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3,339 results for “heterogeneities”
DA Diffusion Simulation for: A fluorescent nanosensor paint reveals the heterogeneity of dopamine release from neurons at individual release sites
<p>Code developed for the revision of:</p> <p>Elizarova, S., Chouaib, A., Shaib, A., Mann, F., Brose, N., Kruss, S., & Daniel, J. A. (2021). A fluorescent nanosensor paint reveals the heterogeneity of dopamine release from neurons at individual release sites. BioRxiv, 2021.03.28.437019. https://doi.org/10.1101/2021.03.28.437019</p>
Statistical analyses of the impact of X-ray damage effects on conformational heterogeneity in room temperature (277 K) and cryo-cooled (100 K) protein crystals
<p>These data are published in support of the manuscript "Evaluating the impact of X-ray damage on conformational heterogeneity in room temperature and cryo-cooled protein crystals" submitted to Acta Crystallographica section D, authors:</p> <p>Filip Yabukarski<sup>1,</sup><sup>#,</sup>*, Tzanko Doukov<sup>5</sup>, Daniel A Mokhtari<sup>1</sup>, Siyuan Du<sup>1</sup>, Daniel Herschlag<sup>1,2,3,4</sup><sup>,</sup>*</p> <p><sup>1</sup>Department of Biochemistry, <sup>2</sup>Department of Chemistry, <sup>3</sup>Department of Chemical Engineering, <sup>4</sup>Stanford ChEM-H, Stanford University, Stanford, California 94305, United States, <sup>5</sup>Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States.</p> <p># Current address: Bristol Myers Squibb, San Diego, California 92121, United States.</p> <p>* Correspondence: fyabukar@stanford.edu, herschla@stanford.edu</p>
Spatial heterogeneity effects on land surface modeling of water and energy partitioning
<p>Related code and data used in the manuscript https://doi.org/10.5194/gmd-2022-4, <Spatial heterogeneity effects on land surface modeling of water and energy partitioning>. The latest source code of ELMv1 is available from https://github.com/E3SM-Project/E3SM (last access: September 2020). If you have any questions, please contact lingchengliwhu@gmail.com</p>
Data from: Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference
<p>1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities.</p> <p>2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species-specific estimates by leveraging detection information among species. Here we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability.</p> <p>3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N-mixture models. Our approach substantially increases precision in estimates of abundance compared to models that do not share detection information among species. We then expand this model, and apply it to repeated detection/non-detection data collected on six species of tits (Paridae) breeding at 119 1 km<sup>2</sup> sampling sites across a <em>P. montanus</em> hybrid zone in northern Switzerland (2004-2020). We find strong impacts of forest cover and elevation on population persistence and colonisation in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonisation probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies.</p> <p>4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper, and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.</p>
Dataset of the article 'Spectroelectrochemistry of water oxidation kinetics in molecular versus heterogeneous oxide iridium electrocatalysts'
<p>Dataset of the article 'Spectroelectrochemistry of Water Oxidation Kinetics in Molecular versus Heterogeneous Oxide Iridium Electrocatalysts', <a href="https://doi.org/10.1021/jacs.2c02006">https://doi.org/10.1021/jacs.2c02006</a>.</p> <p>Abstract: Water oxidation is the step limiting the efficiency of electrocatalytic hydrogen production from water. Spectroelectrochemical analyzes are employed to make a direct comparison of water oxidation reaction kinetics between a molecular catalyst, the dimeric iridium catalyst [Ir<sub>2</sub>(pyalc)<sub>2</sub>(H<sub>2</sub>O)<sub>4</sub>-(µ-O)]<sup>2+</sup> (<strong>Ir<sub>Molecular</sub></strong>,<strong><sub> </sub></strong>pyalc = 2-(2’pyridinyl)-2-propanolate) immobilized on a mesoporous indium tin oxide (ITO) substrate, with that of an heterogenous electrocatalyst, an amorphous hydrous iridium (<strong>IrO<sub>x</sub></strong>) film. For both systems, four analogous redox states were detected, with the formation of Ir(4+)-Ir(5+) being the potential-determining step in both cases. However, the two systems exhibit distinct water oxidation reaction kinetics, with potential-independent first-order kinetics for <strong>Ir<sub>Molecular</sub></strong> contrasting with potential-dependent kinetics for <strong>IrO<sub>x</sub></strong>. This is attributed to water oxidation on the heterogenous catalyst requiring co-operative effects between neighboring oxidized Ir centers. The ability of <strong>Ir<sub>Molecular</sub></strong> to drive water oxidation without such co-operative effects is explained by the specific coordination environment around its Ir centers. These distinctions between molecular and heterogenous reaction kinetics are shown to explain the differences observed in their water oxidation electrocatalytic performance under different potential conditions.</p>
