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The software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the package are described. They include , for simulating isotropic 2D scattering patterns; , to perform operations on 2D images and masks; , a method for variance estimation of structural invariants through parametric resampling; , which computes the pair distance distribution function by a direct Fourier transform of the scattering data; , to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in for Bayesian consensus-based concentration-independent molecular weight estimation; , an shape analysis method that optimizes the search model directly against the scattering data; , an application to set up the initial search volume for multiphase modelling of membrane proteins; , to perform quasi-atomistic modelling of liposomes with elliptical shapes; , which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; , which reconstructs the shape of an unknown intermediate in an evolving system; and and , for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the graphical interface to Qt5, updating - a plugin to run a subset of tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future releases. All these features are implemented in , freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
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http://dx.doi.org/10.1107/S1600576720013412 | DOI Listing |
Vet Ophthalmol
December 2024
Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel.
Purpose: This study describes the ocular findings in dogs and cats diagnosed with Florida spot keratopathy (FSK) at a single institution.
Methods: Affected animals underwent a single comprehensive ophthalmic examination, with no follow-ups conducted. Data on patient demographics and clinical findings were collected and analyzed.
Biophys J
December 2024
School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel. Electronic address:
Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle X-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures.
View Article and Find Full Text PDFCancer Commun (Lond)
December 2024
Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Photonics Center, Boston University, Boston, Massachusetts, USA.
Background: Adaptative desaturation in fatty acid (FA) is an emerging hallmark of cancer metabolic plasticity. Desaturases such as stearoyl-CoA desaturase (SCD) and fatty acid desaturase 2 (FADS2) have been implicated in multiple cancers, and their dominant and compensatory effects have recently been highlighted. However, how tumors initiate and sustain their self-sufficient FA desaturation to maintain phenotypic transition remains elusive.
View Article and Find Full Text PDFNano Lett
December 2024
Department of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
Interparticle ligand exchange can occur during the formation of nanoparticle superlattices (NPSLs), affecting the symmetry of the NPSLs. Here, we report time-resolved small-angle neutron scattering (TR-SANS) measurements of the interparticle exchange kinetics of thiolate ligands among gold nanoparticles (AuNPs) at different temperatures. To track the ligand exchange among AuNPs, two groups of AuNPs were functionalized with hydrogenated and deuterated dodecanethiol, respectively, and then mixed in a solvent mixture of toluene and deuterated toluene for shell contrast.
View Article and Find Full Text PDFHuan Jing Ke Xue
January 2025
Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
The Qinling-Daba Mountain area, an essential ecological conservation zone in China, occupies a pivotal position in the pursuit of carbon neutrality. Using diverse data sources, including temperature, precipitation, solar radiation, and the Normalized Difference Vegetation Index, we refined the CASA model by replacing model indicators. This enhanced model simulated the net primary productivity of vegetation in the Qinling-Daba Mountain area from 2001 to 2022.
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