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82 results for “X-ray structures”
Text-fig. 7. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a) Holotype; seed in lateral view showing seed shape; note that the seed is broken near the lower surface of the hilum (S174345). b) Oblique apical view of micropylar-hilar region of holotype showing slightly ruptured micropylar slit (mi) in the outer integument and two bulging and abraded areas (arrow heads) close to hilum. c) Seed in oblique lateral-raphal view showing the two bulging structures (arrow heads) immediately adjacent to the lower edge of the hilum (S174472). d) Tangential, longitudinal cut (cut at yz0131) through the seed coat of seed in (7c) showing the undulate anticlinal cell walls of the exotesta cells that are thickest towards the outside and thinner towards the inside. Scale bars = 500 µm (a–c); 250 µm (d). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 7. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a) Holotype; seed in lateral view showing seed shape; note that the seed is broken near the lower surface of the hilum (S174345). b) Oblique apical view of micropylar-hilar region of holotype showing slightly ruptured micropylar slit (mi) in the outer integument and two bulging and abraded areas (arrow heads) close to hilum. c) Seed in oblique lateral-raphal view showing the two bulging structures (arrow heads) immediately adjacent to the lower edge of the hilum (S174472). d) Tangential, longitudinal cut (cut at yz0131) through the seed coat of seed in (7c) showing the undulate anticlinal cell walls of the exotesta cells that are thickest towards the outside and thinner towards the inside. Scale bars = 500 µm (a–c); 250 µm (d).
Text-fig. 43. Synchrotron radiation X-ray tomographic microscopy SRXTM images of "Tricarpellate flower sp. 2"; Catefica locality, Portugal. a) Lateral view of floral structure (volume rendering) showing the apical projection of the carpels and the semiinferior organization; b) Apical view of floral structure (volume rendering) showing the triangular shape of the hypanthial rim, the tricarpellate ovary with a single apical style; note that one locule is fully developed while the other two are collapsed; note also slits of unknown nature in the corners of the triangular hypanthial rim (arrows); c) Transverse section (orthoslice xy0712) close to the floral apex showing the locule of the one fully developed carpel with ovules borne along ventral placentae; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; d) Longitudinal section (orthoslice xz0858) through the locule of the one fully developed carpel showing the semi-inferior organization and ovules arranged along the full length of the carpel; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; e) Tangential longitudinal section (orthoslice yz1019) through the one fully developed locule, showing the densely packed ovules and the amorphous substance (asterisk) with which they are associated. Specimen, Catefica 50-S174901 (a–e). Scale bars = 300 Μm (a–e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 43. Synchrotron radiation X-ray tomographic microscopy SRXTM images of "Tricarpellate flower sp. 2"; Catefica locality, Portugal. a) Lateral view of floral structure (volume rendering) showing the apical projection of the carpels and the semiinferior organization; b) Apical view of floral structure (volume rendering) showing the triangular shape of the hypanthial rim, the tricarpellate ovary with a single apical style; note that one locule is fully developed while the other two are collapsed; note also slits of unknown nature in the corners of the triangular hypanthial rim (arrows); c) Transverse section (orthoslice xy0712) close to the floral apex showing the locule of the one fully developed carpel with ovules borne along ventral placentae; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; d) Longitudinal section (orthoslice xz0858) through the locule of the one fully developed carpel showing the semi-inferior organization and ovules arranged along the full length of the carpel; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; e) Tangential longitudinal section (orthoslice yz1019) through the one fully developed locule, showing the densely packed ovules and the amorphous substance (asterisk) with which they are associated. Specimen, Catefica 50-S174901 (a–e). Scale bars = 300 Μm (a–e).
Text-fig. 44. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, d) images of "Hexacarpellate flower". a) Lateral view of flower showing epigynous organization with remains of tepals inserted at top of the hypanthium; b) Detail of apical part of flower showing laminar structures (arrows) that may be stamen bases, adhering to, or fused with, the tepals; c) Longitudinal section (orthoslice yz0540) of flower through the median plane showing the epigynous organization and central axis with ovules (arrows); d) Transverse section (orthoslice xy1250) through the ovary of the flower showing the hexagonal outline, the six locules and ovules (arrows) borne near the center of the gynoecium. Specimen, Catefica 153-S174313 (a–d). Scale bars = 300 Μm (a, c), 100 Μm (b, d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 44. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, d) images of "Hexacarpellate flower". a) Lateral view of flower showing epigynous organization with remains of tepals inserted at top of the hypanthium; b) Detail of apical part of flower showing laminar structures (arrows) that may be stamen bases, adhering to, or fused with, the tepals; c) Longitudinal section (orthoslice yz0540) of flower through the median plane showing the epigynous organization and central axis with ovules (arrows); d) Transverse section (orthoslice xy1250) through the ovary of the flower showing the hexagonal outline, the six locules and ovules (arrows) borne near the center of the gynoecium. Specimen, Catefica 153-S174313 (a–d). Scale bars = 300 Μm (a, c), 100 Μm (b, d).
