PyGOM - A Python Package for Simplifying Modelling with Systems of Ordinary Differential Equations

Ordinary Differential Equations (ODE) are used throughout science where the capture of rates of change in states is sought. While both pieces of commercial and open software exist to study such systems, their efficient and accurate usage frequently requires deep understanding of mathematics and programming. The package we present here, PyGOM, seeks to remove these obstacles for models based on ODE systems. We provide a simple interface for the construction of such systems backed by a comprehensive and easy to use tool--box. This tool--box implements functions to easily perform common operations for ODE systems such as solving, parameter estimation, and stochastic simulation. The package source is freely available and organized in a way that permits easy extension. With both the algebraic and numeric calculations performed automatically (but still accessible), the end user is freed to focus on model development.Comment: 23 pages, 6 figure

A biomechanical model of traumatic contusional injury produced by controlled cerebrocortical indentation in sheep

International audienceA biomechanical model of traumatic contusional injury was used to map axonal damage and neuronal reaction proximal and distal from the contusion. The model uses a precisely controlled and characterised dynamic indentation of the cerebral cortex of anaesthetised sheep. The indentation (16.15-16.50 mm deep; contact speed 1.2-1.24 m/s) is made through a 20 mm craniotomy in the frontal bone. The brain is then perfused-fixed after 6 hours and sectioned at 5 mm intervals. Immunohistochemistry was used to detect axonal injury and neuronal reaction. Quantitation of injury was by an automatic counting algorithm applied to micrographs of each entire section. These maps were cross-checked with manual counts. The injury was characterised by well-defined zones radiating from the impact point; these were a region of haemorrhagic and necrotic tissue, subadjacent penumbra of axonal injury, and distal multi-focal and diffuse areas of neuronal positivity. The model includes precise characterisation of the contact load and the pattern of injury. This will allow future finite element modelling to be used to explore quantitative relationships between several forms of neural damage and the dynamics of the tissue deformation in a finite element model of the insult

Undergraduate teaching of ideal and real fluid flows: The value of real-world experimental projects

This paper describes the pedagogical impact of real-world experimental projects undertaken as part of an advanced undergraduate Fluid Mechanics subject at an Australian university. The projects have been organised to complement traditional lectures and introduce students to the challenges of professional design, physical modelling, data collection and analysis. An overview of two projects is presented : wind tunnel testing of buildings and wave loading on piles. Both studies are undertaken as group work within the undergraduate subject. The pedagogy of the projects is discussed in terms of the classical educational psychology literature concerning project-based learning, collaborative and guided learning and reflection. In terms of learning outcomes, the primary aim is to enable students to deliver a professional report as the final product, where physical model data are compared to ideal-fluid flow calculations and real-fluid flow analyses. Thus the students are exposed to a professional design approach involving a high level of expertise in fluid mechanics, with sufficient academic guidance to achieve carefully defined learning goals, while retaining sufficient flexibility for students to construct there own learning goals. The overall pedagogy is a blend of problem-based and project-based learning, which reflects academic research and professional practice. The assessment is a mix of peer-assessed oral presentations and written reports that aims to maximise student reflection and development. Student feedback indicated a strong motivation for courses that include a well-designed project component

Slow vacular channels from channels from barley mesophyll cells are regulated by 14-3-3 proteins

The conductance of the vacuolar membrane at elevated cytosolic Ca2+ levels is dominated by the slow activating cation selective (SV) channel. At physiological, submicromolar Ca2+ concentrations the SV currents are very small. Only recently has the role of 14-3-3 proteins in the regulation of voltage-gated and Ca2+-activated plasma membrane ion channels been investigated in Drosophila, Xenopus and plants. Here we report the first evidence that plant 14-3-3 proteins are Involved in the down-regulation of ion channels in the vacuolar membrane as well. Using the patch-clamp technique we have demonstrated that 14-3-3 protein drastically reduces the current carried by SV channels, The current decline amounted to 80% and half-maximal reduction was reached within 5 s after 14-3-3-addition to the bath, The voltage sensitivity of the channel was not affected by 14-3-3. A coordinating role for 14-3-3 proteins in the regulation of plasma membrane and tonoplast ion transporters is discussed. (C) 2001 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved