cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/hmager
title: DMP of the TEAMTOX Project - stage before starting the project

description: Le but du projet TEAMTOX est de comprendre les mécanismes de régulation de la production de mycotoxines par un « méta-pathogène » : un « Méta-Fusarium sp. ». Une analyse écophysiologique du Méta-Fusarium sp. , qui regroupe les espèces fongiques du genre Fusarium majoritairement responsables de la fusariose des épis, sera réalisée en considérant le méta-Fusarium sp. comme une entité fongique unique, possédant un fonctionnement propre. En effet, alors que les données bibliographiques suggèrent fortement que les interactions fongiques jouent un rôle clef dans l’étendue des symptômes de la fusariose et la contamination par des mycotoxines, les études menées jusqu’à présent sont essentiellement de type réductionniste ciblant une espèce ou, pour un petit nombre d’entre elles, un couple d’espèces. Il est pourtant assumé que les interactions entre espèces du genre Fusarium conduisent à des effets qui ne vérifient pas l’équation « 1 + 1 = 2 ». Il est urgent de changer d’échelle et de dépasser les approches ciblant une seule espèce. C’est ce challenge qui guide le projet TEAMTOX. Le projet est construit autour de quatre axes expérimentaux avec comme objectif respectif : (1) caractériser la cinétique de distribution des espèces composant le Meta-Fusarium sp. et de sa production de mycotoxines, et analyser les perturbations induites par des modifications de température et de potentiel redox du milieu, (2) identifier les mécanismes moléculaires qui gouvernent la production de mycotoxines du Meta-Fusarium sp., (3) évaluer l’influence de la diversité intraspécifique sur la dynamique du Méta-Fusarium sp., (4) évaluer l’efficacité de solutions de biocontrôle (auparavant identifiées par des approches espèce-centrées) sur le Meta-Fusarium sp. et démontrer la valeur ajoutée de l’approche. La démarche mise en œuvre dans TEAMTOX et les résultats attendus permettront d’augmenter l’efficacité des stratégies de maîtrise de la contamination des récoltes céréalières par des mycotoxines.
DOI: 10.57745/hvpite
title: Plant Health Risks Identification from textual data

description: This corpus is created as part of the BEYOND project. It contains 23 texts annotated for the Named Entity Recognition (NER) and Named Entity Normalisation (NEN) tasks. The annotated entities types are plants, pests, dates and places. The resources for the normalisation are the EPPO Global Database and the GeoNames geographical database. These texts were annotated using the BRAT annotation tool and, therefore, have the brat annotation format. Each annotation file name has a format file_id.ann. The texts cannot be redistributed due to their license terms and conditions. However, you will find the URL to their sources as well as more information about each text in the corpus description.docx file.
DOI: 10.57745/j18jk2
title: MassiveFold data for targets T1249v1 - T250 and T1249v2 - T252

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/gokeqt
title: Interactive dashboard (R Shiny) and simulated dataset of "Towards intercrop ideotypes: non-random trait assembly can promote overyielding and stability of species proportion in simulated legume-based mixtures"

description: Simulated dataset and R Shiny dashborad for visualising data from the article "Towards intercrop ideotypes: non-random trait assembly can promote overyielding and stability of species proportion in simulated legume-based mixtures". The dashboard can can be used to teach basic principles of plant-plant interactions, including competition for light and nutrients and N facilitation related to legumes in intercrops.
DOI: 10.57745/hc64oe
title: Data, computer code and simulation output for the article "To tax or to ban? A Discrete Choice Experiment to elicit public preferences for phasing out glyphosate use in agriculture" by Amalie Bjørnåvold, Maia David, Vincent Mermet-Bijon, Olivier Beaumais, Romain Crastes dit Sourd, Steven Van Passel, and Vincent Martinet

description: This dataset contains the experimental data (survey and choice experiment output), computer code (in R) and simulation output (model estimations) for the Discrete Choice Experiment described in the article "To tax or to ban? A Discrete Choice Experiment to elicit public preferences for phasing out glyphosate use in agriculture" by Amalie Bjørnåvold, Maia David, Vincent Mermet-Bijon, Olivier Beaumais, Romain Crastes dit Sourd, Steven Van Passel, and Vincent Martinet.
DOI: 10.57745/hqjmya
title: A benchmark for elasto-plasticity in finite strain

