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230 results for “structure determination”
Dataset from Reese et al.: "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" - PART 1
<p>Model data from the numerical setup of the tidal Elbe presented in Reese et al. (2023): "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" [1]</p><p>PART 1</p><p>Each file contains data for a full month, as given through the file naming convention: description.YYYYMMDD.nc4</p><p>The numerical model uses terrain-following sigma coordniates, with sigma level 0 being the bottommost layer.</p><p>Certain variables are also given in salinity class bins of dimension salt_s instead of vertical coordinates.</p><p>Explanation of each data type:</p><ul><li> 2D_elv_all: Spatially resolved simulated surface elevation from 08/2012 to 12/2013: Tidal analysis Fig. 4, Table 1 (simulated surface elevation vs. time)<ul><li>5 min snapshots</li></ul></li><li>Elbe_dia_getm_all: Diahaline analysis Fig. 8, 11: on-line GETM computation of u_dia,z^S in September 2012 and June 2013<ul><li>44700s temporal resolution (M2 tidal period); averaged over each period</li></ul></li><li>Elbe_TEF_mean_all: Total Exchange Flow analysis in September 2012 and June 2013, Fig.s 7, 8<ul><li>1-hourly averages</li></ul></li><li>Mixing_mean_all: Physical and numerical Mixing from 08/2012 to 12/2013. Fig. 7, 8, 9, 10, 11<ul><li>44700s temporal resolution (M2 tidal period); averaged over each period</li></ul></li><li>ST_stations: Surface elevation at given location for comparison with observational data at named station from 08/2012 to 12/2013<ul><li>5 min snapshots</li></ul></li><li>SST_stations: Salinity and temperature at given location for comparison with observational data at named station from 08/2012 to 12/2013; Fig. 3, Fig. 5, Table 2<ul><li>30-min snapshots</li></ul></li></ul><p> </p><p>[1] L. Reese, U. Graewe, K. Klingbeil, X. Li, M. Lorenz, H. Burchard, 2023:</p><p> Local mixing determines spatial structure of diahaline exchange flow in a</p><p> mesotidal estuary – a study of extreme runoff conditions.</p><p> J. Phys. Oceanogr., in press.</p>
Dataset from Reese et al.: "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" - PART 2
<p>Model data from the numerical setup of the tidal Elbe presented in Reese et al. (2023): "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" [1]</p><p>PART 2</p><p>Each file contains data for a full month, as given through the file naming convention: description.YYYYMMDD.nc4</p><p>The numerical model uses terrain-following sigma coordniates, with sigma level 0 being the bottommost layer.</p><p>Certain variables are also given in salinity class bins of dimension salt_s instead of vertical coordinates.</p><p>Explanation of each data type:</p><ul><li>Mean_all: Spatially resolved, temporally varying salt distribution in the Elbe estuary: Fig. 6, 10<ul><li>1-hourly averages</li></ul></li></ul><p> </p><p>[1] L. Reese, U. Graewe, K. Klingbeil, X. Li, M. Lorenz, H. Burchard, 2023:</p><p> Local mixing determines spatial structure of diahaline exchange flow in a</p><p> mesotidal estuary – a study of extreme runoff conditions.</p><p> J. Phys. Oceanogr., in press.</p>
Quantum efficiency and vertical position of quantum emitters in hBN determined by Purcell effect in hybrid metal-dielectric planar photonic structures
<p>Data from the article "Quantum efficiency and vertical position of quantum emitters in hBN determined by Purcell effect in hybrid metal-dielectric planar photonic structures", <a href="https://pubs.acs.org/doi/10.1021/acsphotonics.4c01416">ACS Photonics, (2024)</a> - [arXiv:2407.20160]</p>
Armenian: Noun phrase structure and determination
<ul> <li> <p><strong>Basic word order in noun phrase</strong></p> </li> <li> <p><strong>Basic characteristics of definite article</strong></p> </li> <li> <p><strong>Parallels between noun phrase and clause</strong></p> </li> <li> <p><strong>Definite article and specificity</strong></p> </li> <li> <p><strong>Definite article and nominalization</strong></p> </li> <li> <p><strong>Definite article as marker of argumenthood</strong></p> </li> <li> <p><strong>Typological parallels</strong></p> </li> </ul> <p> </p> <p>This lecture is part of the lecture series:</p> <p><em>Glottothèque: Languages of the Anatolia, Caucasus, Iran, Mesopotamia; grammatical snippets online </em>(electronic resource). Bamberg, Cambridge, Göttingen, Moskow, Nicosia, Paris: LACIM network, at https://spw.uni-goettingen.de/projects/lacim/, edited by Christiane Bulut, Anaïd Donabédian-Demopoulos, Geoffrey Haig, Geoffrey Khan, Pollet Samvelian, Stavros Skopeteas, Nina Sumbatova.</p>
