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662 results for “method comparison”
A Detailed Comparison of Multi-Dimensional Boltzmann Neutrino Transport Methods in Core-Collapse Supernovae
<p>This dataset contains results of 1D and 2D static neutrino transport calculations using discrete ordinates and Monte Carlo methods, as described in the 2017 paper by the same name. The results include the neutrino momentum space grids used for the simulations, the full spectral and angular distribution functions, energy-dependent angular moments of the distribution functions, and neutrino heating rates. The HDF5 dataset name corresponds to the simulation of the same name in the 2017 paper, Table 1. Also included are the fluid backgrounds and opacities. See the readme for a description of all quantities in the datasets.</p> <p>There are also two simulation setups including all initial conditions and parameters for 1D and 2D Monte Carlo calculations using the open-source code Sedonu. This accompanies Sedonu commit 8bd509b27aa0461df26b194df65b4526d6c153fe.</p>
Comparison of Fixed Single Cell RNA-seq Methods to Enable Transcriptome Profiling of Neutrophils in Clinical Samples
<p>Monitoring neutrophil gene expression is a powerful tool for understanding disease mechanisms, developing new diagnostics, therapies and optimizing clinical trials. Neutrophils are sensitive to the processing, storage and transportation steps that are involved in clinical sample analysis. This study is the first to evaluate the capabilities of technologies from 10X Genomics, PARSE Biosciences, and HIVE (Honeycomb Biotechnologies) to generate high-quality RNA data from human blood-derived neutrophils. Our comparative analysis shows that all methods produced high quality data, importantly capturing the transcriptomes of neutrophils. 10X FLEX cell populations in particular showed a close concordance with the flow cytometry data. Here, we establish a reliable single-cell RNA sequencing workflow for neutrophils in clinical trials: we offer guidelines on sample collection to preserve RNA quality and demonstrate how each method performs in capturing sensitive cell populations in clinical practice.</p> <p><strong>This dataset includes the FACS, 10X 3', Parse, 10X Flex, and Hive data and analysis.</strong></p>
Supplementary Data for "Comparison of Ensemble-Based Data Assimilation Methods for Sparse Oceanographic Data"
<p>This data set represents the supplementary data for the paper Comparison of Ensemble-Based Data Assimilation Methods for Sparse Oceanographic Data (Section 4) by Florian Beiser, Håvard Heitlo Holm, and Jo Eidsvik.</p><p>It contains the data that is plotted in the manuscript. The code for plotting is provided in the supplementary software.</p>
Supplement to the article "Simulation of marine stratocumulus using the super-droplet method: Numerical convergence and comparison to a double-moment bulk scheme"
<p>This is a supplement to the article "Simulation of marine stratocumulus using the super-droplet method: Numerical convergence and comparison to a double-moment bulk scheme".</p> <p>The time evolution of horizontal distribution of LWP:</p> <ul> <li>SDM_lwp_2d_sdm.mp4: from nine SDM runs with different grid resolutions.</li> <li>SN14_lwp_2d_sn14.mp4: from nine SN14 runs with different grid resolutions.</li> </ul> <p>The time evolution of vertical profiles:</p> <ul> <li>sdm_profile_t.mp4: from nine SDM runs with different grid resolutions.</li> <li>sn14_profile_t.mp4: from nine SN14 runs with different grid resolutions.</li> <li>sdm_incloud_t.mp4: vertical profiles in cloudy areas and cloud holes in SDM runs.</li> <li>sn14_incloud_t.mp4: vertical profiles in cloudy areas and cloud holes in SN14 runs.</li> <li>sdm_50x5_incloud_t.mp4: comparison between original SDM and SDM without sedimentation.</li> </ul>
Data for: Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny
<p>Sequence alignments and gene trees for: Braun et al. "Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny." See README file for detailed description of all files.</p>
RepoFromPaper Comparison with Bidir Method
<p>These are the results of a comparison of link extraction between Bidir method and RepoFromPaper, applied on 150 research papers from the csSe section in Arxiv.org from the year 2023.</p>
