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Recent technological advances in high-throughput data collection give biologists the ability to study increasingly complex systems. A new methodology is needed to develop and test biological models based on experimental observations and predict the effect of perturbations of the network (e.g. genetic engineering, pharmaceuticals, gene therapy). Diverse modeling approaches have been proposed, in two general categories: modeling a biological pathway as (a) a logical circuit or (b) a chemical reaction network. Boolean logic models can not represent necessary biological details. Chemical kinetics simulations require large numbers of parameters that are very difficult to accurately measure. Based on the way biologists have traditionally thought about systems, we propose that fuzzy logic is a natural language for modeling biology. The Union Rule Configuration (URC) avoids combinatorial explosion in the fuzzy rule base, allowing complex system models. We demonstrate the fuzzy modeling method on the commonly studied lac operon of E. coli. Our goal is to develop a modeling and simulation approach that can be understood and applied by biologists without the need for experts in other fields or "black-box" software.

Recent technological advances in high-throughput data collection allow for the study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are required to interpret large and complex data sets. Rationally designed system perturbations (e.g. gene knock-outs, metabolite removal, etc) can be used to iteratively refine hypothetical models, leading to a modeling-experiment cycle for high-throughput biological system analysis. We use fuzzy logic gene network models because they have greater resolution than Boolean logic models and do not require the precise parameter measurement needed for chemical kinetics-based modeling. The fuzzy gene network approach is tested by exhaustive search for network models describing cyclin gene interactions in yeast cell cycle microarray data, with preliminary success in recovering interactions predicted by previous biological knowledge and other analysis techniques. Our goal is to further develop this method in combination with experiments we are performing on bacterial regulatory networks.

DNA chips and microarrays are used to profile gene transcription. Unfortunately, the initial fabrication cost for a chip and the reagent costs to amplify thousands of open reading frames for a microarray are over $100K for a typical 4 Mbase bacterial genome. To avoid these expensive steps, a matrix formulation of a universal hybrid chip-microarray approach to transcript profiling is demonstrated for synthetic data. Initial considerations for application to the 4.3 Mbase bacterium Yersinia pestis are also presented. This approach can be applied to arbitrary bacteria by recalculating a matrix and pseudoinverse. This approach avoids the large upfront expenses associated with DNA chips and microarrays.

From October 1994 to June 1997, a multidisciplinary team of scientists and engineers at Lawrence Livermore National Laboratory were funded through LDRD to develop and integrate technologies for diagnosis and treatment of acute stroke. The project was summarized in a Science and Technology Review article `Brain Attack` that appeared in June 1997 and again in the Center for Healthcare Technologies Report (UCRL-LR-124761). This article is the best overview of the project, epidemiology of stroke and technical progress. Most of the technical progress has been documented in conference papers and presentations and refereed journal articles. Additional technical publication can be expected as our remaining patent applications progress through the US Patent and Trademark Office. The purpose of this report is to provide an appropriate introduction and organization to the numerous publications so that interested readers can quickly find information. Because there is no documentation for the history of this project, this report provides a summary. It also provides the final status report for the LDRD funding.

Air- and space-borne platforms using synthetic aperture radars (SAR) have made interferometric measurements by using either two physical antennas mounted on one air-frame or two passes of one antenna over a scene. A new interferometric technique using one pass of a single-antenna SAR system is proposed and demonstrated on data collected by the NASA-JPL AirSAR. Remotely sensed L-band microwave data are used to show the sensitivity of this technique to ocean surface features and provide a baseline for comparison with work by others using two-antenna systems. >

This note describes several computer scripts to assist when using BibT{sub E}X to maintain bibliographical databases. One set of routines are used to generate a list of items contained in a BibT{sub E}X bib'' file which can then be LAT{sub E}X'ed for reference and printing. Another set of routines are used to grep'' for bibliographical entries in a bib'' file as well as ordering existing bib'' files alphabetically. The codes are shell scripts which are call awk programs and run on sun (unix) computers.

It is shown that if sign modulation is applied in both the sample and transform domains to a signal whose dimension is not an integral multiple of four, then a phase error results in the transformed signal. Although this result is inconsequential to radix-two algorithms, it is extremely important to the increasingly popular prime-radix and mixed-radix fast Fourier transform (FFT) algorithms. >

We have designed computer programs to simulate ultrasound projection scans and to reconstruct the tomographic planar image. We have also used the reconstruction algorithm on actual test data and have obtained a crude but promising image. 11 refs., 9 figs.