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11,506 results for “Dynamics”
Data from: Stimulation-induced cytokine polyfunctionality as a dynamic concept
<p>Cytokine polyfunctionality is a well-established concept in immune cells, especially T cells, and their ability to concurrently produce multiple cytokines has been associated with better immunological disease control and subsequent effectiveness during infection and disease. To date, only little is known about the secretion dynamics of those cells, masked by the widespread deployment of mainly time-integrated endpoint measurement techniques that do not easily differentiate between concurrent and sequential secretion. Here, we employed a single-cell microfluidic platform capable of resolving secretion dynamics of individual PBMCs. To study the dynamics of poly-cytokine secretion, as well as the dynamics of concurrent and sequential polyfunctionality, we analyzed the response at different time points after <em>ex vivo </em>activation. Firstly, we observed simultaneous secretion of cytokines over the measurement time for most stimulants in a subpopulation of cells only. Secondly, polyfunctionality generally decreased with prolonged stimulation times and revealed no correlation with the concentration of secreted cytokines in response to stimulation. However, we observed a general trend towards higher cytokine secretion in polyfunctional cells, with their secretion dynamics being distinctly different from mono-cytokine secreting cells. This study provided insights into the distinct secretion behavior of heterogenous cell populations after stimulation with well-described agents and such a system could provide better understanding for various immune dynamics in therapy and disease.</p>
Immature stages of Culicoides and tidal dynamics in an Amazon beach
<p><span><span><span><span>Data used in the article: </span></span></span></span></p> <p><span><span><span><span><strong>Abundance of immature stages of </strong></span></span></span></span><span><span><span><span><em><strong>Culicoides</strong></em></span></span></span></span><span><span><span><span><strong> Latreille (Diptera, Ceratopogonidae) and their relationship with tidal dynamics on a sandy beach in the Amazonian Coastal Zone</strong></span></span></span></span></p> <p><span><span><span><span><strong>by Costa et al., to be published in the journal <em>Acta Amazonica</em>.</strong></span></span></span></span></p> <p><span><span><span><span>Abstract: The smallest hematophagous insects in the world belong to the </span></span></span></span><span><span><span><span><em>Culicoides</em></span></span></span></span><span><span><span><span> genus, and they are known</span></span></span></span><span><span><span><span> as potential vectors of various diseases globally. These insects are frequent pests on sandy beaches, with young individuals often found in flooded upper areas, edges of brackish waters, and intertidal zones of mangroves, mainly concentrated above the mean water level. In this study we investigated the presence of </span></span></span></span><span><span><span><span><em>Culicoides</em></span></span></span></span><span><span><span><span> Latreille larvae across extensive distances in the intertidal zone of an Amazonian sandy beach – a challenging, high energy, macrotidal environment with fine sediment. The local community links infestations of biting midges to neap tides. Hence, this study aimed to determine if larvae found across the beach intertidal area were associated with these infestations and their periodicity. Samples were collected daily over a two-week cycle of a semidiurnal tide range, extending down to 150 m below the mean high tide water level. Interestingly, young individuals were significantly more abundant during spring tides, contrary to the trend observed with adults, which corroborates the reports of the local community. Adults that </span></span></span></span><span><span><span><span>emerg</span></span></span></span><span><span><span><span>ed </span></span></span></span><span><span><span><span>from sampled juveniles,</span></span></span></span><span><span><span><span> raised </span></span></span></span><span><span><span><span><em>in vitro</em></span></span></span></span><span><span><span><span>,</span></span></span></span><span><span><span> </span></span></span><span><span><span><span>and adults caught using human bait were identified as </span></span></span></span><span><span><span><span><em>C. phlebotomus</em> (Williston)</span></span></span></span><span><span><span><span>, </span></span></span></span><span><span><span><span>confirming that this information may be beneficial to t</span></span></span></span><span><span><span><span>ourism development.</span></span></span></span></p>
Data from: Drivers of population dynamics of at-risk populations change with pathogen arrival
