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1,294 results for “reactions”
Metadata of "Polydopamine/Ethylenediamine Nanoparticles Embedding a Photosynthetic Bacterial Reaction Center for Efficient Photocurrent Generation"
<p>Metadata of "Polydopamine/Ethylenediamine Nanoparticles Embedding a Photosynthetic Bacterial Reaction Center for Efficient Photocurrent Generation"</p>
Metadata of "Effect of chemical substitution on the surface charge of the photosynthetic Reaction Center from Rhodobactersphaeroides: an in-silico investigation"
<p>Metadata of "Effect of chemical substitution on the surface charge of the photosynthetic Reaction Center from Rhodobactersphaeroides: an in-silico investigation"</p>
Dataset: 800 QM/MM minimum energy pathway conformations for the acylation reactions of Toho-1/ampicillin and Toho-1/cefalexin
<p>This dataset consists of 800 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the acylation reactions between a Class A beta-lactamases (Toho-1) and two beta-lactam antibiotic molecules (ampicillin and cefalexin).</p> <p>These files are:</p> <ul> <li>toho_amp.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_amp.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_cex.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>toho_cex.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>energies.zip: the replica energies at B3LYP-D3/6-31+G**/C36 level;</li> <li>chelpgs.zip: the ChElPG charges of all reactant replicas at B3LYP-D3/6-31+G**/C36 level;</li> <li>farrys.zip: the featurzied NumPy arrays for model training;</li> <li>peephole.zip: an example file for how the optimized MEPs look like; </li> <li>dftb3_benchmark.zip: the reference calculations to justify the use of DFTB3/3OB-F/C36 in MEP optimizations, the reference level of theory is B3LYP-D3/6-31G**/C36. </li> </ul> <p>The R1-AE pathways are the acylation uses Glu166 as the general base; the R2-AE pathways uses Lys73 and Glu166 as the concerted base. </p> <p>All QM/MM pathways are optimized at the DFTB3/3OB-f/CHARMM36 level of theory. </p> <p>Z. Song et al Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. <em>ACS Phys. Chem Au</em> 2022, <strong>2</strong>, 4, 316–330. DOI: <a href="https://doi.org/10.1021/acsphyschemau.2c00005">10.1021/acsphyschemau.2c00005</a></p>
Comparative host transcriptomics as a tool to identify candidate biomarkers for immune reactions in leprosy: A meta-analysis study
<p>The dataset consists of R source code for the individual dataset analysis of the studies and their meta-analysis. It also contains supplementary tables and figure.</p>
Data of paper Controlling the interfacial reactions and environment of rare-earth ions in thin oxide films towards wafer-scalable quantum technologies
<p>Data of the figures in the paper :</p> <p>N. Harada, A. Tallaire, D. Serrano, A. Seyeux, P. Marcus, X. Portier, C. Labbé, P. Goldner, and A. Ferrier, <em>Controlling the Interfacial Reactions and Environment of Rare-Earth Ions in Thin Oxide Films towards Wafer-Scalable Quantum Technologies</em>, Mater. Adv. <strong>3</strong>, 300 (2022). doi: 10.1039/D1MA00753J</p>
Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction. Analysis Code, Numerical and Primary data.
<p>Uploaded under this Zenodo DOI is the following:</p> <p>1. the Analysis Code used for Flow Cytometry analysis in the paper, GO complex analysis (Figure 3) and Hit visualization (Figure 1, 2 S1, S4 Figs).</p> <p>2. The primary Flow Cytometry data from both the initial screen (ScreenFlowFCS) and validation experiments (ValidationFlowFCS) are included as .zip files.</p> <p>3. a .zip folder is uploaded that contains all the analysis code for the ChIP-Seq experiments. </p> <p>4. Excel worksheets that contain the numerical source data for all qPCR bar plots.</p>
Genetic basis of growth reaction to drought stress differs in contrasting high-latitude treeline ecotones of a widespread conifer
<p>Raw and filtered SNP data and raw tree ring data of the analysed trees. R scripts for SNP filtering, phenotypic data and genotype-phenotype association analysis. </p>
Novel production pathways for the 64Cu / 67Cu theranostic pair through natZn(n, x) reactions
<p>This repository contains all raw gamma-ray spectra analyzed for the present manuscript, as well as calibration spectra. Further details and analysis code are available on reasonable request. </p> <p> </p> <p>The nuclear decay properties of the 64,67Cu radionuclides are favorable for clinical applications, with 64Cu currently being employed for PET imaging. The combined use of 64Cu with 67Cu as a theranostic pair may enable highly personalized therapeutic treatment, with real-time monitoring of dose delivery. In this study, the natZn(n,x) reactions have been investigated as novel production pathways for the 64,67Cu isotopes. The experiment was performed at the Lawrence Berkeley National Laboratory’s 88-Inch Cyclotron, producing fast neutrons through the deuteron breakup process using deuteron beams of 16 MeV and 33 MeV. This study reports spectrum-averaged cross sections