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1,548 results for “Trajectories”
Data and script:Interactive persistent effects of past land-cover and its trajectory on tropical freshwater biodiversity
<p>This is the unique dataset used to run the analysis of the manuscript: "Interactive persistent effects of past land-cover and its trajectory on tropical freshwater biodiversity". You'll find in the "corumbatai_rb.txt" the catchment's and stream's ID, forest cover (%) within reach contribution areas in 1962, 1972, 1978, 2003 and 2011. The document "aquatic_insects.txt" contains the community data (columns= taxa, rows=sites). We also provide and R code used to analyze the relationship between biodiversity and change in forest cover that occurred across five decades, including landscape trajectories of forest gain and loss.<br> <br> </p>
3x 1 µs all-atom MD trajectories; AMBER ff15ipq & SPC/Eb; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'
<p>Simulation data for "Fitting side-chain NMR relaxation data using molecular simulations" (https://doi.org/10.1101/2020.08.18.256024).</p> <ul> <li>3 x 1 µs all-atom MD simulations of T4 Lysozyme</li> <li>Force field: AMBER ff15ipq with modified methyl rotation barriers<sup>1</sup></li> <li>Water model: SPC/Eb</li> <li>Compressed protein coordinates saved every 1 ps to enable calculation of side-chain NMR relaxation parameters</li> </ul> <p>Contains:</p> <ul> <li>3 x GROMACS .xtc trajectory files for 3 independent simulations</li> <li>3 x corresponding GROMACS .tpr topology files</li> </ul> <p><sup>1</sup> Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2020). Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers. <em>Journal of Chemical Physics</em>, <em>152</em>(8). https://doi.org/10.1063/1.5135379</p>
5x 1 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'
<p>Simulation data for "Fitting side-chain NMR relaxation data using molecular simulations" (https://doi.org/10.1101/2020.08.18.256024).</p> <ul> <li>5 x 1 µs all-atom MD simulations of T4 Lysozyme</li> <li>Force field: AMBER ff99SB*-ILDN with modified methyl rotation barriers<sup>1</sup></li> <li>Water model: TIP4P/2005</li> <li>Compressed protein coordinates saved every 1 ps to enable calculation of side-chain NMR relaxation parameters</li> </ul> <p>Contains:</p> <ul> <li>5 x GROMACS .xtc trajectory files for 5 independent simulations</li> <li>5 x corresponding GROMACS .tpr topology files</li> </ul> <p><sup>1</sup> Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2018). Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. <em>The Journal of Physical Chemistry B</em>, <em>122</em>(19), 5038–5048. https://doi.org/10.1021/acs.jpcb.8b02769</p>
3x 5 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'
<p>Simulation data for "Fitting side-chain NMR relaxation data using molecular simulations" (https://doi.org/10.1101/2020.08.18.256024).</p> <ul> <li>3 x 5 µs all-atom MD simulations of T4 Lysozyme</li> <li>Force field: AMBER ff99SB*-ILDN with modified methyl rotation barriers<sup>1</sup></li> <li>Water model: TIP4P/2005</li> <li>Compressed protein coordinates saved every 1 ps to enable calculation of side-chain NMR relaxation parameters</li> </ul> <p>Contains:</p> <ul> <li>3 x GROMACS .xtc trajectory files for 3 independent simulations</li> <li>3 x corresponding GROMACS .tpr topology files</li> </ul> <p><sup>1</sup> Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2018). Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. <em>The Journal of Physical Chemistry B</em>, <em>122</em>(19), 5038–5048. https://doi.org/10.1021/acs.jpcb.8b02769</p>
Epigenetic Profiling of Social Communication Trajectories and Co-occurring Mental Health Problems: A Prospective, Methylome-wide Association Study
<p>While previous studies suggest that both genetic and environmental factors play an important role in the development of autism-related traits, little is known about potential biological mechanisms underlying these associations. Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC), we examined prospective associations between DNA methylation (DNAm: N-birth=804, N-age7=877) and trajectories of social communication deficits (8-17 years). Methylomic variation at three loci across the genome (false discovery rate=0.048) differentiated children following high (n=80) versus low (n=724) trajectories of social communication deficits. This differential DNAm was specific to the neonatal period and not observed at age 7. Associations between DNAm and trajectory membership remained robust after controlling for co-occurring mental health problems (i.e., hyperactivity/inattention, conduct problems). The three loci identified at birth were not replicated in the Generation R Study. However, to the best of our knowledge, ALSPAC is the only study to date that is prospective enough to examine DNAm in relation to longitudinal trajectories of social communication deficits from late childhood to late adolescence. Although the present findings might point to potentially novel sites that differentiate between a high versus low trajectory of social communication deficits, the results should be considered tentative until further replicated.</p> <p>This dataset contains summary statistics for the methylome-wide association study using DNAm data collected from individuals at age 7.</p> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a zenodo DOI generated for you go to ewascatalog.org/upload</p>
TRACMASS trajectories in the Southern Ocean
<p>Data set of trajectories that are runned with the Lagrangian trajectory code TRACMASS v7.0.0 using data from an EC-Earth run performed following the guidelines of CMIP5. The data are stored according to the output from TRACMASS. </p> <ul> <li>NEMO_ORCA1_trajectories_back_Drake_ini.csv - Contains the initial position of trajectories that are started in the Drake Passage and runned backward to either the Drake Passage again or to 2 degree Celcius. </li> <li>NEMO_ORCA1_trajectories_back_Drake_out.csv - The end position of the trajectories that are started in the Drake Passage and runned backward until they reach the Drake Passage again or 2 degree Celcius. </li> <li>NEMO_ORCA1_trajectories_back_Drake_run.csv - The whole trajectories that are started in the Drake Passage and runned backward until they reach the Drake Passage again or 2 degree Celcius. </li> <li>NEMO_ORCA1_trajectories_Drake_ini.csv - Contains the initial position of trajectories that are started in the Drake Passage and runned forward to either the Drake Passage again or to 25 degree Celcius. </li> <li>NEMO_ORCA1_trajectories_Drake_out.csv - The end position of the trajectories that are started in the Drake Passage and runned forward until they reach the Drake Passage again or 25 degree Celcius. </li> <li>NEMO_ORCA1_trajectories_Drake_run.csv - The whole trajectories that are started in the Drake Passage and runned forward until they reach the Drake Passage again or 25 degree Celcius. </li> </ul>
Data from: Selection biases the prevalence and type of epistasis along adaptive trajectories
The contribution to an organism's phenotype from one genetic locus may depend upon the status of other loci. Such epistatic interactions among loci are now recognized as fundamental to shaping the process of adaptation in evolving populations. Although little is known about the structure of epistasis in most organisms, recent experiments with bacterial populations have concluded that antagonistic interactions abound and tend to de-accelerate the pace of adaptation over time. Here, we use the NK model of fitness landscapes to examine how natural selection biases the mutations that substitute during evolution based on their epistatic interactions. We find that, even when beneficial mutations are rare, these biases are strong and change substantially throughout the course of adaptation. In particular, epistasis is less prevalent than the neutral expectation early in adaptation and much more prevalent later, with a concomitant shift from predominantly antagonistic interactions early in adaptation to synergistic and sign epistasis later in adaptation. We observe the same patterns when re-analyzing data from a recent microbial evolution experiment. These results show that when the order of substitutions is not known, standard methods of analysis may suggest that epistasis retards adaptation when in fact it accelerates it.
Data from: Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar
Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early phase communities. The high dominance-low diversity functional gene communities underwent a transition to low-dominance-high diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.
Simulated Sea Ice (weighted by the Sea ice concentration) and Snow Thickness along the MOSAiC drift trajectory, from AWI-CM-1 and AWI-CM-3 nudged simulations.
