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369 results for “Permeability”
Mechanical data in support of "Permeability Partitioning through the Brittle-to-Ductile Transition and its Implications for Supercritical Geothermal Reservoirs"
<p>This folder contains 4 files with the nechanicakl data produced during the study titled "Mechanical data in support of "Permeability Partitioning through the Brittle-to-Ductile Transition and its Implications for Supercritical Geothermal Reservoirs". Each file correspond to an experiment ran at a different temperature:</p> <p>LG200C.txt: Lanhelin Granite, T = 200C, strain rate 10-6, Initial length = 42.32 mm</p> <p>LG400C.txt: Lanhelin Granite, T = 400C, strain rate 10-6, Initial length = 41.68 mm</p> <p>LG600C.txt: Lanhelin Granite, T = 600C, strain rate 10-6, Initial length = 41.78 mm</p> <p>LG800C.txt: Lanhelin Granite, T = 800C, strain rate 10-6, Initial length = 41.77 mm</p> <p>All data files contain the following columns: time (s), confining pressure (bar), displacement (mm), vertical load (kN), temperature (C), upstream pore pressure (bar), downstream porepressure (bar).</p> <p> </p>
Dataset related to article "Role of ultrastructural determinants of glomerular permeability in ultrafiltration function loss".
<p><em>The files contain the raw data related to the manuscript: "Role of ultrastructural determinants of glomerular permeability in ultrafiltration function loss" available at <a href="https://insight.jci.org/articles/view/137249">https://insight.jci.org/articles/view/13724</a>9.</em></p> <p><strong>Datasets:</strong></p> <p><strong>Scripts for CFD simulation of water passage through the glomerular filtration barrier (GFB) of Wistar, MWF and MWF-treated rats:</strong></p> <p><strong>STL_models</strong> - contains STL models of the unit cell of GFB reconstructed for the three groups of rats (i.e., WIST, MWF and MWFL). The dimensions assumed are presented in tables 2 and 4 in the main text and well explained in the Supplemental Material.</p> <p><strong>CFD_cases</strong> – contains cases in .rar archives for each group of rats; each case includes scripts which needed to run a CFD simulation of steady for incompressible, turbulent flow with porosity treatment, using the <strong><em>porousSimpleFoam</em></strong> solver in OpenFOAM. OpenFOAM version 6 (openfoam.org) was used for generating all data presented in this paper, but scripts should run well with updated versions.</p> <p><strong>Figure 1_Pores morphometrical analysis.xlsx </strong>- dataset for the calculation of distribution of slit pore size. These data are presented in Figure 1. </p> <p><strong>Figure 2_subpodocyte space morphometry.xlsx </strong>- dataset for the quantification of subpodocyte area. These data are presented in Figure 2. </p> <p><strong>Figure 5_CD151 and a3 integrin expression.xlsx </strong>- dataset related to the quantification of CD151, a3 integrin and their colocalization. These data are presented in Figure 5. </p> <p><strong>k_SupplTable2.xlsx</strong> – dataset for the calculation and total and relative permeability of each structural layer of GFB. These data are presented in Supplemental Table 2.</p> <p><strong>Neal-model_graphs_Figure4_SupplFigure3.xlsx</strong> - dataset for the calculation and of hydraulic resistances of GFB using the models of Neal et al. (2007). These data are presented in Figure 4 and Supplemental Figure 3.</p> <p><strong>Table 1_Systemic parameters.xlsx </strong>- dataset related to the systemic parameters. These data are presented in Table 1.</p> <p><strong>Table 2_Morphometric characterization.xlsx </strong>- dataset related to the morphometric characterization of epithelial slit pores and GBM. These data are presented in Table 2. </p> <p> </p> <p><strong>Abstract of the manuscript</strong></p> <p>The epithelial filtration slit is a crucial component of the glomerular capillary membrane, which is essential for maintaining glomerular filtration function. Though chronic kidney diseases are an immense clinical problem, the mechanisms through which structural alterations reduce glomerular water filtration have not yet been understood completely. To investigate the mechanisms underlying filtration function loss, we studied rats with spontaneously occurring progressive kidney disease, either treated with angiotensin II antagonist or untreated, combining high-resolution electron microscopy of the glomerular capillary wall with theoretical water filtration modeling. Under pathological conditions, epithelial filtration pores and the extension of the subpodocyte space were larger than in normal controls. Numerical analyses indicated that these ultrastructural changes increased hydraulic resistance of the glomerular capillary wall by extending coverage of the filtration barrier by the subpodocyte space, with the changes in hydrodynamic forces acting on podocytes likely being responsible for their detachment. Angiotensin II inhibition normalized the subpodocyte space's hydraulic resistance, restored mechanical podocyte load, and preserved CD151-α3 integrin complex assembly, improving podocyte adherence and survival. Our results show that ultrastructural changes in podocytes are major determinants of the hydraulic resistance of the glomerular capillary wall and highlight the mechanism of podocyte loss in kidney disease progression, as well as the mechanisms underlying angiotensin II inhibition.</p>