Crystal structure of natural product Argyrin-D determined by 3D electron diffraction
<p>360° rotation of the Argyrin D model (stick mode with carbon, yellow; nitrogen, blue; oxygen, red; sulfur, gold and hydrogen, white) defined by a 2Fo-Fc map contoured at 1.2 sigma (grey mesh). The model was refined at a resolution of 1.1Å in Phenix using implemented electron scattering factors and restraints to R and Rfree values of 17.3 and 18.6%, respectively.</p>
Overcoming contrast reversals in focused probe ptychography of thick materials: an optimal pipeline for efficiently determining local atomic structure in materials science
<p>Files concerning the publication "Overcoming contrast reversals in focused probe ptychography of thick materials: an optimal pipeline for efficiently determining local atomic structure in materials science"(arxiv:2205.13308 )</p>
BIR-MicroED: selected area electron diffraction tilt series datasets used to determine representative structures of biotin, Cu(II)-serine, Zn(II)-methionine, Zn(II)-histidine, and Co(II)-porphyrin
<div> <div> </div> </div> <div> <p>This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format (except for the data collected from Co(II) porphyrin, which are 300 kV data in .tvips file format). Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature), where the reduced data from each were merged to determine a single representative structure of the compound by microED. Zip files are named according to the format: <em>"CompoundName</em>_<em>AcceleratingVoltage</em>_<em>Temperature_</em>structuredatasets.zip"</p> <p>Diffraction datasets within each folder are named according to the format: <em>CompoundName</em>_structuretiltseries_<em>AcceleratingVoltage</em>_<em>Temperature</em>_crystal#.mrc (or .tvips).</p> <p>All 200 kV datasets were collected with a rotation speed of 1 degree/second and an effective frame rate of 1 frame/second, with the exception of two Zn(II) methionine datasets collected with a frame rate of 3 frames/second. These are noted by the presence of "3fps" in the file name.</p> <p>All 300 kV datasets were collected with a rotation speed of 0.03 degrees/second and a frame rate of 0.5 frames/second.</p> </div>
Data for "Tetramine Aspect Ratio and Flexibility Determine Framework Symmetry for Zn8L6 Self-Assembled Structures"
<p>In the following subdirectories are the input and outputs of cage and face analysis for:</p> <p>Published DOI: <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202217987">10.1002/anie.202217987 </a></p> <p>Code: <a href="https://github.com/andrewtarzia/sca_cage_assembler/tree/cubism-production">sca_cage_assembler</a></p> <p>Previously uploaded in 10.5281/zenodo.8432296 and <a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer">https://github.com/andrewtarzia/citable_data</a></p> <p>NOTES:</p> <ul> <li>the naming convention differs from manuscript:</li> </ul> <table> <tbody> <tr> <th>manuscript tetra-aniline</th> <th>computational label</th> <th>xtal-label</th> </tr> <tr> <td>A</td> <td>5</td> <td>370</td> </tr> <tr> <td>B</td> <td>16</td> <td>326</td> </tr> <tr> <td>C</td> <td>12</td> <td>235</td> </tr> <tr> <td>D</td> <td>3</td> <td>301</td> </tr> <tr> <td>E</td> <td>8</td> <td>257</td> </tr> <tr> <td>F</td> <td>2</td> <td>354</td> </tr> </tbody> </table> <ul> <li>computational labels are often preceded by `quad2_` or `cl1_quad2_`</li> <li>much of the analysis was not used in the manuscript but remains part of the accumulated data</li> </ul> <p> </p> <p>cage_library directory:</p> <ul> <li>_CS.json: information on all cages in the set of diastereomers - properties and whether they optimized successfully.</li> <li>_ligand_measures.json: information on the ligand associated with a set of cage diastereomers.</li> <li>_measures.json: represenets a cleaned up collation of all measures the diastereomers made from a given ligand</li> <li>C_NAME_optc.mol: optimized (at xTB level) structure of each cage.</li> <li>set_dft_run directory contains the input and output of the CP2K optimisations of one set of diastereomers</li> </ul> <p>complex_library directory:</p> <ul> <li>contains the optimised structures of both complexes</li> </ul> <p>ligand_library directory:</p> <ul> <li>contains `_opt.mol` input ligand structures for cage construction</li> <li>for cap, the input was provided manually in `manual/` directory</li> <li>in `face_analysis` directory: <ul> <li>contains manual_complex directory, with necessary input for face construction</li> <li>_long_properties.json files contains the measurements for the named face (in file name)</li> <li>_long_lopt.mol files contain the optimised structure of the named face, on which analysis was performed</li> <li>`long` corresponds to the longer restricted optimization discussed in the SI.</li> </ul> </li> </ul> <p>xray_structures directory:</p> <ul> <li>analysis directory: <ul> <li>contains input .pdb files for xray structure (as single molecules) used in analysis</li> <li>contains `all_xray_csv_data.csv`, which has all data needed on xray structures.</li> </ul> </li> </ul>
