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3,655 results for “Structural data”
Data for: The long-term impacts of deer herbivory in determining temperate forest stand and canopy structural complexity
<p>1. Ungulates place immense consumptive pressure on forest vegetation globally, leaving legacies of reduced biodiversity and simplified vegetative structure. However, what remains unresolved is whether browse-induced changes occurring early in succession ultimately manifest themselves in the developed forest canopy. Understanding the development and persistence of these legacies is critical as canopy structure is an important determinant of forest ecosystem functions like carbon sequestration and wildlife habitat.</p> <p>2. We measured how white-tailed deer (Odocoileus virginianus) browse during stand initiation affected canopy structure, tree species richness, diversity, stem density, and basal area on Pennsylvania's Allegheny Plateau using a portable canopy LiDAR system. We capitalized on an historic deer enclosure experiment where forests were subjected to four deer densities (4, 8, 15, and 25 deer/km2) for ten years following stand initiation.</p> <p>3. Deer browsing impacts on the forest canopy are apparent nearly four decades since stand initiation. The highest deer density treatment experienced a significant reduction in tree species diversity, density, and basal area with stands becoming dominated by black cherry (Prunus serotina). Reductions in overstory diversity and tree density resulted in a more open canopy with low leaf area and high horizontal leaf variability. Canopies were tallest at the lowest and highest deer densities.</p> <p><i>4. Synthesis and Applications</i>: Using a portable canopy LiDAR system and a former deer enclosure experiment, we show that high deer browsing pressure during stand initiation can have a decades-long impact on stand and canopy structure. High deer densities led to stands with lower species diversity and tree density, which resulted in canopies that were taller and less dense. Managers should consider the lasting legacy of ungulate herbivory on canopy structure, as canopy structure influences several important management goals, such as forest carbon sequestration, maintenance of diverse understory communities, and creation of wildlife habitat.</p>
Data: Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon
<p>Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.</p>
Data from: Can matrix structure affect animal navigation between fragments? A dispersal experiment using release platforms
<p>The persistence of species in fragmented landscapes relies on landscape connectivity and individuals' ability in dispersing among habitat patches. Accordingly, matrix structure can affect the orientation of dispersing individuals across the landscape. In this study, we measured the impact of matrix structure on the dispersal performance of the white-eared opossum (Didelphis albiventris). We released individuals in three types of matrix: bare field, corn crops and soybean crops, with distances of 30, 50 and 100 m to the nearest habitat patch. To test if the release height would affect the individuals' dispersal performance, we released animals from the ground and from 2 m high platforms. We released and tracked 14 individuals in bare field on the ground; 30 in corn crops, 22 on the ground and 8 on platforms; 17 on soybeans crop, 12 on the ground and 5 on platforms. The type of matrix influenced the perceptual range. Perceptual range was 100 m in bare field, 50 m in cornfield and less than 30 m in soybean field. The platforms only increased the perceptual range of individuals in the cornfield from 50 to 100 m. Visual and olfactory cues would cause this effect. We conclude that matrix structure affects dispersal performance, and that vertical elements of the matrix, such as scattered trees, may increase orientation in crop fields during inter-patch dispersal.</p>
Data for Structure of Energy Precipitation Induced by Superbolt-Lightning Generated Whistler Waves
<p>This is the dataset for the publication <strong>Structure of Energy Precipitation Induced by Superbolt-Lightning Generated Whistler Waves. </strong>Detailed instruction attached within.</p>
Double-layer structure of the Pt(111)–aqueous electrolyte interface - capacitance data
<p>Original data of Figs. 1, 2, 3, 5, 6 and S2.</p> <p>Codes to generate capacitance data are available at https://theorpubs.lic.leidenuniv.nl/public/katharina.doblhoff-dier/2021_PNAS_meanFieldModel_PtDoubleLayer_withWaterAds/ </p>
Supplementary data from: Diversity, population structure and palaeoecology of the Pleistocene large cervids from the Padang Highlands, Sumatra
