dataesr/scientific-paragraphs-categorization huggingface dataset:
Samples Seventy-two whole-genome sequences from taurine, indicine and crossbred cattle were analyzed. CHCU cattle have been maintained under pedigree control at the "Manuel Fajardo" genetic center that is located in Jiguani (Granma Province) with a current census of ~ 700 animals. Therefore, the genetic relationship between animals can be accurately tracked and we used this information to select 12 unrelated CHCU animals that were sequenced in this work. We also used 15 French Charolais (CHFR)  [12] , six Limousine (LIMS) from France  [13]  and sequences from 39 additional individuals that were downloaded from the sequence read archive (SRA) database [see Additional file 1:.
Bioinformatic analysis All the sequences were mapped against the bovine reference assembly (UMD3. 1. 1) using the Burrows-Wheeler aligner (BWA) v. 0. 7. 12-r1039 software  [14]. PCR duplicates were removed using the Picard MarkDuplicates (v2. 18. 9) program and realigned around InDels with the GATK IndelRealigner tool  [15]. For each individual, SNP calling was done with the SAMtools mpileup and bcftools call (v. 0. 1. 19-96b5f2294a) tools with the following parameters: minimum and maximum depths between 5 × and twice the average sample's depth; a minimum SNP quality of 10; and a minimum mapping quality and minimum base quality of 20. Next, we merged individual gVCF files into a multi-individual VCF file, with all the SNPs from the 72 samples. For this purpose, we followed a two-step approach as detailed in  [16] , using a pipeline available at https ://githu b.
com/migue lpere zenci so/NGSpi pelin e. In brief, to identify whether a position is equal to that in the reference genome, polymorphic or missing, first we generated a fasta file from the gVCF file for each individual and generated a multi-individual VCF file by using the individual file. Once the multiple sample file was obtained, SNPs with more than 20% missing data across samples and populations were removed. Finally, we imputed the missing genotypes and inferred phases with the Beagle 4. 1 software  [17]. Genetic variants that alter transcription factor binding sites (TFBS) were predicted with a custom script using the TFBS models from the JASPAR (JASPAR CORE 2018 collection,  [18] ), HOCOMOCO (version v10,  [19]  and TRANSFAC (version v3. 2 public,  [20]  databases. These databases contain a curated set of TFBS models represented as position weight matrices (PWM), which are derived from published collections of experimentally defined eukaryotic TFBS.
Population genomics We estimated Watterson's nucleotide variability (θ)  [22]  and differentiation values (F ST ,  [23]  between populations with the mstatspop (v. 0. 1beta, https ://githu b. com/ CRAGE NOMIC A/mstat spop) software in consecutive non-overlapping 30-kb windows. This software implements algorithms that allow for missing data  [24]. For the remaining analyses, we imputed missing genotypes with Beagle 4. 1  [17]. The EHH-derived statistics (Rsb, and iHs)  [25]  were computed between CHCU and CHFR for each SNP (https ://githu b. com/CRAGE NOMIC A/Tang_Rsb). As putative selection events, we retained the windows with a 'permutation p-value' lower than 0. 05 among the 2000 windows that contained the SNPs with the largest Rsb value. The 'permutation p-value' was obtained by randomly shuffling the CHCU and CHFR samples and running the Rsb algorithm along the whole genome.
Admixture The software ADMIXTURE v1. 3. 0  [26]  was run in an unsupervised manner with a number of clusters K = 2 using CHCU, BRM, CHFR and CHCA genotypes. We chose K = 2 because we were only interested in ascertaining B. indicus introgression in CHCU. Nevertheless, K = 2 was also the value that resulted in the lowest cross-validation error. The program was run either by including all the SNPs or with pruned data from which SNPs in strong disequilibrium were removed, but the results were identical. To get a more precise map of potential admixture, we used the ELAI software  [27] , which is a partially supervised algorithm that requires data from the putative founder populations (CHFR and BRM) and the potentially admixed population (CHCU). Therefore, ELAI was run using CHCU, CHFR and BRM genotypes only.
indicus in CHCU. This is also reflected when only the BRM, CHFR and CHCU breeds are represented in the PCA plot (Fig. 1b ). To evaluate more precisely the extent and impact of B. indicus introgression into CHCU, we ran the ELAI software  [27] , which provides a map, for each hybrid individual, showing the probability for each SNP to descend from one of the two putative founder populations. The results show that the B. indicus introgression is not homogeneous, neither across individuals nor across chromosomes (Fig. 2 ) and [see Additional.
