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Selected Abstracts369 Tflop/s molecular dynamics simulations on the petaflop hybrid supercomputer ,Roadrunner'CONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 17 2009Timothy C. Germann Abstract We describe the implementation of a short-range parallel molecular dynamics (MD) code, SPaSM, on the heterogeneous general-purpose Roadrunner supercomputer. Each Roadrunner ,TriBlade' compute node consists of two AMD Opteron dual-core microprocessors and four IBM PowerXCell 8i enhanced Cell microprocessors (each consisting of one PPU and eight SPU cores), so that there are four MPI ranks per node, each with one Opteron and one Cell. We will briefly describe the Roadrunner architecture and some of the initial hybrid programming approaches that have been taken, focusing on the SPaSM application as a case study. An initial ,evolutionary' port, in which the existing legacy code runs with minor modifications on the Opterons and the Cells are only used to compute interatomic forces, achieves roughly a 2× speedup over the unaccelerated code. On the other hand, our ,revolutionary' implementation adopts a Cell-centric view, with data structures optimized for, and living on, the Cells. The Opterons are mainly used to direct inter-rank communication and perform I/O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard,Jones pair potential benchmark reached a peak of 369 Tflop/s double-precision floating-point performance on the full Roadrunner system (27.7% of peak), nearly 10× faster than the unaccelerated (Opteron-only) version. Copyright © 2009 John Wiley & Sons, Ltd. [source] The impact of eliminating the global illicit cigarette trade on health and revenueADDICTION, Issue 9 2010Luk Joossens ABSTRACT Aims The purpose of this study was to update global estimates of the illicit cigarette trade, based on recent data, and estimate how many lives could be saved by eliminating it and how much revenue governments would gain. Data sources and methods Our estimates of illicit market share are based on formal and informal sources. Our method for estimating the effect of eliminating the illicit trade on tobacco related deaths is based on West et al. with some minor modifications, and involves calculating the size of the illicit cigarette trade; the effect of eliminating it on the price of cigarettes and thus on consumption; the revenue governments are losing because of it; and the number of tobacco-related premature deaths that would be avoided if this illicit trade were eliminated. Results According to available estimates, the size of the illicit trade varies between countries from 1% to about 40,50% of the market, 11.6% globally, 16.8% in low-income and 9.8% in high-income countries. The total lost revenue is about $40.5 billion a year. If this illicit trade were eliminated governments would gain at least $31.3 billion a year, and from 2030 onwards more than 164 000 premature deaths a year would be avoided, the vast majority in middle- and low-income countries. Conclusions The burden of deaths and lost revenue caused by the illicit cigarette trade falls disproportionately on low- and middle-income countries. Eliminating this trade would avoid millions of premature deaths, and recover billions of dollars for governments. [source] Generalized window advertising for TCP congestion control,EUROPEAN TRANSACTIONS ON TELECOMMUNICATIONS, Issue 6 2002Mario Gerla Congestion in the Internet is a major cause of network performance degradation. The Generalized Window Advertising (GWA) scheme proposed in this paper is a new approach for enhancing the congestion control properties of TCP. GWA requires only minor modifications to the existing protocol stack and is completely backward compatible, allowing GWA-hosts to interact with non-GWA hosts without modifications. GWA exploits the notion of end-host-network cooperation, with the congestion level notified from the network to end hosts. It is based on solid control theory results mat guarantee performance and stable network operation. GWA is able to avoid window oscillations and the related fluctuations in offered load and network performance. This makes it more robust to sustained network overload due to a large number of connections competing for the same bottleneck, a situation where traditional TCP implementations fail to provide satisfactory performance. GWA-TCP is compared with traditional TCP, TCP with RED and also ECN using the ns-2 simulator. Results show that in most cases GWA-TCP outperforms the traditional schemes. In particular, when compared with ECN, it provides smoother network operation and increased fairness. [source] Feedforward networks in financial predictions: the future that modifies the presentEXPERT SYSTEMS, Issue 3 2000Massimo Budcema The main goal of this paper is to show how relatively minor modifications of well-known algorithms (in particular, back propagation) can dramatically increase the performance of an artificial neural network (ANN) for time series prediction. We denote our proposed sets of modifications as the 'self-momentum', 'Freud' and 'Jung' rules. In our opinion, they provide an example of an alternative approach to the design of learning strategies for ANNs, one that focuses on basic mathematical conceptualization rather than on formalism and demonstration. The complexity of actual prediction problems makes it necessary to experiment with modelling possibilities whose inherent mathematical properties are often not well understood yet. The problem of time series prediction in stock markets is a case in point. It is well known that asset price dynamics in financial markets are difficult to trace, let alone to predict with an operationally interesting degree of accuracy. We therefore take financial prediction as a meaningful test bed for the validation of our techniques. We discuss in some detail both the theoretical underpinnings of the technique and our case study about financial prediction, finding encouraging evidence that supports the theoretical and operational viability of our new ANN specifications. Ours is clearly only