Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
641
datasets available to search
ShareScore release 0.9.0
Dataset results
641 results for “data validation”
Data from: Spatial localization of anterior precuneus for bodily self validated with brain stimulation
Open the record for dataset details and reuse information.
Data from: Validation of serum neurofilaments as prognostic & potential pharmacodynamic biomarkers for ALS
<p><span><span><span><span><span><span><span><span><span><span><span><u>Objective</u>. Identify preferred neurofilament assays, and clinically validate serum NfL and pNfH as prognostic and potential pharmacodynamic biomarkers relevant to ALS therapy development. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Methods</u>. Prospective, multi-center, longitudinal observational study of patients with ALS (n=229), primary lateral sclerosis (PLS, n=20) and progressive muscular atrophy (PMA, n=11). Biological specimens were collected, processed and stored according to strict standard operating procedures (SOPs) <sup>1</sup>. Neurofilament assays were performed in a blinded manner by independent contract research organizations (CROs). </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Results</u>. For serum NfL and pNfH measured using the Simoa assay, there were no missing data (i.e. both technical replicates below the lower limit of detection were not encountered). For the Iron Horse and Euroimmun pNfH assays, such missingness was encountered in ~4% and ~10% of serum samples respectively. Mean coefficients of variation (CVs) for pNfH in serum and CSF were ~4-5% and ~2-3% respectively in all assays. Baseline NfL concentration, but not pNfH, predicted the future ALSFRS-R slope and survival. Incorporation of baseline serum NfL into mixed effects models of ALSFRS-R slopes yields an estimated sample size saving of ~8%. Depending on the method used to estimate effect size, use of serum NfL (and perhaps pNfH) as pharmacodynamic biomarkers, instead of the ALSFRS-R slope, yields significantly larger sample size savings.</span></span></span></span></span></span></span></span></span></span></span></p> <p><u>Conclusions</u><span><span><span><span><span><span><span><span><span><span><span>. Serum NfL may be considered a clinically validated prognostic biomarker for ALS. Serum NfL (and perhaps pNfH), quantified using the Simoa assay, have potential utility as pharmacodynamic biomarkers of treatment effect. </span></span></span></span></span></span></span></span></span></span></span></p>
An Empirical Validation of Cognitive Complexity as a Measure of Source Code Understandability - Data, Code and Documentation
<p>Release version of the data, code and documentation used in and generated by our data analysis and literature search to ensure reproducibility, repeatability, and transparency, to be published alongside our paper "An Empirical Validation of Cognitive Complexity as a Measure of Source Code Understandability".</p>
Data from: The island syndrome hypothesis is only partially validated in two rodent species in an inland-island system
<p><span>According to the island syndrome and island rule hypotheses, island isolation and reduced area lead to phenotypic shifts in ecologically relevant traits in insular populations compared to mainland ones. These hypotheses have been built up with oceanic islands in mind or islands where isolation is high and colonization rate relatively limited. This set of hypotheses, however, may not be applicable to other inland-island systems or recently fragmented landscapes. </span></p> <p><span>We investigated how island life leads to phenotypic changes in two rodent metapopulations: deer mice and red-backed voles in a fragmented system on a river in Canada. From 2013 to 2016, we sampled 454 deer mice and 665 red-backed voles spread across 10 islands and six mainland sites on river shores. We compared body mass, tail and hindfoot length, exploration, and reaction towards predators, between individuals from island and mainland sites, and assessed the role of connectivity, isolation and area of islands. </span></p> <p><span>Insular individuals from both species were less aggressive towards potential predators and insular mice were more thorough explorers compared to mainland ones. Male mice were heavier and juvenile mice had longer tails on islands. However, contrary to expectations, we found negative relationships between aggressiveness and juvenile exploration score with patch connectivity for mice. Island connectivity significantly affected tail length of mice through a concave relationship. Finally, vole aggressiveness and exploration of male mice were positively correlated to island isolation. </span></p> <p><span>Our study supports only partially the predictions of the island syndrome hypothesis. It provides empirical evidence that inland-island life can modify traits in deer mice, but less so in red-backed voles in a non-oceanic system. It also raises questions about the direct causal factors of these changes in a naturally fragmented landscape, and urges for more predictive models about phenotypic/genetic divergence among populations in natural and artificial fragmented landscapes.</span></p>
Data from: RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management
