Find research datasets worth reusing

PI3K block restores age-dependent neurovascular coupling defects associated with cerebral small vessel disease

Neurovascular coupling (NVC), a vital physiological process that rapidly and precisely directs localized blood flow to the most active regions of the brain, is accomplished in part by the vast network of cerebral capillaries acting as a sensory web capable of detecting increases in neuronal activity and orchestrating the dilation of upstream parenchymal arterioles. Here, we report a Col4a1 mutant mouse model of cerebral small vessel disease (cSVD) with age-dependent defects in capillary-to-arteriole dilation, functional hyperemia in the brain, and memory. The fundamental defect in aged mutant animals was the depletion of the minor membrane phospholipid phosphatidylinositol 4,5 bisphosphate (PIP2) in brain capillary endothelial cells, leading to the loss of inwardly rectifier K+ (Kir2.1) channel activity. Blocking phosphatidylinositol-3-kinase (PI3K), an enzyme that diminishes the bioavailability of PIP2 by converting it to phosphatidylinositol (3,4,5)-trisphosphate (PIP3), restored Kir2.1 channel activity, capillary-to-arteriole dilation, and functional hyperemia. In longitudinal studies, chronic PI3K inhibition also improved the memory function of aged Col4a1 mutant mice. Our data suggest that PI3K inhibition is a viable therapeutic strategy for treating defective NVC and cognitive impairment associated with cSVD.

Data for: Fear before food: Scale-dependence in elk habitat selection

<ol> <li>Habitat selection is a critical aspect of a species' ecology requiring complex decision-making that is both hierarchical and scale-dependent, since factors that influence selection may be nested or unequal across scales.</li> <li>Elk (Cervus canadensis) ranged widely across diverse habitats in North America prior to European settlement and subsequent eastern extirpation. Most habitat studies have occurred within their contemporary western range, even after eastern elk reintroductions began. As habitat selection can vary by geographic location, available cover, season, and diel period, it is important to understand how a non-migratory, reintroduced population in northern Wisconsin, USA is limited by the lack of variation in topography, elevation, and vegetation.</li> <li>We tested scale-dependent habitat selection on 79 adult elk from 2017–2020. We used resource selection functions across both temporal and spatial scales to understand differences in selection of topographic and environmental features.</li> <li>We found that selection varied both spatially and temporally and elk selected areas with the greatest potential to influence fitness at larger scales (i.e., landscape scale), meaning elk selected areas closer to escape cover and further from "risky" features (e.g., wolf territory centers, county roads and highways). We found stronger avoidance to wolf territory centers during spring, suggesting elk were selecting safer habitats during calving season. We found elk selected habitats with less canopy cover across both spatial scales and all seasons, suggesting that elk selected these areas for better access to forage as forest stands in early seral stages have greater nutritional value and forage biomass than closed-canopy forests and direct solar radiation to provide warmth in the cooler seasons.</li> <li>This study highlights how processes at different spatial and temporal scales influence species' decision-making. It provides insight into the complexity of making informed decisions in which an individual is responding to their immediate environment while simultaneously making decisions in the context of the larger landscape. Scale-dependent behavior is crucial to understand within specific geographic regions as these decisions scale up to influence population dynamics. </li> </ol>

Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency

Environmental circumstances shaping soil microbial communities have been studied extensively. However, due to disparate study designs, it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 of those containing regional plant productivity gradients) to examine i) if similar abiotic or biotic factors predict both large-scale (across sites) and regional-scale (within sites) patterns in bacterial and fungal community composition, and ii) if microbial community composition differs consistently at two levels of regional plant productivity (low vs high). We found that bacteria were consistently associated with certain soil properties and both bacteria and fungi were consistently associated with plant community composition within different sites. Moreover, there was a microbial community signal that clearly distinguished high and low-productivity soils that was shared across different grasslands independent of their location in the world. In this study, we show that there is high congruence between predictors of bacterial and fungal community composition at different spatial scales and that regional productivity differences are typified by characteristic soil microbial communities across the grassland biome. These results suggest that it might be feasible to predict the overall effects of global changes on soil microbial community composition in different grasslands, as well as to discriminate fertile from infertile systems using generally applicable microbial indicators.

