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11,506 results for “Dynamics”
First-passage probability estimation of high-dimensional nonlinear stochastic dynamic systems by a fractional moments-based mixture distribution approach
<p>First-passage probability estimation of high-dimensional nonlinear stochastic dynamic systems is a significant task to be solved in many science and engineering fields, but remains still an open challenge. The present paper develops a novel approach, termed ‘fractional moments-based mixture distribution’, to address such challenge. This approach is implemented by capturing the extreme value distribution (EVD) of the system response with the concepts of fractional<br> moment and mixture distribution. In our context, the fractional moment itself is by definition a high-dimensional integral with a complicated integrand. To efficiently compute the fractional moments, a parallel adaptive sampling scheme that allows for sample size extension is developed using the refined Latinized stratified sampling (RLSS). In this manner, both variance reduction and parallel computing are possible for evaluating the fractional moments. From the knowledge<br> of low-order fractional moments, the EVD of interest is then expected to be reconstructed. Based on introducing an extended inverse Gaussian distribution and a log extended skew-normal distribution, one flexible mixture distribution model is proposed, where its fractional moments are derived in analytic form. By fitting a set of fractional moments, the EVD can be recovered via the proposed mixture model. Accordingly, the first-passage probabilities under different<br> thresholds can be obtained from the recovered EVD straightforwardly. The performance of the proposed method is verified by three examples consisting of two test examples and one engineering problem.</p>
Dynamic interactome of the MHC I peptide loading complex in human dendritic cells - Source Ib
<p>Source data underlying MS data set (Fig.1). Datafile comprises MaxQuant output files.</p>
Tidal channel formation in a rapidly invaded micro-tidal marsh: the role of dynamic vegetation pattern and concurrent channel deepening
<p>The channel formation during the spartina alterniflora invasion influenced by vegetation pattern dynamic and concurrent channel deepening.</p>
Data for Pump–probe x-ray microscopy of photo-induced magnetization dynamics at MHz repetition rates
<p>Datasets and analysis scripts used in publication: Gerlinger et al., <em>Pump–probe x-ray microscopy of photo-induced magnetization dynamics at MHz repetition rates</em></p>
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations: Simulations Topology, Coordinate, Parameters, Input and Output files
<p>The simulation data for the article: Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.</p> <p>ck_metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations with different c(K+), which are newly added runs for resubmission. The corresponding script files and Plumed files are in GitHub.</p> <p>eq_mini.tar.gz: Includes the parameter files required for the equilibration and minimization protocol.</p> <p>standard_md.tar.gz: Includes the topology files and coordinate files for all systems built in the article. Also include the hbfix parameters file required on the MD run, and the MD script file.</p> <p>metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations. The corresponding script files and Plumed files are in GitHub.</p> <p>metad*fe*.tar.gz: Plumed HILLS files and metad.bias data used for drawing the free energy landscapes.</p> <p>ions.tar.gz: Data used for Figure.3 in the manuscript</p> <p>si_data.tar.gz: All data used for SI figures.</p>
Data for: Global change risks a threatened species due to alteration of predator-prey dynamics
<p>Datasets generated and analyzed within the study area located in the Côte-Nord region of Québec, Canada. To identify species-specific movement rules that were implemented in the IBM, we used empirical data collected for caribou, moose, and wolves over the study area.