<p>Invasive alien species (IAS) are among the main causes of global biodiversity loss. Invasive brown (Rattus norvegicus) and black (R. rattus) rats, in particular, are leading drivers of extinction on islands, especially in the case of seabirds where >50% of all extinctions have been attributed to rat predation. Eradication is the primary form of invasive rat management, yet this strategy has resulted in a ~10-38% failure rate on islands globally. Genetic tools can help inform IAS management, but such applications to date have been largely reactive, time-consuming, and costly. Here, we developed a Genotyping-in-Thousands by sequencing (GT-seq) panel for rapid species identification and population assignment of invasive brown and black rats (RapidRat) in Haida Gwaii, an archipelago comprising ~150 islands off the central coast of British Columbia, Canada. We constructed an optimized panel of 443 single nucleotide polymorphisms (SNPs) using previously generated double-digest restriction-site associated DNA (ddRAD) genotypic data (27,686 SNPs) from brown (n=295) and black rats (n=241) sampled throughout Haida Gwaii. The informativeness of this panel for identifying individuals to species and island of origin was validated relative to the ddRAD results; in all comparisons, admixture coefficients and population assignments estimated using RapidRat were consistent. To demonstrate application, 20 individuals from novel invasions of three islands (Agglomerate, Hotspring, Ramsay) were genotyped using RapidRat, all of which were confidently assigned (>98.5% probability) to Faraday and Murchison Islands as putative source populations. These results indicated that a previous eradication on Hotspring Island was conducted at an inappropriate geographic scale; future management should expand the eradication unit to include neighboring islands to prevent re-invasion. Overall, we demonstrated that RapidRat is an effective tool for managing invasive rat populations in Haida Gwaii and provided a clear framework for GT-seq panel development for informing biodiversity conservation in other systems.</p>
Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
<p><i><span>Background</span></i></p> <p><span>The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in <i>de-novo</i> genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (<i>Penaeus monodon</i>) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).</span></p> <p><i><span>Results</span></i></p> <p><span>Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 </span>± 14.7 to 93.0% ± 3.5%<span>), </span>increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7<span>), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.</span></p> <p><i><span>Conclusion</span></i></p> <p><span>Importantly, this assay equips the <em>P. monodon</em> industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as <em>P. monodon</em> breeding programs transition to undertaking genomic selection.</span></p>
Validation Data for WinProp and NYUSIM
<p>Validation of WinProp and NYUSIM<br> ================================</p> <p>This archive contains simulation data the same scenario that is used in the measurement campaign published in [1-3]. The directories correspond to the respective simulators that have been used.</p>
Pilot implementation, monitoring, co-evaluation and validation data_v1
<p>These data have been collected in the context of monitoring and assessing the pilot operation of the INVITE project (H2020 GA 763651) and its OI2lab platform during their 1st deployment round.</p>
Benchmark data for source localization validation
<p>Template data related to the publication :<br> La Fisca et al., A Versatile Validation Framework for ERP and Oscillatory Source Reconstruction Using FieldTrip, 2021</p> <p>Funded by: F.N.R.S - F.R.I.A, Belgium</p>
Ecological niche modeling and first records from Namibia and Zimbabwe validate the amphi-equatorial distribution of Byrsinus pseudosyriacus (Hemiptera: Cydnidae) - Supplementary data
<p><em>Byrsinus pseudosyriacus (</em>Linnavuori, 1977), the most widely distributed Afrotropical species of the genus <em>Byrsinus</em> Fieber, 1860 known hitherto only from the Sudano-Eremian area is for the first time reported in two countries south of the Equator. The species potential distribution map was generated using the ecological niche modelling (ENM) methods that allowed this species to be regarded as amphi-equatorial in distribution<strong>.</strong></p>
Data from: Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments
1.Dispersal distances are commonly inferred from occupancy data but have rarely been validated. Estimating dispersal from occupancy data is further complicated by imperfect detection and the presence of unsurveyed patches. 2.We compared dispersal distances inferred from seven years of occupancy data for 212 wetlands in a metapopulation of the secretive and threatened California black rail (Laterallus jamaicensis coturniculus) to distances between parent-offspring dyads identified with 16 microsatellites. 3.We used a novel autoregressive multi-season occupancy model that accounted for both unsurveyed patches and imperfect detection to quantify patch isolation using buffer radius (BRM) and incidence function (IFM) connectivity measures at 15 scales (1–10, 15, 20, 25, and 30 km). Connectivity measures were then fit as colonization covariates in occupancy models to estimate a model-averaged dispersal distance. 4.As predicted, colonization was more strongly related to connectivity at small spatial scales (< 10 km). AIC weights were greatest at 7 km for BRM and at 4 km for IFM. 5.Model-averaged dispersal distances (BRM = 7.46 km; IFM = 5.48 km) showed good agreement with the mean (± SE) dispersal distance from 23 parent-offspring dyads (5.58 ± 1.92 km), indicating reasonably accurate mean dispersal distances can be inferred from occupancy data when isolation strongly affects colonization.
