cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0x63n54
title: Heterogeneous Stock (HS) Rat Genotypes, Version 4. In Genotype data from: NIDA Center for GWAS in Outbred rats

description: All software versions used to generate the data in this object are noted below and in the Methods section of the associated publication:

fastx_toolkit 0.0.14
cutadapt 4.1
fgbio 1.3.0
bbDuk 38.94
BWA 0.7.17
samtools 1.14
picard 2.25.7
STITCH 1.6.6
GATK 4.2.0
bcftools 1.14
PLINK 1.9
Python 3.10

Demultiplexing was performed using fastx_toolkit and fgbio. Barcode, adapter, and quality trimming was performed using cutadapt and bbDuk. Reads were aligned to the Rattus norvegicus genome assembly mRatBN7.2 using BWA. Read mapping was quantified using samtools. SNP genotypes were imputed using STITCH and a reference panel of consensus variants identified from eight HS rat founder strains. Reference panel SNPs were called using GATK. Variants were filtered using bcftools. Quality control was conducted using Python.
description: This collection contains genotype data collected as part of the NIDA Center for GWAS in Outbred rats and more than 10 additional research projects that use N/NIH heterogeneous stock (HS) outbred rats. We obtain genotypes for DNA samples derived from rats that are phenotyped by different research projects. We use these genotypes to perform genome wide association studies (GWAS) and a number of related analyses. Data in this release contains genotypes for 17,812 N/NIH heterogeneous stock (HS) outbred rats from the breeding colonies MCW: NMcwi:HS RRID:RGD_2314009, and WFU: NMcwiWFsm:HS RRID:RGD_13673907, the University of California San Diego: RRID: RGD_155269102, the University of Tennessee Health Sciences Center, or Oregon Health and Sciences University.
DOI: 10.15468/dl.ve64sb
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Laurencia caduciramulosa Masuda & Kawag.",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 21 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030542-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ed7kqg
title: Occurrence Download

description: A dataset containing 3629570 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gallinago Brisson, 1760"
 ]
}

 The dataset includes 3629570 records from 2033 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030533-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/d1g0ik
title: NMR data of multi-step synthesis of (R)-3-hydroxy-fatty acid derivatives from levoglucosenone

description: This dataset archives NMR data related to synthesis of (R)-3-hydroxydecanoic acid and analogues. These data have been produced during LéGO project which aimed to green up the synthetic pathway of rhamnolipids. Exhibiting outstanding biosurfactant properties, rhamnolipids (RLs) are highly valuable molecules in the cosmetic, pharmaceutic and agricultural sectors. In the latter, they are used to artificially stimulate natural immune system of crops (also known as elicitation). To decipher their mechanisms of action and design novel potent elicitors, a straightforward and green access to model molecules is needed. Herein, starting from cellulose-derived levoglucosenone, we propose an efficient and seven-step synthetic pathway to prepare enantiopure (R)-3-hydroxy-fatty acid chains present in RLs with Michael addition, Baeyer-Villiger oxidation, Bernet-Vasella reaction and cross metathesis homologation as key steps (global yield ranging from 24% to 36%).
DOI: 10.57745/db6ivo
title: Insights into the genomic and phenotypic diversity of Monosporozyma unispora strains isolated from anthropic environments (supporting data)

description: Supporting data from the study of the genomic and phenotypic diversity of a collection of 53 Monosporozyma unispora strains, mainly from cheese, kefir and sourdough.
DOI: 10.57745/dr4r45
title: RPG complété 2022 Région Centre - Val de Loire

description: RPG complété 2022. Complète le RPG campagne 2022 pour les départements de la région Centre-Val de Loire (18, 28, 36, 37, 41, 45). (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2024.
DOI: 10.57745/ebbge8
title: Dataset for common wheat (Triticum aestivum L.) grain and flour characterization using classical and advanced analyses: raw and calculated analytical data SPARQL queries

description: This dataset is composed of the 28 SPARQL queries executed to generate the measurement tables which are included in the files belonging to dataset containing the data tables results of the queries execution. They have the same name. They only differ by their extension. By example, CWG_reception_fallingNumber_raw.sparql is the file including the SPARQL query executed to obtain the table included in the file CWG_reception_fallingNumber_raw.tsv.
DOI: 10.57745/eguuhk
title: Meloidogyne enterolobii scripts

