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265 results for “elemental analysis”
IODP Expedition 361 ICP-AES elemental analysis (solids)
<p>Elemental contents in hard rock and sediment samples was measured by inductively coupled plasma - atomic emission spectrocopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.</p>
Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family
<p>We collected all currently available structures for proteins in the Cytochrome P450 family and annotated their secondary structure elements using SecStrAnnotator software (https://webchem.ncbr.muni.cz/Wiki/SecStrAnnotator). We used 2nnjA as the template domain for the annotation. Based on these annotations, we analysed the occurrence, length distribution, amino acid sequence, and presence of structural irregularities (β-bulges, 3<sub>10</sub>-helices, π-helices) of each secondary structure element class. We also statistically compared the bacterial vs eukaryotic structures. For the secondary structure element classes with sufficient sequence conservation, the most conserved residue is annotated as the reference residue.</p> <p>Main files:</p> <ul> <li><strong>set_ALL.json</strong> - Set-ALL: list of 1012 protein domains belonging to the Cytochrome P450 family (CATH accession 1.10.630.10 + Pfam accession PF00067, accessed on 7 July 2020, one domain per PDB entry)</li> <li><strong>set_NR.json</strong> - Set-NR: non-redundant list of 183 domains (one domain per UniProt ID)</li> <li><strong>domain_lists_table.tsv</strong> - Overview of Set-ALL and Set-NR and separation into subsets Set-NR-Bact (bacterial), Set-NR-Euka (eukaryotic), Set-NR-Arch (archaeal), Set-NR-Viru (viral)</li> <li><strong>structures/template_2NNJ-template.sses.json</strong> - Manually prepared annotation template (domain 2nnjA)</li> <li><strong>structures/template_2NNJ.cif</strong> - Structure of the template domain (2nnjA)</li> <li><strong>annotations_with_reference_residues_ALL.json, annotations_with_reference_residues_ALL.tsv</strong> - Annotation of secondary structure elements for Set-ALL</li> <li><strong>annotations_with_reference_residues_NR.json, annotations_with_reference_residues_NR.tsv</strong> - Annotation of secondary structure elements for Set-NR</li> <li><strong>aligments_NR</strong> - Multiple sequence alignments for each SSE class (Set-NR)</li> <li><strong>logos_NR</strong> - Sequence logos for each SSE class (Set-NR)</li> <li><strong>plots</strong> - Plots of SSE occurrence, length distribution, contained helix types and beta-bulge occurrence (Set-NR), some plots show the comparison between Set-NR-Bact and Set-NR-Euka</li> <li><strong>statistical_tests.ods</strong> - Comparison of SSE occurrence between Set-NR-Bact and Set-NR-Euka by the test of equal proportions and the Fisher test, comparision of the SSE length by the Kolmogorov-Smirnov test and the two-sample Wilcoxon test</li> </ul>
Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabrics reinforced composites
<p>Data behind the publications:</p> <p>Auenhammer, R.M., Mikkelsen, L.P., Asp, L., Blinzler, B. Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabric reinforced composites. <em>Composite Structures, </em><strong>256</strong>, 113136, <a href="https://doi.org/10.1016/j.compstruct.2020.113136">https://doi.org/10.1016/j.compstruct.2020.113136</a>, 2021.</p> <p>Auenhammer, Robert M., Lars P. Mikkelsen, Leif E. Asp, Brina J. Blinzler, Dataset of non-crimp fabric reinforced composites for an X-ray computer tomography aided engineering process, <em>Data in Brief, </em><strong>33</strong>, 106518, <a href="https://doi.org/10.1016/j.dib.2020.106518">https://doi.org/10.1016/j.dib.2020.106518</a>, 2020.</p> <p>Auenhammer, R.M., L.P. Mikkelsen, L.E. Asp, B.J. Blinzler, X-ray tomography based numerical analysis of stress concentrations in non-crimp fabric reinforced composites - assessment of segmentation methods. <em>IOP Conf. Ser.: Mater. Sci. Eng.</em> <strong>942</strong>, 012038, <a href="https://doi.org/10.1088/1757-899X/942/1/012038">https://doi.org/10.1088/1757-899X/942/1/012038</a>, 2020</p> <p>The data-set contain data from three samples: A, E and G. </p> <p>For each sample the data are saved in the follow format</p> <ul> <li>X-ray scan: nii-files</li> <li>SEM scan: tif-files</li> <li>Abaqus files: inp-files </li> <li>X-ray setting: pdf-files</li> <li>SEM settings: hdr-ascii files</li> </ul> <p> </p>
Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods
Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10–15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coalescent. We found that SMRT-ML performed well for UCE data. Our results suggest that UCE data have excellent prospects for the resolution of difficult evolutionary radiations, though specific attention may need to be given to the details of the methods used to estimate species trees.
Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales
The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a non-model system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from eleven exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that while some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources.
Data from: Convergence analysis of a finite element skull model of Herpestes javanicus (Carnivora, Mammalia): implications for robust comparative inferences of biomechanical function
Predictions of skull biomechanical capability based on virtual models constitute a valuable data source for testing hypotheses about craniodental form and feeding behavior. Such comparative analyses also inform dietary reconstruction in extinct species. 3D modeling using Finite Element (FE) methods is a common technique applied to the comparative analysis of craniodental function in extinct and extant vertebrates. However, taxonomically diverse skull models in the literature often are not directly comparable to each other, in part because of distinctions in how boundary conditions are defined, but also because of substantial differences in the number of FEs composing the models. In this study, we test whether a conventional convergence test is adequate in identifying the minimum number of FEs needed to achieve internally stable results for a single species. We constructed a series of skull models of Herpestes javanicus, and simulated unilateral biting across the dentition; the models differed in the number of FEs, degrees of freedom at the joint and bite point constraints, and type of tetrahedral FEs used. We found that convergence patterns differed across constraint types, FE quantities, and bite position simulated. Four-noded tetrahedral (tet-4) FE models with relaxed constraints produced the most stable measurements compared to over-constrained tet-4 models and to relaxed tet-10 models. In absence of an optimal FE quantity from convergence testing, we propose a broadly applicable sub-sampling protocol, whereby average measurement values across multiple models per specimen are used for among-species comparisons. A regime of sampling three low FE quantity models produced the closest estimates of mean measurement values relative to larger model sets, being within the 95% bootstrap estimated confidence intervals. Future studies should focus on identifying sources of variation associated with other FE modeling protocols, so that they can be accounted for before biomechanical attributes from these simulations are used to infer form–function linkage.
Design and Analysis of Chiral and Achiral Metasurfaces with the Finite Element Method
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IODP Expedition 351 Elemental analysis (CHNS)
<p>Fundamental elemental component (total carbon, hydrogen, nitrogen, and sulfur) fluctuations help define the origin, depositional environment, and diagenetic alteration of source materials. To determine C, H, N, and S, solid samples are reacted with a catalyst, separated by chromatography, and detected by thermal conductivity on a FlashEA 1112 CHNS elemental analyzer. Organic carbon can be directly measured on the elemental analyzer by acidification of the sample to drive off carbonate as carbon dioxide before analyzing. Total organic carbon on this report is measured rather than calculated.</p>
Chapter 4 – Characterising the Gamburtsev Subglacial Mountains by detrital apatite, rutile, and titanite U-Pb dating and trace element analysis: How passive tectonics led to inception of the Antarctic Ice Sheet
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Instrumentation Neutron Activation Analysis & Proton Induced X-RAY Emission techniques supported with Machine learning analysis for rare earth/macro/micro elements correlation from O. Sativa Rice varieties in Senegal River valley
<p>data sheet INAA;results</p>
Evaluation of the Ability of CT-based Finite Element Analysis (CTFEA) to Predict Fractures in Patients With Metastases: a Randomized Controlled Study.
ClinicalTrials.gov study NCT03453905. IPD Sharing: NO. Countries: 0. Publications: 8.
Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales
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Data from: Convergence analysis of a finite element skull model of Herpestes javanicus (Carnivora, Mammalia): implications for robust comparative inferences of biomechanical function
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Data from: Comparative finite-element analysis: a single computational modeling method can reliably estimate the mechanical properties of porcine and human vertebrae
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Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods
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CUT&Tag analysis uncovered Pou4f1-bound DNA elements in E16.5 retinas
GEO Series GSE221209. Mus musculus. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Probe level meta analysis of microarray data to understand the role of retrotransposable elements in myelination.
GEO Series GSE245032. Rattus norvegicus. 0 samples. Type: Expression profiling by array; Third-party reanalysis.
Integrated analysis of extrachromosomal DNA elements in SCLC [scCNV]
GEO Series GSE206352. Homo sapiens. 1 samples. Type: Other.
Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq [Human KAS-seq]
GEO Series GSE256228. Homo sapiens. 13 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Analysis of the Drosophila and Human DPR Elements Reveals a Distinct Human Variant Whose Specificity Can Be Enhanced by Machine Learning
GEO Series GSE225570. Drosophila melanogaster. 2 samples. Type: Expression profiling by high throughput sequencing.
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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.