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17,474 results for “Complexes”
An Integrated Structural Model of the DNA Damage Responsive H3K4me3 Binding WDR76:SPIN1 Complex with the Nucleosome
<p>Serial Capture Affinity Purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross linking mass spectrometry (XL-MS) and computational approaches one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were copurified with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected an extensive number of cross-linked sites were found between WDR76, SPIN1, and histones, we first built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we then used the powerful Integrative Modeling Platform to build a structural model of WDR76 and SPIN1 bound to the nucleosome.</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>
Room Temperature NIR Phosphorescence from C64 Nanographene Tetraimide by π-Stacking Complexation with Pt(II)Porphyrin
<p>Additional data to report <a href="https://doi.org/10.1002/anie.202406353">https://doi.org/10.1002/anie.202406353</a>:</p> <p>Near Infrared (NIR) phosphorescence at room temperature is challenging to achieve for organic molecules due to a negligible spin-orbit coupling and a low energy gap leading to fast non-radiative transitions. Here, we show a supramolecular host–guest strategy to harvest the energy from the low-lying triplet state of C<sub>64</sub> nanographene tetraimide <strong>1</strong>. <sup>1</sup>H NMR and X-ray analysis confirmed the 1:2 stoichiometric binding of a Pt(II)porphyrin on the two π-surfaces of <strong>1</strong>. While the free <strong>1</strong> does not show emission in the NIR, the host–guest complex solution shows NIR phosphorescence at 77 K. Further, between 860–1100 nm room temperature NIR phosphorescence (<em>λ</em><sub>max</sub> = 900 nm, <em>τ</em><sub>avg</sub> = 142 µs) was observed for a solid-state sample drop-casted from a preformed complex in solution. Theoretical calculations reveal a non-zero spin-orbit coupling between isoenergetic S<sub>1</sub> and T<sub>3 </sub>of π-stacked [<strong>1</strong>·Pt(II)porphyrin] complex. External heavy atom induced spin-orbit coupling along with rigidification and protection from oxygen in the solid state promotes both the intersystem crossing from the first excited singlet state into the triplet manifold and the NIR phosphorescence from the lowest triplet state of <strong>1</strong>.</p>
CRISPS coding scheme for complex casual leisure search requests — Auxiliary materials
<p>This repository contains auxiliary materials related to the CRISPS coding scheme for complex casual leisure search requests. The CRISPS coding scheme is described in the article "Understanding Complex Casual Leisure Information Needs: An Analysis of Search Requests for Books, Games, Movies and Music" by Toine Bogers (= corresponding author), Maria Gäde, Marijn Koolen, Vivien Petras, and Mette Skov. The article provides a comprehensive analysis of complex search requests in the casual leisure domains of books, games, movies and music using the CRISPS coding scheme.</p> <p>This repository contains the following auxiliary materials:</p> <ul> <li>The CRISPS codebooks for all four domains along with examples for each code and a comparison between the four domains (<strong>codebook.pdf</strong>)</li> <li>The CRISPS coding scheme figures from the article in a single PDF file (<strong>coding-scheme.pdf</strong>)</li> <li>The CRISPS coding scheme from the article in a machine-readable TSV-format (<strong>coding-scheme.tsv</strong>)</li> <li>All 2000 posts along with their assigned CRISPS codes in TSV-format (<strong>all-posts.tsv</strong>)</li> <li>The appendix belonging to the article</li> </ul>
Dataset: Baseline for the Northeast Atlantic (58 – 70° N) intertidal Mytilus species complex (Mytilus spp.) 2021-2022
<p><strong><span>Aim: </span></strong><span>Mussels (<em>Mytilus spp</em>.) are abundant in the North Atlantic, sessile, and sensitive to environmental change, and suitable as sentinels of environment and climate change of costal ecosystems. We aimed to determine the baseline for the Northeast Atlantic (58 – 70° N)<em> Mytilus</em> species complex, and to show the present distribution to surveys conducted 60 years ago. </span></p> <p><strong><span>Location:</span></strong><span> Northeast Atlantic </span></p> <p><strong><span>Methodology: </span></strong><span>Baseline was obtained by investigating a total of 509 stations in the intertidal zone, in four regions comprising the environmental gradient from head of fjord to coast, and distributed over the latitudinal gradient from 58 – 70° N. </span></p> <p><strong><span>Results:</span></strong><span> The baseline shows a range in continuous abundance of mussels from 12 to 36 %, patchy abundance from 26 to 57 % and no or very limited mussel abundance from 26 to 46 % between the four regions. The presence of mussels in the southeast and west region was visualized to previous surveys conducted 60 years ago. The data points to similar past and present presence of mussels in both regions, yet past major mussel fields in the inner section of region southeast was not detected in this study.</span></p> <p><strong><span>Main conclusions:</span></strong></p> <p><span>The baseline of <em>Mytilus spp.</em> in the Northeast Atlantic (58 – 70° N) is now available for future reference. The baseline, plotted to surveys conducted 60 years ago, points to awareness of the population situated in the southeast section of the investigated region. Continued monitoring and modelling are needed to clarify drivers of temporal and spatial variation in the mussel populations along the Northeastern Atlantic coast. </span></p>
Markaṇḍa (Gadchiroli District, Maharashtra). Markaṇḍeśvara temple complex, exterior.
