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750 results for “heterogeneous data”
Data from: Heterogeneity and concordance in locus-specific differentiation and introgression between species of towhees
The maintenance or breakdown of reproductive isolation are observable outcomes of secondary contact between species. In cases where hybrids beyond the F1 are formed, the representation of each species' ancestry can vary dramatically among genomic regions. This genomic heterogeneity in ancestry and introgression can offer insight into evolutionary processes, particularly if introgression is compared in multiple hybrid zones. Similarly, considerable heterogeneity exists across the genome in the extent to which populations and species have diverged, reflecting the combined effects of different evolutionary processes on genetic variation. We studied hybridization across two hybrid zones of two phenotypically well-differentiated bird species in Mexico (Pipilo maculatus and P. ocai), to investigate genomic heterogeneity in differentiation and introgression. Using genotyping by sequencing (GBS) and hierarchical Bayesian models, we genotyped 460 birds at over 41,000 single nucleotide polymorphism (SNP) loci. We identified loci exhibiting extreme introgression relative to the genome-wide expectation using a Bayesian genomic cline model. We also estimated locus-specific FST and identified loci with exceptionally high genetic divergence between the parental species. We found some concordance of locus-specific introgression in the two independent hybrid zones (6-20% of extreme loci shared across zones), reflecting areas of the genome that experience similar gene flow when the species interact. Additionally, heterogeneity in introgression and divergence across the genome revealed another subset of loci under the influence of locally specific factors. These results are consistent with a history in which reproductive isolation has been influenced by a common set of loci in both hybrid zones, but where local environmental and stochastic factors also lead to genomic differentiation.
Data from: Vegetation phenology and nest survival: diagnosing heterogeneous effects through time
Birds should select nest sites that minimize predation risk, but understanding the influence of vegetation on nest survival has proven problematic. Specifically, the common practice of measuring vegetation on nest fate date can overestimate its effect on survival, simply because vegetation at hatched nests grows for a longer period of time than vegetation at nests that were depredated. Here, we sampled the literature to determine the prevalence of this bias in studies of duck breeding ecology. We then used survival data collected from ~2,800 duck nests to empirically evaluate evidence of bias in four different vegetation metrics: vegetation density measured when the nest was found, density when the nest was fated, and date-corrected regression residuals of these two. We also diagnosed the magnitude of vegetation effects on nest survival by restricting analysis to only nests which were fated contemporaneously (thereby removing potential bias in the timing of measurement). Finally, we examined whether systematic phenological differences exist between vegetation at hatched and depredated nests that have the potential to further obfuscate the relationship between vegetation and nest survival. We found evidence for a true positive effect of vegetation density on nest survival that appeared to be inflated when using raw vegetation measurements collected at fate date. However, taken in combination with the literature review, our results suggest that the majority of duck nesting studies have evaluated the role of vegetation on nest survival using a relatively less biased metric—vegetation density when the nest was found. Finally, we found that over the course of a nesting attempt, vegetation increased in density at successful nests, but decreased in density at depredated nests. This seasonal change potentially points to an important new metric for understanding predation risk, but further experimental research is required to fully eliminate potential biases in the timing of vegetation measurements.
Data and code for Heterogeneous selection on exploration behavior within and among West European populations of a passerine bird
<p><span>Heterogeneous selection is often proposed as a key mechanism maintaining repeatable behavioral variation ("animal personality") in wild populations. Previous studies largely focused on temporal variation in selection within single populations. The relative importance of spatial versus temporal variation remains unexplored, despite these processes having distinct effects on local adaptation. Using data from >3500 great tits (<i>Parus major</i>) and 35 nest box plots situated within five West-European populations monitored over 4-18 years, we show that selection on exploration behavior varies primarily spatially, across populations, and study plots within populations. Exploration was, simultaneously, selectively neutral in the average population and year. These findings imply that spatial variation in selection may represent a primary mechanism maintaining animal personalities, likely promoting the evolution of local adaptation, phenotype-dependent dispersal, and nonrandom settlement. Selection also varied within populations among years, which may counteract local adaptation. Our study underlines the importance of combining multiple spatiotemporal scales in the study of behavioral adaptation.</span></p>
