Find research datasets worth reusing

opencc-by-4.0Aug 2024View details →

[Dataset] Intensity and Dimensionality-Dependent Dynamics of Laser-Proton Acceleration in 1D, 2D, and 3D Particle-in-Cell Simulations

The included Jupyter Notebooks (.ipynb) were used to generate figures and make calculations for the work. The resulting image files are saved in Figure_Outputs.tar.gz. The other archives (1D.tar.gz, 2DS.tar.gz, 2DP.tar.gz, 3D.tar.gz, laser_focus.tar.gz, and EField.tar.gz) are compressed directories containing EPOCH PIC simulation outputs for the paper (relevant directories should be extracted to replicate analysis with provided files).   Since the last version, a new figure (Figure 6, an ion phase space) has been added. Notebooks for later figures have been renumbered and the figure outputs have been updated.

opencc-by-4.0Jul 2021View details →

Dataset related to the publication "Accelerated Electrochemical Investigation of Li Plating Efficiency as Key Parameter for Li Metal Batteries Utilizing a Scanning Droplet Cell"

Related to the publication  "Accelerated Electrochemical Investigation of Li Plating Efficiency as Key Parameter for Li Metal Batteries Utilizing a Scanning Droplet Cell" <a href="https://www.zenodo.org/record/5503915">https://www.zenodo.org/record/5503915</a> The file contains raw data of the results shown in Figure 1, 2, 3, 4, 6, 7, 8, S1 and S2.

opencc-by-4.0Dec 2021View details →

accelerations from the accelerometer, orbit determination and CoM offset

accelerations from the accelerometer, orbit determination and CoM offset

opencc-zeroJan 2022View details →

From: Soil fauna accelerate litter mixture decomposition globally, especially in dry environments

More than half of net primary production in terrestrial ecosystems returns to the soil through leaf litter fall and decomposition. In terrestrial ecosystems, litter constitutes a mixture of mainly senescent foliage from multiple species. Yet, the effect of litter mixing on litter decomposition rate remains ambiguous. Quantification of the soil fauna contribution and inclusion of their interaction with litter could remove the prevailing ambiguity, as soil fauna might influence the direction and magnitude of litter mixture effects on decomposition. We carried out a global meta-analysis to elucidate how soil fauna influenced litter mixture decomposition rate based on 55 published studies with 873 fauna inclusion/exclusion comparisons in field litterbag experiments. We hypothesized that soil fauna inclusion in litter mixture experiments would cause a positive change in the magnitude of mixed litter decomposition. That is, the presence of soil fauna would lead to synergistic litter mixture effects while the absence of soil fauna would lead to antagonistic litter mixture effects. Furthermore, we hypothesized that soil fauna would have a greater positive impact on the litter mixture effect in environments with low precipitation. While litter mixture had a neutral effect on decomposition on average across studies, non-additive mixture effects were common, with a key role for soil fauna, which generally enhanced decomposition rate compared to the component single species litters. In contrast, fauna exclusion resulted in a diminished decomposition rate overall. The overall synergistic soil fauna effect on litter mixture decomposition increased under low precipitation. Under high precipitation, the litter mixture effect was positive in the absence of soil fauna but non-significant in the presence of fauna. Climate imposes a great effect on litter mixture, with synergistic effects increasing towards the equator. Synthesis: These results highlight the importance of soil fauna in mixed litter decomposition, most strongly in dry environments. In this era of global climate change, where some regions are projected to become drier, soil fauna might compensate the expected slower decomposition of litter by increasingly enhancing litter mixture decomposition.

opencc-by-4.0Feb 2022View details →

Data, plotting scripts, and figures for "Accelerating Reactive-Flow Simulations using Vectorized Chemistry Integration"

Data, plotting scripts, and figures for the article "Accelerating Reactive-Flow Simulations using Vectorized Chemistry Integration".

opencc-zeroFeb 2022View details →

Data from: Dynamic body acceleration as a proxy to predict the cost of locomotion in bottlenose dolphins

Estimates of the energetic costs of locomotion (COL) at different activity levels are necessary to answer fundamental eco-physiological questions and to understand the impacts of anthropogenic disturbance to marine mammals. We combined estimates of energetic costs derived from breath-by-breath respirometry with measurements of overall dynamic body acceleration (ODBA) from biologging tags to validate ODBA as a proxy for COL in trained common bottlenose dolphins (Tursiops truncatus). We measured resting metabolic rate (RMR); mean individual RMR was 0.71–1.42 times that of a similarly sized terrestrial mammal and agreed with past measurements that used breath-by-breath and flow-through respirometry. We also measured energy expenditure during submerged swim trials, at primarily moderate exercise levels. We subtracted RMR to obtain COL, and normalized COL by body size to incorporate individual swimming efficiencies. We found both mass-specific energy expenditure and mass-specific COL were linearly related with ODBA. Measurements of activity level and cost of transport (the energy required to move a given distance) improve understanding of the COL in marine mammals. The strength of the correlation between ODBA and COL varied among individuals, but the overall relationship can be used at a broad scale to estimate the energetic costs of disturbance and daily locomotion costs to build energy budgets, and investigate the costs of diving in free-ranging animals where bio-logging data are available. We propose that a similar approach could be applied to other cetacean species.

