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43 results for “spatial biology”
Library size confounds biology in spatial transcriptomics data
<p>This dataset contains annotated sub-cellular localised spatial measurements from the Visium, Xenium and CosMx platforms. Specifically, it includes datasets analysed in the publication Bhuva et. al, 2023 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are presented. Data is best accessed through the accompanying <em>SubcellularSpatialData</em> R/Bioconductor package. Region files used to annotate individual transcript detections are presented in the form of <a href="https://geojson.org/">GeoJSON</a> files. </p>
Data for: Temporal consistency and spatial variability in detection: implications for monitoring of macroinvertebrates from shallow groundwater aquifers (Subterranean Biology, 2024)
<p>Original research article: Knüsel M., Alther R., Couton M. & Altermatt F. (2024) Temporal consistency and spatial variability in detection: implications for monitoring of macroinvertebrates from shallow groundwater aquifers. Subterranean Biology 49: 139-161. <a href="https://doi.org/10.3897/subtbiol.49.132515" target="_blank" rel="noopener">https://doi.org/10.3897/subtbiol.49.132515</a></p>
Baseline Spatial Variability Study at the Kellogg Biological Station, Hickory Corners, MI (1988)
Dataset Abstract A spatial variability study conducted across the LTER Main Site area (45 ha) at KBS prior to dividing the site into 1-ha experimental plots. During the 1988 growing season a stratified unaligned sampling scheme was used to collect 400-600 geo-referenced samples across the site (uniformly planted to a single variety of soybeans) for: geomorphological characteristics (microtopography, soil horizon depths, bulk density, texture); soil chemical characteristics (pH, NO3, NH4, total C, total N, moisture, inorganic P, trace metals); soil biological characteristics (N mineralization potentials, microbial biomass C, microbial biomass N, fungal/bacterial ratios, nematodes and other soil invertebrates; seed bank size); plant weed species abundance, weed biomass at peak standing crop); and insect characteristics (major pest and predator species). Most soil samples were taken before crop emergence, plant phenology samples were taken throughout the growing season, biomass samples were taken at physiological maturity, and insect samples were taken continuously. Dried soil and plant samples are archived for potential future analysis. original data source http://lter.kbs.msu.edu/datasets/6
Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas"
<p><strong>Table 1. CCF Specimen, Biological Structure, and Spatial Ontology. </strong>For each ontology, we provide all class names, property names, entity Internationalized Resource Identifier (IRI), definition when available, and entity type.</p> <p><strong>Table 2. 3D Reference Objects. </strong>The 3rd HRA release features 53 <em>Spatial Entities</em> of type <em>Spatial Object Reference</em> that are linked to anatomical structures in the ASCT+B tables plus 43 <em>Spatial Entities</em> of type <em>Extraction Site</em>. For each entity, we provide the spatial entity<em> </em>name, 3D object file name, ID and version number, organ label, sex, and type. Note that a landmark is a <em>Spatial Entity</em> that has been tagged as an <em>Extraction Set</em> for a specific <em>Extraction Site</em>, see <strong>Table 3</strong>.</p> <p><strong>Table 3. Registered Tissue Data. </strong>This table shows 364 <em>Extraction Site </em>entities that either represent the registration location for <em>Tissue Blocks</em> or <em>Registration Sites</em>. For each, we provide consortium name and entity ID, HuBMAP ID if available, and experimental data donor sex as well as HRA data such as organ name, sex, Uberon ID, and GLB file. The data comes from four consortia. HuBMAP data includes 306 tissue blocks, and many of these have derived tissue sections with one or more associated datasets. The 29 well-defined GTEx extraction set sites link to 5,397 datasets. The 26 SPARC blocks link to one paper while the three KPMP tissue blocks link to two data publications. </p>
Data for: Thermal vulnerability in a mountain stream network: Temporal, spatial, and biological data
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Master spatial file for for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)
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Modeled ranges of California plant species and scripts to run the models for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)
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Sequence matrix and tree files for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)
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Data from: Varying the spatial arrangement of synthetic herbivore-induced plant volatiles and companion plants to improve conservation biological control
1.Conservation biological control aims to control pests by promoting wild populations of natural enemies. One challenge is to attract and retain efficient natural enemies in crop fields, which often are a suboptimal environment. Towards this goal, the attract-and-reward strategy relies on combining attractive synthetically produced herbivore-induced plant volatiles (HIPVs) with companion plants (non-crop plants which provide alternative resources to the targeted natural enemies). Although severely overlooked, the spatial arrangement of HIPV dispensers and rewards inside crop fields may strongly influence the foraging behaviour and persistence of natural enemies and thus the success of this pest management strategy. 2.We tested the impact of two contrasting spatial arrangements of HIPV dispensers and rewards, alternatively inside and around a block of target apple trees, on the efficacy of the biological control of Aphis citricola populations by the common predatory ladybird Propylea japonica in apple orchards in northern China. We used synthetic methyl salicylate (MeSA) as an attractant and the companion plant Calendula officinalis as a reward. To better understand how the spatial arrangement of MeSA dispensers and companion plants affected the attraction and foraging behaviour of adult ladybirds, we conducted indoor experiments in a flight mill, an olfactometer and a wind-tunnel. 3.Blocks of target trees treated with MeSA dispensers inside and companion plants around provided the most efficient pest control in orchards, compared with the opposite spatial arrangement. 4.The synthetic MeSA dispenser and the companion plant synergistically attracted ladybirds in the olfactometer and enhanced their flight activity in the flight mill. In the wind-tunnel, MeSA served as a spatial cue for ladybirds to find nearby prey, while companion plants were sought in the absence of prey. 5.Synthesis and applications. The present study will help further improvements of aphid control in apple orchards through a careful spatial arrangement of herbivore-induced plant volatiles dispensers (HIPVs) and rewards (companion plants) in optimized attract-and-reward strategies. Without such assessment, these strategies may be hazardous even with well-identified targeted natural enemies. Associated lab experiments highlight that HIPVs and companion plants interactively influence ladybird foraging pattern, and that their spatial arrangement can modulate the ability of such key predators to find their prey.
