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3,339 results for “heterogeneities”
Edaphic heterogeneity and the evolutionary trajectory of Amazonian plant communities
<p>Fern community data.</p>
Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments
<p><span>Ecological adaptive differentiation alters both the species diversity and intraspecific genetic diversity in forests, thus affecting the stability of forest ecosystems. Therefore, knowledge of the genetic underpinnings of the ecological adaptive differentiation of forest species is critical for effective species conservation. In this study, single-nucleotide polymorphisms (SNPs) from population transcriptomes were used to investigate the spatial distribution of genetic variation in <i>Liriodendron</i> to assess whether environmental variables can explain genetic divergence. We examined the contributions of environmental variables to population divergence and explored the genetic underpinnings of local adaptation using a landscape genomic approach. Niche models and statistical analyses showed significant niche divergence between <i>L. chinense</i> and <i>L. tulipifera</i>, suggesting that ecological adaptation may play a crucial role in driving interspecific divergence. We detected a new fine-scale genetic structure in <i>L. chinense</i>, and divergence of the six groups occurred during the late Pliocene to early Pleistocene. Redundancy analysis (RDA) revealed significant associations between genetic variation and multiple environmental variables. Environmental association analyses identified 67 environmental association loci (EALs; nonsynonymous SNPs) that underwent interspecific or intraspecific differentiation, 28 of which were associated with adaptive genes. These 28 candidate adaptive loci provide substantial evidence for local adaptation in <i>Liriodendron</i>. Our findings reveal ecological adaptive divergence pattern between <i>Liriodendron</i> species and provide novel insight into the role of heterogeneous environments in shaping genetic structure and driving local adaptation among populations, informing future <i>L. chinense</i> conservation efforts. </span></p>
Biologically informed machine learning for identifying human placental cellular heterogeneity and preeclampsia discovery
<p>Single-cell transcripts of 20,518 placental cells and identified 12 major placental cell clusters were collected from the European Bioinformatics Institute (EBI; accession no. EGAS00001002449) (29). Based on the same parameters, we clustered and visualized highly similar cells using t-distribution random neighbourhood embedding (T-SNE) to identify 17 cell subpopulations. we selected nine placental cell clusters that have received more attention from biologists for our study according to the literature survey (Table 1). Considering the sample balance, 7178 single-cell transcriptome data were used to identify human placental cell subpopulations. The samples were randomly divided into a 4809-sample training set and a 2369-sample testing set. The same strategy was applied to split single-cell transcriptomic datasets from healthy and preeclampsia patients (EBI; accession no. EGAS00001002449), with 9852 samples (healthy 4705, preeclampsia 5147) in the training set and 5305 samples (healthy 2473, preeclampsia 2832) in the independent test set</p>
Code and data for 'Bacillus subtilis histidine kinase KinC activates biofilm formation by controlling heterogeneity of single-cell responses'
<p>Code and data used in the paper 'Bacillus subtilis histidine kinase KinC activates biofilm formation by controlling heterogeneity of single-cell responses' https://doi.org/10.1128/mBio.01694-21</p>
Volatile (C, N, Ar) variability in MORB and the respective roles of mantle source heterogeneity and degassing: the case of the Southwest Indian Ridge
<p>Location, isotopic compositions of δ13C and δ18O of CO2, δ15N of N2 and C, N and Ar abundances in vesicles of SWIR basaltic glasses</p>
Mutation and methylation data for study: Assessment of the molecular heterogeneity of E-cadherin expression in invasive lobular breast cancer
<p>Processed mutation data and DNA methylation beta values published with this study.</p>
Data, code, and manual for analysis of image heterogeneity in mass spectrometric imaging.
