Find research datasets worth reusing

opencc-by-4.0Jul 2021View details →

DDISH-GI: Dynamic Distributed Spherical Harmonics Global Illumination - Supplementary Video

A supplementary video for the upcoming publication "DDISH-GI: Dynamic Distributed Spherical Harmonics Global Illumination". The video includes a comparison to a state-of-the-art method and also to the path traced ground truth. Limitations of the proposed method are also shown.

opencc-by-4.0Dec 2020View details →

SOIL-WATERGRIDS v1, mapping dynamic changes in soil moisture and depth of water table from 1970 to 2014, dataset and modelling

SOIL-WATERGRIDS is a comprehensive data product of the monthly estimates of volumetric soil water content at three depths within the root zone and the depth of the water table globally gridded at a resolution of 0.25x025 degree per grid cell from 1970 to 2014. The SOIL-WATERGRIDS data product also provides the full-scale global model (BRTSim, https://sites.google.com/site/thebrtsimproject/home) that allows third party users to assess the entire volumetric soil water content and water table dynamics from land surface to 50 m depth.  This package includes a Technical Documentation with the details about the use of the data product.

opencc-by-4.0May 2021View details →

Data of "Impact of temporal correlations on high risk outbreaks of independent and cooperative SIR dynamics"

The data reported in the paper: Sajjadi et al. (2021) Impact of temporal correlations on high risk outbreaks of independent and cooperative SIR dynamics. PLoS ONE 16(7): e0253563. https://doi.org/10.1371/journal.pone.0253563 Each directory contains the data illustrated in one figure. The data structure and properties are described in .info files within each directory. All the simulations, analyses and illustrations have been conducted via the Epyc package (written in C++ and Python), developed by Sina Sajjadi. Epyc is available under GPLv3, at https://github.com/Sepante/Epyc.

opencc-by-4.0Jul 2021View details →

Amorphous Niobium Oxide Structures Calculated from First Principles using Density Functional Theory and Molecular Dynamics

The dataset contains fifteen different amorphous niobium oxide structures. Nine of the structures have the same stoichiometry as Nb2O5. The other six are defect structures containing 1 or 2 oxygen vacancies, or 1 or 2 interstitial oxygens, or 1 Nb vacancy. Each of the structure files is in the VASP POSCAR file format. Each structure was created using ab-initio molecular dynamics at 5000~K to liquidate the structure, then snapshots of the structure were taken every 2 ps, and geometry optimizations were performed on each individual snapshot. The naming convention is relatively simple: 'conf_x_POSCAR' is a stoichiometric POSCAR, and 'conf_x_oadd1_POSCAR' is a defect structure originating from structure 'x' with a single oxygen interstitial. The defect labels correspond to 1 oxygen interstitial (oadd1), 2 oxygen interstitials (oadd2), 1 oxygen vacancy (ovac1), 2 separated oxygen vacancies (ovac2), 2 nearest neighbor oxygen vacancies (ovac2nn), and 1 Nb vacancy (nbvac).

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Reservoir hosts experiencing food stress alter transmission dynamics for a zoonotic pathogen

Anthropogenic environmental change can significantly alter availability and quality of food resources for reservoir hosts and impact host-pathogen interactions in the wild. The state of the host's nutritional reserves as time of infection is a key factor influencing infection outcomes by altering host resistance. Here we combine experimental and model-based approaches to better understand how an environmental stressor affects host resistance to West Nile virus (WNV). Using American robins (Turdus migratorius), a species considered a superspreader of WNV, we tested the effect of acute food deprivation immediately prior to infection on host viremia. Our results show that robins food deprived of food for 48 hours prior to infection, developed higher virus titers and were infectious longer than robins fed normally. To gain understanding about the epidemiological significance of food stressed hosts, we developed an agent-based model that simulates transmission dynamics of WNV between the avian reservoir host and the mosquito vector. When we simulated a nutritionally stressed host population, the mosquito infection rate rose significantly reaching levels that represent an epidemiological risk. An understanding of the infection disease dynamics in wild populations is critical to predict and predict and mitigate zoonotic disease outbreaks.

opencc-zeroJul 2021View details →

opencc-by-4.0Aug 2021View details →

Molecular dynamics simulations of Liquid crystalline elastomer

This dataset includes the input files for Molecular Dynamics (MD) simulations of liquid crystalline elastomers (LCE) in LAMMPS. The results are incorporated in the journal publication, "Nematic liquid crystalline elastomers are aeolotropic materials" in the Proceedings of the Royal Society A, 2021, authored by L. Angela Mihai, Haoran Wang, Johann Guilleminot, and Alain Goriely.  The files of in.LCE_quench_for_phase_transition and restart.LCE_isotropic_500K are for the MD simulations of quenching isotropic LCE from 500K to 450K under an external field, during which the isotropic-nematic phase transition will happen. The file of restart.LCE_isotropic_500K includes the molecular topologies for a crosslinked LCE with 64 chains.  The files of in.LCE_shear and restart.LCE_nematic_300K are for the MD simulations of shearing the nematic LCEs at 300K. restart.LCE_nematic_300K includes the molecular topologies for nematic LCE with 64 chains.

