Find research datasets worth reusing

opencc-by-4.0Jul 2021View details →

TCTracer: Establishing Test-to-Code Traceability Links Using Dynamic and Static Techniques - Evaluation Data - Empirical Software Engineering 2021

This repository provides the data artefacts for the experiments conducted using our tool TCTracer for the journal paper "TCTracer: Establishing Test-to-Code Traceability links Using Dynamic and Static Techniques" as submitted to the Empirical Software Engineering journal in 2021.

opencc-by-4.0Sep 2021View details →

Water Uptake as a Crucial Factor on Properties of Cryogels of Gelatine Linked by Dextran Dialdehyde

supplementary information

opencc-zeroSep 2021View details →

Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation

Please refer to the publication Shin et al. (2021): "Shin CR, Choi EH, Kim G. et al. (2021). Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation. Scientific Reports 11: 12239. The land snail Ellobium chinense (Pulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of E. chinense has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific E. chinense based on COI and 10 microsatellite markers. The analyses of 140 COI data from South Korea and Japan and 54 microsatellite data from South Korea revealed that E. chinense has high haplotype and low nucleotide diversity without showing any genetic structures that reflect geographical isolations. It strongly implies that the subfamily Ellobiinae may have first appeared around the Eocene Optimum immediately after the Paleocene–Eocene Thermal Maximum (PETM; ca. 55 mya) and the examined E. chinense populations in Northwestern Pacific may have been maintained in a metapopulation under the influence of the Kuroshio warm currents through the Late-Middle Pleistocene (0.350−0.126 mya) and Late Pleistocene (0.126−0.012 mya). We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in COI (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four COI hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure.

opencc-by-3.0Sep 2021View details →

Linked Data Workshops papers (LDOW)

We analyzed the published articles of the Linked Data on the web (LDOW) workshop series and performed a scientometric analysis on them. This dataset includes the metadata of published papers in the LDOW workshops (between 2008 and 2018).

opencc-zeroSep 2021View details →

Wikidata Dump EN labels+desc+aliases+links

RDF dump of wikidata produced with <a href="https://tools.wmflabs.org/wdumps/">wdumps</a>. <a href="https://tools.wmflabs.org/wdumps/dump/1706">View on wdumper</a> entity count: 0, statement count: 0, triple count: 0

opencc-zeroOct 2021View details →

Allo-preening is linked to vocal signature development in a wild parrot

Allo-grooming networks in primate social groups are thought to have favored the evolution of vocal recognition systems, including vocal imitation in humans, as a more effective means of maintaining social bonds in large groups. Select avian taxa converged on vocal learning, but it is not clear what role analogues of allo-grooming might have played. Unlike allo-grooming in most primates, allo-preening in birds is usually limited to pair-bonds. One exception to this is during nestling development when siblings preen each other, but it is unknown how allo-preening influences vocal learning. We addressed this question in wild Green-rumped Parrotlets (Forpus passerinus) in Venezuela. Nestlings learn signature contact calls from adult templates. Large broods, age hierarchies and protracted development in this species create the potential for complex allo-preening networks and a unique opportunity to test how early sociality makes the development of vocal learning labile. From audio-video recordings inside nest cavities and a balanced design of different brood sizes, we quantified allo-preening interactions between marked nestlings, to compare to signature contact calls. Controlling for brood size and age hierarchy, the propensity to preen a larger number of individuals (i.e., out-strength) correlated positively with the age at first contact call. Allo-preening and acoustic similarity matrices did not reveal clear correlations within broods, instead larger broods produced greater contact call diversity. Results indicate that allo-preening elongates the period during which contact calls develop, which might allow individuals time to form a unique signature under the computationally challenging social conditions inherent to large groups.

opencc-by-4.0Oct 2021View details →

Data and code for the manuscript Retrieving Water Vapor From an E-band Microwave Link With an Empirical Model Not Requiring In-situ Calibration

