cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/snrk0v
title: Dataset for the metabolic and physiological characterization of seeds from oilseed rape (Brassica napus L.) plants grown under single or combined effects of drought and clubroot pathogen Plasmodiophora brassicae

description: Faced with the challenges of adapting agriculture to climate change, seed production should have increased resilience to abiotic stress factors and the expected proliferation of pathogens. This concerns both the nutritional quality and seed vigor, two crucial factors in seedling establishment and yield. Both qualities are acquired during seed development, but how environment influences the genetic and physiological determinisms of these qualities remains to be elucidated. With a world production of 71 Mt of seeds per year, oilseed rape (Brassica napus) is the third largest oleaginous crop. But its productivity must cope with several abiotic stresses, among which drought is one of the main constraints in current and future climate scenarios. In addition, clubroot disease, caused by the pathogen Plasmodiophora brassicae, leads to severe yield losses for the Brassica crops worldwide. Clubroot provokes the formation of galls on the infected roots that can restrict the flow of water and nutrients within the plant throughout the growth cycle. In order to get new insights into the impact of single or combined constraints on seed qualities, metabolic profiling assays were run for a collection of 330 seed samples (including developing, mature and imbibed seeds) harvested from plants of two B. napus cultivars (“Express” and “Montego”) that were grown under either drought conditions, the presence of P. brassicae, or a combination of both stresses. Metabolites were identified and quantified by UPLC or GC. In addition, monitoring germination traits was conducted for 60 mature seed lots under in vitro conditions using an automated phenotyping platform. The present dataset contains the raw contents for 42 metabolites (nmol.mg-1 of seed dry weight) filtered and analyzed with statistical tests as well as germination speed and percentages. This dataset is available under accession at Data INRAE. These data will contribute to a better understanding of the crosstalk between the plant responses to water deprivation and/or pathogen attack and how it compromises seed quality. A better understanding of the molecular and physiological responses of the seed to (a)biotic stress on a molecular and physiological will be a first step to meet scientific and technological challenges of adapting seeds to their environment.
DOI: 10.15454/rmiejm
title: Experimental data of Series #5, #6 and #7: Backwater rise related to large wood and eventual releases by overtopping

description: These data describe flow level measurements of experimental runs introducing mixtures of logs in a flume closed by a flexible barrier. For every measurement, water discharge (Q, l/s), flow depth (h, mm) were measured. flume slope (S, %), barrier height (z2, mm), flow depth computed without LW (h0, mm) and total mixture solid volume (Vlw.tot, m3) are given. Each run is labeled by its mixture code, supply mode and repetition index (a, b and c), e.g., "3B(1:7)b" refers to the run with mixture 3B, supply mode 1:7, second repetition. Three Series of experiments are presented: -Series 5 used a low barrier with a height z2=50 mm, releases of large wood were weighted and the equivalent solid volume (Vlw.out, m3) was computed assuming a mean log density of 770 kg/m3. The slope was 2%. -Series 6 used a higher barrier with a height z2=100 mm, no releases were observed. The slope was 2%. -Series 7 used the same higher barrier and shows runs with slope of 4% and 6%.
DOI: 10.15454/s1t0oa
title: RPG complété 2019 département 26

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 26. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/sblx2c
title: Botanical survey in wooded and herbaceous semi-natural habitats

description: The aim was to assess the difference in plant communities in three types of wooded and herbaceous habitats (permanent grassland,hedgerow and forest edge). Plants were surveyed in each of these habitats,in 30 landscapes selected according to a gradient of % of woodland. Botanical surveys were conducted in May and June 2016 in forest edges and hedgerows,and in April and May 2015 and May and June 2016 in permanent grasslands. The surveys comprised abundance-dominance records of all vascular plant species according to the Braun-Blanquet scale in three vegetation layers (herbaceous:0–1 m,shrubs:1–3 m and trees:&gt; 3 m). Data were collected along a 25-m transect on each side of the hedgerows,on a 50-m transect along the forest edges,and wandering freely in grasslands.
DOI: 10.15454/sxka8i
title: Data supplementing the article “Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers” - raw data