description: Overview Finite strain elasto-plastic simulations are critical in fields such as materials science (metal forming, forging, additive manufacturing) and automotive engineering (crash simulations). These simulations are traditionally carried out using computationally intensive finite element analysis (FEA), which limits their use in optimization tasks (e.g., optimal control, design processes) and real-time applications (e.g., tele-operation, personnel training). In this work, we introduce a benchmark dedicated to highly non-linear elasto-plastic simulations, designed to evaluate and develop neural network models tailored for solving elasto-plastic problems under finite strain conditions, ultimately unlocking the potential for real-time optimization and interactive simulations. The datasets include simulations of 1D and 3D elements, featuring quasi-static sequences of applied loads on complex geometries, and the resulting computed quantities: displacements fields, plastic flow coefficient field, stresses. To specifically evaluate the impact of plasticity on different neural networks, the datasets also feature simulations with identical inputs but employing a purely elastic constitutive law. Unzip the data To unzip the split zip archive run : zip -F data.zip --out single-archive.zip and : unzip single-archive.zip Data format The data is stored in the `hd5` format and follows the structure: data/ paperclip/ ├─ meshes/ │ ├─ mesh3d.json //initial 3D mesh ├─ data.hd5 //simulation results ├─ test.hd5 //simulation results (test set) ├─ params.json //parameters used in data generation car_hood/ ├─ meshes/ │ ├─ base.stl //fine mesh, used for simulations. │ ├─ coarse.stl //coarse mesh, on which the results are recorded. │ ├─ bloq0.stl //meshes containing the blocked displacement zones. │ ├─ bloq1.stl │ ├─ bloq2.stl │ ├─ fine_to_coarse.json //conversion table from fine to coarse mesh. ├─ data.hd5 //simulation results ├─ test.hd5 //simulation results (test set) ├─ params.json //parameters used in data generation The HD5 files are organized according to the model: data.hd5/ ├─ data_0/ │ ├─ loads/ //loading │ ├─ elastic/ //elastic results │ ├─ plastic/ //elastoplastic results │ ... Scripts provided Some useful scripts are provided in the code.zip archive. Visualize and use the data A visualization script is available. It can be run as follows: python view_data.py path/to/dataset/ --datum 167 Torch dataloaders are provided in paperclip/loader.py and twizy/loader.py Generate the figures of the paper The figures of the paper can be easily reproduced by running the scripts paperclip/stats.py and twizy/stats.py. Generate new data To generate new data, cast3m is required. The installation can be done here. Fill in the path to the cast3m executable in the file tools/castem.json. Run one of the data generation scripts. Many options are available, detailed in the scripts.
DOI: 10.57745/i1mr1r
title: OSO vecteur 2021 - Département de l'Aveyron

description: Produit vectoriel de l'occupation du sol OSO 2021 sur le département de l'Aveyron
DOI: 10.57745/k7jdgv
title: Please read me first

description: Information on the datasets in the "Dataset pair profiling" collection
DOI: 10.57745/ktgd07
title: IPMWorks H2020 No. 101000339 - IPM Biofortification Strategy 2021-2022 June foliar disease assessment

description: IPMWorks H2020 No. 101000339 – IPM Biofortification Strategy 2021-2022 June foliar disease assessment raw data contains the percentage severity of disease assessments on each leaf layer (Leaf 1-4) in the reference and IPM Biofortification treatment strategies across all tramlines assessed and 5 assessment points within a tramline for the June 2021 assessment. It also includes information on the growth stage of the crop at the time of assessment.
DOI: 10.57745/gu67te
title: Periconia digitata Interproscan annotation

description: Interproscan annotation on 15,520 predicted proteins in the genome of Periconia digitata version used : interproscan-5.51-85.0 options used : -dp disables use of the precalculated match lookup service. All match calculations are run locally. -iprlookup lookup of corresponding InterPro annotation -goterms lookup of corresponding Gene Ontology annotation -pa lookup of corresponding Pathway annotation -f TSV tsv format output file (tabulation-separated values)
DOI: 10.57745/hlt7yr
title: Minimal needed resistive forces data, corrective forces data and abaci in rectilinear motion for different combinations of wheels and resilient floor coverings.