<p>Sea ice thickness (weighted by the Sea ice concentration<i>)</i> and snow (on sea ice) thickness from nudged simulations performed using the coupled climate models AWI-CM-1 (zonal wavenumber truncated at 20) and AWI-CM-3 (T20 truncation; Pithan et al., 2023) with a 1h relaxation time. The model data is collocated to the drift trajectory of the Multidisciplinary Drifting Observatory for the Study of the Arctic Climate (MOSAIC) across the Arctic Ocean, from 01 September 2019 until 31 August 2020. The collocation is done daily, by finding all model grid cells within the area covered by the distributed network of snow and sea ice measuring instruments deployed and maintained during MOSAIC. The sea ice and snow thickness is then spatially averaged for each day. </p><p>Data is provided in three .nc files for each model and variable (wm_ice for sea ice thickness, m_snow for snow thickness) representing ensemble members 1 to 3.</p>
Lagrangian Sequestration Efficiency Trajectories and Extracted Particle Metrics – 2000m Y5 & Y6
<p>A dataset of Lagrangian trajectories used to estimate North Atlantic sequestration efficiency and extracted metrics for the re-entrained and sequestered particles. All variables have long names and units. These files have been used for the analysis in Baker et al. ‘Biological carbon pump sequestration efficiency in the North Atlantic: a leaky or a long-term sink?’ with further information about the methodology available in the paper. Due to the size of the datasets, each DOI only contains two files. This dataset contains the 2000m particles releases for the years 2000 (Y5) and 2001 (Y6).</p>
Lagrangian Sequestration Efficiency Trajectories and Extracted Particle Metrics – 2000m Y19 & Y20
<p>A dataset of Lagrangian trajectories used to estimate North Atlantic sequestration efficiency and extracted metrics for the re-entrained and sequestered particles. All variables have long names and units. These files have been used for the analysis in Baker et al. ‘Biological carbon pump sequestration efficiency in the North Atlantic: a leaky or a long-term sink?’ with further information about the methodology available in the paper. Due to the size of the datasets, each DOI only contains two files. This dataset contains the 2000m particles releases for the years 2014 (Y19) and 2015 (Y20).</p>
Lagrangian Sequestration Efficiency Trajectories and Extracted Particle Metrics – 500m Y19 & Y20
<p>A dataset of Lagrangian trajectories used to estimate North Atlantic sequestration efficiency and extracted metrics for the re-entrained and sequestered particles. All variables have long names and units. These files have been used for the analysis in Baker et al. ‘Biological carbon pump sequestration efficiency in the North Atlantic: a leaky or a long-term sink?’ with further information about the methodology available in the paper. Due to the size of the datasets, each DOI only contains two files. This dataset contains the 500m particles releases for the years 2014 (Y19) and 2015 (Y20).</p>
Lagrangian Sequestration Efficiency Trajectories and Extracted Particle Metrics – 1000m Y5 & Y6
<p>A dataset of Lagrangian trajectories used to estimate North Atlantic sequestration efficiency and extracted metrics for the re-entrained and sequestered particles. All variables have long names and units. These files have been used for the analysis in Baker et al. ‘Biological carbon pump sequestration efficiency in the North Atlantic: a leaky or a long-term sink?’ with further information about the methodology available in the paper. Due to the size of the datasets, each DOI only contains two files. This dataset contains the 1000m particles releases for the years 2000 (Y5) and 2001 (Y6).</p>
A typical result from the high-speed camera HSC for the flight trajectory of a 7 mm diameter projectile propelled from the explosion of 10 g C4 at the entrance of the explosive driven shock tube
<p>The video shows a typical result from the high-speed camera HSC for the flight trajectory of a 7 mm diameter projectile propelled from the explosion of 10 g C4 at the entrance of the explosive driven shock tube. The video depict the magnitude of the displacement which represents the distortion of the air density due to the passage of the shock wave. The displacement is shown in colors where red represents the highest values. The main features of the flow field around the supersonic freely flying projectile, such as the spherical and the detached shock wave in its front are captured with a good spatial resolution. </p>
