Find research datasets worth reusing

opencc-by-4.0Apr 2022View details →

Multiple same-level and telescoping nesting in GFDL's dynamical core (Grids, ICs)

Grids and ICs of the Geoscientific Model Development technical paper: Multiple same-level and telescoping nesting in GFDL's dynamical core. This paper studies the landfall of hurricane Laura (2020) and an Atmospheric river hitting California (2021) using global and regional domains with multiple same level and telescoping nested grids. Files are for the cases shown in this study: 1- Global C48 + nests 2- Global C768 + nests 3- Regional R192 + nests

opencc-by-4.0Sep 2021View details →

Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations

Raw simulations of the acylation step by PETase on a PET dimer model substrate, ran with CP2K 6.1 software at the PBE:AMBER level. Details can be found in the original manuscript (<a href="https://doi.org/10.1021/acscatal.1c03700">https://doi.org/10.1021/acscatal.1c03700</a>): Molecular topology in AMBER Parameter Topology format and Trajectories in CHARMM binary coordinate format DCD. RESIDUE LIST: GLY57 TYR58 SER131 MET132 TRP156 ASP177 SER178 ILE179 ALA180 HID208 MOL262 VMD selection: (name CA C O HA2 HA3 and resname GLY and resid 57) or (name N CA CB H HA HB2 HB3 and resname TYR and resid 58) or (name CA C O OG CB HA HB2 HB3 HG and resname SER and resid 131) or (name N CA SD CE CB CG H HA HB2 HB3 HG2 HG3 HE1 HE2 HE3 and resname MET and resid 132) or (name CB CG CD1 CD2 CE2 CE3 NE1 CZ2 CZ3 CH2 HB2 HB3 HD1 HE1 HE3 HZ2 HZ3 HH2 and resname TRP and resid 156) or (name CG OD1 OD2 CB HB2 HB3 and resname ASP and resid 177) or (name C O and resname SER and resid 178) or (name N CA C O CG2 CD1 CB CG1 H HA HB HG12 HG13 HG21 HG22 HG23 HD11 HD12 HD13 and resname ILE and resid 179) or (name N CA H HA and resname ALA and resid 180) or (name CB CG CD2 ND1 CE1 NE2 HB2 HB3 HD1 HD2 HE1 and resname HID and resid 208) or (name C1 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C2 C20 C3 C4 C5 C6 C7 C8 C9 H1 H10 H11 H12 H13 H14 H15 H16 H17 H2 H3 H4 H5 H6 H7 H8 H9 O1 O2 O3 O4 O5 O6 O7 O8 O9 and resname MOL and resid 262) PYMOL selection: (name CA+C+O+HA2+HA3 & resn GLY & resi 57) | (name N+CA+CB+H+HA+HB2+HB3 & resn TYR & resi 58) | (name CA+C+O+OG+CB+HA+HB2+HB3+HG & resn SER & resi 131) | (name N+CA+SD+CE+CB+CG+H+HA+HB2+HB3+HG2+HG3+HE1+HE2+HE3 & resn MET & resi 132) | (name CB+CG+CD1+CD2+CE2+CE3+NE1+CZ2+CZ3+CH2+HB2+HB3+HD1+HE1+HE3+HZ2+HZ3+HH2 & resn TRP & resi 156) | (name CG+OD1+OD2+CB+HB2+HB3 & resn ASP & resi 177) | (name C+O & resn SER & resi 178) | (name N+CA+C+O+CG2+CD1+CB+CG1+H+HA+HB+HG12+HG13+HG21+HG22+HG23+HD11+HD12+HD13 & resn ILE & resi 179) | (name N+CA+H+HA & resn ALA & resi 180) | (name CB+CG+CD2+ND1+CE1+NE2+HB2+HB3+HD1+HD2+HE1 & resn HID & resi 208) | (name C1+C10+C11+C12+C13+C14+C15+C16+C17+C18+C19+C2+C20+C3+C4+C5+C6+C7+C8+C9+H1+H10+H11+H12+H13+H14+H15+H16+H17+H2+H3+H4+H5+H6+H7+H8+H9+O1+O2+O3+O4+O5+O6+O7+O8+O9 & resn MOL & resi 262)

opencc-by-4.0Jul 2021View details →

Development of a Multi-Level Dynamic Model to Measure the Resilience Level of Transportation Infrastructure Networks

