Cellular automata simulation of topological effects on the dynamics of feed-forward motifs

<p>Abstract</p> <p>Background</p> <p>Feed-forward motifs are important functional modules in biological and other complex networks. The functionality of feed-forward motifs and other network motifs is largely dictated by the connectivity of the individual network components. While studies on the dynamics of motifs and networks are usually devoted to the temporal or spatial description of processes, this study focuses on the relationship between the specific architecture and the overall rate of the processes of the feed-forward family of motifs, including double and triple feed-forward loops. The search for the most efficient network architecture could be of particular interest for regulatory or signaling pathways in biology, as well as in computational and communication systems.</p> <p>Results</p> <p>Feed-forward motif dynamics were studied using cellular automata and compared with differential equation modeling. The number of cellular automata iterations needed for a 100% conversion of a substrate into a target product was used as an inverse measure of the transformation rate. Several basic topological patterns were identified that order the specific feed-forward constructions according to the rate of dynamics they enable. At the same number of network nodes and constant other parameters, the bi-parallel and tri-parallel motifs provide higher network efficacy than single feed-forward motifs. Additionally, a topological property of isodynamicity was identified for feed-forward motifs where different network architectures resulted in the same overall rate of the target production.</p> <p>Conclusion</p> <p>It was shown for classes of structural motifs with feed-forward architecture that network topology affects the overall rate of a process in a quantitatively predictable manner. These fundamental results can be used as a basis for simulating larger networks as combinations of smaller network modules with implications on studying synthetic gene circuits, small regulatory systems, and eventually dynamic whole-cell models.</p

Inquiry as Practice: The Pathway to Redesigning an Educational Leadership Doctoral Research Seminar Series

As faculty of an educational leadership doctoral program (EdD) aligned with the Carnegie Project on the Education Doctorate (CPED) principles, we acknowledge the importance of inquiry to develop scholarly practitioners. Applying the tenet of Inquiry as Practice, our EdD faculty critically examined the doctoral curriculum to explore ways to effectively prepare our doctoral students to learn and apply research methodology meaningfully. This essay details how the review of our research curriculum led to a pedagogical and curriculum redesign of our research seminar series. This revised research seminar series culminates in a course offered every fall/spring semester in the final two years of the program and intentionally has different faculty members teaching each course. We have utilized a backward design to create the themes/content of these seminar courses to better prepare students for their dissertation research

The Politics of Commerce : The Congress of Chambers of Commerce of the Empire, 1886-1914

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Immune-responses to varicella-zoster in the aged

Skin test reactivity and in vitro lymphocyte stimulation responses to varicella-zoster (VZ) were examined in a large normal population ranging in age from 6 months to 93 years. Waning of cellular immunity, as examined by skin delayed hypersensitivity, began at age 40 years. Skin test responses to phytohemagglutinin, however, remained positive into the eighth decade of life. In vitro lymphocyte stimulation responses to VZ were usually positive (stimulation index ≥2.5) until age 60 years, after which time levels, as observed with nonimmune individuals, were often demonstrated. Antibody levels, as measured by fluorescent antibody to membrane antigen, remained positive into the ninth and tenth decades of life. This was especially so with a history of reactivation (zoster) VZ infections, while skin test and in vitro responses were rarely positive in those individuals. Thus cellular, as contrasted with humoral, immunity decreases with advancing age, which may account for a propensity to reactivation of VZ virus