description: The codes used to run the different tools listed in the methods of the paper "High-fidelity annotated genome of the polyploid and quarantine root-knot nematode, Meloidogyne enterolobii" have been deposited and are publicly available at the Recherche Data Gouv institutional collection. For optimal use of DeepConsensus, it is recommended to use a GPU.
DOI: 10.57745/ej4ci3
title: GEDI footprints with corrected geolocation with DEM

description: Data set from Schleich Anouk, Durrieu Sylvie, Maxime Soma and Cédric Vega, "Improving GEDI Footprint Geolocation using a High Resolution Digital Elevation Model" We proposed a geolocation correction method for Global Ecosystem Dynamics Investigation (GEDI) data. The method, called GeoGEDI, is only based on high-resolution digital elevation models (DEMs) and GEDI derived ground elevations. The method does not need any other input, except for a DEM and GEDI Level 2A data. For each footprint, an error map between GEDI ground estimates and reference DEM is computed, and a flow accumulation algorithm is used to retrieve the optimal footprint position. GeoGEDI was tested on footprints in Landes and Vosges, two french forests. The method was applied to GEDI versions 1 (v1) and 2 (v2), by either a single or four full-power laser beam tracks. This dataset is composed of 157 977 GEDI footprints whith positions of unchanged GEDI v1 and v2 releases and the optimal position calculated with our GeoGEDI algorithm.
DOI: 10.57745/eikaq4
title: Distribution of G4s and Mjav repeats on M. javanica contigs

description: The density of Mjav composite repeats per 100kb window is represented by a color gradient with positive values (red) indicating a density in the sense strand and negative values (blue) indicating a density on the reverse complement strand. Gray triangles above bars indicate regions of the contigs where less than 100% of the repeats are on the same strand. The heights of bars in the histogram represent the density of G4-quadruplex forming regions in the same windows.
DOI: 10.57745/evuhca
title: Microtomoscan of Clay-Sulfate Rock after Exposure to NaCl in the Desiccator for 62 Days, Part 2

description: microtomosan
DOI: 10.57745/fke8u7
title: High-Performance Size-Exclusion Chromatography (HP-SEC) analysis of lignins

description: Lab-extracted organosolv lignins have been analysed using high-performance size-exclusion chromatography. This dataset includes: - 1 file explaining the method; - 1 file summarizing the molecular weight (Mw) and the polydispersity index (Mw/Mn) for acetylated lab-extracted organosolv lignin samples.
DOI: 10.57745/eo2sbc
title: Data from the paper entitled 'Glycaemic effects of a 156-km ultra-trail race in athletes: an observational field study'

description: Objectives We aimed to explore the impact of an ultra-endurance race on continuously measured glycaemia and to understand potential physiological mechanisms, as well as the consequences for performance and behavioural alertness. Methods Fifty-five athletes (78% men, 43.7 +/- 9.6 years) ran a 156-km ultra-trail race (‘Trail Scientifique de Clécy’: six 26-km laps, total elevation +6000 m). Participants wore a masked continuous glucose monitoring sensor from the day before the race until 10 days post-race. Blood was taken at rest, during refuelling stops after each lap, and after 24-h recovery. Running intensity (% heart rate reserve), performance (lap times), psychological stress and behavioural alertness were explored. Linear mixed models and logistic regressions were carried out. Results No higher risk of hypo or hyperglycaemia was observed during the exercise phases of the race (i.e., excluding stops for scientific measurements and refuelling) compared with resting values. Laps comprising a greater proportion of time spent at maximal aerobic intensity were nevertheless associated with more time &gt;180 mg/dL (P=0.021). A major risk of hyperglycaemia appeared during the 48-h post-race period compared with pre-race (P&lt;0.05), with 31.9% of the participants spending time &gt;180 mg/dL during recovery vs. 5.5% during resting. Changes in circulating insulin, cortisol and free fatty acids followed profiles comparable with those usually observed during traditional aerobic exercise. However, creatine phosphokinase, and to a lesser extent lactate dehydrogenase, increased exponentially during the race (P&lt;0.001) and remained high at 24-h post-race (P&lt;0.001; respectively 43.6 and 1.8 times higher vs. resting). Glycaemic metrics did not influence physical performance nor behavioural alertness. Conclusion Ultra-endurance athletes were exposed to hyperglycaemia during the 48-h post-race period, possibly linked to muscle damage and inflammation. Strategies to mitigate muscle damage or subsequent inflammation before or after ultra-trail races could limit recovery hyperglycaemia and hence its related adverse health consequences.
DOI: 10.57745/fdpixy
title: Varietal parameterization of eleven modern French wheat cultivars in the STICS crop model