The recent increase in disasters is making the largest critical infrastructure system namely the transportation infrastructure system susceptible to unexpected damage. Discontinuation of services provided by transportation infrastructures will create significant societal, economic, and collateral damages. Therefore, this study aims to identify dimensions to measure the resilience of the transportation infrastructures. This study also aims to develop a model to measure the resilience of the transportation infrastructures resilience. To fulfill the aims of this study, a questionnaire was developed which was supported by a comprehensive literature review. 92 valid responses were received and analyzed qualitatively and quantitatively. Statistically significant variables were used to develop a resilience measurement tool. The developed tool will provide relative resilience measures for multiple projects which will help in identifying the most vulnerable segment of the transportation infrastructure network. Exploratory factor analysis (EFA) was performed to identify the constructs and structural equation modeling (SEM) was used to develop the model. Without previous experience in reconstruction works, handling integrated assets becomes very critical. Also, such inexperience makes it difficult to handle emergency resources properly. However, such issues regarding integrated assets can be resolved by investing in locating integrated assets away from the roadways, so if a break in a railroad crossing or utility line occurs or emergency repairs are needed, the impact on the roadway operations can be minimized. To avoid issues related to access to previous disaster data for the roadway this study suggess investing in preparing an interactive online platform for recording and reviewing data related to disasters as well as previous resilience enhancing activities for the roadway with easy access credentials. The findings of this study will support practitioners and decision-makers in investing in the appropriate resilience enhancement activity project for funding and investment.

opencc-by-4.0Feb 2022View details →

Modelling dynamic precipitation in pre-aged aluminium alloys

Calculation of precipitation kinetics under deformation This repository contains the data plotted in https://doi.org/10.1016/j.actamat.2022.118036 as well as the code used to generate them. The code can be run reading the instructions contained in README.txt

A simple method to describe the COVID-19 trajectory and dynamics in any country based on Johnson cumulative density function fitting

A simple method is utilised to study and compare COVID-19 infection dynamics between countries based on curve fitting to publicly shared data of confirmed COVID-19 infections. The method was tested using data from 80 countries from 6 continents. We found that Johnson cumulative density functions (CDFs) were extremely well fitted to the data (R2 > 0.99) and that Johnson CDFs were much better fitted to the tails of the data than either the commonly used normal or lognormal CDFs. Fitted Johnson CDFs can be used to obtain basic parameters of the infection wave, such as the percentage of the population infected during an infection wave, the days of the start, peak and end of the infection wave, and the duration of the wave's increase and decrease. These parameters can be easily interpreted biologically and used both for describing infection wave dynamics and in further statistical analysis. The usefulness of the parameters obtained was analysed with respect to the relation between the gross domestic product (GDP) per capita, the population density, the percentage of the population infected during an infection wave, the starting day and the duration of the infection wave in the 80 countries. We found that all the above parameters were significantly associated with GDP per capita, but only the percentage of the population infected was significantly associated with population density. If used with caution, this method has a limited ability to predict the future trajectory and parameters of an ongoing infection wave.

Cascading drought-heat dynamics during the 2021 Southwest United States Heatwave

In June of 2021 the southwest United States experienced a record-breaking heatwave. This heatwave came at a time when the region was in severe drought. As drought alters the surface energy budget in ways that affect lower atmosphere temperature and circulations, it is possible that the combined drought-heat event was a cascading climate hazard, in which preexisting drought exacerbated the heatwave. We apply satellite observation and numerical experiments with the Weather Research and Forecasting (WRF) model to test for land-atmosphere feedbacks during the heatwave consistent with drought influence. We find a modest positive drought-heat effect, as WRF simulations that include the drought have marginally higher air temperatures than those that exclude the initial drought conditions, with more substantial effects in wetter, forested areas. Evidence of drought-heat-drought coupled feedbacks was similarly modest in our simulations, as accounting for drought preconditioning led to a small reduction in simulated precipitation in the region. The files in this dataset are the output of our analyses and numerical modeling presented in this study.

