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3,655 results for “Structural data”
Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.
DNA Stack Data Structure: Data Set of Polyacrylamide Gels
<p>Data set to accompany paper: A Last-In First-Out Stack Data Structure Implemented in DNA, Lopiccolo and Shirt-Ediss et al., Nature Comms 12, 4861 (2021). <a href="https://doi.org/10.1038/s41467-021-25023-6">doi:10.1038/s41467-021-25023-6</a>.</p> <p>The data set contains 32 polyacrylamide gel experiments (reaction sequences and gel images) used for creating the electrophoretic mobility graph in Figure S13 of the SI of the above paper.</p>
Supplementary Data for "Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein"
<p>Supplementary Data for "Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein", Journal of Biomolecular Structure and Dynamics, 2021, 10.1080/07391102.2021.1942213</p> <p>A random selection of 10 representative structures from each MSM state of STING/CDN complexes is provided in .pdb file format. The selected MSM representatives are aligned and available as PyMOL session files.</p>
Data from: High-speed surface reconstruction of a flying bird using structured light
<p>Animal flight requires aerodynamic power, which is challenging to determine accurately <i>in vivo</i>. Existing methods rely on approximate calculations based on wake flow field measurements, inverse dynamics approaches, or invasive muscle physiological recordings. In contrast, the external mechanical work required for terrestrial locomotion can be determined more directly by using a force platform as an ergometer. Based on an extension of the recent invention of the aerodynamic force platform, we now present a more direct method to determine the <i>in vivo</i> aerodynamic power by taking the dot product of the aerodynamic force vector on the wing with the representative wing velocity vector based on kinematics and morphology. We demonstrate this new method by studying a slowly flying dove, but it can be applied more generally across flying and swimming animals as well as animals that locomote over water surfaces. Finally, our mathematical framework also works for power analyses based on flow field measurements.</p>
Data from: Structural and functional brain connectome in motor neuron diseases: a multicenter MRI study
Objective. To investigate structural and functional neural organization in amyotrophic lateral sclerosis (ALS), primary lateral sclerosis (PLS) and progressive muscular atrophy (PMA) patients. Methods. 173 ALS, 38 PLS, 28 PMA sporadic patients and 79 healthy controls were recruited from three Italian centers. Subjects underwent clinical, neuropsychological and brain MRI evaluations. Using graph analysis and connectomics, global and lobar topological network properties and regional structural and functional brain connectivity were assessed. The association between structural and functional network organization and clinical/cognitive data was investigated. Results. Compared to healthy controls, ALS and PLS patients showed altered structural global network properties, as well as local topological alterations and decreased structural connectivity in sensorimotor, basal ganglia, frontal and parietal areas. PMA patients showed preserved global structure. Patient groups did not show significant alterations of functional network topological properties relative to controls. Increased local functional connectivity was observed in ALS patients in the precentral, middle and superior frontal areas, and in PLS patients in the sensorimotor, basal ganglia and temporal networks. In both ALS and PLS patients, structural connectivity alterations correlated with motor impairment, while functional connectivity disruption was closely related to executive dysfunctions and behavioral disturbances. Conclusions. This multicenter study showed widespread motor/extra-motor network degeneration in ALS and PLS, suggesting that graph analysis and connectomics might represent a powerful approach to detect upper motor neuron degeneration, extra-motor brain changes and network reorganization associated with the disease. Network-based advanced MRI provides an objective in vivo assessment of motor neuron diseases, delivering potential prognostic markers.
Data from: Habitat and social factors shape individual decisions and emergent group structure during baboon collective movement
For group-living animals traveling through heterogeneous landscapes, collective movement can be influenced by both habitat structure and social interactions. Yet research in collective behavior has largely neglected habitat influences on movement. Here we integrate simultaneous, high-resolution, tracking of wild baboons within a troop with a 3-dimensional reconstruction of their habitat to identify key drivers of baboon movement. A previously unexplored social influence – baboons' preference for locations that other troop members have recently traversed – is the most important predictor of individual movement decisions. Habitat is shown to influence movement over multiple spatial scales, from long-range attraction and repulsion from the troop's sleeping site, to relatively local influences including road-following and a short-range avoidance of dense vegetation. Scaling to the collective level reveals a clear association between habitat features and the emergent structure of the group, highlighting the importance of habitat heterogeneity in shaping group coordination.
