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376 results for “local scales”
King Rail (Rallus elegans) presence in the Midwestern United States is predicted by local-scale factors and avian community
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Supplementary material 1 from: Erdélyi A, Hartdégen J, Malatinszky Á, Vadász C (2023) Historical reconstruction of the invasions of four non-native tree species at local scale: a detective work on Ailanthus altissima, Celtis occidentalis, Prunus serotina and Acer negundo. One Ecosystem 8: e108683. https://doi.org/10.3897/oneeco.8.e108683
Derived data of Ailanthus altissima, Celtis occidentalis, Prunus serotina and Acer negundo from the National Forestry Database and its archives.
Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior: resources and main figure data
<p><strong>Summary:</strong></p> <p>Neural population dynamics relevant for behavior vary over multiple spatial and temporal scales across 3-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice. We developed a semi-automated micro-CT based strategy to precisely localize positions of each optical fiber. This highly-customizable approach enables investigation of multi-scale spatial and temporal patterns of cell-type and neurotransmitter specific signals over arbitrary 3-D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum volume which revealed distinct, modality specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics through our fiber arrays enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and spatial localization of behavioral function across large circuits. </p> <p><strong>Files included: </strong></p> <ul> <li>Vu, M-A. et al. (2023) - Key Resources Table.xlsx -- key resources used in this study</li> <li>README_figure_data_and_analysis.txt --a description of the organization of the files within this repository</li> <li>README_preprocessing_code.txt -- details about the preprocessing pipeline (including registration and localization pipelines) and annotation of the preprocessed data structure</li> <li>preprocessing_code.zip -- contains all the preprocessing code</li> <li>Fig01.zip -- preprocessed data and analysis code for main Figure 1</li> <li>Fig03.zip -- preprocessed data and analysis code for main Figure 3</li> <li>Fig04.zip -- preprocessed data and analysis code for main Figure 4</li> <li>Fig05.zip -- preprocessed data and analysis code for main Figure 5</li> <li>Fig06.zip -- preprocessed data and analysis code for main Figure 6</li> <li>Fig07.zip -- preprocessed data and analysis code for main Figure 7</li> <li>SuppFig01.zip -- preprocessed data and analysis code for supplemental Figure 1</li> <li>SuppFig02.zip -- preprocessed data and analysis code for supplemental Figure 2</li> <li>SuppFig03.zip -- preprocessed data and analysis code for supplemental Figure 3</li> <li>SuppFig04.zip -- preprocessed data and analysis code for supplemental Figure 4</li> <li>SuppFig05.zip -- preprocessed data and analysis code for supplemental Figure 5</li> <li>SuppFig06.zip -- preprocessed data and analysis code for supplemental Figure 6</li> <li>SuppFig07.zip -- preprocessed data and analysis code for supplemental Figure 7</li> </ul> <p>Each .zip file contains a folder corresponding to a figure. Within each figure folder will be a folder corresponding to the letter (e.g., A, B, C) of the panel within the figure. In addition to the panel folders, when applicable, there may also be a folder containing general-use functions or scripts, or interim results .mat files, that are called by the scripts within the subfolders. In each subfolder there will be 3 things:</p> <ol> <li>a folder of preprocessed data (see README_preprocessing_code.txt)</li> <li>a folder of the analysis scripts that analyzed the preprocessed data and generated the figure</li> <li>a README text file detailing the contents of both folders and the analysis workflow.</li> </ol> <p> </p>
Data from: Turnover and nestedness drive plant diversity benefits of organic farming from local to landscape scales
<p>Biodiversity-benefits of organic farming have mostly been documented at the field scale. However, these benefits from organic farming to species diversity may not propagate to larger scales, because variation in the management of different crop types and semi-natural habitats in conventional farms might allow species to cope with intensive crop management. We studied flowering plant communities using a spatially replicated design in different habitats (cereal, ley and semi-natural grasslands) in organic and conventional farms, distributed along a gradient in proportion of semi-natural grasslands. We developed a novel method to compare the rates of species turnover within and between habitats, and between the total species pools in the two farming systems. We found that the intra-habitat species