for the 64,67Cu isotopes, as well as for 20 additional reaction products from neutron irradiation of natural zinc, zirconium, indium, yttrium and aluminum, more than half of which are measured for the first time. The well-characterized monitor reactions of 89Y(n,2n)88Y, 27Al(n,x)24Na, and natZr(n,x)89Zr were employed to determine the neutron fluence, using the recommendations from the IRDFF-II dosimetry library, and all activities were measured through γ-ray spectroscopy using a high-purity germanium detector. The results are compared to previous experiments from the EXFOR and TENDL-2019 databases, and calculations using ALICE-2017, CoH-3.5.3, EMPIRE-3.2.3, and TALYS-1.9. This work shows that natZn(n,x)64,67Cu is a viable pathway for producing these isotopes, and offers a potential ”tunable” ratio of 64Cu:67Cu for various applications.</p>
Deep Learning for Reaction-Diffusion Glioma Growth Modeling: Towards a Fully Personalized Model? — Supporting Data
<p>Supporting data for Martens et al. Deep Learning for Reaction-Diffusion Glioma Growth Modelling: Towards a Fully Personalised Model? arXiv:2111.13404.</p>
Machine learning the quantum flux-flux correlation function for catalytic surface reactions
<p>This dataset contains information on each of the 14 reactions used in the paper, the geometries for these reactions, the product of the quantum reaction rate constant and canonical reactant partition function and the flux-flux correlation function time series values for each reaction-temperature combination.</p> <p><strong>reaction_details.csv</strong></p> <p>This is a .csv file containing additional details on the reactions used in this paper. Each row contains one reaction/temperature combination, of which there are 55.</p> <p> </p> <p>Column descriptions:</p> <ul> <li>reaction_number: Reaction identifier number used in this work</li> <li>reaction: The chemical reaction equation</li> <li>metal_surface: atomic symbol of metal surface</li> <li>facet_number: Miller indices of surface</li> <li>reactants: Python dictionary object of reactants and their quantities</li> <li>products: Python dictionary object of products and their quantities</li> <li>reaction_energy [eV]: reaction energy in electron-volts</li> <li>activation_energy [eV]: activation energy of reaction in electron-volts</li> <li>temperature [K]: The randomly assigned temperature a calculation was run for</li> <li>kQ_Cff [1/au]: The calculated integrated reaction rate product at corresponding temperature {1,2,3,4} in units 1/(au time).</li> <li>reaction_split: Train/test placement of that reaction/temperature combination for reaction split</li> <li>temperature_split:<strong> </strong>Trian/test placement of that reaction/temperature combination for temperature split</li> <li>catalysishub_reactionID: Catalysis Hub reaction ID identifier for referencing catalysis hub database</li> <li>doi:<strong> </strong>digital object identifier of original publication for which DFT calculations were performed</li> </ul> <p> </p> <p> </p> <p><strong>Flux_flux_correlation_functions:</strong></p> <p>Directory containing flux-flux correlation function time series values for each reaction temperature combination. Values are organized in subdirectories, one for each of the 14 reaction. In each subdirectory .csv files are labeled by reaction number and temperature in Kelvin. Each csv file contains a column with time points [au of time] and the corresponding flux-flux correlation function value in units [1/(au of time)<sup>2</sup>].</p> <p> </p> <p><strong>Geometries:</strong></p> <p>Directory containing geometry files for each reaction. Geometries of reactants on the surface were shifted respect to those supplied by catalysis hub to create continuous reaction pathways where necessary. Geometry files are organized in subdirectories for each reaction. When complete nudged elastic band (NEB) minimum energy paths (MEP) were not available ,subdirectories contain a products.xyz, reactants.xyz, and TSstar.xyz file (reactions 1 to 11) otherwise the complete set of NEB MEP images labeled neb{n}.xyz is given (reactions 12, 13, 14).</p> <p> </p> <p> </p>
Supplementary Information for "G-type Halohydrin Dehalogenases Catalyze Ring Opening Reactions of Cyclic Epoxides with Diverse Anionic Nucleophiles"
<p>This is the external Supplementary Information for our publication "G-type Halohydrin Dehalogenases Catalyze Ring Opening Reactions of Cyclic Epoxides with Diverse Anionic Nucleophiles".</p> <p>The .zip files contain the raw NMR data for all compounds as well as the protein structural data described in the manuscript.</p>
Dataset for: Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR
<p>A dataset is reported for a rapid isothermal method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. The procedure uses an unprecedented reverse transcription–free (RTF) approach for converting genomic RNA into DNA. This involves the formation of an RNA/DNA heteroduplex whose selective cleavage generates a short DNA trigger strand, which is then rapidly amplified using the exponential amplification reaction (EXPAR). Deploying the RNA-to-DNA conversion and amplification stages of the RTF-EXPAR assay in a single step results in the detection, via a fluorescence read-out, of single figure copy numbers per microliter of SARS-CoV-2 RNA in under 10 min. In direct three-way comparison studies the assay has been found to be faster than both PCR and loop-mediated isothermal amplification (LAMP), while being just as sensitive. The assay protocol involves the use of standard laboratory equipment and is readily adaptable for the detection of other RNA-based agents.</p>
Raw data for "Interplay of Kinetic and Thermodynamic Reaction Control Explains Incorporation of Dimethylammonium Iodide into CsPbI3"
<p>Raw solid-state NMR and XRD data, and input files for DFT and MD calculations shown in https://doi.org/10.1021/acsenergylett.2c00877</p>
Data from: Operando Proton Transfer Reaction-Time of Flight-Mass Spectrometry of Carbon Dioxide Reduction Electrocatalysis
<p>Seven top-level folders</p> <p>GC-PTR-TOF-MS<br> - Raw data and Jupyter Notebook used for analysis of GC-PTR-TOF-MS data</p> <p>LSV-PTR-TOF-MS<br> - Raw data and Jupyter Notebook used for analysis of PTR-TOF-MS data under linear sweep voltammetry</p> <p>MSCP-PTR-TOF-MS<br> - Raw data and Jupyter Notebook used for analysis of PTR-TOF-MS data under multi-step chronopotentiometry</p> <p>PTR-TOF-MS-Calibration<br> - Raw data and Jupyter Notebook used for analysis of PTR-TOF-MS calibration data</p> <p>SEM<br> - Raw images from scanning electron microscope</p> <p>Stability<br> - Raw data of electrochemical stability</p> <p>TEM<br> - Raw images from transmission electron microscopy</p>
Data for: Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms
<p><span>Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals' response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies non-zero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, </span><span>result in </span><span>flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits, and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experiments <em>in</em> <em>silico</em>. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral or no plasticity, without any additional knowledge of the traits assessed and species' biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopod <em>Idotea balthica</em> sampled from two </span><span>geographical locations </span><span>with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments, or correlated to fitness.</span></p>
Limited sex differences in plastic responses suggest evolutionary conservatism of thermal reaction norms: A meta-analysis in insects
<p>Temperature has a profound effect on the growth and development of ectothermic animals. However, the extent to which ecologically-driven selection pressures can adjust thermal plastic responses in growth schedules is not well understood. Comparing temperature-induced plastic responses between sexes provides a promising but underexploited approach to evaluating the evolvability of thermal reaction norms: males and females share largely the same genes and immature environments but typically experience different ecological selection pressures. We proceed from the idea that substantial sex differences in plastic responses could be interpreted as resulting from sex-specific life-history optimization, whereas similarity among the sexes should rather be seen as evidence of an essential role of physiological constraints. In this study, we performed a meta-analysis of sex-specific thermal responses in insect development times, using data on 161 species with comprehensive phylogenetic and ecological coverage. As a reference for judging the magnitude of sex-specificity in thermal plasticity, we compared the magnitude of sex differences in plastic responses to temperature with those in response to diet. We show that sex-specific responses of development times to temperature variation are broadly similar. We also found no strong evidence for sex-specificity in thermal responses to depend on the magnitude or direction of sex differences in development time. Sex differences in temperature-induced plastic responses were systematically less pronounced than sex differences in responses induced by variations in larval diet. Our results point to the existence of substantial constraints on the evolvability of thermal reaction norms in insects as the most likely explanation. If confirmed, the low evolvability of thermal response is an essential aspect to consider in predicting evolutionary responses to climate warming.</p>
Thermodynamic database and calculator of free energies and potentials for redox reactions involving iron minerals in aqueous media (IMTD)