description: This repository contains new xml plant files for the STICS crop model with eleven new modern French winter wheat cultivars. The description of the calibration approach is also provided.
DOI: 10.57745/bic6mb
title: Réponses Enquête Données de la recherche Université de Strasbourg et Université Côte d’Azur

description: Objet : Le jeu de données intitulé «Réponses Enquête Données de la recherche Université de Strasbourg et Université Côte d’Azur» au format .ods comprends 496 réponses complètes à un questionnaire en ligne (environ 60 questions) portant sur les pratiques des chercheurs concernant leurs données de recherche. L’enquête, administrée sous Lime Survey entre novembre 2019 et février 2020, a été adressée à l’ensemble des doctorants et personnels exerçant des activités de recherche au sein de l’Université de Strasbourg et Université Côte d’Azur. Nature : Le fichier anonymisé contient de nombreuses données qualitatives sur les aspects suivants : 1. caractéristiques du répondant (statut, classe d’âge, champ disciplinaire, responsabilités, genre) 2. type des données 3. gestion (stockage, archivage, description) des données 4. usage et partage des données (y compris freins et intentions de partage) 5. besoins (formation, etc.) Portée : L’intérêt de ce jeu de données est de concerner toutes les disciplines scientifiques et d’avoir été collecté au niveau local de deux universités, ce qui permet une analyse comparative inter-établissements. Dans cet esprit, et dans le but de faciliter la collecte de données similaires, une version améliorée du questionnaire est librement accessible et importable sous Lime Survey. Cette version peut être aisément utilisée et/ou adapté à d’autres établissements (le questionnaire a ainsi été adapté au cas des universités de Nantes et du Mans, ainsi qu’à INRAe et au Synchrotron SOLEIL) Ce jeu de donnée est associé aux fichiers complémentaires suivants : - Fichier Readme.txt pour en expliquer l’usage (fichier nécessaire à l’exploitation du jeu de donnée) - Version .html du questionnaire originel en anglais et en français (idem : fichier nécessaire) - Questionnaire amélioré en format .lss importable sous Lime Survey - Rapport final correspondant est disponible sur HAL («Enquête sur les Données de la Recherche au sein de deux universités françaises. Université de Strasbourg; Université Nice Côte d'Azur », id : hal-03997711, déposé le 20 février 2023)
DOI: 10.57745/cvlvdl
title: RPG complété 2020 Région Rhône-Alpes

description: RPG complété 2020. Complète le RPG campagne 2020 pour les départements de la région Rhône-Alpes (01, 07, 26, 38, 42, 69, 73, 74). (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2022.
DOI: 10.57745/eql6ht
title: Raw data - Operando X-ray Absorption Study of TiO₂-Supported Au, Cu, and Au–Cu Catalysts for Butadiene Selective Hydrogenation

description: Raw dataset of the data presented in the article entitled "Operando X-ray Absorption Study of TiO₂-Supported Au, Cu, and Au–Cu Catalysts for Butadiene Selective Hydrogenation" by Abdallah Nassereddine et al. in ChemCatChem in 2025. This dataset contains all raw quick-XAS data acquired on ROCK beamline in SOLEIL synchrotron. The complementary mass spectrometry data are provided. The STEM HAADF data presented throughout the article have also present.
DOI: 10.57745/fchdxu
title: Two-photon interference from a quantum emitter in hexagonal boron nitride

description: Data from all figures from the article: C. Fournier, S. Roux, K. Watanabe, T. Taniguchi, S. Buil, J. Barjon, J.-P. Hermier, A. Delteil, "Two-photon interference from a quantum emitter in hexagonal boron nitride", Phys. Rev. Applied 19, L041003 (2023). Fig.1: spectroscopy of the quantum emitter studied in the publication. Fig. 2: time-resolved photon counting data. (b) Fluorescence decay. (c) Hanbury Brown and Twiss correlations. (d) Hong-Ou-Mandel correlations in parallel and orthogonal configurations. Fig. 3a: HOM visibility as a function of the time filter width. Fig. 3b: simulation of the visibility decay as a function of the emitter dephasing time.
DOI: 10.57745/dsuq0a
title: Large-Eddy Simulations of boundary layers with coherent structures