<p>Markaṇḍa (Gadchiroli District, Maharashtra). Markaṇḍeśvara temple complex, exterior from the south-west showing outer wall and subsidiary shrines.</p>
Kanheri (Bombay, Maharashtra, India). Plan of Kanheri caves complex
<p>Kanheri (Bombay, Maharashtra, India). Plan of Kanheri caves complex, dated 1881 and published in Campbell, James M. <em>Gazetteer of the Bombay Presidency</em>. Bombay: Government Central Press, 1896.</p>
Computational data for selection of PBE+50HFX functional for studying Ru-Cl/H-PR3 complexes
<p>The dataset provides all relevant computational data for selecting the hybrid GGA functional (PBE) with 50% HF exchange and saturated (def2TZVP) basis set as the most reasonable level of theory that reproduces the current golden standard of CCSD(T) results for Ru-Cl/H-PR3 complexes.<br> The file <strong>inventory</strong> gives you an overview of the data entries provided. <br> The PDF file <strong>labelling.pdf</strong> defines the symbols used for labelling various complexes.<br> In brief, the archive content is as follows:</p> <p><strong>basis sets</strong> - definition of BS1 to BS5 <br> <strong>Z-matrix definitions</strong> - definition of internal coordinates for isomers considered<br> <strong>operational procedures</strong> - operation procedures for how to derive atomic orbital compositions</p> <p><strong>density functionals</strong> - optimized structures calculated using various density functionals<br> <strong>wave functions</strong> - optimized structures calculated at various levels of wave function theory<br> <strong>population analyses</strong> - summary of electronic structure analysis<br> <strong>difference density</strong> - manipulated cube files used for electron density contours</p> <p><strong>CCDB</strong> - optimized structures of XRD characterized Ru-Cl/H-PR3 complexes<br> <strong>chemical speciation</strong> - structural optimization and energetics of reaction pathways</p>
Supporting data and codes for: A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology, hybrid sterility and possible introgression
<p>This GitHub repository includes R codes and datasets for the paper: A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology, hybrid sterility and possible introgression</p>
CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA-seq data: Codes and processed data
<p>Codes and processed data to reproduce the analysis discussed in: </p> <p>Wegmann <em>et Al.</em>,<strong> CellSIUS provides sensitive and specific detection of rare cell<br> populations from complex single cell RNA-seq data</strong>, Genome Biology 2019 (Accepted)<br> </p>
The complex non-collinear magnetic orderings in Ba2YOsO6: A new approach to tuning spin-lattice interactions and controlling magnetic orderings in frustrated complex oxides
<p><strong>Project abstract</strong>: Frustrated magnets are one class of fascinating materials that host many intriguing phases such as spin ice, spin liquid and complex long-range magnetic orderings at low temperatures. In this work we use first-principles calculations to find that in a wide range of magnetically frustrated oxides, at zero temperature a number of non-collinear magnetic orderings are more stable than the type-I collinear ordering that is observed at finite temperatures. The emergence of non-collinear orderings in those complex oxides is due to higher-order exchange interactions that originate from second-row and third-row transition metal elements. This implies a collinear-to-noncollinear spin transition at sufficiently low temperatures in those frustrated complex oxides. Furthermore, we find that in a particular oxide Ba2YOsO6, experimentally feasible uniaxial strain can tune the material between two different non-collinear magnetic orderings. Our work predicts new non- collinear magnetic orderings in frustrated complex oxides at very low temperatures and provides a mechanical route to tuning complex non-collinear magnetic orderings in those materials. <br> <br> <strong>About this entry</strong>: We provide the input files of our DFT calculations for the studied complex oxides. The structures in POSCAR format and the INCAR files for all stabilized magnetic orderings in our study are all included. These files can be directly used into DFT calculations with VASP. Only the versions of PAW potentials are included in POT.info files owing to the VASP license restrictions.</p>