turnover did not differ between organic and conventional farms, but that organic farms had a significantly higher inter-habitat turnover of flowering plant species compared to conventional ones. This was mainly driven by herbicide-sensitive species in cereal fields in organic farms, as these contained 2.5 times more species exclusive to cereal fields compared to conventional farms. The farm-scale species richness of flowering plants was higher in organic than conventional farms, but only in simple landscapes. At the inter-farm level, we found that 36% of species were shared between the two farming systems, 37% were specific to organic farms while 27% were specific to conventional ones. Thus, our results suggest that that both community nestedness and species turnover drive changes in species composition between the two farming systems. These large-scale shifts in species composition were driven by both species-specific herbicide and nitrogen sensitivity of plants. Our study demonstrates that organic farming should foster a diversity of flowering plant species from local to landscape scales, by promoting unique sets of arable-adapted species that are scarce in conventional systems. In terms of biodiversity conservation, our results call for promoting organic farming over large spatial extents, especially in simple landscapes, where such transitions would benefit plant diversity most<b>. </b></p>
Functional Ultrasound Localization Microscopy reveals brain-wide neurovascular activity on a microscopic scale
<p>Matlab script to process fULM dynamic maps and compute activation maps. Two dataset are provided : one from a whiskers stimulation experiment in rats and one from a visual stimulation experiment in rats.</p>
Long distance migration is a major factor driving local adaptation at continental scale in a Pacific Salmon
<p><span>Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (<i>Oncorhynchus kisutch</i>) across its entirety North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed increased rate of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.</span></p>
Distribution. Known only from type locality on S coast of Seram I, Indonesia. Descriptive notes. Head-body 123 mm, tail 128 mm, ear 14-6 mm, hindfoot 26-2 mm; weight 65 g (all mensural data are from holotype). Pavel's Seram Mosaic-tailed Rat is very small-bodied, with dorsal pelage soft and brightly colored rufescent reddish brown, hairs with graybases, and venter contrastingly pure white; tail is slightly longer than head-body length, all black in color, tail scales raised, one hair per scale, scale hairs very short. Upper surfaces of feet are dark gray; hindfeet broad, with first digit long. Cranium is relatively narrow, with nasal profile flat; teeth very small. Single known specimen (the holotype), a pregnant female, has four mammae. in Muridae
Distribution. Known only from type locality on S coast of Seram I, Indonesia. Descriptive notes. Head-body 123 mm, tail 128 mm, ear 14-6 mm, hindfoot 26-2 mm; weight 65 g (all mensural data are from holotype). Pavel's Seram Mosaic-tailed Rat is very small-bodied, with dorsal pelage soft and brightly colored rufescent reddish brown, hairs with graybases, and venter contrastingly pure white; tail is slightly longer than head-body length, all black in color, tail scales raised, one hair per scale, scale hairs very short. Upper surfaces of feet are dark gray; hindfeet broad, with first digit long. Cranium is relatively narrow, with nasal profile flat; teeth very small. Single known specimen (the holotype), a pregnant female, has four mammae.
FIGURE. Petalidium mannheimerae, morphology of flowers from different localities in the Richtersveld, Northern Cape, South Africa (A–D), and leaf morphology (E). A. Flower in lateral view (Sun Valley). B. Flower in front view (Sun Valley). C. Flower in front view (Kosies). D. Flowers (Umdaus). E. Branchlet showing leaves being semi-succulent, the blade subconduplicate to conduplicate, recurved towards apex, the margins with isolated, robust, stalked glandular trichomes. Scale bar = 5 mm. Photographs by M. Koekemoer (A–C), N. Jürgens (D), & W. Swanepoel (E). in Petalidium mannheimerae (Acanthaceae), a new species from Namibia and South Africa, with notes on the taxonomic identity of P. parvifolium
FIGURE. Petalidium mannheimerae, morphology of flowers from different localities in the Richtersveld, Northern Cape, South Africa (A–D), and leaf morphology (E). A. Flower in lateral view (Sun Valley). B. Flower in front view (Sun Valley). C. Flower in front view (Kosies). D. Flowers (Umdaus). E. Branchlet showing leaves being semi-succulent, the blade subconduplicate to conduplicate, recurved towards apex, the margins with isolated, robust, stalked glandular trichomes. Scale bar = 5 mm. Photographs by M. Koekemoer (A–C), N. Jürgens (D), & W. Swanepoel (E).
