Find research datasets worth reusing

Uncertainty-aware molecular dynamics from Bayesian active learning: Phase Transformations and Thermal Transport in SiC

Machine learning interatomic force fields are promising for combining high computational efficiency and accuracy in modeling quantum interactions and simulating atomic level processes. Active learning methods have been recently developed to train force fields efficiently and automatically. Among them, Bayesian active learning utilizes principled uncertainty quantification to make data acquisition decisions. In this work, we present an efficient Bayesian active learning workflow, where the force field is constructed from a sparse Gaussian process regression model based on atomic cluster expansion descriptors. To circumvent the high computational cost of the sparse Gaussian process uncertainty calculation, we formulate a high-performance approximate mapping of the uncertainty and demonstrate a speedup of several orders of magnitude. As an application, we train a model for silicon carbide (SiC), a wide-gap semiconductor with complex polymorphic structure and diverse technological applications in power electronics, nuclear physics and astronomy. We show that the high pressure phase transformation is accurately captured by the autonomous active learning workflow. The trained force field shows excellent agreement with both \textit{ab initio} calculations and experimental measurements, and outperforms existing empirical models on vibrational and thermal properties. The active learning workflow is readily generalized to a wide range of systems, accelerates computational understanding and design.

Supplementary material 1 from: Di Lorenzo T, Di Marzio W, Piccini L, Messana G, Sáenz M, Galassi D (2018) Survival, metabolic rates and locomotory activities of a groundwater-obligate copepod species under long-term exposures to tetrachloroethylene. ARPHA Conference Abstracts 1: e29966. https://doi.org/10.3897/aca.1.e29966

Survival, metabolic rates and locomotory activities of a groundwater-obligate copepod species under long-term exposures to tetrachloroethylene

Supplementary material 1 from: Kotov S, Gontova T, Kononenko N, Chernyavski E, Chikitkina V (2022) Phytochemical analysis and anti-allergic activity of a combined herbal medicine based on bur-marigold, calendula and hawthorn. Pharmacia 69(1): 237-247. https://doi.org/10.3897/pharmacia.69.e77624

HPLC results for dry extracts of the bur-marigold herb, calendula flowers, hawthorn leafand flowers and combined extract

Mammals adjust diel activity across gradients of urbanization

Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator-prey dynamics. Yet, changes in animal behavior within the shorter 24-hour light-dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While spatial habitat is a fundamental consideration in wildlife management and conservation, temporal habitat is often ignored. We formulated a temporal resource selection model to quantify the diel behavior of eight mammal species across ten U.S. cities. We found high variability in diel activity patterns within and among species and species-specific correlations between diel activity and human population density, impervious land cover, available greenspace, vegetation cover, and mean daily temperature. We also found that some species may modulate temporal behaviors to manage both natural and anthropogenic risks. Our results highlight the complexity with which temporal activity patterns interact with local environmental characteristics, and suggest that urban mammals may use time along the 24-hour cycle to reduce risk, adapt, and therefore persist in human-dominated ecosystems.

opencc-by-4.0Dec 2020View details →

Revisiting the impact of rapid releases on software development activities

This repository contains the data used in our work entitled ["Revisiting the impact of rapid releases on software development activities"]

