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4,753 results for “SHAPE”
Data from: "Distance decay effects predominantly shape spider but not carabid community composition in crop fields in north-western Europe"
Open the record for dataset details and reuse information.
Exo-Metabolomics Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
<p>Exo-Metabolomics Data for "<em>Phocaeicola vulgatus</em> shapes the long-term growth dynamics and evolutionary adaptations of <em>Clostridioides difficile</em>"</p>
Illumina Sequencing Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
<p>Illumina Sequencing Data for "<em>Phocaeicola vulgatus</em> shapes the long-term growth dynamics and evolutionary adaptations of <em>Clostridioides difficile</em>"</p>
Invasive macroalgae shape chemical and microbial waterscapes on coral reefs
<p><span>Over the past decades, human impacts have changed the structure of tropical benthic reef communities <a name="_Hlk166256162"></a>towards coral depletion and macroalgal proliferation. However, how these changes have modified chemical and microbial waterscapes is poorly known. Here, we assessed how the experimental removal of macroalgal assemblages influences the chemical and microbial composition of two reef boundary layers, the benthic and the momentum<em>. </em>Chemical and microbial waterscapes were spatially structured, both horizontally and vertically, according to macroalgal dominance and boundary layers. Microbes associated with reef degradation were enriched in the boundary layers surrounding macroalgal-dominated substrata. Dominant macroalgae were surrounded by a distinct chemical pool of diverse lipid classes (e.g., diterpenoids and glycerolipids) and labile organic matter (e.g., organooxygen compounds), which diffused from algal tissues to boundary layers according to their polarity. Finally, our results highlighted strong co-variations between specific algal-derived metabolites and planktonic microbes, giving insight into their roles in coral reef functioning and resilience. </span></p>
Role of individual and population heterogeneity in shaping dynamics of multi-pathogen shedding in an island endemic bat
<p>Dataset for the manuscript "<strong>Role of individual and population heterogeneity in shaping dynamics of multi-pathogen shedding in an island endemic bat</strong>", including information of the bat samples and infection data.</p>
Behavioral flexibility in solitary foraging ants: how experience, colony size and food distribution shape individual and collective performance
<p>To deal with the unpredictability of available food resources, animals must adjust their behavior to optimize foraging efficiency. Various mechanisms can influence an individual’s food acquisition behaviour, and thus our knowledge of their combined impact on foraging efficiency remains limited. In this study, we conducted laboratory experiments with seven colonies of the solitary foraging ant Dinoponera quadriceps. Foragers were individually observed in semi-controlled experiments where food was offered in aggregated or dispersed distributions. During the experiments, individual participation was voluntary (i.e. ants were free to enter or not the experimental arena), giving us an opportunity to assess internal processes such as motivation. Besides, behavioral traits such as foraging activity, exploration of food patches, and performance were recorded across repeated trials. We found that solitary foragers of D. quadriceps were highly efficient (retrieving food in 77.38% of the trips), especially when exploiting aggregated and abundant food resources. However, individual foraging success declined when more conspecific foragers were present and with longer foraging experience. Foragers increased their exploration levels in environments with larger numbers of dispersed prey items. Individual foraging activity was higher with more experience and in smaller colonies with fewer foragers. Furthermore, foragers and colonies exhibited low but consistent differences in levels of activity, exploration, and success rates. These findings provide a comprehensive view of how different factors combine to give rise to complex behaviors such as foraging. Additionally, they emphasize the importance of individual traits for effective task performance within social groups, an understudied topic.</p>
Abiotic conditions along altitude shape plant-fungal associations by influencing both fungal availability and association strength
