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1,350 results for “Intermediate”
Intermediate processing stage of horizontal particle flux data collected using a snow particle counter on board the R/V Akademik Tryoshnikov in the Southern Ocean during the austral summer of 2016/17 as part of the Antarctic Circumnavigation Expedition (ACE).
<p><strong>Dataset abstract</strong></p> <p>Flux of particles (snow, rain and other particles including sea spray) were recorded passing through a photo-electric snow particle counter installed on board the R/V Akademik Tryoshnikov as part of the Antarctic Circumnavigation Expedition (ACE). Data were recorded from January to March 2017 in the Southern Ocean. Here we present an intermediate step in data processing, with relative horizontal particle flux of particles with a size between 36 – 2000 μm averaged over one-minute periods. Data are presented in daily files.</p> <p><strong>Dataset contents</strong></p> <ul> <li>SPC_HPF_1min_YYYY_MM_DD.csv, data files, comma-separated values</li> <li>data_file_header.txt, metadata, text</li> <li>README.txt, metadata, text</li> </ul> <p><strong>Dataset license</strong></p> <p>This one-minute averaged horizontal particle flux dataset from ACE is made available under the Creative Commons Attribution 4.0 International License (CC BY 4.0) whose full text can be found at https://creativecommons.org/licenses/by/4.0/</p>
Diffraction images used to solve the structures published in the article "An Epoxide Intermediate in Glycosidase Catalysis"
<p>Raw diffraction images used for generating the structures published in the article "An Epoxide Intermediate in Glycosidase Catalysis" (available <a href="https://doi.org/10.1021/acscentsci.0c00111">here</a>). Full single-crystal datasets, including images that were not used in the final analyses, are published. The software used for the processing of each dataset is listed in their respective PDB entries.</p> <p> </p> <p>If you find this useful, please contact me at <a href="mailto:lukasz.sobala@hirszfeld.pl">lukasz.sobala@hirszfeld.pl</a>, I am just interested in how these data are used!</p>
DATA SET: Peripheral microcirculatory alterations are associated with the severity of acute respiratory distress syndrome in COVID-19 patients admitted to intermediate respiratory and intensive care units
<p>This repository contains the data sets of the article:</p> <p>Mesquida, J., Caballer, A., Cortese, L. <em>et al.</em> Peripheral microcirculatory alterations are associated with the severity of acute respiratory distress syndrome in COVID-19 patients admitted to intermediate respiratory and intensive care units. <em>Crit Care</em> <strong>25, </strong>381 (2021). https://doi.org/10.1186/s13054-021-03803-2</p>
Measurement of the bound-state beta decay of 205Tl(81+): intermediate and result data
<p>The data presented here is the intermediate and result data from the measurement of the bound-state beta decay of 205Tl(81+), experiment G-20-0E121, which was performed at the Experimental Storage Ring (ESR) at the GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt (Germany) in the frame of FAIR Phase-0. The experimental measurement was done from the 26th March 2020 to 6th April 2020.</p> <p><strong>Intermediate Data:</strong> During the experiment, the ESR monitored the beam via three main detectors: the non-destructive 245 MHz Schottky resonator, the DC Current Transformer (DCCT), and a Multi-Wire Proportional Chamber (MWPC). In particular:</p> <ol> <li>Schottky data: the integrated Schottky noise power density for the 205Tl(81+) peak and the 205Pb(82+) peak is provided for each storage measurement. The full Schottky spectrum can be made available on request. As described in the related works below, the Schottky data became saturated above a certain threshold due to a mismatched amplifier in the NTCAP DAQ. This results in non-exponential decay of Schottky peaks for high intensities. </li> <li>DCCT data: the entire beam current in the ring was monitored using the DCCT. The DCCT was recorded using a scalar counter and thus has a non-zero offset value, which we determined to be 28.199 µA from a period with no beam. The DCCT is intended to be used as a diagnostic tool, and is not as precise as other, purpose-built detectors.