Supplementary material 1 from: Gutjahr S, Schmidt S, Hahn H (2014) A proposal for a groundwater habitat classification at local scale. Subterranean Biology 14: 25-49. https://doi.org/10.3897/subtbiol.14.5429
Graphic output of a hierarchical cluster analysis (single linkage) of faunistic data.: Explanation note: Cluster analysis of the ecological goups' faunistic data based on a Bray-Curtis-similarity-matrix (calculated using a dummy variable).
Data associated with "The importance of terrain and climate for predicting soil organic carbon is highly variable across local to continental scales"
<p>The zipped folder contains the processed soil datasets including covariates, soil depths, and SOC concentrations for training the deep learning models described in the paper "The importance of terrain and climate for predicting soil organic carbon is highly variable across local to continental scales". </p> <p>"soil_profile/" contains a table including the geolocations of all the soil profiles in this study. "patch_data/" and "point_data/" contain the covariates to feed the models with patch input and point input respectively. "depth/" contains the upper and lower depths of the soil samples. "y/" contains the target variable - SOC concentration of the soil samples. The data files with suffix "_1" is a small subset of their counterparts without "_1" (10 % in sample size) used for model hyperparameters tuning.</p>
Quantifying Winter Forage Resources for Reindeer: Developing a Method to Estimate Ground Lichen Cover and Biomass at a Local Scale
<p>Data and R scripts used in the paper Quantifying Winter Forage Resources for Reindeer: Developing a Method to Estimate Ground Lichen Cover and Biomass at a Local Scale (https://doi.org/10.1016/j.tfp.2024.100768).</p>
Cumulative arrival time distribution data for "Upscaling transport in heterogeneous media featuring local-scale dispersion: flow channeling, macro-retardation and parameter prediction"
<div> <div>This archive contains arrival time CDF data for a variety of transport simulations in heterogeneous Darcy flow fields, alongside metadata describing the flow fields. The flow fields were spatially periodic, intersected by uniformly-spaced imaginary planes. Arrival times represent length of time from particle departure from one plane until arrival at the next.</div> <div> </div> <div>Consult the README.md file at the top level of the archive for more information. The file format used to store the CDF data is documented in the Python script at the top level of the archive.</div> </div>
Research data for: "Band Structure Interpolation using Optimized Local Orbitals from Linear-Scaling Density-Functional Theory"
<p>This file was created by Laura E. Ratcliff on 23rd March 2018. It contains the input files employed for the ONETEP and CASTEP calculations in the above publication.</p> <p>Directory Listing:</p> <p>castep/</p> <p>Contains the input files used to generate the CASTEP reference data.</p> <p>onetep/</p> <p>Contains the input files used to generate all of the ONETEP data, where filenames are labelled with the number of repeat CNT units, val (cond) indicates a valence (conduction) calculation and the suffixes follow a similar labelling convention to that employed in the manuscript.</p>
X-ray Binary Luminosity Function Scaling Relations for Local Galaxies Based on Subgalactic Modeling
<p>Property maps (SFR and M*) and processed Chandra images for the 38 galaxies from Lehmer et al. (2019).</p>
Data and code for figures of "Scale-tailored localization and its observation in non-Hermitian electrical circuits"
<p>The main data and code for figures of "Scale-tailored localization and its observation in non-Hermitian electrical circuits" are provided here.</p>
Data from: Regional climate and local-scale biotic acceptance explain native-exotic diversity relationships in Australian annual plant communities
Native and exotic species richness is expected to be negatively related at small spatial scales where individuals interact, and positive at larger spatial scales as a greater variety of habitats are sampled. However, a range of native-exotic richness relationships (NERRs) have been reported, including positive at small scales and negative at larger scales. We present a hierarchical metacommunity framework to explain how contrasting NERRs may emerge across scales and study systems, and then apply this framework to NERRs in an invaded winter annual plant system in south-west Western Australia. We analysed NERRs at increasing spatial scales from neighbourhoods (0.09 m2) to communities (225 m2) to metacommunities (>10 ha) within a multi-level structural equation model. In contrast to many previous studies, native and exotic richness were positively related at the neighbourhood scale and were not significantly associated at larger scales. Heterogeneity in soil surface properties was weakly, but positively, associated with native and exotic richness at the community-scale. Metacommunity exotic richness increased strongly with regional temperature and moisture availability, but relationships for native richness were negative and much weaker. Thus, we show that neutral NERRs can emerge at larger scales due to differential climatic filtering of native and exotic species pools.
