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4,010 results for “Stabilization”
The Role of Buffer, Pyridoxal 5'-Phosphate and Light on the Stability of the Silicibacter Pomeroyi Transaminase
<p>Transaminases are pyridoxal 5’-phosphate (PLP)-dependent enzymes that transfer amino-functions. The transaminase from <em>Silicibacter pomeroyi</em> (SpATA) exhibits a broad substrate spectrum. In this work we examined the effect of different conditions (light, buffer and PLP-concentration) on the stability of SpATA, as well as the causes for these effects. The enzyme was stored either in TRIS or CHES with 0–10 mM added PLP at 22 °C. The samples were either kept dark or they were exposed to light. The results show that invariably, all samples kept in darkness exhibited longer half-life times than the ones exposed to light. An increase in the half-life from 8 h to 720 h could be achieved solely by keeping the sample dark. Especially samples in CHES buffer inactivated faster in light the more PLP was present, due to the degradation of PLP. In TRIS however, an imine-bond between TRIS and PLP protects PLP from degradation.</p>
Relaxation effects in twisted bilayer molybdenum disulfide: structure, stability, and electronic properties
<p><strong>Abstract</strong></p> <p>Manipulating the interlayer twist angle is a powerful tool to tailor the properties of layered two-dimensional crystals. The twist angle has a determinant impact on these systems' atomistic structure and electronic properties. This includes the corrugation of individual layers, formation of stacking domains and other structural elements, and electronic structure changes due to the atomic reconstruction and superlattice effects. However, how these properties change with the twist angle, <em>θ</em>, is not yet well understood. Here, we monitor the change of twisted bilayer (tBL) MoS<sub>2</sub> characteristics as a function of <em>θ</em>. We identify distinct structural regimes, each with particular structural and electronic properties. We employ a hierarchical approach ranging from a reactive force field through the density-functional-based tight-binding approach and density-functional theory. To obtain a comprehensive overview, we analyzed a large number of tBLs with twist angles in the range of <span class="math-tex">\(\theta=0.2^\circ\dots59.6^\circ\)</span>. Some systems include up to half a million atoms, making structure optimization and electronic property calculation challenging. For <span class="math-tex">\(13^\circ \lessapprox \theta \lessapprox 47^\circ\)</span>, the structure is well-described by a moiré regime composed of two rigidly twisted monolayers. At small twist angles (<span class="math-tex">\(\theta\leq3^\circ\)</span> and <span class="math-tex">\(57^\circ\leq\theta\)</span>), a domain-soliton regime evolves, where the structure contains large triangular stacking domains, separated by a network of strain solitons and short-ranged high-energy nodes. The corrugation of the layers and the emerging superlattice of solitons and stacking domains affects the electronic structure. Emerging predominant characteristic features are Dirac cones at <em>K</em> and kagome bands. These features flatten for <em>θ</em> approaching 0<sup>∘</sup> and 60<sup>∘</sup>. Our results show at which range of <em>θ</em> the characteristic features of the reconstruction, namely extended stacking domains, the soliton network, and superlattice, emerge and give rise to exciting electronics. We expect our findings also to be relevant for other tBL systems.</p> <p>DOI: 10.1088/2053-1583/aceb75</p> <p><strong>Overview</strong></p> <p>This repository contains calculation files, optimized structures, and visualization movies for studies of twisted-bilayer MoS<sub>2</sub>, focussing on structural properties and electronic structure. Each directory has its own README.md file with additional information, separated by what data is included and the method used.</p> <p><strong>Geometry optimization</strong></p> <ul> <li>Directory `calc_structure_optimization_ReaxFF`: calculation files of the structure optimization of all studied structures, done with ReaxFF.</li> <li>Directory `calc_structure_optimization_DFT`: validation calculation files of the ReaxFF-optimized structures using DFT optimization.</li> </ul> <p><strong>Electronic structure calculations</strong></p> <ul> <li>Directory `calc_electronic_properties_DFT`: calculation files of electronic structure calculations on the DFT level.