</li> <li>MWPC data: for most storage measurements, a MWPC detector was placed downstream of the gas target on the outside of the ring to detect electron recombination products. The provided data is the detection rate on the anode.</li> <li>The gas target density, as recorder by a scaler counter, is also included.</li> </ol> <p>The intermediate data on all three of these detectors plus the gas target density is provided in the tar.gz repository, with individual ROOT files for each storage time. The ROOT files have the naming format "Storage time_MMDD_HH.root". Each file contains 5 TGraph objects.</p> <p><strong>Result Data: </strong>The result data provides all the necessary individual measurement and correction values to extract a bound-state beta-decay rate from the corrected ratios. It is provided in two forms:</p> <ol> <li>BSBD_205Tl-result_data.ods is an ODS table for easy visualisation.</li> <li>BSBD_205Tl-final_vals.txt is a text file used by the Monte Carlo analysis script provided in <a href="https://doi.org/10.5281/zenodo.11560338" target="_blank" rel="noopener">DOI 10.5281/zenodo.11560338</a>.</li> </ol> <p>The "Ratio" column is the corrected 205Pb/205Tl decay ratio for each storage, following Equation (1) of <a href="https://www.nature.com/articles/s41586-024-08130-4" target="_blank" rel="noopener">Leckenby et al. (2024) Nature 635:321–326</a>. 1 sigma error bars, both including and not-including the estimated contamination variation, are provided.</p> <p>Please refer to the related works below or contact the authors for more details.</p>
Dataset Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T
<p>Scientific Reports - Nature - DOI : 10.1038/s41598-018-37825-8</p> <p>##################################<br> "Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T"<br> ##################################</p> <p>E. Najdenovska*, C. Tuleasca*, J. Jorge, P. Maeder, J.P. Marques, T. Roine, D. Gallichan, J.-P. Thiran, M. Levivier, and M. Bach Cuadra</p> <p>*Equally contributed authors</p> <p><br> Copyright (c) - All rights reserved. University of Lausanne. 2018.</p> <p><br> To reproduce the analyses presented in the referred study, in this repository you could find the MR images acquired from nine young healthy subjects (YS1-YS5), four elderly healthy subject (ES1-ES4) and two drug-resistant tremor patients treated treated with Vim radiosurgery by Gamma Knife (P1 and P2).</p> <p>The provided dataset includes the following NifTI files:</p> <p>- MPRRAGE @3T<br> - DWI @3T (together with the corresponding bvals and bvecs)<br> - MP2RAGE @7T<br> - SWI @7T<br> - binary masks of the manual delineation of both left and right Vim respectively that were done on the SWI (as NifTI files as well).</p> <p>Additionally, for the young cohort (YS1-YS5) we include as well the images used for building the quadrilateral of Guiot:<br> - T2-w @3T<br> - T2 CISS @3T</p> <p>For the patients (P1 and P2), a follow-up MPRAGE (acquired at 3T) with Gadolinium enhancement is also provided.</p> <p>——————————————<br> Notes:<br> 1. For YS3 MP2RAGE at 7T is missing, instead MPRAGE at 3T was used</p> <p>2. The code performing the thalamic nuclei clustering could be found in Zenodo (DOI: 10.5281/zenodo.123768)</p>
Intermediate processing steps of quality-checking of Antarctic Circumnavigation Expedition (ACE) cruise track data.