Data from: Connectivity explains local ant community structure in a Neotropical forest canopy: a large-scale experimental approach
Understanding how habitat structure and resource availability affect local species distributions is a key goal of community ecology. Where habitats occur as a mosaic, variation in connectivity among patches influences both local species richness and composition, and connectivity is a key conservation concern in fragmented landscapes. Similarly, availability of limiting resources frequently determines species co-existence or exclusion. For primarily cursorial arthropods like ants, gaps between neighboring trees are a significant barrier to movement through the forest canopy. Competition for limited resources such as nest sites also promotes antagonistic interactions. Lianas (woody vines) connect normally isolated neighboring tree crowns and often have hollow stems inhabited by ants. We used two large-scale liana removal experiments to determine how connectivity and nest site availability provided by lianas affect arboreal ant species richness, species composition, and β-diversity in a lowland tropical forest in Panama. Removing lianas from a tree crown reduced ant species richness up to 35%, and disproportionately affected species that require large foraging areas. Adding artificial connectivity to trees mitigated the effects of liana removal. Ant colonization of artificial nests was higher (73% occupied) in trees without lianas vs. trees with lianas (28% occupied). However, artificial nests typically were colonized by existing polydomous, resident ant species. As a result, nest addition did not affect ant community structure. Collectively, these results indicate that lianas are important to the maintenance of arboreal ant diversity specifically by providing connectivity among neighboring tree crowns. Anticipated increases in liana abundance in this forest could increase the local (tree-level) species richness of arboreal ants, with a compositional bias toward elevating the density of broad-ranging specialist predators.
Data from: Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment
We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.
Text-fig. 12. Ranges of the length of the dp4 based on data from the literature. Vertical scale in Ma, the samples are from the Siwaliks (black) and Turkey, Greece and Arabia (red). Type localities of species are indicated with an asterisk. The Y and Z sites are from Baskin (1996), its size ranges are composed of data from several localities and the vertical arrowed broken line indicates the age range of these sites. in An Exceptional Large Sample Of The Early Miocene Ctenodactyline Rodent Sayimys Giganteus, Specific Variation And Taxonomic Implications
Text-fig. 12. Ranges of the length of the dp4 based on data from the literature. Vertical scale in Ma, the samples are from the Siwaliks (black) and Turkey, Greece and Arabia (red). Type localities of species are indicated with an asterisk. The Y and Z sites are from Baskin (1996), its size ranges are composed of data from several localities and the vertical arrowed broken line indicates the age range of these sites.
Local-scale patterns of coastal hypoxia in an upwelling region
<p>GENERAL INFORMATION</p> <p>Title of Dataset: Replication data for: </p> <p>- Sea Surface Temperature (SST, daily) MODIS-Aqua (2016-2019)</p>
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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.