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6,452 results for “Application”
Prairie manure application impacts on floral abundance, plant growth, plant community structure, insect and spider community abundance and activity density in experimental plots in Ames, Iowa (2021-2022).
This dataset contains results from a two-year field experiment at Iowa State University’s Horticulture Research Station to evaluate the effects of dairy manure application on native prairie plant and insect communities. We established replicated 4 m² plots across two field types, an established tallgrass prairie and a tilled crop field, and applied four manure treatments (weekly, biweekly, once per season, and control) using liquid slurry from a local dairy farm. Plant responses were monitored through weekly measurements of mortality, ground cover, floral abundance, plant height, and visual obstruction. Insect communities were sampled biweekly using vacuum suction for foliage and flower visitors and pitfall traps for ground-dwelling arthropods. Collected insects were identified to order, with Hymenoptera and Carabidae further resolved to family or genus.
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
<p>Data used to test the robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data, described in <a href="https://doi.org/10.1186/s13059-020-1949-z">Holland et al. 2020</a>.</p> <p>The folder <em>data </em>contains<em> </em>raw data and the folder <em>output</em> contains intermediate and final results of all analyses. </p> <p>The associated analyses code and more information are available on <a href="https://github.com/saezlab/FootprintMethods_on_scRNAseq">GitHub</a>.</p> <p> </p> <p><strong>Abstract</strong></p> <p><strong>Background</strong></p> <p>Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way.</p> <p><strong>Results</strong></p> <p>To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community.</p> <p><strong>Conclusions</strong></p> <p>Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used.</p> <p> </p> <p>For questions related to the data please write an email to christian.holland@bioquant.uni-heidelberg.de or use the <a href="https://github.com/saezlab/FootprintMethods_on_scRNAseq/issues">GitHub issue system</a>.</p>
A New Method for Accurate and Efficient Modeling of the Local Ocean Induction Effects. Application to Long-Period Responses from Island Geomagnetic Observatories
<p>Dataset presented in Figures 3-7, S1 and S3 in the recently submitted AGU paper "A New Method for Accurate and Efficient Modeling of the Local Ocean Induction Effects. Application to Long-Period Responses from Island Geomagnetic Observatories".</p>
The MedAfriCarbon radiocarbon database and web application. Archaeological dynamics in Mediterranean Africa, ca. 9600-700 BC
<p>MedAfriCarbon radiocarbon database and web app are outcomes of the <em>MedAfrica Project —Archaeological deep history and dynamics of Mediterranean Africa, ca. 9600-700 BC</em>. The dataset presented here includes a collection of <strong>1584</strong> calibrated archaeological 14C dates from <strong>1587</strong> samples collected from <strong>368</strong> sites located in Mediterranean Africa (plus some additional dates whose published information is incomplete). The majority of the dates are linked to cultural and environmental variables, notably the presence/absence of different domestic/wild species and specific material culture.</p> <ul> <li><strong>1.0.3</strong> _27 Feb 2020_– Official public JOAD release (includes JOAD DOI and volume numbers). Includes a few minor error corrections.</li> <li><strong>1.0</strong> _30 Jan 2020_— First public release of the dataset on Zenodo.</li> </ul>
Applications on the F-Droid Website (May-June 2019)
<p>The applications on the f-droid website (https://f-droid.org/en/). These applications were scraped around May-June 2019</p>
Datasets from Approximate equality of character strings and its application to record linkage in metadata of scientific publications thesis
