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11,506 results for “Dynamics”
Temporal dynamics of mother-offspring relationships in Bigg's killer whales: opportunities for kin-directed help by post-reproductive females
<p>Age-related changes in the patterns of local relatedness (kinship dynamics) can be a significant selective force for shaping the evolution of life history and social behaviour. In humans and some species of toothed whales, average female relatedness increases with age which can select for a prolonged post-reproductive lifespan in older females due to both the costs of reproductive conflict and the benefits of late-life helping of kin. Killer whales (<em>Orcinus</em> <em>orca</em>) provide a valuable system for exploring social dynamics related to such costs and benefits in a mammal with an extended post-reproductive female lifespan. We use >40 years of demographic data to investigate the opportunities for helping and harming in the mammal-eating Bigg's killer whale by quantifying how mother-offspring social relationships change with offspring age. Our results suggest a high degree of male philopatry and female-biased budding dispersal in Bigg's killer whales, with some variability in the dispersal rate for both sexes. These patterns of dispersal provide opportunities for late-life helping of particularly adult sons, while partly mitigating the costs of mother-daughter reproductive conflict. This is an important step towards understanding the evolution of menopause in the few species it occurs.</p>
Efficient GPU Offloading with OpenMP for a Hyperbolic Finite Volume Solver on Dynamically Adaptive Meshes
<p>We identify and show how to overcome an OpenMP bottleneck in the administration of GPU memory. It arises for a wave equation solver on dynamically adaptive block-structured Cartesian meshes, which keeps all CPU threads busy and allows all of them to offload sets of patches to the GPU. Our studies show that multithreaded, concurrent, non-deterministic access to the GPU leads to performance breakdowns, since the GPU memory bookkeeping as offered through OpenMP's map clause, i.e., the allocation and freeing, becomes another runtime challenge besides expensive data transfer and actual computation. We, therefore, propose to retain the memory management responsibility on the host: A caching mechanism acquires memory on the accelerator for all CPU threads, keeps hold of this memory and hands it out to the offloading threads upon demand. We show that this user-managed, CPU-based memory administration helps us to overcome the GPU memory bookkeeping bottleneck and speeds up the time-to-solution of Finite Volume kernels by more than an order of magnitude.</p>
Data and Code for Blaszczak et al. 2023, Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience
<p>Data and code for analyses in Blaszczak et al. 2023, Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience.</p> <p>See publication and ReadMe file for analysis description and further details. </p> <p>bioRxiv pre-print: Blaszczak, J.R., Yackulic, C., Shriver, R., & R.O. Hall, Jr. 2023. Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience. https://doi.org/10.1101/2023.04.11.535773</p>
Spatio-temporal Dynamics of Coworking Spaces Development: The Case of Selected Central European Capitals
<p>The dataset provides geolocation coordinates and years of activity of coworking spaces in the selected Central European capitals - Bratislava, Budapest, Prague, and Warsaw.</p>
Cortex-wide neural dynamics predict behavioral states and provide a neural basis for resting-state dynamic functional connectivity
<p><strong>GENERAL INFORMATION</strong></p> <p>This data is described in the following publication: </p> <p><strong>Cortex-wide neural dynamics predict behavioral states and provide a neural basis for resting-state dynamic functional connectivity</strong>, Somayeh Shahsavarani<sup>1,2,5</sup>, David N. Thibodeaux<sup>1,5</sup>, Weihao Xu<sup>1</sup>, Sharon H. Kim<sup>1</sup>, Fatema Lodgher<sup>1</sup>, Chinwendu Nwokeabia<sup>1</sup>, Morgan Cambareri<sup>1</sup>, Alexis J. Yagielski<sup>1</sup>, Hanzhi T. Zhao<sup>1</sup>, Daniel A. Handwerker<sup>2</sup>, Javier Gonzalez-Castillo<sup>2</sup>, Peter A. Bandettini<sup>2,3</sup>, Elizabeth M. C. Hillman<sup>1,4,6,*</sup> Cell Reports (2023): <a href="https://doi.org/10.1016/j.celrep.2023.112527">https://doi.org/10.1016/j.celrep.2023.112527</a></p> <p><br> 1. Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Biomedical Engineering, Columbia University, New York, NY, USA<br> 2. Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA<br> 3. Functional MRI Core Facility, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA<br> 4. Department of Radiology, Columbia University Irving Medical Center, New York, NY, USA<br> 5. These authors contributed equally<br> 6. Lead contact<br> *Correspondence: elizabeth.hillman@columbia.edu</p> <p>Preprocessing and analysis code that generated / can be used with this data is posted at: <br> GitHub: <a href="https://doi.org/10.5281/zenodo.7860561">https://doi.org/10.5281/zenodo.7860561</a></p> <p><strong>DATA OVERVIEW </strong></p> <p>This dataset comprises simultaneous neuronal and hemodynamic data collected using wide-field optical mapping (WFOM) techniques. The data were obtained from head-fixed mice that were allowed to behave spontaneously without any external stimulation. For more detail, please refer to the Readme file.</p>
A climatology of thermodynamic vs. dynamic Arctic wintertime sea ice thickness effects during the CryoSat-2 era: Data
<p>Data for:</p> <p>Anheuser, J., Liu, Y., and Key, J.: A climatology of thermodynamic vs. dynamic Arctic wintertime sea ice thickness effects during the CryoSat-2 era, submitted to: The Cryosphere. 2022</p> <p>Code can be found at:</p> <pre>https://doi.org/10.5281/zenodo.7987926</pre>
Dynamic light scattering datasets used to assess the Raynals software
<p>Updated - 23/04/2023<br> This folder contains the associated data from Burastero et al., 'Raynals, an online tool for the analysis of dynamic light scattering'</p> <p>The experimental datasets can be found at ./experimentalData/<br> The artificially generated datasets at ./SimulatedDataDLS_case1 and ./SimulatedDataDLS_case2</p> <p>To produce the experimental datasets, we performed measurements on Carbonic Anhydrase, Bovine Serum Albumin, Gold Nanoparticles, and three in-house samples: A protein with a beta-Propeller domain, a coiled-coil like protein, and an intrinsically disordered protein.</p> <p>Additionally, you'll find R scripts to generate Fig. 3, Fig. 5, and Fig. S1 to S4.<br> </p>
Datasets for Work "Predicting Pulsed-Laser Deposition SrTiO3 Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction"
<p>RHEED raw dataset and Gaussia fitting parameter dataset for samples "treated_213nm", "treated_81nm" and "untreated_162nm" in the work "Predicting Pulsed Laser Deposition SrTiO<sub>3 </sub>Homoepitaxy Growth Dynamics using High-Speed Reflection High-Energy Electron Diffraction."</p>
Extended ensemble molecular dynamics study of ammonia–cellulose I complex crystal models: free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase.
<p>The data deposited here accompany the manuscript "Extended ensemble molecular dynamics study of ammonia–cellulose I complex crystal models: free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase" and include the molecular dynamics trajectories and the AMBER topology (parm) files. Detailed file contents are summarized in the README file.</p>
Data for: Age structure eliminates the impact of coinfection on epidemic dynamics in a freshwater zooplankton system
<p>Parasites often coinfect host populations, and, by interacting within hosts, might change the trajectory of multi-parasite epidemics. However, host-parasite interactions often change with host age, raising the possibility that within-host interactions between parasites might also change, influencing the spread of disease. We measured how heterospecific parasites interacted within zooplankton hosts and how host age changed these interactions. We then parameterized an epidemiological model to explore how age-effects altered the impact of coinfection on epidemic dynamics. In our model, we found that in populations where epidemiologically relevant parameters did not change with age, the presence of a second parasite altered epidemic dynamics. In contrast, when parameters varied with host age (based on our empirical measures), there was no longer a difference in epidemic dynamics between singly and coinfected populations, indicating that variable age structure within a population eliminates the impact of coinfection on epidemic dynamics. Moreover, infection prevalence of both parasites was lower in populations where epidemiologically relevant parameters changed with age. Given that host-population age structure changes over time and space, these results indicate that age-effects are important for understanding epidemiological processes in coinfected systems and that studies focused on a single age group could yield inaccurate insights.</p>
10 ns Molecular Dynamics simulations of mAMCase at pH 2.0 and 6.5 in complex with GlcNAc6.
