cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/cfwbaa
title: Données de réplication pour : Agriculture increases the bioavailability of silicon, a beneficial element for crop, in temperate soils

description: These data concern the study 'Agriculture increases the bioavailability of Silicon, a beneficial element for crop, in temperate soils' published in nature communication. This work was performed in the frame of the French ANR BioSiSol project (ANR-14-CE01-0002) and is based on data from the RMQS program (French Soil Quality Monitoring Network). The French Soil Quality Monitoring Network (RMQS) is a national program for the assessment and long-term monitoring of the quality of French soils. This network is based on the monitoring of 2240 sites representative of French soils and their land use. These sites are spread over the whole French territory (metropolitan and overseas) along a systematic square grid of 16 km x 16 km cells. The network covers a broad spectrum of climatic, soil and land-use conditions (croplands, permanent grasslands, woodlands, orchards and vineyards, natural or scarcely anthropogenic land and urban parkland). The physical, chemical and biological properties of the soil are measured on each site. These soil analyses were carried out by the Soil Analysis Laboratory of INRAE (Arras, France). The spatial and temporal variability of soil properties are explained by biophysical variables, sources of contamination, history of land-use and management practices on each plot. The first sampling campaign in metropolitan France took place from 2000 to 2009 and the second campaign has begun in 2016. At each site, 25 core samples were taken by layer with an auger within a 20 m × 20 m plot and combined into a composite sample. Analyses used in this study only concern the surface layer (generally 0–30 cm layer) of samplings from the first campaign in metropolitan France. The analyses of total Si and available Si were made in 2016 on samples stored from the first sampling campaign. The dataset published contains all the raw data used in the statistical analysis in order to make them available for any further study. The table contains soil properties (total and available Si, particle size fraction, organic carbon content ...), observations about soil and land use, and spatial coordinates. We warn the user that coordinates published here are theoretical coordinates, the RMQS site can be located until 1 km around this point. Real coordinates can not be made publicly available because of confidential information.
DOI: 10.15454/cyablu
title: Supplemental Dataset S1 - Holstein cow dimensions

description: This dataset contains the dimensions of 307 Holstein cow. All dimensions, measured with a rod, are expressed in cm. The dataset contains four columns: Height (for height at withers); Length(for diagonal body length); Width_should (for width at shoulder); Width_belly (for width at belly).
DOI: 10.15454/f7cavn
title: Consumer home practices related with infant food safety in France

description: Online survey among a panel of 1,304 French citizens on home practices concerning four store-bought infant foods (powdered infant formula, sterilized vegetable mixed with fish, infant cereals, fruit puree), in relation to infant food safety. The survey is composed of 50 individual questions. The survey was designed using the Limesurvey tool. It was then launched in June 2021 by the Crowdpanel polling company in order to ensure a representative sample of the French population. Answers to the survey are provided in csv format.
DOI: 10.15454/bbc2ri
title: RPG complété 2019 département 59

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 59. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/bmh6ym
title: RPG complété 2018 département 05

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 05. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/d2toav
title: Données des performances d'élevage des porcs à l'engraissement plein air de 2017 à 2020 de l'Installation Expérimentale ASTER Mirecourt