Multi-complex integrative structure determination of the human HDAC1/2 interactome
<p><span><span>Histone deacetylases (HDACs) 1 and 2</span><span> are Class I HDACs that are members of several transcriptional regulatory complexes including coREST, MIER, NuRD, and SIN3. The interaction of each HDAC within the complex is undefined. Our studies </span><span>utilize Affinity Purification and Crosslinking Mass Spectrometry to define HDAC1 and 2 interactions. We</span><span> determined the structures of NuRD, SIN3A, and coREST by integrative structural modeling. </span><span>Lastly, we characterize MHAP1, previously known as C16orf87, define it as a novel member of the MIER HDAC complex, </span><span>and also</span><span> obtain a</span></span> <span><span>structural model for an </span><span>HDAC1:MIER1: MHAP</span><span>1 complex. </span></span><span> </span></p>
Structural determinants of ivabradine block of the open pore of HCN4
<p>Dataset underlying findings published in:<br>"Structural determinants of ivabradine block of the open pore of HCN4", PNAS (DOI: https://doi.org/10.1073/pnas.2402259121)</p>
Microcrustaceans structure determined by the type and trophic state of lakes - Upper Paranapanema River, Brazil
<p><span>The study was conducted in a segment of the Paranapanema River basin, in southeastern Brazil, focusing on five lakes spanning an eight-kilometer stretch, to understand the different organisms' responses to distinct conditions of aquatic environments. Sampling was carried out bimonthly over the course of a year.</span></p>
Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state.
<p>Initial coordinates, molecular dynamics trajectories and representative snapshots resulting from the study "Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state." by Pasquadibisceglie and Polticelli.</p> <p>The MD folders contain the parameter/topology (parm7) and initial coordinates (rst7) for the molecular dynamics simulations. Moreover, a NetCDF trajectory "prod.nc" of the production phase is also included.<br> In detail:<br> - MD0 -> SLC25A29 in absence of ligands;<br> - MD1, MD3, MD4 -> SLC25A29-ARG complex;<br> - MD1-LYS, MD3-LYS, MD4-LYS -> SLC25A29-LYS complex.</p> <p>The folder PDB_figures contains the PDB files used to produce the figures presented in the manuscript.</p>
Crystallographic datasets on crystal structures measured, determined, and resolved in multiplication
<p>There are data on:</p> <p>1.Catena-[(μ3-(DL)-mandelato)-silver(i)]<br> Bojidarka Ivanova, Michael Spiteller, CCDC 1918624: Experimental Crystal Structure Determination, DOI: 10.5517/ccdc.csd.cc22dh33<br> B.Ivanova, M.Spiteller, CCDC 771414: Experimental Crystal Structure Determination, 2011, DOI: 10.5517/cctwqbq<br> B.Ivanova, M.Spiteller, Polyhedron, 2011, 30, 241, DOI: 10.1016/j.poly.2010.10.008</p> <p><br> Sample 1; single crystal 1 (CCDC 1918624): BI37b<br> Sample 1; single crystal 2: (CCDC 2256450): BI38new<br> Sample 1; single crystal 3 (CCDC 771414): BI54a</p> <p>2. Diaqua-bis(cyclohexane-1,2-diamine)-zinc(ii) dinitrate<br> Bojidarka Ivanova, Michael Spiteller, Journal of Molecular Structure, 2021, 131488, DOI: 10.1016/j.molstruc.2021.131488<br> diaqua-bis(cyclohexane-1,2-diamine)-zinc(ii) dinitrate (CCDC 1576255)</p> <p>Sample 1; single crystal 1 (CCDC 1576255): 39a (BI39a.p4p)<br> Sample 1; single crystal 2: BI39.p4p</p> <p>3.Hexa-aqua-zinc(ii) bis(hydrogen 5-sulfosalicylate) monohydrate <br> M.Lamshoft, J.Storp, B.Ivanova, M.Spiteller, Polyhedron, 2011, 30, 2564, DOI: 10.1016/j.poly.2011.07.003<br> M.Lamshoft, J.Storp, B.Ivanova, M.Spiteller, CCDC 864677: Experimental Crystal Structure Determination, 2011, DOI: 10.5517/ccy0rth<br> Hexa-aqua-zinc(ii) bis(hydrogen 5-sulfosalicylate) monohydrate (CCDC 864677)</p> <p>Sample 1; single crystal 1 (CCDC 864677): 200-13a<br> Sample 1; single crystal 2: (CCDC 2256451): 200-8 (200-8.p4p)<br> Sample 1; single crystal 3: (CCDC 2256449): 200-15 </p> <p> </p> <p> </p>
Obuasi case study data: Performance of neutral SNP barcodes to determine genetic diversity and structure of Plasmodium falciparum in Africa
<p>A small number of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the genotyping and relatedness analysis of <em>Plasmodium</em> <em>falciparum</em> in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries characterised by moderate-to-high transmission. Using haplotypes generated from the MalariaGEN <em>P. falciparum</em> Community Project version 6 database, 52.3% of infections were multiclonal, generating high frequencies of mixed-allele calls (MACs) per isolate. Both multiclonality and low heterozygosity of SNPs impeded haplotype construction for analyses of relatedness. Although fewer SNPs provided usable data, these SNP barcodes weakly identified genetic differentiation across large geographic distances. However, both minor and major alleles' frequencies were temporally unstable. We conclude that these standardised SNP barcodes are vulnerable to ascertainment bias. While large numbers of SNPs acquired by whole-genome sequencing and computational methods to construct haplotypes present a way forward, these approaches may not be practical or cost-effective for surveillance on large scales in malaria-endemic areas. </p>
Variation among strains of Borrelia burgdorferi in host tissue abundance and lifetime transmission determine the population strain structure in nature
<p class="MsoNormal">Pathogen life history theory assumes a positive relationship between pathogen load in host tissues and pathogen transmission. Empirical evidence for this relationship is surprisingly rare due to the difficulty of measuring transmission for many pathogens. The comparative method, where a common host is experimentally infected with a set of pathogen strains, is a powerful approach for investigating the relationships between pathogen load and transmission. The validity of such experimental estimates of strain-specific transmission is greatly enhanced if they can predict the pathogen population strain structure in nature.</p> <p class="MsoNormal"><em>Borrelia burgdorferi</em> is a multi-strain, tick-borne spirochete that causes Lyme disease in North America. This study used 11 field-collected strains of <em>B. burgdorferi</em>, a rodent host (<em>Mus musculus, </em>C3H/HeJ) and its tick vector (<em>Ixodes scapularis</em>) to determine the relationship between pathogen load in host tissues and lifetime host-to-tick transmission (HTT). Mice were experimentally infected via tick bite with 1 of 11 strains. Lifetime HTT was measured by infesting mice with <em>I. scapularis </em>larval ticks on 3 separate occasions. The prevalence and abundance of the strains in the mouse tissues and the ticks were determined by qPCR. We used published databases to obtain estimates of the frequencies of these strains in wild <em>I. scapularis</em> populations.</p> <p>Spirochete loads in ticks and lifetime HTT varied significantly among the 11 strains of <em>B. burgdorferi</em>. Strains with higher spirochete loads in the host tissues were more likely to infect feeding larvae, which molted into nymphs with a higher probability of <em>B. burgdorferi</em> infection (<em>i.e.</em>, higher HTT). Our laboratory-based estimates of lifetime HTT were predictive of the frequencies of these strains in wild <em>I. scapularis</em> populations. For <em>B. burgdorferi</em>, the strains that establish high abundance in host tissues and that have high lifetime transmission are the strains that are most common in nature.</p>
Using sea level to determine the strength, structure and variability of the Cape Horn Current
<p>This is the data used in the paper ('Using sea level to determine the strength, structure and variability of the Cape Horn Current').</p>
The structural determinants of PH domain-mediated regulation of Akt revealed by segmental labeling
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Supplementary data from: Early vertebrate biomineralisation and eye structure determined by synchrotron X-ray analyses of Silurian jawless fish
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Data from: Hydrological dynamics, wetland morphology and vegetation structure determine riparian arthropod communities in constructed wetlands
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Contrasting light demands determine the coordination of plants’ non-structural carbohydrates and economic strategy over the range of solar spectral composition
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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.