<p>This directory contains all files required to analyze the 10 ns MD simulations of mouse AMCase at pH 2.0 and 6.5 presented in <strong>Figure 5</strong> in the manuscript <a href="https://www.biorxiv.org/content/10.1101/2023.06.03.542675">Díaz et al.<em> </em>(2023)</a>.</p> <p>All simulations were performed using Molecular Operating Environment (Chemical Computing Group) and simulation data was analyzed using Graphpad Prism. Structure models were analyzed using PyMOL. Figures were compiled using Adobe Illustrator.</p> <p> </p> <p>Files included in this directory:</p> <p><strong>Figures</strong></p> <p>- contains PDFs of Asp138 X1 angle distribution, Asp138 X1 angle timecourse, PNGs of representative structure models from pH 2.0 <em>active</em> conformation simulation and pH 6.5 <em>inactive</em> conformation simulation with and without distances labeled.</p> <p><strong>MOE</strong></p> <p>- README.txt defines what each variable in "<strong>Production_phX_Conformation.xlsx</strong>" represents</p> <p><strong>/MOE/pHX_Conformation</strong></p> <p>- contains the starting structure for each simulation, a video of the 10 ns simulation, different variables measured during the simulation as an Excel (.xlsx) and Moe databasse (.mdb) files.</p> <p><strong>PyMOL</strong></p> <p>- contains all structure models, 2mFo-DFc maps, mFo-DFc maps, PyMOL script, and PyMOL session used to generate <strong>Figure 5</strong>.</p> <p> </p> <p><strong>MD.pzfx</strong></p> <p>- contains raw data from 10 ns simulations at pH 2.0 and pH 6.5 with Asp138 starting conformation in the <em>active </em>or <em>inactive </em>conformation.</p> <p> </p> <p>Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu</p> <p>James Fraser, jfraser@fraserlab.com</p>
Interactive Molecular Dynamics Simulation Movie using MDsrv - BioGem
<p>The protein structure and molecular dynamics simulation trajectories used to make interactive movie using MDsrv and NGL Viewer.</p> <p>https://www.youtube.com/watch?v=m62lg6ZInAI</p>
Input and Output simulation data of the THOR GCM for the paper Dynamical and radiative effects resulting from the deep non-hydrostatic vs deep quasi-hydrostatic equations in the global circulation model THOR with an added non-grey radiative transfer scheme
<p>The input and ouput simulation data of the THOR GCM for Dynamical and radiative effects resulting from the deep non-hydrostatic vs deep quasi-hydrostatic equations in the global circulation model THOR with an added non-grey radiative transfer scheme</p> <p>Global circulation models (GCMs) play an important role in contemporary investigations of exoplanet atmospheres. Different GCMs evolve various sets of dynamical equations which can result in obtaining different atmospheric properties between models. In this study, we investigate the effect of different dynamical equation sets on the atmospheres of hot Jupiter exoplanets. We compare GCM simulations using the quasi-primitive dynamical equations (QHD) and the deep Navier-Stokes equations (NHD) in the GCM THOR. We utilise a two-stream non-grey "picket-fence" scheme to increase the realism of the radiative transfer scheme. We perform GCM simulations covering a wide parameter range grid of system parameters in the population of exoplanets. Our results show significant differences between simulations with the NHD and QHD equation sets at lower gravity, higher rotation rates or at higher irradiation temperatures. The parameter exploration shows the relevance of choosing dynamical equation sets dependent on system and planetary properties.Climate states of hot Jupiters seemed to be more diverse than previously thought. There are exceptions to prograde superrotation. Overall, our study shows the evolution of different climate states which arise just due to different selection of Navier-Stokes equations and approximations. We show the shortcomings of approximations in GCMs made for Earth, but used for non Earth-like planets.</p>
MPIData: Increased Dynamic Range
<p>This data repository contains magnetic particle imaging data. The files are stored in the <a href="https://arxiv.org/pdf/1602.06072.pdf">MDF file format</a> and the folder structure is organized as an <a href="https://github.com/MagneticParticleImaging/MPIFiles.jl">MDF store</a>. The data is used in this code example: <a href="https://github.com/IBIResearch/IncreasedDynamicRange">https://github.com/IBIResearch/IncreasedDynamicRange</a></p>
Dataset to reproduce firgures for the paper "A unifying method to study Respiratory Sinus Arrhythmia dynamics implemented in a new toolbox"