<p>Successful wildlife conservation in an era of global change requires understanding determinants of species population growth. However, when populations are faced with novel stressors, factors associated with healthy populations can change, necessitating shifting conservation strategies. For example, emerging infectious diseases can cause conditions previously beneficial to host populations to increase disease impacts. Here, we paired a population dataset of 265 colonies of the federally endangered Indiana bat (<em>Myotis sodalis</em>) with 50.7 logger-years of environmental data to explore factors that affected colony response to white-nose syndrome (WNS), an emerging fungal disease. We found variation in colony responses to WNS, ranging from extirpation to stabilization. The severity of WNS impacts was associated with hibernaculum temperature, as colonies of cold hibernacula declined more severely than those in relatively warm hibernacula, an association that arose following pathogen emergence. Interestingly, this association was opposite that of a sympatric bat species, the little brown bat (<em>Myotis lucifugus</em>), illustrating that environmental dependence of disease can vary by species in a multi-host community. Simulating future colony dynamics suggests that most extirpations have already occurred, as the pathogen has been present for several years in most colonies, and that relatively small colonies are more susceptible to extirpation. Overall, this study illustrates that emerging infectious diseases can change the factors associated with host population growth, including through novel environmental associations that vary by host species. Consideration of these shifting associations and differences between impacted species will be essential to the conservation of host communities challenged by emerging infectious disease. </p>
Human population dynamics in Upper Paleolithic Europe inferred from fossil dental phenotypes
<p>Despite extensive archaeological research, our knowledge of the human population history of Upper Paleolithic Europe remains limited, primarily due to the scarce availability and poor molecular preservation of fossil remains. As teeth dominate the fossil record and preserve genetic signatures in their morphology, we compiled a large dataset of 450 dentitions dating between ~47-7 thousand years ago (kya), outnumbering existing skeletal and paleogenetic datasets. We tested a range of competing demographic scenarios using a newly developed coalescent-based machine-learning Approximate Bayesian Computation (ABC) framework designed specifically for use with phenotypic data. Mostly in agreement with, but also challenging some of the hitherto available evidence, we identified a population turnover in western Europe at ~28 kya, isolates in western and eastern refugia between ~28-14.7 kya, and bottlenecks during the Last Glacial Maximum. Methodologically, this study marks the pioneering application of ABC to skeletal phenotypes, paving the way for exciting new research avenues.</p>
Molecular Dynamics Simulation and Docking Studies Reveals Inhibition of NF-kB signaling as a Promising Therapeutic Drug Target for reduction in Cytokines Storms
<p><span>The complexes of the top identified molecules with NF-kB-kB site, as well as all the designed molecules used in the screening process. </span></p>
Data from: Spatio-temporal dynamics in syntopy are driven by variability in rangeland conditions
<p>Sympatry is the most common form of niche differentiation and can exist as broad sympatry (shared geographical region) or direct sympatry (i.e., syntopy (shared resource patch)). Syntopy may be highly dynamic, particularly in environments that experience stochastic events that increase variability in abiotic conditions and vegetation. We examined how estimates of syntopy varied across space and time in a rangeland system within the Southern Great Plains, USA over a three-year period (2013-2015). We modeled annual estimates of syntopy between three functionally similar (ground-foraging Galliformes) species (northern bobwhite (<em>Colinus virginianus)</em>, scaled quail (<em>Callipepla squamata)</em>, and lesser prairie-chicken (<em>Tympanuchus pallidicinctus)</em>. Niche similarity representing increased syntopy was greatest during years with increased drought conditions (2013-2014). Niche differentiation was greatest in 2015 in which rangelands experienced the greatest amount of precipitation. Syntopy estimates were driven by variability in vegetation cover estimates, representing changes in rangeland conditions related to abiotic conditions. Our results suggest that syntopy can be highly dynamic across space and time and can be driven by variability in abiotic conditions (i.e., precipitation). Furthermore, these results suggest that habitat is in a state of non-equilibrium. Finally, we highlight that climate refuges that promote demographic resiliency through intraspecific changes in resource use are fundamental drivers of spatio-temporal patterns in community dynamics, particularly across similar functional species.</p>