Data set related to the manuscript "Mesoscopic simulations of the in situ NMR spectra of porous carbon based supercapacitors: Electronic structure and adsorbent reorganisation effects"
<p>Graphical files in the agr format for all the figures in the manuscript entitled "Mesoscopic simulations of the in situ NMR spectra of porous carbon based supercapacitors: Electronic structure and adsorbent reorganisation effects". Examples of input files for the lattice simulations are also provided.</p>
Sample locations and structural data
<p>Available data compile sample locations and structural measurements from several field campains between 2016 and 2018. The area of interest is in the westernmost part of the Mediterranean region, in the Betic Cordillera (Andalucia, Spain).</p> <p> </p> <p>The full dataset is linked to a publication in <em>Tectonics</em> Journal (Bessière et al., 2021):</p> <p>" Exhumation of the Ronda peridotite during hyper-extension: New structural and thermal constraints from the Nieves Unit (western Betic Cordillera, Spain)"</p>
Data from: Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta: Sphagnaceae) relative to taxonomy and geography
METHODS <p>RADseq analyses were applied to a sample of 384 collections representing the European, North American, and (to a lesser extent) Asian ranges of the complex. The data were subjected to maximum likelihood phylogenetic analyses and analyses of genetic structure using the software, STRUCTURE, and multivariate ordination approaches.</p> RESULTS <p>Defined phylogenetically, the S. recurvum complex includes S. angustifolium , S. fallax , S. flexuosum , S. pacificum , and S. recurvum , as distinct clades with little evidence of admixture within them. In addition, we resolved another clade, sister to either S. pacificum or S. fallax , that is currently unnamed and is referred to in this paper as S. "pseudopacificum." We confirm that S. balticum , a species not generally included in the S. recurvum complex, and S. obtusum , never associated with the complex by previous authors, are nested within it among the core species. Species with geographic ranges that span Europe, eastern North America, and Western North America exhibit a sister-group relationship between amphi-Atlantic and Pacific clades. European plants within S. flexuosum form a clade that is nested within a paraphyletic group of eastern North American plants; this species does not occur in western North America.</p> CONCLUSIONS <p>We recognize seven species in the amended S. recurvum complex, including S. balticum and S. obtusum , in addition to the informal clade, S. "pseudopacificum". Although we detected some geographically-correlated phylogenetic structure within widespread morphospecies, our RADseq data support the interpretation that these species have intercontinental geographic ranges. Please be aware that if you ask to have your user record removed, we will retain your name in the records concerning manuscripts for which you were an author, reviewer, or editor. In compliance with data protection regulations, you may request that we remove your personal registration details at any time. (Use the following URL: https://www.editorialmanager.com/ajb/login.asp?a=r). Please contact the publication office if you have any questions.</p>
Data from: Morphology and distribution of scales, dermal ossifications, and other non-feather integumentary structures in non-avialan theropod dinosaurs
<p class="MsoBodyText">Modern birds are typified by the presence of feathers, complex evolutionary innovations that were already widespread in the group of theropod dinosaurs (Maniraptoriformes) that include crown Aves. Squamous or scaly reptilian-like skin is, however, considered the plesiomorphic condition for theropods and dinosaurs more broadly. Here, we review the morphology and distribution of non-feathered integumentary structures in non-avialan theropods covering squamous skin and naked skin as well as dermal ossifications. The integumentary record of non-averostran theropods is limited to tracks, which ubiquitously show a covering of tiny reticulate scales on the plantar surface of the pes. This is consistent also with younger averostran body fossils, which confirm an arthral arrangement of the digital pads. Among averostrans, squamous skin is confirmed in<i> </i>Ceratosauria (<i>Carnotaurus</i>), Allosauroidea (<i>Allosaurus, Concavenator, Lourinhanosaurus</i>), Compsognathidae (<i>Juravenator</i>), and Tyrannosauroidea (<i>Santanaraptor, Albertosaurus, Daspletosaurus, Gorgosaurus, Tarbosaurus, Tyrannosaurus</i>), whereas dermal ossifications consisting of sagittate and mosaic osteoderms are restricted to <i>Ceratosaurus.