description: L’installation expérimentale est une exploitation de 240ha en agriculture biologique depuis 2004 sur laquelle est conduite une expérimentation-système à l’échelle de la ferme. Un système de polyculture-polyélevage y est conçu dans une logique d'autonomie et d'économie de gamme en priorisant un usage des terres à destination de l’alimentation humaine. Le projet sur l’installation expérimentale articule (i) la conception-évaluation d’un système basé sur la diversification des productions animales (bovins, ovins et porcins) et végétales (prairies et cultures annuelles telles que le blé meunier, l’avoine, lentilles colza, tournesol, cameline) raisonnées en complémentarités à l’échelle de l’ensemble de la ferme et (ii) des conduites d’élevage innovantes : (i) élevage d’un troupeau d’une centaine de vaches laitières en monotraite alimentées exclusivement à base d’herbe (pâturage et foins) et dont les veaux femelles sont élevés sous vaches nourrices, (ii) une troupe d’environ 130 brebis et agnelles conduites en plein air intégral et complémentarité avec le troupeau bovin (pâturage mixte ovins-bovins au printemps, pâturages des prairies peu portantes l’hiver et des couverts intermédiaires en été). Une troupe d’une trentaine de porcs par an élevés en pâturage sur luzerne assure le rôle de détritivore de l’ensemble du système via la valorisation des productions non commercialisables (issus de tri, lait colostral). L’expérimentation système est conduite selon une démarche de conception « pas à pas » où une place importante est donnée à l’acquisition d’expérience dans l’action par les expérimentateurs. Ces deux caractéristiques, échelle ferme entière et conception “pas à pas”, font de l’installation expérimentale de Mirecourt un lieu où savoirs et expériences issus de la pratique ont une place importante. Les données des performances de l’atelier porc proviennent des données recueillies lors des années 2017 à 2020 soit 5 troupes sur l'atelier porcin. Elles concernent des données de croissance, de conduite mais également de qualité de viande.
DOI: 10.15454/dd9j5t
title: Data from: Consistent functional clusters explain the effects of biodiversity on ecosystem productivity in a long-term experiment

description: R-codes used in the paper "Consistent functional clusters explain the effects of biodiversity on ecosystem productivity in a long-term experiment", by Benoît Jaillard, Philippe Deleporte, Forest Isbell, Michel Loreau and Cyrille Violle, published in Ecology, 2021, and copy of the R-package functClust. The R-codes used in the paper published in Ecology must be run in the order: "1.format.R", "2.fclust.R", "3.ftest.R", then "4.fboot.R". The file "io.R" and the package "functClust" should be previously installed. The package functClust presents a method for clustering components belonging to an interactive system for their effects on an emergent, systemic performance. The package contains four main functions: (i) fclust, that fits a tree of components to observed assemblage performances; (ii) fclust_plot, that plots the results obtained using the function fclust; (iii) fclust_write and fclust_read, that save and load the results obtained using the function fclust.
DOI: 10.15454/dyncen
title: Milk microfiltration operation experimental data annotated from the scientific litterature including controlled parameters

description: This dataset comprises 934 milk microfiltration operation experimental data annotated from the scientific litterature including controlled parameters (Volume Reduction factor, VRF, Transmembrane Pressure, TMP, Permeation flux, Jp, …). It has been used to learn a Bayesian Network linking those variables.
DOI: 10.15454/eb1bak
title: RPG complété 2018 département 35

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 35. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/ffwe8q
title: Replication data for Bergès et al. Submitted to PLOS ONE

description: Data from Sandy Bergès PhD thesis used in Bergès et al. (submitted to PLOS ONE). Experiments performed in PHENOPSIS (C2M44 and C2M45).
DOI: 10.15454/bmliqi
title: Carabid beetles have hump-shaped responses to disturbance and resource gradients within agricultural landscapes - Dataset

description: Data from the project SEBIOPAG-PHYTO to analyse effects of cropping systems on carabid distributions within agricultural landscapes
DOI: 10.15454/cxgqwc
title: Membrane processes for the concentration of VFAs occurring in effluents of biotechnological acidogenic processes

description: Relatively scarce VFA concentration in actual fermentation broths hinders their potential exploitation as bio-based substrates. Nanofiltration and reverse osmosis approaches can represent suitable solutions for the concentration of VFAs; thus, dedicated NF and RO membrane-based cross-flow filtration was applied by laboratory pilot-scale plant with the aim of getting scalable results for preliminary feasibility evaluation studies. Experiments dedicated to the obtainment of robust evidences about the role and optimal values of main process parameters were carried out under total recirculation and concentration mode, using multicomponent solutions and different spiral wound membranes. The role of main process parameters (P, pH, membrane type) on process performances has been studied. Furthermore, the collected data was used to develop a semi-empirical model describing the mass transfer of the single VFAs. Finally, process design cases have been evaluated. Scalable experimental data was collected during operational parameter screening, which allowed defining pH as a key process parameter. The screening was followed by the development of a semiempirical model useful for NF/RO process design and simulation. Indeed, the model was used as to evaluate the concentration performances when utilizing (A) only RO modules or (B) RO + NF modules. Best overall economic performances were observed for the latter process configuration.
DOI: 10.15454/daaup1
title: R ressources improve dendrograms

description: R programms to improve dendrogram drawing
DOI: 10.15454/dk0b4k
title: Production and stabilization of highly concentrated cultures of Ligilactobacillus salivarius from the scientific literature, including experimental manufacturing conditions and survival rates.

