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388 results for “Data element”
Simulation data of Schmidt et al., A three-dimensional finite element formulation coupling electrochemistry and solid mechanics on resolved microstructures of all-solid-state lithium-ion batteries, DOI: https://doi.org/10.1016/j.cma.2023.116468
<p>This data set includes the simulation results of the relevant simulations published in the paper: "Schmidt et al., A three-dimensional finite element formulation coupling electrochemistry and solid mechanics on resolved microstructures of all-solid-state lithium-ion batteries, DOI: https://doi.org/10.1016/j.cma.2023.116468".</p> <p>Please refer to the paper for the details of the model as well as the parameterization of the model for the respective simulations.</p> <p>The provided lzip archive is structured into separate folders, one per simulation. Each folder contains the output data and a short README.txt with further hints. For information on the compression algorithm and how to uncompress it lzip please refer to https://en.wikipedia.org/wiki/Lzip.</p>
Data for: Mimicking functional elements of the natural flow regime promotes native fish recovery in a regulated river
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Data from: Taphonomic controls on a multi-element skeletal fossil record
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Data from: Transposable element diversity and activity patterns in neotropical salamanders
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Finite Element model data for Academic Rotor bladed-disc system
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Data from: DCDC2 READ1 regulatory element: how temporal processing differences may shape language
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Data for: Intra- and interspecific variation in trace element concentrations in feathers of North European Trans-African migrants
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Data from: Walrus teeth as biomonitors of trace elements in Arctic marine ecosystems
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Data from: Hybrid incompatibility between D. virilis and D. lumei is stronger in the presence of transposable elements
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Data supplement for Wind Energy Science Paper 'Implementation of the blade element momentum model on a polar grid and its aeroelastic load impact'
<p>Contains the data for most figures in the article, as well as a plotting file written in python that generates the figures.</p>
Discrete Element Model for subglacial till: code and data
<p>This is a permanent archive of the code and data for the Discrete Element Model, Sphere, developed by Anders Damsgaard, and used for simulations of deforming subglacial till. File is compressed in the tar.bz2 format.</p> <p>The Sphere code and documentation can be found at <a href="https://src.adamsgaard.dk/sphere/">https://src.adamsgaard.dk/sphere/</a> .</p> <p>Run sphere/python/MyVisualization.py to generate the figures in sphere/Images/.</p>
Data for the article "Commensurability between element symmetry and the number of skyrmions governing skyrmion diffusion in confined geometries"
<p>Data for the article "Commensurability between element symmetry and the number of skyrmions governing skyrmion diffusion in confined geometries" (<a href="https://arxiv.org/abs/2009.03995">[2009.03995] Commensurability governing skyrmion diffusion in confined geometries (arxiv.org)</a>)</p>
Data from: Conodont size, trophic level and the evolution of platform elements.
Conodonts are among the first vertebrates to have evolved mineralized tooth-like structures. Among these, the so-called P1 elements are known to have been used to break down food, and display a wide variety of morphologies. In particular, the repeated independent evolution of platform-like P1 elements have been suggested to correspond to similar functional constraints linked to diet. To test this hypothesis of convergence, we measured size (as element length) for various conodont taxa, and used it as a proxy for trophic level. We then tested the correlation between size and platform presence/absence, both on raw data and in a phylogenetic context. Retaining or excluding the platform traits from the character matrix has limited impact on the resulting phylogeny. Contrary to platform presence/absence, size shows no phylogenetic signal. Using the raw data, size and platform presence appear positively correlated. That correlation however is no longer significant if one corrects for the phylogeny. We conclude that platform presence cannot be explained by an enlargement of the conodont element, be it via a trophic level change or developmental constraints. This suggests that conodonts as a whole, and in particular platform-bearing conodonts, were an ecologically diverse group and that the various known platform types are likely to reflect different, rather than convergent, ecological niches.
Data from: Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects
Background: Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. Results: Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6 % in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58 % in the malaria mosquito (Diptera) and the migratory locust (Orthoptera), and a possible relationship between the content and diversity of TEs and the genome size. Conclusion: While most insect orders exhibit a characteristic TE composition, we also observed intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera. Our findings shed light on common patterns and reveal lineage-specific differences in content and evolution of TEs in insects. We anticipate our study to provide the basis for future comparative research on the insect TE repertoire.
Data from: The fire ant social supergene is characterized by extensive gene and transposable element copy number variation
In the fire ant Solenopsis invicta, a supergene composed of ~600 genes and having two variants, SB and Sb, regulates colony social form. In single queen colonies all individuals carry only the SB allele, while in multiple queen colonies, some individuals carry the Sb allele. In this study we characterized genes with copy number variation between SB and Sb-carrying individuals. We showed extensive acquisition of gene duplicates in Sb genome, with some likely involved in polygyne-related phenotypes. We found 260 genes with differences in copy number between SB and Sb, of which 239 are in greater copy number in Sb. We observed TE accumulation on Sb, likely due to the accumulation of repetitive elements on the non-recombining chromosome. We found a weak correlation between TE copy number and differential expression, suggesting some TEs may still be proliferating in Sb, however many of the duplicated TEs were already silenced. Among the 115 non-TE genes with higher copy in Sb, enzymes responsible for cuticular hydrocarbon synthesis were highly represented. These include a desaturase and an elongase; both potentially responsible for differential queen odor and likely beneficial for polygyne ants. These genes seem to have translocated into the supergene from other chromosomes and proliferated by multiple duplication events. While the presence of transposable elements (TEs) in supergenes is well documented, little is known about duplication of non-TE genes and their possible adaptive role. Overall, our results suggest that gene duplications may be an important factor leading to monogyne and polygyne ant societies.