</i> Naked, non-scale bearing skin is found in the contentious tetanuran <i>Sciurumimus</i>, possibly ornithomimosaurians (<i>Pelecanimimus</i>) and tyrannosauroids (<i>Santanaraptor</i>), and also on the patagia of scansoriopterygids (<i>Ambopteryx, Yi</i>). Scales are surprisingly conservative among non-avialan theropods compared to some dinosaurian groups (e.g., hadrosaurids); however, the limited preservation of tegument on most specimens hinders further interrogation. Scale patterns vary between and/or within body regions in <i>Carnotaurus</i>, <i>Concavenator</i> and <i>Juravenator</i>, and include polarised, snake-like ventral scales on the tail of the latter two genera. Unusual but more uniformly-distributed patterning also occurs in <i>Tyrannosaurus</i>, whereas feature scales are present only in <i>Albertosaurus</i> and <i>Carnotaurus.</i> Few theropods currently show compelling evidence for the cooccurrence of scales and feathers (e.g., <i>Juravenator,</i> <i>Sinornithosaurus</i>), although reticulate scales were probably retained on the mani and pedes of many theropods with a heavy plumage. Feathers and filamentous structures appear to have replaced widespread scaly integuments in maniraptorans<i>.</i> Theropod skin, and that of dinosaurs more broadly, remains a virtually untapped area of study and the appropriation of commonly-used techniques in other palaeontological fields to the study of skin holds great promise for future insights into the biology, taphonomy and relationships of these extinct animals.</p>
Data for "Advanced Structural Health Monitoring Method by Integrated Isogeometric Analysis and Distributed Fiber Optic Sensing"
<p>This dataset includes the experiment and simulation data of a new structural health monitoring system using distributed fiber optic sensing (DFOS) and Isogeometric Analysis (IGA).</p> <p>The experiment setup was a 5mm thick PVC pipe with a fiber optic cable wrapped around the outer surface of the pipe. The PVC pipe was subjected to an applied deformation and the distributed strains along the optical fiber was measured with a Neubrescope (NBX7031) instrument using Rayleigh backscattering technology.</p> <p>The simulation was performed using the in-house code JWRIAN-IGA developed in Joining and Welding Research Institute, Osaka University. The simulated data includes deformation, stress and strain distributions of the pipe, and projected one-dimensional fiber strains. The visualization files are post-processed with ParaView software.</p>
data for Newbury et al Short term fitness effects of bipartite interactions shape network structure of mutualistic and antagonistic communities
<p>speciescountdata.csv contains colony couts and plasmid detection from the main experiment.</p> <p>evonet.csv conatins colony counts of bacteria with and without plasmid pkjk5 from commuities where donors were o/ p ancestral/evolved. </p> <p>AOPV.csv contains optical density data for species a,o,p and v. column 1 is time in hours. Then columns alternate between a, o, p, s, v, a+,o+,p+,s+,v+,s+,v+ (where + denotes plasmid carriage) until column 49. After which the same patten continues, but these were grown with tetracycline. s did not grow at all in the 96-well plate this data was taken from. This is likely due to experimental error, so an additional well plate was used just for s (S.scv).</p> <p>S.csv contains optical density data for species s. column 1 is time in hours. then there are 6 colulmns of s and 6 columns of s+ until column 49. After this the same pattern continues but bacteria were grown with tetracycline.</p>
Structural Basis for Membrane Recruitment of ATG16L1 by WIPI2 in Autophagy Raw GUV Data
<p>Raw GUV data of fluorescent protein imaged on a Nikon A1 confocal microscope with a 63 × Plan 359 Apochromat 1.4 NA objective. Three biological replicates were performed for each experimental 360 condition. Identical laser power and gain settings were used during the course of all conditions.</p>
Fault trace data and supplementary table and figures of "Fault trace corrugation and segmentation as a measure of fault structural maturity"
<p>Fault trace data and supplementary information to the paper "Fault trace corrugation and segmentation as a measure of fault structural maturity" by Manighetti I., Mercier A., and de Barros L., Sept. 2021</p>
Data from: Fear dynamically structures the ocean's pelagic zone
