cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/9otynj
title: Supplemental dataset used for transcriptomic analysis of HrpG* regulon in 17 Xanthomonas strains

description: This dataset includes generated genome annotation for the 17 strains as Data S1, and comparative statistics and orthogroup analyses for these genomes, performed using OrthoFinder, as Data S2. R scripts utilized for analyzing the data, are stored in a code repository in Data S5. Comparative statistics and orthogroup information for 675 publicly available Xanthomonas genomes which include a type T3SS are detailed in Data S6, along with their respective genome accession numbers. Raw DESeq2 results and MultiQCs of read mapping, PCA, MA and Volcano plots are available in Data S3. Finally, information on the coverage of hrpG*/hrpG transcript reads against the endogenous hrpG gene is available id Data S4.
DOI: 10.57745/6xakms
title: P. senegalensis stock assessment in Ghana - Côte d’Ivoire by length frequencies analysis - Rectified pseudo-cohort analysis LBB –

description: In this report, included within WP1 - DEMERSTEM, we apply two data-poor adapted and length-based methods, which are first introduced, before application to the P. senegalensis stock of Ghana - Côte d’Ivoire.
DOI: 10.57745/9xjxjy
title: IPMWorks H2020 No. 101000339 - IPM Biofortification Strategy 2021-2022 diary

description: IPMWorks H2020 No. 101000339 – IPM Biofortification Strategy 2021-2022 diary raw data contains the dates of all treatments, assessments and harvest. Information on the country where the case study was completed, main crop of focus, organisations involved in the case study and the year/s when the case study was completed are contained within.
DOI: 10.57745/51cz5x
title: Data for : Conservation agriculture affects multitrophic interactions driving the efficacy of weed biological control

description: This is the data and R script used for the submission of the paper "Conservation agriculture affects multitrophic interactions driving the efficacy of weed biological control" (submission to Journal of Applied Ecology). The repository includes a dataset guide, the dataset and the R script used to analyse the data.
DOI: 10.57745/77afbh
title: PROspective - agronomic management dataset

description: Agronomic management dataset from the PROspective's long-term field experiment. // The PROspective's field experiment is a randomised block experiment divided into 2 sub-devices “With_N” and “Without_N” including 24 plots of 10 m × 9 m in 4 blocks of replicates and a fifth block devoted to following of the nitrogen dynamic with bare plots or control plots without mineral fertilization. The following organic waste products are randomly distributed within each block: Sewage sludge (SLU), Co-compost of sewage sludge with green waste and wood chips (GWS), Co-compost of the home-sorted fermentable fraction of municipal solid waste and green waste, also called biowaste compost (BIOW), Farmyard manure from a dairy farm (FYM), Compost of farmyard manure (CFYM), No organic amendment (control, or CN). // Two phases were carried out during 2000-2019 as presented in the table in attached file (PROspective_Experimental_treatments_FR_EN), with the treatments randomly distributed in the 2 sub-devices; with additional biowaste digestate (DIG) applied from 2015 in the sub-device “without_N.
DOI: 10.57745/8zmxsa
title: Experimental and modelling study of phenol combustion and oxidation

description: Despite of its central importance in the chemistry of aromatic compounds and fuels derived from biomass, only few experimental studies on phenol combustion can be found in literature. In this paper, unique measurements of the adiabatic laminar burning velocities of phenol are presented, together with the first experimental study of the oxidation of this molecule in a jet-stirred reactor. The burning velocities were measured with a flat-flame burner using the heat-flux method for a fresh gas temperature of 398 K and equivalence ratios from 0.7 to 1.35. In the reactor experiments, the oxidation of a stoichiometric mixture of phenol highly diluted in helium was investigated at temperatures between 600 and 1100 K at near-atmospheric pressure. The mole fraction of the reactants, as well as 32 products, mainly carbon monoxide, carbon dioxide, methane, acetylene ethylene, acrolein, cyclopentadiene, benzene, naphthalene and dibenzofuran, were recorded. Based on previous literature work, a new detailed kinetic model is developed based on several published sub-mechanisms and updated considering rate constants taken from recent literature studies or calculated at the CBS-QB3 or G4 level of theory. This model leads to a significantly improved prediction of the phenol burning velocities compared to literature models, as well as a reasonable prediction of most species mole fractions during phenol oxidation in the jet-stirred reactor. Sensitivity analyses as well as flow rate analyses are discussed to explain the obtained model improvements.
DOI: 10.57745/9ryy9o
title: Production de projections hydro-climatiques en Outre-Mer