description: These data supplement the article “Aquatic biofilms as passive environmental DNA samplers: application to benthic macroinvertebrate communities in rivers” Sinziana F. Rivera, Valentin Vasselon, Nathalie Mary, Olivier Monnier, Fréderic Rimet & Agnès Bouchez submitted to “Molecular Ecology Resources” journal.------------------ The directory is composed of: “38_samples_fastq:files”: contains raw demultiplexed fastq files (R1. fastq and R2. fastq) for each of the 38 samples used in this study to produce OTUs and taxonomic inventories.----------------------------- “Samples id.xlsx”: contains the samples ID of the fastq files---------------------------- “Inventories.xlsx”: contains single and multi-habitat morphological inventories as well as molecular inventories resulting from the study
DOI: 10.15454/pxde4k
title: Habitat choice versus habitat transformation in a nest-building species: which matters most?

description: Animals of many species lay their eggs in nests built to provide their offspring a suitable microhabitat during a critical phase of development. Nest characteristics result from two processes: habitat choice and modification that may impact differently nest suitability for eggs. This field-based study aimed to estimate their independent effects and their interaction effects on the suitability of sea lamprey nests in retaining eggs. Physical variables linked to both habitat choice and habitat modification affected nest suitability but higher effect sizes indicated the prevalence of habitat modification. The most retentive nests were built on habitats with slower current (habitat choice) and had steeper slope between the deepest part of the nest (pit) and the downstream mound (habitat modification); the positive effect of the steep slope increasing with flow velocity in the nest. Our results show that habitat choice and habitat modification must be taken into account in evolutionary or conservation studies that analyse nest building animals. This data compiles the code + datasets used for the analysis.
DOI: 10.15454/q4butz
title: Effects of plant functional group removal on structure and function of soil communities across contrasting ecosystems

description: We used a biodiversity manipulation experiment that has been running for 19 years across a chronosequence consisting of 30 forested islands in two adjacent lakes in the boreal zone of northern Sweden This experiment involves a full factorial combination of three different plant functional group removals (8 treatments in total) i.e., tree root removal (performed by root trenching), ericaceous shrub removal (performed manually), and feather moss removal (performed manually) This dataset includes five sheets: PLFA = Measure of PLFA markers + bacterial and fungal biomasses (nmol g-1) Nematode = Nematode biomass (ind g-1) and trophic community composition Metabarcoding= OTU count FungalAssignation = Assignation of eah OTU to a fungal guild EnvVar = Plant biomass and soil abiotic factors + outputs variables (i.e., decomposition rates + SIR + NMR) All the details are provided in the sheet Information
DOI: 10.15454/qr1xms
title: Survey on Legumes in Institutional Food Services

description: French and English versions of a survey built to collect data and information on the practices, brakes and levers regarding the use of legumes in French institutional food services (catering sector). The legumes consider are: pulses (lentils, beans, chickpeas, split peas, beans, faba beans) and soybeans. The survey was addressed to Central or on-site kitchens (chefs, kitchen managers, purchasing or nutrition managers) during spring-summer 2019. Near 400 complete answers were collected and are available on request.
DOI: 10.15454/rzkkwg
title: Annotation data about Multi Criteria Assessment Methods used in Social Science, Agriculture and Food, Rural Development and Environment : the French National Institute for Agricultural Research (INRA-SAE2) experience

description: This data article contains annotation data characterizing Multi Criteria Assessment Methods proposed in the scientific literature by INRA researchers belonging to the Social Science, Agriculture and Food, Rural Development and Environment department. Those researchs aim to on the one hand, to understand the functioning and social and economic developments of agriculture, food processing industries, agribusinesses, food with close links to local and global environmental stakes, and on the other hand, to shed light on public debates and public and private decisions.
DOI: 10.15454/skhgkz
title: Horses form cross-modal representations of adults and children

description: Data analysed in the the article 'Horses form cross-modal representations of adults and children' submitted for publication in the journal Animal Cognition
DOI: 10.15454/svdtou
title: Statistiques spatio-temporelles sur les propriétés agronomiques des sols agricoles en France issues de la Base de Données d'Analyses de Terre (BDAT)