Benchmark Multi-Omics Datasets for Methods Comparison
<p><strong>Pathway Multi-Omics Simulated Data</strong></p> <p>These are synthetic variations of the TCGA COADREAD data set (original data available at <a href="http://linkedomics.org/data_download/TCGA-COADREAD/">http://linkedomics.org/data_download/TCGA-COADREAD/</a>). This data set is used as a comprehensive benchmark data set to compare multi-omics tools in the manuscript "pathwayMultiomics: An R package for efficient integrative analysis of multi-omics datasets with matched or un-matched samples".</p> <p>There are 100 sets (stored as 100 sub-folders, the first 50 in "pt1" and the second 50 in "pt2") of random modifications to centred and scaled copy number, gene expression, and proteomics data saved as compressed data files for the R programming language. These data sets are stored in subfolders labelled "sim001", "sim002", ..., "sim100". Each folder contains the following contents: 1) "indicatorMatricesXXX_ls.RDS" is a list of simple triplet matrices showing which genes (in which pathways) and which samples received the synthetic treatment (where XXX is the simulation run label: 001, 002, ...), (2) "CNV_partitionA_deltaB.RDS" is the synthetically modified copy number variation data (where A represents the proportion of genes in each gene set to receive the synthetic treatment [partition 1 is 20%, 2 is 40%, 3 is 60% and 4 is 80%] and B is the signal strength in units of standard deviations), (3) "RNAseq_partitionA_deltaB.RDS" is the synthetically modified gene expression data (same parameter legend as CNV), and (4) "Prot_partitionA_deltaB.RDS" is the synthetically modified protein expression data (same parameter legend as CNV).</p> <p> </p> <p><strong>Supplemental Files</strong></p> <p>The file "cluster_pathway_collection_20201117.gmt" is the collection of gene sets used for the simulation study in Gene Matrix Transpose format. Scripts to create and analyze these data sets available at: <a href="https://github.com/TransBioInfoLab/pathwayMultiomics_manuscript_supplement">https://github.com/TransBioInfoLab/pathwayMultiomics_manuscript_supplement</a></p> <p> </p>
Performance comparison of optimization methods on variational quantum algorithms
<p>This repository contains the code, data and notebooks to reproduce the plots from the manuscript "Performance comparison of optimization methods on variational quantum algorithms"</p>
Data from: How to date a crocodile – estimation of neosuchian clade ages and a comparison of four time-scaling methods
<p>Clade ages within the crocodylomorph clade Neosuchia have long been debated. Molecular and morphological studies have yielded remarkably divergent results. Despite recent advances, there has been no comprehensive relative comparison of the major time calibration methods available to estimate clade ages based on morphological data. We used four methods (cal3, Extended Hedman [EH], smoothed Ghost-Lineage-Analysis [sGLA] and the Fossilised Birth-Death model [FBD]) to date clade ages derived from a published crocodylomorph supertree and a new neosuchian phylogeny. All time-scaling methods applied here agree on the origination of Neosuchia during the Late Triassic/Early Jurassic, and the presence of the major extant eusuchian groups (Crocodyloidea, Gavialoidea, Alligatoroidea, and Caimaininae) by the end of the Late Cretaceous. The number of distinct lineages present before the K/Pg boundary is less certain, with support for two competing scenarios in which Crocodylinae, Tomistominae and Diplocynodontinae either: 1) diverged from other eusuchian lineages before the K/Pg boundary; or 2) evolved during a 'burst' of diversification after the K/Pg event. Cal3 and FBD are identified as the most suitable methods for time-scaling phylogenetic trees dominated by fossil taxa. Extended Hedman estimates are substantially older than the others, with larger standard deviations and a strong vulnerability to taxon sampling and topological changes. sGLA has similar problems and cannot be recommended either. We conclude that a detailed understanding of phylogenetic relationships, tree reconstruction methods, and good taxonomic coverage (in particular the inclusion of the oldest taxon in each clade) is essential when evaluating the results of such dating analyses.</p>
