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1,552 results for “patch”
Natural image patches
<p>Matlab file of 70000 natural image patches of size 14x14 in gray scale.</p> <p>The data can be loaded using the following Python code (Result is a numpy array of size 196x70000).</p> <p><strong>import </strong>scipy </p> <p>data = scipy.io.loadmat('NaturalImage.mat')['rawImages']</p> <p> </p>
Next-generation Sequencing Data Associated with "Genome Editing Outcomes Reveal Mycobacterial NucS Participates in a Short-Patch Repair of DNA Mismatches"
Open the record for dataset details and reuse information.
Density-dependent within-patch movement behavior of two competing species
<p class="MsoNormal">Movement behavior is central to understanding species distributions, population dynamics and coexistence with other species. At present, relatively little is known about how conspecific and interspecific competitor density affect movement behavior. We conducted releases of two species of competing <em>Tribolium</em> flour beetles at different densities, alone and together in homogeneous microcosms, and tested whether their recaptures-with-distance were well described by a random-diffusion model. We also determined whether mean displacement distances varied with the release density of conspecific and heterospecific beetles. A diffusion model provided a good fit to the redistribution of <em>T. castaneum</em> and <em>T. confusum </em>at all release densities, explaining an average of >60% of the variation in recaptures. For both species, mean displacement (directly proportional to the diffusion rate) exhibited a humped-shaped relationship with conspecific density. Finally, we found that both species of beetle impacted the within-patch movement rates of the other species, but it depended on density. For <em>T. castaneum</em> in the highest density treatment, the addition of equal numbers of <em>T. castaneum</em> or <em>T. confusum</em> had the same effect, with mean displacements reduced by approximately one-half. The same result occurred for <em>T. confusum</em> released at an intermediate density. In both cases, it was total beetle abundance, not species identity that mattered to mean displacement. We suggest that displacement or diffusion rates that exhibit a nonlinear relationship with density or depend on the presence or abundance of interacting species should be considered when attempting to predict the spatial spread of populations.</p>
Data from: Upland Sandpipers select for later time since fire and experience high nest survival in grasslands managed with patch-burn grazing
<p>Upland Sandpipers (<em>Bartramia longicauda</em>) are a grassland obligate shorebird that nests in dense vegetation structure near recently disturbed areas and could benefit from management practices that promote heterogenous vegetation structure. Although, Upland Sandpipers primary breeding range is generally managed for livestock production using traditional practices that lack patchy disturbances to facilitate higher levels of structural heterogeneity. Patch-burn grazing (PBG) could be an alternative management practice for Upland Sandpiper conservation for its ability to create areas of dense vegetation structure near recently disturbed areas. However, limited information is available regarding nest production of Upland Sandpipers within a PBG framework. To assess the compatibility of PBG with Upland Sandpiper conservation, we estimated nest site selection and survival of Upland Sandpiper nests on private lands managed with PBG in the unglaciated plains region of North Dakota. We located 59 nests from 2017–2020. Upland Sandpipers avoided 1 year since fire (YSF) patches and selected for 2 and 3 YSF patches for nest sites. Additionally, nest site selection decreased with increased bare ground and at intermediate distances to the nearest Upland Sandpiper nest. Upland Sandpipers experienced high overall nest survival during the study with 51 of 59 nests successfully hatching, which limited our ability to make inferences between daily survival rates and variables of interest. Our findings suggest that PBG can provide suitable nesting cover for Upland Sandpipers in later YSF patches despite annual prescribed fire and livestock grazing during the nesting season. PBG seems a suitable grassland management strategy that should be included in conservation planning within Upland Sandpiper's breeding distribution.</p>
Data from: Complex patch geometries maximize species richness at the expense of forest specialists