description: L’objectif du projet Explore2 est de donner à voir le climat et l’hydrologie naturelle futurs, à horizon 2100, sur une maille de 8 km x 8 km ; en se basant sur les résultats du 5ème rapport du GIEC et en utilisant une approche multi-modèles et multi-scénario pour assurer la robustesse scientifique de l’exercice et pouvoir associer des incertitudes aux simulations calculées. Etant donné le retour d’expériences du projet Explore 2070 sur les territoires d’Outre-Mer (OM) et malgré les progrès faits depuis 10 ans, le projet Explore2 ne pourra pas produire de projections hydro climatiques à horizon 2100 sur les territoires ultra-marins, mais uniquement en France métropolitaine. La principale raison est l’existence d’un certain nombre de verrous scientifiques, comme le manque de données d’observation disponibles par exemple, indispensables à la validation des modèles utilisés ; des explications détaillées sont présentées en section 3 de ce rapport. Il a été proposé, dans le cadre du projet Explore2, d’établir une feuille de route pour les territoires ultra-marins afin de remédier à la situation et de pouvoir programmer, dès que possible dans les années à venir, la réalisation d’un exercice scientifiquement robuste du type Explore2 dans chacun de ces territoires. Afin de permettre l’élaboration de ces feuilles de route, nous avons commencé notre « Zoom Outre-Mer » du projet Explore2 par la réalisation de ce rapport de connaissances comportant trois principales parties : - Recueil de connaissances dans les territoires ultra-marins des projets ayant été menés ou encore en cours sur le thème « adaptation au changement climatique et gestion des ressources en eau » (section 2, page 8) ; ce travail a été réalisé par une médiatrice scientifique de l’OiEau sur la base de recherches bibliographiques et d’interviews ciblées de porteurs de projets en OM, - Analyse des freins actuels à la réalisation d’un exercice de type Explore2 en OM (section 3, page 14) ; ce travail a été réalisé par le coordinateur du volet scientifique d’Explore 2 d’INRAE, - Perspectives pour établir des feuilles de route pour chaque territoire ultra-marins, en vue de l’élaboration de projections hydro-climatiques dans ces territoires (section 4, page 19) ; ce travail sera mené par la coordinatrice du volet « Accompagnement des acteurs » d’Explore2 de l’OiEau.
DOI: 10.57745/a7hiwl
title: Diatom endemism: an assessment in high-altitude alpine lakes covering a large geographical range

description: Fasq files, metadata, and communities datatables.
DOI: 10.57745/7kzvmp
title: Meloidogyne incognita gene predictions

description: Results of EuGene annotation on the M. incognita nuclear genome contigs. Predictions of gene models in M. incognita, M. javanica, M. arenaria and M. luci genomes were done with the fully automated pipeline EuGene-EP version 1.6.5 (Sallet et al., 2019). EuGene has been configured to integrate similarities with known proteins of Caenorhabditis elegans (PRJNA13758) downloaded from Wormbase ParaSite (Howe et al., 2017) as well as the “nematoda” section of UniProtKB/Swiss-Prot library (UniProt Consortium, 2018), with the prior exclusion of proteins that were similar to those present in RepBase (Bao et al., 2015). We used as transcriptional evidence, transcriptome data for M. incognita, as it is the Meloidogyne species with the most comprehensive expression data available. RNA-seq data from pre-parasitic J2, J2-J3 and adult female stages (Blanc-Mathieu et al., 2017) were assembled de novo using Trinity (Haas et al., 2013) followed by a cleanup that retains for each trinity locus only the transcript that gives the longest ORF. The dataset of M. incognita assembled transcriptome was aligned on the genomes of the four Meloidogyne species using Gmap (Wu and Watanabe, 2005) and except for M. incognita the option "cross-species" was used. Only alignments spanning 30% of the transcript length with at least 97% identity were retained. The EuGene default configuration was edited to set the “preserve” parameter to 1 for all datasets, the “gmap_intron_filter” parameter to 1, the minimum intron length to 35 bp, and to allow the non-canonical donor splice site “GC”. Finally, the Nematode specific Weight Array Method matrices were used to score the splice sites (available at this URL: http://eugene.toulouse.inra.fr/Downloads/WAM_nematodes_20171017.tar.gz).
DOI: 10.57745/87kzfh
title: Cemov cohort

