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1,454 results for “large scale”
Chronic Circadian Misalignment Results in Reduced Longevity and Large-Scale Changes in Gene Expression in Drosophila
GEO Series GSE124065. Drosophila melanogaster. 12 samples. Type: Expression profiling by high throughput sequencing.
Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients
GEO Series GSE158055. Homo sapiens. 284 samples. Type: Expression profiling by high throughput sequencing.
Large-scale analysis of longitudinal skin gene expression in systemic sclerosis reveals relationships of immune cell and fibroblast activity with skin thickness and a trend towards normalization over
GEO Series GSE181549. Homo sapiens. 339 samples. Type: Expression profiling by array.
Large-scale rewiring of innate immunity circuitry and microRNA regulation during initial rice blast infection [smallRNA-Seq]
GEO Series GSE77332. Oryza sativa Indica Group. 10 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage [ChIP-seq]
GEO Series GSE103969. Mus musculus. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
10XG CRAM files for "Characterization of large-scale structural variants using Linked-Reads" (Part 2 of 2)
<p>Here we propose novel algorithms to characterize large (>40 Kbp) interspersed segmental duplications, (> 80 Kbp) inversions, (> 100 Kbp) deletions, and (> 100 Kbp) translocations using Linked-Read sequencing data. Linked-Read sequencing provides long range information, where Illumina reads are tagged with barcodes that can be used to assign short reads to pools of larger (30-50 Kbp) molecules.</p> <p><br> Our methods rely on split molecule sequence signature that we have previously described. Similar to the split read, split molecules refer to large segments of DNA that span an SV breakpoint. Therefore, when mapped to the reference genome, the mapping of these segments would be discontinuous.</p> <p><br> We redesign our earlier algorithm, VALOR, to specifically leverage Linked-Read sequencing data to discover large <br> structural variation. We implement our new algorithms in a new software package, called VALOR2. </p>
Dataset: Learning to Solve Large-Scale Security-Constrained Unit Commitment Problems
<p>This package contains the instance data used for the experiments presented in the paper <em>Learning to Solve Large-Scale Security-Constrained Unit Commitment Problems</em>, by Alinson S. Xavier, Feng Qiu and Shabbir Ahmed.</p>
Companion Web Page for "Empirical Evidence of Large-Scale Diversity in API Usage of Object-Oriented Software"
<p>dataset-jars-scam2013.zip:</p> <ul> <li>Content: 3 418 Jar files, which include 382 774 different types (classes or interfaces).</li> <li>Source: All Jar files present on a machine used for performing software mining experiments for 7 years.</li> </ul> <p>type-usages-20130622.zip:</p> <ul> <li>Content: All the type-usages, filtered by type of the type-usage</li> </ul> <p>Software:</p> <ul> <li>Software to extract type-usages: <a href="https://github.com/monperrus/typeusage">https://github.com/monperrus/typeusage</a></li> </ul> <p> </p> <p>Paper:</p> <pre>@inproceedings{Mendez2013, title = {Empirical Evidence of Large-Scale Diversity in API Usage of Object-Oriented Software}, author = {Mendez, Diego and Baudry, Benoit and Monperrus, Martin}, url = {<a href="https://hal.archives-ouvertes.fr/hal-00844753/file/article.pdf">https://hal.archives-ouvertes.fr/hal-00844753/file/article.pdf</a>}, booktitle = {{International Conference on Source Code Analysis and Manipulation (SCAM'2013)}}, pages = {10}, year = {2013}, doi = {<a href="https://doi.org/10.1109/SCAM.2013.6648183">10.1109/SCAM.2013.6648183</a>}, } </pre>
The role of perception and action on the use of allocentric information in a large-scale virtual environment
<p>Final allo weights, filtered as explained in the manuscript</p>
A large-scale depth-based multimodel audio-visual corpus in mandarin
<p>A large-scale depth-based multimodel audio-visual corpus in mandarin,.</p> <p>This file have depth-based Lip point data. The rest of the data is being collated and will be made public soon.</p> <pre>If the dataset is useful for your research, please cite our work: @inproceedings{Jianrong2018A, title={A Large-Scale Depth-Based Multimodal Audio-Visual Corpus in Mandarin}, author={Jianrong Wang and Liyuan Wang and Ju Zhang and Jianguo Wei and Ruiguo Yu}, booktitle={2018 IEEE 20th International Conference on High Performance Computing and Communications; IEEE 16th International Conference on Smart City; IEEE 4th International Conference on Data Science and Systems (HPCC/SmartCity/DSS)}, year={2018}, }</pre> <p> </p>
Large-scale analyses provide no evidence for gene-gene interactions influencing type 2 diabetes risk
<p>Summary statistics for "Large-scale analyses provide no evidence for gene-gene interactions influencing type 2 diabetes risk"</p> <p> </p>
Using Galaxy to Perform Large-Scale Interactive Data Analyses - An update
<p>Datasets and workflows supporting the protocols described in the article "Using Galaxy to Perform Large‐Scale Interactive Data Analyses - An update".</p>
Figure 4 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 4 Image processing and indices of the radula of Chiton articulatus.