Datasets for the paper: "Rock-matrix porosity and permeability of the hydrothermally altered, upper oceanic crust, Oman ophiolite"
<p>This dataset includes all the data used for the paper submitted to the Journal of Geophysical Research: Solid Earth, entitled: <strong>Rock-matrix porosity and permeability in the hydrothermally altered, upper oceanic crust, Oman ophiolite. </strong></p> <p>One excel file is provided with the following tables on separate sheets:</p> <p>Table 1: Sample locations, alteration types, and petrophysical analyses</p> <p>Table S1: Trace element Zirconium and Yttrium analysis for this study’s sample set in Figure S1</p> <p>Table S2: Outcrop upscale results from image analysis</p> <p>Table S3: Sample bulk rock geochemistry</p>
(EMPIR 19ENG06 HEFMAG) Data sets of measurements of magnetic loss and complex permeability on amorphous and nanocrystalline samples up to the MHz range
<p>We measured the magnetic losses and the complex permeability of amorphous and nanocrystalline ribbons from DC to 1 GHz by combined application of fluxmetric and transmission line methods. Two transverse field annealed Co-based amorphous alloys, ~13 µm and ~25 µm tick and two nanocrystalline Finemet type alloys, ~13 µm and ~20 µm tick, endowed with defined transverse magnetic anisotropy, were characterized. </p>
Accumbal calcium-permeable AMPA receptors orchestrate neuronal ensembles underlying social attachment
Open the record for dataset details and reuse information.
Dataset of gas permeability and flux simulation of poplar tension wood
<p>The datasets generated during the study <Relationship between pore structure and gas permeability in poplar (<em>Populus deltoides</em> CL.'55/65') tension wood>.</p> <p> </p>
Dataset associated to Bioinspired electro-permeable glycans on carbon: Fouling control for sensing in complex matrices
<p>This dataset is associated to the publication "Bioinspired electro-permeable glycans on carbon: Fouling control for sensing in complex matrices" performed in Trinity College, Dublin, Ireland. The dataset contains raw data associated to the measures contained in the article: X ray photoelectron spectroscopy, Atomic force microscopy, cyclic voltammetries. This publication has emanated from research conducted with the financial support of Science Foundation Ireland (SFI) grant No. <a href="https://www.sciencedirect.com/science/article/pii/S0008622319311455#gs1">13/CDA/2213</a>. AM and JAB gratefully acknowledge support from the School of Chemistry and the Irish Research Council Grant No. <a href="https://www.sciencedirect.com/science/article/pii/S0008622319311455#gs2">GOIPG/2014/399</a>, respectively. EW is grateful for support by the Undergraduate Research Bursary Program of the Royal Society of Chemistry and Nuffield Foundation. Use of the XPS of Prof. I. V. Shvets and C. McGuinness provided under SFI Equipment Infrastructure funds. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. <a href="https://www.sciencedirect.com/science/article/pii/S0008622319311455#gs6">799175</a> (HiBriCarbon). The results of this publication reflect only the authors’ view and the Commission is not responsible for any use that may be made of the information it contains.</p>
Melt Focusing Along Permeability Barriers at Subduction Zones and the Location of Volcanic Arcs: Numerical models
<p>The dataset includes 2-D subduction zone models calculated by Comsol Mutiphysics®, slab geometry, subduction parameters, and the prediction results.</p> <p>Each numerical model solves the thermal structure of 31 subduction zones. The 2-D slab geometry of each subduction zone is obtained from the compilations of global subduction geometries based on earthquake catalogs Slab 1.0 and Slab2 (Hayes et al., 2012; 2018). Each slab geometry is imported in the corresponding Comsol model as a text file format. Below the point where the slab depth data is unavailable, the slab interface is simply defined as a straight line with the same dip to the bottom of the computation domain. The subduction parameters used in the models are available in Table 1.</p> <p>Using the calculated thermal structure at 30 Ma, we approximate the locations of the arc as the apices of 5 isotherms at 100°C interval within 800°C – 1200°C. The predicted arc locations from each isotherm are reported in Table 2 as the horizontal distance from the trench. The actual arc location in each model is defined as the point on the surface where the slab interface reaches the subarc slab depth <em>H</em> in Table 1 and reported as the horizontal distance from the trench in Table 2. The slab water loss depth and rate obtained from van Keken et al. (2011) are presented in Table 2. In case of the maximum temperature above the water loss depth is higher than the experimentally-derived melting condition, 800°C, we report the horizontal distance from the trench. The width of the horizontal distance of slab water loss depth is assumed as the expected melting region. </p>
Dataset for "Studying the effect of membrane permeability with a GPU-based Bloch-Torrey simulator"
<p>This dataset contains the results of the GPU-based simulations of diffusion in cardiac tissue. The data was used for the work presented at the ISMRM 27th Annual Meeting in 2019.</p>
