cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/liuhey
title: Module de calcul des besoins en plants et semences d'après un plan de culture maraîcher (en lien avec l'outil Pépinière-Mesclun)

description: Ce tableur (en format .xlsx) permet, à partir de l'assolement, de prévoir les quantités de semences et de plants à acheter pour une année et également de prévoir les semis à réaliser en pépinière dans le cadre d’une production de plants. S'il peut s'utiliser seul, ce module peut fonctionner à partir de l'onglet "assolement" de l'export en .xlsx de l'outil de planification Pépinière https://pepiniere.outils-mesclun.fr/
DOI: 10.57745/lyhm4w
title: Dataset of 2D effective elasticity tensor from discrete simulations of quasi-brittle area elements

description: This dataset contains 76,356 effective elasticity tensors describing the degradation of quasi-brittle materials. The elasticity tensors are gathered from discrete (beam-particle) simulations of 2D area elements. Those simulations aim at reproducing the mechanical degradation of quasi-brittle materials submitted to complex (multi-axial and non-proportional) mechanical loads. Two types of data are given in this dataset: the damaging loadings and the effective elasticity tensors. Each damaging loading is stored in a CSV file. It contains a temporal index, the strain applied to the area elements, and the stress in response. The evolutions of each effective elasticity tensor are also stored in CSV files. It mainly contains the evolution of the effective elasticity tensor components during the associated damaging loading. It is also indexed with the same temporal index as in the damaging loadings files. The README.md file contains more details on the data and can be found below.
DOI: 10.57745/mhtn16
title: Random forest models for predicting the flow intermittence in the 6 European Drying River Networks

description: Random forest models to predict the state of flow (0=dry, 1=flowing) are the reach scales and at daily time step in the 6 European DRNs
DOI: 10.57745/mjekaz
title: Données de réplication pour : Experimental analysis of genetic and environmental interactions on leaf elongation and reproductive development in Lolium perenne

description: The dataset originates from an experiment aimed to investigate the genetic diversity of perennial ryegrass phenology in response to different environments. In particular, we studied effect of duration of exposure to non inductive treatments on leaf elongation and appearance rate, spikelets production and heading date. This work provides original data for perennial grasses and highlights the interactions between the vegetative and reproductive development. Our results could be used to develop and/or calibrate phenological models of grasslands.
DOI: 10.57745/mkll9i
title: Image data set of "Semi-automatic quantification of 3D Histone H3 phosphorylation signals during cell division in Arabidopsis root meristems"

description: This set of images corresponds to wholemount immunolocalized Col0 untreated root tips obtained using an anti-tubulin antibody (B-5-1-2 mouse monoclonal anti-tubulin, Sigma-Aldrich), an anti-Histone H3 (Phospho S10) antibody (rabbit polyclonal anti-H3S10ph antibody) and stained with DAPI. Root tips Z-stacks were acquired using an SP8 confocal laser microscope (Leica Microsystems). For simultaneous detection of DAPI, microtubules and H3S10ph signals, samples were excited respectively at 405 nm, 488 nm or 561 nm, with an emission band of 420-446 nm, 495-540 nm or 570-620 nm, using PMT detectors for both DAPI and H3S10ph, and a hybrid detector for microtubules. All 3D stacks were acquired as 12 bits images to get a high dynamic range of the H3S10ph signal, ensuring that no pixel was saturated in this channel. All 3D stacks were acquired with using the same zoom, the same voxel size (350 µm x 350 µm x 350 µm) and the same settings and PMT level for the H3S10ph channel.
DOI: 10.57745/n3h2hv
title: Raw datas of 30 samples from RNASeq reads

description: 30 Samples of RNA-Seq sequencing (Illumina). with 3 replicates. 37 : F. succinogenes + Levucell 4h 39 : S. ruminantium + Levucell 4h 41 : Co-culture + Levucell 4h 43 : F. succinogenes 4h 45 : S. ruminantium 4h 47 : F. succinogenes + S. ruminantium 4h 49 : F. succinogenes + Levucell 48h 51 : Co-culture + Levucell 48h 57 : F. succinogenes 48h 59 : F. succinogenes + S. ruminantium 48h
DOI: 10.57745/n9vzcs
title: Effect of an extract from chickpeas cooking wastewater containing galacto-oligosaccharides, an inulin-derived product containing fructo-oligosaccharides, and sucrose on the resistance of L. bulgaricus CFL1 to freezing, freeze-drying and dried storage

