Find research datasets worth reusing

Data from: Changing with the times: Seasonal environmental gradients unveil dynamic bat assemblages and vulnerability

Uncovering the temporal and spatial dynamics of biological communities in response to biotic and abiotic drivers is essential to predict the effects of environmental change on biodiversity. Similarly, estimating species vulnerability in the face of such dynamics is crucial for implementing effective conservation actions. We explored how bat diversity changes over the year across an altitudinal gradient and identified the environmental drivers that shape bat communities. By analysing species' marginality within the biophysical niche space, we evaluated bats' vulnerability to foreseeable environmental changes. Our results suggest that altitude, the proportion of forest cover and shrubs cover are the main drivers shaping bat communities year-round. Additionally, while some bat species are restricted to a single ecological assemblage (or ecological preferences group), others show greater plasticity throughout the year. Importantly, we found that although bats associated with highland habitats and forests could be particularly vulnerable to environmental changes (in particular Myotis mystacinus), this vulnerability correlates poorly with their national conservation status. We suggest that species' ecological plasticity is critical for the resilience of biological communities exposed to environmental changes and should be considered when planning tailored conservation strategies.

opencc-by-4.0Apr 2023View details →

Dataset on flow dynamics in rivers with riffle-pool morphology: results from case studies and field experiments on the Tagliamento River, Italy

Riffle-pool sequences in rivers, formed due to interactions between river flow, alluvium and vegetation, provide vital ecological services to aquatic organisms and therefore are considered as fundamental habitats in fluvial ecosystems. Nevertheless, the knowledge of associated riffle-pool hydrodynamics is limited because of a lack of high-resolution data collected in rivers and scaling effects present in laboratory studies. Here we present a dataset on turbulent flow structure in riffle-pool sequences of a natural river. Two case studies and two field-based experiments were carried out in a side branch of the braided gravel-bed Tagliamento River in Italy. Our case studies deliver detailed information about the there-dimensional structure of mean and turbulent flows in natural riffle-pool/run and pool-riffle/glide transitions. Field-based experiments completed with the in-stream flume models of a riffle-pool transition and a shallow jet model provide a methodological bridge for linking simplified hydrodynamic theories of shallow jets to complex flow structure documented by our case studies. Therefore, this dataset enables examination of scaling effects and can be widely used for validation of numerical models.

Data and code from: Dynamics of cortical contrast adaptation predict perception of signals in noise

Neurons throughout the sensory pathway adapt their responses depending on the statistical structure of the sensory environment. Contrast gain control is a form of adaptation in the auditory cortex, but it is unclear whether the dynamics of gain control reflect efficient adaptation, and whether they shape behavioral perception. Here, we trained mice to detect a target presented in background noise shortly after a change in the contrast of the background. The observed changes in cortical gain and behavioral detection followed the dynamics of a normative model of efficient contrast gain control; specifically, target detection and sensitivity improved slowly in low contrast, but degraded rapidly in high contrast. Auditory cortex was required for this task, and cortical responses were not only similarly affected by contrast but predicted variability in behavioral performance. Combined, our results demonstrate that dynamic gain adaptation supports efficient coding in auditory cortex and predicts the perception of sounds in noise.

Data set for Dynamic Service Restoration of Distribution Networks with Volt-Var Devices, Distributed Energy Resources, and Energy Storage Systems

Two power distribution systems are presented. The first system consists of 53 nodes and 61 branches, while the second system consists of 404 buses and 430 branches. Both distribution systems offer extensive applications in problems related to multi-time service restoration, Volt/Var devices, and distributed energy resource operation.

DYNAMIC TZ Cluster RCT Dataset

De-identified dataset from the DYNAMIC Tanzania cluster-randomized controlled trial evaluating the impact of the ePOCT+ package on antibiotic prescription (superiority analysis) and clinical failure (non-inferiority analysis) compared to usual care. Study conducted in the Mbeya and Morogoro regions of Tanzania between December 2021 to October 2022.

Dynamic nuclear polarization by two-pulse phase modulation - Data

Experimental data associated Redrouthu et al. Dynamic nuclear polarization by two-pulse phase modulation, The Journal of Chemical Physics, doi: 10.1063/5.0153053.

Emulator of PR-DNS: Accelerating Dynamical Fields with Neural Operators in Particle-Resolved Direct Numerical Simulation

The codes directory includes the various machine learning models, such as FNO, UNet and ResNet. R128_init1 and R128_init2 are the PR-DNS time step simulations at different initial conditions. R64_init2, R128_init2 and R256_init2 are the PR-DNS time step simulations at different resolutions.