<p><span>Fear of predation can have wide-ranging ecological effects.</span><span>This is especially true in the ocean's pelagic zone, the Earth's largest habitat, where vertical gradients in light and primary productivity force numerous taxa to migrate vertically each night to feed at the surface while minimizing risk from visual predators.</span><span> Despite its importance, and the fact that it is driven by spatial differences in perceived risk,</span><span> diel vertical migration (DVM) is rarely considered within the "landscape of fear"</span><span> framework</span><span>. It is also far from the only such process in the pelagic zone. We used continuous, year-long records from an upward-looking echosounder and broadband hydrophone at a cabled observatory off Central California, USA, to observe avoidance reactions by several groups of pelagic animals to the presence of their predators. As expected, vertical migration was ubiquitous, but we also observed behaviors at shorter and longer time-scales which were best explained by fear of predation. The presence of foraging odontocetes induced immediate diving behavior in mesopelagic sound-scattering layers, and schools of epipelagic fishes induced similar behaviors in layers of zooplankton and mesopelagic micronekton. At longer time scales, the presence of fish schools significantly deepened vertical migration, rearranging life throughout the water column. We argue that behavioral reactions to predation risk are common in the pelagic zone at a range of spatiotemporal scales and that our understanding of food webs and biogeochemical cycling in this immense biome will be incomplete unless we account for fear.</span></p>
Raw data for Investment casting of periodic aluminum cellular structures using slurry-cast table salt moulds
<p>This dataset includes the raw data used to draw the conclusions of the paper entitled "Investment casting of periodic aluminum cellular structures using slurry-cast table salt moulds". </p> <p>The work presents a precision-casting process specifically designed to manufacture periodic cellular structures.</p>
Dataset of Bnet values of 93,978 PDB-REDO structures analysed in "Quantifying and comparing radiation damage in the Protein Data Bank"
<p>Dataset of Bnet values, plus associated metadata (resolution, Rwork, Rfree, temperature, etc.), for 93,978 PDB-REDO structures analysed in the publication "Quantifying and comparing radiation damage in the Protein Data Bank"</p>
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
<p class="MsoNormal"><strong><u><span>Aim:</span></u></strong><span> Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow.</span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Taxon:</span></u></strong><span> <em>Dascyllus marginatus </em>(endemic) and <em>Dascyllus abudafur </em>(widespread)<em>.</em></span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Location:</span></u></strong><span> Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Methods:</span></u></strong><span> We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Results:</span></u></strong><strong><span> </span></strong><em><span>Dascyllus marginatus </span></em><span>inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. <em>Dascyllus abudafur</em> species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of <em>D. marginatus </em>had an order of magnitude higher genetic differentiation compared to <em>D. abudafur</em>, as well as several outlier loci (suggesting selective pressure), which were absent in <em>D. abudafur</em> despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Main conclusions:</span></u></strong><span> The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.</span></p>
Data for "Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics"
<p>We provide the raw data for the paper "Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics". The files hold time tagged and time resolved single photon data from experiments on immobilized structures as well on free diffusion structures. The files have PicoQuant's .ptu files-format.</p> <p>Additionally we provide the python scripts used to analyze these data sets.</p>
Data Used in "Close view of of the lightning attachment process unveils the streamer zone fine structure"
<p>This page contains high-speed video files as .gif and .cine files, for the complete video of Figure 2 (Movie S1 and S3). It also contains the video (Movie S2) from a second high-speed (Phantom V711) looking in a different direction that saw other UUL leaders not registered by the Phantom V2012 camera. There is also an Excel file containing the data analysis. The data uploaded here is sufficient to reproduce the results of the paper titled "Close view of of the lightning attachment process unveils the streamer zone fine structure", submitted for publication in Geophysical Research Letters.</p> <p><em>Instructions to watch the videos</em>: <strong>Movie S1.cine </strong>and<strong> Movie S2.cine:</strong></p> <p>Download and use the software Phantom Camera Control (PCC) available at:</p> <p><a href="https://www.phantomhighspeed.com/resourcesandsupport/phantomresources/pccsoftware">https://www.phantomhighspeed.com/resourcesandsupport/phantomresources/pccsoftware</a></p> <p>The Phantom Camera Control (PCC) software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems.</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.