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57 results for “empirical study data”
Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available. As their recommendation was mainly based on simulated data, we sought to replicate findings in two large-scale empirical studies. In our empirical data, SVA did not fully correct for cell-type effects, its performance was somewhat unstable, and it carried a risk of missing true signals caused by removing variation that might be linked to actual disease processes. By contrast, a reference-based correction method performed well and did not show these limitations. A disadvantage of this approach is that if reference methylomes are not (publicly) available, they will need to be generated once for a small set of samples. However, given the notable risk we observed for cell-type confounding, we argue that, to avoid introducing false-positive findings into the literature, it could be well worth making this investment.
Data from: Empirical and Bayesian approaches to fossil-only divergence times: a study across three reptile clades
Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.
Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)
Species tree methods are now widely used to infer the relationships among species from multi-locus datasets. Many methods have been developed, which differ in whether gene and species trees are estimated simultaneously or sequentially, and in how gene trees are used to infer the species tree. While these methods perform well on simulated data, less is known about what impacts their performance on empirical data. We used a dataset including five nuclear genes and one mitochondrial gene for 22 species of Batrachoseps to compare the effects of method of analysis, within-species sampling and gene sampling on species tree inferences. For this dataset, the choice of inference method had the largest effect on the species tree topology. Exclusion of individual loci had large effects in *BEAST and STEM, but not in MP-EST. Different loci carried the greatest leverage in these different methods, showing that the causes of their disproportionate effects differ. Even though substantial information was present in the nuclear loci, the mitochondrial gene dominated the *BEAST species tree. This leverage is inherent to the mtDNA locus and results from its high variation and lower assumed ploidy. This mtDNA leverage may be problematic when mtDNA has undergone introgression, as is likely in this dataset. By contrast, the leverage of RAG1 in STEM analyses does not reflect properties inherent to the locus, but rather results from a gene tree that is strongly discordant with all others, and is best explained by introgression between distantly related species. Within-species sampling was also important, especially in *BEAST analyses, as shown by differences in tree topology across 100 subsampled datasets. Despite the sensitivity of the species tree methods to multiple factors, five species groups, the relationships among these, and some relationships within them, are generally consistently resolved for Batrachoseps.
Scripts and data from the study 'Characterisation of magnetic atomic and molecular beamlines for the extraction of empirical scattering-matrices' (PCCP manuscript number CP-ART-04-2024-001785)
<p>This repository contains the data used for the article "Characterisation of magnetic atomic and molecular beamlines for the extraction of empirical scattering-matrices" and includes the code for generating the figures in the publication.</p>
Data accompanying "An empirical pipeline for choosing the optimal clustering threshold in RADseq studies"
<p>Data files accompanying "An empirical pipeline for choosing the optimal clustering threshold in RADseq studies"</p>
Empirical Study Data for Test Program-Based Generative Fuzzing for Differential Testing of the Kotlin Compiler
<p>Empirical Study Dataset for MSc. Thesis titled "Test Program-Based Generative Fuzzing for Differential Testing of the Kotlin Compiler". The data contains automatically generated Kotlin files, the results of differentially testing the generated files, and aggregated data containing file information, and compilation features.</p>
Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)
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Data from: Empirical and Bayesian approaches to fossil-only divergence times: a study across three reptile clades
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Data from: Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications
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Data from: Ecological divergence, adaptive diversification, and the evolution of social signaling traits: an empirical study in arid Australian lizards
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Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
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Data from: Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses
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Data from: Finding clarity in ecological outcomes using empirical integrated social-ecological systems: a case study of agriculture-dependent grassland birds
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Data from: Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes
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Data from: Empirical studies on the network of social groups: the case of Tencent QQ
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Data for: Gene tree estimation error with ultraconserved elements: An empirical study on Pseudapis bees
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Replication package with data used in the study: "The effect of code smells on the relationship between design patterns and defects. An empirical study"