Data from: The importance of population heterogeneities in detecting social learning as the foundation of animal cultural transmission
<p class="MsoNormal"><span>High levels of within-population behavioural variation can have drastic demographic consequences, thus changing the evolutionary fate of populations. A major source of within-population heterogeneity is personality. Nonetheless, it is still relatively rarely accounted for in social learning studies that constitute the most basic process of cultural transmission. Here, we perform in female mosquitofish (<em>Gambusia holbrooki</em>) a social learning experiment in the context of mate choice, a situation called mate copying, and for which there is strong evidence that it can lead to the emergence of persistent traditions of preferring a given male phenotype. </span><span class="TexteCourant1Car"><span>When accounting for the </span></span><span>global</span><span class="TexteCourant1Car"> <span>tendency of females to prefer lager males </span></span><span>but ignoring differences in personality we detected no evidence for mate copying. However, when accounting for the bold-shy dichotomy, we found that bold females did not show any evidence for mate copying, while shy females showed significant amounts of mate copying. This illustrates how the presence of variation in personality can hamper our capacity to detect mate copying. We conclude that mate copying may be more widespread than we thought because many studies ignored the presence of within-population heterogeneities.</span></p>
Demographic consequences of heterogeneity in conspecific density dependence among mast fruiting tropical trees
<p>The role of conspecific density dependence (CDD) in the maintenance of species richness is a central focus of tropical forest ecology. However, tests of CDD often ignore the integrated effects of CDD over multiple life-stages and their long-term impacts on population demography. We combined a 10-year time series of seed production, seedling recruitment and sapling and tree demography of three dominant Southeast Asian tree species that adopt a mast fruiting phenology. We used these data to construct individual-based models that examine the effects of CDD on population growth rates (λ) across life-history stages. Recruitment was driven by positive CDD for all species, supporting the predator satiation hypothesis, while negative CDD affected seedling and sapling growth of two species, significantly reducing λ. This negative CDD on juvenile growth overshadowed the positive CDD of recruitment, suggesting the cumulative effects of CDD during seedling and sapling development has greater importance than the positive CDD during infrequent masting events. Overall, CDD varied between positive and negative across life-history stages for all species, suggesting that assessments of CDD on transitions between just two stages (e.g. seeds-seedlings or juveniles-mature trees) likely misrepresents the importance of CDD on population growth and stability.</p>
A comparative phylogenomic analysis of birds reveals heterogeneous differentiation processes among Neotropical Savannas
<p>The main objective of this study is to evaluate biogeographic hypotheses of diversification and connection between isolated savannas north (Amazonian savannas) and south (Cerrado core) of the Amazon River. To achieve our goal, we employed genomic markers (genotyping by sequencing) to evaluate the genetic structure, population phylogenetic relationships, and historical range shifts of four Neotropical passerines with peri-Atlantic distributions: the Narrow-billed Woodcreeper (<em>Lepidocolaptes angustirostris</em>), the Plain-crested Elaenia (<em>Elaenia cristata</em>), the Grassland Sparrow (<em>Ammodramus humeralis</em>), and the White-banded Tanager (<em>Neothraupis fasciata</em>). The population genetic analyses indicated that landscape (e.g., geographic distance, landscape resistance, and percentage of tree cover) and climate metrics explained divergence among populations in most species, but without indicating a differential role between current and historical factors. Our results did not fully support the hypothesis that isolated populations at Amazonian savannas have been recently derived from the Cerrado core domain. Intraspecific phylogenies and gene flow analyses supported multiple routes of connection between the Cerrado and Amazonian savannas, rejecting the hypothesis that the Atlantic corridor explains the peri-Atlantic distribution. Our results reveal that the biogeographic history of the region is complex and cannot be explained by simple vicariant models.</p>