<p>Habitat loss and fragmentation are the greatest threats to reptiles and amphibians (herpetofauna) around the globe, but especially in the Neotropics where high diversity and ongoing land-use change coincide. Persistence of biodiversity in fragmented systems relies both on characteristics of habitat patches, and on the permeability of the landscape that separates the patches (the 'matrix'). We sought to understand: (a) how the herpetofauna community differs between forest reserves, patches, corridors, and matrices, and (b) the landscape characteristics that increase suitability of a habitat patch. We conducted herpetofauna surveys in patches, corridors, matrices, and preserves (54 total sites) in a fragmented landscape in Costa Rica for three seasons. We recorded 1663 individuals of 52 species. We found that the herpetofauna community differed, and had lower richness and abundance, in the matrix compared to the other three habitat types. Patches and corridors supported a similar community to the forest preserves, demonstrating the conservation value of small forest remnants. Water body presence was an important predictor of richness and abundance in both patches and matrices. While total richness increased in patches with more edge, this was driven by the response of generalist species, whereas the prime indicator species of forest preserves decreased in patches with complex shapes. The differing response to landscape characteristics between specialist and generalist species demonstrates the importance of considering specific taxa when setting conservation goals, rather than using richness measures alone. Our findings can help guide preservation of forest fragments to optimize biodiversity conservation in mixed forest-pastoral landscapes.</p>
Supplementary Videos to Transient Attracting Profiles in the Great Pacific Garbage Patch
<h1>Summary</h1> <p>This repository contains supplementary videos to the publication Transient Attracting Profiles in the Great Pacific Garbage Patch (<a href="https://doi.org/10.5194/egusphere-2024-1215" target="_blank" rel="noopener">Kunz et al., 2024, preprint</a>). TRansient Attracting Profiles (TRAPs, <a href="http://doi.org/10.1038/s41467-020-16281-x" target="_blank" rel="noopener">Serra et al. (2020)</a>, <a href="https://doi.org/10.1063/1.4951720" target="_blank" rel="noopener">Serra and Haller (2016)</a>) have been computed using the TRAPs detection software by <a href="https://github.com/MattiaSerra/TRAPs" target="_blank" rel="noopener">Mattia Serra (2020)</a>. Raw TRAPs were further post-processed, tracked and analysed using software by <a href="https://github.com/kunzluca/trapsgpgp" target="_blank" rel="noopener">Luca Kunz (2024)</a>. The videos provided here display:</p> <ol> <li><strong>SV1_TRAPS_TRAJECTORIES.mp4</strong>: Coloured lines represent the trajectories of propagating TRAPs, colours indicate the estimated total lifetime of a TRAP. Ephemeral TRAPs appear as flickering points.</li> <li><strong>SV2_TRAPS_VORTICITY_DRIFTERS.mp4</strong>: Black lines indicate TRAPs upon a colourmap of the relative voriticity field ζ. Filled and empty black circles represent the 24-hourly positions of drogued and undrogued GDP drifters. The video shows the simultaneous motion of TRAPs, drifters and the relative vorticity field.</li> <li><strong>SV3_TRAPS_VORTICITY_EDDIES.mp4</strong>: Black lines indicate TRAPs upon a colourmap of the relative voriticity field ζ. Blue lines indicate the speed contour of cyclonic, pink lines the speed contour of anticyclonic mesoscale eddy detections. The video shows the simultaneous propagation of TRAPs, mesoscale eddy detections and the relative vorticity field.</li> </ol> <p>For related datasets, see: <a href="https://doi.org/10.5281/zenodo.10993736">https://doi.org/10.5281/zenodo.10993736</a></p> <h1>Source data</h1> <p>Raw TRAPs and relative vorticity are derived from daily snapshots of near-surface geostrophic + Ekman currents from the product Global Total Surface and 15m Current (COPERNICUS-GLOBCURRENT) from Altimetric Geostrophic Current and Modeled Ekman Current Reprocessing that is provided by the E.U. Copernicus Marine Service (<a href="https://doi.org/10.48670/moi-00050" target="_blank" rel="noopener">CMEMS, 2022a</a>). Surface drifter positions have been consulted from the Global Drifter Program (<a href="https://doi.org/10.25921/7ntx-z961" target="_blank" rel="noopener">Lumpkin and Centurioni, 2019</a>). Mesoscale eddy detections have been consulted from the Mesoscale Eddy Trajectory Atlas (META3.2 DT) which is produced by SSALTO/DUACS and distributed by AVISO+ with support from CNES, in collaboration with IMEDEA (<a href="https://doi.org/10.24400/527896/a01-2022.005.220209" target="_blank" rel="noopener">AVISO+, 2022</a>).</p> <h1>Acknowledgements</h1> <p>This work is a contribution to the project <a href="https://www.trr-energytransfers.de/research/area-l/l3" target="_blank" rel="noopener">L3 Meso- to submesoscale turbulence in the ocean</a> of the Collaborative Research Centre TRR 181 Energy Transfer in Atmosphere and Ocean funded by the German Research Foundation (DFG) and has been conducted in collaboration with <a href="https://theoceancleanup.com/" target="_blank" rel="noopener">The Ocean Cleanup</a>.</p> <h1>Please cite</h1> <p>When using the videos, please cite</p> <p>Kunz, L., Griesel, A., Eden, C., Duran, R., and Sainte-Rose, B.: Transient Attracting Profiles in the Great Pacific Garbage Patch, Ocean Sci., 20, 1611–1630, <a href="https://doi.org/10.5194/os-20-1611-2024">https://doi.org/10.5194/os-20-1611-2024</a>, 2024. </p> <p>and provide a link to the repository.</p> <p> </p>
