Find research datasets worth reusing

Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death

This dataset accompanies the article entitled Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death, published in ACS Cent. Sci. (<a href="https://doi.org/10.1021/acscentsci.2c01078">https://doi.org/10.1021/acscentsci.2c01078</a>). subboxes_overview.xlsx:  This spreadsheet contains information about the protein composition of each sub-box. BOX_GEOMETRIES.zip: Starting structures (saved in Gromos87 .gro format) used for the production runs of the all-atom sub-boxes. PROTEIN_COM_MSD.zip: Text files containing the mean square displacements (MSDs) of the centers of mass (COMs) of individual proteins, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds while the MSD values are given in nm2. For each sub-box, the protein numbering corresponds to the subboxes_overview.xlsx spreadsheet. CHAIN_COM_MSD.zip: Text files containing the mean square displacements (MSDs) of the centers of mass (COMs) of individual polypeptide chains, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds while the MSD values are given in nm2. For each sub-box, the chain numbering corresponds to the subboxes_overview.xlsx spreadsheet. CHAIN_ROTACF.zip: Text files containing the rotational autocorrelation functions for individual polypeptide chains, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds; the autocorrelation functions were calculated using a second-order Legendre polynomial. For each sub-box, the chain numbering corresponds to the subboxes_overview.xlsx spreadsheet.

opencc-by-4.0Nov 2022View details →

Learning Dissipative Dynamics in Chaotic Systems (Datasets)

We present the datasets for NeurIPS 2022 paper <a href="https://arxiv.org/abs/2106.06898">"Learning Dissipative Dynamics in Chaotic Systems."</a> In this work, we propose a machine learning framework, which we call the Markov Neural Operator (MNO), to learn the underlying solution operator for dissipative chaotic systems, showing that the resulting learned operator accurately captures short-time trajectories and long-time statistical behavior. In our work, we present results in the finite-dimensional toy system Lorenz-63. We showcase results on the 1D Kuramoto–Sivashinsky (KS) and on the 2D Navier-Stokes (Kolmogorov flows) PDEs. We present the datasets for Lorenz-63, KS, and Navier-Stokes (Reynolds numbers 40, 500, and 5000). The data is stored as .npy and .mat files: <ul> <li>L63.mat: Lorenz-63 data (one long trajectory of 10000 seconds)</li> <li>KS.mat: 1D Kuramoto–Sivashinsky data (1200 trajectories, 500 time-steps each)</li> <li>2D_NS_Re40.npy: 2D Navier-Stokes data (200 trajectories, 500 time-steps each) at 64 x 64 spatial resolution.</li> <li>2D_NS_Re500.npy: 2D Navier-Stokes data (1000 trajectories, 500 time-steps each) at 64 x 64 spatial resolution with Reynolds number 500.</li> <li>2D_NS_Re5000.npy: 2D Navier-Stokes data (100 trajectories, 500 time-steps each) at 128 x 128 spatial resolution with Reynolds number 5000.</li> </ul>

On equilibrating non-periodic molecular dynamics samples for coupled particle-continuum simulations of amorphous polymers: dataset