Data from: Individual heterogeneity in fitness in a long-lived herbivore
<p><span><span><span><span><span><span><span><span><span><span><span>Heterogeneity in the intrinsic quality and nutritional condition of individuals affects reproductive success and consequently fitness. Black brant (<i>Branta bernicla nigricans</i>) are long-lived, migratory, specialist herbivores. Long migratory pathways and short summer breeding seasons constrain the time and energy available for reproduction, thus magnifying life-history trade-offs. These constraints, combined with long lifespans and trade-offs between current and future reproductive value, provide a model system to examine the role of individual heterogeneity in driving life-history strategies and individual heterogeneity in fitness. We used hierarchical Bayesian models to examine reproductive trade-offs, modeling the relationships between within-year measures of reproductive energy allocation and among-year demographic rates of individual females breeding on the Yukon-Kuskokwim Delta, Alaska using capture-recapture and reproductive data from 1988 to 2014. We generally found that annual survival tended to be buffered against variation in reproductive investment, while breeding probability varied considerably over the range of clutch size-laying date combinations. We provide evidence for relationships between breeding probability and clutch size, breeding probability and nest initiation date, and an interaction between clutch size and initiation date. Average lifetime clutch size also had a weak positive relationship with apparent survival probability. Our results support the use of demographic buffering strategies for black brant. These results also indirectly suggest associations among environmental conditions during growth, fitness, and energy allocation, highlighting the effects of early growth conditions on individual heterogeneity, and subsequently, lifetime reproductive investment.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Neurotransmitter content heterogeneity within an interneuron class shapes inhibitory transmission at a central synapse
<p>Neurotransmitter content is deemed the most basic defining criterion for neuronal classes, contrasting with the intercellular heterogeneity of many other molecular and functional features. Here we show, in the adult mouse brain, that neurotransmitter content variegation within a neuronal class is a component of its functional heterogeneity. Most Golgi cells (GoCs), the well-defined class of cerebellar interneurons inhibiting granule cells (GrCs), contain cytosolic glycine, accumulated by the neuronal transporter GlyT2, and GABA in various proportions. To assess the functional consequence of this neurotransmitter variation, we paired GrCs recordings with optogenetic stimulations of single GoCs, which preserve the intracellular transmitter mixture. We show that the strength and decay kinetics of GrCs IPSCs, which are entirely mediated by GABA<sub>A</sub> receptors are negatively correlated to the presynaptic expression of GlyT2 by GoCs. We isolate a slow spillover component of GrCs inhibition that is also affected by the expression of GlyT2, leading to a 56 % decrease in relative charge. Acute manipulations of cytosolic GABA and glycine supply recapitulate the modulation of IPSC charge, supporting the hypothesis that presynaptic loading of glycine negatively impact the GABAergic transmission in mixed interneurons through a competition for vesicular filling. Our results suggest that heterogeneity of neurotransmitter supply within the GoC class may provide a presynaptic mechanism to tune the gain of the stereotypic granular layer microcircuit, thereby expanding the realm of possible dynamic behavior.</p>
A modified Beer–Lambert–Bouguer law for nonrandom distributions and its application in gap probability calculations for heterogeneous canopies
<p>This repository contains the data, codes and files required to reproduce the results of the manuscript "A modified Beer–Lambert–Bouguer law for nonrandom distributions and its application in gap probability calculations for heterogeneous canopies" submitted to the Journal of Advances in Modeling Earth Systems (JAMES).</p>
Data from: Filtering ground noise from LiDAR returns produces inferior models of forest aboveground biomass in heterogenous landscapes