<p>This chapter deals with the dentognathic remains of the large deer from the Padang Highland caves in Sumatra. By means of a multiproxy approach we attempt to more fully document the presence and characteristics of the cervid family during the Late Pleistocene in this region. We used linear and geometric morphometric techniques to investigate variation, taxonomic position and body size trends in a dataset of upper and lower molars. Dental mesowear was used to assess dietary prefence in a sub-sample. The results suggest the Padang Highland cervids belonged to multiple populations of an early stock of <em>Rusa</em> deer of the size of <em>Rusa unicolor</em>, but morphologically similar to <em>Rusa timorensis</em>. <em>Rusa</em> sp. was reconstructed as a mixed feeder with an increase of the grazing component with age. </p>
NGS Data from: Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage
<p><span><span>We engineered gRNAs with highly stable hairpins in their constant parts and further enhanced their stability by chemical modifications. The 'Genome-editing Optimized Locked Design' (GOLD)-gRNA increases genome editing efficiency up to around 1000-fold (from 0.08% to 80.5%) with a mean increase across different other targets of 7.4-fold. The related NGS data is deposited </span></span>here.</p>
Data of "Electronic Structure and Epitaxy of CdTe shells on InSb Nanowires"
<p>This folder contains the figure data of "Data of "Electronic Structure and Epitaxy of CdTe shells on InSb Nanowires""</p>
Structural Basis for the Inhibition of IAPP Fibril Formation by the Co-Chaperonin Prefoldin - Experimental Data
<p>Experimental data (EM, AFM, BLI, ThT and Cell viability assays, as well as docking models) used for the study :</p> <p><strong>Structural Basis for the Inhibition of IAPP Fibril Formation by the </strong><strong>Co-Chaperonin Prefoldin</strong></p> <p>by Ricarda Törner, Tatsiana Kupreichyk, Lothar Gremer, Elisa Colas Debled, Daphna Fenel, Sarah Schemmert, Pierre Gans<sub>, </sub>Dieter Willbold, Guy Schoehn, Wolfgang Hoyer, Jerome Boisbouvier</p>
Data from: Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure
<p><strong>General information</strong></p> <p>This deposition contains the datasets that were used in the statistical analysis of the manuscript entitled <strong>Traces of genetic but not epigenetic adaptation in the invasive goldenrod <em>Solidago canadensis</em> despite the absence of population structure </strong>published in Frontiers in Ecology and Evolution (doi: <a href="https://doi.org/10.3389/fevo.2022.856453">10.3389/fevo.2022.856453</a>).</p> <p><strong>Uploaded files</strong></p> <ul> <li><strong>README</strong> file to explain the datasets</li> <li><strong>AFLP/MSAP metadata</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLPMSAP_meta_data.txt</li> <li><strong>AFLP scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLP_scoring_data.txt</li> <li><strong>MSAP scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data.txt</li> <li><strong>MSAP mix1-scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data_mix1.txt</li> <li>All files were combined in a <strong>.zip file</strong></li> </ul>
Data from: Population genomic evidence of selection on structural variants in a natural hybrid zone
<p><span>Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two </span><em>Lycaeides</em> butterfly taxa (<em>L. melissa</em> and Jackson Hole <em>Lycaeides</em>) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviated from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole <em>Lycaeides</em> ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole <em>Lycaeides</em>. Excess Jackson Hole <em>Lycaeides</em> ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.</p>
Data from: The influence of historical dispersal on the phylogenetic structure of tree communities in the tropical Andes
We test for evidence of the Tropical Niche Conservatism or the Out of The Tropics hypotheses in structuring patterns of tree community composition along a 2000+ meter elevational gradient in the northern tropical Andes. By collecting and integrating data on the presence-absence of tree species within plots with phylogenetic information, we analyzed: 1) patterns of phylogenetic dispersion and species diversity along the elevational gradient based on indexes of net relatedness, nearest taxon relatedness, and species richness (α-diversity); and 2) the replacement of lineages along the gradient using the PhyloSorensen metric (β-diversity). More specifically, we established 20 0.25-ha permanent tree inventory plots between 750 and 2802 m asl where all individuals with Diameter at Breast Height (DBH) ≥ 10 cm were measured and identified. We then used a series of linear models to test for changes in α and β diversity between plots in relation to elevation. Neither the net relatedness index nor the nearest taxon index showed a significant relationship with elevation. However, there was greater phylogenetic over-dispersion at intermediate elevations; this likely reflects the mixing of species with contrasting origins from tropical and temperate lineages. β-diversity between plots was negatively related to the corresponding difference in elevation, indicating that closely related lineages occupy similar ranges of elevation and temperature. We conclude that the immigration of lineages from extra-tropical regions have significant effects in determining the phylogenetic structure of tree communities in tropical Andean forests.