<p>These files contains the description of the data and scripts to reproduce the analyses of:<br>"Abiotic conditions along altitude shape plant-fungal associations by influencing both fungal availability and association strength" which can be found here: <a href="https://doi.org/10.1111/1365-2745.70075">https://doi.org/10.1111/1365-2745.70075</a></p> <p>As detailed in the study, the data consist of fungal DNA data from ten high and low <em>Bistorta vivipara </em>populations across Fennoscandia. Species-level fungal OTUs have been identified applying ITS2-based metabarcoding to the different parts of the focal plant <em>B. vivipara </em>(bulbils, leaves and roots) and its surrounding soil and leaves of surrounding plants. In total, the data contains data on 253 fungal OTUs across 641 sampling units.</p> <p>The README file describes the contents of the metadata and explains how the scripts are to be run in order to reproduce the results of the study.</p> <p> </p>
Supplementary data: The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer's disease
<p>Supplementary data for: The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease. </p> <p>Supplementary_Table1_QC: Excel sheet containing QC metrics for the RNA-seq data and the other containing QC metrics for the ATAC-seq data. </p> <p>Supplementary_Table2_DEGs: Excel sheet containing DeSeq2 differential expression analysis results for the following comparisons: APOE2 vs APOE3, APOE4 vs APOE3, APOE4 vs APOE2, APOE-KO vs APOE3. </p> <p>Supplementary_Table3_MAGMA_geneset_analysis_res: CSV file containing MAGMA gene set analysis results using the differentially expressed genes (FDR < 0.05) for the comparisons outlined in Supplementary_Table2_DEGs and three independent AD GWAS. </p> <p>Supplementary_Table4_DARs: Excel sheet containing DeSeq2 differential accessibility analysis results for the following comparisons: APOE2 vs APOE3, APOE4 vs APOE3, APOE4 vs APOE2, APOE-KO vs APOE3. </p> <p>Supplementary_Table5_sLDSC_res.csv: CSV file containing s-LDSC results using the consensus set of ATAC-seq peaks with three brain disorder GWAS (Alzheimer's disease, autism spectrum disorder, and amyotrophic lateral sclerosis). </p> <p>Supplementary_Table6_WGCNA_clusterProfiler_pathway_enrichment.csv: CSV file containing pathway enrichment results using two WGCNA-identified modules that were significantly upregulated in APOE2-expressing microglia. </p> <p>Supplementary_Table7_homer_motifEnrichment_res.xlsx: Excel sheet containing Homer motif enrichment analysis results using top 100 peaks with increased and decreased chromatin accessibility for APOE2 vs APOE3, APOE4 vs APOE3, and APOE4 vs APOE2.</p>
Artificial Image Data of 2-D Shapes with Different Orientations
<p>1000 images for each of 5 different shapes:</p> <ul> <li>arrow (no rotational symmetry)</li> <li>semicircle (no rotational symmetry)</li> <li>double arrow (2-fold rotational symmetry)</li> <li>triangle (3-fold rotational symmetry)</li> <li>pentagon (5-fold rotational symmetry)</li> </ul> <p>Ground truth orientations and numbers of symmetries are given in groundtruths.csv.</p>
Data from: Host-parasite dynamics shaped by temperature and genotype: quantifying the role of underlying vital rates
<p>1. Global warming challenges the persistence of local populations, not only through heat-induced stress, but also through indirect biotic changes. We study the interactive effects of temperature, competition and parasitism in the water flea <i>Daphnia magna</i>.</p> <p>2. We carried out a common garden experiment monitoring the dynamics of <i>Daphnia</i> populations along a temperature gradient. Halfway through the experiment, all populations became infected with the ectoparasite <i>Amoebidium parasiticum</i>, enabling us to study interactive effects of temperature and parasite dynamics. We combined Integral Projection Models with epidemiological models, parameterized using the experimental data on the performance of individuals within dynamic populations. This enabled us to quantify the contribution of different vital rates and epidemiological parameters to population fitness across temperatures and <i>Daphnia</i> clones originating from two latitudes.</p> <p>3. Interactions between temperature and parasitism shaped competition, where Belgian clones performed better under infection than Norwegian clones, mainly due to higher survival. Infected <i>Daphnia</i> populations performed better at higher than at lower temperatures, mainly due to an increased host capability of reducing parasite loads. Temperature strongly affected individual vital rates, but effects largely cancelled out on a population-level. In contrast, parasitism strongly reduced fitness through consistent negative effects on all vital rates. As a result, temperature-mediated parasitism was more important than the direct effects of temperature in shaping population dynamics. Both the outcome of the competition treatments and the observed extinction patterns support our modeling results.</p> <p>4. Our study highlights that shifts in biotic interactions can be equally or more important for responses to warming than direct physiological effects of warming, emphasizing that we need to include such interactions in our studies to predict the competitive ability of natural populations experiencing global warming.</p>
