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11,506 results for “Dynamics”
Fig. 2 in Population dynamics of Prochilodus nigricans (Characiformes: Prochilodontidae) in the Putumayo River
Fig. 2. Size frequency distribution for both Prochilodus nigricans females and males in the upper Putumayo River between 2009 and 2017.
Fig. 1 in Population dynamics of Prochilodus nigricans (Characiformes: Prochilodontidae) in the Putumayo River
Fig. 1. Geographic location of the study area around Puerto Leguízamo in the Putumayo River, Colombian Amazon.
The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks
<p>Actomyosin networks give cells the ability to move and divide. These networks contract and expand while being driven by active energy-consuming processes such as motor protein walking and actin polymerization. Actin dynamics is also regulated by actin-binding proteins, such as the actin-related protein 2/3 (Arp2/3) complex. This complex generates branched filaments thereby changing the overall organization of the network. In this work, the spatiotemporal patterns of dynamical actin assembly accompanying the branching-induced reorganization caused by Arp2/3 were studied using a computational model (MEDYAN); this model simulates actomyosin network dynamics as a result of chemical reactions whose rates are modulated by rapid mechanical equilibration. We show that branched actomyosin networks relax significantly more slowly than do unbranched networks. Also, branched networks undergo rare convulsive movements, “avalanches”, that release strain in the network. These avalanches are associated with the more heterogeneous distribution of mechanically-linked filaments displayed by branched networks. These far-from equilibrium events arising from the marginal stability of growing actomyosin networks provide a possible mechanism of the “cytoquakes” recently seen in experiments.</p>
Figures for "Simultaneous Observation of Nuclear and Electronic Dynamics by Ultrafast Electron Diffraction"
<p>This is the data underlying figures for the manuscript "Simultaneous Observation of Nuclear and Electronic Dynamics by Ultrafast Electron Diffraction". Data is kept in MATLAB .mat format.</p>
Dataset in the manscript titiled Magnetic field effect on plume dynamics and optical emission of laser-produced tungsten plasma in vacuum
<p>This is the data in the manuscript titiled "Magnetic field effect on plume dynamics and optical emission of laser-produced tungsten plasma in vacuum"submitted to POP </p>
3-Dimensional Organization and Dynamics of the Microsporidian Polar Tube Invasion Machinery
<p>These are additional videos for the <strong>3-Dimensional Organization and Dynamics of the Microsporidian Polar Tube Invasion Machinery </strong>manuscripts. There are 6 separate zip files. The description of each file is listed below.</p> <p><strong>1. Incomplete PT germination:</strong> contains incomplete PT germination videos of <em>A. algerae, E. hellem,</em> and <em>E. intestinalis</em> (3 videos for each species)</p> <p><strong>2. Nuclear live-cell imaging: </strong>contains 3 videos of nuclear movement inside <em>A. algerae</em> spores, and 7 videos for nuclear translocation through the PT</p> <p><strong>3. PT germination of <em>A. algerae</em>: </strong>contains 20 videos of the complete PT germination from<em> A. algerae</em></p> <p><strong>4. PT germination of <em>E. hellem</em>:</strong> contains 20 videos of the complete PT germination from <em>E. hellem</em></p> <p><strong>5. PT germination of <em>E. intestinalis</em>:</strong> contains 20 videos of the complete PT germination from <em>E. intestinalis</em></p> <p><strong>6. Shrinkage of the <em>E. hellem</em> PT:</strong> contains 20 videos of the PT shrinkage events observed in <em>E. hellem</em></p>
CESM coupled simulation dataset with new (Mod_cp) and original (F09) dynamical coupling scheme from atmosphere, ocean and ice.
