Find research datasets worth reusing

Antimicrobial resistance monitoring results complementing the European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021 – Germany

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision (EU) 2020/1729. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision (EU) 2020/172. The quantitative minimum inhibitory concentration (MIC) data from dilution methods, as well as the voluntary reporting of and Whole Genome Sequencing (WGS) data are included. Reporting authorities contributing to 2021 AMR data collection: Federal Institute for Risk Assessment

Antimicrobial resistance monitoring results complementing the European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021 – Estonia

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision (EU) 2020/1729. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision (EU) 2020/172. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. Reporting authorities contributing to 2021 AMR data collection: Veterinary and Food Board

Antimicrobial resistance monitoring results complementing the European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021 – Finland

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision (EU) 2020/1729. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision (EU) 2020/172. The quantitative minimum inhibitory concentration (MIC) data from dilution methods, as well as the voluntary reporting of and Whole Genome Sequencing (WGS) data are included. Reporting authorities contributing to 2021 AMR data collection: Finnish Food Authority

Antimicrobial resistance monitoring results complementing the European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021 – Luxembourg

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision (EU) 2020/1729. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision (EU) 2020/172. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. Reporting authorities contributing to 2021 AMR data collection: Administration des services vétérinaires

Comment on 'The central role of forests in the 2021 European floods'

Data belonging to the article: Staal, A. & Koren, G. (2023). Comment on 'The central role of forests in the 2021 European floods'. Environmental Research Letters 18, 048002. DOI:10.1088/1748-9326/acc260 The files contain: - The moisture sources in mm for the study area of Insua-Costa et al. (2022, ERL 17, 064053), 'box', for 1-15 July of each year during 2006-2021 and the 2021 event as described in Insua-Costa et al. (2022). - The moisture sources in mm for the Meuse basin for July of each year during 2006-2021. - The moisture sources in mm for the Rhine basin for July of each year during 2006-2021. - The masks used in Staal & Koren (2023). For further details, see Staal & Koren (2023) and the attributes of the netcdf files.

opencc-zeroMar 2023View details →

Biotic and abiotic data for: European Benthic survey of seagrass-lucinid mutualism

Coastal ecosystem functioning often hinges on habitat-forming foundation species that engage in positive interactions (e.g. facilitation and mutualism) to reduce environmental stress. Seagrasses are important foundation species in coastal zones but are rapidly declining with losses typically linked to intensifying global change-related environmental stress. There is growing evidence that loss or disruption of positive interactions can amplify coastal ecosystem degradation as it compromises its stress-mitigating capacity. Multiple recent studies highlight that seagrass can engage in a facultative mutualistic relationship with lucinid bivalves that alleviate sulphide toxicity. So far, however, the generality of this mutualism, and how its strength and relative importance depend on environmental conditions, remains to be investigated. Here we study the importance of the seagrass-lucinid mutualistic interaction on a continental scale using a field survey across Europe. We found that the lucinid bivalve Loripes orbiculatus is associated with the seagrasses Zostera noltii and Zostera marina across a large latitudinal range. At locations where the average minimum temperature was above 1°C, L. orbiculatus was present in 79% of the Zostera meadows; whereas, it was absent below this temperature. At locations above this minimum temperature threshold, mud content was the second most important determinant explaining the presence or absence of L. orbiculatus. Further analyses suggest that the presence of the lucinids have a positive effect on seagrass biomass by mitigating sulphide stress. Finally, results of a structural equation model (SEM) support the existence of a mutualistic feedback between L. orbiculatus and Z. noltii. We argue that this seagrass-lucinid mutualism should be more solidly integrated into management practices to improve seagrass ecosystem resilience to global change as well as the success of restoration efforts.

