cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/wirxic
title: RMQS1 16S taxonomy

description: RMQS: The French Soil Quality Monitoring Network (RMQS) is a national program for the assessment and long-term monitoring of the quality of French soils. This network is based on the monitoring of 2,240 sites representative of French soils and their land use. These sites are spread over the whole French territory (metropolitan and overseas) along a systematic square grid of 16 km x 16 km cells. The network covers a broad spectrum of climatic, soil and land-use conditions (croplands, permanent grasslands, woodlands, orchards and vineyards, natural or scarcely anthropogenic land and urban parkland). The first sampling campaign in metropolitan France took place from 2000 to 2009. Dataset: This dataset contains taxonomic affiliation (genus;family;order;class;phylum) for 16S rDNA (Archaea + Bacteria) dataset of 1,842 sites of the RMQS. Soil 16S rDNA gene was sequenced using pyrosequecing (GS FLX Titanium - Roche 454) at Genosocope. Bioinformatics analysis was performed using BIOCOM-PIPE (previously named GNS-PIPE) metabarcoding pipeline. Sequences taxonomic affiliation is based on Silva r132 database (see this zenodo repository for details). Taxonomic affiliation was performed on a rarefied dataset (10,000 reads). See associated articles for details, as well as Terrat et.al. (2014). Raw sequencing data are available at EBI. File structure: Taxonomy was splitted across five files with one line per site and one column per taxa (rmqs1_taxonomy_). Each line sums to 10,000 (rarefaction defined threshold). Three supplementary columns are present: Unknown: not matching any reference. Unclassified: missing taxa between genus and phylum. Environmental: matched to sample from environmental study, generally with only a phylum name. Five metadata files describe upper taxonomic level for each taxa (rmqs1_taxonomy_.metadata.tsv). Details: Some sites sample could not be collected, they do not appear in dataset. Some sites did not pass laboratory or bioinformatics step to attain 10k sequences before taxonomic assignation, they dot not appear in the dataset. One can link this dataset with 10.15454/QSXKGA to get each sample physico-chemical property, landuse, coordinates, or filtering sites using its site_officiel column. Sites with ID longer than 4 number are supplementary sites that are not in the center of the cells (e.g. 10797 and 20797 that came from cell 797).
DOI: 10.57745/ww5s3x
title: In-depth characterization of 4 carbon nanomaterials (MWCNT, DWCNT, FLG, GNP) chemically modified by oxidation with KMnO4

description: Double-walled carbon nanotubes (DWCNTs), multi-walled carbon nanotubes (MWCNTs), few-layer graphene (FLG) and graphene nanoplatelets (GNPs) were chemically modified by refluxing in potassium permanganate at 0.2 M for 40 min rigorously in the same way. The oxidized samples have been characterized by means of several complementary characterization techniques : transmission electron microscopy (TEM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA) under air and TGA coupled with a mass spectrometry (TGA-MS) under He. The dataset provides morphological, structural and chemical characterizations of the four chemically treated carbon nanomaterials.
DOI: 10.57745/vtmyp0
title: Urban soil desealing

description: The research project DESSERT (Desealing of soils, ecosystem services and territory resilience – 2020-2024) supported by the French Agency for Ecological Transition (Ademe) aims to inventory practices of soil desealing, and to acquire scientific knowledge on desealed soils to provide tools to help urban stakeholders to design and implement soil desealing practices. Within this project, the present work aims at improving our knowledge on current desealing practices in urban environments. To do so, information on soil desealing operations was collected using an online survey and direct interaction with urban operators. Quantitative and qualitative data were gathered and analysed to draw a first picture of soil desealing practices. Two complementary strategies were carried out to compile data on desealing operations. (1) Online questionnaire run over a period of 4 months (June 7th to September 17th, 2021). Email reminders were made during the questionnaire's accessibility period. The questionnaire included sixty questions, mostly semi-open question (multiple choice with single or multiple answers) or text question. Due to the structure of the questionnaire, each question is independent from the others. (2) Case studies of soil desealing were collected through direct interaction with consulting firms, partners of the DESSERT project. The desealing projects described were added to the feedbacks collected from the online questionnaire.
DOI: 10.57745/vufbgr
title: MassiveFold data for target T1235 - T290

