H.J.W. Spoelder

Estimation of protein secondary structure and error analysis from circular dichroism spectra.

The estimation of protein secondary structure from circular dichroism spectra is described by a multivariate linear model with noise (Gauss-Markoff model). With this formalism the adequacy of the linear model is investigated, paying special attention to the estimation of the error in the secondary structure estimates. It is shown that the linear model is only adequate for the alpha-helix class. Since the failure of the linear model is most likely due to nonlinear effects, a locally linearized model is introduced. This model is combined with the selection of the estimate whose fractions of secondary structure summate to approximately one. Comparing the estimation from the CD spectra with the X-ray data (by using the data set of W.C. Johnson Jr., 1988, Annu. Rev. Biophys. Chem. 17, 145-166) the root mean square residuals are 0.09 (alpha-helix), 0.12 (anti-parallel beta-sheet), 0.08 (parallel beta-sheet), 0.07 (beta-turn), and 0.09 (other). These residuals are somewhat larger than the errors estimated from the locally linearized model. In addition to alpha-helix, in this model the beta-turn and other class are estimated adequately. But the estimation of the antiparallel and parallel beta-sheet class remains unsatisfactory. We compared the linear model and the locally linearized model with two other methods (S. W. Provencher and J. Glöckner, 1981, Biochemistry 20, 1085-1094; P. Manavalan and W. C. Johnson Jr., 1988, Anal. Biochem. 167, 76-85). The locally linearized model and the Provencher and Glöckner method provided the smallest residuals. However, an advantage of the locally linearized model is the estimation of the error in the secondary structure estimates.

Virtual instrumentation: a survey of standards and their interrelation

Many standards exist in the field of instrumentation. The ever increasing scale of integration of processing power with instrumentation has opened ways to extend and transform the functionality of instruments in software, i.e. create a virtual instrument. Controlling and standardizing this virtual instrument requires a multi-level definition. In this paper we review some of the most relevant developments in this field.

Some aspects of pseudo random binary array based surface characterization

In this paper, we report on an algorithm which we have developed to model three-dimensional (3-D) scenes with color-coded Pseudo Random Binary Arrays (PRBAs). The algorithm comprises three steps: first, a graph recovery, then an iterative reinspection, and finally application of the PRBA information. The combination of these three steps allows the algorithm to become auto adaptive to the surface studied. This approach also opens ways to dynamically adapt a PRBA to the surface studied in order to achieve optimal resolution.

A new instrument to measure the shape of the cornea based on pseudorandom color coding

We have developed a prototype instrument providing a new way to measure the shape of the cornea. Our approach exploits properties of pseudorandom binary arrays (PRBAs). Encoded in a colored pattern (stimulus) that is mirrored to the eye, a large PRBA allows for unique identification of unambiguously characterized positions both in stimulus and reflected image. This is used to come to an integral reconstruction of the cornea. It is demonstrated that the new technique contributes to a very robust measurement method.

A study of the robustness of pseudo random binary array based surface characterization

In this article we report on aspects of the use of colour coded Pseudo Random Binary Arrays (PRBAs) to model three dimensional scenes. We will evaluate the accuracy and the robustness of the pattern recognition phase in the process. Emphasis will be on the added value of the use of PRBAs as a tool to make the image processing robust and highly noise insensitive.

A new PRBA-based instrument to measure the shape of the cornea

We have developed a prototype-instrument providing a new way to measure the shape of the cornea. Our approach exploits properties of pseudo random binary arrays (PRBAs). Encoded in a coloured pattern (stimulus) that is mirrored to the eye PRBAs allow for unique characterization of positions both in the stimulus and the reflected image. This is used to come to an integral reconstruction of the cornea. It is demonstrated that the new technique contributes to a very robust measurement method.

Man multi-agent interaction in VR: a case study with RoboCup

We discuss the use of virtual reality (VR) techniques for interaction between humans and a multi-agent system in the context of RoboCup. The goal of RoboCup is to let teams of cooperating autonomous agents play a soccer match, using either robots or simulated players. We use RoboCup to study distributed collaborative applications, which allow multiple users at different geographic locations to cooperate, by interacting in real time through a shared simulation program. Our objective is to construct a VR environment in which humans at different locations can play along with a running RoboCup simulation in a natural way. The simulation system consists of the Soccer Server and a set of processes modeling the players. The server keeps track of the state of the game: provides the players with information on the game, and enforces the rules. The players request state information and autonomously calculate a behavior, sending the server commands that consist of accelerations, turns and kicks. The server discretizes time into slots, only one command is executed per time slot. We have developed a 3D visualization system that allows a user in a CAVE to interact with the soccer simulation software.

Knowledge-based animation of articulated anthropomorphic models for virtual reality applications

This paper presents development aspects of a semi-autonomous animated avatar for real-time interactive virtual environment applications.

SIGNOR: a tool for visualization of concepts of system and signal theory

A tool called SIGNOR, which was developed as a visual signal processing package for a course in signals and systems theory for graduate students, is described. The tool incorporates a generic visual programming environment with a generalized method of interfacing. In the current version of SIGNOR the authors achieve real-time responses for 16-bit samples and up to 40-kHz read/write operations. The generic character of the setup enables the students to easily incorporate their own procedures within the tool. This combination makes SIGNOR a very successful tool.<<ETX>>

Visualization in corneal topography

The anterior surface of the eye (cornea) is extremely important for good sight. Instruments measuring corneal shape conventionally visualize the surface characteristics by mapping the instantaneous radius of curvature onto a rainbow colour scale. This technique is known to have important drawbacks. Firstly, not corneal shape itself is visualized, but rather second order surface properties. Secondly, the type of colouring produces well documented artifacts. We discuss visualization techniques for a more direct representation of the data. In a three part display, shape deviations are presented as a height surface in one window, height lines superimposed over the input image in another, and a colour mapped representation of the mean normal radius of curvature in a third. With the aid of some typical examples, it is shown that these visualizations are easy to interpret by the physician and overcome the limitations of the conventional techniques.