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1,868 results for “Spatial Data”
Data from "Understanding and controlling spatial resolution, sensitivity, and surface selectivity in resonant-mode photothermal-induced resonance spectroscopy"
<p>Dataset of PTIR spectra used for the article "Understanding and controlling spatial resolution, sensitivity, and surface selectivity in resonant-mode photothermal-induced resonance spectroscopy", L. Quaroni, Ana. Chem. 2020, 92, 5, 3544-3554</p>
Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales
<p>Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate population persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and thus has direct implications for the spatial scales of management plans. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach based on mitochondrial control region sequences and 4,339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units – the Atlantic, eastern Gulf, and western Gulf – that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighboring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.</p>
Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios
<p>All total 152 datasets are collected in the benchmarking study.</p> <p>Every dataset contains two parts: the gene expression matrix (or well-established model by dynwrap for trajectory) and the data information including the data id, repository, accession number, URL, technology platform, species, organ (source), cell number, gene number, data type, ERCC spike-in, dilution factor, volume, group condition, treatment, batch information and cluster labels.</p> <p>There are 23 datasets (data79-data101) for evaluating the simulation ability for cell trajectories which are derived from another Zenodo repository (https://zenodo.org/record/1443566).</p>
The second data release from the European Pulsar Timing Array II. Customised pulsar noise models for spatially correlated gravitational waves
<p>Aims: The nanohertz gravitational wave background (GWB) is expected to be an aggregate signal of an ensemble of gravitational waves emitted predominantly by a large population of coalescing supermassive black hole binaries in the centres of merging galaxies. Pulsar tiNanohertz ming arrays (PTAs), which are ensembles of extremely stable pulsars at approximately kiloparsec distances precisely monitored for decades, are the most precise experiments capable of detecting this background. However, the subtle imprints that the GWB induces on pulsar timing data are obscured by many sources of noise that occur on various timescales. These must be carefully modelled and mitigated to increase the sensitivity to the background signal. Methods: In this paper, we present a novel technique to estimate the optimal number of frequency coefficients for modelling achromatic and chromatic noise, while selecting the preferred set of noise models to use for each pulsar. We also incorporated a new model to fit for scattering variations in the Bayesian pulsar timing package temponest. These customised noise models enable a more robust characterisation of single-pulsar noise. We developed a software package based on tempo2 to create realistic simulations of European Pulsar Timing Array (EPTA) datasets that allowed us to test the efficacy of our noise modelling algorithms. Results: Using these techniques, we present an in-depth analysis of the noise properties of 25 millisecond pulsars (MSPs) that form the second data release (DR2) of the EPTA and investigate the effect of incorporating low-frequency data from the Indian Pulsar Timing Array collaboration for a common sample of ten MSPs. We used two packages, enterprise and temponest, to estimate our noise models and compare them with those reported using EPTA DR1. We find that, while in some pulsars we can successfully disentangle chromatic from achromatic noise owing to the wider frequency coverage in DR2, in others the noise models evolve in a much more complicated way. We also find evidence of long-term scattering variations in PSR J1600-3053. Through our simulations, we identify intrinsic biases in our current noise analysis techniques and discuss their effect on GWB searches. The analysis and results discussed in this article directly help to improve the sensitivity to the GWB signal and they are already being used as part of global PTA efforts.</p>
Data from: Emergent spatial patterns can indicate upcoming regime shifts in a realistic model of coral community
<p class="western"><span>Increased stress on coastal ecosystems, such as coral reefs, seagrasses, kelp forests and other habitats can make them shift towards degraded, often algae-dominated or barren communities. This has already occurred in many places around the world, calling for new approaches to identify where such regime shifts may be triggered. Theoretical work predicts that the spatial structure of habitat-forming species should exhibit changes prior to regime shifts,</span><span><em> </em></span><span>such as an increase in spatial autocorrelation. However, extending this theory to marine systems requires theoretical models connecting field-supported ecological mechanisms to data and spatial patterns at relevant scales. To do so, we built a spatially-explicit model of sub-tropical coral communities based on experiments and long-term datasets from Rapa Nui (Easter Island, Chile), to test whether spatial indicators could signal upcoming regime shifts in coral communities. Spatial indicators anticipated degradation of coral communities following increases in frequency of bleaching events or coral mortality. However, they were generally unable to signal shifts that followed herbivore loss, a widespread and well-researched source of degradation, likely because herbivory, despite being critical for the maintenance of corals, had comparatively little effect on their self-organization. Informative trends were found both under equilibrium and non-equilibrium conditions, but were determined by the type of direct neighbor interactions between corals, which remain relatively poorly documented. These inconsistencies show that while this approach is promising, its application to marine systems will require detailed information about the type of stressor, and filling current gaps in our knowledge of interactions at play in coral communities. </span></p>
Spatial metatranscriptomics resolves host-bacteria-fungi interactomes, Source Data
<p>Source Data for a publication: Spatial metatranscriptomics resolves host-bacteria-fungi interactomes. </p> <p>Includes the data sets to generate the results. </p> <p>Contains five different experiment types:</p> <p>- Pst bacterial infiltration experiment<br> - Enrichment experiment with different array types<br> - Comparison between SmT vs. Amp-seq<br> - Outdoor-grown leaf experiments<br> - Sterile leaf experiment</p> <p>For each of the experiments are included (if generated, see the README file):<br> - Gene count matrices<br> - Microbial taxa count matrices<br> - Bright field images<br> - Alignment files (Spot files)<br> - Putative microbial reads and related probe information<br> - Data for enrichment analysis<br> - Fluorescent images and corresponding fluorescent values</p>
