cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/hnv8v0
title: Deliverable D3.1 Assessment Indicators - Baseline - CS-Aut

description: This file is part of the deliverable D3.1 of the European H2020 FAIRCHAIN. It structures all the data relevant for the description of the initial value chain (baseline) of the case study in Austria (CS-Aut). The description of the baseline covers the dimensions of co-creation business models and sustainability including environmental, economic and social perspectives.
DOI: 10.57745/hzgcc1
title: DATASET - Biogeomorphic assessment of stable natural streambank structures in the Alps

description: This dataset comprises the data gathered in the field for Juliette Rousset's PhD thesis. It encompasses all the measured and observed variables during the field campaign in June 2022, which aims to describe the biogeomorphological components of natural vegetation-stabilised streambanks in the Alps. The 21 sites visited in the Massif de la Vanoise were characterised by topographic surveys (cross section and slope), granulometric surveys and vegetation surveys.
DOI: 10.57745/fchsnr
title: Data from: Increasing landscape heterogeneity as a win-win solution to manage trade-offs in biological control of crop and woodland pests

description: Datasets synthetise the data collected in the MUESLI project and are separated according to the ecosystems in which they were collected. The project was about biological pest control assesssement in cereal fields and woodlands and biodiversity. R script is also provided, it corresponds to statistical analyses used on previous datasets and presented in the article.
DOI: 10.57745/gfnmas
title: SEIBIOTE healthy subjects

description: Abstract
DOI: 10.57745/glmvcd
title: Essential genes of Salmonella Typhimurium grown on tryptone soy agar

description: File presenting the genes and insertions considered to be essential or non-essential or to give a growth advantage or disadvantage for Salmonella Typhimurium. These data were obtained with a saturated Tn-Seq library grown on tryptone soy agar containing kanamycin at 50 micrograms per milliliter. Two files are available for chromosomal data and two others for plasmid virulence data (information for insertions and for genes). These analyzes were obtained with TRANSIT software (V3.2.0)
DOI: 10.57745/fa9dra
title: XyloDensMap: a georeferenced dataset for the wood density of 110,000 trees from 156 European species in France

description: The XyloDensMap collaboration has assembled a dataset of 110,763 individual tree records of wood density from 156 species, across a broad range of ecological conditions in France, reflecting a large set of European climates. Data include the measurement of the average anhydrous wood density (mass of dry wood divided by the dry volume) and an estimate of the basic wood density (mass of dry wood divided by the green volume, estimated using volumetric shrinkage coefficients gathered from a literature review) of radial wood cores extracted from tree stem at a conventional breast height on 20,697 forest plots of the French National Forest Inventory (NFI). Additional information on stand’s geographical position, climatic conditions, tree age, height and circumference at stem breast height are provided. Further, wood shrinkage has been measured around one spatially systematic fraction (1/4th) of the collected cores, providing data for further refined modelling of this shrinkage, in addition to reference values available in the literature. The dataset is composed of three comma-separated files, one R code, and one metadata file. 1. The first file (xdm_individual_density_data.csv) provides tree- or stand-level information for each of the 110,763 increment cores, along with the corresponding mean anhydrous wood density (WD0), weighted mean anhydrous wood density (WD0w), mean basic wood density (WDb), weighted mean basic wood density (WDbw) and the wood volumetric shrinkage (WS) used to convert anhydrous into basic wood density. Missing values are denoted by NA. 2. The second file (xdm_species_density_data.csv) provides statistics at species level for the mean weighted basic wood density (WDbw). 3. The third file (xdm_individual_shrinkage_data.csv) provides the wood volumetric shrinkage measured on a subset of 23,828 wood cores. These values can be used as an alternative to the default literature shrinkage values used to estimate the basic wood density, either by estimating volumetric shrinkage means by tree species (see example in the fourth file), or by a more sophisticated modelling approach taking into account individual tree or core attributes. 4. The fourth file (xdm_R_import_and_manipulate_data.R) is an R code designed to guide the user through data import and manipulation, with examples of data operations and visualizations, a theoretical example of biomass calculation using the species wood density means provided in the second file, and an example of recalculation of the basic wood density using the shrinkage values contained in the third file instead of the shrinkage values of the literature. 5. The fifth file (xdm_metadata.txt) is a metadata file containing all definitions and units for each table and each variable.
DOI: 10.57745/gsmefn
title: Phobos orbital measurement using MARSIS data

description: This dataset is composed of MARSIS measurements of Phobos's position. It combines the two tables present in Desage et al. (2024) paper on this subject. This data can be used as control points for Phobos' orbitography.
DOI: 10.57745/gvl2ee
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overview We built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels. This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota. Materials and Methods Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230) The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al. Metagenomic assembly Metagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed. Non-redundant gene catalog Genes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded. Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details). Functionnal annotation KEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database) Metagenomic Species Using the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered. Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles. Taxonomic annotation of Metagenomic Species MGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if &gt; 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
DOI: 10.57745/h8cbg1
title: Responses of the hyper-diverse community of canopy-dwelling Hymenoptera to oak decline