Data from: A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements
Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe. This clade has had a challenging taxonomic history, but the current classification consists of ~77 species in three families, the Travuniidae, Paranonychidae, and Nippononychidae. Travunioidea classification has traditionally been based on structure of the tarsal claws of the hind legs. However, it is now clear that tarsal claw structure is a poor taxonomic character due to homoplasy at all taxonomic levels. Here, we utilize DNA sequences derived from capture of ultraconserved elements (UCEs) to reconstruct travunioid relationships. Data matrices consisting of 317–677 loci were used in maximum likelihood, Bayesian, and species tree analyses. Resulting phylogenies recover four consistent and highly supported clades; the phylogenetic position and taxonomic status of the enigmatic genus Yuria is less certain. Based on the resulting phylogenies, a revision of Travunioidea is proposed, now consisting of the Travuniidae, Cladonychiidae, Paranonychidae (Nippononychidae is synonymized), and the new family Cryptomastridae Derkarabetian & Hedin, fam. n., diagnosed here. The phylogenetic utility and diagnostic features of the intestinal complex and male genitalia are discussed in light of phylogenomic results, and the inappropriateness of the tarsal claw in diagnosing higher-level taxa is further corroborated.
Data and plotting scripts used in "High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling"
<p>Raw performance data and plotting scripts used to generate the figures in the paper "High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling"</p>
Data and plotting scripts used in "High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling"
<p>Raw performance data and plotting scripts used to generate the figures in the paper "High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling"</p> <p>A previous version of this dataset (corresponding to an earlier revision of the paper) is available as https://doi.org/10.5281/zenodo.50533.</p>
Data for: The suppression of a selfish genetic element increases a male's mating success in a fly
<p>X chromosome meiotic drive (XCMD) kills Y-bearing sperm during spermatogenesis, leading to the biased transmission of the selfish X chromosome. Despite this strong transmission, some natural XCMD systems remain at low and stable frequencies, rather than rapidly spreading through populations. The reason may be that male carriers can have reduced fitness, as they lose half of their sperm, only produce daughters, and may carry deleterious alleles associated with XCMD. Thus, females may benefit from avoiding mating with male carriers, yielding a further reduction in fitness. Genetic suppressors of XCMD, which block the killing of Y sperm and restore fair Mendelian inheritance, are also common and could prevent the spread of XCMD. However, whether suppressed males are as fit as a wild-type male remains an open question, and the effect that genetic suppressors may have on a male's mating success is rarely considered. Here, we investigate the mating ability of XCMD males and suppressed XCMD males in comparison to wild-type males in the fruit fly <em>Drosophila subobscura</em>, where drive remains at a stable frequency of 20% in wild populations where it occurs. We use both competitive and non-competitive mating trials to evaluate male mating success in this system. We found no evidence that unsuppressed XCMD males were discriminated against. Remarkably, however, their suppressed XCMD counterparts had a higher male mating success compared to wild-type controls. Unsuppressed XCMD males suffered 12% lower offspring production in comparison to wild-type males. This cost appears too weak to counter the transmission advantage of XCMD, and thus the factors preventing the spread of XCMD remain unclear.</p>
Data from: high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery
<p>Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps. This makes it difficult to decipher the impact of these elements on the dynamics of genome evolution. The increased capacity of long-read sequencing technologies to span highly repetitive regions of the genome should provide novel insights into patterns of TE diversity. Here we report the generation of highly contiguous reference genomes using PacBio long read and Omni-C technologies for three species of sparrows in the family Passerellidae. To assess the influence of sequencing technology on TE annotation, we compared these assemblies to three chromosome-level sparrow assemblies recently generated by the Vertebrate Genomes Project and nine other sparrow species generated using a variety of short- and long-read technologies. All long-read based assemblies were longer in length (range: 1.12-1.41 Gb) than short-read assemblies (0.91-1.08 Gb). Assembly length was strongly correlated with the amount of repeat content, with longer genomes showing much higher levels of repeat content than typically reported for the avian order Passeriformes. Repeat content for the Bell's sparrow (31.2% of genome) was the highest level reported to date for a songbird genome assembly and was more in line with woodpecker (order Piciformes) genomes. CR1 LINE elements retained from an expansion that occurred 25-30 million years ago were the most abundant TEs in the song sparrow genome. Although the other five sparrow species also exhibit evidence for a spike in CR1 LINE activity at 25-30 million years ago, LTR elements stemming from more recent expansions were the most abundant elements in these species. LTRs were uniquely abundant in the Bell's sparrow genome deriving from two recent peaks of activity. Higher levels of repeat content (79.2-93.7%) were found on the W chromosome relative to the Z (20.7-26.5) or autosomes (16.1-30.9%). These patterns support a dynamic model of transposable element expansion and contraction underpinning the seemingly constrained and small sized genomes of birds. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.</p>
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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.