Dataset (III) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist

MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a> Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files) dataset I: systems SRL+Co, C-100 and BAY-1797 dataset I: each file contains all branched replicas and the main replica. dataset1:  C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b). dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches. dataset I: system SRL+Co ;each file contains one main replica dataset I: system BAY-1797; each file contains one main replica dataset II:system SRL ; each file contains one main replica. dataset III:system C-100+Co (compound 100 in presence of SRC-1 coactivator) ; each file contains one main replica.

opencc-by-4.0May 2022View details →

Dynamic data of body weight and feed intake in fattening pigs and the determination of energetic allocation factors using a dynamic linear model

This is the R script (DLM_script.R) to characterize the evolution of the energetic allocation factor (αt) which represents the link between the cumulative net energy available (estimated from feed intake) and cumulative weight gain during fattening period. The data for the 100 fattening pigs are stored in the csv file (DataAxiom.csv) and structured as follows: <ul> <li>ID: pig identification number;</li> <li>Fattening_group.Pen : fattening group and pen number for a given ID;</li> <li>t (day): time in days since the transfer to fattening room;</li> <li>Wt (kg) : median weight in kg at day t for a given ID;</li> <li>FIt (kg day-1) : total feed intake in kg at day t for a given ID.</li> </ul> For detail description of the procedure please see article.

CeA Psilocin fiber photometry study: Data and custom code from experiments looking at changes in calcium dynamics in response to an air puff events

Psilocybin, and its active metabolite psilocin, have been shown to elicit rapid and long-lasting symptom improvements in a variety of affective psychiatric illnesses. However, the specific mechanisms behind these therapeutic effects remain relatively unknown. The central amygdala (CeA) is a primary output region within the extended amygdala that is heavily dysregulated in affective psychiatric disorders. Here, we utilized fiber photometry to measure changes in CeA reactivity to an aversive air puff stimulus after psilocin administration, both acutely and at varying prolonged time points. We found that administration of psilocin increased reactivity acutely in females, but not males. Additionally, we show that one dose of psilocin produced decreases in reactivity in males, but not females, 28-days post administration, with decreases seen as early as 2-days post administration. We further report stimulus-specific changes in CeA reactivity after psilocin with differential responsivity to an aversive air puff stimulus and an auditory stimulus. We also measured changes in behavioral response to the air puff stimulus and report sex differences in exploratory behavior but not threat responding or general locomotion. This study provides evidence that a single dose of psilocin can elicit sex-specific, dynamic, and enduring changes in CeA reactivity to an aversive stimulus. These data are an important step towards dissecting circuit-based mechanisms underlying the effects of psychedelics.

opencc-by-4.0Dec 2021View details →

Global annual mean Absolute Dynamic Topography of permanently ice-free Oceans 1993 to 2020

The text, data and figure disclosed are part of the manuscript “Intensification of the South Pacific Subtropical Gyre Circulation (1993–2020) Revealed by Satellite Altimetry” by Wolfgang Schneider, Freddy Hernández-Vaca, José Garcés-Vargas, and Iván Pérez-Santos, which was submitted to the Journal of Geophysical Research: Oceans   The time series presented below were generated using E.U. Copernicus Marine Service Information, namely “Absolute Dynamic Topography” which was retrieved from the following Copernicus Marine Environment Monitoring Service (CMEMS) ftp site.   ftp://my.cmems-du.eu/Core/SEALEVEL_GLO_PHY_L4_MY_008_047/cmems_obs-sl_glo_phy-ssh_my_allsat-l4-duacs-0.25deg_P1D/1993/01/

Data for "Quantum-corrected thickness-dependent thermal conductivity in amorphous silicon predicted by machine learning molecular dynamics simulations"

This is the data set for the preprint <a href="https://arxiv.org/abs/2206.07605">arXiv:2206.07605</a> [cond-mat.mtrl-sci], obtained by the GPUMD code. Here are 6 directories.     1). NEMD     2). NEPpotential     3). PDOS     4). kappa-quenchRate     5). kappa-size     6). kappa-temperature      1). NEMD directory contains calculations of ballistic conductance using NEMD method, where 6 independent cycles are run to average. 2). NEPpotential directory is the trained NEP potential. 3). PDOS directory contains phonon density of states of a-Si samples generated by the quench rate of 10^{11} K/s. 4). kappa-quenchRate directory contains HNEMD calculations of a-Si samples which are prepared using melt-quench temperature protocols with the quench rates covering from 10^{11} to 5x10^{12} K/s. In each case, 3 independent cycles are run. 5). kappa-size directory contains HNEMD calculations based on different supercells. 6 independent cycles are run. 6). kappa-temperature directory contains HNEMD calculations of a-Si samples which are prepared for different targeted temperatures using slow quench rate of 10^{11} K/s.

