Find research datasets worth reusing

Unraveling the decarboxylation dynamics of the fluorescein dianion with fragment action spectroscopy

The raw action spectra of Fl2- recorded by monitoring the yields of electrons, Fl- and Fl-CO2-, as well as the photoelectron image of Fl2- at 320 nm.

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution

Supplementary Tables for article "Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution"

opencc-zeroApr 2023View details →

Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Flavivirus Helicases -- Output Files

These are the output files generated using the input files and Galaxy workflows for flavivirus helicase simulations, from:  <pre>https://doi.org/10.5281/zenodo.7493015</pre>

Predicting Pulsed Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction - sample untreated_162nm

RHEED intensity image dataset of sample untreated_162nm in work "Predicting Pulsed Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction."

Predicting Pulsed Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction - sample treated_81nm

RHEED intensity image dataset of sample t0.08 in work "Predicting Pulsed Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction."

Vortex dynamics induced by scanning SQUID susceptometry

We measured the local magnetic response of a niobium thin film by applying a millitesla-scale AC magnetic field using a micron-scale field coil and detecting the response with a micron-scale pickup loop in a scanning superconducting quantum interference device (SQUID) susceptometry measurement. Near the film's critical temperature, we observed a step-like nonlinear and dissipative magnetic response due to the dynamics of a small number of vortex-antivortex pairs induced in the film by the local applied AC field.  We modeled the dynamics of the measurement using a combined two-dimensional London-Maxwell and time-dependent Ginzburg-Landau approach, allowing us to construct a detailed real-space picture of the vortex motion causing the observed dissipative response. This work pushes scanning SQUID susceptometry of two-dimensional superconductors beyond the regime of linear response and lays the foundation for microscopic studies of vortex dynamics and pinning in superconducting devices and more exotic materials systems.

opencc-zeroApr 2023View details →

Mathematical model results for: Dynamic fibronectin assembly and remodeling by leader neural crest cells prevents jamming in collective cell migration

Collective cell migration plays an essential role in vertebrate development, yet the extent to which dynamically changing microenvironments influence this phenomenon remains unclear. Observations of the distribution of the extracellular matrix (ECM) component fibronectin during the migration of loosely connected neural crest cells (NCCs) lead us to hypothesize that NCC remodeling of an initially punctate ECM creates a scaffold for trailing cells, enabling them to form robust and coherent stream patterns. We evaluate this idea in a theoretical setting by developing an agent-based model that incorporates reciprocal interactions between NCCs and their ECM. ECM remodeling, haptotaxis, contact guidance, and cell-cell repulsion are sufficient for cells to establish streams in silico, however additional mechanisms, such as chemotaxis, are required to consistently guide cells along the correct target corridor. Further investigations of the model imply that contact guidance and differential cell-cell repulsion between leader and follower cells are key contributors to robust collective cell migration by preventing stream breakage. Global sensitivity analysis and simulated underexpression/overexpression experiments suggest that long-distance migration without jamming is most likely to occur when leading cells specialize in creating ECM fibers, and trailing cells specialize in responding to environmental cues by upregulating mechanisms such as contact guidance. This dataset contains summary statistics, movies, parameter values, and photos obtained from individual realizations of the mathematical model.

opencc-zeroApr 2023View details →

Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling

<div class="abstract"> Old growth forests are declining globally, threatening dependent wildlife. Many arboreal old‐growth obligates, such as the threatened red tree vole, are difficult to monitor for changes in habitat occupancy, and abundance. Yet, conservation planning relies on this information to prevent population declines. We integrated a range of species, habitat, and landscape change information to develop a dynamic habitat‐population model. The spatial individual‐based model simulated dynamic patterns of occupancy that responded to annual habitat maps, describing 36 years of observed change. We simulated population dynamics and local movement to characterize changes in occupancy and abundance, and the capacity of remaining habitat to support red tree voles. Red tree vole redistribution patterns strongly corresponded to wildfire footprints and timber extraction locations. Population strongholds are likely to exist in clumped pockets of old‐growth forest that were unaffected by wildfire and in protected old forest reserves. However, the exact number and locations of local clusters remain uncertain. Simulated population losses occurred at different paces in different places, underscoring the need for recurring evaluation of population changes with field occupancy surveys and modeled evaluations that can anticipate potential connectivity and extirpation thresholds. This modeling approach was effective at leveraging existing information for a data‐light species to assess how historical changes to the quantity, quality, and configuration of habitat likely influenced the potential landscape capacity, species abundance, and distribution. Dynamic individual‐based modeling can benefit conservation planning for red tree vole and other reclusive forest species by providing biologically nuanced assessments of abundance and distribution. Such models can also project the long‐term benefits and impacts of spatially explicit land management plans. </div> <div class="abstract"></div>