Flashy male Jamaican anoles (Anolis grahami) show accelerated telomere attrition

Data on Jamaican Anoles dewlap size and colouration, bite force and telomere attrition

Supplemental data and code for Improved air quality in China can enhance solar power performance and accelerate carbon neutrality targets

Supplemental data and code for Improved air quality in China can enhance solar power performance and accelerate carbon neutrality targets

opencc-zeroMay 2022View details →

Hurricane disturbance accelerated the thermophilization of a Jamaican montane forest

Thermophilization – changes in community composition towards greater relative abundances of species associated with warmer environments – has been described for plants and animals in many locations around the world. Disturbances of various kinds have increased rates of thermophilization in temperate sites, and this has been proposed, but not demonstrated, for some tropical environments. In this study, we tested whether disturbance by a Category four hurricane in 1988 (Hurricane Gilbert) increased thermophilization in a Jamaican montane forest by using pre- and post-hurricane data collected over four decades (1974–2014). We analysed tree species composition in permanent plots at c. 1580 m elevation in Jamaica's Blue Mountains. There were 66 tree species with stem diameters ≥3 cm at breast height. We used published data on the altitudinal distribution of 62 species (94% of genetic individuals (genets)) to calculate the mean community altitude scores (MCAS) of the trees recorded in each census, as well as the MCAS of the survivors, recruits and dead trees after each decade. We found that thermophilization did occur (i.e., MCAS decreased significantly over time), and that this was due both to a decreasing MCAS of recruits through the four decades (significantly lower than expected in the last three decades) as well as a high MCAS of trees that died. Thermophilization was fastest in the post-hurricane decade, during which time there was marked and significant increase in the MCAS of dead trees; this change was above and beyond expectations of long-term successional dynamics. The rate of compositional change equates to an overall decrease in MCAS of 1.6 m yr-1 over the forty-year study period. We conclude that this Jamaican montane forest is undergoing thermophilization (likely due to rising temperature) and that the hurricane-caused disturbance accelerated thermophilization through differential mortality.

opencc-by-4.0Jun 2022View details →

All-atom accelerated molecular dynamics (aMD) simulations of Filamin-A (FLNa) actin-binding Domain, immunoglobulin-like Domains 3, 4, 5, 21 and 24 to investagate the impact of known missense mutations associated with periventricular nodular heterotopia in the liveborn males

Data includes all of the wild-type and mutant trajectories of accelerated all-atom molecular dynamics (aMD) simulations of Filamin-A (FLNa, the product of FLNA gene located on chromosome X). Wild-type proteins are from the PDB structures with IDs: 4M9P, 3HOP, 3CNK. The mutations, including R484Q that we discovered in a Turkish family, were formerly found in the liveborn males with FLNA-associated periventricular nodular heterotopia (PNH), who survived with the only copy of mutated FLNA. To understand how these mutations lead to the PNH and simultaneously allow their survival, we performed these MD simulations for the wild-type and mutant systems. Systems were prepared in Visual Molecular Dynamics (VMD 1.9.3) by placing them in a TIP3P water box with approximately 20 Å thickness from the protein surface and neutralizing the system by adding counter ions in the form of NaCl. Of note, only protein parts were kept for the submission to reduce the size of files. Nanoscale Molecular Dynamics (NAMD 2.13-CUDA) was used to perform MD simulations with CHARMM36m force field. For pressure and temperature controls, Nosé-Hoover Langevin barostat and Langevin thermostat were used. ShakeH algorithm of NAMD was applied for water molecule constraints. 12 Å cut-off distance was used for van der Waals interactions. Switching function starts at 10 Å and reaches zero at 14 Å. Integration time-step was 2 fs. To compute the long-range Coulomb interactions, the particle-mash Ewald method was used. After a 10000-step minimization with conjugate gradient algorithm and an equilibration for 1 ns at 298 K under NVT ensemble, production simulations were run along 100 ns. Only the production simulations were supplied in this dataset. Further details are available in the regarding configuration files. Resulting analysis files and scripts are included with the carbon alpha-containing dcd files of the simulations. This dataset is not used directly for any study, but they are preliminary results for the usage of aMD to understand rare disease mechanisms. Related publications: <pre>Zenodo repo of classical MD for these variants: https://doi.org/10.5281/zenodo.4483108</pre> Journal article based on classical MD: Gerlevik U, Saygı C, Cangül H, Kutlu A, Çaralan EF, Topçu Y, et al. (2022) Computational analysis of missense filamin-A variants, including the novel p.Arg484Gln variant of two brothers with periventricular nodular heterotopia. PLoS ONE 17(5): e0265400. https://doi.org/10.1371/journal.pone.0265400

