Find research datasets worth reusing

opencc-by-4.0Oct 2016View details →

Figure 1 in Albania: another European country with the occurrence of Buchonomyia thienemanni Fittkau, 1955

Figure 1. Shkumbin River, view of the sampling site of B. thienemanni. Photo: K. Trnková

opencc-zeroDec 2022View details →

The genomics of adaptation to climate in European great tit (Parus major) populations

The recognition that climate change is occurring at an unprecedented rate means that there is increased urgency in understanding how organisms can adapt to a changing environment. Wild great tit (Parus major) populations represent an attractive ecological model system to understand the genomics of climate adaptation. They are widely distributed across Eurasia and they have been documented to respond to climate change. We performed a Bayesian genome-environment analysis, by combining local climate data with SNP genotype data from 20 European populations (broadly spanning the species' continental range). We found 36 unique putative climate adaptation genes that were associated with variation in climate. Following an enrichment analysis of biological process Gene Ontology (GO) terms, we identified over-represented terms and pathways among the genes putatively under selection for climate adaptation. Because many different genes and GO terms are associated with climate variables, it seems likely that climate adaptation is polygenic and genetically complex. Our findings also suggest that geographical climate adaptation has been occurring since great tits left their Southern European refugia at the end of the last ice age. Finally, we show that substantial climate-associated genetic variation remains, which will be essential for adaptation to future changes.

opencc-zeroDec 2022View details →

Normalised absorbance ratios of IgG for myxoma and rabbit hemorrhagic disease viruses: Longitudinal dataset wild European rabbits

This study addresses the long-term dynamics of humoral immunity to two viral pathogens of the European rabbit, an endangered keystone species of major ecological relevance. Such studies are particularly challenging in free-ranging species, and a combination of longitudinal capture-mark-recapture and semi-quantitative serology was used to address this question. Over 600 normalised absorbance ratios of indirect ELISA, obtained from 505 individual rabbits in 7 populations over five years were analysed using linear mixed models. The results support a lifelong acquired humoral immunity to myxoma virus and rabbit hemorrhagic disease virus upon natural infection and suggest the presence of maternal immunity to the latter in wild juvenile rabbits. These results contribute to understanding the epidemiology of two viral diseases threatening this keystone species and assist in developing conservation programs.

Data for: Food Anticipatory Behaviour on European Seabass in Sea Cages: Activity-, Positioning- and Density-based approaches

Telemetry and sensory data data for: Food Anticipatory Behaviour on European Seabass in Sea Cages: Activity-, Positioning- and Density-based approaches Please read the README.txt file before working with the data.

Techno-economic evaluation and resource assessment of hydrogen production through offshore wind farms: A European perspective - Supplementary material

This is the additional material provided with the journal article "Techno-economic evaluation and resource assessment of hydrogen production through offshore wind farms:  A European perspective" published in Renewable and Sustainable Energy Reviews (<a href="https://doi.org/10.1016/j.rser.2023.113699">https://doi.org/10.1016/j.rser.2023.113699</a>). Datasets are provided as NetCDF files for European maps and CSVfor Economically Attractive Resource curves. European and National plots are provided as PDF files.

opencc-by-4.0Dec 2022View details →

Reproducibility of the wet part of the soil water retention curve: a European interlaboratory comparison (dataset)

The soil water retention curve (SWRC) is a key soil property required for predicting basic hydrological processes. The SWRC is often obtained in the laboratory with non-harmonized methods. Moreover, procedures associated with each method are not standardized. This can induce a lack of reproducibility between laboratories using different methods and procedures or using the same methods with different procedures. The goal here was to estimate the inter- and intralaboratory variability of the measurement of the wet part (from 10 to 300 hPa) of the SWRC. An interlaboratory comparison was carried out between 14 laboratories, using artificially constructed, porous reference samples that were transferred between laboratories according to a statistical design. The retention measurements were modelled by a series of linear mixed models using a Bayesian approach. This allowed the detection of sample-to-sample variability, interlaboratory variability, intralaboratory variability and the effects of sample changes between measurements. Here we present the dataset containing measured data from the interlaboratory comparison, R code to implement models, and final model results.

openJun 2023View details →

Homo sapiens expanded into the Northern European Plains by 45,000 years ago

1,322 morphologically unidentified fragmentary bone specimens were analyzed using MALDI-TOF and a subset of 341 bone specimens with LC-MS/MS in order to characterize their proteome for species identification and potential hominin specimens related to the LRJ transitional period derived from the site Ilsenhöhle Ranis, Germany (50°39.7563’N, 11°33.9139’E).