description: This dataset contains the R scripts and both the database of Hymenoptera taxa traits and the database of plot and stand characteristics used for the article "Responses of the hyper-diverse community of canopy-dwelling Hymenoptera to oak decline". The article is currently published in the peer-reviewed journal "Insect Conservation and Diversity". During the CANOPEE project, the P2E and INRAE EFNO teams sampled canopy-dwelling Hymenoptera in three oak-dominated forests in France (Orléans, Marcenat and Vierzon). Various types of traps (green multi-funnel and flight interception traps) were suspended in the canopy (above 10-15 m) of oak trees from April to September 2019. Collected Hymenoptera were sorted at the family or subfamily level by the P2E team and then identified to the lowest taxonomic level (species, morphospecies or genus) by specialist identifiers (listed as contributors). The analyses of the responses of Hymenoptera communities to oak decline were performed by Elodie Le Souchu and Jérémy Cours, and Aurélien Sallé supervised the work.
DOI: 10.57745/hmqvcs
title: Transcriptomic, Proteomic and Metabolic data of Gammarus fossarum

description: Metabolic pathways are targets of environmental contaminants throughout biodiversity. However, due to the lack of available genomic data in many environmental sentinel species, the systematic reconstruction of their metabolic pathways remains limited. It is thus essential to gain a better picture of the metabolism of sentinel species in order to improve our understanding of pollution impacts on the ecosystems. In this study, we used a multi-omics approach to reconstruct the metabolic network of Gammarus fossarum and map the main metabolic pathways expressed in the cephalon, gills, caeca, intestines and male and female gonads. We performed a de novo assembly of RNA-seq data from a previous study and acquired new shotgun proteomic data from male and female G. fossarum organs. The new transcriptome assembly reduced RNA contaminants and transcript redundancy allowing the adaptation of the genomic tool CycADS for metabolic pathway reconstruction to the transcriptomic data. Additionally, we integrated proteomic data and analyzed the expression profile in organs to identify organ-specific metabolic profiles. This dataset contains the de novo transcriptome assembly, proteomic and functional annotation data for Gammarus fossarum, together with the reconstructed metabolic networks of the GamfoCyc metabolic database (available in the ArthropodaCyc collection) and integrated mass spectrometry data.
DOI: 10.57745/jkrwyo
title: Questionnaire pour mener un retour d'expérience sur les impacts d'une inondation auprès d'agriculteurs

description: Ce questionnaire a été élaboré par l'équipe de l'observatoire so-ii suite à l'inondation du 19 septembre 2020 sur le territoire d'étude de so-ii (bassin versant du Lez et Bassin de l'Or, département de l'Hérault). Les enquêteurs ont réalisé les entretiens avec chaque agriculteur en face à face. L'outil utilisé par les enquêteurs est le logiciel limesurvey (fichier .lss du questionnaire). Pour sa diffusion, nous avons également publié une version en ligne à : https://sondages.inrae.fr/index.php/756321?lang=fr. À noter que la version actuelle du questionnaire n'est pas activable sur la plateforme sondages INRAE en raison de sa taille. Nous recommandons de l'utiliser sur un serveur en local permettant de l'activer et de l'utiliser en mode hors ligne. Une version adaptée à sondages INRAE est à venir. Cette étude s'inscrit dans la Tâche d'Observation REX de so-ii. Plus d'informations à : http://so-ii.org/to-rex/ Pour toute question, n'hésitez à nous contacter à : so-ii@so-ii.org
DOI: 10.57745/jmbuzk
title: Data from: Environmental filtering and landscape composition drive multifaceted diversity of bird assemblages in vineyards

description: Bird assemblages observed during the springs of 2013, 2014 and 2015 in vineyard plots in Burgundy (France). These plots were located in a landscape gradient comprising more or less semi-natural environments. Each row in the dataset represents one plot one year. Columns C to BA contain the abundances of bird species identified by their abbreviated scientific name. Column BB is plot area (m2). Columns BC and BD contain within plot proportions of woodland and shrubland. Columns BE to BI contain proportions of respective landscape elements within 1000m.
DOI: 10.57745/l0fljd
title: Genome-wide genotyping data renew knowledge on genetic diversity of a worldwide alfalfa collection and give insights on genetic control of phenology traits