Wave, Flow, and Sediment Dynamics under Strong Winds on a tidal beach

The data are saved as matlab data file. 1) ssc_fit.mat is used for producing figure 2. 2) Reynolds_shear_stress.mat is used for producing figures 3 and 10. 3) hydrodynamics.mat is used for producing figure 4. 4) shear_stress_&_ssc.mat is uesd for producing figures 5 and 8. 5) SSF.mat is used for producing figures 6 and 11. 6) breaking_wave_criteria.mat is used for producing figure 7. 7) mob_number.mat is used for producing figure 9.

Ocean Gateways and Ocean Circulation Dynamics: Unveiling the Deep Water-Mass properties in the Western Equatorial Pacific and Eastern Indian Ocean since the middle

File contains a dataset related to census counts and stable isotopes that we used to write our manuscript.

Equilibrium Molecular Dynamics of aqueous glycerol menisca

This dataset contains the results of Molecular Dynamics simulations of quasi-2D water-glycerol liquid meniscus, confined between silica-like surfaces. The goal of the simulations is to observe and quantify liquid density layering close to solid surfaces. The pattern "Glycerol***" refers to the mass fraction of glycerol ("000": pure water, "100": pure glycerol). Each folder contains configuration files and compressed output molecular trajectories. Post-processing is performed on density maps binned on-the-fly using a customized Gromacs version (<a href="https://github.com/pjohansson/gromacs-flow-field">https://github.com/pjohansson/gromacs-flow-field</a>); frames are placed in a tarball ("wat-gly-*p-eq.tar.gz"). The zipped folder 'scripts.zip' contains a self-contained library of functions to read density maps and a Jupyter notebook with an example of density reading and plotting. Simulations are performed with Gromacs. We refer to the code documentation for further information (<a href="https://manual.gromacs.org/">https://manual.gromacs.org/</a>).

Population dynamics and social organization of sambar (Rusa unicolor unicolor) in Horton Plains National Park, Sri Lanka

We estimated the population density and investigated the social organization of sambar (Rusa unicolor unicolor) in Horton Plains National Park (HPNP), Sri Lanka. Distance sampling was conducted along six strip transects every month for a period over three years (2018–2020) to estimate the density of the sambar population in grasslands of HPNP (9.4 km2), while the antler stage of males and the behaviour of individuals were recorded to describe the population's reproductive stage and hence the social organization. Population density estimates showed relative stability over the three years and varied over the seasons but with consistent peaks from year to year with the highest population densities recorded in November-December (212.93 ± 25.38 animals/km2 in 2018, 187.91 ± 28.51 in 2019, and 179.76 ± 31.85 in 2020). The highest percentage of males in hard antlers was observed from November through January, while the percentage of antlers cast sambar peaked from March to April each year. Hinds were observed with newborn calves throughout the year, but the highest number of newborn calves were recorded from July to August each year, while the number of calves counted each year varied from 210–267 individuals. The mean group size was variable throughout each year with the largest groups recorded from September to December (up to 52), the period accompanied by the most observations of mating and sparring behaviour. Although on a tropical island, HPNP is situated on a rolling plateau landscape in the highlands, where sambar showed a degree of reproductive seasonality somewhat similar to temperate cervid species.

opencc-by-4.0Jan 2021View details →

Dataset: Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion

This dataset is related to "Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion" and contains the raw data obtained.

Long-term seedling and small sapling census data from the Barro Colorado Island 50 ha Forest Dynamics Plot, Panama

Tropical forests are well known for their high woody plant diversity. Processes occurring at early life stages are thought to play a critical role in maintaining this high diversity and shaping the composition of tropical tree communities. To evaluate hypothesized mechanisms promoting tropical tree species coexistence and influencing composition, we initiated a census of woody seedlings and small saplings in the permanent 50-ha Forest Dynamics Plot (FDP) on Barro Colorado Island (BCI), Panama. Situated in old-growth, lowland tropical moist forest, the BCI FDP was originally established in 1980 to monitor trees and shrubs ≥1 cm diameter at 1.3 m above ground (dbh) at ca. 5-yr intervals. However, critical data on the dynamics occurring at earlier life stages were initially lacking. Therefore, in 2001 we established a 1-m2 seedling plot in the center of every 5 x 5 m section of the BCI FDP. All freestanding woody individuals ≥20 cm tall and <1 cm dbh (hereafter referred to as seedlings) were tagged, mapped, measured, and identified to species in 19,313 1-m2 seedling plots. Because seedling dynamics are rapid, we censused these seedling plots every 1–2 years. Here we present data from the 14 censuses of these seedling plots conducted between the initial census in 2001 to the most recent census, in 2018. This data set includes nearly 1M observations of ~185,000 individuals of >400 tree, shrub, and liana species. These data will permit spatially-explicit analyses of seedling distributions, recruitment, growth, and survival for hundreds of woody plant species. In addition, the data presented here can be linked to openly-available, long-term data on the dynamics of trees and shrubs ≥1cm dbh in the BCI FDP, as well as existing data sets from the site on climate, canopy structure, phylogenetic relatedness, functional traits, soil nutrients, and topography.

