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573 results for “Structure analysis”
Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
<p><strong>Summary</strong></p> <p>Uganda is endowed with a large population of goats from predominantly indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture of the exotic breed Boer is still limited. Using a medium density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Ugandan goat breeds. Samples from five indigenous Ugandan goat breeds including Mubende (n=29), Kigezi (n=29), Small East African (n=29), Sebei (n=29) and Karamojong (n=15), and the exotic breed Boer (n=13) from different agro-ecological regions of Uganda were genotyped using the GoatSNP50 BeadChip. Analysis of genotype data revealed high levels of polymorphism with the proportion of polymorphic SNPs ranging from 0.885 in Kigezi to 0.928 in Sebei. The overall mean genetic diversity indices across breeds for <em>H<sub>O</sub></em> and <em>H<sub>E</sub></em> was 0.355±0.147 and 0.384±0.143 respectively. Principle components, genetic distances and ADMIXTURE analyses revealed weak population sub-structuring among the breeds. Principle components separate Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong are tightly entangled together while Mubende occupies a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. ADMIXTURE and four population test analyses further revealed gene-flow from Boer to Ugandan indigenous goat breeds and varying levels of admixture among the Ugandan indigenous breeds. Generally, moderate to high levels of genetic variability were observed in the Ugandan goat breeds. Our findings provide useful insight to devise strategies to maintain genetic diversity in local goat breeds from Uganda and to design appropriate breeding programs to exploit within breed diversity and heterozygote advantage in cross-breeding schemes.</p>
Biases of STRUCTURE software when exploring introduction routes: Datasets, STRUCTURE outputs, simulation and analysis pipeline
<p>This archive is associated with the article “Biases of STRUCTURE software when exploring introduction routes of invasive species”. Authors: Eric Lombaert, Thomas Guillemaud & Emeline Deleury.</p> <p>The file contains the 22,500 simulated datasets, the corresponding 900,000 STRUCTURE outputs and the summary statistics files. It also contains SIM_STRUCT which is a home-made pipeline developed for the purpose of carrying out analyzes as described in the manuscript. It can be used to simulate and summarize datasets, and to perform STRUCTURE analyses in batch on those simulated datasets. It is currently based on several softwares such as DIYABC, ARLSUMSTAT and STRUCTURE, as well as on some home-made PERL scripts. A tutorial is included.<br> See the Readme file for details.</p>
Supporting dataset: "Analysis of tide and offshore storm-induced water table fluctuations for structural characterization of a coastal island aquifer"
<p>Included in this repository are supporting field data and final model input files used to produce the results of the manuscript:</p> <p>Trglavcnik, V., Morrow, D., Weber, K. P., Li, L., & Robinson, C. E. (2017), "Analysis of tide and offshore storm-induced water table fluctuations for structural characterization of a coastal island aquifer."</p> <p>This dataset contains:</p> <ul> <li>SableIsland_data.xlsx <ul> <li>Data used to produce figures in the above manuscript. </li> </ul> </li> <li>Final_SS.zip <ul> <li>Input files for the final model (see Figure 3 in manuscript), steady-state SEAWAT simulation. </li> </ul> </li> <li>Final_PBC.zip <ul> <li>Input files for the final model, transient SEAWAT simulation with a sinusoidal tidal boundary implemented by the Periodic Boundary Condition package (developed for MODFLOW by Post, 2011).</li> </ul> </li> </ul> <p>All data and files are licensed under Creative Commons Attribution Share Alike 4.0 International.</p> <p> </p> <p> </p>
Data for "Structure, short-range order, and phase stability of the Al$_x$CrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis"