Data from: Irregular forest structures originating after fire: an opportunity to promote alternatives to even-aged management in boreal forests
<p><span>1. Even-aged silviculture based on short-rotation clearcuts had severely altered boreal forests. Silvicultural alternatives (e.g., continuous cover or retention forestry) has the potential to restore and protect the habitats and functions of boreal forests. These alternatives are however often restricted to structurally complex old-growth forest, which are particularly threatened by anthropogenic disturbances. Increasing the use of alternatives to even-aged silviculture in early-successional stands could help recruit more structurally complex forests, with characteristics closer to the old-growth. In this article, we therefore evaluate the potential for silvicultural alternatives to even-aged management in boreal forests that burned less than a century ago.</span></p> <p><span>2. We analyzed 1085 field plots in a 243000 km<sup>2</sup> area situated in the boreal forest of eastern Canada. These plots burned 30 to 100 years before the survey and had not been subjected to previous or subsequent anthropogenic disturbance; they hence represent young primary forests. The main patterns of tree diameter distribution variation within the plots were identified using k-means clustering. Stand structure, tree species composition, and environmental variables that most explained the differences among the clusters were identified with a random forest model, and then compared using Kruskal-Wallis and Fisher's exact tests.</span></p> <p><span>3.</span> <span>The majority (>75 %) of the plots presented an irregular structure of stem diameters (i.e., non-normally distributed, with many small diameter trees). The understorey was generally dominated by black spruce (<em>Picea mariana</em> [Mill.] BSP), a shade-tolerant species. Irregular structures were observed in both forests of high and low productivity, implying that different processes (e.g., early regeneration, variable tree growth) can lead to observed early irregular structure. Regular structures were generally characterized by a higher productivity and abundance in hardwood species compared to the irregular structures. </span></p> <p><span>4. <em>Synthesis and application</em>: Many boreal forests of eastern Canada progress towards an irregular structure in the decades following the last stand-replacing fire. A substantial part of these early-successional forests may be suitable for alternatives to even-aged silviculture that better maintains habitats and functions of preindustrial boreal forests. </span></p>
Data for: Biogeographic history predicts bee community structure across floral resource gradients in southeast Australia
<p><strong><span>Aim:</span></strong><span> Plants populations are declining in their native ranges around the globe through the expansion of agriculture, urbanization, and plant invasions. We test the hypothesis that animal species that have spent more of their evolutionary history in a region are more dependent on native plants, particularly those plants that have spent more of their evolutionary history in the region, and are therefore more negatively impacted by native plant decline. </span></p> <p><strong><span>Location:</span></strong><span><strong> </strong>Yarra Valley landscapes, Australia</span></p> <p><strong><span>Methods</span></strong><span><strong>:</strong> We test the presence and pattern of phylogenetic signal in native bee community responses to local flower density of ancient Australian plant lineages and the amount of native vegetation in the surrounding landscape across farm and native vegetation sites. We also test phylogenetic signal in the frequency of bee visitation to flowers from ancient Australian plant lineages. We compare the patterns of phylogenetic signal to the current understanding of bee biogeographic histories to evaluate our hypothesis. </span></p> <p><strong><span>Results:</span></strong><span> There was significant phylogenetic signal in responses to flower density of plants from ancient Australian lineages, and the frequency of visitation to these flowers, with most species from the ancient Australian bee clade being positively associated with these flowers. This is consistent with our hypothesis. Significant phylogenetic signal in response to native vegetation in the surrounding landscape was driven primarily by the more recently arrived bee linages, with ancient lineages able to persist on some farms where ancient Australian flowers were present (e.g. on roadsides). </span></p> <p><strong><span>Main conclusions:</span></strong><span> Bee species that have spent more of their evolutionary history in Australia are more dependent on ancient Australian plant lineages and so most negatively impacted by the decline of these plants. This may be a broader phenomenon because phylogenetic conservatism in host plant use, the main assumption underlying our hypothesis, is common among herbivorous arthropods (~500,000 species).</span></p>
Structural measurements and stress inversion data from Condit and French, GRL 2022
<p>Structural measurements and stress inversion results of vein sets used for mechanical inversions in Condit and French, <em>In review - </em> At Geophysical Research Letters </p>
Data for: The formation of "mega‐flocks" depends on vegetation structure in montane coniferous forests of Taiwan
<p>A mixed-species bird flock is a social assemblage where two or more bird species are moving together while foraging and might benefit from increased foraging efficiency and antipredator vigilance. A "mega-flock," which includes flocking species from different vegetation layers, often exhibits high species diversity. Mechanisms for the formation of mega-flocks have not yet been explored. In this study, we evaluated the influence of vegetation structure and bird species diversity/richness in driving the occurrence of mega-flocks. We investigated the composition of mixed-species flocks, local bird communities, and vegetation structure in five vegetation types of two high-elevation sites in central Taiwan. (For more details, please see the paper which has been published in Ecology and Evolution, entitled "The formation of "mega-flocks" depends on vegetation structure in montane coniferous forests of Taiwan." Doi: https://doi.org/10.1002/ece3.8608)</p>
Research Data for "Molecular Dynamics Study of Structure and Reactions at the Hydroxylated Mg(0001)/Bulk Water Interface"
