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11,506 results for “Dynamics”
Datasets associated with the manuscript "Discovering SARS-CoV-2 neoepitopes and the associated TCR-pMHC recognition mechanisms by combining single-cell sequencing, deep learning, and molecular dynamics simulation techniques"
<p>meta_data_TCR-pMHC_from_STCRDab.tsv, TCR-pMHC structures used for contacts analysis.</p><p>tcr_gliph_input_sars2.tsv, input files (TCR sequences and related information) used for clustering TCRs targeting SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_input_non-sars2.tsv, input files used for clustering TCRs targeting non-SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_output*, output files from the GLIPH software, including the recognized TCR clusters by GLIPH (convergence-group.txt), the linkage information of TCR clusters (clone-network.txt), and the recognized motif in TCR clusters (kmer.txt).</p><p>md_trajs.tar, structures and MD simulation trajectories of TCR-614-pMHC and TCR-204-pMHC complexes.</p>
04/04 - Spatial and Amplitude Dynamics of Neurostimulation: Insights from the Acute Intrahippocampal Kainate Seizure Mouse Model
<p>Dataset #4 of 4</p>
02/04 - Spatial and Amplitude Dynamics of Neurostimulation: Insights from the Acute Intrahippocampal Kainate Seizure Mouse Model
<p>Dataset #2 of 4</p>
Molecular dynamics simulations of BmGtsf1L peptide interacting with eTD1 of BmVreteno
<p>AF-eTD1 of BmVreteno and the ten last residues of BmGtsf1L.</p><p>GRO file and files for 10 simulations runs. Processed XTC files. </p>
Raw data for analysis in AI-NERD: Elucidation of Relaxation Dynamics Beyond Equilibrium Through AI-informed X-ray Photon Correlation Spectroscopy
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Molecular dynamics initialization files to reproduce simulations in "Anillin-Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study"
<p>Molecular dynamics initialization files to reproduce simulations in "Anillin-Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study" by Aaron R. Hall, Yeol Kyo Choi, Wonpil Im, and Dimitrios Vavylonis, Structure (2024) https://doi.org/10.1016/j.str.2023.11.010</p>
Assessing the interaction of oceanic and riverine processes on coastal phytoplankton dynamics in the East China Sea
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Assessing the interaction of oceanic and riverine processes on coastal phytoplankton dynamics in the East China Sea
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Data and code for the publication "Assessing the Behavior of Microplastics in Fluvial Systems: Infiltration and Retention Dynamics in Streambed Sediments" - Part 2(2)
<p><strong>Background</strong></p><p>The dataset contains data on Microplastic transport experiments run in an experimental flume of the University of Bayreuth. It was analysed in the paper by J.P. Boos, F. Dichgans, J.H. Fleckenstein, B.S. Gilfedder and S. Frei, "Assessing the Behavior of Microplastics in Fluvial Systems: Infiltration and Retention Dynamics in Streambed Sediments", currently under review in Water Resources Research</p><p> </p><p><strong>Description of the dataset</strong></p><p>This dataset contains data used for individual particle detection, and is a companion of the main dataset (10.5281/zenodo.10083568). The files need to be downloaded and merged into the given folder structure. Put the folder "1Pix" along with the folder "10Pix" to the folder in "210812/Data-FIS/matlab/2_Experiment/exp/".</p><p> </p><p><strong>Disclaimer</strong></p><p>The data and code are provided as is without any warranty.</p><p> </p><p><strong>Funding</strong></p><p>Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) -– Project Number 391977956 –- SFB 1357.</p>
Data and code for the publication "Assessing the Behavior of Microplastics in Fluvial Systems: Infiltration and Retention Dynamics in Streambed Sediments" - Part 1(2)