European Reference Genome Atlas Community - Phase 1 Members - 2020-2023

This dataset presents a comprehensive list of members registered as part of the European Reference Genome Atlas (ERGA, erga-biodiversity.eu) Community during ERGA Phase 1, which spanned from 2020 to 2023. The dataset includes information on the various roles undertaken by these members, particularly those who played a key role in establishing ERGA. Founding members are individuals who joined ERGA prior to the first leadership elections in February 2021, and they were instrumental in building the initial structure of ERGA. Some of these founding members were also involved in the establishment of different ERGA Committees. The dataset further includes details about the current and former core members and chairs of the ERGA committees. Additionally, it provides a list of the current (2023) and former Council members, along with the countries or regions they represent. The dataset is organised in alphabetical order for ease of reference. The co-authors of this dataset encompass both current and former ERGA Council members, listed in alphabetical order, and the current ERGA chair, as the last author.

Supplementary figures for 'Domino: A new framework for the automated identification of weather event precursors, demonstrated for European extreme rainfall.'

Supplementary dynamics and skill plots for the paper 'Domino: A new framework for the automated identification of weather event precursors, demonstrated for European extreme rainfall', submitted to QJRMS.

opencc-by-4.0Jul 2023View details →

Associated data underlying the article "OPEN GOVERNMENT DATA (OGD) IN EUROPEAN EDUCATIONAL PROGRAMS CURRICULUM CURRENT STATE AND PROSPECTS"

Associated data underlying the article Rizun, Nina; Ciesielska, Magdalena; Alexopoulos, Charalampos; Saxena,Stuti; Papageorgiou, Georgios  International Conference on Open Data (ICOD 2022): Book of abstracts, Faculty of Law, University of Zagreb, Zagreb, Croatia, pp. 26-29 (978-953-270-167-8). <pre><a href="https://doi.org/10.5281/zenodo.8069910">https://doi.org/10.5281/zenodo.8069910</a></pre> It is everybody’s knowledge now that Open Government Data (OGD) pertains to the availability of datasets pertaining to government operations and functioning via license-free formats (Afful-Dadzie and Afful-Dadzie, 2017) and these datasets are linked with different themes contingent upon the area of administration like energy, education, climate, tourism, environment, infrastructure, etc. (Ubaldi, 2013). Governments have been benchmarking their OGD initiatives across standard indices like ODIN, OKFN, Open Data Barometer, etc. (Lnenicka et al., 2022; Lnenicka and Nikiforova, 2021) and ample research exists on assessing the quality of OGD portals from the demand (i.e. the governments’ efforts at maintaining the quality of datasets) and supply (i.e. the perceptions of users regarding the quality of datasets) side (Crusoe et al., 2019; de Souza et al., 2022; Islam et al., 2021; Kaasenbrood et al., 2015; Khurshid et al., 2022; Lnenicka et al., 2022; Purwanto et al., 2020; Saxena and Janssen, 2017; Shehata and Elgllab, 2021; Talukder et al., 2019; Weerakkody et al., 2017; Wirtz et al., 2016; Wirtz et al., 2018; Wirtz et al., 2019; Zuiderwijk et al., 2015). Given the magnitude of academic interest on OGD- especially in the last 10 years- it remains to be assessed as to how far has the domain progressed in the academic environs and surprisingly, no research has been conducted to elucidate the infusion of this very significant domain- that is relatable to the extent to which the governments are forwarding their claims regarding the furtherance of transparent and corruption-free administration apart from bolstering citizen participation, collaboration and trust (Gil-Garcia et al., 2020; Hellberg and Hedstrom, 2015) besides serving as a means for value creation and innovation by a range of stakeholders (Jetzek et al., 2012; Jetzek et al., 2014) - in the diverse platforms that are meant for furthering academic dialogue and discussion.

opencc-by-4.0Jul 2023View details →

Modelling results for the paper "The impact of methane leakage on the role of natural gas in the European energy transition"

This data file represents the modelling results of the paper "The impact of methane leakage on the role of natural gas in the European energy transition" that is accepted to Nature Communications.