Text-fig. 33. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a, c) and scanning electron microscope (SEM, b, d) images of Paisia pantoporata (a–c) and?Paisia sp. (d); Catefica locality, Portugal. a) Lateral view (volume rendering) of flower showing the carpels (c) and the fleshy tepals (t) that have a slightly bulge near the base; b) Pollen grains in situ from stamen showing scattered pores and spiny supratectal ornamentation; c) Transverse section (orthoslice xz1024) through flower showing the pentamerous organization with five tepals (green) five stamens (yellow) and five carpels (red) all on the same radii; d) Lateral view of floral structure with three free carpels borne on the swollen receptacle that has poorly defined facets at the apex indicating the former presence of perianth parts. Specimens, Catefica 49-S101214 (a, c), Catefica 50-S170188 (b), Catefica MM125-P0292 (d). Scale bars = 300 Μm (a, c, d), 6 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 33. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a, c) and scanning electron microscope (SEM, b, d) images of Paisia pantoporata (a–c) and?Paisia sp. (d); Catefica locality, Portugal. a) Lateral view (volume rendering) of flower showing the carpels (c) and the fleshy tepals (t) that have a slightly bulge near the base; b) Pollen grains in situ from stamen showing scattered pores and spiny supratectal ornamentation; c) Transverse section (orthoslice xz1024) through flower showing the pentamerous organization with five tepals (green) five stamens (yellow) and five carpels (red) all on the same radii; d) Lateral view of floral structure with three free carpels borne on the swollen receptacle that has poorly defined facets at the apex indicating the former presence of perianth parts. Specimens, Catefica 49-S101214 (a, c), Catefica 50-S170188 (b), Catefica MM125-P0292 (d). Scale bars = 300 Μm (a, c, d), 6 Μm (b).
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b).
Supplementary data for article 'Estimating and abstracting the 3D structure of feline bones using neural networks on X-ray (2D) images'
<p>3D DICOM volumes (CT scans) of feline femora, PNGs generated from them as DRRs using MeVisLab, and STLs generated from the DICOM volumes with MIMICS or MeshLab. Software to work with these files can be found at http://doi.org/10.5281/zenodo.3829423</p>
X-ray structure ensemble refinement of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P21212)
<p>X-ray structure ensemble refinement of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P21212). Raw diffraction images are available on Zenodo: 10.5281/zenodo.4086066. A single conformer model was deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV8">7AV8</a>. Refinement was carried out with <a href="https://www.phenix-online.org/documentation/reference/ensemble_refinement.html">phenix.ensemble_refinement</a> and the repository contains all input and output files:</p> <p>Input:</p> <ul> <li>mx8421v63_xPHIPAx1521_free.mtz</li> <li>refine9.pdb</li> </ul> <p>Output:</p> <ul> <li>PHIPA-P21212_ensemble_refinement_ensemble.geo</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.pdb</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.mtz</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.log</li> </ul>
Atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years ‘on the shelf’
<p>These are the raw diffraction images for crystals 1 and 2 underpinning PDBe code 5LXW.</p>
Raw output data for "Covalency in actinide(IV) hexachlorides in relation to the chlorine K-edge X-ray absorption structure", DOI: 10.1039/D1SC06454A
<p>This repository contains raw output files related to the following article:</p> <p>Authors: Dumitru-Claudiu Sergentu and Jochen Autschbach<br> Title: Covalency in Actinide(IV) Hexachlorides in Relation to Chlorine K-Edge X-ray Absorption Structure<br> DOI: https://doi.org/10.1039/D1SC06454A</p> <p>Each archive: 1) ThCl6.rar 2) UCl6.rar 3) NpCl6.rar and 4) PuCl6.rar<br> contains output data produced by ADF (raw DFT outputs associated with the article, the ADF program can be found at: https://www.scm.com/product/adf/) and OpenMolcas (raw RASSCF and RASSI outputs associated with the article, the OpenMolcas program can be found at: https://gitlab.com/Molcas/OpenMolcas). Each folder in the archives contains 00README.txt files describing its content(s).</p> <p> </p> <p> </p>
Data for publication: Nanomechanical and Structural Study of Au38 Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity
<p>Original data of Figures published in:</p> <p><strong>Nanomechanical and Structural Study of Au<sub>38</sub> Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity</strong></p> <p>Journal of Colloid and Interface Science, 2022, Michal Swierczewski<sup>,</sup> Alexis Chenneviere, Lay-Theng Lee, Plinio Maroni and Thomas Bürgi*<sup>[</sup></p> <p> </p>
Compounds with multi-target activity from X-ray structures, corresponding analog series, and associated scaffolds
<p>A total of 702 crystallographic ligands with activity against multiple targets from different protein families (multi-family ligands) were extracted from the Protein Data Bank (PDB). These ligands are made available as aromatic non-stereo SMILES strings together with their target information. A subset of these ligands were also found in the ChEMBL database yielding additional target annotations. Target and family assignments were made following the UniProt classification scheme. In addition, 133 analog-series-based (ASB) scaffolds were derived from series of PDB ligands and structural analogs identified in ChEMBL, which are also made available. For each ASB scaffold, the number of analogs, targets, and target families is provided (union of PDB and ChEMBL annotations).</p>
Expression test and purification of SETDB1 catalytic domain constructs' for structural studies by X-ray crystallography.
