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11,506 results for “Dynamics”
In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter
<p>Structural models and MD trajectories analyzed in the original article "In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter". Topologies and trajectories were stripped of the water molecules.</p> <p>- "alphafold2" contains the c-state and m-state models obtained with alphafold2 and colabfold_advanced, respectively;</p> <p>- "slc25a20_cstate" contains the parameter/topology file (slc25a20_cstate_nowat.parm7), the MD simulations of the c-model of the slc25a20 apo protein (prod1_nowat_skip10.nc, prod2_nowat_skip10.nc), and the representative structure used to analyzed the transmembrane helices (cstate1.pdb);</p> <p>- "slc25a20_mstate" contains the parameter/topology file (slc25a20_mstate_nowat.parm7), the MD simulations of the m-state model of the slc25a20 apo protein (prod1_nowat_skip10.nc, prod2_nowat_skip10.nc), and the representative structure used to analyzed the transmembrane helices (cstate2.pdb);</p> <p>- "slc25a20_car" contains the parameter/topology file (slc25a20_carn_nowat.parm7, slc25a20_carn2_nowat.parm7), the MD simulations of the slc25a20-carnitine complex (prod1_nowat_skip2.nc, prod2_nowat_skip2.nc), and a representative structure (snapshot_slc25a20-car.pdb);</p> <p>- "slc25a20_pcar" contains the parameter/topology file (slc25a20_pcarn_nowat.parm7, slc25a20_pcarn2_nowat.parm7), the MD simulations of the slc25a20-propionylcarnitine complex (prod1_nowat_skip2.nc, prod2_nowat_skip2.nc), and a representative structure (snapshot_slc25a20-pcar.pdb).</p> <p>If you include these data in your manuscript, please cite: Pasquadibisceglie A, Quadrotta V and Polticelli F "In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter"</p>
Supplementary material 6 from: Rusch JC, Strand DA, Laurendz C, Andersen T, Johnsen SI, Edsman L, Vrålstad T (2022) Exploring the eDNA dynamics of the host-pathogen pair Pacifastacus leniusculus (Decapoda) and Aphanomyces astaci (Saprolegniales) under experimental conditions. NeoBiota 79: 1-29. https://doi.org/10.3897/neobiota.79.82793
Agent levels of Aphanomyces astaci in individuals of Pacifastacus leniusculus used in the experiment
A basic community dynamics experiment: Disentangling deterministic and stochastic processes in structuring ecological communities
<p>Community dynamics are governed by two opposed processes: species sorting, which produces deterministic dynamics leading to an equilibrium state, and ecological drift, which produces stochastic dynamics. Despite a great deal of theoretical and empirical work aiming to demonstrate the predominance of one or the other of these processes, the importance of drift in structuring communities and maintaining species diversity remains contested. Here we present the results of a basic community dynamics experiment using floating aquatic plants, designed to measure the relative contributions of species sorting and ecological drift to community change over about a dozen generations. We found that species sorting became overwhelmingly dominant as the experiment progressed, and directed communities towards a stable equilibrium state maintained by negative frequency-dependent selection. The dynamics of any particular species depended on how far its initial frequency was from its equilibrium frequency, however, and consequently the balance of sorting and drift varied among species.</p>
Online Fusion of Multi-resolution Multispectral Images with Weakly Supervised Temporal Dynamics
<p>This is the data set for experiments of satellite images of Oroville dam site in paper: Online Fusion of Multi-resolution Multispectral Images with Weakly Supervised Temporal Dynamics. Inside the zip file, there are 3 folders: 'HD-IMG-Database-Landsat-8', 'HD-IMG-Database-Landsat-8-Qest' and 'MODIS_250'.</p>
Data From: Active sinking particles: Flow and transport dynamics due to sessile suspension feeders on sinking aggregates
<p>Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in waste-water treatment plants. In both these contexts, the sinking aggregates are "active," since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories, and mass transfer to these "active sinking particles," has not previously been studied. Here we use a novel scale-free vertical-tracking microscope (a.k.a. Gravity Machine, Krishnamurthy et al. "Scale-free vertical tracking microscopy." Nature Methods (2020)) to follow model sinking aggregates (agar spheres) with attached protists (<em>Vorticella convallaria</em>), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached \vortc causes significant changes to the flow around aggregates in a dynamic manner and reshapes mass transport boundary layers. Furthermore, we find that activity-mediated local flows along with sinking modify the encounter and plume cross-sections of the aggregate and induce sustained aggregate rotations. Overall our work shows the important role of biological activity in shaping the near-field flows around aggregates with potentially important effects on aggregate fate and material fluxes.</p>
Precise dynamical masses of new directly imaged companions from combining relative astrometry, radial velocities, and HIPPARCOS-Gaia eDR3 accelerations
