Visual insights into high-resolution earthquake Simulations.

This study focuses on the visualization of a series of large earthquake simulations collectively called TeraShake. The simulation series aims to assess the impact of San Andreas Fault earthquake scenarios in Southern California. We discuss the role of visualization in gaining scientific insight and aiding unexpected discoveries.     

Exploiting ILP, TLP, and DLP with the polymorphous trips architecture

The Tera-op reliable intelligently adaptive processing system (TRIPS) architecture seeks to deliver system-level configurability to applications and runtime systems. It does so by employing the concept of polymorphism, which permits the runtime system to configure the hardware execution resources to match the mode of execution and demands of the compiler and application.     

Combustion synthesis of advanced materials: Part I. Reaction parameters

An explanation of combustion (self propagating high temperature) synthesis (SHS) is given together with a historical perspective of the examination of such exothermic reactions. The application of thermochemical functions has been used to predict theoretically the maximum adiabatic temperature, T_ad. This, combined with a knowledge of the ignition temperature, T_ig, and the actual combustion temperature, T_c, has been used to determine the heat loss from the SHS reaction and the amount of heat needed to raise the adjacent, cold, reactant layer to the ignition temperature in order to maintain the self sustaining nature of the propagating mode of the reaction. The pertinent reaction parameters that control self propagating high temperature (combustion) synthesis reactions have been examined. These include: reactant particle size and shape; powder mixing and compaction; green density; reaction stoichiometry; impurities; volatiles and diluents; reaction environment; mode and technique of ignition; heating rate; and the effect of these parameters on the generation of heat, exothermicity and control of the SHS reaction.     

Role of IL-4 and IFN-gamma in modulation of immunity to Borrelia burgdorferi in mice

Because T cells appear to modulate the severity of murine Borrelia burgdorferi infections, we decided to examine the possible involvement of T cell-associated cytokines in disease outcome. Comparison of in vitro B. burgdorferi Ag-induced cytokine production in disease-susceptible and -resistant strains revealed striking differences; spleen cells from susceptible C3H mice produced significantly higher levels of IL-2 and IFN-gamma and lower levels of IL-4 than spleen cells from resistant BALB/c mice. Lymph node responses were even more divergent, with C3H mice producing high levels of IFN-gamma, and BALB/c mice producing little or none. This apparent Th1/Th2 cytokine imbalance was also reflected in vivo, since serum from C3H had significantly higher levels of B. burgdorferi-specific IgG2a Ab and lower levels of IgG1 Ab than serum from BALB/c mice. In vivo studies confirmed the importance of IL-4 in early control of spirochete growth, since treatment of either strain with neutralizing anti-IL-4 mAb led to increased joint swelling and higher spirochete burdens in joints compared with those in control mAb-treated mice. In contrast, IFN-gamma may hinder early control of spirochete growth in susceptible C3H mice, since treatment of mice with neutralizing anti-IFN-gamma mAb reduced both joint swelling and joint spirochete burdens compared with those in control mAb-treated mice. These studies indicate opposing roles for IL-4 and IFN-gamma in the modulation of spirochete growth and disease development in B. burgdorferi-infected mice and suggest that differential cytokine production early in infection may contribute to strain-related differences in susceptibility.     

Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, an HO endonuclease-induced double-strand break can be repaired by at least two pathways of nonhomologous end joining (NHEJ) that closely resemble events in mammalian cells. In one pathway the chromosome ends are degraded to yield deletions with different sizes whose endpoints have 1 to 6 bp of homology. Alternatively, the 4-bp overhanging 3' ends of HO-cut DNA (5'-AACA-3') are not degraded but can be base paired in misalignment to produce +CA and +ACA insertions. When HO was expressed throughout the cell cycle, the efficiency of NHEJ repair was 30 times higher than when HO was expressed only in G1. The types of repair events were also very different when HO was expressed throughout the cell cycle; 78% of survivors had small insertions, while almost none had large deletions. When HO expression was confined to the G1 phase, only 21% were insertions and 38% had large deletions. These results suggest that there are distinct mechanisms of NHEJ repair producing either insertions or deletions and that these two pathways are differently affected by the time in the cell cycle when HO is expressed. The frequency of NHEJ is unaltered in strains from which RAD1, RAD2, RAD51, RAD52, RAD54, or RAD57 is deleted; however, deletions of RAD50, XRS2, or MRE11 reduced NHEJ by more than 70-fold when HO was not cell cycle regulated. Moreover, mutations in these three genes markedly reduced +CA insertions, while significantly increasing the proportion of both small (-ACA) and larger deletion events. In contrast, the rad5O mutation had little effect on the viability of G1-induced cells but significantly reduced the frequency of both +CA insertions and -ACA deletions in favor of larger deletions. Thus, RAD50 (and by extension XRS2 and MRE11) exerts a much more important role in the insertion-producing pathway of NHEJ repair found in S and/or G2 than in the less frequent deletion events that predominate when HO is expressed only in G1.     

A formal model of asynchronous communication and its use in mechanically verifying a biphase mark protocol

We present a formal model of asynchronous communication between two digital hardware devices. The model takes the form of a function in the Boyer-Moore logic. The function transforms the signal stream generated by one processor into that consumed by an independently clocked processor, given the phases and rates of the two clocks and the communications delay. The model can be used quantitatively to derive concrete performance bounds on communications at ISO protocol level 1 (physical level). We use the model to show that an 18-bit/cell biphase mark protocol reliably sends messages of arbitrary length between two processors provided the ratio of the clock rates is within 5% of unity.