Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies.

The growing body of experimental and computational studies suggested that the cross-neutralization antibody activity against Omicron variants may be driven by balance and tradeoff of multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with the epitope residues remain scarcely characterized. In this study, we performed molecular dynamics simulations, ensemble-based deep mutational scanning of SARS-CoV-2 spike residues and binding free energy computations for two distinct groups of broadly neutralizing antibodies : E1 group (BD55-3152, BD55-3546 and BD5-5840) and F3 group (BD55-3372, BD55-4637 and BD55-5514).

AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes.

Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2, which combines randomized alanine sequence masking with shallow multiple sequence alignment subsampling to expand the conformational diversity of the predicted structural ensembles and capture conformational changes between apo and holo protein forms.

Assessing Structures and Conformational Ensembles of Apo and Holo Protein States Using Randomized Alanine Sequence Scanning Combined with Shallow Subsampling in AlphaFold2 : Insights and Lessons from Predictions of Functional Allosteric Conformations.

Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2 that combines randomized alanine sequence masking with shallow multiple sequence alignment subsampling to expand the conformational diversity of the predicted structural ensembles and capture conformational changes between apo and holo protein forms.

Rigorous Models for Vapor Diffusion in Polymers with Immobilization and Chemical Potential Gradients.

Two key phenomena─immobilization and concentration-dependent mixing free energies─simultaneously alter the sorption thermodynamics and diffusion of vapors in materials. This interrelation is leveraged to fit a unified model simultaneously capturing both sorption dynamics and the equilibrium isotherms. This transport model incorporates quasi-equilibrated immobilization reactions and considers Fick's law rigorously in terms of chemical potential gradients rather than concentration gradients.

Predicted Fracture Tendency of Naturally Occurring Aluminum Surface Coatings under Tensile Loading.

Naturally occurring coatings on aluminum metal, such as its oxide or hydroxide, serve to protect the material from corrosion. Understanding the conditions under which these coatings mechanically fail is therefore expected to be an important aspect of predictive models for aluminum component lifetimes. To this end, we develop and apply a molecular dynamics (MD) modeling framework for conducting tension tests that is capable of isolating factors governing the mechanical strength as a function of coating chemistry, defect morphology, and variables associated with the loading path.

Clarifying mechanisms and kinetics of programmable catalysis.

Programmable catalysis-the purposeful oscillation of catalytic potential energy surfaces (PES)-has emerged as a promising method for the acceleration of catalyzed reaction rates. However, theoretical study of programmable catalysis has been limited by onerous computational demands of integrating the stiff differential equations that describe periodic cycling between PESs. This work details methods that reduce the computational cost of finding the limit cycle by ≳10×.

A chemo-mechanical model for describing sorption hysteresis in a glassy polyurethane.

Hysteretic sorption and desorption of water is observed from 0 to 95% relative humidity and 298-333 K on a glassy polyurethane foam. It is postulated that sorption-induced swelling of the glassy polyurethane increases the concentration of accessible hydrogen-bonding adsorption sites for water. The accessibility of sites is kinetically controlled due to the restricted thermal motions of chains in the glassy polymer, causing a difference in accessible site concentrations during sorption and desorption.

Readability of Online Materials in Spanish and English for Breast Reduction Insurance Coverage.

Introduction: Breast reduction surgery aims to alleviate physical discomfort and improve the quality of life for individuals with macromastia. Insurance coverage plays a crucial role in making this surgery accessible, but navigating the complex approval process can be challenging. Online resources have become a primary information source, but limited research exists on the adequacy of online materials, particularly for Spanish-speaking patients.

Patient Understanding of Provider Credentials and Selection of Plastic Surgery Providers.

Background: Many physicians who are not board-certified plastic surgeons have started performing aesthetic procedures, leading to unsafe practices that jeopardize patients' health.

Methods: Patients of a cosmetic and reconstructive private plastic surgery practice were asked to complete a survey that assessed their understanding of plastic surgeon credentials and advertising practices, and what influences their choice of a plastic surgeon.

Results: Eighty-five patients completed the survey, with 37.

A patient-centredness improvement study for efficacy of behaviour change for healthy lifestyle and weight loss in a student-run free clinic.

Background: Primary care is the ideal place to implement behaviour change interventions for weight management. However, most primary care physicians are not managing patient weight as a standard of care due to lack of knowledge, skills and reimbursement. Generating more physicians who are familiar and comfortable with providing weight management is essential in leveraging a global change.

Characterization of a Vivid Homolog in Botrytis cinerea.

Blue light-signaling pathways regulated by members of the light-oxygen-voltage (LOV) domain family integrate stress responses, circadian rhythms and pathogenesis in fungi. The canonical signaling mechanism involves two LOV-containing proteins that maintain homology to Neurospora crassa Vivid (NcVVD) and White Collar 1 (NcWC1). These proteins engage in homo- and heterodimerization events that modulate gene transcription in response to light.