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380 results for “DIAMOND”
Crystal Structures of SARS-CoV-2 main protease with screening fragments and COVID Moonshot compounds from the XChem facility at Diamond Light Source
<p>Bulk repositiory of structures of SARS-CoV-2 main protease in complex with fragment molecules from inital XChem screen and designed COVID Moonshot inhibtor compounds. Each structure has a PDB ID, coordinate file, structure factor file, ligand restraint (cif) and PANDDA event maps (as appropriate).</p><p>2023-10-26 - updated to include <strong>all </strong>initial fragment screening hits alongside follow up compounds</p>
The training dataset and HamGNN model for diamond silicon
Open the record for dataset details and reuse information.
MAP. Distribution of Chinese Skleroprotopus species. Star, S. confucius; triangle, S. laticoxalis laticoxalis; square, S. laticoxalis longus; circle, S. membranipedalis; hexagon, S. securifer sp. nov.; diamond, S. serratus. in The millipede genus Skleroprotopus Attems, 1901 (Diplopoda, Julida, Mongoliulidae) in China, with description of a new species
MAP. Distribution of Chinese Skleroprotopus species. Star, S. confucius; triangle, S. laticoxalis laticoxalis; square, S. laticoxalis longus; circle, S. membranipedalis; hexagon, S. securifer sp. nov.; diamond, S. serratus.
Viral RefSeq databases for Centrifuge, Kraken2 and DIAMOND
<p>Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. </p> <p>In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. </p> <p>Across most simulations, more than 228 out of the 233 simulated viruses are recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovers only around one third. Overall, Centrifuge and Kraken2 have the best performance with the highest values of sensitivity and precision. We found that deamination damage has little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieves the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend to verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.</p>
Source data and code for "A diamond voltage imaging microscope"
<p>This data set contains both the source data and code used to generate figures and establish the conclusions of "A diamond voltage imaging microscope" (DOI: https://doi.org/10.1038/s41566-022-01064-1). It contains:</p> <p>- Raw source data (e.g., video data, fluorescence spectra).</p> <p>- Processed source data (e.g., calibration maps, calculated vales of contrast, sensitivity, etc).</p> <p>- Analysis code used to generate processed source data (this includes both MATLAB and Python scripts. MATLAB scripts require at least version R2021A).</p> <p>- Simulation code (Python) used to fit the equivalent RC circuit model described in the work to the experimental data.</p>
FIGURE. Distribution maps of Drosera species in northern Brazil (AM and RR states). a, D. amazonica (circles) and D. roraimae (triangles). b, D. biflora (stars), D. esmeraldae (diamonds) and D. hirticalyx (triangles). in A synopsis of the genus Drosera (Droseraceae) in Brazil
FIGURE. Distribution maps of Drosera species in northern Brazil (AM and RR states). a, D. amazonica (circles) and D. roraimae (triangles). b, D. biflora (stars), D. esmeraldae (diamonds) and D. hirticalyx (triangles).
FIGURE. Distribution maps of Drosera species endemic to Minas Gerais. a, D. ascendens (circles), D. quartzicola (triangles) and D. villosa (stars). b, D. camporupestris (triangles) and D. graomogolensis (circles). c, D. chimaera (stars), D. schwackei (triangles) and D. spirocalyx (diamonds). d, D. graminifolia (triangles), D. magnifica (star) and D. spiralis (circles). in A synopsis of the genus Drosera (Droseraceae) in Brazil
FIGURE. Distribution maps of Drosera species endemic to Minas Gerais. a, D. ascendens (circles), D. quartzicola (triangles) and D. villosa (stars). b, D. camporupestris (triangles) and D. graomogolensis (circles). c, D. chimaera (stars), D. schwackei (triangles) and D. spirocalyx (diamonds). d, D. graminifolia (triangles), D. magnifica (star) and D. spiralis (circles).
Supplementary material 1 from: Lambert SM, Hutter CR, Scherz MD (2017) Diamond in the rough: a new species of fossorial diamond frog (Rhombophryne) from Ranomafana National Park, southeastern Madagascar. Zoosystematics and Evolution 93(1): 143-155. https://doi.org/10.3897/zse.93.10188
File S1 : Explanation note: This file contains a PDF-embedded interactive 3D model of the skeleton of the holotype of Rhombophryne nilevina sp. n., KU 340897, generated via X-ray micro-Computed Tomography. The model can be opened in Adobe® Acrobat Pro or Reader, versions IX and above. To activate it, click the image.
FIGURE 1 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada
FIGURE 1. Sampling localities of populations included for morphological (a) and DNA (b) collections within the hydrological Great Basin and surrounding states. a) Colors indicate species-specific populations measured for morphological analysis. b) Colors correspond with localized species and B. boreas colors correspond with major mtDNA haplotype clades (ONV- Oregon- NW Nevada (yellow), HL-Humboldt-Lahontan (blue), M-Mojave (aqua)) identified in Tracy et al. (in progress) molecular study of B. boreas diversity. Maps created using ArcGIS software by ESRI (2011: Release 10).