The spatial analysis of biological interactions: morphological variation responding to the co-occurrence of competitors and resources
By sharing geographic space, species are forced to interact with one another and the contribution of this process to evolutionary and ecological patterns of individual species is not fully understood. At the same time, species turnover makes that species composition varies from one area to another, so the analysis of biological interaction cannot be uncoupled from the spatial context. This is particularly important for clades that show high degree of specialization such as hummingbirds, where any variation in biotic pressures might lead to changes in morphology. Here, we describe the influence of biological interactions on the morphology of Hylocharis leucotis by simultaneously considering potential competition and diet resources. We characterized the extent of local potential competition and local available floral resources by correlating two measurements of hummingbird diversity, floral resources and the size of morphological space of H. leucotis along its geographic distribution. We found that H. leucotis shows an important morphological variability across its range and two groups can be recognized. Surprisingly, morphological variation is not always linked to local hummingbird richness or the phylogenetic similarity of. Only in the southern part of its distribution, H. leucotis is morphologically more variable in those communities where it coexist with closely related hummingbird species. We also found that morphological variation in H. leucotis is independent from the availability of floral resources. Our results suggest that abiotic factors might be responsible for morphological differences across populations in Hylocharis leucotis being biological interactions of minor importance.
Individual-level leaf trait variation and correlation across biological and spatial scales
<p>Even with increasing interest in the ecological importance of intraspecific trait variation (ITV) for better understanding ecological processes, few studies have quantified ITV in seedlings and assessed constraints imposed by trade-offs and correlations among individual-level leaf traits. Estimating the amount and role of ITV in seedlings is important to understand tree recruitment and long-term forest dynamics. We measured ten different size, economic, and whole leaf traits (lamina and petiole) for more than 2800 seedlings (height ≥ 10 cm and diameter at breast height < 1 cm) in 283 seedling plots, and then quantified the amount of ITV and trait correlations across two biological (intraspecific and interspecific) and spatial (within and among plots) scales. Finally, we explored the effects of trait variance and sample size on the strength of trait correlations. We found about 40% (6~63%) variation in leaf-level traits was explained by ITV across all traits. Lamina and petiole traits were correlated across biological and spatial scales, whereas leaf size traits (e.g., lamina area) were weakly correlated with economics traits (e.g., specific lamina area); <a name="_Hlk61031779">lamina mass ratio was strongly related to the petiole length</a>. Trait correlations varied among species, plots, and different scales but there was no evidence that the strength of trait relationships was stronger at broader than finer biological and spatial scales. While larger trait variance increased the strength of correlations, the sample size was the most important factor that was negatively related to the strength of trait correlations. Our results showed that a large amount of trait variation was explained by ITV, which highlighted the importance of considering ITV when using trait-based approaches in seedling ecology. In addition, sample size was an important factor that influenced the strength of trait correlations, which suggests that comparing trait correlations across studies should consider the differences in sample size.</p>
Regenerating tropical forests are consistently affected by biological invasions across spatial scales
<p>Here we present our raw data (obtained via fieldwork) and all our analysis from the manuscript entitled “Regenerating tropical forests are consistently affected by biological invasions across spatial scales”. This manuscript is available as a preprint (<a href="https://doi.org/10.32942/X2SC76">https://doi.org/10.32942/X2SC76</a>) and as a published paper in Biological Invasions (https://doi.org/10.1007/s10530-024-03257-x). </p> <p>We investigated the effects of white-popinac (<em>Leucaena leucocephala</em> (Lam.) de Wit) invasions on regenerating areas of Atlantic Forest, considering local and regional scales, and beta-diversity.</p> <p>To reproduce the results, please see instructions in the READ_ME.txt file. </p>
(raw dataset) "Spatial biology of Ising-like synthetic genetic networks"
<p>This is the raw data for the manuscript Simpson et al "Spatial biology of Ising-like synthetic genetic<br> networks"</p>
Individual-level leaf trait variation and correlation across biological and spatial scales
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Data from: Comparative landscape genomics reveals species-specific spatial patterns and suggests human-aided dispersal in a global hotspot for biological invasions
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Data from: Landscape-scale interactions of spatial and temporal cropland heterogeneity drive biological control of cereal aphids
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The spatial analysis of biological interactions: morphological variation responding to the co-occurrence of competitors and resources
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Data from: Varying the spatial arrangement of synthetic herbivore-induced plant volatiles and companion plants to improve conservation biological control
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Data from: Biological pest control and yields depend on spatial and temporal crop cover dynamics
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Рис. 5. Суточная активность поΑземной поΛевки (на примере синхронной активности ♀ № 1 и № 3, ♂ № 4; июΛь 2000 г., манеж БиНИИ) Fig. 5. Daily activity of the common pine vole (on the example of synchronous activity of ♀ No. 1 and 3, ♂ No. 4; July 2000, measured in a pen at the Scientific Research Institute of Biology) in Spatial Organization Of Common Pine Vole (Microtus Subterraneus Selys-Longchamps, 1836) Colonies
Рис. 5. Суточная активность поΑземной поΛевки (на примере синхронной активности ♀ № 1 и № 3, ♂ № 4; июΛь 2000 г., манеж БиНИИ) Fig. 5. Daily activity of the common pine vole (on the example of synchronous activity of ♀ No. 1 and 3, ♂ No. 4; July 2000, measured in a pen at the Scientific Research Institute of Biology)
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.