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13,587 results for “specification”
Patient-specific genome-scale metabolic models reconstructed for 8 TCGA tumor types
<p>TCGA_reconstructedGEMs: 3,599 cancer patient-specific GEMs for 8 different tumor types reconstructed using the TCGA (The Cancer Genome Atlas) RNA-seq data and generic human GEM 'Recon 2M.2'</p>
Updated Data corresponding to a study on 'Rapid Patient-Specific FEM Meshes from 3D iPhone Scans'
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Data from: A Deep Learning Approach for Fast Muscle Water T2 Mapping with Subject Specific Fat T2 Calibration from Multi-Spin-Echo Acquisitions
<p>This repository contains the imaging data (in NIfTI) and analysis code to reproduce the work presented in <em>"A Deep Learning Approach for Fast Muscle Water T2 Mapping with Subject Specific Fat T2 Calibration from Multi-Spin-Echo Acquisitions"</em> by <strong>Marco Barbieri, Melissa T. Hooijmans, Kevin Moulin, Tyler E. Cork, Daniel B. Ennis, Garry E. Gold, Feliks Kogan and Valentina Mazzoli.</strong></p> <p>Citation: "Barbieri, M., Hooijmans, M.T., Moulin, K. <em>et al.</em> A deep learning approach for fast muscle water T2 mapping with subject specific fat T2 calibration from multi-spin-echo acquisitions. <em>Sci Rep</em> 14, 8253 (2024). https://doi.org/10.1038/s41598-024-58812-2"</p> <p>The source code for setting up the Deep Learning application can be found in the GitHub repository https://github.com/barma7/Deep_Learning_for_Muscle_T2_mapping.git</p>
Subregions specific dynamics of striatal dopamine
<div> <div> <div> <p>Transient increases in dopamine within the striatum can encode reward prediction errors, critical signals for updating predictions of future rewards. However, it is unclear how this mechanism can provide suitable feedback for predictions across a wide range of time horizons: from seconds or less (if singing a song) to potentially hours or more (if hunting for food). Here we report that dopamine transients in distinct striatal subregions convey prediction errors over distinct time scales. Dopamine dynamics systematically accelerated from ventral to dorsal- medial to dorsal-lateral striatum, in the tempo of their spontaneous fluctuations, their temporal integration of prior rewards, and their discounting of future rewards. This spectrum of time scales for evaluative computations can help achieve efficient learning and adaptive motivation for a wide range of behaviors.</p> </div> </div> </div>
Differential cross-reactivity to the influenza B virus haemagglutinin underpins lineage-specific susceptibility between birth cohorts
<p>Data and code relataing to "Differential cross-reactivity to the influenza B virus haemagglutinin underpins lineage-specific susceptibility between birth cohorts" Edler et al study https://www.biorxiv.org/content/10.1101/2023.08.25.554879v1<br><br></p> <p> </p>
Culture Graph Interchange Format Specification
<p>For the federated acquisition of data for the <a href="https://nfdi4culture.de/resources/knowledge-graph.html">Culture Knowledge Graph</a> <strong>we propose an easy to use, lightweight interchange format</strong> based on <a href="https://schema.org/">schema.org</a> for the harvesting of resources from data collections with key attributes (IRIs, names, dates and terms from controlled vocabularies). The <strong><em>Culture Graph Interchange Format</em></strong> <strong>(CGIF)</strong> has the added benefit of automatically making the data eligible for <a href="https://datasetsearch.research.google.com/">Google Dataset Search</a> and to significantly improve the findability of websites and datasets through search engine optimization.</p> <p>This is the data publication (source files, figures, post-use materials) of the CGIF specification. The web version is available at <a href="https://nfdi4culture.de/go/E3712">https://nfdi4culture.de/go/E3712 </a></p>
Specification and Verification for Unrestricted Algebraic Effects and Handling
<p>This is the supporting data from a paper submission to ICFP24, including the source code and the benchmarks. </p> <p>The benchmark examples can be found in folder "src/demo/".</p>
Decoding the Brain Mosaic: Region and Cell Type-Specific Dysregulation Patterns in Stress and Psychiatric Disorders
