysis with CuKa radiation at room temperature. The data were analyzed by Rietveld method using Fullprof program. 17  good agreement between the observed and the calculated proles was remarked. This is due to the excellent goodness of t (c 2 ), conrming the high quality of renement. From this gure, we can deduce that the x ¼ 0. 15 sample is a mixture of orthorhombic and rhombohedral structures, respectively, with Pbnm and R 3c space groups, around 2q ¼ 32. In this region, the system showed a sign of multi-phased behavior with no complete splitting into the double line of the intense peak. This result is in concordance with that observed in ref. 18. The relative amount of the orthorhombic phase was 81.
5. 0, Bruker-AXS, Karlsruhe, Germany), in Bragg-Brentano reflection geometry with Cu Kα radiation (λ = 1. 5418 Å). Moreover, NPD was used to characterize the crystal structure concerning possible atomic vacancies and displacement factors. High-resolution patterns were collected in the D2B diffractometer at the Institut Laue-Langevin, Grenoble, France, in the high-flux configuration with a neutron wavelength λ = 1. 549 Å at 298 K (RT) for PbTe. Typically, 2 g of the samples were measured in a vanadium can. Diffraction data were analyzed using the Rietveld method employing the FULLPROF program (version Sept 2018, Grenoble, France). The line shape of the diffraction peaks was modeled by a pseudo-Voigt function. The following parameters were refined in the final run for all the atoms: scale factor, zero shift, background points, pseudo-Voigt corrected for asymmetry parameters, half-width, unit-cell parameters, and isotropic displacement factors.
Acknowledgments: We are grateful to the  Spanish Ministry of Science, Innovation and Universities (MICIIN)  for granting the projects  MAT2017-84496-R  and  RTI2018-097895-B-C43 , and to ILL for making all facilities available for the neutron diffraction experiments. J. G. thanks  MICINN  for granting the FPI contract  PRE2018-083398. TEM measurements were performed in the  Centro Nacional de Microscopía Electrónica (CNME) at the Universidad Complutense de Madrid (UCM).
Background: Hepatitis E virus (HEV) is one of the major causes of acute hepatitis in humans worldwide with a casefatality rate of 1-4% in the general population that might reach 30% in pregnant women. In the past decade in Africa, studies have shown that HEV infects not only humans but also animals. A systematic review summarizing the epidemiological data of HEV has been only performed in humans residing in Africa. We will perform this systematic review and meta-analysis to assess the prevalence of HEV infection in animal species in Africa. Methods: This review will include cross-sectional studies among different animal species that reported the prevalence of HEV in Africa. We will consider published and unpublished studies from January 1, 2000 to present. A comprehensive search of PubMed, Excerpta Medica, African Journals Online, and Africa Index Medicus will be conducted to identify all relevant articles.
Bibliographic database searches A comprehensive search of MEDLINE through PubMed, Excerpta Medica, African Journals Online, and Africa Index Medicus will be conducted to identify all relevant articles published on HEV in animals living in Africa from January 1, 2000 to present, without any linguistic restrictions. A search strategy based on the combination of relevant terms will be designed and applied. Text words and medical subject header terms will be used. The following terms and their variants will be used for hepatitis E virus: "HEV," "Hepatitis E," and "Hepatitis E. " Individual country names for the 54 African countries and names of African sub-regions such as "West Africa" or "East Africa" will also be used as additional key search terms for more abstracts on the subject. The names of African countries will be introduced in both English and the languages relevant to each country, for example, "Ivory Coast" and "Côte d'Ivoire.
" When country names have changed over time, old, and new names will be included, such as "Zaire" and "Democratic Republic of Congo". Abstracts of all eligible articles will be reviewed and full texts of articles will be available. The main search strategy in PubMed/MEDLINE is shown in Table  1. This search strategy will be adapted for search in other databases. A filter will be applied to select studies in animals. We have built the search strategy for electronic databases as per PRESS (Peer Review of Electronic Search Strategies) guidelines  [9].
