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311 results for “function dataset”
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>
dataset for bioRxiv preprint titled 'Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease'
<p>This data supports the Figures in the preprint titled</p> <p><strong>Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease</strong></p> <p><strong>working abstract</strong></p> <p>The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies. It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease, which is a critical dynamic region involved in non-specific polypeptide binding during invasion and infection of the host cell. In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV). We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.</p>
Dataset presented in the recently submitted AGU manuscript "Constraining the crustal and mantle conductivity structures beneath islands by a joint inversion of multi-source magnetic transfer functions"
<p>Dataset (observed tippers, solar quiet global-to-local transfer functions, and global Q responses) presented in the recently submitted AGU manuscript "Constraining the crustal and mantle conductivity structures beneath islands by a joint inversion of multi-source magnetic transfer functions".</p>
De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation - DATASET
<p>All models used for the paper "De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation".</p>
Dataset: Facile functionalization of carbon electrodes for efficient electroenzymatic hydrogen production
<p>This dataset contains all of the data used to create the plots in both (i) the main article and (ii) the supporting information.</p> <p>The corresponding journal article can be found here:</p> <p><a href="https://doi.org/10.1021/jacsau.2c00551">https://doi.org/10.1021/jacsau.2c00551</a> </p>
Dataset: Core excitations and ionizations of uranyl in Cs2UO2Cl4 from relativistic embedded damped response time-dependent density functional theory and equation of motion coupled cluster calculations
<p>This dataset collects the unprocessed (= outputs from calculations) results discussed in the paper titled "Core excitations and ionizations of uranyl in Cs2UO2Cl4 from relativistic embedded damped response time-dependent density functional theory and equation of motion coupled cluster calculations", by Wilken Aldair Misael and Andre Severo Pereira Gomes. It also contains the figures used in the manuscript.</p>
dataset relate to article: "Functional Characterization of Two Variants at the Intron 6-Exon 7 Boundary of the KCNQ2 Potassium Channel Gene Causing Distinct Epileptic Phenotypes"
<p><strong>Sequencing Analysis performed at Fondazione Besta and carried out as part of the study mentioned at title</strong></p>
Protein Function Embeddings: First Beta Release of Datasets
<p>This release corresponds to the datasets generated from a thesis work that explores how information for protein functions can be exploited through embeddings so that the produced information can be used to improve protein function annotations. The underlying hypothesis here is that any pair of proteins with high sequence similarity will also share a similar biological function which would be reflected by the corresponding protein embeddings. The comparison and evaluation of this is done using two text-driven embedding approaches: Word2doc2Vec and Hybrid-Word2doc2Vec.</p>
Dataset of Thermography captures the differential sensitivity of dryland functional types to changes in rainfall event timing and magnitude
<p>The folder contains all data that have been used in the article "<strong>Thermography captures the differential sensitivity of dryland functional types to changes in rainfall event timing and magnitude" </strong>published in the "New Phytologist" journal.</p> <p>https://doi.org/10.1111/nph.19127</p>
Dataset to the article "Omnidirectional endpoint force control through Functional Electrical Stimulation" by Marek Sierotowicz and Claudio Castellini
<p>The present .zip files contains the anonimized datasets of a static force output control test facilitated through FES.</p> <p>In addition, the DataExtraction MATLAB code is meant to provide the synchronisation offsets for the logs.</p> <p>The data is sampled from 3 anonymized participants, who all signed informed consent forms.</p> <p>The experiment was carried out in compliance with the standards of the Declaration of Helsinki, and was approved by the ethical committee of the Friedrich-Alexander Universität Erlangen-Nürnberg (approval ID 22-304-S).</p> <p> </p>
Search-based Software Testing Driven by Automatically Generated and Manually Defined Fitness Functions - Dataset and Results
<p>This dataset contains the replication package for the paper: Federico Formica, Tony Fan, and Claudio Menghi. 2023. "Search-based Software Testing Driven by Automatically Generated and Manually Defined Fitness Functions".</p> <p>The dataset contains:</p> <ul> <li>The models used in the evaluation section.</li> <li>All the results obtained by running Athena-S on the models.</li> <li>The scripts that automatically analyze the results file and produce the tables and figures used in the paper.</li> </ul>
Regression Datasets: Strength as a Function of Liquid Water Content in Different Snow Types
<p>This repository contains two datasets used for determining the shear strength of different snow types as a function of liquid water content. It also contains one dataset with additional information pertaining to our experiment, including site and condition details. <strong>Please read the 'Read me.txt' file before using these datasets.</strong></p>
Targeted social immunity is associated with a pathogen-specific erosion of individual immune function in ants - dataset
<p>Complete dataset of quantitative data and R scripts used to generate the figures and statistics of the publication, sorted by figure panel number. Information about data structure are including in the scripts. </p>
Assessing consistency across functional screening datasets in cancer cells
Open the record for dataset details and reuse information.
