cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/t3vcb0
title: In situ pelagic dataset from continuous monitoring: a mesocosm experiment in Lake Geneva (MESOLAC)

description: This dataset corresponds to a data series produced from automated data loggers during the MESOLAC experimental project. In July 2019 we deployed nine pelagic mesocosms (about 3000 l, 3m depth) in Lake Geneva near the shore of Thonon le Bains, France, to simulate predicted climate scenarios (i.e. extreme events) and assess the response of pelagic communities, ecosystems functioning and resilience. The experiment lasted 4 weeks (July 4 – 30, 2019) and the design consisted of three treatments each replicated 3 times: a control treatment (no treatment applied – named C) and two different treatments simulating extreme weather events. The high intensity treatment (named H), aimed at reproducing short and intense weather events such as violent storms. It consisted of a short-term intense stress applied during the first week, with high pulse of dissolved organic carbon (5x increased concentration), light reduction up the 95% and water column manual mixing. The medium intensity treatment (named M), simulated less intense and more prolonged exposures such as during flood events. It was maintained during the 4 weeks and consisted of 1.5x increased concentration of dissolved organic carbon, light reduction up to 70 % and water column manual mixing. During the experiment, automated data loggers were placed in the mesocosms at different depths for continuous environmental monitoring of temperature, dissolved oxygen and CO2. Here these data are presented in the dataset file, ordered by treatment (Control, High and Medium) and replicates. For each time point the measured parameters are listed in columns, a summary table of all the measures is provided as well in the excel dataset file.
DOI: 10.15454/t6obby
title: Projet Artisols - Coefficient de dispersion par canton - Occitanie - 2015 à 2019

description: Le projet ArtiSols, soutenu par la Région Occitanie et le Fonds Européen de Développement Régional (FEDER), s’inscrit dans une démarche d’évaluation et de qualification du processus d’artificialisation des sols en région Occitanie. Piloté par INRAE (UMR TETIS), ce projet rassemble des établissements de recherche (INRAE, CNRS, INPT), des services de l’État (DRAAF Occitanie) et de la Région Occitanie (Direction de l’Aménagement, du Foncier et de l’Urbanisme), et les aménageurs BRL et CACG. Le coefficient de dispersion représente le rapport entre la surface des espaces artificialisés (taches urbaines) morcelés, définis ici pour une emprise inférieure à 3 hectares, et celle des espaces artificialisés denses supérieurs ou égales à 3 hectares. Cet indicateur a été calculé par canton et pour les années 2015 à 2019.
DOI: 10.15454/ojjtey
title: Scenarios for the introduction of environmental DNA-based tools in aquatic biomonitoring (SYNAQUA France-Switzerland workshops)

description: The French-Swiss project SYNAQUA (INTERREG France-Switzerland 2017-2019) focuses on the development and the validation of genomic tools for water quality biomonitoring based on diatoms and oligochaetes. As part of the work-package dedicated to stakeholders and public awareness and involvement, three foresight participative seminars were organized in Lyon and Paris in early 2019. These seminars aimed to design various feared and desired scenarios of genomic tools development in France (and to a lesser extent in Switzerland), then to build an ideal but realistic one, favouring a better biomonitoring. The outcome of the seminars included an action plan along six fields of action: the development, experimentation and normalisation of methods based on eDNA; the regulation and organisation of biomonitoring allowing a good implementation of these tools; the training and mobilisation of professionals; the awareness-building and involvement of policy and decisions makers; the awareness-building and involvement of civil society; the set-up of an implementation mechanism for the overall plan, insuring a steady and consistent progress. The “ideal scenario”, based on a good complementarity between genomic and traditional methods, requires a strong collaboration between all the concerned professionals, especially between researchers and operators, as well as political will and funds to support the process of development. To secure such an involvement, it is necessary to demonstrate how these methods will improve the preservation and restauration of aquatic environments and the overall quality of life and health of the population, with an optimized use of financial resources.
DOI: 10.15454/r5jdyx
title: MeatPartTool Software: Tutorial

description: This report explain how to deal with the MeatPartTool software : - settings and first launch - Interface description - Opening an existing database - Selection of an individual - Access to allocation factors - Create a new individual
DOI: 10.15454/sqghh1
title: Metabarcoding data analysis of fungal communities associated with pedunculate oak (Quercus robur) and maritime pine (Pinus pinaster) in the ORPHEE experimental site.

