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11,506 results for “Dynamics”
Fishtrap Creek thermal dynamics - scripts and data sets
<p>This repository contains data sets and scripts used in the analysis reported in an article titled "Predicting latent and sensible heat fluxes in stream temperature models -- current challenges and potential solutions"</p>
Unique dynamics and exocytosis properties of GABAergic synaptic vesicles revealed by three-dimensional single vesicle tracking
<p>This data set includes x, y, and z trajectories of all GABAergic synaptic vesicles that we used for the study. These GABAergic synaptic vesicles in inhibitory presynaptic terminals of living primary hippocampal neurons were labeled by single quantum dots (QDs) conjugated with anti-VGAT antibody under electrical stimulation, and were tracked three-dimensionally by using a dual-focus imaging in real-time. Each trajectory data indicates x, y, and z positions (nanometer-scale) over time from the start of imaging to the moment of vesicle fusion. The electrical stimulation to the neurons was applied for 120 s, starting from 20 s.</p>
ss-PDMFA: size-specific, probabilistic, dynamic material flow analysis
<p><strong>Description of the dataset:</strong></p> <p>This dataset is related to the following publication:</p> <p>Title: Size-specific, dynamic, probabilistic material flow analysis of titanium dioxide releases into the environment</p> <p>Authors: Yuanfang Zheng, Bernd Nowack </p> <p>Submitted to the journal Environmental Science & Technology in November 2020.</p> <p>The files contain input files, final codes and raw results of the ss-PDMFA model.</p> <p> </p>
Data for "Sub-7-femtosecond conical-intersection dynamics probed at the carbon K-edge"
<p>Data sets underlying Figs. 1-4, and S1-S6, S8-S20 of the paper entitled "Sub-7-femtosecond conical-intersection dynamics probed at the carbon K-edge".</p>
Data from" Euphotic Zone Metabolism in the North Pacific Subtropical Gyre Based on Oxygen Dynamics"
<p>This data set provides measurements of oxygen to argon molar ratios from discrete samples collected within the mixed layer at the long-term sampling site (Station ALOHA) of the Hawaii Ocean Time-Series program, within the North Pacific Subtropical Gyre, between November 2013 and January 2019 (near-monthly cruises). Samples were measured by membrane inlet mass spectrometry following Ferrón et al. (2015). Version 2 had corrected longitude data (in decimal degrees east). Version 3 includes a new file with estimated rates of net community production, gross oxygen production and community respiration for the mixed layer.</p>
DEVILS: a tool for the visualization of large datasets with a high dynamic range
<p>This repository accompanying the article “DEVILS: a tool for the visualization of large datasets with a high dynamic range” contains the following:</p> <ul> <li>Extended Material of the article</li> <li>An example raw dataset corresponding to the images shown in Fig. 3</li> <li>A workflow description that demonstrates the use of the DEVILS workflow with BigStitcher.</li> <li>Two scripts (“CLAHE_Parameters_test.ijm” and a “DEVILS_Parallel_tests.groovy”) used for Figure S2, S3 and S4.</li> </ul>
Phyloseq R object accompanying the paper Temporal Dynamics Cloacal Microbiota 16S metataxonomics
<p>This ready to load <strong>phyloseq</strong> R S4 object contains the ASV table, taxonomy table and sample metadata. This data was build using the DaDa2 (version 1.6.0) and phyloseq (version 1.223) R packages using our raw MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA673103.</p> <p>The accompanying (peer-reviewed) scientific article can be found here: </p> <ul> <li>https://www.frontiersin.org/articles/10.3389/fmicb.2020.626713/abstract </li> <li>DOI: 10.3389/fmicb.2020.626713</li> </ul> <p> </p> <p><strong>Study/paper</strong> </p> <p>J. Schreuder, F.C. Velkers, A. Bossers, R.J. Bouwstra, W.F. de Boer, P. van Hooft, J.A. Stegeman, S.D. Jurburg.</p> <p>Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing.<br> The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 % and 4.4 % of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.</p>
All-atom Molecular Dynamics Simulations of SARS-CoV-2 Spike Receptor-binding Domain bound with ACE2
