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7,195 results for “SET”
Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing
1. The simplicity and cost efficiency of Illumina amplicon sequencing has greatly contributed to the advancement of DNA barcoding and metabarcoding applications. However, current amplicon sequencing based barcoding approaches are usually restricted to short, single-locus fragments, limiting their taxonomic and phylogenetic resolution. 2. Here, we establish a cost efficient and simple multiplex PCR protocol for arthropod systematics by Illumina amplicon sequencing. We introduce primer sets, including several new, generic primers, to reliably amplify nine loci across a wide range of arthropods. Using a diverse collection of arthropod species from 19 orders, we test loci for amplification efficiency and estimate the effect of cross-species amplification bias on taxon recovery from bulk community samples. We then explore the taxonomic and phylogenetic utility of the primer sets, focusing on a dataset of spiders that includes both deep and recent divergences. 3. The set of loci provides good phylogenetic support across a wide taxonomic spectrum, making it a useful addition to COI for resolving lineages within a comparative context. All loci recover sequences for the majority of arthropod taxa in separate PCRs. However, cross-species amplification bias in some primers prevents an exhaustive taxon recovery from bulk community samples. 4. Our protocol makes it possible to generate multilocus datasets for large numbers of arthropod taxa for a fraction of the price and workload of Sanger sequencing. This opens up the possibility for parallel phylogenetic and taxonomic analysis of large collections of arthropods, but also enables rapid exploratory analyses of target lineages. Primers for metabarcoding applications should be carefully evaluated for their performance in bulk community samples and chosen to minimize cross-species amplification bias.
Data from: Assimilating MODIS data-derived minimum input data set and water stress factors into CERES-Maize model improves regional corn yield predictions
Crop growth models and remote sensing are useful tools for predicting crop growth and yield, but each tool has inherent drawbacks when predicting crop growth and yield at a regional scale. To improve the accuracy and precision of regional corn yield predictions, a simple approach for assimilating Moderate Resolution Imaging Spectroradiometer (MODIS) products into a crop growth model was developed, and regional yield prediction performance was evaluated in a major corn-producing state, Illinois, USA. Corn growth and yield were simulated for each grid using the Crop Environment Resource Synthesis (CERES)-Maize model with minimum inputs comprising planting date, fertilizer amount, genetic coefficients, soil, and weather data. Planting date was estimated using a phenology model with a leaf area duration (LAD)-logistic function that describes the seasonal evolution of MODIS-derived leaf area index (LAI). Genetic coefficients of the corn cultivar were determined to be the genetic coefficients of the maturity group [included in Decision Support System for Agrotechnology Transfer (DSSAT) 4.6], which shows the minimum difference between the maximum LAI derived from the LAD-logistic function and that simulated by the CERES-Maize model. In addition, the daily water stress factors were estimated from the ratio between daily leaf area/weight growth rates estimated from the LAD-logistic function and that simulated by the CERES-Maize model under the rain-fed and auto-irrigation conditions. The additional assimilation of MODIS data-derived water stress factors and LAI under the auto-irrigation condition showed the highest prediction accuracy and precision for the yearly corn yield prediction (R2 is 0.78 and the root mean square error is 0.75 t ha-1). The present strategy for assimilating MODIS data into a crop growth model using minimum inputs was successful for predicting regional yields, and it should be examined for spatial portability to diverse agro-climatic and agro-technology regions.
Data from: A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restriction-site associated DNA sequencing (RAD-seq) to develop an economical single-nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with post-clustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof-of-concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/ Q. prinoides and Q. stellata) among natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa; and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD-seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.