opencc-by-4.0Aug 2023View details →

Data for Torppa et al. 2023 'Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety'

The dataset consists of the data that supports the findings of the article 'Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety’ written by Torppa et al. and published in Plant and Soil in 2023. The data consists of arbuscular mycorrhizal colonization, fatty acid and community data, as well as soil and crop nutrient and yield data.

Data for: The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype

Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant Persicaria maculosa by varying two key resources light and soil moisture in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e., the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes (although the precise proportion of parental versus immediate DETs varied among genotypes). By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptome level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.

Linking temperature dependence in fitness effects of mutations to thermal niche adaptation

Fitness effects of mutations may generally depend on temperature that influences all rate-limiting biophysical and biochemical processes. Earlier studies suggested that high temperatures may increase the availability of beneficial mutations ("more beneficial mutations"), or allow beneficial mutations to show stronger fitness effects ("stronger beneficial mutation effects"). The "more beneficial mutations" scenario would inevitably be associated with increased proportion of conditionally beneficial mutations at higher temperatures. This in turn predicts that populations in warm environments show faster evolutionary adaptation but suffer fitness loss when faced with cold conditions, and those evolving in cold environments become thermal-niche generalists ("hotter is narrower"). Under the "stronger beneficial mutation effects" scenario, populations evolving in warm environments would show faster adaptation without fitness costs in cold environments, leading to a "hotter is (universally) better" pattern in thermal niche adaptation. We tested predictions of the two competing hypotheses using an experimental evolution study in which populations of two model bacterial species, Escherichia coli and Pseudomonas fluorescens, evolved for 2,400 generations at three experimental temperatures. Results of reciprocal transplant experiments with our P. fluorescens populations were largely consistent with the "hotter is narrower" prediction. Results from the E. coli populations clearly suggested stronger beneficial mutation effects at higher assay temperatures, but failed to detect faster adaptation in populations evolving in warmer experimental environments (presumably because of limitation in the supply of genetic variation). Our results suggest that the influence of temperature on mutational effects may provide insight into the patterns of thermal niche adaptation and population diversification across thermal conditions.

opencc-zeroSep 2023View details →

White-tailed deer responses to predator cues depend upon past land use and contemporary fire regime

Prey can assess immediate risk of predation by detecting cues of predator presence, and it is expected that prey should invest in costly antipredator behaviors when a cue of predator presence is detected. Features of the habitat in which the cue is detected, such as vegetative concealment, serve as indirect cues of risk and can mediate how prey respond to direct cues of predator presence. Past agricultural land use and contemporary fire regime are common disturbances that may modify prey perceptions of risk and could therefore alter prey responses to direct cues of predator presence. We examined whether the overlap of these two disturbances affected white-tailed deer (Odocoileus virginianus) responses to cues of predator presence by measuring deer vigilance and foraging bout duration in response to coyote (Canis latrans) vocalizations across 20 woodlands that varied in past land use and contemporary fire regime. Frequent fire regimes consistently increased deer visibility to predators across both land-use history contexts. Deer exhibited no behavioral response to the predator cue in habitats containing infrequent fire regimes or agricultural legacies. Deer responded to the cue in frequently burned woodlands without agricultural legacies through increased vigilance and duration spent at a foraging location. These findings reveal that land-use legacies and contemporary fire regimes can mediate how prey respond to direct cues of risk. They also suggest that prey may balance the uncertainty associated with cues of predation risk with the urgency of responding to a potential attack by being vigilant and remaining in place.

opencc-by-nc-nd-4.0Nov 2022View details →

Angle Dependent Spectral Reflectance Material Dataset based on 945 nm Time-of-Flight Camera Measurements