<p><strong>Dataset abstract</strong></p> <p>The Antarctic Circumnavigation Expedition (ACE), undertaken in the austral summer of 2016/2017 recorded the cruise track using two independent geo-location instruments: one using GLobal NAvigation Satellite Systems (GLONASS; hereafter referred to as GLONASS) and another primarily using the Global Positioning System (GPS; hereafter referred to as the Trimble GPS). Daily log files were recorded in real-time from both instruments during the expedition and added to MySQL database tables. Following the expedition, quality-checking work has been undertaken to provide a one-second resolution set of positions for the cruise track. This dataset presents the intermediate files that were produced during the quality-checking, therefore it could be used to check the processing steps that have been undertaken, but should not be used as a final source of the cruise track data. Both the original raw data files and final quality-checked cruise track can be found in related datasets.</p> <p><strong>Dataset contents</strong></p> <ul> <li>ace_INSTRUMENT_YYYY-MM-DD.csv – daily files for each instrument that were output from the database, data file, comma-separated values</li> <li>ace_INSTRUMENT_concatenated_YYYY-MM.csv – input files concatenated by month and instrument, data file, comma-separated values</li> <li>flagging_data_ace_INSTRUMENT_YYYY-MM-DD.csv – daily output files for each instrument with flagged data points, data file, comma-separated values</li> <li>track_data_combined_overall_flags_YYYY-MM.csv – instrument data combined with overall data flag for each month, data file, comma-separated values</li> <li>track_data_prioritised_YYYY-MM.csv – prioritised data files with overall data flag for each month, data file, comma-separated values</li> <li>ace_INSTRUMENT_manual_position_errors.csv – files containing the manually-observed errors, metadata, comma-separated values</li> <li>in_port.csv - dates on when the ship was stationary in port, metadata, comma-separated values</li> <li>README.txt – metadata, text file</li> <li>data_file_header.txt – metadata, text file</li> </ul> <p><strong>Dataset license</strong></p> <p>This dataset containing intermediate processing files of the ACE cruise track is made available under the Creative Commons Attribution 4.0 International License (CC BY 4.0) whose full text can be found at https://creativecommons.org/licenses/by/4.0/</p>
The Unfolding Journey of Superoxide Dismutase 1 Barrels Under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions With Crowders
<p>This data accompanies the article entitled <em>The Unfolding Journey of Superoxide Dismutase 1 Barrels Under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions With Crowders</em>, published in J. Phys. Chem. Lett. (<a href="https://doi.org/10.1021/acs.jpclett.0c00699">https://doi.org/10.1021/acs.jpclett.0c00699</a>).</p> <p><strong>01_SOD1bar_unfolding_REST2.zip: </strong>The zip archive includes REST2 trajectories for the three systems investigated in the paper: 1:1 packing, 2:1 packing, and the dilute case. The trajectories are saved in the GROMACS XTC file format, separately for each temperature (i=0,...,23). Given the large trajectory sizes, only protein coordinates (SOD1bar + crowders) are reported, and the output frequency is reduced to 100 ps. A starting geometry (in the Gromos87 GRO format) after equilibration of the initial packing is provided for each REST2 simulation (conf_prot.gro). Moreover, for each REST2 simulation, an xarray (http://xarray.pydata.org) dataset, saved in the netCDF file format, is included with computed fraction of native contacts, secondary structure content, and the Calpha RMSD of the barrel core (beta sheets beta1 - beta8) with respect to the crystal structure.</p> <p><strong>02_SOD1bar_geometries_representative_unfolding.zip:</strong> Representative SOD1bar geometries along the unfolding pathway (presented in Figure 3 of the paper).</p> <p><strong>03_SOD1bar_geometries_loopVII.zip: </strong>SOD1bar geometries with varying loop VII conformation which were isolated from dilute REST2 and which are presented in Figure S9 of the paper.</p>
Intermediate depth earthquakes at the Hikurangi subduction zone, New Zealand
<p>This dataset contains a catalogue of intermediate depth earthquakes in the Hikurangi Subduction Zone, New Zealand, as well as computed focal mechanisms.</p> <p>If you use this dataset please cite the following paper:</p> <p>Mark, O.K., Illsley‐Kemp, F., Townend, J. and Barker, S.J., 2024. Evidence From Intermediate‐Depth Earthquakes of Slab‐Derived Fluids Beneath the Taupō Volcanic Zone. <em>Journal of Geophysical Research: Solid Earth</em>, <em>129</em>(5), p.e2023JB028586.</p>
