cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/bivuoq
title: Replication data for: "Characterization of bacterial communities of cold-smoked salmon during storage"

description: Information data on the diversity of bacterial communities present on 45 samples of cold-smoked salmon produced in 3 different food processing plants and cold-smoked salmon chemical content. The aim of this study was to evaluate the bacterial community of cold smoked salmon by using 16S rRNA gene metabarcoding. This dataset also contains statistical outputs
DOI: 10.15454/9ymh8m
title: Water temperature on the Yères river (Seine-Maritime county - France)

description: The data consists of Yeres river water temperature since 1997 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 Yères is 39,8 km long and has a mean slope of 0,25%. It drains a basin of 309 km2 and flows north-west from Aubermesnil-aux-Erables and ends into the English Channel at Criel-sur-Mer. It lies within a chalky geological zone and is fed from alluvial deposits. The mean flow is 2,71 m3/s, with the highest mean flow in February (mean = 3,69 m3/s) and the lowest in September (mean = 1.82 m3/s).
DOI: 10.15454/ahkbtq
title: Business Model Canvas examples

description: Three characteristic triggers were selected to build business concepts by business model canvas around them. Selected triggers: 1. Avoiding or reducing pollution 2. Environmental awareness and need for sustainable development 3. Market need & opportunity
DOI: 10.15454/d270ce
title: Frimouss Peach

description: Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INRA UMR 1115 PSH (Plantes et Systemes de culture Horticoles, Avignon)
DOI: 10.15454/cj26oo
title: Recombinant Lactococcus lactis delivering hCAP18 cDNA alleviates DNBS-induced colitis in C57BL/6 mice by promoting IL17A and IL10 cytokine expression

description: In this study, we attempted to alleviate chemically induced colitis in mice using a recombinant probiotic strain that delivered hCAP18 cDNA under the control of the cytomegalovirus promoter (LL-Probi-H1:hCAP18) to the host cells. We investigated whether the alleviation of symptoms could be explained through modification of the host gut microbiota by hCAP18. Feces from mice were collected at day 7, before DNBS colitis induction, for 16S DNA sequencing. Total bacterial DNA was extracted from mouse fecal samples according to the protocol described by Godon et al. (Godon et al., Appl Environ Microbiol., 63(7):2802-13, 1997). The V3-V4 hyper-variable region of the 16S rRNA gene was amplified by using the following primers: forward primer CTTTCCCTACACGACGCTCTTCCGATCTACGGRAGGCWGCAG and reverse primer GGAGTTCAGACGTGTGCTCTTCCGATCTTACCAGGGTATCTAATCCT. The PCR reactions were carried out using 10 ng of fecal DNA, 0.5 μM primers, 200 µM dNTP, and 0.5 U of the DNA-free Taq-polymerase, MolTaq 16S DNA Polymerase (Molzym). Amplifications started at 94°C for 60 sec, followed by 30 cycles at 94°C for 60 s, 65°C for 60 s, 72°C for 60 s, and finishing with a step at 72°C for 10 min. The resulting PCR products were purified, quantified and sent to the @BRIDGe platform (INRAE, Jouy-en-Josas) for sequencing using Illumina MiSeq technology (Illumina, CA, USA).
DOI: 10.15454/bgmnqy
title: Data used in Mollier et al., (2022). JVS

description: Data used in the article "Former croplands have stronger legacy effects on soil and understory plant communities and traits than former meadows and pastures in French montane forests" published in Journal of vegetation science. The data include botanical surveys (L), site descriptions (R) and species identifiers that were used to match the different trait databases.
DOI: 10.15454/di74ps
title: Données de réplication pour : Matériels Supplémentaires pour Livrable 2 OFB PhytoDOM 2021

description: Ce dossier contient les matériels supplémentaires présentés dans le livrable 2 OFB pour le projet phytoDOM, reprenant les activités de l'année 2021.
DOI: 10.15454/fqmc9w
title: Milling itineraries for a collection of biomasses including kinetics - Product characterisation D50, span and elongation
DOI: 10.15454/fgtihr
title: Transcriptome of the the tick synganglion

description: This
DOI: 10.15454/fd9fhu
title: Growth and annual valorisation of Breton grasslands simulated by STICS, and associated climate

description: The present data sets result from the study "Les prairies françaises : Production, exportation d’azote et risques de lessivage" and were used to build models for predicting the ten-day growth of grass from knowledge of the climate and the annual valuation of grasslands. They are limited to the Brittany region and the 1984-2013 period.
DOI: 10.15454/fk7whw
title: data_moisture_regimes_Zymoseptoria_tritici_Boixel_et_al._2020