<p>This upload contains all replication material for "The software for interactive evaluation of mass spectrometric imaging heterogeneity" (forthcoming).</p> <p><strong>Authors:</strong> E.S. Zhvansky, E.V. Zhdanova, M.S. Belenikin, M.A. Shamraeva, S.V. Silkin, K.V. Bocharov, A.A. Sorokin.</p> <p><strong>Code, manual, and data are located within Interactive_CSMM.zip</strong><strong>.</strong> Code is written MATLAB R2019b and Python 3.5.2.</p> <p>Please find the README.md for code using and the code to replicate the main findings of the paper described below:</p> <ul> <li>imzml2mat.py in conversion directory for file conversion.</li> <li>CSMM.m for application start.</li> <li>40TopL,10TopR,30BottomL,20BottomR-centroid.mat - data in conversion/Data directory for reproducing the results.</li> <li>User_manual.pdf - manual.</li> <li>mp4 files - screencasts.</li> </ul>
Representing surface heterogeneity in land-atmosphere coupling in E3SMv1 single-column model over ARM SGP during summertime - E3SM SCM data and code
<p>This dataset contains post-processed E3SM single-column model output and code used to produce the figures in the manuscript that we are targeting Geoscientific Model Development to submit. </p>
Raw data for "Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics"
<p>This is the raw data for the paper "Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics".</p> <p>There are 5 directories. Three correspond to the CAG repeats with different length (20, 31 and 47). The "scramble47" directory stores data for the scrambled sequence. "Electrostatics" has data for the electrostatics run (see details in Extended Data Fig. 9).</p> <p>Each directory of CAG contains multiple sub-directories corresponding to different concentrations.</p> <p> </p>
Heterogeneous histories of recombination suppression on stickleback sex chromosomes
<p>How consistent are the evolutionary trajectories of sex chromosomes shortly after they form? Insights into the evolution of recombination, differentiation, and degeneration can be provided by comparing closely related species with homologous sex chromosomes. The sex chromosomes of the threespine stickleback (<em>Gasterosteus aculeatus</em>) and its sister species, the Japan Sea stickleback (<em>G. nipponicus)</em>, have been well characterized. Little is known, however, about the sex chromosomes of their congener, the blackspotted stickleback (<em>G. wheatlandi</em>). We used pedigrees to obtain experimentally phased whole genome sequences from blackspotted stickleback X and Y chromosomes. Using multispecies gene trees and analysis of shared duplications, we demonstrate that Chromosome 19 is the ancestral sex chromosome and that its oldest stratum evolved in the common ancestor of the genus. After the blackspotted lineage diverged, its sex chromosomes experienced independent and more extensive recombination suppression, greater X-Y differentiation, and a much higher rate of Y degeneration than the other two species. These patterns may result from a smaller effective population size in the blackspotted stickleback. A recent fusion between the ancestral blackspotted stickleback Y chromosome and Chromosome 12, which produced a neo-X and neo-Y, may have been favored by the very small size of the recombining region on the ancestral sex chromosome. We identify six strata on the ancestral and neo-sex chromosomes where recombination between the X and Y ceased at different times. These results confirm that sex chromosomes can evolve large differences within and between species over short evolutionary timescales.</p>
Data from: Landscape heterogeneity filters functional traits of rice arthropods in tropical agroecosystems
<p>Biological control services of agroecosystems depend on the functional diversity of species traits. However, the relationship between arthropod traits and landscape heterogeneity is still poorly understood, especially in tropical rice agroecosystems which harbour a high diversity of often specialized species. We investigated how landscape heterogeneity, measured by three metrics of landscape composition and configuration, influenced body size, functional group composition, dispersal ability and vertical distribution of rice-arthropods in the Philippines.</p> <p> </p> <p>We found that landscape composition and configuration acted to filter arthropod traits in tropical rice agroecosystems. Landscape diversity and rice habitat fragmentation were the two main gradients influencing rice-arthropod traits, indicating that different rice-arthropods have distinct habitat requirements. Whereas small parasitoids and species mostly present in the rice-canopy were favoured in landscapes with high compositional heterogeneity, predators and medium-sized species occupying the base of the rice plant, including planthoppers, mostly occurred in highly fragmented rice habitats. We demonstrate the importance of landscape heterogeneity as an ecological filter for rice-arthropods, identifying how the different components of landscape heterogeneity selected for or against specific functional traits. However, the contrasting effects of landscape parameters on different groups of natural enemies indicate that not all beneficial rice-arthropods can be promoted at the same time when using a single land management strategy. Increasing compositional heterogeneity in rice landscapes can promote parasitoids but may also negatively affect predators. Future research should focus on identifying trade-offs between fragmented rice habitats and structurally diverse landscapes to maximize the presence of multiple groups of beneficial arthropods.</p>
Dataset for a manuscript entitled Variation in CO2 and CH4 Fluxes Among Land Cover Types in Heterogeneous Arctic Tundra in Northeastern Siberia
<p>Dataset for the manuscript Variation in CO<sub>2</sub> and CH<sub>4</sub> Fluxes Among Land Cover Types in Heterogeneous Arctic Tundra in Northeastern Siberia authored by Sari Juutinen, Mika Aurela, Juha-Pekka Tuovinen, Viktor Ivakhov, Maiju Linkosalmi, Aleksi Räsänen, Tarmo Virtanen, Juha Mikola, Johanna Nyman, Emmi Vähä, Marina Loskutova, Alexander Makshtas, and Tuomas Laurila</p> <p>Dataset consists of CO2 and CH4 flux data measured mainly using chamber method in arctic tundra</p>
Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish
<p>Supplementary material for paper entitled "Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish".</p> <p>Raw data, scripts, models and results are made available along with supplementary figures.</p>
Model-based analysis of tuberculosis genotype clusters in the United States reveals high degree of heterogeneity in transmission, and state-level differences across California, Florida, New York, and Texas.