Abstract: (from [1]) In the context of fracture simulations of polymers, the molecular mechanisms in the vicinity of the crack tip are of particular interest. Nevertheless, to keep the computational cost to a minimum, a coarser resolution must be used in the remaining regions of the numerical sample. For the specific case of amorphous polymers, the Capriccio method bridges the gap between the length and time scales involved at the different levels of resolution by concurrently coupling molecular dynamics (MD) with the finite element method (FEM). Within the scope of the Capriccio approach, the coupling to the molecular MD region introduces non-periodic, so-called stochastic boundary conditions (SBC). In similarity to typical simulations under periodic boundary conditions (PBC), the SBC MD simulations must reach an equilibrium state before mechanical loads are exerted on the coupled systems. In this contribution, we hence extensively study the equilibration properties of non-periodic MD samples using the Capriccio method. We demonstrate that the relaxation behavior of an MD-FE coupled MD domain utilizing non-periodic boundary conditions is rather insensitive to the specific coupling parameters of the method chosen to implement the boundary conditions. The behavior of an exemplary system equilibrated with the parameter set considered as optimal is further studied under uniaxial tension and we observe some peculiarities in view of creep and relaxation phenomena. This raises important questions to be addressed in the further development of the Capriccio method.   Contact: Felix Weber Institute of Applied Mechanics Friedrich-Alexander-Universität Erlangen-Nürnberg Egerlandstr. 5 91058 Erlangen Germany   Context: This dataset contains the results presented in [1] and related data. Content: Throughout this data set, Lammps [2] real units are used. The following folders contain the results obtained under periodic boundary conditions: - biax_PBC: biaxial loading  - equil_PBC: equilibration - ut_PBC: uniaxial tension Each simulation directory contains: - input.prm: input parameters of the specific simulation (read by the input file) - job.out: simulation log file - meta.info: meta data of the specific simulation run - Lammps input file (*.in) of the specific simulation - Lammps data file (*.data, molecular style) of the investigated sample - LAMMPS_out: resulting Lammps data and restart (*.rst) files and simulation results (Lammps thermo_out) in  tabulated form, an overview of the columns is given in the respective folders The following folders contain the results obtained under stochastic boundary conditions using the Capriccio method [3]: - best: equilibration with the parameter set considered to be most suitable for the MD-FE coupled equilibration - biax: biaxial loading - bridging: equilibration with different adaptivity levels of the bridging domain - descr_obs: equilibration with a Lagrangian frame for the description of the observation region - dpd: equilibration with different thicknesses of the dissipative particle dynamics (DPD) region - friccoeff: equilibration with different friction coefficients applied in the dissipative particle dynamics region - fur: equilibration with different numbers of fur beads  - gausspoints: equilibration with different numbers of quadrature points per direction  - min: equilibration applying an initial, static energy minimization - nodes: equilibration with a higher number of finite element nodes - shifted: equilibration with particle systems obtained at different positions and points in time within the periodic master system - smdcub: equilibration with different remaining stiffness ratios for the cubic modified weighting factor - smdlin: equilibration with different remaining stiffness ratios for the linear modified weighting factor - timestepsize: equilibration with different molecular dynamics time step sizes - ut: uniaxial tension - ut_friccoeff: uniaxial tension with different friction coefficients applied in the dissipative particle dynamics region - weighting: equilibration with different energy weighting functions - youngsmod: equilibration with different Young's moduli Each simulation directory contains: - input_files: Abaqus [4] input file (*.inp) and Lammps data file (*.data, molecular style) of the investigated sample - MD_data: Results evaluated in the molecular dynamics region. MD_data contains the following subfolders:  anchorforces (dumped force components on the anchor points (AP) in kcal/mol, files anchorforce_[load step]_[MD-FE iteration].AF),  data (resulting Lammps data files *.[load step].[MD-FE iteration].data), Density (dumped mass density in the observation region in kg/m^3),  Energy (dumped total (kinetic + potential), angle, bond, and pair energies in kcal/(mol*Angstrom)), Strain (integral strains in the observation region in x-, y-, and z-direction calculated by means of the Matlab [5] script calc_OBSstrain.m), Stress (stresses in the observation region in MPa), and Temperature (temperature in the observation region in K) - job.out: simulation log file - meta.info: meta data of the specific Lammps simulation Information on the subfolders is given in the respective folders. References: [1] F. Weber, M. Ries, C. Bauer, C. R. Wick, S. Pfaller, "On equilibrating non-periodic molecular dynamics samples for coupled particle-continuum simulations of amorphous polymers", Forces in Mechanics, 2023, 10, 100159. [2] A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer,  S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, S. J. Plimpton, "LAMMPS - a flexible simulation tool  for particle-based materials modeling at the atomic, meso, and continuum scales", Computer Physics Communications, 2022, 271, 108171. [3] S. Pfaller, M. Rahimi, G. Possart, P. Steinmann, F. Müller-Plathe, M. C. Böhm, "An Arlequin-based method to couple molecular dynamics  and finite element simulations of amorphous polymers and nanocomposites", Computer Methods in Applied Mechanics and Engineering,  2013, 260, 109-129.  [4] Dassault Systèmes, "Abaqus documentation", URL: https://abaqus-docs.mit.edu/2017/English/SIMACAEEXCRefMap/simaexc-c-docproc.htm. [5] The MathWorks, Inc, "MATLAB. The Language of Technical Computing", URL: https://de.mathworks.com/help/matlab/. Funding: This research was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 377472739/GRK 2423/1-2019. The authors are very grateful for this support. Sebastian Pfaller is furthermore funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 396414850 (Individual Research Grant ’Identifikation von Interphaseneigenschaften in Nanokompositen’).

