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7,378 results for “case”
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
<p>With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage <i>in silico</i>. We tested the performance of four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the <i>Vitis</i> clade at the genus level and Vitaceae at the family level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, coupled with incredibly low sequencing costs, we showcase that deep genome skimming (DGS) is as effective for capturing large datasets of SCNs as the widely used Hyb-Seq approach, in addition to capturing plastomes, mtDNA, and entire nrDNA repeats. DGS may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach.</p>
Panel: "Broken for All:: The case for persistent identifiers for digital cultural heritage resources AND Developer Track Session 2
<p>This video contains two sessions from Open Repositories 2021:</p> <p><strong>Panel: "Broken for All": the case for persistent identifiers for digital cultural heritage resources</strong><br> <em>Turner, Adrian (1); Holmes-Wong, Deborah (2); Rafique, Zahid (2); Kunze, John (1); Lohnash, Megan (3); McKinley, Matthew (4), Lund, <em>Allison</em> (5)</em><br> <em>1: California Digital Library; 2: University of Southern California Libraries; 3: California Revealed; 4: Omeka; 5: Metropolitan New York Library Council </em><br> Cultural heritage institutions within the United States have made significant investments in building unique digital collections, broadly disseminating them on the web and through networks such as the Digital Public Library of America (DPLA). The items within these collections are referenced and cited in a range of sources -- from Wikipedia and scholarly articles, to archival finding aids and classroom lesson plans. However, the application of persistent identifier schemes (e.g. DOI, ARK) for unique digital resources is relatively uncommon within the gallery, library, archive, and museum communities. Relatedly, many repositories and digital asset management systems (DAMS) widely used in these communities simply do not support persistent identifier schemes "out of the box." Hence, the URLs for the items are extremely fragile. If the collections are migrated to a different repository, the URLs can easily break -- impacting downstream networks, confounding researchers, and compounding the problem of link rot. This panel will discuss the critical role of persistent identifiers in digital collections management and dissemination and some of the challenges in applying them. It will feature case studies demonstrating how commonly-available licensed and open-source repositories can be adapted to support them.</p> <p><strong>Developer Track Session 2:</strong></p> <p><strong>Constructing a Repository Test Strategy Built on Docker Containers</strong><br> <em>Brady, Terrence W</em><br> <em>California Digital Library, United States of America</em><br> The Merritt Digital Preservation system comprises a dozen microservices and supporting services. Our team found that it was not cost effective to maintain and patch a fleet of servers to support a development environment. Our solution was to replace our development server environment with a stack of dockerized services. Once the stack was containerized, we discovered that we were able to create 3 variants of our development stack with different persistence strategies for database content and cloud storage. With these variants, the team has been able to support a variety of testing scenarios.<br> <br> <strong>Deploying a Serverless Application as a Docker Image</strong><br> <em>Brady, Terrence W</em><br> <em>California Digital Library, United States of America</em><br> A serverless application consists of a defined runtime (such as Ruby 2.7 or Python 3) and a package of code. This presentation will illustrate 3 types of code packages of different complexity and will describe the challenges of bundling more complicated dependencies such as binary files. In December 2020, the AWS Lambda serverless architecture began to support Docker images as a deployment package. This packaging approach makes it possible to run tests against a code package before it is deployed. This presentation will demonstrate the test and deployment process for a serverless application within the Merritt digital preservation system. Other repository teams hosting their applications on AWS may discover some useful patterns for testing and deploying serverless code to AWS Lambda.