Find research datasets worth reusing

Molecular Dynamics snapshots of the Glycine receptor MD-open state

Molecular Dynamics snapshots (10 files .pdb) of the Glycine receptor MD-open state full-length, used in computational electrophysiology experiments to explore conductance and permeation pathways.   Associated with: “Lateral fenestrations in the extracellular domain of the glycine receptor contribute to the main chloride permeation pathway” Adrien H. Cerdan, Laurie Peverini,  Jean-Pierre Changeux, Pierre-Jean Corringer, Marco Cecchini

Spatiotemporal dynamics of odor representations in the human brain revealed by EEG decoding

This is the data and script that reproduces the results of the paper: Kato et al., PNAS 2022, Spatiotemporal dynamics of odor representations in the human brain revealed by EEG decoding. As the results of each analysis that are needed for other analysis are also contained in this folder,  each sub-section of the script can be run independently (e.g., you can plot OERP waveforms or GFPs without executing preprocessing).  Refer to README.txt for detailed discription.

opencc-zeroMay 2022View details →

dryad32/100

Dataset for analysing spatiotemporal dynamics of large carnivores in Kasungu National Park, Malawi

Effective conservation management requires an understanding of the spatiotemporal dynamics driving large carnivore density and resource partitioning. In African ecosystems, reduced prey populations and the loss of competing guild members, most notably lion (Panthera leo), are expected to increase levels of competition between remaining carnivores. Consequently, intraguild relationships can be altered, potentially increasing the risk of further population decline. Kasungu National Park (KNP), Malawi, is an example of a conservation area that has experienced large-scale reductions in both carnivore and prey populations, leaving a resident large carnivore guild consisting of only leopard (Panthera pardus) and spotted hyaena (Crocuta crocuta). Here we quantify the spatiotemporal dynamics of these two species and their degree of association, using a combination of co-detection modelling, time-to-event analyses, and temporal activity patterns from camera trap data. Detection of leopard and spotted hyaena was significantly associated with the detection of preferred prey and competing carnivores, increasing the likelihood of species interaction. Temporal analyses revealed sex-specific differences in temporal activity, with female leopard activity patterns significantly different to those of spotted hyaena and male conspecifics. Heightened risk of interaction with interspecific competitors and male conspecifics may have resulted in female leopards adopting temporal avoidance strategies to facilitate co-existence. Female leopard behavioural adaptations increased overall activity levels and diurnal activity rates, with potential consequences for overall fitness and exposure to sources of mortality. As both species are currently found at low densities in KNP, increased risk of competitive interactions, that infer a reduction in fitness, could have significant implications for large carnivore demographics. Protection of remaining prey populations is necessary to mitigate interspecific competition and avoid further alterations to the large carnivore guild.

opencc-by-4.0Mar 2022View details →

The role of ocean and atmospheric dynamics in the marine-based collapse of the last Eurasian Ice Sheet

EIS_reconstruction.zip:  .shp files of Eurasian Ice Sheet reconstruction 20-14 ka (1 ka time step) EIS_thickness.zip:  .shp files of Eurasian Ice Sheet thickness for 19 ka, 18 ka, 16 ka and 15 ka. Supplementary Data 1: An Excel spreadsheet containing radiocarbon dates from the North Sea Supplementary Data 2:  An Excel spreadsheet containing radiocarbon dates from the Mid Norwegian margin Supplementary Data 3: An Excel spreadsheet containing radiocarbon dates from the Svalbard-Kara Sea-Barents Sea Supplementary Data 4:   An Excel spreadsheet containing model output GIA adjusted Supplementary Data 5:  An Excel spreadsheet containing Model output GIA adjusted -20% Supplementary Data 6:  An Excel spreadsheet containing Model output GIA adjusted +20%

opencc-by-4.0Jan 2022View details →

Numerical data for dynamic rupture simulations of the 2016 Kumamoto earthquake

Numerical data used to generate Figures in the manuscript entitled "The origin of large, long-period near-fault ground velocities during surface-breaking strike-slip earthquakes".

