Characterizing distributed shared memory performance: a case studyof the Convex SPP1000

In a distributed shared memory (DSM) multiprocessor, the processors cooperate in solving a parallel application by accessing the shared memory. The latency of a memory access depends on several factors, including the distance to the nearest valid data copy, data sharing conditions, and traffic of other processors. To provide a better understanding of DSM performance and to support application tuning and compiler development for DSM systems, this paper extends microbenchmarking techniques to characterize the important aspects of a DSM system. We present an experiment-based methodology for characterizing the memory, communication, scheduling, and synchronization performance, and apply it to the Convex SPP1000. We present carefully designed microbenchmarks to characterize the performance of the local and remote memory, producer-consumer communication involving two or more processors, and the effects on performance when multiple processors contend for utilization of the distributed memory and the interconnection network     

A practical look at ATPG

Book Reviewed: Digital Logic Testing and Simulation, 2nd edition, by Alexander Miczo (Wiley-Interscience, 2003, ISBN 0-471-43995-9, 696 pp., $115).     

A bi-labeling based XPath processing system

We present BLAS, a Bi-LAbeling based XPath processing System. BLAS uses two labeling schemes to speed up query processing: P-labeling for processing consecutive child (or parent) axis traversals, and D-labeling for processing descendant (or ancestor) axis traversals. XML data are stored in labeled form and indexed. Algorithms are presented for translating XPath queries to SQL expressions. BLAS reduces the number of joins in the SQL query translated from a given XPath query and reduces the number of disk accesses required to execute the SQL query compared with the traditional XPath processing using D-labeling alone. We also propose an approximate P-labeling scheme and the corresponding query translation algorithm to handle XML data trees that contain a large number of distinct tag names, and/or are very deep. This extension captures a spectrum of XPath-to-SQL query translation schemes, ranging from existing schemes that do not use P-labels to the one that uses exact P-labels. Experimental results demonstrate the efficiency of the BLAS system.     

On the computer simulation of the P–C isotherms of ZrFe2 type hydrogen storage materials

This paper deals with computer simulation of the P–C isotherms of some ZrFe₂ type (Zr(Fe_1−xCr_x)₂, Zr_1−xTi_xFe_1.4Cr_0.6, Zr_1−2xMm_xTi_xFe_1.4Cr_0.6 : x00.4) of hydrogen storage materials. A feasible mathematical model has been developed to simulate the P–C isotherms. The randomized variables in the model applied for simulating the P–C isotherms of the above-mentioned ZrFe₂ type hydrogen storage materials correspond to change in enthalpy (ΔH) and entropy (ΔS) of hydride formation. Several ZrFe₂ type materials as in above have been synthesized and their P–C isotherms, enthalpy and entropy change has been evaluated experimentally in order to have input data for simulation. A special software was developed to simulate the P–C isotherms using the said model. A close match between the experimentally observed and simulated P–C isotherms for the above said ZrFe₂ type alloys has been obtained.     

Process Lethality Prediction for Escherichia coli O157:H7 in Raw Franks During Cooking and Fully Cooked Franks During Post-cook Pasteurization

ABSTRACT: Thermal inactivation D (decimal reduction time at a certain heating temperature) values of Escherichia coli O157:H7 at 55 °C to 70 °C were 21.36 to 0.031 min in raw franks and 24.91 to 0.038 min in fully cooked franks. Although statistically significant differences were found on the D values of E. coli O157:H7 between raw and fully cooked franks, the z value of E. coli O157:H7 in raw franks (5.07 °C) and fully cooked franks (5.08 °C) was not significantly different. The obtained D and z values were used to validate the process lethality of the pathogen in the raw franks that were processed according to a multistage cooking/cooling schedule or in the fully cooked franks that were pasteurized in-packages via steam. In this study, the calculated process lethality for both the cooking (process lethality = 254 min) and post-cook pasteurization (process lethality = 39 min) processes was far greater than the processing time that was needed for achieving a 7D reduction of E. coli O157:H7 during cooking and post-cook pasteurization of the franks.     

Reaction and total cross sections for low energy pi + and pi - on isospin zero nuclei

We calculated the electrostatic force between a planar interface, such as a planar-supported lipid bilayer membrane, and the tip of a stylus on which another lipid bilayer or some other biomacromolecular system might be deposited. We considered styli with rounded tips as well as conical tips. To take into account the effect of dynamical hydrogen-bonded structures in the aqueous phase, we used a theory of nonlocal electrostatics. We used the Derjaguin approximation and identified the systems for which its use is valid. We pointed out where our approach differs from previous calculations and to what extent the latter are inadequate. We found that 1) the nonlocal interactions have significant effects over distances of 10-15 A from the polar zone and that, at the surface of this zone, the effect on the calculated force can be some orders of magnitude; 2) the lipid dipoles and charges are located a distance L from the hydrophobic layer in the aqueous medium and this can have consequences that may not be appreciated if it is ignored; 3) dipoles, located in the aqueous region, can give rise to forces even though the polar layer is unchanged, and if this is ignored the interpretation of force data can be erroneous if an attempt is made to rationalize an observed force with a knowledge of an uncharged surface; 4) the shape of the stylus tip can be very important, and a failure to take this into account can result in incorrect conclusions, a point made by other workers; and 5) when L is nonzero, the presence of charges and dipoles can yield a force that can be nonmonotonic as a function of ionic concentration.     