Data from: Incorporating capture heterogeneity in the estimation of autoregressive coefficients of animal population dynamics using capture-recapture data
<p>Population dynamics models combine density-dependence and environmental effects. Ignoring sampling uncertainty might lead to biased estimation of the strength of density-dependence. This is typically addressed using state-space model approaches, which integrate sampling error and population process estimates. Such models seldom include an explicit link between the sampling procedures and the true abundance, which is common in capture-recapture settings. However, many of the models proposed to estimate abundance in the presence of capture heterogeneity lead to incomplete likelihood functions and cannot be straightforwardly included in state-space models.</p> <p>We assessed the importance of estimating sampling error explicitly by taking an intermediate approach between ignoring uncertainty in abundance estimates and fully specified state-space models for density-dependence estimation based on autoregressive processes. First, we estimated individual capture probabilities based on a heterogeneity model, using a conditional multinomial likelihood, followed by a Horvitz-Thompson estimate for abundance. Second, we estimated coefficients of autoregressive models for the log abundance. Inference was performed using the methodology of integrated nested Laplace approximation (INLA). We performed an extensive simulation study to compare our approach with estimates disregarding capture history information, and using R-package VGAM, for different parameter specifications. The methods were then applied to a real dataset of gray-sided voles <em>Myodes rufocanus</em>from Northern Norway.</p> <p>We found that density-dependence estimation was improved when explicitly modelling sampling error in scenarios with low process variances, in which differences in coverage reached up to 8% in estimating the coefficients of the autoregressive processes. In this case, the bias also increased assuming a Poisson distribution in the observational model. For high process variances, the differences between methods were small and it appeared less important to model heterogeneity.</p>
Data for: A test of Sensory Drive in plant-pollinator interactions: habitat heterogeneity shapes pollinator preference for a floral visual signal
<p>DATA:</p> <p>FinnKoski_PollData_Final: Pollinator visitation data to floral arrays analyzed</p> <p>Spectra used for vismodels.zip: reflectance spectra of flowers and floral backgrounds, irradiance spectra</p> <p>ColorContrastData: visual contrast data analyzed</p> <p>CODE: </p> <p>vismod_code.R : code used for visual system modeling and calculation of contrast</p> <p>SAS_modelcode.R: SAS code used to analyze pollinator visitation data and color contrast data</p>
Data Sets for: Complete Description of the LaCl3-NaCl Melt Structure and the Concept of a Spacer Salt that Causes Structural Heterogeneity
<p>Data Sets for published figures and sample input files for PIM and AIMD simulations in paper <a href="https://doi.org/10.1021/jacs.2c09987">https://doi.org/10.1021/jacs.2c09987</a></p> <p> </p> <p>Complete Description of the LaCl3–NaCl Melt Structure and the Concept of a Spacer Salt That Causes Structural Heterogeneity</p> <p>Matthew S. Emerson, Shobha Sharma, Santanu Roy*, Vyacheslav S. Bryantsev*, Alexander S. Ivanov*, Ruchi Gakhar*, Michael E. Woods, Leighanne C. Gallington, Sheng Dai, Dmitry S. Maltsev, and Claudio J. Margulis*</p> <p> </p>
Supplementary Data for "The heterogeneous K/U and Th/U ratios in different mantle reservoirs".
<p>Supplementary data tables for Ma et al. (2023) associated with the paper entitled "The heterogeneous K/U and Th/U ratios in different mantle reservoirs".</p>
Data for Structural Features of Interfacial Water Predict the Hydrophobicity of Chemically Heterogeneous Surfaces
<p>Scripts, raw and processed data, Jupyter notebooks, and force field files for the simulations performed in:</p> <p>B. C. Dallin, A. S. Kelkar, and R. C. Van Lehn. “Structural Features of Interfacial Water Predict the Hydrophobicity of Chemically Heterogeneous Surfaces.” <em>Chemical Science </em><strong>2023</strong>.</p>
Intermediary and supplemental data for publication "Heterogenous circulating miRNA changes in ME/CFS converge on a unified cluster of target genes and may be a result of modulation by latent herpesviruses: A computational analysis"
<p>Intermediary and supplemental data for publication "Heterogenous circulating miRNA changes in ME/CFS converge on a unified cluster of target genes and may be a result of modulation by latent herpesviruses: A computational analysis"</p>
Data for manuscript "Investigate on the Compression-shear Coupled Stress Waves Propagating in Heterogeneous Rock" submitted to JGR
<p>In the manuscript "Investigate on the Compression-shear Coupled Stress Waves Propagating in Heterogeneous Rock", the true triaxial experimental testing system is employed to measure the longitudinal wave velocities of three samples: granite (i), mortar model material (ii, MMM), and mortar model material with coarse aggregates (iii, MMMA), under different triaxial confining pressures. Here, the initial electrical signal data received on the strain gauge is provided and recorded. The measured position is consistent with that shown in Figure D1 in the manuscript.</p>
Data for: Link between glucose metabolism and EMT drives triple negative breast cancer migratory heterogeneity
