mlegp: statistical analysis for computer models of biological systems using R

Microfoundations of the weakening educational gradient in fertility

The disappearance of the social gradient in fertility represents a paradigm shift that has called into question the validity of theories that predicted a decline in fertility with increased access to education and resources. Emerging theories have tried to explain this trend by highlighting a potential change in the fertility preferences of more educated couples. In this paper we add additional elements to this explanation. Using a computational modelling approach, we show that it is still possible to simulate the weakening social gradient in fertility, in the context of steady declines in family size preferences. Our results show that one of the key drivers of the change in the education-fertility relationship can be found in the transition to an increasingly regulated fertility regime. As the share of unplanned births decreases over time, the negative association between education and fertility weakens and the mechanisms that positively connect educational attainment with desired fertility become dominant.

Demographic models of the reproductive process: Past, interlude, and future

After 30 years of active development, mechanistic models of the reproductive process nearly stopped attracting scholarly interest in the early 1980s. In the following decades, fertility research continued to thrive, relying on solid descriptive work and detailed analysis of micro-level data. The absence of systematic modelling efforts, however, has also made the field more fragmented, with empirical research, theory building, and forecasting advancing along largely disconnected channels. In this paper we outline some of the drivers of this process, from the popularization of user-friendly statistical software to the limitations of early family building models. We then describe a series of developments in computational modelling and statistical computing that can contribute to the emergence of a new generation of mechanistic models. Finally, we introduce a concrete example of this new kind of model, and show how they can be used to formulate and test theories coherently and make informed projections.

High-resolution computational modeling of immune responses in the gut

Background

Helicobacter pylori causes gastric cancer in 1–2% of cases but is also beneficial for protection against allergies and gastroesophageal diseases. An estimated 85% of H. pylori–colonized individuals experience no detrimental effects. To study the mechanisms promoting host tolerance to the bacterium in the gastrointestinal mucosa and systemic regulatory effects, we investigated the dynamics of immunoregulatory mechanisms triggered by H. pylori using a high-performance computing–driven ENteric Immunity SImulator multiscale model. Immune responses were simulated by integrating an agent-based model, ordinary, and partial differential equations.

Results

The outputs were analyzed using 2 sequential stages: the first used a partial rank correlation coefficient regression–based and the second a metamodel-based global sensitivity analysis. The influential parameters screened from the first stage were selected to be varied for the second stage. The outputs from both stages were combined as a training dataset to build a spatiotemporal metamodel. The Sobol indices measured time-varying impact of input parameters during initiation, peak, and chronic phases of infection. The study identified epithelial cell proliferation and epithelial cell death as key parameters that control infection outcomes. In silico validation showed that colonization with H. pylori decreased with a decrease in epithelial cell proliferation, which was linked to regulatory macrophages and tolerogenic dendritic cells.

Conclusions

The hybrid model of H. pylori infection identified epithelial cell proliferation as a key factor for successful colonization of the gastric niche and highlighted the role of tolerogenic dendritic cells and regulatory macrophages in modulating the host responses and shaping infection outcomes.