<p>Data associated with "Structure, short-range order, and phase stability of the AlxCrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis", published in npj Comput. Mater. <strong>10</strong>, 271 (2024).</p>
Elasto-plastic residual stress analysis of selective laser sintered porous materials based on 3D-multilayer thermo-structural phase-field simulations
<p>The supporting data and utilities from the publication "Elasto-plastic residual stress analysis of selective laser sintered porous materials based on 3D-multilayer thermo-structural phase-field simulations" are recorded in this dataset. </p> <p>Non-isothermal phase-field simulations of SLS process on SS316L material and subsequent elasto-plastic calculations were performed to analyze the development of plastic deformation and residual stress in SLS produced components during the processing. The dependence of the fusion zone, residual stress and plastic strain on the processing parameters namely, Beam power (Unit: Watts) and Scan speed (Unit: mm/s) were investigated. </p> <p>To promote FAIR research data principles, the processed simulation data from the thermo-elasto-plastic calculations for all the process parameter sets (hereby refered as P-v sets) are curated in this dataset. The raw temporal data obtained from the processing simulations and the elasto-plastic could not be included in this dataset due to its high volume. However, the corresponding raw data can be requested by contacting the creators of this dataset (Yangyiwei Yang: <a href="mailto:yangyiwei.yang@mfm.tu-darmstadt.de">yangyiwei.yang@mfm.tu-darmstadt.de</a> and Somnath Bharech: <a href="mailto:somnath.bharech@tu-darmstadt.de">somnath.bharech@tu-darmstadt.de</a>).</p> <p>This dataset includes: </p> <ul> <li><code>average_value.csv</code>: Contains average values of mechanical properties (such as residual stress, plastic strain) for the powder bed and the fused strut of all the process parameter sets.</li> <li><code>mesostructures_tep_sls.zip</code> : Contains resampled mesostructures obtained at the last time step of the SLS processing simulations with thermo-elasto-plastic calculations for the P-v sets reported in the aforementioned investigation. Nomenclature of the sub-directories indicating the P-v sets follows: <code>tep_<beam power>-<scan speed></code>. Each of these sub-directories contain the mesostructures from last time step of the thermo-elasto-plastic analysis of each of the four layer scans and is named as: <code>TP_layer{1..4}_output_final.e</code>. These files can be opened using Paraview v.5.8.1 or higher. The nodal values are explained as follows:</li> </ul> <table> <tbody> <tr> <td><strong>Nodal value name</strong></td> <td><strong>Symbol</strong></td> <td><strong>Description</strong></td> <td><strong>Unit</strong></td> </tr> <tr> <td>T</td> <td>\(T\)</td> <td>Temperature field normalized by \(T_M\)</td> <td>-</td> </tr> <tr> <td>c</td> <td>\(\rho\)</td> <td>Substance order parameter</td> <td>-</td> </tr> <tr> <td>eps_ij </td> <td>\(\varepsilon\)</td> <td>Strain</td> <td>-</td> </tr> <tr> <td>epsp_ij</td> <td>\(\varepsilon^\text{pl}\)</td> <td>Plastic strain</td> <td>-</td> </tr> <tr> <td>peeq</td> <td>\(p_\text{e}\)</td> <td>Accumulated plastic strain</td> <td>-</td> </tr> <tr> <td>sigma_ij </td> <td>\(\sigma\)</td> <td>Stress</td> <td>MPa</td> </tr> <tr> <td>vonmises</td> <td>\(\sigma_\text{e}\)</td> <td>von Mises stress </td> <td>MPa</td> </tr> <tr> <td>u</td> <td>\(\mathbf{u}\)</td> <td>Displacement</td> <td>µm</td> </tr> </tbody> </table> <p> </p>
Input data of the multi-patch geometries used in: A. Farahat, H. M. Verhelst, J. Kiendl, M. Kapl, Isogeometric analysis for multi-patch structured Kirchhoff–Love shells, Computer Methods in Applied Mechanics and Engineering 411 (2023) 116060 DOI: 10.1016/j.cma.2023.116060
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Fig. 2. A in A preliminary study of genetic structure and relatedness analysis of Nutria (Myocastor coypus) in Upo Wetland
Fig. 2. A bar plot representing the estimated membership coefficients of nutria individuals (K=2).