Precessional dynamics of geometrically scaled magnetostatic spin waves in two-dimensional magnonic fractals

Open data for "Precessional dynamics of geometrically scaled magnetostatic spin waves in two-dimensional magnonic fractals" published in PRB 105, 174415 (2022)

Dynamic implicit modeling of tunnel unfavorable geology based on multi-source data fusion using support vector machine

This is the relevant data of the article "Dynamic implicit modeling of tunnel unfavorable geology based on multi-source data fusion using support vector machine"

Data for "Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase"

Molecular dynamics data associated with the publication: "Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase" Trajectores were generated in GROMACS, and the carbon alpha coordinates were extracted and aligned with the JEDi analysis software. Details of the simulations and analysis are given in the publication. Data in apo.zip contains trajectories for 32 total trajectories of TEM-1, TEM-2, TEM-10, and TEM-52 beta-lactamase, each starting form different 8 crystal structures Data in holo.zip contains 16 trajectories of TEM-1, TEM-2, TEM-10, and TEM-52 beta-lactamase in complex with ampicillin, amoxicillin, cefotaxime, and ceftazidime each. Trajectories files are in comma delimited format, with rows representing degrees for freedom (789 total), and columns representing samples (10000 per trajectory file). Supervised Projective Learning for Orthogonal Completeness (SPLOC) software for analysis as performed in the publication can be found at: https://github.com/BioMolecularPhysicsGroup-UNCC/MachineLearning/tree/master/SPLOC

Research Data for Martin and Edmonds, 2022, Earth Surface Dynamics.

Research data for: Martin, H.K and Edmonds, D.A., 2022. The push and pull of abandoned channels: How floodplain processes and healing affect avulsion dynamics and alluvial landscape evolution in foreland basins. Earth Surface Dynamics. Available at: https://doi.org/10.5194/esurf-2021-82. Consists of .gif animations and some .csv files for all model output used to generate figures for the paper.

opencc-by-4.0Jul 2021View details →

Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids

Source data and source code for the graphs in "Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids".

dryad32/100

Data from: Retinoic acid-induced protein 14 controls dendritic spine dynamics associated with depressive-like behaviors

Dendritic spines are the central postsynaptic machinery that determines synaptic function. The F-actin within dendritic spines regulates their dynamic formation and elimination. Rai14 is an F‑actin-regulating protein with a membrane‑shaping function. Here, we identified the roles of Rai14 for the regulation of dendritic spine dynamics associated with stress-induced depressive-like behaviors. Rai14-deficient neurons failed to maintain a proper dendritic spine density in the Rai14+/- mouse brain, resulting in impaired functional synaptic activity. Rai14 was protected from degradation by complex formation with Tara, and accumulated in the dendritic spine neck, thereby enhancing spine maintenance. Concurrently, Rai14 deficiency in mice altered gene expression profile relevant to depressive conditions and increased depressive-like behaviors. Moreover, Rai14 expression was reduced in the prefrontal cortex of the mouse stress model, which was blocked by antidepressant treatment. Thus, we propose that Rai14-dependent regulation of dendritic spines may underlie the plastic changes of neuronal connections relevant to depressive-like behaviors.

opencc-zeroMay 2022View details →

In silico investigation of Alsin RLD conformational dynamics and phosphoinositides binding mechanism

Raw data of the publication "In silico investigation of Alsin RLD conformational dynamics and phosphoinositides binding mechanism"

Hierarhical method and Dynamic Programming methods for AI-SPRINT GPU Scheduler

This repository includes the source code and the datasets of the Hierarchical method and the Dynamic Programming methods used to obtain the results reported in the article "Scheduling Deep Learning Jobs Training in the Cloud: Comparing Multiple Approaches". The two methods constitute a part of the GPU Scheduler developed in the context of the AI-SPRINT project.

Neural dynamics differentially encode phrases and sentences in spoken language comprehension

Data used to plot the summarized figures in the research article, Neural dynamics differentially encode phrases and sentences in spoken language comprehension.