opencc-by-4.0Jul 2023View details →

Contrasting Patterns of Pierce's Disease Risk in European Vineyards Under Global Warming

Data associated to the publication Contrasting Patterns of Pierce’s Disease Risk in European Vineyards Under Global Warming

opencc-by-3.0Jul 2023View details →

Research compendium for 'Hussain et al. (2023) A pan-European dataset revealing variability in lithic technology, toolkits, and artefact shapes ~15-11 kya'

Research compendium for 'A pan-European dataset revealing variability in lithic technology, toolkits, and artefact shapes ~15-11 kya' Compendium DOI: <a href="https://doi.org/10.5281/zenodo.7940337">https://doi.org/10.5281/zenodo.7940337</a> The files at the URL above will generate the results as found in the publication. The files hosted at <a href="https://github.com/yesdavid/1511NAC_Dataset">https://github.com/yesdavid/1511NAC_Dataset</a> are the development versions and may have changed since the paper was published. Maintainer of this repository: David N. Matzig (<a href="mailto:david.matzig@cas.au.dk">david.matzig@cas.au.dk</a>; <a href="http://orcid.org/0000-0001-7349-5401">http://orcid.org/0000-0001-7349-5401</a>) Published in: Shumon T. Hussain, Felix Riede, David N. Matzig, Miguel Biard, Philippe Crombé, Federica Fontana, Daniel Groß, Thomas Hess, Mathieu Langlais, Javier Fernández-Lopéz de Pablo, Ludovic Mevel, William Mills, Martin Moník, Nicolas Naudinot, Caroline Posch, Tomas Rimkus, Damian Stefański, Hans Vandendriessche. A pan-European dataset revealing variability in lithic technology, toolkits, and artefact shapes ~15-11 kya. Sci Data 10, 593 (2023). <a href="https://doi.org/10.1038/s41597-023-02500-9">https://doi.org/10.1038/s41597-023-02500-9</a>. Abstract: Comparative macro-archaeological investigations of the human deep past rely on the availability of unified, quality-checked datasets integrating different layers of observation. Information on the durable and ubiquitous record of Paleolithic stone artefacts and technological choices are especially pertinent to this endeavour. We here present a large expert-sourced collaborative dataset for the study of stone tool technology and artefact shape evolution across Europe between ~15.000 and 11.000 years before present. The dataset contains a compendium of key sites from the study period, and data on lithic technology and toolkit composition at the level of the cultural taxa represented by those sites. The dataset further encompasses 2D shapes of selected lithic artefact groups (armatures, endscrapers, and borers) shared between cultural taxa. These data offer novel possibilities to explore within- and between-region patterns of material culture change to reveal scale-dependent processes of long-term technological evolution in mobile hunter-gatherer societies at the end of the Pleistocene. Our dataset facilitates state-of-the-art quantitative analyses and showcases the benefits of collaborative data collation and synthesis. Keywords: Europe; Pleistocene-Holocene transition; Late Glacial archaeology; lithic technology; comparison; macro-archaeology; taxonomy; cultural evolution; digital methods; computational morphometrics; collaborative research; open science Overview of contents and how to reproduce: This repository contains data (<code>1_data</code>) and code (<code>2_scripts</code>) for the paper, as well as the <code>1511NAC_Dataset</code> folder. The <code>1511NAC_Dataset</code> folder contains all relevant data for the readers to start their own analyses using the dataset. After downloading the complete repository, the results can be reproduced using <code>1511NAC_dataset.Rproj</code> and the existing folder structure. The required packages and their versions which have been used in this study are listed below and in the <code>DESCRIPTION</code>-file. All analyses and visualisations presented in this paper were prepared in R 4.2.2 under Ubuntu 18.04.5 LTS (64-bit). Required R-packages and their versions: <code>data.table</code> (>= 1.14.8), <code>dplyr</code> (>= 1.1.2), <code>forcats</code> (>= 1.0.0), <code>ggforce</code> (>= 0.4.1), <code>ggplot2</code> (>= 3.4.2), <code>ggpointgrid</code> (>= 1.2.0), <code>ggridges</code> (>= 0.5.4), <code>magrittr</code> (>= 2.0.3), <code>Momocs</code> (>= 1.4.0), <code>outlineR</code> (>= 0.1.0), <code>raster</code> (>= 3.6-20), <code>readr</code> (>= 2.1.4), <code>remotes</code> (>= 2.4.2), <code>rgeos</code> (>= 0.6-2), <code>rworldmap</code> (>= 1.3-6), <code>sp</code> (>= 1.6-0). Licenses: Code: MIT <a href="http://opensource.org/licenses/MIT">http://opensource.org/licenses/MIT</a>, copyright holder: David Nicolas Matzig (2023). Data and intellectual work: Creative Commons Attribution 4.0 International License (<a href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</a>), copyright holder: the authors (2023).