<p>This folder contains data used in the paper "Molecular Dynamics Study of Structure and Reactions at the Hydroxylated Mg(0001)/Bulk Water Interface" (Title subject to change). Some details on the structure are as follows:</p> <p>The folder "figures" contains data to create various figures in the main paper. Each file contains a json object, where keys "0", "1", etc. refer to the 1st/2nd subplot for a figure. The values are then another json object with the data used to create the relevant plot; the most useful of which is the "data" key which contains the plot data.</p> <p>The folder "md_traj" contains the molecular dynamics trajectory. The file "traj.exyz" is a standard format which can be opened with various software. "traj.json" contains the same information in an in-house format used by the author. The "thermo_data.json" contains various thermodynamics properties over the simulation, such as temperatures and kinetic energies. Units are femtoseconds, Angstrom, electron-volts and Kelvin.</p> <p>The folder "react_traj" contains trajectories in the same formats as "md_traj", but each are limited to time-windows where reactions occurred (so each trajectory will only be hundreds of femtoseconds long at most). The subfolder "full_traj" contains the trajectories with all atoms present, whilst "trimmed_traj" contains trajectories with most atoms removed (the atoms included are those nearest the reaction).We include these "trimmed_traj" files as it is difficult to find the reacting molecules when visualising all atoms in the simulation.</p> <p>The folder "opt_geoms" contains geometries for various structures used in the paper (in *.exyz format). These also contain *.json files; these contain information on how the calculations were carried out in a format used by the author (they are small files primarily included for the benefit of the author).</p> <p> </p> <p> </p>
Data from: Design of cinnamaldehyde amino acid Schiff base compounds based on the quantitative structure–activity relationship
Cinnamaldehyde amino acid Schiff base (CAAS) is a new class of safe, bioactive compounds which could be developed as potential antifungal agents for fungal infections. To design new cinnamaldehyde amino acid Schiff base compounds with high bioactivity, the quantitative structure–activity relationships (QSARs) for CAAS compounds against Aspergillus niger (A. niger) and Penicillium citrinum (P. citrinum) were analysed. The QSAR models (R2 = 0.9346 for A. niger, R2 = 0.9590 for P. citrinum,) were constructed and validated. The models indicated that the molecular polarity and the Max atomic orbital electronic population had a significant effect on antifungal activity. Based on the best QSAR models, two new compounds were designed and synthesized. Antifungal activity tests proved that both of them have great bioactivity against the selected fungi.
Data from: How structured is the entangled bank? The surprisingly simple organization of multiplex ecological networks leads to increased persistence and resilience
Species are linked to each other by a myriad of positive and negative interactions. This complex spectrum of interactions constitutes a network of links that mediates ecological communities' response to perturbations, such as exploitation and climate change. In the last decades, there have been great advances in the study of intricate ecological networks. We have, nonetheless, lacked both the data and the tools to more rigorously understand the patterning of multiple interaction types between species (i.e., "multiplex networks"), as well as their consequences for community dynamics. Using network statistical modeling applied to a comprehensive ecological network, which includes trophic and diverse non-trophic links, we provide a first glimpse at what the full "entangled bank" of species looks like. The community exhibits clear multidimensional structure, which is taxonomically coherent and broadly predictable from species traits. Moreover, dynamic simulations suggest that this non-random patterning of how diverse non-trophic interactions map onto the food web could allow for higher species persistence and higher total biomass than expected by chance and tends to promote a higher robustness to extinctions.
Data from: Phylogenetic structure of vertebrate communities across the Australian arid zone
AIM: To understand the relative importance of ecological and historical factors in structuring terrestrial vertebrate assemblages across the Australian arid zone, and to contrast patterns of community phylogenetic structure at a continental scale. LOCATION: Australia. METHODS: We present evidence from six lineages of terrestrial vertebrates (five lizard clades and one clade of marsupial mice) that have diversified in arid and semi-arid Australia across 37 biogeographical regions. Measures of within-lineage community phylogenetic structure and species turnover were computed to examine how patterns differ across the continent and between taxonomic groups. These results were examined in relation to climatic and historical factors, which are thought to play a role in community phylogenetic structure. Analyses using a novel sliding-window approach confirm the generality of processes structuring the assemblages of the Australian arid zone at different spatial scales. RESULTS: Phylogenetic structure differed greatly across taxonomic groups. Although these lineages have radiated within the same biome – the Australian arid zone – they exhibit markedly different community structure at the regional and local levels. Neither current climatic factors nor historical habitat stability resulted in a uniform response across communities. Rather, historical and biogeographical aspects of community composition (i.e. local lineage persistence and diversification histories) appeared to be more important in explaining the variation in phylogenetic structure. While arid-zone assemblages show an overall tendency towards phylogenetic clustering, this pattern was less pronounced at finer spatial scales. MAIN CONCLUSIONS: By focusing within different taxonomic groups and between those groups within regions, we show that although the vertebrate lineages we examined exhibited high diversity and low turnover across the arid zone, the underlying phylogenetic structure differs between regions and taxonomic groups, suggesting that taxon-specific histories are more important than habitat stability in determining patterns of phylogenetic community relatedness.
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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.