Selection of studies to include in the review The selection of studies will be managed using EndNote X7. Two researchers will independently identify the articles and sequentially review their titles and/or abstracts to determine their eligibility. The full text of articles potentially eligible will be acquired. These researchers will independently assess the full text of each study to determine eligibility, and in a consensual way, select which studies to include. Existing disagreements will be resolved by a third author. We will use a selection guide to ensure that the selection criteria are reliably applied by all evaluators. Eligible studies in languages other than English, French, or Spanish will be translated using Google Translate and considered for inclusion.
Assessment of methodological quality and reporting of data An adapted version of the risk of bias tool for prevalence studies developed by Hoy et al. [10]  will be used to evaluate included studies for methodological quality and risk of bias. The defined items will be scored with 0 for 'no' and 1 for 'yes. ' The total score of each article will be calculated by the sum of its items. The studies will be ranked according to their total score as low risk, moderate risk, and high risk for scores of 8-10, 5-7, and 0-4, respectively. Two review authors will assess the risk of bias and disagreements will be solved through a consensus or by an arbitration of a third review author.
Data extraction and management Two researchers will extract data concerning: 1. Details of the author: name of first author and year of publication; 2. Characteristics of the study: recruitment site (country, city), setting (rural and/or urban), sampling method (random, systematic); 3. Characteristics of participants: species, number of animals examined, number of animals infected with hepatitis E virus, age distribution, proportion of male animals, criteria for inclusion, and exclusion of animals. When only primary data (number of animals examined and number of animals infected with hepatitis E) are provided, these data will be used to calculate prevalence estimates. The data will be extracted using a preconceived, piloted, and standardized data abstraction form. In case of missing data, we will contact directly the corresponding author to request the information.
Data synthesis including assessment of heterogeneity The data will be analyzed using the "meta" packages of the R statistical software (version 3. 3. 3, The R Foundation for statistical computing, Vienna, Austria). The prevalence of HEV infection will be recalculated on the basis of numerators and denominators provided by individual studies. To minimize the effect of studies with extremely small or extremely large prevalence estimates on the overall estimate, the variance in study-specific prevalence will be stabilized with Freeman-Tukey arcsinetransformation before pooling the data with the random effects meta-analysis model  [11]. Heterogeneity will be assessed by the chi-square test on Cochran's Q test  [12] , which will be quantified by I 2 values, assuming I 2 values of 25, 50, and 75% respectively representative low, medium, and high heterogeneity  [13].
This was further confirmed by a more detailed stoichiometric model of the respiratory pathway, including alternative oxidase and uncoupling proteins  (Colombié et al. , 2017). In grape berry, reducing power equivalents (NADH and NADPH) were also associated with major carbon fluxes, thus supporting a strong link between central metabolism and pyridine nucleotides  (Soubeyrand et al. , 2018). In the present work, as a first attempt to clarify the importance of pyridine nucleotides in the developing fruit, we used a developmental fruit series of nine growth stages of tomato fruit (var. Moneymaker) and measured pyridine nucleotide pools. We further examined quantitative data for transcript and protein levels previously obtained by RNAseq and proteomics  (Belouah et al. , 2019)  and revealed changes in NAD(P) metabolism during fruit development.
Protein Extraction and Quantification Total proteins from tomato pericarp were extracted as in  (Faurobert et al. , 2007). LC-MS/MS analyses were performed with a NanoLC-Ultra System (Nano-2D Ultra, Eksigent, Les Ulis, France) coupled with a Q Exactive Mass Spectrometer (Thermo Electron, Waltham, MA, USA) as in  (Havé et al. , 2018). For each sample, 800 ng (4 μl from a 0. 200 ng. μl -1 solution) of protein digest were loaded onto a Biosphere C18 pre-column (0. 1 × 20 mm, 100 Å, 5 μm; Nanoseparation) at 7. 5 μl. min -1 and desalted with 0. 1% (v/v) formic acid and 2% ACN. After 3 min, the pre-column was connected to a Biosphere C18 nanocolumn (0. 075 × 300 mm, 100 Å, 3 μm; Nanoseparation). The raw MS output files and identification data were deposited online using the PROTICdb database (http:// moulon.
inra. fr/protic/tomato_fruit_development). Protein identification was performed using the protein sequence database of S. lycopersicum Heinz assembly v 2. 40 (ITAG2. 4) downloaded from https://solgenomics. net/ (34,725 entries). A contaminant database, which contains the sequences of standard contaminants, was also interrogated. Criteria used for protein identification were (1) at least two different peptides identified with an E-value smaller than 0. 01, and (2) a protein E-value (product of unique peptide E-values) smaller than 10 -5. Using reversed sequences as a decoy database, the false discovery rate for peptide and protein identification was respectively 0. 05 and 0%.