Bats partition activity in space and time in a large, heterogeneous landscape

Diverse species assemblages theoretically partition along multiple resource axes to maintain niche separation between all species. Temporal partitioning has received less attention than spatial or dietary partitioning but may facilitate niche separation when species overlap along other resource axes. We conducted a broad-scale acoustic study of the diverse and heterogeneous Great Smoky Mountains National Park in the Appalachian Mountains. Between 2015 and 2016, we deployed acoustic bat detectors at 50 sites (for a total of 322 survey nights). We examined spatiotemporal patterns of bat activity (by phonic group: Low, Mid, and Myotis) to test the hypothesis that bats partition both space and time. Myotis and Low bats were the most spatially and temporally dissimilar, while Mid bats were more general in their resource use. Low bats were active in early successional openings or low-elevation forests, near water, and early in the evening. Mid bats were similarly active in all land cover classes, regardless of distance from water, throughout the night. Myotis avoided early successional openings and were active in forested land cover classes, near water, and throughout the night. Myotis and Mid bats did not alter their spatial activity patterns from 2015 to 2016, while Low bats did. We observed disparate temporal activity peaks between phonic groups that varied between years and by land cover class. The temporal separation between phonic groups relaxed from 2015 to 2016, possibly related to changes in the relative abundance of bats or changes in insect abundance or diversity. Temporal separation was more pronounced in the land cover classes that saw greater overall bat activity. These findings support the hypothesis that niche separation in diverse assemblages may occur along multiple resource axes and adds to the growing body of evidence that bats partition their temporal activity.

Representative giant virus genomes for "Resolving environmental drivers and ecological patterns of active viruses infecting protists in the Southern Ocean"

Nucleotide FASTA files of each representative giant virus genomes used in "Resolving environmental drivers and ecological patterns of active viruses infecting protists in the Southern Ocean".

Dataset from Research: Effect of active lecture and webquest on learning outcomes in higher education

Dataset in a xlsx file used by Remedios Aguilar-Moya & collaborators in the research “Effect of direct instruction and webquest on learning outcomes in higher education”.

Dataset: Multi-Stakeholder Validation of Entrustable Professional Activities for a Family Medicine Care of the Elderly Residency Program: A Focus Group Study

ZOOM Meeting transcripts from 5 stakeholder group meetings used in the study.

opencc-by-4.0Apr 2021View details →

Coordination of two opposite flagella allows high-speed swimming and active turning of individual zoospores

This contains the datasets of zoospores swimming in water at global scale and during a turning event. We also include the Matlab files for computing the data of global scale data and the simulation for zoospore spreading.

Active flutter suppression for light sport airplanes by a control surface split

The DataSet contains Matlab files to carried out a Modal Analysis, Flutter Analysis, Active Flutter Suppression and Dynamical response for developed mathematical model of the airplane.

Oil-gas prices and economic activity in selected European countries – evidence form time and frequency domain causality

Data sets related with research: Oil-gas prices and economic activity in selected European countries – evidence form time and frequency domain causality. - file name: Data - Time Series - DEU, NOR, POL results of Breitung-Candelon test

Experimental evolution reveals differential evolutionary trajectories in male and female activity levels in response to sexual selection and metapopulation structure

Behavior is central to interactions with the environment and thus has significant consequences for individual fitness. Sexual selection and demographic processes have been shown to independently shape behavioral evolution. However, while some studies have tested the simultaneous effects of these forces, no studies have investigated their interplay in behavioral evolution. We applied experimental evolution in the seed beetle Callosobruchus maculatus to investigate, for the first time, the interactive effects of sexual selection intensity (high (polygamy) vs. minimal (enforced monogamy)) and metapopulation structure (yes/no) on the evolution of movement activity, a crucial behavior involved in multiples functions (e.g., dispersal, predator avoidance or resource acquisition) and thus, closely related to <a>fitne</a>ss. We found that the interactive effects of the selection regimes did not affect individual activity, which was assayed under two different environments (absence vs. presence of conspecific cues from both sexes). However, contrasting selection regimes led to sex- and context-dependent divergence in activity. The relaxation of sexual selection favored an increase in female, but not male, movement activity that was consistent between environmental contexts. In contrast, selection associated with the presence/absence of metapopulation structure led to context-dependent responses only in male activity. In environments containing cues from conspecifics, males from selection lines under population subdivision showed increased levels of activity compared to those assayed in an environment devoid of conspecifics cues, while the opposite was true for males from panmictic lines. These results underscore that both the effects of sexual selection and population spatial structure may be crucial in shaping sex-specific behavioral evolution.