Funding MPE and SERO were funded by  MINECO  grant  AGL2016-78709-R  and from the  EU  through the  BFU2016-77236-P (MINECO/AEI/FEDER ,  EU)  and the  "Centro de Excelencia Severo Ochoa   2016-2019″  award  SEV-2015-0533. LCRA is funded by " Don Carlos Antonio López" Graduate program  (BECAL) from Paraguay. YRC was funded by the  European Union   H2020  Research and  Innovation programme under Marie Skłodowska-Curie grant (P-Sphere ) agreement No  6655919. This work was partially funded by the  Animal Genetics Division of INRAE  as part of the  CHACUBA  project. Y. Rodriguez-Valera  was funded by the  France Embassy in Havana (Cuba)  and  INRAE.
Acknowledgements We gratefully acknowledge  I. Aguilar  for her help with ICP measurements. R. D. is grateful to  Jean-Pascal Rueff  and  Jonas Sottmann  for assistance on the GALAXIES beamline at  SOLEIL Synchrotron  ( Proposals 99200153  and  99210084 ). E. S. thanks  M. Deschamps  and  D. Massiot  ( CEMHTI ) for fruitful discussions. A. M. A. thanks AICF of  Skoltech  for providing access to transmission electron microscopy equipment. J. -M. T. acknowledges funding from the  European Research Council (ERC)  ( FP/2014) / ERC  Grant-Project  670116-ARPEMA. The authors thank  Thomas Marchandier ,  Khagesh K. Kumar , and  Jordi Cabana  for fruitful and insightful discussions on anionic redox. This work used the 11-BM mail service of the  Advanced Photon Source , a  US Department of Energy (DOE) Office of Science User Facility  operated for the  DOE Office of Science by Argonne National Laboratory  under contract no.
Available nuclear data for molybdenum included in the nuclear data libraries are not of sufficient quality for reactor physics or criticality safety issues and indeed information about uncertainties and covariance is either missing or leaves much to be desired. Therefore, IRSN and JAEA performed experimental measurements on molybdenum at the J-PARC (Japan Proton Accelerator Research Complex) facility in Japan. The aim was to measure capture cross section and transmission of natural molybdenum at the ANNRI (Accurate Neutron-Nucleus Reaction measurement Instrument) in the MLF (Material Life and science Facility) of J-PARC. The measurements were performed on metallic natural molybdenum samples with various thicknesses. A NaI detector, placed at a flight-path length of about 28 m, was used for capture measurements and a Li-glass detector (flight-path length of about 28.
Thus, accurate nuclear data of molybdenum isotopes in a wide energy range are of great importance. As an example, molybdenum isotopes are among the greatest contributors to the global nuclear data uncertainty on calculated k eff in UPu-MoZr deposits configurations. The available nuclear data for molybdenum included in the nuclear data libraries are not of sufficient quality for reactor physics or criticality safety issues and indeed information about uncertainties and covariance are either missing or leaves much to be desired. Therefore, IRSN and JAEA performed experimental measurements on molybdenum at the J-PARC (Japan Proton Accelerator Research Complex) facility in Japan. The aim was to measure the capture cross section and transmission of natural molybdenum.
The evaluation presented in this work takes into account the spin channel issue in the fitting procedure by the SAMMY code  [3]. It is of great importance since it can reflect the interferences in the entrance channels. The quantum numbers j, l, and s are provided in Table  IV  for 95 Mo and 97 Mo. The neutron spin and parity is 1/2+. Table  IV. Channel spins for molybdenum isotopes. Isotope (I=5/2+) l s (1/2+I) j  95 Mo, 97 Mo 0 2 2+ 3 3+ 1 2 1- 2 2- 3 2 3- 3 3 4-.
FUTURE WORK AND PERSPECTIVES Capture cross sections measurements were also performed at the J-PARC facility and the data reduction process is in progress. A SAMMY fitting will be performed on these measurements in order to provide more accurate capture data for molybdenum isotopes. Besides, additional measurements on 95 Mo, 96 Mo, and 97 Mo enriched samples are already envisioned for the next years. The SAMMY fitting procedure has currently been applied to the J-PARC measured data in the 0-600 eV energy range. Future works will consist of extending the evaluation to higher energies covering at least the range of resonance parameters up to 2145 eV. It is expected that this range could be extended beyond this energy to account for resonances identified in the measured data. The production of covariance data for transmission and capture cross sections for molybdenum is essential for criticality safety applications.