<p>Intracellular and environmental cues result in heterogeneous cancer cell populations with different metabolic and migratory behaviors. While glucose metabolism and EMT have previously been linked, we aim to understand how this relationship fuels cancer cell migration. We show that while glycolysis drives single-cell migration in confining microtracks, fast and slow cells display different migratory sensitivities to glycolysis and oxidative phosphorylation inhibition. Phenotypic sorting of highly and weakly migratory subpopulations (MDA<sup>+</sup>, MDA<sup>-</sup>) reveals that more mesenchymal, highly migratory MDA<sup>+</sup> preferentially use glycolysis while more epithelial, weakly migratory MDA<sup>-</sup> utilize mitochondrial respiration. These phenotypes are plastic and MDA<sup>+</sup> can be made less glycolytic, mesenchymal, and migratory and MDA<sup>-</sup> can be made more glycolytic, mesenchymal, and migratory via modulation of glucose metabolism or EMT. These findings reveal an intrinsic link between EMT and glucose metabolism that controls migration. Identifying mechanisms fueling phenotypic heterogeneity is essential to develop targeted metastatic therapeutics.</p>
Data and Code for "Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica"
<p>Data and Code for "Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica"</p>
SCM data for "Representing the subgrid surface heterogeneity of precipitation in a general circulation model"
<p>Single Column Model output from simulations described in the paper, "Representing the subgrid surface heterogeneity of precipitation in a general circulation model," by Nathan Arnold, Randal Koster, and Atanas Trayanov. </p>
A Deep Learning Approach to Afternoon Convection Prediction Using Heterogeneous Weather Data: Taking the Important Areas in Taiwan as an Example
<p>The following partial dataset is provided by the authors for the Afternoon Convection Prediction method presented in the paper.</p> <p>afternoon_rainfall_label is labeled as afternoon convection data</p> <p>weather_image is weather images</p>
Data for: Spatial heterogeneity and infection patterns on epidemic transmission disclosed by a combined contact-dependent dynamics and compartmental model
<p>Epidemics, such as COVID-19, have caused significant harm to human society worldwide. A better understanding of epidemic transmission dynamics can contribute to more efficient prevention and control measures. Compartmental models, which assume homogeneous mixing of the population, have been widely used in the study of epidemic transmission dynamics, while agent-based models rely on a network definition for individuals. In this study, we developed a real-scale contact-dependent dynamic (CDD) model and combined it with the traditional susceptible-exposed-infectious-recovered (SEIR) compartment model. </p>
Data for: Consistently heterogeneous structures observed at multiple spatial scales across fire-intact reference sites
<p>Geospatial polygons representing fire-suppressed control sites against which fire-intact reference sites were compared in Chamberlain et al. (2023). Control sites represent areas with 1) no record of fire history, 2) no record of late 20th century or early 21st century timber management, and 3) no "Fast Change" detected by the Landscape Change Monitoring System dataset. All sites are predominantly within the yellow pine and mixed-conifer zone of California's Sierra Nevada, USA. Polygon boundaries were defined using the NHDPlusV2 catchments, and were manually reshaped using aerial imagery to ensure that polygons were > 100 ha, represented primarily forested areas, and excluded major roads, infrastructure, and major rock outcrops.</p> <p>Detailed description of the methods used to produce this dataset provided in:<br> Chamberlain, C.P., Cova, G.R., Cansler, C.A., North, M.P., Meyer, M.D., Jeronimo, S.M.A., Kane, V.R., 2023. Consistently heterogeneous structures observed at multiple spatial scales across fire-intact reference sites. Forest Ecology and Management.</p>
Data for Overestimation of Black Carbon Light Absorption due to Mixing State Heterogeneity.
<p>Data for Overestimation of Black Carbon Light Absorption due to Mixing State Heterogeneity. </p>
Additional data - Using a micro-device with a deformable ceiling to probe stiffness heterogeneities within 3D cell aggregates
<p>Additional data for the article <em>"Using a micro-device with a deformable ceiling to probe stiffness heterogeneities within 3D cell aggregates" </em>by Jain, Belkadi et al.</p> <p><strong>additionaldata_jain-belkadi_2023/data_fig_3/data_fig_3_bc:</strong> One .tif file per spheroid shown in Fig 3b,c. the air cavity pressure levels are the following (respectively for each frame): 0 (mbar), -50, -100, -150, -200, -250, -300, -450, -500, 0</p> <p><strong>additionaldata_jain-belkadi_2023/data_fig_3/data_fig_3_def: </strong>One .tif file for the cyclic compression of the spheroids.</p> <p><strong>additionaldata_jain-belkadi_2023/data_fig_4_d: </strong>One folder per spheroid. See readme.txt</p>
Data from: Spatial variability in a plant-pollinator community across a continuous habitat: high heterogeneity in the face of apparent uniformity
Open the record for dataset details and reuse information.
Data from: Environmental heterogeneity decreases reproductive success via effects on foraging behaviour
Open the record for dataset details and reuse information.
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.