Find research datasets worth reusing

Reconstructing locomotor ecology of extinct avialans: a case study of Ichthyornis comparing sternum morphology and skeletal proportions

Avian skeletal morphology is associated with locomotor function, including flight style, swimming and terrestrial locomotion, and permits informed inferences on locomotion in extinct taxa. The fossil taxon Ichthyornis (Avialae: Ornithurae) has long been regarded as highly aerial, with flight similar to terns or gulls (Laridae), and skeletal features resembling foot-propelled diving adaptations. However, rigorous testing of locomotor hypotheses has yet to be performed on Ichthyornis, despite its notable phylogenetic position as one of the most crownward stem birds. We analysed separate datasets of 3D sternal shape (geometric morphometrics) and skeletal proportions (linear measurements across the skeleton), to examine how well these data types predict locomotor traits in Neornithes. We then used this information to infer locomotor capabilities of Ichthyornis. We find strong support for both soaring and foot-propelled swimming capabilities in Ichthyornis. Further, sternal shape and skeletal proportions provide complementary information on avian locomotion: skeletal proportions allow better predictions of the capacity for flight, whereas sternal shape predicts variation in more specific locomotor abilities such as soaring, foot-propelled swimming, and escape burst flight. These results have important implications for future studies of extinct avialan ecology, and underscore the importance of closely considering sternum morphology in investigations of fossil bird locomotion.

Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)"

Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)" alignments: alignments used for BEAST ("bayes") and PopArt ("popart"). The "popart" folder also has a traits file per each species. bayesian_plots: TSVs ("tsv") and PDF files ("ogs") generated by BEAST. The "tsv" folder also has the scripts for plotting the results in R. easysfs: scripts, population file and results from the VCF to SFS conversione done by easySFS. fineRADstructure: fineRADstructure input files and output PDF plots ("plots") for C. formosanus ipyrad and Stacks ("stacks") data.  logs: logs for ipyrad, ModelTest, PGDspider, PopArt ("popart") and Stacks ("stacks"). The "popart" folder also have the generated networks in a TXT file. The "stacks" folder also has ODS files for calculating the amount of loci per each M/n fixed value. snapclust: STR files used with R for snapclust. Scripts included. stairway_plot: input (blueprint files) and outputs for Stairway Plot 2 analyses. The C. formosanus folder ("chordodes") also has scripts for R plotting. vcfs: VCF and HDF5 files used in this study. Also scripts for filtering/converting data and plotting the PCA with ipyrad (activate python first!) for C. formosanus. "acutogordius" = A. taiwanensis "chordodes" = C. formosanus "gordius" = G. chiashanus

Using inbreeding to test the contribution of non-additive genetic effects to additive genetic variance: A case study in Drosophila serrata

Additive genetic variance, VA, is the key parameter for predicting adaptive and neutral phenotypic evolution. Changes in demography (e.g., increased close-relative inbreeding) can alter VA, but how depends on the, typically unknown, gene action and allele frequencies across many loci. For example, VA increases proportionally with the inbreeding coefficient when allelic effects are additive, but larger (or smaller) increases can occur when allele frequencies are unequal at causal loci with dominance effects. Here, we describe an experimental approach to assess the potential for rare, recessive alleles to inflate VA under inbreeding. Applying a powerful paired pedigree design in Drosophila serrata, we measured 11 wing traits on half-sibling families bred via either random or sibling mating, differing only in homozygosity (not allele frequency). Despite close inbreeding and substantial power to detect small VA, we detected no deviation from the expected additive effect of inbreeding on genetic (co)variances. Our results suggest the average dominance coefficient is very small relative to the additive effect, or that allele frequencies are relatively equal at loci affecting wing traits. We outline the further opportunities for this paired pedigree approach to reveal the characteristics of VA, providing insight into historical selection and future evolutionary potential.