Data and code for the manuscript Retrieving Water Vapor From an E-band Microwave Link With an Empirical Model Not Requiring In-situ Calibration accepted for publication to Earth and Space Science in October 2021. The dataset contains 7 month of total losses (transmitted - received power levels) and retrieved water vapor density from a 4.87 km long full-duplex E-band commercial microwave link (CML) operating at 73.5 and 83.5 GHz in Prague, CZ. The CML was operated as a part of a mobile phone backhaul. Furthermore, observations of air temperature, and air relative humidity from sites close to the CML end nodes are provided. Finally, theoretical gaseous attenuation calculated from the air temperature and relative humidity is included as a part of the dataset. Data are stored in semicolon-delimited csv files. Time stamps are in UTC time in the format yyyy-mm-dd HH:MM:SS. All time series are regular and have 5-min temporal resolution. Metadata are stored in text files. The code is in a form of R Markdown files and html notebooks. Results presented in the manuscript Retrieving Water Vapor From an E-band Microwave Link With an Empirical Model Not Requiring In-situ Calibration and in its Supporting information are fully reproducible using this dataset.

opencc-by-4.0Apr 2024View details →

IPBES Global Assessment in Linked Open Data format

This dataset contains the Thematic Assessment Report on Invasive Alien Species and their Control of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services in linked open data format. The structure of the file follows the IPBES ontology version 06: <a href="https://github.com/IPBES-Data/IPBES_Ontology">https://github.com/IPBES-Data/IPBES_Ontology</a> The report is published in 2019 and consists of 6 chapters and a Summary for Policy Makers. For more information about the report, see: <a href="https://www.ipbes.net/global-assessment">https://www.ipbes.net/global-assessment</a> For any questions and enquiries, please contact the IPBES Data and Knowledge Unit <a href="mailto:aidin.niamir@senckenberg.de">aidin.niamir@senckenberg.de</a>

CPSV-AP 2.0 based public service descriptions of the Region of Epirus (Greece) as linked data

It comprises a set of 45 CPSV-AP 2.0 based public service descriptions as linked data. The fields of the included public service descriptions were adapted from a regional public service catalogue, namely "The Citizen's Guide of the Region of Epirus", in order to comply with CPSV-AP 2.0 data model. The public service descriptions that are included in the linked dataset are not updated as the intended usage of the linked dataset is for research or educational activities and not for providing valid information to citizens.

The versatility of pulses: Are consumption and consumer perceptions in different European countries related to the actual climate impact of different pulse types? Author links open overlay panel

Pulses support sustainable production and consumption. Their culinary versatility creates a wide range of possibilities for new products, bridging consumers’ preparation barriers. However, this potential is often intangible for consumers who have little knowledge about plant-based foods. Based on an online survey in Denmark, Germany, Poland, Spain, and the United Kingdom (N = 4,226), this study aimed to investigate consumer utilization and perception of pulses as a versatile, low-carbon food relative to objective life cycle assessment (LCA) measures of 12 pulse types. The most popular pulse types, with specific preferences across countries, were lentils, kidney beans, and chickpeas, typically consumed at home and purchased in dried or canned form. Respondents associated pulses with being healthy and natural, but sustainability was not an essential attribute related to the perception of pulses. LCA revealed a low environmental impact caused by pulse production and consumption, with marginal variations between types and produce. Respondents were unaware of the nuances in the environmental impact of different pulse types, generally perceiving uncommon pulses to be relatively more sustainable than others. In conclusion, a low consumption combined with a misconception of pulses’ environmental impact may demand different promotional strategies including clear communication to inform consumers.

opencc-zeroNov 2022View details →

Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms

Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful but nevertheless produced substantial datasets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (> 515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (> 11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.

Geochemical, timescales data in orthopyroxenes from Kizimen 2010 eruption and database of studies linking diffusion timescales with monitoring signals.

This dataset comprises the geochemical data on whole rock analysis, melt inclusions, residual glasses, magnetites and orthopyroxenes in samples from the 2010 eruption of Kizimen volcano (Kamchatka), as well as the timescales modelled in the orthopyroxenes and a database of studies linking diffusion timescales with monitoring signals, associated with the publication: Ostorero, L., Balcone-Boissard, H., Boudon, G. et al. Correlated petrology and seismicity indicate rapid magma accumulation prior to eruption of Kizimen volcano, Kamchatka. Commun Earth Environ 3, 290 (2022). https://doi.org/10.1038/s43247-022-00622-3

Wikidata dump extension (enwiki section links)