Vorlesung "Un-Menschliche Lebensformen" als podcast - RVL02 Shapes Of Water
<p>Gekürzte und edierte Fassung der Vorlesungsstunde mit "Pans Labyrinth" (Fortsetzung und Ende), "The Little Mermaid" und "The Shape Of Water".</p> <p>Musik (royalty free): "Taiko Drums" <a href="https://youtu.be/M8VvZObWtZM">https://youtu.be/M8VvZObWtZM</a>; Kevin MacLeod "Spellbound" <a href="https://youtu.be/3TESYVp-WhY">https://youtu.be/3TESYVp-WhY</a></p>
Light availability and light demand of plants shape the arbuscular fungal communities in their roots
<p>Plants involved in the arbuscular mycorrhizal (AM) symbiosis trade photosynthetically derived carbon for fungal-provided soil nutrients. However, little is known about how plant light demand and ambient light conditions influence root-associating AM fungal communities.</p> <p>We conducted a manipulative field experiment to test whether plants' shade tolerance influences their root AM fungal communities in open and shaded grassland sites. We found similar light-dependent shifts shifts in AM fungal community structure for experimental bait plant roots and the surrounding soil. Yet, deviation from the sorrounding soil towards lower AM fungal beta-diversity in the roots of shade-intolerant plants in shade suggested preferential carbon allocation to specific AM fungi in conditions where plant-assimilated carbon available to fungi was limited. We conclude that favourable environmental conditions widen the plant biotic niche, as demonstrated here with optimal light availability reducing plants' selectivity for specific AM fungi, and promote compatibility with a larger number of AM fungal taxa.</p> <p>The deposited dataset contains the raw fungal sequence table for each sample and information on the characteristics of the sample (light treatment, sample type, sampling point in time etc).</p>
Supplementary data to "Geometric morphometrics of bilateral asymmetry in Eunotia bilunaris (Eunotiales, Bacillariophyceae) as a tool for the quantitative assessment of teratogenic deviations in frustule shapes"
<p>The supplementary data consist of the files "data.txt" and "R_script.odt" including the landmark coordinates and the R script used for the analyses described in the paper submitted to Symmetry.</p> <p> </p>
Anthropogenic land‐use change shapes bird diversity along the eastern Himalayan altitudinal gradient
<p>Globally, the conversion of natural forest into agricultural land and human settlement has altered avian diversity and structure often leading to functional and/or phylogenetic homogenisation. While the effects of land-use change on avian functional and phylogenetic diversity is well studied in the tropics, it is poorly understood and scarcely studied in the Himalayas, let alone in the eastern Himalayan bird communities.</p> <p>This dataset comprises observations of 336 bird species from a replicated point-count transect survey conducted between 2019 and 2020 in Bhutan. We used a multispecies occupancy model to estimate occupancy probability while accounting for detection probability. The detection-corrected z-matrix was used to calculate functional and phylogenetic diversity. </p> <p>Our study shows that bird community occupancy along the elevational gradient is negatively associated with human land use (agriculture and settlement). Bird assemblages were functionally and phylogenetically clustered at higher elevations. Agriculture and settlement harboured higher functional and phylogenetic diversity whereas forests had phylogenetically diverse communities within functionally convergent traits.</p> <p>The higher functional and phylogenetic diversity in agriculture and settlement suggests that bird diversity offers an opportunity for a broad range of ecosystem services. Protection of forests abutting human settlements and agriculture will help preserve higher phylogenetic diversity. We recommend that agricultural practices that safeguard and improve bird-friendly habitats should be promulgated. Educational programmes on the importance of the roles of birds should be implemented and integrating bird conservation with farm production will help conserve bird diversity in human-dominated landscapes. To enhance the conservation value of working landscapes in the Himalayas, avitourism can be explored further. </p>