<p>Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of of SARS-CoV2 Spike Protein/ACE2 complex (PDB ID: 6M0J). In order to decrease the size of the file only protein rajectories were provided. Simulation has been performed with Desmond. Protein 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 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 simulation.</p>
Dataset for article: Perakakis P., Idrissi S., Vila J., Ivanov Ch.P. (2012). Dynamical patterns of human postural responses to emotional stimuli. Psychophysiology, 49 (9), pp. 1225–1229
<p>Dataset for article: Perakakis P., Idrissi S., Vila J., Ivanov Ch.P. (2012). Dynamical patterns of human postural responses to emotional stimuli. Psychophysiology, 49 (9), pp. 1225–1229</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 80 wt% C12E5, T=298K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Dynamic testing of a four-storey building with reinforced concrete and unreinforced masonry wall: Data set
<p>This paper presents a publically available data set recorded during the shake-table test of a structure with reinforced concrete (RC) and unreinforced masonry (URM) walls. The shake-table test, performed at the TREES laboratory of EUCENTRE (Pavia, Italy), was part of a larger research initiative at EPFL (Lausanne, Switzerland) that addresses the seismic behaviour of mixed RC-URM structures. The half-scale test unit was subjected to several shakings of different intensity levels. The paper presents the geometry of the test unit, the properties of the construction materials, the instrumentation, and outlines the organization of the recorded data. Two sets of data are available: the unprocessed data and a second set of processed data where conventional and optical measurements are synchronised. This second set contains also some derived data, which allows to quickly plot key quantities such as base shear and top displacement. The aim of the paper is to provide all information required by the reader for analysing the test data and using it for validation purposes of numerical and mechanical models. The performance of the test unit is described in a companion paper.</p>
Domain-specific model selection for structural identification of the Rab5-Rab7 dynamics in endocytosis - Additional Files
<p>Additional files from the manuscript titled "Domain-specific model selection for structural identification of the Rab5-Rab7 dynamics in endocytosis" published in BMC Systems Biology:</p> <ul> <li>Data containing delimited time points and measurements used for fitting the different model structures</li> <li>Supplementary material containing additional figures and tables</li> <li>Archive containing the complete library, the incomplete model and the task used for modeling the Rab5-Rab7 switch</li> </ul> <p> </p>
Dataset and Figures for article: Ivanov P.Ch., Yuen, A., Perakakis, P., (2014). Impact of stock market structure on intertrade time and price dynamics. PLoS ONE 9(4): e92885
<p>Dataset and Figures for article: Ivanov P.Ch., Yuen, A., Perakakis, P., (2014). Impact of stock market structure on intertrade time and price dynamics. PLoS ONE 9(4): e92885</p>
Lipid center-of-mass trajectory: long-time dynamics
<p>This file contains the center-of-mass coordinates of the lipid molecules in a Molecular Dynamics simulation of a hydrated lipid bilayer. The simulated system consists of 2033 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) molecules and 57952 water beads (equivalent to 231808 water molecules), using the coarse-grained representation of the MARTINI force field. Note that the mass of a POPC molecule is significantly higher (936 g/mol) in this representation than the mass of a real POPC molecule (760 g/mol). The simulation was performed in an NVT ensemble at T = 320 K.</p> <p>This trajectory stores the long-time dynamics of the lipid centers of masses, sampled at a time step of 18 ps up to a total length of 600 ns. The short-time dynamics are available at http://dx.doi.org/10.5281/zenodo.61742.