Figure 10 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 10 List of collaborators in the project.
Figure 5 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 5 Equipment used to take pictures of each chiton and example of some chitons photographed.
Figure 1 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 1 Specimens of the mollusc Chiton articulatus in its habitat on the intertidal rocky shore.
Data from: Large scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine
Objective: To identify a plasma metabolomic biomarker signature for migraine. Methods: Plasma samples from 8 Dutch cohorts (n = 10,153: 2,800 migraine patients and 7,353 controls) were profiled on a 1H-NMR-based metabolomics platform, to quantify 146 individual metabolites (e.g., lipids, fatty acids, and lipoproteins) and 79 metabolite ratios. Metabolite measures associated with migraine were obtained after single-metabolite logistic regression combined with a random-effects meta-analysis performed in a nonstratified and sex-stratified manner. Next, a global test analysis was performed to identify sets of related metabolites associated with migraine. The Holm procedure was applied to control the family-wise error rate at 5% in single-metabolite and global test analyses. Results: Decreases in the level of apolipoprotein A1 (β −0.10; 95% confidence interval [CI] −0.16, −0.05; adjusted p = 0.029) and free cholesterol to total lipid ratio present in small high-density lipoprotein subspecies (HDL) (β −0.10; 95% CI −0.15, −0.05; adjusted p = 0.029) were associated with migraine status. In addition, only in male participants, a decreased level of omega-3 fatty acids (β −0.24; 95% CI −0.36, −0.12; adjusted p = 0.033) was associated with migraine. Global test analysis further supported that HDL traits (but not other lipoproteins) were associated with migraine status. Conclusions: Metabolic profiling of plasma yielded alterations in HDL metabolism in migraine patients and decreased omega-3 fatty acids only in male migraineurs.
Data from: A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success
In summer 2012, we initiated a large-scale field experiment in southern Ontario, Canada, to determine whether exposure to clothianidin seed-treated canola (oil seed rape) has any adverse impacts on honey bees. Colonies were placed in clothianidin seed-treated or control canola fields during bloom, and thereafter were moved to an apiary with no surrounding crops grown from seeds treated with neonicotinoids. Colony weight gain, honey production, pest incidence, bee mortality, number of adults, and amount of sealed brood were assessed in each colony throughout summer and autumn. Samples of honey, beeswax, pollen, and nectar were regularly collected, and samples were analyzed for clothianidin residues. Several of these endpoints were also measured in spring 2013. Overall, colonies were vigorous during and after the exposure period, and we found no effects of exposure to clothianidin seed-treated canola on any endpoint measures. Bees foraged heavily on the test fields during peak bloom and residue analysis indicated that honey bees were exposed to low levels (0.5–2 ppb) of clothianidin in pollen. Low levels of clothianidin were detected in a few pollen samples collected toward the end of the bloom from control hives, illustrating the difficulty of conducting a perfectly controlled field study with free-ranging honey bees in agricultural landscapes. Overwintering success did not differ significantly between treatment and control hives, and was similar to overwintering colony loss rates reported for the winter of 2012–2013 for beekeepers in Ontario and Canada. Our results suggest that exposure to canola grown from seed treated with clothianidin poses low risk to honey bees.
Data from: Social spider webs harbor largely consistent bacterial communities across broad spatial scales
Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbor microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbors compositionally distinct microbes from the more ephemeral capture webs in the desert social spider Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harbored similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey, and web samples. These data suggest that social spider webs can harbor characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.
Data from: Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
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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.