Stigma shape shifting in sages (Salvia: Lamiaceae) – hummingbirds guided the evolution of New World floral features
<p><span><span><span><span><span><span><span><span><span><span><span>A fundamental question in evolutionary biology is how clades of organisms exert influence on one another. The evolution of the flower and subsequent plant/pollinator coevolution are major innovations that have operated in flowering plants to promote species radiations at a variety of taxonomic levels in the Neotropics. Here we test the hypothesis that pollination by Neotropical endemic hummingbirds drove the evolution of two unique stigma traits in correlation with other floral traits in New World Salvia (Lamiaceae). We examined morphometric shapes of stigma lobing across 400 Salvia spp., scored presence and absence of a stigma brush across Salvia, and used a suite of phylogenetic comparative methods to detect shape regime shifts, correlation of trait shifts with BayesTraits and phylogenetic generalized least square regressions, and the influence of scored pollinators on trait evolution using OUwie. We found that a major Neotropical clade of Salvia evolved a correlated set of stigma features, with a longer upper stigma lobe and stigmatic brush, following an early shift to hummingbird pollination. Evolutionary constraint is evident as subsequent shifts to bee pollination largely retained these two features. Our results support the hypothesis that hummingbirds guided the correlative shifts in corolla, anther connective, style and stigma shape in Neotropical Salvia, despite repeated shifts back to bee pollination. </span></span></span></span></span></span></span></span></span></span></span></p>
Evolution of body size and wing shape trade-offs in arsenurine silkmoths
<p>One of the key objectives in biological research is understanding how evolutionary processes have produced Earth's diversity. A critical step towards revealing these processes is an investigation of evolutionary tradeoffs – that is, the opposing pressures of multiple selective forces. For millennia, nocturnal moths have had to balance successful flight, as they search for mates or host plants, with evading bat predators. However, the potential for evolutionary trade-offs between wing shape and body size are poorly understood. In this study, we used phylogenomics and geometric morphometrics to examine the evolution of wing shape in the wild silkmoth subfamily Arsenurinae (Saturniidae) and evaluate potential evolutionary relationships between body size and wing shape. The phylogeny was inferred based on 782 loci from target capture data of 42 arsenurine species representing all 10 recognized genera. After detecting in our data one of the most vexing problems in phylogenetic inference – a region of a tree that possesses short branches and no "support" for relationships (i.e., a polytomy), we looked for hidden phylogenomic signal (i.e., inspecting differing phylogenetic inferences, alternative support values, quartets, and phylogenetic networks) to better illuminate the most probable generic relationships within the subfamily.</p> <p>We found there are putative evolutionary trade-offs between wing shape, body size, and the interaction of fore- and hindwing shape. Namely, body size tends to decrease with increasing hindwing length but increases as forewing shape becomes more complex. Additionally, the type of hindwing (i.e., tail or no tail) a lineage possesses has a significant effect on the complexity of forewing shape. We outline possible selective forces driving the complex hindwing shapes that make Arsenurinae, and silkmoths as a whole, so charismatic.</p>
Ecological and evolutionary processes shape belowground springtail communities along an elevational gradient
<p> The data sets were analyzed during the current study. Data from: Ecological and evolutionary processes shape belowground springtail communities along an elevational gradient</p>
Data from: The evolution of egg shape in birds: Evolutionary constraints and adaptations
<p>Using accurate measures of size and shape, we studied the eggs of 955 extant species across the avian phylogeny, including 39 of the 40 orders, and 78% of the 249 families. We show that the elongation component of egg shape is largely the result of constraints imposed by the female's anatomy during egg formation, whereas asymmetry is mainly an adaptation to conditions during the incubation period. Thus, egg elongation is related to the size of the egg in relation to the size of the female's oviduct and also to either the shape of her pelvis or general body conformation associated with her mode of locomotion. Egg asymmetry is related mainly to clutch size and the structure of the incubation site, factors that influence thermal efficiency during incubation and the risk of breakage. Importantly, general patterns across the phylogeny do not always reflect the trends within families and orders. We argue that the analysis of avian egg shape is most profitably conducted within taxa where all species share similar life histories and ecologies, as there is no single factor that influences egg shape in the same way in all birds.</p>
