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3,339 results for “heterogeneities”
Example data for "Characterization of tumour heterogeneity through segmentation-free representation learning on multiplexed imaging data"
<p>This repository includes two example dataset and configurations for running CANVAS (https://github.com/tanjimin/CANVAS).</p> <p>The repostory is structured as follows:</p> <p>├── Kim_2022<br>│ ├── configs<br>│ │ ├── config.yaml<br>│ │ └── preprocess<br>│ │ ├── channels_vis_strength.yaml<br>│ │ └── selected_channels_w_color.yaml<br>│ └── data<br>│ └── raw_data<br>│ ├── common_channels.txt<br>│ └── image_files<br>└── Sorin_2023<br> ├── configs<br> │ ├── config.yaml<br> │ └── preprocess<br> │ ├── channels_vis_strength.yaml<br> │ └── selected_channels_w_color.yaml<br> └── data<br> └── raw_data<br> ├── common_channels.txt<br> └── image_files</p> <p> </p> <p>The source IMC data from this repository are from Kim et al. 2022 (https://www.nature.com/articles/s41592-022-01657-2) and Sorin et al. 2023 (https://www.nature.com/articles/s41586-022-05672-3). They are avaiable at: https://zenodo.org/records/4110560 and https://zenodo.org/records/7760826.</p>
Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity
<p>We acquired 10x Visium spatial transcriptomics (ST) data from 9 patients with invasive adenocarcinomas [1–5] to explore the role of the tumour microenvironment (TME) on intratumor heterogeneity (ITH) and drug response in breast cancer. By leveraging a new version of Beyondcell [6] (<a href="https://github.com/cnio-bu/beyondcell" target="_blank" rel="noopener">cnio-bu/beyondcell</a>), a tool for identifying tumour cell subpopulations with distinct drug response patterns, we predicted sensitivity to over 1,200 drugs while accounting for the spatial context and interaction between the tumour and TME compartments. Moreover, we also used Beyondcell to compute spot-wise functional enrichment scores and identify niche-specific biological functions.</p> <p>Here, you can find:</p> <p>In signatures folder:</p> <ul> <li><strong>SSc breast:</strong> Collection of gene signatures used to predict sensitivity to > 1,200 drugs derived from breast cancer cell lines.</li> <li><strong>Functional signatures:</strong> Collection of gene signatures used to compute enrichment in different biological pathways.</li> </ul> <p>In visium folder:</p> <ul> <li><strong>Visium objects:</strong> Processed ST Seurat objects with deconvoluted spots, SCTransform-normalised counts, and clonal composition predicted with SCEVAN [7]. These objects, together with the signatures, were used to compute the Beyondcell objects.</li> </ul> <p>In single-cell folder:</p> <ul> <li><strong>Single-cell objects:</strong> Raw and filtered merged single-cell RNA-seq (scRNA-seq) Seurat objects with unnormalised counts used as a reference for spot deconvolution.</li> </ul> <p>In beyondcell folder:</p> <ul> <li><strong>Beyondcell </strong><strong>sensitivity </strong><strong>objects</strong> with prediction scores for all drug response signatures in SSc breast.</li> <li><strong>Beyondcell functional objects </strong>with enrichment scores for all functional signatures.</li> </ul>
Accounting for sampling heterogeneity suggests a low palaeolatitude origin for dinosaurs
<p>All code and data for manuscript: Accounting for sampling heterogeneity suggests a low palaeolatitude origin for dinosaurs </p>
Vulnerable but not equal: mountain lakes exhibit heterogeneous patterns of phytoplankton responses to climate change
Open the record for dataset details and reuse information.
DATASET - Climate heterogeneity shapes the diversity of specialist beetle species across mountains in Malaysia
Open the record for dataset details and reuse information.
Intermittent, Heterogeneous, and Transient River-Groundwater Transitions from Disconnection to Connection
<p>This repository includes the data for model setup and HYDRUS-2D input/output files.</p> <p>The first version was released on 05/24/2024. The second version was released on 12/17/2024. </p>
Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure Data and Code
<p>This dataset includes all data used for the creation of "Including dynamic population and environmental heterogeneity in continuum models of collective behaviour with applications to locust foraging and group structure" as well as a snapshot of the code used.<br><br>Each zip should be unzippable and the code should operate with only the contents of the zip file.</p>
Wing with Root Holes - Hierarchical, random and bifurcation tiling with heterogeneity in micro-structures construction via functional composition.
