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4,753 results for “SHAPE”
FIGURE 6. Scale-shaped sclerites under polarized light showing concentric extinction patterns. A in A review of the genus Trichogorgia (Cnidaria, Octocorallia), including descriptions of new species
FIGURE 6. Scale-shaped sclerites under polarized light showing concentric extinction patterns. A: Stephanogorgia diomedea (USNM 75108); B: Trichogorgia lyra (USNM 52875); C: S. wainwrighti (USNM 1112682); D: T. muzikae sp. nov. (USNM 77155, holotype).
Astrea: automatic generation of SHACL shapes from ontologies
<p> This resource is Astrea-KG, a Knowledge Graph that publishes a set of mappings that encode the equivalent conceptual restrictions among ontology constraint patterns and SHACL constraints patterns.</p>
Dataset: Seismic Performance of Slender RC U-shaped Walls with a Single-Layer of Reinforcement
<p>This dataset contains the experimental data for two large-scale reinforced concrete U-shaped wall specimens tested at the Earthquake Engineering and Structural Dynamics Laboratory (EESD Lab), École Polytechnique Féderale de Lausanne (EPFL) in Switzerland. This dataset contains supplementary material for the journal paper titled, "Seismic Performance of Slender RC U-shaped Walls with a Single-Layer of Reinforcement", which contains some of the experimental observations and results. Thus, this dataset also contains MATLAB files associated with calculating the results presented in the journal paper and the corresponding figures and plots. The abstract for the journal paper is below:</p> <p>Reinforced concrete walls are typically used to resist the lateral loading induced by wind and earthquake actions. While most walls feature two vertical reinforcement layers, in some regions the use of slender reinforced concrete walls with a single vertical layer of reinforcement is current construction practice or has been in the past. The seismic performance of such elements is largely unknown given the paucity of experimental research that has been conducted on walls with a single layer of reinforcement, particularly for non-rectangular walls, such as the popular U-shaped wall. This paper presents the results of two slender reinforced concrete U-shaped walls tested at the Earthquake Engineering and Structural Dynamics Laboratory (EESD Lab), École Polytechnique Féderale de Lausanne (EPFL) in Switzerland. Both wall specimens were unconfined and detailed with a single-layer of vertical reinforcement to replicate some of the current construction practices being conducted in Colombia. Both walls reached ultimate drifts larger than 2.5-3.0% and initially failed due to buckling of the longitudinal reinforcement at the flange ends. The buckling length was 700-800 mm, which corresponded to 44-50 bar diameters.</p>
Summer aridity rather than management shapes fitness-related functional traits of the threatened mountain plant Arnica montana
<p>Semi-natural mountain grasslands are increasingly exposed to environmental stress under climate change. However, which are the environmental factors that limit plants in these grasslands? Also, is the present management effective against these changes? Fitness-related functional traits may offer a way to detect changes in performance and provide new insights into their vulnerability to climate change. We investigated changes in performance and variability of functional traits of the mountain grassland target species <em>Arnica montana</em> along a climate gradient in Central German low mountain ranges. This gradient represents at its lower end climate conditions that are expected at its upper end under future climate change. We measured vegetative, generative and physiological traits to account for multiple ways of plant response to the environment. Using mixed effects and multivariate models, we evaluated changes in trait values among individuals as well as the variability of their populations in order to assess performance under changing summer aridity and different management regimes.</p> <p>Fitness-related performance of most traits showed strongly positive associations with reduced summer aridity at higher elevations, while only specific leaf area and leaf dry matter content showed no association. This suggests a higher performance level at less arid montane sites and that the physiological traits are less sensitive to this climate change factor. The coefficient of variation of almost all traits declined steadily with decreasing site aridity. We suggest that this reduced variability indicates a lower environmental stress level for <em>A. montana</em> towards its environmental optimum at montane elevations, especially because the trait performance increased simultaneously. Surprisingly, management factors and habitat characteristics had only low influence on both trait performance and variability. In summary, summer aridity had a stronger effect to shape the trait performance and variability of <em>A. montana</em> under increased environmental stress than management and other habitat characteristics.</p>
Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
<p><em>Austropuccinia psidii</em>, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. <em>Austropuccinia</em><em> psidii</em> has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into <em>A. psidii</em> pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in transposable elements and a very low overall GC content of 33.8%. The overall gene content is highly conserved, when compared to other closely related Pucciniales, yet the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how transposable elements shaped the genome evolution of <em>A. psidii</em> and provide a greatly needed resource for strategic approaches to combat disease spread. Please cite the authors if using this data: https://academic.oup.com/g3journal/article/11/3/jkaa015/6007476</p>