description: This dataset comprises experimental data gathered from 17 scientific articles, including different strains of this lactic acid bacteria, manufacturing scale (laboratory or pilot), fermentation conditions (medium composition, temperature, pH value and neutralizing solution for controlled pH, harvesting time), cooling and concentration conditions (temperature, speed, time,), composition of protective solutions, stabilization operating conditions (freezing and or drying), storage conditions (temperature and time). Survival rates (and functionality when available) at different steps of the production process are also included. This dataset has been used to discuss on the principal issues and future research challenges for improving the production and long-term preservation at the industrial scale of L. salivarius, and probably of other probiotics
DOI: 10.15454/ek58pi
title: RPG complété 2018 département 18

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 18. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020
DOI: 10.15454/bdnct2
title: Transcriptomic analysis of Faecalibacterium prausnitzii A2-165 grown in acetate poor vs rich conditions

description: The bacterial strain Faecalibacterium prausnitzii (DSM No. 17677, DSMZ collection, Braunschweig, Germany) was cultured under anaerobic conditions (anaerobic chamber: N2 = 90%, CO2 = 5% and H2 = 5%) at 37°C, in brain heart infusion broth (BHI, 37g/L, Difco) supplemented with yeast-extract (5g/L, Difco) cellobiose (1mg/mL, Sigma), maltose (1 mg/mL, Sigma) and cysteine (0.5 mg/mL, Sigma), namely the BHIS medium. The strain was defrosted and cultivated at a 10% inoculation in 10 mL BHIS for 24 hours at 37°C, followed by a 1% inoculation in 10mL BHIS for overnight growth (16-18 hours). The experimental cultures were then made at 2% inoculation in 50 mL BHIS medium with or without supplemented sodium-acetate solution (20 mM, Sigma, (10, 11)), namely the BHISA medium, at the time of inoculation.
DOI: 10.15454/cgwvah
title: Tree diversity and density affect damage caused by the invasive pest Cameraria ohridella in urban areas

description: Dataset, supplementary tables and R code of the preprint "Tree diversity and density affect damage caused by the invasive pest Cameraria ohridella in urban areas".
DOI: 10.15454/chmtkh
title: RPG complété 2018 département 14

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 14. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/dcvdzn
title: Dataset of an experimental evolution on the effect of fungicide-resistance composition of populations on the durability of anti-resistance strategies on the wheat pathogen Zymoseptoria tritici

description: Data and R scripts supporting the analysis of both the qualitative and quantitative evolution, through experimental evolution, of fungicides resistances within three different population of distinct composition. The population genetics, population size and resistance phenotypic profiles were considered to bring new insights for the management of resistance (in particular mlultiple resistance) through selection pressure diversity, in front of various population composition. Also, some additional analysis on mfs1 expression were carried out to potentially explain some resistance phenotypic profile (enhanced efflux)
DOI: 10.15454/dwb4ut
title: CNVMaize Indels Affymetrix Axiom Array

description: These three datasets describe the content of Indel Affymetrix Axiom array corresponding to the publication "High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® Axiom® array " of Mabire, Duarte et al., 2019. The Affymetrix Axiom array contain 105,927 Indels interogated by 662,772 probes.
DOI: 10.15454/eb8yxf
title: Vegetation, browsing and hunting survey data on GNB plots.