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Statistical analysis code for output from a model used to simulate foot-and-mouth disease dynamics in the United Kingdom

Epidemics can sometimes be managed through reductions of host density, such as social distancing for human diseases, reducing plant density through cultural and genetic means, and host culling for epizootics. These approaches allow for a certain density of hosts to remain within a targeted area. By contrast, total ring depopulation is often used as a management strategy for emerging infectious diseases in livestock. In this study, we explore the trade-offs of a density-based culling strategy to determine if fewer livestock farms can be culled within rings while maintaining a decrease in disease transmission. To do so, we evaluated a farm-density-based ring culling strategy to control foot-and-mouth disease (FMD) in the United Kingdom. This strategy may allow for some farms within rings around infected premises (IPs) to escape depopulation, with the aim to prevent over-culling during outbreaks. Using a spatially-explicit, stochastic, state-transition simulation algorithm originally developed by Keeling et al. 2001 to model FMD spread in the United Kingdom, we simulated this reduced-farm-density, or "target density" strategy. We modeled FMD disease spread in four counties in the UK (Aberdeenshire, Cumbria, Devon, and North Yorkshire) that have different farm demographies. We ran 740,000 simulations in a full-factorial analysis of epidemic impact measurements (i.e. culled animals, culled farms, epidemic length) and cull strategy parameters (i.e. target farm density, daily farm cull capacity, cull radius). We found that all of the cull strategy parameters were drivers of epidemic impact. We found that outbreaks in Cumbria had higher epidemic impacts and were more likely to take off compared with other counties with more outbreaks being likely to take off in Cumbria. Most importantly, in all counties, our proposed target density strategy was more effective at combatting FMD compared with traditional 'total ring depopulation' when considering average culled animals and culled farms. The differences in epidemic impact between the counties are likely driven by farm demography, especially differences in cattle and farm density. This target density strategy can be applied to many different systems, including other livestock and agricultural systems, to reduce host density as opposed to over-culling hosts.

opencc-zeroAug 2021View details →

opencc-by-4.0Aug 2021View details →

Data for: High-order geometric integrators for representation-free Ehrenfest dynamics

Data for publication: S. Choi and J. Vaníček, High-order geometric integrators for representation-free Ehrenfest dynamics,<a href="https://aip.scitation.org/doi/10.1063/5.0061878"> J. Chem. Phys. 155, 124104 (2021)</a>. Contains the data for reproducing the figures in the above-mentioned publication.

opencc-by-4.0Jan 2021View details →

Insights from Transient Absorption Spectroscopy into Electron Dynamics Along the Ga-Gradient in Cu(In,Ga)Se2 Solar Cells: Data

Excel file with data to all figures published in our article found at https://doi.org/10.1002/aenm.202003446 (Advanced Energy Materials), Synopsis user manual, Matlab code to analyse and fit data

openother-openAug 2021View details →

A suburban soundscape reveals altered acoustic dynamics during COVID-19 lockdown

Abstract The 2020 COVID-19 pandemic and resulting national and international movement restrictions provide a unique opportunity to investigate the consequences of changing anthropogenic noise regimes on animal communities and soundscapes. Here I use this lockdown period as a natural experiment to investigate changes to soundscape intensity, structure, and dynamics during restricted human activity (lockdown) in suburban Nottingham, UK. Using 11 common acoustic indices, I tested for differences in the richness and evenness of the soundscape during COVID-19 lockdown, and I measured changes in soundscape dynamics by comparing the temporal variability of acoustic indices during versus after lockdown. Regardless of how the soundscape was summarised, there were significant differences in the intensity, evenness, and temporal variability of the soundscape during COVID-19 lockdown, principally driven by changes to anthropogenic noise. I recorded a shift away from a dominance of anthropophony towards more intense biological sounds during lockdown, and the lockdown soundscape was generally more even, particularly because of changes to the magnitude of the diurnal cycle. These preliminary results from a mass human confinement experiment provide an early glimpse into how suburban soundscapes are impacted by noise pollution. In time, globally distributed longer-term monitoring efforts will reveal the generality of these findings, facilitating a mechanistic understanding of the impacts of anthropogenic noise on the world’s natural and human-dominated soundscapes. Methods The dataset contains standardised acoustic index values for 11 commonly used acoustic indices, based on AudioMoth recordings taken during two periods around the COVID-19 lockdown (May 2020) and after restrictions had been lifted (Oct 2020) in suburban Nottingham, UK. I analysed the difference in acoustic index values during versus after the lockdown and compared their temporal variability using standardised effect sizes for the difference between these two time periods. I did this on the whole dataset and on several hourly subsets of the dataset (see the manuscript for further details).  Usage notes See readme file for further details and main manuscript for descriptions of data.