Research Data/Code for "Scale-bridging within a complex model hierarchy for investigation of a metal-fueled circular energy economy by use of Bayesian model calibration with model error quantification"
<p>This repository contains research data and code for supplementing the manuscript <br>"Scale-bridging within a complex model hierarchy for investigation of a metal-fueled circular energy economy by use of Bayesian model calibration with model error quantification" <br>by L. Gossel, E. Corbean, S. Dübal, P. Brand, M. Fricke, H. Nicolai, C. Hasse, S. Hartl, S. Ulbrich, and D. Bothe. </p> <p>There is a corresponding preprint available on Arxiv: https://doi.org/10.48550/arXiv.2404.13092</p> <p><br>Users are referred to the manuscript for background information. This repository shall enable reproduction of the reported results and does not stand alone. </p> <p>Please read important information in the README in the top-level directory. </p> <p>Funded by the Hessian Ministry of Higher Education, Research, Science and the Arts - cluster project Clean Circles. </p>
Supplementary Material: Knobs and dials of retrieving JWST transmission spectra. I. The importance of p-T profile complexity
<p>This is supplementary material to <a title="Schleich et al. (2024)" href="https://www.aanda.org/articles/aa/abs/2024/10/aa51845-24/aa51845-24.html" target="_blank" rel="noopener">Schleich et al. (2024)</a>. The content of the provided data repository (also described in the file "content.txt") is as follows:</p> <p> </p> <h2>ADDITIONAL ANALYSIS</h2> <p>This folder contains a collection of ancillary data products for the evaluation of the retrievals performed in this work.</p> <ul> <li>'bayes-factor' contains the data tables for evaluating the Bayes' factor for each separate collection of models(*)</li> <li>'corner-plots' contains a collection of all corner plots associated with the individual input cases</li> <li>'fit-residuals' contains all fit residuals for the individual atmospheric retrievals performed in this work (used to make Fig. C.1)</li> <li>'resampled-pt-profiles' contains resampled p-T profiles to generate Figs. 6 and F.1</li> <li>'retrieval-accuracy' contains additional plots related to the accuracy of each retrieval (used to make Fig. 5, as well as Figs. E.1 - E.5)</li> </ul> <p><br>(*) SIDE NOTE:<br>Table headers in the "bayes-factor" data tables reference evidence reported from MultiNest (variable "Z"), and calculated Bayes factor (variable R). The case with log(R) = 0 is necessarily the reference case, and outliers are marked in a binary table with 1 (|log(R)| > 5) or 0 (|log(R)| < 5). In all cases, "log" refers to the natural logarithm.</p> <ul> <li>If someone actually reads this, I'm sorry. I also spent way too much time trying to track down if the values reported in MultiNest are natural or base-10 logarithm. I have now been convinced that it is worth it, always, to either specify "ln" for the base-e logarithm, or give the base of your logarithm if your write it down (i.e. log_10(X)) -Simon.</li> </ul> <h1> </h1> <h2>RETRIEVAL RESULTS</h2> <p>This folder contains the data products associated with the retrieval runs for each synthetic spectrum. The sub-directories are aranged by the following keys:</p> <ul> <li>'drs' and 'pandexo' refere to the two noise cases considered</li> <li>'inv-t' and 'norm-t' refere to the two underlying p-T profiles used to make the synthetic spectra</li> <li>'hpc', 'mpc', and 'lpc' refere two the three cloud-top pressure cases considerd</li> </ul> <p>Each individual folder contains (1) the TauREx parameter files for running retrievals using the selection of p-T profiles, (2) a folder called 'results', which containts the associated data products, and (3) a folder called 'chains', which stores the ancillary data products associated with the MultiNest sampling runs of each retrieval.