<p><strong>Background</strong></p><p>The dataset contains data on Microplastic transport experiments run in an experimental flume of the University of Bayreuth. It was analysed in the paper by J.P. Boos, F. Dichgans, J.H. Fleckenstein, B.S. Gilfedder and S. Frei, "Assessing the Behavior of Microplastics in Fluvial Systems: Infiltration and Retention Dynamics in Streambed Sediments", currently under review in Water Resources Research</p><p> </p><p><strong>Description of the dataset</strong></p><p>This dataset is the main dataset used for the analysis. There is a twin archive connected to this one, which contains the dataset which was used for the individual particle detection routines (10.5281/zenodo.10081788). The files have to be downloaded and merged into the folder structure.</p><p>The following data is included</p><ul><li>individual experimental data and results in the folders<ul><li><strong>210812</strong> (10 µm, coarse sand, low-flow)</li><li><strong>220727</strong> (1 µm, coarse sand, low flow)</li><li><strong>220803</strong> (3 µm, coarse sand, low-flow)</li><li><strong>220818</strong> (1 µm, fine sand, low-flow)</li><li><strong>220901</strong> (1 µm, coarse sand, high-flow)</li></ul></li><li><strong>Comparison</strong> (comparing individual results of the experiments)</li><li><strong>Scripts</strong> (contains the individual matlab scripts)</li><li><strong>labbook.xlsx</strong> (contains metadata on the experiments, which are read out in the matlab scripts)</li></ul><p> </p><p><strong>Description of the code</strong></p><p>The matlab scripts *.m contain the code to read and analyse all experimental data. The scripts are divided for the different input file types.</p><ul><li>Main scripts to analyze experimental data<ul><li><strong>Experiment_Main.m </strong>Main routine for individual experiments, reading and analysing Fluorometer, Levelogger, Flowmeter, Ultrasonics PIV</li><li><strong>Experiment_Main_Compare.m </strong>Comparison of individual experiment results</li></ul></li><li>FIS-dataset<ul><li><strong>FIS_Cal_Individual.m: </strong>Realizes individual calibrations of one experiment</li><li><strong>FIS_Cal_Result.m: </strong>Merges individual calibrations of one experiment</li><li><strong>Experiment_FIS.m: </strong>Load data of one experiment, detect interfaces. Followed by<ul><li><strong>Experiment_FIS_1pix</strong>: Individual particle detection (for 10 µm experiment, no binning)</li><li><strong>Experiment_FIS_10pix</strong>: Particle cloud analysis (all experiments, binning 10 Pix * 10 Pix)</li></ul></li><li><strong>Experiment_FIS_10pix_compare.m: </strong>Compare results of particle cloud analysis for all experiments.</li></ul></li><li>Fluo-data<ul><li><strong>Fluo_Cal.m </strong>Realizes calibration for Fluorometer devices</li></ul></li><li>PIV-dataset<ul><li><strong>PIV_individual.m </strong>Individual analysis of Particle Image Velocimetry (in total 9 different subdatasets, from 3 camera positions, and each 3 different illumination positions)</li><li><strong>PIV_merge.m </strong>Merge<strong> </strong>9 individual results of PIV for a result for one experiment</li></ul></li><li>Profiler-dataset<ul><li><strong>Profiler.m </strong>Analyses data from bedform profiling (merging individual measurements after the experiment)</li><li><strong>Profiler_Compare.m </strong>Compares bedform elevations and metrics between the 5 experiments (acquired after the experiment)</li><li><strong>Profiler_Time.m </strong>Analyses temporal change of bedform elevation during the experiment</li></ul></li></ul><p> </p><p><strong>Disclaimer</strong></p><p>The data and code are provided as is without any warranty.</p><p> </p><p><strong>Funding</strong></p><p>Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) -– Project Number 391977956 –- SFB 1357.</p>
Fig. 2 in The Composition, Diversity And Community Dynamics Of Limnetic Zooplankton In A Tropical Caldera Lake (Lake Taal, Philippines)
Fig. 2. Average abundance (Ind. / l) and number of species of Copepoda, Cladocera and Rotifera from the upper 40 m in Lake Taal in the year 2008. The Copepoda were grouped into nauplii, Calanoida and Cyclopoida.