description: In France, farmers commission about 250,000 soil-testing analyses per year to assist them managing soil fertility. The number and diversity of origin of the samples make these analyses an interesting and original information source regarding cultivated topsoil variability. Moreover, these analyses relate to several parameters strongly influenced by human activity (macronutrient contents, pH...), for which existing cartographic information is not very relevant. Compiling the results of these analyses into a database makes it possible to re-use these data within both a national and temporal framework. A database compilation relating to data collected over the period 1990-2014 has been recently achieved. So far, commercial soil-testing laboratories approved by the Ministry of Agriculture have provided analytical results from more than 3,600,000 samples. After the initial quality control stage, analytical results from more than 1,900,000 samples were available in the database. The anonymity of the landholders seeking soil analyses is perfectly preserved, as the only identifying information stored is the location of the nearest administrative city to the sample site. We present in this dataset a set of statistical parameters of the spatial distributions for several agronomic soil properties. These statistical parameters are calculated for 4 different nested spatial entities (administrative areas: e.g. regions, departments, counties and agricultural areas) and for 5 time periods (1990-1994, 1995-1999, 2000-2004, 2005-2009, 2010-2014). Two kinds of agronomic soil properties are available: the first one correspond to the quantitative variables like the organic carbon content, and the second one corresponds to the qualitative variables like the texture class. For each spatial unit and temporal period, we calculated the following statistics sets: the first set is calculated for the quantitative variables and corresponds to the number of samples, the mean, the standard deviation and, the 2-,4-,10-quantiles; the second set is calculated for the qualitative variables and corresponds to the number of samples, the value of the dominant class, the number of samples of the dominant class, the second dominant class, the number of samples of the second dominant class.
DOI: 10.15454/tdivwk
title: NMR spectra of plasma, liver and muscle of rainbow trout fed a plant-based diet supplemented with spirulina

description: Representative 500 MHz 1H-NMR spectra of plasma and polar extracts of liver and muscle of rainbow trout fed a plant-based diet supplemented with 0% (PB) and 15% spirulina (SPI-15).
DOI: 10.15454/qcj6sw
title: CIRM-BIA : Plan de Gestion des Données

description: Plan de Gestion des Données du CIRM-BIA (Bactéries d'Intérêt Alimentaire.)
DOI: 10.15454/somfsu
title: A ready-to-use database for mothur: Diat.barcode_rbcL_263bp_mothur based on Diat.barcode v9

description: Ready to use database adapted from Diat.barcode v9 for MOTHUR
DOI: 10.15454/t090gw
title: Plan de gestion des données de l'Unité Expérimentale Forêt Pierroton (PGD UEFP)

description: Plan de gestion des données de l'Unité Expérimentale Forêt Pierroton (PGD UEFP) L'UEFP est une unité expérimentale de l’Institut National de la Recherche pour l'Agriculture l'Alimentation et l'Environnement (INRAE), rattachée au département ECODIV (Ecologie et Diversité) (https://doi.org/10.15454/1.5483264699193726E12). Elle constitue un support aux recherches menées sur les écosystèmes forestiers. L'UEFP génère une grande quantité de données, de nature variée et ayant une grande importance patrimoniale. Ces données sont organisées dans différents systèmes d'information. Vous pouvez citer le DOI de ce PGD UEFP.
DOI: 10.15454/tjqv83
title: RPG complété 2019 département 11

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 11. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021
DOI: 10.15454/rzdfor
title: Clustered IMG VR v3 file: IMGVR70

description: How this file was created? All proteins (n=66,585,678) were retrieved from IMG/VR v3 database (https://genome.jgi.doe.gov/portal/IMG_VR/IMG_VR.home.html) version IMG_VR_2020-10-12_5.1 (https://doi.org/10.1093/nar/gkaa946). We used MMseqs2 (https://doi.org/10.1038/nbt.3988) for similarity-based clustering with a threshold of 70% identity (using default greedy mode and 80% reciprocal coverage of target and query). We then extracted one representative sequence per cluster (n=16,555,061) to build the IMGVR70.fa file.
DOI: 10.15454/sh6vgx
title: RPG complété 2018 département 13