CoUDlabs_WP8_T812_IKT_001 Permeable pavement clogging assessment using sediments with different properties
<p>This dataset includes raw and processed data from a series of laboratory tests that were conducted to develop and assess new and existing methods for analysing pavement performance and to gain insights into how these systems operate during their lifetime. The test method and specification used are based on the standards set by the Deutsches Institut für Bautechnik (DIBt), the German Institute for Construction Engineering. The tests are focused on determining hydraulic permeability and material retention of a cobblestone pavement with permeable joints under different sources of contamination, such as plastic dust and particulate sediments with different granulometries. The work is part of a joint research line between IKT and UDC towards the development of standardised methods to assess the long-term behaviour of different permeable pavement types during their lifetime. Data may be used to increase knowledge on permeable pavement clogging, allowing for developing improved design and maintenance strategies to optimise the long-term performance of permeable pavements.</p><p>This dataset is a result from the Joint Research Activity 3 (WP8, Improving Resilience and Sustainability in Urban Drainage solutions), Task 8.1.2. (Development of Scalable Measurement Protocols to Assess the Pollutant Retention and Release potentials of Urban Drainage Structures) within Co-UDlabs project, funded under the European Union's Horizon 2020 research and innovation program under grant agreement No 101008626. </p>
Normalized water permeability of hydrate-bearing sediments
<p>This dataset include some normalized water permeability, hydrate saturation, porosity and the water saturation of hydrate-bearing sediments </p>
Longyearbyen CO2 Lab - Porosity, permeability, density and mechanical data
<p>Porosity, permeability, density and mechanical testing measurements on core samples taken from the Longyearbyen CO2 Lab boreholes/drillcore.</p> <p>Sources are indicated in the file name, as are the included data types.</p>
Permeability of granular mixtures under shear - videos for shear rate 213 s-1
<p>A granular column comprising Ballotini glass beads of diameters 250 μm, 125 μm, 90 μm and 63 μm is sheared at shear rate 213 s-1, while simultanouesly being fluidised with an increasing air flux rate. The data set includes videos of the granular column for each size fraction.</p>
Permeability of granular mixtures under shear - videos for zero shear rate
<p><strong>Videos of fluidisation experiments</strong></p> <p>A static granular column comprising Ballotini glass beads of diameters 250 μm, 125 μm, 90 μm and 63 μm is fluidised with an increasing air flux rate. The data set includes videos of the granular column for each size fraction.</p>
Permeability of granular mixtures under shear
<p><strong>Data set for fluidisation experiments</strong></p> <p>A granular column cmprising Ballotini glass beads of diameters 250 μm, 125 μm, 90 μm and 63 μm is sheared at a range of shear rates, γ˙ = 0, 16, 49, 115, 213 s−1, whilst simultaneously being fluidised with an increasing air flux rate. The data set includes the values of the pressure gradient across the granular column, Δp (Pa) and the corresponding air flux rate, Q (L min-1), for each size fraction and each shear rate.</p> <p> </p>
reduced permeability
<p># permeability reduction</p> <p>Matlab scripts to simulate the reduced permeability of porous granular media due to ice or hydrate. The functions are organized in two classes, including:<br> - `soil.m`. Calculate the soil freezing curves using a Monte Carlo method on synthetic soil models.<br> - `frw.m`. Calculate the permeabilities of the synthetic soil models, ice-free or ice-bearing, and compare the results against published models and measurements.<br> - `duct.m`. Examples showing the calculations in straight ducts of simple cross-sections.</p> <p>Parameters and data for calculations are in:<br> - `param.json`. All relevant parameters.<br> - `data/conductivity.xlsx`. Digitized measurements used for validation.<br> - `data/kr_finney.mat`. Simulated permeability reduction of Finney pack.<br> - `data/mc`. Simulated Monte Carlo results to calculate the soil freezing curves.<br> - `data/deposit`. Synthetic soil models, including the mono-dispersed Finney pack, and poly-dispersed synthetic soil.</p> <p>For details of the code, refer to the paper *Estimating permeability of partially frozen soil using floating random walks* published in Water Resources Research. </p> <p>This repository can also be found on <a href="https://gitlab.com/jzchenjz/permeability-reduction">GitLab</a>.</p>
Role of internal loop dynamics in antibiotic permeability of outer membrane porins
<p>Representative structures for Markov State models for wild type and mutants of OmpF "Coupling of internal loop dynamics and antibiotic permeation in outer membrane porins"</p>
Source molecular simulation data for calculating energy and friction profiles and permeability coefficients through model lipid membranes