</p> <p>For a detailed description of the simulation, see the thesis of Sławomir Stachura, available at http://www.theses.fr/2014PA066239</p> <p>Two analyses of this simulation have already been published:</p> <ul> <li>S. Stachura and G.R. Kneller Anomalous lateral diffusion in lipid bilayers observed by molecular dynamics simulations with atomistic and coarse-grained force fields Mol. Sim. 40, 245-250 (2014) (http://dx.doi.org/10.1080/08927022.2013.840902)</li> <li>S. Stachura and G.R. Kneller Probing anomalous diffusion in frequency space J. Chem. Phys. 143, 191103 (2015) (http://dx.doi.org/10.1063/1.4936129)</li> </ul> <p>This work was funded by the French Agence Nationale de la Recherche (Contract No. ANR- 2010-COSI-01-001).</p> <p><strong>Trajectory data</strong></p> <p>The trajectory is stored in an HDF5 file that uses the ActivePapers conventions (http://www.activepapers.org/). Any HDF5-compatible software can be used to read the trajectory data. The ActivePapers software is only required to re-use the included conversion script.</p> <p>The trajectory is contained in the group<br /> /data/POPC_martini_nvt</p> <p>It is stored in H5MD/MOSAIC format. The positions and time labels are contained in the following datasets:<br /> /data/POPC_martini_nvt/particles/universe/position/value<br /> /data/POPC_martini_nvt/particles/universe/position/time</p> <p>For a complete specification of the H5MD/MOSAIC format, see:<br /> http://nongnu.org/h5md/index.html<br /> http://mosaic-data-model.github.io/mosaic-specification/h5md_mosaic_module.html</p> <p><strong>Plots</strong></p> <p>Two 3D plots are provided to give an overview of the lipid motions:<br /> /documentation/all_lipids.pdf<br /> shows all the lipid center-of-mass positions once every 0.3 ps.<br /> /documentation/one_lipids.pdf<br /> shows a single lipid center of mass position every 10 ps.</p>
Lipid center-of-mass trajectory: short-time dynamics
<p>This file contains the center-of-mass coordinates of the lipid molecules in a Molecular Dynamics simulation of a hydrated lipid bilayer. The simulated system consists of 2033 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) molecules and 57952 water beads (equivalent to 231808 water molecules), using the coarse-grained representation of the MARTINI force field. Note that the mass of a POPC molecule is significantly higher (936 g/mol) in this representation than the mass of a real POPC molecule (760 g/mol). The simulation was performed in an NVT ensemble at T = 320 K.</p> <p>This trajectory stores the short-time dynamics of the lipid centers of masses, sampled at a time step of 0.03 ps up to a total length of 300 ps. The long-time dynamics are available at http://dx.doi.org/10.5281/zenodo.61743.</p> <p>For a detailed description of the simulation, see the thesis of Sławomir Stachura, available at http://www.theses.fr/2014PA066239</p> <p>Two analyses of this simulation have already been published:</p> <ul> <li>S. Stachura and G.R. Kneller Anomalous lateral diffusion in lipid bilayers observed by molecular dynamics simulations with atomistic and coarse-grained force fields Mol. Sim. 40, 245-250 (2014) (http://dx.doi.org/10.1080/08927022.2013.840902)</li> <li>S. Stachura and G.R. Kneller Probing anomalous diffusion in frequency space J. Chem. Phys. 143, 191103 (2015) (http://dx.doi.org/10.1063/1.4936129)</li> </ul> <p>This work was funded by the French Agence Nationale de la Recherche (Contract No. ANR- 2010-COSI-01-001).</p> <p><strong>Trajectory data</strong></p> <p>The trajectory is stored in an HDF5 file that uses the ActivePapers conventions (http://www.activepapers.org/). Any HDF5-compatible software can be used to read the trajectory data. The ActivePapers software is only required to re-use the included conversion script.</p> <p>The trajectory is contained in the group<br /> /data/POPC_martini_nvt</p> <p>It is stored in H5MD/MOSAIC format. The positions and time labels are contained in the following datasets:<br /> /data/POPC_martini_nvt/particles/universe/position/value<br /> /data/POPC_martini_nvt/particles/universe/position/time</p> <p>For a complete specification of the H5MD/MOSAIC format, see:<br /> http://nongnu.org/h5md/index.html<br /> http://mosaic-data-model.github.io/mosaic-specification/h5md_mosaic_module.html</p> <p><strong>Plots</strong></p> <p>Two 3D plots are provided to give an overview of the lipid motions:<br /> /documentation/all_lipids.pdf<br /> shows all the lipid center-of-mass positions once every 3 ps.<br /> /documentation/one_lipids.pdf<br /> shows a single lipid center of mass position every 0.3 ps.</p>