a preliminary step. Further developments of ANN architectures with more and more sophisticated 'learning to learn' characteristics are now under study and test. [source] Novel polyketides synthesized with a higher plant stilbene synthaseFEBS JOURNAL, Issue 13 2001Hiroyuki Morita The physiological function of the stilbene synthase (STS) from groundnut (Arachis hypogaea) is the formation of resveratrol. The enzyme uses 4-coumaroyl-CoA, performs three condensations with malonyl-CoA, and folds the resulting tetraketide into a new aromatic ring system. We investigated the capacity for building novel and unusual polyketides from alternative substrates. Three types of products were obtained: (a) complete reaction (stilbene-type), (b) three condensations without formation of an aromatic ring (CTAL-type pyrone derailment), and (c) two condensations (BNY-type pyrone derailment). All product types were obtained from 4-fluorocinnamoyl-CoA and analogs in which the coumaroyl moiety was replaced by furan or thiophene. Only type (b) and (c) products were synthesized from other 4-substituted 4-coumaroyl-CoA analogs (-Cl, -Br, -OCH3). Benzoyl-CoA, phenylacetyl-CoA, and medium chain aliphatic CoA esters were poor substrates, and the majority of the products were of type (c). The results show that minor modifications can be used to direct the enzyme reaction to form a variety of different and new products. Manipulation of the biosynthesis of polyketides by synthetic analogs could lead to the development of a chemical library of pharmaceutically interesting novel polyketides. [source] Elders assessment of an evolving model of oral healthGERODONTOLOGY, Issue 4 2007Mario A Brondani Objectives:, To evaluate qualitatively a model of oral health through focus groups among elders. Methods:, The participants (30 women and 12 men; mean age: 75 years) attended one of six focus groups to discuss the relevance of the model to their oral health-related beliefs and experiences, and transcripts of the narratives were analysed systematically for the components, associations and recommendations emerging from the discussions. Results:, The groups confirmed the relevance of the original components of the model with minor modifications, but felt that for completeness it required four additional components: diet; economic priorities; personal expectations; and health values and beliefs. They recommended that the negative connotations of limited activity, impairment and restricted participation were modified with the positive terms activity and participation, and they suggested that ellipses rather than concentric circles more aptly illustrate the dynamic and overlapping importance of the various components in the model. Conclusion:, The original model required additional components and graphic representation to accommodate all of the experiences and beliefs relating to the oral health of the elders who participated in this qualitative study. [source] Identification of evolutionary sequential systems,part 1: unified approachINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 9 2001Claude Baron Abstract Logical identification covers a wide range of applications dealing with constrained transformation processes between internal and external models of sequential systems. In this paper, we consider the differential identification approach whose purpose is to measure the influence of minor modifications of the internal or external models of an existing system. This class of identification is dedicated to sensitivity analysis: learning, redesign, diagnosis, etc. Thus, it reveals all its interest for the study of systems which have to adapt themselves to an evolving environment. This paper presents an overall view of the different differential identification approaches and their corresponding applications. We will propose a new resolution technique based on genetic simulation. In a second paper, we will focus on some experiments performed with a genetic identification tool. Copyright © 2001 John Wiley & Sons, Ltd. [source] Artificial neural networks applications in building energy predictions and a case study for tropical climatesINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 10 2005Melek Yalcintas Abstract This study presents artificial neural network (ANN) methods in building energy use predictions. Applications of the ANN methods in energy audits and energy savings predictions due to building retrofits are emphasized. A generalized ANN model that can be applied to any building type with minor modifications would be a very useful tool for building engineers. ANN methods offer faster learning time, simplicity in analysis and adaptability to seasonal climate variations and changes in the building's energy use when compared to other statistical and simulation models. The model herein is presented for predicting chiller plant energy use in tropical climates with small seasonal and daily variations. It was successfully created based on both climatic and chiller data. The average absolute training error for the model was 9.7% while the testing error was 10.0%. This indicates that the model can successfully predict the particular chiller energy consumption in a tropical climate. Copyright © 2005 John Wiley & Sons, Ltd. [source] NMR-based analysis of structure of heteroleptic triple-decker (phthalocyaninato) (porphyrinato) lanthanides in solutionsMAGNETIC RESONANCE IN CHEMISTRY, Issue 7 2010Kirill P. Birin Abstract A novel approach for the structural analysis of heteroleptic triple-decker (porphyrinato)(phthalocyaninato) lanthanides(III) in solutions is developed. The developed approach consists in molecular mechanics (MM+) optimization of the geometry of the complex taking into account the lanthanide-induced shift (LIS) datasets. LISs of the resonance peaks in 1H NMR spectra of a series of symmetric complexes [An4P]Ln[(15C5)4Pc]Ln[An4P], where An4P2, is 5,10,15,20-tetrakis(4-methoxyphenyl)porphyrinato-dianion, [(15C5)4Pc]2, is 2,3,9,10,16,17,24,25-tetrakis(15-crown-5)phthalocyaninato-dianion and Ln = La, Ce, Pr, Nd, Sm, Eu, are analyzed. Analysis of LISs showed two sets of protons