Dynamic antagonism between key repressive pathways maintains the placental epigenome (source data and custom code)

DNA and Histone-3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb Repressive Complexes regulate the CpG-rich promoters of developmental genes. In contrast to this general framework, the extraembryonic lineages display noncanonical, globally intermediate DNA methylation levels that includes disruption of local Polycomb domains. To better understand this unusual landscape’s molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse Trophoblast Stem Cells (TSCs). We find that the extraembryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized appearance, our data point to a highly controlled equilibrium between counteracting repressors within extraembryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.

Post-translocation dynamics of black-tailed prairie dogs (Cynomys ludovicianus): A successful conservation and human-wildlife conflict mitigation tool

Prairie dogs have declined by 98% throughout their range in the grasslands of North America. Translocations have been used as a conservation tool to reestablish colonies of this keystone species and to mitigate human-wildlife conflict. Understanding the behavioral responses of prairie dogs to translocation is of utmost importance to enhance the persistence of the species and for species that depend on them, including the critically endangered black-footed ferret. In 2017 and 2018, we translocated 658 black-tailed prairie dogs on the Lower Brule Indian Reservation in central South Dakota, USA, a black-footed ferret recovery site. Here, we describe and evaluate the effectiveness of translocating prairie dogs into augered burrows and soft released within presumed coteries to reestablish colonies in previously occupied habitat. We released prairie dogs implanted with passive integrated transponders (PIT tags) and conducted recapture events approximately 1-month and 1-year post-release. We hypothesized that these methods would result in a successful translocation and that prairie dogs released as coteries would remain close to where they were released because of their highly social structure. In support of these methods leading to a successful translocation, 69% of marked individuals were captured 1-month post-release, and 39% were captured 1-year post-release. Furthermore, considerable recruitment was observed with 495 unmarked juveniles captured during the 1-year post-release trapping event, and the reestablished colony had more than doubled in area by 2021. Contrary to our hypothesis, yet to our knowledge a novel finding, there was greater initial movement within the colony 1-month post-release than expected based on recapture locations compared to published average territory size; however, 1-year after release most recaptured individuals were captured within the expected territory size when compared to capture locations 1-month post-release. This research demonstrates that while translocating prairie dogs may be socially disruptive initially, it is an important conservation tool.

Supplementary data to: Soil Moisture to Runoff (SM2R) A data-driven model for runoff estimation across poorly gauged Asian water towers based on soil moisture dynamics

This data archive includes simulated monthly runoff anomaly using the Soil Moisture to Runoff model during 1981‒2020 over the representative drainage basin in each water tower. Please see Readme for more data information. For calculation details please see the publication.

Dynamics and recovery of forest understory biodiversity over 17 years following varying levels of retention harvesting

1. Retention harvesting is advocated as an alternative to intensive timber harvesting, such as clear-cutting, to better maintain or facilitate recovery of biodiversity and other ecological values in managed forests. However, it is not clear how long the benefits of retention harvests persist. 2. We investigated responses of understory vascular plant cover, richness, diversity (inverse Simpson index), and composition to a gradient in dispersed retention (2% [clear-cut], 10%, 20%, 50% and 75% retention; unharvested reference [100% retention]) at 3, 6, 11, and 17 years after harvest, in four boreal mixed wood forest types (deciduous (broadleaf)-dominated, deciduous-dominated with conifer understory, mixed, and conifer-dominated) in western Canada. 3. Understory cover and richness tended to increase in the short-term (3 years), peaked at 6–11 years with differences following the gradient of harvesting intensity, then plateaued or declined in the second decade (17 years), by which time there were minimal or no differences among harvesting levels, including the reference. Responses for diversity were minimal. In contrast, composition varied along the gradient of harvesting intensity and showed little recovery towards the unharvested condition over the 17-year period. Generally, for plant community composition, clear-cut and lower retention treatments (10%, 20%) were similar to one another but differed from the higher retention and unharvested reference treatments. 4. Synthesis and applications. Retention harvests can moderate the negative impacts of harvesting and facilitate the recovery of biodiversity. Our results suggest that for the cover, richness and diversity of understory vascular plants, this moderating influence is weak and short-lived. However, higher levels of retention can temper changes in understory composition relative to the unharvested forest, but full recovery is likely to be slow and will be complicated by post-harvest regeneration dynamics.

Data from: Like a rolling stone: Colonization and migration dynamics of the gray reef shark (Carcharhinus amblyrhynchos)

Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here we investigated the evolutionary history of the endangered gray reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RAD-seq loci in 173 individuals in the Indo-Pacific (IP). We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo-Australian Archipelago (IAA) where two stepping-stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm~10 per generation) throughout the range, and an isolation-by-distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long-distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (FST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the gray reef shark should be designed on a range-wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon-associated Carcharhinus melanopterus, known for its restricted dispersal ability. C. melanopterus exhibits a similar RE dynamic but is characterized by stronger genetic structure and a non-homogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as a source of biodiversity and of life history traits in shaping the extent of genetic structure and diversity.

