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.     

Anaerobic biodecolorization of textile reactive anthraquinone and phthalocyanine dyebaths under hypersaline conditions.

The biological decolorization of two industrial, spent textile reactive dyebaths was investigated using a suspended-growth, halophilic mixed culture fed with glucose. Dyebath I contained mainly Reactive Blue 19 (RB19), an anthraquinone dye, whereas dyebath II contained mainly Reactive Blue 21 (RB21), a phthalocyanine dye. Batch assays under anaerobic conditions with the two neutralized dyebaths resulted in 87 and 37% extent of decolorization for dyebaths I and II, respectively. The rate of glucose utilization and the extent of acetate production were impacted in the presence of each dyebath as compared to the control culture. However, dyebath decolorization occurred despite moderate culture inhibition. Reuse of a biologically renovated RB19-containing dyebath in the dyeing process resulted in reproducible but not identical cotton fabric shades as compared to a standard dyeing (i.e., control) using fresh water. This difference is attributed to a variable degree of RB19 aggregation during the dyeing process and is not related to the efficiency of the biodecolorization process. Further improvement of the redyeing efficiency will lead to the development of an in-plant, closed-loop decolorization system resulting in significant water conservation and minimization of textile pollutants such as salt and dyes.     

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.     

Analysis and synthesis of on-chip spiral inductors

This paper presents a physically based compact model for estimating high-frequency performance of spiral inductors. The model accurately accounts for skin and proximity effects in the metal conductors as well as eddy current losses in the substrate. The model shows excellent agreement with measured data mostly within 10% across a variety of inductor geometries and substrate dopings up to 20 GHz. A web-based spiral inductor synthesis and analysis tool COILS, which makes use of the compact models, is presented. An optimization algorithm using binary searches speeds up the synthesis of inductor designs.     

The Metaflow architecture

The Metaflow architecture, a unified approach to maximizing the performance of superscalar microprocessors, is introduced. The Metaflow architecture exploits inherent instruction-level parallelism in conventional sequential programs by hardware means, without relying on optimizing compilers. It is based on a unified structure, the DRIS (deferred-scheduling, register-renaming instruction shelf), that manages out-of-order execution and most of the attendant problems. Coupling the DRIS with a speculative-execution mechanism that avoids conditional branch stalls results in performance limited only be inherent instruction-level parallelism and available execution resources. Although presented in the context of superscalar machines, the technique is equally applicable to a superpipelined implementation. Lightning, the first implementation of the Metaflow architecture, which executes the Sparc RISC instruction set is described