cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/hxdw3c
title: Growth kinetics and mycotoxins dataset investigating ecophysiological behaviour of Fusarium spp under abiotic environmental constraints

description: This repository contains data and code used for the article “Ecophysiological behaviour of major Fusarium species in response to combinations of temperature and water activity constraints.” by Garcia M-A, Mahmoud R and al. Description of files is available in README-repository.docx.
DOI: 10.57745/itavno
title: Evolution de l’abondance de Pseudotolithus elongatus en Guinée / Guinée-Bissau

description: Le présent document décrit l’utilisation des modèles linéaires généralisés (GLM) pour la création d’indices d’abondance du stock de Bobo(Pseudotolithus Elongatus) en Guinée et Guinée Bissau. Les modèles GLM permettent de prendre en compte les variations de protocole d’échantillonnage dans l’observation des captures des flottilles de pêche concernées. Les données utilisées proviennent, d’une part des campagnes scientifique démersales réalisées dans les deux pays depuis les années 1980, et d’autre part des données de captures et d’effort des pêcheries artisanales maritimes et industrielles disponibles pour les deux pays.
DOI: 10.57745/jupe21
title: Accompagnement de lecture des fiches Incertitudes

description: Ce document a pour objectif d’accompagner la lecture des fiches incertitudes produites avec l’ensemble de projections hydroclimatiques d’Explore2 obtenus avec la méthode de correction ADAMONT. Le lecteur pourra consulter le rapport Explore2 dédié aux incertitudes pour des informations complémentaires (Evin et al., 2024) ainsi que les notices de lecture des illustrations produites (Reverdy et al., 2023a,b).
DOI: 10.57745/k6fdlg
title: Minimal dataset for SQuIRE usage on Prunus Marouch

description: This dataset is composed of 3 files: (1) the sequence genome of Marouch (.fasta) (2) the annotation of Marouch genome (.gff3) (3) the rmsk informations from RepeatMasker software for Marouch genome. These three files are the minimal input to use SQuIRE as explain here: https://github.com/Elie-Bordron/SQuIRE_usage
DOI: 10.57745/k7vll2
title: Weed control, protein and forage yield of seven grass species in lucerne-grass associations

description: • Association of grass species with lucerne is a way to limit weed occurrence • Lucerne-grass associations give forage yield and quality, close to that of pure lucerne • Grass species differed for their direct and associated effects on the species of the association • Grass species with a small direct effect on grass production and a large positive associated effect on lucerne production favoured high forage and protein production
DOI: 10.57745/kamghr
title: The effects of earthworm species on organic matter transformations and soil microbial communities are only partially related to their bioturbation activity

description: This dataset was acquired to investigate the effects of earthworm species on soil bioturbation, biogeochemical transformations of soil organic matter, and soil microbial communities under controlled conditions. Six earthworm species (Lumbricus terrestris, Allolobophora chlorotica, Octolasion cyaneum, Octodrilus complanatus, Aporrectodea caliginosa meridionalis and Microscolex dubius) were incubated in soil cores with soil and alfalfa litter for 6 weeks, at 16 °C. The soil is a silty loam sampled in an agricultural plot in Estrées-Mons, northern France. Two series of soil cores were performed, including controls (3 with litter and without earthworm, 3 without litter and without earthworm per series). At the end of the incubation period, the entire cores were scanned using a medical scanner for bioturbation measurements. All images were processed the same way to compute the number of macropores (set of connected voxels), the volume of burrows (sum of all the macropore volume), the vertical barycentre of the burrow system (the centre of mass of the burrow system when only the vertical dimension is taken into account), the diameter (assessed as the median of the diameter of all vertical pores with a circularity 0.8) and burrow system continuity (number of burrows whose vertical length was higher than 30% of the depth of the soil core). In cores with earthworms, the soil was sampled from three different compartments: surface casts, the drilosphere (i.e., soil surrounding burrows, up to 4 mm from the burrow walls), and surrounding bulk soil. In control cores without earthworms, the soil was sampled from three different depths: surface (0-2 cm from the soil surface), middle (8-12 cm) and bottom (18-22 cm). Biogeochemical measurements, performed on the different soil compartments, included : soil humidity, dissolved organic carbon (C), total C, total nitrogen (N), mineral N, organic N contents, C to N ratio, nitrate (NO3-) and ammonium (NH4+) contents at the time if sampling and after 8 days in incubation at 20°C, carbon dioxide (CO2) fluxes measured with Isotope-ratio mass spectrometry (IRMS) method after 46, 91, 136, and 181 hours of microcosm incubation at 20°C, CO2 fluxes measured with sodium hydroxide (NaOH) traps after 46, 94, 142, and 190 hours of microcosm incubation at 20°C. Microbiological measurements, performed on the different soil compartments, included: total DNA concentration in soil, 16S rRNA copy number, 18S rRNA copy number, bacterial operational taxonomic unit (OUT) composition, and Shannon index, calculated on bacterial OTU. This work was supported by the the AgroEcoSystem Division of INRAE through the funding of the “GloWorms” project.
DOI: 10.57745/lbz5gt
title: Impact des digestats de méthanisation sur la qualité biologique des sols : Evaluation d’impact à court terme en conditions contrôlées (Mésocosmes)

