Specifying concurrent systems with TSL

The Task Sequencing Language (TSL), which lets programmers specify constraints on the behavior of concurrent programs, is described. The constraints, specified by high-level annotations to Ada programs, are monitored at runtime; when a violation is detected, control is returned to the user, along with information about the nature of the violation. It is argued that such a tool is a necessary crutch for human reasoning capabilities when dealing with the complexities of concurrent process interaction. The first large-scale application of TSL, the specification and validation of a distributed tasking supervisor for Ada, is described     

Virtual machine monitors: current technology and future trends

Developed more than 30 years ago to address mainframe computing problems, virtual machine monitors have resurfaced on commodity platforms, offering novel solutions to challenges in security, reliability, and administration. Stanford University researchers began to look at the potential of virtual machines to overcome difficulties that hardware and operating system limitations imposed: This time the problems stemmed from massively parallel processing (MPP) machines that were difficult to program and could not run existing operating systems. With virtual machines, researchers found they could make these unwieldy architectures look sufficiently similar to existing platforms to leverage the current operating systems. From this project came the people and ideas that underpinned VMware Inc., the original supplier of VMMs for commodity computing hardware. The implications of having a VMM for commodity platforms intrigued both researchers and entrepreneurs.     

New energy transfer dyes for DNA sequencing

We have synthesized a set of four energy transfer dyes and demonstrated their use in automated DNA sequencing. The donor dyes are the 5- or 6-carboxy isomers of 4'-aminomethylfluorescein and the acceptor dyes are a novel set of four 4,7-dichloro-substituted rhodamine dyes which have narrower emission spectra than the standard, unsubstituted rhodamines. A rigid amino acid linker, 4-aminomethylbenzoic acid, was used to separate the dyes. The brightness of each dye in an automated sequencing instrument equipped with a dual line argon ion laser (488 and 514 nm excitation) was 2-2.5 times greater than the standard dye-primers with a 2 times reduction in multicomponent noise. The overall improvement in signal-to-noise was 4- to 5-fold. The utility of the new dye set was demonstrated by sequencing of a BAC DNA with an 80 kb insert. Measurement of the extinction coefficients and the relative quantum yields of the dichlororhodamine components of the energy transfer dyes showed their values were reduced by 20-25% compared with the dichlororhodamine dyes alone.     

Protein crystal growth in microgravity-temperature induced large scale crystallization of insulin

One of the major stumbling blocks that prevents rapid structure determination using x-ray crystallography is macromolecular crystal growth. There are many examples where crystallization takes longer than structure determination. In some cases, it is impossible to grow useful crystals on earth. Recent experiments conducted in conjunction with NASA on various Space Shuttle missions have demonstrated that protein crystals often grow larger and display better internal molecular order than their earth-grown counterparts. This paper reports results from three Shuttle flights using the Protein Crystallization Facility (PCF). The PCF hardware produced large, high-quality insulin crystals by using a temperature change as the sole means to affect protein solubility and thus, crystallization. The facility consists of cylinders/containers with volumes of 500, 200, 100, and 50 ml. Data from the three Shuttle flights demonstrated that larger, higher resolution crystals (as evidenced by x-ray diffraction data) were obtained from the microgravity experiments when compared to earth-grown crystals.     

Human expression recognition from motion using a radial basisfunction network architecture

In this paper a radial basis function network architecture is developed that learns the correlation of facial feature motion patterns and human expressions. We describe a hierarchical approach which at the highest level identifies expressions, at the mid level determines motion of facial features, and at the low level recovers motion directions. Individual expression networks were trained to recognize the "smile" and "surprise" expressions. Each expression network was trained by viewing a set of sequences of one expression for many subjects. The trained neural network was then tested for retention, extrapolation, and rejection ability. Success rates were 88% for retention, 88% for extrapolation, and 83% for rejection.     