opencc-by-4.0Dec 2021View details →

Melanocortin 1 receptor activation protects against alpha-synuclein pathologies in models of Parkinson's disease

Raw data for the manuscript "Melanocortin 1 receptor activation protects against alpha-synuclein pathologies in models of Parkinson’s disease"

opencc-by-4.0Apr 2022View details →

Data for the original research article 'Enhanced anaerobic digestion of dairy wastewater in a granular activated carbon amended sequential batch reactor'

All data that support the findings of the study 'Enhanced anaerobic digestion of dairy wastewater in a granular activated carbon amended sequential batch reactor' published in GCB Bioenergy Journal are openly available in the file.

opencc-zeroApr 2022View details →

Fire decreases soil enzyme activities and reorganizes microbially-mediated nutrient cycles: a meta-analysis

The biogeochemical signature of fire shapes the functioning of many ecosystems. Fire changes nutrient cycles not only by volatilizing plant material, but also by altering organic matter decomposition—a process regulated by soil extracellular enzyme activities (EEAs). However, our understanding of fire effects on EEAs and their feedbacks to nutrient cycles is incomplete. We conducted a meta-analysis with 301 field studies and found that fire significantly decreased EEAs by ~20-40%. Fire decreased EEAs by decreasing soil microbial biomass and organic matter substrates. Soil nitrogen-acquiring EEA decreased alongside decreasing available nitrogen, likely from fire-driven volatilization of nitrogen and decreased microbial activity. Fire decreased soil phosphorus-acquiring EEA but increased available phosphorus, likely from pyro-mineralization of organic phosphorus. These findings suggest that fire suppresses soil microbes and consumes their substrates, thereby slowing microbially-mediated nutrient cycles (especially phosphorus) via decreased EEAs. These changes can become increasingly important as fire regimes in many ecosystems continue to shift in response to global change.

opencc-zeroApr 2022View details →

Data from: Responses to artificial selection for locomotor activity: A focus on death feigning in red flour beetle

Whole-organism performance, including locomotor activity, is an important fitness trait in many animals. Locomotor activity is often classified into sprint speed and locomotor endurance and differences in sprint speed and locomotor endurance affect on other traits such as life-history traits. Previous studies found that locomotor endurance, sprint speed, and brain dopamine (DA) levels are correlated with artificial selection for death-feigning (an anti-predator behavior that we refer to as "death-feigning syndrome") in some insect species. Thus, if the syndrome has a genetic basis, death feigning, sprint speed, and brain DA levels may be affected by artificial selection for locomotor endurance. We artificially selected for locomotor endurance over 10 generations in the red flour beetle Tribolium castaneum, and established higher (H) and lower activity (L) strains, then compared their death-feigning behavior, sprint speed, and brain DA levels. H-strain beetles exhibited significantly shorter duration of death-feigning, and significantly higher sprint speed, suggesting variation in death-feigning syndrome. Surprisingly, although brain DA expression affects various animal behaviors, we found no significant differences in the brain DA expressions of H- and L-strain beetles. Thus, our results imply genetic correlations between locomotor endurance, sprint speed, and death feigning, but not with brain DA expression, suggesting that differences in the biogenic amine results of our previous studies may reflect differences in behavioral expression mechanisms.

opencc-by-4.0Apr 2022View details →

Seismic evidence on crustal architecture of east-southern Tibet and implications for active landform construction since Late Miocene

This is the receiver function data set for "Seismic evidence on crustal architecture of east-southern Tibet and implications for active landform construction since Late Miocene"

opencc-by-4.0May 2022View details →

The datasets used in the manuscript named "Fidelity of Global Tropical Cyclone Activity in a High-Resolution Reanalysis Dataset CRA40 in Comparison with Multiple Other Reanalysis Datasets"

The datasets after tracking the TC events in five reanalyses: ERA5, JRA55, CFSR, MERRA2, CRA40.