Data for: "Land-use intensity influences European tetrapod food-webs"

These .Rdata files enable to reproduce results from our article " Signatures of land use intensity on european tetrapod food-web architectures" along with the R code provided at: https://github.com/ChrisBotella/foodwebs_vs_land_use - raw_data : Raw data including GBIF and iNaturalist occurrences and IUCN enveloppes used to select sites and generate species presence/absence. We provide this file for transparency and reproducibility of our methodology. - preprocessed_data: preprocessed data (obtained from raw_data) used to generate our article Figures along with the next file. - TrophicNetworksList : .Rdata containing a list of igraph objects, each igraph is a foodweb associated to a site identify by the list element name.  - MultiRegMatrices: .Rdata containing especially the pre-computed matrix Y of cells (rows) by food web metrics (columns) and the covariate design matrix X (for the linear regressions) in order to facilitate and accelerate the reproduction of the analyses.

opencc-zeroDec 2022View details →

Data from: Climatic water availability mainly drives context-dependency of tree functional diversity effects on soil organic carbon storage in European forests

The interplay of forest stand and environmental factors shape soil organic C (SOC) storage in forest ecosystems but little is known about their relative impacts in different soil layers. Moreover, how environmental factors modulate the impact of stand factors, particularly species mixing, on SOC storage, is largely unexplored. In this study conducted in 21 forest triplets (two-species mixed stand and respective monocultures nearby) distributed in Europe, we tested the hypothesis that stand factors (functional identity and diversity) have stronger effects on topsoil (FF+0-10 cm) C storage than environmental factors (climatic water availability, clay+silt content, oxalate-extractable Al - Alox) but that the opposite occurs in the subsoil (10-40 cm). We also tested the hypothesis that functional diversity improves SOC storage under high climatic water availability, clay+silt contents, Alox. We characterized functional identity as the proportion of broadleaved species (beech and/or oak), and functional diversity as the product of broadleaved and conifer (pine) proportions. The results show that functional identity was the main driver of topsoil C storage while climatic water availability had the largest control on subsoil C storage. Contrary to expectations, functional diversity decreased topsoil C storage under increasing climatic water availability but the opposite was observed in the subsoil. Functional diversity effects on topsoil C increased with increasing clay+silt content, while its effects on subsoil C was negative at increasing Alox content. This suggests that functional diversity effect on SOC storage along environmental gradients depends on the specific environmental factor and the soil depth under consideration.

opencc-zeroApr 2023View details →

Data from: European bee diversity: Taxonomic and phylogenetic patterns

Aim Wild bees still face striking shortfalls in knowledge of biodiversity in key regions of the world. This includes Europe, where despite a long tradition of data gathering, the continental scale distribution patterns of wild bees have not been systematically analysed to date. This study aims to characterise large-scale biodiversity patterns to: (i) understand spatial-temporal heterogeneity in large-scale databases, (ii) locate genuine diversity hotspots and their relationship with biogeographical patterns or habitats of interests, and (iii) identify understudied species and areas to further design conservation actions for most at risk species in key regions. Location Europe Taxon Bees Methods We present a continental and standardised study of bee taxonomic and phylogenetic diversity patterns in Europe, using a large compilation of occurrence records of nearly three million validated occurrence records for 1,515 wild bee species. Results Southern and eastern Europe suffer from the largest gaps in data availability while northern and western regions benefit from better historical coverage. Our models show that higher wild bee diversity in Europe is hosted in xeric, warm areas, as highlighted by a clear latitudinal gradient. However, phylogenetic diversity is predicted to be more homogenous across Europe than taxonomic diversity, suggesting that policies and strategies targeted to protect species richness may differ from those targeting greater phylogenetic diversity. Main conclusions This study represents a significant advance in the characterisation of wild bee distribution patterns across Europe and is an important stepping stone towards the design of more targeted survey efforts and conservation actions of this key group of pollinators. This, in turn, will provide the data necessary to improve the spatiotemporal coverage in a context of ongoing and future Europe-wide monitoring schemes, to ultimately develop cost-effective, coordinated and evidence-based conservation actions and tailored habitat management actions that can be implemented on a smaller scale.

opencc-by-4.0Mar 2018View details →

Skeletal Variation and Adaptation in Europeans: Upper Paleolithic to the Twentieth Century

