Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors.

The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa.

SARS-CoV-2 variant transition dynamics are associated with vaccination rates, number of co-circulating variants, and convalescent immunity.

Background: Throughout the COVID-19 pandemic, the SARS-CoV-2 virus has continued to evolve, with new variants outcompeting existing variants and often leading to different dynamics of disease spread.

Methods: In this paper, we performed a retrospective analysis using longitudinal sequencing data to characterize differences in the speed, calendar timing, and magnitude of 16 SARS-CoV-2 variant waves/transitions for 230 countries and sub-country regions, between October 2020 and January 2023. We then clustered geographic locations in terms of their variant behavior across several Omicron variants, allowing us to identify groups of locations exhibiting similar variant transitions.

Transition from susceptible-infected to susceptible-infected-recovered dynamics in a susceptible-cleric-zombie-recovered active matter model.

The susceptible-infected (SI) and susceptible-infected-recovered (SIR) models provide two distinct representations of epidemic evolution, distinguished by whether or not the number of susceptibles always drops to zero at long times. Here we introduce a new active matter epidemic model, the "susceptible-cleric-zombie-recovered" (SCZR) model, in which spontaneous recovery is absent but zombies can recover with probability γ via interaction with a cleric. Upon colliding with a zombie, both susceptibles and clerics enter the zombie state with probability β and α, respectively.