The dataset contains angle dependent spectral reflectance measurements of materials in the infrared spectrum at a wavelength of 945 nm taken by a time-of-flight camera for an angle range of 0° to 80° in incremental steps of 10°, mounted on an adjustable angle measurement device. Each data file is structured in columns with two parameters: reflectance (%) and incidence angle (°). For each single material measurement a description file is attached in a separate ZIP-file. The extended dataset include new materials such as vehicle varnish and moss rubber. This new version further includes pictures for almost each of the measurements to depict the measurement setup and environmental conditions during the data acquisition. They are provided in a separate ZIP-file.   Note: Please always use the latest version!

opencc-by-4.0Jul 2023View details →

Raw data of the publication titled "First-row d6 metal complex enables photon upconversion and initiates blue light-dependent polymerization with red light"

Raw data of the publication in Angew. Chem. Int. Ed. titled "First-row d6 metal complex enables photon upconversion and initiates blue light-dependent polymerization with red light "

Dataset: Bioelectrocatalytic CO2 Reduction by Mo-Dependent Formylmethanofuran Dehydrogenase

Supporting information for article <a href="https://doi.org/10.1002/anie.202311981">https://doi.org/10.1002/anie.202311981</a>

opencc-zeroSep 2023View details →

Rapid and reversible humidity-dependent colour change by water film formation in a scaled springtail: Image compilations and video recordings

Colour is often not a static trait but can change over time either through biotic or abiotic factors. Humidity-dependent colour change can occur through either morphological change (e.g. to feather barbules in birds) or by the replacement of air by water causing a shift in refractive index, as seen in arthropod multilayer cuticles or scales. The scaled springtail Lepidocyrtus cyaneus has scales that produce color largely via thin film interference from their lamina. We observed a marked colour change from golden to violet/purple colouration in humid conditions. Light microscopy, microspectrophotometry, contact angle goniometry and optical modelling indicate that the formation of a thin film of water on top of the hydrophilic scales increases their laminar thin film thickness, causing a shift towards violet/purple colour. Evaporation of the water film causes the metallic golden colour to return. This constitutes a remarkably rapid colour change (in the order of seconds), only limited by the speed of water film condensation and evaporation, that may serve as inspiration for new dynamically coloured materials and sensors.

Mitochondrial responses to long-term and cyclic hypoxia depend on the oxidized fuel in a hypoxia-tolerant marine bivalve Crassostrea gigas

These are the metadata for a publication "Mitochondrial responses to long-term and cyclic hypoxia depend on the oxidized fuel in a hypoxia-tolerant marine bivalve Crassostrea gigas" under consideration for publication in the Scientific reports. Sessile benthic organisms like oysters inhabits intertidal zone transitioning between aquatic and terrestrial condition during tidal movements exposing the organisms to alternating hypoxia and reoxygenation (H/R) episodes thereby altering the respiratory chain activities and metabolome compositions. Our study investigated the effects of constant long-term H/R stress (90 min at ~0% O2, and 10 min reoxygenation) and constant cyclic H/R stress (5 cycles of 15 min at ~0% O2, and 10 min reoxygenation) on isolated mitochondria from the gill and the digestive gland of C. gigas respiring on different substrates (pyruvate, palmitate, and succinate). Both gill and the digestive gland mitochondria exposed to constant long-term H/R suppressed OXPHOS respiration especially during Complex I oxidation with no change in ROS efflux but an increase FEL. In the gill mitochondria oxidizing Complex I substrates, exposure to constant cyclic H/R prompted a significant drop after the first H/R cycle. In contrast, succinate-driven respiration only showed significant decline after the fifth H/R cycle. ROS efflux and FEL however saw little to no change after constant cyclic H/R. This observation from our study further suggests succinate as a potential stress fuel under H/R stress and might assist in post-hypoxic recovery of oysters mitigating oxidative stress and supporting rapid ATP re-synthesis during oxygen fluctuations such as commonly observed in intertidal zones. Additionally, our study revealed that constant long-term hypoxia is more damaging than constant cyclic hypoxia.