Data and code for changes in contact patterns shape the dynamics of the novel coronavirus disease 2019 outbreak in China
<p>Data and code for the paper "changes in contact patterns shape the dynamics of the novel coronavirus disease 2019 outbreak in China" published in Science.</p>
Softness and Weight from Shape: Material Properties Inferred from Local Shape Features
<p>Dataset relative to the following publication:</p> <p>Schmidt, F., Fleming, R. W., & Valsecchi, M. (2020). Softness and Weight from Shape: Material Properties Inferred from Local Shape Features. <em>Journal of Vision, 20(6):2</em>, 1-20. https://doi.org/10.1167/jov.20.6.2</p> <p>Each experiment folder contains the data relative to one experiment, the rating scale images and videos, and a text file with comments. The stimuli folder contains image files of all experimental stimuli.</p>
Watershed shapes for the Great Lakes Runoff Inter-comparison Project for Lake Erie (GRIP-E)
<p>This dataset provides the shapefiles of the 46 calibration and 7 validation watersheds used within the Great Lakes Runoff Inter-comparison Project for Lake Erie (GRIP-E).</p> <p>The watersheds draining towards the following WSC and USGS gauge stations have been used for:</p> <p><strong>1a. calibration of objective 1</strong> (low-human impact)<br> (28 stations in total; 13 of them in both objective 1 and 2)<br> 02GA010 02GA018 02GA038 02GA047 02GB007<br> 02GC002 02GC010 02GC018 02GD004 02GE007<br> 02GG002 02GG003 02GG006 02GG009 02GG013<br> 04159492 04159900 04160600 04161820 04164000<br> 04165500 04166100 04177000 04196800 04197100<br> 04207200 04208504 04213000</p> <p><strong>1b. calibration of objective 2</strong> (most-downstream gauges closest to Lake Erie)<br> (31 stations in total; 13 of them in both objective 1 and 2)<br> 02GB001 02GB007 02GC002 02GC007 02GC018<br> 02GC026 02GE007 02GG003 02GG009 02GG013<br> 04159900 04160600 04165500 04166500 04174500<br> 04176500 04177000 04193500 04195820 04198000<br> 04199000 04199500 04200500 04208504 04209000<br> 04212100 04213000 04213500 04214500 04215000<br> 04215500</p> <p><strong>2. (spatial) validation</strong><br> (7 stations in total)<br> 02GE003 04167000 04168000 04185000 04195500<br> 04201500 04208000</p> <p>===============================================================</p> <p>These data have been derived under the Great Lakes Runoff Intercomparison Project for Lake Erie (GRIP-E) led by Juliane Mai and Bryan Tolson (both University of Waterloo) and funded under the Integrated Modelling Program for Canada (IMPC) within the Global Water Futures program.</p>
Videos to accompany publication "The Synthesis of Complex Shape Deployments in Sign Language" (Filhol & McDonald, 2020)
<p>Videos to accompany publication "The Synthesis of Complex Shape Deployments in Sign Language" (Filhol & McDonald, 2020)</p>
Shape file for AMoD dispatching in Zurich
<p>Shape file to re-run the simulations for our upcoming paper <strong>Automated Mobility on Demand: A comprehensive simulation study of cost, behaviour and system impact for Zurich</strong></p>
From smart apes to human brain boxes. A uniquely derived brain shape in late hominins clade: supplementary material
<p>DATA.rda: an RData file containing the phylogenetic tree, the landmark and semilandmark sets used in the analyses of the endocast shape (123 specimens), the semilandmark sets used in the asymmetry analyses (120 specimens), the vector of the corresponding ECV values and a mesh containing the triangulated semilandmark configuration.</p> <p>script.R: the annotated script used to replicate the analyses reported in this study.</p>
Stan code from: Simulation modeling reveals the evolutionary role of landscape shape and species dispersal on genetic variation within a metapopulation
Different shapes of landscape boundaries can affect the habitat networks within them and consequently the spatial genetic-patterns of a metapopulation. In this study, we used a mechanistic framework to evaluate the effects of landscape shape, through watershed elongation, on genetic divergence among populations at the metapopulation scale. Empirical genetic data from four, sympatric stream-macroinvertebrates having aerial adults were collected from streams in Japan to determine the roles of species-specific dispersal strategies on metapopulation genetics. Simulation results indicated that watershed elongation allows the formation of river networks with fewer branches and larger topographic constraints. This results in decreased interpopulation connectivity but a lower level of spatial isolation of distal populations (e.g., those found in headwaters) occurring in the landscapes examined. Distal populations had higher genetic divergence when their downstream-biased dispersal (relative to upstream- and/or overland-biased dispersal) was high. This underscores the importance of distal populations influencing genetic divergence at the metapopulation scale for species having downstream-biased dispersal. In turn, lower genetic divergence was observed under watershed elongation when the genetic isolation of distal populations was decreased in such species. This strong association between landscape shape and evolutionary processes highlights the importance of natural, spatial architecture in assessing the effectiveness of conservation and management strategies.
