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349 results for “comparative method”
Supplementary material: How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature
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Data from: Pollinator shifts, contingent evolution, and evolutionary constraint drive floral disparity in Salvia (Lamiaceae): evidence from morphometrics and phylogenetic comparative methods
Switches in pollinators have been argued to be key drivers of floral evolution in angiosperms. However, few studies have tested the relationship between floral shape evolution and switches in pollination in large clades. In concert with a dated phylogeny, we present a morphometric analysis of corolla, anther connective, and style shape across 44% of nearly 1,000 species of Salvia (Lamiaceae) and test four hypotheses of floral evolution. We demonstrate that floral morphospace of New World (NW) Salvia is largely distinct from that of Old World (OW) Salvia and that these differences are pollinator driven; that shifts in floral morphology sometimes mirror shifts in pollinators; that anther connectives (key constituents of the Salvia staminal lever) and styles co-evolved from curved to linear shapes following shifts from bee to bird pollination; and that morphological differences between NW and OW bee flowers are partly the legacy of constraints imposed by an earlier shift to bird pollination in the NW. The distinctive staminal lever in Salvia is a morphologically diverse structure that has evolved in concert with both the corolla and style, under different pollinator pressures, and in contingent fashion.
Data from: Phylogenetic comparative methods on phylogenetic networks with reticulations
The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.
Comparative Analysis of Methods to Estimate Geodetic Strain Rates from GNSS Data in Italy
<p>This dataset comprises GNSS velocity field and strain rate maps for Italy.</p> <p><strong>List of Files:</strong></p> <ol> <li> <p><strong>velocity_dataset.dat</strong></p> <ul> <li>GNSS velocity field of stations with time series longer than 4.5 years.</li> <li>Columns: Longitude (degrees), Latitude (degrees), East component of velocity (mm/yr), North component of velocity (mm/yr), Uncertainty on the East component (mm/yr), Uncertainty on the North component (mm/yr), Station Name.</li> </ul> </li> <li> <p><strong>velocity_dataset_filtr.dat</strong></p> <ul> <li>Filtered velocity field.</li> <li>Columns: Longitude (degrees), Latitude (degrees), East component of velocity (mm/yr), North component of velocity (mm/yr), Uncertainty on the East component (mm/yr), Uncertainty on the North component (mm/yr), Station Name.</li> <li>Stations ending with 'GPM' represent velocity values obtained by merging neighboring stations.</li> </ul> </li> <li> <p><strong>strain_rate_nn.dat (strain_rate_visr.dat, strain_rate_wav.dat)</strong></p> <ul> <li>Strain rate computed on cells spaced by 0.025°.</li> <li>Suffixes in the file names: 'nn' refers to the Nearest Neighbor method, 'visr' refers to the VISR method, and 'wav' refers to the Wavelet-based method</li> <li>Columns: Longitude (degrees), Latitude (degrees), exx (east) component of the strain rate tensor (nstr/yr), exy (east, north) component of the strain rate tensor (nstr/yr), eyy (north) component of the strain rate tensor, second invariant of the strain rate (nstr/yr), most extensive eigenvalue (nstr/yr), most compressive eigenvalue (nstr/yr), angle between north and the direction of the eigenvector corresponding to the most compressive eigenvalue (degrees, positive clockwise).</li> </ul> </li> </ol> <p><strong>Reference:</strong></p> <p>For further details, please refer to the article "Comparative Analysis of Methods to Estimate Geodetic Strain Rates from GNSS Data in Italy", published in <em>Annals of Geophysics</em>.</p>
Thesis data: Enhancing Vulnerability Detection: A Comparative Study of Change Identification Methods Across Granularity Levels
<p>Starting dataset used within the thesis; Enhancing Vulnerability Detection: A Comparative Study of Change Identification Methods Across Granularity Levels.</p> <p>Results of manual annotation of and extract of nonPatchTaggedCommitLinks within the NVD CVE dataset.</p>
Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction"
