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3,655 results for “Structural data”
Data from: Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters
Marine Archaea are important players among microbial plankton and significantly contribute to biogeochemical cycles, but details regarding their community structure and long-term seasonal activity and dynamics remain largely unexplored. In this study, we monitored the inter-annual archaeal community composition of abundant and rare biospheres in northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA and rRNA. A detailed analysis of the rare biosphere structure showed that the rare archaeal community was composed of three distinct fractions. One contained the rare Archaea that became abundant at different times within the same ecosystem; these cells were typically not dormant, and we hypothesize that they represent a local seed bank that is specific and essential for ecosystem functioning through cycling seasonal environmental conditions. The second fraction contained cells that were uncommon in public databases and not active, consisting of aliens to the studied ecosystem and representing a non-local seed bank of potential colonizers. The third fraction contained Archaea that were always rare but actively growing; their affiliation and seasonal dynamics were similar to the abundant microbes and could not be considered a seed bank. We also showed that the major archaeal groups, Thaumarchaeota Marine Group-I (MGI) and Euryarchaeota Group-II.B (MGII.B) in winter and Euryarchaeota Group-II.A (MGII.A) in summer, contained different ecotypes with varying activities. Our findings suggest that archaeal diversity could be associated with distinct metabolisms or life strategies, and that the rare archaeal biosphere is composed of a complex assortment of organisms with distinct histories that affect their potential for growth.
Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species
The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the ITS region, frequently used in plant phylogenetics, is now recognised as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analysed datasets from the Saccharomyces Genome Resequencing Project, characterising rDNA sequence variation within multiple strains of the baker's yeast <i>Saccharomyces cerevisiae</i> and its nearest wild relative <i>Saccharomyces paradoxus</i> in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterisation of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intra-species phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridisation events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multi-locus rDNA systems.
Data from: Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum L., Solanaceae) in southern India: implications for conservation
[No abstract entered]
Data from: Causes and consequences of fine-scale population structure in a critically endangered freshwater seal
[No abstract entered]
Data from "Cooperative Management of Ecosystem Services: Coalition Formation, Landscape Structure and Policies"
<p>Simulated data generated to perform the simulations of the paper "Bareille, F., Zavalloni, M., Raggi, M., & Viaggi, D. (2021). Cooperative management of ecosystem services: coalition formation, landscape structure and policies. Environmental and Resource Economics, 79(2), 323-356."</p>
Global structure of magnetotail reconnection revealed by mining space magnetometer data
<p>Data associated with the manuscript titled "Global structure of magnetotail reconnection revealed by mining space magnetometer data". For each of the 26 IDR events, files are included that detail: time intervals identified using the nearest-neighbor search and the resulting subset of magnetometer data and their associated weights, files containing the fit set of coefficients and parameters for the model, and the digital model output data that were used in constructing the figures. The compiled magnetometer database used in this study is available on the SPDF website. This study extended this database with the addition of MMS magnetometer data which has also been included in the Zenodo archive. The SMR and SML indices obtained from the SuperMAG web page are also included in the Zenodo archive.</p>
Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
<p>Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (<i>Zonotrichia leucophrys</i>) subspecies: <i>Z. l. gambelii, Z. l. oriantha, </i>and <i>Z. l. pugetensis</i>. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned<i> </i>sparrows<i> </i>do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.</p>
Data used for the paper "Birth and decline of magma oceans in planetesimals. Part 2: Structure and thermal history of early accreted small planetary bodies". Submitted to JGR - Planets.