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 13. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/syp4pe
title: CIRCASA DELIVERABLE D2.2: “Assessing barriers and solutions to the implementation of SOC sequestration options”

description: Report on the key barriers and solutions for the implementation of SOC sequestration options across different geographic zones and what knowledge gaps need to be filled to overcome barriers.
DOI: 10.15454/tbgljc
title: Spirulina ingredient composition by 500 and 1000 MHz NMR analysis

description: Analysis of spirulina hydroethanolic extract by liquid 1D and 2D NMR at 500 and 1000 MHz to aid the identification of low molecular weight metabolites/compounds. The spirulina ingredient is a dried biomass of Arthrospira platensis cultivated in autotrophic conditions.
DOI: 10.15454/tveugj
title: Données dendrométriques et phénologiques d'un dispositf de pin maritime et bouleau verruqueux

description: La forêt des Landes étant presque exclusivement composée de peuplements purs, elle est plus vulnérable à des problèmes sanitaires et à des parasites comme la chenille processionnaire du Pin. Une alternative à ce problème pourrait être le mélange d’essences, comme on en trouve sur le dispositif Orphée. Nous nous servirons donc de ce dispositif (plus particulièrement des modalités Pins / Bouleaux / Pin-Bouleaux), pour étudier les effets de l’eau et des mélanges d’essences sur la croissance radiale et l’évolution phénologique des arbres.
DOI: 10.15454/rbu9iz
title: RPG complété 2019 département 73

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 73. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/revp8s
title: RPG complété 2018 département 33

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 33. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/s7p0hg
title: Dataset of an experiment on sheep/cattle mixed-grazing mechanisms

description: This is the dataset of the 'MeMiPat' experiment about the mechanisms of sheep-cattle mixed-grazing. The experiment was conducted in France in 2019-2020 (Auvergne region). The dataset contains data about animal growth, parasitism and grazing behaviour.
DOI: 10.15454/sezg3p
title: Adaptation of Lactobacillus Bulgaricus CIRM-BIA1592 to cow milk versus soymilk environments

description: Lactobacillus Bulgaricus (CIRM-BIA1592) adaptation to cow milk versus soymilk environments was studied thanks to proteomics. Bacteria were harvested at the begining of stationary phase. Protein trypsin digestion were performed in solution. The data set contains 22 files of NanoLC-MS/MS analysis, acquired on a Qexactive mass spectrometer. Design: 2 classes (cow milk:"lait", soymilk: "soja"), 4 biological replicates for cow milk, 3 biological replicates for soymilk. All samples were injected at least 3 times.
DOI: 10.15454/sm6ocr
title: Bioinformatic and statistical scripts to analyze acorn mycobiota structure and composition

description: This dataset contains R-scripts to perform bioinformatic and statistical analysis on acorn associated fungal communities (Fort et al., Maternal effects and environmental filtering shape seed fungal communities in oak trees. Submitted). Bioinformatic script was applied to raw sequences after paired-end sequences were joined using PEAR v0.9.10 (Zhang et al., 2014). Raw sequences are available at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551388. Metadata and ASV tables are also provided allowing to use statistical analysis scripts without running the bioinformatic steps.
DOI: 10.15454/stwmj9
title: Integrated signals calculated from 1H NMR quantitative analysis for PHB and PHBV3% commercial product and PHBV18%

description: Integrated signals calculated from 1H NMR quantitative analysis. 1H NMR spectra of PHB and PHBV copolymers carried out on a Bruker spectrometer Ascend III HD operating at 400 MHz. The 1H NMR spectra were recorded at 25°C, 3 kHz for spectral width, 1600 Hz for transmitter frequency offset, 3 s for acquisition time and 4 scans. Quantitative conditions were obtained with a 30° pulse (3 µs) and a relaxation delay at 1 s (D1). 1H decoupling applied during acquisition (waltz16 with a pulse of 90µs).
DOI: 10.15454/ta2eso
title: French freshwater macroinvertebrates surveys series