description: Ce jeu de données contient les résultats d'une expérimentation en conditions contrôlées (mésocosme) ayant pour objectif d'étudier à court terme (42 jours) l'impact de digestats de méthanisation en tenant compte du type de sol sur la qualité biologique et écologique des sols agricoles en utilisant des bio-indicateurs opérationnels (nématodes, lombriciens, litterbag).
DOI: 10.57745/levtcu
title: Head length (HL) and total length (TL) measurements on 17 crocodylian species ( 7,368 measuerments))

description: The database include compiled 7,368 Head Lenght (HL) and Total Lenght (TL) measured from captured individuals of 17 different crocodylian species: Alligator mississippiensis (USA (Florida): 1 650, USA (Georgia): 744), Caiman crocodilus (Brazil: 459), Crocodylus acutus (Belize: 259, Mexico (Atlantic): 493, Mexico (Pacific): 154), Crocodylus intermedius (Venezuela: 403), Crocodylus john-stoni (Australia: 588), Crocodylus moreletii (Belize: 390, Mexico: 207), Crocodylus niloticus (Egypt: 65, Gabon: 20, South Africa: 228, Tanzania: 5, Uganda: 22), Crocodylus palustris (India: 23, Iran: 57), Crocodylus porosus (Australia: 370), Crocodylus rhombifer (Cuba: 196), Crocodylus suchus (Côte d’Ivoire: 24, Ghana: 37, Niger: 36, Uganda: 19), Gavialis gangeticus (India: 308, Nepal: 45), Mecistops leptorhynchus (Gabon: 159), Melanosuchus niger (Brazil: 104, Ecuador: 63), Osteolaemus tetraspis (Gabon: 106), Paleosuchus pal-pebrosus (Brazil: 149), and Paleosuchus trigonatus (Brazil: 87). Additional data: ID, Country, Localisation, Sex, Proprietary, Date
DOI: 10.57745/gztjmf
title: SicpaOpenData for Python

description: The Sicpa_OpenData libraries facilitate the publication of data to the INRAE dataverse in a transparent way 1/ by simplifying the creation of the metadata document from the data already present in the information systems, 2/ by simplifying the use of the dataverse.org APIs. Available as a WHL file, the SicpaOpenData for Python library can be used from all the developments of the Python ecosystem
DOI: 10.57745/hubgdm
title: Supplementary tables "Milking interval and milk lipolysis"

description: 2 supplementary tables : Supplementary table 1. Milk nitrogen composition of cows submitted to different milking times and intervals Supplementary table 2. Milk fatty acids of cows submitted to different milking times and intervals
DOI: 10.57745/ig5ul8
title: Lidar data acquired by drone in the Louchats forest, Gironde, France

description: Acquisition date : 2022/07/06 Sensor :Yellowscan, Surveyor - GNSS-inertial station: Applanix APX-15 UAV - Lidar: Velodyne VLP16 (Puck) : Wavelength: 905 nm / 300,000 pulses per second (300 kHz) / 2 echoes per pulse / Angle of view: 360 deg - Accuracy: 4cm Vector: DJI Matrice 600 Pro drone Flight conditions : - Trajectory design: double grid, distance between lines: 40 m - Speed: 5m/s - Flight height: 50m above ground level, constrained by IGN DTM at 5m spatial resolution -Flight planning software: UGCS-4.0.134 Pre-processing software : - Applanix POSPac UAV 8.4: trajectory post-processing based on the UAV's GNSS inertial unit data, using a reference GNSS base station. The correction solution for each trajectory is exported as an ASCII SBET (Smoothed Best Estimated Trajectory) file. - Yellowscan CloudStation V2106.0.0: The SBET file is integrated into the software to generate point clouds in .las format projected in RGF93/Lambert 93.
DOI: 10.57745/ilfcp4
title: High-throughput sequencing data, codes and scripts used for statistical analyses, associated with the article entitled "Gene copy number variations at the within-host population level modulate gene expression in a multipartite virus" by Gallet et al. (2022)