description: MassiveFold data generated for CASP16, in collaboration with CAPRI . 8040 predictions were generated for the target = 1005 x 8 sets of parameters. - a description of the setup can be found in `MassiveFold_CASP16_Abstract.pdf` - `README.txt` describes the contents of the main `MassiveFold.tar.gz` file - the main `MassiveFold.tar.gz file contains all the predictions, divided into 8 folders named after the conditions. It contains predictions as well as pickle files, sequence alignments, rankings and plots. The README.txt file describes the contents of this tar.gz. - the `only_pdbs_MassiveFold.tar.gz` is the result of the `gather_runs.py` script, without the pickle files. It contains a list of all the pdb files and ranking files with scores. - `gather_runs.py` allows to gather the runs, to use preferentially to the one included in the main `MassiveFold.tar.gz` at the time of the prediction phase, because it has been updated - `combined_scores.csv` file contains the CASP assessment for the target (from https://predictioncenter.org/) - `CAPRI_assessment.csv` file contains the CAPRI assessment for the target (from https://www.capri-docking.org/assessment/) - `CAPRI_scoring.pdb.gz` is a multi-pdbs containing all the MassiveFold predictions for the target. It was used for the CAPRI scoring phase.
DOI: 10.57745/we8ax8
title: PHODE-21 Data

description: Data for PHODE-21 project
DOI: 10.57745/rllzrm
title: Matches of Minc repeat on Mluci contigs

description: Results of a BLASTn search with the M. incognita repeat as a query against the M. luci contigs. Positions of the composite repeats, their orientation and presence / absence of the 3 constitutive motifs are indicated.
DOI: 10.57745/tckstd
title: PigLet case study for ASTERICS

description: This case study focuses on fetal development in late gestation in pig species (Lefort et al. 2020). The study addresses the question of delayed development in mammalian that may impact survival ability at birth. Two ages at late gestation were studied, 90 and 110 days (birth is expected at 114 days). Two genetic lines were included, LW for Large White, with higher risk of delayed development, and MS for Meishan, more robust. Studied piglets were of four genotypes: LWLW, MSMS, and the crossed piglets LWMS and MSLW. The data is composed of in four datasets corresponding to metabolomic analyses (NMR) performed on plasma, urine, and amniotic fluid samples of 444 piglets and to a metadata file providing information on piglets and on the design of the experiment. In addition, the data collection also contains the results of the analysis performed with ASTERICS https://asterics.miat.inrae.fr under the UID `piglet_usecase`.
DOI: 10.57745/w7fb4w
title: JACS correction notices - Dataset (2000-2023)

description: On April 8, 2023, we collected 1083 correction notices issued by the JACS (Journal of the American Chemical Society) since 2000, which includes 1061 Additions/Corrections and 22 Retractions. These notices refer to 1068 publications (53% of which are Articles, 45% are Communications, and less than 2% are other document types). The correction notices are labeled as adequate or not depending on how they are displayed in the Web of Science, Scopus, PubMed. The initial publications they are related to are labeled as adequate or not depending on how they are displayed on the JACS website and across other venues (i.e., the Web of Science, Scopus, PubMed, OpenAlex and Crossref).
DOI: 10.57745/wrn3dd
title: Epreuve : Fluence d'action

description: Mise à disposition de l'épreuve de Fluence d'action ainsi que le tableur calculant les normes et l'article publié. Cette épreuve permet d'évaluer les capacités de fluence d'action et contribuer à identifier les performances de patients ayant une démence fronto-temporale de ceux ayant une maladie d'Alzheimer.
DOI: 10.57745/wtdv2x
title: Outil de saisie pour l'inventaire de cycle de vie des produits de la pêche

description: Ce tableur a pour objectif de guider la récolte des données et de réaliser les calculs de base pour l'établissement d'un inventaire du cycle de vie de l'activité de pêche à l'échelle d'un navire et d'une campagne de pêche, jusqu'au débarquement du poisson. Il porte sur la description d'un triplet comprenant une espèce cible, une zone de pêche et un engin de pêche. Il comporte huit onglets: Guide d'utilisation, informations, détail navire, description de la saison, activités de pêche, apparaux de pêche, conservation et transformation. Le tableur permet la concaténation des données pour un transfert vers un logiciel de calcul d'analyse du cycle de vie. The purpose of this spreadsheet is to guide data collection and perform the basic calculations required to draw up a life cycle inventory of fishing activity on the scale of a vessel and a fishing campaign, right up to the landing of the fish. It describes a triplet comprising a target species, a fishing area and a fishing gear. It comprises eight tabs: user guide, information, vessel details, season description, fishing activities, fishing gear, preservation and processing. The spreadsheet allows data to be concatenated for transfer to a life cycle assessment calculation software.
DOI: 10.57745/x4qwkz
title: Life Cycle Assessment of new fermented food products mixing cow milk and pea protein sources

