Multiagent systems with workflows

Industry and researchers have two different visions for the future of Web services. Industry wants to capitalize on Web service technology to automate business processes via centralized workflow enactment. Researchers are interested in the dynamic composition of Web services. We show how these two visions are points in a continuum and discuss a possible path for bridging the gap between them.     

Cross-reactivity of ten anti-prostate-specific antigen monoclonal antibodies with human glandular kallikrein

OBJECTIVES: Prostate-specific antigen (PSA) is commonly used as a marker for prostate disease. Prostate epithelium expresses both PSA and human glandular kallikrein (hK2) proteins, which share 80% sequence homology. The immunologic cross-reactivity of these two proteins could potentially interfere with determination of PSA levels in diagnoses of prostate cancer. We set out to determine the extent of this cross-reactivity for a panel of 10 anti-PSA monoclonal antibodies (mAbs). METHODS: Enzyme-linked immunosorbent assay (ELISA), sandwich assays, and western transfer techniques were used to assess the PSA/hK2 cross-reactivity of the anti-PSA mAbs. RESULTS: We did not detect the hK2 protein with any of the 10 anti-PSA mAbs under western transfer conditions. In ELISA experiments, 8 of 10 mAbs exhibited hK2 cross-reactivity under certain conditions. However, no combination of mAbs tested in sandwich assays exhibited a signal in hK2 cross-reactivity experiments greater than 0.1% of the PSA signal. CONCLUSIONS: We have evaluated 10 anti-PSA mAbs and determined that despite the 80% homology between PSA and hK2 proteins, cross-reactivity with hK2 by these antibodies would not significantly affect the determination of PSA levels by means of sandwich assays.     

On the phase composition of polymethylsiloxane derived ceramics

The pyrolysis products of polymethylsiloxanes (PMS) have been studied in order to characterize their phase composition from the viewpoint of equilibrium thermodynamics. Dilatometry measurements and redox analyses with PbO have been conducted and the results analysed and compared with respect to the second law of thermodynamics. In agreement with equilibrium thermodynamics, which shows that there is no ternary compound in the Si–O–C system, the experimental results imply that the pyrolysis residue is an amorphous or nanocrystalline composite consisting of a SiO2-phase matrix with embedded SiC and C particles. These findings seem to contradict the accepted scientific opinion of ternary silicon-oxycarbide phases.     

Parallel programming inPanda

Distributed systems are an alternative to shared-memory multiprocessors for the execution of parallel applications.Panda is a run-time system that provides architectural support for efficient parallel and distributed programming. It supplies fast user-level threads and a means for transparent and coordinated sharing of objects across a homogeneous network. The paper motivates the major architectural choices that guided our design. The problem of sharing data in a distributed environment is discussed, and the performance of the mechanisms provided by thePanda prototype implementation is assessed.     

Acceleration of ungapped extension in Mercury BLAST

The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data efficiently is becoming an increasingly difficult task. There are many available software tools that molecular biologists use for comparing genomic data. This paper focuses on accelerating the most widely used such tool, BLAST. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections to specialized hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone.This paper presents the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and runs at 100 MHz on available FPGAs, making it an effective and powerful component for accelerating biosequence comparisons. The performance of this stage is 25× that of the standard software distribution, yielding close to 50× performance improvement on the complete BLAST application. The sensitivity is essentially equivalent to that of the standard distribution.     

Surface Chemical Study of Sheet Molded Composite (SMC) as Related to Adhesion

Surfaces of commercial sheet molded composite (SMC) materials have been characterized by X-ray photoelectron spectroscopy (XPS) before and after various surface treatments. Surface treatments included cleaning with methylene chloride, abrasion using methylene chloride and a Scotch Brite ® abrasive pad, and application of an isocyanate primer. The pretreated SMC materials were bonded using a polyurethane adhesive. Bonded coupons were tested under a variety of conditions using the lap shear technique. Lap shear test results for specimens bonded following the abrasion and primer pretreatment indicated a favorable fracture force and mode of failure. Surface analysis studies were used to characterize the pretreated and failed surfaces.     

Biosequence Similarity Search on the <Emphasis Type="BoldItalic">Mercury</Emphasis> System

Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described.     

Rainbow trout cytochrome P450s: purification, molecular aspects, metabolic activity, induction and role in environmental monitoring

Cytochromes P450 (P450s or CYPs) constitute a superfamily of heme-thiolate proteins that play important roles in oxidative metabolism of endogenous and exogenous compounds. This review provides some limited history but addresses mainly the research progress on the cytochrome P450s in rainbow trout (Oncorhynchus mykiss), their purification, structures at the primary level, role in metabolism, responses to chemicals and environmental pollutants, application to biomonitoring and the effect of various factors on their expression or activities. Information obtained to date suggests that the rainbow trout P450 systems are as complex as those seen in mammals. Fourteen P450s have been purified from liver or trunk kidney to relatively high specific content. cDNAs belonging to seven different P450 families have been documented from trout liver, kidney and ovary. Two CYP1A genes, nine cDNAs containing open reading frames, and a cDNA fragment were entered into GenBank. Among them, CYP2K1, CYP2K3, CYP2K4, CYP2M1, CYP3A27 and CYP4T1 are the most recently described forms. CYP2K1, CYP2M1 and CYP4T1 represent newly identified P450 subfamilies first described in the rainbow trout. In many cases, the cloned rainbow trout P450s have subsequently been expressed in heterologous expressions systems such as COS-7 cells, yeast and baculovirus infected insect cells. Some of the overexpressed P450 isoforms have been partially characterized. Potential future research directions are discussed.     

Detection of ATP by “in line” 31P magnetic resonance spectroscopy during oxygenated hypothermic pulsatile perfusion of pigs’ kidneys

Object

To demonstrate that adenosine triphosphate (ATP), which provides a valuable biomarker for kidney viability in the context of donation after cardiac death (DCD) transplantation, can be detected by means of ³¹P magnetic resonance spectroscopy (MRS) if kidneys are perfused with oxygenated hypothermic pulsatile perfusion (O₂+HPP).

Materials and methods

Porcine kidney perfusion was carried out using a home made, MR-compatible HPP-machine. Consequently, kidney perfusion could be performed continuously during magnetic resonance imaging and magnetic resonance spectroscopy recording. ³¹P MR spectroscopy consisted of 3-dimensional chemical shift imaging (CSI), which allowed for the detection of ATP level in line. ³¹P CSI was performed at 3?tesla in 44?min with a nominal voxel size of 6.1?cc.

Results

³¹P CSI enabled the detection of renal ATP when pO₂ was equal to 100?kPa. With pO₂ of 20?kPa, only phosphomonoester, inorganic phosphate and nicotinamide adenine dinucleotide could be found. Semi-quantitative analysis showed that ATP level was 1.3?mM in normal kidney perfused with pO₂ of 100?kPa.

Conclusions

This combined technology may constitute a new advance in DCD organ diagnostics prior to transplantation, as it allows direct assessment of ATP concentration, which provides a reliable indicator for organ bioenergetics and viability. In this study, kidneys presenting no warm ischemia were tested in order to establish values in normal organs. The test could be easily integrated into the clinical environment and would not generate any additional delay into the transplantation clinical workflow.