Tangara Sydney Trains T set
Low Poly Tangara. The Tangara (an Aboriginal Australian word meaning to go) is a class of electric multiple unit operated by Sydney Trains in Sydney, Australia. The Tangaras were delivered between 1988 and 1995, and are third-generation trains. A Tangara is a double-deck four-car set, with the two outer cars being driving control trailers (carrying a D prefix) fitted with one pantograph each and the middle two cars being non-control motor cars (carrying a N prefix). They are equipped with air conditioning and chopper control. Two subclasses of Tangara were built, the suburban sets targeted as T sets, and outer-suburban sets originally targeted as G sets. The T sets replaced the first generation of Sydney's electric rolling stock. The G sets were converted to suburban use and were re-targeted as additional T sets. Unlike most other Sydney Trains rolling stock the seats on the suburban T sets are fixed, meaning that half the seats face backwards. Source: Objaverse 1.0 / Sketchfab
Data set for ISOP paper
<p>Data to reproduce results in the ISOP paper</p>
FEM data sets for heat generation due to plastic deformation and the and associated contact temperature during a normal impact between an elastic-perfectly-plastic particle and a rigid surface.
<p>This dataset contains essential data from the Finite Element Method (FEM) model predicting heat generation due to plastic deformation during the normal impact of a deformable spherical particle and a rigid flat substrate. Part of this data was processed and featured in a publication of a journal article (https://doi.org/10.1016/j.ijimpeng.2023.104831). The following is the description of the data files and the associated figures in the original paper. </p><p>'Energy_Vy200_1200 .xlsx' and 'Temp_Vy200_1200 .xlsx' - data for the evolution of heat and nodal temperature, respectively for varying impact velocities. Data was used for Figs.5 -7 in the published paper.</p><p>'Energy_YM_5_1000.xlsx' and 'Temp_YM_5_1000.xlsx' - data for the evolution of heat and nodal temperature, respectively for varying Young moduli. Data was used for Figs. 8 and 9 in the published paper.</p><p>'Energy_YS_50_800.xlsx' , 'Temp_YS_50_800.xlsx' - data for the evolution of heat and nodal temperature, respectively for varying yield strengths. Data was used for Figs. 10 and 11 in the published paper.</p><p>'Energy_Den_500_8000.xlsx' , 'TempC_Den_500_8000.xlsx'- data for the evolution of heat and nodal temperature, respectively for varying densities. Data was used for Figs. 12 and 13 in the published paper.</p><p>'Temp_TC.xlsx' , 'Temp_HC.xlsx' - data for the evolution of nodal temperatures for varying thermal conductivity and specific heat capacities, respectively. Data was used for Figs. 14 -17 in the published paper.</p><p> </p><p> </p><p> </p><p> </p><p> </p>
Complete Data Set for the Master Thesis: Acceptance of Robotics in Tourism
<p>Data Set for the Master Thesis <i>Acceptance of Robotics</i> reseached and written by Elena Schiffmann. </p><p>Use only with permission. </p>
Augment Single-cell RNA-seq data with Surface Protein Levels using Gene set-based Deep Learning and Transfer Learning Methods
<p><span>Necessary data, scripts and saved models for "Augment Single-cell RNA-seq data with Surface Protein Levels using Gene set-based Deep Learning and Transfer Learning Methods" manuscript.</span></p>
Model Counting Competition 2020: Full Instance Set
<p>The dataset contains all instances that the organizers of the competition received or collected during the preparation phase of the Model Counting Competition 2020. The dataset includes short benchmark descriptions (00_description.{pdf,txt,md}) by the submitters/collectors (00_authors.txt).</p><p>For a more details, we refer to the report<br>Fichte, Hecher, Hamiti: The Model Counting Competition 2020.</p><p>-----<br>Changelog:</p><p>2023-10-17 (v2): We updated the instances to the most recent competition format in preparation for the report on the competitions 2021-2023. Note that the old instance set contained various instances with incorrect headers (less variables or clauses than in the actual data), unterminated lines, or a few broken lines. We corrected these instances by scripts that are available on github (daajoe:mc_format_tools).</p>
Data Set of paper_photoelectrocatalytic disinfection of water using titania nanotube photoanodes with carbon cathodes and determination of the radicals produced
Open the record for dataset details and reuse information.
