Application Level Fault Tolerance in Heterogeneous Networks of Workstations

We have explored methods for checkpointing and restarting processes within the distributed object migration environment (Dome), a C++ library of data parallel objects that are automatically distributed over heterogeneous networks of workstations (NOWs). System level checkpointing methods, although transparent to the user, were rejected because they lack support for heterogeneity. We have implemented application level checkpointing which places the checkpoint and restart mechanisms within Dome's C++ objects. Application level checkpointing has been implemented with a library-based technique for the programmer and a more transparent preprocessor-based technique. Dome's implementation of checkpointing successfully checkpoints and restarts processes on different numbers of machines and different architectures. Results from executing Dome programs across a NOW with realistic failure rates have been experimentally determined and are compared with theoretical results. The overhead of checkpointing is found to be low, while providing substantial decreases in expected runtime on realistic systems.     

Sequence clustering strategies improve remote homology recognitions while reducing search times

Sequence databases are rapidly growing, thereby increasing thecoverage of protein sequence space, but this coverage is unevenbecause most sequencing efforts have concentrated on a smallnumber of organisms. The resulting granularity of sequence spacecreates many problems for profile-based sequence comparisonprograms. In this paper, we suggest several strategies thataddress these problems, and at the same time speed up the searchesfor homologous proteins and improve the ability of profile methodsto recognize distant homologies. One of our strategies combinesdatabase clustering, which removes highly redundant sequence,and a two-step PSI-BLAST (PDB-BLAST), which separates sequencespaces of profile composition and space of homology searching.The combination of these strategies improves distant homologyrecognitions by more than 100%, while using only 10% of theCPU time of the standard PSI-BLAST search. Another method, intermediateprofile searches, allows for the exploration of additional searchdirections that are normally dominated by large protein sub-familieswithin very diverse families. All methods are evaluated witha large fold-recognition benchmark.     

MRT of experimental liver abscesses: a comparison of a new blood pool contrast medium with gadolinium-DTPA in animal experiments

PURPOSE: In an experimental pyogenic liver abscess model, the signal intensities were compared intraindividually and interindividually after the application of a new blood pool contrast agent, 24-gadolinium-DTPA (diethylenetriamine-pentaacetic acid) cascade polymer, and after the application of gadopentetate dimeglumine. METHODS: In 20 rabbits with experimentally induced liver abscesses, the relative signal intensities of the liver, abscess centre, abscess wall and portal vein were assessed before and between 30 seconds and 60 minutes after injection of a 25 mumol/kg dose of gadolinium polymer and of 100 mumol/kg of gadolinium-DTPA, respectively. Measurements were performed at 1.5 Tesla, using a head coil and a Flash-2-D sequence. RESULTS: The interindividual comparison (unpaired T-test, p < 0.05) yielded significant differences of the relative signal intensities of the abscess centre (at any time point after contrast-media application), abscess wall (between 15 and 60 minutes after contrast media application), and portal vein (between 30 seconds and 7.5 minutes after contrast media application). The interindividual comparison showed a significantly higher abscess centre-liver contrast (between 30 seconds and 12.5 minutes after contrast media application) and a significantly higher abscess wall-centre contrast (between two and 7.5 minutes after contrast media application) after the application of gadolinium polymer compared with gadopentetate dimeglumine. CONCLUSION: In this animal model, the higher abscess centre-liver contrast after the application of gadolinium polymer was the basis for a better and prolonged visibility of the abscesses, as compared with images acquired after injection of gadopentetate dimeglumine.     

An SS1-SS2 {beta}-barrel structure for the voltage-activated potassium channel

To examine the feasibility of a ß structure for thepore-lining region of the voltage-gated potassium channel, wehave characterized a family of 12 antiparallel ß-barrels.Each is comprised of four identical pairs of ß-strandsorganized with approximate 4-fold symmetry about a channel axis.The Cand N-termini of the ß-strand pairs are assumedto be at the extracellular end of the channel, and each pairis connected by a hairpin turn at the intracellular end of thechannel. The models differ in the residues located in the hairpinturn and in the orientation of the two strands of each pairin the barrel, i.e. whether the C-terminus of a pair is clockwise(CW) or counterclockwise (CCW) from the N-terminus when thechannel is viewed from outside the cell. Following known structureprecedents and potential energy predictions, the barrel is assumedto be right-twisting in all cases. All models have crowded layersof inward-projecting aromatic sidechains near the center ofthe channel which could regulate channel selectivity. The modelswith an odd number of amino acids in the hairpin turn have theadvantage of predicting that F433 points into the barrel, butthe disadvantage that V438 does not. Of these models, two ofthe models are most consistent with the external tetraethylanunonhim(TEA) block data, and of those, one (T439 CCW 3:5) is most consistentwith the internal TEA block data.     