<p>Supplementary Online Tables for the doctoral thesis "Decoding the Brain Mosaic: Region and Cell Type-Specific Dysregulation Patterns in Stress and Psychiatric Disorders" by Nathalie Gerstner. </p> <p>This repository includes complete lists of differentially expressed and differential hub genes, alongside the results of enrichment analysis for 8 brain regions examined in a mouse model for transcriptomic alterations following glucocorticoid stimulation (Online Tables 1-30). Additionally, the repository encompasses the complete results of differential expression and chromatin accessibility analyses across various cell types examined in postmortem brain tissue of the orbitofrontal cortex (Online Tables 31-37). These findings delineate the transcriptomic and epigenomic changes between psychiatric cases and controls, as well as between donors with high and low genetic risk for psychiatric disorders.</p> <p>The lists of all genes tested in the respective studies, not just the significant ones, can be found in the "GRactivation_MouseBrain_tables.zip" and the "SingleNuc_PostmortemBrain_Tables.zip" archives.</p> <p> </p>
Subspecies-specific BayesR posterior probabilities of inclusion for a composite population of tropically adapted beef heifers
<p>Many of the world's agriculturally important plant and animal populations consist of hybrids of subspecies. Cattle in tropical and sub-tropical regions for example, originate from two subspecies, <em>Bos taurus indicus </em>(<em>Bos indicus</em>)<em> </em>and <em>Bos taurus taurus (Bos taurus). </em>Methods to derive the underlying genetic architecture for these two subspecies are essential to develop accurate genomic predictions in these hybrid populations. We propose a novel method to achieve this. First, we use haplotypes to assign SNP alleles to ancestral subspecies of origin in a multi-breed and multi-subspecies population. Then we use a BayesR framework to allow SNP alleles originating from the different subspecies differing effects. Applying this method in a composite population of <em>B. indicus</em> and <em>B. taurus </em> hybrids, our results show that there are underlying genomic differences between the two subspecies, and these effects are not identified in multi-breed genomic evaluations that do not account for subspecies of origin effects. The method slightly improved the accuracy of genomic prediction. More significantly, by allocating SNP alleles to ancestral subspecies of origin, we were able to identify four SNP with high posterior probabilities of inclusion that have not been previously associated with cattle fertility and were close to genes associated with fertility in other species. These results show that haplotypes can be used to trace subspecies of origin through the genome of this hybrid population and, in conjunction with our novel Bayesian analysis, subspecies SNP allele allocation can be used to increase the accuracy of QTL association mapping in genetically diverse populations.</p>
Figure 2. Rubicon and Pacer RH domain have inverted pRAB7A binding specificity [FINAL]
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Alkyl lipid distribution, elemental composition and compound-specific 14C isotope composition in marine and terrestrial sedimentary archives from sub-Antarctic South Georgia
<p>The dataset comprises elemental data, alkyl lipid data and radiocarbon (14C) data that was obtained on sediment samples from sub-Antarctic South Georgia. The sediments were collected from a range of different sites, including lakes, peat deposits, a marine inlet and a fjord during RV Polarstern expedition PS81 in 2013. More details on the study sites, sampling and data evaluation can be found in Berg et al. (submitted manuscript to JGR Biogeochemistry).</p>
Inferring Incorrectness Specifications for OO Programs
<div> <p>This is the supporting data for OOPSLA24 submission: Inferring Incorrectness Specifications for OO Programs. </p> <p>It includes the source code and benchmarks presented in the paper. </p> <p> </p> </div>
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics (output data)
<p>This contains the output results of CalicoST (inferred CNAs and cancer clones), results of comparison methods, and CNAs inferred from WES data of 13 samples across four cancer types.</p> <p>In this updated version, we also included the simulated data and the results from CalicoST and other methods in CalicoST_simulation_deposit.zip. README contains the details of deposited files.</p>
Colorectal cancer patients-derived immunity-organoid platform unveils cancer-specific tissue markers associated with immunotherapy resistance.
