A checkpointing-enabled and resource-aware Java Virtual Machine for efficient and robust e-Science applications in grid environments

Object-oriented programming languages presently are the dominant paradigm of application development (e. g., Java,. NET). Lately, increasingly more Java applications have long (or very long) execution times and manipulate large amounts of data/information, gaining relevance in fields related with e-Science (with Grid and Cloud computing). Significant examples include Chemistry, Computational Biology and Bio-informatics, with many available Java-based APIs (e. g., Neobio). Often, when the execution of such an application is terminated abruptly because of a failure (regardless of the cause being a hardware of software fault, lack of available resources, etc.), all of its work already performed is simply lost, and when the application is later re-initiated, it has to restart all its work from scratch, wasting resources and time, while also being prone to another failure and may delay its completion with no deadline guarantees. Our proposed solution to address these issues is through incorporating mechanisms for checkpointing and migration in a JVM. These make applications more robust and flexible by being able to move to other nodes, without any intervention from the programmer. This article provides a solution to Java applications with long execution times, by extending a JVM (Jikes research virtual machine) with such mechanisms. Copyright (C) 2011 John Wiley & Sons, Ltd.

Boulder deposition during major tsunami events

A remarkable accumulation of marine boulders located above the present spring tide level has occurred in two coastal lowlands of the Algarve (Portugal). The size-interval of the particles studied here is seldom reported in the literature in association with extreme events of coastal inundation, thus making this study of relevance to many other coasts worldwide. The spreads of boulders extend several hundred meters inland and well beyond the present landward limit of storm activity. The marine origin of the boulders is demonstrated by well-developed macro-bioerosion sculpturing and in situ skeletal remains of endolithic shallow marine bivalves. The good state preservation of the fossils within the boulders indicates that abrasion duringtransport and redeposition was not significant. We envisage boulder deposition as having taken place during the Lisbon tsunami of ad 1755 through the simultaneous landward entrainment of coarse particles from nearshore followed by rapid shoreward suspended-dominated transport and non-graded redeposition that excluded significant sorting by weight or boulder dimensions. We use numerical hydrodynamic modeling of tsunami (and storm) waves to test the observational data on boulder dimensions (density, size, distribution) on the most likely processes of sediment deposition. This work demonstrates the effectiveness of the study of boulder deposits in tsunami reconstruction. Copyright (C) 2011 John Wiley & Sons, Ltd.

Chromatographic behaviour of monoclonal antibodies against wild-type amidase from Pseudomonasaeruginosa on immobilized metal chelates

The aim of this work was to devise a one-step purification procedure for monoclonal antibodies (MAbs) of IgG class by immobilized metal affinity chromatography (IMAC). Therefore, several stationary phases were prepared containing immobilized metal chelates in order to study the chromatographic behaviour of MAbs against wild-type amidase from Pseudomonas aeruginosa. Such MAbs adsorbed to Cu(II), Ni(II), Zn(II) and Co(II)-IDA agarose columns. The increase in ligand concentration and the use of longer spacer arms and higher pH values resulted in higher adsorption of MAbs into immobilized metal chelates. The dynamic binding capacity and the maximum binding capacity were 1.33 +/- 0.015 and 3.214 +/- 0.021 mg IgG/mL of sedimented commercial matrix, respectively. A K(D) of 4.53 x 10(-7) M was obtained from batch isotherm measurements. The combination of tailor-made stationary phases of IMAC and the correct selection of adsorption conditions permitted a one-step purification procedure to be devised for MAbs of IgG class. Culture supernatants containing MAbs were purified by IMAC on commercial-Zn(II) and EPI-30-IDA-Zn(II) Sepharose 6B columns and by affinity chromatography on Protein A-Sepharose CL-4B. This MAb preparation revealed on SDS-PAGE two protein bands with M(r) of 50 and 22 kDa corresponding to the heavy and light chains, respectively. Copyright (C) 2011 John Wiley & Sons, Ltd.