Data from: Development of a sustainability assessment algorithm and its validation using case studies on cryogenic machining
This work presents a comprehensive structure for evaluating the sustainability of machining processes. Industries can contribute towards developing a sustainable future by using algorithms that evaluate the sustainability of their processes. Inspired by the literature, the proposed model involves a set of metrics that are critical in evaluating the impact of a process on society, environment, and economy. The flexibility of this model allows decision-makers to use the available responses to identify the most favorable process. The entropy weight method was suggested for objectively calculating the weights of each indicator. A multi-criteria decision-making method i.e., Technique for Order Preference based on Similarity to Ideal Solution (TOPSIS), was used to rank processes in the decreasing order of their sustainability. The proposed algorithm was successfully validated with case studies from the published literature. A MATLAB code was also created so that industries may expeditiously apply this method to evaluate the sustainability of machining processes.
Paraphyletic species no more – genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)
<p>Rapid speciation events, with taxa generated over a short time period, are among the most investigated biological phenomena. However, molecular systematics often reveals contradictory results compared with morphological/phenotypical diagnoses of species under scenarios of recent and rapid diversification. In this study, we used molecular data from an average of over 29,000 loci per sample from RADseq to reconstruct the diversification history and delimit the species boundary in a short-winged grasshopper species complex (<i>Melanoplus </i>Scudderi group), where Pleistocene diversification has been hypothesized to generate more than 20 putative species with distinct male genitalic shapes. We found that based on a maximum likelihood molecular phylogeny that each morphological species indeed forms a monophyletic group, contrary to the result from a previous mitochondrial DNA sequence study. By dating the diversification events, the species complex is estimated to have diversified during the Late Pleistocene, supporting the recent radiation hypothesis. Furthermore, coalescent-based species delimitation analyses provide quantitative support for independent genetic lineages, which corresponds with the morphologically-defined species. Our results also showed that male genitalic shape may not be predicted by evolutionary distance among species, indicating that this trait is not only labile, but also implying that selection may play a role in character divergence. Additionally, our findings suggest that the rapid speciation events in this flightless grasshopper complex might be associated primarily with the fragmentation of their grassland habitats during the Late Pleistocene. Collectively, our study highlights the importance of integrating multiple sources of information to delineate species, especially for a species complex that diversified rapidly, and whose divergence may be linked to ecological processes that create geographic isolation (i.e., fragmented habitats), as well as selection acting on characters with direct consequences for reproductive isolation (i.e., genitalic divergence).</p>
Data from: Validation of grain yield QTL from soft winter wheat using a CIMMYT spring wheat panel
Validation of quantitative trait loci (QTLs) is an essential step in marker-assisted breeding. The objectives of this study were to validate grain yield (GY) QTLs previously identified in soft red winter wheat (Triticum aestivum L.) through biparental and association mapping using the spring wheat association mapping initiative (WAMI) panel from CIMMYT, Mexico, and to identify allele combinations of the validated QTLs that resulted to the highest GY. Linked single-nucleotide polymorphisms for IWA3560 (3A), IWA1818 (4B), and IWA755 (6B) were significantly associated (P < 0.001) with GY, grain number, and thousand-grain weight in the WAMI. Lines possessing the favorable allele for the QTL at the 3A, 4B, and 6B loci (ACG allele combination) validated on the WAMI had the highest mean GY at 4.55 t ha−1, but three other haplotypes (ACA, GCA, and GCG) differing by one or two alleles in the validated QTL regions were not significantly different. These results validate GY QTLs across winter and spring wheat through genome-wide association analysis and further demonstrate the potential for pyramiding favorable alleles for the genetic improvement of wheat breeding populations.