<p>This is a replication package with data used in a study by T. Alkhaeir and B. Walter "The effect of code smells on the relationship between design patterns and defects. An empirical study"</p> <p>This dataset contains the following folders:</p> <ul> <li> <p>"Analyzed systems" folder:</p> <ul> <li> <p>For each subject system (Ant-1.7, JEdit-4.2, Lucene-2.4, Camel-1.6, Log4j-1.2, Xalan-2.7, Poi-3.0, Ivy-2.0, Xerces-2.0, Velocity-1.6), we identify the following datasets: SDP, nSDP, SnDP, and nSnDP. Each dataset is represented by a separate csv file.</p> </li> <li> <p>Those csv files include raw data about every class in every release. Each file includes columns which represent:</p> <ul> <li> <p>System: The analyzed system</p> </li> <li> <p>className: A fully qualified class name</p> </li> <li> <p>Pattern: if the class is part of any pattern the cell contains the name of the pattern, and “null” otherwise</p> </li> <li> <p>Smell: if the class is part of affected by any smell the cell contains the name of the smell, and “null” otherwise</p> </li> <li> <p>Bugs: Number of defects reported inside the class (extracted from the PROMISE dataset)</p> </li> </ul> </li> </ul> </li> <li> <p>A "detailed analysis" folder:</p> <ul> <li> <p>For each pattern, we report all the classes which participate in it in all the analyzed systems. The csv files inside this folder follow the same structure as the other csv files reported above</p> </li> </ul> </li> </ul> <p><br> </p>
Data from: How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards
Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g., anoles, basilisks, iguanas, and spiny lizards) but relationships among families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1179 to approximately 2.4 million characters per matrix and approximately 30% to 60% total missing data. We then compared mean branch support for interfamilial relationships under these 15 different sampling strategies for both concatenated (maximum likelihood) and species tree (NJst) approaches (after showing that mean branch support appears to be related to accuracy). We found that both approaches had the highest support when including loci with up to 50% missing taxa (matrices with ∼40–55% missing data overall). Thus, our results show that simply excluding all missing data may be highly problematic as the primary guiding principle for the inclusion or exclusion of taxa and genes. The optimal strategy was somewhat different for each approach, a pattern that has not been shown previously. For concatenated analyses, branch support was maximized when including many taxa (44) but fewer characters (1.1 million). For species-tree analyses, branch support was maximized with minimal taxon sampling (16) but many loci (4789 of 4921). We also show that the choice of these sampling strategies can be critically important for phylogenomic analyses, since some strategies lead to demonstrably incorrect inferences (using the same method) that have strong statistical support. Our preferred estimate provides strong support for most interfamilial relationships in this important but phylogenetically challenging group.
Data from: Empirical and theoretical study of Atelostomate (Echinoidea, Echinodermata) plate architecture: using graph analysis to reveal structural constraints
Describing patterns of connectivity among organs is essential for identifying anatomical homologies among taxa. It is also critical for revealing morphogenetic processes and the associated constraints that control the morphological diversification of clades. This is particularly relevant for studies of organisms with skeletons made of discrete elements such as arthropods, vertebrates, and echinoderms. Nonetheless, relatively few studies devoted to morphological disparity have considered connectivity patterns as a level of morphological organization or developed comparative frameworks with proper tools. Here, we analyze connectivity patterns among apical plates in Atelostomata, the most diversified clade among irregular echinoids. The clade comprises approximately 1600 fossil and Recent species (e.g., 25% of post-Paleozoic species of echinoids) and shows high levels of morphological disparity. Plate connectivity patterns were analyzed using tools and statistics of graph theory. To describe and explore the diversity of connectivity patterns among plates, we symbolized each pattern as a graph in which plates are coded as nodes that are connected pairwise by edges. We then generated a comparative framework as a morphospace of connections, in which the disparity of plate patterns observed in nature was mapped and analyzed. Main results show that apical plate patterns are both highly disparate between and within atelostomate groups and limited in number; overall, they also constitute small, compact, and simple structures compared to possible random patterns. Main traits of the evolution of apical plate patterns reveal the existence of strong morphogenetic constraints that are phylogenetically determined. In contrast, evolutionary radiations within atelostomates were accompanied by a clear increase in disparity, suggesting a release of some constraints at the origin of clades.
Data from: Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations
Understanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we can anticipate that they will be increasingly used in the future. Here we compile a series of biotic and abiotic paleodatasets that can be used as explanatory variables in these models and use simulations to assess the statistical properties of the approach when applied to these paleodatasets. We demonstrate that environment-dependent models perform well in recovering environment-dependent speciation and extinction parameters, as well as in correctly identifying the simulated environmental model when speciation is environment-dependent. We explore how the strength of the environment-dependency, tree size, missing taxa, and characteristics of the paleoenvironmental curves influence the performance of the models. Finally, using these models, we infer environment-dependent diversification in two empirical phylogenies: temperature-dependence in Cetacea and δ 13C-dependence in Ruminantia. We illustrate how to evaluate the relative importance of abiotic and biotic variables in these two clades and interpret these results in light of macroevolutionary hypotheses. Given the important role paleoenvironments are presumed to have played in species evolution, our statistical assessment of how environment-dependent models behave is crucial for their utility in macroevolutionary analysis.
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.