description: Data for the manuscript : Emotional overeating affected nine in ten female students during the COVID-19 University closure: A cross-sectional study in France
DOI: 10.57745/9bv2mt
title: The gradient of vertical velocities and acoustic events in the solar photosphere: a comparison between the MHD simulation and Hinode observations

description: We present a scientific dataset allowing to investigate the gradient of vertical velocities and acoustic events of the solar photosphere. For that purpose, we used results of a MHD numerical simulation and a sequence of observations (spectroscopic scans) from Hinode (JAXA/NASA) at disk centre. The simulation and observations appear to be in good agreement; they exhibit upward and downward gradients respectively in intergranules and granules, together with sporadic acoustic events (upward propagating waves) mainly in intergranular lanes. Such events are derived from the computation of amplitudes and phase lags of waves between two altitudes, providing the phase, group velocities and the energy flux, under some assumptions.
DOI: 10.57745/9vei7s
title: RT-qPCR Data (raw, merged, normalized and analyzed) associated to " Contribution of the Galleria mellonella model to decipher host pathogen interactions from Staphylococcus aureus derivative extracellular vesicles "

description: All RT-QPCR data generated during the infection of Galleria mellonella larvae with TBS buffer (TBS), Staphylococcus aureus HG003 (SA), EVs produced by Staphylococcus aureus HG003 (EV) and non infected. At 2, 24, and 72 h post-injection (hpi), two living larvae were randomly selected in each group for monitoring key larvae immune system actors. Experiment was conducted in biological triplicates. Total RNA was directly extracted from the hemolymph (HL) and the fat body (FB) larval content using the phenol-chloroform method. Dataset comprises raw, filtered, normalized and analyzed RT-qPCR data.
DOI: 10.57745/9weilt
title: ABC model for sea lamprey population estimate using a simple nest count during the spawning season

description: Data used for the manuscript entitled "ABC model for sea lamprey population estimate using a simple nest count during the spawning season". "Model.R" is the main model script, with the model code, the graphs presented in the article, and the sampling schemes simulation. "Sensitivity analysis.R" is the script for sensitivity analysis, using the data from "sensitivity_data.xlsx".
DOI: 10.57745/6pdazb
title: Independent validation of ATE score diagnostic accuracy for predicting the absence of intra-atrial thrombi before catheter ablation of atrial fibrillation

description: The purpose of the data collection was to assess the diagnostic accuracy of the ATE score for exclusion of intra-atrial thrombi before catheter ablation of atrial fibrillation. Demographics, clinical, biological, procedural, and score data were collected. Categorical data were used for gender, clinical history, clinical condition, procedural data, and diagnostic of intra-atrial thrombus. Continuous data were used for age, d-Dimer level, CHADS2, CHA2DS2VASc, and ATE Score. The primary outcome was the number of patients with atrial thrombus and a zero ATE score at most 48 hours before ablation. The secondary outcomes were 1) the number of patients with atrial thrombus among patients with a zero CHADS2VASC score at most 48 hours before ablation, 2) the number of patients with atrial thrombus among patients with a zero CHADS2 score. In this dataset, transesophageal echography detected 29 atrial thrombi in a population of 3,072 patients (incidence rate 0.94% [95%CI 0.63-1.35]). Considering a zero ATE score as a negative result, the negative predictive value was 99.8%.
DOI: 10.57745/7dt6qc
title: Jeu de données températures Nivelle

description: Petit fleuve côtier de 39 km de long, la Nivelle est une rivière à migrateurs (saumon, alose, truites de mer) et ses populations sont suivies depuis le début des années 80. Ce Dataset présente un classeur Excel qui décrit les relevés de températures qui sont effectués quotidiennement depuis juillet 2009 sur plusieurs points de la Nivelle, en complément des mesures effectuées sur l’Aquapôle depuis 1984 : - La très haute Nivelle avec un Thermo-enregistreur sur Le Lapitxuri à proximité de la station de l’Inrae. - La Nivelle intermédiaire avec une sonde en amont du barrage d’Urrutienea (Darguy). - L’affluent principal le Lurgorrieta au niveau de l’ancienne conserverie. - La basse Nivelle sur la station de piégeage d’Uxondoa. En complément de tous ces thermo-enregistreurs qui prennent des valeurs de température de l’eau de la Nivelle, une sonde pour la mesure de l’air a également été mise en place en juillet 2009 sur l’Aquapôle. Pour la plupart de ces thermo-enregistreurs le pas de temps retenu entre 2 mesures est d’une heure.
DOI: 10.57745/7ucrmf
title: Greenhouse gas emissions factors of land use and land-use change for French agricultural land uses and crops