Data from: Validity of the Diplostomoidea and Diplostomida (Digenea, Platyhelminthes) upheld in phylogenomic analysis
Higher systematics within the Digenea, Carus 1863 have been relatively stable since a phylogenetic analysis of partial nuclear ribosomal markers (rDNA) led to the erection of the Diplostomida Olson, Cribb, Tkach, Bray, and Littlewood, 2003. However, recent mitochondrial (mt) genome phylogenies suggest this order might be paraphyletic. These analyses show members of two diplostomidan superfamilies are more closely related to the Plagiorchiida La Rue, 1957 than to other members of the Diplostomida. In one of the groups implicated, the Diplostomoidea Poirier, 1886, a recent phylogeny based on mt DNA also indicates the superfamily as a whole is non-monophyletic. To determine if these results were robust to additional taxon sampling, we analyzed mt genomes from seven diplostomoids in three families. To choose between phylogenetic alternatives based on mt genomes and the prior rDNA-based topology, we also analyzed hundreds of ultra-conserved elements (UCEs) assembled from shotgun sequencing. The Diplostomida was paraphyletic in the mt genome phylogeny, but supported in the UCE phylogeny. We speculate this mitonuclear discordance is related to ancient, rapid radiation in the Digenea. Both UCEs and mt genomes support the monophyly of the Diplostomoidea and show congruent relationships within it. The Cyathocotylidae Muhling, 1898 are early diverging descendants of a paraphyletic clade of Diplostomidae Poirier, 1886, in which were nested members of the Strigeidae Railliet, 1919; the results support prior suggestions that the Crassiphialinae Sudarikov, 1960 will rise to the family level. Morphological traits of diplostomoid metacercariae appear to be more useful for differentiating higher taxa than those of adults. We describe a new species of Cotylurus Szidat, 1928, resurrect a species of Hysteromorpha Lutz, 1931, and find support for a species of Alaria Schrank, 1788 of contested validity. Complete rDNA operons are provided as a resource for future studies.
Data for figures and tables in: "Validation of the Scientific Program for the Dark Energy Spectroscopic Instrument"
<p>Supplementary material to DESI's publication 'Validation of the Scientific Program for the Dark Energy Spectroscopic Instrument' to comply with the data management plan.</p>
Experimental data from the initial validation of spark-eclib, a new framework for distributed metaheuristics in Spark
<p>This repository contains the experimental data obtained from two series of experiments to validate and profile <a href="https://doi.org/10.5281/zenodo.8431048"><strong>spark-eclib</strong></a>, a framework written in Scala to support the development of distributed population-based metaheuristics and their application to the global optimization of large-scale problems in Spark clusters:</p> <ul> <li>Experiments to validate the proposal of a generic topology for distributed PSO algorithms.</li> <li>Experiments to profile the parallel implementations of a PSO template.</li> </ul>
Profiling of pancreatic adenocarcinoma using artificial intelligence-based integration of multi-omic and computational pathology features - Validation Data Sets
<p>Two public validation cohorts were utilized in the MT-Pilot study, the Cancer Genome Atlas (TCGA) and cohort-1 Johns Hopkins University (JHU). These datasets included DNA, RNA, clinical data, and tissue protein analytes analyzed for survival outcome prediction using AI/Machine Learning modeling. </p>
Research data supporting article on implementation and validation of OpenMC cell-based R2S shutdown dose rate capabilities
<p>This file contains an archive of all research data that supports the article on implementation and validation of a cell-based R2S shutdown dose rate workflow in OpenMC.</p>
Data and Codes for Experimentally Validated Inverse design of Multi Property Fe-Co-Ni alloys: Data and codes release v1.0.1
<p>Data and Codes for Experimentally Validated Inverse design of Multi-Property Fe-Co-Ni alloys</p>
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.