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8,038 results for “Validity”
Data from: On the objectivity, reliability, and validity of deep learning enabled bioimage analyses
<p>Bioimage analysis of fluorescent labels is widely used in the life sciences. Recent advances in deep learning (DL) allow automating time-consuming manual image analysis processes based on annotated training data. However, manual annotation of fluorescent features with a low signal-to-noise ratio is somewhat subjective. Training DL models on subjective annotations may be instable or yield biased models. In turn, these models may be unable to reliably detect biological effects. An analysis pipeline integrating data annotation, ground truth estimation, and model training can mitigate this risk. To evaluate this integrated process, we compared different DL-based analysis approaches. With data from two model organisms (mice, zebrafish) and five laboratories, we show that ground truth estimation from multiple human annotators helps to establish objectivity in fluorescent feature annotations. Furthermore, ensembles of multiple models trained on the estimated ground truth establish reliability and validity. Our research provides guidelines for reproducible DL-based bioimage analyses.</p>
Model Validation Framework Evaluation Result
<p>CSV Files with the results of the Model Validation Framework Evaluation</p>
Viral Validation: How the New Journal 'Rapid Reviews: COVID-19′ Accelerates Peer Review and Publishing
<p><strong>Episode Summary:</strong></p> <p>In this episode we talk to Professor Stefano Bertozzi, editor-in-chief Rapid Reviews: COVID-19 (RR:C19). This new open access overlay journal from the MIT Press is aiming to publish expert peer reviews of new COVID-19 research which will help validate and accelerate the discovery of high impact, useful studies. We discussed how the journal will work, the role human and AI input will play, and the importance of pan-disciplinary content. </p> <p><strong>Episode Links:</strong></p> <ul> <li><a href="https://rapidreviewscovid19.mitpress.mit.edu/">Rapid Reviews: COVID-19 Journal</a></li> <li><a href="https://mitpress.mit.edu/">MIT Press</a></li> <li><a href="https://publichealth.berkeley.edu/people/stefano-bertozzi/">Professor Stefano Bertozzi</a> <ul> <li><a href="https://twitter.com/StefBertozzi">Twitter</a></li> </ul> </li> </ul>
Data set for validation of a Python script for computation of Protein-Ligand Interaction Fingerprints
<p><strong>1. Data set for for validation of the Protein-Ligand Interaction Fingerprints, which includes examples of protein structures (original PDB and equilibrated) and molecular dynamics trajectories (equilibration and ligand dissociation generated using Random Acceleration MD simulations, RAMD)</strong></p> <p><strong>mdifp_validation_data.tar.gz - </strong>archive that contains benchmark dataset for evaluation of the protein-ligand IFP protocol (PDB structures of protonated complexes, ligands, and MOL2 files of ligands) published in D. B. Kokha, B. Doser, S. Richter, F. Ormersbach, X. Cheng, R. C. Wade "A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories" J. Chem. Phys. <strong>153</strong>, 125102 (2020); <a href="https://doi.org/10.1063/5.0019088">https://doi.org/10.1063/5.0019088</a></p> <p>(2020) <a href="https://arxiv.org/abs/2006.11066">arXiv:2006.11066</a> </p> <p><strong>2YKI </strong>- protein-ligand complex , PDB ID 2YKI<br> - 2yki_MOE.pdb complex with hydrogen added and energy minimized using MOE software (https://www.chemcomp.com/)<br> - ligand_2yki_MOE.mol2 and ligand_2yki_MOE.pdb - ligand structure with hydrogens prepered by MOE software (https://www.chemcomp.com/)</p> <p><strong>6EI5</strong> - MD trajectory of the protein-ligand complex generated from PDB ID 6EI5<br> - ref-min.pdb minimized structure<br> - ref.prmtop topology file<br> - moe.mol2 - ligand structure in mol2 format<br> - amber2namd2.dcd generated MD trajectory </p> <p><strong>SAD_3-RAMD-03-2020.pkl </strong>- a pkl dataset with IFPs generated from RAMD dissociation trajectory of the complex PDB ID: 5LQ9 (trajectories from the paper Front. Mol. Biosci., 2019 DOI:10.3389/fmolb.2019.00036)</p> <p><strong>HSP90_Gromacs.zip </strong>- an archive that contains three pkl data sets of protein-ligand IFPs (for three HSP90 complexes; PDB ID: 5J64, 5J86, 5LQ9) generated from RAMD dissociation trajectories simulated using new Gromacs-RAMD engine (https://github.com/HITS-MCM/gromacs-ramd)</p> <p>The rest of the files contains data obtained from simulation of the complex of <strong>GPCR muscarinic receptor M2 (PDB ID:4MQT);</strong> immersed in a mixed membrane: 50% CHL, 30% POPC, 20% POPE) with a small molecule agonist iperoxo. <br> - <strong>IXO.pdb and moe.mol2 </strong>- PDBand MOL2 structure of iperoxo<br> - <strong>AMBER_eq.tar.gz</strong> - structure of the equilibrated complex generated using AMBER software<br> -<strong> NAMD_eq.tar.gz </strong>- two equilibration trajectories in dcd format generated using NAMD software <br> - <strong>RAMD_eq.tar.gz </strong>- dissociation tarjectoris of iprtoxo from the M2 protein generated from the last snapshot of two NAMD equilibration trajectories (for each case 2 RAMD dissociaiton trajectories are available) </p> <p>( *csv files were added erroneously and do not belong to the project)</p>
Quo Vadis, Methodology? The Key Role of Manipulation Checks for Validity Control and Quality of Science
<p>Data set and code book related to the article "Quo Vadis, Methodology? The Key Role of Manipulation Checks for Validity Control and Quality of Science"</p>
FIGURE 3. Isotomurus graminis from Iran. A in Isotomurus graminis Fjellberg (Collembola: Isotomidae) new for Iran, key to Iranian species in genus with comment on the validity of photographic records
FIGURE 3. Isotomurus graminis from Iran. A, habitus of specimen fixed in alcohol (lateral view); B, post antennal organ in head indicate with arrow (40x); C, trichobothria present on abdomen IV, arrow indicates two trichobothria (40x); D, tibiotarsus distally and empodial complex of hind leg (posterior view)(40x).
