Find research datasets worth reusing

opencc-by-4.0Jun 2023View details →

Edge illumination X-ray phase contrast imaging with alternative gratings: dataset

This dataset contains results from Edge illumunation X-ray phase contrast simulations with alternative gratings, as shown in 'Setup.png' The simulations are performed with the monte-carlo software Gate. Postprocessing is done in Matlab. Four different grating geometries were simulated: Conventional, sheared, curved and folded gratings. As phantom, a row of Aluminum cylinders is chosen. The simulation parameters can be found in the excel-file 'Simulation_parameters.xlsx'. The folder 'gate' contains the macros that where used for the monte carlo-simulation. The folder 'matlab' contains the results of post-processing in matlab for each grating geometry. They can be opened with the file 'results_script.m The folder 'results' contains images of the results for each geometry, including, flatfield, projection, threefold contrast and fitting parameters. <table> <tbody> <tr> <td>This research was supported by EU Interreg Flanders - Netherlands Smart*Light (0386), Fonds wetenschappelijk onderzoek (G090020N, G094320N), and Agentschap Innoveren \& Ondernemen (Vlaio) (HBC.2020.2159). Nathanaël Six and Ben Huyge have a PhD fellowship of the FWO (11D8319N, 1S46122N).</td> </tr> </tbody> </table>

opencc-by-4.0Jun 2023View details →

Supplementary Data for "Assessing weathering, pedogenesis, and silt generation in granitoid-hosted soils from contrasting hydroclimates"

Supplementary data includes original sample names and locations, raw geochemical and granulometric data, and calculated geochemical data represented as figures for the manuscript titled "Assessing weathering, pedogenesis, and silt generation in granitoid-hosted soils from contrasting hydroclimates". All datasets are in the same excel file on separate tabs. All data were processed according to established procedures cited in the manuscript text. All software used is open access: ImageJ, adobe illustrator, and Microsoft excel.

opencc-by-4.0Mar 2023View details →

scNCL transfers labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization

Data used in our manuscript. 'scNCL_data' folder contains gene expression data (with protein) and gene activitiy data (with protein). 'GLUE_data' folder contains gene expression data and raw chromatin accessibility data.  'HFA-resampling' folder contains multiple independent sampling of HFA-subset dataset. 'Accuray on HFA-subsets.xlsx' file contains accuray results of all compared methods on HFA-subsets datasets.

opencc-zeroJul 2023View details →

Flower strip effectiveness for pollinating insects in agricultural landscapes depends on established contrast in habitat quality: A meta-analysis

Flower strips have become a prevalent measure in agricultural landscapes to counteract biodiversity loss and especially promote pollinators. Although their benefits for pollinating insects have been frequently evaluated and reported, generalized conclusions about optimal settings for effective flower strips are still difficult. From the perspective of pollinators, flower strips vary distinctly in habitat quality, and the same applies for the control sites selected for scientific studies. In this study, we used a meta-analytic approach based on a systematic review of recent studies (2009-2020) to analyze the relationship between flower strip effectiveness for pollinators and the contrast in habitat quality between flower strips and control sites. We extracted 350 data entries from 29 out of 172 studies based on available data for richness or abundance of the pollinator taxa groups Apiformes, Lepidoptera and Syrphidae as response variables, for both flower strips and control treatments. All flower strips and control treatments were assigned a habitat quality score including information on spatial dimension, floral resources and management. Moreover, we included information on landscape complexity as measured by percent cover of semi-natural habitats in the studied landscape. In general, our results of meta-analytical models showed an increasing effect size of flower strips on pollinators for higher contrasts in habitat quality between flower strips and control treatments. This relationship was consistent across pollinator taxa and different levels of landscape complexity. Altogether, in terms of pollinator habitat quality, high-quality flower strips were more attractive than low-quality flower strips, and the reported effectiveness of flower strips decreased from low-quality to high-quality control treatments. We recommend that results of future studies evaluating flower strips for pollinators are always linked with the contrast in habitat quality between selected flower strips and control treatments.