description: This dataset contains experimental data on the on the biological, physical and biochemical characterization of Lactobacillus delbrueckii subsp. bulgaricus CFL1 in the presence of three protective formulations: a galacto-oligosaccharides-contining extract from chickpeas cooking wastewater (GOS), produced in the frame of PREMIUM project (777657) (Martins et al 2023), a commercial fructo-oligosaccharides product from inulin (FOS), and sucrose, and at different steps of the stabilization process (freezing, freeze-drying and two weeks of storage at 28°C). The data set includes i) biological activity (culturability, acidifying activity, viability), ii) physical properties of the matrix (glass transition temperature and water content), iii) biochemical composition (Fourier transform infrared features), iv) biophysical (membrane integrity and phospholipid organization) and fermentation data (optical density and acidification rate as a function of time).
DOI: 10.57745/na1uy3
title: Metagenetic data and bacterial quantification of 310 Label Rouge broiler carcass samples

description: The dataset provides the 16S metagenetic data of sequencing of 310 Label Rouge broiler carcass samples, collected in a French slaughterhouse between 2023 and 2024. It includes 16S rRNA metabarcoding data from broiler carcass rinses before and after 7 days of storage at 4°C. Amplicons from the region V3-V4 of 16S rRNA were sequenced with Illumina MiSeq technology. The dataset also includes Campylobacter et Total Mesophilic Aerobic flora quantification on agar plates before and after refrigerated storage. The data were collected to identify bacterial species that correlate positively or negatively with Campylobacter on chicken meat.
DOI: 10.57745/nhwiqn
title: Dataset and code for publication entitled "Fostering temporal crop diversification to reduce pestice use" in Nature Communications

description: Two csv tables and one R script used for analysis. The additionnal table "table_description" describes the columns of the two csv files
DOI: 10.57745/o4xabu
title: Replication Data for: Bayesian inference for parameter identification in mechanistic models, examplified using a cow’s lifetime performance model

description: An eleven-columns CSV file for 43 cows with animal id, values of Age (days), Dry Matter Intake (DMI, Kg DM/d), Parity, Days in Milk (DIM), Milk (Kg /day), Milk protein (PC_Milk, %), Milk fat (Fat_Milk, %), Milk lactose(Lac_Milk, %), Body Weight (BW, Kg), and Body Condition Score (BCS, 1 to 5 scale).
DOI: 10.57745/ok3zhq
title: Recurrent restrictive dieting induces a changes in fecal and cecal microbiota in mice

description: C57BL/6 mice underwent 3 cycles of 1 week of WD (45% kcal from fat) exposure separated by 2 weeks of chow diet exposure (group CYCL) or stay under chow diet for 7 weeks (group CTRL). Food intake and body weight were monitored daily. In a first experiment, feces were collected 4 days before each reintroduction of the WD and the fecal microbiota composition was analyzed through 16S sequencing. In a second set of experiment, before the third cycle of WD of CYCL mice and in CTRL mice of the same age cecal samples were collected and the cecal microbiota composition was analyzed through 16S sequencing. Then, cecal samples from the CYCL and CTRL mice from a 3rd set of experiment were transplanted in naive mice to decipher whether differences in food intake behavior could be transmitted through the gut microbiota. Cecal microbiota of donor and recipient mice were collected and the microbiota composition was analyzed through 16S sequencing.
DOI: 10.57745/kto26y
title: Soil characteristics - French Guyana

description: Soil physical and chemical characteristics in cores extracted at Paracou, to a depth of 9 m
DOI: 10.57745/lordna
title: Four HMM models for basidiomycete sesquiterpene cyclases

description: Sesquiterpene cyclases (STC) catalyze the removal of inorganic diphosphate (PPi) from farnesyl diphosphate, and the cyclization of the resulting carbocation. In fungi, STC that share a common ancestor catalyze a same cyclization mechanism: • clade 1 STC catalyze the 1,10-cyclization of (2E,6E)-FPP carbocation; • clade 2 STC catalyze the 1,10-cyclization of the (3R)-NPP carbocation; • clade 3 STC catalyze the 1,11 cyclization of (2E,6E)-FPP carbocation (trans-humulyl-type cyclases); • clade 4 STC catalyze the 1,6 or 1,7 cyclization of the (3R)-NPP carbocation. Here, we provide robust HMM models for the identification of STC genes in basidiomycete genomes. Their classification into one of the four clades will give indication for the prediction of their cyclisation mechanism.
DOI: 10.57745/mcaqmi
title: Creating common understanding and action in bark beetle damage study

description: Creating common understanding and action in bark beetle damage study in English and Finnish
DOI: 10.57745/mxmxbk
title: RPG complété 2020 Région Pays de la Loire