Model output and analysis scripts for "High-latitude precipitation as a driver of multicentennial variability of the AMOC in a climate model of intermediate complexity"
<p>Here, we provide annually averaged model output from a 3000-year control simulation of PlaSim–LSG, a climate model of intermediate complexity. Processed variables and a Jupyter notebook to reproduce all figures of the manuscript (Mehling et al.: "High-latitude precipitation as a driver of multicentennial variability of the AMOC in a climate model of intermediate complexity") can also be found in this repository.</p> <p>In addition, a Python implementation of the three-box model proposed in the manuscript can be found in the notebook <em>boxmodel.ipynb</em>.</p>
From the hot carrier solar cell to the intermediate band solar cell, passing through the multiple-exciton generation solar cell and then back to the hot carrier solar cell: the Dance of the Electro-chemical Potentials
<p>Presentation titled "From the hot carrier solar cell to the intermediate band solar cell, passing through the multiple-exciton generation solar cell and then back to the hot carrier solar cell: the Dance of the Electro-chemical Potentials" given by Antonio Marti at the 36th European PV Solar Energy Conference and Exhibition in Marseille, in September 2019.</p>
Research data for "Intermediates of Forming Transition Metal Dichalcogenides Heterostructures Revealed by Machine Learning Simulations"
<p>This dataset supports the paper "Intermediates of Forming Transition Metal Dichalcogenides Heterostructures Revealed by Machine Learning Simulations". </p> <p><strong>Included Files:</strong></p> <ul> <li><strong>ocp_active.zip</strong>: Modified version of ocp (https://github.com/Open-Catalyst-Project/ocp) tailored for active learning applications.</li> <li><strong>deployed.pth</strong>: Pre-trained model used in the experiments.</li> <li><strong>chemiscopy_run.py</strong>: Script integrating the chemiscopy and nequip modules, designed for dataset visualization.</li> <li><strong>new_energy.py</strong>: Modified version of the nequip module, featuring a repulsive potential function.</li> <li><strong>test_datasets.extxyz</strong> & <strong>train_datasets.extxyz</strong>: The test and training datasets in extxyz format.</li> </ul> <p>How to use the modified version of the nequip module:</p> <p>To train this version of the potential function, it is recommended to use nequip<=0.5.6 (on Linux). The NequIP training files need to be updated as follows:</p> <pre><code>model_builders: - new_energy.EnergyModel - StressForceOutput min_bond_len: 1.8</code></pre> <p>Then run:</p> <p><code>export PYTHONPATH=${PYTHONPATH}:$PWD</code><br><code>nequip-train config.yml # Train the potential function</code><br><code>nequip-deploy build --train-dir nequipresultsdir build.pth # Deploy the trained model</code></p>
Alphafold2_ab_initio iterative predictions for folding intermediate identification
<p>PDB ids starts from 1 and 8, rmsds, plddts, t-sne embeddings.</p> <p>Check related biorxiv preprint: AlphaFold2 knows some protein folding principles; DOI: https://doi.org/10.1101/2024.08.25.609581.</p>
Intermediate data products for: Moored Turbulence Measurements using Pulse-Coherent Doppler Sonar (Zippel et al. 2021, Journal of Atmospheric and Oceanic Technology)
<p>This repository contains some of the intermediate data products needed to reproduce the results in the <em>Journal of Atmospheric and Oceanic Technology</em> article "Moored Turbulence Measurements using Pulse-Coherent Doppler Sonar" by S.F. Zippel, J. T. Farrar, C. J. Zappa, U. Miller, L. St. Laurent, T. Ijichi, R. A. Weller, L. McRaven, S. Nylund, and D. Le Bel. Specifically, this material should allow reproduction of Figures 3, 5-7, 12 and 13. Reproduction of Figures 8-11 also requires data from associated glider deployments nearr the SPURS-1 mooring, which may be requested from co-author L. St. Laurent.</p> <p>Code to do the analysis and make the plots is here: https://github.com/zippelsf/MooredTurbulenceMeasurements</p> <p>Matlab data files:</p> <p>(1) 677404_burst1865.mat</p> <p>Single-burst data used for the example spectral fit in Figure 7. The burst was collected during the SPURS-1 project at 21.5m depth. The data collection and processing methods are described in detail in Section 2. </p> <p>(2) 811604_burst0510.mat (Single-burst data used in the unwrapping example, Figure 5)</p> <p>(3) 8116_dissipation_timeseries.mat (Used for associated ancillary data in Figure 6)</p> <p>(4) 913411_burst2879.mat (Single-burst data, used for ancillary data to make Figure 3).</p> <p>(5) BuoyancyFlux_b.mat</p> <p>Ocean buoyancy flux estimates for SPURS-2 dataset, created from the 1-hr "met" and "flux" files available on the UOP website, and using the Gibbs SeaWater (GSW) toolbox to estimate "alpha" and "beta". The estimated buoyancy fluxes were used for Figure 12.