Fig. 1 in A preliminary study of genetic structure and relatedness analysis of Nutria (Myocastor coypus) in Upo Wetland
Fig. 1. Maps denoting Upo Wetland where nutrias were collected.
Structural Analysis of USP5 Zf-UBD
<p>Analysis of the <a href="https://zenodo.org/record/1209986#.Wr1Pqy7wapo">solved structure</a> of USP5 zinc finger ubiquitin binding domain (Zf-UBD) in crystallization conditions of 1.8 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 5.5, 1.7 mM l-glutathione reduced, l-glutathione-oxidized to determine if the ubiquitin binding pocket is accessible through solvent channels for inhibitor screening. </p>
Fine vertical structures at the cloud heights of Venus revealed by radio holographic analysis of Venus Express and Akatsuki radio occultation data -- dataset
<p>The data used in the figures in the paper "Fine vertical structures at the cloud heights of Venus revealed by radio holographic analysis of Venus Express and Akatsuki radio occultation data" by Imamura et al. (J. Geophys. Res)</p> <p>The description of the columns in the files are given in the header section.</p>
Supplementary data for: Graphene Microelectrode Arrays, 4D Structured Illumination Microscopy, and a Machine Learning Spike Sorting Algorithm Permit the Analysis of Ultrastructural Neuronal Changes During Neuronal Signalling in a Model of Niemann-Pick Disease Type C
<p>Supplementary example data for the work presented in "<em>Graphene Microelectrode Arrays, 4D Structured Illumination Microscopy, and a Machine Learning Spike Sorting Algorithm Permit the Analysis of Ultrastructural Neuronal Changes During Neuronal Signalling in a Model of Niemann-Pick Disease Type C</em>". </p> <p><strong>Abstract: </strong></p> <p>Simultaneously recording network activity and ultrastructural changes of the synapse is essential for advancing our understanding of the basis of neuronal functions. However, the rapid millisecond-scale fluctuations in neuronal activity and the subtle sub-diffraction resolution changes of synaptic morphology pose significant challenges to this endeavour. Here, we use specially designed graphene microelectrode arrays (G-MEAs), which are compatible with high spatial resolution imaging across various scales as well as permit high temporal resolution electrophysiological recordings to address these challenges. Furthermore, alongside G-MEAs, we have developed an easy-to-implement machine learning algorithm to efficiently process the large datasets collected from MEA recordings. We demonstrate that the combined use of G-MEAs, machine learning (ML) spike analysis, and four-dimensional (4D) structured illumination microscopy (SIM) enables monitoring the impact of disease progression on hippocampal neurons which have been treated with an intracellular cholesterol transport inhibitor mimicking Niemann-Pick disease type C (NPC), and show that synaptic boutons, compared to untreated controls, significantly increase in size, leading to a loss in neuronal signalling capacity.</p> <p> </p>
Interactive Outputs for "Automated Mixture Analysis via Structural Evaluation"
<p>HTML files with interactive outputs related to the mixture assignments discussed in the paper "Automated Mixture Analysis via Structural Evaluation."</p>
Constant plane shift model: structure analysis of martensitic phases in Ni50Mn27Ga22Fe1 beyond non-modulated building blocks
<p>Difraction data for lattice parameter calculation, Origin files</p>
Microsatellite-based analysis of genetic structure and gene flow of Mythimna separata (Walker) (Lepidoptera: Noctuidae) in China
<p>The oriental armyworm, <i>Mythimna separata</i>, is a serious agricultural pest in China. Seasonal and roundtrip migration has recently led to sudden, localized outbreaks and crop losses. To evaluate genetic differentiation between populations in eastern and western China and elucidate gene flow, the genetic structure of 20 natural populations from nine provinces was examined using seven microsatellite markers. The results indicated high genetic diversity. However, little to moderate (0 < <i>F</i><sub>ST</sub> < 0.15) genetic differentiation was detected, and there was no correlation between genetic distance and geographical distance. Bayesian clustering analysis identified three groups whereas discriminant analysis of principal components identified ten clusters that were considered as two clear‐cut clusters and one admixed group. Gene flow occurred frequently in most population pairs, and an asymmetrical migration rate was detected in several pairwise population comparisons. The bottleneck test showed that few populations had experienced recent bottlenecks. Correspondingly, large‐scale and long‐distance migration of <i>M. separata</i> has caused low genetic differentiation and frequent gene exchange. Our findings are important for studying genetic evolution and help to improve predictions of <i>M. separata</i> outbreaks in China.</p>