description: The dataset is composed with 400 cultivated accessions (378 cultivars and 22 landraces) whose fall (autumn) dormancy was mainly between 3 and 7 on a 1-11 scale. Their origin, based on the place they have been collected (landraces) or initially selected and registered (cultivars) was Europe (318 accessions), North America (45 accessions), South America (16 accessions), China (17 accessions), Middle East (3 accessions) and Japan (1 accession). In addition, 617 accessions representing advanced breeding material obtained by five European breeders were included. All the 1017 accessions were genotyped and used for genetic structure study while only the 400 ‘cultivated accessions’ were phenotyped for phenology and used for GWAS and GS studies. All accessions have been coded by a unique identifier (EUCLEG_ID) with the format: EUC_MS_xxxx, EUC referring to the EU project EUCLEG (H2020, N°737212, 2017-2021), MS to Medicago sativa, and xxx a number from 001 to 1017.
DOI: 10.57745/ftixs5
title: Viral OTU from blood and fecal human samples

description: This repository contains the viral OTU assembled from the viromes produced from human blood and fecal samples. 14 were healthy subjects and 15 were Crohn's disease patients. The analysis of these results is presented in the bioRxiv manuscript described below. Data are organized as one file per vOTU, in the gff format (annotations plus DNA sequence)
DOI: 10.57745/g0un8a
title: Fourier Transformed Mid-InfraRed Transmission (MIR-Trans) spectroscopy analysis of lignins

description: Lab-extracted organosolv lignins have been analysed using mid-infrared transmission spectroscopy. This dataset includes: - 1 file explaining the method; - MIR-Trans spectra in .CSV format (one per lignin sample).
DOI: 10.57745/gixysm
title: LCA_data_Belgium_CS_Large_scale_baseline

description: This dataset contains the data related to the LCA of the baseline scenario for the Belgium CS of FAIRCHAIN project: - Raw data; - LCI; - LCIA; - Possible extra data (sensitivity analysis, etc.). These data are used to produce LCA results described in Deliverable D5.2 of FAIRCHAIN.
DOI: 10.57745/gttjar
title: Maize silage supplementation in grazing dairy cows: milk production, pasture intake, behaviour and methane emissions

description: This dataset includes raw and analysed data from 2 grazing experiments on dairy cows carried out at the INRAE PEGASE experimental dairy farm of Méjusseaume (Le Rheu, France, https://doi.org/10.15454/yk9q-pf68), in spring 2021 and 2022. These experiments were part of the GrASTech project, in the 2018 Joint Call of the Cofund ERA-Nets FACCE ERA-GAS (Grant N° 696356), ICT-AGRI 2 (Grant N° 618123) and SusAn (Grant N° 696231). The first experiment aimed to study the effect of partial mixed ration (PMR) supplementation level (0, 4 and 8 kg DM/d), based on maize silage and soyabean meal (85:15 ratio on a DM basis), cows being at pasture day and night (access time to pasture of 19 h/d). The second experiment aimed to study the effect of the moment of maize silage supplementation (5 kg DM/d; morning vs. evening milking) when cows grazed either only during daytime or during day and night (access time to pasture of 7 vs. 19 h/d). Twenty-four lactating Holstein dairy cows were used in each experiment, according to a 3 × 3 (Experiment 1) or a 4 × 4 (Experiment 2) Latin square design. Milk production and composition, pasture intake (n-alkanes method), grazing behaviour (Lifecorder and Feed’Live devices), and methane emissions (Laser Methane Detector) were measured individually at each period. The dataset is composed of 18 Microsoft® Excel files, corresponding to different types and levels of information: dates of experimental periods, treatments description, cow characteristics, cow measurements, herbage measurements, feed characteristics, weather, methane emissions, daily pattern of feeding behaviour.
DOI: 10.57745/gxqo6f
title: process of information integration in old people with dementia: impact of Physical Activity

description: Physical activity enhances cognitive performance and reduces the progression of dementia symptoms (Liu et al., 2020; Swinnen et al., 2021; Henskens et al., 2018). The aim of this research is to investigate the impact of physical activity on the judgment processes of older people with dementia. The aim is to assess the effect of physical activity on their information integration abilities. Three groups of old people participated in this study. An "active" group, consisting of older people with dementia (N=9), received three "throwing training" sessions per week. An "inactive" group, also comprising old people with dementia (N=7), did not engage in any physical activity. Healthy old people (N=13) formed the control group who conducted the assessment only once at T0 (0 months) to obtain baseline results. At 3-month intervals, using a judgment scale, the judgment of success in throwing tasks combining three pieces of information (in cognito) was assessed for the two other groups. The same scenarios were presented in real-life conditions (in vivo) to the "active" group, who performed these throws. Comparative statistical analyses were conducted at T0, T3, and T6. The study revealed a difference in judgment processes between old people with dementia and healthy old people. It also demonstrated a difference in judgment processes between old people with dementia who received physical activity and those who did not. Training in real-life throwing scenarios (in vivo) facilitated information integration in the judgment task (in cognito). Physical practice positively affects judgment processes. It preserved information integration ability in old people with dementia.
DOI: 10.57745/i3sbmd
title: Experimental data on larval development in Palaemon serratus