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-zeroJul 2023View details →

Data from: Remotely sensed environmental measurements detect decoupled processes driving population dynamics at contrasting scales

The increasing availability of satellite imagery has supported a rapid expansion in forward-looking studies seeking to track and predict how climate change will influence wild population dynamics. However, these data can also be used in retrospect to provide additional context for historical data in the absence of contemporaneous environmental measurements. We used 167 Landsat-5 Thematic Mapper (TM) images spanning 13 years to identify environmental drivers of fitness and population size in a well-characterized population of banner-tailed kangaroo rats (Dipodomys spectabilis) in the southwestern United States. We found evidence of two decoupled processes that may be driving population dynamics in opposing directions over distinct time frames. Specifically, increasing mean surface temperature corresponded to increased individual fitness, where fitness is defined as the number of offspring produced by a single individual. This result contrasts with our findings for population size, where increasing surface temperature led to decreased numbers of active mounds. These relationships between surface temperature and (i) individual fitness and (ii) population size would not have been identified in the absence of remotely sensed data, indicating that such information can be used to test existing hypotheses and generate new ecological predictions regarding fitness at multiple spatial scales and degrees of sampling effort. To our knowledge, this study is the first to directly link remotely sensed environmental data to individual fitness in a nearly exhaustively sampled population, opening a new avenue for incorporating remote sensing data into eco-evolutionary studies.

opencc-by-4.0Aug 2023View details →

Dataset: Periodic variation of mesoscale ultraviolet contrast at the cloud top of Venus

Filename: mean_A_283.txt : wavelength of 283 nm mean_A_365.txt : wavelengths of 365 nm Description: Empirical equigonal UV albedo of Venus as a function of the phase angle determined from Akatsuki UVI data. Format (text file):   1st column: Phase angle (deg) 2nd column: A:Mean albedo 3rd column: SD:Standard deviation   Filename: period1_283nm.txt : Period 1, 283 nm period1_365nm.txt : Period 1, 365 nm period2_283nm.txt : Period 2, 283 nm period2_365nm.txt : Period 2, 365 nm Description: Time series of the standard deviation of mesoscale UV contrast and the mean brightness of Venus. Format (text file): 1st column: Image file name 2nd column: Elapsed time (h) 3rd column: Phase angle (deg) 4th column: Standard deviation (W/m2/str/m) 5th column: Standard deviation in AM 6th column: Standard deviation in PM 7th column: Mean brightness (W/m2/str/m) 8th column: Mean brightness in AM 9th column: Mean brightness in PM   Filename: uvi_20160425_131340_283_l3b_v10.nc uvi_20160425_151341_283_l3b_v10.nc uvi_20160425_171339_283_l3b_v10.nc uvi_20160506_101341_283_l3b_v10.nc uvi_20160506_121340_283_l3b_v10.nc uvi_20160506_141343_283_l3b_v10.nc uvi_20160517_141339_283_l3b_v10.nc uvi_20160517_161339_283_l3b_v10.nc Description: 2.02-micrometer mapped data taken by the IR2 camera onboard Akatsuki in Level-3 netCDF format. The data have been corrected for the point-spread function, the flat-field pattern, and the detector temperature dependence by Sato et al. (2020, Icarus, 345, 113682, https://doi.org/10.1016/j.icarus.2020.113682). Format (binary file): netCDF The file names indicate the year, date and time of each observation.

opencc-by-4.0Aug 2023View details →

Non-Contrast CT Scans Dataset for Subarachnoid Hemorrhage: Bleeding Segmentation

This dataset comprises non-contrast CT scans of patients admitted with subarachnoid hemorrhage. All scans are provided in the NIfTI format. Details of the image preprocessing, which encompasses anonymization, resampling, skull stripping, and intensity normalization, are available at <a href="https://github.com/smcch/Subarachnoid_Hemorrhage_segmentation_and_mortality_prediction">https://github.com/smcch/Subarachnoid_Hemorrhage_segmentation_and_mortality_prediction</a>. Each scan is accompanied by a corresponding NIfTI volume, showcasing the expert manual segmentation of the hemorrhage.

opencc-by-4.0Aug 2023View details →

Contrasting impacts of climate change on protection forests of the Italian Alps: Supporting Data