Research Data for "Molecular Dynamics Study of Structure and Reactions at the Hydroxylated Mg(0001)/Bulk Water Interface"

This folder contains data used in the paper "Molecular Dynamics Study of Structure and Reactions at the Hydroxylated Mg(0001)/Bulk Water Interface" (Title subject to change). Some details on the structure are as follows: The folder "figures" contains data to create various figures in the main paper. Each file contains a json object, where keys "0", "1", etc. refer to the 1st/2nd subplot for a figure. The values are then another json object with the data used to create the relevant plot; the most useful of which is the "data" key which contains the plot data. The folder "md_traj" contains the molecular dynamics trajectory. The file "traj.exyz" is a standard format which can be opened with various software. "traj.json" contains the same information in an in-house format used by the author. The "thermo_data.json" contains various thermodynamics properties over the simulation, such as temperatures and kinetic energies. Units are femtoseconds, Angstrom, electron-volts and Kelvin. The folder "react_traj" contains trajectories in the same formats as "md_traj", but each are limited to time-windows where reactions occurred (so each trajectory will only be hundreds of femtoseconds long at most). The subfolder "full_traj" contains the trajectories with all atoms present, whilst "trimmed_traj" contains trajectories with most atoms removed (the atoms included are those nearest the reaction).We include these "trimmed_traj" files as it is difficult to find the reacting molecules when visualising all atoms in the simulation. The folder "opt_geoms" contains geometries for various structures used in the paper (in *.exyz format). These also contain *.json files; these contain information on how the calculations were carried out in a format used by the author (they are small files primarily included for the benefit of the author).

Simulation input files and analysis scripts for "Small ionic radii limit time step in Martini 3molecular dynamics simulations"

Simulation input files and analysis scripts for "Small ionic radii limit time step in Martini 3molecular dynamics simulations". See <a href="https://aip.scitation.org/doi/10.1063/5.0095523">https://aip.scitation.org/doi/10.1063/5.0095523</a> for details. NOTE: some combinations of settings result in simulations that crash!

Acoustic Mid-Ocean Dynamics Experiment (AMODE), 1991, North Atlantic: High-frequency Baroclinic Mode-1 Amplitudes

A netcdf data file of high-frequency (> 1 cpd) baroclinic mode-1 amplitude in the western North Atlantic derived from ocean acoustic tomography data collected during the Acoustic Mid-Ocean Dynamics Experiment (AMODE) in 1991.  AMODE consisted of a pentagonal array of six moored instruments deployed between Puerto Rico and Bermuda.  These are baroclinic amplitudes averaged over paths several hundred kilometers long.  As documented in: Dushaw, B. D., & Worcester, P. F. (1998). Resonant diurnal internal tides in the North Atlantic. Geophys. Res. Lett., 25 , 2189–2192. doi: 10.1029/98GL01583 Dushaw, B. D., Worcester, P. F., Cornuelle, B. D., Howe, B. M., & Luther, D. S. (1995). Baroclinic and barotropic tides in the central North Pacific Ocean determined from long-range reciprocal acoustic transmissions.J. Phys. Oceanogr.(25), 631–647.  doi: 10.1175/1520-0485(1995)025&lang;0631: BABTIT&rang;2.0.CO;2 Dushaw, B. D. (2003). On the mapping and wavenumber resolution of line-integral data for observations of low-mode internal tides. J. Atmos. Oceanic Tech., 20 , 1043–1059. doi: 10.1175/1458.1 Dushaw, B. D. (2006). Mode-1 internal tides in the western North Atlantic Ocean. Deep-Sea Res. Part I , 53 , 449–473. doi: 10.1016/j.dsr.2005.12.009 Dushaw, B. D., Worcester, P. F., & Dzieciuch, M. A. (2011). On the predictability of mode-1 internal tides. Deep-Sea Res. Part I (58), 677–698. doi: 10.1016/j.dsr.2011.04.002 Dushaw, B. D.  (2015).  An empirical model for mode-1 internal tides derived from satellite altimetry: Computing accurate tidal predictions at arbitrary points over the world oceans (Tech. Rep. No. Technical Memorandum TM 1-15).  Applied Physics Laboratory, University of Washington, Seattle, WA. http://www.apl.washington.edu/project/project.php?id=tm\ 1-15 Hendershott, M. (1981). Long waves and ocean tides. In B. A. Warren & C. Wunsch (Eds.), Evolution of physical oceanography: Scientific surveys in honor of Henry Stommel (pp. 292–341). Cambridge, MA: MIT Press. These data can be used to derive accurate estimate for baroclinic tide amplitudes in the open ocean.  The file includes 15 time series of 100 to 300 day record length.  The purpose of this upload is to allow others to estimate tides from these data to test baroclinic tidal models.  Other than a simple high-pass filter, the time series is unfiltered, but the baroclinic tides account for 30-80% of the variance, depending on the amplitude of the tide on the acoustic path.