How to estimate body condition in large lizards? Argentine black and white tegu (Salvator merianae, Duméril and Bibron, 1839) as a case study

Body condition is a measure of the health and fitness of an organism represented by available energy stores, typically fat. Direct measurements of fat are difficult to obtain non-invasively, thus body condition is usually estimated by calculating body condition indices (BCIs) using mass and length. The utility of BCIs is contingent on the relationship of BCIs and fat, thereby validation studies should be performed to select the best-performing BCI before application in ecological investigations. We evaluated 11 BCIs in 883 Argentine black and white tegus (Salvator merianae) removed from their non-native range in South Florida, United States. Because the length-mass relationship in tegus is allometric, a segmented linear regression model was fit to the relationship between mass and length to define size classes. We evaluated percent, residual, and scaled fat and determined percent fat was the best measure of fat because it was the least associated with snout-vent length (SVL). We evaluated performance of BCIs with the full dataset and within size classes and identified Fulton's K as the best-performing BCI for our sampled population, explaining up to 19% of the variation in fat content. Overall, we found that BCIs: 1) maintained relatively weak relationships with measures of fat and 2) splitting data into size classes reduced the strength of the relationship (i.e., bias) between percent fat and SVL but did not improve the performance of BCIs. We postulate that the weak performance of BCIs in our dataset was likely due to the weak association of fat with SVL, the body plan and life-history traits of tegus, and potentially inadequate accounting of available energy resources. We caution against assuming that BCIs are strong indicators of body condition across species and suggest that validation studies be implemented, or that alternative or complementary measures of health or fitness should be considered.

An Exploratory Study on the Usage and Readability of Messages Within Assertion Methods of Test Cases

This is the code and dataset that accompanies the study: "An Exploratory Study on the Usage and Readability of Messages Within Assertion Methods of Test Cases." This study has been accepted for publication at the 2023 International Workshop on Natural Language-based Software Engineering. Following is the abstract of the study: Unit testing is a vital part of the software development process and involves developers writing code to verify or assert production code. Furthermore, to help comprehend the test case and troubleshoot issues, developers have the option to provide a message that explains the reason for the assertion failure. In this exploratory empirical study, we examine the characteristics of assertion messages contained in the test methods in 20 open-source Java systems. Our findings show that while developers rarely utilize the option of supplying a message, those who do, either compose it of only string literals, identifiers, or a combination of both types. Using standard English readability measuring techniques, we observe that a beginner's knowledge of English is required to understand messages containing only identifiers, while a 4th-grade education level is required to understand messages composed of string literals. We also discuss shortcomings with using such readability measuring techniques and common anti-patterns in assert message construction. We envision our results incorporated into code quality tools that appraise the understandability of assertion messages.

Data for: Post-migratory nonbreeding movements of birds: a review and case study

Seasonal migrations are fascinating and ecologically important, but many migratory species are declining as climate change and land-use change alter the habitats used by migrants across the annual cycle. While some migratory birds use a single wintering site, others undertake large-scale post-migratory movements during the nonbreeding season. Technological advances that enable tracking individual birds are uncovering more examples of post-migratory nonbreeding movements. Documenting these movements is important for conservation, which requires understanding when and where migrants use habitats throughout their range. Here, we reviewed existing literature and collected information on the post-migratory nonbreeding movements of 92 migratory bird species from 18 orders across six continents. Among these records, the most commonly reported drivers of movements were resource availability and climate. This strong dependence of post-migratory nonbreeding movements on birds' abiotic and biotic environments suggests that environmental change will impact the patterns of these movements and potentially the fitness of species that undertake them. We also reviewed post-migratory nonbreeding movements in North American-breeding thrushes from the genus Catharus to examine the drivers of these movements in five closely related migratory species. We find that species that are less territorial are more likely to use multiple sites during the nonbreeding season; however, there is little evidence for dietary, evolutionary, or environmental differences between thrush species that move during winter and those that are stationary. While we believe our study represents the most comprehensive list of species exhibiting post-migratory nonbreeding movements to date, biases in sampling, a lack of common terminology for these movements, and the still-nascent availability of inexpensive, lightweight tracking devices mean that there are probably many more populations that undertake such movements. Future research into the consequences of post-migratory nonbreeding movements for individual fitness and ecosystem services would advance our understanding of their conservation importance and their evolution.

opencc-by-4.0Jan 2023View details →

A Case Study on AI Engineering Practices: Developing an Autonomous Stock Trading System

The field note data related to a case study on AI engineering practices. During the case study, an autonomous stock trading system was developed, while 10 AI engineering practices were applied. We used field notes to document the application of each practice. Additionally, we documented any challenges we experienced. <ul> <li>field-notes-practices.csv: the documented experiences with the AI engineering practices containing the name of the practice, the perceived effectiveness of the practice on an ordinal scale (--, -, 0, +, ++), a description of how it was applied and its effects, and the date when it was applied (in DD.MM.YYYY format).</li> <li>field-notes-challenges.csv: the documented challenges experiences during the case study containing the date (in DD.MM.YYYY format), a description of the challenge, the source that made us became aware of the challenge, the solution we used to overcome the challenge, and a description of the frequency of occurrence.</li> </ul>

