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123 results for “structuring mechanisms”
Data from: Mechanical and structural adaptations to migration in the flight feathers of a Palaearctic passerine
<p>Current avian migration patterns in temperate regions have been developed during the glacial retreat and subsequent colonization of the ice-free areas during the Holocene. This process resulted in a geographic gradient of greater seasonality as latitude increased that favoured migration-related morphological and physiological (co)adaptations. Most evidence of avian morphological adaptations to migration comes from the analysis of variation in the length and shape of the wings, but the existence of intra-feather structural adjustments has been greatly overlooked despite their potential to be under natural selection. To shed some light on this question, we used data from European robins Erithacus rubecula overwintering in Campo de Gibraltar (Southern Iberia), where sedentary robins coexist during winter with conspecifics showing a broad range of breeding origins and, hence, migration distances. We explicitly explored how wing length and shape, as well as several functional (bending stiffness), developmental (feather growth rate) and structural (size and complexity of feather components) characteristics of flight feathers varied in relation to migration distance, which was estimated from the hydrogen stable isotope ratios of the summer-produced tail feathers. Our results revealed that migration distance not only favoured longer and more concave wings, but also promoted primaries with a thicker dorsoventral rachis and shorter barb lengths, which in turn conferred more bending stiffness to these feathers. We suggest that these intra-feather structural adjustments could be an additional, largely unnoticed, adaptation within the avian migratory syndrome that might have the potential to evolve relatively quickly to facilitate the occupation of seasonal environments.</p>
Data presented in Crustal structure and anisotropy measured by CHINArray and implications for complicated deformation mechanisms beneath the eastern Tibetan margin
<p>The dataset includes the raw waveforms and receiver functions presented in the paper Crustal structure and anisotropy measured by CHINArray and implications for complicated deformation mechanisms beneath the eastern Tibetan margin, submitted to JGR Solid Earth.</p><p>Contact: Zengsijia@cug.edu.cn</p><p> </p>
Azole resistance mechanisms and population structure of Aspergillus fumigatus on retail plant products
<p><em>Aspergillus fumigatus </em>is a ubiquitous saprotroph and human-pathogenic fungus that is life-threatening to the immunocompromised. Triazole-resistant <em>A. fumigatus</em><em> </em>was found in patients without prior treatment with azoles, leading researchers to conclude that resistance had developed in agricultural environments where azoles are used against plant pathogens. Previous studies have documented azole-resistant <em>A. fumigatus </em>across agricultural environments, but few have looked at retail plant products. Our objectives were to determine if azole-resistant <em>A. fumigatus </em>is prevalent<em> </em>in retail plant products produced in the United States (U.S.), as well as to identify the resistance mechanism(s) and population genetic structure of these isolates. Five hundred twenty-five isolates were collected from retail plant products and screened for azole resistance. Twenty-four isolates collected from compost, soil, flower bulbs, and raw peanuts were pan-azole resistant. Resistant isolates had the TR<sub>34</sub>/L98H, TR<sub>46</sub>/Y121F/T289A, G448S, and H147Y <em>cyp51A </em>alleles, all known to underly pan-azole resistance, as well as WT alleles, suggesting that non-cyp51A-mechanisms contribute to pan-azole resistance in some isolates. Minimum spanning networks showed two lineages containing isolates with TR alleles or the F46Y/M172V/E427K allele, and discriminant analysis of principle components (DAPC) identified three primary clusters. This is consistent with previous studies detecting three clades of <em>A. fumigatus</em> and identifying pan-azole-resistant isolates with TR alleles in a single clade. We found pan-azole resistance in U.S. retail plant products, particularly compost and flower bulbs, which indicates the risk of exposure to these products for susceptible populations and that highly resistant isolates are likely distributed worldwide on these products.</p>
Data and code for the article "Hierarchical tensile structures with ultralow mechanical dissipation"