Tracked trajectories Oxyrris marina
<div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div>Datasets containing the tracked trajectories for each experimental replicate with <em>Oxyrris marina</em> analyzed in the article: <strong>The distinctive chemotactic responses of three marine herbivore protists to DMSP and related compounds.</strong></div> <div><br>Nomenclature:</div> <div><br>O + _ + 1 letter identifying the compound + concentration in uM+ _ + experimental replicate number<br>for example: O_D20_R1 stands for "Oxyrris marina, DMSP, 20 uM, third replicate"</div> <div><br>The compounds are identified with:<br>D --> DMSP, M--> DMS, A --> Acrylate</div> <div><br>The datasets are saved as Pandas dataframe and can be opened with the library Pickle</div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div> <div> </div> </div> </div> </div> </div> <div> <div> <div> </div> </div> <div> </div> </div> </div> </div> <div> <div> <div> <div> </div> <div> <div> <div> <div> <div> <div> <div> <div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div>
MD simulation trajectory for POPC bilayer with 128 lipid molecules (CHARMM36, Gromacs 5.1)
<p>Equilibrated POPC lipid bilayer ran with Gromacs 5.1.2 with CHARMM36 lipid forcefield.<br> The simulation is composed of 128 POPC at full hydratation and ran for 500ns at 303K, data saved every 10ps.<br> This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
Adjustments in end-effector trajectory and underlying joint angle synergies after a target switch: Order of adjustment is flexible
<p>These are the data files used to perform the analyses for the paper: 'Adjustments in end-effector trajectory and underlying joint angle synergies after a target switch: Order of adjustment is flexible'.</p>
Molecular Dynamics trajectories and portable binary run input (TPR) files for the dual role of anionic lipids in amyloid aggregation
<h1>About this repository</h1> <p>We conducted Coarse-Grained molecular dynamics simulations to study the aggregation of the amyloid-beta fragment, Aβ16-22 (K16LVFFAE22), on mixed lipid bilayers composed of POPC and POPS. Three bilayer compositions were examined: 0% PS-100% PC, 10% PS-90% PC and 30% PS-70% PC. Simulations were performed using GROMACS 2019.4, employing the WEPROM forcefield for peptide modeling and WEPMEM for lipid modeling. For each POPS percentage, four independent replicas were run for 3000 ns. </p> <h1><strong>Contents</strong></h1> <h3>> Abeta_PCPS.zip </h3> <p>This zip file contains three main folders: 0PS, 10PS, and 30PS. These represent different percentages of PS present in the lipid bilayer.</p> <p>Each folder contains:</p> <p>1. Initial structures:<br> - em1.gro: Lipid bilayer without peptides<br> - eq1.gro: Lipid bilayer at 95 Ų area-per-lipid (APL)<br> - em2.gro: Lipid bilayer at 95 Ų APL with 16 peptides<br> - eq2.gro: Final equilibrated structure with peptides (used for production)</p> <p>2. Supporting files:<br> - index.ndx: Index groups for peptides and lipid bilayer<br> - run.pdf: Structure file for VMD visualization</p> <p>3. Four replica folders (replica1 to replica4), each containing:<br> - red.tpr: Binary input for analysis (peptides and lipid bilayer only)<br> - full_trj_pbc.xtc: Trajectory file (peptides and lipid bilayer only, centered in box)</p> <p>Note: The `.tpr` files were created using the `gmx convert-tpr` tool.</p> <p><strong>To access the source files with which these simulations were set-up, and a brief tutorial, see: </strong><a href="https://github.com/suhasgotla/heparin_amyloid_self-assembly">https://github.com/meenaljainumd/PCPS_amyloid_aggregation</a></p>
Dataset for paper "Direct multiple shooting for computationally efficient train trajectory optimization" (Kouzoupis et al.)
Open the record for dataset details and reuse information.
Molecular Dynamics Trajectories for GPR6 with Ligand S1P
<p>Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling</p> <p>Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
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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.