CONCLUSIONS New differential experiments were performed at J-PARC facility on natural molybdenum samples of various thicknesses in the frame of a JAEA-IRSN collaboration. The transmission measurements were analyzed and the SAMMY fitting procedure was already applied on the 0-600 eV energy range. On-going work is focused on the capture experimental data analysis and on the extension of the evaluation to higher energies covering at least the range of resonance parameters up to 2145 eV. Resonance parameter covariances for the evaluated isotopes will also be derived. The impact of the new molybdenum isotopes evaluation on benchmark calculation will be studied using integral experiments involving natural molybdenum in various neutron energy spectra. This collaborative work between IRSN and JAEA will help to address issues concerned to criticality safety and reactor physics applications thru more accurate data and uncertainties.
e. , Control (C) and Walker 256 tumour-bearing (W), while two other groups were fed a leucine-rich diet, i. e. , Leucine Control (L) and Leucine Walker 256 tumour-bearing (LW). The minimal number of animals per group was six. The animals were monitored daily, weighed three times/week and given food and water ad libitum. Food intake was measured three times/week per week, and functional activities were assessed one week before (to assess the health condition) and 18 days after tumour and diet administration (endpoint moment) (Figure  1 ). The final endpoint criteria utilised in the present study, the 18th day of tumour evolution, were determined based on the data derived from daily observations of discomfort symptoms such as piloerection, diarrhoea or constipation, hunched posture, tremors, closed eyes, and red tears (chromodacryorrhea).
The animals were randomly distributed into four experimental groups. Two groups were fed a control diet, i. e. , Control (C) and Walker 256 tumour-bearing (W), while two other groups were fed a leucine-rich diet, i. e. , Leucine Control (L) and Leucine Walker 256 tumour-bearing (LW). The minimal number of animals per group was six. The animals were monitored daily, weighed three times/week and given food and water ad libitum. Food intake was measured three times/week per week, and functional activities were assessed one week before (to assess the health condition) and 18 days after tumour and diet administration (endpoint moment) (Figure  1 ). The final endpoint criteria utilised in the present study, the 18th day of tumour evolution, were determined based on the data derived from daily observations of discomfort symptoms such as piloerection, diarrhoea or constipation, hunched posture, tremors, closed eyes, and red tears (chromodacryorrhea).
Muscle Functional Analysis 2. 2. 1. Catwalk Walking Test The catwalk walking test (Noldus Inc. , Wageningen, The Netherlands) is an automated tool that quantifies gait parameters. Rats were placed in an illuminated-walkway glass floor with a video camera (Gevicam GP-3360; Gevicam Inc. , Milpitas, CA, USA). The camera positioned under the walkway at a distance of 56 cm recorded the paws prints automatically by using the CatWalkTM XT10. 6 software, as the animal crossed the pathway in a calibrated 20 × 10 cm length lane. The maximum intensity measurements were analysed, which represent the intensity of the full paw. The maximum contact area (cm 2 ) corresponded to the max area of a paw that came into contact within the glass floor and the print area (cm 2 ). The surface area of the complete paw print of both tumour-bearing groups (W and LW) was compared with the gait patterns at the initial time point (pretumour inoculation) and the endpoint moment (18 days after tumour inoculation).
Behaviour Test (Video Recording System and Analysis) Animal behaviour was assessed by night vision cameras placed in front of each individual cage at an adequate height. The cameras recorded all rats' nocturnal behaviour. The video recording system was activated one week before the experiment started. Video files were analysed using the video tracking software EthoVisionXT12 (Noldus Information Technology, Utrecht, The Netherlands) to assess the total distance covered (cm), the average velocity (cm/s) and the time spent in movement (s) of both tumour-bearing groups (W and LW). All tumour-group data were compared to behaviour at the initial time point (pretumour inoculation) and at the endpoint moment (18 days after tumour inoculation).