Trends in properties of para-substituted 3-(phenylhydrazo)pentane-2,4-diones

Trends between the Hammett's sigma(p) and related normal sigma(n)(p), inductive sigma(I), resonance sigma(R), negative sigma(-)(p) and positive sigma(+)(p) polar conjugation and Taft's sigma(o)(p) substituent constants and the N-H center dot center dot center dot O distance, delta(N-H) NMR chemical shift, oxidation potential (E-p/2(ox), measured in this study by cyclic voltammetry (CV)) and thermodynamic parameters (pK, Delta G(0), Delta H-0 and Delta S-0) of the dissociation process of unsubstituted 3-(phenylhydrazo)pentane-2,4-dione (HL1) and its para-substituted chloro (HL2), carboxy (HL3), fluoro (HL4) and nitro (HL5) derivatives were recognized. The best fits were found for sigma(p) and/or sigma(-)(p) in the cases of d(N center dot center dot center dot O), delta(N-H) and E-p/2(ox), showing the importance of resonance and conjugation effects in such properties, whereas for the above thermodynamic properties the inductive effects (sigma(I)) are dominant. HL2 exists in the hydrazo form in DMSO solution and in the solid state and contains an intramolecular H-bond with the N center dot center dot center dot O distance of 2.588(3)angstrom. It was also established that the dissociation process of HL1-5 is non-spontaneous, endothermic and entropically unfavourable, and that the increase in the inductive effect (sigma(I)) of para-substitutents (-H < -Cl < -COOH < -F < -NO2) leads to the corresponding growth of the N center dot center dot center dot O distance and decrease of the pK and of the changes of Gibbs free energy, of enthalpy and of entropy for the HL1-5 acid dissociation process. The electrochemical behaviour of HL1-5 was interpreted using theoretical calculations at the DFT/HF hybrid level, namely in terms of HOMO and LUMO compositions, and of reactivities induced by anodic and cathodic electron-transfers. Copyright (C) 2010 John Wiley & Sons, Ltd.

Wind turbines equipped with fractional-order controllers: Stress on the mechanical drive train due to a converter control malfunction

This paper is on variable-speed wind turbines with permanent magnet synchronous generator (PMSG). Three different drive train mass models and three different topologies for the power-electronic converters are considered. The three different topologies considered are respectively a matrix, a two-level and a multilevel converter. A novel control strategy, based on fractional-order controllers, is proposed for the wind turbines. Simulation results are presented to illustrate the behaviour of the wind turbines during a converter control malfunction, considering the fractional-order controllers. Finally, conclusions are duly drawn. Copyright (C) 2010 John Wiley & Sons, Ltd.

The influence of experience and training in a group of novice observers: a jackknife alternative free-response receiver operating characteristic analysis

Purpose - The study evaluates the pre- and post-training lesion localisation ability of a group of novice observers. Parallels are drawn with the performance of inexperienced radiographers taking part in preliminary clinical evaluation (PCE) and ‘red-dot’ systems, operating within radiography practice. Materials and methods - Thirty-four novice observers searched 92 images for simulated lesions. Pre-training and post-training evaluations were completed following the free-response the receiver operating characteristic (FROC) method. Training consisted of observer performance methodology, the characteristics of the simulated lesions and information on lesion frequency. Jackknife alternative FROC (JAFROC) and highest rating inferred ROC analyses were performed to evaluate performance difference on lesion-based and case-based decisions. The significance level of the test was set at 0.05 to control the probability of Type I error. Results - JAFROC analysis (F(3,33) = 26.34, p < 0.0001) and highest-rating inferred ROC analysis (F(3,33) = 10.65, p = 0.0026) revealed a statistically significant difference in lesion detection performance. The JAFROC figure-of-merit was 0.563 (95% CI 0.512,0.614) pre-training and 0.677 (95% CI 0.639,0.715) post-training. Highest rating inferred ROC figure-of-merit was 0.728 (95% CI 0.701,0.755) pre-training and 0.772 (95% CI 0.750,0.793) post-training. Conclusions - This study has demonstrated that novice observer performance can improve significantly. This study design may have relevance in the assessment of inexperienced radiographers taking part in PCE or commenting scheme for trauma.