<p>Airborne LiDAR has become an essential data source for large-scale, high-resolution modeling of forest aboveground biomass and carbon stocks, enabling predictions with much higher resolution and accuracy than can be achieved using optical imagery alone. Ground noise filtering -- that is, excluding returns from LiDAR point clouds based on simple height thresholds -- is a common practice meant to improve the 'signal' content of LiDAR returns by preventing ground returns from masking useful information about tree size and condition contained within canopy returns. However, ground returns may be helpful for making accurate aboveground biomass predictions in heterogeneous landscapes that include a patchy mosaic of vegetation heights and land cover types.<br> <br> In this paper, we applied several ground noise filtering thresholds while mapping forest AGB across New York State (USA), a heterogenous landscape composed of both contiguously forested and highly fragmented areas with mixed land cover types. We fit random forest models to predictor sets derived from each filtering intensity threshold and compared model accuracies, paying attention to how changes in accuracy correlated with landscape structure. We observed that removing ground noise via any height threshold systematically biases many of the LiDAR-derived variables used in AGB modeling, with mean correlation (Spearman's $\rho$) between variables increasing from 0.183 to 0.266. We found that that ground noise filtering yields models of forest AGB with lower accuracy than models trained using predictors derived from unfiltered point clouds, with RMSE increasing by up to 2.2 Mg ha^-1^ statewide. Although we only modeled AGB for forest cover types, models fit to predictors derived from filtered point clouds performed worse as landscape heterogeneity (as measured by patch density and edge density) increased, suggesting ground returns are particularly useful when modeling edge forests. Our results suggest that ground filtering should be a carefully considered decision when mapping forest AGB, particularly when mapping heterogeneous and highly fragmented landscapes, as ground returns are more likely to represent useful 'signal' than extraneous 'noise' in these cases.</p>
Data from: Large trees and forest heterogeneity facilitate prey capture by California spotted owls
<p>Predators are among the most threatened animal groups globally, with prey declines contributing to their endangerment. However, assessments of the habitat conditions that influence the successful capture of different prey species are rare, especially for small, cryptic predators. Accordingly, most predator conservation plans are based on the relative importance of habitats inferred from coarse-scale <a name="_Hlk99628060"></a>studies that do not consider habitat features contributing to hunting success, which can vary among prey species. To address this limitation, we integrated high-resolution GPS tracking and nest video monitoring to characterize habitat features at prey capture locations during the nestling provisioning stage for the Spotted Owl (<em>Strix occidentalis</em>) a small, cryptic predator that has been at the center of a decades-long forest management conflict in western North America. When all prey species were considered collectively, males provisioning nests tended to capture prey: (<em>i</em>) in areas with more large-tree forest, (<em>ii</em>) in areas with more medium trees/medium canopy forest, and (<em>iii</em>) at edges between conifer and hardwood forests. However, when we considered the owl's two key prey species separately, males captured woodrats (<em>Neotoma fuscipes</em>) and Humboldt flying squirrels (<em>Glaucomys oregonensis</em>) in areas with markedly different habitat features. Our study provides clarity for forest management in mixed-ownership landscapes because different prey species achieve high densities in different habitat types. Specifically, our results suggest that promoting large trees, increasing forest heterogeneity, and creating canopy gaps in forests with medium trees/high canopy cover could benefit Spotted Owls and their prey, which has the ancillary benefit of enhancing forest resilience. Combining high-resolution GPS tagging with video-based information on prey deliveries to breeding sites can strengthen conservation planning for small predators by more rigorously defining those habitat features that are associated with successful prey acquisition.</p>
Heterogeneous cavitation from atomically smooth liquid-liquid interfaces
<p>Original research data on "Heterogeneous cavitation from atomically smooth liquid-liquid interfaces"</p> <p> </p> <p>Magnetic beads: diameter 4.5 µm<br> Framerate 5x10^6 fps<br> scale: 1px = 1.45 µm</p> <p>PFOB: 1-Bromoheptadecafluorooctane<br> Framerate 5x10^6 fps<br> scale: 1px = 1.60 µm</p> <p>4H-PFOB: 1H,1H,2H,2H-Perfluorooctyl bromide<br> Framerate 5x10^6 fps<br> scale: 1px = 1.23 µm</p> <p>"Luminity": Perfluteren 150 µl/ml<br> Framerate 5x10^6 fps<br> scale: 1px = 1.60 µm</p> <p>single_Interface: 4H-PFOB (left;laser impact) and water (right)<br> Framerate 5x10^6 fps<br> scale: 1px = 1.33 µm</p> <p>multi_cav: PFOB droplets<br> Framerate 5x10^6 fps<br> scale: 1px = 1.34 µm</p>