Data for: Host infection dynamics and disease induced mortality modify species contributions to the environmental reservoir

Environmental pathogen reservoirs exist for many globally important diseases and can fuel epidemics, influence pathogen evolution, and increase the threat of host extinction. Species composition can be an important factor that shapes reservoir dynamics and ultimately determines the outcome of a disease outbreak. However, disease-induced mortality can change species communities, indicating that species responsible for environmental reservoir maintenance may change over time. Here we examine reservoir dynamics of Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome in bats. We quantified changes in pathogen shedding, infection prevalence and intensity, host abundance, and the subsequent propagule pressure imposed by each species over time. We find that highly shedding species are important during pathogen invasion, but contribute less over time to environmental contamination as they also suffer the greatest declines. Less infected species remain more abundant, resulting in equivalent or higher propagule pressure. More broadly, we demonstrate that high infection intensity and subsequent mortality during disease progression can reduce the contributions of high-shedding species to long-term pathogen maintenance.

opencc-zeroDec 2022View details →

Data from: Negative interactions and virulence differences drive the dynamics in multispecies bacterial infections

Bacterial infections are often polymicrobial, leading to intricate pathogen-pathogen and pathogen-host interactions. There is increasing interest in studying the molecular basis of pathogen interactions and how such mechanisms impact host morbidity. However, much less is known about the ecological dynamics between pathogens and how they affect virulence and host survival. Here we address these open issues by co-infecting larvae of the insect model host Galleria mellonella with one, two, three, or four bacterial species, all of which are opportunistic human pathogens. We found that host mortality was always determined by the most virulent species regardless of the number of species and pathogen combinations injected. In certain combinations, the more virulent pathogen simply outgrew the less virulent pathogen. In other combinations, we found evidence for negative interactions between pathogens inside the host, whereby the more virulent pathogen typically won a competition. Taken together, our findings reveal positive associations between a pathogen's growth inside the host, its competitiveness towards other pathogens, and its virulence. Beyond being generalizable across species combinations, our findings predict that treatments against polymicrobial infections should first target the most virulent species to reduce host morbidity, a prediction we validated experimentally.

opencc-by-4.0Jul 2023View details →

AutoParams: An Automated Web-Based Tool To Generate Parameters for Molecular Dynamics Simulations

Dataset of thirteen (13) compounds used to test the AutoParams webserver.  Includes initial PDB files, generated parameters (mol2/frcmod files), and resulting AMBER-formatted MD inputs (prmtop/inpcrd).  Additionally, includes 2D structure in PNG format and canonical SMILES string in .smi file format.

opencc-zeroJul 2023View details →

Data for: Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow (Ammospiza caudacuta)

Determining factors that shape a species' population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110-135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson's Sparrow (A. nelsoni) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range.

opencc-by-4.0Jul 2023View details →

Dataset of dynamical structure factor of Lieb-Liniger model

This dataset contains all data and scripts to plot the figures of the article arXiv:2303.09208

opencc-zeroJul 2023View details →

Data from: Fission-fusion dynamics in sheep: The influence of resource distribution and temporal activity patterns

Fission-fusion events, i.e. changes to the size and composition of animal social groups, are a mechanism to adjust the social environment in response to short-term changes in the cost-benefit ratio of group living. Furthermore, the time and location of fission-fusion events provide insight into the underlying drivers of these dynamics. Here, we describe a method for identifying group membership over time and for extracting fission-fusion events from animal tracking data. We applied this method to high-resolution GPS data of free-ranging sheep (Ovis aries). Group size was highest during times when sheep typically rest (mid-day and at night), and when anti-predator benefits of grouping are high while costs of competition are low. Consistent with this, fission and fusion frequencies were highest during early morning and late evening, suggesting that social restructuring occurs during periods of high activity. However, fission and fusion events were not more frequent near food patches and water resources when adjusted for overall space use. This suggests a limited role of resource competition. Our results elucidate the dynamics of grouping in response to social and ecological drivers, and we provide a tool for investigating these dynamics in other species.