Datasets of the article "Sub-millisecond Photoinduced Dynamics of Free and EL222-bound FMN by Stimulated Raman and Visible Absorption Spectroscopies"

Femtosecond-stimulated Raman spectra (FSRS) and visible transient absorption (visTA) spectra of free FMN (flavin mononucleotide), FMN bound to EL222-WT, and FMN bound to EL222-C78A. The dataset includes also the lifetime distributions, decay-associated difference spectra (DADS), and evolution-associated difference spectra (EADS). Please check the README file for more information. If you use any of these data, please cite:  Liu, Y.; Chaudhari, A.S.; Chatterjee, A.; Andrikopoulos, P.C.; Picchiotti, A.; Rebarz, M.; Kloz, M.; Lorenz-Fonfria, V.A.; Schneider, B.; Fuertes, G. Sub-Millisecond Photoinduced Dynamics of Free and EL222-Bound FMN by Stimulated Raman and Visible Absorption Spectroscopies. Biomolecules 2023, 13, 161. https://doi.org/10.3390/biom13010161

input data for topo_drag.f90 using GFDL dynamical cores

Use XXX=150 for T85, and XXX=300 for T42. Remember to change the file names in the source code or rename these input files accordingly.

Data from: Microbial population dynamics decouple growth response from environmental nutrient concentration

To explore the diversity of microbial growth responses, we have compiled 247 measurements of half-saturation concentrations K and maximum growth rates gmax from previously-published studies (see Methods). The data includes a wide range of resources, including sources of carbon, nitrogen, phosphorus, metals, and vitamins, with phosphate, glucose, and nitrate having the largest number of measurements due to their emphasis in marine and laboratory systems. Organisms include prokaryotes and eukaryotes as well as autotrophs and heterotrophs. This data has been analyzed in a companion research article. For data plots and a discussion of results, please refer to: <div class="csl-bib-body"> <div class="csl-entry">Fink, Justus Wilhelm, Noelle A. Held, and Michael Manhart. "Microbial Population Dynamics Decouple Growth Response from Environmental Nutrient Concentration." Proceedings of the National Academy of Sciences 120, no. 2 (January 10, 2023). <a href="https://doi.org/10.1073/pnas.2207295120">https://doi.org/10.1073/pnas.2207295120</a>.</div> </div>

Dataset of "Stabilized explicit 𝑢−𝑝𝑤 solution in soil dynamic problems near the undrained-incompressible limit"

Dataset of "Stabilized explicit 𝑢−𝑝𝑤 solution in soil dynamic problems near the undrained-incompressible limit"

Figures from the paper "The diversity of canonical and ubiquitous progress in computer vision: A dynamic topic modeling approach"(v2))

Figures from the paper  "The diversity of canonical and ubiquitous progress in computer vision: A dynamic topic modeling approach". The second version: Corrections to Figure 1. (fig1-> fig_v2).

Improving spectral library search untargeted metabolomics identification by dynamic tolerance peak matching and false discovery estimation

The unprocessed and processed benchmarking data used in the paper of "Improving spectral library search untargeted metabolomics identification by dynamic tolerance peak matching and false discovery estimation"

Data: Large old trees increase growth under shifting climatic constraints: Aligning tree longevity and individual growth dynamics in primary mountain spruce forests

In a world of accelerating changes in environmental conditions driving tree growth, tradeoffs between tree growth rate and longevity could curtail the abundance of large, old trees (LOTs), with potentially dire consequences for biodiversity and carbon storage. However, the influence of tree-level tradeoffs on forest structure at landscape scales will also depend on disturbances, which shape tree size and age distribution, and on whether LOTs can benefit from improved growing conditions due to climate warming. We analyzed temporal and spatial variation in radial growth patterns from ~5000 Norway spruce (Picea abies (L.) H. Karst) live and dead trees from the Western Carpathian primary spruce forest stands. We applied mixed-linear modeling to quantify the importance of LOT growth histories and stand dynamics (i.e. competition and disturbance factors) on lifespan. Finally, we assessed regional synchronization in radial growth variability over the 20th century, and modelled the effects of stand dynamics and climate on LOTs recent growth trends. Tree age varied considerably among forest stands, implying an important role of disturbance as an age constraint. Slow juvenile growth and longer period of suppressed growth prolonged tree lifespan, while increasing disturbance severity and shorter time since last disturbance decreased it. The highest age was not achieved only by trees with continuous slow growth, but those with slow juvenile growth followed by subsequent growth releases. Growth trend analysis demonstrated an increase in absolute growth rates in response to climate warming, with late summer temperatures driving the recent growth trend. Contrary to our expectation that LOTs would eventually exhibit declining growth rates, the oldest LOTs (>400 years) continuously increase growth throughout their lives, indicating a high phenotypic plasticity of LOTs for increasing biomass, and a strong carbon sink role of primary spruce forests under rising temperatures, intensifying droughts, and increasing bark beetle outbreaks.