Single column 1D radiative transfer simulations for a case study of multilayer mixed-phase cloud in Punta Arena Chile

This data set contain the input files and output simulations from a single column 1D radiative transfer simulations using the Rapid Radiative Transfer Model for General Circulation Model (GCM) applications (RRTMG). The simulations are focused on a selected case study of multiple-layer mixed phase cloud observed in Punta Arenas Chile. The input parameters of the simulations are based on remote sensing observations, which were synergistically used with the Cloudnet and VOODOO algorithm to derive macro and microphysical properties of clouds. The atmospheric profiles of temperature, pressure, and ozone are from ERA5 (European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis) and values of surface albedo from CERES (Clouds and the Earth's Radiant Energy System) SYN1deg Ed. 4.1.

opencc-zeroMar 2023View details →

Data from: Sulfur isotopic discrimination factors differ among avian tissues and diets: Insights from a case study in Gentoo Penguins (Pygoscelis papua)

The use of stable isotopes of sulfur (δ34S) to infer avian diets, foraging habitats, and movements is relatively uncommon, resulting in a lack of information on patterns of δ34S incorporation in avian tissue. In a controlled study of Gentoo Penguins (Pygoscelis papua), we found that diet-tissue isotopic discrimination factors (Δ34Sdiet-tissue) differed among egg components and feathers synthesized from a common diet, ranging from -0.4 to -1.7 ‰. We also found that methodical choices such as lipid extraction and prey tissue selection influenced calculated Δ34Sdiet-tissue values. Specifically, Δ34Sdiet-tissue values were lower (i.e., more negative) when calculated using whole fish relative to fish muscle and lipid-extraction biased egg yolk, but not fish tissue, δ34S values. Δ34Sdiet-tissue values obtained for Gentoo Penguins fed a marine fish diet were generally lower than those reported for freshwater-fish-consuming Double-crested Cormorants (Phalacrocorax auritus), the only other bird species in which Δ34Sdiet-tissue has been quantified. We found support for the hypothesis that tissue Δ34Sdiet-tissue values are inversely related to dietary δ34S values in birds, similar to what has been observed in mammals. Given this relationship, the discrimination factors reported here for Gentoo Penguins may be broadly applicable to other avian species with a similar marine diet. Finally, we provide recommendations for future studies seeking to quantify Δ34Sdiet-tissue in avian tissues and guidance to allow for greater application of sulfur stable isotope analysis in ornithological research.

opencc-zeroMar 2023View details →

Data from: The role of niche breadth in oak phylogeography: Quercus glaucoides as a study case

The amount of genetic diversity and its distribution among populations has been associated to species' attributes such as mating system, dispersal ability and geographic range size. Another attribute that could contribute to explain intraspecific phylogeographic patterns is niche breadth, but this relationship barely has been tested. Here, we studied a Mexican oak (Quercus glaucoides) with a comparatively narrow climatic niche breadth. Genetic diversity and structure were assessed, as well as historical demography dynamics and connectivity. Then, we tested for a general correlation of genetic diversity and structure with niche breadth, using our data and previous results from other co-distributed Mexican oaks with variable niche breadths. Methods Descriptors of genetic diversity and structure were obtained from 21 Q. glaucoides populations using chloroplast DNA (cpDNA) and nuclear microsatellites (nSSRs). Historical demography dynamics were inferred with approximate Bayesian computation (ABC) and past potential distribution models. To test for an association between niche breadth and phylogeographic patterns, we used genetic diversity and differentiation values of Q. glaucoides plus those previously published for other ten species. Niche breadth was estimated for all species and linear regressions were performed. Results Genetic diversity calculated from nSSRs (HO= 0.539; HE= 0.714) was among the lowest, and cpDNA differentiation (NST= 0.88) was the highest so far obtained for comparable Mexican oaks. Moderate changes in demographic size and distribution shifts throughout the last glacial cycle were inferred, explaining some of the observed genetic patterns. A positive correlation of HO and a negative correlation of NST with niche breadth were detected across species. Main conclusions Distinct phylogeographic patterns in Q. glaucoides could be explained because a narrower niche may cause lower historical effective population sizes and more fragmented distributions in comparison to species with a wider niche breadth, even with similar range sizes.

opencc-by-4.0Mar 2023View details →

Cloudnet products and VOODOO enhancements for a case study of multilayer mixed-phase cloud in Punta Arena Chile