Two residues that may ligate Ca2+ in transmembrane domain six of the plasma membrane Ca(2+)-ATPase

In order to identify Ca2+ ligands in the putative transmembrane domain 6 of the plasma membrane Ca2+ pump, amino acids Asn879, Met882, Asp883, and Ser887 were singly altered. Asn879, Met882, and Asp883 were chosen because the corresponding amino acids have been proposed as Ca2+ ligands in the sarcoplasmic reticulum Ca2+ pump (Clarke, D. M., Loo, T. W., and MacLennan, D. H. (1990) J. Biol. Chem. 265, 6262-6267). For the alterations, a fully active truncated version of the pump was used, because the interaction of Ca2+ with the pump could be studied without interference from calmodulin binding. The mutants at Asn and Asp did not carry out ATP-supported Ca2+ uptake and formed no acylphosphate from [gamma-32P]ATP, suggesting that, like the corresponding amino acids in the sarcoplasmic reticulum Ca2+ pump, these two are Ca2+ ligands. However, all the mutants at the position of Met882 showed some activity. Indeed, the Met882--> Ile mutant was fully active at a saturating Ca2+ concentration and only the K1/2 for Ca2+ activation was shifted slightly upward. Converting the Met to Thr (which is the corresponding residue in the sarcoplasmic reticulum Ca2+ pump) reduced the activity to 20% of the wild type, further emphasizing the differences between the two Ca2+ pumps. The mutant Ser887--> Ala was expressed in greater amounts than, and had a specific activity about 50% higher than, the wild type, indicating that this serine also could not be a Ca2+ ligand and could not replace the missing Thr at position Met882.     

New insights into the compartmentation of glutamate and glutamine in cultured rat brain astrocytes

Studies from several groups have provided evidence that glutamate and glutamine are metabolized in different compartments in astrocytes. In the present study we measured the rates of 14CO2 production from U-[14C]glutamate and U-[14C]glutamine, and utilized both substrate competition experiments and the transaminase inhibitor aminooxyacetic acid (AOAA) to obtain more information about the compartmentation of these substrates in cultured rat brain astrocytes. The rates of oxidation of 1 mM glutamine and glutamate were 26.4 +/- 1.4 and 63.0 +/- 7.4 nmol/h/mg protein, respectively. The addition of 1 mM glutamate decreased the rate of oxidation of glutamine to 26.3% of the control rate, demonstrating that glutamate can effectively compete with the oxidation of glutamine by astrocytes. In contrast, the addition of 1 mM glutamine had little or no effect on the rate of oxidation of glutamate by astrocytes, demonstrating that the glutamate produced intracellularly from exogenous glutamine does not dilute the glutamate taken up from the media. The addition of 5 mM AOAA decreased the rate of 14CO2 production from glutamine to 29.2% of the control rate, consistent with earlier studies by our group. The addition of 5 mM AOAA decreased the rate of oxidation of concentrations of glutamate < or = 0.1 mM by approximately 50%, but decreased the oxidation of 0.5-1 mM glutamate by only approximately 20%, demonstrating that a substantial portion of glutamate enters the tricarboxylic acid (TCA) cycle via glutamate dehydrogenase (GDH) rather than transamination, and that as the concentration of glutamate increases the relative proportion entering the TCA cycle via GDH also increases. To determine if the presence of an amino group acceptor (i.e. a ketoacid) would increase the rate of metabolism of glutamate, pyruvate was added in some experiments. Addition of 1 mM pyruvate increased the rate of oxidation of glutamate, and the increase was inhibited by AOAA, consistent with enhanced entry of glutamate into the TCA cycle via transamination in the presence of pyruvate. Enzymatic studies showed that pyruvate increased the activity of mitochondrial aspartate aminotransferase (AAT). Overall, the data demonstrate that glutamate formed intracellularly from glutamine enters the TCA cycle primarily via transamination, but does not enter the same TCA cycle compartment as glutamate taken up from the extracellular milieu. In contrast, extracellular glutamate enters the TCA cycle in astrocytes via both transamination and GDH, and can compete with, or dilute, the oxidation of glutamate produced intracellularly from glutamine.     

Developmental and behavioral effects of prenatal primidone exposure in the rat

Pregnant Sprague-Dawley rats were administered primidone (PRM) by oral gavage on gestation days 8-17 in doses of 0.40, and 80 mg/kg. Although these doses of PRM did not produce significant differences in litter size, birth weight, mortality, date of attainment of developmental landmarks or measures of preweaning reflex and motor development, there were a number of significant differences that developed as the animals approached and entered adulthood. When tested as adults, the 80 mg/kg male rats showed a deficit in the performance of an eight-arm radial maze task. These same animals showed a significant reduction in open field activity when tested as adults. In addition, both male and female PRM-treated animals showed reduced body weights at different periods corresponding to onset of sexual maturation during development. These findings are consistent with the larger body of literature reporting on the neurobehavioral teratology of phenobarbital, including its ability to produce lesions in the hippocampus and endocrine dysfunction resulting in reproductive deficits. These results suggest that PRM produces its adverse effects as a result of its metabolism to phenobarbital, which in turn affects the limbic system.