Turning summer into winter: nutrient dynamics, temperature, density dependence, and invasive species drive bioenergetic processes and growth of a keystone coldwater fish

A combination of global changes such as species invasions, climate change, and nutrient pollution have altered ecosystems, food webs, and the bioenergetic processes that control growth. These changes are especially pronounced in freshwater ecosystems and often lead to rapid variation in fish growth and dependent ecosystems services such as fishery yield. Understanding the mechanisms driving growth responses to environmental change is important for interpreting past dynamics and sustainably managing ecosystems. This study uses integrated bioenergetics and growth modeling to understand how nutrient dynamics, species invasions, and changing temperatures have altered growth of the keystone pelagic whitefish (Coregonus wartmanni) in Lake Constance, Germany from 1925 to 2020. Growth variation was modeled by allowing covariates to alter temperature-dependent consumption, while size-specific metabolism varied only with temperature. Consumption and growth increased strongly to a maximum with phosphorous, and this effect was stronger when intraspecific competition (measured as whitefish biomass) was low. Increasing whitefish biomass reduced growth under mesotrophic conditions, but had no effect under oligotrophic conditions. In contrast, increasing competition with invasive three-spined stickleback (Gasteosteus aculeauts) was predicted to reduce growth even under oligotrophic conditions. The invasion has effectively turned summer into winter for whitefish, with older fish ceasing to grow and younger fish losing up to 10% of their body weight during the normal growing season in subsequent years. Warming is predicted to further reduce whitefish growth due to competition with invasive stickleback, which would further alter zooplankton food availability and reduce already low fishery yields. These results demonstrate the importance of considering biotic interactions and synergistic effects in global change studies, as well as the value of mechanistic-based models for understanding effects. Similar growth responses to ecosystem change are likely within and across ecosystems, and bioenergetic models can help understand effects to support informed ecosystem management.

Extended conformational states dominate the Hsp90 chaperone dynamics

aMD and cgMD simulation trajectories for publication "Extended conformational states dominate the Hsp90 chaperone dynamics" Jussupow et al. doi: 10.1016/j.jbc.2022.102101

DNA replication dynamics during erythrocytic schizogony in the malaria parasites Plasmodium falciparum and Plasmodium knowlesi

Malaria parasites are unusual, early-diverging protozoans with non-canonical cell cycles. They do not undergo binary fission, but divide primarily by schizogony. This is a mode of replication involving asynchronous production of multiple nuclei within the same cytoplasm, culminating in a single mass cytokinesis event. The rate and efficiency of parasite replication is fundamentally important to malarial disease, which tends to be severe in hosts with high parasite loads. Here, we have studied for the first time the dynamics of schizogony in two human malaria parasite species, Plasmodium falciparum and Plasmodium knowlesi. These differ in their cell-cycle length, the number of progeny produced and the genome composition, among other factors. Comparing them could therefore yield new information about the parameters and limitations of schizogony. We report that the dynamics of schizogony differ significantly between these two species, most strikingly in the gap phases between successive nuclear replications, which are longer in P. falciparum and shorter, but more heterogenous, in P. knowlesi. In both species, gaps become longer as schizogony progresses, whereas each period of active replication grows shorter. In both species there is also extreme variability between individual cells, with some schizonts producing many more nuclei than others, and some individual nuclei arresting their replication for many hours while adjacent nuclei continue to replicate. The efficiency of schizogony is probably influenced by a complex set of factors in both the parasite and its host cell.