description: RPG complété 2020. Complète le RPG campagne 2020 pour les départements de la région Pays de la Loire (44, 49, 53, 72, 85). (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2022.
DOI: 10.57745/onngwz
title: Script and data used for the article "Comparison of enrichment methods for efficient nitrogen fixation on a biocathode"

description: Data and R scripts used for the analysis and graphic representation used in the article "Comparison of enrichment methods for efficient nitrogen fixation on a biocathode"
DOI: 10.57745/oz2h51
title: De ville en ville : Itinéraire de Marguerite de Valois en Flandres

description: Ces données décrivent l'itinéraire de Marguerite de Valois en Flandres représenté dans l'application web De ville en ville à l'adresse https://citedesdames.github.io/de-ville-en-ville/?site=1. Elles ont été produites de 2019 à 2024, dans le cadre du projet de recherche Cité des dames, créatrices dans la cité, financé par l'I-Site FUTURE de l'Université Gustave Eiffel, par Nicole Dufournaud, Philippe Gambette et Caroline Trotot. Le texte de l'extrait des Mémoires de Marguerite de Valois relatif au voyage des Flandres a été mis à disposition par Éliane Viennot et le repérage des noms de lieux y a été effectué avec des contributions d'Isabelle Qin.
DOI: 10.57745/mhjpa6
title: Fermented vegetables metavirome - microbial enumeration

description: This dataset contains the microbial enumeration and pH of twelve fermented vegetables: four cabbages (sauerkraut), four carrots, and four turnips (sauerruben). Serial dilutions of samples mixed in saline sterile water were plated on three solid media: Plate Count Agar for aerobic bacteria, MRS agar for lactic acid bacteria and YEGC for fungal populations. After incubation, the colonies formed were counted to calculate the concentration in colony forming unit per gram of sample. These data were further characterized during the Agence Nationale de la Recherche (ANR) Metasimfood project (https://www.metasimfood.inrae.fr/) to estimate the microbial composition and concentration of fermented vegetables, and are subsequently made publicly available for academic research purposes on fermented foods.
DOI: 10.57745/mlzfro
title: Reducing pest pressure and insecticide use by increasing hedgerows in the landscape - dataset

description: Data set for the publication of the article "Reducing pest pressure and insecticide use by increasing hedgerows in the landscape" Details about the dataset are provided in the associated publication.
DOI: 10.57745/n6y6qr
title: Database for systematic map of inland navigation effects on freshwater biodiversity

description: Database of the systematic map of the literature on the effects of inland navigation on freshwater ecosystems
DOI: 10.57745/nd3m71
title: Rev-erb-α antagonism in alveolar macrophages protects against pneumococcal infection in elderly mice

description: Crude data related to the sudy "Rev-erb-α antagonism in alveolar macrophages protects against pneumococcal infection in elderly mice" (Cell Reports, 2025)
DOI: 10.57745/nhvpcr
title: EcoTroph-Dyn unexploited ecosystems

description: R scripts to run the EcoTroph-Dyn model in a theoretically unexploited ecosystem and analyze climate change effects. WARNING: In this repository, you will find an original implementation of the EcoTroph_Dynamic modelling framework, which is completely independent of the EcoTroph Package (https://cran.r-project.org/web/packages/EcoTroph/index.html). EcoTroph-Dyn is a simplified semi-empirical model of the flow of biomass through the food web, from primary producers to top predators (Gascuel 2005, Gascuel et al. 2011). It has been used in particulate to assess the ecosytem impact of fishing. In this implementation of EcoTroph-Dyn, biomass and production of upper trophic levels (at each trophic level) are calculated based on the trophic transfer efficiency and the flow kinetic at each trophic level, using sea water temperature, net primary production and transfer efficiency of high trophic levels (see du Pontavice et al 2021 https://doi.org/10.1111/gcb.15576) as the model inputs. The details and the theoretical basis about the implementation of EcoTroph-Dynamic available in this repository would be presented in Guibourd de luzinais et al. (2024). How to run those scripts? 1.Open the R script: EcoTroph_Dynamic_core_function.R. 2. Run the first lines and the fonctions called "create_data_envi",and "ecotroph_dynamic_core". 3. Use ecotroph with the examples at the end of the script (3 examples) or use your own data following the details in the R script. REFERENCES Du Pontavice, H., Gascuel, D., Reygondeau, G., Stock, C., & Cheung, W. W. L. (2021). Climate‐induced decrease in biomass flow in marine food webs may severely affect predators and ecosystem production. Global Change Biology, 27(11), 2608–2622. https://doi.org/10.1111/gcb.15576. Gascuel, D., Bozec, Y.-M., Chassot, E., Colomb, A., & Laurans, M. (2005). The trophic spectrum: Theory and application as an ecosystem indicator. ICES Journal of Marine Science, 62(3), 443–452. https://doi.org/10.1016/j.icesjms.2004.12.013. Gascuel, D., Guenette, S. & Pauly, D. (2011). The trophic-level-based ecosystem modelling approach: theoretical overview and practical uses. ICES J. Mar. Sci.. DOI: https://doi.org/10.1093/icesjms/fsr062. Guibourd de Luzinais, V., Gascuel, D., Reygondeau, G., D., & Cheung, W. W. L. (2024). Large potential impacts of Marine Heatwaves on ecosystem functioning. manuscript submitted for publication in Global Change Biology.
DOI: 10.57745/nqlfo1
title: OSO vecteur 2021 - Département des Hautes-Alpes