<p>Script and data to generates the figures displayed in the pre-print.</p>
Data for: Effects of biotic interactions on plant fecundity depend on spatial and functional structure of communities and time since disturbance
<p><span>Biotic interactions in plant communities affect individual fitness and community dynamics. Interactions between plants vary in space, over time and with organisational complexity. Yet it is challenging to quantify temporal, spatial and functional determinants of different types of interactions between long-lived perennial plant species and their effect on lifetime fecundity. We studied how plant-plant, pollinator- and seed predator-mediated interactions affect year-to-year variation in three fecundity components (cone production, seed set and seed survival) during post-fire recovery. Age-stratified data on the three fecundity components were collected in 19 even-aged communities comprising 20 serotinous <em>Protea </em>shrub species in the South African Fynbos. We analyse data on these fecundity components with neighbourhood models to infer the sign and strength of interactions throughout post-disturbance recovery, the neighbour plant traits that shape them and the spatial scale at which interactions take place. For each fecundity component, these models describe how neighbourhood effects change over time and with spatial distance between plants. For each focal plant, we then predicted neighbourhood effects on individual fecundity components and cumulative reproductive output at different post-fire stand ages. Competitive effects on cone production and seed set increased with post-fire stand age as biomass and floral resources for pollinators build up. In contrast, neighbourhood effects on seed survival were weak throughout post-disturbance recovery. Plant-plant interactions were shaped by neighbour traits related to resource acquisition, whereas animal-mediated interactions depended on neighbour traits related to resource availability for pollinators and seed predators. The spatial scale of the interactions increased from plant-plant over predator-mediated to pollinator-mediated interactions. The joint effect of these interactions on cumulative reproductive output caused the proportion of focal plants experiencing competition to increase with time since fire. We show that temporal changes in biotic interactions throughout post-disturbance recovery of perennial plant communities depend on functional traits and can be integrated to neighbourhood effects on lifetime fecundity. Studying the temporal, spatial and functional determinants of neighbourhood effects on lifetime fecundity is important for predicting not only individual plant fitness, but also population and community dynamics in changing environments. </span></p>
Supplementary Website, Data, and Scripts for the Paper "Hierarchical and Hybrid Organizational Structures in Open-Source Software Projects: A Longitudinal Study"
<p>Supplementary website containing result plots and data, anonymized raw data, and scripts used to produce the results of the paper "Hierarchical and Hybrid Organizational Structures in Open-Source Software Projects: A Longitudinal Study".</p>
Crystal structure PDB 8PPS, dimeric RbdA EAL, diffraction data and processing
Open the record for dataset details and reuse information.
Dual-Transformer Architecture for Cross-Modal Learning on Tree-Structured Data in Regression Tasks
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Raw data for "Unsteady secondary flow structure at a large river confluence"
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ChEMBL Data for 'Achieving Well-Informed Decision-Making in Drug Discovery: A Comprehensive Calibration Study using Neural Network-Based Structure-Activity Models'
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FIGURE 248 in World genera of Mastigitae: review of morphological structures and new ecological data (Coleoptera: Staphylinidae: Scydmaeninae)
FIGURE 248. Phylogenetic hypothesis for Mastigitae, after Jałoszyński et al. (2018).
FIGURES 214–216 in World genera of Mastigitae: review of morphological structures and new ecological data (Coleoptera: Staphylinidae: Scydmaeninae)
FIGURES 214–216. Mastigini, behavior. Adults of Palaeostigus palpalis feeding on dead caterpillars.
FIGURES 200–201 in World genera of Mastigitae: review of morphological structures and new ecological data (Coleoptera: Staphylinidae: Scydmaeninae)
FIGURES 200–201. Mastigini, larva of Palaeostigus palpalis in dorsal (200) and lateral (201) views.
FIGURE 247 in World genera of Mastigitae: review of morphological structures and new ecological data (Coleoptera: Staphylinidae: Scydmaeninae)
FIGURE 247. †Baltostigini, example of extinct species; lateral habitus of Baltostigus antennatus.
FIGURE 166 in World genera of Mastigitae: review of morphological structures and new ecological data (Coleoptera: Staphylinidae: Scydmaeninae)
FIGURE 166. Mastigini, distribution of extant species. Palaeostigus.
FIGURE 236 in World genera of Mastigitae: review of morphological structures and new ecological data (Coleoptera: Staphylinidae: Scydmaeninae)
FIGURE 236. Mastigini, larva of Stenomastigus longicornis in lateral view.
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.