Data Analysis of mRNA and Protein Profiles Datasets consisted of 22,877 transcript and 2,375 protein profiles and were made publicly available via GEO repository  (Barrett et al. , 2013)  with the accession number GSE12873 (https:// www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE128739) for the transcripts. The proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE  (Perez-Riverol et al. , 2019)  partner repository with the dataset identifier PXD012877. Prior to uni-and multivariate statistical analyses, mRNA and protein data were pre-processed to normally distributed data by performing median normalization, cube-root transformation, and Pareto scaling of the data intensities as described previously  (Belouah et al. , 2019). Normalized datasets were then used to construct score plots of principal component analysis (PCA) for transcriptomic and proteomic overview using MetaboAnalyst v 4.
0 (http://www. metaboanalyst. ca/), or dendrograms of clustering analysis by Pearson's correlation with complete clustering linkage using MeV v 4. 9. 0 (http://mev. tm4. org/). Significant markers of both transcripts and proteins were determined by ANOVA after discarding false positives (P < 0. 01 corrected for multiple testing by Bonferroni method). Details of ANOVA P values are given in Supplemental Tables  S1-3. Transcript and protein features of NAD-dependent functions were selected by identifying domains (InterPro and GO) that were annotated to bind or process pyridine nucleotides using Assembly v 2. 40 (ITAG v 2. 4) from Sol Genomics (https://solgenomics. net/) and UniProt (https://www. uniprot. org/). Data mining of publicly available gene expression data was conducted using Tomato Expression Atlas (http://tea.
Raw data of mRNA profiles evidenced very low expression values for AO in tomato fruit, as compared to NIC and NaPT, and more remarkably, as compared to actinand enolase-related genes (Figure  S3A ). Complementarily, data mining of expression profiles from published datasets (http://tea. solgenomics. net/; Fernandez-Pozo et al. , 2017) confirmed that the NAD + biosynthesis gene AO was expressed at low levels in fruit tissues as compared to other genes (Figure  S3B ), which can explain the absence of proteomic hits in our dataset. Furthermore, we analyzed transcriptional changes of NAD + catabolism involved in signaling and metabolism of nicotinate including 13 genes of PARPs, SIR, NDXs, NaGTs, NMTs, and NaMe esterase that demethylates NaMe into Na (Figure  3B )  (Gakière et al. , 2018b). Clustering analysis (Pearson's correlation with complete clustering) unveiled three main significant clusters (ANOVA with Bonferroni correction, P < 0.
Flux map and spectral properties Flux maps and spectra extracted with a simple aperture contain a large amount of stellar flux from sources close to the nebula. To better disentangle stellar background and ionized gas emission, we employ pPXF (Python version 6. 7. 12, dated 9 July 2018,  Cappellari & Emsellem 2004; Cappellari 2017) , the penalized pixel-fitting method that is widely used for full-spectrum fitting with the goal of extracting kinematics of gas and stars and to estimate stellar populations. We chose to describe the spectra with two sets of templates: 1. The stellar background was modelled using the empirical stellar library MILES  (Sánchez-Blázquez et al. 2006; Falcón-Barroso et al. 2011). We took the full library of individual stars which samples the expected range of stars in NGC 6656 well enough.
Since the AO data has a slightly different wavelength coverage and a broad gap in the region of NaD and in this case did not actually improve S/N or FWHM significantly, we chose not to include them in the combined deep dataset. The contour lines in Fig. 1  give the combined [N ii]λλ6548,6583 emission flux after subtracting the stellar background. In this map, the nebula appears as an ellipse of 2. 5 ×2 , corresponding to 0. 04 pc×0. 03 pc at the cluster distance of 3. 2 kpc  (Cudworth 1986). Fig. 1  also shows the [N ii]λ6583 spectral layer after subtracting the mean flux of the adjacent layers. While this map does not rely on model assumptions, it contains stronger residuals from the bright star above the nebula. We make the datacube created from all non-AO observations and the extracted spectrum publicly available.