Data from: Specialization and niche overlap across spatial scales: revealing ecological factors shaping species richness and coexistence in Australian songbirds
1. Ecological specialization enables the partitioning of resources and thus can facilitate the coexistence of species and promote higher species richness. Specialization and niche partitioning are expected to exert a decisive influence on local spatial scales, while species richness at regional scales should be shaped mostly by historical factors and abiotic conditions. Moreover, specialization is expected to be particularly important in communities that are exceptionally species rich for their environmental conditions. Concurrently, niche overlap in these communities should be minimized to enable species coexistence. 2. We tested these hypotheses by studying specialization-richness relationship and niche overlap in assemblages of 298 species of songbirds (Passeriformes) across Australia. We used local (2-6 ha) to regional (bioregions) spatial scales, and detailed data on habitat, diet, and foraging behaviour (method, substrate, and stratum). 3. We expected the richness-specialization relationship to be particularly strong i) on local spatial scales and ii) in communities exceptionally species rich for given environmental conditions (approximated by moisture and vegetation complexity). We also expected iii) low niche overlap in assemblages with specialized species. 4. Only the third prediction was partly supported. First, while the specialization and species richness were often positively related, the strength and the direction of the relationship changed between traits and across spatial scales. The strength of the specialization-richness relationship was consistently positive only in foraging stratum, and it increased towards smaller spatial scales only in case of habitat and diet. Simultaneously, species in local communities demonstrated high overlap in habitat and diet. Second, we did not find particularly strong specialization-richness relationships in exceptionally species rich communities. Third, we found the expected negative relationship between specialization and overlap in foraging stratum and substrate (in local communities), suggesting that species partition ecological space locally in terms of where they find food. 5. Our expectations were only weakly supported. Specialization on foraging stratum was probably important in facilitating species co-existence. Conversely, although species were often specialized on habitat and diet, high overlap in these traits did not preclude their local coexistence. Overall, specialization and overlap in foraging traits were more important for species coexistence than habitat or diet.
Data from: Recombination rate variation shapes barriers to introgression across butterfly genomes
Hybridisation and introgression can dramatically alter the relationships among groups of species, leading to phylogenetic discordance across the genome and between populations. Introgression can also erode species differences over time, but selection against introgression at certain loci acts to maintain post-mating species barriers. Theory predicts that species barriers made up of many loci throughout the genome should lead to a broad correlation between introgression and recombination rate, which determines the extent to which selection on deleterious foreign alleles will affect neutral alleles at physically linked loci. Here we describe the variation in genealogical relationships across the genome among three species of Heliconius butterflies: H. melpomene, H. cydno and H. timareta, using whole genomes of 92 individuals, and ask whether this variation can be explained by heterogeneous barriers to introgression. We find that species relationships vary predictably at the chromosomal scale. By quantifying recombination rate and admixture proportions, we then show that rates of introgression are predicted by variation in recombination rate. This implies that species barriers are highly polygenic, with selection acting against introgressed alleles across most of the genome. In addition, long chromosomes, which have lower recombination rates, produce stronger barriers on average than short chromosomes. Finally, we find a consistent difference between two species pairs on either side of the Andes, which suggests differences in the architecture of the species barriers. Our findings illustrate how the combined effects of hybridisation, recombination and natural selection, acting at multitudes of loci over long periods, can dramatically sculpt the phylogenetic relationships among species.
