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2,960 results for “elements”
Data from: Convergence analysis of a finite element skull model of Herpestes javanicus (Carnivora, Mammalia): implications for robust comparative inferences of biomechanical function
Predictions of skull biomechanical capability based on virtual models constitute a valuable data source for testing hypotheses about craniodental form and feeding behavior. Such comparative analyses also inform dietary reconstruction in extinct species. 3D modeling using Finite Element (FE) methods is a common technique applied to the comparative analysis of craniodental function in extinct and extant vertebrates. However, taxonomically diverse skull models in the literature often are not directly comparable to each other, in part because of distinctions in how boundary conditions are defined, but also because of substantial differences in the number of FEs composing the models. In this study, we test whether a conventional convergence test is adequate in identifying the minimum number of FEs needed to achieve internally stable results for a single species. We constructed a series of skull models of Herpestes javanicus, and simulated unilateral biting across the dentition; the models differed in the number of FEs, degrees of freedom at the joint and bite point constraints, and type of tetrahedral FEs used. We found that convergence patterns differed across constraint types, FE quantities, and bite position simulated. Four-noded tetrahedral (tet-4) FE models with relaxed constraints produced the most stable measurements compared to over-constrained tet-4 models and to relaxed tet-10 models. In absence of an optimal FE quantity from convergence testing, we propose a broadly applicable sub-sampling protocol, whereby average measurement values across multiple models per specimen are used for among-species comparisons. A regime of sampling three low FE quantity models produced the closest estimates of mean measurement values relative to larger model sets, being within the 95% bootstrap estimated confidence intervals. Future studies should focus on identifying sources of variation associated with other FE modeling protocols, so that they can be accounted for before biomechanical attributes from these simulations are used to infer form–function linkage.
Data from: Genome-wide identification of microsatellites and transposable elements in the dromedary camel genome using whole genome sequencing data
Transposable elements (TEs) along with simple sequence repeats (SSRs) are prevalent in eukaryotic genome, especially in mammals. Repetitive sequences form approximately one-third of the camelid genomes, so study on this part of genome can be helpful in providing deeper information from the genome and its evolutionary path. Here, in order to improve our understanding regarding the camel genome architecture, the whole genome of the two dromedaries (Yazdi and Trodi camels) was sequenced. Totally, 92- and 84.3-Gb sequence data were obtained and assembled to 137,772 and 149,997 contigs with a N50 length of 54,626 and 54,031 bp in Yazdi and Trodi camels, respectively. Results showed that 30.58% of Yazdi camel genome and 30.50% of Trodi camel genome were covered by TEs. Contrary to the observed results in the genomes of cattle, sheep, horse, and pig, no endogenous retrovirus-K (ERVK) elements were found in the camel genome. Distribution pattern of DNA transposons in the genomes of dromedary, Bactrian, and cattle was similar in contrast with LINE, SINE, and long terminal repeat (LTR) families. Elements like RTE-BovB belonging to LINEs family in cattle and sheep genomes are dramatically higher than genome of dromedary. However, LINE1 (L1) and LINE2 (L2) elements cover higher percentage of LINE family in dromedary genome compared to genome of cattle. Also, 540,133 and 539,409 microsatellites were identified from the assembled contigs of Yazdi and Trodi dromedary camels, respectively. In both samples, di-(393,196) and tri-(65,313) nucleotide repeats contributed to about 42.5% of the microsatellites. The findings of the present study revealed that non-repetitive content of mammalian genomes is approximately similar. Results showed that 9.1 Mb (0.47% of whole assembled genome) of Iranian dromedary's genome length is made up of SSRs. Annotation of repetitive content of Iranian dromedary camel genome revealed that 9,068 and 11,544 genes contain different types of TEs and SSRs, respectively. SSR markers identified in the present study can be used as a valuable resource for genetic diversity investigations and marker-assisted selection (MAS) in camel-breeding programs.
Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.
FIGURE 17. Rharodesmus tabarkensis n in Rharodesmus Schubart, 1960 — a tropical element in the North African fauna: a new species from Tunisia and notes on the family Pyrgodesmidae (Diplopoda: Polydesmida)
FIGURE 17. Rharodesmus tabarkensis n. sp. mandible. Arrow pointing at the molar hook.
FIGURE 17 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 17. Female terminalia of Paraleia fumosa sp. n., lateral view. Paratype. Scale 0.1 mm.
FIGURE 20 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 20. Male terminalia of Paraleia tonnoiri sp. n., ventral view. Holotype. Scale 0.1 mm.
FIGURE 16 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 16. Male terminalia of Paraleia fumosa sp. n., ventral view. Holotype. Scale 0.1 mm.
FIGURE 1 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 1. Habitus. Female paratype of Paraleia fumosa sp. n., lateral view. Scale 1 mm.
FIGURE 13 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 13. Male terminalia of Paraleia bolivari sp. n., ventral view. Paratype. Scale 0.1 mm.
FIGURE 23 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 23. Female terminalia of Paraleia sp., lateral view. Paratype. Scale 0.1 mm.
FIGURE 19 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 19. Female terminalia of Paraleia denticulata sp. n., lateral view. Paratype. Scale 0.1 mm.
FIGURE 18 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 18. Male terminalia of Paraleia denticulata sp. n., ventral view. Paratype. Scale 0.1 mm.
FIGURE 15 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 15. Female terminalia of Paraleia bolivari sp. n., ventral view. Paratype. Scale 0.1 mm.
FIGURE 21 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 21. Female terminalia of Paraleia nidorosa sp. n., lateral view. Holotype. Scale 0.1 mm.
FIGURE 14 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 14. Female terminalia of Paraleia bolivari sp. n., lateral view. Paratype. Scale 0.1 mm.
FIGURE 22 in Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes
FIGURE 22. Female terminalia of Paraleia sharkeyi sp. n., lateral view. Paratype. Scale 0.1 mm.
Atmospheric trace elements in Pudong, Shanghai
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Design and Analysis of Chiral and Achiral Metasurfaces with the Finite Element Method
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STATIC DESCRIPTIONS OF A THREE-PHASE TRANSFORMER TAKEN INTO ACCOUNT OF SENSITIVE ELEMENTS
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A LA-BTC MOF AS A SENSOR ELEMENT OF AN ELECTRONIC NOSE FOR SELECTIVE ADSORPTION OF BIOMARKERS OF DISEASES: MOLECULAR DYNAMICS SIMULATIONS OF ADSORPTION
<p>The MD trajectories calculated for all the La-BTC MOF-biomarker simulation systems </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.