Retrieving 2D laterally varying structures from multi-station surface wave dispersion curves using multiscale window analysis
<p>Here are the waveform data used in the Geophysical Journal International paper entitled "Retrieving 2D laterally varying structures from multi-station surface wave dispersion curves using multiscale window analysis". The dataset is used for the reader who wants to reproduce the result in the paper.</p>
Supplemental material to 'A variational rigid-block modelling approach to nonlinear elastic and kinematic analysis of failure mechanisms in historic masonry structures subjected to lateral actions'
<p>This repository contains the data necessary to reproduce the content of the article:</p> <blockquote> <p>A variational rigid-block modelling approach to nonlinear elastic and kinematic analysis of failure mechanisms in historic masonry structures subjected to lateral actions (2021). Earthquake Engineering & Structural Dynamics, 1–23. <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/eqe.3512">https://doi.org/10.1002/eqe.3512</a></p> </blockquote> <p>The file <strong>01_Dataset.zip</strong> contains the dataset. The companion document <strong>00_Dataset_description.pdf </strong>describes the content of the dataset, guiding the analyst to its use in order to (i) reproduce the article's results and (ii) compare the article's results to new results brought by the analyst, e.g. by comparison with other numerical models.</p> <p>Version history</p> <p>v2: updated references in 00_dataset description.pdf </p>
Data for "Advanced Structural Health Monitoring Method by Integrated Isogeometric Analysis and Distributed Fiber Optic Sensing"
<p>This dataset includes the experiment and simulation data of a new structural health monitoring system using distributed fiber optic sensing (DFOS) and Isogeometric Analysis (IGA).</p> <p>The experiment setup was a 5mm thick PVC pipe with a fiber optic cable wrapped around the outer surface of the pipe. The PVC pipe was subjected to an applied deformation and the distributed strains along the optical fiber was measured with a Neubrescope (NBX7031) instrument using Rayleigh backscattering technology.</p> <p>The simulation was performed using the in-house code JWRIAN-IGA developed in Joining and Welding Research Institute, Osaka University. The simulated data includes deformation, stress and strain distributions of the pipe, and projected one-dimensional fiber strains. The visualization files are post-processed with ParaView software.</p>
Results of the analysis of the structure of biomass after microwave-assisted hydrotropic pretreatment.
<p>Results of analyzes of the structure of lignocellulosic biomass of various origins. The analyzes include the use of FTIR, SEM, XRD and NMR techniques. The work was supported by the National Science Centre, Poland, grant No. 2020/37/B/NZ9/00372.</p>
Tissue-engineered vocal fold replacement in swine: Methods for functional and structural analysis.
<p>S2 Data. 5534 pig squeal events investigated in this study, provided in a folder structure sorted by pigs, pre- / post-treatment and recording date as .wav files.</p>
Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis
<p>Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to inter-specific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. There has been concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here we apply genome-wide single nucleotide polymorphism (SNP) genotyping to a set of 385 wild and captive dingoes from across Australia and then carry out comparisons to domestic dogs, and perform ancestry modelling and biogeographic analyses to characterize population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes, challenging previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in southeastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policy makers to assess and inform dingo management policy and legislation moving forwards.</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.
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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.