SOFA--an open source framework for medical simulation.

SOFA is a new open source framework primarily targeted at medical simulation research. Based on an advanced software architecture, it allows to (1) create complex and evolving simulations by combining new algorithms with algorithms already included in SOFA; (2) modify most parameters of the simulation--deformable behavior, surface representation, solver, constraints, collision algorithm, etc.--by simply editing an XML file; (3) build complex models from simpler ones using a scene-graph description; (4) efficiently simulate the dynamics of interacting objects using abstract equation solvers; and (5) reuse and easily compare a variety of available methods. In this paper we highlight the key concepts of the SOFA architecture and illustrate its potential through a series of examples.

DNAid: a Macintosh full screen editor featuring a built-in regular expression interpreter for the search of specific patterns in biological sequences using finite state automata.

DNAid is a full screen and multi-window sequence editor designed as an aid for the easy manipulation of DNA and protein sequences on Macintosh computers. In addition to the classical editing capabilities, powerful analysis and search functions are available from within the editor. Restriction mapping, translation and alignment of homologous sequences are supported by DNAid, furthermore a pattern matching language is included which allows searches for user-defined strict or fuzzy signals within biological sequences. Patterns are translated into finite state automata which allow very efficient searches.

[Membrane phosphatidylethanolamine methylase in blood leukocytes and alveolar macrophages of asthmatic patients]. / Etude de la phosphatidyl ethanolamine méthylase (PEMT) membranaire sur les leucocytes sanguins et les macrophages alvéolaires chez le sujet asthmatique.

Phosphatidyl ethanolamine methylase (PEMT) is an enzyme involved in the methylation of membrane phospholipids which plays a very important role in the modulation of the activity of the beta-receptors and the production of phosphatidylcholine, substrate of phospholipase A2. This report describes a study of PEMT on the membranes of blood leucocytes and alveolar macrophages obtained by bronchoalveolar washings in different types of asthma: allergic, intrinsic and occupational. This was accompanied by parallel study of respiratory function tests and the level of bronchial reactivity to carbachol in asthma sufferers as well as other alveolar biological parameters: phospholipid fractions of surfactant, angiotensin conversion enzyme and protein/albumin ratio. The authors found a significant increase (in comparison with controls) in PEMT activity both in macrophages and leucocytes in cases of intrinsic asthma. However, there was no correlation between the level of activity of the enzyme and the degree of bronchial hyper-reactivity. There was no change in alveolar phospholipid environment. In the light of these findings, the role of membrane activation of the alveolar macrophage is discussed in the physiopathology of intrinsic asthma.