description: Differential tolerance to altered moisture regimes during early infection stages in the fungal pathogen Zymoseptoria tritici. In planta responses of 48 genetically distinct isolates from Irish and Israelian populations originating from two contrasted Euro-Mediterranean climatic zones locations to four altered moisture regimes exerted on wheat seedlings during the first three days after inoculation. INRA BIOGER "Epidemiology of wheat diseases". Corresponding authors: Anne-Lise Boixel (anne-lise.boixel@inra.fr) and Frédéric Suffert (frederic.suffert@inra.fr).
DOI: 10.15454/efvswm
title: FR-Bil environmental data for the 2020 summer

description: This dataset contains half-hourly environmental measurement for the 2020 summer at the ICOS site FR-Bil used in a paper which present canopy surface temperature measurement and its impact on the canopy stomatal conductance. It regroup half-hourly measurement of canopy surface temperature, sapflux, latent heat of vaporization and other environmental variables continuously measured by ICOS such as radiation, dendrometric, air temperature and relative humidity ( all accessible on the carbon portal).
DOI: 10.15454/g6ngsz
title: Differential Adaptation of Propionibacterium freudenreichii CIRM-BIA to cow's milk versus soymilk envirnments modulates its stress tolerance and proteome

description: Propionibacterium freudenreichii 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 19 files of NanoLC-MS/MS analysis, acquired on a Qexactive mass spectrometer. Design: 2 classes (cow milk:"lait", soymilk: "soja"), 3 biological replicates. All samples were injected 3 times
DOI: 10.15454/gcyurm
title: Metabarcoding datasets and bioinformatic scripts for the LEARN_BIOCONTROL project

description: Metabarcoding datasets describing the foliar mycobiome of grapevine (Vitis vinifera L.) leaves collected in the LEARN-BIOCONTROL project. Bioinformatic scripts used to analyze the sequence data. Raw and filtered ASV table in the QIIME2 and R phyloseq formats.
DOI: 10.15454/ipmiox
title: Dataset of a three-year experiment about Zymoseptoria tritici sexual crosses on wheat according to the virulence or avirulence of the parental strains against a recently broken-down qualitative resistance gene

description: The raw data used for the analysis of the intensity of asexual multiplication and the intensity of sexual reproduction of Zymoseptoria tritici
DOI: 10.15454/izjit7
title: Stakeholders' preferences survey about new technology acceptance and potential development for waste management in wine production in Languedoc Roussillon, France

description: This dataset contains results of a survey conducted in order to understand the new technology acceptance and potential development for waste management in wine production. A total of six wine-makers and technical centers, two distilleries and three public decision-makers have been interviewed in the Languedoc-Roussillon in July and August 2018. All industries interviewed were close from the city of Montpellier, within a 150 km radius. Interviews were composed of approximately twenty questions evaluating interviewees’ knowledge about new by-products and valorization processes, but also about their preferences, expectations, demands and constraints regarding these new valorization possibilities. Each survey took about 45 minutes to be completed. After having interviewed all stakeholders, all data has been stored in the “NoAWVote”, a software specifically developed for the NoAW project to aggregate stakeholders’ preferences (Karanikolas et al. 2018)
DOI: 10.15454/ilh0ne
title: RPG complété 2018 département 81

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 81. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/ihvm9p
title: Consumer perception data about food packaging functionalities for fresh strawberries: consumers' answers to poll for Plastic not closed
DOI: 10.15454/ku1p28
title: MassJ : Julia package for mass spectrometry data treatment and analysis

description: MassJ is a package for loading, processing and plotting mass spectrometry data. It provides a range of functionalities such as: * Getting information on the file * Load a file * Averaging mass spectra based on various criteria that may be combined * Chromatogram * Processing the data - smoothing - baseline correction - peak-picking * Calculation of isotopic distribution
DOI: 10.15454/ioblws
title: Replication data for the article: "Biological control at work: demonstrating the complementary effects of natural enemies on two contrasting pests and the damage they cause"

description: This dataset includes all data and R code to reproduce the analyses and graphics presented in the article "Biological control at work: demonstrating the complementary effects of natural enemies on two contrasting pests and the damage they cause". Mesmin, X., Maret, M., Vincent, M., Daniel, L., Gardin, P., Raitif, J., Faloya, V., Cortesero, A.-M., Le Ralec, A. (2021). Journal of Pest Science._____Data are available either as separate csv files or as a compact RData directly usable in the R code (provided as Rmd).
DOI: 10.15454/jrb3p4
title: Supplementary tables to manuscript: “Crop and wild plants/weed species-associated viromes in a horticultural context: diversity, prevalence and stability over a two-year period”

description: Supplementary tables to manuscript in Chapter 1.
DOI: 10.15454/ixgwvt
title: Study of the Faux in the Verzy Forest (Fagus sylvatica variety tortuosa) - Supporting information