FAIRmat Tutorial 7: Molecular Dynamics Trajectories and Workflows in NOMAD
<p>The FAIRmat consortium is committed to extending the NOMAD infrastructure to a wide variety of materials science data. To support soft matter simulations (e.g., atomistic molecular dynamics simulations), a number of challenges arise, primarily due to the volume and variety of data. The FAIRmat team is working to overcome these challenges, and the NOMAD infrastructure is now equipped with new metadata, features, and tools specifically designed to ease the FAIR treatment of trajectory data and workflows. Parsers have been implemented for two of the most popular molecular dynamics codes (Gromacs and Lammps), with plans for quick expansion to additional codes within the next year. The NOMAD Metainfo now describes the system’s hierarchical structure (in terms of bond topology) through the concept of fixed chemical bonds defined within classical force fields. The NOMAD GUI provides a bespoke overview page for molecular dynamics data, which includes tools that ease visualization of the system topology and automatically displays structural, dynamic, and thermodynamic observables that can assist in a fast assessment of system equilibration. Additionally, a native workflow visualizer allows the user to connect individual simulation entries into complex workflows. Finally, the NOMAD Python module facilitates custom trajectory analysis, for instance in a Jupyter notebook, with functions that convert a NOMAD archive entry to an instance of the MDAnalysis data class.</p> <p>This tutorial invites both experienced and completely novice NOMAD users to learn about these new features for molecular dynamics trajectories. A brief introduction to the FAIRmat consortium and the NOMAD infrastructure will be given, followed by guided and interactive tutorials highlighting the various features described above</p> <p><strong>Disclaimer:</strong> NOMAD is being continuously developed based on input and feedback from the scientific community. Hence the features, services or interface may have changed since the time of recording of this video. For up-to-date information please consult our latest tutorials and the NOMAD documentation <a href="https://nomad-lab.eu/prod/v1/docs/">https://nomad-lab.eu/prod/v1/docs/</a></p>
Data for Huang, Luo, et al., Dopamine-mediated interactions between short- and long-term memory dynamics, Nature, 2024
<p>Zip files contain voltage imaging traces and on-ball behavioral data from the five main figures in Huang, Luo, et al., Dopamine-mediated interactions between short- and long-term memory dynamics, Nature, 2024</p>
Test data for "Imaging of cellular dynamics in vitro and in situ: from a whole organism to sub-cellular imaging with self-driving, multi-scale microscopy"
<p>This repository contains test data associated with analysis code of low- and high-resolution self-driving multi-scale data from our manuscript "Imaging of cellular dynamics <em>in vitro</em> and <em>in situ</em>: from a whole organism to sub-cellular imaging with self-driving, multi-scale microscopy"</p> <p>by Stephan Daetwyler, Hanieh Mazloom-Farsibaf, Felix Y. Zhou, Dagan Segal, Etai Sapoznik, Bingying Chen, Jill M. Westcott, Rolf A. Brekken, Gaudenz Danuser and Reto Fiolka</p> <p> </p> <p>Code repository: <a href="https://github.com/DaetwylerStephan/multi-scale-image-analysis">https://github.com/DaetwylerStephan/multi-scale-image-analysis</a></p> <p>Documentation: <a href="https://daetwylerstephan.github.io/multi-scale-image-analysis/">https://daetwylerstephan.github.io/multi-scale-image-analysis/</a></p> <p>Preprint: <a href="https://www.biorxiv.org/content/10.1101/2024.02.28.582579v1.full">https://www.biorxiv.org/content/10.1101/2024.02.28.582579v1.full</a></p>
Bayesian analysis of (3+1)D relativistic nuclear dynamics with the RHIC beam energy scan data
<p>This dataset contains the MCMC chain (LHD+HPP) without any constraints on the parameters for the (3+1)D Bayesian inference study for the RHIC beam energy scan program.<br>We also provide the nine trained emulator objects, which were generated with the code available at <a title="GPBayesTools-HIC: v1.1.0" href="https://doi.org/10.5281/zenodo.12807892" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12807892</a>.<br>The training data is given in pickle format as dictionaries for the training points. The first 1000 points in the files correspond to the Latin Hypercube design points and the last 100 points are points sampled from the posterior distribution.</p>
Somatic hypermutation-mediated paratope flexibility improves the cross-reactivity of human malaria antibodies -- Molecular Dynamics dataset