<p>Datasets used in "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction".</p> <p>The provided zip file contains:</p> <ul> <li><strong>Datasets 1–3:</strong> For each dataset, directories include input sequences (FASTA), multiple sequence alignments (MSAs in AFA format), and normalized predicted structures from six deep learning tools. Dataset 3 also contains references - RNA chains extracted from complexes. These folders also include a CSV file with all metrics for all RNAs and tools.</li> <li><strong>Dataset 4:</strong> A text file listing the PDB IDs of RNAs included in this dataset, which is a subset of Dataset 3.</li> <li><strong>Dataset complexes:</strong> RNA chains extracted from predicted complexes, where predictions are made by AlphaFold 3 web server and, in some cases, RoseTTAFoldNA. There are also job files for the AlphaFold 3 web server used to obtain these predictions. Same as for previous datasets, this folder also includes a CSV file with all metrics for these RNA chains.</li> </ul> <p>The structure of the dataset and details of each folder are explained in the included README file.</p> <p> </p>
Research methods and Comparative examination of pinniped craniofacial musculature and its role in aquatic feeding
<p>Secondarily aquatic tetrapods have many unique morphological adaptations for life underwater compared to their terrestrial counterparts. A key innovation during the land-to-water transition was feeding. Pinnipeds, a clade of air-breathing marine carnivorans that includes seals, sea lions, and walruses, have evolved multiple strategies for aquatic feeding (e.g., biting, suction feeding). Numerous studies have examined pinniped skull and dental specializations for underwater feeding. However, data on the pinniped craniofacial musculoskeletal system and its role in aquatic feeding are rare. Therefore, the objectives of this study were to conduct a comparative analysis of pinniped craniofacial musculature and examine the function of the craniofacial musculature in facilitating different aquatic feeding strategies. We performed anatomical dissections of 35 specimens across six pinniped species. We describe 32 pinniped craniofacial muscles—including facial expression, mastication, tongue, hyoid, and soft palate muscles. Pinnipeds broadly conform to mammalian patterns of craniofacial muscle morphology. Pinnipeds also exhibit unique musculoskeletal morphologies—in muscle position, attachments, and size—that likely represent adaptations for different aquatic feeding strategies. Suction feeding specialists (bearded and northern elephant seals) have a significantly larger masseter than biters. Further, northern elephant seals have large and unique tongue and hyoid muscle morphologies compared with other pinniped species. These morphological changes likely help generate and withstand suction pressures necessary for drawing water and prey into the mouth. In contrast, biting taxa (California sea lions, harbor, ringed, and Weddell seals) do not exhibit consistent craniofacial musculoskeletal adaptations that differentiate them from suction feeders. Generally, we discover that all pinnipeds have well-developed and robust craniofacial musculature. Pinniped head musculature plays an important role in facilitating different aquatic feeding strategies. Together with behavioral and kinematic studies, our data suggest that pinnipeds' robust facial morphology allows animals to switch feeding strategies depending on the environmental context—a critical skill in a heterogeneous and rapidly changing underwater habitat.</p>
Supplementary material 1 from: Venere P, Valente G, Vitorino C, Cabral-de-Mello D, Oliveira C, Souza I, Martins C (2012) Comparative cytogenetics of ten species of cichlid fishes (Teleostei, Cichlidae) from the Araguaia River system, Brazil, by conventional cytogenetic methods. Comparative Cytogenetics 6(2): 163-181. https://doi.org/10.3897/compcytogen.v6i2.1739
Table with synthesis of karyotypic traits of cichlids.
ROS-specific Huntingtin Interactions: Comparing transfection methods for inducible expression of huntingtin-specific chromobody
<p>Optimization step in the development of an inducible system expressing YFP-tagged huntingtin-specific intrabodies for stable transfection in TruHD fibroblasts.</p>
Figure 1 in Prevalence of Blastocystis sp. in Morocco: Comparative assessment of three diagnostic methods and characterization of parasite forms in Jones' culture medium
Figure 1. Dispersion of intestinal parasitic species among infected individuals.