<p>The datasets were produced in my thesis project. The thesis (in Czech language) explores the application of approximate string matching in scientific publication record linkage process. An introduction to record matching along with five commonly used metrics for string distance (Levenshtein, Jaro, Jaro-Winkler, Cosine distances and Jaccard coefficient) are provided. These metrics are applied on publication metadata from V3S current research information system of the Czech Technical University in Prague. Based on the findings, optimal thresholds in the F1, F2 and F3-measures are determined for each metric.</p> <p>Thesis citation:<br> DOBIÁŠOVSKÝ, Jan. <em>Approximate equality of character strings and its application to record linkage in metadata of scientific publications</em> [online]. Praha, 2020 [cit. 2020-05-04]. Masters thesis. Charles University. Faculty of Arts. Institute of Information Studies and Librarianship.</p> <p> </p>
Video S3 - Organic Pellet Application to Carrington Island Spawning Site
<p><strong>Video S3.</strong> Suppression of invasive lake trout by treatment of spawning sites with organic pellets to kill embryos in an IPM approach. Because only a few weeks are available to safely work on Yellowstone Lake following the peak of lake trout spawning each autumn, we expanded the embryo suppression research to include a comprehensive treatment of a spawning site with organic pellets by helicopter (with long line and seeder/spreader) to better understand the logistical constraints that may be faced when attempting large-scale, multi-site applications in the future. Dr. Christopher Guy of the USGS Montana Cooperative Fishery Research Unit describes the Carrington Island spawning site. During an October 2019 experimental treatment, all of the rocky substrate at this spawning site (0.5 ha) was treated with 18,000 kg of organic (soy and wheat gluten) pellets in less than one day. The pellets induce organic decomposition and decline in dissolved oxygen concentration, which is lethal to lake trout embryos, curtailing recruitment from the site. Relative to the expansive lake areas intensively gillnetted over a 22-week season (> 60 km of gill nets set daily), lake trout embryo suppression targets relatively small sites during a period of 2–3 weeks in autumn where the majority of a future year class is concentrated. Broad-scale application of pellets in autumn may reduce lake trout recruitment and enhance population suppression as part of an IPM approach targeting multiple lake trout life stages because the area of the 14 verified spawning sites is only 11.4 ha (0.03% of lake surface area).</p>
Application-Motivated, Holistic Benchmarking of a Full Quantum Computing Stack: Experimental Data
<p>Full experimental dataset for the publication "Application-Motivated, Holistic Benchmarking of a Full Quantum Computing Stack". The archive `application_motivated_benchmarks.zip` contains the following files and directories:</p> <p>- uncompiled_log.csv</p> <p>Gives IDs for the uncompiled circuits initially generated for use in our<br> experiments, along with the properties of the circuits.</p> <p>- properties_log.csv</p> <p>Gives IDs for device property files, along with the device and the time at which<br> they were collected.</p> <p>- compiled_log.csv</p> <p>Gives the calculated figures of merits for the compiled and run circuits.<br> Compiled circuits are identified by the ID of the uncompiled circuit, the<br> compilation strategy used, and the device compiled onto. Device property IDs at<br> the time of compilation and run are given.</p> <p>- circuits/</p> <p>Contains a subdirectory for each uncompiled circuit. Each subdirectory has files<br> of 2 forms.<br> <br> - uncompiled.qasm is the uncompiled circuit.<br> - files of the form 'strategy'_'device'.qasm are the compiled circuits.</p> <p>- data/</p> <p>Contains a subdirectory for each uncompiled circuit. Each subdirectory has files<br> of 3 forms.</p> <p> - prob_vector.csv contains the ideal output probability distribution.<br> - files of the form 'strategy'_'device'.csv contain the shot counts for<br> each compiled circuit when run on the real device.<br> - files of the form 'strategy'_'device'_simulated.csv contain the shot<br> counts for each compiled circuit when run using a classical simulator<br> with noise model build from device properties at the time of the real<br> run.</p> <p>- device_properties/</p> <p>Contains json files detailing device properties for each device property ID.</p> <p> </p>