description: Simulations of atmospheric boundary layers used in Brient et. al (2023). The model used is the MESO-NH model 4 simulations - BOMEX_sel_Ru0x0.1.V0301.008.nc4 The reference BOMEX marine cumulus case (Siebesma et al., 2003) at t=8h - BOMEX_sel_Ru0x0.1.V0301.008.nc4 The BOMEX case where horizontal large-scale winds are set to zero (t=8h) - FIRE_sel_Ls2x0.1.V0301.012.nc4 The reference FIRE marine stratocumulus case (Duynkerke et al., 2004) at t=12h - FIRE_sel_Ls2x0.1.V0301.021.nc4 The FIRE case at t=21h - IHOP_sel_Ru0x0.1.V0301.006.nc4 The reference IHOP clear-sky continental convective case (Couvreux et al., 2005) at t=12h (t+6h)
DOI: 10.57745/eh9krw
title: Multipartite virus full genome reconstitution dataset

description: This repository contains data files and scripts used to analyse these data from manuscript ‘Non-concomitant host-to-host transmission of multipartite virus genome segments may lead to complete genome reconstitution’ by Jérémy Di Mattia, Babil Torralba, Michel Yvon, Jean-Louis Zeddam, Stéphane Blanc and Yannis Michalakis.
DOI: 10.57745/daeb1z
title: 2015 LiDAR point-cloud for Draix-Bleone Observatory

description: This dataset contains a high resolution LiDAR point cloud that was acquired on April 7th, 2015 in Draix-Bleone Observatory, from a helicopter flight using instrument Riegl LMS Q680i. It covers an area of 252 ha and includes the Laval, Moulin, Roubine and Brusquet catchments of Draix-Bleone Observatory. The point cloud was classified into soil and vegetation points using Terrasolid tools. The original point cloud has a density of 160 points/m2 and the filtered point cloud excluding vegetation points has a density of 40 pts/m2. Data is provided in RGF93 coordinates.
DOI: 10.57745/dzim2l
title: Camera images from embedded Camera on a drone flying in front of walls and nettings in simulation and experimental data

description: This data set contains .png images taken from a drone when flying in an arena with nets on one side and plane walls on the others. The data were acquired during several flights made on different days, in a real arena or in simulations (https://gazebosim.org/home). Several parameters change across the data-sets, from orientation of the camera, type of texture used to the field-of-view of the camera. The data are used in a journal paper in order to show a way to detect the presence of a netting via the use of the optic flow (motion parallax) taken on several layers. The software used for data acquisition onboard the drone was python 2.7, while the system VICON tracker VRPN 3.1.1 was used for position recording (https://www.vicon.com/support/faqs/how-does-tracker-work-with-vrpn/). The camera used was a global shutter camera ELP USBGS720P02-L36 with a 3.6 mm objective. More details about the setup and experimental conditions can be founded in "codes/readme". Basic codes are given in the "codes" folder in order to extract and link the data between images and csv file, taking into account the experimental bias in the data acquisition. This project wasn't financed by a specific research project but was done during my PhD thesis.
DOI: 10.57745/eqyvlp
title: Datasets of the AMOBIO research programme: the multi-criteria analysis of the effects of flow obstacles on stream physical and biological conditions in France