description: Vascular vegetation and bryophyte monitoring data, ungulate browsing and associated hunting data on GNB plots, for the publication "Effects of stand structure and ungulates on understory vegetation in managed and unmanaged forest" in Ecological Applications.
DOI: 10.15454/cstxu2
title: M. incognita candidate effector proteins

description: Accession numbers of M. incognita candidate effectors. These proteins are predicted to be secreted based on the presence of a signal peptide for secretion and absence of transmembrane domains. Furthermore at least one motif known to be enriched in effector proteins is present in the 100 first amino acids. A separate subset of those specific to plant-parasitic nematode species is also provided.
DOI: 10.15454/dc9pyl
title: Consumer perception data about food packaging functionalities for fresh strawberries - Plastic rigid lid consumers’ arguments
DOI: 10.15454/dmywpb
title: Données lidar acquises par drone au pied du Pic St Loup (34)

description: Acquisitions Lidar par drones sur la commune de Cazevielle, au pied du Pic-St-Loup (34). Survol financé par le Projet SenthyMed , CNES. Acquisition les 23 et 25 juin 2021. Télépilotes unité TETIS, Montpellier : Samuel Alleaume : samuel.alleaume@inrae.fr Audrey Jolivot : audrey.jolivot@cirad.fr . Capteur : Yellowscan, Surveyor • Centrale GNSS-inertielle : Applanix APX-15 UAV • Lidar : Velodyne VLP16 (Puck) : Longueur d’onde:905 nm / 300 000 pulses par seconde (300 kHz) / 2 échos par pulse / Angle de vue : 360 deg • Précision : 4cm Vecteur : drone DJI Matrice 600 Pro 4 zones couvertes d'une quinzaine d'hectares. Densité de point de 200 à 250 point par m2.
DOI: 10.15454/dsfc9q
title: Comparative shelf-life study on falafel and fresh beef

description: Comparative shelf-life study on falafel: PHBV tray vs reference material Comparative shelf-life study on fresh beef: PHBV tray vs reference material
DOI: 10.15454/dw23pe
title: Supplementary table 1 - Yu et al., 2021, Journal of Dairy Science

description: Supplementary table 1 - Yu et al., 2021, Journal of Dairy Science Title : Semi-industrial production of a native and microbiologically safe infant formula powder using membrane filtration
DOI: 10.15454/enhraw
title: Plan de Gestion de Données de la plateforme PHENOBOIS

description: Ce dataset contient le Plan de Gestion de Données de la plateforme PHENOBOIS.
DOI: 10.15454/fgrkay
title: Emergence dates observed along an altitudinal transect in Mont Ventoux, France, for the pine processionary moth between 1970 and 1984

description: The dataset provides the date of procession in situ and the date of emergence in a common garden for caterpillars sampled in 6 sites located along an altitudinal gradient in Mont Ventoux, France, for the pine processionary moth Thaumetopoea pityocampa. The experimental protocol was followed yearly between 1970 and 1984. Due to prolonged diapause, some of the individuals emerged up to 4 years after field sampling.
DOI: 10.15454/fifrqo
title: Community and environmental data of field competition-dispersal experiment RNN Cousseau

description: Plant community and environmental data from the field competition-dispersal experiment in Molinia caerulea wet meadow (National Nature Reserve of Etang de Cousseau)
DOI: 10.15454/c8ipii
title: Tree architecture, canopy shape, vegetation indices and canopy surface temperature related traits in response to soil drying in an apple tree core-collection