</p> <p>(6) BuoyancyFlux_c.mat</p> <p>Ocean buoyancy flux estimates for SPURS-1 dataset, created from the 1-hr "met" and "flux" files available on the UOP website, and using the Gibbs SeaWater (GSW) toolbox to estimate "alpha" and "beta". The estimated buoyancy fluxes were used for Figure 12.</p> <p>(7) SPURS1_dissipation_grid_v1d.mat</p> <p>Gridded TKE dissipation rates for SPURS-1 dataset. Processing of these data is described extensively in Section 2. Data used in Figures 8-13. Dissipation rates also available on NASA's PODAAC.</p> <p>(8) spurs1_met_1hr.mat (Processed met data from SPURS-1 mooring. Also available on WHOI's UOP website.)</p> <p>(9) SPURS2_dissipation_grid_v1c.mat</p> <p>Gridded TKE dissipation rates for SPURS-2 dataset. Processing of these data is described extensively in Section 2. Data used in Figures 12. Dissipation rates also available on NASA's PODAAC.</p>
ConFiRMa dataset_04: simulation of tests on CRM strengthened masonry buildings with the OOFEM code (intermediate, multi-layer level modelling)
<p>The Dataset collects the input files developed for the simulation of tests on one, two and three stroeys masonry buildings strengthened through Composite Reinforced Mortar with the free open-source code OOFEM (intermediate, multi-layer level modelling).</p> <p>OOFEM Version 2.5 (https://doi.org/10.5281/zenodo.4339630) was used for running the analyzes.</p> <p>ReadMe file provides a description of the different input files.</p>
Intermediate data for: Environment and shipping drive eDNA beta-diversity among commercial ports
<p>Intermediate data generated by Paul Czechowski as part of MEC-22-0945.R1 using code stored at <a href="https://github.com/macrobiotus/ships_and_bugs">GitHub</a>, most recently release with <a href="https://doi.org/10.5281/zenodo.7600608">DOI: 10.5281/zenodo.7600608 </a> . Pre-print with linked final manuscript version available at BioRxiv via <a href="https://doi.org/10.1101/2021.10.07.463538">DOI: 10.1101/2021.10.07.463538</a>. Please refer to the published manuscript for a full list of available digital resources associated with this work.</p>
Data and analysis scripts for: Recent acceleration in global ocean heat accumulation by mode and intermediate waters
<p>The folder contains the MATLAB code and data to re-create Figures 1-9 and S1-3 within the publication by <em>Li, Z., England, M. H., & Groeskamp, S. Recent acceleration in global ocean heat accumulation by mode and intermediate waters, Nature Communications</em>, 2023.</p>
Software Plagiarism Detection on Intermediate Representation Data Set
<p>This data set contains the necessary files used for the bachelor's thesis Software Plagiarism Detection on Intermediate Representation.</p> <p>This includes the data sets for the tests, the implemented code and scripts for the evaluation as well as referenced work.</p> <p> </p>
Summary of measured and modeled light curve parameters for diffuse, direct, and intermediate light curves for 14 whole-canopy 1mx1m plots sampled near the shrub LTER sites at Toolik Field Station, Alaska, summer 2012.
14 1m x 1m shrub plots were sampled the summer of 2012 under direct and diffuse light conditions. Light response curves were measured under each light condition for each plot using a Li-Cor 6400 to measure net ecosystem exchange (NEP); these measurements were modelled using a saturatingMichaelis-Menton formula. The best fit parameters for those models are contained here (Pmax, K, RE, Eo, and light compensation point) for each individual NEP light response curve (direct, diffuse, and intermediate light conditions) measured with corresponding NDVI , LAI, diffuse light fraction, and average temperature. Sorting variables and curve ID numbers for each curve match the corresponding data in the flux data file.
Tree-Ring Data for Co-Occurring White Spruce and Paper Birch at an Intermediate Aged Stand in the Bonanza Creek LTER Regional Site Network - 2018
This dataset contains tree ring widths of co-occurring white spruce and Alaska paper birch. The data were published as part of a 2021 article in Journal of Ecology.
Data to "Choroidal changes in intermediate age-related macular degeneration patients with drusen or pseudodrusen."
<p>This record contains experimental and analysis scripts (written in Matlab) as well as raw and processed data to reproduce the results shown in:</p> <p>Rosa R., Corazza P., Musolino M., Mochi C., Maiello G., Traverso C. E., & Nicolò M. Choroidal changes in intermediate age-related macular degeneration patients with drusen or pseudodrusen. European Journal of Ophthalmology. (in press)</p> <p> </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.