3D Models of the Anonymous yellow coffin set in the Los Angeles County Museum of Art (LACMA)
<p>3D Models of <a href="https://collections.lacma.org/node/229429" target="_blank" rel="noopener"><strong>Anonymous yellow coffin set (inner lid and mummy board)</strong></a> in the <strong>Los Angeles County Museum of Art</strong> </p> <p>The 3D models consider only the external upper part of coffin lids as far down as the lower part of the crossed forearms. </p> <p>The dataset contains:</p> <ol> <li>zip files with the 3D models generated with the software Agisoft Metashape 1.8.3 (.jpg; .mtl; .obj);</li> <li>.tif files with the orthophtgraphs of the coffins textured and not textured</li> <li>Exported Report of 3D models (.pdf)</li> <li>.pdn file with the overlapped layers (orthophotographs textured and not textured, drawings and points) generated with the open source paint. net</li> </ol> <p>The dataset is part of the results of the <a href="https://facesrevealed.museoegizio.it/"><strong>Faces Revealed</strong> <strong>Project</strong></a>. The project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 895130</p> <p><strong>If you publish material based on datasets contained in this archive, then, in your acknowledgements, please cite the original source, referring to it through the following DOI: 10.5281/zenodo.10590118</strong></p>
Selected data sets for Marsh et al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'
<p>Data sets used in the for the manuscript <strong>Marsh<em> </em>et<em> </em>al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'</strong>. The DOIs that link to all other data sets used in the publication are available in Tables S2-5 of the supplementary information. The z-score standardised data, and outputs of RMarkdown documents outline all the steps in the processing and analysis of the data are available at https://zenodo.org/uploads/13161799.</p> <p> </p> <p>This repository contains data used for:</p> <h3><strong><em>Mean canopy height</em></strong></h3> <p>Canopy height and vertical profiles of forest structure were compiled using airborne remote sensing with LiDAR collected by NERC’s Airborne Research Facility (ARF) in November 2014, using a Leica ALS50-II LiDAR. A Beer-Lambert approximation was used to convert point clouds to plant area density (PAD) distributions, a similar measure to leaf-area index, but where methods do not distinguish between leaves and branches or trunks. LiDAR measurements for the carbon plots were converted to rasters with 0.5 × 0.5 m cell size. Plots were rotated to a North-South axis if necessary</p> <h3><br><em><strong>Spectral diversity</strong></em></h3> <p>Spectral measurements were made on five leaves attached to tree branches used to measure leaf chemical traits. Leaves were randomly selected but we avoided damaged and young plant material to avoid potential confounding factors. Reflectance spectra (350–2500 nm) were acquired using a FieldSpec 4, produced by Analytical Spectral Devices (ASD, Boulder, Colorado, USA). The spectroradiometer's contact probe was mounted on a clamp and firmly pushed down onto the sample against a black background so that no extraneous light was included in the measurement. Spectral measurements were taken halfway between the petiole and leaf tip, and between the main vein and the leaf edge, with the abaxial surface pointing towards the probe. The readings were calibrated against a Spectralon white reference panel every five samples. Leaf reflectance measured at 430 nm, 660 nm, 1450, 1980 nm and 2350 nm align closely with absorption features for pigments, water content, proteins and cellulose. Spectral diversity calculated from these absorption features can provide an integrated measure of the functional trait variability within plant communities and may be used as a proxy for functional diversity.</p> <p> </p> <h3><em><strong>Liana abundance</strong></em></h3> <p>Percentage liana cover for large canopy and emergent trees. The four quadrants of the canopy were scored as 0 (no lianas), 1 (1-20%), 2 (20-40%), 3 (40-60%), 4 (60-80%) and 5 (80-100%).