This data set contains the Cloudnet and VOODOO enhanced products from observations during the the long-term ground-based remote-sensing field experiment Dynamics, Aerosol, Cloud and Precipitation Observations in the Pristine Environment of the Southern Ocean (DACAPO-PESO) in Punta Arenas, Chile.

opencc-by-4.0Mar 2023View details →

Case study result data set for Energy Systems (submitted) article "Influence of hydrogen import prices on hydropower systems in climate-neutral Europe"

The data set contains result data for the European system in a long term climate-neutral European energy system (scenario year 2050) as described in the publication "Influence of hydrogen import prices on hydropower systems in climate-neutral Europe". The results have been generated with the model SCOPE SD of Fraunhofer Institute for Energy Economics and Energy System Technology IEE.  Abbreviations: <ul> <li>BEV - Battery Electric Vehicles</li> <li>CCGT - Combined Cycle Gas Turbine</li> <li>CHP - Combined heat and power</li> <li>con - consumption</li> <li>gen - generation</li> <li>HighCLEQ - High import prices / clustered-equivalent hydropower units</li> <li>HighEQ - High import prices / equivalent hydropower units</li> <li>LowCLEQ - Low import prices / clustered-equivalent hydropower units</li> <li>LowEQ - Low import prices / equivalent hydropower units</li> <li>MedCLEQ - Medium import prices / clustered-equivalent hydropower units</li> <li>MedEQ - Medium import prices / equivalent hydropower units</li> <li>OCGT - Open Cycle Gas Turbine</li> <li>PHEV - Plug-In Hybrid Vehicles</li> <li>PS - Pumped Storage</li> <li>w/ - with</li> <li>w/o - without</li> <li>yr - year</li> </ul>

opencc-zeroMar 2023View details →

Incorporating pyrodiversity into wildlife habitat assessments for rapid post-fire management: A woodpecker case study

Spatial and temporal variation in fire characteristics – termed pyrodiversity – are increasingly recognized as important factors that structure wildlife communities in fire-prone ecosystems, yet there have been few attempts to incorporate pyrodiversity or post-fire habitat dynamics into predictive models of animal distributions and abundance to support post-fire management. We use the black-backed woodpecker – a species associated with burned forests – as a case study to demonstrate a pathway for incorporating pyrodiversity into wildlife habitat assessments for adaptive management. Employing monitoring data (2009–2019) from post-fire forests in California, we developed three competing occupancy models describing different hypotheses for habitat associations: (1) a static model representing an existing management tool, (2) a temporal model accounting for years since fire, and (3) a temporal-landscape model which additionally incorporates emerging evidence from field studies about the influence of pyrodiversity. Evaluating predictive ability, we found superior support for the temporal-landscape model, which showed a positive relationship between occupancy and pyrodiversity and interactions between habitat associations and years since fire. We incorporated this new temporal-landscape model into an RShiny application to make this decision-support tool accessible to decision-makers: <a href="https://birdpop.org/pages/bbwoPredPostFireDist.php">https://birdpop.org/pages/bbwoPredPostFireDist.php</a>.

opencc-by-4.0Mar 2023View details →

CRLC: Cross-resolution national-scale land-cover mapping based on noisy label learning: a case study of China

CRLC are the 10-meter resolution land cover maps for China in 2020 achieved by a deep classification network. The maps include eight land cover classes: 1: Cropland 2: Forest 3: Grass/shrubland 5: Wetland 6: Water bodies 8: Impervious 9: Bareland 10: Snow/ice   Reference: <pre>@article{liu2023cross, title={Cross-resolution national-scale land-cover mapping based on noisy label learning: A case study of China}, author={Liu, Yinhe and Zhong, Yanfei and Ma, Ailong and Zhao, Ji and Zhang, Liangpei}, journal={International Journal of Applied Earth Observation and Geoinformation}, volume={118}, pages={103265}, year={2023}, publisher={Elsevier} }</pre>

opencc-zeroApr 2023View details →

Detecting ecological traps in human-altered landscapes: A case study of the thick-billed longspur nesting in croplands