<p>Data and codes for the publication</p>
Dataset and additional files/softwares required for the paper "LeSICiN: A Heterogeneous Graph-based Approach for Automatic Legal Statute Identification from Indian Legal Documents"
<p>This dump contains all files and softwares required for running the codes for the paper "LeSICiN: A Heterogeneous Graph-based Approach for Automatic Legal Statute Identification from Indian Legal Documents". Specifically, these codes are available at https://github.com/Law-AI/LeSICiN.</p> <p>LeSICiN is a deep neural network for the task of Legal Statute Identification which also uses graphical properties of the document-statute citation network for training and predictions.</p> <p>We have three datasets --- train, dev and test. These are all .jsonl files with each instance dict per line; each instance dict contains the unique id, list of sentences and cited labels of the particular instance. Also, there is a fourth file --- secs.jsonl, which stores the text of all the statutes in similar format.</p> <p>schemas.json list out the metapath schemas for fact and section type nodes, while type_map.json maps the id of each node to its type (Act/Chapter/Topic/Section/Fact). </p> <p>label_tree.json and citation_network.json list out the edges for the two parts of the network in the format of a 3-tuple ('source id', 'relationship type', 'target id')</p> <p>"ils2v.bin" is the pretrained sent2vec vectorizer that can generate a 200-dim vector for each sentence</p>
Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors - Scripts & Source data
<p>Source data and scripts to reproduce the figures that are part of the publication "Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors".</p> <p>Journal of Cell Science (2022) 135, jcs259685, DOI: 10.1242/jcs.259685</p> <p> </p> <p>An earlier version of this work is published as a preprint: "Heterogeneity and dynamics of ERK and Akt activation by G protein-coupled receptors depend on the activated heterotrimeric G proteins", DOI: <a href="https://doi.org/10.1101/2021.07.27.453948">10.1101/2021.07.27.453948</a></p>
Data sets for 'Mechanical Compliance of Individual Fractures in a Heterogeneous Rock Mass from Production-type Full-waveform Sonic Data', submitted to JGR: Solid Earth
<p>Synthetic and field FWS data sets are supplied for validation of proposed methods for compliance estimation of individual fractures. Each zip contains ‘ReadMe.txt ‘, which illustrates the files and corresponding parameters. More details about the setup in the submitted paper ‘Mechanical Compliance of Individual Fractures in a Heterogeneous Rock Mass from Production-type Full-waveform Sonic Data’.</p>
Effect of heterogeneous substrate adhesivity of follower cells on speed and tension profile of leader cells in primary keratocyte collective cell migration
<p><span>In single keratocyte motility, membrane tension is reported to be high at cell-fronts and believed to establish front coherence. To understand role of membrane mechanics in collective cell migration, we study membrane height fluctuations in cell sheets from fish scales using interference reflection microscopy (IRM). We report the monolayer to have cells lacking substrate adhesion and show that such "non-sticky" cells can form bridges between leader cells and far-away follower cells. Do such interactions alter motility and membrane mechanics in such leaders? We find non-significant, but reduced speed for leaders with "non-sticky" followers in comparison to other leaders. Cells show high phenotypic variability in their membrane fluctuation tension profiles. On average, this tension is found to be lower at cell fronts than the mid-section. However, leaders with non-sticky followers are more prone to display higher tension at their front and have a negative correlation between cell speed and front-mid tension difference. We, thus, conclude that intracellular tension gradients are heterogeneous in cell sheets and substrate adhesivity of followers can control the coupling of the gradient to cell speed.</span></p>
Data from: Scale-dependence of landscape heterogeneity effects on plant invasions