opencc-zeroSep 2023View details →

The effects of sex on extinction dynamics of Chlamydomonas reinhardtii depend on the rate of environmental change

The continued existence of sex, despite many the costs it entails, still lacks an adequate explanation, as previous studies demonstrated that the effects of sex are environment-dependent: sex enhances the rate of adaptation in changing environments, but the benefits level off in benign conditions. To the best of our knowledge, the potential impact of different patterns of environmental change on the magnitude of these benefits received less attention in theoretical studies. In this paper, we begin to explore this issue by examining the effect of the rate of environmental deterioration (negatively correlated with population survival rate), on the benefits of sex. To investigate the interplay of sex and the rate of environmental deterioration, we carried out a long-term selection experiment with a unicellular alga (Chlamydomonas reinhardtii), by manipulating mode of reproduction (asexual, facultative or obligate sexual) and the rate of environmental deterioration (an increase of salt concentration). We monitored both the population size and extinction dynamics. The results revealed that the relative advantage of sex increased at the intermediate rate and plateaued at the highest rate of environmental deterioration. Obligate sexual populations had the slowest extinction rate under the intermediate rate of environmental deterioration, while facultative sexuality was favoured under the high rate-treatment. To the best of our knowledge, our study is the first to demonstrate that the interplay of sex and the rate of environmental deterioration affects the probability of survival, which indicates that mode of reproduction may be an important determinant of survival of the anthropogenic-induced environmental change.

Data-driven characterization and correction of the orientation dependence of magnetization transfer measures using diffusion MRI

These are the produced plots for every subjects and every sessions of the study. Here are the characterization plots, the corrected plots, and the tractometry plots.

Database of Short Term Damage Equivalent Loads (DEL) of IWT7.5MW wind turbine depending on wind, TI, yaw and derating

Two datasets for short term damage equivalent loads (DEL) and energy production of the IWT7.5 MW research wind turbine (https://doi.org/10.24406/IWES-N-518562) are provided. dataset_Derating is a subset of dataSet_Derating_withYaw. The damage equivalent loads are computed with the rainflow counting algorithm applied to time series loads. They are based on Miner's rule. Further details can be found in:  Requate, N., Meyer, T., and Hofmann, R.: From wind conditions to operational strategy: Optimal planning of wind turbine damage progression over its lifetime, Wind Energ. Sci., accepted for publication, 2023.  In the paper, the dataset_Derating was used to create surrogate models. A fullfactorial approach to simulate different parameter-combination was applied.  Information about the signals and units is provided in the yml files. The range of parameters is given by python code in the yml file.  For each set of parameters, 6 different 10 minute-realizations of a turbulent wind field ("seeds") were created. The turbine was then simulated separately for each turbulent wind field. Each folder contains the short term DELs for each 10 minute simulation and the aggregated short term DELs over all 6 wind realizations. Outliers from simulation error were removed. The data was originally intended to create surrogate models of the variation of outputs values throughout the parameter space. Further usage is possible and encouraged.

opencc-zeroOct 2023View details →

Dataset: Plant-mediated effects of fire and fragmentation drive plant–pollinator interaction β-diversity in fire-dependent pine savannas