</p> <p>"DataFinal_SSF_Species_season.csv" (6 files) were used to develop Step Selection Functions for caribou, moose, and wolves to assess habitat selection. <span>SSFs</span><span> were estimated from data for the real animals and provide the relative probability of selection among a set of options based on the comparison of observed and random steps (i.e., the linear segment between successive locations at 8-h interval) using conditional</span><span> logistic regression </span><span>(Fortin et al. 2005). Details on GPS data and SSF models can be found in the article in Appendix S1: Section S2. </span></p> <p>SSFs compare resource characteristics of observed (scored 1) and random (scored 0) locations presented in column case. Habitat characteristics (columns conif_dense, conif_open, mixed, open, other, fire010, fire1020, fire20, cut010, cut1020, cut20) was extracted from the Canadian National Forest Inventory (NFI) forest cover maps. Land cover maps were updated every year by adding roads, recent (<5 years), regenerating (6–20 years) and old (21–50 years) cutblocks/fires based on information provided annually by local forestry companies and from the Canadian National Fire Database (CNFDB). Columns dist0_0.25, dist0.25_0.50, dist0.5_1.00, dist1.00_1.5, and dist1.5 are a set of 5 dichotomous covariables representing the classes of distance to the nearest road (i.e., 1) ≤250 m, 2) 251–500 m, 3) 501–1000 m, 4) 1001–1500 m and 5) >1500 m as the reference category).</p> <p>"DataFinal_IBM_Caribou_Season.csv" (2 files) corresponded to the IBM outputs with the proportion of caribou agent killed (Prop.Caribou_killed, number of caribou killed/total number of caribou), in function of the different scenarios (CC,LUC,Year,Season,Scenario) and the response (Behavioral-Numerical responses or Behavioral response). The columns Prop.CutsRoads, Prop.Fire, Prop.Broadleaf, Homogenization, Isolation correspond to the different variable we tested to predict the cumulative impact of anthropogenic disturbance and climate change. To explore how changes in forest structure and composition impacted the proportion of caribou killed, we used the proportion of areas disturbed by cuts and roads (Prop.CutsRoads), burned areas (Prop.Fire), and landscape characteristics, such as the proportion of deciduous vegetation (Prop.Broadleaf), landscape homogenization (Homogenization) and isolation (Isolation) of mature conifer stands.</p>
Data set for graphene/GO polymer molecular dynamics simulation
<p>Lammps input files and log files for molecular dynamics simulations of graphene and graphene-oxide nano ribbons for paper "Molecular dynamics reveals the origin of the enhancement of polymer properties by graphene". Log files include stress-strain behaviour during uniaxial strain. </p> <p> </p>
Single-cell RNA sequencing of Sox17-expressing lineages reveals distinct gene regulatory networks and dynamic developmental trajectories
<p>Two seurat objects contains single-cell RNA sequencing data that captures <em>Sox17</em>-expressing lineages during embryogenesis.</p> <p>sox17_integrated_Figure2B.rds :</p> <p>This is a seurat object that contains single-cell RNA sequencing data from integration of GFP+ cells produced from <em>Sox17<sup>GFPCre</sup></em> allele marking cells that currently express <em>Sox17</em> or short-term progeny of <em>Sox17­-</em>expressing progenitors and TdTomato+ cells produced from <em>R26<sup>LSL.TdTomato</sup></em> reporter allele in the presence of <em>Sox17<sup>GFPCre</sup></em> marking long-term progeny of <em>Sox17</em>-expressing progenitors. Inferred cell types in this seurat object reflects Figure 2B in the article.</p> <p>sox17_Prox1_endoderm_Figure5A.rds :</p> <p>This is a seurat object that contain single-cell RNA sequencing data from integration of <em>Sox17</em>- and <em>Prox1</em>-expressing endoderm dataset. Prox-1 expressing endoderm data is from the Willnow et al. <em>Nature</em>(2021). Inferred cell types in this seurat object reflects Figure 5A in the article.</p>
Brief Communication: Monitoring active layer dynamic using a lightweight nimble Ground-Penetrating Radar system. A laboratory analog test case
<p>GPR dataset from Leger et al., 2023 (https://tc.copernicus.org/preprints/tc-2022-214/)</p> <p> </p>
Charge Transport in Water-NaCl Electrolytes with Molecular Dynamics Simulations
<p>LAMMPS input-file, and log-files used in "Charge Transport in Water-NaCl Electrolytes with Molecular Dynamics Simulations"</p> <p> </p> <p>DOI: 10.1021/acs.jpcb.2c08047</p>
Data from: The Reissner fiber under tension in vivo shows dynamic interaction with ciliated cells contacting the cerebrospinal fluid
<p>The Reissner fiber (RF) is an acellular thread positioned in the midline of the central canal that forms together with cerebrospinal fluid (CSF)-contacting neurons (CSF-cNs) an axial sensory system detecting curvature in the spinal cord. How these components interact is unknown. Using <em>in vivo</em> imaging in larval zebrafish, we show that RF is under tension and resonates dorsoventrally. Focal RF ablations trigger retraction and relaxation of the fiber cut ends, with larger retraction speeds for rostral ablations. We built a mechanical model that estimates RF stress diffusion coefficient at 10 mm<sup>2</sup>/s and reveals that tension builds up rostrally along the fiber. After RF ablation, CSF-cN spontaneous activity decreased and ciliary motility changed, suggesting physical interactions between RF and cilia projecting into the central canal. We observed that motile cilia were caudally-tilted and frequently interacted with RF. We propose that the numerous ependymal motile monocilia contribute to RF heterogenous tension via weak interactions. Our work demonstrates that under tension, the Reissner fiber dynamically interacts with motile cilia generating CSF flow and spinal sensory neurons.</p>