<p>1. Coupled models simulate air-sea interaction by coupling components models together. However, in state-of-the-art models such as CESM, the atmospheric model contains dynamic core and physic parameterization that are not differentiated during air-sea interaction. The dynamics-physics (D-P) coupling in CAM causes the prognostic winds of the dynamic core be interpolated onto non-staggered locations. We propose a new dynamical coupling scheme (denoted as Mod_cp) that eliminates the extra interpolation during D-P coupling for the atmosphere-ocean interaction, reducing the numerical diffusion during the dynamics-physics coupling for air-sea interactions.</p> <p>2. Using new and original dynamical coupling scheme, two coupled simulations (100 years) were conducted. Climatology of atmosphere (cam), ocean (ocn) and sea ice (ice) model simulations are archived here (last 50 years). The resolution is around 1 latitude x 1 longitude.</p> <p>3. B1850_mod_cp denotes the simulation with new dynamical coupling scheme, B1850_f09_g16 denotes the simulation with original scheme.</p>
All Atom Molecular Dynamics Simulations of Ritonavir at the Binding Pocket of SARS-CoV2 Main Protease
<p>Data includes all of the trajectories (2000) of classical all-atom molecular dynamics (MD) simulations of ritonavir at the binding pocket of SARS-CoV2 main protease target. In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained by Glide/SP docking program. Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 ns production run was performed for the simulation.</p> <p> </p>
Dynamic representation of Höfler diagram
<p>Höfler Diagram in flash format (.exe). Classical representation of cell water potential, osmotic potential and wall pressure in a dynamic view during a cell loosing water. </p>
Investigating the dynamics of microbial consortia in spatially structured environments - Source Data
<p>Source data and model code for the following publication:</p> <p><strong>Investigating the dynamics of microbial consortia in spatially structured environments</strong></p>
Local structure and dynamics in methylammonium, formamidinium and cesium tin(II) mixed−halide perovskites from 119Sn solid−state NMR
<p>Raw and processed NMR data in Bruker Topspin format</p>
Dynamical network analysis reveals key microRNAs in progressive stages of lung cancer
<p>This repository contains clinical data of LUAD samples (phnotype.csv; TCGA-LUAD.survival.tsv), microRNA targets data of RNAs-RNAs relationships (mirna-lnc.txt; mirna-mrna.csv), and RNAs expression data of LUAD (ENSG_ID.txt; ENSG_ID_LNC.txt; idMap.data; TCGA-LUAD.htseq_fpkm.tsv; TCGA-LUAD.mirna.tsv) used in <em>Dynamical network analysis reveals key microRNAs in progressive stages of lung cancer</em>.</p> <p> </p>
All Atom Molecular Dynamics Simulations of inhibitor N3 at the binding pocket of SARS-CoV2 Main Protease (PDB ID: 6LU7)
<p>Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of inhibitor N3 at the binding pocket of SARS-CoV2 main protease target (PDB ID: 6LU7). In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained from RCSB PDB (PDB ID: 6LU7). Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 100 ns production run was performed for the simulations.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (with unbound ligand)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer with unbound ligands. Simulation starts from the crystal pose (PDB: 5FII) and is motivated by this paper:</p> <p>Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Data from: Estimating dispersal and evolutionary dynamics in diploporan blastozoans (Echinodermata) across the Great Ordovician Biodiversification Event
<p><b>Echinoderms make up a substantial component of Ordovician marine invertebrates, yet their speciation and dispersal history as inferred within a rigorous phylogenetic and statistical framework is lacking. We use Biogeographic Stochastic Mapping (BSM; implemented in the R package BioGeoBEARS) to infer ancestral area relationships and the number and type of dispersal events through the Ordovician for diploporan blastozoans and related species. The BSM analysis was divided into three time slices to analyze how dispersal paths changed before and during the Great Ordovician Biodiversification Event (GOBE) and within the Late Ordovician mass extinction intervals. The best-fit biogeographical model incorporated jump dispersal, indicating this was an important speciation strategy. Reconstructed areas within the phylogeny indicate the first diploporan blastozoans likely originated within Baltica or Gondwana. Dispersal, jump dispersal, and sympatry