FIGURES 1. A & B in Isotomurus graminis Fjellberg (Collembola: Isotomidae) new for Iran, key to Iranian species in genus with comment on the validity of photographic records
FIGURES 1. A & B: Different views of grassland sites on which Isotomurus graminis was found showing varied vegetation found on the Golil-Sarany protected rangelands in North Khorasan, Iran.
FIGURE 2 in Isotomurus graminis Fjellberg (Collembola: Isotomidae) new for Iran, key to Iranian species in genus with comment on the validity of photographic records
FIGURE 2. Location of protected area in Iran and IRS-P6 LISS III satellite image of Golil-Sarany protected rangelands.
Design and Validation of an Assessment Tool for Educational Mobile Applications Used with Autistic Learners
<p>Appendix A and B, supplementary material to the publication:</p> <p>Sanromà-Giménez, M., Lázaro Cantabrana, J. L., Usart Rodríguez, M., & Gisbert-Cervera, M. (2021). Design and Validation of an Assessment Tool for Educational Mobile Applications Used with Autistic Learners. <em>Journal of New Approaches in Educational Research,</em> 10(1), doi: 10.7821/naer.2021.1.574</p>
FD-detector: Dataset gathered running measurements in the wild and Emulations for validation
<p>This file contains two folders: the dataset and emulation setup.</p> <p>The dataset is composed of warts files, resulting from traceroutes run with Scamper on NLNOG RING nodes. On the other hand, the emulations were performed on GNS3.</p>
Datasets from: Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode
<p>Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (<i>metaMATE</i>) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. <i>metaMATE</i> requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mtDNA haplotypes) or non-authentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. <i>metaMATE</i> (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of non-authentic ASVs and the collateral effects on the removal of authentic ASVs. The output from <i>metaMATE</i> facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the <i>metaMATE</i> software, available at https://github.com/tjcreedy/metamate).</p>
FIGURE 3 in First record of the West Nile virus bridge vector Culex modestus Ficalbi (Diptera Culicidae) in Belgium, validated by DNA barcoding
FIGURE 3. NJ tree based on COI sequences downloaded from BOLD, including Culex species recorded from Belgium (Boukraa et al. 2015) and sequences of Cx. modestus (Table 1). Bootstrap values are indicated above the branches. The blue square gives a zoom view of the un-collapsed tree.
FIGURE 2 in First record of the West Nile virus bridge vector Culex modestus Ficalbi (Diptera Culicidae) in Belgium, validated by DNA barcoding
FIGURE 2. The small vernal pond vegetated with common cattail (Typha latifolia) where the Cx. modestus larva was collected.
FIGURE 1 in First record of the West Nile virus bridge vector Culex modestus Ficalbi (Diptera Culicidae) in Belgium, validated by DNA barcoding
FIGURE 1. (A) Posterior part of the mounted Cx. modestus larva. Zoom on the diagnostic characteristic of the siphon, showing disarrayed insertion points of the ventral siphonal setae. (B) Posterior part of a mounted Cx. pipiens larva.
