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369 results for “Permeability”
Field-based evidence for intra-slab high-permeability channel formation at eclogite-facies conditions during subduction
<p>Bulk rock analysis of metamorphic rock samples (major and trace element)</p>
Code and Data from Bhakti et al. on landscape permeability of urban landscape, v. 1.0
<p>This repository shares the code and data from the paper Bhakti et al. (in review), on integrating land cover, animal behavior, and master plan regulations to assess urban landscape permeability for birds. The paper is under review on Landscape and Urban Planning.</p> <p>Bhakti, T.; Pena, J.C.; Niebuhr, B.B.; Sampaio, J.; Goulart, F.F.; Azevedo, C.S.; Ribeiro, M.C., and Antonini, Y. Combining land cover, animal behavior, and master plan regulations to assess landscape permeability for birds. In review.</p>
Semi-analytical modeling of rate-dependent relative permeability in heterogeneous formations
<p>Numerical codes and results for MS: Semi-analytical modeling of rate-dependent relative permeability in heterogeneous formations</p>
Data from: Apolipoprotein M-bound sphingosine-1-phosphate regulates blood-brain barrier paracellular permeability and transcytosis
The blood-brain barrier (BBB) is formed by the endothelial cells lining cerebral microvessels. Here, we report that the BBB permeability is modified by apolipoprotein M (apoM)-bound sphingosine 1–phosphate (S1P). We used two-photon microscopy to monitor changes in BBB permeability in apoM-deficient mice (apoM-/-), showing significant increases in paracellular BBB permeability to small molecules without structural changes in junctional complexes between endothelial cells. Lack of apoM-bound S1P increased vesicle-mediated transfer of albumin across endothelium of brain pial and penetrating arterioles, whereas transcytosis in capillaries and venules remained unchanged. S1PR1 agonist SEW2871 rapidly normalized BBB permeability along both the paracellular and transcellular routes in apoM-/- mice. Thus, apoM-bound S1P maintains low paracellular BBB permeability for small molecules in all cerebral microvessels and low levels of adsorptive transcytosis in penetrating arterioles. Modulation of apoM/S1P-dependent signaling may be a novel strategy for the protection of brain endothelial cells to preserve the BBB function.
Long-time Delays in Induced Earthquakes Caused by Low-Permeability Bodies: Insights from the Xinfengjiang Reservoir, China
<p>This version adds waveforms of the catalog earthquakes from 2014 to 2018.</p>
Experimental and numerical investigations into the influence of temperature on the permeability of hydrate-bearing sediments
<p>Induced by heat injection and climate change, temperature change in hydrate reservoir significantly affects the permeability. A combination of experimental tests and fluid-mechanical-thermal coupling simulations is applied to investigate the temperature influence. The numerical and experimental data is listed here. Results show that the permeability decreases with increasing temperature with a quadratic function relation. Moreover, higher hydrate saturation will promote this reduction. In principle, the increase of temperature leads to linear narrowing of pore throats, further causes the quadratic function relation between permeability and temperature. Higher hydrate saturation will increase the thermal expansion and reduce the initial size of pore throats, which results in a more significant temperature sensitivity. The reduction of permeability may affect the advancement of decomposition front and the release of methane into atmosphere. Accordingly, a theoretical model is developed to describe the permeability-temperature relation, which offers a support for production estimation and environmental assessment.</p>
Introducing a transition domain for describing the solute exchange between macropores/fractures and matrix in dual-permeability system
<p>出口 1 至 5 的浓度值和出口处的总浓度记录在"实验数据"中。图 8 至 10 中的仿真结果数据记录在"仿真结果"中。构建数值模型的方法记录在"数值模拟"中,需要 COMSOL Multiphysics 将其打开。</p>
Innovative Strategies for Blood-Brain Barrier (BBB) Permeability Modeling: Harnessing the Power of Machine Learning-based q-RASAR Approach
<p>In the current research, we have unveiled an advanced technique termed the quantitative Read-Across Structure-Activity Relationship (q-RASAR) framework to harnesses the power of machine learning (ML) for significantly enhancing the precision of predictions related to blood-brain barrier (BBB) permeability. It is important to emphasize that the central objective of this study is not to introduce another model for predicting BBB permeability. Instead, our focus is on highlighting the improvement in predicting the BBB permeability of organic compounds by introducing the q-RASAR approach. This innovative methodology strives to enhance the precision of evaluating neuropharmacological implications and streamline the drug development process. In this investigation, we developed an ML-based q-RASAR PLS model using a dataset comprising 1012 compounds of diverse classes of heterocyclic and aromatic hydrocarbons, obtained from the