FIGURE 5 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada
FIGURE 5. Discriminant function analysis (DFA). Cross validated DFA using 14 size corrected morphological characters measured from 380 live adult toads (Fig. 1a) examined within the hydrological Great Basin Bufo (Anaxyrus) boreas species complex. Species identified as B. boreas (red circle), B. nelsoni (blue diamond), B. exsul (green circle), and B. williamsi (yellow square).
FIGURE 4 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada
FIGURE 4. Photographs of Bufo (Anaxyrus) williamsi sp. nov. holotype (CAS 259271). Adult male toad presented live: (a) dorsal view and (b) ventral view; and preserved: (c) dorsal view and (d) ventral view. Photographs taken by M.R.Gordon.
Reprocessed / rebinned to 0.5 degree images: Beta-Lactamase X-ray diffraction data recorded at Diamond Light Source I04 as part of commissioning & development
<p>Derived from https://zenodo.org/record/841060; made more compact (though no longer "raw" data) for use in tutorials</p>
FIGURE 3 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada
FIGURE 3. Molecular examination of Bufo (Anaxyrus) boreas species complex.The TCS haplotype network was constructed using 246 sequences (1622 aligned sites) obtained from toad sampling (Fig.1b) resulting in 72 unique haplotypes, with circle sizes corresponding with the number of individuals of a particular haplotype. Haplotype colors correspond geographically (Fig. 1b) and to localized species (B. canorus (purple), B. exsul (green) and B. nelsoni (orange)) and highlight the genetic divergence of B. williamsi (red). The condensed phylogeny identifying Great Basin Bufo (Anaxyrus) boreas species complex major haplotype clades: maximum likelihood of 10 samples (1436 aligned sites) using GTR +G+I evolutionary model. The terminals are identified by taxon name and followed by locality of collection for B. boreas. Bufo williamsi, noted with a red circle, is sister to boreas of the HL clade. Heavy bars correspond with major haplotype clades.
FIGURE 2 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada
FIGURE 2. Bufo (Anaxyrus) boreas species complex distribution. a) Bufo (Anaxyrus) boreas distribution (shown in brown) across the Western United States with hydrological Great Basin shown with black outline and hash mark interior; b) Bufo (Anaxyrus) boreas species complex and ranges for toads including new species, illustrating the narrow distribution of localized endemics. Spatial data for all toads except B. williamsi provided by IUCN (2015). Images taken by M.R.Gordon except B. canorus with photo credit to G. Nafis.
FIGURE 6 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada
FIGURE 6. Major and minor groups identified: Bayesian inference phylogenetic tree constructed from analyses from unique haplotype sequences of 1622bp fragment of the control region of the mitochondrial genome (Fig. 1b; n = 308). Posterior probabilities are shown. Haplotype number (n = 72) and sampling locality comprise terminal ends of tree and two haplotypes of the root are shown. Minor groups include localized species: Bufo (Anaxyrus) nelsoni (green), B. exsul (orange), B. canorus (purple), B. williamsi (red) and undescribed divergent species (black). Large bars identify major groups, which include populations of B. boreas, sampled within the hydrological Great Basin (Fig. 1b).
Data from crystal of Leucine-Rich Repeat Protein from Leptospira interrogans recorded during routine commissioning on Diamond Light Source beamline I04
<p>Samples as part of ongoing research / collaboration; for more details see https://www.ncbi.nlm.nih.gov/pubmed/26057675</p>
Imaging the atomic structure and local chemistry of platelets in natural type Ia diamond
<p>The upload contains raw data for the manuscript entitled "Imaging the atomic structure and local chemistry of platelets in natural type Ia diamond" accepted for publication in Nature Materials.</p>
Diamond-turned GaAs WGMR with million optical Q factor, L. M. Platt, M. I. Suresh, F. Azeem, L. S. Trainor, and H. G. L. Schwefel, Zenodo 2024
<p>Data sets corresponding to plotted figures in the manuscript titled "Single-point-diamond-turned GaAs disk resonator with a million optical quality factor," by L. M. Platt et al. </p>
Replication Data for: (111)-oriented, single crystal diamond tips for nanoscale scanning probe imaging of out-of-plane magnetic fields
<p>Data repository for: <strong>(111)-oriented, single crystal diamond tips for nanoscale scanning probe imaging of out-of-plane magnetic fields</strong></p> <p><em>Data description.pdf </em>describes the uploaded data.<br> <em>Data.xlsx</em> is the data represented in the paper.</p>
FIG. 3 in Plasma Vitellogenin and Testosterone in Diamond-backed Terrapins (Malaclemys terrapin) during the Nesting Season in Coastal New Jersey
FIG. 3. Plasma testosterone (A) and vitellogenin (B) concentrations in relation to midline plastron length in Diamond-backed Terrapins captured during early (June; green triangles), middle (early July; blue squares), and late (late July–early August; red circles) nesting season at the Cape May Peninsula, New Jersey and the Hackensack Meadowlands, New Jersey.
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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)
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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.