Engineered nanoparticles are advantageous for biotechnology applications including biomolecular sensing and delivery. However, testing compatibility and function of nanotechnologies in biological systems requires a heuristic approach, where unpredictable protein corona formation prevents their effective implementation. We develop a random forest classifier trained with mass spectrometry data to identify proteins that adsorb to nanoparticles based solely on the protein sequence (78% accuracy, 70% precision). We model proteins that populate the corona of a single-walled carbon nanotube (SWCNT)–based nanosensor and study the relationship between the protein’s amino acid–based properties and binding capacity. Protein features associated with increased likelihood of SWCNT binding include high content of solvent-exposed glycines and nonsecondary structure–associated amino acids. To evaluate its predictive power, we apply the classifier to identify proteins with high binding affinity to SWCNTs, with experimental validation. The developed classifier provides a step toward undertaking the otherwise intractable problem of predicting protein-nanoparticle interactions.
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http://dx.doi.org/10.1126/sciadv.abm0898 | DOI Listing |
Open Forum Infect Dis
January 2025
Division of Infectious Diseases, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
Background: Identifying risk factors for mortality in patients with bacteremia (SAB) is crucial due to its high fatality. However, data on risk factors for infection-attributable deaths considering competing risk events such as non-infection-attributable deaths remain limited. We performed a competing risk analysis to elucidate risk factors associated with 30-day infection-attributable mortality in a large cohort of patients with SAB.
View Article and Find Full Text PDFFront Immunol
December 2024
College of Pharmacy, University of Houston, Houston, TX, United States.
Background: Proton pump inhibitors (PPIs) are one of the most used drugs worldwide. While generally considered safe, the usage of PPIs is associated with several adverse outcomes including acute infectious diseases. PPIs influence macrophage and neutrophil function although a systematic review has never been undertaken.
View Article and Find Full Text PDFTheranostics
January 2025
Department of Nephrology, China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Beijing, 100029, China.
The tertiary structure of normal podocytes prevents protein from leaking into the urine. However, observing the complexity of podocytes is challenging because of the scale differences in their three-dimensional structure and the close proximity between neighboring cells in space. In this study, we explored podocyte-secreted angiopoietin-like 4 (ANGPTL4) as a potential morphological marker via super-resolution microscopy (SRM).
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December 2024
African Society for Bioinformatics and Computational Biology, Cape Town, South Africa.
Introduction: Dengue Fever continues to pose a global threat due to the widespread distribution of its vector mosquitoes, and . While the WHO-approved vaccine, Dengvaxia, and antiviral treatments like Balapiravir and Celgosivir are available, challenges such as drug resistance, reduced efficacy, and high treatment costs persist. This study aims to identify novel potential inhibitors of the Dengue virus (DENV) using an integrative drug discovery approach encompassing machine learning and molecular docking techniques.
View Article and Find Full Text PDFCureus
December 2024
Department of Critical Care Medicine, Citizens Specialty Hospital, Hyderabad, IND.
Background: Sepsis is a life-threatening condition arising from a dysregulated host response to infection leading to organ dysfunction. Traditional clinical signs are often unreliable for detecting sepsis, necessitating the exploration of more accurate biomarkers. Furthermore, currently, recommended screening scores perform poorly, necessitating more effective biomarkers to identify sepsis.
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