Impact of spatio-temporal shade dynamics on winter wheat growth and yield
<p>During two growing seasons (2013-2014, 2014-2015), an artificial shade structure was installed on the experimental farm of Gembloux Agro-Bio Tech to evaluate winter wheat growth, productivity and quality under shade. During both seasons, global radiation (MJ/m²/days) at crop canopy level was measured with quantum sensors (CS300- Campbell Scientific Inc., USA – accuracy ± 5 % for the daily global radiation) and recorded every minute by a data logger (CR1000 - Campbell Scientific Inc., USA). These data are compiled at a daily time scale for each treatment (CS: constant shade, PS: periodic shade, NS: no shade) into the tables “<em>GR_2013_2014.txt</em>” and “<em>GR_2014_2015.txt</em>”.</p> <p>During the cropping season, we sampled winter wheat to assess aboveground biomass, dry matter dynamics, final yield, yield components (thousand grain yield, grain size, and spike per m²) and grain protein content. These data are compiled in the two tables “<em>sampling_2013_2014.txt</em>” and “<em>sampling_2014_2015.txt</em>”. Samples were taken from three adjacent sowing lines of 40 cm. To assess dry matter distribution (g/m²), wheat plants were subdivided into spikes (<em>DM_Spike_g_m2</em>) and straw (<em>DM_Straw_g_m2</em>), dried and weighed. The final yield is expressed in t/ha at 0% humidity (<em>Yield_t_ha_0%</em>). We assessed the proportion of grain size using 3 sieves: 2.2, 2.5, 2.8 mm (<em>Grain_weight_seive_2.2mm, Grain_weight_seive_2.5mm, Grain_weight_seive_2.8mm</em>). Thousand grain weight at 0% humidity was calculated on subsamples from the harvested plots (<em>TGW_g_0%</em>). Protein content (%) analysis was performed with near-infrared reflectance spectroscopy technique (<em>Protein_content_%).</em></p> <p>Detailed information on the experimental design will be available in the following paper: “Impact of spatio-temporal shade dynamics on wheat growth and yield, perspectives for temperate agroforestry” in European Journal of Agronomy.</p>
2nd_dataset-Minimal radius of magnetic skyrmions: statics and dynamics
<p>In a broad range of applied magnetic fields and material parameters isolated magnetic skyrmions<br> condense into skyrmion lattices. While the geometry of isolated skyrmions and their lattice<br> counterparts strongly depend on field and Dzyaloshinski–Moriya interaction, this issue has not been<br> adequately addressed in previous studies. Meanwhile, this information is extremely important for<br> applications, because the skyrmion size and the interskyrmion distance have to be tuned for skyrmion<br> based memory and logic devices. In this investigation we elucidate the size and density-dependent<br> phase diagram showing traditional phases in field versus material parameters space by means of<br> Monte-Carlo simulations on a discrete lattice. The obtained diagram permits us to establish that, in<br> contrast to the continuum limit, skyrmions on a discrete lattice cannot be smaller than some critical<br> size and have a very specific shape. These minimal skyrmions correspond to the micromagnetic<br> configuration at the energy barrier between the ferromagnetic and the skyrmionic states.<br> Furthermore, we use atomistic Landau–Lifshitz–Gilbert simulations to study dynamics of the<br> skyrmion annihilation. It is shown that this procees consists of two stages: the continuous skyrmion<br> contraction and its discontinuous annihilation. The detailed analysis of this dynamical process is<br> given.</p>
Individual work of Bachelor students monitored using a dynamic assessment dashboard
<p>This document explain how data were generated and how to interpret them. </p> <p><strong>LICENSE: CC0</strong><br> But if you want to combine data with other datasets, feel free to use them as if they were published under CC0 license. <br> Data were published in February 2017. At that time, Zenodo only provided CC BY, CC BY-SA, CC BY-NC, CC BY-ND and CC BY-NC-ND. No CC0 option was available.