Manuscript data for "PASV: Automatic protein partitioning and validation using conserved residues"
<p>Manuscript data for "PASV: Automatic protein partitioning and validation using conserved residues"</p>
Data from: Development and validation of warning system of ventricular tachyarrhythmia in patients with heart failure with heart rate variability data
Implantable-cardioverter defibrillators (ICD) detect and terminate life-threatening ventricular tachyarrhythmia with electric shocks after they occur. This puts patients at risk if they are driving or in a situation where they can fall. ICD's shocks are also very painful and affect a patient's quality of life. It would be ideal if ICDs can accurately predict the occurrence of ventricular tachyarrhythmia and then issue a warning or provide preventive therapy. Our study explores the use of ICD data to automatically predict ventricular arrhythmia using heart rate variability (HRV). A 5 minute and a 10 second warning system are both developed and compared. The participants for this study consist of 788 patients who were enrolled in the ICD arm of the Sudden Cardiac Death – Heart Failure Trial (SCD-HeFT). Two groups of patient rhythms, regular heart rhythms and pre-ventricular-tachyarrhythmic rhythms, are analyzed and different HRV features are extracted. Machine learning algorithms, including random forests (RF) and support vector machines (SVM), are trained on these features to classify the two groups of rhythms in a subset of the data comprising the training set. These algorithms are then used to classify rhythms in a separate test set. This performance is quantified by the area under the curve (AUC) of the ROC curve. Both RF and SVM methods achieve a mean AUC of 0.81 for 5-minute prediction and mean AUC of 0.87-0.88 for 10-second prediction; an AUC over 0.8 typically warrants further clinical investigation. Our work shows that moderate classification accuracy can be achieved to predict ventricular tachyarrhythmia with machine learning algorithms using HRV features from ICD data. These results provide a realistic view of the practical challenges facing implementation of machine learning algorithms to predict ventricular tachyarrhythmia using HRV data, motivating continued research on improved algorithms and additional features with higher predictive power.
Data from: Multivariate ratio analysis reveals Trigonoderus pedicellaris Thomson (Hymenoptera, Chalcidoidea, Pteromalidae) as a valid species
We demonstrate by multivariate ratio analysis (MRA) the validity of two female colour morphs as separate species in what was previously regarded as a single species, Trigonoderus cyanescens (Förster, 1841) (Hymenoptera: Pteromalidae). As a result, T. pedicellaris Thomson, 1878 stat.r., is resurrected from synonymy under T. cyanescens and T. filatus binubilatus Erdős, 1960 syn.n. is synonymized with T. cyanescens. More than 20 characters were measured as part of two MRA dataset analyses. The first analysis excluded all measurements related to the gaster, whereas the second included gaster length, gaster breadth and seventh gaster tergite breadth. The first analysis revealed that the best separating morphometric ratios for the two species are head breadth:metatibia length and OOL:parastigma length, whereas the second analysis revealed OOL:gaster length as the second best separating ratio. The measurement error of all characters was below the admissible level of 30%. Gaster length proved to be a good character for separating the two groups, showed the lowest measurement error, and its percentage coefficient of variation was not greater than for other characters. This indicates that gaster length should not be discarded out-of-hand as a morphometric character in Pteromalidae. The variables that gave the best separating ratios included different body parts; therefore we suggest that the body of a specimen should be taken as a whole for use in MRA analyses, where each distance measurement can interact freely with any other. A key, figures and re-descriptions of T. cyanescens and T. pedicellaris are provided.
Data from: Exploitation of a turbot (Scophthalmus maximus L.) immune-related expressed sequence tag (EST) database for microsatellite screening and validation
In this study, we identified and characterized 160 microsatellite loci from an expressed sequence tag (EST) database generated from immune-related organs of turbot (Scophthalmus maximus). A final set of 83 new polymorphic microsatellites were validated after the analysis of 40 individuals from Atlantic origin including both wild and farmed individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analyzed loci showed deviations from Mendelian segregation after analysis of five full-sib families including ~92 individuals/family. The markers are used to consolidate the turbot genetic map and, since they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) at 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.
Data from: A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies
The main objective of this work was to develop and validate a robust and reliable 'from benchtop-to-desktop' metabarcoding workflow to investigate the diet of invertebrate-eaters. We applied our workflow to fecal DNA samples of an invertebrate-eating fish species. A fragment of the COI gene was amplified by combining two minibarcoding primer sets to maximize the taxonomic coverage. Amplicons were sequenced by an Illumina MiSeq platform. We developed a filtering approach based on a series of non-arbitrary thresholds established from control samples and from molecular replicates in order to address the elimination of cross-contamination, PCR/sequencing errors and mistagging artifacts. This resulted in a conservative and informative metabarcoding dataset. We developed a taxonomic assignment procedure that combines different approaches and that allowed the identification of ~75% of invertebrate COI variants to the species level. Moreover, based on the diversity of the variants, we introduced a semi-quantitative statistic in our diet study, the Minimum Number of Individuals (MNI), which is based on the number of distinct variants in each sample. The metabarcoding approach described in this paper may guide future diet studies that aim to produce robust datasets associated with a fine and accurate identification of prey items.
Data from: Development, validation, and evaluation of an assay for the detection of wood frogs (Rana sylvatica) in environmental DNA
We developed and describe a qPCR assay for the detection of wood frogs (Rana sylvatica) using environmental DNA (eDNA) sampling. A single primer set was designed to amplify a 115-bp region of the wood frog cytochrome B gene and assessed for target specificity. There was no evidence of amplification in 11 non-target species. We evaluated the utility of the primer set in qPCR assay by conducting geo-referenced eDNA field surveys in Interior Alaska. Results indicate that the assay consistently detects wood frog DNA in the environment to 1.83 × 10−3 pg/μL. The assay provides a complement to traditional survey methods and can be readily applied in a wider conservation and management context.
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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.