description: The objective of this project is help solve the mystery of the twisted beech phenotype, a mutant dwarf tree - Fagus sylvatica variety tortuosa – so far reported in several forests in France, Germany, Sweden and Denmark (see https://en.wikipedia.org/wiki/Faux_de_Verzy). The most famous stand is located in Verzy (25km south of Reims, France) where hundreds of Faux (their given name from the old French "fagus") characterized by their tortuous trunks and branches pending to the ground, have been preserved by the national forest office. More precisely, we aim at discovering the molecular bases of the mutation by comparing (i) the genomes of wild types (straight trees) and dwarf mutants, and (ii) genomic features (transcriptome, methylomes, mobilomes, small RNA populations, genomes) of six genotypes displaying both the mutant and wild type phenotypes. We hypothesized that the reversion of the mutation, resulting in a straight branch standing up from the typical igloo shape of the mutant, is caused by a somatic mutation in or near the mutated locus.
DOI: 10.15468/dl.gjcecy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Nycticeinops happoldorum (Hutterer, Decher, Monadjem & Astrin, 2019)",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028407-250525065834625/datasets/export for details.
DOI: 10.15454/l79x2k
title: Biotic Stress and Grain-Legumes WoS DataSet 1980-2018

description: The text file corresponds to the search query capturing the main biotic stress research theme on grain-legumes (both soya and pulses, see Species Grain-Legumes WoS dataset) to be applied on the WoS (Web of Knowledge). This search query is restricted to the main types of scientific literature documents, namely the types: article, book, book chapter, and review. This translated into the query DT = ("Article" OR "Book" OR "Book Chapter" OR "Review"); the time range selected is 1980-2018 (PY = "1980-2018"). Biotic Stress theme refers to various subjects on weeds, diseases and pests life traits and control in crops. UT file corresponds to the results of this search query (UT refers to a WoS unique identifier for each record retrieved) after a post-processing step which eliminated the records captured by the Wos KeyWord Plus : ie, the UT file correspond to records containing terms of the search query only in title, abstract, and (regular) keywords. See the related publication for more information.
DOI: 10.15454/kmau1g
title: Bioinformatic scripts to analyze metabarcoding data of fungal communities associated with two grapevine varieties (Vitis vinifera ‘Regent’ and ‘Cabernet-Sauvignon’)

description: This archive provides the bioinformatic scripts used to analyze a metabarcoding dataset (available at https://www.ncbi.nlm.nih.gov/bioproject/678415) representing foliar fungal communities associated with two grapevine varieties (Vitis vinifera ‘Regent’ and ‘Cabernet-Sauvignon’) inoculated with powdery mildew (Erysiphe necator) under various drought conditions. The raw and filtered ASV tables are provided in QIIME2 format and R phyloseq format. Summary statistics and interactive taxonomic plots (.qzv files) can be viewed in the QIIME2view interface.
DOI: 10.15454/jqpbow
title: Bioinformatic and statistical scripts to analyze the leaf-associated fungal community of wild plant populations

description: This dataset contains R-scripts to perform bioinformatic and statistical analysis on leaf-associated fungal communities of wild plant populations (Ma et al. Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Submitted). Raw sequences are available at https://doi.org/10.15454/X23KJF. Metadata and ASV tables are also provided allowing to use statistical analysis scripts without running the bioinformatic steps.
DOI: 10.15454/nshuaq
title: Bioinformatic scripts to assess the effect of the cropping system on both community and network α- and β-properties of fungal microbiota

description: These bioinformatics scripts were applied to the sequences available at https://doi.org/10.15454/3DPFNJ. They are based on several softwares, including SparCC (Friedman and Alm 2012) and DADA2 (Callahan et al. 2016). The code corresponds to R and R markdown files. These scripts were used to assess the effect of the cropping system on both community and network α- and β-properties of the foliar fungal microbiota of grapevine (Pauvert et al. Microbial networks inferred from metabarcoding data lack replicability: consequences for next-generation biomonitoring, Submitted).
DOI: 10.15454/nbnshh
title: Données de réplication pour: Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)

description: Along with these data, the script MusDakar.r is a template provided as supplementary material of the following article: Claire Stragier, Sylvain Piry, Anne Loiseau, Mamadou Kane, Aliou Sow, Youssoupha Niang, Mamoudou Diallo, Arame Ndiaye, Philippe Gauthier, Marion Borderon, Laurent Granjon, Carine Brouat Karine Berthier (2020). Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa). bioRxiv. DOI:10.1101/557066. [Version 4 of this preprint has been peer-reviewed and is recommended by Peer Community In Ecology, see DOI: 10.24072/pci.ecology.100044] This script is provided under the CC-BY licence, in order to illustrate the main analyses presented in this article. Thanks for refering to the article above if you use, adapt or redistribute this script.
DOI: 10.15454/pmvcfi
title: Apple FBo-Hi elite material mid-density genotypic data