</p> <p> We note that for the "drs_inv-t_mpc" case, the chains for the isothermal, 2-point, and 4-point runs have been lost</p> <p> </p> <h2>SYNTHETIC SPECTRA</h2> <p>This folder contains data products associated with the sample of synthetic transmission spectra.</p> <ul> <li>'pt-profile_*.csv' are csv-files containing the p-T points used to make Figure 1 , and to generate the synthetic transmissions spectra</li> <li>'forward-models' contains TauREx parameter files and forward models for the sample of synthetic transmission spectra. Each of the sub-directories also contains a faux-spectrum representing the wavelength-map of NIRSpec PRISM <ul> <li>'no-clouds' contains contains the above for generating Figure 3.</li> <li>'inv-t' contains forward models using the "inverse" p-T profile</li> <li>'norm-t' contains forwrad models using the "monotonic" p-T profile</li> </ul> </li> </ul>
Navigating the complex policy landscape for carbon farming in The Netherlands and the EU -- Open Research Europe Extended Data-- Tables 1-6, Figures 1-2
<p>This is extended data for the article entitle 'Navigating the complex policy landscape for carbon farming in The Netherlands and the EU' submitted to Open Research Europe by Eise Spijker. </p>
Data and Software for: 'A NICER View of PSR J1231−1411: A Complex Case'
<p>Posterior sample files associated with the publication "A NICER View of PSR J1231−1411: A Complex Case" by Salmi et al. (2024b; <a href="https://doi.org/10.48550/arXiv.2409.14923">arXiv.2409.14923</a>; <a href="https://doi.org/10.3847/1538-4357/ad81d2">https://doi.org/10.3847/1538-4357/ad81d2</a>).</p> <p>Also included are: the data products; the numeric model files including the telescope calibration products; model modules in the Python language using the X-PSI framework; and Jupyter analysis notebooks.</p> <p>Please refer to the README for detailed information.</p>
Experimental data related to the publication: "Phase Composition of AlTiNbMoV, AlTiNbTaZr and AlTiNbMoCr Refractory Complex Concentrated Alloys: A Correlation of Predictions and Experiment
<h2>EDS data</h2> <ul> <li>SPC and SPD files: EDAX Genesis raw data for EDS maps of as-sintered condition (Figures 1, 5 and 10).</li> <li><em>EDS_homogenized.h5</em> file: EDAX APEX raw data for maps (Figures 2, 6 and 11) and linescans (Figures 3, 7 and 12) of the homogenized condition</li> </ul> <h2>XRD data</h2> <p>ASCII tab-separated files for XRD diffractograms (Figures 4, 9 and 14). Contains measured intensity and calculated intensities for the displayed phases.</p> <h2>CALPHAD data</h2> <p>ASCII tab-separated files to recreate Figure 15 (resulting phase fractions only).</p> <p> </p>
Ternary π–π Stacking Complexes by Allosteric Regulation in Multilayer Nanographenes
<p>Additional data to report <a href="https://doi.org/10.1021/jacs.4c11119">https://doi.org/10.1021/jacs.4c11119</a>:</p> <p>Construction of π–π stacking supramolecular complexes with more than two components is challenging due to the weak and directionless nature of dispersion interactions. Here we report ternary complexes of a ditopic nanographene tetraimide (<strong>1</strong>), α-substituted phthalocyanine (<strong>Pc</strong>) and polyaromatic hydrocarbons (PAHs) in solution and crystalline state via allosteric regulation. Binding of one <strong>Pc</strong> give rise to significant distortion and conformational changes in <strong>1</strong> that in turn lead to the inhibition of the second binding of <strong>Pc</strong>. The conformational changes associated with first binding allowed an allosteric binding of a third component (PAHs) to form ternary complexes in solution. <sup>1</sup>H NMR titration revealed a moderately high thermodynamic stability for the ternary complexes in CDCl<sub>3</sub>. Competition between allosterically regulated ternary complexes ([<strong>Pc·1</strong>·PAH]) and 1:2 stoichiometric binary complexes of <strong>1</strong> with PAHs ([PAH·<strong>1</strong>·PAH]) were elucidated. Further, selective formation of ternary complexes in solution led to the generation of ternary cocrystals from a 1:1:1 mixture of three components in solution. Our work shows that large π-conjugated nanographenes designed with allosteric recognition sites allow the construction of multilayer ternary complexes in solution and solid-state even with dispersive π–π interactions.</p>