<p>This microstructure has been created using tools and algorithms developed at the Technion, and are part of the IRIT geometric modeling kernel (<a href="https://www.cs.technion.ac.il/~irit/">https://www.cs.technion.ac.il/~irit/</a>).</p> <p>This specific wing is a functional composition of trivariate spline tiles inside a macro trivariate shape of a wing. The root tiles have through vertical holes in them.</p> <p>Model is provided in STL format.</p>
Three‐dimensional soil heterogeneity modulates responses of grassland mesocosms to an experimentally imposed drought extreme
<p>Heterogeneity is an intrinsic characteristic of soils, which regulates plant diversity and ecosystem functioning. However, whether soil heterogeneity also modulates responses of plant communities to climate change, including climate extremes, remains largely an open question. Here, we explore responses of plant communities to drought extremes across four levels of spatial soil heterogeneity, with cell sizes varying from very small to very large, i.e. 0, 12, 24 and 48 cm. These were created in mesocosms by alternating nutrient-rich and nutrient-poor substrate in three dimensions. A seed mixture of 24 grassland species was evenly sown on each mesocosm in spring. In late summer, a three-week drought was imposed with a rainout shelter. During the drought, soil water content at the mesocosm scale decreased more at intermediate (12 and 24 cm) than at small or large (0 and 48 cm) cell sizes, which was reflected in increased senescence and drought-induced heat stress. These responses could be traced to greater plant biomass coupled with higher water demand at those intermediate cell sizes, likely related to between-cell access to nutrients and effects of diversity and community composition. Our results indicate that soil heterogeneity can modulate the impact of drought extremes on plant communities, though more research is needed on the transition between intermediate and extreme cell sizes, where heterogeneity effects seem to change most. We propose that soil heterogeneity be considered more explicitly in studies of changing precipitation regimes.</p>
Resource availability and heterogeneity shape the self‐organisation of regular spatial patterning
<p>Explaining large-scale ordered patterns and their effects on ecosystem functioning is a fundamental and controversial challenge in ecology. Here, we coupled empirical and theoretical approaches to explore how competition and spatial heterogeneity govern the regularity of colony dispersion in fungus-farming termites. Individuals from different colonies fought fiercely, and inter-nest distances were greater when nests were large and resources scarce—as expected if competition is strong, large colonies require more resources, and foraging area scales with resource availability. Building these principles into a model of inter-colony competition showed that highly ordered patterns emerged under high resource availability and low resource heterogeneity. Analysis of this dynamical model provided novel insights into the mechanisms that modulate pattern regularity and the emergent effects of these patterns on system-wide productivity. Our results show how environmental context shapes pattern formation by social-insect ecosystem engineers, which offers one explanation for the marked variability observed across ecosystems.</p>
A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs (Recorded Talk)
<p>This entry contains the recording of the presentation that was presented at the 2020 Intelligent Systems for Molecular Biology as part of the Bio-Ontologies COSI (https://www.iscb.org/ismb2020).</p>
HeteroGen: Transpiling C to Heterogeneous HLS Code with Automated Test Generation and Program Repair
<p>This artifact submission includes 1. an error study, 2. a fuzzing-based test generation tool, and 3. a code-editing tool for error removal.</p>
Dataset for Spatial Heterogeneity of Uplift Pattern in the Western European Alps Revealed by InSAR Time Series Analysis
<p>ZIP file with InSAR raw and smoothed final velocity solution values</p>
data for modeling scale of representation of heterogeneity on simulated salinity and saltwater circulation in coastal aquifers
<p>This is the modeling data for modeling scale of representation of heterogeneity on simulated salinity and saltwater circulation in coastal aquifers. We setup a series of SEAWAT models to see the scale-dependent heterogeneity in simulations of saltwater circulation and cautions</p>
Data from: Resource heterogeneity but not inbreeding affects growth and grouping behaviour in socially foraging juvenile cichlid fish
