A Retargetable Compilation Methodology for Embedded Digital Signal Processors Using a Machine-Dependent Code Optimization Library

We address the problem of code generation for embedded DSP systems. Such systems devote a limited quantity of silicon to program memory, so the embedded software must be sufficiently dense. Additionally, this software must be written so as to meet various high-performance constraints. Unfortunately, current compiler technology is unable to generate dense, high-performance code for DSPs, due to the fact that it does not provide adequate support for the specialized architectural features of DSPs via machine-dependent code optimizations. Thus, designers often program the embedded software in assembly, a very time-consuming task. In order to increase productivity, compilers must be developed that are capable of generating high-quality code for DSPs. The compilation process must also be made retargetable, so that a variety of DSPs may be efficiently evaluated for potential use in an embedded system. We present a retargetable compilation methodology that enables high-quality code to be generated for a wide range of DSPs. Previous work in retargetable DSP compilation has focused on complete automation, and this desire for automation has limited the number of machine-dependent optimizations that can be supported. In our efforts, we have given code quality higher priority over complete automation. We demonstrate how by using a library of machine-dependent optimization routines accessible via a programming interface, it is possible to support a wide range of machine-dependent optimizations, albeit at some cost to automation. Experimental results demonstrate the effectiveness of our methodology, which has been used to build good-quality compilers for three fixed-point DSPs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Compiling for Reduced Bit-Width Queue Processors

Embedded systems are characterized by the requirement of demanding small memory footprint code. A popular architectural modification to improve code density in RISC embedded processors is to use a reduced bit-width instruction set. This approach reduces the length of the instructions to improve code size. However, having less addressable registers by the reduced instructions, these architectures suffer a slight performance degradation as more reduced instructions are required to execute a given task. On the other hand, 0-operand computers such as stack and queue machines implicitly access their source and destination operands making instructions naturally short. Queue machines offer a highly parallel computation model, unlike the stack model. This paper proposes a novel alternative for reducing code size by using a queue-based reduced instruction set while retaining the high parallelism characteristics in programs. We introduce an efficient code generation algorithm to generate programs for our reduced instruction set. Our algorithm successfully constrains the code to the reduced instruction set with the addition of only 4% extra code, in average. We show that our proposed technique is able to generate about 16% more compact code than MIPS16, 26% over ARM/Thumb, and 50% over MIPS32 code. Furthermore, we show that our compiler is able to extract about the same parallelism than fully optimized RISC code.     

Influence of side chain length on fluorescence intensity of ROMP-based polymeric nanoparticles and their tumor specificity in in-vivo tumor imaging

In this study, amphiphilic brush-like copolymers conjugated with short alkyl or long polymeric chains of various lengths are synthesized using ring-opening metathesis polymerization (ROMP) of substituted norbornadiene monomers followed by chemical transformations. These amphiphilic copolymers form spherical self-assemblies in aqueous media with diameters of 132-244 nm. The low critical aggregation concentration of these assemblies (2.5 × 10(-3) -1.4 × 10(-5) g/L) indicates that they are quite stable in dilute conditions. An appropriate length of polymer side chain that conjugates the polymer backbone with a hydrophobic ICG (indocyanine green) moiety enhanced the fluorescence intensities of these self-assemblies in aqueous solution as well as in tumor-bearing mice. A longer side chain conjugated with tumor targeting agents could significantly affect the tumor specificity of self-assemblies to a greater extent. The self-assemblies bearing hydrophilic tumor targeting agents, such as a glucosamine molecule and a cyclic RGD (arginine-glycine-asparatic acid) peptide, accumulated in tumor tissues with high selectivity, while those having a hydrophobic targeting agent, such as folate moieties, accumulated in tumor sites with low selectivity. The results demonstrated here unambiguously indicate that the fluorescence intensity and tumor specificity of self-assemblies are strongly affected by the length of side chains that conjugate with dyes and targeting agents.     

Immobilization of alkaline phosphatase on magnetic particles by site-specific and covalent cross-linking catalyzed by microbial transglutaminase

Bacterial alkaline phosphatase (BAP) was site-specifically and covalently immobilized on magnetic particles (MPs) using the enzymatic reaction of microbial transglutaminase (MTG). Immobilization efficiency was affected by the chemical surface treatment of MPs and immobilized BAP exhibited more than 90% of the initial activity after 10 rounds of recycling.     

Application of femtosecond laser ablation for detaching grown protein crystals from glass capillary tube

We developed a novel technique for detaching protein crystals from glass capillary tube using the counter diffusion crystallization technique by femtosecond laser irradiation. X-ray diffraction analysis demonstrated that femtosecond laser irradiation has little effect on crystallinity. This technique will contribute to progress in structural genomics as a powerful tool.     

Transgenic melon (cucumis melo L.) and potential for expression of novel proteins important to food industry

Abstract

Melon (Cucumis melo L.) is an important fruit crop cultivated widely in every region of the world. Our laboratory is targeting this species for production of novel proteins important to food industry. Prior to expression of protein of interest in transgenic melon an efficient genetic transformation system has to be developed. In this context we are testing a wide variety of promoters fused to reporter gene for β‐glucuronidase (GUS) for expression specifically in melon fruits. In this study in melon, salicylic acid‐inducible promoter region of pathogenesis‐related protein gene (PR1a) of tobacco fused to β‐glucuronidase (GUS) gene was introduced into melon via Agrobacterium‐mediated gene transfer using a binary vector system. Gene transfer was effective when Agrobacterium virulence factors like acetosyringone (100 μM) and low pH (5.2) were provided during the co‐culture step. Transformed shoots were recovered from benzyladenine‐induced cut cotyledons using kanamycin gene as a selective marker. Regeneration of shoots from cotyledons was stimulated by providing 10 mM proline in the shoot organogenesis medium. Southern and Northern blot analysis of transformants confirmed the presence of β‐glucuronidase gene in two selected clones J‐3 and PR‐G. The transformants also showed high β‐glucuronidase activity after salicylic acid treatment. Thiamine, a previously known inducer of pathogenesis‐related protein, stimulated β‐glucuronidase in J‐3 but not PR‐G melon transformants tested in this study. These studies showed that tobacco PR1a promoter region can be expressed in melon and it was stimulated by salicylic acid. This indicates the potential to use the promoter region of tobacco PR1a for genetic improvement of melon for specific food processing‐related characteristics or for expression of novel food‐related proteins. The promoter region could be used to drive specific target genes under stress or salicylic acid induced conditions.