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1,552 results for “patch”
Dataset for the Manuscript: Structural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut (in revision)
<p>This dataset provides the classical and QM/MM MD simulation trajectory data to the manuscript:</p> <p><strong>Structural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut</strong></p> <p>The data set contains classical MD simulations of AM0627 with three substrate peptides P1, P2, P9, and BT4244 with glycopeptides, as well as QM/MM metadynamics simulations for our manuscript. PDB files for Figures 4,5 and Figure S5-8,10 are also included.</p>
Patch quality and habitat fragmentation shape the foraging patterns of a specialist folivore
<p><span>Research on use of foraging patches has focused on why herbivores visit or quit patches, yet little is known about visits to patches over time. Food quality, as reflected by higher nutritional quality and lower plant defences, and physical patch characteristics, which offer protection from predators and weather, affect patch use and hence should influence their revisitation. Due to the potentially high costs of moving between patches, fragmented habitats are predicted to complicate foraging decisions of many animals. We aimed to determine how food quality, shelter availability and habitat fragmentation influence tree reuse by a specialist folivore, the koala, in a fragmented agricultural landscape. We GPS- tracked 23 koalas in northern New South Wales, Australia and collated number of revisits, average residence time, and average time-to-return to each tree. We measured tree characteristics including food quality (foliar nitrogen and toxic formylated phloroglucinol compounds, FPCs concentrations), tree size and tree connectedness. We also modelled the costs of locomotion between trees. Koalas re-visited isolated trees with high leaf nitrogen disproportionately often. They spent longer time in trees with high leaf nitrogen, and in large trees used for shelter. They took longer to return to trees with low leaf nitrogen. Tree connectivity reduced travel costs between patches, being either individual or groups of trees. FPC levels had no detectable effect on patch revisitation. We conclude that food quality and shelter drive koala tree re-visits. Scattered, isolated trees with nutrient-rich leaves are valuable resource patches for koalas despite movement costs to reach them. </span></p>
Text-fig. 18. Stereo images of fossil marine gastropod steinkerns from White Patch Fossil Site 1. in Stratigraphy, Chronology And Palaeontology Of The Tertiary Rocks Of The Cheringoma Plateau, Mozambique
Text-fig. 18. Stereo images of fossil marine gastropod steinkerns from White Patch Fossil Site 1.
Data from: Which plumage patches provide information about condition and success in a female fairy-wren?
<p>Recent evidence suggests that female ornaments can commonly act as signals. However, how signaling functions might be affected by the tendency for reduced ornament elaboration in relation to males is less well understood. We address this in mutually ornamented purple-crowned fairy-wrens. We investigated putatively ornamental (tail, ear coverts, crown) and non-ornamental (throat, back) plumage patches in females and compared our findings to previous studies in males. Both sexes have brown backs, buff-white throats, and turquoise-blue tails (bluer in males), while ear coverts are rufous in females and black in males. Both sexes also have a seasonal crown (slate-grey in females, black-and-purple in males). Dominant (breeder) females expressed more complete and greyer (more ornamented) crowns, although variation in coloration should not be discriminable by individuals. Unexpectedly, subordinates showed more colorful (saturated) rufous ear coverts, which should be discriminable. Condition dependence was only evident for crown completeness (% slate-grey cover). Females with more reddish-brown backs were more reproductively successful. Variation in plumage characteristics did not explain differential allocation by mates or chances of gaining dominance. Our outcomes were not entirely consistent with findings in males. The most notable disparity was for the crown, a signal used in male-male competition that in females seems to be expressed as an incomplete version of the male crown that is not associated with fitness benefits. Our study shows that in a species, multiple traits can vary in their information content and that female ornaments can sometimes be less informative than in males, even those that are produced seasonally.</p>
[3/3] Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation
<p>Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation</p>
[2/3] Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation
<p>Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation</p>
[1/3] Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation
<p>Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation</p>
Surface patch characteristics
<p>Introduction on how geometric characteristics are evaluated for a point cloud, which can be, e.g., a surface patch. First part shows how principal components depend on the data. When principal components are computed for every individual surface patch, they can be used to find dimensionality and direction estimates for them. The end part of the animation shows how the principal components of neighboring surface patches can be used for a more accurate direction estimate by finding a direction that perpendicular to the plane spanned by the smallest principal components.</p> <p>This animation was produced by the Inverse Problems research group in the Department of Mathematics at Tampere University of Technology (http://math.tut.fi/inversegroup).</p> <p>Animation created using Blender (http://www.blender.org).</p> <p>Music:<br> Brittle Rille Kevin MacLeod (http://incompetech.com)<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p> <p>Sound effects:<br> Whooshes - 18 - Wooshes - Various.wav<br> by koroshiya1 at http://www.freesound.org/<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p> <p>door_slam.wav<br> by primeval_polypod at http://www.freesound.org/<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p>