<p>1. Spatial food distribution determines resource profitability, defensibility and encounter rate of foragers. Clumped food distribution can promote aggressiveness and resource monopolisation, in turn increasing within-group variation in food intake and growth. However, the effects of food distribution may depend on foraging strategies. Little is known about the impact of spatial food heterogeneity on growth and grouping behaviour in social foragers in the absence of monopolisation.</p> <p>2. Social foraging is present in many fishes, particularly at early juvenile life stages when fish are especially sensitive to environmental variation. Here, a heterogeneous food distribution may impair foraging success and growth and juveniles may increase sociability to attain social information about food resources.</p> <p>3. We examined the impact of the spatial distribution of food as well as inbreeding on growth and social behaviour in juveniles of the cichlid fish <i>Pelvicachromis pulcher. </i>Inbred individuals often show poorer performance than outbred individuals (inbreeding depression), but inbreeding effects can be environment-dependent. In the experiment, in- and outbred fish were reared in a split-clutch design either under homogeneously distributed or spatially clumped food conditions for eight weeks starting one week after juveniles could actively feed. We documented growth and performed a shoaling assay and a sociality test (choice between a large vs. a small shoal) after six weeks.</p> <p>4. Spatial food distribution did not affect within-group body length variation, but individuals reared under clumped food conditions were smaller. Shoals of the different feeding conditions differed in social behaviour. Shoals of the clumped treatment group showed higher variation in inter-individual distances compared to shoals of the homogeneous treatment group. Furthermore, focal fish of the clumped treatment adjusted their association preference to the position of the groups' largest individual. We did not find significant inbreeding or environment-dependent inbreeding effects regarding growth or social behaviour.</p> <p>5. Our study suggests that a clumped food distribution can impede localisation of food resources and thus growth in juvenile social foragers. Accordingly, in heterogeneous environments, the use of social information may be highly relevant to increase individuals' foraging success potentially explaining orientation on successful foragers, i.e. large individuals. Inter-individual variation in juvenile social behaviour may precede variation in food monopolisation capability and in growth emerging at later life stages.</p>
Combining molecular data sets with strongly heterogeneous taxon coverage enlightens the peculiar biogeographic history of stoneflies (Insecta: Plecoptera)
<p class="Standard1">Extant members of the ancient insect order of stoneflies exhibit a disjunct, antitropical distribution, with one major lineage exclusively occurring in the Southern Hemisphere and the other, with few exceptions, on the Northern continents. Here, we address the biogeographic distribution and phylogenetic relationships of stoneflies using a phylogenetic workflow that combines both transcriptomic and Sanger sequence datasets with heterogeneous taxon coverage. We used a dataset comprising 2997 genes derived from the transcriptomes of 30 species and Sanger sequences of seven genes for 498 species. The backbone phylogeny was mainly inferred from the transcriptomic data, whereas the Sanger nucleotide sequence data provided high species density for divergence time estimation and diversification analyses. Our results show that the biogeographic pattern we observe today is primarily more likely shaped by long-distance over-land dispersal than by vicariance. We inferred that the ancestors of extant stoneflies originated in the Northern Hemisphere approximately 265 Ma and were presumably restricted to this area due to climatic and geographic boundaries. Our analyses suggest that with the break-up of Pangaea around 200 Ma and the associated climatic and geographical changes, two groups of stoneflies, the Anarctoperlaria and the Notonemouridae, dispersed to Gondwana and subsequently went extinct on the northern continents. Both groups likely dispersed across Gondwana before its break-up into the modern continents. At least one member of another group of 'northern' stoneflies, the Acroneuriinae, seems to have migrated from North America to South America around 67 Ma. We found four major net diversification rate shifts, indicating rapid radiation patterns that hampered a robust phylogenetic placement of these stonefly groups. Our study provides the first conclusive evolutionary explanation for the unique distribution pattern of stoneflies.</p>
Data from: Deep learning unlocks X‐ray microtomography segmentation of multiclass microdamage in heterogeneous materials
<p>Four-dimensional quantitative characterization of heterogeneous materials using <i>in situ</i> synchrotron radiation computed tomography can reveal 3D sub-micron features, particularly damage, evolving under load, leading to improved materials. However, dataset size and complexity increasingly require time-intensive and subjective semi-automatic segmentations. Here, we present the first deep learning (DL) convolutional neural network (CNN) segmentation of multiclass microscale damage in heterogeneous bulk materials, teaching on advanced aerospace-grade composite damage using ≈65,000 (trained) human-segmented tomograms. The trained CNN machine segments complex and sparse (<<1% of volume) composite damage classes to ≈99.99% agreement, unlocking both objectivity and efficiency, with nearly 100% of the human time eliminated, which traditional rule-based algorithms do not approach. The trained machine is found to perform as well or better than the human due to 'machine-discovered' human segmentation error, with machine improvements manifesting primarily as new damage discovery and segmentation augmentation/extension in artifact-rich tomograms. Interrogating a high-level network hyperparametric space on two material configurations, we find DL to be a disruptive approach to quantitative structure-property characterization, enabling high-throughput knowledge creation (accelerated by two orders of magnitude) via generalizable, ultra-high-resolution feature segmentation.</p>