<p>4493 Manuscript Data<br>====================</p> <p>author: Anton Hanke<br>size of uncompressed folder: ~19Gb.<br>DOI: 10.5281/zenodo.11470585</p> <p># Standard MD simulation data</p> <p>Standard Simulations were generated with gromacs 2021.5 using the charmm36m forcefield Juli 2021 release tarball (https://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2021.ff.tgz).<br>Post processed (PBC) simulations are structured as follows:<br>Mature generally refers to the wildtype 4493 antibody.</p> <p>- simulations/standardMD<br> |<br> |- prod.mdp example production mdp file used to run all production simulations.<br> |<br> |- mature Mature simulation set. (folder and file naming the same in all simulation directories)<br> | |- {peptide}_{replicate}_prod.gro {peptide} = peptide; {replicate} = standard MD replicate<br> | |- {peptide}_{replicate}_prod.tpr<br> | `- {peptide}_{replicate}_prod_align_noPBC.xtc (10Frames/ns)<br> |<br> |- mature_rerun Additional set of replicates with the wildtype 4493.<br> |- matureCapped Set of simulations with termini capped peptides<br> |- mature_nanpv2 Set of simulations with NPDP similar positioning of NANP<br> |- wo_pep Set of simulations without peptides for germline and mature<br> `- germline Set of germline simulations.</p> <p><br># RAMD simulation data</p> <p>RAMD simulations were generated with gromacs_2020.5 patched with RAMDv2 modified to account for the connected multiple ligand groups.<br>(Source code provided as tar file ./sw/gromacs_ramd_patchv2.tar.gz)</p> <p>Not all trajectories contain an unbinding event (gromacs CUDA bug.). <br>These trajectories were not considered in the analysis of simulations. </p> <p>- simulations/ramd<br> |<br> |- prod.mdp Exemplary production mdp file with RAMD settings, these were used in all trajectories w/<br> | differing RAMD random seed.<br> |<br> |- mature_2.625kcalmolA_4.0_3.0<br> | |- {peptide}_{replicate}_prod_{startFrame}.gro {peptide} = peptide; {replicate} = standard MD replicate; {startFrame} = Frame in standard MD used to start simulation.<br> | |- {peptide}_{replicate}_prod_{startFrame}.tpr<br> | |- {peptide}_{replicate}_prod_{startFrame}.ndx<br> | |- {peptide}_{replicate}_prod_{startFrame}_align_noPBC.xtc (100Frames/ns) Files omited due to size -- available on request.<br> | `- {peptide}_{replicate}_prod_{startFrame}_lastframe.pdb Last frame of the processed RAMD trajectory.<br> `- gl_2.625kcalmolA_4.0_3.0</p> <p><br># Analysis</p> <p>- analysis<br> |<br> |- entropie Quasi harmonic entropy estimation.<br> | |- inp Concatenated & Bootstrapped, coarse-grained and aligned trajectories of all systems<br> | |- out CPPTRAJ runs to calculate QHE on the bootstrapped trajectories<br> | |- run_complex.sh Script running analysis.<br> | |- ana.py Script to calculte average and std of QHE for each system. (generates *.out *.tsv *.png)<br> | |- cg.py Script used to bootstrap, coarse-grain align and build average structure with.<br> | `- delta_entropies.ods Excel file used to calculate Tab 1. in Main text of paper from entropies.out.<br> |<br> |- mmpbsa MMPBSA calculations (MM + SolvEnergy) with gmx_MMPBSA<br> | |- inp Input trajectories and topologies processed for MMPBSA<br> | |- out/gmx_mmpbsa Output directories in which gmx_MMPBSA was run.<br> | | ` *.dat Output files containing calculated energy terms from gmx_MMPBSA.<br> | |- mmpbsa.in MMPBSA input file used to run analysis.<br> | |- plot_results.py Python script to plot correlation of MMPBSA output with experimental data<br> | |- pca_eig_extr.py Script to reduce simulations to regions of high probability density within trajectory (not used in the present analysis)<br> | |- slurm-91315023.out Log file of the analysis run<br> | `- run_mmpbsa.sh Shell script to run the MMPBSA analysis (generates input and output file trees).<br> |<br> `- ramd RAMD analysation.<br> |- run.sh Shell script to run the analysis<br> |- run_ramd_ana.py Python script called by `run.sh` to run the analysis using `ramdAnalysis.py`<br> |- contact_clusters.py Python script to generate plots based on output of the analysis.<br> |- ramdAnalysis.py Python module containing analysis classes called/used within `run_ramd_ana.py`<br> | Based on tauRAMD & Fingerprint analysis by Dr. Daria Khokh (https://doi.org/10.1021%2Facs.jctc.8b00230; https://doi.org/10.1063%2F5.0019088)<br> |- abrun.* Log files from the present run<br> |- *.svg; *.png Analysis output files.<br> |- tramd_patchv2/ Output PDB structures from the analysis (excluded due to size, available on request)<br> `- representatives.pse Pymol session of cluster representatives along unbinding for germline and wildtype with contact probabilities within the<br> cluster mapped as b-factor.</p> <p># Figures</p> <p>- figure_pdbs PDB files (and pymol sessions) used to generate figures in the papers main text.</p>
Data set for "SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics"
<p>Please see README.txt for detailed information about the contents of this data repository.</p>
Dynamic interplay of cNHEJ and MMEJ pathways of DNA double-strand break repair during embryonic development in zebrafish.
