A program package for molecular simulations of biological molecules was developed. The package, "PEACH version 4 with ABINIT-MP version 20021029," was constructed by incorporating ABINIT-MP, a program for the fragment molecular orbital (FMO) method [Chem.Phys. Lett. 313 (1999) 701], into PEACH, a program package for classical molecular dynamics simulations (MD). A few capabilities of the package were demonstrated. First, high parallel efficiency of FMO was demonstrated in a single point calculation of a protein. Second,FMO-MD simulations [Chem. Phys. Lett. 372 (2003) 342] of a peptide were performed with and without explicit solvent, and the simulations showed the influence of the solvent on the electronic state of the peptide.
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http://dx.doi.org/10.1016/j.compbiolchem.2004.01.003 | DOI Listing |
Respir Res
January 2025
School of Engineering, University of Warwick, Coventry, CV4 7AL, UK.
Introduction And Objectives: High flow nasal cannula (HFNC) therapy is an increasingly popular mode of non-invasive respiratory support for the treatment of patients with acute hypoxemic respiratory failure (AHRF). Previous experimental studies in healthy subjects have established that HFNC generates flow-dependent positive airway pressures, but no data is available on the levels of mean airway pressure (mP) or positive end-expiratory pressure (PEEP) generated by HFNC therapy in AHRF patients. We aimed to estimate the airway pressures generated by HFNC at different flow rates in patients with AHRF, whose functional lung volume may be significantly reduced compared to healthy subjects due to alveolar consolidation and/or collapse.
View Article and Find Full Text PDFJ Transl Med
January 2025
Medical College of YiChun University, Xuefu Road No 576, Yichun, 336000, Jiangxi, People's Republic of China.
Background: Artificial sweeteners (AS) have been widely utilized in the food, beverage, and pharmaceutical industries for decades. While numerous publications have suggested a potential link between AS and diseases, particularly cancer, controversy still surrounds this issue. This study aims to investigate the association between AS consumption and cancer risk.
View Article and Find Full Text PDFJ Transl Med
January 2025
Dental School, The University of Western Australia, 17 Monash Avenue, Nedlands, WA, 6009, Australia.
Background: Treatment of deep carious lesions poses significant challenges in dentistry, as complete lesion removal risks compromising pulp vitality, while selective removal often reduces the longevity of restorations. Herein, we propose a minimally invasive approach using High-Intensity Focused Ultrasound (HIFU) for microscale removal of carious dentine. Concurrently, HIFU's antimicrobial effects against associated cariogenic biofilms and the corresponding thermal and biological impacts on surrounding tissues were investigated.
View Article and Find Full Text PDFNature
January 2025
Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China.
Mimicking the superstructures and properties of spherical biological encapsulants such as viral capsids and ferritin offers viable pathways to understand their chiral assemblies and functional roles in living systems. However, stereospecific assembly of artificial polyhedra with mechanical properties and guest-binding attributes akin to biological encapsulants remains a formidable challenge. Here we report the stereospecific assembly of dynamic supramolecular snub cubes from 12 helical macrocycles, which are held together by 144 weak C-H hydrogen bonds.
View Article and Find Full Text PDFNPJ Syst Biol Appl
January 2025
Center for Interdisciplinary Digital Sciences (CIDS), Department Information Services and High-Performance Computing (ZIH), Dresden University of Technology, 01062, Dresden, Germany.
Predicting the biological behavior and time to recurrence (TTR) of high-grade diffuse gliomas (HGG) after maximum safe neurosurgical resection and combined radiation and chemotherapy plays a pivotal role in planning clinical follow-up, selecting potentially necessary second-line treatment and improving the quality of life for patients diagnosed with a malignant brain tumor. The current standard-of-care (SoC) for HGG includes follow-up neuroradiological imaging to detect recurrence as early as possible and relies on several clinical, neuropathological, and radiological prognostic factors, which have limited accuracy in predicting TTR. In this study, using an in-silico analysis, we aim to improve predictive power for TTR by considering the role of (i) prognostically relevant information available through diagnostics used in the current SoC, (ii) advanced image-based information not currently part of the standard diagnostic workup, such as tumor-normal tissue interface (edge) features and quantitative data specific to biopsy positions within the tumor, and (iii) information on tumor-associated macrophages.
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