Creating surface patches
<p>Animation that shows how a point cloud can be partitioned into subsets called surface patches. These surface patches can be used to describe the local geometric properties of the point cloud. As each patch knows its neighbors, the patches can also be used to move along the point cloud through set expansion.</p> <p>This animation was produced by the Inverse Problems research group in the Department of Mathematics at Tampere University of Technology (http://math.tut.fi/inversegroup).</p> <p>Animation created using Blender (http://www.blender.org).</p> <p>Music:<br> The Complex Kevin MacLeod (http://incompetech.com)<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p>
Secondary data_exploration depth and size of outside patch
<p>Dataset containing secondary data regarding cell distribution. This data was used for the generation the plots about cell distribution related to the article: <strong>The distinctive chemotactic responses of three marine herbivore protists to DMSP and related compounds.</strong> Therefore, provides information about the spatial distribution and the zones of accumulation of three cultured dinoflagellates (<em>Karlodinium armiger, Gyrodinium dominans</em> and<em> Oxyrrhis marina</em>) responding DMSP gradients diffusing from a microcapillary. </p> <p>Nomenclature:</p> <p>lambda_in: <span>the depth of exploration inside the capillary (λ<sub>in</sub>) </span></p> <p>lambda_out: <span>the size of the cell patch outside of it (λ<sub>out</sub>)</span></p> <p>concentration: uM</p>
Data of SST patch experiments, Part3: control experiment
<p>This dataset is control experiments of the SST patch experiments, which can be used to test the statistical significances between the differences in conjugate patch experiments.</p>
patch-ch4
<p>Data and analysis code supporting "High spatial variability in wetland methane fluxes is tied to vegetation patch types"</p>
Input data of the multi-patch geometries used in: A. Farahat, H. M. Verhelst, J. Kiendl, M. Kapl, Isogeometric analysis for multi-patch structured Kirchhoff–Love shells, Computer Methods in Applied Mechanics and Engineering 411 (2023) 116060 DOI: 10.1016/j.cma.2023.116060
Open the record for dataset details and reuse information.
Fungal trait-environment relationships in wood-inhabiting communities of boreal forest patches
<p>Fungal traits can provide a mechanistic understanding of how wood-inhabiting fungi interact with their environment and how that influences community assembly in deadwood. However, fungal trait exploration is relatively new and almost no studies measure fungal traits in their environment. In this study we tested species- and trait-environment relationships in reproducing fungal communities inhabiting 571 Norway spruce (<em>Picea abies</em>) logs in 55 isolated forest patches (0.1-9.9 ha) of different naturalness types, located in Northern boreal Sweden. The studied patches were (1) semi-natural set-aside patches within highly managed landscapes, or (2) old-growth natural patches located in an unmanaged landscape. We tested species and trait relationships to deadwood substrate and forest patch variables. We measured mean fruit body size and density for each of the 19 species within communities. Traits assembled in relation to log decay stage and forest patch naturalness, illustrating the important role of deterministic environmental filtering in shaping reproducing wood-inhabiting fungal communities. Early decay stage communities had larger, less dense, annual fruiting bodies of half-resupinate type and were more often white-rot fungi. Species rich mid decay stage communities had mixed trait assemblages with more long lived perennial fruit bodies of intermediate size, and both brown- and white-rot fungi equally represented. Finally, late decay stage communities had smaller, denser and perennial fruit bodies, more often of the brown-rot type. The relationships between the studied traits and decay stages were similar in both set-aside and natural patches. However, set-aside semi-natural patches in highly managed landscapes more frequently supported species with smaller, perennial, and resupinate fruit bodies compared to natural patches in an unmanaged landscape.</p> <p><em>Synthesis</em></p> <p>We found that log decay stage was the primary driver of fungal community assembly of species and traits in isolated forest patches. Our results suggest that decay stage filters four reproduction traits (fruit body density, size, lifespan and type) and one resource-use trait (white or brown rot). Our results highlights, for the first time, that communities with diverse fungal reproductive traits are maintained foremost across all deadwood decay stages under different forest naturalness conditions.</p>
Data used in the publication "The sensitivity of streamer inception on the initial electron-ion patch"
<p>This data was used to generate the Figures in the publication "The sensitivity of streamer inception on the initial electron-ion patch".</p>
A Dataset of Multiple Types of Linux Kernel Patches
<p>We share a dataset of a nine-year history of patches (666,550 patches produced from December 2008 to December 2017) and related discussion recorded by the LKML project on the Linux kernel patchwork. To better help future studies, we analyzed the review results of these patches, and marked three types: accepted patches, rejected patches, and patches that are rejected because of the communication problem.</p>
Data of the Paper "How to Communicate when Submitting Patches: an Empirical Study of the Linux Kernel"
<p>This repository includes the data of the paper "How to Communicate when Submitting Patches: an Empirical Study of the Linux Kernel".</p> <p>It contains three parts:</p> <ol> <li>Related online documents.</li> <li>Original questionnaire of the survey.</li> <li>Survey results.</li> </ol> <p> </p>
Fig. 1 in The importance of isolated patches for maintaining local bird biodiversity and ecosystem function: a case study from the Pernambuco Center of Endemism, Northeast Brazil
Fig. 1. Rarefaction curve based at Mata do Cedro abundance and richness, state of Alagoas, Brazil.