description: This dataset corresponds to the genotypic data used for the elite material in the FBo-Hi panel used by Cazenave et al (2021) "Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple" G3: Genes, Genomes, Genetics. The dataset was obtained using the 20K apple SNP array (Bianco et al, 2014). These data were obtained in the frame of the EU seventh Framework Programme project FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops (http://www.fruitbreedomics.com/).
DOI: 10.15454/meiik0
title: GéoDispo, un nouvel outil pour géoréférencer facilement les objets d'étude (plantes ligneuses par exemple) dans les dispositifs expérimentaux de terrain

description: Dans la plupart des dispositifs expérimentaux (sylviculture, viticulture, arboriculture), les objets d'étude (dans ces cas des plantes ligneuses) sont identifiés dans un repère orthogonal spécifique au dispositif, avec des coordonnées de type XY qui ne permettent pas directement leur importation et leur positionnement cartographiques dans des SIG. On peut pallier ce problème en procédant au relevé des coordonnées de tous les individus dans le système de localisation mondial (Global Positioning System, GPS) ou en réalisant un géoréférencement directement sous SIG. La première solution est très coûteuse en matière de temps et la seconde requiert une procédure particulière réservée aux utilisateurs avertis. GéoDispo permet de transformer facilement les coordonnées XY de tous les individus en coordonnées Lambert-93, à partir des coordonnées GPS de seulement quatre objets d’étude. GéoDispo se présente sous la forme d'un tableur Excel® comprenant quatre feuilles explicitant les conditions d’utilisation, le mode opératoire, l’outil « Géoréférencer » et enfin les équations utilisées. GéoDispo peut fonctionner avec tous les systèmes de coordonnées cartographiques de référence. Abstract Geographic information system (SIG) are pretty used to analyse experimental devices in the field. However they need that coordinates of each studied object take part of a coordinate system of geodesique reference, as for example Lambert-93. In most of existing experimental devices, studied objects are identified within an orthogonal grid in the device, with coordinates like XY unmachable with the use of SIG. In order to point out sometimes thousand of GPS coordinates, a simple device has been set out : GeoDispo. It allows transforming easily XY coordinates of every items in Lambert-93 coordinates from GPS coordinates of only four studied objects. GéoDispo is an Excel® spreadsheet and comprises four sheets that explane use conditions, how to use mode, « Georeferencer » tool and also equations used. GeoDispo can work with every system of cartographic coordinates.
DOI: 10.15454/o78myf
title: Typology of European livestock production areas

description: This typology of European livestock production areas was made during the collective scientific assessment of the 'Role, impacts and services provided by European livestock production' that was carried out by INRA at the request of the French ministries responsible for Agriculture and the Environment, in cooperation with the French Environment and Energy Management Agency (ADEME). Based on Eurostat data for 2010 processed at the NUTS3 level (or NUTS2 level for Germany, Belgium and the Netherlands), each area was characterised by its livestock density (in livestock units (LU) per hectare of UAA) and by the proportion of permanent grassland (sensu largo i.e., including rangelands) within the UAA. This led us to distinguish six types of livestock production areas, and to represent areas where UAA is less than 20% of total area (Hercule et al., 2017 INRA Prod. Anim. 30, 285-302; Dumont et al., 2019 Animal, accepted). Serbia, Macedonia, Bosnia-Herzegovina and Albania were not considered in Eurostat 2010 and were therefore excluded from the analysis. French West Indies, Guiana, Madeira, and Canary Islands were also not considered.
DOI: 10.15454/mypxwp
title: Estimated counts and sea trout individual data from the upstream trap on the Bresle (France).

description: Data consists of sea trout yearly estimated counts for smolts and spawners from 1984 to 2017 on the Bresle river and individual data on spawners from 1981 to 2017. It was 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) on salmonids. 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/qstxwf
title: Impact of feeding strategies on young rabbit and its gut microbiota

description: You will find all the datasets presented in the study of Paës et al, "Establishment of hindgut bacterial ecosystems and acquisition of microbial functions in the infant rabbit: impact of early-life nutrition and polysaccharides ingestion" and described in the data paper "Multiomics analysis of postnatal nutrition impact on rabbit development at the weaning transition" With this experiment, we aimed to study the effects of post-natal feeding strategies on the co-maturation of the host and its microbiota in a rabbit model. Multi-level data were collected : phenotypic data (growth, feeding behaviour,oxidative stress, blood nutritional status, immunoglobulins concentrations), data on the gut microbiota and metabolome profiling as well as transcript profilings.