dominated the BSM inference through the Ordovician, while dispersal paths varied in time. Long-distance dispersal events in the Early Ordovician indicate distance was not a significant predictor of dispersal, whereas increased dispersal events between Baltica and Laurentia are apparent during the GOBE, indicating these areas were important to blastozoan speciation. During the Late Ordovician, there is an increase in dispersal events among all paleocontinents. The drivers of dispersal are attributed to oceanic and epicontinental currents. Speciation events plotted against geochemical data indicate that blastozoans may not have responded to climate cooling events and other geochemical perturbations, but additional data will continue to shed light into the drivers of early Paleozoic blastozoan speciation and dispersal patterns.</b></p>
Hippocampal CA1 pyramidal cell demonstrating dynamic mode switching (Berteau & Bullock 2020)
<p>Zenodo record for Berteau Bollock 2020 model on github and modeldb:</p> <p>The code for Berteau & Bullock 2020 is available on github</p> <p><a href="https://github.com/ModelDBRepository/245071">https://github.com/ModelDBRepository/245071</a></p> <p>and ModelDB</p> <p><a href="https://modeldb.yale.edu/245071">https://modeldb.yale.edu/245071</a></p>
Uncovering dryland woody dynamics using optical, microwave, and field data: Prolonged above-average rainfall paradoxically contributes to woody plant die-off in the western Sahel
<p>Data accompanying the paper:</p> <p>Bernardino, P., Brandt, M., De Keersmaecker, W., Horion, S., Fensholt, R., Storms, I., Wigneron, JP., Verbesselt, J. and Somers, B. 2020. Uncovering dryland woody dynamics using optical, microwave, and field data: Prolonged above-average rainfall paradoxically contributes to woody plant die-off in the western Sahel. <em>Remote Sensing</em>, 12(14), 2332.</p>
Data from: Cerebrospinal fluid dynamics disorders: relationship to Alzheimer biomarkers and cognition
Objectives: To determine the frequency high-convexity tight sulci (HCTS) in a population based sample and whether the presence of HCTS and related features influenced participants' cognitive status and classification within the new Alzheimer-biomarker framework. Methods: We analyzed 684 participants, ≥50, enrolled into the prospective population-based Mayo Clinic Study of Aging, who underwent structural MRI, amyloid PET imaging, and tau- PET imaging. A fully automated machine-learning algorithm that had been developed previously in-house was used to detect neuroimaging features of HCTS. Based on PET and MRI measures, participants were classified as having normal (A−) or abnormal (A+) amyloid, normal (T−) or abnormal (T+) tau, and normal (N−) or abnormal (N+) neurodegeneration. The neuropsychological battery assessed domain-specific and global cognitive scores. Gait speed also was assessed. Analyses were adjusted for age and sex. Results: 45/684 participants (6.6%) were classified with HCTS based on the automated algorithm. Patients with HCTS were older than patients without HCTS (mean [SD], 78.0 [8.3] vs 71.9 [10.8] years; P<.001). More were cognitively impaired after age and sex adjustment (27% vs 9%; P=.005). Amyloid PET status was similar with and without HCTS, but tau PET SUVR was lower for those with HCTS after age and sex adjustment (P<.001). Despite a lower tau SUVR, HCTS patients had lower Alzheimer disease (AD) signature cortical thickness. Using the AT(N) framework, HCTS was overrepresented in the T−(N)+ group, regardless of amyloid status. Conclusions: The HCTS pattern represents a definable subgroup of non-AD pathophysiology (i.e., T−[N]+) that is associated with cognitive impairment. HCTS may confound clinical and biomarker interpretation in AD clinical trials.
Data set for "Dynamic perceptual feature selectivity in primary somatosensory cortex upon reversal learning"
<p>This repository contains the data used to generate the figures and well as the main codes that were used for analyses.</p>
Complementary data to "Molecular dynamics trajectories for 630 drug-membrane potentials of mean force"
<p>Missing data from "Molecular dynamics trajectories for 630 drug-membrane potentials of mean force"</p> <p>Hoffmann, Christian; Centi, Alessia; Menichetti, Roberto; Bereau, Tristan (2020): Molecular dynamics trajectories for 630 drug-membrane potentials of mean force. figshare. Collection.</p> <p>https://doi.org/10.6084/m9.figshare.c.4641551.v1</p> <p>Includes:</p> <ul> <li>'bsResult.xvg' of DIM_P2-P3 in DLPC</li> </ul>
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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.