Interaction β-diversity is a measure essential for understanding and conserving species interactions and ecosystem functioning. Interaction β-diversity explains the variation in species interactions across spatial and temporal gradients, resulting from species turnover or interaction rewiring. Each component of interaction β-diversity has different ecological implications and practical consequences. While interaction β-diversity due to species turnover is related to assembly processes and fragmentation, rewiring can support high biodiversity and confer resilience to ecological networks. However, it is unclear whether both components respond to the same or different ecological drivers. Here, we assessed the ecological drivers of plant–pollinator interaction β-diversity and its components across 24 sites in 9 longleaf pine (LLP) savannas in north and central Florida. We evaluated the effects of flowering plant composition and flower abundance, vegetation, fire regime, soil moisture, terrain characteristics, climate, spatial context and geographic location. We used path analysis to evaluate the drivers of spatial interaction β-diversity and its main components. We then used generalized linear mixed models to assess the temporal patterns of spatial β-diversity among sites within preserves. We found that plant–pollinator networks in LLP savannas are highly variable across space and time, mainly due to species turnover and possibly in response to abiotic gradients and dispersal boundaries. Flower abundance and flowering plant composition, geographic location, fire seasonality, soil moisture, and landscape context were the main drivers of plant–pollinator β-diversity, highlighting the role of fire management and habitat connectivity in preserving plant–pollinator networks.

opencc-by-4.0Jul 2023View details →

Data set "Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra"

This data set accompanies the publication "Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra" by Julia Brüggemann, Maria Chekmeneva, Mario Wolter, and Christoph R. Jacob (TU Braunschweig, Germany) It contains the following files: Directory 01_structures:     - xyz files of all considered molecular structures. Directory 02_2d-ir_data_and_code:     - updated version of the code of calculating 2D-IR spectra, initially published in DOI: 10.5281/zenodo.7328312, which can be used to obtain the 2D-IR spectra shown in the publication and its supporting information.

opencc-zeroOct 2023View details →

Effects of large mammal exclusion on seedling communities depend on plant species traits and landscape protection in human-modified Costa Rican forests

<ol> <li>Large terrestrial herbivorous mammals (LTH-mammals) influence plant community structure by affecting seedling establishment in mature tropical forests. Many of these LTH-mammals frequent secondary forests, but their effects on seedling establishment in them are understudied, hindering our understanding of how LTH-mammals influence forest regeneration in human-modified landscapes.</li> <li>We tested the hypothesis that the strength of LTH-mammals' effects on seedling establishment depends on landscape protection, forest successional stage, and plant species' traits using a manipulative field experiment in six 1-ha sites with varying successional age and landscape protection. In each site, we established forty seedling plot-pairs, with one plot excluding LTH-mammals and one not, and monitored seedlings of 116 woody species for 26 months.</li> <li>We found significant effects of LTH-mammal exclusion on seedling survival contingent upon the protection of forests at the landscape level and forest stage. After 26 months, survival differences between LTH-mammal exclusion and non-exclusion treatments were greater in protected than unprotected landscapes. Additionally, plant species' traits were related to the LTH-mammals' differential effects, as LTH-mammals reduced the survival of seedlings of larger-seeded species the most. Overall, LTH-mammals' effects translated into significant shifts in community composition as seedling communities inside and outside the exclosures diverged. Moreover, lower density and higher species diversity were found as early as 12 and 18 months outside than inside exclosures.</li> <li> Synthesis and applications. Insight into the interactions between LTH-mammals and seedling communities in forest regeneration can be instrumental in planning effective restoration efforts. We highlight the importance of landscape protection in seedling survival and the role of LTH-mammals in promoting seedling diversity in mature forests but also in secondary successional forests. The findings suggest that conservation efforts and possibly trophic rewilding can be important approaches for preserving diversity and influencing the trajectory of secondary tropical forest succession. However, we also caution that an overabundance of LTH-mammals may adversely impact the pace of forest succession due to their preference for large-seeded species. Therefore, a comprehensive wildlife management plan is indispensable. Additionally, longer-term studies on LTH-mammals are necessary to understand the effects of temporal fluctuations that are undetected in short-term studies.</li> </ol>

opencc-by-4.0Oct 2023View details →

Serial Dependence in face-gender classification revealed in low-beta frequency EEG

Dataset and MATLAB scripts for publication. Contact giacomo.ranieri@unifi.it for any additional information.