<p><span>Fastq sequences from zebrafish embryos corresponding to 9 amplicons sequenced by </span><span>Illumina MiSeq. DNA sample were obtained from non-treated wildtype controls (ctrl) or from wildtype (WT), polq mutants, lig3 mutant or lig4 mutant injected with Cas9 protein and a pool of 5 or 4 different sgRNA (numbered from 1#1 to 5#2). Each target site corresponds to one amplicon. </span></p>
Dynamic Crosstalk Between Female Gonadal Hormones and Vaginal Microbiota Across Various Reproductive Phases
<p>Vaginal samples for 16S rRNA sequencing are collected from 150 healthy women across five reproductive phases: follicular phase, luteal phase, early pregnancy, lactation, and menopause, with 30 samples per group.</p>
Dynamically chiral phosphonic acid-type metallo-β-lactamase inhibitors
<p>NMR raw data files (FID), X-ray data, computational structural files</p>
Data and codes for the work: "Quasiparticle dynamics in a superconducting qubit irradiated by a localized infrared source"
<p>All data and codes used for the work can be found here. </p> <p> </p> <ul> <li>For figures 2 and SM6, one must unzip the files and change the directory in the codes accordingly.</li> <li>For figures 3, SM7 and SM8, one should use the file "Figure3_data.h5", already containing the analysis of the raw data of the pulsed experiment, which is also contained inside the zip file.</li> <li>Comsol 6.2 was used to create the simulation file for the sample temperature.</li> </ul>
Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
<p>Data and analysis code repository for: </p> <p>Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation</p> <p>https://doi.org/10.1101/255380</p>
Quantum Chemical Topology of the Electron Localization Function in the Field of Attosecond Electron Dynamics
<p>Movies accompaning publication of the Article "Quantum Chemical Topology of the Electron Localization Function in the Field of Attosecond Electron Dynamics". Journal of Physical Chemistry Letters, ACS, DOI:10.1021/acs.jpclett.7b03379</p> <p><strong>Collision of water molecule by alpha particle. Time-Dependent Density Functional Theory simulations.</strong></p> <p><strong>Water molecule</strong></p> <p>- Collision of gas phase H<sub>2</sub>O with 100 MeV alpha particle. ELF isosurface of 0.88.</p> <p>Full duration of movie: 5fs. 1E2MeV_H2O_view1.mpeg</p> <p>- Collision of gas phase H<sub>2</sub>O with 1 MeV alpha particle. ELF isosurface of 0.88.</p> <p>Full duration of movie: 5fs. 1E0MeV_H2O_view1.mpeg</p> <p> </p> <p>- Collision of gas phase H<sub>2</sub>O with 0.1 MeV alpha particle. ELF isosurface of 0.70.</p> <p>Full duration of movie: 5fs. 1E-1MeV_H2O_view1.mpeg</p> <p>- Collision of gas phase H<sub>2</sub>O with 0.05 MeV alpha particle. ELF isosurface of 0.8.</p> <p>Full duration of movie: 5fs. 5E-2MeV_H2O_view1.mpeg</p> <p>- Collision of gas phase H<sub>2</sub>O with 0.01 MeV alpha particle. ELF isosurface of 0.8.</p> <p>Full duration of movie: 5fs. 1E-2MeV_H2O_view1.mpeg</p> <p><strong>Movies - guanine </strong></p> <p>Color code: Carbon in green, oxygen in red, nitrogen in blue, hydrogen and alpha particle in white. The ELF attractor are shown in yellow.</p> <p> </p> <p>- Collision of gas phase guanine with 1 MeV alpha particle. ELF isosurface of 0.8. Case i) the alpha particle impacts the central C=C bond. Full duration of movie: 430as. </p> <p>gua_1MeV_C=C_view1.mpeg, gua_1MeV_C=C_view2.mpeg</p> <p>- Collision of gas phase guanine with 1 MeV alpha particle. ELF isosurface of 0.8. Case ii) the alpha particle impact the 6-member ring N atom. Full duration of movie: 430as. </p> <p>gua_1MeV_6RN_view1.mpeg, gua_1MeV_6RN_view2.mpeg</p> <p>- Collision of gas phase guanine with 0.1 MeV alpha particle. ELF isosurface of 0.8. Case i) the alpha particle impacts the central C=C bond. Full duration of movie: 1.5fs. </p> <p>gua_01MeV_C=C_view1.mpeg, gua_01MeV_C=C_view2.mpeg</p> <p>- Collision of gas phase guanine with 0.1 MeV alpha particle. ELF isosurface of 0.8. Case ii) the alpha particle impact the 6-member ring N atom. Full duration of movie: 1.5fs. </p> <p>gua_01MeV_6RN_view1.mpeg, gua_01MeV_6RN_view2.mpeg</p>
Supplemental Tables Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines
<p>Supplemental tables for paper titled "Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines"</p>
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria
<p>Code and data for Frenoy & Bonhoeffer 2018 (Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria, in PLoS Biology)</p> <p>See README for details and steps to reproduce the full analysis from the raw data</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.