description: The aim of the ACV Carbone project, funded by ADEME, was to develop a method to estimate greenhouse gas emissions from both direct land-use changes and land-management changes, to be implemented in Agribalyse, the French agricultural and food life cycle inventory database. The proposed method uses spatially explicit land-conversion data at the departmental scale with a shared-responsibility allocation approach and regionalised carbon stocks, in line with recent developments in carbone accounting methods for life cycle assessment. We calculated three types of emissions factor (EF) per unit area associated with land use and land-use change : (i) specific EFs when the department of production and previous land use are known (for five agricultural land-use categories, 14 previous land-use categories and 94 departments), (ii) mean departmental EFs when the department of production is known but previous land use is not (for five agricultural land-use categories and 94 departments) and (iii) mean supra-departmental EFs when the department of production and previous land use are unknown (for more than 80 crops and 178 variants at the national scale). The EFs are consistent with international life cycle assessment and carbon accounting guidelines for land use and land-use change, but carbon dioxide removals must be excluded. We recommend using these EFs to assess the climate change impacts of agricultural products.
DOI: 10.57745/8w5hts
title: Development of sequenced-based microsatellite genotyping protocol

description: Sequence-based microsatellite genotyping is a powerful method for efficient genotypic data production in non-model species. We described an optimized laboratory and bioinformatics workflow for time and cost effective development of sequence-based microsatellite genotyping protocol.
DOI: 10.57745/adrabs
title: Data associated to the communication "Calculating the effect of nutritional and hormonal challenges on lactation persistency of dairy cows"

description: These data sets (.csv) contains milk yield and persistency data of 4 distinct experiments (1 file per experiment). For more information, the associated published papers are: - For (EXPA) Herve et al. 2019. Milk yield loss in response to feed restriction is associated with mammary epithelial cell exfoliation in dairy cows. J Dairy Sci. 102:2670-2685; - For (EXPB) Dessauge et al. 2011. Effects of nutrient restriction on mammary cell turnover and mammary gland remodeling in lactating dairy cows. J Dairy Sci, 94, 4623-4635; - For (EXPC) Lacasse et al. 2011. Effect of the prolactin-release inhibitor quinagolide on lactating dairy cows. J Dairy Sci. 94:1302-9; - For (EXPD) Yart et al. 2013. Changes in mammary secretory tissue during lactation in ovariectomized dairy cows. Steroids. 78:973-81. Also a short communication paper (Gaillard et al. "Calculating the effect of nutritional and hormonal challenges on lactation persistency of dairy cows") has been submitted to J. Dairy Sci. to present lactation persistency values calculated as the slope of the milk yield (MY) curve smoothed with the fda package on R (penalty of 1e+2, the knots are the days). A complementary file ("ANNEXES Graphs") allows to vbisualize the milk production and persistency over the experimental periods for each experiment.
DOI: 10.57745/6hnonq
title: Source Data for G4 density in M. incognita

description: We used the G4-Hunter software76 with a window size of 25 and a minimal score of 1.2 to detect regions possibly forming G4-quadruplexes on the composite terminal repeats as well as the whole genome sequences of Meloidogyne incognita. Using an in-house script, we retrieved only the non-overlapping positions, distant by more than 25 bp, and the score for each G4-quadruplex position, and we plotted their frequency using Rstudio.
DOI: 10.57745/6xs4hv
title: Replication data for the publication "Harmonized disposable income dataset for Europe at subnational level"

description: These files contain auxiliary data to reproduce the results of the publication: "Harmonized disposable income dataset for Europe at subnational level". They contain 42 country-level folders containing input data and a "Global_Input" folder with inputs shared by many countries.
DOI: 10.57745/9dgkgp
title: Distribution of telomeric repeats and proteins across nematode species

description: Distribution of the canonical (TTAGGC)n telomeric repeats and telomere-associatted proteins across 69 nematode species. Sources of genomes and predicted proteomes as well taxonomic classification are provided. - First sheet: Full details of the source for genomes and proteomes and evidence for presence / absence of the TTAGGC repeat and telomere-associated proteins. - Second sheet: Consensus final decision for presence / absence of the TTAGGC repeat and telomere-associated proteins.
DOI: 10.57745/a6k7il
title: RPG complété 2020 Région Hauts-de-France