description: In this study, we analyzed the diversity and composition of fungal communities collected from leaves of pedunculate oak (Quercus robur) and needles of maritime pine (Pinus pinaster) in 48 experimental forest plots. These plots were part of the ORPHEE experimental site (44.73742 N, 0,77504 E Cestas, France) and were planted in monocultures or in mixtures of 2 to 5 tree species. Following fungal ITS1 amplification with ITS1F-ITS2 primers, 3/16th runs of single-end 454 sequencing were performed (Roche GS junior). The metabarcoding data we obtained were analyzed using QIIME. Raw and filtered ASV Tables are available here. Sample ID corresponds to species_block_plot (https://treedivnet.ugent.be/ExpORPHEE.html)
DOI: 10.15454/tghblr
title: Projet Artisols - Occupation des sols en Occitanie - 2019

description: Le projet ArtiSols, soutenu par la Région Occitanie et le Fonds Européen de Développement Régional (FEDER), s’inscrit dans une démarche d’évaluation et de qualification du processus d’artificialisation des sols en région Occitanie. Piloté par INRAE (UMR TETIS), ce projet rassemble des établissements de recherche (INRAE, CNRS, INPT), des services de l’État (DRAAF Occitanie) et de la Région Occitanie (Direction de l’Aménagement, du Foncier et de l’Urbanisme), et les aménageurs BRL et CACG. La cartographie de l'occupation des sols est produite sur l'ensemble de la région Occitanie pour l'année 2019. Cette donnée raster résulte d'une classification par méthode d'apprentissage profond à partir d'imagerie très haute résolution spatiale (1.5m) SPOT 6/7. Des post-traitements ont été effectués afin de mieux caractériser les classes relatives à l'artificialisation. Des fichiers de style (nomenclature et symbologie) compatibles SIG sont également mis à disposition.
DOI: 10.15454/pgkktk
title: TREEPEACE: Heritability and genetic architecture of reproduction-related traits in a temperate oak species

description: The dataset contains data characterizing the reproduction of 342 trees monitored during four years, from 2014 to 2017, within a full-sib family of pedunculated oak (Quercus robur) situated at the experimental unit of Bourran, France. Trees were planted within a randomized incomplete block design comprising 8 blocks with 47 ± 6 individuals per block. Seed production (Ntot), the total mass of seed produced (Mtot), the mean mass of one seed (Ma) and the seed production normalized per tree diameter (Ntot/D) were assessed for every tree of the design. These data have been collected as part of the TreePeace ERC project (#FP7-339728) leads by Antoine Kremer (2018-04-13). The data has been submitted to the public QuercusMap database, available at http://mapedigree.pierroton.inra.fr/qmap. Go to Phenotypic data menu, Data per plantation site and select Bourran2 as plantation site and Reproduction as class of trait.
DOI: 10.15454/sr56zy
title: Retinal cholesterol and glaucoma in the rat

description: This dataset was produced in the context of a project aiming at investigating retinal cholesterol metabolism in a experimental model of glaucoma in the rat. It contains the data generated during the study at different time points and using various techniques: RT-qPCR, Western blot, gas chromatography.
DOI: 10.15454/srhcuh
title: Science for policy 1: FaST hidden benefits: needs based targeting of cleaner water through better use of nutrients - datasets