description: The compressed archive contains three subdirectories: The subdirectory data/ contains the final datasets, which consist in sequencing data of twenty parallel lineages of faba bean necrotic stunt virus (FBNSV), passaged from faba bean (Vicia faba) plants to alfalfa (Medicago truncatula) plants. All files are text files with tab separators. The subdirectory data/ also contains the R script parse_data.R, which purpose is to parse the sequencing data for subsequent analyses. The subdirectory abc/ contains the source files of the TmprlDiffABC software package, which purpose is to perform stochastic simulations mimicking the passage from faba bean (Vicia faba) plants to alfalfa (Medicago truncatula) plants. The subdirectory abc/ also contains the R script abc_inference.R which purpose is to perform ABC inference, using both the observed and the simulated statistics. The subdirectory test/ contains the source files of the TmprlDiffSEL software package, which purpose is to test the null hypothesis that the locus-specific differentiation measured at each SNP between the faba bean and the alfalfa samples is only due to genetic drift. The subdirectory test/ also contains the R script neutrality_test.R which purpose is to parse the outputs of the TmprlDiffSEL analyses.
DOI: 10.57745/j7coat
title: ABQTL_BREEDWHEAT

description: données phénotypiques, données génotypiques
DOI: 10.57745/jdq4ko
title: Simulated hydrological variables and flow intermittence indicators for the reconstruction period (1960-2021) for the 6 European catchments studied in the DRYvER project

description: Hydrological models outputs for the reconstruction period (1960-2021) for the 6 European catchments studied in the DRYvER project.
DOI: 10.57745/jecjui
title: Germination kinetics of red clover diversity panel

description: This dataset decribes the germination curves of a representative, diverse collection of red clover accessions. Germinated seeds were counted at regular intervals using the automated phenotyping platform PHENOSEM (SFR QUASAV, Angers, https://www.geves.fr/tools/phenosem/) (Demilly et al., 2015, https://hal.science/hal-01209985 on 4x25 seeds that were imbibed at 15°C. The description of the diversity collection of red clover is described in Nay et al., 2023, https://doi.org/10.3389/fpls.2023.1128823.
DOI: 10.57745/jnmrzi
title: Evolution of granulometry of plastic fragments sampled during the composting experiment

description: The materials batch of the composting experiment containing the compostable plastics was regularly sampled during the process. These sampling was done using the standardized method NF EN 12579:(12579:2013, 2013). For a batch of compost (max 580 m³) it recommends taking 12 elementary samples, each weighing 1 kg, from various locations. The quartering method described in ASTM C702/C702M:2018 (C702/C702M:2018, 2018) was used to reduce the sample size without creating a systematic bias due to product heterogeneity and obtain a representative final sample of around 10 kg per batch and per sampling time. All the compost samples were air-dried. They were then passed through a series of sieves with decreasing mesh sizes to obtain eight fractions ranging from 10 mm to 0.2 mm. Each fraction was weighed, and its water content was determined.
DOI: 10.57745/kcsbzh
title: ESR10_Exp1_pH

description: pH data
DOI: 10.57745/m4ivee
title: Données de réplication pour : "Exploring two regimes of water mobility in unsaturated expansive clay using NMR relaxometry"

description: Set of experimental and bibliographic data used in the publication "Exploring two regimes of water mobility in unsaturated expansive clay using NMR relaxometry". Data-treatment files are also provided. The user needs to decompress the .zip files. Files with format (.sce) correspond to SciLab files. Scilab is free and open source software for numerical computation providing a powerful computing environment for engineering and scientific applications. SciLab was used to perform the graphics and data analysis of NMR relaxometry experiments. More information about SciLab in: https://www.scilab.org/about
DOI: 10.57745/hlnfn3
title: Data set "Forage, freedom of movement and social interactions remain essential fundamentals for the welfare of high-level sport horses "