Input files for the ForClim model (version 4.0.1) used in the associated paper. They can be used to to reproduce results of the simulation study. The ForClim model, including the source code, executable and documentation, is freely available under an Open Access license from the website of the original developers at <a href="https://ites-fe.ethz.ch/openaccess/">https://ites-fe.ethz.ch/openaccess/</a>. The original climatic dataset used to generate the ForClim input climate files at each site in South Tyrol is freely available at <a href="https://doi.pangaea.de/10.1594/PANGAEA.924502">https://doi.pangaea.de/10.1594/PANGAEA.924502</a> while the CHELSA climate data for future scenarios are available at <a href="https://www.chelsa-climate.org">https://www.chelsa-climate.org</a>. If interested in using this dataset for a research study or a project, please contact <a href="https://www.marco-mina.com">Marco Mina</a> ----------------------------------------------------------------------- Hillebrand L, Marzini S, Crespi A, Hiltner U & Mina M (2023) Contrasting impacts of climate change on protection forests of the Italian Alps. Frontiers in Forests and Global Change, 6, 2023  <a href="https://doi.org/10.1111/gcb.16197">https://doi.org/</a><a href="https://doi.org/10.3389/ffgc.2023.1240235">10.3389/ffgc.2023.1240235</a> ABSTRACT. Protection forests play a key role in protecting settlements, people, and infrastructures from gravitational hazards such as rockfalls and avalanches in mountain areas. Rapid climate change is challenging the role of protection forests by altering their dynamics, structure, and composition. Information on local- and regional-scale impacts of climate change on protection forests is critical for planning adaptations in forest management. We used a model of forest dynamics (ForClim) to assess the succession of mountain forests in the Eastern Alps and their protective effects under future climate change scenarios. We investigated eleven representative forest sites along an elevational gradient across multiple locations within an administrative region, covering wide differences in tree species structure, composition, altitude, and exposition. We evaluated protective performance against rockfall and avalanches using numerical indices (i.e., linker functions) quantifying the degree of protection from metrics of simulated forest structure and composition. Our findings reveal that climate warming has a contrasting impact on protective effects in mountain forests of the Eastern Alps. Climate change is likely to not affect negatively all protection forest stands but its impact depends on site and stand conditions. Impacts were highly contingent to the magnitude of climate warming, with increasing criticality under the most severe climate projections. Forests in lower-montane elevations and those located in dry continental valleys showed drastic changes in forest structure and composition due to drought-induced mortality while subalpine forests mostly profited from rising temperatures and a longer vegetation period. Overall, avalanche protection will likely be negatively affected by climate change, while the ability of forests to maintain rockfall protection depends on the severity of expected climate change and their vulnerability due to elevation and topography, with most subalpine forests less prone to loosing protective effects. Proactive measures in management should be taken in the near future to avoid losses of protective effects in the case of severe climate change in the Alps. Given the heterogeneous impact of climate warming, such adaptations can be aided by model-based projections and high local resolution studies to identify forest stand types that might require management priority for maintaining protective effects in the future.

opencc-by-4.0Mar 2019View details →

Contrasting the magnetism in La2−xSrxFeCoO6(x=0,1,2) double perovskites: The role of electronic and cationic disorder

Data sets for original figures in the article 'Contrasting the magnetism in La2−xSrxFeCoO6 (x=0,1,2) double perovskites: The role of electronic and cationic disorder' published in <a href="https://doi.org/10.1103/PhysRevB.99.184411">Phys. Rev. B 99, 184411 (2019)</a>. The file name of each xls file corresponds to the figure number in the published article. The files can be opened using the Excel program. If there are sub-figures, or multiple frames in each figure, the data of each sub-figure is stored in separate sheets within one xls file. The files with the file extension 'vesta' can be opened using the freely available program <a href="https://jp-minerals.org/vesta/en/">VESTA</a>.

opencc-by-4.0Sep 2023View details →

CAKE: clustering scRNA-seq data via combining contrastive learning with knowledge distillation

All datasets used in our paper "CAKE: clustering scRNA-seq data via combining contrastive learning with knowledge distillation"

Data from: Contrasting sap flow characteristics between pioneer and late-successional tree species in secondary tropical montane forests of Eastern Himalaya, India

Abstract The interactive role of life-history traits and environmental forcing on plant-water relations is crucial for understanding species response to climate change but remains poorly understood in secondary tropical montane forests (TMFs). Comparing contrasting life-history traits (pioneer vs late-successional species) in a biodiverse Eastern Himalayan secondary TMF, we investigated sap flow responses in co-occurring pioneer species, Symplocos racemosa (n=5) and Eurya acuminata (n=5), and late-successional species, Castanopsis hystrix (n=3), using modified Granier's Thermal Dissipation probes. The fast-growing pioneers S. racemosa and E. acuminata) had 2.1- and 1.6-times higher sap flux density than the late-successional C. hystrix, respectively, and exhibited characteristics of long-lived pioneer species. Significant radial and azimuthal variability in sap flow (V) between species was observed and attributed to life history traits and the canopy's access to sunlight. Nocturnal V (1800-0500 hr) was 13.8 % of daily V and is attributed to stem recharge for evening V (1800-2300 hr) and to endogenous stomatal controls for pre-dawn V (0000-0500 hr). Both the shallow-rooted pioneer species exhibited midday depression in V attributed to photosensitivity and diel moisture stress response. In contrast, deep-rooted C. hystrix transpired unaffected across the dry season likely accessing groundwater. Thus, the secondary broadleaved TMFs, with the dominance of shallow-rooted pioneers, are more prone to the negative impacts of drier and warmer winters than primary forests, which are dominated by deep-rooted species. The study provides an empirical understanding of life-history traits and microclimate modulating plant-water use in widely distributed secondary TMFs in Eastern Himalaya and highlights their vulnerability against warmer winters and reduced snowfall due to climate change.