<p><span>Invasive alien species are amongst the most concerning threats to native biodiversity worldwide, and the level of landscape heterogeneity is considered to affect spatial patterns of their occurrence and spread. However, as previous studies on these associations report contrasting results, the role of landscape heterogeneity on its susceptibility to invasions remains poorly understood. Landscape heterogeneity is usually described by two measures: configuration and composition. Both measures may differently affect invasive species and these impacts may be additionally scale-dependent. Nevertheless, their relative contribution to invasion patterns is poorly known. We investigated the effect of two landscape heterogeneity components: configuration (edge density) and composition (number and evenness of land-cover types) measured at different spatial scales (from within 0.25 km to 5 km of the studied localities) on the local abundance of one of the most invasive alien plant species in Europe, the North American goldenrods (<em>Solidago canadensis</em> and <em>S. gigantea</em>). Using publicly available geospatial environmental data and a novel method based on remote analysis of Google Street View images, we collected and analyzed large dataset on goldenrod occurrence along 1347 roadside transects in agricultural landscapes of Poland. Both the compositional and configurational heterogeneity were positively associated with the local abundance of goldenrods, however the effect size of these relationships was dependent on spatial scale. While abundance-heterogeneity associations were most pronounced at the largest spatial scale for compositional heterogeneity, the pattern was the opposite for configurational heterogeneity. Landscape heterogeneity is a clear correlate of plant invasion potential, with occurrences of invasive plants generally higher in more heterogeneous landscapes. However, scale-dependence of this association means that researchers and practitioners may miss the association if only concentrating on a single spatial scale. While increasing heterogeneity of rural landscapes is widely introduced as a way to promote farmland biodiversity, we show that it may also support invasive plants and thus conflict with original goals of biodiversity-oriented strategies. Therefore, we suggest implementing regular management and eradication schemes in most heterogeneous landscapes. Finally, we demonstrate how remote analysis of plant invasions using existing imagery can advance our understanding of invasion biology.</span></p>
Environmental heterogeneity shapes physiological traits in tropical direct-developing frogs
<p><span><span><span><span><span><span><span><span><span><span><span>1. Tropical ectotherm species tend to have narrower physiological limits than species from temperate areas. As a consequence, tropical species are considered highly vulnerable to climate change since minor temperature increases can push them beyond their physiological thermal tolerance. Differences in physiological tolerances can also be seen at finer evolutionary scales, such as among populations of ectotherm species along elevation gradients, highlighting the physiological sensitivity of such organisms.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>2. Here we analyze the influence of elevation and bioclimatic domains, defined by temperature and precipitation, on thermal sensitivities of a terrestrial direct-developing frog (<i>Craugastor loki)</i> in a tropical gradient. We address the following questions: <i>i</i>) Does preferred temperature vary with elevation and among bioclimatic domains? <i>ii</i>)<i> </i>Do thermal tolerance limits, i.e. critical thermal maximum and critical thermal minimum vary with elevation and bioclimatic domains?, and <i>iii</i>) Are populations from high elevations more vulnerable to climate warming? </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>3. We found that along an elevation gradient body temperature decreases as environmental temperature increases. The preferred temperature tends to moderately increase with elevation within the sampled bioclimatic domains. Our results indicate that the ideal thermal landscape for this species is located at mid-elevations, where the thermal accuracy (<i>db</i>) and thermal quality of the environment (<i>de</i>) are suitable. The critical thermal maximum is variable across elevations and among the bioclimatic domains, decreasing as elevation increases. Conversely, the critical thermal minimum is not as variable as the critical thermal maximum. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>4. Populations from the lowlands may be more vulnerable to future increases in temperature. We highlight that the critical thermal maximum is related to high temperatures exhibited across the elevation gradient and within in each bioclimatic domain, therefore, it is a response to high environmental temperatures.</span></span></span></span></span></span></span></span></span></span></span></p>
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.