description: data set of the research article "Forage, freedom of movement and social interactions remain essential fundamentals for the welfare of high-level sport horses"
DOI: 10.57745/ida8tn
title: Stable isotope analyses - Escherichia coli - T4

description: The dataset comprises two tables : -one with the isotopic composition of Escherichia coli cells grown on minimal medium with various proportions of 13C-glucose, as measured by Isotope Ratio Mass Spectropmetry (IRMS) -one with the density of T4 DNA in a CsCl gradient, according to the rate of 13C-glucose in the culture medium used for host growth
DOI: 10.57745/ifejl8
title: Prediction of the structure of polymer-coated cardboards produced by thermocompression using I-optimal design of experiment

description: This dataset contains the data (two excel files) related to the publication : Prediction of the structure of polymer-coated cardboards produced by thermocompression using I-optimal design of experiment.
DOI: 10.57745/ihwwbf
title: Temperature-dependent zero-field splittings in graphene

description: Data associated to the publication : Temperature-dependent zero-field splittings in graphene C. Bray, K. Maussang, C. Consejo, J. A. Delgado-Notario, S. Krishtopenko, I. Yahniuk, S. Gebert, S. Ruffenach, K. Dinar, E. Moench, J. Eroms, K. Indykiewicz, B. Jouault, J. Torres, Y. M. Meziani, W. Knap, A. Yurgens, S. D. Ganichev, and F. Teppe Phys. Rev. B 106, 245141 (2022)
DOI: 10.57745/iq1kwp
title: Scenarios co-designed during a Dynamix workshop

description: Data from scenarios co-designed with two groups of farmers (Parmiers, Mirepoix) on crop-livestock integration at landscape level. They were designed during a workshop with the serious game Dynamix in 2017 in Ariège (south of France). These data are part of a long-term follow-up of the farms and may not be adequate to use in another situation.
DOI: 10.57745/isna0c
title: Tilleul (lime tree, Tilia europaea)

description: fichier d'impression 3D : bois de Tilleul File for 3D printer: lime tree
DOI: 10.57745/j8erw1
title: Genetic diversity and population structure of Botryosphaeria dothidea and Neofusicoccum parvum on English walnut (Juglans regia L.) in France

description: Although widespread in nut orchards abroad and in other French crops such as vineyards, dieback disease has been recently reported in France on walnut trees, causing severe yield losses since 2015 onwards. The emergent nature of this disease encouraged us to explore its sources and pathways, based on a population genetic study. This dataset contains genotypes of B. dothidea and N. parvum strains collected from French walnut trees (both symptomatic and asymptomatic walnut husks and twigs; 381 strains), French vineyards (48 strains) , Spanish walnut trees and Californian walnut and almond trees (24 strains). Genotypes were obtained the microsatellite marker sequencing technology developed and implemented at the Genome Transcriptome Facility of Bordeaux. A total of 11 loci were used for B. dothidea, and 27 loci for N. parvum. The dataset also contains metadata (e.g. collection date, origin) on each strain. For each species, the genotype tables are constructed as follow: the name of the strains (1st column); the name of the loci identified as PROJECT-SPECIES-NUMBER OF THE LOCI (1st line); and the allele for each locus coded using a three-digit number. A different code represents a different allele in terms of microsatellite repeats. An allele coded with "0" corresponds to a missing data.
DOI: 10.57745/jbph2q
title: Data Management Plan for the Metabolic Profiling and Metabolomic Platform (P2M2)

description: Le Plan de Gestion de Données (PGD) de la plateforme de profilage métabolique et de métabolomique (P2M2) écrit avec DMP OPIDoR est un document qui décrit les pratiques de gestion de la plateforme . Ce document détaille les protocoles utilisés pour la collecte, le stockage, l'analyse, l'interprétation et le partage des données métabolomiques collectées par la plateforme. Il décrit également les métadonnées associées aux données métabolomiques, telles que les informations sur les échantillons, les conditions d'analyse et les protocoles utilisés pour chaque type d'analyse métabolomique. Le PGD de P2M2 répertorie les politiques de partage de données, les licences d'utilisation des données, ainsi que les protocoles de sécurité et de confidentialité qui sont mis en place pour protéger les données des utilisateurs. En résumé, le PGD de P2M2 définit les règles et les procédures que les utilisateurs de la plateforme doivent suivre pour garantir la qualité, la traçabilité et la réutilisabilité des données métabolomiques collectées et produites par la plateforme.
DOI: 10.57745/jiyl1i
title: Phenotypic data corresponding to two aggressiveness components (infection efficiency and latency period) of Puccinia striiformis f. sp. tritici assessed under warm and cold thermal regimes, allowing comparison of 10 European isolates collected between 2010 and 2020 in Europe with three 'old' reference isolates