Diel greenhouse gas emissions demonstrate a strong response to vegetation patch types in a freshwater wetland
<p>Data supporting submitted research paper. "All_flux_variables.csv" includes all plot data and is organized by the date/time of sample, campaign number, and sample location in rows and data collected as headers in the columns. "Flux_tower_data.csv" are meterological variables include in data analysis collected by a flux tower on sight. All other files are time series data for water pH (n = 2), water temperature (n = 3-5). Refer to the "metadata.csv" for units and descriptions of data in files. </p>
Hyperspectral images of patches at different stages of degraded alpine meadows
<p>This data contains hyperspectral images of degraded alpine meadow patches in four stages, which are:active patches (Stage 0), inactive patches (Stage 1), recovering patches (Stage 2), and healthy alpine meadow (Stage 3).</p>
Landscape context affects patch habitat contributions to biodiversity in agroecosystems
<p>Effective conservation schemes are needed to advance dual objectives of biodiversity conservation and agronomic production in agricultural landscapes. Understanding how plant and arthropod taxa respond to both local habitat patch characteristics and landscape complexity is crucial for planning effective agri-environment schemes. This study investigated the relative effects of local (≤ 100 m from patch habitat center) and landscape (≤ 5 km from patch habitat center) variables on diversity of plants and arthropods within non-crop habitat patches (i) at different spatial extents ranging from 0.1 km to 5 km, while (ii) quantifying differential effects of local and landscape variables on unique components of diversity (i.e. species richness and abundance), and accounting for (iii) unique components of landscape extent (0.1, 0.5, 1, 2 and 5 km radii) and complexity (i.e. landscape composition and configuration). Landscape variables were significantly correlated with local plant and arthropod species richness and abundance at all spatial extents. Biodiversity responses to landscape variables were largely scale-dependent, as pairwise comparisons were significantly different between all spatial extents except between 1-km and 2-km extents, and correlations were lowest at the 5-km extent. Partial R-squared values for predicting local biodiversity were highest when both local and landscape variables were included as predictors of species richness and abundance, underscoring the importance of considering both local and landscape effects on local diversity. Landscape configuration variables accounted for more variation in plant and arthropod species richness than composition variables. However, models performed best when composition and configuration were considered together rather than alone, suggesting that both components of landscape complexity should be considered for identifying and managing conservation areas in crop fields. Conservation schemes that incentivize farmers to create or conserve small patch habitat within crop fields may be more effective when combined with landscape-scale designs that enhance landscape complexity across the Northern Great Plains. Local conservation efforts should be coordinated with landscape-level efforts to ultimately enhance biodiversity and desired ecosystem service outcomes across agricultural landscapes.</p>
Animation for "Rapid Evolution of Bald Patches in a Major Solar Eruption"
<p>Animation of Figure 1 and 4 of Lee, Sun, & Kazachenko (2020), ApJL, "Rapid Evolution of Bald Patches in a Major Solar Eruption".</p> <p>Animation 1. The animation (18 s, 88 frames) shows bald patch (BP) evolution from 10:49:30 UT to 13:00:00 UT. The background shows the positive (negative) polarity B_z in white (black). Vectors show B_h with foot points in the positive (negative) B_z in blue (red). The polarity inversion line (PIL) and BPs are shown by the green line and yellow/orange circles, respectively. The gray contour is for B_z = 300 G. The X9.3 flare has a GOES start, peak, and end time in soft X-ray flux at 11:53 UT, 12:02 UT, and 12:10 UT, respectively. Prior to the flare, Region 1 gradually built more BPs along the PIL. Throughout the duration of the flare and afterwards, BPs in Region 1 disintegrated. BPs in Region 2 largely remained the same and survived the flare. The large amount of pixel masking occurring in the central regions of the AR and extending into both polarities during the flare is an artifact of flare ribbons, leading to many masked pixels. It can be seen in more detail in the Animation 4.</p> <p>Animation 4. The animation (18 s, 88 frames) shows the flare ribbon evolution from 10:49:30 UT to 13:00:00 UT. During the onset of eruption, ribbons developed along the PIL within Region 1 and exterior to the PIL in Region 2. Prior to the flare peak, flare ribbons propagated along and separated away from the PIL covering the entirety of Region 1 and Region 2.</p>
Community patch‐dynamics governs direct and indirect nutrient recycling by aggregated animals across spatial scales