description: RPG complété 2020. Complète le RPG campagne 2020 pour les départements de la région Hauts-de-France (02, 59, 60, 62, 80). (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2022.
DOI: 10.57745/akjdio
title: Breedwheat

description: Phenotype and genotype datasets from the Breedwheat Project
DOI: 10.57745/9hrbag
title: High resolution spectra of the [6297-6303] and [6361-6367] Angström domains (including forbidden Oxygen lines) of the Sun and brightest stars

description: We present a dataset of high resolution spectra of the Sun (many centre to limb positions) and ten bright stars of the domains [6297-6303] and [6361-6367] Angtröm, including Oxygen lines. Solar spectra were obtained in the quiet Sun at various distances from disk centre with the ground based Meudon Solar Tower and Themis telescope (12 mÅ resolution) and with the Solar Optical Telescope (SOT) onboard the Hinode satellite (21 mÅ resolution). Spectra of 10 bright stars (magnitude &lt; 2) were also got with Themis at 12 mÅ resolution. These spectral domains contain the faint and forbidden Oxygen OI lines (6300.31 Å and 6363.79 Å) that are useful for the research of Oxygen abundance. The spectra shown here are freely available in scientific FITS format to the research community.
DOI: 10.57745/9li35d
title: Sapin de Vancouver (grand fir, Abies grandis)

description: Fichier d'impression 3D de bois de SAPIN file for 3D printer : fir wood
DOI: 10.57745/ar1mpb
title: Données de réplication pour : First evidence of large-scale PAH trends in French soils

description: Here, we share the first selection of nation-wide maps of soil Polycyclic aromatic hydrocarbons (PAH) in France. Results were obtained within the French National Soil Monitoring Network, which is the first European network monitoring systematically soil PAHs. We used advanced geostatistics to map PAH distribution over the whole French territory. 4 maps are provided in a raster format. The projection is lambert 2, SRID 2154. The resolution is 5 km.
DOI: 10.57745/arp784
title: Ho3+-doped Y3NbO7 transparent ceramic elaborated by air pre-sintering and post-HIP treatment as potential LASER gain material at 2 μm

description: Data set from Cornet L., Guené-Girard S., Heintz J. M., Boulesteix R., Maître A. and Jubera V. Ho3+-doped Y3NbO7 transparent ceramic elaborated by air pre-sintering and post-HIP treatment as potential LASER gain material at 2 μm. Optical Materials (Amsterdam, Netherlands) 2023 vol. 144, p. 114319. Hal-04197983 Dataset production context : In the framework of the development of new laser materials at the lowest limit of the mid-IR range, the cubic Y3NbO7 matrix has been doped by trivalent holmium. Fine powders were prepared through a liquid phase synthesis and highly densified using a two-stage sintering process: i) natural sintering was performed in air to reach relative density higher than 95%; ii) Hot Isostatic Pressure was applied to obtain fully dense and, consequently, transparent ceramics. The resulting microstructures were examined and then related to sintering parameters such as temperature and pressure. Refractive index, transmission and luminescence properties were measured and presented for the first time on a bulk material. These encouraging results showed that the Ho3+-doped Y3NbO7 compound is a promising potential candidate as a new laser material. For more information see the article.
DOI: 10.57745/7meynt
title: Extraction of the CowNflow dataset for the paper Animal-24-21504 by Ferreira et al.

description: This dataset represents the subset fo the CowNflow dataset used for determining nitrogen and truly digestible protein efficiencies of dairy cows fed fresh herbage- or maize forage-based diets though a meta-analysis (paper Animal-24-21504 by Ferreira et al.).
DOI: 10.57745/b6rcw8
title: Inoculation of synthetic community of bean seeds

description: We performed 4 experiments during which bacterial synthetic communities were inoculated on bean seeds. Experiment 1 : Inoculation of 35 single bacterial strains on bean seeds - Effect on seedling microbiota assembly Experiment 2 : Inoculation of one SynCom (14 strains) on bean seeds - Effect of inoculum concentration, inoculation fluid and seed disinfection on seed microbiota Experiment 3 : Inoculation of one SynCom (14 strains) on bean seeds sown in soil - Effect of inoculum concentration on seedling microbiota assembly Experiment 4 : Inoculation of twelve SynComs of increasing richness (3, 5, 8 or 11 strains) on bean seeds sown in soil - Effect of SynCom richness on seedling microbiota assembly We performed amplicon sequencing on the gyrB gene to characterize bacterial communities on the Illumina MiSeq platform. Embargo on the data in ENA until September 30th 2023.