AIDER (Aerial Image Dataset for Emergency Response Applications)
<p><strong>AIDER </strong>(<strong>A</strong>erial <strong>I</strong>mage <strong>D</strong>ataset for <strong>E</strong>mergency <strong>R</strong>esponse applications): The dataset construction involved manually collecting all images for four disaster events, namely Fire/Smoke, Flood, Collapsed Building/Rubble, and Traffic Accidents, as well as one class for the Normal case.</p> <p>The aerial images for the disaster events were collected through various online sources (e.g. google images, bing images, youtube, news agencies web sites, etc.) using the keywords ”Aerial View” or ”UAV” or”Drone” and an event such as Fire”,”Earthquake”,”Highway accident”, etc. Images are initially of different sizes but are standardized prior to training. All images where manually inspected to first contain the event that was of interested and then to have the event centered at the image so that any geometric transformations during augmentation would not remove it from the image view. During the data collection process the various disaster events were captured with different resolutions and under various condition with regards to illumination and viewpoint. Finally, to replicate real world scenarios the dataset is imbalanced in the sense that it contains more images from the Normal class.</p> <p>This subset includes around 500 images for each disaster class and over 4000 images for the normal class. This makes it an imbalanced classification problem.</p> <p>It is advised to further enhance the dataset that random augmentations are probabilistically applied to each image prior to adding it to the batch for training. Specifically there are a number of possible transformations such as geometric (rotations, translations, horizontal axis mirroring, cropping and zooming), as well as image manipulations (illumination changes, color shifting, blurring, sharpening, and shadowing).</p>
Source data for road transportation applications (road surface assessment, authentication of automotive vehicles)
<p>This data set records the driving using an Inertial Measurement Units of 12 different vehicles on the road infrastructure of the European Commission Joint Research Centre.</p> <p>The data set is described more in detail in the paper:</p> <p>Baldini, G.; Geib, F.; Giuliani, R. Continuous Authentication of Automotive Vehicles Using Inertial Measurement Units. <em>Sensors</em> <strong>2019</strong>, <em>19</em>, 5283.</p> <p><a href="https://doi.org/10.3390/s19235283">https://doi.org/10.3390/s19235283</a></p> <p>Please, cite this paper if you use this data set.</p>
Scalasca trace analysis of HemeLB application execution with 13824 MPI processes on SuperMUC-NG
<p>The CompBioMed HPC CoE flagship application HemeLB was run with a 6.4 micron resolution "circle of Willis" geometry dataset on LRZ's SuperMUC-NG supercomputer, and its execution performance with 13824 MPI processes on 288 dual 24-core compute nodes measured by Score-P (using SIONlib) and analysed by Scalasca trace analyzer.</p>
UI Dark Patterns and Where to Find Them: A Study on Mobile Applications and User Perception
<p>UI Dark Patterns and Where to Find Them: A Study on Mobile Applications and User Perception</p> <p> </p> <p>This dataset contains:</p> <ul> <li>survey_data.xlsx: Read-only spreadsheet containing the answers of 541 participants of our online survey (48 participants opted to not make their answers publicly available);</li> <li>classification_data.xlsx: Read-only spreadsheet containing the overall and the individual categorization of 240 mobile apps with respect to the presence of dark patterns; and,</li> <li>Videos.zip: videos of 15 apps (10 minutes each) used to classify the apps. The complete set of videos is considerably large and can be provided upon request.</li> </ul>
dataset for paper Vanhaebost J, Faouzi M, Mangin P, Michaud K: New reference tables and user-friendly Internet application for predicted heart weights. Int J Legal Med 2014, 128(4):615-620.