description: Life Cycle Assessments (LCA) were performed to assess the environmental performance of 4 new fermented food products that mix animal (milk) and plant (pea) protein sources in different ratios (100% Pea, 75% Pea-25% Milk, 50% Pea-50% Milk, 25% Pea-75% Milk). The system perimeter goes from the agricultural production of the ingredients to the ready-to-eat products. Environmental impact results were obtained for 1 kg of ready-to-eat product, for all the environmental indicators calculated by the EF 3.0 Method on the SimaPro software. Life cycle inventories included the different flows in the LCA (raw materials, energy, water, cleaning products, packaging, transport, wastes). Foreground data have been acquired on the manufacturing site, background data were taken from the Ecoinvent 3.6 database. The dataset contains details on products, processes, equipment, infrastructures, mass and energy flows, Life Cycle Inventories (LCI) and Life Cycle Impact Assessment (LCIA) results.
DOI: 10.57745/x9fwag
title: Long-distance wind dispersal of Culicoides from EHDV-infected areas in France

description: The dataset was used to investigate the magnitude of Culicoides wind dispersal in the context of Epizootic Hemorrhagic Disease Virus (EHDV) emergence in France, retrospectively and prospectively in 2024. This dataset is a subset of a bigger wind connectivity matrix, which estimates when and how often two locations anywhere in Europe could be connected by wind, based on HYSPLIT simulations adapted to Culicoides survival conditions. The subsets were performed according to the source zone and the period/year considered in the paper entitled: ‘Windborne dispersion of Culicoides midges in Europe: case study with EHDV in France’.
DOI: 10.57745/vekhqs
title: Meloidogyne enterolobii E1834 genome structure analysis

description: Genome structure analysis was conducted using MCScanX (Wang et al., 2012), with default settings. First, the whole proteome of M. enterolobii, predicted by EuGene, was self-blasted with an E-value cutoff of 1e-25, a maximum of 5 aligned sequences, and maximum 1 high-scoring pair (hsp). Subsequently, we used gene location information extracted from the GFF3 annotation file of EuGene, along with homology information based on the all-versus-all BLASTP analysis, to identify and categorize each duplicated protein-coding gene into one of five groups using the duplicate_gene_classifier program implemented in the MCScanX package. The use of MCScanX reveals that a majority of gene duplicates create whole duplicated blocks, rather than dispersed independent duplications. Following the classification established by the duplicate_gene_classifier program implemented in the MCScanX package, 39,532 of the protein-coding genes (around 86.10%) are predicted to be duplicated at least once. Furthermore, a majority of these coding genes (75.6%) show a duplication depth of two (meaning for these genes, two other copies exist), further reinforcing the idea that the genome is triploid.
DOI: 10.57745/vnmvjv
title: Principales caractéristiques des exploitations engagées dans des Signes Officiels de Qualité et d'Origine (SIQO) agrégées par produit à partir des données du Recensement Agricole 2020

description: Les indicateurs portent sur les exploitations engagées dans des signes officiels de qualité et d'origine (SIQO) hors agriculture biologique en 2020. Les types de SIQO concernés sont les Appellations d’Origine Protégées (AOP), les Indications Géographiques Protégées (IGP), les Labels Rouges (LR) et les Spécialités Traditionnelles Garanties (STG). Les indicateurs sont relatifs à la taille des exploitations, les caractéristiques du chef d'exploitation (âge, formation, sexe), les activités de diversification (transformation, externalisation, circuits courts) et les autres démarches de qualité et environnementales. Ils sont agrégés par produit SIQO (1 produit = 1 cahier des charges). Les indicateurs portant sur moins de trois exploitations sont soumis au secret statistiques (ss). Sources et méthodologie: Appariement réalisé sur le CASD entre les données du recensement agricole 2020 et les données de l'INAO/ODR-INRAE sur les opérateurs habilités en signe de qualité et d'origine au 4ème trimestre 2020. Clé d’appariement : numéro SIRET. Année : 2020. Ne sont retenus que les opérateurs ayant déclaré un SIQO (AOP, IGP, Label Rouge) dans le recensement agricole 2020 et retrouvés dans la base des opérateurs habilités de l'INAO avec le même signe de qualité pour l'habilitation (sauf vins AOP/IGP toléré). Cela représente un peu plus de 80% des déclarants SIQO au RA ( voir document technique sur le bilan de l’appariement). Pour plus d’informations sur les données disponibles sur les SIQO, vous pouvez consulter le site de l’Observatoire Territorial des SIQO, fruit du partenariat entre l’INAO et INRAE.
DOI: 10.57745/we0vk8
title: Replication data for Impact of a Brief Early-life Motor Training on Mouse Neuromuscular Development.