<p>The VLT/SPHERE reduced images using the Geneva reduction pipeline, GRAPHIC, used to obtain the astrometry and photometry as published in Rickman et al. 2022. Each .fits file has been cosmetically corrected (i.e. bad pixels), background-subtracted, and flat-fielded. These files correspond to the 'flux frames' of the imaging observing sequence that was used to calculate the astrometry and photometry for each companion. The raw data are also available on the ESO archive with the relevant program numbers as listed in Rickman et al. 2022.</p>
Explosive Cenozoic origin and diversity-dependent diversification dynamics shaped the evolution of Australian skipper butterflies
<p><span>Australia was predominantly tropical for most of the early Cenozoic, then transitioned to a cooler and drier climate in the Oligocene. In response to this increasing aridity, some lineages adapted to more xeric ecosystems, contracted, or became restricted to increasingly fragmented mesic refugia, or went extinct. Yet, the lack of macroevolutionary studies at a continental scale precludes a better understanding of Australian biodiversity patterns and processes during the Cenozoic. Here, we infer a robust dated phylogenomic tree for a radiation of Australian endemic butterflies, the Trapezitinae skippers, to test the impact of biotic and abiotic drivers on Cenozoic diversification dynamics in Australia. These butterflies originated during the Eocene (<em>ca</em>. 42 Ma) in the mesic biome of Australia. Trapezitinae exploded in diversity during a cool, dry period in the late Oligocene and early Miocene, then experienced a sharp deceleration in speciation. Xeric ecosystems appear to have been colonized more recently, supporting the hypothesis of arid and semi-arid biomes as evolutionary sinks. Temperature-dependent and phytophagy-dependent diversification models received little support. Instead, we find evidence for diversity-dependent processes with a declining diversification in Trapezitinae likely linked to limited ecological opportunities following a rapid initial burst of diversification.</span></p>
Pupillary dynamics reflect the impact of temporal expectation on detection strategy - data
<p>This repository contains data from work that investigated how humans can extract hidden temporal cues from the occurrences of probabilistic targets and utilize them to inform target detection in a complex acoustic stream, using a combination of behavioral measures and pupillometry. It accompanies the article entitled: " <strong>Pupillary dynamics reflect the impact of temporal expectation on detection strategy</strong>" from the same authors. It contains:<br> - preprocessed pupil data for all subjects<br> - similarly matched behavior data for all subjects<br> - custom code for both behavioral and pupil analysis</p>
Raw dataset for "Rehybridization dynamics into the pericyclic minimum of an electrocyclic reaction imaged in real-time"
<p>The dataset contains raw diffraction images in .tiff format. Each image file name contains three numbers, separated by "_". The first number refers to the order in which the images were taking in laboratory time. The second number refers to the absolute translation stage position in millimeters in the optical beam path of the pump beam. The stage position can be converted into a pump-probe delay time (taking into account the speed of light and a factor of 2 for the beam path, since the pulses move back and forth on the stage). Larger stage position values correspond to the optical pump pulse arriving later with respect to the probe pulse. Time zero was determined to be at 156.26 mm using a solid reference sample.</p>
Data for Sleep cycle-dependent vascular dynamics and the predicted effects on perivascular cerebrospinal fluid flow and solute transport
<p>Datasets containing derived data and results used by code in: https://github.com/AlexandraVallet/PVSflow for "Sleep cycle-dependent vascular dynamics and the predicted effects on perivascular cerebrospinal fluid flow and solute transport", Bojarskaite et al. 2023. Please see github for instructions. </p>
Data from: Observed and dark diversity dynamics over millennial time scales: Fast-life history traits linked to expansion lags of plants in northern Europe
<p>Global change drivers (e.g. climate and land use) affect the species and functional traits observed in a local site but also its dark diversity—the set of species and traits locally suitable but absent. Dark diversity links regional and local scales and, over time, reveals taxa under expansion lags by depicting the potential biodiversity that remains suitable but is absent locally. Since global change effects on biodiversity are both spatially and temporally scale dependent, examining long-term temporal dynamics in observed and dark diversity would be relevant to assessing and foreseeing biodiversity change. Here, we used sedimentary pollen data to examine how both taxonomic and functional observed and dark diversity changed over the past 14500 years in northern Europe. We found that taxonomic and functional observed and dark diversity increased over time, especially after the Late Glacial and during the Late Holocene. However, dark diversity dynamics revealed expansion lags related to species' functional characteristics (dispersal limitation and stress intolerance) and an extensive functional redundancy when compared to taxa in observed diversity. We highlight that assessing observed and dark diversity dynamics is a promising tool to examine biodiversity change across spatial scales, its possible causes, and functional consequences.</p>