Heterogeneous environmental seascape across a biogeographic brake influences the thermal physiology and tolerances to ocean acidification in an ecosystem
<p><b>Aim:</b> Understanding how spatio-temporal environmental variability influences stress tolerance, local adaptation, and phenotypic variation among populations is a key challenge for evolutionary ecology and climate change biology. Coastal biogeographic breaks are natural laboratories to explore this fundamental research question due to the contrasting environmental conditions experienced by natural populations across these regions.</p> <p><b>Location:</b> In the South East Pacific (SEP) coast a major break (30º-32ºS) is characterized by extreme natural variability in sea surface temperature (SST) and carbonate chemistry parameters related to temporal and spatial dynamics in upwelling events. Calcifying organisms inhibiting this zone are exposed to marked fluctuations and clines in SST that together with naturally acidified waters can impact their metabolism, calcification and fitness, making them particularly prone to the effects of climate change (e.g., ocean acidification, OA). We investigated to what extent the spatial and temporal environmental variability (in SST and seawater carbonate conditions) that characterizes the biogeographic break in the SEP, influences intra-specific differences in the thermal ecology and the tolerances to OA of the limpet <i>Scurria araucana</i>.</p> <p><b>Methods: </b>During two years, we conducted field surveys of limpet populations at sites across the SEP break (27ºS, 30ºS and 32ºS). We collected individuals from each population to test for geographic differences in morphometric (e.g., total buoyancy weight, shell length) and physiological (e.g., oxygen consumption rate, cardiac activity, and thermal performance curves; TPC) responses to local environmental conditions (Tº and pH/pCO<sub>2</sub>) and to simulated OA scenarios.</p> <p><b>Results:</b> Populations of <i>S. Araucana </i>exhibit high tolerance to OA with no signal of geographic influence on this attribute. However, inter-population differences in thermal physiology (metabolic rates and performances) where found across the biogeographic break in the SEP coast. Limpets from the central part of the break (30ºS) exhibit higher thermal performance compared to limpets from populations at both sides of the break.</p> <p><b>Main conclusions:</b> Variation in SST has a greater effect shaping inter-population differences in thermal physiology of the limpet <i>S. araucana</i>. These physiological differences<i> </i>are aligned the thermal heterogenous seascape along the biogeographic break in the SEP. Contrary, temporal and spatial variation in seawater carbonate conditions does not influence inter-population differences in phenotypic response populations, but an overall high tolerance to OA.</p>
Heterogeneous genetic structure in eastern North American peatmosses (Sphagnum)
<p><span><span><span>Bryophytes generally have broad geographic ranges that suggest high dispersal ability. The aim of this study was to test hypotheses about dispersal limitation, as indicated by isolation by distance (IBD), in four spore producing species of the moss genus <i>Sphagnum</i> (<i>S. carolinianum</i>, <i>S. missouricum</i>, <i>S. macrophyllum</i>, <i>S. pylaesii</i>), and to assess whether plants in the southern United States harbor high levels of unique alleles and/or other indicators of exceptional genetic diversity. IBD was detected in all four species, but regional patterns of genetic structure were very species-specific. One species, <i>S. macrophyllum</i>, exhibited differentiation between northern and southern genetic groups that appear to reflect more ancient phylogenetic diversification.</span></span></span></p>
Root allocation and foraging precision in heterogeneous soils
<p>Root growth patterns respond to small-scale resource heterogeneity and the presence of roots of neighboring plants, but how a plant integrates its responses to these cues is not well understood. In the presence of neighbors, plants may shift allocation to roots as a consequence of plant size and root:shoot allometry, as a response to resource depletion by neighbors, or through a direct response to neighbor presence. The same response pathways also have the potential to alter proliferation in resource-rich patches in soil.</p> <p>Four species of grassland plants were grown in the greenhouse as single plants, monocultures, and mixtures. Root length allocation as a function of shoot mass was examined for background soil and fertilized patches. Plants grown with same-species neighbors followed the same allometric trajectory as single plants for root length in background soil, so any change in root allocation was due only to reduced plant size. Root proliferation in patches declined with neighbors, consistent with a response to resource depletion. Mixtures overproduced roots in both background soil and in patches, relative to plants of the same size in monocultures.</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.