Data for 'Comparative Analysis of Single-Cell RNA Sequencing Methods'
<p>Raw sequencing data to "Comparative Analysis of Single-Cell RNA Sequencing Methods". </p> <p>https://www.ncbi.nlm.nih.gov/pubmed/28212749</p> <p> </p> <p>In addition to the GEO submission https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75790, you can find here raw bam files for UMI-methods tagged with cell barcode and UMI sequences.</p> <p>MD5 checksum: f10825509952fffd9c4dc0c1dcb9eb8e</p>
Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods
<p>Understanding variation in rates of evolution and morphological disparity is a goal of macroevolutionary research. In a phylogenetic comparative methods framework, we present three explicit models for linking the rate of evolution of a trait to the state of another evolving trait. This allows testing hypotheses about causal influences on rates of phenotypic evolution with phylogenetic comparative data. We develop a statistical framework for fitting the models with generalized least-squares regression, and use this to discuss issues and limitations in the study of rates of evolution more generally. We show that the power to detect effects on rates of evolution is low in that even strong causal effects are unlikely to explain more than a few percent of observed variance in disparity. We illustrate the models and issues by testing if rates of beak-shape evolution in birds are influenced by brain size, as may be predicted from a Baldwin effect in which presumptively more behaviorally flexible large-brained species generate more novel selection on themselves leading to higher rates of evolution. From an analysis of morphometric data for 645 species we find evidence that both macro- and microevolution of the beak are faster in birds with larger brains, but with the caveat that there are no consistent effects of relative brain size.</p>
Data and code for: Feeding, mating, and animal wellbeing: New insights from Phylogenetic Comparative Methods
<p class="MsoNormal">Some species tend to thrive in captivity, while others risk health and reproductive problems. This enables the use of P<span>hylogenetic Comparative Methods (PCMs) </span>to identify aspects of natural biology that predispose species to faring poorly or well. Risk factors can then suggest new ways to improve animal care. A steady trickle of studies has applied PCMs to animal welfare over the last two decades, Lewis et al. (1) <span>providing the latest. Here we contextualise this new work and suggest further research it might inspire.</span></p> <p class="MsoNormal"><span>Provided here are the data and R code for Figure 1 provided in a commentary on: (1) Lewis, K., M.O. Parker, L. Proops, and S.D. McBride, <em>Risk factors for stereotypic behaviour in captive ungulates</em>. Proceedings of the Royal Society B: Biological Sciences, 2022. 289(1983): p. 20221311.</span></p>
Stowaways S1. Methods & Comparative Materials
<p>A full description of biometric methods utilized in the Stowaways manuscript, including formulae following previously published protocols and comparative material dataset.</p>
A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods
<p>This repository contains all the datasets used for benchmarking drug repositioning methods based on heterogeneous networks, including drug-drug similarity, disease-disease similarity, and drug-disease associations.</p> <p>The repository consists of:</p> <ol> <li>Name or keyword information for drugs and diseases information contained in the dataset</li> <li>Inputs needed for different drug repositioning methods: multiple drug similarity matrices,multiple disease similarity matrices, and drug-disease associations matrices.</li> </ol> <p> </p> <p> </p> <blockquote> <p><strong>Please cite us :</strong><br>Yinghong Li, Yinqi Yang, Zhuohao Tong, Yu Wang, Qin Mi, Mingze Bai, Guizhao Liang, Bo Li, Kunxian Shu, A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods, <em>Briefings in Bioinformatics</em>, Volume 25, Issue 3, May 2024, bbae172, <a href="https://doi.org/10.1093/bib/bbae172">https://doi.org/10.1093/bib/bbae172</a></p> </blockquote>
Comparing Two Different Methods to Prescribe Exercise
ClinicalTrials.gov study NCT04286919. IPD Sharing: NO. Countries: 1. Publications: 30.
Comparative Efficacy of Water & Indigo Carmine vs. Water or Air Method on Adenoma Detection Rate (ADR) - a Randomized Controlled Trial (RCT)
ClinicalTrials.gov study NCT01607255. IPD Sharing: NO. Countries: 1. Publications: 13.
A Comparative Study of Papacarie® and the Conventional Method for Dental Caries Treatment
ClinicalTrials.gov study NCT01641861. IPD Sharing: NO. Countries: 1. Publications: 1.
A Study Comparing Two Methods of Placing an Interscalene Nerve Catheter for Postoperative Pain Control in Patients Who Undergo Open Shoulder Surgery.
ClinicalTrials.gov study NCT01696188. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Trial Comparing Different Methods of Support With Stopping Smoking (PORTSSS/Stop Together Trial)
ClinicalTrials.gov study NCT00775944. IPD Sharing: Not stated. Countries: 1. Publications: 16.
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.