<p>Data and code for the article "Hierarchical tensile structures with ultralow mechanical dissipation", consisting of all the ringdown measurements, spectra and codes for data analysis and generation of the fabrication GDS masks.</p>
A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2
<p>Data produced and analyzed in the manuscript "A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2" by Pasquadibisceglie et al.</p> <p><br> If you include these data in your manuscript, please cite: Pasquadibisceglie A, Leccese A and Polticelli F (2022) A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2. <em>Front. Chem.</em> 10:1004815. doi: 10.3389/fchem.2022.1004815</p>
Encapsulation Enhances the Catalytic Activity of C-N Coupling: Reaction Mechanism of a Cu(I)/Calix[8]arene Supramolecular Catalyst - XYZ Structure files
<p>XYZ Structures corresponding to DOI: 10.1002/cctc.202200662</p>
Input data of the multi-patch geometries used in: A. Farahat, H. M. Verhelst, J. Kiendl, M. Kapl, Isogeometric analysis for multi-patch structured Kirchhoff–Love shells, Computer Methods in Applied Mechanics and Engineering 411 (2023) 116060 DOI: 10.1016/j.cma.2023.116060
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6th International Conference "Fracture Mechanics of Materials and Structural Integrity" (June 3–6, 2019, Lviv, Ukraine)
<p><strong>12.06.2019</strong></p> <p>03–06 червня 2019 року у м. Львові відбулася 6-та Міжнародна конференція з механіки руйнування матеріалів і цілісності конструкцій (“Fracture Mechanics of Materials and Structural Integrity”, FMSI 2019). Співорганізаторами конференції виступили Європейське товариство з цілісності конструкцій (European Structural Integrity Society, ESIS), Українське товариство з механіки руйнування матеріалів, Фізико-механічний інститут імені Г.В. Карпенка НАН України та Національний університет “Львівська політехніка”.</p> <p><em>Матеріали прес-служби НАН України</em></p>
T2* and quantitative susceptibility mapping in an equine model of post-traumatic osteoarthritis: prediction of mechanical and structural properties
<p>Dataset for the manuscript titled "T2* and quantitative susceptibility mapping in an equine model of post-traumatic osteoarthritis: assessment of mechanical and structural properties"</p>
Molecular Simulation Elaborating the Structural Mechanism of Spiri forming nitrilase from Bacillus safensis
<p><span>Nitrilases are indispensable in the biocatalytic hydrolysis of nitrile compounds, which presents promising applications in industrial biocatalysis and environmental remediation. In this study, we conduct an extensive investigation into the structural and functional properties of <em>Bacillus safensis </em>nitrilase (<em>BsNIT</em>), highlighting its assembly, substrate binding mechanisms, stability, evolutionary relationships, and active site conservation. Using a combination of molecular modeling and extensive molecular dynamics simulations, we unveil the intricate architecture of <em>BsNIT</em>, which exhibits a left-handed spiri-forming structure stabilized by interchain interactions and salt-bridge formations. The substrate-binding pocket, surrounded by aromatic residues, displays multifaceted accessibility through distinct channels. Our simulations reveal substrate-specific catalytic orientations, with glutaronitrile and 4-cyanobutanoic acid displaying stable binding, while benzonitrile exhibits a propensity for rapid product diffusion. Analysis of active site conservation emphasizes the functional significance of preserved catalytic residues, providing insights into <em>BsNIT</em>'s catalytic efficiency. This comprehensive study offers a thorough understanding of <em>BsNIT</em>'s structure-function relationships, paving the way for future advancements in enzyme engineering and bioremediation strategies targeting nitrile pollutants.</span></p>
Data from: Parallel mechanisms signal a hierarchy of sequence structure violations in the auditory cortex
<p>The brain predicts regularities in sensory inputs at multiple complexity levels, with neuronal mechanisms that remain elusive. Here, we monitored auditory cortex activity during the local-global paradigm, a protocol nesting different regularity levels in sound sequences. We observed that mice encode local predictions based on stimulus occurrence and stimulus transition probabilities, because auditory responses are boosted upon prediction violation. This boosting was due to both short-term adaptation and an adaptation-independent surprise mechanism resisting anesthesia. In parallel, and only in wakefulness, VIP interneurons responded to the omission of the locally expected sound repeat at sequence ending, thus providing a chunking signal potentially useful for establishing global sequence structure. When this global structure was violated, by either shortening the sequence or ending it with a locally expected but globally unexpected sound transition, activity slightly increased in VIP and PV neurons respectively. Hence, distinct cellular mechanisms predict different regularity levels in sound sequences.</p>