Island biogeography predicts skull gigantism and shape variation in meadow voles (Microtus pennsylvanicus) through ecological release and allometry
Island Rule describes the graded trend of gigantism in small-bodied species to dwarfism in large-bodied species inhabiting islands, but causal explanations remain unresolved. We used geometric morphometrics to quantify cranial morphology of 544 meadow vole (<i>Microtus pennsylvanicus</i>) samples across 11 island and 3 mainland populations from the Outer Lands of New England (Atlantic) and the Alexander Archipelago of Alaska (Pacific). We compared the thermoregulation and endurance (TRE) and ecological release (ER) hypotheses using all-subsets linear models employing residual randomization permutation procedures (rrpp), and Akaike Information Criterion (AIC) for model selection. We decoupled direct and indirect effects of island variables on size using path analysis. We evaluated shape with Principal Components Analysis (PCA) and Procrustes ANOVA on Procrustes shape coordinates, then assessed the impact of static allometry and TRE and ER variables on shape. Six Atlantic island populations exhibit significant signals of gigantism with the largest voles occurring on the smallest islands lacking predators. ER explains 63% of cranial size differences. Island area has a significant total effect on size by influencing the number of mammalian predators, resulting in a 0.011 increase in unit centroid size for a 100 km<sup>2</sup> decrease in island area. This corresponds to a predicted 0.9% change in size for every 100 km<sup>2</sup>. Given static allometry, cranial shape does not respond to insularity independent of size. These results suggest that Island Rule is a latent evolutionary process whose manifestation depends on nuanced biogeographic and ecological contexts that have important conservation and taxonomic implications.
Understanding parapatry: How do environment and competitive interactions shape Iberian vipers' distributions?
<p><b>Aim</b>: To assess if the parapatry of the three viper species present in the Iberian Peninsula is mainly caused by environmental conditions, historical events, interspecific competition among them, or a combination of these factors.</p> <p><b>Location</b>: The Iberian Peninsula</p> <p><b>Taxon</b>: <i>Vipera aspis</i>, <i>V. latastei,</i> and <i>V. seoanei</i>.</p> <p><b>Methods</b>: We applied the concept of favourability of occurrence to produce commensurate distribution units unaffected by the prevalence of different species in the Iberian Peninsula. We compared the favourability of each species individually with the favourability of occurrence of more than one species co-occurring in their overlapping ranges, and identified the areas in which sympatric coexistence, environmental segregation, and competitive exclusion are predicted to occur.</p> <p><b>Results</b>:<i> </i>The main driver of the parapatric pattern was competitive exclusion, which was mediated by gradual changes in the environmental conditions favouring each species.<i> </i>The para-Mediterranean<i> V. aspis </i>presented fragmented favourable areas outside its range that seemed to be unoccupied due to competitive exclusion by the other vipers. The Mediterranean <i>V. latastei</i> appeared to be limited by competition with the other viper species and by the environment in northwestern Iberia. <i>V. seoanei</i> prevented the other two species becoming established in the north-western quarter of the Iberian Peninsula due to its better adaption to the humid conditions in this region. Some areas of sustainable coexistence were detected, mainly in the upper reaches of the River Ebro.</p> <p><b>Main conclusions</b>: Each species is better adapted to particular conditions. However, the existence of ecotones forces them to occur sympatrically and compete for resources. The parapatric pattern is a result of the evolutionary history of the species and of strong competitive interactions between them, which form 'competitive-exclusion barriers'. However, these barriers are environmentally dependent, so changes in the environment could rapidly affect the limits of the species distribution.</p>
ScienceDex guides
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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.