Related papers: Antibiotic resistance: Insights from evolution exp…
Purpose: Antimicrobial resistance is a major global health concern, affecting hospital admissions and treatment success. This study aims to introduce an experimental setup for monitoring bacterial activity over time using image-based…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
The contribution to an organism's phenotype from one genetic locus may depend upon the status of other loci. Such epistatic interactions among loci are now recognized as fundamental to shaping the process of adaptation in evolving…
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis,…
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular…
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,"…
The evolution of the adaptive immune system is characterized by changes in the relative abundances of the B- and T-cell clones that make up its repertoires. To fully capture this evolution, we need to describe the complex dynamics of the…
Epidemic spreading over populations networks has been an important subject of research for several decades, and especially during the Covid-19 pandemic. Most epidemic outbreaks are likely to create multiple mutations during their spreading…
The spreading of evolutionary novelties across populations is the central element of adaptation. Unless population are well-mixed (like bacteria in a shaken test tube), the spreading dynamics not only depends on fitness differences but also…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We here present a generic stochastic model…
The gap in statistics between multi-variate and time-series analysis can be bridged by using entropy statistics and recent developments in multi-dimensional scaling. For explaining the evolution of the sciences as non-linear dynamics, the…
The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore…
In the studies of dynamics of pathogens and their interactions with a host immune system, an important role is played by the structure of antigenic variants associated with a pathogen. Using the example of a model of antigenic variation in…
Mastitis is a billion dollar health problem for the modern dairy industry, with implications for antibiotic resistance. The use of AI techniques to identify the early onset of this disease, thus has significant implications for the…
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…
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to…
A fundamental problem in technological studies is how to measure the evolution of technology. The literature has suggested several approaches to measuring the level of technology (or state-of-the-art) and changes in technology. However, the…
This paper introduces a stochastic adaptive dynamics model for the interplay of several crucial traits and mechanisms in bacterial evolution, namely dormancy, horizontal gene transfer (HGT), mutation and competition. In particular, it…
Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…