<p>Animals can have pervasive effects on ecosystems as they modify their biogeochemical and physical environments. In particular, when animals occur in high densities these effects can result in dramatic changes in the physical environment and biogeochemical hotspots or hot moments. While most research to date has focused on the direct role of animals in biogeochemical cycles, few have examined how animals indirectly influence biogeochemical cycles across scales.</p> <p>Freshwater mussels occur as spatially heterogeneous, dense and species-rich aggregations in many river ecosystems worldwide. Here we examined how mussel communities (1) directly influence the flux of particulate and dissolved nutrients and (2) indirectly effect the flux of N<sub>2</sub> production, via denitrification, across a gradient of mussel biomass and differences in community composition at the patch- (0.25 m<sup>2</sup>) and stream reach-scales (60-80 m).</p> <p>We combined measurements of ammonia (N) and soluble reactive phosphorous (P) excretion and C, N, and P biodeposition rates for ten species with biomass and distribution estimates for seven mixed-species aggregations to quantify direct mussel contributions to biogeochemical cycling and the spatial heterogeneity of their impact. Additionally, we sampled sediments at a fine spatial scale to determine how mussel biomass and richness influence potential denitrification (indirect flux) rates at the patch- and reach-scales.</p> <p>We predicted that increasing mussel biomass would lead to greater direct and indirect fluxes of nutrients, manifesting in heterogeneous nutrient redistribution within and among stream reaches. We also predicted that variation in community composition would result in differential nutrient excretion and egestion stoichiometries.</p> <p>Our results indicate that mussel aggregations directly influence soluble and particulate nutrient fluxes with community composition, particularly phylogenetic tribe composition, controlling the stoichiometry. Mussel aggregations also indirectly influenced nutrient fluxes as greater mussel biomass and species richness resulted in higher denitrification rates as mediated by their interactions with the sediments and enhancement of nutrient availability. Our results underscore the importance of patchy communities in acting as biogeochemical control points.</p>
A patch-dynamic metacommunity perspective on the persistence of mutualistic and antagonistic bipartite networks
<p>The structure of interactions between species within a community plays a key role in maintaining biodiversity. Previous studies have found that the effects of these structures might substantially differ depending on interaction type, for example, a highly connected and nested architecture stabilizes mutualistic communities, while the stability of antagonistic communities is enhanced in modular and weakly connected structures. Here we show that, when network dynamics are modelled using a patch-dynamic metacommunity framework, the qualitative differences between antagonistic and mutualistic systems disappear, with nestedness and modularity interacting to promote metacommunity persistence. However, the interactive effects are significantly weaker in antagonistic metacommunities. Our model also predicts an increase in connectance, nestedness and modularity over time in both types of interaction, except in antagonistic networks where nestedness declines. At steady state, we find a strong negative correlation between nestedness and modularity in both mutualistic and antagonistic metacommunities. These predictions are consistent with the structural trends found in a large dataset of real-world antagonistic and mutualistic communities.</p>
Data from: Plant life history traits rather than soil legacies determine colonisation of soil patches in a multi-species grassland
<p class="MsoNoSpacing">Interactions between plants and soil biota are increasingly shown to play critical roles in plant species co-existence processes. Plant species co-existence is thought to be promoted via biotic legacies that plant species leave behind in the soil after a plant disappears. These soil legacies are hypothesised to supress colonisation success when the preceding plant is of the same species, that is, when a plant species encounters its own, species-specific soil antagonists.</p> <p class="MsoNoSpacing">However, colonisation of vacant spots in plant communities is in the first place determined by the ability of plants to reach such vacant locations. We currently lack an understanding of the explicit role of soil legacy effects and their relative contribution to colonisation processes in plant communities consisting of plant species inherently differing in colonisation ability.