Dynamics of the temperature of the leather tissue weldability during storage for 15 days after salting in the experimental curing mixture and in the control curing liquid
<p>Dynamics of the temperature of the leather tissue weldability during storage for 15 days after salting in the experimental curing mixture and in the control curing liquid</p>
Empirical Dataset of 1200 hours of Experiment: Reliability and Performance Measurements of Dynamic Routing Applications
<p>This artifact presents the empirical measurements of an experiment with 1200 hours of runtime. We repeated the experiment 200 runs, each for 6 hours. The data folder provides the empirical data, and the plots folder gives the distribution of reliability and performance measurements in 200 runs. </p> <p><strong>For reliability</strong>, we simulate component crashes and measure the request loss. To simulate component crashes, we generate a random number for each service and router and stop the docker container if the generated number is below a crash probability (0.5% in this study). </p> <p><strong>For performance</strong>, we consider the round-trip time of requests going through several services until the requests are processed.</p> <p>The experiment cases are: </p> <p>Four levels of call frequency <span class="math-tex">\(cf\)</span>: 10, 25, 50, 100 requests/second (r/s)</p> <p>Three levels of service: 3, 5, 10<br> the number of services <span class="math-tex">\(n_{serv}\)</span> in a call sequence</p> <p>Three architectures: <br> Central Entity (CE): one router <span class="math-tex">\(n_{rout} = 1\)</span><br> Dynamic Routers (DR): three routers <span class="math-tex">\(n_{rout} = 3\)</span><br> Sidecar Architecture (SA): 1 router per service <span class="math-tex">\(n_{rout} = n_{serv}\)</span></p>
Joshi et al 2023: Dynamic synchronization between hippocampal representations and stepping
<p>Data and code accompanying Joshi et al 2023, 'Dynamic synchronization between hippocampal representations and stepping'. Please contact Abhilasha Joshi (abhilasha.joshi@ucsf.edu) with any questions.</p>
Quaternary diversity dynamics of Australian reptiles - Electronic supplement
<p>Supplement paper 2</p> <p><em>Electronic data files</em></p> <p>File ES2.1 - Metadata for the included specimens (.xlsx)</p> <p>File ES2.2 – Folder containing surface models (.ply) of the crania of the included specimens, landmark pairs, and sliding landmark data</p> <p>File ES2.3a – 3D landmark coordinates of maxillae (.tps)</p> <p>File ES2.3b – 3D landmark coordinates of maxillae (missing data estimated, curves equidistant) (.tps)</p> <p>File ES2.4a – 3D landmark coordinates of frontals (.tps)</p> <p>File ES2.4b – 3D landmark coordinates of frontals (missing data estimated, curves equidistant) (.tps)</p> <p>File ES2.5 – R code for evaluating landmark estimation (.R)</p> <p>File ES2.6 – R code for estimating effects of sample size (.R)</p> <p>File ES2.7 – R code for estimating effects of missing landmarks (.R)</p> <p>File ES2.8 – Results of landmark estimation performance analyses (.csv)</p> <p>File ES2.9 – Pairwise Procrustes distances of different groupings and CVA results (maxillae; .xlsx)</p> <p>File ES2.10 - Pairwise Procrustes distances of different groupings and CVA results (frontals; .xlsx)</p> <p>File ES2.11 - Pairwise Procrustes variances of different groupings (maxillae; .xlsx)</p> <p>File ES2.12 - Pairwise Procrustes variances of different groupings (frontals; .xlsx)</p> <p>File ES2.13 – Results of sample size analyses (.csv)</p> <p>File ES2.14 – Results of missing landmarks analyses (.csv)</p> <p>File ES2.15 – Results of estimation vs. deletion analyses (.xlsx)</p> <p> </p> <p>Supplement paper 3</p> <p><em>Electronic data files</em></p> <p>File ES3.1 – Metadata for the included specimens (.csv)</p> <p>File ES3.2 – Folder containing landmark file (.tps) and bilateral landmark pairs (.txt)</p> <p>File ES3.3 – Metadata for the specimens included in compactness analyses and results of the compactness measurements (.csv)</p> <p>File ES3.4 – ImageJ Macro for measuring vertebral compactness (.ijm)</p> <p>File ES3.5 – Accuracy of classifications