opencc-by-4.0Aug 2021View details →

(VIDEOS) Dynamics of hydroxyapatite and carbon nanotubes interacting

These files correspond to the dynamics results for all the structures studied in the paper: <ul> <li>W.G. Knupp, M.S. Ribeiro, M. Mir, I. Camps. Dynamics of hydroxyapatite and carbon nanotubes interaction. Applied Surface Science 495 (2019) 143493. DOI: <a href="https://doi.org/10.1016/j.apsusc.2019.07.235">10.1016/j.apsusc.2019.07.235</a></li> </ul> The nomenclature to identify the systems is: <ul> <li>HAP, for hydroxyapatite.</li> <li>CNT, for pristine carbon nanotube.</li> <li>HAP+CNT, for the complex hydroxyapatite interacting with pristine carbon nanotube.</li> <li>HAP+CNTOHx, for hydroxyapatite interacting with -OH functionalized carbon nanotube.</li> <li>HAP+CNTCOOHx, for hydroxyapatite interacting with -COOH functionalized carbon nanotube.</li> <li>x = 5%, 10%, 15%, 20%, 25% represents the concentration of -OH or -COOH, respectively.</li> </ul>

Figure 1 in Life history dynamics and biogeography of a nudibranch with contrasting developmental modes: A hypothesis for the evolution of larval types

Figure 1. Map of the lower Gulf of Maine with the distribution of Dendronotus frondosus and Dendronotus sp. from subtidal and intertidal habitats near the coasts of Maine (ME) and New Hampshire (NH), USA and New Brunswick (NB) and Nova Scotia (NS), Canada. See Table I to reference site numbers and Cartesian coordinates. Sites for seasonal monitoring of hydroid and nudibranch abundance include York (2), West Quoddy Head (12) and Eastport (13), Maine.

Figure 5 in Life history dynamics and biogeography of a nudibranch with contrasting developmental modes: A hypothesis for the evolution of larval types

Figure 5. Summary of the larval dispersal potential of Dendronotus frondosus and Dendronotus sp. in laboratory cultures at 10°C (Sisson 2002b, 2004). The ''egg-to-juvenile'' period lasts from spawn deposition through larval settlement and metamorphosis.

Figure 3 in Life history dynamics and biogeography of a nudibranch with contrasting developmental modes: A hypothesis for the evolution of larval types

Figure 3. Abundance of spawn masses deposited by Dendronotus spp. at: (a) York, Maine, (b) Eastport, Maine and (c) the intertidal site at West Quoddy Head, Lubec, Maine.

Figure 4 in Life history dynamics and biogeography of a nudibranch with contrasting developmental modes: A hypothesis for the evolution of larval types

Figure 4. Weekly mean (¡SD), minimum and maximum water temperature (in °C) at the subtidal sampling sites in York and Eastport, Maine.

Figure 2 in Population dynamics, age structure and sex ratio of the bromeliad-dwelling jumping spider, Psecas chapoda (Salticidae)

Figure 2. Mean number (¡SE) of Psecas chapoda per Bromelia balansae with no inflorescence, from May 1998 to April 2000 (N53516 spiders).

Figure 1 in Population dynamics, age structure and sex ratio of the bromeliad-dwelling jumping spider, Psecas chapoda (Salticidae)

Figure 1. Fluctuations in the number of Psecas chapoda and egg sacs (log) on bromeliads with and without inflorescence, and the frequency (%) of bromeliads in bloom (with inflorescence or infrutescence) between May 1998 and April 2000 (N53516 spiders and 314 egg sacs).

Figure 5 in Population dynamics, age structure and sex ratio of the bromeliad-dwelling jumping spider, Psecas chapoda (Salticidae)

Figure 5. Mean number (¡SE) of spiders Psecas chapoda on bromeliads that produced inflorescence between August and December and on bromeliads that did not produce inflorescence until December, in 1998 (A) and 1999 (B). The frequency (%) of bromeliads that bloomed up to December is also shown.

Figure 4 in Population dynamics, age structure and sex ratio of the bromeliad-dwelling jumping spider, Psecas chapoda (Salticidae)

Figure 4. Phenogram of the Psecas chapoda population on plants of Bromelia balansae without inflorescence, from May 1998 to April 2000 (N53516 spiders).