Supplemental material to 'A variational rigid-block modelling approach to nonlinear elastic and kinematic analysis of failure mechanisms in historic masonry structures subjected to lateral actions'
<p>This repository contains the data necessary to reproduce the content of the article:</p> <blockquote> <p>A variational rigid-block modelling approach to nonlinear elastic and kinematic analysis of failure mechanisms in historic masonry structures subjected to lateral actions (2021). Earthquake Engineering & Structural Dynamics, 1–23. <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/eqe.3512">https://doi.org/10.1002/eqe.3512</a></p> </blockquote> <p>The file <strong>01_Dataset.zip</strong> contains the dataset. The companion document <strong>00_Dataset_description.pdf </strong>describes the content of the dataset, guiding the analyst to its use in order to (i) reproduce the article's results and (ii) compare the article's results to new results brought by the analyst, e.g. by comparison with other numerical models.</p> <p>Version history</p> <p>v2: updated references in 00_dataset description.pdf </p>
Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms: Molecular dynamics coordinate and trajectory files
<p>Molecular dynamics files associated with the publication: Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms</p>
Vascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides
<p>MD simulation data for vascular KATP channel focusing on Kir6.1-pore and SUR2B in the presence and absence of MgADP. </p>
Data for "Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota"
<p>MD simulation data of OxlT. Trajectory data and NAMD input files are included. The first 500 ns trajectory that starts from the occluded conformation with a transition to the outward-open conformation is in the OxlT-occ directory. The 200 ns trajectories that start from the outward-open conformation with different protonation states of K355 are in the OxlT-out directory. </p>
Data for: A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA
<p><span>Productive transcriptional elongation of many cellular and viral mRNAs requires transcriptional factors to extract pTEFb from the 7SK snRNP by modulating the association between the HEXIM protein and the 7SK snRNA. Here we report the structure of the HEXIM arginine-rich motif in complex with the apical stemloop-1 of 7SK (7SK-SL1<sup>apical</sup>) and detail how the HIV transcriptional regulator Tat from various subtypes overcome the structural constraints required to displace HEXIM. While most interactions between 7SK and HEXIM and Tat are similar, critical differences exist that guide function. First, the conformational plasticity of 7SK enables the formation of three different base pair configurations at a critical remodeling site, which allows for the modulation required for HEXIM binding and its subsequent displacement by Tat. Furthermore, the specific sequence variations observed in various Tat subtypes all converge on remodeling 7SK at this region. Second, we show that HEXIM primes its own displacement by causing specific local destabilization upon binding </span>— <span>a feature that is then exploited by Tat to bind 7SK more efficiently. Overall, our study details the molecular environment presented by HEXIM and uncovers a destabilization-driven displacement strategy that increases the conformational sampling of 7SK-snRNP, which may allow diverse transcriptional factors to competitively regulate pTEFb.</span></p>
Response mechanism of residual strength to meso-structure of shear surface in gravelly slip zone of ancient landslide
<p>Response mechanism of residual strength to meso-structure of shear surface in gravelly slip zone of ancient landslide-Original data</p>
Data for: A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA
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Data from: Structural and mechanical properties facilitate shock wave damping by helmet-like orbital hoods in snapping shrimp
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Data from: Grassland restoration characteristics influence phylogenetic and taxonomic structure of plant communities and suggest assembly mechanisms
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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.