Dataset for nonlinear dynamic analysis to quantify workload in pedaling

The dataset contains raw data and the data underlying the figures and tables of the following research article:  "Quantifying workload using nonlinear dynamical measures of biomechanical parameters during cycling on a roller trainer" Journal: PLOS ONE Manuscript Nr: PONE-D-22-23944

Data set: The opening dynamics of the lateral gate regulates the activity of rhomboid proteases

Dataset: The opening dynamics of the lateral gate regulates the activity of rhomboid proteases Input: MD simulations + docking results

opencc-zeroMay 2023View details →

Defensive symbiosis in the wild: seasonal dynamics of parasitism risk and symbiont-conferred resistance

Parasite-mediated selection can rapidly drive up resistance levels in host populations, but fixation of resistance traits may be prevented by costs of resistance. Black bean aphids (Aphis fabae) benefit from increased resistance to parasitoids when carrying the defensive bacterial endosymbiont Hamiltonella defensa. However, due to fitness costs that come with symbiont infection, symbiont-conferred resistance may result in either a net benefit or a net cost to the aphid host, depending on parasitoid presence as well as on the general ecological context. Balancing selection may therefore explain why in natural aphid populations, H. defensa is often found at intermediate frequencies. Here we present a two-year field study where we set out to look for signatures of balancing selection in natural aphid populations. We collected temporally well-resolved data on the prevalence of H. defensa in A.f. fabae and estimated the risk imposed by parasitoids using sentinel hosts. Despite a marked and consistent early-summer peak in parasitism risk and significant changes in symbiont prevalence over time, we found just a weak correlation between parasitism risk and H. defensa frequency dynamics. H. defensa prevalence in the populations under study was, in fact, better explained by the number of heat days that previous aphid generations were exposed to. Our study grants an unprecedentedly well-resolved insight into the dynamics of endosymbiont and parasitoid communities of A.f. fabae populations, and it adds to a growing body of empirical evidence suggesting that not only parasitism risk but rather multifarious selection is shaping H. defensa prevalence in the wild.

Regulation of T7 gp2.5 Binding Dynamics by its C-terminal tail, Template Conformation and Sequence

Bacteriophage T7 single-stranded DNA-binding protein (gp2.5) binds to and protects transiently exposed regions of single-stranded DNA (ssDNA) while dynamically interacting with other proteins of the replication complex. We directly visualize fluorescently labelled T7 gp2.5 binding to ssDNA at the single-molecule level. Upon binding, T7 gp2.5 reduces the contour length of ssDNA by stacking nucleotides in a force-dependent manner, suggesting T7 gp2.5 suppresses the formation of secondary structure. Next, we investigate the binding dynamics of T7 gp2.5 and a deletion mutant lacking 21 Cterminal residues (gp2.5-Δ21C) under various template tensions. Our results show that the base sequence of the DNA molecule, ssDNA conformation induced by template tension, and the acidic terminal domain from T7 gp2.5 significantly impact on the DNA binding parameters of T7 gp2.5. Moreover, we uncover a unique template-catalyzed recycling behaviour of T7 gp2.5, resulting in an apparent cooperative binding to ssDNA, facilitating efficient spatial redistribution of T7 gp2.5 during the synthesis of successive Okazaki fragments. Overall, our findings reveal an efficient binding mechanism that prevents the formation of secondary structures by enabling T7 gp2.5 to rapidly rebind to nearby exposed ssDNA regions, during lagging strand DNA synthesis.

opencc-by-nc-4.0May 2023View details →

Regulation of T7 gp2.5 Binding Dynamics by its C-terminal tail, Template Conformation and Sequence

