Infrastructure Aware Scientific Workflows and Infrastructure Aware Workflow Managers in Science Gateways

The workflow interoperability problem was successfully solved by the SHIWA project if the workflows to be integrated were running in the same grid infrastructure. However, in the more generic case when the workflows were running in different infrastructures the problem has not been solved yet. In the current paper we show a solution for this problem by introducing a new type of workflow called infrastructure-aware workflow. These are scientific workflows extended with new node types that enable the on-the-fly creation and destruction of the required infrastructures in the clouds. The paper shows the semantics of these new types of nodes and workflows and also how they can solve the workflow interoperability problem. The paper also describes how these new type of workflows can be implemented by a new service called Occopus, and how this service can be integrated with the existing SHIWA Simulation Platform services like the WS-PGRADE/gUSE portal to provide the required functionalities of solving the workflow interoperability problem.     

Practical verification of decision-making in agent-based autonomous systems

We present a verification methodology for analysing the decision-making component in agent-based hybrid systems. Traditionally hybrid automata have been used to both implement and verify such systems, but hybrid automata based modelling, programming and verification techniques scale poorly as the complexity of discrete decision-making increases making them unattractive in situations where complex logical reasoning is required. In the programming of complex systems it has, therefore, become common to separate out logical decision-making into a separate, discrete, component. However, verification techniques have failed to keep pace with this development. We are exploring agent-based logical components and have developed a model checking technique for such components which can then be composed with a separate analysis of the continuous part of the hybrid system. Among other things this allows program model checkers to be used to verify the actual implementation of the decision-making in hybrid autonomous systems.     

Comparison of the enthalpic relaxation of poly(lactide–co‐glycolide) 50:50 nanospheres and raw polymer

The phenomenon of enthalpic relaxation was evaluated for poly(lactide‐co‐glycolide) (PLGA, 50:50), in terms of storage of nanospheres for use as a controlled drug delivery system. Samples were stored for different times and temperatures below the glass transition temperature (T_g). Relaxation occurred at a significant rate up to 15 degrees below the T_g of 39.2°C. The effect of polymer morphology was considered by comparing the relaxation kinetics of the raw polymer with that of nanospheres formed using a novel technique. The nanospheres were shown to have a larger change in heat capacity at the glass transition and a longer average relaxation time than that of the raw polymer, and the relationship between these two parameters was discussed. For both the raw polymer and the nanospheres, relaxation was found to occur at a significant rate at room temperature. The storage of this system at subambient temperatures was therefore deemed important for maintaining the physicochemical properties of the system. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 1868–1872, 2002     

Fracture strength of silicon carbide microspecimens

Polycrystalline silicon carbide tensile microspecimens 3.1 mm long were produced by deep reactive ion etching of wafers on the order of 150 /spl mu/m thick. The gage sections, which were nominally 200 /spl mu/m wide, were either straight, slightly curved, or contained double notches in order to vary the size of the highly stressed region. The fracture stresses of 190 specimens from three process runs were measured in a novel test setup. The average local fracture strengths for the last run were: straight 0.38/spl plusmn/0.13 GPa, curved 0.47/spl plusmn/0.15 GPa, notched 0.78/spl plusmn/0.28 GPa. The corresponding Weibull characteristic strengths were, 0.42 GPa, 0.53GPa, and 0.88 GPa with respective moduli 3.3, 3.4, and 3.1. These results show a clear increase in the strength of the material as the size of the highly stressed region decreases. Fractographic analyzes showed failures initiating from the bottoms of side grooves left by the etching process. The grains of the material were quite heterogeneous, varying from a few microns in size to columnar grains through the entire specimen thickness. The curved specimens were used as the base for predicting the probability of failure of the other two shapes. While the Weibull approach was quite accurate for the straight shape, it over-predicted the strengths of the notched specimens. Given the microstructure of the material relative to the size of the specimen, a continuum analysis is questionable.     