<br> <br> <strong>Live Demo: Create a Developer Workspace Challenge</strong><br> <em>Pottinger, Hardy Joseph</em><br> <em>California Digital Library, University of California, Office of the President, United States of America</em><br> Creating a developer workspace, a place in which you can write and test your code, can seem a daunting task. Sure, someone might have done it before, and they might even share their notes with you, but following those notes and arriving in the same place is like following a treasure map and expecting to get rich. There’s a better way, and I’m willing to prove it. This demo aims to show the process one goes through to craft a development environment with pretty much any tool, but will use Lando to conserve time. Lando is a way to bootstrap a useable development environment. It's built on Docker, and is like Docker-Compose, but much more transparent. It handles the boring details and helps you actually start developing with code in your favorite IDE, and all the services you need in Docker. It's all about making the life of a developer easier. It won't give you an application container you can deploy, but you will develop a deeper understanding of how all the pieces fit together, and you'll have a tool which can deploy those pieces to dev/stage/prod if you wish. The audience will participate in this demo.<br> <br> <strong>Building Scalable Serverless Digital Repositories using Amplify Open-source Framework</strong><br> <em>Chen, Yinlin; Jiang, Tingting; Hunter, Lee</em><br> <em>Virginia Tech, United States of America</em><br> We develop digital repositories to disseminate different types of digital content and to promote the principles of open access. Our goal is not to provide access to information to just one individual institution or group but to anyone and everyone. With that ambitious goal in mind, how do we enable our digital repositories to have the high availability and flexible scaling capabilities necessary to face unforeseen demand? How do we utilize only the resources we need without the waste of overprovisioning resources? These are some of the most challenging issues that we face. To achieve our goals, we moved from the traditional monolithic, server-based approach to serverless cloud infrastructure. By leveraging the services that AWS provides we have been able to boost the performance of our repositories 10x compared to that of our previous implementation that was hosted in-house. Our repositories now automatically scale up and down to meet any kind of traffic demands, without our intervention. In this talk, we will demonstrate our scalable serverless digital repositories and show the opportunities to explore and reflect on the ways that repositories enable openness for all.</p>
ARTICONF Crowd Journalism Use Case final version - Focus Group Dataset
<p>This dataset corresponds to a focus group and beta testing session conducted on the ARTICONF crowd journalism use case final version. The members participating in this discussion are from various sectors and industries. </p>
Dataset for "Modeling Neighborhood-Scale Shallow Geothermal Energy Utilization - A Case Study in Berlin"
<p>Dataset with prepared ogs simulations used in the paper "Modeling Neighborhood-Scale Shallow Geothermal Energy Utilization - A Case Study in Berlin".</p> <p>Plese read the README file in the folder first.</p>
Fig. 4 in Are plant adaptations to growing on serpentine soil rare or common? A few case studies from New Caledonia
Fig. 4. — Guioa (WELZEN 1990), showing soil preferences as in Fig. 1.
Fig. 3 in Are plant adaptations to growing on serpentine soil rare or common? A few case studies from New Caledonia
Fig. 3. — Cupaniopsis (modified from ADEMA 1991), showing soil preferences as in Fig. 1.
Real-time GNSS troposphere products: ZTD and gradients - hurricane Lorenzo case study
<p>This dataset contains multi-GNSS real-time products, i.e. ECEF coordinates, zenith total delay (ZTD), and horizontal gradients, together with their uncertainties estimated every 1 minute for a subset of EPN stations during two test periods (21 days long each):</p> <p>1) Day of year (DoY) 201 - 221, 2019</p> <p>2) DoY 266 - 286, 2019.</p> <p>The processing strategy can be found in https://link.springer.com/article/10.1007/s10291-020-01014-w, under to "advanced strategy" configuration.</p> <p>For convenience, products are stored in 2 formats (but each contains identical data):</p> <p>1. Self-explanatory netCDF format (https://www.unidata.ucar.edu/software/netcdf/docs/file_format_specifications.html), which follows the parameter naming convention of the troposphere SINEX v2 format: https://www.pecny.cz/WWW_FIL/TRO-SINEX/old/sinex_tro_2017-05-28-JD.pdf. Each file contains data for all stations but only for one test period.</p> <p>2. Semicolon delimited text files, with a self-explanatory header line. Each file contains daily products for one station.</p>
Figure 3 in Deforestation affects biogeographical regionalization: a case study contrasting potential and extant distributions of Mexican terrestrial mammals
Figure 3. Mexican regionalization based on consensus cladogram of t1.