description: This dataset is part of both Deliverable 4.3 and 5.3 and was produced by the WP4 team of the Landmark H2020 project. It contains the following shapefile: PO1_GAEC5.shp The shapefile gives an estimation of the change in soil function performance across the EU in agricultural soils after implementation of the GAEC5 under the proposed CAP. This spatial variation is represented in change in z-scores compared to the current supply on a NUTS1 level. To implement the scenario, for each crop within each environmental zone the 20% area with the lowest values of the N Cycling indicator are selected from the current SF supply map and this indicator is increased to the lowest values in the other 80% of the same crop – environmental zone combination. In a second step, for each crop within each environmental zone the 20% area with the lowest values of the water purification indicator from the current SF supply map are selected and this indicator is increased to the lowest values in the other 80% of the crop – environmental zone combination, while maintaining the N Cycling improvements. This simulates potential improvements in both N Cycling and water purification due to the implementation of the Farm Sustainability Tool for Nutrients (GAEC 5) Z-scores are calculated from the spatial SF maps for each of the NUTS1 zones. The z-scores give the signed fractional number of standard deviations by which SF means for a NUTS1 zone are above or below the mean value and allow us indicate which areas have a higher or lower soil function performance compared to the mean value. Z-scores from the current SF maps and scenario maps were then compared to each other to calculate the change in z-scores. This change in z-scores is given in the shapefiles and describes the relative change in soil function performance. Positive values indicate an improvement in soil functioning compared to the current situation, negative values a decrease. More information regarding calculation and interpretation of both this dataset and the soil function maps used to calculate the z-scores can be found in: Vrebos D., F. Bampa, R. Creamer, A. Jones, E. Lugato, L. O’Sullivan, P. Meire, R.P.O. Schulte, J. Schröder and J. Staes (2018). Scenarios maps: visualizing optimized scenarios where supply of soil functions matches demands. LANDMARK Report 4.3. and Jones A. et al. (2019). An options document to propose future policy tools for functional soil management. LANDMARK 5.3. All available from www.landmark2020.eu.
DOI: 10.15454/udmkhl
title: Le semis direct sous couvert : pratiques culturales et problèmes malherbologiques. Enquête nationale auprès des agriculteurs.

description: The data presented in this document represent the responses to an online questionnaire broadcast in France between November 2018 and March 2019. The questionnaire was aimed at farmers in the French territory who were using direct seeding under cover (SDSC) or who had experience with SDSC. The questionnaire focused on the agronomic and weed science aspects of the transition to SDSC. It asked farmers to describe their agronomic practices, their weed management and the main problematic weeds for three periods: (1) before the adoption of the SDSC (2) during the first years of SDSC and (3) when farmers felt that they had mastered their weed management. Farmers were also asked to describe their use of glyphosate on their SDSC plots during the survey period (2018-2019). The data includes the 425 complete responses. Of the 425 responses, 143 farmers felt that they had mastered their weed management.
DOI: 10.15454/v0vnly
title: RPG complété 2018 département 95

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 95. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020
DOI: 10.15454/ve2mlh
title: Enriched gene ontology terms in upregulated genes at the transition from J2 to J3-J4 larval stages

description: Analysis of differentially represented (over and under) Gene Ontology (GO) terms in the genes showing significant up-regulation at the transition between the the pre-parasitic J2 and J3-J4 stage. GO over and under representation of terms are according to the hypergeometric test as implemented in the GofuncR Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/GOfuncR.html). Results are separated by: - Molecular Function - Biological Process - Cellular Component And, in each ontology, under, over and all differentially expressed GO terms are given. All the files are in table separated values format, with the last common providing the accession numbers of proteins annotated with the GO term under consideration.
DOI: 10.15454/vypxij
title: Code from Structure of multilocus genetic diversity in predominantly selfing populations

description: We provide here scripts allowing forward simulations of temporal samples in several demographic scenarios using SLiM 2.6, and converting the output into microsatellite data following the stepwise mutation model. The demographic scenarios simulated are: - isolated population of constant demographic size (isolated_pop_input.sh); - isolated population undergoing bottlenecks (bottleneck_input.sh); - population of constant demographic size in an island model of migration (migration_input.sh); - population in an island model undergoing admixture or extinction-recolonization events (admixture_input.sh). R scripts to convert SLiM output into microsatellite data (readCustomSlimOutput.R and slim2microsat.R), as well as scripts to perform diversity analyses (DivStats.R, percentLD.R and MLGFS.R) are also provided. A readme file describing the details of each script is provided.
DOI: 10.15454/tfyh9n
title: Transposable element annotation of Botrytis cinerea B05.10

description: The TEdenovo was launched on Botrytis cinerea strain B05.10 whole genome (18 chromosomes, NCBI bioProject PRJNA264284, assembly ASM83294v1). The TE Consensus library from the TEdenovo (36 consensus) was filtered out for consensus sequences classified as SSR, or noCat built from less than 10 fragments (HSPs). The library of the remaining 26 consensus sequences was used to annotate TE copies in the whole genome using TEannot pipeline. Using results of this first TEannot pipeline, we manually eliminate redondancy by filtering out 5 consensus classified class I LTR, one noCat and 6 consensus classified class II MITE containing more than 30 % of micro/mini satellites. We finally kept 15 consensus sequences used to launched a second TEannot pipeline. Genome assembly website: http://fungi.ensembl.org/Botrytis_cinerea/Info/Index Genome annotation files and TE consensus ID mapping between previous and new classification are available for download.
DOI: 10.15454/ucrzo7
title: Replication data for:Organic farming expansion drive arthropod abundance not diversity in agricultural landscapes