description: Produit vectoriel de l'occupation du sol OSO 2021 sur le département des Hautes-Alpes
DOI: 10.57745/ofsisa
title: supplementary_table

description: Supplementary table from the meta-analysis of factors structuring equine strongyles populations
DOI: 10.57745/ot1ifb
title: Water transit time tracing model using wetness adaptive StorAge Selection functions

description: A model using StorAge Selection (SAS) functions in order to estimate water transit time distributions through a mesoscale catchment under Mediterranean climate, prone to flash floods. This dataset contains the model code, forcing data as well as results of a sensitivity analysis. The article describing this model will be linked once published.
DOI: 10.57745/pjrwcu
title: Mass spectrometry analyses of pectin soluble degradation products released by PsAA17 LPMOs

description: We provide the raw data of the mass spectrometry analyses (MS and MS/MS) of pectin soluble degradation products released by PsAA17 LPMOs. Data are deposited in the Waters instrument manufacturer's format (.raw). They can be converted to .mzml format using a free converter.
DOI: 10.57745/qvvtd6
title: Deliverable D3.1 Assessment Indicators - Baseline - CS-Gre

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 Greece (CS-Gre). The description of the baseline covers the dimensions of co-creation business models and sustainability including environmental, economic and social perspectives.
DOI: 10.57745/r0vpgy
title: Phenotyping data of symbiotic and aposymbiotic Dioscorea sansibarensis in gnotobiotic or greenhouse conditions.

description: Phenotyping data of symbiotic and aposymbiotic D. sansibarensis under gnotobiotic conditions. Raw data used in Acar et al. 2023 https://doi.org/10.1101/2023.09.04.555865 File description: - phenotyping_data_greenhouse_Acar et al 2023-corrected.ods : Automated phenotyping data of Dioscorea sansibarensis in greenhouse conditions. Data from apoymbiotic plants were collected alongside symbiotic and inoculated plants at the TPMP high-throughput phenotyping facility in Toulous, France. Colorimetric data extracted from segmented image analysis with the IPSO_PHEN software. See Readme.txt for details. - phenotyping_data_gnotobiotic_Acar_et al 2023-corrected : Dioscorea sansibarensis symbiotic and aposymbiotic plants were grown in sterile containers. Phenotyping data was collected at the end of the experiment. See Readme.txt for details.
DOI: 10.57745/ktfzqd
title: Fichiers QGIS et Excel des cas d'étude d'application du protocole d'aide à la décision pour le traitement des embâcles (protocole de Wohl et al. 2019 adapté par Benaksas et Piton 2022)

description: Chaque archive se rapporte à un cas d'étude du rapport de Benaksas & Piton (2022), à savoir: Le Bresson (Isère) Torrent de montagne et Alloix (Isère) Ruisseau de montagne, Le Lagamas (Hérault) Ruisseau méditerranéen, La Brague (Alpes-Maritimes) Rivière méditerranéenne, La Clamoux (Aude) Rivière torrentielle méditerranéenne. Chaque archive contient trois documents maîtres et les fichiers sources associés permettant de faciliter l'application du protocole de Wohl et al. (2019) tel que adapté par Benaksas & Piton (2022): Le fichier export_csv_vers_shp.qgz est un projet QGIS qui a facilité la transformation en données SIG des fichiers textes (format .csv) importés de l'application Epicollect 5 tel que décrit dans l'Annexe C du rapport de Benaksas et Piton (2023) , L'autre fichier ".gqz" est un projet QGIS qui facilite l'affichage et l'interprétation des données SIG compilées préalablement aux missions de terrains et sur le terrain via l'application Epicollect 5 tel que décrit dans les Annexe C et D u rapport de Benaksas et Piton (2023) , ResultatsProtocole_epicollecte.xlsx est un tableur Excel qui a facilité la notation des indicateurs de l'approche multicritère, qui permet la modification éventuelle des pondérations entre sous-critères, et qui a mené le calcul des scores pondérés fournis dans le rapport et a préparé les sorties graphiques fournies dans le rapport. Nota: Le cas d'étude du Bréda (Isère) rivière de montagne affluent de l'Isère ayant servi à caler le protocole, les données associées à ce cas d'étude ne sont pas homogènes et ne sont ainsi pas mis librement à disposition. Elles peuvent éventuellement être mises à disposition sur demande directe à Guillaume Piton.
DOI: 10.57745/lzbptc
title: Participatory soil citizen science