Figure 2 in The first substantiated case of trans-oceanic tortoise dispersal
Figure 2. Map showing probable dispersal route.
Figure 3 in The first substantiated case of trans-oceanic tortoise dispersal
Figure 3. Aldabra tortoise at sea off Alphonse in December 2005. Photograph: J. Gerlach.
Figure 2 in The first cases of gynandromorphism in oil-collecting bees (Hymenoptera, Apidae: Centridini, Tapinotaspidini)
Figure 2. Gynandromorph of Epicharis (Epicharitides) iheringii Friese: (A) Habitus in lateral view. (B) Head in frontal view. (C) Metasoma in dorsal view.
Figure 1 in The first cases of gynandromorphism in oil-collecting bees (Hymenoptera, Apidae: Centridini, Tapinotaspidini)
Figure 1. Gynandromorph of Lophopedia nigrispinis (Vachal): (A) Habitus in lateral view. (B) Head in frontal view. (C) Foreleg right basitarsus in inner view. (D) Foreleg left basitarsus in inner view. (E) Left middle leg in inner view. (F) Right hind leg in external view. (G) Left hind leg in external view. (H) Right middle leg in inner view. Scale bars: (A) 2 mm. (B) 1 mm. (C) 0.25 mm. (D-H) 0.5 mm.
Location of ground stations, targets and spacecraft for Spire case study 2021
<p>Locations of ground stations, targets, and spacecraft for the analysis presented in article: "Dynamical influence driven space system design"</p>
paperChain - Video Animation - Circular Case 2 (SPAIN)
<p>This animation video summarises in approximately two minutes the most relevant results of the implementation of paperChain's Circular Case.</p> <p> </p>
Data from dissertation: 'Landscape and Aboveground Biomass Dynamics of Brazilian Savanna using airborne LIDAR and MapBiomas datasets : case study of Rio Vermelho Watershed, Brazil'
<p>This dissertation was submitted to University of Manchester as part of MSc GIS program</p> <p>This repository contains:</p> <p>1) Contains the R language code used in the dissertation (CHM_&_LiDAR_metric.R; Landscape_metric.R; Generalized_Linear_Model.R; Random_Forest_Model.R).</p> <p><br> 2) Canopy Height Model (CHM) and 56 LiDAR metric raster files with a resolution of 1m (CHM_&_LiDAR_metric_2014.zip; CHM_&_LiDAR_metric_2018.zip), the original LiDAR data come from Brazil project supported by the Brazilian Agricultural Research Corporation (EMBRAPA), the US Forest Service, USAID, and the US Department of State.</p> <p><br> 3) AGB raster files with a resolution of 10m (AGB_2014.tif; AGB_2018.tif; AGB_dynamic.tif), field plots used for AGB estimation come from Sabrinado Couto de Miranda from University of Goiás State (UEG), Brazil, and her team.</p> <p><br> 4) Landscape metric interpolation raster file (SHDI.tif; SHEI.tif; AREA_CV.tif; CIRCLE_MN.tif; SHAPE_MN.tif) with a resolution of 10m, land cover map Map come from Biomas team for landscape metric calculation.</p>
Impacts of biomass burning in peninsular Southeast Asia on PM2.5 concentration and ozone formation in southern China during springtime – A case study
<p>Abstract: Biomass burning (BB) affects fine particulate matter (PM<sub>2.5</sub>) and ozone (O<sub>3</sub>) formations by emitting their gaseous precursors and primary aerosols. Impacts of BB in peninsular Southeast Asia (BB-PSEA) are evaluated on the PM<sub>2.5</sub> and O<sub>3</sub> formations in southern China, using a source-oriented WRF-Chem model to simulate an air pollution episode from 21 to 25 March 2015. The source-oriented model separates the emission from the BB-PSEA and other sources and is able to evaluate the effect of aerosol-radiation interactions (ARI) and aerosol-photolysis interactions (API) from the BB-PSEA. Comparisons with observations reveal that the model performs well in simulating the air pollution episode. Sensitivity experiments show that BB-PSEA increases