Elevated CO2 does not alter behavioural lateralization in free‐swimming juvenile European sea bass ( Dicentrarchus labrax) tested in groups

Rising concentrations of atmospheric carbon dioxide (CO2) equilibrate with oceanic CO2, contributing to ocean acidification (OA). OA can induce changes in fish behavioural lateralization (an expression of brain functional asymmetries) manifested in a left or right turning preference in detour tests. However, recent works find no such effects, and other work demonstrates assessment of turning preferences by detour tests to be a flawed methodology. Behavioural lateralization and OA effects on lateralization therefore need to be assessed with alternative paradigms. Here, we investigate left-right turning preferences of N=260 free-swimming juvenile European sea bass (Dicentrarchus labrax) reared in either: ambient conditions; OA conditions; or reared in ambient conditions but tested in OA water. Fish were observed free-swimming in groups of 10 individuals in a circular tank, and individuals' turning preferences were quantified using trajectory data from video. In contrast to early studies, and in support of recent comprehensive work on coral reef fishes, we show that near future OA levels have no effect on behavioural lateralization (left–right turning preference) in juvenile European sea bass.

A qualitative assessment of calcification across species and sexes of European Bufo toads using the micro-CT technique

Micro-computed tomography is a powerful tool towards the detailed reconstruction of internal and external morphology, in particular for ossified and other dense tissues. Here, we document and compare the amount of calcification in the skin of the head and the parotoids (the external skin glands) in males and females of the common and spined toads, Bufo bufo and B. spinosus. In some anurans including Bufo species, a specific acellular calcified tissue layer (the Eberth-Katschenko layer) within the dermis has been documented. Using micro-CT scan and standard histological techniques, we detected additional calcium deposits located in the dermal layer stratum spongiosum, above the Eberth-Katschenko layer. The data show that the level of calcification and the presence of the additional calcium deposits is size- and sex-related, increasing in the order from B. bufo males, B. spinosus males, B. bufo females to B. spinosus females. The least variable are B. spinosus females that have dense additional calcium deposits in parotoids, dorsal and ventral skin, as armour protecting their heads. Three-dimensional volume renderings and cross-sectional slices obtained by micro-CT scan used in this study indicate that this approach is a promising technique for further studies on Bufo skin anatomy and geographic variation in skin calcification.

Data for: Use of viscera from hunted roe deer by vertebrate scavengers in summer in central European mountainous mixed forest

Carrion is a valuable resource in forests, providing sustenance for vertebrate and invertebrate scavenger communities and contributing to ecosystem functions, such as nutrient cycling. Intensive ungulate hunting, and thereby extraction of carcasses, removes large quantities of potential carrion from the system, denying a valuable resource from scavenger fauna. It may be possible to reduce the loss and negative consequences to forest biodiversity by retaining evisceration residues from hunted deer, where full carcasses cannot be retained. However, what roll evisceration residues play as a resource for scavengers in temperate forests is not well understood. In this study, we exposed 47 carrion samples from hunted roe deer, in front of triple sets of camera traps, to examine how hunting remains are removed and fed upon by vertebrate scavengers. Overall, 70 % of the samples were completely removed from experimental sites by vertebrates. We detected twelve vertebrate taxa feeding on evisceration residues, including martens (Martes spp.), red kites (Milvus milvus) and garden dormice (Eliomys quercinus). Common buzzards (Buteo buteo) and Eurasian jays (Garrulus glandarius) were the most frequent feeders on carrion samples, while red foxes (Vulpes vulpes) displaced the largest proportion of samples. Finally, we found a range of insectivorous bird and mammal species using hunting remains as a source for invertebrate prey, while not scavenging on the remains directly. We demonstrate that evisceration residues can be a valuable resource for a wide range of taxa and suggest that viscera retention from hunted game may contribute to resource provisioning for scavengers in forest ecosystems.