Using coverage information to predict the cost-effectiveness ofregression testing strategies

Selective regression testing strategies attempt to choose an appropriate subset of test cases from among a previously run test suite for a software system, based on information about the changes made to the system to create new versions. Although there has been a significant amount of research in recent years on the design of such strategies, there has been very little investigation of their cost-effectiveness. The paper presents some computationally efficient predictors of the cost-effectiveness of the two main classes of selective regression testing approaches. These predictors are computed from data about the coverage relationship between the system under test and its test suite. The paper then describes case studies in which these predictors were used to predict the cost-effectiveness of applying two different regression testing strategies to two software systems. In one case study, the TESTTUBE method selected an average of 88.1 percent of the available test cases in each version, while the predictor predicted that 87.3 percent of the test cases would be selected on average     

Multidimensional visual representations for underwater environmental uncertainty

We investigate how to represent the resulting multivariate information and multidimensional uncertainty by developing and applying candidate visual techniques. Although good techniques exist for visualizing many data types, less progress has been made on how to display uncertainty and multivariate information - this is especially true as the dimensionality rises. At this time, our primary focus is to develop the statistical characterizations for the environmental uncertainty (described only briefly in this article) and to develop a visual method for each characterization. The mariner community needs enhanced characterizations of environmental uncertainty now, but the accuracy of the characterizations is still not sufficient, and therefore formal user evaluations cannot take place at this point in development. We received feedback on the applicability of our techniques from domain experts. We used this in conjunction with previous results to compile a set of development guidelines.     

Variability in function measurements of three sensory foot nerves in neuropathic diabetic patients

Although most short, linear peptide fragments of proteins are unstructured in aqueous solution, a number of immunogenic and antigenic peptides have been shown to have conformational preferences for structured forms. By using mainly NMR and CD spectroscopy, it has been possible to detect and quantify quite small populations of beta-turn, helical, and nascent helical conformations. Recent studies have been published indicating that the presence of structured forms is correlated with the location of T cell and/or B cell epitopes in peptide sequences. X-ray crystal structures of complexes between peptides and anti-peptide antibodies frequently show the peptides bound in beta-turn conformations, and the presence of helix in one peptide-antibody complex has been shown by NMR spectroscopy. Studies of peptides free in solution and bound to anti-peptide antibodies in the crystal indicate that the structure of the principal neutralizing determinant of HIV-1 probably includes at least one beta-turn in a highly conserved region. These results can potentially be used in the design of peptide-based vaccines.     

NMR-based metabolomics: a powerful approach for characterizing the effects of environmental stressors on organism health

It is important to assess the chronic effects of chemical, physical, and biological stressors on organisms in the environment. Appropriate methods must enable rapid, inexpensive, and multibiomarker analyses of organism health. Here we investigate withering syndrome in red abalone (Haliotis rufescens), an important wild and farmed shellfish species along the Pacific coast, using a metabolomic approach that combines the metabolic profiling capabilities of nuclear magnetic resonance spectroscopy (NMR) with pattern recognition methods. Foot muscle, digestive gland, and hemolymph samples were collected from healthy, stunted, and diseased abalone, and the extracts were analyzed by NMR. Following spectral preprocessing, principal components analyses of the metabolite profiles were conducted. Our results confirm that NMR-based metabolomics can successfully distinguish the biochemical profiles of the three groups of animals, in every type of tissue or biofluid studied. Furthermore, this discovery-based approach successfully identified novel metabolic biomarker profiles associated with withering syndrome. The application of these methods for investigating other environmental stressors is discussed, as are the advantages of NMR-based metabolomics for biomonitoring, particularly in conjunction with gene and protein expression profiling.     

Multimodal interaction for 2D and 3D environments [virtual reality]

The allure of immersive technologies is undeniable. Unfortunately, the user's ability to interact with these environments lags behind the impressive visuals. In particular, it's difficult to navigate in unknown visual landscapes, find entities, access information and select entities using six-degrees-of-freedom (6-DOF) devices. We believe multimodal interaction-specifically speech and gesture-will make a major difference in the usability of such environments