opencc-zeroJul 2022View details →

Accelerating ice loss from peripheral glaciers in North Greenland

In recent decades, Greenland's peripheral glaciers have experienced large-scale mass loss, resulting in a substantial contribution to sea-level rise. Only 4% of Greenland's ice cover are small peripheral glaciers that are distinct from the ice sheet proper. Despite comprising this relatively small area, these small peripheral glaciers are responsible for 11% of the ice loss associated with Greenland's recent sea-level rise contribution. Using the satellite laser platforms ICESat and ICESat-2, we estimate that ice loss from these Greenland glaciers increased from 27±6 Gt/yr (2003–2009) to 42±6 Gt/yr (2018–2021). Here, we provide the laser altimetry assessment of changing ice loss rates from Greenland peripheral glaciers that bridges both the ICESat and ICESat-2 periods of Feb 2003 – Dec 2021. We provide peripheral glaciers elevation changes including correction for firn compaction, elastic uplift rates from present-day mass changes, and long-term past ice changes (Glacial Isostatic Adjustment- GIA). We provide: (1) Mean elevation change rates of the Greenland peripheral glaciers during, Feb 2003 - Oct 2009, Oct 2008 - Apr 2019, and Oct 2018 – Dec 2021 obtained from ICESat and ICESat-2 data. The grid resolution is 500x500 meters. (2) Mean elastic uplift rates of the bedrock (in mm/yr) due to ice loss during, Feb 2003 - Oct 2009, Oct 2008 - Apr 2019, and Oct 2018 – Dec 2021. (3) Mean firn compaction rates in m/yr during, Feb 2003 - Oct 2009, Oct 2008 - Apr 2019, and Oct 2018 – Dec 2021. (4) Glacial Isostatic Adjustment- GIA rates in mm/yr from the GNET-GIA empirical model of Khan et al. (2016). (5) Time series of mean surface air temperature in degrees Celcius during May-September in north, northwest, southeast, southwest, and northwest Greenland from RACMO2.3p2.

opencc-by-4.0Jul 2022View details →

LISFLOOD-FP 8.1: New GPU accelerated solvers for faster fluvial/pluvial flood simulations - video supplement

These are video supplement files to Sharifian et al. (2022), to give step-by-step instructions on how to download and install LISFLOOD-FP8.2, and reproduce the simulations for representative case studies. For a full description of the methodology and case studies, please refer to the manuscript.

A computational study of accelerating, steady and fading negative streamers in ambient air

This dataset contains the data used to generate the results presented in the article "A computational study of accelerating, steady and fading negative streamers in ambient air". This dataset includes (1) the source code; (2) two transport data files, which contain a list of included reactions, with their reaction rate coefficients, and transport coefficients; (3) configuration files for running the simulations and (4) output log files, which contain information about the physics and numerical properties of the simulations.

opencc-by-4.0Aug 2022View details →

Supplementary Materials: Next Generation Computational Tools for the Modeling and Design of Particle Accelerators at Exascale

Supplementary materials (aka data artifact or data archive) for our NAPAC22 publication: "Next Generation Computational Tools for the Modeling and Design of Particle Accelerators at Exascale" (Paper ID: TUYE2). Work supported by the Exascale Computing Project (17-SC-20-SC), a joint project of the U.S. Department of Energy's Office of Science and National Nuclear Security Administration, responsible for delivering a capable exascale ecosystem, including software, applications, and hardware technology, to support the nation's exascale computing imperative. This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under U.S. Department of Energy Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility located at Lawrence Berkeley National Laboratory, operated under Contract No. DE-AC02-05CH11231.