description: These data are the minimal resistive forces and the correctives forces for different types of wheel in rectilinear motion on various floors. 44 different wheels were tested, varying diameter (80mm, 100mm, 160mm and 200mm), tread (solid rubber, elastic-tyre, thermoplastic rubber, synthetic rubber, injected polyurethane, casted polyurethane and polyamide) and bearing (sleeve bearing, cone ball bearing and precision ball bearing). 5 differents floors were tested: a flat, smooth and horizontal steel plate and 4 resilient floor coverings (3 PVC multilayer floor coverings and 1 monolayer rubber floor covering). The resistive forces were obtained at steady state (where acceleration is zero for a constant velocity was 2,5km/h, i.e. at uniform rectilinear motion) using an original motorised test bench. Forces were measured with a six-axis force sensor. The tests were carried out, for each wheel and flooring for 5different loads: (13kg, 24kg, 37kg, 49kg and 62 kg). Average forces were then calculated from 3 round-trips. Combining these results with a mechanical model of a cart, permits to modelize the minimal pushing force to move it. The corrective forces, defined like being the difference between the resistive forces (obtained for a given couple wheel/floor on a floor covering) and the resistive forces (obtained for the same couple on the flat, smooth and horizontal steel plate), were deducted from the resistive forces results. Corrective forces abacus are the average corrective forces, for a specific tread and wheel bearing, in function of base foam hardness A/15 of floor covering, and for various loads carried by the wheel. The combination of the datas of the corrective forces abacus and of a pushing force’s model permits to evaluate the corresponding effort on floor coverings, knowing the pushing force of a four wheels manual handling equipment obtained when it moves on a steel plate. All the abaci are given (.csv files and image in .jpeg). An example of a trial for measuring resisitve forces with the test bench is shown by a short movie.
DOI: 10.57745/hxn1xt
title: Analysis report and associated Rmarkdown for Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils

description: Rmarkdown analytical report for article: Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils ABSTRACT Soil microbial communities respond quickly to natural and/or anthropic-induced changes in environmental conditions, with potential impacts in terms of soil functioning. However, most studies are limited to specific microbial groups, mainly bacteria and fungi, thus the in situ dynamics of the whole microbial community remains to be documented. Here, we investigated the response of the soil microbial community (archaea, bacteria, fungi, protists and viruses) to wheat straw input in a 4-month in-situ field study. We employed global metagenomics to characterise the whole soil microbial diversity, and compared the results with those previously obtained using high throughput amplicon sequencing on the same soil samples. Taxonomic patterns at the community, phyla and genus levels, were concordant between the two methodologies but global metagenomics was more sensitive and allowed studying all the microbial groups simultaneously, showing the considerable potential of this approach for the fine analysis of microbial population dynamics in situ. Microorganisms from each taxonomic group were affected directly or indirectly by the amendment. Land-use histories impacted the soil communities and their responses to amendment. Lastly, both inter and intra-domain trophic interactions could be inferred from our dataset. In particular, we observed the multiplication of viral sequences in the early phase of straw decomposition, in parallel to that of copiotrophic bacteria, suggesting a “kill-the-winner” dynamic that, to our knowledge, had not been observed before in soils. Our study highlights that top-down regulation by microbial predators or viruses might play a key role in soil microbiota dynamics and structure.
DOI: 10.57745/i5yvjh
title: Guide d'annotation des Bulletins de Santé du Végétal

description: Ce document présente le schéma d'annotation et les instructions à suivre pour l'annotation manuelle du corpus des Bulletins de Santé du Végétal (BSV). Il est destiné aux experts qui réalisent l'annotation, ainsi qu'aux personnes qui développent des méthodes de traitement automatique pour la prédiction et l'évaluation des annotations. L'annotation concerne les entités nommées, leur normalisation à l'aide de référentiels, ainsi que les relations sémantiques entre entités. Les instructions sont illustrées par des exemples tirés du corpus des BSV.
DOI: 10.57745/i7o9f5
title: Données pour Bien-être des chirurgiens dentistes français

description: Données collectées après une enquête nationale auprès des chirurgiens dentistes mesurant leur bien-être, leur résilience, leur anxiété et dépression, leur stress perçu et leurs stratégies d'adaptation au stress
DOI: 10.57745/gcyg3q
title: Triticum aestivum trait Corpus