description: Phenotypic data corresponding to two aggressiveness components (infection efficiency and latency period) of Puccinia striiformis f. sp. tritici assessed under warm and cold thermal regimes, allowing comparison of 10 European isolates collected between 2010 and 2020 in Europe with three 'old' reference isolates. Related publication: Meyer KJG, Leconte M, Vidal T, Goyeau H, Suffert F. 2024. Is thermal aptitude a pivotal driver in the establishment of recent Puccinia striiformis f. sp. tritici lineages in Europe?  Journal of Plant Pathology / bioRxiv (https://doi.org/10.1101/2023.08.11.552914)
DOI: 10.57745/kh3wrf
title: Supporting data for "Ruminant microbiome data are skewed and unFAIR, undermining their usefulness for sustainable production improvement"

description: In this study, we explored the metadata of microbiome studies from farmed ruminants to determine global representativeness and summarized information according to ruminant species, geographic location, body site, and host information.
DOI: 10.57745/kpfabr
title: Overview of packaging supplier selection

description: Overview of the identification of potential packaging suppliers
DOI: 10.57745/kpqfr6
title: OSO vecteur 2021 - Département de l'Aube

description: Produit vectoriel de l'occupation du sol OSO 2021 sur le département de l'Aube
DOI: 10.57745/kpzjef
title: RAMIFIC Data used by Poirier-Pocovi Magalie

description: The data was collected during the Ramific project in 2017 and was used to produce the results published in the following article: "A new architectural index to statistically compare variations in branching profile of the main stem between rapeseed plants"
DOI: 10.57745/m3pesu
title: Metabarcoding data for diatom samples in "Recommendations for the preservation of environmental samples in diatom metabarcoding studies"

description: Fastq files obtained by metabarcoding of 216 samples from " Baricevic, Chardon et al., 2022. Recommendations for the preservation of environmental samples in diatom metabarcoding studies. MBMG". Metabarcoding was done as follow: A 312 bp fragment of the rbcL chloroplastic gene was amplified from DNA extracts using Takara LA Taq® polymerase and an equimolar mix of the forward primers Diat_rbcL_708F_1, 708F_2, 708F_3 and the reverse primers R3_1, R3_2 (Vasselon et al. 2017a), following the protocol of Chardon et al. (2020). For each DNA sample, a single step PCR ampliﬁcation was performed in triplicate in a ﬁnal volume of 25 μl. After validating PCR amplification, 19 µl of each PCR product per sample were pooled together and 50 µl of this pool were transferred into an individual well of a 96-well microplate. The resulting three plates with 216 samples were sent to “GenoToul Genomics and Transcriptomics” (GeT-PlaGe, Auzeville, France) where library preparation, final library pool and the sequencing with Illumina MiSeq System with paired-end sequencing kit (V2, 250 bp × 2) were performed.
DOI: 10.57745/hhnt10
title: Labeled Temporal Brain Networks

description: Labeled Temporal Brain Networks This dataset contains a collection of temporal brain networks of 100 subjects. Each subject has a label representing their biological sex ("M" for male and "F" for female) and age range (22-25, 26-30,31-35 and 36+). The networks are obtained from resting-state fMRI data from the Human Connectome Project (HCP) and are undirected and weighted. The number of nodes is fixed at 202, instead the edge weights change their values over time. Dataset structure The networks.zip file contains the networks as .txt files in the following format: the first line of each .txt file contains the number of nodes and the number of snapshots of the network divided by a space. The following lines contain the list of edges of the network in the form i,j,t,w, meaning that the edge between node i and node j at time t has weight w. The labels are contained in the file labels.txt, where there are three columns separated by a space, where the first column is the identifier of a subject, the second is the biological sex, and the last is an age range. Acknowledgments Data were provided by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University. The authors are grateful to the OPAL infrastructure from Université Côte d'Azur for providing resources and support. This work has been supported by the French government, through the UCA DS4H Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-17-EURE-0004.
DOI: 10.57745/hm1gxx
title: CTPS

description: CTPS