Muscle Morphological Analyses 2. 4. 1. Light Microscopy Muscle samples were removed from animals and immersed in a fixative solution (4% paraformaldehyde in 0. 1 M phosphate-buffered saline (PBS), pH 7. 4) for 24 h at 4 • C. Then, tissues were dehydrated in graded alcohol concentrations, embedded in paraffin (Leica Microsystems, Heidelberg, Germany), and sectioned at a width of 3 µm. The sections were mounted on slides and stained with hematoxylin-eosin. A cross-sectional area of myofibre was measured for each muscle sample using at least 200 fibres per muscle sample (average number ± SD of fibre analyses for each group). Analyses were performed using Image Pro-Plus Premium software (v. 3. 01, Media Cybernetics, Silver Spring, MD, USA) after capturing the image with a Leica microscope (Leica DMLM, Wetzlar, Germany) using 20× magnification.
Statistical Analysis Data are expressed as mean ± SEM. Differences between three or more groups were analysed by variance test ANOVA, followed by Tukey post hoc test and by t-test for comparison between 2 groups (W vs. LW). For all statistical analyses, p < 0. 05 was considered significant. The statistical analyses were performed using the software Graph Pad Prism 9. 0 (Graph-Pad Software, Inc. , San Diego, CA, USA). All comparisons among the four groups processed by ANOVA were presented as Supplementary Figures  S1-S6. The result section only presented the comparison between LW vs. W, showing the specific leucine effect.
These data are then added and compared to previous screen data to assess what we know about the distribution of Cardinium in field and laboratory populations and the suitability of specific midge species for further investigation pertaining to the endosymbiont. Culicoides specimens were collected between 2007 and 2016 from sites spanning France, South Africa and the United Kingdom (Table  1 ). Details of Culicoides collection methods, storage and species identification can be found in  Pilgrim et al. (2017). DNA extracts from a previous study by  Lewis et al. (2014) , describing positive Cardinium infection in C. pulicaris and C. punctatus from the United Kingdom, were used to validate screening assays. Amplification of the host COI gene was initially assessed as a means of quality control by conventional PCR assay.
COI amplicons from the Pulicaris complex were Sanger sequenced to determine cryptic species, which are difficult to distinguish morphologically. To this end, individuals were designated as belonging to a particular species if their COI haplotype had >99% sequence identity to previously designated DNA barcodes. DNA extracts, which passed quality control, were then screened for Cardinium using conventional and nested primers amplifying partial sequences of the Gyrase B (GyrB) gene (Primer sequences and PCR cycling conditions in File S1). Prevalence estimates were defined by the nested PCR data and categorised into no infection (0%), polymorphic infection (>0. 1% and < 100%) and fixation (100%). Collection sites of Culicoides populations were then plotted against Cardinium infection prevalence based on the nested PCR assay and mapped geographically.
, 2009) , in which all previously described sequences of Culicoides clustered (Fig. 1 ) (Genbank accession numbers [https://www. ncbi. nlm. nih. gov/genbank/]: LR877462-LR877465). The C. imicola GyrB sequence obtained from South Africa in this study (LR877465) was identical to both of those obtained from Kenya (KR026927) and Israel (JN166963), indicating a global infection. Likewise, the Cardinium sequences obtained from C. punctatus from Wolverhampton, U. K. (LR877464) had 100% identity to the sequence reported in the same species by  Lewis et al. (2014; HG380244). Mee et al. (2015)  have previously suggested that Cardinium strains group by geography; by contrast, we find a sporadic distribution of strains with respect to location. For example, the C. bysta and C. newsteadi strains (LR877462 and LR877463) identified from Corsica, group with strains from Israel and Japan, respectively (JN166964 and AB506792).
Acknowledgements We thank  Kenneth Sherlock ,  Georgette Kluiters ,  Steve Price ,  Lukasz Lukomski , the  Direction générale de l'alimentation (DGAL)  and the national veterinary services (France) for their support with the collection of midge samples. We are grateful to  Jan Chirico  and  Mats Ander  for the identification of  Culicoides from Sweden, Ignace Rakotoarivony (CIRAD)  for the identification of Culicoides from France and  Karien Labuschagne  for the identification of Culicoides from South Africa. This work was supported by a  BBSRC   Doctoral Training Partnership studentship  ( BB/M011186/1 ) awarded to JP. The authors declare no conflict of interest.