description: This dataset contains the observed abundances of different freshwater macroinvertebrates taxa in French streams and rivers, extracted from the national surveys, with IBGN protocol (sampling_method). Macroinvertebrates are described at the family level (Taxon). It covers 305 survey sites (site_ID), from 1992 to 2017. The sites have been selected to match the 2 following criteria: shortest time-serie is 10 years and the smallest number of sample occasions is 8 (sampling_date). Coordinates of sampling points are WGS84 decimal degrees (X_coordinate, Y_coordinate).
DOI: 10.15454/tgaby7
title: Data on migratory fish from the Bresle river (1981 to 2021; Seine-Maritime and Somme county - France)

description: The data consists of data on migratory fish from the Bresle river since 1981 collected for the Environmental Research Observatory (ORE) on Diadromous Fish in Coastal rivers (DiaPFC). ORE DiaPFC is a research infrastructure focused on studying the influence of human-induced and environmental changes (mainly agriculture and climate). The River Bresle is 72 km long and has a mean slope of 0,26%. It drains a basin of 750 km2 and flows north-west through the Normandy-Picardy plateau ending into the English Channel at Le Tréport. It lies within a chalky geological zone and is fed from alluvial deposits. The water quality is generally fair, except for the occasional pollution by chronic agricultural run-offs. The mean flow is 7,3m3/s, with the highest mean flow in February (mean = 9,4 m3/s) and the lowest in September (mean = 6.4 m3/s).
DOI: 10.15454/thncac
title: Hatching-data_Gautier-et-al_FIM

description: Hatching rates of Globodera pallida in native and recolonized soils (A, D, F and J) for each replicate in each modality (dose 1, dose 2 and control).
DOI: 10.15454/trtriy
title: Decision-aiding

description: Tools and presentations for the implementation of a multi-criteria support approach with examples of applications to the case of nature-based solutions (developed within the H2020 NAIAD project). The package includes: - A series of spreadsheets presenting examples of a (hierarchic) multicriteria decision-making model (AHP-like) applied to NBS choice and assessment (developped within the H2020 NAIAD project). - A series of generic spreadsheets which allow to calculate preferences as in AHP method for 2 to 7 criteria (developped within the H2020 NAIAD project) - A practical kit to be used to explain the principles of hierarchic multicriteria decision-making and implement it in an interactive way with decision-makers (developped within the H2020 NAIAD project).
DOI: 10.15454/rymvus
title: Initial root density along intact soil profile (mixed forest, Chamrousse, French Alps)

description: Root density distribution in closed and open forest at Chamrousse, French Alps
DOI: 10.15454/sonfvf
title: Gene expression and genetic divergence oak species highlights adaptive genes to soil water constraints

description: These files includes normalized values for RNAseq data, Fold change Ratio and Gene set enrichment analysis. Supplementary file 8 include Fst value for the differentially expressed genes and their associated effect analysed in the paper entitled "Water stress-associated isolation barriers between two sympatric oak species".
DOI: 10.15454/t6ambc
title: Dataset: Lipids, antioxidants and color of meat from cull-cows

description: This data set presents values of the fatty acids composition and of indicators of lipid oxidation determined in the Longissimus dorsi and Semitendinosus of Normand cull-cows at slaughter (with or without pre-slaughter stress), after muscle ageing and after meat storage periods under different packaging conditions.
DOI: 10.15454/tckbtk
title: Phenology Data - INRAE Colmar - UE 871 AV - BDD PHETEC

description: Ce modèle est défini pour la base de données PHETEC – Grandes cultures. Données d'observation de la phénologie de plusieurs cultures (Maïs, Blé et Orge) observées par l'Unité Expérimentale Agronomique et viticole 871 de Colmar entre les années 2002 et 2010. Les données sont issues des parcelles qui n'ont pas été utilisés pour des expérimentations. Elles sont issus de la base de données Phetec et sont accessibles via le Portal de données TEMPO (https://tempo.pheno.fr/) Le fichier est composé de plusieurs feuilles. Les données de phénologie ont plusieurs métadonnées associées pour aider à leur compréhension.