description: Citizen science is a participatory research method that actively involves and engages the public in scientific enquiry to generate new knowledge or understanding. For the program EJP SOIL, we review past and current citizen science projects on agricultural soils across Europe. We conducted a web-based survey and described the 39 reviewed European citizen science projects in the light of the ten principles of citizen science and identified success factors for citizen science.
DOI: 10.57745/mcd8yt
title: NMR metabolomic and starch data of young leaf of maize hybrids cultivated in the field with early sowing

description: Metabolomic and starch analyses of young leaves of maize plants cultivated in the field with early sowing in 2013 and 2014. Analyses performed on the genetic diversity of a core panel of 30 European hybrids and a commercial hybrid in AMAIZING ANR project (https://amaizing.fr/). Proton NMR analyses of leaf extracts. Starch analyses of pellets.
DOI: 10.57745/motpxm
title: DATA: Harmful self-pollination drives gynodioecy in European chestnut, a self-incompatible tree

description: Fruit set data used in the research article entitled: Self-interference and female advantage in chestnut.
DOI: 10.57745/mqxhg9
title: Deciphering the respective roles of coating weight and number of layers on the mass transfer properties of polyvinyl alcohol coated cardboards

description: This dataset gathers 7 files containing all the data presented in the scientific article entitled “Deciphering the respective roles of coating weight and number of layers on the mass transfer properties of polyvinyl alcohol coated cardboards”.
DOI: 10.57745/nhrnor
title: Fabas forest plots acquired during the HYPERBIO project

description: This dataset was collected during the TOSCA HYPERBIO project supported by CNES, in collaboration with ONERA/DOTA and TETIS Lab. The FABAS forest is located in the “Vallées et Coteaux de Gascogne” (Haute-Garonne, France), belonging to the ZA PYGAR long-term socio-ecological research site (LTSER) (Ouin et al. 2021). The forest was sampled in 2019 to acquire a set of square plots in which the dominant tree species with their percentage of coverage at canopy level were estimated. A non-random sampling strategy was applied in order to select plots in forest stands of different composition (tree species), structure (heights), openness, and topography (steep or flat). We sampled a total of 44 plots. Each plot was defined as a square of 40 m x 40 m. Plots were located using a Garmin GPSMap 62st receiver (3–5 m accuracy) and distributed over forest stands. The surveys were carried out in april (19th, 23th, 24th, 26th), may (2nd, 9th) and july (18th) in 2019. For each plot, the % tree cover of the dominant tree species at canopy level was estimated by one or two observers with a minimum range of 5 %. A maximum of 5 dominant species were recorded. The total % of tree cover within each plot may not reach 100 % because of over-mixed species or uncovered areas. The % cover of understory vegetation was also recorded with no information on the species.
DOI: 10.57745/nqhb1i
title: Module de dimensionnement et d'évolution de la charge de travail à partir de la planification en cultures maraîchères (en lien avec l'outil Pépinière-Mesclun)

description: Le module Dimensionnement_ Travail (en format .xlsx ou .ods) permet à partir de son plan de cultures en maraîchage de visualiser les surfaces nécessaires en plein champ et sous abri pour dimensionner le système de production (en cas d’installation) et visualiser les pics de travail semaine après semaine en considérant l’évolution des surfaces implantées, en cours de culture et récoltées. Cette dernière fonctionnalité permet une première approche de l’impact des choix de diversification et d’intégration de couverts sur l’évolution de la charge de travail. Etant donné la variabilité des temps de travail en maraîchage selon les contextes, il n’a pas été possible de produire une estimation quantitative du volume de travail horaire au cours du temps mais des fourchettes de temps de travail par unité de surface pour différents systèmes de production sont fournies pour nourrir la réflexion. Ce module est conçu pour s'utiliser à partir de l'onglet "assolement" du fichier d'export généré par l'outil Pépinière-Mesclun (https://pepiniere.outils-mesclun.fr/ ). L'usage de ce module est détaillé dans le premier onglet "Préambule".