Picard–Vessiot extensions of artinian simple module algebras

AbstractThis paper pursues Takeuchi's Hopf algebraic approach [M. Takeuchi, A Hopf algebraic approach to the Picard–Vessiot theory, J. Algebra 122 (1989) 481–509] to the Picard–Vessiot (PV) theory for differential equations, to involve the PV extensions of difference equations. Differential fields and total difference rings in the standard PV theory are unified here by artinian simple (AS) module algebras over a cocommutative, pointed smooth Hopf algebra

Computational Analysis of Cardiovascular Hemodynamics

The human body requires a complex circulatory system to supply nutrients to, and to remove metabolic waste products from, its tissues. Given this primary purpose, circulatory function is closely related to the hemodynamic characteristics of blood vessels. This includes not only macroscale fluid dynamics, but also mass transfer in the microvasculature. Many experimental and clinical studies have examined these characteristics of vascular function. Over the past 50 years, mathematical modeling has become a powerful adjunct to such studies, as modeling provides a rational framework within which to analyze the cardiovascular system

The primary structure of superoxide dismutase purified from anaerobically maintained Bacteroides gingivalis

AbstractThe superoxide dismutase (SOD) of Bacteroides gingivalis can use either iron or manganese as a cofactor in its catalytic activity. In this study, the complete amino acid sequence of this SOD purified from anaerobically maintained B. gingivalis cells was determined. The proteins consisted of 191 amino acid residues and had a molecular mass of 21 500. The sequence of B. gingivalis SOD showed 44–51% homology with those for iron-specific SODs (Fe-SODs) and 40–45% homology with manganese-specific SODs (Mn-SODs) from several bacteria. However, this sequence homology was considerably less than that seen among the Fe-SOD (65–74%) or Mn-SOD family (42–60%). This indicates that B. gingivalis SOD, which accepts either iron or manganese as metal cofactor, is a structural intermediate between the Fe-SOD and Mn-SOD families

Revision of the taxonomic status of Synthesium elongatum (Ozaki, 1935) (Brachycladiidae), an intestinal digenean of narrow-ridged finless porpoise (Neophocaena asiaeorientalis)

Synthesium elongatum (Brachycladiidae) is an intestinal digenean described from the finless porpoise (Neophocaena asiaeorientalis) in Japan. Few records of this species exist and there is a remarkable morphological similarity between S. elongatum and S. tursionis, such that a synonymy between the species has been suggested previously. However, no morphological and/or molecular analysis has been carried out to clarify the taxonomic status of S. elongatum. In this study, we collected specimens of Synthesium sp. from N. asiaeorientalis in western Japan. The specimens possess lobed testes within the third quarter of the body, a round ovary, and vitellaria extending to level of uterine field,which are diagnostic characters for both S. elongatum and S. tursionis. They were morphologically identified to S. elongatum or S. tursionis due to the fact that the available morphometric data for both species overlap remarkably. A molecular analysis of the mitochondrial ND3 gene showed that the pairwise nucleotide distances between these specimens and S. tursionis were small,and phylogenetic analysis showed that these specimens and S. tursionis are in the same clade. Therefore, it was indicated that S. elongatum and S. tursionis are the same species and,consequently, S. elongatum is a synonym of S. tursionis

A CellML simulation compiler and code generator using ODE solving schemes

Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully simulate a model, boundary conditions and ordinary differential equation (ODE) solving schemes have to be combined with it. Though boundary conditions can be described in CellML, it is difficult to explicitly specify ODE solving schemes using existing tools. In this study, we define an ODE solving scheme description language-based on XML and propose a code generation system for biological function simulations. In the proposed system, biological simulation programs using various ODE solving schemes can be easily generated. We designed a two-stage approach where the system generates the equation set associating the physiological model variable values at a certain time t with values at t + Δt in the first stage. The second stage generates the simulation code for the model. This approach enables the flexible construction of code generation modules that can support complex sets of formulas. We evaluate the relationship between models and their calculation accuracies by simulating complex biological models using various ODE solving schemes. Using the FHN model simulation, results showed good qualitative and quantitative correspondence with the theoretical predictions. Results for the Luo-Rudy 1991 model showed that only first order precision was achieved. In addition, running the generated code in parallel on a GPU made it possible to speed up the calculation time by a factor of 50. The CellML Compiler source code is available for download at http://sourceforge.net/projects/cellmlcompiler