Fig. 2 in The importance of isolated patches for maintaining local bird biodiversity and ecosystem function: a case study from the Pernambuco Center of Endemism, Northeast Brazil
Fig. 2. Functional dendrogram of species of birds found at Mata do Cedro, state of Alagoas, Brazil.
EOL Dinosauria Patch (dino)
<p>Dinosaurs, including extinct birds to complement coverage of the COL & IOC data sets.</p> <h3>References</h3> <p>Averianov, Alexander, and Hans-Dieter Sues. 2019. Morphometric Analysis of the Teeth and Taxonomy of the Enigmatic Theropod Richardoestesia from the Upper Cretaceous of Uzbekistan. Journal of Vertebrate Paleontology 39(3): e1614941. <a href="https://doi.org/10.1080/02724634.2019.1614941">https://doi.org/10.1080/02724634.2019.1614941</a></p> <p>Baron, Matthew G., David B. Norman, and Paul M. Barrett. 2017. A New Hypothesis of Dinosaur Relationships and Early Dinosaur Evolution. Nature 543(7646):501–6. <a href="https://doi.org/10.1038/nature21700">https://doi.org/10.1038/nature21700</a></p> <p>Benton, Michael. 2014. Vertebrate Palaeontology. John Wiley & Sons. Brocklehurst, Neil, Paul Upchurch, Philip D. Mannion, and Jingmai O__Connor. 2012. The Completeness of the Fossil Record of Mesozoic Birds: Implications for Early Avian Evolution. PLoS ONE 7(6). <a href="https://doi.org/10.1371/journal.pone.0039056">https://doi.org/10.1371/journal.pone.0039056</a></p> <p>Brusatte, Stephen L., Jingmai K. O__Connor, and Erich D. Jarvis. 2015. The Origin and Diversification of Birds. Current Biology 25(19): R888–98. <a href="https://doi.org/10.1016/j.cub.2015.08.003">https://doi.org/10.1016/j.cub.2015.08.003</a></p> <p>Fastovsky, D.E., Weishampel, D.B., 2016. Dinosaurs: A Concise Natural History, third ed. New York: Cambridge University Press. Foth, Christian, and Oliver W. M. Rauhut. 2017. Re-Evaluation of the Haarlem Archaeopteryx and the Radiation of Maniraptoran Theropod Dinosaurs." BMC Evolutionary Biology 17. <a href="https://doi.org/10.1186/s12862-017-1076-y">https://doi.org/10.1186/s12862-017-1076-y</a></p> <p>Jarvis, Erich D., Siavash Mirarab, Andre J. Aberer, Bo Li, Peter Houde, Cai Li, Simon Y. W. Ho, et al. 2014. Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds. Science 346(6215):1320–31. <a href="https://doi.org/10.1126/science.1253451">https://doi.org/10.1126/science.1253451</a></p> <p>Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, and A. O. Mooers. 2012. The Global Diversity of Birds in Space and Time. Nature 491(7424): 444–48. <a href="https://doi.org/10.1038/nature11631">https://doi.org/10.1038/nature11631</a></p> <p>Jønsson, Knud A., Pierre-Henri Fabre, Robert E. Ricklefs, and Jon Fjeldså. 2011. Major Global Radiation of Corvoid Birds Originated in the Proto-Papuan Archipelago. Proceedings of the National Academy of Sciences 108(6):2328–33. <a href="https://doi.org/10.1073/pnas.1018956108">https://doi.org/10.1073/pnas.1018956108</a></p> <p>Ksepka, Daniel T., Julia A. Clarke, Sterling J. Nesbitt, Felicia B. Kulp, and Lance Grande. 2013. Fossil Evidence of Wing Shape in a Stem Relative of Swifts and Hummingbirds (Aves, Pan-Apodiformes). Proceedings of the Royal Society B: Biological Sciences 280(1761). <a href="https://doi.org/10.1098/rspb.2013.0580">https://doi.org/10.1098/rspb.2013.0580</a></p> <p>Langer, Max C., Martín D. Ezcurra, Oliver W. M. Rauhut, Michael J. Benton, Fabien Knoll, Blair W. McPhee, Fernando E. Novas, Diego Pol, and Stephen L. Brusatte. 