description: Replication data for the paper entitled: Impact of a Brief Early-life Motor Training on Mouse Neuromuscular Development published in PloS Biology. Electrophysiological data from lumbar motoneurons recorded in newborn mice, analysis of myelin sheath and MyHC in hindlimb muscles.
DOI: 10.57745/wqxg3j
title: MassiveFold data for target H1233 - T280

description: MassiveFold data generated for CASP16, in collaboration with CAPRI . 8040 predictions were generated for the target = 1005 x 8 sets of parameters. - a description of the setup can be found in `MassiveFold_CASP16_Abstract.pdf` - `README.txt` describes the contents of the main `MassiveFold.tar.gz` file - the main `MassiveFold.tar.gz file contains all the predictions, divided into 8 folders named after the conditions. It contains predictions as well as pickle files, sequence alignments, rankings and plots. The README.txt file describes the contents of this tar.gz. - the `only_pdbs_MassiveFold.tar.gz` is the result of the `gather_runs.py` script, without the pickle files. It contains a list of all the pdb files and ranking files with scores. - `gather_runs.py` allows to gather the runs, to use preferentially to the one included in the main `MassiveFold.tar.gz` at the time of the prediction phase, because it has been updated - `combined_scores.csv` file contains the CASP assessment for the target (from https://predictioncenter.org/) - `CAPRI_assessment.csv` file contains the CAPRI assessment for the target (from https://www.capri-docking.org/assessment/) - `CAPRI_scoring.pdb.gz` is a multi-pdbs containing all the MassiveFold predictions for the target. It was used for the CAPRI scoring phase.
DOI: 10.57745/tny0ya
title: MassiveFold data for target T1266

description: MassiveFold data generated for CASP16, in collaboration with CAPRI . 8040 predictions were generated for the target = 1005 x 8 sets of parameters. - a description of the setup can be found in `MassiveFold_CASP16_Abstract.pdf` - `README.txt` describes the contents of the main `MassiveFold.tar.gz` file - the main `MassiveFold.tar.gz file contains all the predictions, divided into 8 folders named after the conditions. It contains predictions as well as pickle files, sequence alignments, rankings and plots. The README.txt file describes the contents of this tar.gz. - the `only_pdbs_MassiveFold.tar.gz` is the result of the `gather_runs.py` script, without the pickle files. It contains a list of all the pdb files and ranking files with scores. - `gather_runs.py` allows to gather the runs, to use preferentially to the one included in the main `MassiveFold.tar.gz` at the time of the prediction phase, because it has been updated - `combined_scores.csv` file contains the CASP assessment for the target (from https://predictioncenter.org/)
DOI: 10.57745/v1uq7j
title: ATHEM Result Files

description: Files used to build the ATHEM Resources
DOI: 10.57745/xaasrz
title: Photos of large plastic fragments sampled during the composting experiment and identified by FTIR

description: Large plastic fragments were sampled during the composting experiment and chemically identified by Fourier Transform Infrared Spectroscopy. The dataset contains the photos of the fragments. The identification of the samples is available in the dataset "Identification of large plastic fragments sampled during the composting experiment", https://doi.org/10.57745/M3MYBU.
DOI: 10.57745/v2w0ek
title: PGD de l’Unité Expérimentale de la Fage (UEF)