Acoustic Mid-Ocean Dynamics Experiment (AMODE), 1991, North Atlantic: High-frequency Barotropic Currents

A netcdf data file of high-frequency (> 1 cpd) barotropic currents in the western North Atlantic derived from ocean acoustic tomography data collected during the Acoustic Mid-Ocean Dynamics Experiment (AMODE) in 1991.  AMODE consisted of a pentagonal array of six moored instruments deployed between Puerto Rico and Bermuda.  These are barotropic currents averaged over paths several hundred kilometers long.  As documented in: Dushaw, B. D., Egbert, G. D., Worcester, P. F., Cornuelle, B. D., Howe, B. M., & Metzger, K. (1997). A TOPEX/POSEIDON global tidal model (TPXO.2) and barotropic tidal currents determined from long-range acoustic transmissions. Prog. Oceanogr., 40 , 337–367. doi: 10.1016/S0079-6611(98)00008-1 these data can be used to derive accurate estimate for barotropic tidal currents in the open ocean.  The file includes 15 time series of 100 to 300 day record length.  See also: Stammer, D., & Coauthors. (2014). Accuracy assessment of global barotropic ocean tide models. Rev. Geophys., 52 , 243–282. doi: 10.1002/2014RG000450 which compares tidal current harmonic constants derived from these data to those derived from several global tidal models.  The purpose of this upload is to allow others to estimate tides from these data to test other tidal models.  Other than a simple high-pass filter, the time series is unfiltered, but the barotropic tides account for 80-90% of the variance.

opencc-by-4.0Aug 2021View details →

Data from: Nonprehensile Manipulation of Parts on a Horizontal Circularly Oscillating Platform with Dynamic Dry Friction Control

Data from the paper "Nonprehensile Manipulation of Parts on a Horizontal Circularly Oscillating Platform with Dynamic Dry Friction Control"  <a href="https://doi.org/10.3390/s21165581">https://doi.org/10.3390/s21165581</a> This paper presents a novel method for nonprehensile manipulation of parts on a circularly oscillating platform when the effective coefficient of dry friction between the part and the platform is being dynamically controlled. Theoretical and experimental analyses have been performed to validate the proposed method and to determine the control parameters that define the characteristics of the part’s motion. A mathematical model of the manipulation process with dynamic dry friction control was developed and solved. The modeling showed that by changing the phase shift between the function for dynamic dry friction control and the function defining the circular motion of the platform, the part can be moved in any direction as the angle of displacement can be controlled in a full range from 0 to 2π. The nature of the trajectory and the mean displacement velocity of the part mainly depend on the width of the rectangular function for dynamic dry friction control. To verify the theoretical findings, an experimental setup was developed, and experiments of manipulation were carried out. The experimental results qualitatively confirmed the theoretical findings. The presented analysis enriches the classical theories of nonprehensile manipulation on oscillating platforms, and the presented findings are relevant for mechatronics, robotics, mechanics, electronics, medical, and other industries.

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