<p>Dataset provided to reproduce figures <br> for the paper "A unifying method to study Respiratory Sinus Arrhythmia dynamics implemented in a new toolbox"</p> <p>Jupyter notebooks are available here:<br> https://github.com/samuelgarcia/physio_benchmark</p> <p>Human dataset<br> =============</p> <p>Context: A research aimed to decipher the impact of respiration on brain oscillations</p> <p>Data collection methods: ECG and Respiration of 15 healthy adults subjects <br> (age : 30.9 +/- 9.5 yo).All participants gave informed consent to take part to the study, and all experiments<br> were approved by the national french committee (CPP number 4090). They were sitting quietly and instructed just<br> to relax. Recording lasted 5 minutes. Respiration signal was recorded from a nasal sensor<br> (Sensortechnics GmbH, Puchheim , Germany) at a sampling rate of 1000 Hz, amplified by actiCHamp<br> Plus amplifier (Brain Products GmbH, Gilching, Germany). ECG signal was recorded from 3 skin electrodes<br> (right forearm, left forearm, left iliac region), at a sampling rate of 1000 Hz (same amplifier).</p> <p>Structure of files: tabular separated values text files.<br> The first columns correspond to the ECG signal, the second is the respiratorysignal.<br> The sampling rate is 1000Hz</p> <p>Data manipulations: The original dataset has longer durationand and contain channels (EEG).<br> This sub-dataset was extracted from the original using the neo python package from the VHDR brain product format.<br> Signal tarces haven't been preprocessed they correspond to the "raw" signal.</p> <p><br> Data confidentiality and permissions: Experiments were approved by the national french committee (CPP number 4090)</p> <p><br> Animal dataset<br> ==============</p> <p>Context: The dataset was recorded to validate the device telemetric jacket from Etisense.</p> <p>Data collection methods: ECG and Respiration of 1 adult rat were recorded. Recording lasted 30 seconds during<br> freely behaving. Respiration signal and ECG were recorded from a thoraco-abdominal telemetric<br> jacket at which it was habituated before. Recorded were done at a sampling rate of 500 Hz, amplified by<br> Etisense acquisition unit (Etisense, MedTech company, Lyon, France).</p> <p>Structure of files: tabular separated values text files.<br> The first columns correspond to the ECG signal, the second is the respirator signal.<br> The sampling rate is 500Hz</p> <p><br> Data manipulations:<br> The dataset was extracted from the original HDF5 structure.<br> The ECG signal correcpond to the "raw" traces from the HDF5 files.<br> The respiratory signal was originaly sample at 200Hz on the device and resample with linear interpolation<br> to 500Hz to be easy aligned with the ECG signal.</p> <p>Data confidentiality and permissions: Experiments were carried according to the ethical guidelines of the<br> European Communities Council Directive of 24 November 1986 (86/609/EEC), as well as the approval 16979 of the<br> Lyon 1 University CEEA-55 ethical committee and of the Ministry of Higher Education, Research and Innovation.<br> </p>
Figure 1 in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)
Figure 1. Seasonal dynamics of the average abundance of spionid polychaetes S. gynobranchiata in the innermost part of the Sevastopol Bay (2006–2007).
Figure 2 in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)
Figure 2. Multi-annual dynamics of the average abundance of S. gynobranchiata in the Sevastopol Bay (2007–2013).
Figure 4. S in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)
Figure 4. S. gynobranchiata: А, a body fragment of an egg-carrying female; В, a 3–chaetiger larva just hatched from egg capsule; С, a 3–chaetiger larva on the 2nd day; D, a 5–chaetiger larva equipped with anal cirri; E, a 9–chaetiger larva; F, a 13–chaetiger larva making a tube. Scale: А- F – 100 µm.
Figure 3 in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)
Figure 3. Distribution of polychaete worms S. gynobranchiata (density in ind.·m-2) in the Sevastopol Bay: A – in 2007; B – in 2008; C – in 2013.
Dynamics of macrophage polarization in Salmonella infection: row data
<p>Experimental metadata of the manuscript " <strong>Dynamics of macrophage polarization support <em>Salmonella</em> persistence in a whole living organism</strong> " by Leiba et al.</p>
ScienceDex guides
Understand access before you commit
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.