</li> <li>Directory `calc_electronic_properties_DFTB`: calculation files of electronic structure calculations on the DFTB level</li> </ul> <p><strong>Results</strong></p> <ul> <li>Directory `structures_rigidly_twisted`: structure files in cif format of the rigidly twisted (flat) systems, labeled by their twist angle.</li> <li>Directory `structures_fully_optimized`: structure files in cif format of the fully ReaxFF-optimized systems, labeled by their twist angle.</li> <li>Directory `movies`: visualization of the change of the interlayer distance landscape and the strain fields with the twist angle.</li> <li>Additionally, the script `plot_interlayer_distance.py` is included, which was used to create the individual frames of the movie showing the interlayer distance.</li> </ul>
Data from: A stabilizing eco-evolutionary feedback loop in the wild
<p><span>Eco-evolutionary dynamics are predicted to involve feedback loops, where ecological changes driven by rapid evolution feed back to shape further evolution. However, direct experimental evidence for such loops in the wild is lacking. Here, we show that eco-evolutionary dynamics in a plant-feeding arthropod community involve a negative feedback loop. Specifically, adaptation in cryptic coloration in an abundant stick-insect species mediates bird predation, with local maladaptation increasing predation. In turn, the abundance of arthropods is reduced by predation. Here, we experimentally manipulate arthropod abundance to show that these community-level changes feedback to affect stick-insect evolution. Specifically, low arthropod abundance increases the strength of selection on crypsis, increasing local adaptation of stick insects in a negative feedback loop. Our results suggest that eco-evolutionary feedbacks are able to stabilize complex systems by preventing consistent directional change and therefore increasing resilience.</span></p>
Stability and change in male fertility patterns by cognitive ability across 32 birth cohorts
<p>The relationship between cognitive ability (CA) and childbearing remains unsettled. Using Norwegian administrative registers with population coverage, we study how male lifetime fertility patterns differ across cognitive score groups, and how these changed across the 1950–1981 birth cohorts, covering a period characterized by rapid social and economic change. The analyses reveal systematic differences in fertility and fertility timing across CA groups, with high-scoring males having delayed but ultimately higher fertility than lower-scoring males. This pattern remains stable over time despite strong trends towards delayed and reduced fertility. The overall positive relationship between CA and fertility is primarily driven by high rates of childlessness in the lowest-scoring group, with low-scoring males showing higher rates of parity progression conditional on having children.</p>
Changes in vertical and horizontal diversities mediated by the size structure of introduced fish collectively shape food-web stability
<p><span>Species introductions can alter local food-web structure by changing the vertical or horizontal diversity within communities, largely driven by their body size distributions. Increasing vertical and horizontal diversities is predicted to have opposing effects on stability. However, their interactive effects remain largely overlooked. We investigated the independent and collective effects of vertical and horizontal diversities on food-web stability</span><span> in alpine lakes stocked with variable body size distributions of introduced fish species. I</span><span>ntroduced predators destabilize food-webs by </span><span>increasing vertical diversity through food chain lengthening</span><span>. Alternatively, increasing horizontal diversity results in more </span><span>stable food-web topologies. A non-linear interaction between vertical and horizontal diversities </span>suggests that increasing vertical diversity is most destabilizing when horizontal diversity is low<span>.</span> <span>Our findings suggest </span>that the size structure of introduced predators drives their impacts on stability by modifying the structure of food-webs, and highlights the <span>interactive effects of vertical and horizontal diversities on stability.</span></p>
FireProtDB + PDB Structural Protein Stability Dataset
