A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series

The rates of cell growth, division, and carbon loss of microbial populations are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In recent years, size-structured matrix population models (MPMs) have gained popularity for estimating division rates of microbial populations by mechanistically describing changes in microbial cell size distributions over time. Motivated by the mechanistic structure of these models, we employ a Bayesian approach to extend size-structured MPMs to capture additional biological processes describing the dynamics of a marine phytoplankton population over the day-night cycle. Our Bayesian framework is able to take prior scientific knowledge into account and generate biologically interpretable results. Using data from an exponentially growing laboratory culture of the cyanobacterium Prochlorococcus, we isolate respiratory and exudative carbon losses as critical parameters for the modeling of their population dynamics. The results suggest that this modeling framework can provide deeper insights into microbial population dynamics provided by size distribution time-series data.

An Adaptive Modeling Framework for Bearing Failure Prediction

Rolling element bearings are a common component in rotating equipment, a class of machines that is essential in a wide range of industries. Detecting and predicting bearing failures is then vital for reducing maintenance and production costs due to unplanned downtime. In previous literature, significant efforts have been devoted to building data-driven health models from historical bearing data. However, a common limitation is that these methods are typically tailored to specific failure instances and have limited ability to model bearing failures between repairs in the same system. In this paper, we propose a multi-state health model to predict bearing failures before they occur. The model employs a regression-based method to detect health state transition points and applies an exponential random coefficient model with a Bayesian updating process to estimate time-to-failure distributions. A model training framework is also introduced to make our proposed model applicable to more bearing instances in the same system setting. The proposed method has been tested on a publicly available bearing prognostics dataset. Case study results show that the proposed method provides accurate failure predictions across several system failures, and that the training approach can significantly reduce the time necessary to generate an effective, generalized model.

Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework

Current metabolic modeling tools suffer from a variety of limitations, from scalability to simplifying assumptions, that preclude their use in many applications. We recently created a modeling framework, Linear Kinetics-Dynamic Flux Balance Analysis (LK-DFBA), that addresses a key gap: capturing metabolite dynamics and regulation while retaining a potentially scalable linear programming structure. Key to this framework’s success are the linear kinetics and regulatory constraints imposed on the system. However, while the linearity of these constraints reduces computational complexity, it may not accurately capture the behavior of many biochemical systems. Here, we developed three new classes of LK-DFBA constraints to better model interactions between metabolites and the reactions they regulate. We tested these new approaches on several synthetic and biological systems, and also performed the first-ever comparison of LK-DFBA predictions to experimental data. We found that no single constraint approach was optimal across all systems examined, and systems with the same topological structure but different parameters were often best modeled by different types of constraints. However, we did find that when genetic perturbations were implemented in the systems, the optimal constraint approach typically remained the same as for the wild-type regardless of the model topology or parameterization, indicating that just a single wild-type dataset could allow identification of the ideal constraint to enable model predictivity for a given system. These results suggest that the availability of multiple constraint approaches will allow LK-DFBA to model a wider range of metabolic systems.

Spatiotemporal Associations between Local Safety Level Index and COVID-19 Infection Risks across Capital Regions in South Korea

This study aims provide understanding of the local-level spatiotemporal evolution of COVID-19 spread across capital regions of South Korea during the second and third waves of the pandemic (August 2020~June 2021). To explain transmission, we rely upon the local safety level indices along with latent influences from the spatial alignment of municipalities and their serial (temporal) correlation. Utilizing a flexible hierarchical Bayesian model as an analytic operational framework, we exploit the modified BYM (BYM2) model with the Penalized Complexity (PC) priors to account for latent effects (unobserved heterogeneity). The outcome reveals that a municipality with higher population density is likely to have an elevated infection risk, whereas one with good preparedness for infectious disease tends to have a reduction in risk. Furthermore, we identify that including spatial and temporal correlations into the modeling framework significantly improves the performance and explanatory power, justifying our adoption of latent effects. Based on these findings, we present the dynamic evolution of COVID-19 across the Seoul Capital Area (SCA), which helps us verify unique patterns of disease spread as well as regions of elevated risk for further policy intervention and for supporting informed decision making for responding to infectious diseases.

A Graph-Based Framework for Multiscale Modeling of Physiological Transport

Trillions of chemical reactions occur in the human body every second, where the generated products are not only consumed locally but also transported to various locations in a systematic manner to sustain homeostasis. Current solutions to model these biological phenomena are restricted in computability and scalability due to the use of continuum approaches in which it is practically impossible to encapsulate the complexity of the physiological processes occurring at diverse scales. Here, we present a discrete modeling framework defined on an interacting graph that offers the flexibility to model multiscale systems by translating the physical space into a metamodel. We discretize the graph-based metamodel into functional units composed of well-mixed volumes with vascular and cellular subdomains; the operators defined over these volumes define the transport dynamics. We predict glucose drift governed by advective–dispersive transport in the vascular subdomains of an islet vasculature and cross-validate the flow and concentration fields with finite-element–based COMSOL simulations. Vascular and cellular subdomains are coupled to model the nutrient exchange occurring in response to the gradient arising out of reaction and perfusion dynamics. The application of our framework for modeling biologically relevant test systems shows how our approach can assimilate both multi-omics data from in vitro–in vivo studies and vascular topology from imaging studies for examining the structure–function relationship of complex vasculatures. The framework can advance simulation of whole-body networks at user-defined levels and is expected to find major use in personalized medicine and drug discovery.