* To whom correspondence may be addressed: g.j.l.wuite@vu.nl # The first three authors should be regarded as joint first authors Abstract Bacteriophage T7 single-stranded DNA-binding protein (gp2.5) binds to and protects transiently exposed regions of single-stranded DNA (ssDNA) while dynamically interacting with other proteins of the replication complex. We directly visualize fluorescently labelled T7 gp2.5 binding to ssDNA at the single-molecule level. Upon binding, T7 gp2.5 reduces the contour length of ssDNA by stacking nucleotides in a force-dependent manner, suggesting T7 gp2.5 suppresses the formation of secondary structure. Next, we investigate the binding dynamics of T7 gp2.5 and a deletion mutant lacking 21 C-terminal residues (gp2.5-Δ21C) under various template tensions. Our results show that the base sequence of the DNA molecule, ssDNA conformation induced by template tension, and the acidic terminal domain from T7 gp2.5 significantly impact on the DNA binding parameters of T7 gp2.5. Moreover, we uncover a unique template-catalyzed recycling behaviour of T7 gp2.5, resulting in an apparent cooperative binding to ssDNA, facilitating efficient spatial redistribution of T7 gp2.5 during the synthesis of successive Okazaki fragments. Overall, our findings reveal an efficient binding mechanism that prevents the formation of secondary structures by enabling T7 gp2.5 to rapidly rebind to nearby exposed ssDNA regions, during lagging strand DNA synthesis. Data Set Description This data set contains the raw data and analysis code for the single-molecule study of the binding dynamics of T7 gp2.5 and its interactions with single-stranded DNA (ssDNA). The experiments utilized a custom-built setup combining dual optical trapping, confocal microscopy, and microfluidics. Methodology The single-molecule experiments were performed at room temperature in a 5-channel microfluidic flow cell using a custom-built experimental setup that combines dual optical trapping, confocal microscopy, and microfluidics for single-molecule assays. Data analysis was conducted using Python, Origin, and MATLAB. Detailed methodology and instrument specifications are provided in the associated publication. Data Set Structure - `Raw_Data/`: Contains raw data files in TDMS format. - `Data_Analysis_Code/`: Contains the code used for data analysis and figure generation. File Formats - Raw data files are in TDMS format. Usage Notes Along with the raw data, we also provided the analysis code which generates the figures. Users should be aware of the required citations, license terms, and ethical considerations when using this data set. Acknowledgments This work was financially supported by: ‘Crowd management: The physics of genome processing in complex environments’ of Stichting voor Fundamenteel Onderzoek der Materie, China Scholarship Council (funding No. 201704910912) and the European Union H2020 Marie-Sklowdowska Curie International Training Network AntiHelix, Grant Agreement n. 859853. Author Contributions J.C-D., L X., M.T.J.H., and G.J.L.W. conceptualized the research; J.C-D., and L.X. collected data; I.H. built the combined optical trapping and confocal microscope instrument and developed the MATLAB code for the analysis of kymograph data; S.A.S. and A.v.O. provided purified wild type T7 gp2.5 and tested their biochemical activity; S-J L. provided purified gp2.5-Δ21C and tested their biochemical activity; L X. J.C-D., and M.T.J.H. analyzed the data; J.C-D., L X., M.T.J.H., and G.J.L.W. wrote the manuscript; G.J.L.W. supervised the project; the manuscript is read, revised and confirmed by all the

Determinants of corporate shares market value dynamics during periods of decline and return to the original values of shares market

Determinants of corporate shares market value dynamics during periods of decline and return to the original values of shares market

openother-ncMay 2023View details →

TauBench: A Dynamic Benchmark for Graphics Rendering (Dataset)

TauBench is a dynamic graphics rendering benchmark dataset, targeted especially towards rendering methods relying on the reuse of temporal data. Path traced reference frames for the dataset are available at <a href="https://zenodo.org/record/7907164">https://zenodo.org/record/7907164</a>. The related conference paper (describing TauBench 1.0) is available at <a href="https://zenodo.org/record/6223036">https://zenodo.org/record/6223036</a>. More information about the 1.1 update and about the dataset in general can be found at <a href="https://webpages.tuni.fi/vga/taubench">https://webpages.tuni.fi/vga/taubench</a>.

Molecular dynamics trajectories of MTDH-SND1 protein-protein interaction inhibitors

This includes the prmtop and MD trajectories (production stage) and Amber outfiles of L1-L12, C26-A6/2, and MTDH peptide, GaMD trajectories of the protein, and the umbrella sampling trajectories of L5 and C26-A6/2. To reduce the file size, the trajectory files had been compressed using “xz” algorithm, and frames were saved by one frame per 1ns. However, for reference, one additional larger traj file with higher saving frequency for L5 was also uploaded. The input files and input coordinate files were uploaded as a separate attachment at http://pubs.acs.org.

Decomposition and nutrient dynamics of stumps and coarse roots of Eucalyptus plantations in southern China

This study aimed to (1) quantify the stocks of biomass and nutrients from Eucalyptus stumps and coarse roots along a chrono-sequence of 0–6-year-old clear-cutting stands and (2) estimate the loss rate of biomass and nutrients,  as well as the nutrient dynamics of stumps and coarse roots, to elucidate (1) if the biomass of coarse roots is higher than that of stumps and (2) if there is faster decomposition and nutrient loss rate from stumps from than coarse roots. Conclusion: Stumps and coarse roots serve as significant nutrients stocks that decay at varying rates. The loss of nutrients must be considered while analyzing the decomposition dynamics following clear-cutting in Eucalyptus plantations. This dataset is related to a research paper submitted to Annals of Forest Science.

Predicting Pulsed-Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction - gaussian_fit_parameters - sample untreated_162nm

RHEED raw dataset and Gaussia fitting parameter dataset for sample "untreated_162nm" in work "Predicting Pulsed Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction."

Compressed Datasets for Work "Predicting Pulsed-Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction"

Compressed version of RHEED image datasets and Gaussia fitting parameter datasets for samples "treated_213nm", "treated_81nm" and "untreated_162nm" in the work "Predicting Pulsed Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction."