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706 results for “molecular complexes”
Molecular and Taxonomic Reevaluation of the Digitaria filiformis Complex (Poaceae) including a Globally Extinct, Single Site Endemic from New Hampshire, USA, and a New Species from Mexico
<p>We examine the <em>Digitaria filiformis </em>complex, to determine the proper taxonomic rank and rarity of each taxon. The taxonomy of the <em>D. filiformis </em>complex is highly debated and includes two widespread species, <em>D. filiformis </em>and <em>D. villosa</em>; a possibly extinct species endemic to a single-site in New Hampshire, <em>D. laeviglumis</em>; and a rare species of southern Florida and the West Indies, <em>D.</em><em> dolichophylla. </em>We conducted morphologic comparisons and molecular analysis of the four members of the <em>D. filiformis</em> complex, together with specimens from Mexico and Venezuela purportedly identified as <em>D. laeviglumis</em> (morphology only). Based on results of phylogenetic analyses of plastid and nuclear ITS sequences and morphologic comparisons, we recognize five species in the <em>D. filiformis </em>complex, including a newly described Mexican endemic <em>D. glabrifloris. </em>After field investigation we have moved the global rank of <em>D. laeviglumis </em>from globally historical (GH) to extinct (GX), as there is virtually no likelihood of rediscovery. <em>Digitaria</em><em> dolichophylla </em>is much rarer than previously recognized, moving from secure (T5) to imperiled with extinction (G2).</p>
Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (replicate 1)
<p>Replicate simulation 1/4</p> <p>Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation. </p> <p>Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.</p>
Dataset related to article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant".
<p><em>The files contain raw data related to the article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant", available from <a href="https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/full">https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/ful</a>l.</em></p> <p>File <strong>"Genetic and clinical data"</strong>:</p> <ul> <li>In the sheet "485 aHUS patients" are reported data obtained from the screening of 485 unrelated patients with aHUS including rare variants (RVs) in complement disease-associated genes (<em>CFH, CD46, CFI, C3, CFB </em>and <em>THBD</em>), the presence of <em>CFH-CFHR</em> genomic rearrangements and/or anti-FH antibodies.</li> <li>In the sheet "Pedigrees with c.286+2T>G" are listed all pedigrees carrying the c.286+2T>G variant, the diseases status of all subjects and the age of disease onset of patients. In bold are indicated pedigrees (n=7) used to study the penetrance of aHUS in c.286+2T>G carriers.</li> <li>In the sheet "Haplotypes" are reported genotypes used to evaluate the association between the presence of <em>CFH-H3</em> and <em>CD46<sub>GGAAC</sub></em> risk haplotypes and aHUS. Results of this analysis are reported in Table 3 of the published paper.</li> <li>In the sheet "Raw data Fig.2" are reported data of "platelet count" and "serum creatinine" of the proband used to elaborate Figure 2.</li> </ul> <p>In the file <strong>"C3 and C5b-9 deposition"</strong> is reported the quantification of serum-induced C3 and C5b-9 deposition on human microvascular endothelial cell line (HMEC-1). The fluorescent staining was evaluated with Image J and expressed as pixel<sup>2 </sup>per field analyzed. The fields with the lowest and highest values were excluded from calculation. These values were used to elaborate data included in Table 2 and in Figure 5.</p> <p>In the file <strong>"CD46 protein expression"</strong> are reported data of CD46 expression on peripheral blood mononuclear cells (PBMCs) isolated from the proband, his relatives and healthy volunteers. Data of specific expression of CD46 (evaluated for SCR1 or for SCR4 as reported in the materials and methods section) are indicated as median fluorescence intensity (MFI) percentage compared with the control.</p> <p>In the ppt file <strong>"cDNA amplification and sequencing results"</strong> is reported:</p> <ul> <li>the agarose gel image of the amplified cDNA from the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> <li>Electropherograms obtained from the cDNA sequencing of the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> </ul> <p>Additional data will be made available by the authors, without undue reservation, to any qualified researcher. </p>
Research data supporting: "Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles"
<p>This repository contains the set of data shown in the paper <strong>"Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles"</strong>, published on The Journal of Physical Chemistry B (DOI:10.1021/acs.jpcb.2c08726).</p>
The Complex Geometry and Dynamical Role of Stellar Wind Bubbles in Turbulent Molecular Clouds
<p>Research Data Management Package for paper in Monthly Notices of the Royal Astronomical Society with same title and author list</p>
Gaussian-accelerated Molecular Dynamics simulations of CCR8-CCL1-Gprotein complex in a POPC lipid bilayer
<p>Gaussian-accelerated Molecular Dynamics simulations of the CCR8-CCL1-Gprotein complex in a POPC lipid bilayer. Simulation system was prepared with OpenMM v7.7 and simulations were performed using the GaMD-OpenMM package (https://github.com/MiaoLab20/gamd-openmm) with a modification to include the MDTraj h5 file formate reporter as the output file format. These simulations were then converted to pdb topologies and dcd trajectories using MDTraj. </p><p>Files include:</p><p>CCL1_CCR8_noSer23_oriented_repaired1_system.pdb : system topology</p><p>CCL1_CCR8_config.xml : config for running GaMD-OpenMM</p><p>CCL1_CCR8_N_1ns_imaged_structure.pdb : initial topology/structure</p><p>CCL1_CCR8_N_1ns_imaged_trajectory.dcd : trajectory file</p><p> </p><p>Simulations can be loaded in python using MDTraj:</p><p>import mdtraj</p><p>trj = mdtraj.load(<dcd file>, top=<pdb file>)</p>
Dataset from the paper entitled "Complex structure of molten FLiBe (2 LiF – BeF2) examined by experimental neutron scattering, X-ray scattering, and deep neural network-based molecular dynamics"
<p>Dataset from the paper entitled "Complex structure of molten FLiBe (2 LiF – BeF2) examined by experimental neutron scattering, X-ray scattering, and deep neural network-based molecular dynamics". These data include experimental total scattering measurements and molecular dynamics simulations on the molten structure of FLiBe. </p>
Figures 7–12 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figures 7–12. Fifth sternites of male: 7, Phortica hani Zhang & Shi; 8, Phortica floccipes Cao & Chen sp. nov.; 9, Phortica hirtotibia Cao & Chen sp. nov.; 10, Phortica panda Cao & Chen sp. nov.; 11, Phortica longicauda Cao & Chen sp. nov.; 12, Phortica longiseta Cao & Chen sp. nov. The scale bars = 0.1 mm.
Figures 24, 25 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figures 24, 25. Phortica longiseta Cao & Chen sp. nov., male. 24, epandrium, surstylus, and cercus; 25, hypandrium, gonopods, paramere, aedeagus, and aedeagal apodeme. For abbreviations see Figs 14 and 15. Scale bars = 0.1 mm.
Figure 27 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figure 27. Single maximum parsimony tree based on the concatenated DNA sequences (tree length = 831, consistency index = 0.7714, retention index = 0.7497).
Figures 22, 23 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figures 22, 23. Phortica longicauda Cao & Chen sp. nov., male. 22, epandrium, surstylus, and cercus; 23, hypandrium, gonopods, paramere, aedeagus, and aedeagal apodeme. For abbreviations see Figs 14 and 15. Scale bars = 0.1 mm.
Figures 16, 17 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figures 16, 17. Phortica hirtotibia Cao & Chen sp. nov., male. 16, epandrium, surstylus, and cercus; 17, hypandrium, gonopods, paramere, aedeagus, and aedeagal apodeme. For abbreviations see Figs 14 and 15. Scale bars = 0.1 mm.
Figures 1–6 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figures 1–6. Hindlegs of male. For details of the parts denoted by letters a–e see the descriptions of individual species.
Figures 13–15 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figures 13–15. Phortica floccipes Cao & Chen sp. nov., male. 13, arista; 14, epandrium (epand), surstylus (sur), cercus (cerc), and tenth sternite (st 10) (lateral view); 15, hypandrium (hypd), gonopods (gon), paramere (pm), aedeagus (aed), and aedeagal apodeme (aed a) (lateral view). Scale bars = 0.1 mm.
Figures 18, 19 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figures 18, 19. Phortica pinguiseta Cao & Chen sp. nov., male. 18, epandrium, surstylus, and cercus; 19, hypandrium, gonopods, paramere, aedeagus, and aedeagal apodeme. For abbreviations see Figs 14 and 15. Scale bars = 0.1 mm.
Figures 20, 21 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figures 20, 21. Phortica panda Cao & Chen sp. nov., male. 20, epandrium, surstylus, and cercus; 21, hypandrium, gonopods, paramere, aedeagus, and aedeagal apodeme. For abbreviations see Figs 14 and 15. Scale bars = 0.1 mm.
Research data supporting: "Machine learning of microscopic structure-dynamics relationships in complex molecular systems"
<p>This repository contains the set of data and the code to reproduce the results shown in "Machine learning of microscopic structure-dynamics relationships in complex molecular systems" published on Machine Learning: Science and Technology (DOI: 10.1088/2632-2153/ad0fa5).</p>
Figure 8 in Distribution and molecular differentiation of Culex pipiens complex species in the Middle and Eastern Black Sea Regions of Turkey
Figure 8. Unrooted haplotype network for CQ11. Each circle represents a haplotype, and lines above each link indicate mutations.
Figure 7 in Distribution and molecular differentiation of Culex pipiens complex species in the Middle and Eastern Black Sea Regions of Turkey
Figure 7. Phylogenetic tree based on a 151-bp region within the CQ11 microsatellite region of Culex pipiens. The tree was constructed using the maximum likelihood method, and bootstrap values are shown as numbers on the tree.
Figure 5. Unrooted haplotype network. Each circle represents a in Distribution and molecular differentiation of Culex pipiens complex species in the Middle and Eastern Black Sea Regions of Turkey
Figure 5. Unrooted haplotype network. Each circle represents a haplotype, and the lines above each link indicate one mutation. Small black dots indicate intermediate, missing, or unsampled haplotypes.
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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.