Data from: Group density, disease, and season shape territory size and overlap of social carnivores
<p>1. The spatial organization of a population can influence the spread of information, behaviour, and pathogens. Territory size and territory overlap, components of spatial organization, provide key information as these metrics may be indicators of habitat quality, resource dispersion, contact rates, and environmental risk (e.g., indirectly transmitted pathogens). Furthermore, sociality and behaviour can also shape space use, and subsequently, how space use and habitat quality together impact demography.</p> <p>2. Our study aims to identify factors shaping the spatial organization of wildlife populations and assess the impact of epizootics on space use. We also use network analysis to describe spatial organization and connectivity of social groups.</p> <p>3. Here, we assessed the seasonal spatial organization of Serengeti lions and Yellowstone wolves at the group level. We examine the factors predicting mean territory size and mean territory overlap for each population using generalized additive models. We further explore the mechanisms by which disease perturbations could cause changes in spatial organization.</p> <p>4. We demonstrate that lions and wolves were similar in that group-level factors, such as number of groups, shaped spatial organization more than population-level factors, such as population density. Factors shaping territory size were slightly different than factors shaping territory overlap; for example, wolf pack size was an important predictor of territory overlap, but not territory size. Lion spatial networks were more highly connected, while wolf spatial networks varied seasonally. We found that resource dispersion may be more important for driving territory size and overlap for wolves than for lions. Additionally, canine distemper epizootics may alter lion spatial organization, highlighting the importance of including behavioural and movement ecology in studies of pathogen transmission dynamics.</p> <p>5. We provide insight about when we might expect to observe the impacts of resource dispersion, disease perturbations, and other ecological factors on spatial organization. Our work highlights the importance of monitoring and managing social carnivore populations at the group level. Future research should elucidate the complex relationships between demographics, social and spatial structure, abiotic and biotic conditions, and pathogen infections. </p>
The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote skulls
Cranial morphology is remarkably varied in living amniotes, ranging from short-faced mammals to the elongate snouts of crocodylians. This diversity of shapes is thought to correspond with feeding ecology, a relationship repeatedly demonstrated at smaller phylogenetic scales, but one that remains untested across amniote phylogeny. Using a combination of 2D geometric and linear morphometrics, we investigate the links between phylogenetic relationships, diet, and skull shape in an expansive dataset of extant amniotes with teeth: mammals, lepidosaurs, and crocodylians. We find that both phylogeny and diet have statistically significant effects on skull shape, although these effects differ depending on the dataset analyzed. The three major clades largely partition morphospace, each plotting in separate regions with limited overlap. Mammals and squamates extensively diversify within their respective regions. Among all three groups, dietary generalists often occupy clade-specific central regions of morphospace. Some parallel changes in skull shape occur in clades with distinct evolutionary histories but similar diets. However, members of a given clade often present distinct skull shape solutions for a given diet, and the vast majority of species retain the unique aspects of their ancestral skull plan, underscoring the limits of morphological convergence due to ecology in amniotes. These data demonstrate that certain skull shapes may provide functional advantages suited to particular diets, but accounting for both phylogenetic history and ecology can provide a more nuanced approach for inferring the ecology and functional morphology of cryptic or extinct amniotes.
Seed shape in the Caryophyllales-Cardioid
<p>A summary of seed shape in the Caryophyllales with interest in the species whose seeds have cardioid-shape.</p>
Variation in the strength of allometry drives rates of evolution in primate brain shape - Supplementary Material
<p>Large brains are a defining feature of primates, as is a clear allometric trend</p> <p>between body mass and brain size. However, important questions on the</p> <p>macroevolution of brain shape in primates remain unanswered. Here we</p> <p>address two: (i), does the relationship between the brain size and its shape</p> <p>follow allometric trends and (ii), is this relationship consistent over evolutionary</p> <p>time? We employ three-dimensional geometric morphometrics and</p> <p>phylogenetic comparative methods to answer these questions, based on a</p> <p>large sample representing 151 species and most primate families. We found</p> <p>two distinct trends regarding the relationship between brain shape and</p> <p>brain size. Hominoidea and Cercopithecinae showed significant evolutionary</p> <p>allometry, whereas no allometric trends were discernible for Strepsirrhini,</p> <p>Colobinae or Platyrrhini. Furthermore,we found that in the taxa characterized</p> <p>by significant allometry, brain shape evolution accelerated, whereas for taxa in</p> <p>which such allometrywas absent, the evolution of brain shape decelerated.We</p> <p>conclude that although primates in general are typically described as largebrained,</p> <p>strong allometric effects on brain shape are largely confined to the</p> <p>order's representatives that display more complex behavioural repertoires.</p>
Data from: Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)
<p>Little is known about intraspecific <span class="il">variation</span> within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50 km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic <span class="il">variation</span> at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with <span class="il">sex</span>, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in <span class="il">otolith</span> <span class="il">shape</span>, but further sampling is required to disentangle potential confounding influence of age. This study is the first step towards understanding intraspecific <span class="il">variation</span> within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in <span class="il">sex</span>, age, and gene flow between the nearshore and offshore environments.</p>
Auditory cortex shapes sounds responses in the inferior colliculus
The extensive feedback from the auditory cortex (AC) to the inferior colliculus (IC) supports critical aspects of auditory behavior, but has not been extensively characterized. Previous studies demonstrated that activity in IC is altered by focal electrical stimulation and pharmacological inactivation of AC, but these methods lack the ability to selectively manipulate projection neurons. We measured the effects of selective optogenetic modulation of cortico-collicular feedback projections on IC sound responses in mice. Activation of feedback increased spontaneous activity and decreased stimulus selectivity in IC, whereas suppression had no effect. To further understand how microcircuits in AC may control collicular activity, we optogenetically modulated different cortical neuronal subtypes, specifically parvalbumin-positive (PV) and somatostatin-positive (SOM) inhibitory interneurons. We found that modulating either type of interneuron did not affect IC sound-evoked activity. Combined, our results identify that activation of excitatory projections, but not inhibition-driven increases in cortical activity, affects collicular sound responses.
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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.