<p>The heart weight is the most important parameter in the determination of cardiac hypertrophy. The obtained heart weight value should be compared against tables of normal weights by age, gender and body weight and height</p> <p>In the study by Vanhaebost<em> et al</em>. has been shown in the Swiss population that the heart weight increases along with the increase of the body weight, body height, BMI and body surface area (BSA). The mean heart weight is greater in men than in women at a similar body weight. The reference tables for predicted heart weights obtained from this study are presented as an user-friendly internet application (<a href="http://calc.chuv.ch/Heartweight">http://calc.chuv.ch/Heartweight</a>) enabling the comparison of heart weights observed at autopsy with the reference values.</p>
Application of contact-resonance AFM methods to polymer samples (Raw Data)
<p>Raw data and figures of the article "Application of contact-resonance AFM methods to polymer samples", published in Beilstein Journal of Nanotechnology on 12 Nov 2020</p> <p> </p> <p>The raw data can be opened with the software "Igor Pro"</p>
The dataset of figures for "The GPU version of LICOM3 under HIP framework and its large-scale application" (updated)
<p>A high-resolution (1/20°) global ocean general circulation model with Graphics processing units (GPUs) code implementations is developed based on the LASG/IAP Climate system Ocean Model version 3 (LICOM3) under Heterogeneous-compute Interface for Portability (HIP) framework. The dynamic core and physics package of LICOM3 are both ported to the GPU, and 3-dimensional parallelization is applied. The HIP version of the LICOM3 (LICOM3-HIP) is 42 times faster than what the same number of CPU cores dose, when 384 AMD GPUs and CPU cores are used. The LICOM3-HIP has excellent scalability; it can still obtain speedup of more than four on 9216 GPUs comparing to 384 GPUs. In this phase, we successfully performed a test of 1/20° LICOM3-HIP using 6550 nodes and 26200 GPUs, and at the grand scale, the model’s time to solution can still obtain an increasing, about 2.72 simulated years per day (SYPD). The high performance was due to putting almost all of computation processes inside GPUs, and thus greatly reduces the time cost of data transfer between CPUs and GPUs. At the same time, a 14-year spin-up integration following the phase 2 of Ocean Model Intercomparison Project (OMIP-2) protocol of surface forcing has been conducted, and the preliminary results have been evaluated. We found that the model results have little differences from the CPU version. Further comparison with observations and lower-resolution LICOM3 results suggests that the 1/20° LICOM3-HIP can not only reproduce the observations, but also produce much smaller scale activities, such as submesoscale eddies and frontal scales structures.</p>
A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae
<p><b><i>Premise of the study</i></b><b>: </b>Putatively single-copy nuclear (SCN) loci, identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment<i> </i>in the distantly related <i>Memecylon</i> and <i>Tibouchina</i> (Melastomataceae).</p> <p><b><i>Methods</i></b>: We present a two-tiered pipeline. First, we identified putatively SCN loci using MarkerMiner and transcriptomes from distantly related species in Melastomataceae. Published loci and genes of functional significance were added (384 total loci). Second, using HybPiper, we retrieved 689 homologous template sequences for these loci using genome-skimming data from within the focal clades.</p> <p><b><i>Results</i></b>: We sequenced 193 loci from both <i>Memecylon</i> and <i>Tibouchina</i>, with probes designed from 56 template sequences successfully targeting sequences in both clades. Probes designed from genome-skimming data within a focal clade were more successful than probes designed from other sources.</p> <p><b><i>Discussion: </i></b>Our pipeline successfully identified and targeted SCN loci in <i>Memecylon </i>and <i>Tibouchina</i>, enabling phylogenomic studies in both clades and potentially across Melastomataceae. This pipeline could be easily applied to other clades with few genomic resources. </p>
Design of perfused PTFE vessel-like constructs for in vitro applications
<p>The design of a vessel-like construct for further use in perfused tissue models using PTFE membranes and collagen is presented. Endothelial cells were able to adhere to the tube’s wall, resisted perfusion, and formed an endothelial barrier delaying diffusion of fluorescently labeled molecules.</p>
New genetic markers for Sapotaceae phylogenomics: more than 600 nuclear genes applicable from family to population levels
<p>Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short tandem repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from<em>Capurodendron delphinense</em> and <em>Bemangidia lowryi</em>, both from the Tseboneae tribe, as well as the published <em>Manilkara zapota</em> transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (<em>C. delphinense</em>) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. All together, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.</p>
User Interaction Evaluation of 3D Handicraft Products Application
<p>The dataset for analysis during the study for evaluation of 3D handicraft products application for smartphones usage</p>
Research data supporting for Application of electron tomography of dislocations in beam-sensitive quartz to the determination of strain components
<p>This archives contains all the raw data (micrographs) supporting the publication</p>
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.