description: We reared groups of 50 larvae from Palaemon serratus females (5 young and 5 old) at 3 temperatures (14, 18 and 22°C) with 3 Artemia-based diets: nauplii (N), metanauplii enriched with algal mix (ME) or not (M). We weighed larvae from each female at hatching ("Hatching.csv") and of each juveniles at metamorphosis ("Metamorphosis_data_per_larvae.csv"). For each group, we followed developmental pathways, metamorphosis rate and average duration of development (Metamorphosis_data_per_vessel.csv"). We then analysed the FA composition of larvae at metamorphosis ("Metamorphosis_FA_mg-micro-g-1.csv").
DOI: 10.57745/ihqapy
title: Instances and detailed results for the whole testbed of "A Branch-Price-and-Cut algorithm for the Kidney Exchange Problem"

description: Instances and detailed results for the whole testbed of "A Branch-Price-and-Cut algorithm for the Kidney Exchange Problem". The .zip contains a readme with the informations about the format used to generate the instances. The .xlsx contains a readme sheet to help the interpretation of the results.
DOI: 10.57745/j0zrri
title: DATA from Saclay's Divergent Selection Experiments analysed in Desbiez-Piat et al. 2023

description: Empirical description of phenotypic shifts in selection experiments have nourished quantitative genetics models. These models have shown that long-term selection responses depend both on the initial standing variance as well as the flux of incoming mutations, and that quantifying the proportion of genetic variance due to latter is essential to understanding the seeming absence of selection limits. There are however at least two important things to keep in mind when interpreting selection experiments: first correlative responses to selection on non-focal traits can perturb the selection response on the focal trait and second, generations and selection environments are confounded so that genotype by environment interactions are ignored. Here we used the Saclay Divergent Selection Experiments (DSE) on maize flowering time that display striking selection responses over 18 generations and combined yearly measurements of flowering time (DSEYM), measurements of 11 traits on a subset of 308 DSE genotypes measured for two consecutive years in common gardens (DSECG), as well as genotyping data to track the fate of individual mutations in pedigrees, with four main objectives: (1) to quantify the relative contribution of standing variation and de novo mutational variance to the selection response; (2) to approximate the distribution of phenotypic effects of de novo mutations; (3) to study the impact of GxE interactions in the observed selection response; (4) to describe how trait correlations modulate the exploration of the phenotypic space. In agreement with theoretical predictions, we experimentally validated two successive phases in the selection response: one governed by the fixation of standing variants whose contribution quickly reached a plateau, and the second governed by the fixation of de novo mutations sustaining the selection response. The distribution of selected phenotypic effects confirmed the expected enrichment of fixation of beneficial mutations with an average effect of +0.278 and +0.299 days to flowering, depending on the genetic background; but also revealed fixation of unfavorable mutations reaching up to 25% of incoming mutations. Accumulation of genetic load may be due to antagonistic pleiotropy whereby mutations that were fixed in the selection environment (DSEYM) turn to be unfavorable in evaluation environment (DSECG). Finally, we found that global patterns of correlations between-traits are conserved across genetic backgrounds but exhibit a temporal pattern. Traits that are weakly or uncorrelated with flowering time allow stochastic exploration of the phenotypic space, owing to the microenvironment-specific fixation of standing variants and a pleiotropic mutational input.
DOI: 10.57745/jo3jkz
title: Fermented vegetables metavirome - epifluorescence microscopy dataset

description: This dataset contains the estimation of viral load from twelve fermented vegetables: four cabbages (sauerkraut), four carrots, and four turnips (sauerruben). Viral fractions were extracted from the samples, and dilution of it in phage buffer was filtrated on 0.02 μm Anodisc filters before 1X SYBR Gold coloration. Each sample was observed using an epifluorescence microscope and ten images were captured per slide. The number of virus-like particles was counted and then related to the initial weight of the fermented vegetable, taking into account the ratio between the image area and the filter area, as well as the sample dilution factor. These data were further characterized during the Agence Nationale de la Recherche (ANR) Metasimfood project (https://www.metasimfood.inrae.fr/) to estimate the viral load of fermented vegetables, and are subsequently made publicly available for academic research purposes on fermented foods.
DOI: 10.57745/joz1na
title: Long term monitoring of near surface soil temperature in the french Alps

description: Monitoring of near-surface soil temperature in seasonaly snow-covered, mountain ecosystems located in the French Alps. Data are part of several research projects and monitoring programs examining the impact of climate change on snow cover dynamics, microclimate, species distribution and ecosystem functioning. Data include a GPS position, a date and time in UTC and a near-surface soil temperature (in °C) measured at 5 cm belowground using stand-alone temperature data logger.