Conversion of the North American prairies to cropland remains a prominent threat to grassland bird populations. Yet, a few species nest in these vastly modified systems. The thick-billed longspur (Rhynchophanes mccownii) is an obligate grassland bird whose populations have declined 4% annually during the past 50 years. Thick-billed longspurs historically nested in recently disturbed or sparsely vegetated patches within native mixed-grass prairie, but observations of longspurs in spring cereal and pulse crop fields during the breeding season in northeastern Montana, USA suggest such fields also provide cues for habitat selection. Maladaptive selection for poor-quality habitat may contribute to ongoing declines in longspur populations, but information on thick-billed longspur breeding ecology in crop fields is lacking. We hypothesized that these crop fields may function as ecological traps; specifically, we expected that crop fields may provide cues for territory selection, but frequent human disturbance and increased exposure to weather and predators would have negative consequences for reproduction. To address this hypothesis, we compared measures of habitat selection (settlement patterns and trends in abundance) and productivity (nest density, nest survival, and number of young fledged) between crop fields and native grassland sites during 2020–21. Across both years, settlement patterns were similar between site types and occupancy ranged from 0.52 ± 0.17SE to 0.99 ± 0.01 on April 7 and 30, respectively. Early season abundance differed by year, and changes in abundance during the breeding season appeared to be associated with precipitation-driven vegetation conditions rather than habitat type. While an index of nest density was lower in crop than native sites, the number of young fledged per successful nest (2.9 ± 0.18SE) and nest survival (0.24 ± 0.03 SE; n=222 nests) were similar for crop and native sites. Collectively, the data did not support our ecological trap hypothesis: longspurs did not exhibit a clear preference for crop sites and reproductive output was not significantly reduced. Our results indicate that croplands may provide alternative breeding habitat within a human-dominated landscape.

opengpl-2.0Mar 2023View details →

On the Performance of NVRAM-based Operating Systems: A Case Study with Linux and FreeBSD

All artefacts regarding "On the Performance of NVRAM-based Operating Systems: A Case Study with Linux and FreeBSD". <ul> <li>Changes to Linux</li> <li>Changes to FreeBSD</li> <li>Testsetup and benchmarks</li> <li>Measurements</li> </ul>

Data supporting "Machine Learning-based Modeling of Olfactory Receptors: Human OR51E2 as a Case Study"

Simulation data and input files in support of the Manuscript:"Machine Learning-based Modeling of Olfactory Receptors: Human OR51E2 as a Case Study". The archive is organized in 6 different folders: 1. 7x7_rmsd, which contains a tcl script (to be run in VMD) to compute the 7x7 RMSD matrix (see Wang et al. J Struct. Bio, (2017)). 2. a100_plumed, which contains PLUMED input files to compute A100 index on OR51E2 trajectories. 3. initial_structures, which contains the 6 different conformation for hOR51E2 obtained by the different predictors in the pdb format. 4. mdp_files, which contains the GROMACS mdp files to perform all the protocol described in the paper. 5. topologies, which contains the 6 different topologies (in .top format) and the initial conformation (in .gro format) for the hOR51E2 embedded in the membrane and solvated. 6. trajectories, which contains the 18 (6 systems, 3 replicas per system) different trajectories with the sodium in place close to D692.50 without solvent and ions (in .xtc format with a frame every 100 ps) and a reference conformation (in .gro format). Here we have also added the trajectory for the SwissModel-derived simulation without sodium ion in place, where we observed the ion binding. This last trajectory contains also solvent and ions, but with a lower printing frequency (1 ns).

opencc-by-4.0Apr 2023View details →

Historical data set for the Flumendosa case study in Sardinia, Italy.

The files COUT, WTMP, EVAP, CTMP contain the outflow, outflow water temperature, evapotranspiration and corrected air temperature of the sub basins respectively. CCIN, CCON, CCTN, CCTP, CCPP, CCSP, CCSS, CCTS are the concentrations of inorganic ang organic nitrogen; the total nitrogen and phosphorus;  the particulate and soluble phosphorus and the suspended and total sediment. CPRC is the corrected precipitation and UPVAP the evapotranspiration from the upstream area of each sub basin.

opencc-by-4.0Apr 2023View details →

Primewater Flumendosa (Sardinia) case study historical data

Historical data for the Flumendosa (sardinia, Italy) PrimeWater case study. The files COUT, WTMP, EVAP, CTMP contain the outflow, outflow water temperature, evapotranspiration and corrected air temperature of the sub basins respectively. CCIN, CCON, CCTN, CCTP, CCPP, CCSP, CCSS, CCTS are the concentrations of inorganic ang organic nitrogen; the total nitrogen and phosphorus;  the particulate and soluble phosphorus and the suspended and total sediment. CPRC is the corrected precipitation and UPVAP the evapotranspiration from the upstream area of each sub basin.