Geo-referenced crop-nutrient response function dataset for Tropical Africa
Open the record for dataset details and reuse information.
Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome - datasets
<p>This is an archive of the repository held under https://github.com/dmnfarrell/gordon-group/tree/master/mbovis_annotation</p> <p>It contains a notebook and required input files for updating the MTB/Mbovis AF2122/97 genomes with new protein product annotations from literature.</p> <p>D Farrell UCD February 2020</p> <p>Updates to M.bovis genome (Aug 2019):<br> added 611 product annotations<br> added 689 gene names<br> added 5 manually edited entries from pdb hits<br> removed locus_tags for repeat_region features<br> added prefix to tRNA and mobile_element features for consistency</p> <p><br> References<br> Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome (https://www.biorxiv.org/content/10.1101/757823v1)</p>
Dataset for Manthan: A Data Driven Approach for Boolean Function Synthesis (CAV-20 paper)
<p>The data set consists of 609 benchmarks used for experimental evaluation of <a href="https://arxiv.org/abs/2005.06922">paper</a> titled 'Manthan: A Data-Driven Approach for Boolean Function Synthesis" published in International Conference of Computer-Aided Verification (CAV), 2020 . The benchmarks are from following sources:</p> <ul> <li>Prenex-2QBF track of<a href="http://www.qbflib.org/qbfeval17.php"> QBFEval-17</a> and <a href="http://www.qbflib.org/qbfeval18.php">QBFEval-18</a></li> <li>Arithmetic set (Srivastava, Gulwani, Foster 2013).</li> <li>Disjunctive set (Akshay, Charkraborty, John, Shah 2017).</li> <li>Factorization set (Akshay, Charkraborty, John, Shah 2017).</li> </ul>
Dataset for a systematic technology review of Function-as-a-Service platforms
<p>Description</p> <p>This dataset comprises the results of analysis of 3 commercial and 7 open source FaaS platforms. The included Excel sheet lists the results grouped into multiple classification categories and dimensions. The data for each platform reside in a separate tab, and for every collected fact there is a corresponding link to the documentation or software repository.</p>
Dataset for "Analytic High-order Geometric Derivatives with Polarizable Embedding in a Response Function Framework"
<p>This dataset contains data for the article "Analytic High-order Geometric Derivatives with Polarizable Embedding in a Response Function Framework"</p>
Dataset for Ongole at al. - Functional traits predict tree-level phenological strategies in a mesic Indian savanna
<p>Leaf phenology influences terrestrial primary production by determining the period of carbon uptake. While dominant leaf habit (evergreen/deciduous) is predictable at large scales based on environmental factors, there is substantial variability in the timing of key events such as leaf flush and senescence at smaller site-level scales. How much of this variability is explained by species functional traits related to a plant's carbon economy? We monitored leaf phenology for 113 individual trees of eleven dominant species in an Indian mesic savanna. Specifically, we related leaf functional traits and wood density to the (i) timing of leaf flush, leaf maturity, peak canopy and senescence, (ii) duration of leaf deployment, (iii) duration from start of senescence to leaflessness, and (iv) time to attainment of peak mature canopy following leaf flush. We expected species that use resources conservatively (low specific leaf area (SLA), high leaf dry matter content, low leaf nitrogen and high wood density) to senesce later and retain their leaves longer. For all species, leaflessness was most pronounced in early dry season and leaf flushing occurred in the late dry season. Species with high leaf carbon and dry matter content showed earlier leaf maturation, attained peak mature canopies sooner and deployed leaves longer. Species with high SLA, leaf nitrogen and low wood density showed earlier senescence but relationships were weak. In this savanna, phenology at fine scales was indeed associated with species functional traits relating to carbon investment, but these relationships were strong only when intra-specific variation in phenology was low.</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.