IrLumDB: a dataset of bis-cyclometalated iridium(III) complexes luminescence properties
<h1><strong>If you use this dataset, please cite our paper</strong>: <a href="https://doi.org/10.1039/D5TC00305A">https://doi.org/10.1039/D5TC00305A</a></h1> <p>IrLumDB contains data about 1454 experimentally measured luminescence spectra of 1287 unique iridium(III) complexes reported in the 340 literature papers.</p> <p><br>The 13 columns of this dataset are explained as follows:</p> <ol> <li>L1 — SMILES representation of the L1 ligand attached to the iridium ion</li> <li>L2 — SMILES representation of the L2 ligand attached to the iridium ion</li> <li>L3 — SMILES representation of the L3 ligand attached to the iridium ion</li> <li>Counterion — SMILES representation of the counterion (if the complex molecule is charged)</li> <li>Abbreviation_in_the_article — the original abbreviation depicting the complex in the article</li> <li>Charge — the total charge of the complex molecule</li> <li>Max_wavelength(nm) — value of maximal luminescence wavelength reported in the article</li> <li>PLQY — value of quantum yield reported in the article</li> <li>tau(s*10^-6) — value of excited state lifetime reported in the article</li> <li>Solvent — solvent media for luminescence measurements reported in the article</li> <li>DOI — DOI of a data source for given values</li> <li>Notes — additional notes for presented data</li> <li>PLQY_in_train — photoluminescence quantum yields which we consider suitable for ML purposes (for all the PLQY’s for which inert atmosphere is stated in the source article “1” is stated, otherwise “0” is stated).</li> </ol> <p>An appendix to the dataset (Synthesized_complexes.csv) contains data about 33 experimentally measured luminescence spectra of 33 unique iridium(III) complexes synthesized by our research group.</p> <p><br>Additional remarks:</p> <ul> <li>The iridium(III) complexes reported in this dataset are bis-cyclometalated Ir(III) complexes, which usually contain two bidentate cyclometalated ligands and one bidentate ancillary ligand; for these L1 and L2 correspond to the cyclometalated ligands and L3 corresponds to the ancillary ligand. </li> <li>Several ligands make formally covalent bonds with the Ir(III) ion. For these a negatively charged bond-forming atom is drawn in the SMILES of corresponding ligand.</li> <li>The vast majority of quantum yield and excited state lifetime measurements were claimed to be performed in deoxygenated solutions at room temperature. If not, the conditions for measurements are presented in the ”notes” column.</li> </ul>
Reproduction package for: 'Exploring Waveform Variations among Neutron Star Ray-tracing Codes for Complex Emission Geometries'
<p>Data files, python scripts and notebooks to reproduce the code output comparisons performed in "Exploring Waveform Variations among Neutron Star Ray-tracing Codes for Complex Emission Geometries" by Choudhury et al. (2024; <a href="https://doi.org/10.3847/1538-4357/ad7255" target="_blank" rel="noopener"><em>ApJ</em> <strong>975</strong> 202</a>, <a href="https://doi.org/10.48550/arXiv.2406.07285" target="_blank" rel="noopener">arXiv.2406.07285</a>).</p> <p>Please refer to the README for detailed information.</p> <p>N.B. The neutral hydrogen column density (${\rm N}_{\rm H}$) value is mentioned in the paper to be $0.2 \times 10^{20} {\rm cm}^{-2}$, whereas all the analyses in the paper, as reflected in this Zenodo package, actually uses ${\rm N}_{\rm H} = 2 \times 10^{20} {\rm cm}^{-2}$.</p>
Verification of library complexity in the HEK-Cas9 sublibraries - sequence data of the generated sublibraries A and B
<p>Sequence data of the generated HEK-Cas9 sublibraries A and B, linked to the manuscript 10.1128/mbio.01925-24: The <em>Bordetella</em> effector protein BteA induces host cell death by disruption of calcium homeostasis by Martin Zmuda, Eliska Sedlackova, Barbora Pravdova, Monika Cizkova, Marketa Dalecka, Ondrej Cerny, Tania Romero Allsop, Tomas Grousl, Ivana Malcova, and Jana Kamanova</p>
ScienceDex guides
Understand access before you commit
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.