description: Datasets from the AMOBIO research programme (2021 – 2024) in partnership between the French Biodiversity Office (OFB) and the National Research Institute for Agriculture, Food and the Environment (INRAE) entitled: « Multi-criteria analysis of the effects of flow obstacles on stream physical and biological conditions in France ». Flow obstacles are ubiquitous and increasing in rivers around the world, fragmenting and altering freshwater habitats quality and availability yet that are essential for biological communities and human societies. This research programme aims to better understand the direct and indirect effects, at different spatial scales, of the multifaceted flow obstacle pressure (dams, weirs and bridges) on stream physical conditions (hydromorphology, hydrology, water temperature and physicochemical water quality) and on the taxonomic and functional composition of three major river communities in France (benthic diatoms and macroinvertebrates and fish). This programme also seeks to integrate the natural (structure of the dendritic river network, natural cover) and anthropic (urbanization, agriculture) complexity of watersheds. The datasets includes two files (and their respective metadata): 1) a national dendritic network (NETWORK_AMOBIO, and its metadata METADATA_NETWORK_AMOBIO, please download the original file if you want to see all spreadsheets) in a tidy graph format (sfnetworks package) compiling thousands of sampling stations associated with environmental data and/or pressure indicators (biological samplings, water quality measurements, inventory of flow obstacles, hydrological and water temperature measurements, characterization and risk of hydromorphological alterations of watercourses) from national WFD monitoring systems (ROE, CARHYCE, SYRAH-CE, TIGRE, SCHAPI, etc.) ; 2) a table (METRICS_AMOBIO, and its metadata METADATA_METRICS_AMOBIO) providing information for each biological sampling station on taxonomic and functional variables for biological communities and metrics of pressures and/or environmental characterizations (obstacle pressure, water quality, hydrology, water temperatures, hydromorphology, land uses and natural cover) at different spatial and temporal scales The scientific and technical report of the program describes the methods of data construction and shows the first results (Dézerald O., Bourillon B., Mirabel A., Moussay M., Kreutzenberger K., 2025). In the face of the current erosion of biodiversity, these data represent a major development for a better understanding of the human impacts on aquatic ecosystems in the multi-stress and multi-scales context of watersheds. They also provide important perspectives on both fundamental and applied research as well as on the management and preservation of watercourses and biodiversity.
DOI: 10.57745/fd6xqs
title: Data of Pinus pinaster root architecture after outplanting: 3D-digitised root systems of 284 saplings aged three to five years from seed

description: Planting is a widespread propagation technique, even for long-life woody plants. Yet, cultivation in containers and outplanting can cause root deformations and subsequently alter anchorage. We set up an original method to characterise the root deformations and their relationships with anchorage in 3D-digitised root systems of 1-m tall saplings. We applied this method to 236 three- to five-year-old outplanted Pinus pinaster saplings first reared in containers with vertical slits and ribs from 15 commercial planted stands, and to 48 saplings from a control seeded-in-place stand. The data set contains the root characteristics of the 284 saplings.
DOI: 10.57745/de9spe
title: Identification de stations hydrométriques et piézomètres pour l’évaluation des modélisations hydrologiques et hydrogéologiques

description: Les modèles qui simulent des débits et des niveaux piézométriques en temps futur ont besoin d’être évalués en comparant de la manière la plus objective les données simulées en temps présent à des données observées sur un ensemble de points de mesure. Tous les points de mesure ne peuvent pas contribuer à cette évaluation. Les modèles mobilisés dans Explore2 simulent une ressource naturelle : le contrôle doit s’opérer là où l’empreinte anthropique est faible. Le rapport mentionne les modalités de sélection des séries journalières de débits et de niveaux piézométriques. Outre des critères de représentativité hydrologique, la sélection s’est appuyée sur des critères de longueur de chronique, des informations sur la qualité des mesures, des indicateurs de pression sur la ressource (prélèvements en eau) ou de potentielles perturbations (présence d’ouvrages hydrauliques en amont) et une expertise des usages sur les bassins versants ou à proximité de piézomètres. La sélection croise les informations disponibles dans les bases de données nationales (BNPE, HYDRO, ADES), internationale (AQUASTAT) ou constituées par les partenaires (EDF, INRAE). Les séries candidates de débits ont ensuite fait l’objet d’une ultime analyse de chaque série par deux individus (identification de données aberrantes par comparaison aux données de pluie et température, et aux sorties d’un modèle). Finalement, à la date du 1er juillet 2022, 611 séries de débits et 227 séries de niveau piézométrique ont été retenues pour évaluer les modèles hydrologiques.
DOI: 10.57745/dehdr9
title: Microniche of génépis (Alpine wormwoods) in the Southern Alps

description: This dataset corresponds to field measurements of the ecological conditions where Alpine wormwoods grow (Artemisia eriantha, A. genipi, A. glacialis, A. umbelliformis), in the southern Alps, to study niche overlap and differentiation of these four congeneric species. Details on the authors of the data: Data acquisition: Samson Acoca-Pidolle, Isabelle Boulangeat, Louis Clouet, Ninon Fontaine, Perrine Gauthier, John Thompson Soil analyses: Ninon Fontaine, Perrine Gauthier, Raphaëlle Leclerc, Virginie Pons Data curation: Ninon Fontaine