Data from: Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences

Background During evolution, genes can experience duplications, losses, inversions and gene conversions. Why certain genes are more dynamic than others is poorly understood. Here we examine how several Sgs genes encoding glue proteins, which make up a bioadhesive that sticks the animal during metamorphosis, have evolved in Drosophila species. Results We examined high-quality genome assemblies of 24 Drosophila species to study the evolutionary dynamics of four glue genes that are present in D. melanogaster and are part of the same gene family – Sgs1, Sgs3, Sgs7 and Sgs8 – across approximately 30 millions of years. We annotated a total of 102 Sgs genes and grouped them into 4 subfamilies. We present here a new nomenclature for these Sgs genes based on protein sequence conservation, genomic location and presence/absence of internal repeats. Two types of glue genes were uncovered. The first category (Sgs1, Sgs3x, Sgs3e) showed a few gene losses but no duplication, no local inversion and no gene conversion. The second group (Sgs3b, Sgs7, Sgs8) exhibited multiple events of gene losses, gene duplications, local inversions and gene conversions. Our data suggest that the presence of short "new glue" genes near the genes of the latter group may have accelerated their dynamics. Conclusions Our comparative analysis suggests that the evolutionary dynamics of glue genes is influenced by genomic context. Our molecular, phylogenetic and comparative analysis of the four glue genes Sgs1, Sgs3, Sgs7 and Sgs8 provides the foundation for investigating the role of the various glue genes during Drosophila life.

Data for "Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states"

This deposit contains all the single-molecule trajectories reported in "Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states", Science Advances, 2023. To access the tracks, open the mat file in MATLAB. This contains a MATLAB table with the following fields: summary_table.cell_protein{i} identifies the ith dataset i.e. cell line + protein + treatment. summary_table.X{i}{j} is an Nx2 array of x and y coordinates (in microns) for track j in condition i. N is the number of localizations in that track. Time interval between localizations is 200 ms. Details on data acquisition and tracking parameters can be found in the associated manuscript.

Dataset for 'Effects of bubble plumes on lake dynamics, near-bottom turbulence, and transfer of dissolved oxygen at the sediment-water interface'

The dataset associated with the article "Effects of bubble plumes on lake dynamics, near-bottom turbulence, and transfer of dissolved oxygen at the sediment-water interface".

Data for: "Dynamics of collective motion across time and species"

This repository contains the data accompanying the paper: Papadopoulou M., Fürtbauer I., O’Bryan L., Garnier S., Georgopoulou D., Bracken A., Christensen C., and King A.J. (2022) "Dynamics of collective motion across time and species". Phil. Trans. R. Soc. B 20220068 <a href="https://doi.org/10.1098/rstb.2022.0068">https://doi.org/10.1098/rstb.2022.0068</a> This work is supported by an Office for Naval Research (ONR) Global Grant (N629092112030) awarded to AJK.

Examining the Influence of Focal Point Location on Heat Transfer Dynamics in Phase Change Material: A Dataset Publication

Dataset including experimental data from small-scale solar facade module that consists of several components: Fresnel lens; cone-shaped air gap; aerogel (semi-transparent) as insulation layer; PCM container. Variations of the experimental settings in test setups are different cone diameter (2, 3 and 4 cm) and insulation layer thickness is (3,5 and 7cm). Nine different compositions  were tested in laboratory to evaluate the ompact of focal point location. The focal point has been described with three different values that reflect its location on the inner and outer surfaces and in the middle of the PCM container. The corresponding figures can be found in the paper The Effect of Fresnel Lens Focal Point Location on Heat Transfer in Phase Change Material (PCM) Enhanced Dynamic Solar Facade. This study has been supported by Fundamental and Applied Research project ‘Smart building EnVElope with solaR Energy STorage (EVEREST)’, project No. lzp-2019/1-0363, funded by the Latvian Council of Science.