<p>Database of free energies of formation for iron minerals and associated aqueous species, which are used in a tableu style spreadsheet to calculate free energies of redox reactions involving iron minerals, which in turn are used to calculate free energies and formal potentials for these reactions, under specified environmental conditions.</p> <p>The database and calculators were assembled by students and postdocs (Jeff Hudson, Ania Pavitt, Ying Lan, and Miranda Bradley) working under direction of Professor Paul G. Tratnyek at the Oregon Health & Science University, Portland, Oregon, USA. Drew Latta, Thomas Robinson, and Michelle Scherer contributed to the database and extended the calculations.</p> <p>Early versions of this tool were used in several publications, including (i) Fan, D., Y. Lan, P. G. Tratnyek, R. L. Johnson, J. Filip, D. M. O'Carroll, A. N. Garcia, and A. Agrawal. 2017. <em>Environ. Sci. Technol.</em> 51(22): 13070–13085. [DOI: 10.1021/acs.est.7b04177] and (ii) Bradley, M. J., and P. G. Tratnyek. 2019. <em>ACS Earth & Space Chemistry</em> 3(3): 688-699. [DOI: 10.1021/acsearthspacechem.8b00200].</p> <p>This tool is provided as a spreadsheet in .xlsx format. The file includes six sheets. The first contains background, constants, and calculations that apply throughout the remaining tabs. The second contains free energies of formation from various authoritative sources, and a mechanism for designating “recommend values”. The third contains a tableu that calculates free energies of redox reactions using the recommended free energy of formation and user-specified stoichiometries. The fourth calculates free energies and formal potentials of the redox reactions using the standard potentials, and specific solution conditions. The last tab summarizes previous published formal potentials from a variety of sources. </p> <p>While the database was checked thoroughly, it still is unlikely to be completely accurate. For critical applications, we recommend that you track-down the primary sources (listed on the first tab of the spreadsheet) and use them for data, conditions, and other caveats. Obviously, we do not accept any responsibility for what anyone does with information obtained from this document.</p> <p>In the future, if significantly corrections or additions are made to this document, we may publish it here as new versions. If the contributions of others result in major improvements, we are open to adding new authors to those versions. Feel free to contact us with corrections, suggests, or offers to help.</p> <p>The development of this version of the tool was funded through grants from the Strategic Environmental Research and Development Program (SERDP) and the U.S. Department of Energy.</p>
The 48Ca+181Ta reaction: Cross section studies and investigation of neutron-deficient 86≤Z≤93 isotopes
<p>Example for RDM developments:</p> <p>Small result datasets given. Under development metadata schema provided</p> <p>This example dataset describes alpha-decaying chains from an experiment performed at the SHE Physics group at GSI Helmholtzzentrum fuer Schwerionenforschung GmbH. The reaction 48Ca+181Ta was used to produce neutron deficient isotopes of Np, Pa and U. The 48Ca beam was delivered by the UNILAC at a variety of selected energies with 5Hz repitition rate and 5ms pulse width. The evaporation residues were implanted into the focal plane detection system, COMPASS, where their alpha-decay signatures were measured.Further details are given in the linked publication.</p> <p>The data format is in comma-separated values format. Columns are as Energy(keV), Counts per energy bin, decay time (seconds) and counts per decay time bin. The decaying nucleus is given for each chain.</p>
Development of a desorption electrospray ionization –multiple-reaction-monitoring mass spectrometry (DESI-MRM) workflow for spatially mapping oxylipins in pulmonary tissue
<p>Data from desorption electrospray ionization mass spectrometry – multiple-reaction-monitoring mass spectrometry (DESI-MRM) analysis of oxylipins in guinea pig lung tissue following<em> in vivo</em> exposure to house dust mite extract.</p> <p>Data are provided as Waters *.raw data folders, each incuding an 'Analyte .txt' file, which is generated from processing within MassLynx (Waters). The 'ion_library.txt' file includes details about the MRM transitions and is required for processing the data with quantMSImageR (<span><a href="https://github.com/targeted-lipidomics/quantMSImageR"><span>https://github.com/targeted-lipidomics/quantMSImageR</span></a></span><span>).</span></p>
Data Set for the Journal Article "Heron: Visualizing and Controlling Chemical Reaction Explorations and Networks"
<p>This data archive contains all data newly created in the following publication:</p> <p>Charlotte H. Müller, Miguel Steiner, Jan P. Unsleber, Thomas Weymuth, Moritz Bensberg, Katja-<br>Sophia Csizi, Maximilian Mörchen, Paul L. Türtscher, and Markus Reiher, "Heron: Visualizing and<br>Controlling Chemical Reaction Explorations and Networks", in preparation.</p> <p>The directory contents are as follows:</p> <ul> <li>steered_eschenmoser.tar.xz: Dump of the database created during the steered exploration</li> <li>steered_exploration_protocol_chemoton_3.1.json: Protocol used for the steered exploration</li> </ul>
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.