A test for the statistical significance of DNA sequence similarities for application in databank searches

A method is developed, based on word-searching, which provides a rapid test for the statistical significance of DNA sequence similarities for use in databank searching. The method makes allowance for the lengths and dinucleotide compositions of the sequences being compared. A way is also described to calculate the power of the test, i.e. the probability of detecting a given similarity as being statistically significant. The effects on the power of the test of the scoring method, word length, sequence length, and sequence composition are examined. A novel scoring method is shown to be superior to the method currently used in most word-searching algorithms.     

Static and pulsed pressures measured using electrically conducting rubbers

A method of measuring static and pulsed pressures using electrically conducting rubber sensors is proposed. The method is based on a change in the volume resistivity of a filled rubber under the action of external pressure. The pressure-induced change in resistance of the rubber sensor is proportional to the applied pressure and can be measured by a bridge circuit. Using this method, it is possible to evaluate the degree of homogeneity of the pressure distribution over a solid surface. This is achieved by distributing rubber sensors over the given surface.     

An experiment for showing some kind of artificial understanding

In this paper we design an experiment which can be depicted as a simple scenario, a very limited 'world'. In this world, there are an actor that can pursue a project and an observer that is keeping its eyes on the actor. We try to show in the experiment that the observer can to some degree understand the actor based on its knowledge and some metaphors, i.e. understand what the actor is doing and why. As the conclusion of this experiment, we try to show some features of 'understanding'. These are (1) that 'understanding' has to be based on some preliminary knowledge; (2) that 'understanding' is a process of incremental learning; (3) that, as for symbolic systems, some metaphors are necessary for mapping real entities into concepts in mind.     

Standing on Solid Ground

The new Editor in Chief of IEEE Micro introduces himself and the first issue of 2007. He thanks outgoing Editor in Chief Pradip Bose for his outstanding work on Micro during his tenure. He assesses the current state of the microarchitecture field, speculates on the future, and asks readers for their suggestions on topics the magazine should cover in coming issues.     

Bioavailability and Toxicity of Metal Nutrients during Anaerobic Digestion

This paper investigates the effect of chelating agents on the bioavailability of Fe and Cu during anaerobic digestion. The results on metal speciation and methane production in anaerobic serum bottles showed that biomass was able to grow in the presence of citrate 1?mM and nitrilotriacetic acid (NTA) 1?mM, suggesting that the binding sites at the cell surface competed efficiently for the metals with the chelating agents added. The presence of free ethylenediaminetetraacetic acid 1?mM inhibited methanogenesis, and this seemed to be related to a loss in metal uptake capacity. Although the addition of soluble microbial products (SMP) did not change metal distribution in anaerobic systems, it caused an increase in the rate of methane production, and it is believed that direct uptake of Cu-SMP complexes was responsible for this increase. The best protection against Cu toxicity occurred when stoichiometric amounts of NTA, which should complex and solubilize most of the Cu, was added, and it is likely that NTA prevented lethal concentrations of Cu from being adsorbed onto the cell and hence internalized.     

An intrinsic observer for a class of Lagrangian systems

We propose a new design method of asymptotic observers for a class of nonlinear mechanical systems: Lagrangian systems with configuration (position) measurements. Our main contribution is to introduce a state (position and velocity) observer that is invariant under any changes of the configuration coordinates. The observer dynamics equations, as the Euler-Lagrange equations, are intrinsic. The design method uses the Riemannian structure defined by the kinetic energy on the configuration manifold. The local convergence is proved by showing that the Jacobian of the observer dynamics is negative definite (contraction) for a particular metric defined on the state-space, a metric derived from the kinetic energy and the observer gains. From a practical point of view, such intrinsic observers can be approximated, when the estimated configuration is close to the true one, by an explicit set of differential equations involving the Riemannian curvature tensor. These equations can be automatically generated via symbolic differentiations of the metric and potential up to order two. Numerical simulations for the ball and beam system, an example where the scalar curvature is always negative, show the effectiveness of such approximation when the measured positions are noisy or include high frequency neglected dynamics.