</p> <p class="MsoNoSpacing">In experimental, outdoor plant communities consisting of eight grassland species, we tested the effect of five differently conditioned soil patches on plant species colonisation success over three consecutive growing seasons. We found that colonisation success was largely determined by the species' reproductive strategy, lateral spread and growth rate, and not by the plant species that conditioned the soil patch. Fast spreading, clonal plant species reached the soil patches first and initially attained the highest biomass inside the patch. One year later, slower spreading plant species colonised the patch via seedlings. Species with intrinsically high growth rates attained the highest biomass, decreasing biomass of the initial colonisers. While subtle differences between conditioned soil patches did occur, these were not strong enough to overcome the inherent differences in colonisation ability between the various plant species.</p> <p class="MsoNoSpacing"><strong>Synthesis:</strong><em> </em>Our results reject the hypothesis that colonisation of vacant soil patches in plant communities is strongly affected by the legacy that is left behind by the preceding plant species. Instead, plant species life history strategy plays a prominent role, driving sequential plant species replacements. Based on our results and recent accounts in literature we present a conceptual model for local cyclic dynamics in grassland communities, where soil legacy plays a role in affecting the performance of established plant species rather than colonisation of vacant patches.</p>
Empirical tests of habitat selection theory reveal that conspecific density and patch quality, but not habitat amount, drive long-distance immigration in a wild bird
<p>Individuals that disperse long distances from their natal site must select breeding patches with no prior knowledge of patch suitability. Despite decades of theoretical studies examining which cues dispersing individuals should use to select breeding patches, few empirical studies have tested the predictions of these theories at spatial scales relevant to long-distance dispersal in wild animal populations. Here, we use a novel assignment model based on multiple intrinsic markers to quantify natal dispersal distances of Wood Thrush (<i>Hylocichla mustelina</i>) breeding in forest fragments. We show that long-distance natal dispersal in this species is more frequent than commonly assumed for songbirds and that habitat selection by these individuals is driven by density-dependence and patch quality but not the amount of habitat surrounding breeding patches. These results represent an important contribution to understanding habitat selection by dispersing individuals, especially with regards to long-distance dispersal.</p>
Incubation mound-building by the Australian megapode (Malleefowl, Leipoa ocellata) creates novel, resource-rich patches in a semi-arid woodland
<p> Desert ecosystems are characterised by a patchy distribution of resources. Nutrient sinks associated with landscape modulators (trees) differ markedly from the resource-poor interpatch matrix. Fauna can also act as landscape modulators, modifying patch dynamics by redistributing resources via 'ecosystem engineering'. In semi-arid woodlands, malleefowl (<em>Leipoa ocellata</em>: Megapodiidae) reconfigure surface characteristics by scavenging leaf litter to construct large incubation mounds. The extent to which this movement of resources creates a novel patch and alters extant patches is largely unknown. Ecosystem engineering effects by megapodes have been little studied, but are potentially great, particularly in drylands, where mammalian engineers are known to enhance ecosystem function and drive restoration.</p> <p>We measured vegetation, ground cover, and soil chemistry at malleefowl mounds and four extant microsites (trees and open areas close to, and far from, mounds) and predicted that: 1) malleefowl mounds would represent enriched, yet novel, microsites; 2) the characteristics of tree and open patches close to the mounds would differ from those away from the mounds, because of the diminishing intensity of disturbance; and 3) effects at tree and open patches close to the mound would be shorter-term, compared to the more substantial high-resource patch formation occurring at the mound, but we expected all effects would diminish with time since malleefowl activity.</p> <p>We found that: 1) malleefowl mounds were novel microsites with soil chemistry more similar to tree-modulated patches, and groundcover and vegetation variables more similar to the open, interpatch matrix; 2) effects extended to tree and open patches near the mound, but most effects were short lived; and 3) some novel mound attributes (e.g., soil pH, phosphorus, nitrogen, carbon) were greater at mounds, irrespective of their age, while less plant cover and richness on young mounds dissipated with age.</p> <p><strong><em>Synthesis</em></strong>: Mound-building megapodes can modulate the distribution of locally derived resources and create a novel microsite. Engineering effects can enhance spatial heterogeneity and ecosystem function over broad spatial and temporal scales, and may assist with ecological restoration, particularly in depauperate, arid systems.</p>
Simulations for: Patched 1 regulates Smoothened by controlling sterol binding to its extracellular cysteine-rich domain.