Dimerization the ACE-2 with Different RBD Mounts: A Dynamic Simulation Perspective on SARS-Cov-2 Infecting Details
<p>The system construction and dynamic simulation data of paper "Dimerization the ACE-2 with Different RBD Mounts: A Dynamic Simulation Perspective on SARS-Cov-2 Infecting Details"(manuscript, ci-2023-00041c) are prepared.</p>
data for the submission in Marine Geology: Turbulence and Fine Sediment Dynamics in a Coastal Benthic Boundary Layer
<p>Data used for the plots and tables can be found in the submission in Marine Geology:Turbulence and Fine Sediment Dynamics in a Coastal Benthic Boundary Layer. The data are saved as matlab data file.</p>
Input parameters for manuscript "Understanding drug skin permeation enhancers using Molecular Dynamics Simulation"
<p>Input parameters used for Gromacs simulations in publication with title: "Understanding drug skin permeation enhancers using Molecular Dynamics Simulation"</p>
LAMMPS trajectories for "The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA"
<p><strong>LAMMPS trajectory data for:</strong><br> <strong>The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA</strong><br> Jasmine Cubuk<sup>1,2</sup>, Jhullian J. Alston<sup>1,2</sup>, J. Jeremías Incicco<sup>1,2</sup>, Alex S. Holehouse<sup>1,2</sup>, Kathleen B Hall<sup>1</sup>, Melissa D. Stuchell-Brereton<sup>1,2</sup>, Andrea Soranno<sup>1,2,*</sup></p> <p><sup>1</sup>Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110, Saint Louis, MO, USA</p> <p><sup>2</sup>Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA</p> <p><strong>Corresponding author: </strong>Andrea Soranno (soranno@wustl.edu)<br> <strong>Questions about simulations: </strong>Alex Holehouse (alex.holehouse@wustl.edu)</p> <p><strong>Preprint link: </strong><a href="https://doi.org/10.1101/2023.02.10.527914">https://doi.org/10.1101/2023.02.10.527914</a></p> <p><strong>GitHub link to simulation info:</strong> <a href="https://github.com/holehouse-lab/supportingdata/tree/master/2023/cubuk_2023">https://github.com/holehouse-lab/supportingdata/tree/master/2023/cubuk_2023</a></p> <p><strong>Funding: </strong>This research was supported by the NIH National Institute on Allergic and Infectious Diseases with R01AI163142 (to A.S., A.S.H.) and by the NIH National Cancer Institute F99CA264413 (to J.J.A.).</p> <p> </p>
Estimation of the nucleation location and rupture extent of the 1850 Xichang, Sichuan, China, earthquake by dynamic rupture simulations on a multi-segment stepover structure
<p>These datasets accompany the Zemuhe fault surface coordinates that were used for construction of the fault geometry model, the observational fault surface slip of the 1850 Xichang M 7.5 earthquake and the intensity distribution in Estimation of the nucleation location and rupture extent of the 1850 Xichang, Sichuan, China, earthquake by dynamic rupture simulations on a multi-segment stepover structure submitted to Earth and Space Science by Yu et al. (2023). The data is structured as follows:</p> <p>Once unzipped the data within the archive are six txt files: fault_surface_slip_Feng.txt, which is from Feng et al. (2000); fault_surface_slip_Ren.txt, which is from Ren and Lin (2010), fault_surface_slip_Yu.txt, which is from Yu et al., (2001); intensity.txt, which is from Feng et al. (2000); landslides.txt, which is from Guo et al. (2014) and Cao (2015); zemuhe_fault_surface_coordinates.txt, which is from Working group for geologic mapping on Zemuhe fault (2000). The file folder stress_configuration contains the initial stress setup for the model in Figure 5e.</p>
Laser Ablation Inductively Coupled Plasma Mass Spectrometric Quantification of Isotope Trace Elements in Human Carcinoma Tissue - Stochastic Dynamics and Theoretical Analysis (SUPPORTING INFORMATION)
<p>Supporting information file of publication [https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4334866]. </p>
Data for "Water dynamics in highly concentrated protein systems – insight from Nuclear Magnetic Resonance relaxometry
<p>Raw data (<sup>1</sup>H magnetization versus time) for "Water dynamics in highly concentrated protein systems – insight from Nuclear Magnetic Resonance relaxometry".</p> <p>The files include information about concentration and temperature.</p> <p><em>Int. J. Mol. Sci.</em> <strong>2023</strong>, <em>24</em>(4), 4093; https://doi.org/10.3390/ijms24044093</p> <p> </p>
Quadrupole transitions and quantum gates protected by continuous dynamic decoupling data
<p>Experimental and theoretical data for the creation of the Figures in the article: Quadrupole transitions and quantum gates protected by continuous dynamic decoupling</p>
Yu_et_al_2023_molecular_dynamics_simulation_data
<p>The molecular dynamics simulation data set accompanying Yu et al, 2023, containing (i) representative coordinates and measurements described therein, (ii) selected simulation trajectories, and (iii) LAMMPS input files.</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.