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Systems Biology Commons

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Full-Text Articles in Systems Biology

'In' Or 'As' Space?: A Model Of Complexity, With Philosophical, Simulatory, And Empirical Ramifications, Charles H. Smith Jan 2015

'In' Or 'As' Space?: A Model Of Complexity, With Philosophical, Simulatory, And Empirical Ramifications, Charles H. Smith

DLPS Faculty Publications

A General Systems model based on ideas originating with the writings of Benedict de Spinoza is described, starting with its philosophical underpinnings, and proceeding on to its relation to modern systems concepts, including attempts to simulate the relationships posed, and measure real world structures. Central to the idea is the notion that spatial extension may not have a prior existence, but emerges only through an entropy maximization process in which information and energy exchange is balanced among some limited number of subsystems that in sum comprise any given functioning complex system. Related published empiricism concerning geographical/geological systems – the hypsometry …


Adding Upstream Sequence And A Downstream Reporter To The Bile Acid Inducible Promoter Of Clostridium Scindens Vpi 12708, Bryan Patrick Mason Aug 2009

Adding Upstream Sequence And A Downstream Reporter To The Bile Acid Inducible Promoter Of Clostridium Scindens Vpi 12708, Bryan Patrick Mason

Masters Theses & Specialist Projects

Bile acids in the small intestines of animals serve to breakdown fats and fatsoluble vitamins. Most of the bile acids are reabsorbed into the enterohepatic circulation, but approximately five percent of these bile acids pass into the large intestine. These bile acids are swiftly deconjugated by the bacterial population, and then subjected to further intestinal bacterial chemical modifications. The most significant of these modifications are 7α-dehydroxylations which form secondary bile acids (deoxycholate and lithocholate). Much research has illuminated the 7α-dehydroxylation pathway: of particular interest is the bile acid inducible operon, for which Clostridium scindens VPI 12708 serves as the model …


Where Do They Go When They Die?, Meridith L. Bartley Jan 2009

Where Do They Go When They Die?, Meridith L. Bartley

Mahurin Honors College Capstone Experience/Thesis Projects

Food webs and matrices are vital to understanding feeding relationships and ecology. Adjacency matrices can be employed to present the direct relationships between predators and prey; these binary matrices utilize 0’s to denote no direct link and 1’s to denote a direct link. We analyzed a variety of published food webs ranging from pine forests in the United States to tussock grasslands in New Zealand. The food webs varied in number of distinguishable taxa present, functional diversity, climates and habitats. Consequently, we expect that our results are not specific to a given system. The published food webs lack flows from …