<p><strong>Atomistic simulations of Smoothened:</strong></p> <p>Atomistic molecular dynamics simulations of glycosylated mouse Smoothened (mSMO) and human Smoothened (hSMO) in distinct liganded states:</p> <p>- mSMO in an apo state (mSMO_apo)</p> <p>- mSMO with TMD cholesterol bound (mSMO_chol_TMD)</p> <p>- mSMO with CRD cholesterol bound (mSMO_chol_CRD)</p> <p>- mSMO with cholesterol bound to the CRD and TMD (mSMO_2chol_TMD_CRD)</p> <p>- mSMO bound to CRD cholesterol and Smoothened agonist (SAG) (mSMO_chol_CRD_SAG)</p> <p>- mSMO bound to CRD and TMD cholesterols, SAG and an intracellular nanobody (mSMO_2chol_SAG_nanobody)</p> <p>- mSMO bound to CRD and TMD cholesterol and with an additional cholesterol bound at a proposed 'mid' position (mSMO_3chol)</p> <p>- hSMO bound to CRD cholesterol and SAG (hSMO_chol_CRD_SAG)</p> <p> </p> <p>All simulations were run for 5x 300 ns. The active mSMO conformation was obtained from the Protein Data Bank (PDB ID: 6O3C). The hSMO structure was determined using X-ray crystallography as outlined within this study. </p> <p><strong>File description for each system:</strong></p> <p>- md_fit_firstframe.pdb : Initial frame used for atomistic simulations (replicate 1, each replicate equilibrated independently). </p> <p>- md_fit_<em>X</em>.xtc : Gromacs trajectory file for each replicate (X=replicate number). </p>
Data from: Prey encounters and spatial memory influence use of foraging patches in a marine central place forager
<p class="MsoNormal">Given the patchiness and long-term predictability of marine resources, memory of high-quality foraging grounds is expected to provide fitness advantages for central place foragers. However, it remains challenging to characterise how marine predators integrate memory with recent prey encounters to adjust fine-scale movement and use of foraging patches. Here, we used two months of movement data from harbour seals (<em>Phoca vitulina</em>) to quantify the repeatability in foraging patches as a proxy for memory. We then integrated these data into analyses of fine-scale movement and underwater behaviour to test how both spatial memory and prey encounter rates influenced the seals' Area Restricted Search (ARS) behaviour. Specifically, we used one month's GPS data from 29 individuals to build spatial memory maps of searched areas, and archived accelerometry data from a subset of five individuals to detect prey catch attempts, a proxy for prey encounters. Individuals were highly consistent in the areas they visited over two consecutive months. Hidden Markov Models showed that both spatial memory and prey encounters increased the probability of seals initiating ARS. These results provide evidence that predators use memory to adjust their fine scale movement and this ability should be accounted for in movement models.</p>
Patch clamp dataset for: A massively parallel assay accurately discriminates between functionally normal and abnormal variants in a hotspot domain of KCNH2
<p><span>Many genes, including <em>KCNH2</em>, contain </span><span>'hotspot' domains associated with a high density of variants associated with disease. This has led to the suggestion that variant location can be used as evidence supporting classification of clinical variants. However, it is not known what proportion of all potential variants in hotspot domains cause loss of function. Here, we have used a massively parallel trafficking assay to characterize all single-nucleotide variants in exon 2 of <em>KCNH2, </em>a known hotspot for variants that cause long QT syndrome type 2 and an increased risk of sudden cardiac death<em>. </em>Forty-two percent of <em>KCNH2</em> exon 2 variants caused at least 50 % reduction in protein trafficking and 65% of these trafficking defective variants exerted a dominant-negative effect when co-expressed with a WT <em>KCNH2</em> allele as assessed using a calibrated patch clamp electrophysiology assay. The massively parallel trafficking assay was more accurate (AUC of 0.94) than bioinformatic prediction tools (REVEL and CardioBoost, AUC of 0.81) in discriminating between functionally normal and abnormal variants. Interestingly, over half of variants in exon 2 were found to be functionally normal, suggesting a nuanced interpretation of variants in this 'hotspot' domain is necessary. Our massively parallel trafficking assay can provide this information prospectively.</span></p>
Data from: Forest loss and treeless matrices cause the functional impoverishment of sapling communities in old-growth forest patches across tropical regions