</p> <p> </p> <h3><em><strong>Leaf-area index<br></strong></em></h3> <p>Leaf area index (LAI) for carbon plots was derived from hemispherical photos (Sigma 8mm SRL fish eye lens and Canon EOS 600D digital camera, mounted on a tripod at 1 m height). Between 5-27 photos were taken over time in each subplot. Images were processed with Hemisfer® software (www.wsl.ch/dienstleistungen/produkte/software/hemisfer/index_EN). LAI was calculated with the method by Thimonier et <em>al</em>. (2010) <em>European Journal of Forest Research</em> 129, 543–562 (2010), with a canopy clumping correction applied from Chen & Cihlar (1995) <em>IEEE Transactions on Geoscience and Remote Sensing</em> 33, 777–787.</p> <p> </p> <h2>Funding</h2> <p>Analyses were carried out, and data were collected, as part of the BALI (Biodiversity And Land-use Impacts on tropical ecosystem function) using the following funding:</p> <ul> <li>NERC's Human Modified Tropical Forests research programme (grant number NE/K016377/1 awarded to the BALI consortium)</li> <li>MHN was supported by a PhD scholarship from the Conselho Nacional de Pesquisa e Desenvolvimento (CNPq, grant No. 201516/2014-4) from Brazil</li> </ul>
Table 1: Q-Set Statements
<p><span>In <a name="_Hlk179116558"></a>Table 1, we list and examine the statements comprising the Q-set. </span><a name="_Hlk177752677"></a>Table 1 answers the questions: What are the statements that formed the final Q-set? How does each statement demonstrate the conflict between logics and, thus, the reason for its inclusion in the Q-set?</p>
Data Set_Exploring the Molecular Mechanisms of Endothelial Dysfunction Affecting Myocardial Infarction by Integrating Multiple Datasets with In Vivo Experimental Validation
Open the record for dataset details and reuse information.
Ozone data set
<p>Ground-level O<sub>3</sub> observation data during summertime (June–August) of 2014–2019 were retrieved from Beijing Municipal Ecological and Environmental Monitoring Center, ultimately comprising 31 air quality stations.</p>
Set de datos 2 - a (anfibios), b (reptiles), Capitulo II, Tesis doctoral Javier Maximiliano Cordier
<p>Bases de datos de respuesta en abundancia frente a cambios en uso de suelo y cobertura, y variados rasgos biologicos, para anfibios y reptiles. Tesis Doctoral Javier Maximiliano Cordier, Capítulo II.</p>
data_set_for_revision_of_manuscript_contrail_formation_within_cirrus_Verma_Burkhardt_26112021
<p>This data set has new figures used in the revision of the manuscript 'contrail formation within cirrus'. and data relevent to paper is in the below given DOI.</p> <pre><strong>https://doi.org/10.5281/zenodo.5744985</strong></pre> <p> </p>
Parallel, Portable Algorithms for Distance-2 Maximal Independent Set and Graph Coarsening: Rebuttal Material
<p>Additional material with rebuttal of IPDPS22 submission, "Parallel, Portable Algorithms for Distance-2 Maximal Independent Set and Graph Coarsening".</p>
S2-Agri - Pixel-Set
<p>Dataset of satellite image time series for parcel-based crop type classification, in pixel set format.</p> <p>See related <a href="https://openaccess.thecvf.com/content_CVPR_2020/papers/Garnot_Satellite_Image_Time_Series_Classification_With_Pixel-Set_Encoders_and_Temporal_CVPR_2020_paper.pdf">article</a> for further details.</p>
data set for Magnon heat transport in a 2D Mott insulator
<p>data set for the paper Magnon heat transport in a 2D Mott insulator</p> <p>source code for generating the data:</p> <p><a href="https://github.com/wenowang96/Determinant-QMC">https://github.com/wenowang96/Determinant-QMC</a></p> <p>Publication: Phys. Rev. B <strong>105</strong>, L161103</p> <p> </p> <p>refer to <a href="https://github.com/wenowang96/DQMC_analysis_data">https://github.com/wenowang96/DQMC_analysis_data</a> (the folder ''magnon-heat-transport'') for follow up updates.</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.