opencc-by-4.0Sep 2023View details →

Contrasting carbon dioxide removal potential and nutrient feedbacks of simulated ocean alkalinity enhancement and macroalgae afforestation

PISCES model outputs supporting the associated publication. Files are for the following simulations: historical control (CTL), OAE without nutrient addition (OAE), OAE with nutrient addition (OAE_Fe_Si), macroalgae afforestation without nutrient feedbacks (MACRO) and macroalgae afforestation with nutrient feedbacks (MACRO_N_P). The following outputs are provided at monthly resolution: air-sea carbon flux (Cflx), export flux at 100m (EPC100) and depth integrated net primary production of phytoplankton (INTPP). In addition masks of the regions of OAE (mask_OAE) and macroalgae afforestation (mask_MACRO) are provided. All files have been regridded from the original eORCA025 grid to a regular 360x180 degree grid.

Multi-colony tracking of two pelagic seabirds with contrasting flight capability illustrates how windscapes shape migratory movements at an ocean-basin scale

Migration is a common trait among many animals allowing the exploitation of spatiotemporally variable resources. It often implies high energetic costs to cover large distances, for example between breeding and wintering grounds. For flying or swimming animals, the adequate use of winds and currents can help reduce the associated energetic costs. Migratory seabirds are good models because they dwell in habitats characterized by strong winds while undertaking very long migrations. We tested the hypothesis that seabirds migrate through areas with favourable winds. To that end, we used a multi-colony geolocator tracking dataset of two North Atlantic seabirds with contrasting flight capabilities, the black-legged kittiwake (Rissa tridactyla) and the Atlantic puffin (Fratercula arctica), and wind data from the ERA5 climate reanalysis model. Both species had on average positive wind support during migration. Their main migratory routes were similar and followed seasonally prevailing winds. The general migratory movement had a loop-shape at the scale of the North Atlantic, with an autumn route (southward) along the east coast of Greenland, and a spring route (northward) closer to the British Isles. While migrating, both species had higher wind support in spring than in autumn. Kittiwakes migrated farther and benefited from higher wind support than puffins on average. The variation in wind conditions encountered while migrating was linked to the geographical location of the colonies. Generally, northernmost colonies had better wind support in autumn while the southernmost colonies had a better wind support in spring, with some exceptions. Our study helps in understanding how the physical environment shapes animal migration, which is crucial to further predict how migrants will be impacted by ongoing environmental changes.

Contrasting laboratory and field outcomes of bat–moth interactions

Predator–prey interactions are important but difficult to study in the field. Therefore, laboratory studies are often used to examine the outcomes of predator–prey interactions. Previous laboratory studies have shown that moth hearing and ultrasound production can help prey avoid being eaten by bats. We report here that laboratory behavioral outcomes may not accurately reflect the outcomes of field bat–moth interactions. We tested the success rates of two bat species capturing moths with distinct anti-bat tactics using behavioral experiments. We compared the results with the dietary composition of field bats using next‐generation DNA sequencing. Rhinolophus episcopus and Rhinolophus osgoodi had a lower rate of capture success when hunting for moths that produce anti-bat clicks than for silent eared moths and earless moths. Unexpectedly, the success rates of the bats capturing silent eared moths and earless moths did not differ significantly from each other. However, the field bats had a higher proportion of silent eared moths than that of earless moths and that of clicking moths in their diets. The difference between the proportions of silent eared moths and earless moths in the bat diets can be explained by the difference between their abundance in bat foraging habitats. These findings suggest that moth defensive tactics, bat countertactics, and moth availability collectively shape the diets of insectivorous bats. This study illustrates the importance of using a combination of behavioral experiments and molecular genetic techniques to reveal the complex interactions between predators and prey in nature.