<p>Landscape-level disturbances, such as forest loss, can profoundly alter the functional composition and diversity of biotic assemblages. In fact, the landscape-moderated functional trait selection (LMFTS) hypothesis states that landscape-level disturbances may act as environmental filters that select a set of species with disturbance-adapted attributes while causing the loss of species with disturbance-sensitive attributes, ultimately compromising ecosystem functioning. However, the impact of landscape patterns on the functional composition and diversity of tropical regenerating trees (saplings) is unknown.</p> <p>Using a multiscale approach to identify the best spatial scale (i.e. the scale of effect), we tested the effect of forest cover, matrix openness and forest patch density (fragmentation) on functional composition and functional diversity of tree saplings in old-growth forest patches (n = 59) in three Mexican rainforest regions with different degree of deforestation. For 368 species and ~23,000 individuals, we compiled information from global and national databases on six functional traits related to seed dispersal and plant establishment and calculated their community abundance-weighted mean (CWMs) and three complementary functional diversity indices.</p> <p>Forest loss and matrix openness reduced functional richness and evenness, but only in the two most deforested regions. Overall, fragmentation had contrasting effects on functional diversity and composition, but correlated negatively with some functional traits in the most deforested region. Importantly, in the regions with high-to-intermediate degree of deforestation, functional composition experienced major changes: maximum height, seed mass, fruit size and wood density decreased, and SLA increased, in forest patches surrounded by open matrices in highly deforested and fragmented landscapes. This caused a shift of community traits towards more disturbed-adapted attributes.</p> <p><em>Synthesis and applications</em>. In agreement with the LMFTS hypothesis, our results confirm that landscape modifications in regions undergoing high and long-lasting deforestation greatly impoverish the functional composition and diversity of sapling communities. The shift from communities composed mainly by conservative attributes towards communities with a higher prevalence of disturbance-adapted attributes disrupts the future community structure and jeopardizes critical ecosystem functions. Management practices focused on preventing deforestation, increasing forest cover, and promoting treed matrices are necessary to preserve the functionality of these species-rich but increasingly threatened rainforests.</p>
Data from: Patch size drives colonization by aquatic insects, with minor priority effects of a cohabitant
<p>Patch size is one of the most important factors affecting the distribution and abundance of species, and recent research has shown that patch size is an important niche dimension affecting community structure in aquatic insects. Building on this result, we examined the impact of patch size in conjunction with presence of larval anurans on colonization by aquatic insects. Hyla chrysoscelis (Cope's gray treefrog) larvae are abundant and early colonists in fishless lentic habitats, and these larvae can fill multiple ecological roles. By establishing larvae in mesocosms prior to colonization, we were able to assess if H. chrysoscelis larvae have priority effects on aquatic insect assemblages. We conducted a series of three experiments in naturally-colonized experimental landscapes to test whether (1) H. chrysoscelis larval density affects insect colonization, (2) variation in patch size affects insect colonization, and (3) the presence and larval density of H. chrysoscelis shifts colonization of insects between patches of different size. Larval density independently had almost no effect on colonization, while patch size had species-specific effects consistent with prior work. When larvae and patch size were tested in conjunction, patch size had numerous, often strong, species-specific effects on colonization; larval density had effects largely limited to the assemblages of colonizing beetles and water bugs, with few effects on individual species. Higher larval densities in large mesocosms shifted some insect colonization to smaller patches, resulting in higher beta diversity among small patches in proximity to high density large mesocosms. This indicates establishing H. chrysoscelis larvae prior to insect colonization can likely create priority effects that slightly shape insect communities. Our results support the importance of patch size in studying species abundances and distributions, and also indicate that colonization order plays an important role in determining the communities found within habitat patches.</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.