description: Data set on natural enemy communities that have been collected in vineyards over the growing season 2015 (project "SOLUTION"). The data set also contains data on management intensity and landscape composition around focal vineyards.
DOI: 10.15454/v6aotg
title: PGD Unité Expérimentale Arboricole

description: Ce dataset contient le PGD de l'Unité Expérimentale Arboricole
DOI: 10.15454/vi7yrb
title: FirmiData: Annotation of ICEs and IMEs in 40 Firmicutes genomes

description: Manually curated reference annotation of Integrative Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs) and other degenerated ICEs and IMEs in 40 Firmicutes genomes.
DOI: 10.15454/w6swzh
title: Horizontal gene transfer candidates in M. incognita

description: Analysis of horizontal gene transfer (HGT) candidates on the M. incognita predicted proteins from (Blanc-Mathieu et al. 2017), using Alienness (Rancurel et al. 2017) on a Diamond search against the NCBI's nr library. The following parameters were used in Alienness Taxonomic group of interest: 33208 (Metazoa; HGT of non metazoan origin in a metazoan species) Taxonomic group to exclude: 33283 (Tylenchomorpha; to ignore self hits to plant-parasitic nematodes in Clade 12) Additional taxonomic groups to classify potential donors: 3041 (Chlorophyta); 35493 (Streptophyta) M. incognita proteins with an AI&gt;0 have a better hit to non-metazoa than metazoa and this can include possible HGT M. incognita proteins with an AI&gt;14 have a better hit to non-metazoa than metazoa, with a magnitude of difference &gt;1E6 and this can be considered likely HGT
DOI: 10.15454/w8hen1
title: CANOPY-A_Grignon_2016-2017_AGRONOMIE

description: Données expérimentales issues de l'essai CANOPY-A conduit à Grignon en 2016-2017 par l'UMR AGRONOMIE sur 4 génotypes de colza x 5 traitements azotés.
DOI: 10.15454/qh1mv7
title: Raw data - defense gene expression under multiinfection - Robijn

description: Raw experimental data on defense gene transcrirts in potato cv Robijn under multiple infections
DOI: 10.15454/uueiqn
title: Plastics in a circular economy: mitigating the ambiguity of widely-used terms from stakeholders consultation

description: This dataset is associated with a study which aims to examine, through stakeholders consultation, the widely used definitions of four terms related to plastics sustainability: ‘bio-based plastics', ‘bioplastics’, ‘biodegradable plastics’ and ‘plastics recycling’ and to mitigate their potential ambiguity for diverse scientific communities and sectors of activity. For the three terms ‘bio-based plastics', ‘biodegradable’ and ‘recycling’, consolidated definitions were elaborated based on the feedback of online survey and analysis of the pro and con arguments given by face-to-face interviews with 18 experts followed by an online survey of 122 stakeholders. Acceptance of the consolidated definitions was higher than the official ones with an increase of acceptance from 43 to 81% for bio-based plastics, from 47 to 61% for biodegradable plastics, and from 28 to 60 % for plastics recycling. The terms ‘biodegradable’ and ‘recycling’ remain ambiguous even after consolidation of the definition.This highlights that more discussions are necessary to achieve a consensual and fair definition of such complex properties and mechanisms. In the term ‘Bioplastics’ the prefix ‘bio’, referring either to the origin of the resources or the end of life of the material, remains difficult to understand and we prefer to advise against its use, especially with non-expert people (e.g. consumers and the public at large), in favour of the use of ‘bio-based plastics’ or ‘biodegradable plastics’.
DOI: 10.15454/v70zst
title: Monolith Aboveground Biomass

description: Dry aboveground biomass per plant species in monoliths
DOI: 10.15454/vt1csa
title: Monitoring of Electric Resistivity of trees in Auvergne (France)

description: Monitoring of Electric Resistivity values of tree trunks (silver fir) in Auvergne (France). Wood moisture content in heartwood and sapwood in silver fir (Auvergne, France)
DOI: 10.15454/qsmewd
title: RPG complété 2019 département 07