Supporting Information: Mapping conduits in two-dimensional heterogeneous karst aquifers using hydraulic tomography
<p>This file contains the supplementary data for a article submitted to Journal of Hydrology.</p>
Detecting and reducing heterogeneity of error in acoustic classification: Data
<ol> <li>Passive acoustic monitoring can be an effective method for monitoring species, allowing the assembly of large audio datasets, removing logistical constraints in data collection, and reducing anthropogenic monitoring disturbances. However, the analysis of large acoustic datasets is challenging, and fully automated machine-learning processes are rarely developed or implemented in ecological field studies. One of the greatest uncertainties hindering the development of these methods is spatial generalisability – can an algorithm trained on data from one place be used elsewhere?</li> <li>We demonstrate that heterogeneity of error across space is a problem that could go undetected using common classification accuracy metrics. Secondly, we develop a method to assess the extent of heterogeneity of error in a random forest classification model for six Amazonian bird species. Finally, we propose two complementary ways to reduce heterogeneity of error, by (i) accounting for it in the thresholding process and (ii) using a secondary classifier that uses contextual data.</li> <li>We found that using a thresholding approach that accounted for heterogeneity of precision error reduced the coefficient of variation of the precision score from a mean of 0.61±0.17 (SD) to 0.41±0.25 in comparison to the initial classification with threshold selection based on F-score. The use of a secondary, contextual classification with thresholding selection accounting for heterogeneity of precision reduced it further still, to 0.16±0.13, and was significantly lower than the initial classification in all but one species. Mean average precision scores increased, from 0.66±0.4 for the initial classification, to 0.95±0.19, a significant improvement for all species.</li> <li>We recommend assessing - and if necessary correcting for - heterogeneity of precision error when using automated classification on acoustic data to quantify species presence as a function of an environmental, spatial or temporal predictor variable.</li> </ol>
Morphing of Stiffness-Heterogeneous Liquid Crystal Elastomers Via Mechanical Training and Locally Controlled Photopolymerization
<p>This dataset contains experimental and simulation data that support the findings of the study.</p> <p>Experimental data: stress-strain tests of highly crosslinked and lightly crosslinked liquid crystal elastomers.</p> <p>Simulation data: Codes (user element subroutine, .inp files) used for the finite element modeling of liquid crystal elastomer structures using the commercial software ABAQUS/Implicit.</p>
Supporting dataset: Towards the Optimal Representation of Sub-Grid Heterogeneity in Land Surface Models - Upper Colorado River Basin study case
<p>Supporting files for the manuscript "Towards the Optimal Representation of Sub-Grid Heterogeneity in Land Surface Models - Upper Colorado River Basin study case." The dataset contains the ESCF derived from the original 800 HydroBlocks simulations used to train/test the random forest models (RFM) to compute the annual mean ESCFs for soil moisture content, sensible heat, latent heat, and runoff, as well as the obtained RFM to compute the resulting number of tiles for a given configuration over the study domain. Besides, the dataset includes the ESCFs for the quasi-fully distributed simulation (QFD) and the input data layers required to run HydroBlocks simulations over the study domain.</p>
Companion data of Exploiting system level heterogeneity to improve the performance of a GeoStatistics multi-phase task-based application
<p>This is the companion data repository for the paper entitled <strong>Exploiting system level heterogeneity to improve the performance of a GeoStatistics multi-phase task-based application</strong> by Lucas Leandro Nesi, Lucas Mello Schnorr, and Arnaud Legrand. The manuscript has been accepted for publication in the <a href="https://oaciss.uoregon.edu/icpp21/">ICPP 2021</a>.</p>
Companion data for Communication-Aware Load Balancing of the LU Factorization over Heterogeneous Clusters
<p>This is the companion data repository for the paper entitled <strong>Communication-Aware Load Balancing of the LU Factorization over Heterogeneous Clusters</strong> by Lucas Leandro Nesi, Lucas Mello Schnorr, and Arnaud Legrand. The manuscript has been accepted in the <a href="https://icpads2020.comp.polyu.edu.hk/">ICPADS 2020</a>.</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.