<p>Dataset compiled and curated for use in the ThermoMPNN paper: <a href="https://doi.org/10.1073/pnas.2314853121">https://doi.org/10.1073/pnas.2314853121</a>: </p> <p>Dataset for training models for prediction of thermodynamic stability changes (ddG) of protein point mutations given a wildtype protein structure (PDB) file. Data was assembled by matching sequence-based ddG measurements in <a href="https://loschmidt.chemi.muni.cz/fireprotdb/">FireProtDB</a> to structures from the <a href="https://www.rcsb.org/">RCSB Protein Data Bank </a>(PDB). For details, see the Methods section of our manuscript.</p> <p>Citing this work: If you choose to use this dataset for your own research, please cite this repository and the ThermoMPNN paper: <a href="https://doi.org/10.1073/pnas.2314853121">https://doi.org/10.1073/pnas.2314853121</a>.</p> <p> </p> <p>Contents:</p> <p>pdbs/ directory contains all PDB files</p> <p>csvs/ directory contains all CSVs with mutation data</p> <p>csvs/4_fireprotDB_bestpH.csv is the main (full) dataset file with 3,438 mutations across 100 proteins.</p> <p>csvs/fireprot_splits.pkl contains the dataset splits (train/val/test) used in our study</p> <p>csvs/splits/ contains csvs for each of the splits (train/val/test/homologue-free) indexed from the full dataset csv.</p> <p>Important CSV columns:</p> <ul> <li>pdb_id_corrected: corresponds to the PDB in the pdbs/ directory (after curation and disambiguation)</li> <li>ddG: ddG value for mutation (mutant - WT)</li> <li>wild_type: wild-type amino acid (1-letter code)</li> <li>mutation: mutant amino acid (1-letter code)</li> <li>pdb_position: 0-based index of the mutated residue in the PDB file (may be different from position in the original FireProtDB sequence entry)</li> </ul> <p> </p>
MarTREC Publication forBio-Inspired Stabilization of Levee Slope on Expansive Yazoo Clay at the Maritime and Multimodal Transportation Infrastructure in Mississippi
<p>The link considers the data file for the MarTREC Project: Bio-Inspired Stabilization of Levee Slope on Expansive Yazoo Clay at the Maritime and Multimodal Transportation Infrastructure in Mississippi.</p> <p>PI: Dr. Sadik Khan</p> <p>Funding Agency: This material is based upon work supported by the U.S. Department of Transportation under Grant Award Number DTRT13-G-UTC50. The work was conducted through the Maritime Transportation Research and Education Center at the University of Arkansas.</p>
Dataset for "Stabilizing the inverted phase of a WSe2/BLG/WSe2 heterostructure via hydrostatic pressure"
<p>Measurement dataset for the article "Stabilizing the inverted phase of a WSe2/BLG/WSe2 heterostructure via hydrostatic pressure".</p>
Changes in NT-proBNP, Safety, and Tolerability in HFpEF Patients With a WHF Event (HFpEF Decompensation) Who Have Been Stabilized and Initiated at the Time of or Within 30 Days Post-decompensation (PA
ClinicalTrials.gov study NCT03988634. IPD Sharing: YES. Countries: 2. Publications: 6.
Comparison of Sacubitril/Valsartan Versus Enalapril on Effect on NT-proBNP in Patients Stabilized From an Acute Heart Failure Episode.
ClinicalTrials.gov study NCT02554890. IPD Sharing: YES. Countries: 1. Publications: 8.
Data from: Dominant species stabilize pollination services through response diversity, but not cross-scale redundancy
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Data from: The pathogenic E139D mutation stabilizes a non-canonical active state of the multi-domain phosphatase SHP2
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Data from: Functional diversity shapes the stability of reef fish biomass under global change
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Can predators stabilize host-parasite interactions? Changes in aquatic predator identity alters amphibian responses and parasite abundance across life stages
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Data from: Stability of fecal microbiota during degradation in ex situ Cheetahs in the US
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Examining the diversity, stability and functioning of marine fish communities across a latitudinal gradient
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Data from: Evolutionary stability inferred for a free ranging lizard with sex-reversal
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G-matrix stability of clinally diverging populations of an annual weed
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Site-specific structure and stability constrained substitution models improve phylogenetic inference
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Data from : Variation in salmon migration phenology bolsters population stability but is threatened by drought
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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.