This file contains bone structural data and associated contextual information for 2177 European skeletons dating from about 32,000 years before present to the late 20th century. They were collected as part of a project funded primarily by the US National Science Foundation and carried out between 2007 and 2015. The primary publication associated with this file is: Ruff, C. B. (ed.) (2018) Skeletal variation and adaptation in Europeans: Upper Paleolithic to the Twentieth Century. Hoboken: Wiley Blackwell.  Please see the attached Notes file for more information on collaborators and contacts, as well as descriptions of data variables and other notes.

opencc-by-4.0Apr 2023View details →

Statistics for different european teams

This dataset was generated through web scraping with the intention to provide data in order to analyze the teams performance.

opencc-zeroApr 2023View details →

Supplementary materials for: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians

Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera Discoglossus, Rana, Lissotriton and Triturus using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species' systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.

Where are we now with European forest multi-taxon biodiversity and where can we head to? - Supplementary Material

Supplementary material of the paper "WHERE ARE WE NOW WITH EUROPEAN FOREST MULTI-TAXON BIODIVERSITY AND WHERE CAN WE HEAD TO?"

Supplementary materials for Detrital garnet geochronology by in-situ U-Pb and Lu-Hf analysis: A case study from the European Alps

Figure S2. Interactive 3D version of Fig.2 from main text, using the same symbology. To open, unzip folder and launch the .xhtml file in any internet browser. Use scroll wheel to zoom, left-click and drag to rotate. Table S1. Analytical parameters for garnet U-Pb and Lu-Hf analysis. Table S2. Isotopic and trace-element data. Table S3. Raman data.

European offshore wind farms and marine energy deployements

Three distinct dataset used to forecast the development of marine energy in Europe in the upcoming three decades: - European offshore wind farms - tidal energy converter deployements in Europe - wave energy converter deployements in Europe

Pig population data complementing the annual report on the epidemiological analyses of African swine fever (ASF) in the European Union - Bulgaria

This dataset contains swine population data. Reporting authorities contributing to the data collection: <ul> <li>ASF2022_BG - Bulgarian Food Safety Agency (BFSA)</li> </ul>

Continuous increase in evaporative demand shortened the growing season of European ecosystems in the last decade

Datasets provided above are processed data during the conducting analysis for our paper entitled "Continuous increase in evaporative demand shortened the growing season of European ecosystems in the last decade". Here is the abstract of the paper: Despite previous reports on European growing seasons lengthening due to global warming, evidence shows that this trend has been reversing in the past decade due to increased transpiration needs. We used an innovative method along with space-based observations to determine the timing of greening and dormancy and then to determine existing trends and causes. Early greening still occurs, albeit at slower rates than before. However, a recent (2011-2020) shift in the timing of dormancy has caused the season length to decrease back to 1980s levels. This shortening of season length is attributed primarily to higher atmospheric water demand in summer that suppresses transpiration even for soil moisture levels as of previous years. Transpiration suppression implies that vegetation is unable to meet the high transpiration needs. Our results have implications for future management of European ecosystems (e.g., net carbon balance and water and energy exchange with atmosphere) in a warmer world.

opencc-by-4.0Dec 2022View details →

European migration scenarios with probabilistic uncertainty assessment – Data Description

This open data deposit contains the data and code accompanying used in the report: Bijak (2023): European migration scenarios with probabilistic uncertainty assessment, QuantMig Project Deliverable D9.4. The cover note should be read in conjunction with the report, available via www.quantmig.eu, and with the individual readme files in the data folders that can be found within this Zenodo repository (DOI: 10.5281/zenodo.7954150).

Results of article : "Prospective European District Heating Scenarios based on Geographical Analysis"

Results of the paper "Prospective European District Heating scenarios based on geographical analysis". Three scenarios are generated : Ambitious, Circular, and Conservative. For each scenario, there is a gpkg file and an excel file. The gpkg file is the whole dataset of inputs and results, each row being a European city. The excel summarizes the results for each EU27+UK country.