<p>Energy files from GROMACS molecular dynamics simulations with enhanced free energy sampling contain time-dependent evolution of the free energy profiles and friction profiles (and other energies and simulation properties) that were used for calculating permeability coefficients in the publication https://www.biorxiv.org/content/10.1101/2021.07.16.452599v1</p> <p>Simulation system contains a lipid POPC or DPPC bilayer with a varying amount of cholesterol (specified as mol% in the file name). Hydrophobic level of the permeating particle is specified as "level-I", "level-II" etc. When unspecified in the file name, the particle is hydrophobic level "III". Lipids D-C14-PC denote PC lipids with both tails monounsaturated of length 14 carbon atoms. DOPC is equivalent to D-C18-PC. (Detailed description in the publication)</p> <p>Adaptive Weighted Histogram (AWH) method was used to sample the free energy profile of translocating small molecule through the lipid bilayer.</p> <p>GROMACS tool `gmx awh` reads the files and provides the described profiles.</p> <p>Files were generated by GROMACS `mdrun` simulation engine version 2019.3.</p> <p> </p> <p>Coarse-grained MARTINI 3.0 model was used for modeling the biomolecular interactions.</p> <p>Scripts to perform the simulations and the files with initial configurations and simulation settings are stored in a public GitHub repository depozited on Zenodo.org: <a href="https://doi.org/10.5281/zenodo.5082249">https://doi.org/10.5281/zenodo.5082249</a>.</p> <p> </p> <p>Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).</p> <p>Lindahl, V., Lidmar, J. & Hess, B. Accelerated weight histogram method for exploring free energy landscapes. J. Chem. Phys. 141, 044110 (2014).</p> <p>Souza, P. C. T. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat. Methods 18, 382–388 (2021).</p> <p>Melcr, J. Git repository with analysis scripts for MD simulations of permeability through lipid membranes. (2021) doi:<a href="https://doi.org/10.5281/zenodo.5082249">https://doi.org/10.5281/zenodo.5082249</a>.</p>
Results of core filtration tests to assess the reduction in permeability due to colloid migration
<p>Results of filtration tests of three core samples, filtered liquid - deionized water and kerosene. Filtration installation - AFS-300. Filtering conditions inside files. Core samples are registered in IGSN, the numbers and type of fluid are indicated in the file name. Prior to filtration, the samples are saturated under vacuum for 24 hours. Before filtration, the samples were kept in an AFS-300 core holder at confining and pore pressure for 24 hours.</p> <p>New data added (08/03/2022)</p>
From nature reserve to mosaic management: improving matrix survival, not permeability, benefits regional populations under habitat loss and fragmentation
<p>Although matrix improvement in fragmented landscapes is a promising conservation measure, matrix permeability (willingness of an organism to enter the matrix) and movement survival in the matrix are usually aggregated. Consequently, it is unknown which matrix property needs to be improved. It also remains unclear whether matrix upgrading from dispersal passage to providing reproduction opportunities has large conservation benefits and whether there are interactive effects between habitat and matrix management.</p> <p>We examined matrix effects on regional populations across a gradient of habitat loss and fragmentation using simulation experiments that integrated demographic processes and movement modeling based on circuit theory. We separately modified the levels of matrix permeability and movement survival to evaluate their individual effects. We also altered the amount and configuration of not only habitat but also improved matrix to assess their effects on population vital rates (size, survival and density).</p> <p>In binary landscapes comprising habitat and unimproved matrix, matrix movement survival had larger effects on population vital rates than matrix permeability. Increasing movement survival increased vital rates, yet, increasing matrix permeability decreased vital rates. Increased permeability required corresponding increased movement survival to offset potential negative population outcomes.</p> <p>When subsets of the matrix functioning as dispersal passage only (where no reproduction opportunities existed) were improved, increasing matrix permeability but holding movement survival constant reduced all vital rates, especially with increasing habitat fragmentation. In contrast, when movement survival increased, vital rates increased given strong habitat fragmentation. The benefits of upgrading dispersal passage to provide reproduction opportunities for population survival were greatest when habitat amount was moderate. We also found synergetic effects between amounts of habitat and improved matrix, and the benefits of matrix improvement were promoted when improvement was achieved in a spatially aggregated manner.</p> <p><em>Synthesis and applications</em>: Matrix improvement and connectivity modeling aimed at increasing movement survival will likely bring larger conservation benefits than those for improving permeability alone. Buffering and connecting habitat remnants with improved matrix could provide benefits as long as movement survival is increased. Simultaneous implementation of habitat management and matrix improvement would yield synergistic conservation benefits.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.