Synthesis and characterization of rabies virus glycoprotein-tagged amphiphilic cyclodextrins for siRNA delivery in human glioblastoma cells: in vitro analysis

In man brain cancer is an aggressive, malignant form of tumour, it is highly infiltrative in nature, is associated with cellular heterogeneity and affects cerebral hemispheres of the brain. Current drug therapies are inadequate and an unmet clinical need exists to develop new improved therapeutics. The ability to silence genes associated with disease progression by using short interfering RNA (siRNA) presents the potential to develop safe and effective therapies. In this work, in order to protect the siRNA from degradation, promote cell specific uptake and enhance gene silencing efficiency, a PEGylated cyclodextrin (CD)-based nanoparticle, tagged with a CNS-targeting peptide derived from the rabies virus glycoprotein (RVG) was formulated and characterized. The modified cyclodextrin derivatives were synthesized and co-formulated to form nanoparticles containing siRNA which were analysed for size, surface charge, stability, cellular uptake and gene-knockdown in brain cancer cells. The results identified an optimised co-formulation prototype at a molar ratio of 1:1.5:0.5 (cationic cyclodextrin:PEGylated cyclodextrin:RVG-tagged PEGylated cyclodextrin) with a size of 281±39.72nm, a surface charge of 26.73±3mV, with efficient cellular uptake and a 27% gene-knockdown ability. This CD-based formulation represents a potential nanocomplex for systemic delivery of siRNA targeting brain cancer.

Damage detection in structures using a transmissibility-based Mahalanobis distance

In this paper, a damage-detection approach using the Mahalanobis distance with structural forced dynamic response data, in the form of transmissibility, is proposed. Transmissibility, as a damage-sensitive feature, varies in accordance with the damage level. Besides, Mahalanobis distance can distinguish the damaged structural state condition from the undamaged one by condensing the baseline data. For comparison reasons, the Mahalanobis distance results using transmissibility are compared with those using frequency response functions. The experiment results reveal quite a significant capacity for damage detection, and the comparison between the use of transmissibility and frequency response functions shows that, in both cases, the different damage scenarios could be well detected. Copyright (c) 2015 John Wiley & Sons, Ltd.

Multi-agent management system for electric vehicle charging

This paper proposes an implementation, based on a multi-agent system, of a management system for automated negotiation of electricity allocation for charging electric vehicles (EVs) and simulates its performance. The widespread existence of charging infrastructures capable of autonomous operation is recognised as a major driver towards the mass adoption of EVs by mobility consumers. Eventually, conflicting requirements from both power grid and EV owners require automated middleman aggregator agents to intermediate all operations, for example, bidding and negotiation, between these parts. Multi-agent systems are designed to provide distributed, modular, coordinated and collaborative management systems; therefore, they seem suitable to address the management of such complex charging infrastructures. Our solution consists in the implementation of virtual agents to be integrated into the management software of a charging infrastructure. We start by modelling the multi-agent architecture using a federated, hierarchical layers setup and as well as the agents' behaviours and interactions. Each of these layers comprises several components, for example, data bases, decision-making and auction mechanisms. The implementation of multi-agent platform and auctions rules, and of models for battery dynamics, is also addressed. Four scenarios were predefined to assess the management system performance under real usage conditions, considering different types of profiles for EVs owners', different infrastructure configurations and usage and different loads on the utility grid (where real data from the concession holder of the Portuguese electricity transmission grid is used). Simulations carried with the four scenarios validate the performance of the modelled system while complying with all the requirements. Although all of these have been performed for one charging station alone, a multi-agent design may in the future be used for the higher level problem of distributing energy among charging stations. Copyright (c) 2014 John Wiley & Sons, Ltd.