freely accessible B3DB database (accessible at <a href="https://github.com/theochem/B3DB">https://github.com/theochem/B3DB</a>) to predict BBB permeability during the lead discovery phase for central nervous system (CNS) drugs. The model's predictive capability underwent validation using two external sets, encompassing a total of 1,130,315 compounds, including synthetic compounds and natural products (NPs) for data gap filling and other two external sets comprising 116 drug-like/drug compounds from FDA and ChEMBL databases to assess the model's reliability. This study aimed to bridge the data gap by employing a predictive model to estimate the impact of brain-plasma concentration ratios on BBB permeability for both synthetic compounds and natural products (NPs). To further enhance predictability, we have developed various other ML-based q-RASAR models. The insights from the developed model highlight the pivotal roles played by hydrophobicity, electronic effects, degree of ionization and steric factors as essential features facilitating the traversal of the blood-brain barrier. This research not only advances our understanding of the molecular determinants influencing the permeability of central nervous system drugs but also establishes a versatile computational platform for the rapid assessment of diverse compounds, facilitating informed decision-making in the realms of drug development and design.</p>
An Analytical Formulation for Correcting the Relative Permeability of Gas-Water Flow in Propped Fractures Considering the Effect of Brinkman Flow
<p>Brinkman flow can impose a strong effect on the fluid transportation within propped fractures, as well as on the well productivity.</p>
An Analytical Formulation for Correcting the Relative Permeability of Gas-Water Flow in Propped Fractures Considering the Effect of Brinkman Flow
<p><span><span>·<span> </span></span></span><span>The viscous shear from fracture walls and the resistance from propping materials induce Brinkman flow in propped fractures</span><span>.</span></p> <p><span><span>·<span> </span></span></span><span>Neglecting the effect of Brinkman flow can cause significant errors in evaluating the gas-water relative permeability in propped fractures.</span></p> <p><span><span>·<span> </span></span></span><span>An analytical formulation is proposed to correct the relative permeability of gas-water flow in propped fractures considering Brinkman flow.</span></p>
Permeability, acoustic emission and wave velocities during compaction of porous sandstone
Open the record for dataset details and reuse information.
Controls of Grain Breakage on Shear Band Morphology and Permeability Evolution in Fault Gouges
<p>The simulations are designed and run within the software platform PFC (https://www.itascacg.com/software/PFC). The data set is composed of results of two-dimensional (2D) Discrete Element Method (DEM) modeling performed by Li et al., with the licensed commercial <em>Particle Flow Code </em>2D version 6.0 (PFC2D 6.0) from Itasca Consulting Group, Ltd. </p>
Dataset for the manuscript of the "Permeability evolution of methane and water vapor when simultaneously transporting in shale"
<p>Dataset for the manuscript of the "Permeability evolution of methane and water vapor when simultaneously transporting in shale"</p>
Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations
<p>Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: tar -zcvf terpenoidpermeability.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*log" --exclude="*xsc" --exclude="*coor" --exclude="*vel" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*ppm" --exclude="*png" --exclude="*pdf" --exclude="*catchy*" --exclude="*svg" --exclude="*restart*" --exclude="*history" --exclude="core.*" --exclude="FFTW_NAMD*" --exclude="*avi" --exclude="*mp4" Terpenoid-Permeability, which intentionally excludes large files. The full dataset that includes trajectories is available upon request.</p> <p>The data is split into two directories initially "<strong>build</strong>" and "<strong>Simulations</strong>"</p> <ul> <li>"<strong>build</strong>" directory is the part where initial system for unbiased and biased simulation were build using "<strong>resolvate.tcl</strong>" and "<strong>smd-single-build-system.tcl</strong>" respectively.</li> <li>"<strong>Simulations</strong>" directory has the different namd files for running unbiased simulation, steered molecular dynamics and replica exchange umbrella sampling.</li> </ul> <p>The folder structure was generated using "<strong>gendirs*.py</strong>".<br> The unbiased simulations were run using "<strong>run.namd</strong>".<br> Steered molecular dynamics namd files were with name "<strong>step*.namd</strong>" and colvars configuration file are named "<strong>step*.conf</strong>".<br> <br> Replica exchange moleuclar dynamics (REUS) system was generated using "<strong>buildreplicas.tcl</strong>".<br> Replica windows size and force constant were written into a namd configuration file using "<strong>reus-genscript.py</strong>".<br> REUS general configuration file containing the parameters and forcefield is named as "<strong>base.namd</strong>".<br> Colvars for REUS are in "<strong>replicadistZcolvars.conf</strong>".<br> Umbrella sampling is performed with "<strong>umbrella.namd</strong>".</p>