Chalcogenide Glasses Based on Germanium Disulfide for Second Harmonic Generation

High second‐order susceptibilities are created by thermal poling in bulk germanium disulfide based chalcogenide glasses. Experimental conditions of the poling treatment (temperature, voltage, time) were optimized for each glass composition. The second‐order nonlinear signals were recorded by using the Maker fringes experiment and a second‐order coefficient χ⁽²⁾ up to 8 pm V^–1 was measured in the Ge₂₅Sb₁₀S₆₅ glass. This value is obtained using a simulation based on accurate knowledge of the thickness of the nonlinear layer. Two mechanisms are proposed to explain the creation of a nonlinear layer under the anode: the formation and the migration of charged defects towards the anode may mainly occur in Ge₂₀Ga₅Sb₁₀S₆₅ and Ge₂₅Ga₅S₇₀ glasses, whereas the migration of Na⁺ ions towards the cathode may be responsible for the accumulation of negative charges under the anode in Ge₃₃S₆₇ and Ge₂₅Sb₁₀S₆₅ glasses. Different electronic conductivity behaviors seem to be at the origin of the phenomenon. In parallel, the potential effect of the poling treatment on the structural and electronic properties is studied using Raman spectroscopy and secondary ion mass spectroscopy measurements.     

Virtual reality is for real

Some current applications work in the computer-rendered environments known as virtual reality (VR) are examined. Caterpillar Inc., a manufacturer of earth-moving and construction equipment is using VR to assess interior visibility on new prototypes. The Big Three among US automobile makers are joining with a US Army vehicle center, United Technologies' automotive division, the University of Michigan, and a dozen other smaller companies to form a consortium for industrial VR. Boeings' new airliner, the 777, to be rolled out next year, is its first to be designed without the use of a full-scale physical mockup; VR was used instead. Military, medical, and entertainment applications of VR are growing     

Monoclonal antibodies to bovine growth hormone potentiate hormonal activity in vivo by enhancing growth hormone binding to hepatic somatogenic receptors

Administration of GH complexed with monoclonal antibodies (MABs) potentiates the in vivo actions of the hormone. In particular, growth and serum IGF-I concentrations of GH-treated hypophysectomized rats are increased by concomitant injection of anti-GH MABs. Among 37 anti-bovine GH (bGH) MABs, we selected one MAB with the most potentiating effects to investigate the mechanisms responsible for this phenomenon. Hypophysectomized rats were killed 18 h after a single s.c. injection of bGH (100 micrograms/rat), alone or complexed with increasing doses of MAB (4, 40, 400 micrograms/rat; MAB:bGH molar ratio: 0.005, 0.05, 0.5). IGF-I was measured by radioimmunoassay in acid-extracted sera and livers, whereas liver IGF-I mRNA was quantified by Northern blot hybridization. The in vivo occupancy of liver somatogenic (GH) receptors was derived from the determinations of total and free 125I-labelled bGH binding to liver homogenates treated with 4 mol MgCl2/l or water. Injection of MAB-bGH complexes enhanced body weight gain and raised serum IGF-I, liver IGF-I and liver IGF-I mRNA more than bGH alone (1.6-, 6-, 10- and 7-fold increases at the highest dose of MAB, compared with bGH alone; P < 0.001). These potentiating effects of the MAB were dose-dependent and significant potentiation of the growth response was already observed with the lowest dose of MAB. In vivo occupancy of liver GH receptors was markedly higher 18 h after injection of MAB-bGH complexes than after bGH alone, and this effect was also dose-dependent (receptor occupancy of 28%, 37% and 83% after 4, 40 and 400 micrograms of MAB respectively compared with 6% after bGH alone; P < 0.05, 0.05 and 0.001 respectively). In contrast, the in vitro binding of 125I-labelled bGH to liver homogenates was decreased in the presence of high doses of MAB. We conclude that low amounts of MABs complexed with bGH potentiate the stimulation by the hormone of liver IGF-I synthesis and secretion in a dose-dependent manner. These effects are mediated, at least in part, through changes in hormone-receptor interaction in vivo, leading to enhanced and/or prolonged binding of bGH to its somatogenic receptors.