<p><strong>Experiment: </strong>Expression test and purification of SETDB1 catalytic domain constructs’ for structural studies by X-ray crystallography.</p> <p><strong>Aim:</strong> In the present section of this study, we focused on the development of efficient bacterial expression systems to produce large amounts of soluble SETDB1 catalytic domain for structural studies. This report involves a summary of expression test results of different fragments of SETDB1 and purification of various fusion proteins.</p>
Data and Scripts for the Article "Structural Descriptors and Information Extraction from X-ray Emission Spectra: Aqueous Sulfuric Acid"
<p>Data and scripts for the article titled "Structural Descriptors and Information Extraction from X-ray Emission Spectra: Aqueous Sulfuric Acid".</p> <p>For further details on the contents, see the "readme.md"-file.</p> <p>Article available at <a href="https://doi.org/10.1039/D4CP02454K">10.1039/D4CP02454K</a>.</p>
X-ray diffraction data on the crystal structures of Tris-bound β-glucosidase from Thermoanaerobacterium saccharolyticum
<p>X-ray diffraction data of Tris-bound β-glucosidase from Thermoanaerobacterium saccharolyticum</p> <p>Data type: raw data<br>Data format: cbf</p> <p>Data <br>1. TsaBgl-Tris Data I <br>2. TsaBgl-Tris Data II<br>3. TsaBgl-Tris Data III </p>
Effect of intense x-ray free-electron laser transient gratings on the magnetic domain structure of Tm:YIG
<p>Dataset for the publication "Effect of intense x-ray free-electron laser transient gratings on the magnetic domain structure of Tm:YIG" by V. Ukleev, et al.</p>
RNA 3D structure modeling by fragment assembly with Small Angle X-ray Scattering restraints
<p>Structure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution RNA 3D structure determination efforts, however, are not keeping up with the pace of discovery of new non-coding RNA sequences. This increases the importance of computational approaches and low-resolution experimental data, such as from the Small Angle X-ray Scattering experiments. We present RNA Masonry, a computer program and a web service for a fully automated modeling of RNA 3D structures. It assemblies RNA fragments into geometrically plausible models that meet user-provided secondary structure constraints, restraints on tertiary contacts and Small Angle X-ray Scattering data. We illustrate the method description with detailed benchmarks and its application to structural studies of viral RNAs with SAXS restraints.</p>
Identifying the variety of jovian X-ray auroral structures: tying the morphology of X-ray emissions to associated magnetospheric dynamics
<p>The data used in Weigt et al., study <strong><em>"Identifying the variety of jovian X-ray auroral structures: tying the morphology of X-ray emissions to associated magnetospheric dynamics"</em>.</strong> The README.pdf explains what data is used to produce each Figure in the article with links to the Chandra archive and other data repositories. Pipeline to analyse data can be found here: </p> <pre><a href="https://doi.org/10.5281/zenodo.7380282">https://doi.org/10.5281/zenodo.7380282</a> </pre>
Supplementary data from: Early vertebrate biomineralisation and eye structure determined by synchrotron X-ray analyses of Silurian jawless fish
Open the record for dataset details and reuse information.
A two-frame movie of X-ray induced structural dynamics in single free nanoparticles
Open the record for dataset details and reuse information.
Raw data: Electronic and Structural Property Comparison of a Novel vs. a Commercial Iridium-based OER Catalysts Enabled by Operando Ir L3-edge X-ray Absorption Spectroscopy
<p>Raw data for the manuscript titled:</p> <p><strong>Electronic and Structural Property Comparison of a Novel vs. a Commercial Iridium-based OER Catalysts Enabled by <em>Operando </em>Ir L3-edge X-ray Absorption Spectroscopy</strong></p> <p> </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)
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DANDI Archive for NWB datasets
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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.