description: The Taec corpus is a dataset of 540 Pubmed abstracts about bread wheat with manual annotations of species, phenotypes, and traits in the BioNLP-ST format. It is intended to learn and evaluate named entity recognition and linking methods in the plant trait domain.
DOI: 10.57745/hanqe7
title: NOMAD-Outcome_GA101024283_Recensement_posts_Facebook_CAPE_et_CLPMR_2013-2022

description: Ce fichier excel recense tous les posts Facebook publiés par les comités logement de Parc-Extension (CAPE, Comité d'action de Parc-Extension) et du Plateau Mont-Royal (CLPMR, Comité logement du Plateau Mont-Royal) entre 2008 et 2023. Le recensement des publications Facebook de ces deux groupes s'inscrit dans le cadre d'une recherche sur les mobilisations de quartier pour le droit au logement qui porte le nom de NOMAD-Outcome, Explaining the Outcomes of Neighbourhood Mobilization Against Displacement, et qui est financée avec des fonds européens (Marie Sklodowska Curie Action).
DOI: 10.57745/hhn3g5
title: MAGATT - Marker Assisited Gene Annotation Transfert for Triticeae

description: Test data for the MAGATT pipeline. Source code: https://forgemia.inra.fr/umr-gdec/magatt Documentation: https://umr-gdec.pages.mia.inra.fr/magatt/
DOI: 10.57745/hw3mzl
title: Mass spectrometry analyses of oxidized species produced with PsAA7 LPMOs from GalA and GalA DP3

description: We provide the raw data of the mass spectrometry analyses (MS) of oxidized species released by PsAA7 LPMOs from GalA and GalA DP3. 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/id1ls6
title: Ice texture data from ice core, NEEM, Greenland, 2007-2012

description: NEEM (North Greenland Eemian Ice Drilling) was an international ice core research project in Greenland. As other projects like GRIP and NGRIP, this ice core had the goal to extract informations and data about the last interglacial period. The project was directed and organized by the Danish former Centre for Ice and Climate at the Niels Bohr Institute and US NSF, Office of Polar Programs. It was supported by funding agencies and institutions in Belgium (FNRS-CFB and FWO), Canada (NRCan/GSC), China(CAS), Denmark (FIST), France (IPEV, CNRS/INSU, CEA and ANR), Germany (AWI), Iceland (RannIs), Japan (NIPR), South Korea (KOPRI), the Netherlands (NWO/ ALW), Sweden (VR), Switzerland (SNF), the United Kingdom (NERC) and the USA (US NSF, Office of Polar Programs) and the EU Seventh Framework programmes Past4Future and WaterundertheIce The coring site was located in North West Greenland (camp position 77.45°N 51.06°W). The drilling took place between 2007 and 2012. For more information about the project: https://neem.dk/, NEEM community members (doi:https://doi.org/10.1038/nature11789 ). The data provided here is published in Montagnat et al., (2014) (doi:https://doi.org/10.5194/tc-8-1129-2014) The dataset contains texture data (crystallographic orientations) measured on thin sections of ice extracted along the 2540 m depth ice core. The ice core has been subdivided and stored into core sections (also called “bags”) of 0.55 m long.
DOI: 10.57745/ijonlv
title: Data on 2341 grass fields from 100 mountain-area dairy farms in France: agricultural uses and geographical characteristics

description: Data collected by survey from 100 dairy farmers located in a mountainous area (France), including 72 farmers engaged in the traditional Salers system and 28 farmers engaged in a specialised dairy system. The questionnaire covered all uses of all grass fields during the entire outdoor period, considering ‘field’ as an area that was used in the same way throughout the entire period. Cutting dates, grazing dates, animal categories and numbers were recorded using a grazing and harvesting schedule. We also recorded key geographical and physical characteristics of each field, i.e. main slope, altitude, area, and distance from the farmstead. Each field in the presented database is thus described by 47 quantitative and qualitative variables. Further information on data collection and processing is available in the associated publication in Data in Brief (https://doi.org/10.1016/j.dib.2023.109242).
DOI: 10.57745/it6ita
title: Data for - MuFFIN - Modelling Foraging Fitness in Marine Predators