</p> <p> </p> <p><strong>HOW DATA WERE COLLECTED</strong><br> Data provided in this dataset were collected in Fall 2016 as part of the Bachelor course 'Formation des usagers en bibliothèques' taught at the University of applied sciences Geneva (Information Sciences Department). <br> Data were generated by the interaction of the students with DAD, the Dynamic assessment dashboard, software to be released in 2017 (https://github.com/grolimur/DAD). Only data related to individual activities are published in this set. They were then cleaned and anonymised.</p> <p>The activities.csv file is provided for information purpose.</p> <p>Data are provided in 2 formats:</p> <p>* Comma-spearated values (submissions.csv)<br> * SQLite (submissions.sqlite)</p> <p>CSV is not correctly read by Excel, it's recommended to convert it into an .xslx file before using it. <br> SQLite is provided in order to apply different sorting and filters to the data. It can be read using SQLite manager for Firefox (https://addons.mozilla.org/en-US/firefox/addon/sqlite-manager/).</p> <p> </p> <p><strong>CODEBOOK</strong><br> Here is the name, the meaning and the possible values of the columns (name - description [possible values]).</p> <p>ID - database row ID [(database unique row ID)]<br> ActivityID - unique activity ID [1, 2, 3, 4, 10, 14, 16, 21, 22, 23, 41]<br> StudentID - unique anonymous student ID [#50 to #72]<br> date - recorded by the database [timestamp]<br> year - year extracted from date [2016, 2017]<br> month - month extracted from date [01, 11, 12]<br> day - day extracted from date [1 to 31]<br> weekday - weekday calculated from date [1, 2, 3, 4, 5, 6, 7]<br> hour - hour extracted from date - 00 to 23]<br> minute - minute extracted from date [00 to 59]<br> second - second extracted from date [00 to 59]<br> gr - group activity or not [0]<br> validated - was the submission validated or not [-1 or 1]<br> week - week number [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, H1, H2]</p> <p><em>ActivityID meaning</em><br> Activities are described in activities.csv. This file conatins only individual activities description. <br> The 2 activities iwth the bonus particularity are not present in the data because students didn't need to apply for them. A bonus was automatically added when activity 1 AND 2 AND 3 AND 4 (bonus = activity 5) as well as when activities 21 AND 22 AND 23 (activity 24) were completed.</p> <p><em>Date format</em><br> The date is formatted like YYYY-MM-DD hh:mm:ss.</p> <p><em>Weekday meaning</em><br> 1 stands for Monday, 2 for Tuesday and so on until 7 for Sunday.</p> <p><em>Group meaning</em><br> 0 stands for 'individual activity' and 1 would stand for group activity'. <br> Only entries with gr="0" appears in this dataset.</p> <p><em>Validated meaning</em><br> -1 stands for 'rejected' and 1 for 'validated'.</p> <p><em>Week meaning</em><br> The course lasts 10 weeks. 1 stands for the 1st week and so on until 10 that stands for the 10th week. <br> H1 and H2 stand for the Christmas holiday weeks that took place between week 8 and 9. <br> No submission were sent in weeks 1, 2 and 10.</p> <p> </p>
Data and results for manuscript "Flow dynamics in hyper-saline aquifers: hydro-geophysical monitoring and modeling"
<p>The paper presents a general methodology that will help understand how freshwater and saltwater may interact in natural porous media, with a particular view at practical applications such as the storage of freshwater underground in critical areas such as semi-arid zones around the Mediterranean sea. The methodology is applied to a case study in Sardinia and shows how a mix of advanced monitoring and mathematical modeling tremendously advance our understanding of these systems.</p> <p>This package contains the raw cross-hole time-lapse ERT data, additional field data, the ERT inversion results of the field data as well as the modeling data in terms of the concentration distribution of the density-dependent flow and transport model and the inverted synthetic ERT monitoring results.</p>
Supplementary material 1: Elevation data of FSN Dynamics Plot from: Tree Diversity and Dynamics of the Forest of Seu Nico, Viçosa, Minas Gerais, Brazil - Biodiversity Data Journal 3: e5425 (31 July 2015) https://doi.org/10.3897/BDJ.3.e5425
X, Y and elevation values of all vertices from 100 subplots from the one hectar FSN Dynamics Plot relative to starting point forming the northwestern vertex
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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.