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Dataset for Effects Effects of Soft Tissue Mobilization with TECAR Therapy Using Bracelet Electrodes in Women with Chronic Non-specific Neck Pain
<p>This dataset contains anonymized data from a randomized controlled trial (RCT) evaluating the effectiveness of combining Soft Tissue Mobilization Techniques (STMT) with Capacitive and Resistive Electric Transfer Therapy (TECAR) in women with Chronic Non-Specific Neck Pain (CNSNP). Data include assessments at baseline, the 5th week, and the 6th-month follow-up for variables related to pain intensity, disability, and range of motion (ROM).</p>
Figure 5 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 5. Evolutionary trends and patterns of repeat distribution in the karyotype of Anguis and Pseudopus. The summary presents: the distribution pattern of interstitial telomeric repeats (ITRs) in macrochromosomes (red arrowheads), the presence of constitutive heterochromatin in the centromeric region of chromosome No. 2 (black arrowheads), and the number and topology of 18S rDNA sites (green signals). Phylogenetic relationships follow Gvoždík et al. (2023). Although all six species share 2n = 44 and macrochromosome morphology differs only subtly, several species-specific repeat accumulation patterns have been observed. A, The common ancestor of Anguis and Pseudopus had 10 macro- and 12 microchromosome pairs, and its metacentric chromosome No. 1 likely possessed ITRs in the centromeric region. B, Accumulation of ITRs on chromosomes Nos 2, 4, and 7, and heterochromatin on chromosome No. 2; translocation and accumulation of rDNA sites on microchromosomes in the Anguis ancestor. C, Accumulation (in A. cephallonica) or elimination (in the A. fragilis species complex ancestor) of ITRs on pair Nos 5 and 9 and of rDNA sites on one of the microchromosome pairs. An asterisk indicates two possible directions of chromosomal changes. D, Elimination of ITRs on pair No. 1 in the A. fragilis species complex ancestor. E, Elimination of ITRs on chromosomes Nos 2 and 7; elimination of heterochromatin on chromosome No. 2 in the common ancestor of A. colchica and A. graeca. F, Accumulation of ITRs on chromosome No. 3 in the ancestor of A. fragilis and A. veronensis. Anguis veronensis represents a composite ITR pattern of A. cephallonica and A. fragilis, providing support for the hypothesis of past contact between Italian and Peloponnese slow worms (Gvoždík et al. 2023), with remnants of these interactions likely persisting. An alternative hypothesis proposes a shared repeat pattern among all Anguis species, wherein the detection of ITRs depends on the repeat abundance and reveals accumulations only above the detection limit.
Figure 2 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 2. Distribution of constitutive heterochromatin (first column from the less side), GC/AT-positive regions (second column), telomeres and ITRs (third column), and 18S rDNA gene clusters (fourth column) in Anguis and Pseudopus (males, UN for unknown sex). First column (A, E, I, M, Q, U): presence (full arrowhead) and absence (empty arrowhead) of centromeric heterochromatin in chromosome pair No. 2. Second column (B, F, J, N, R, V): diffused GC+ pattern in distal part of pair No. 2 (empty arrowhead) or strong signal (full arrowhead) in the telomeric region of pair No. 1. Third column (C, G, K, O, S, W): ITRs (full arrowhead). Fourth column (D, H, L, P, T, X): hybridization of 18S rDNA on three pairs of microchromosomes (full arrowheads) and additional weak signal on another microchromosome pair (empty arrowheads). Where available, females do not differ from males and are shown in Supporting Information (Fig. S3).
Figure 4 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 4. Chromosome painting with Varanus komodoensis (VKO) macrochromosome probes on Anguis fragilis (AFR) and Pseudopus apodus (PAP) chromosomes. The probe identity is indicated (number and letter correspond to VKO chromosome and flow-sorted peak, respectively). Arrowheads mark the hybridization signal on the AFR (A–E) and PAP (F) homeologous chromosomes. Note that each of the probes VKO 1, 2, and 3 marks two different pairs of chromosomes, whereas the probes VKO 6 + 7 and 8 + 7 mark different arms of the same chromosome pair. The hybridization signal of the probes VKO 6 + 7 and 8 + 7 does not clearly overlap in Anguis, but it marks chromosome pair No. 7 in Pseudopus.
MD Source Data for "Subunit-specific conductance of single HCN pacemaker channels at femtosiemens resolution"
<p>This dataset is the MD source data for the research paper ''Subunit-specific conductance of single HCN pacemaker channels at femtosiemens resolution''. It includes the following parts:</p> <ol> <li>Figures.zip. This file provides high resolution MD related figures, including main figures and supplementary figures.</li> <li>Figure_source_data.zip. This is the source data for the figures in the paper.</li> <li>Homology_Modelling_result.zip. This file provides the input (rHCN4, PDB ID: 7NP3) and output files (mHCN1-4, hHCN4) of homology modelling.</li> <li>MD_input.zip. This is the MD setup input data. It includes starting structure, topology file, .mdp file and force field file. Due to the limitation of storage space (50 GB), it is a pity we couldn't upload all trajectories files (~180 GB). But these files are enough for rerunning the MD simulations.</li> <li>Movie 1. K+ permeation in mHCN2 channel during a 250 ns trajectory.</li> </ol>
Figure 3 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 3. Male (A, C, E, G) and female (B, D, F, H) comparative genomic hybridization in four Anguis species. Male-specific DNA is labelled with fluorescein d-UTP (green), and female-specific DNA with Cy3 d-UTP (red). The yellow regions reflect regions of accumulated repetitive elements existing in equilibrium in the male and female genomes. Slightly reddish (E, F) or greenish (G, H) regions indicate certain enrichment of the repetitive fraction in the genome of one of the individuals.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.