description: This repository contains information on the raw GPS-Time Depth Recorder-accelerometer data collected from two penguin species, The Little penguin (Eudyptula minor) and the Adélie penguin (Pygoscelis adeliae) published in: "The role of individual variability on the predictive performance of machine learning applied to large bio-logging datasets." Article DOI: 10.1038/s41598-022-22258-1 Marianna Chimienti * , Akiko Kato, Olivia Hicks, Frédéric Angelier, Michaël Beaulieu, Jazel Ouled-Cheikh, Coline Marciau, Thierry Raclot, Meagan Tucker, Danuta Maria Wisniewska, Andre Chiaradia, Yan Ropert-Coudert *Corresponding author. marianna.chimienti@cebc.cnrs.fr This study was supported by: H2020-Marie Skłodowska-Curie Individual Fellowship, project number 890284, "Modelling Foraging Fitness in Marine predators (MuFFIN)", awarded to Marianna Chimienti Nature of dataset: quantitative Purpose of dataset: collect movement data from penguin species Scope of dataset: quantify movement patterns in penguin species while foraging during the breeding season
DOI: 10.57745/ivwyl4
title: Integrating Adaptation Pathways and Ostrom's Framework for Sustainable Governance of Social-Ecological Systems in a Changing World

description: Supplementary S1: Raw social-ecological data and 4th tier SES analysis. Contains one zip file: Supplementary.S1.SESF.Analysis.zip Supplementary S2: details of data, GIS analysis and survey documents used for constructing the modeling the structure and dynamics of the hedgerow network in the study site. Supplementary.S2.Model.Application.Study.Site.pdf Supplementary S3: Raw physical and ecological data, GIS analysis and survey used for modeling the structure and dynamics of the hedgerow network in the two sites. Contains three types of files: Spreadsheet presenting the physical, GIS and ecological survey of the hedgerows present in the study sites during summer 2021: Hedgerows.Geo.Phys.Ecol.data.Peri.Urban.and.Rural.1989.2000.2019.xlsx Files summarizing information used for the GIS analysis (with QGIS) of all the hedgerows present in the study, and the spreadsheets allowing the estimation of the transition rates between hedgerow types: QGIS.data.full.zip pdf file showing a QGIS picture output of the evolution of the hedgerow network for rural and urban sites in between the four years (1946, 1989, 2000, 2019): Supplementary.S2.Pictures.GIS.Land.Use.Hedgerows.Rural.and.PeriUrban.1946.1989.2000.2019.pdf Supplementary S4: Octave or Matlab code used to reproduce the results Supplementary.S4.Octave-Matlab.Code.zip Supplementary S5: supplementary results Supplementary.S5.Results.pdf
DOI: 10.57745/jncwc4
title: IPMWorks H2020 No. 101000339 - IPM Biofortification Strategy 2021-2022 Field plan

description: IPMWorks H2020 No. 101000339 – IPM Biofortification Strategy 2021-2022 Field plan raw data contains the layout of the field where the case study was conducted, including tramlines where different treatment strategies were used. Information on the products applied within each treatment strategy and rate of application are included within.
DOI: 10.57745/js5hlr
title: Data set related to the article: "Performance, meat quality and blood parameters in four strains of organic broilers differ according to range use"

description: This dataset is the base of a peer-reviewed article. In the tab "Slaughter data" are presented the data per animal of the measures collected at the slaughter house. In the second tab "Weight" is presented the weight per animal at three different age.
DOI: 10.57745/kovf5b
title: Beech chips

description: Properties of the beech chips used for experiments in rotary kilns and drums
DOI: 10.57745/hou0ef
title: Operating methods and conditions for fermentation

description: This dataset presents the conditions and monitoring of alcoholic and acetic fermentations of apple and grape pomaces into wine and vinegar. Measurements include pH, Brix, alcohol content, acidity levels, fermentation temperature, and cooling water temperature. These measurements were conducted over the years 2021, 2022, and 2023. Measurements were carried out on two 10L pilot acetifiers from Frings and a semi-industrial acetifier from Gilson
DOI: 10.57745/hsrsvw
title: Tilleul à petites feuilles (small-leaves lime, Tilia cordata)

description: Fichier d'impression 3D : Bois de Tilleul à petite feuille file for 3D printer : Tilia cordata wood