Imaging the onset of oscillatory signaling dynamics during mouse embryo gastrulation

A fundamental requirement for embryonic development is the coordination of signaling activities in space and time. A notable example in vertebrate embryos is found during somitogenesis, where gene expression oscillations linked to the segmentation clock are synchronized across cells in the presomitic mesoderm (PSM) and result in tissue-level wave patterns. To examine their onset during mouse embryo development, we studied the dynamics of the segmentation clock gene Lfng during gastrulation. To this end, we established an imaging setup using selective plane illumination microscopy (SPIM) that enables culture and simultaneous imaging of up to four embryos (SPIM-for- 4). Using SPIM-for-4, combined with genetically encoded signaling reporters, we detected the onset of Lfng oscillations within newly formed mesoderm at presomite stages. Functionally, using chemical inhibition and genetic mutants, we found that initial synchrony and first ~6-8 oscillation cycles occurred even when Notch-signaling was impaired, revealing similarities to previous findings made in zebrafish embryos. Finally, we show that a spatial period gradient is already present at the onset of oscillatory activity, providing a potential mechanism accounting for our observation that wave patterns build up gradually over the first oscillation cycles.

opencc-by-4.0Mar 2022View details →

Data from: Omnidirectional Manipulation of Microparticles on a Platform Subjected to Circular Motion Applying Dynamic Dry Friction Control

Data from the paper "Omnidirectional Manipulation of Microparticles on a Platform Subjected to Circular Motion Applying Dynamic Dry Friction Control" <a href="https://doi.org/10.3390/mi13050711">https://doi.org/10.3390/mi13050711</a> Currently used planar manipulation methods that utilize oscillating surfaces are usually based on asymmetries of time, kinematic, wave, or power types. This paper proposes a method for omnidirectional manipulation of microparticles on a platform subjected to circular motion, where the motion of the particle is achieved and controlled through the asymmetry created by dynamic friction control. The range of angles at which microparticles can be directed, and the average velocity were considered figures of merit. To determine the intrinsic parameters of the system that define the direction and velocity of the particles, a nondimensional mathematical model of the proposed method was developed, and modeling of the manipulation process was carried out. The modeling has shown that it is possible to direct the particle omnidirectionally at any angle over the full 2π range by changing the phase shift between the function governing the circular motion and the dry friction control function. The shape of the trajectory and the average velocity of the particle depend mainly on the width of the dry friction control function. An experimental investigation of omnidirectional manipulation was carried out by implementing the method of dynamic dry friction control. The experiments verified that the asymmetry created by dynamic dry friction control is technically feasible and can be applied for the omnidirectional manipulation of microparticles. The experimental results were consistent with the modeling results and qualitatively confirmed the influence of the control parameters on the motion characteristics predicted by the modeling. The study enriches the classical theories of particle motion on oscillating rigid plates, and it is relevant for the industries that implement various tasks related to assembling, handling, feeding, transporting, or manipulating microparticles.

opencc-zeroJul 2022View details →

Seasonal dynamics of the wild rodent faecal virome

Viral discovery studies in wild animals often rely on cross‐sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host–virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long‐term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3‐month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.

opencc-by-4.0Jul 2022View details →

Data for "The effect of a weak asthenospheric layer on surface kinematics, subduction dynamics and slab morphology in the lower mantle"

Dataset associated with the paper entitled "The effect of a weak asthenospheric layer on surface kinematics, subduction dynamics and slab morphology in the lower mantle" by Cerpa, N. G., Sigloch, K., Garel, F., Heuret, A., Davies, D. R., and Mihalynuk, M. Please, contact Nestor Cerpa (nestor.cerpa@umontpellier.fr) for additional information

opencc-by-4.0Jul 2022View details →

Molcular Dynamics Data for Therapeutic High Affinity T Cell Receptor Targeting a KRAS G12D Cancer Neoantigen

This folder contains the starting structures and input scripts required to simulate the wild-type and G12D KRAS peptide bound TCR-pHLA complexes, as performed in this study. Starting_Structures - This folder contains the amber parameter/topology files used to simulate each system (.prmtop) and the coordinates of the starting structure both as amber coordinate file (.rst) and PDB file (.pdb). MD_Inputs - This folder contains the amber MD inputs used to run the md simulations.  MMPBSA_inputs - This folder contains the input files for running MMPBSA with the MMPBSA.py script in amber. The mmpbsa.in script was used for calculating overall binding energy whereas the mmpbsa_decomp.in script was used for calculating the per-residue contribution to binding energy.