Data from: Microbial activity contributes to spatial heterogeneity of wetland methane fluxes
<p>The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these greenhouse gas emissions, it remains unclear what drives these large within-site variations, creating a knowledge-gap that impedes a mechanistic understanding of wetland fluxes. While geophysical variables including water table depth (WTD) and soil temperature are known to correlate with CH<sub>4</sub> flux, measurable variance in these parameters declines as spatial and temporal scales become finer. Here, we leveraged depth-stratified gene abundance and gene expression measurements of methanogenesis and methanotrophy to investigate CH<sub>4</sub> flux variance at an ombrotrophic peat bog. Our results show that the flux variance was strongly correlated to methanogen abundance and that peat depth also exerted significant control over CH<sub>4</sub> flux, methanogen abundance, and the relationship between the two. Correlations between CH<sub>4</sub> flux and either WTD or soil temperature were absent or minimal. These findings suggest that microbial factors likely underlie localized variance in wetland CH<sub>4</sub> flux, and that a greater reliance on biological predictors could improve our ability to understand wetland methane fluxes at finer scales than is currently possible.</p>
Single-cell and spatially resolved transcriptomic data of mouse regenerative livers under normal and fibrotic conditions
<p>A single-cell spatial-temporal transcriptomic atlas of liver regeneration under normal and fibrotic condition, including a total of 30 mouse liver samples obtained from 15 normal and 15 fibrotic mice at timepoints Day 0, 1, 2, 3, and 7 after a partial hepatectomy (PHx) procedure with three replicates for each time point, followed by the scRNA-seq and SRT sequencing for each sample using the Stereo-seq platform. </p>
Data for "Spatial and Temporal patterns of Southern Ocean Ventilation"
<p>This contains the trajectory data used in the paper "Spatial and temporal patterns of Southern Ocean Ventilation" which has been submitted to GRL</p>
Codes and data for: Spatial Relationships between Coseismic Slip, Aseismic Afterslip, and On-fault Aftershock Density in Continental Earthquakes
<p>This code is an accompanyment to the paper: Spatial Relationships between Coseismic Slip, Aseismic Afterslip, and On-fault Aftershock Density in Continental Earthquakes. The code serves to allow reproduction of figures in the paper, and the repository also serves as a store for the data analysed. Readers are welcome to edit/adapt/incorporate the code freely, but please cite our paper. Use of, or reference to, any of the datasets included here should also be accompanied by a reference to the original source (i.e. the work by the original authors), which can be found in our paper.</p> <p>The code should be run sequentially and is not unbreakable, please take care. The methods outlined in the paper give a guide to the workflow, please contact me should you have additional questions.</p> <p>DATA (also referenced in the accompanying paper):</p> <ul> <li>Seismic catalogs are provided pre-processed in the folder 'catalogs'. These originate from: <ul> <li>The Northern California Earthquake Catalog (NCEC) (Waldhauser & Schaff, 2008; Waldhauser, 2009)</li> <li>The California Integrated catalog by the Southern California Seismic Network (SCSN) (SCEDC, 2013)</li> <li>The International Seismological Centre Bulletin (ISC)</li> </ul> </li> <li>Slip models (coseismic slip and afterslip) are provided in the folder 'SlipModels': <ul> <li>Many of these are availible freely online and are referenced in the accompanying paper</li> <li>Additional coseismic slip models are availible from the SRCMOD database (Mai & Thingbaijam, 2014)</li> <li>Chris Rollins (the El Mayor Cucapah afterslip paper) and Daniele Cheloni (the L'Aquila afterslip paper) were kind enough to allow me to include their models in this repository.</li> </ul> </li> </ul> <p>Again, we thank the following individuals who provided, or helped find, coseismic and afterslip models: Roland B ̈urgmann, Daniele Cheloni, Nicola D’Agostino, Semih Ergintav, Wangpeng Feng, Elizabeth Hearn, Junle Jiang, Fred Pollitz, Chris Rollins, Elisa Trasatti, Kang Wang, Sam Wimpenny, and Han Yue.</p> <p> </p>
Spatial Modeling of Groundwater Potential in the North of Minas Gerais, Brazil: An Integrated Approach Using Machine Learning and Environmental Data
<p>This database is associated with the article published in the Revista Brasileira de Cartografia (RBC), entitled: Spatial Modeling of Groundwater Potential in the North of Minas Gerais, Brazil: An Integrated Approach Using Machine Learning and Environmental Data. This database contains the Groundwater flow rasters and the covariates used in spatial modeling. This database is associated with the article published in the Revista Brasileira de Cartografia (RBC), entitled: Spatial Modeling of Groundwater Potential in the North of Minas Gerais, Brazil: An Integrated Approach Using Machine Learning and Environmental Data. This database contains the Groundwater flow rasters and the covariates used in spatial modeling.</p>
Spatial uncertainty in herbarium data: Simulated displacement but not error distance alters estimates of phenological sensitivity to climate in a widespread California wildflower
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Data from: Combining thermal and hydric constraints for spatially predicting the activity suitability of Neotropical Leptodactylid frogs
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Data from: Species-specific variation in germination rates contributes to spatial coexistence more than adult plant water use in four closely-related annual flowering plants
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Data from a flexible framework to assess patterns and drivers of beta diversity across spatial scales
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Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species
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Data from: Soil nutrient availability rather than spatial nutrient heterogeneity shapes the intraspecific response of root architectural, morphological, and mycorrhizal traits in <em>Vaccinium myrtillus</em>
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Data from: Two for the price of one: eDNA metabarcoding reveals temporal and spatial variability of mussel and fish co-distributions in Michigan riverine systems
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Data from: Spatial structure imposes sex-specific costs but does not reduce interlocus sexual conflict
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Data from: Cortical reactivation of spatial and non-spatial features coordinates with hippocampus to form a memory dialogue
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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.