description: Plan de Gestion de Données de l’Unité Expérimentale de la Fage (PGD UEF) L'UEF est une unité expérimentale de l'Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), rattachée au département de Génétique Animale (GA) : https://uef.isc.inrae.fr/ Elle est le support de recherches menées sur les ovins laitiers et allaitants. Le PGD de l'infrastructure décrit l'organisation et les moyens mobilisés pour la mise en œuvre de la politique de gestion et de valorisation des données : https://doi.org/10.57745/V2W0EK
DOI: 10.57745/xepnuh
title: Dexi-Dairy indicator handbook - Sustainability tree and selected indicators for assessing European specialised dairy farms

description: The MilKey project aims at assessing the environmental, economic, and social sustainability of European dairy production systems, and at identifying ‘win-win’ farming practices for sustainable and greenhouse gas (GHG) optimised milk production. In this context, a holistic model was developed to evaluate the sustainability of specialised dairy farms and was entitled DEXi-Dairy. This model has the potential of aiding the identification of GHG and nitrogen (N) emission mitigation options and assessing their effects across multiple sustainability aspects. DEXi-Dairy covers the three sustainability pillars, i.e., environmental, economic, and social. Based on the ‘DEX’ multi-criteria methodology, the model is detailed under the form of a tree structure represented by four main hierarchical layers, i.e., branches, principles, criteria, and indicators. DEXi-Dairy was built following a participatory and interdisciplinary approach by MilKey project partners. It was then tested on three case study farms from Ireland, France, and Germany, respectively, using data from 2020. The DEXi-Dairy indicator handbook describes the sustainability tree and selected indicators to assess dairy production systems over a production year. Overall, this document can be used as a basis to replicate and expand the sustainability assessment framework developed as part of the MilKey project.
DOI: 10.57745/xgdgrr
title: Flow intermittence indicators from the reconstruction simulations (1960-2021) in the Lepsämänjoki DRN (Finland)

description: Statistical monthly and yearly flow intermittence indicators calculated from the simulated daily state of flow in the Lepsämänjoki DRN (Finland). Indicators for the reconstruction period (1960-2021).
DOI: 10.57745/xs7ivp
title: Données de réplication pour : Bean crop residues (stubble) for feeding sheep during dry season shortage in Cuba

description: The feasibility of feeding sheep with bean stubble produced during the dry season of Cuba was evaluated under real-farm conditions in Moron (Ciego de Avila, Cuba). The dataset present the choice of farms the municipality, the crop residue yields per farm, the results from an experimentation with animals evaluating the voluntary bean stubble intake (supplemented with sugarcane molasses), the results from an animal behaviour trial in the scope of that experimentation, as well as the carcass yield and composition at the end of the experiment. Finally, an assessment is presented with regard the potential meat sheep production to be expected if sheep flocks are fed with such high volumes of crop residues produced in the region, after bean harvest every year.
DOI: 10.57745/vlwj51
title: RMQS1 molecular microbial biomass

description: RMQS: The French Soil Quality Monitoring Network (RMQS) is a national program for the assessment and long-term monitoring of the quality of French soils. This network is based on the monitoring of 2,240 sites representative of French soils and their land use. These sites are spread over the whole French territory (metropolitan and overseas) along a systematic square grid of 16 km x 16 km cells. The network covers a broad spectrum of climatic, soil and land-use conditions (croplands, permanent grasslands, woodlands, orchards and vineyards, natural or scarcely anthropogenic land and urban parkland). The first sampling campaign in metropolitan France took place from 2000 to 2009. Dataset: Soil DNA was extracted and quantified from soils sampled from the center of RMQS grid cells (between 0 and 20cm). A specific and standardized DNA extraction procedure was used so that all samples could be compiled and interpreted in terms of molecular microbial biomass (MMB). See Horrigue et.al. 2016 for details. Values were re-extracted from GenoSol platform database, each value corresponding to the last MMB measure performed between 2012 and 2018. File structure: Two columns tabulated file with a MMB value per sample. id_site: sample/site unique identifier across RMQS. Stripped down from a longer identifier containing campaign number and site type. biomass: molecular microbial biomass measured in microgram of DNA per gram of soil. Details: Some sites sample could not be collected, they do not appear in dataset. Sites with ID longer than 4 number are supplementary sites that are not in the center of the cells (e.g. 10797 and 20797 that came from cell 797). Some of them can replace missing official site (e.g. 12258 is in the dataset, but not 2258. See dataset doi:10.15454/QSXKGA for filtering sites using its site_officiel column.