Data availability statement The data that support the findings of this study are openly available in figshare at: http://doi. org/10. 6084/m9. figshare. 13187069, http://doi. org/10. 6084/m9. figshare. 13142684, and http://doi. org/10. 6084/m9. figshare. 13130306. Accession numbers generated in this study: LR877462-LR877465.
Research strategy For articles look-up, we used the Scopus and PubMed databases and their research systems to conduct our bibliographic search. To do so, we searched for relevant articles dealing with national HIS performance (performance is understood here as organizational, technical and behavioral determinants). In the bibliographic research system of these databases, we used the following keywords: "health", "information", "systems", "system", "africa", "developing countries", "Africa". Using the filters provided by the search engines (for example the publication date), relevant articles were selected on the basis of the criteria described in Table  1. To lookup the databases, we exclusively relied on the logical operator "OR", because the use of the logical operator "AND" or the combination of both logical operators "OR" and "AND" enabled us to obtain a reduced number of articles, which were unfortunately not relevant for our study.
e. , technical, organizational and behavioral for the analysis of the 14 articles selected in our study, we opted to examine only the organizational and technical determinants. The behavioral determinants were not examined, as they required the administration of a questionnaire to the various actors involved in the HIS. This was not adapted to our study, whose approach was to review the literature. The selected articles were examined using a grid validated by all the reviewers. On that grid, the two selected determinants for the study were evaluated on the specific aspects dealt with these articles, namely HIS governance (HIS legal framework, national HIS strategies, etc. ), data quality (data completeness, data reliability, data relevance, data accuracy, data timeliness, etc. ), information technology (IT), data warehouses, HIS evaluation and DHIS digital solution (Fig.
In Zanzibar, paper-based forms were used to collect data from health facilities and made available to health districts, which were then filled in the DW. To overcome the errors which may occur with a manual process associated with the use of paper forms, the Zanzibar Ministry of Health had undertaken a project to use the OpenMRS clinical management software at the health facility level for processing and recording data in the DHIS warehouse. However, this OpenMRSbased project is experiencing difficulties in its implementation due to limited local technical capacity  [17]. Sierra Leone has had an approach that takes into account the context of unequal distribution of technical infrastructures throughout the country. The adapted and validated digital DHIS solution served as a repository for the national HIS at all levels of the health system.
The adaptation of DHIS was done in such a way that in areas with a digital infrastructure, this repository exchanged data with a hospital management software (HMS), such as OpenMRS where the SDX-HD standard facilitates this data exchange. The DHIS solution also provides the ability to enter data from paper or mobile phones. It is therefore a model that allows data to be recorded at all levels and aggregated in one place  [18]. This evolutionary approach, based on a collaborative architecture, has enabled Sierra Leone health system to have increasingly accurate health data that is accepted by several organizations that use it. Six other countries (Ghana, Mozambique, Rwanda, Tanzania, Zambia and Mozambique) which received support from the International Health Partnership have used the DHIS software to implement their HIS.
Main lessons learned The implementation of an HIS must take into account the process of data collection, analysis processing and transmission at all levels of the health pyramid. It must support decision-making in health planning, epidemiological monitoring and evaluation of health actions. This requires that the development of HIS be supported by sufficient governance with policies integrating HISrelated aspects, including harmonized indicators, forms (electronic or paper-based) for integrated data collection, and databases that are easy to use and accepted by users. From the conducted literature review, it mainly emerges that governance, a crucial element for an efficient HIS, has not been sufficiently taken into account in most of the projects to set HIS upin Developing Countries. The weak involvement of all stakeholders, together with weak leadership expressed by States and insufficient coordination of HIS actors are among the main factors that have often threatened the sustainability of these HIS  [10].
Funding information RDD received support from the  Conseil Interprofessionnel du Vin de Bordeaux (CIVB)  under the  CIVB  project " Recherche , experimentation, etudes et outils," and from the  EU  in the framework of the  Marie-Curie FP7 COFUND People Programme , through the award of an  AgreenSkills/AgreenSkills+fellowship  under grant agreement number  FP7-609398. QR received support from the cluster  SysNum of Bordeaux University. SL was supported by  JCJC  grant  ANR-16-CE35-0012  " STEEP ," and FF, JBR, and AD received support from  ANR-18-CE32-0004  " ArchiV. ".