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 07. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/uu2fqt
title: Data set - Collembola abundances and traits in various land uses

description: This dataset is composed by an excel files with 6 sheets: (i) "abundance" is a data table that groups the collembolan communities in 758 sampled sites (minimum of 3 replicates by site), (ii) "trait" provides information on the functional traits of several collembolan species. These data are largely extracted from the BETSI trait database (https://portail.betsi.cnrs.fr/), (iv) "site" is a table giving information on the different characteristics of the sites and (v) a table summarising the origin of the data (13 different projects) and (vi) list of abbreviations.
DOI: 10.15454/vyeybk
title: A dataset from a 3-year network of field measurements of soil organic nitrogen mineralization under a mild oceanic temperate climate

description: Soil organic nitrogen (SON) mineralization is a function of soil properties, land use and climate, which led to monitor a network of 137 cultivated fields covering the wide diversity of soils, crop rotations and cropping practices throughout Brittany (France). SON mineralization was quantified by the mineral N balance calculated for a maize crop not fertilized with N; it was determined by measuring soil mineral N (SMN) in the 0-90 cm soil profile in March (Ni) and October (Nf) and N uptake by the maize crop, and predicting nitrate leaching (Nleached) using the STICS model. The experimental design was based on estimating SON for three consecutive years (2012-2014) to improve the accuracy of measuring mineralization.
DOI: 10.15454/wy0ljl
title: PaSim

description: This dataset contains the files necessary to use PaSim, namely the software and its user guide. IDDN: IDDN.FR.001.220024.000.R.P.2012.000.10000
DOI: 10.15454/y3rpe3
title: SWOT analysis of case studies

description: Tabulated results of the SWOT analysis of case studies
DOI: 10.15454/vvnqhr
title: Data from: Benefits and drawbacks of osmotic adjustment in Propionibacterium freudenreichii

description: Propionibacterium freudenreichii CIRM-BIA 129 and CIRM-BIA 1025 osmoadaptation in chemically defined medium (MMO) and osmoadaptation in the presence of glycine betaine (GB) were studied thanks to proteomics. Bacteria were harvested at the begining of stationary phase. Protein trypsin digestion were performed in solution. The data set contains 87 files of NanoLC-MS/MS analysis, acquired on a Qexactive mass spectrometer. Design: 3 classes (control:"MMO", osmoadaptated: "NaCl" and osmoadapted in the presence of Glycine betaine: "GB"), 5 or 4 biological replicates. All samples were injected 3 times
DOI: 10.15454/w9qyhb
title: Frayères Nivelle

description: Petit fleuve côtier de 39 km de long, la Nivelle est une rivière à saumon et sa population est suivi depuis le début des années 80. Afin d’estimer l’état de la population, chaque année, des suivis sont effectués sur le cours principal de la rivière et ses principaux affluents. Le présent Datatset a pour objectif de présenter les recensements de frayères des poissons qui viennent pondre sur la Nivelle entre fin novembre et mi-janvier. Chaque année à cette période, la Nivelle, son affluent principal le Lurgorrieta ainsi que deux affluents majeurs (sorrimenta et opalazio) sont scrutés afin d’identifier le maximum de nids de femelles de saumons qui sont creusés dans le lit de la rivière, majoritairement en tête de radier. Durant la saison de reproduction, au moins trois descentes complètes (à pied dans la rivière et pour partie en canoé en partie aval de la Nivelle) sont effectuées sur les portions susceptibles d’accueillir ces frayères à savoir : - La Nivelle sur toute la portion entre Ascain (pont romain) et le barrage infranchissable d’Urrutienea en aval de Dantcharia. - Le Lurgorrieta entre sa confluence avec la Nivelle et le barrage infranchissable d’Harrieta à Sare. - Le Sorrimenta et l’Opalazio sur le premier kilomètre en amont de leur confluence avec la Nivelle. Le classeur Excel mis à disposition dans ce Dataset inventorie toutes les frayères de saumons identifiées sur la Nivelle et ses affluents entre 1983 (date des premiers relevés). A ces identifications sont associées certaines informations comme l’année, la zone de découverte, les coordonnées GPS (degrés décimaux), le secteur (par rapport au plan cadastral de la Nivelle découpé en tronçon), la quantité de frayères identifiées par site ainsi que les observations.