The dataset contains mappings between Wikidata entities and Wikipedia sections. The mappings come in addition to the existing Wikidata sitelinks referencing Wikipedia pages. The creation of the present dataset stems from the observation that only a fraction of Wikidata entities has a corresponding Wikipedia article in any language (we refer to the remaining entities, without an article, as orphans). However, a substantial number of orphan entities are indeed available in Wikipedia, but not at the page level; orphan entities can be described within existing Wikipedia articles in the form of sections, subsections, and paragraphs of a more generic concept or fact. The dataset provides a fine-grained mapping between Wikidata orphan entities and Wikipedia (sub)-sections. Mappings are provided for English language. The dataset is available in JSON and RDF formats and complies with the Wikibase data model. In the JSON representation, an entity contains two fields: id (the unique identifier of an entity) and sectionlinks (links to Wikipedia sections). Each sectionlink record comprises a list of records1 with three fields: site, title, and url. A section title is appended to the page title separated with # symbol. Such a compound title is then URL-encoded and added to the URL path. Following the Wikidata guidelines, each entity is encoded as a single line. Example: <pre><code class="language-json">{ "id": "Q715509", "sectionlinks": { "enwiki": [ { "site": "enwiki", "title": "Places in Harry Potter#Azkaban", "url": "https://en.wikipedia.org/wiki/Places_in_Harry_Potter#Azkaban" } ], } }</code></pre>   The RDF dump is serialized using the Turtle format and stores nodes describing Wikipedia links. Section titles are added in the same manner as described above. Example: <pre><code><https://en.wikipedia.org/wiki/Places_in_Harry_Potter#Azkaban> a schema:Article ; schema:about wd:Q715509 ; schema:inLanguage "en" ; schema:isPartOf <https://en.wikipedia.org/> ; schema:name "Places in Harry Potter#Azkaban"@en . <https://en.wikipedia.org/> wikibase:wikiGroup "wikipedia" . </code></pre>   1 As opposed to sitelinks, where each entity can be mapped with a unique Wikipedia page (one-to-one mapping), in sectionlinks we  allow a one-to-many mapping, i.e., an entity can be mapped to multiple sections. For example, Tennis racket concept can be mapped to Tennis#Rackets and Racket (sports equipment)#Tennis sections.

Exploring links between climatic predictability and the evolution of within- and transgenerational plasticity

In variable environments, phenotypic plasticity can increase fitness by providing tight environment-phenotype matching. However, adaptive plasticity is expected to evolve only when the future selective environment can be predicted based on the prevailing conditions. That is, the juvenile environment should be predictive of the adult environment (within-generation plasticity) or the parental environment should be predictive of the offspring environment (transgenerational plasticity). Moreover, environmental predictability can also shape transient responses such as stress responses in an adaptive direction. Here, we test links between environmental predictability and the evolution of adaptive plasticity by combining time series analyses and a common garden experiment using temperature as a stressor in a temperate butterfly (Melitaea cinxia). Time series analyses revealed that across-season fluctuations in temperature over 48 years are overall predictable. However, within the growing season, temperature fluctuations showed high heterogeneity across years with low autocorrelations and the timing of temperature peaks was asynchronous. Most life-history traits showed strong within-generation plasticity for temperature and traits such as body size and growth rate broke the temperature-size rule. Evidence for transgenerational plasticity, however, was weak and detected for only two traits each in an adaptive and non-adaptive direction. We suggest that the low predictability of temperature fluctuations within the growing season likely disfavours the evolution of adaptive transgenerational plasticity but instead favours strong within-generation plasticity.

The missing link in biogeographic reconstruction: Accounting for lineage extinction rewrites history

Aim In the most widely used family of methods for ancestral range estimation (ARE), dispersal, speciation and extirpation events are estimated from information on extant lineages. However, this approach fails to consider the geographic distribution of extinct species and their position on the phylogenetic tree, an omission that could compromise reconstruction. Here, we present a method that models the geographic distribution of extinct species and we quantify the potential inaccuracy in ancestral range estimation when extinction rates are above zero. Location Global applications, with an example from the Americas. Taxon All taxa, with an example from hummingbirds (Amazilia). Methods Methods capable of explicitly modelling extinct branches along with their reconstructed geographic information (GeoSSE) have been overlooked in ARE analysis, perhaps due to the inherent complexity of implementation. We develop a user-friendly platform, which we term LEMAD (Lineage Extinction Model of Ancestral Distribution) that generalizes the likelihood described in GeoSSE for any number of areas and under several sets of geographic assumptions. We compare LEMAD and extinction-free approaches using extensive simulations under different macroevolutionary scenarios. We apply our method to revisit the historical biogeography of Amazilia hummingbirds. Results We find that accounting for the lineages removed from a tree by extinction improves reconstructions of ancestral distributions, especially when rates of vicariant speciation are higher than rates of in situ speciation, and when rates of extinction and range evolution are high. Rates of in situ and vicariant speciation are accurately estimated by LEMAD in all scenarios. North America as the most likely region for the common ancestor of hummingbirds. Main conclusions Methods that neglect lineage extinction are less likely to accurately reconstruct true biogeographic histories of extant clades. Our findings on an empirical dataset reconcile the Eurasian origin of Amazilia with biogeographic reconstructions when lineage extinction is considered.