PM<sub>2.5</sub> concentrations by 39.3 μg m<sup>-3</sup> (68.0%) in Yunnan Province (YNP) and 8.4 μg m<sup>-3</sup> (24.1%) in other downwind areas (ODA) in southern China (including the provinces of Guizhou, Guangxi, Hunan, Guangdong, Jiangxi, Fujian, and Zhejiang) on the regional average. The PM<sub>2.5</sub> enhancement is mainly contributed by primary aerosols in YNP but by secondary aerosols in the ODA. The BB-PSEA increases O<sub>3</sub> concentrations of 18.1 μg m<sup>-3 </sup>(19.4%) in YNP and decreases O<sub>3 </sub>concentrations in the ODA by 3.7 μg m<sup>-3</sup> (5.3%). The O<sub>3</sub> increase in YNP is contributed by the gaseous emissions of the BB-PSEA, and the O<sub>3</sub> decrease in the ODA is caused by the effects of ARI and API of the BB-PSEA. The NH<sub>3</sub> emissions from the BB-PSEA plays a key role in enhancing secondary inorganic aerosols in southern China, and also determine the PM<sub>2.5</sub> increase in the ODA.</p>
Same Side Stance Classification Adversarial Test Cases
<p>This dataset contains 175 cases. It is manually created to reveal the ability of models to solve different types of <strong>adversarial</strong> cases for same side stance predictions more systematically. The examples selected here are derived from the dataset used in the <a href="https://sameside.webis.de/">Same Side Stance Classification</a> shared task.</p> <p>We have selected <strong>25</strong> distinct arguments from the <em>"gay marriage"</em> topic that are short and express their stance clearly. For each selected argument, we construct new arguments of four distinct types to obtain two pairs, one with the same stance, and one with an opposing stance:</p> <ul> <li><strong>Negation</strong>: a simple negation of the argument.</li> <li><strong>Paraphrase</strong>: alters important words from the argument to synonymous expressions with the same stance.</li> <li><strong>Argument</strong>: uses an argument from the same topic and stance, but semantically completely different regarding the first one.</li> <li><strong>Citation</strong>: repeats or summarizes the first argument and then expresses agreement or rejection (a case frequently occurring in the dataset).</li> </ul> <p>The types <em>Paraphrase</em>, <em>Argument</em>, and <em>Citation</em> are also formulated in a negated version to create additional test instances for the opposite stance.</p>
FIGURE 8 in Infestation Of Sphingidae (Lepidoptera) By Otopheidomenid Mites In Intertropical Continental Zones And Observation Of A Case Of Heavy Infestation By Prasadiseius Kayosiekeri (Acari: Otopheidomenidae)
FIGURE 8: Unusual infestation of P. kayosiekeri on prothorax, Pachylioides resumens (Sphingidae) (VP09-23). Seven mites are attached to the hairs (high magnification, Guatemala) (many mites removed for identification).
FIGURE 9 in Infestation Of Sphingidae (Lepidoptera) By Otopheidomenid Mites In Intertropical Continental Zones And Observation Of A Case Of Heavy Infestation By Prasadiseius Kayosiekeri (Acari: Otopheidomenidae)
FIGURE 9: Several Prasadiseius species mites in the left proximal half of the forewing and left wing base-tympanic-first abdominal cavity area (several mites shown within the circle) (low magnification).
FIGURE 7 in Infestation Of Sphingidae (Lepidoptera) By Otopheidomenid Mites In Intertropical Continental Zones And Observation Of A Case Of Heavy Infestation By Prasadiseius Kayosiekeri (Acari: Otopheidomenidae)
FIGURE 7: Large infestation of P. kayosiekeri on the prothorax of Pachylioides resumens (Sphingidae) in low magnification (Guatemala) (many mites were removed for identification).
ScienceDex guides
Understand access before you commit
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.