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Item Response Theory (IRT) and Factor Analysis (FA) are two major frameworks used to model multi-item measurements of latent traits. While the relationship between two-parameter IRT models and dichotomized FA models is well established, IRT…
Survival analysis is one of the most important fields of statistics in medicine and the biological sciences. In addition, the computational advances in the last decades have favoured the use of Bayesian methods in this context, providing a…
Chemotaxis enables marine bacteria to increase encounters with phytoplankton cells by reducing their search times, provided that bacteria detect noisy chemical gradients around phytoplankton. Gradient detection depends on bacterial…
A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions…
Marine viruses shape the structure of the microbial community. They are, thus, a key determinant of the most important biogeochemical cycles in the planet. Therefore, a correct description of the ecological and evolutionary behavior of…
We predict the Fried physical frailty phenotype health deficits (FPFP5: slow gait, weakness, weight loss, low activity, and exhaustion) using two measures of frailty: frailty index (FI) or frailty phenotype (FP). The FP theorizes that the…
Rapid environmental change and advances in data-driven analysis highlight the need not only to use computational tools, but also to foster understanding of the natural world and inspire creativity. Photosynthesis, the process that fuels…
Phagocytosis is a fundamental process of the innate immune system, yet the physical determinants that govern the engulfment of soft, deformable targets remain poorly understood. Existing theoretical models typically approximate targets as…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Bacteriophages spreading through populations of bacteria offer relatively simple, tuneable systems for testing mathematical models of range expansion. However, such models typically assume a static state into which to expand, which is not…
Sepsis is a life-threatening host response to infection associated with high mortality, morbidity, and health costs. Its management is highly time-sensitive since each hour of delayed treatment increases mortality due to irreversible organ…
We seek to understand the probability an individual benefits from treatment (PIBT), an inestimable quantity that must be bounded in practice. Given the innate uncertainty in the population-level bounds on PIBT, we seek to better understand…
The classification of diabetes and prediabetes by static glucose thresholds obscures the pathophysiological dysglycemia heterogeneity, primarily driven by insulin resistance (IR), beta-cell dysfunction, and incretin deficiency. This review…
Blood biomarkers are an essential tool for healthcare providers to diagnose, monitor, and treat a wide range of medical conditions. Current reference values and recommended ranges often rely on population-level statistics, which may not…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
The paper proposes an estimator to make inference of heterogeneous treatment effects sorted by impact groups (GATES) for non-randomised experiments. The groups can be understood as a broader aggregation of the conditional average treatment…
Certain defense mechanisms of phages against the immune system of their bacterial host rely on cooperation of phages. Motivated by this example we analyse invasion probabilities of cooperative parasites in host populations that are…
This paper introduces PyGAD, an open-source easy-to-use Python library for building the genetic algorithm. PyGAD supports a wide range of parameters to give the user control over everything in its life cycle. This includes, but is not…
Why are living systems complex? Why does the biosphere contain living beings with complexity features beyond those of the simplest replicators? What kind of evolutionary pressures result in more complex life forms? These are key questions…