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669 results for “substitution”
Computed data for "Structural and Electronic Impacts of the Axial Substitution at the Phosphorus Center of C(sp3)-Bridged P-Heterotriangulenes"
<p>Computed structures and TD-DFT raw data of the article "Structural and Electronic Impacts of the Axial Substitution at the Phosphorus Center of C(sp3)-Bridged P-Heterotriangulenes" published in Eur. J. Org.Chem. <a href="https://doi.org/10.1002/ejoc.202400368">https://doi.org/10.1002/ejoc.202400368</a></p>
Dataset of the publication: Tailoring spin waves in 2D transition metal phosphorus trichalcogenides via atomic-layer substitution
<p>Dataset of the publication: Tailoring spin waves in 2D transition metal phosphorus trichalcogenides via atomic-layer substitution</p> <p>DOI: 10.1039/d2dt02482a</p> <p>A. M. Ruiz, DL. Esteras, A. Rybakov, J. J. Baldov </p> <p>Dalton Trans., 54, 44, 16816-16823 (2022)</p>
Carbon-Substituted Amines of the Cobalt Bis(dicarbollide) Ion: Stereochemistry and Acid–Base Properties
<p>Analytical dataset for "Carbon-Substituted Amines of the Cobalt Bis(dicarbollide) Ion: Stereochemistry and Acid–Base Properties"</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>
Structure and stability constrained substitution models outperform traditional substitution models used for evolutionary inference
<p>The current knowledge about how protein structures influence sequence evolution is rarely incorporated into substitution models adopted for phylogenetic inference, which are commonly based on independent with the same substitution process and ignore the known variation of the evolutionary rates across sites with different structural properties. In previous works, we presented site-specific substitution models of protein evolution based on selection on the folding stability of the native state (Stab-CPE), which predict more realistically the evolutionary variability across protein sites. However, those Stab-CPE present qualitative differences from observed data, probably because they ignore changes in the native structure, despite empirical studies suggesting that conservation of the native structure is a strong selective force. Here we present novel structurally constrained substitution models (Str-CPE) based on Julián Echave's model of the structural change due to a mutation as the linear response of the protein to a perturbation and on the explicit model of the perturbation generated by a specific amino-acid mutation. Compared to our previous Stab-CPE models, the novel Str-CPE models are more stringent (they predict lower sequence entropy and substitution rate), provide higher likelihood to multiple sequence alignments (MSA) of the wild-type protein, and better predict the observed substitution rates. Next, we combine Str-CPE and Stab-CPE models to obtain structure and stability constrained substitution models (SSCPE) that fit the empirical MSAs even better. Importantly, these SSCPE models present a relevant improvement of the phylogenetic likelihood for all ten protein families that we analyzed with the program RAxML-NG. We implemented the SSCPE models in the program Prot evol, freely available at <a href="https://github.com/ugobas/Prot_evol">https://github.com/ugobas/Prot_evol</a>.</p>
Supplementary material from: Wolz D, Seidel-Greiff R, Behnisch T, Kruppke I, Kuznik I, Bertram P, Jäger H, Gude M, Cherif C (2024) Potentials of Polyacrylonitrile Substitution by Lignin for Continuous Manufactured Lignin/Polyacrylonitrile-Blend-Based Carbon Fibers
<p>This material contains all research data concerning the analyses conducted in the work taht was published as "<strong>Potentials of Polyacrylonitrile Substitution by Lignin for Continuous Manufactured Lignin/Polyacrylonitrile-Blend-Based Carbon Fibers</strong>" in the <strong>MDPI</strong> journal <strong>Fibers.</strong></p> <p>Process data cannot be included for reasons of confidentiality.</p>
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group. in Distribution of extracellular enzyme-producing bacteria in the digestive tracts of 4 brackish water fish species
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group.