The role of high-contrast male facial stripes in mitigating female aggression in the jumping spider, Plexippus paykulli

Vibrant male coloration and energetic courtship displays set jumping spiders apart from most arachnids, which typically rely on non-visual stimuli. Like many other spiders, female salticids engage in sexual cannibalism, making courtship a risky but necessary endeavor for males. In this study, we investigated the relationship between male coloration and female aggression to better understand the interplay of attraction and aversion during courtship. Many male jumping spiders sport conspicuous coloration or high-contrast patterns that are reminiscent of the coloration of many aposematic insects. The faces of Plexippus paykulli males are adorned with bold vertical stripes they direct toward females during courtship. We hypothesized that these stripes could function as a sensory trap, leveraging female aversion to the signal to reduce the likelihood of cannibalism. We tested whether spiders exhibit an aversion to stripes in the context of predation by manipulating prey coloration and testing spider preference for prey based on the presence or absence of stripes. Then we conducted two courtship experiments by manipulating male facial coloration to determine whether the presence of male stripes affects female aggression and likelihood of mating. We also manipulated female foraging drive in each courtship experiment (either diet or mating status) to see whether common sources of natural variation among females influenced response to courting males. We found that spiders showed an aversion to stripes while foraging but that this aversion does not confer reduced aggression from females toward striped males vs. males with stripes obscured. However, stripes did affect the likelihood of male reproductive success, as striped males mounted females more frequently than non-striped males. Finally, female condition influenced female response to courting males, with hungrier females showing higher aggression and previously mated females being mounted less frequently than non-mated females.

opencc-by-4.0Sep 2023View details →

Videos For: One-shot recognition of any material anywhere using contrastive learning with physics-based renderin

Demonstration Video: Image Recognition of Materials States And Types From Single Example Identifying the state of the material in the main video by matching it to a few reference images (top). Each image contains a specific material state or type. The best match image is marked green. Based on the net for identifying similarity between any material state and type. The code for the net and the trained model used for this is available at: https://github.com/sagieppel/Contrastive-learning-for-one-shot-materials-and-textures-similarity-recognition-from-images Paper : One-shot recognition of any material anywhere using contrastive learning with physics-based rendering. https://arxiv.org/abs/2212.00648

opencc-by-4.0Oct 2023View details →

Dataset for Paul et al., "Revisiting the applicability and constraints of molybdenum and uranium-based paleo redox proxies: comparing two contrasting sill fjords", Biogeosciences, 2023

The datafile contains the solid phase data for Gullmar Fjord (GF-117) and Koljö Fjord (KF-43), presented in Figures 3, 4 and 6 in the publication: <ol> <li>pore water data (SO42-, ΣH2S, Fe, Mn, Mo, and U)</li> <li>solid-phase carbon and nitrogen data (TOC, TN, C/N, OCterr and OCphyt)</li> <li>solid-phase sequential extraction data (Mo, U, Fe, Mn, Al, Ca, and S)</li> <li>Mo and U-Enrichment Factors (EF)</li> </ol>

opencc-zeroOct 2023View details →

Data from: Contrasting impacts of short- and long-term large herbivore exclusion on understory net CO2 exchange in a boreal forest

Across boreal forests, trees are the main living biomass carbon (C) stock, but the understory vegetation can contribute significantly to the C cycling and net forest carbon dioxide (CO2) balance. The patchy understory vegetation which consists of sunlit (i.e., lichen-like) and shaded habitats (i.e., dwarf shrub-like) is often altered by ungulate grazers. Grazers may influence understory CO2 exchange, and consequently, the forest CO2 balance. Grazing affects differently the biomass of slow growing lichens compared to the faster growing mosses and dwarf shrubs, and therefore the effects of grazing on CO2 exchange in the patchy understory vegetation could vary temporally. We studied how excluding grazing for short- and long-term affects the CO2 exchange and vegetation biomass in the understory of an oligotrophic Scots pine forest. We measured growing season (2019, 2020) CO2 exchange across sunlit and shaded habitats inside fences that had excluded large grazers for 0–1 and 25–26 years and in the adjacent grazed area. In addition, we measured the height of understory vegetation. We found that short-term grazer exclusion increased ecosystem CO2 source fluxes only in the shaded habitats. However, long-term exclusion of grazing decreased CO2 net release regardless of the habitat type. Furthermore, grazer exclusion increased moss depth immediately which coincided with an abrupt intensification of CO2 net release. Considering the impacts of grazing over both short- and long-term may help to forecast C fluxes more accurately which may be relevant for informed climate solutions regionally and even on a larger scale.