Natural history of coronary atherosclerosis using quantitative angiography in men, and implications for clinical trials of coronary regression. The Harvard Atherosclerosis Reversibility Project Study Group

Previous studies of the natural history of coronary disease generally relied on estimates of percent stenosis derived from visual assessment of the coronary angiogram. In a study of 26 patients, serial quantitative angiography was performed 3 years apart to determine changes in both absolute measurements of the luminal diameter and relative percent stenosis. Initially, the mean minimal diameter of 74 coronary obstructions was 1.94 +/- 0.09 mm, the mean "normal" reference diameter was 3.06 +/- 0.11 mm, and the mean percent stenosis was 37%. At follow-up, there was a mild reduction of 0.12 +/- 0.04 mm (6%) in the minimal diameter (p < 0.005), and an increase in percent stenosis to 39% (p = 0.03). The average diameter of 85 arterial segments without a focal obstruction either initially or at follow-up showed mild but significant progression (-0.11 +/- 0.04 mm; p = 0.02). Using a minimal change of 0.27 mm in arterial diameter as a categoric variable, progression occurred in 26% of 74 arterial segments, no significant change in 65%, and regression in 9%. The only significant determinant of disease progression was the initial severity of disease. Obstructed arteries with a larger initial minimal diameter and presumably milder disease progressed more rapidly than did those with a smaller diameter (r = -0.42; p = 0.0002). There was no effect of age on the rate of progression (r = 0.02; p = NS).(ABSTRACT TRUNCATED AT 250 WORDS)     

Long-Chain and Very Long-Chain Ceramides Mediate Doxorubicin-Induced Toxicity and Fibrosis

Doxorubicin (Dox) is a chemotherapeutic agent with cardiotoxicity associated with profibrotic effects. Dox increases ceramide levels with pro-inflammatory effects, cell death, and fibrosis. The purpose of our study was to identify the underlying ceramide signaling pathways. We aimed to characterize the downstream effects on cell survival, metabolism, and fibrosis. Human fibroblasts (hFSF) were treated with 0.7 µM of Dox or transgenically overexpressed ceramide synthase 2 (FLAG-CerS2). Furthermore, cells were pre-treated with MitoTempo (MT) (2 h, 20 µM) or Fumonisin B1 (FuB) (4 h, 100 µM). Protein expression was measured by Western blot or immunofluorescence (IF). Ceramide levels were determined with mass spectroscopy (MS). Visualizations were conducted using laser scanning microscopy (LSM) or electron microscopy. Mitochondrial activity was measured using seahorse analysis. Dox and CerS2 overexpression increased CerS2 protein expression. Coherently, ceramides were elevated with the highest peak for C24:0. Ceramide- induced mitochondrial ROS production was reduced with MT or FuB preincubation. Mitochondrial homeostasis was reduced and accompanied by reduced ATP production. Our data show that the increase in pro-inflammatory ceramides is an essential contributor to Dox side-effects. The accumulation of ceramides resulted in a lipotoxic shift and subsequently mitochondrial structural and functional damage, which was partially reversible following inhibition of ceramide synthesis.     

Secret key rates of free‐space optical continuous‐variable quantum key distribution

In this letter, we derive the maximal achievable secret key rates for continuous‐variable quantum key distribution (CVQKD) over free‐space optical (FSO) quantum channels. We provide a channel decomposition for FSO‐CVQKD quantum channels and study the SNR (signal‐to‐noise ratio) characteristics. The analytical derivations focus particularly on the low‐SNR scenarios. The results are convenient for wireless quantum key distribution and for the quantum Internet.     

Vicinal disulfide turns

The formation of a disulfide bond between adjacent cysteineresidues is accompanied by the formation of a tight turn ofthe protein backbone. In nearly 90% of the structures analyzeda type VIII turn was found. The peptide bond between the twocysteines is in a distorted trans conformation, the omega torsionangle ranges from 159 to –133°, with an average valueof 171°. The constrained nature of the vicinal disulfideturn and the pronounced difference observed between the oxidizedand reduced states, suggests that vicinal disulfides may beemployed as a ‘redox-activated’ conformational switch. Received December 16, 2002; revised June 30, 2003; accepted July 30, 2003.