Data for: Fitness costs of female competition linked to resource defence and relatedness of competitors

Female reproductive success is often limited by access to resources and this can lead to social competition both within and between kin groups. Theory predicts that both resource availability and relatedness should influence the fitness consequences of social competition. However, testing key predictions requires differentiating the effects of these two factors. Here we achieve this experimentally by manipulating the social environment of house mice, a facultative communal breeding species with known kin discrimination ability. Our results support the hypothesis that resource defence can be costly for females, potentially trading off against maternal investment. When competition for nest sites was more intense, subjects: 1) were more active during resting phases, 2) responded more strongly to simulated territory intrusions via competitive signalling, and 3) produced smaller weaned offspring. However, we found no evidence that the propensity for kin to cooperate was influenced by relatedness of rivals. Communal breeding between sisters occurred independently of the relatedness of competitors, and costs of competition with non-kin were not mitigated by greater inclusive fitness benefits. Rather, communally breeding sisters weaned fewer offspring when competing with unrelated females, indicating that competition with non-kin is more costly overall. Our findings thus demonstrate that social competition has fitness costs and that associating with kin is beneficial to avoid negative fitness consequences of competing with non-kin, in addition to more widely recognised kin-selected benefits.

Dietary plasticity linked to divergent growth trajectories in a critically endangered sea turtle

Foraging habitat selection and diet quality are key factors that influence individual fitness and metapopulation dynamics through effects on demographic rates. There is growing evidence that sea turtles exhibit regional differences in somatic growth linked to alternative dispersal patterns during the oceanic life stage. Yet, the role of habitat quality and diet in shaping somatic growth rates is poorly understood. Here, we evaluate whether diet variation is linked to regional growth variation in hawksbill sea turtles (Eretmochelys imbricata), which grow significantly slower in Texas versus Florida (USA), through novel integrations of skeletal growth, gastrointestinal content (GI), and bulk tissue and amino acid (AA)-specific stable nitrogen (δ15N) and carbon (δ13C) isotope analyses. We also used AA δ15N ΣV values (heterotrophic bacterial re-synthesis index) and δ13C essential AA (δ13CEAA) fingerprinting to test assumptions about the energy sources fueling hawksbill food webs regionally. GI content analyses, framed within a global synthesis of hawksbill dietary plasticity, revealed that relatively fast-growing hawksbills stranded in Florida conformed with assumptions of extensive spongivory for this species. In contrast, relatively slow-growing hawksbills stranded in Texas consumed considerable amounts of non-sponge invertebrate prey and appear to forage higher in the food web as indicated by isotopic niche metrics and higher AA δ15N-based trophic position estimates internally indexed to baseline N variation. However, regional differences in estimated trophic position may also be driven by unique isotope dynamics of sponge food webs. AA δ15N ΣV values and δ13CEAA fingerprinting indicated minimal bacterial resynthesis of organic matter (ΣV < 2) and that eukaryotic microalgae were the primary energy source supporting hawksbill food webs. These findings run contrary to assumptions that hawksbill diets predominantly comprise high microbial abundance sponges expected to primarily derive energy from bacterial symbionts. Our findings suggest alternative foraging patterns could underlie regional variation in hawksbill growth rates, as divergence from conventional sponge prey might correspond with increased energy expenditure and reduced foraging success or diet quality. As a result, differential dispersal patterns may infer substantial individual and population fitness costs and represent a previously unrecognized challenge to the persistence and recovery of this critically endangered species.

opencc-zeroJan 2023View details →

Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age

The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We used resequenced whole genomes to investigate how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpeckers, species co-distributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (1) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (2) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.

opencc-zeroFeb 2023View details →

Data from: Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos

Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyze geographic variation in genome size, genetic diversity, and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity, and increased self-fertilization, but we show that this is not the case for Poa annua. Microsatellite data indicated low population genetic structure and lack of isolation-by-distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality, and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of autogamy declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are likely tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy likely benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.