Synergistic homovalent and heterovalent substitution effects on piezoelectric and relaxor behavior in lead-free BaTiO3 ceramics
<p>This study investigates lead-free BaTiO3 (BT) perovskite ceramics, unraveling the synergistic effects arising from simultaneous homovalent (Zr) and heterovalent (Nb) substitution. Focusing on piezoelectric, ferroelectric, and relaxor behaviors, this research employs a comprehensive suite of analyses, including temperature-dependent<br>dielectric measurements, polarization-electric field hysteresis loops, and bipolar strain measurements. Significantly, our study unveils that the simultaneous substitution of Zr and Nb in the BT lattice induces roomtemperature relaxor behavior at relatively low concentrations (5 % Zr and 3 % Nb), yielding higher permittivity and larger maximum polarization compared to single element (Zr or Nb) substituted BT relaxors. Bipolar strain measurements showcase substantial large-signal d33* values (~250 pm/V) across a broad temperature range (–50 ◦C to 30 ◦C) for BT ceramics with simultaneous 5 % Zr and 2 % Nb substitution. This research advances understanding of homovalent and heterovalent substitution in BT ceramics and opens avenues for tailoring properties to suit specific applications. </p>
Towards substitution of invasive telemetry: An integrated home cage concept for unobtrusive monitoring of objective physiological parameters in rodents - Minimal dataset
<p>Minimal dataset for unobtrusive monitoring of vital parameters in rodents.</p>
Virtual Reality as a Substitute for Procedural Sedation During Epidural Steroid Injections
ClinicalTrials.gov study NCT04887285. IPD Sharing: YES. Countries: 1. Publications: 2.
Site-specific structure and stability constrained substitution models improve phylogenetic inference
Open the record for dataset details and reuse information.
Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans
Open the record for dataset details and reuse information.
Model executable, output, drivers and parameters for modeling organism acclimation to changing availability of and requirements for substitutable and interdependent resources
Files used to generate the data for figures in: Rastetter, EB, Kwiatkowski, BL. An approach to modeling resource optimization for substitutable and interdependent resources. Ecological Modelling (2020). https://doi.org/10.1016/j.ecolmodel.2020.109033. This paper presents a hierarchical approach to modeling organism acclimation to changing availability of and requirements for substitutable and interdependent resources. Substitutable resources are resources that fill the same metabolic or stoichiometric need of the organism. Interdependent resources are resources whose acquisition or expenditure are tightly linked (e.g., light, carbon dioxide, and water in photosynthesis and associated transpiration). We illustrate the approach by simulating the development of vegetation with four substitutable sources of nitrogen that differ only in the cost of their uptake and assimilation.
Hydrogen storage properties of Mn and Cu for Fe substitution in TiFe0.9 intermetallic compound - Raw Dataset related to publication
<p>Data type: Experimental measurements and Rietveld Refinement. Date format: .opj, .pcr, .dat (Software FullProf package outputs). Origin of the data: Experimental x-ray diffraction patterns, and kinetic measurements of hydrogen absorption. Data generated by a Bruker D8 Advance Bragg Brentano diffractometer using Cu-Kα radiation (λ=1.5418 Å), and a home-made Sieverts’ type apparatus from CNRS, ICMPE, Thiais, France. Software needed to plot the data: Origin. Software needed to analyse the data: FullProf package.</p>
Oxygen vacancy substitution linked to ferric iron in bridgmanite at 27 GPa
<p>1.1.1 The article file in gold open access publication and supplementary information</p> <p>1.1.2 Data of electron microprobe analysis, Mossbauer spectrscopy and power X-ray diffraction are added</p> <p>1.1.3 SEM images are added</p>
Fundamental hydrogen storage properties of TiFe-alloy with partial substitution of Fe by Ti and Mn - Raw Dataset related to publication
<p>Data type: Experimental measurements and Rietveld Refinement. Date format: .xls, .xlsm,.opj, .pcr, .dat (Software FullProf package outputs). Origin of the data: Experimental EMPA, x-ray diffraction patterns, and kinetic measurements of hydrogen absorption. Data generated by electron probe micro-analysis (Cameca SX100), a Bruker D8 Advance Bragg Brentano diffractometer using Cu-Kα radiation (λ=1.5418 Å), and a home-made Sieverts’ type apparatus from CNRS, ICMPE, Thiais, France. Software needed to plot the data: Origin and Excel. Software needed to analyse the data: FullProf package.</p>