Results of statistical analyses of the comparison of phosphorous measurement laboratory methods
<p>The study in the related article compares the phosphorus (P) analysis methods of ammonium lactate (AL), Mehlich 3 (M3); water extraction (P-WA(P)&P-WA(PO<sub>4</sub>)), cobalt hexamine (CoHex) and X-ray fluorescence (XRF, as an estimate of total soil P). The ratio of the P-content/XRF was calculated and compared with the whole dataset first. Based on the comparison of all the data there were significant differences between the results of P-WA(P) and P-WA(PO<sub>4</sub>) vs M3 and AL, CoHex vs M3 and CoHex vs AL methods (p<0.001). The influencing factors were also analysed for a more in-depth understanding of their role (CaCO<sub>3</sub>-content, pH, soil texture and clay content). The file contains the results of the statistical analyses.</p>
Comparison of Monitoring Methods during L-DED of Inconel 718
<p>Videos showing 4 different monitoring techniques during L-DED (BeAM Magic 2.0) of Inconel 718</p>
Comparison of Fixed Single Cell RNA-seq Methods to Enable Transcriptome Profiling of Neutrophils in Clinical Samples - Time course data
<p>Monitoring neutrophil gene expression is a powerful tool for understanding disease mechanisms, developing new diagnostics, therapies and optimizing clinical trials. Neutrophils are sensitive to the processing, storage and transportation steps that are involved in clinical sample analysis. This study is the first to evaluate the capabilities of technologies from 10X Genomics, PARSE Biosciences, and HIVE (Honeycomb Biotechnologies) to generate high-quality RNA data from human blood-derived neutrophils. Our comparative analysis shows that all methods produced high quality data, importantly capturing the transcriptomes of neutrophils. 10X FLEX cell populations in particular showed a close concordance with the flow cytometry data. Here, we establish a reliable single-cell RNA sequencing workflow for neutrophils in clinical trials: we offer guidelines on sample collection to preserve RNA quality and demonstrate how each method performs in capturing sensitive cell populations in clinical practice.</p> <p><strong>This dataset includes only the 10X Flex time course data and analysis.</strong></p>
Raw data from Incineration Ash-Inter Comparison Results for Metal Concentrations by ICP-mS method
<p>The dataset contains the raw data of all consortium member for metal concentrations on loaded filters.</p> <p>These data relate to the journal article <strong>Novel preparation of a candidate reference material of PM10 and PM2.5 airborne particulate filters loaded with incineration ash. Inter comparison results for metal c</strong>once<strong>ntrations</strong> by Alexandre Bescond, Caroline Oster, Paola Fisicaro, Sharon Goddard, Paul Quincey, Lamprini-Areti Tsakanika, Theopisti Lymperopoulou, Maria Ochsenkuehn-Petropoulou. <a href="https://doi.org/10.3390/atmos12010067">https://doi.org/10.3390/atmos12010067</a></p> <p>Theses datas was produced with ICP-MS devices for the determination of metal concentration on loaded filters. The filters was produced by LNE with an aerosol disperser.</p>
Data Archive for: Hurricane Laura (2020): A Comparison of Drop Size Distribution Moments Using Ground and Radar Remote Sensing Retrieval Methods
<p>This archive corresponds to the data described in Brauer et al. (2021) to be published in <em>Journal of Geophysical Research: Atmospheres.</em> Please see the included readme.txt file for details about each data file.</p>
Molecular dynamics-generated ensemble dataset of ubiquitin; for "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles"
<p>The molecular dynamics-generated ensemble dataset (229Mb zip file) for ubiquitin, used in the manuscript "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles", submitted to the Journal of Chemical Information and Modeling (JCIM). The dataset consists of 6 .dcd files, and one .pdb file. </p>
Comparison of Root End Sealing Ability of three Retrograde Filling Materials in Teeth with Root Apices Resected at 900 using dye penetration method under fluorescent microscope.
