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The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining mutational processes, horizontal gene transfer and resource consumption, is one of the…

Populations and Evolution · Quantitative Biology 2020-03-09 Ramsès Djidjou-Demasse , Samuel Alizon , Mircea T. Sofonea

Consumption of antimicrobial drugs, such as antibiotics, is linked with antimicrobial resistance. Surveillance of antimicrobial drug consumption is therefore an important element in dealing with antimicrobial resistance. Many countries lack…

Information Retrieval · Computer Science 2018-03-12 Niels Dalum Hansen , Kåre Mølbak , Ingemar Cox , Christina Lioma

Antibiotics are a vital class of drugs closely associated with the prevention and treatment of bacterial infections. Accurate prediction of molecular antimicrobial activity remains a key challenge in the pursuit of novel antibiotic…

Quantitative Methods · Quantitative Biology 2025-09-23 R. He

Near-field hydrodynamic interactions between bacteria and no-slip solid surfaces are the main mechanism underlying surface entrapment of bacteria. In this study, we employ a chiral two-body model to simulate bacterial dynamics near the…

Soft Condensed Matter · Physics 2026-02-25 Baopi Liu , Lu Chen , Haiqin Wang

Skin and soft tissue infections (SSTIs) are among the most frequently observed diseases in ambulatory and hospital settings. Resistance of diverse bacterial pathogens to antibiotics is a significant cause of severe SSTIs, and treatment…

Machine Learning · Computer Science 2022-03-01 Farnaz H. Foomani , Shahzad Mirza , Sahjid Mukhida , Kannuri Sriram , Zeyun Yu , Aayush Gupta , Sandeep Gopalakrishnan

How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can…

Biological Physics · Physics 2019-09-12 Stanislaw Makarchuk , Vasco C. Braz , Nuno A. M. Araújo , Lena Ciric , Giorgio Volpe

This work introduces a new statistical physics lattice model of bacteria interacting with anti-microbial drugs that can reproduce qualitative features of resistance emergence and whose model parameters and outputs can be measured with…

Populations and Evolution · Quantitative Biology 2017-05-17 Roberto C. Alamino

Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…

Machine Learning · Statistics 2020-04-13 Travis E. Gibson , Georg K. Gerber

The concepts and methods of Systems Biology are being extended to neuropharmacology, to test and design drugs against neurological and psychiatric disorders. Computational modeling by integrating compartmental neural modeling technique and…

Neurons and Cognition · Quantitative Biology 2007-05-23 Peter Erdi , Tamas Kiss , Janos Toth , Balazs Ujfalussy , Laszlo Zalanyi

Fecal Microbiota Transplant (FMT) is an FDA approved treatment for recurrent Clostridium difficile infections, and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to priming the…

From soap-covered dishes to freshly cleaned floors, surfactants can make surfaces slippery; yet, the underlying mechanism remains poorly understood. Here, we identify the molecular origin behind this ubiquitous phenomenon using macroscopic…

A study of the induced effect of different types of weak magnetic field exposure on bacterial growth is performed, comparing the relative changes after removal from the magnetic fields. This investigation is relevant to understand the…

Biological Physics · Physics 2019-12-03 Samina Masood , Iram Saleem , Derek Smith , Wei-Kan Chu

Rapid antimicrobial susceptibility testing (AST) is urgently needed for treating infections with correct antibiotics and slowing down the emergence of antibiotic-resistant bacteria. Here, we report a phenotypic platform that rapidly…

Learning how proteins fold will hardly have any impact in the way conventional -- active site centered -- drugs are designed. On the other hand, this knowledge is proving instrumental in defining a new paradigm for the identification of…

Biomolecules · Quantitative Biology 2012-03-16 R. A. Broglia

Many bacterial species readily develop biofilms that act as a protective matrix against external challenge, e.g. from antimicrobial treatment. Therefore, biofilms are often responsible for persistent and recurring infections. Established…

The human microbiome has an important role in determining health. Mediation analyses quantify the contribution of the microbiome in the causal path between exposure and disease; however, current mediation models cannot fully capture the…

Applications · Statistics 2023-01-09 Yuka Moroishi , Zhigang Li , Juliette C. Madan , Hongzhe Li , Margaret R. Karagas , Jiang Gui

Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of…

Quantitative Methods · Quantitative Biology 2024-09-12 Jeff Meilander , J. Gregory Caporaso

Since penicillin was discovered about 90 years ago, we have become used to using drugs to eradicate unwanted pathogenic cells. However, using drugs to kill bacteria, viruses or cancer cells has the serious side effect of selecting for…

Populations and Evolution · Quantitative Biology 2017-08-02 Matti Gralka , Diana Fusco , Stephen Martis , Oskar Hallatschek

Dynamics of a bubble impacting and sliding a tilted surface has been investigated through experimental and computational methods. \textcolor{blue}{Specifically, shear stress generated on the wall has been calculated and compared with…

Fluid Dynamics · Physics 2018-10-30 Ehsan Esmaili , Pranav Shukla , Joseph D. Eifert , Sunghwan Jung

Antibiotic resistance, which is a serious healthcare issue, emerges due to uncontrolled and repeated antibiotic use that causes bacteria to mutate and develop resistance to antibiotics. The Antibiotics Time Machine Problem aims to come up…

Optimization and Control · Mathematics 2025-01-22 Deniz Tuncer , Burak Kocuk