using CVA (.xlsx)</p> <p>File ES3.6 – Results of Procrustes ANOVAs testing for influences of taxonomic groupings, size, and the interaction of grouping and size on vertebral shape (.txt)</p> <p>File ES3.7– Typicality probabilities of fossils belonging to extant species (.xlsx)</p> <p>File ES3.8 – Procrustes distances between fossils of different sites / groupings and extant species (.xlsx)</p> <p>File ES3.9 – Procrustes variance in juvenile versus adult specimens (.xlsx)</p> <p>File ES3.10 – Phylogenetic signal of shape results (.txt)</p> <p>File ES3.11 – Results of the trajectory analyses (.xlsx)</p> <p> </p> <p>Supplement paper 4</p> <p><em>Electronic data files</em></p> <p>File ES4.1 – Metadata for tissue specimens and data for correlation analyses (.csv)</p> <p>File ES4.2 – Folder containing surface models (.ply) of the included crania</p> <p>File ES4.3 – Metadata for alcohol specimens (maxillae) (.csv)</p> <p>File ES4.4 – Metadata for alcohol specimens (<em>Rankinia</em> maxillae) (.csv)</p> <p>File ES4.5 – Metadata for alcohol specimens (<em>Rankinia</em> crania) (.csv)</p> <p>File ES4.6 – 3D landmark coordinates of maxillae (.tps)</p> <p>File ES4.7 – Folder containing 3D landmark files and landmark pairs of population cluster analyses</p> <p>File ES4.8 – Procrustes distances between genera means, plus statistics (.xlsx)</p> <p>File ES4.9 – R code for evaluating landmark estimation (.R)</p> <p>File ES4.10 – Occurrence points used for creating the niche models (.csv)</p> <p>File ES4.11 – Folder containing SNAPP tree files (.trees) and log files (.log) of the 4 SNAPP runs</p> <p>File ES4.12 – Model outputs of SSDM ensemble models using different GCMs (.xlsx)</p> <p> </p> <p>Supplement paper 5</p> <p><em>Electronic data files</em></p> <p>File ES5.1 – Supplementary references (.docx)</p> <p>File ES5.2 – Body size, microhabitat and spiny tail data of the 2877 squamate species used in the study (.csv)</p> <p>File ES5.3 – Tree file (.tre)</p> <p>File ES5.4 – Results of the D statistic (.csv)</p> <p>File ES5.5 – Results of the fitPagel funtion (.csv)</p> <p>File ES5.6 – Phylogenetic ANOVA results (spiny tails vs microhabitat) (.csv)</p> <p>File ES5.7 – Phylogenetic ANOVA results (spiny tails vs. body size) (.csv)</p> <p>File ES5.8 – Phylogenetic logistic regression results (.csv)</p> <p>File ES5.9 – Phylogenetic ANOVA results (microhabitat vs body size) (.csv)</p> <p>File ES5.10 – Results of the HiSSE models (.csv)</p>
Data supporting "COMBI-Tweez: high-precision single-molecule mechanical manipulation and imaging for dynamic chiral biopolymers"
<p>Experimental data for our paper on COMBI-Tweez</p>
How does thermal pressurization of pore fluids affect 3D strike-slip earthquake dynamics and ground motions?
<p>BSSA-TP-31Mar2023-zenodo.tar.gz has all the input files required to simulate forty-nine dynamic rupture models. Note that "SeisSol_release_generatedKernels_dhsw_hybrid_none_9_5" and "TP-3D-final_withXML" are SeisSol executable (compiled on Shaheen II at KAUST) and mesh files respectively. Every simulation folder should have empty "logs" and "output" folders where simulation outputs will be stored.</p>
The Vegetation Dynamics in Response to Cooling Events from the Medieval Warm Period to the Little Ice Age in Southeast China
<p>Full palynological dataset from three-peats (Wangdongyang peat bog: WDY, 27°40′48″N、119°38′15″E, elevation: 1303 m; Xiyaohu peat bog: XYH15, 28°44′N, 115°40′E, elevation: 735m and XYH14 is close to XYH15; Yuhuashan peat bog: YHS2, 27°50′29″N, 115°38′54.98″E, elevation: 882 m) in the southeast of China.</p> <p>The dataset contains raw counts for pollen and ferns.</p>
SNP table and metadata for: Geographically consistent hybridization dynamics between the Black-crested and Tufted Titmouse with evidence of hybrid zone expansion
<p>We studied hybridization between the Black-crested and Tufted titmouse across two geographically distinct transects that differ in the timing of secondary contact by hundreds to thousands of years. We found that hybridization patterns correspond to localized hybrid swarms and that the titmouse hybrid zone is likely slowly expanding over time, a product of short post-natal dispersal distances coupled with weak or absent selection against admixture.</p>
Ultrafast formation dynamics of D3+ from the light-driven bimolecular reaction of the D2-D2 dimer
<p>All the raw data for the main figures of our literature of "Ultrafast formation dynamics of D<sub>3</sub><sup>+</sup> from the light-driven bimolecular reaction of the D<sub>2</sub>-D<sub>2</sub> dimer". Molecular dynamics trajectories and the initial configurations are supplied.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.