Pan-European database for pathogenic microbial taxa in birds and bats

The spatially extensive multidimensional database of the prevalence of pathogenic microbial taxa for humans and wildlife in birds and bats was compiled by systematically reviewing publications for 121 pathogenic taxa. It covered pathogenic taxa mostly at the genus level (species level for most of the viruses), including sampling from ~450,000 host individuals of 376 bird species and 39 bat species. Data S1. Taxonomic details of the covered bird and bat species and pathogen prevalence of the most studied pathogenic microbial taxa in these host species. Data S2. Taxonomic details and sample sizes of the covered pathogenic microbial taxa. Data S3. Pan-European database for pathogenic microbial taxa from systematic review. Data S4. Input data for modelling. The filtered dataset follows the protocol illustrated in "Database quality control" of Methods in the corresponding article. Because the database includes endangered species that were listed by the IUCN as anything from Threatened or more severe, the geographical coordinates in the datasets were required by the platform to be masked as numbers with a scale of 1. The finer resolution coordinates (with a scale of 4) can be requested by contacting the corresponding author: Yanjie Xu (<a href="mailto:yanjie.xu5@gmail.com">yanjie.xu5@gmail.com</a> or <a href="mailto:yanjie.xu@helsinki.fi">yanjie.xu@helsinki.fi</a>). The comprehensive methods about the data collection and database quality control are illustrated in the corresponding article. Xu, Y., Poosakkannu, A., Suominen, K.M., Laine V.N., Lilley T.M., Pulliainen A.T. & Lehikoinen, A. (2023). Continental-scale climatic gradients of pathogenic microbial taxa in birds and bats. Ecography. https://doi.org/10.1111/ecog.06783

opencc-zeroAug 2023View details →

Data from: Phenotypic drought stress prediction of European beech (Fagus sylvatica) by genomic prediction and remote sensing

Current climate change species response models usually do not include evolution. We integrated remote sensing with population genomics to improve phenotypic response prediction to drought stress in the key forest tree species European beech (Fagus sylvatica L.). We used whole-genome sequencing of pooled DNA from natural stands along an ecological gradient from humid-cold to warm-dry climate. We phenotyped stands for leaf area index (LAI) and moisture stress index (MSI) for the period 2016–2022. We predicted this data with matching meteorological data and a newly developed genomic population prediction score in a Generalised Linear Model. Model selection showed that the addition of genomic prediction decisively increased the explanatory power. We then predicted the response of beech to future climate change under evolutionary adaptation scenarios. A moderate climate change scenario would allow persistence of adapted beech forests, but not worst-case scenarios. Our approach can thus guide mitigation measures, such as allowing natural selection or proactive evolutionary management.

opencc-zeroAug 2023View details →

Data and Code from: Sheltered or suppressed? Tree regeneration in unmanaged European forests

Tree regeneration is a key demographic process influencing long-term forest dynamics. It is driven by climate, disturbances, biotic factors, and their interactions. Thus, predictions of tree regeneration are challenging due to complex feedbacks along the wide climatic gradients covered by most tree species. We developed statistical models based on >50,000 recruitment events observed for 24 tree species in an extensive permanent plot network (6,540 plots from 299 unmanaged European temperate, boreal, and subalpine forests) covering a wide climatic gradient. This repository stores csv files with response and explanatory variables and R-Scripts that are needed to run the analysis and create the figures that are presented in the accompanying article titled "Sheltered or suppressed? Tree regeneration in unmanaged European forests" which was published in Journal of Ecology in 2023. Our study shows that competition between trees towards climatic stress decreases systematically but depends on species stress tolerance to climate and shade. These findings explain within- and between-species differences in tree recruitment patterns in European temperate forests. Moreover, our findings imply that projections of forest dynamics along wide climatic gradients and under climate change must accommodate both competition and positive interactions, as they strongly affect rates of community turnover.

Fig. 8 in Sex-ratio and body size plasticity in two cold-adapted ground beetles co-occurring in a periglacial area of the European Alps (Coleoptera: Carabidae)

Fig. 8 – Linear regression graph between elytra width of Nebria castanea females and the soil pH.