Acknowledgements. We thank the anonymous referee for the constructive report which helped to improve the quality of the work. We also thank  Frederic V. Hessman  and  Francis R. Stephenson  for the helpful discussions. FG, SK and SD acknowledge support from the  German Research Foundation (DFG)  through projects  KA 4537/2-1  and  DR 281/35-1. SK gratefully acknowledges funding from a  European Research Council  consolidator grant ( ERC-CoG-646928-Multi-Pop ). PMW, SK, SD and BG also acknowledge support from the  German Ministry for Education and Science (BMBF Verbundforschung)  through projects  MUSE-AO , grants  05A14BAC  and  05A14MGA , and  MUSE-NFM , grants  05A17MGA  and  05A17BAA. JB acknowledges support by  FCT/MCTES  through national funds by this grant  UID/FIS/04434/2019  and through the  Investigador FCT  Contract No.
Spatial cluster analysis This was performed using Kulldorffʼs scan statistic in SaTScan (v. 9. 1. 1) (http://www. satsc an. org/)  [22]. A discrete Poisson model was used to analyse the spatial distribution of adult mosquito catches (females and males were combined) in standard, non-adapted BGSTs and larval/pupal mortality in ABS. The program compares the occurrence of adult mosquito catches (or larvae/ pupae dead) over the number of sites (BGST or ABS) inside a randomly generated cluster circle compared to the rest of the population. The unit of analysis was the sampling site (BGST or ABS). An infinite number of cluster circles are generated with a maximum diameter set to values between 10-250 m, adapted to the area of study. Clusters represented hot or cold spots representing greater or less than expected adult mosquito numbers or juvenile mortality.
Only clusters with no geographical overlap were accepted. A relative risk of observed lower (cold spot) or higher (hot spot) numbers of events (here adult mosquitoes or larval mortality) than expected from the whole study area is calculated and a likelihood ratio test performed. For BGST catches only a spatial analysis was performed. For Funchal, information on larval/pupal mortality was available every 48 h and thus a spatio-temporal analysis was performed. Additional analyses on larval/pupal mortality were performed fitting BGST adult mosquito catches in the nearest BGST as a covariate. A Bonferroni correction was applied when multiple analyses were performed on the same data set.
Funding Funded by a  European Union   FP7  grant through the  DENFREE consortium  (European Union 7th FP, grant  282378 ). Fundação para a Ciência e  Tecnologia (FCT) , through  GHTM -UID/Multi/04413/2013  has partially funded the work and GS is supported by a  FCT doctoral grant  ( SFRH/BD/98873/2013 ).
The band structure calculations were performed using the SPR-KKR package  [25]  that is based on the Korringa-Kohn-Rostoker method, which uses the Green's function formalism within the multiple scattering theory and the Dirac equation, thus fundamentally containing all relativistic effects, such as spin-orbit coupling. The bulk potential that was used as an input to simulate the ARPES spectra within the one-step model of photoemission  [26, 27]  results from calculations performed within the local density and atomic sphere approximations. The model of Rundgren-Malmström  [28]  was used to describe the crystal potential in the surface region. The relaxation of the surface was taken into account using the structural data given in  [29]. For the bulk, the lattice parameters in the hexagonal description (a=4.
Acknowledgments The research leading to these results has received funding from the  European Community 's  Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement No. 312284. JB and HE acknowledge financial support by the  Deutsche Forschungsgemeinschaft   SPP1666 priority program  (Grants No. EB144/26  and  EB154/32 ). JM and LN would like to thank the Computational and  Experimental Design of Advanced Materials with New Functionalities  ( CZ. 02. 1. 01/0. 0/0. 0/15_003/0000358 )co-funded by the  European Regional Development Fund as part of the Ministry of Education, Youth and Sports of Czech Republic. OH, KH and MCR acknowledge funding from the  'Investment for the Future' programme of the Agence Nationale de la Recherche  (contract No  11-EQPX-0034-PATRIMEX ).
| Mouse platelet aggregation Wild-type mice received ticagrelor (100 mg/kg) by oral gavage 18 and 6 hours before experiments. Mouse PRPs were obtained from citrate anticoagulated mouse blood and diluted (1/7) into Tyrode's buffer. Light transmission aggregation was performed on 96-well plates using the EnSight multimode plate reader (PerkinElmer, Waltham, MA). groups. One-way ANOVA was used for comparison between different groups. Acute coronary syndrome patient data were adjusted for age and sex prior to statistical analysis. Correlations were assayed using Pearson's method. The stepwise method for multivariable linear regression models was used to calculate the linear association between CD40L parameters and cardiovascular risk factors.