openNov 2021View details →

Accelerating DNA-PAINT imaging with a deep neural network

(<a href="https://zenodo.org/api/files/7030c526-533f-44ce-8b8c-01a979fd6b6f/RawFrames_P5-IS_20pM.tif?versionId=55a12821-8472-42f5-91b5-eabda1516e2b">RawFrames_P5-IS_20pM.tif</a>) Raw DNA-PAINT SMLM frames with isolated emitters taken on TOM20 labelled MNTB neuronal rat tissue with P5 imaging strand at 20 pM concentration.  (<a href="https://zenodo.org/api/files/7030c526-533f-44ce-8b8c-01a979fd6b6f/Binned_HighDensity_30kpatches.tif?versionId=ac01dd00-3c44-4059-a1b1-3b1045fa636d">Binned_HighDensity_30kpatches.tif</a> and <a href="https://zenodo.org/api/files/7030c526-533f-44ce-8b8c-01a979fd6b6f/Binned_HighDensity_30kpatches.csv?versionId=31e792fc-fab5-43cd-af81-a271595586d0">Binned_HighDensity_30kpatches.csv</a>) Artificially summed high-density emitter patches with the corresponding emitter coordinates used for training the DeepSTORM neural network.   (DeepSTORM_model_metadata.mat and DeepSTORM_model_weights_best.hdf5) The trained model metadata and weights used for all predicted images in the study. (Figure 4_Large_super-resolution_image.png) The large super-resolution image in Figure 4 and Figure S4. (High-density-frames_Images 1 - 5 .tif) Five high-emitter density raw frames for alpha-tubulin and TOM20 of 400 frames each. (<a href="https://zenodo.org/api/files/b98093d2-f689-4fef-8222-220c07ca4fe9/Ground-truth-rendered_Image4_Tubulin.tif">Ground-truth-rendered_Image 1 - 5</a>.tif) Five ground truth images rendered in Picasso (drift-corrected, linked localisations, pixel size 13.37 nm/pixel) for alpha-tubulin and TOM20. (<a href="https://zenodo.org/api/files/e726ff9b-45ba-4d3a-b3ba-3e6eaca03d35/Low%20density%20frames%20for%20GT%20images.zip">Low density frames for GT images.zip</a>) Five low-emitter density (0.5 nM) raw frames for alpha-tubulin and TOM20 of 10000 frames each which were used to render ground truth images. (<a href="https://zenodo.org/api/files/e726ff9b-45ba-4d3a-b3ba-3e6eaca03d35/Bassoon_Homer_datasets.zip">Bassoon_Homer_datasets.zip</a>) Three Bassoon and Homer datasets each with a ground truth image and the corresponding high-density raw frames (5 nM, 800 frames).

opencc-by-4.0Aug 2022View details →

Machine Learning Constructs Color Features to Accelerate Development of Long-Term Continuous Water Quality Monitoring

This is a machine learning method for predicting the concentration of colored pollutants based on RGB and kmeans methods. This dataset includes raw images of pollutants as well as characteristic data of pollutants, as well as code for the model. You can see the contents of the zip file for details.

Plasma electron contribution to beam emittance growth from Coulomb collisions in plasma-based accelerators

This dataset contains some supplementary material for the paper published in the journal Physics of Plasmas. There are two folders in the compressed file. One includes two input files that are used for the open-source particle-in-cell code WarpX(https://github.com/ECP-WarpX/WarpX/). The other includes figure files, and the plotting scripts.

opencc-zeroSep 2022View details →

Higher phage virulence accelerates the evolution of host resistance

Pathogens vary strikingly in their virulence and the selection they impose on their hosts. While the evolution of different virulence levels is well studied, the evolution of host resistance in response to different virulence levels is less understood and as of now mainly based on observations and theoretical predictions with few experimental tests. Increased virulence can increase selection for host resistance evolution if resistance costs are outweighed by the benefits of avoiding infection. To test this, we experimentally evolved the bacterium Vibrio alginolyticus in the presence of two variants of a filamentous phage that differ in their virulence. The bacterial host exhibited two alternative defence strategies: (1) super infection exclusion (SIE) whereby phage-infected cells were immune to subsequent infection at a cost of reduced growth, and (2) surface receptor mutations (SRM) providing resistance to infection by preventing phage attachment. While SIE emerged rapidly against both phages, SRM evolved faster against the high compared to the low virulence phage. Using a mathematical model of our system we show that increasing virulence strengthens selection for SRM due to the higher costs of infection suffered by SIE immune hosts. Thus, by accelerating the evolution of host resistance, more virulent phages caused shorter epidemics.

opencc-by-4.0Jul 2022View details →

LISFLOOD-FP 8.1: New GPU accelerated solvers for faster fluvial/pluvial flood simulations - simulation results

Simulation result data for Sharifian et al. (2022) for the following case studies: 1- Lower Triangle catchment 2- Upper Lee catchment 3- Eden catchment 4- Glasgow urban area 5- Cockermouth urban area