Micropalstic ingestion by small species causes large detrimental effects on marine food web dynamics
<p>Model parameter and program for the article.</p>
Figure 3. Chlorophyll-a in First observation and seasonal dynamics of the new invasive planktonic copepod Oithona davisae Ferrari and Orsi, 1984 along the southern Black Sea (Anatolian Coast)
Figure 3. Chlorophyll-a distributions during the sampling period.
Figure 2 in First observation and seasonal dynamics of the new invasive planktonic copepod Oithona davisae Ferrari and Orsi, 1984 along the southern Black Sea (Anatolian Coast)
Figure 2. The average monthly sea surface temperature in 2007 and 2015 (°C).
Dynamics of dominance: maneuvers, contests, and assessment in the posture-scale movements of interacting zebrafish
<p>This is the dataset of the paper "<strong>Dynamics of dominance</strong>:<strong> </strong><i><strong>maneuvers, contests, and assessment in the posture-scale movements of interacting zebrafish</strong></i>".</p><h2>Contents</h2><h4>Very useful data</h4><ol><li>tracking_results.zip. This file contains the tracking results for all 22 experiments. <strong>This is the most useful file to download.</strong></li><li>fight_detection_data.zip. This file contains the data that was originally clustered to build the fight detector (see the paper). This is the same data that you need if you want to use the fight detector yourself.</li></ol><h4>Other data</h4><ol><li>Files of the form FishTank*.zip. These contain the raw output of idtracker.ai and SLEAP that were used to track the experiments. These files are only useful if you want to re-track from the very beginning. Even then, a slightly modified verison of this data is available in tracking_results.zip (for all experiments), and that may be what you want. These files are mainly for posterity.</li><li>PCA_data.zip. This is cached data that can be recomputed from the trajectory data. See the paper, and the code in the github.</li><li>tmat_and_infomap_generation_data.zip & infomap_data.zip & infomap_tau_sweep_data.zip. These contain the output of the calculations for the main infomap calculation, and the tau sweep calculation. See the paper and github.</li></ol><p> </p><h2>Code</h2><p>See <a href="https://github.com/liamshock/Dynamics_of_dominance">https://github.com/liamshock/Dynamics_of_dominance</a></p>
A LA-BTC MOF AS A SENSOR ELEMENT OF AN ELECTRONIC NOSE FOR SELECTIVE ADSORPTION OF BIOMARKERS OF DISEASES: MOLECULAR DYNAMICS SIMULATIONS OF ADSORPTION
<p>The MD trajectories calculated for all the La-BTC MOF-biomarker simulation systems </p>
The structure and dynamics of scientific collaborations in Europe (PhD. Dataset)
<p>The dataset comprises articles used in the qualitative analysis within the doctoral thesis entitled The Structure and Dynamics of Scientific Collaborations in Europe (Pințoiu-Mihăilă Bianca-Elena, 2023). These articles capture networks of authors and co-authors who have published on COVID-19 between 2020 and 2021. They also encompass information regarding the relationship between the number of prevention measures recommended by researchers and those implemented by the Romanian, Italian, or Swedish governments. The articles were found on the Web of Science using a search algorithm incorporating keywords such as COVID-19 and [country], publication year (for 2020 and 2021), document type (articles), Web of Science Category (Multidisciplinary Science, Sociology, and all other categories containing the term "policy"), sorted by country.</p>
Active learning molecular dynamics-assisted insights into ultralow thermal conductivity of two-dimensional covalent organic frameworks
<p>This is a training sets for monolayer COF-5, which could be used for NEP trainging.</p>
Data for the publication "Mechanical communication within the microtubule through network-based analysis of tubulin dynamics"
<p>Repository containing all the necessary data to replicate the study "Mechanical communication within the microtubule through network-based analysis of tubulin dynamics", published in Biomechanics and Modeling in Mechanobiology (https://doi.org/10.1007/s10237-023-01792-5).</p>
Dissecting the chiral recognition of TLR4/MD2 with Neoseptin-3 enantiomers by molecular dynamics simulations
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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.