Molecular dynamics simulation trajectory data for "Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function"
<p>Trajectories and input files corresponding to entries in Supplementary Table S1.</p>
Effects of fluid rheology and pore connectivity on rock permeability
<p></p> <p>The pore structure data associated with Figure 12 and Figure 13.</p>
Gas permeability and mechanical properties of dust grains at hyper- and zero-gravity
<p>Two-phase flow experimental data obtained from the TEMPusVoLA facility over the course of three Zero-gravity parabolic flight campaigns (<strong>PFCs</strong>). The experiment, designated 'System 1' , contains low-pressure gas and analogue dust particles (of diverse compositions, shapes, and sizes) that experience a low-pressure gas cross-wind normal to the gravitational force vector. During steady flight, the particles pack into the lower end of the chamber and the layer of granular media creates a pressure differential, which is used to extract permeability coefficients in both the continuum and molecular-diffusion dominated regimes. We compare the permeability both with and without the effect of gravity and make comparisons with the conditions on low-gravity objects in the solar system, such as planetesimals and the dust particles that comprise them. In particular, we are able to compare and contrast the cohesiveness of the dust-regolith analogue types, which has consequences for formation theories of Solar-system bodies. </p> <p> </p> <p><strong>Data products: </strong></p> <p><strong>Pressure, acceleration</strong></p> <p>Each file corresponds to a particular parabolic flight campaign and day of flight. The 4th Swiss PFC lasted 1 day in 2020. The 75 ESA PFC lasted 3 days in 2021, and the the 78th ESA PFC lasted 3 days in 2022. Data was obtained in System 1 during all flights of all campaigns, and for a set of 12-16 parabolas. On each parabola, we studied the sample in one out of three chambers and changed the gas mass flux rate after cycling through all three samples. The below files were used to correlate changes in sample gas permeability with changes in gravitational loading. </p> <p>-- Raw pressure files output from 6-channel pressure logger measuring pressure as function of time as .csv files: DATALOG_DATE. </p> <p>-- Raw acceleration files output from accelerometer measuring gravitational load on aircraft.</p> <p><strong>Imaging data</strong></p> <p>-- Movie sequences obained with high-resolution thor-labs camera. All three chambers were imaged, despite only one chamber being subject to active gas flow at any given time. movie1 and movie 2 are referenced in the associated publication. </p> <p><strong>Multimeter data</strong></p> <p><strong>-- </strong>Output from photo-diodes measured across 9 channels using a Keithley Multimeter/Multiplexor. Acquisition speed was 27 Hz. </p>
Data from: Is population structure in the European white stork determined by flyway permeability rather than translocation history?
European white stork are long considered to diverge to eastern and western migration pools as a result of independent overwintering flyways. In relatively recent times, the western and northern distribution has been subject to dramatic population declines and country-specific extirpations. A number of independent reintroduction programs were started in the mid 1950s to bring storks back to historical ranges. Founder individuals were sourced opportunistically from the Eastern and Western European distributions and Algeria, leading to significant artificial mixing between eastern and western flyways. Here we use mitochondrial and microsatellite DNA to test the contention that prior to translocation, eastern and western flyways were genetically distinct. The data show a surprising lack of structure at any spatial or temporal scale suggesting that even though birds were moved between flyways, there is evidence of natural mixing prior to the onset of translocation activities. Overall a high retention of genetic diversity, high Nef, and an apparent absence of recent genetic bottleneck associated with early 20th century declines suggest that the species is well equipped to respond to future environmental pressures.
Digital rock dataset for use in machine learning research of permeability prediction
<p>Datasets and codes for the paper "Hierarchical homogenization with deep-learning-based surrogate model for rapid estimation of effective permeability from digital rocks"</p>
Numerical results data of 'Impact of Injection Pressure and Polyaxial Stress on Hydraulic Fracture Propagation and Permeability Evolution in Greywacke: Insights from Discrete Element Models of a Laboratory Test'
<p>Numerical results data of '<strong>Impact of Injection Pressure and Polyaxial Stress on Hydraulic Fracture Propagation and Permeability Evolution in Greywacke: Insights from Discrete Element Models of a Laboratory Test</strong>'</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.