Also, residual confounding may be present if there were relevant covariates that were not considered or were imprecisely measured. Additionally, not all biomarkers (including sCD40L, pCD40L, and rCD40L) were measured in all participants, so precision was limited for some analyses. In particular, sCD40L was not measured in the populations where pCD40L and rCD40L were evaluated due to the constraints related to the experimental conditions for obtaining platelet solutions. Our findings are evidence that P2Y12 inhibitors may preclude secondary thrombotic events by preventing platelet aggregation and reducing pCD40L and rCD40L levels. The importance of pCD40L and/or locally released rCD40L still remains to be clearly determined. Our data showing that blocking CD40L reduces arterial thrombus from healthy human blood samples treated or not treated with a P2Y12 inhibitor support this hypothesis.
Having in hand an RH panel and composed of 100 clones and the NGS assembly, we sequenced the 100 duck RH hybrid clones enabling to genotype directly the assembly scaffolds. We describe in the following section, the different steps of this mapping by RH sequencing procedure: from the raw sequence data to the retention pattern for the scaffold-markers to the construction of the maps, pseudomolecules and finally a validation of the resulting assembly. Following previous work, we use a comparative mapping approach to order the scaffolds along chromosomes using the chicken genome as reference  [23].
Aligning the duck scaffolds to the chicken genome All the 19,479 duck scaffolds were aligned to the chicken (Gallus gallus-4. 0, GCA 000002315. 2 assembly), zebra finch (taeGut3. 2. 4 assembly) and turkey (Turkey 2. 01, GCA 000146605. 1 assembly) genome using the Last software  [53]. Large conserved segments are expected between these two closely related species (respectively 80 and 90 million years). However, because of sequence divergence and also of incompleteness of the current assemblies these conserved segments are split into a larger number of local conservation fragments captured by local alignments. In order to recover large conserved segments between the duck scaffolds and the chicken genome we chained the alignments using the chaining algorithm developed in  [54]. Briefly, starting with local sequence similarities, conserved segments are chained using an adaptation of the Longest Increasing Subsequence (LIS) algorithm transformed into a general purpose dynamic programming algorithm that identifies high-scoring chain of segments occurring in the same order in both species (see Supplementary information, section 2).
The probes were purified using spin column G50 Illustra 11/22 (Amersham Biosciences). Probes were ethanol precipitated, resuspend in 50% formamide hybridization buffer (for FISH on chicken metaphases) or in 40% formamide hybridization buffer for heterologous FISH. Probes were hybridised to chicken metaphase slides for 17 hours at 37 • C and to duck metaphases for 48H in the Hybridizer (Dako). Chromosomes were counterstained with DAPI in antifade solution (Vectashield with DAPI, Vector). The hybridised metaphases were screened with a Zeiss fluorescence microscope and a minimum of twenty spreads was analysed for each experiment. Spot-bearing metaphases were captured and analysed with a cooled CCD camera using Cytovision software (Leica Biosystem).
The mean GC content of A. ceratii genome was calculated to be 55. 9%, which is in the range of published dinoflagellate transcriptomes (23) but relatively higher compared to Symbiodinium spp. (43. 6 to 50. 5%)  (20) (21) (22)  and Hematodinium sp. (approximately 47%) draft genomes (Table  1 )  (14). Gene predictions identified 19,925 protein-coding genes and 39 transfer RNAs (tRNAs). We also mapped the transcript data obtained previously  (16, 19)  to the scaffolds and found that 12,200 transcripts mapped to this assembly. Despite the relatively small size, by dinoflagellate standards, the genome assembly appears to be largely complete, containing 89. 1% of CEGMA (core eukaryotic gene mapping approach) conserved proteins  (24). This is slightly higher than the Hematodinium genome (85. 9%)  (14).