description: This dataset comes from a core-collection of 241 apple tree varieties mostly consisting of French local or old dessert apple varieties. The collection was assessed in 2017 in the field (4-years old trees), with four trees per variety. In July 2017, irrigation was withheld for two trees per variety, while the two other trees were maintained well-irrigated. Airborne imaging (thermal and multispectral) was deployed at four dates during the month of July (on 5th, 12th, 17th and 27th July). Vegetation indices (NDVI, GNDVI, MCARI2) were calculated from multispectral images. Mean canopy surface temperature (TS) was computed from thermal images, and differences between canopy surface and air temperature (TSTA) were then calculated to account for potential climate variations between dates. Two measurement campaigns were performed with a T-LiDAR scanner: one in October 2017 on leafy trees, and one in February 2018. Summer variables provided information on the canopy shape: alpha hull volume (a_volume), convex hull volume (c_volume) and plant height (height). c_volume represents the maximal space occupation of the tree, whereas a_volume represents the volume filled by leaves within this convex hull. For assessing light interception variables, we computed the STAR (Silhouette to Total Leaf Area Ratio). Finally, a convexity index (ci) correlated with STAR was computed as the ratio a_volume/c_volume. Winter scans were used to estimate tree architecture-related variables: the number of axes (nb_axes) and the total cumulative axis length (total_length) per tree. Along with genotypic data (https://doi.org/10.15454/F5XIVJ), this dataset was used to perform GWAS to detect SNPs associated with tree architecture, light interception and canopy surface temperature with the ultimate goal of assessing to which extent these architectural and functional traits do or do not share a common genetic origin (Coupel-Ledru et al., 2022). All methods regarding images and scans processing can be found in: Coupel-Ledru et al., 2019 Hort Res, DOI : 10.1038/s41438-019-0137-3 ; Pallas et al., 2020 Acta Hort, DOI: 10.17660/ActaHortic.2020.1281.82 ; Coupel-Ledru et al. 2022 New Phyt (in press).
DOI: 10.15454/cucg3s
title: RPG complété 2019 département 10

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 10. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021
DOI: 10.15454/dpill6
title: Do non-native plants affect terrestrial arthropods in the sub-Antarctic Kerguelen Islands?

description: Abundances of arthropods collected in pitfall traps and in yellow pans within vegetation dominated by either native plant species or non-native plant species in Kerguelen archipelago during the summer 2017-2018
DOI: 10.15454/e3sapw
title: Ecopics Plots and Map

description: Map of altitudinal bands and GPS coordinates of field sites at Massif de Belledonne, France
DOI: 10.15454/e6yrkx
title: Screening of phytophagous and xylophagous insects guts microbiota abilities to degrade lignocellulose in bioreactor - raw sequencing reads

description: Raw Illumina MiSeq sequencing reads (paired) for Screening of phytophagous and xylophagous insects guts microbiota abilities to degrade lignocellulose in bioreactor. Names used correspond to the publication. 5 insects were used for screening : Beetle, Chafer, Cockroach, Cricket and Locust, with 4 samples each. Initial barial content (T0), end composition with blank reactor (BR) without lignocellulosic substrate, and end composition (2 biological replicates) of a wheat-straw reactor (WSR1 and WSR2). 3 insects were used for fed-batch reactors : Chafer, Cockroach and Locust. Samples are available for blank reactors (BR) and wheat straw reactors (WS) at different time points : initial reactor content (T0a and T0b for WS replicates, T0 for BR) and end content of each fed-batch cycles (SBR-Na and SBR-Nb for WS replicates, SBR-N for BR).
DOI: 10.15454/edikcu
title: Data for "Realised genetic gains on growth, survival, feed conversion ratio and quality traits after ten generations of multi-trait selection in rainbow trout Oncorhynchus mykiss, fed a standard diet or a “future” fish-free and soy-free diet."

description: This dataset contains growth, body composition (including fatty acids profile), survival, processing yields and feed efficiency data of an experiment comparing selected (Generation 10) and unselected (Generation 0) rainbow trout from the breeding programme of "les Sources de l'Avance (Aqualande group, France). These two fish lines are compared with two different feeds in a 2x2 factorial design. The Standard feed is the industry standard, produced by Aqualia (France). The Future feed is a feed free of fishmeal, fish oil and soy products, produced by INRAE NuMeA (Donzacq, France)
DOI: 10.15454/cos00o
title: Crosscut matching

description: Crosscut est un ensemble de scripts python et R pour faire l'appariement entre les simulations ADAMONT de la neige adaptées aux pratiques de gestion du manteau neigeux en station de sports d'hiver. Elle a été développée dans le cadre des travaux partagés entre l'INRAE et Météo France et consolidée à l'issue des travaux de thèse de P. Spandre et elle est utilisée dans le cadre du service ClimSnow (TM). -- Crosscut is a set of python and R scripts to match ADAMONT snow simulations adapted to snowpack management practices in ski areas. It was developed in the framework of shared work between INRAE and Météo France and consolidated at the end of P. Spandre's PhD work and is used in the ClimSnow (TM) service.