An unusual amino acid substitution within hummingbird cytochrome c oxidase alters a key proton-conducting channel
<p>Hummingbirds in flight exhibit the highest metabolic rate of all vertebrates. The bioenergetic requirements associated with sustained hovering flight raise the possibility of unique amino acid substitutions that would enhance aerobic metabolism. Here, we have identified a non-conservative substitution within the mitochondria-encoded cytochrome <i>c</i> oxidase subunit I (COI) that is fixed within hummingbirds, yet exceedingly rare among other vertebrates. This unusual change is also rare among metazoans, but can be identified in several clades with diverse life histories. We performed atomistic molecular dynamics simulations using bovine and hummingbird COI models, thereby bypassing experimental limitations imposed by the inability to modify mtDNA in a site-specific manner. Intriguingly, our findings suggest that COI amino acid position 153 (bovine numbering system) provides control over the hydration and activity of a key proton channel in COX. We discuss potential phenotypic outcomes linked to this intriguing alteration encoded by the hummingbird mitochondrial genome.</p>
Synthesis of Ti3AuC2, Ti3Au2C2 and Ti3IrC2 by noble-metal substitution reaction in Ti3SiC2 for high-temperature-stable ohmic contacts to SiC
<p>Repository data for paper "Synthesis of Ti<sub>3</sub>AuC<sub>2</sub>, Ti<sub>3</sub>Au<sub>2</sub>C<sub>2</sub> and Ti<sub>3</sub>IrC<sub>2</sub> by noble-metal substitution reaction in Ti<sub>3</sub>SiC<sub>2</sub> for high-temperature-stable ohmic contacts to SiC".</p> <p>Detailed information:</p> <p>Data from calculations include relaxed structures, electronic band-structure (selected compounds), electronic density of states and crystal overlap Hamilton population (selected compounds). In addition, spin-orbit coupling used for selected compounds. Data fro each compound are found in separate zip files. Scripts used to extract data are found in tools.zip.</p> <p>EDX-mapping:<br> Fig1d.xlsx</p> <p>XRD data:<br> Fig1h.xlsx, Fig2g.xlsx, FigS3.xlsx, FigS7a.xlsx</p> <p>I/V-measurements:<br> Fig4c.xlsx, FigS7b.xlsx, FigS13.xlsx</p> <p>Electrical resistance:<br> FigS5.xlsx, FigS14.xlsx</p>
data for publication "Benefits of biobased fertilizers as substitutes for synthetic nitrogen fertilizers: Field assessment combining minirhizotron and UAV-based spectrum sensing technologies"
<p>Dataset for the scientific publication "Benefits of biobased fertilizers as substitutes for synthetic nitrogen fertilizers: Field assessment combining minirhizotron and UAV-based spectrum sensing technologies" in the Journal Frontiers of Environmental Science. </p><p><a href="https://doi.org/10.3389/fenvs.2022.988932">https://doi.org/10.3389/fenvs.2022.988932</a></p>
ESCOTT mutational effect predictions for ProteinGym Substitutions Dataset with Colabfold MSAs
<p>This dataset includes all escott calculations for ProteinGym dataset and the calculations were performed with v1.6.0 of PRESCOTT package. </p> <p>ProteinGym dataset contains 72 proteins and there are 87 experiments performed on these 72 proteins.</p> <p>This dataset is organized into three folders:<br>1-predictions<br>2-analyses<br>3-figures-and-csv-files</p> <p>'predictions' folder has 72 subdirectories, one for each protein.<br>Let's use BLAT as an example to show the most essential files in each protein folder inside 'predictions'.<br>You can find the following files in BLAT_ECOLX_full_11 directory:<br> *aliBLAT.fasta (input file): This is the MSA file used for the calculations and it was obtained with Colabfold.<br> *ranked_0.pdb (input file): This is the pdb model used to deduce structural parameters by escott algorithm.<br> *BLAT_ECOLX_Stiffler_2015.mut (input file): This file is a list of mutations in simple text format. <br> *BLAT_jet.res (data file): This file contains trace(tjet), cv and pc parameters for each amino acid in a protein. This data is produced and used by escott.<br> *BLAT_ECOLX_Stiffler_2015_normPred_evolCombi.txt (output file): This file contains raw (unprocessed) escott predictions. This file is the most important output of escott algorithm.<br> *BLAT_ECOLX_Stiffler_2015_singleline.csv (experimental data file): We compare our escott predictions to the experimental measurements given in this file.<br> <br> <br>'analyses' folder contains 3 types of analyses that we used in our study:<br>1-secondary-structure-analysis<br>2-escott-averages-analysis<br>3-amino-acid-type-analysis</p> <p>'figures-and-csv-files' folder contains png files and their data in csv format.</p>
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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.