<p>Checking the depth of dye penetration and thereby evaluating the sealing ability of retrograde materials</p>
A Comparison of Passive and Active Dust Sampling Methods for Measuring Airborne MRSA in Pig Farms
<p>Study Abstract:</p> <p>Authors: Anne Rittscher, Abel A. Vlasblom, Birgitta Duim, Peter Scherpenisse, Isabella van Schothorst, Inge M. Wouters, Liese Van Gompel, Lidwien A.M. Smit</p> <p> Methicillin resistant strains of <em>Staphylococcus aureus </em>(MRSA) are resistant to most b-lactam antibiotics. Pigs are an important reservoir of livestock associated MRSA (LA-MRSA), which is genetically distinct from both hospital and community acquired MRSA. Occupational exposure to pigs on farms can lead to LA-MRSA carriage by workers. There is a growing body of research on MRSA found in the farm environment, the airborne route of transmission, and its implication on human health. This study aims to compare two sampling methods used to measure airborne MRSA in the farm environment; passive dust sampling with electrostatic dust fall collectors (EDCs), and active inhalable dust sampling using stationary air pumps with Teflon filters.</p> <p>Paired dust samples using EDCs and GSP samplers, totaling 87 samples, were taken from seven Dutch pig farms, in multiple compartments housing pigs of varying ages. Total nucleic acids of both types of dust samples were extracted and targets indicating MRSA (<em>femA, nuc, mecA</em>) and total bacterial count (16S rRNA) were quantified using quantitative Real Time PCRs.</p> <p>MRSA could be measured in all stationary pump samples and in 94% of the EDCs, additionally MRSA was present on every farm sampled. There was a strong positive relationship between the paired MRSA levels found in EDCs and those measured on filters (Normalized by 16S rRNA; Pearson’s correlation coefficient r=0.94, Not Normalized; Pearson’s correlation coefficient r=0.84).</p> <p>This study suggests that EDCs can be used as an affordable and easily standardized method for quantifying airborne MRSA levels in the pig farm setting.</p>
Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi
<p>Limiting harm to organisms via genetic sampling is an important consideration for rare species. Nondestructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the Unionid freshwater mussel, Texas Pigtoe (<em>Fusconaia askewi</em>). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared to swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence) while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.</p>
Establishing peat-forming plant communities: A comparison of wetland reclamation methods in Alberta's oil sands region
<p>The Sandhill Wetland (SW) and Nikanotee Fen (NF) are two wetland research projects designed to test the viability of peatland reclamation in the Alberta oil sands post-mining landscape. To identify effective approaches for establishing peat-forming vegetation in reclaimed wetlands, we evaluated how plant introduction approaches and water level gradients influence species distribution, plant community development, and establishment of bryophyte and peatland species richness and cover. Plant introduction approaches included seeding with a <em>Carex aquatilis</em>-dominated seed mix, planting <em>C. aquatilis</em> and <em>J. balticus</em> seedlings, and spreading a harvested moss layer transfer. Establishment was assessed six years after introduction at SW and five years after introduction at NF. A total of 51 species were introduced to the reclaimed wetlands, and 122 species were observed after five and six years. The most abundant species in both reclaimed wetlands was <em>C. aquatilis</em>, which produced dense canopies and occupied the largest water level range of observed plants. Introducing <em>C. aquatilis</em> also helped to exclude marsh plants such as <em>Typha latifolia</em> that has little to no peat accumulation potential. <em>Juncus balticus</em> persisted where the water table was lower and encouraged formation of a diverse peatland community and facilitated bryophyte establishment. Various bryophytes colonized suitable areas, but the moss layer transfer increased cover of desirable peat-forming mosses. Communities with the highest bryophyte and peatland species richness and cover (averaging 9 and 14 species, and 50% to 160% cover respectively) occurred where summer water level was between -10 and -40 cm. Outside this water level range, a marsh community of <em>Typha latifolia</em> dominated in standing water and a wet-meadow upland community of <em>Calamagrostis canadensis</em> and woody species established where the water table was deeper. Overall, the two wetland reclamation projects demonstrated that establishing peat-forming vascular plants and bryophytes is possible, and community formation is dependent upon water level and plant introduction approaches. Future projects should aim to create microtopography with water tables within 40 cm of the surface and introduce vascular plants such as <em>J. balticus</em> that facilitate bryophyte establishment and support development of a diverse peatland plant community.</p>
Comparison Between the Caudal Block and Other Methods of Postoperative Pain Relief in Children Undergoing Circumcision
ClinicalTrials.gov study NCT06086106. IPD Sharing: YES. Countries: 1. Publications: 7.
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.