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In information theory, a signature is characterized by the information content as well as noise statistics of the communication channel. Biosignatures have analogous properties. A biosignature can be associated with a particular attribute of a pathogen or a host. However, the signature may be lost in backgrounds of similar or even identical signals from other sources. In this paper, we highlight statistical and signal processing challenges associated with identifying good biosignatures for pathogens in host and other environments. In some cases, it may be possible to identify useful signatures of pathogens through indirect but amplified signals from the host. Discovery of these signatures requires new approaches to modeling and data interpretation. Finally, an understanding of pathways (or gene networks) that are modified through host–pathogen interactions will result in better detectors as well as opportunities in vaccines and therapeutics.

The DNA sequence of the human genome has been determined. This significant scientific milestone has been a multidisciplinary effort sponsored by both public and private investments. Engineering and computer science contributions have been essential to success, especially with the accelerated schedules of the Human Genome Project. A tutorial summary of the biological and health implications of sequencing the human genome is presented together with examples of how genome data from human and other organisms are already used. Engineering contributions to sequencing are identified as well as predictions of how engineering methods may contribute to the "postsequencing" era of biology.

An efficient method for accurately calculating the center-of-rotation, or projection center, for parallel computed tomography projection data, or sinograms, is described. This method uses all the data in the sinogram to estimate the center by a least-squares technique and requires no previous calibration scan. The method also finds the object's center-of-mass without reconstructing its image. Since the method uses the measured data, it is sensitive to noise in the measurements, but that sensitivity is relatively small compared to other techniques. Examples of its use on simulated and actual data are included. For fan-beam data over 360 degrees , two related methods are described to find the center in the presence or absence of a midline offset. >

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.

Summary form only given. Two techniques have been used to design telescope arrays for imaging applications. The first technique is applicable to arrays with a relatively small ( approximately 10), number of apertures and is essentially an exhaustive search with a simple inline test that allows the search space to be pruned by an order of magnitude. In the second technique, arrays of a large number of apertures are designed by combining the results from several arrays with fewer apertures. The criteria is that the best array would maximize the distance from the origin to the position of the first zero in the transfer function (TF). This criterion has been selected to accommodate reconstruction of image phases from phase-difference averages, a process that is sensitive to zeros in the TF. For telescopes with a large number of individually steerable mirrors, the dominant cost moves away from the fabrication of a mirror and towards the cost of beam combination systems and civil engineering. In order to reduce these costs, a fractal-based approach that encourages modular and replicated subsystems has been adopted. >

A class of hybrid domain-iterative algorithms for 2-D image reconstruction is described. The consistent iterative reconstruction-reprojection (CIRR) algorithm was designed and implemented along with other classical domain-iterative methods. The algorithms are tested on the hollow projections problem, where simple object models are assumed known. Results show that the CIRR algorithm is robust and accurate, and converges quickly. >

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.