Self-organization of self-clearing beating patterns in an array of locally interacting ciliated cells formulated as an adaptive Boolean network

On Attractor Detection and Optimal Control of Deterministic Generalized Asynchronous Random Boolean Networks

Deterministic asynchronous Boolean networks play a crucial role in modeling and analysis of gene regulatory networks. In this paper, we focus on a typical type of deterministic asynchronous Boolean networks called deterministic generalized asynchronous random Boolean networks (DGARBNs). We first formulate the extended state transition graph, which captures the whole dynamics of a DGARBN and paves potential ways to analyze this DGARBN. We then propose two SMT-based methods for attractor detection and optimal control of DGARBNs. These methods are implemented in a JAVA tool called DABoolNet. Two experiments are designed to highlight the scalability of the proposed methods. We also formally state and prove several relations between DGARBNs and other models including deterministic asynchronous models, block-sequential Boolean networks, generalized asynchronous random Boolean networks, and mixed-context random Boolean networks. Several case studies are presented to show the applications of our methods.

A quantitative interspecies comparison of the respiratory mucociliary clearance mechanism

Collectively coordinated ciliary activity propels the airway mucus, which lines the luminal surface of the vertebrate respiratory system, in cranial direction. Our contemporary understanding on how the quantitative characteristics of the metachronal wave field determines the resulting mucociliary transport is still limited, partly due to the sparse availability of quantitative observational data. We employed high-speed video reflection microscopy to image and quantitatively characterize the metachronal wave field as well as the mucociliary transport in excised bovine, porcine, ovine, lapine, turkey and ostrich samples. Image processing techniques were used to determine the ciliary beating frequency (CBF), the velocity and wavelength of the metachronal wave and the mucociliary transport velocity. The transport direction was found to strongly correlate with the mean wave propagation direction in all six species. The CBF yielded similar values (10–15 Hz) for all six species. Birds were found to exhibit higher transport speeds (130–260 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\upmu$$\end{document}μm/s) than mammals (20–80 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\upmu$$\end{document}μm/s). While the average transport direction significantly deviates from the tracheal long axis in mammals, no significant deviation was found in birds. The metachronal waves were found to propagate at about 4–8 times the speed of mucociliary transport in mammals, whereas in birds they propagate at about the transport speed. The mucociliary transport in birds is fast and roughly follows the TLA, whereas the transport is slower and proceeds along a left-handed spiral in mammals. The longer wavelengths and the lower ratio between the metachronal wave speed and the mucociliary transport speed provide evidence that the mucociliary clearance mechanism operates differently in birds than in mammals.