2017. Untangling the Dinosaur Family Tree. Nature 551(7678): E1–3. <a href="https://doi.org/10.1038/nature24011">https://doi.org/10.1038/nature24011</a></p> <p>Mayr, Gerald. 2014. The origins of crown group birds: Molecules and fossils. Palaeontology 57:231–242. <a href="https://doi.org/10.1111/pala.12103">https://doi.org/10.1111/pala.12103 </a></p> <p>Mayr, Gerald. 2016. Avian Evolution: The Fossil Record of Birds and Its Paleobiological Significance. 1st ed. John Wiley & Sons, Ltd, 2016. <a href="https://doi.org/10.1002/9781119020677">https://doi.org/10.1002/9781119020677</a> </p> <p>Mayr, Gerald, Thomas Lechner, and Madelaine Böhme. 2020. The Large-Sized Darter Anhinga pannonica (Aves, Anhingidae) from the Late Miocene Hominid Hammerschmiede Locality in Southern Germany. PLOS ONE 15(5):e0232179. <a href="https://doi.org/10.1371/journal.pone.0232179">https://doi.org/10.1371/journal.pone.0232179</a></p> <p>Mayr, Gerald, and Marco Pavia. 2014. On the True Affinities of Chenornis graculoides Portis, 1884, and Anas lignitifila Portis, 1884—an Albatross and an Unusual Duck from the Miocene of Italy. Journal of Vertebrate Paleontology 34(4):914–23. <a href="https://doi.org/10.1080/02724634.2013.821076">https://doi.org/10.1080/02724634.2013.821076</a></p> <p>Nesbitt, Sterling J., Daniel T. Ksepka, and Julia A. Clarke. 2011. Podargiform Affinities of the Enigmatic Fluvioviridavis platyrhamphus and the Early Diversification of Strisores (Caprimulgiformes + Apodiformes). PLoS ONE 6(11). <a href="https://doi.org/10.1371/journal.pone.0026350">https://doi.org/10.1371/journal.pone.0026350</a></p> <p>Paleobiology Database, PBDB, accessed at <a href="https://paleobiodb.org">https://paleobiodb.org </a></p> <p>Pietri, Vanesa L. De, and Gerald Mayr. 2014. The Phylogenetic Relationships of the Early Miocene Stork Grallavis edwardsi, with Comments on the Interrelationships of Living Ciconiidae (Aves). Zoologica Scripta 43(6):576–85. <a href="https://doi.org/10.1111/zsc.12074">https://doi.org/10.1111/zsc.12074</a></p> <p>Pietri, VL De, R. P. Scofield, S. J. Hand, A. J. D. Tennyson, and T. H. Worthy. 2016. Sheathbill-like Birds (Charadriiformes: Chionoidea) from the Oligocene and Miocene of Australasia." Journal of the Royal Society of New Zealand 46(3–4):181–99. <a href="https://doi.org/10.1080/03036758.2016.1194297">https://doi.org/10.1080/03036758.2016.1194297</a></p> <p>Suárez, William. 2020. The Fossil Avifauna of the Tar Seeps Las Breas de San Felipe, Matanzas, Cuba. Zootaxa 4780(1):1–53. <a href="https://doi.org/10.11646/zootaxa.4780.1.1">https://doi.org/10.11646/zootaxa.4780.1.1</a></p> <p>Warheit, Kenneth I. 2002. The Seabird Fossil Record and the Role of Paleontology in Understanding Seabird Community Structure. CRC Press. Worthy, Trevor H., and Jacqueline M. T. Nguyen. 2020. An Annotated Checklist of the Fossil Birds of Australia.Transactions of the Royal Society of South Australia 144(1):66–108. <a href="https://doi.org/10.1080/03721426.2020.1756560">https://doi.org/10.1080/03721426.2020.1756560</a></p> <p>Yuri, Tamaki, Rebecca T. Kimball, John Harshman, Rauri C. K. Bowie, Michael J. Braun, Jena L. Chojnowski, Kin-Lan Han, et al. 2013. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2(1):419–44. <a href="https://doi.org/10.3390/biology2010419">https://doi.org/10.3390/biology2010419</a></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.