in the molecule with opposite signs of shift. Two-nuclei analysis of LISs testifies isostructurality of the whole series of investigated complexes in solution despite contraction of the lanthanide ions. Model-free separation of contact and dipolar contributions of LISs was performed with one-nucleus technique and did not show changes in contact and dipolar terms within the investigated series. MM+ optimization of the molecular structure allowed the interpretation of features of LIS for each particular group of protons. Parameterization of MM + -optimized model of molecule with values of structure-dependent dipolar contributions of LIS allows the development of the precise structural model of the triple-decker complex in solution. This approach allows the determination of the geometry and structure of the sandwich macrocyclic tetrapyrrolic complexes together with conformational analysis of flexible peripheral substituents in solutions. The developed method can be applied with minor modifications for the determination of structural parameters of other types of lanthanides(III) complexes with tetrapyrrolic ligands and also supramolecular systems based on them. Copyright © 2010 John Wiley & Sons, Ltd. [source] Major depression: emerging therapeuticsMOUNT SINAI JOURNAL OF MEDICINE: A JOURNAL OF PERSONALIZED AND TRANSLATIONAL MEDICINE, Issue 3 2008Srijan Sen MD Abstract The first effective antidepressants, monoamine oxidase inhibitors and tricyclic antidepressants, were identified 50 years ago, largely through serendipity. These medications were found to improve mood in a little more than half of depressed patients after a few weeks of chronic use. Almost all antidepressants prescribed today were developed through minor modifications of these original antidepressants and, like monoamine oxidase inhibitors and tricyclic antidepressants, act primarily through monoaminergic mechanisms. Although there have been improvements in side-effect profiles and overdose toxicity, these newer medications have not provided substantial advances in the efficacy and speed of the antidepressant effect for patients. Over the last 2 decades, our understanding of the neurobiology underlying depression has expanded exponentially. Given this expansion, we may be nearing an inflection point in antidepressant drug development, at which useful medicines will be designed through a rational understanding of the biological systems. In this review, we discuss the biological basis and preclinical and clinical evidence for a series of promising classes of antidepressants developed primarily out of a pathophysiologically informed approach. Mt Sinai J Med 75:203,224, 2008. © 2008 Mount Sinai School of Medicine [source] Polarization transfer for sensitivity-enhanced MRS using a single radio frequency transmit channelNMR IN BIOMEDICINE, Issue 5 2008D. W. J. Klomp Abstract Polarization transfer techniques are used to enhance sensitivity and improve localization in multinuclear MRS, by transferring polarization from highly polarized or even hyperpolarized nuclei to less sensitive spin systems. Clinical MR scanners are in general not equipped with a second radio frequency (RF) transmit channel, making the conventional implementation of polarization transfer techniques such as distortionless enhanced polarization transfer (DEPT) impossible. Here we present a DEPT sequence using pulses sequentially that can be used on a single RF transmit channel (SC-DEPT). Theoretical simulations, phantom measurements, and in vivo results from human brain at 3,T show that the SC-DEPT method performs as well as the conventional DEPT method. The results indicate that an independent second RF transmit channel for simultaneous pulsing at different nuclear frequencies is not needed for polarization transfer, facilitating the use of these methods with common clinical systems with minor modifications in the RF architecture. Copyright © 2007 John Wiley & Sons, Ltd. [source] One-plasmid tunable coexpression for mycobacterial protein,protein interaction studiesPROTEIN SCIENCE, Issue 11 2009Yong Chang Abstract A single plasmid that allows controlled coexpression has been developed for use in mycobacteria. The tetracycline inducible promoter, PtetO, was used to provide tetracycline-dependent induction of one gene, while the Psmyc, Pimyc, or Phsp promoters were used to provide three different levels of constitutive expression of a second gene. The functions of these four individual promoters were established using green fluorescent protein (GFP) and a newly identified red fluorescence inducible protein from Geobacillus sterothermophilus strain G1.13 (RFIP) as reporters. The tandem use of GFP and RFIP as reporter genes allowed optimization of the tunable coexpression in Mycobacterium smegmatis; either time at a fixed inducer concentration or changes in inducer concentration could be used to control the protein:protein ratio. This single vector system was used to coexpress the two-protein Mycobacterium tuberculosis stearoyl-CoA ,9 desaturase complex (integral membrane desaturase Rv3229c and NADPH oxidoreductase Rv3230c) in M. smegmatis. The catalytic activity was found to increase in a manner corresponding to increasing the level of Rv3230c relative to a fixed level of Rv3229c. This system, which can yield finely tuned coexpression of the fatty acid desaturase complex in mycobacteria, may be useful for study of other multicomponent complexes. Furthermore, the tunable coexpression strategy used herein should also be applicable in other species with minor modifications. [source] Coupling of ion-molecule reactions with liquid chromatography on a quadrupole ion trap mass spectrometerRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2008Yuriy Pyatkivskyy We report for the first time a coupling of gas-phase ion-molecule reactions with chromatographic separations on a quadrupole ion trap mass spectrometer. The interface was accomplished by using a pulsed valve for the introduction of a volatile neutral into the ion trap. The pulsed valve controller is synchronized with the mass spectrometer software. The setup requires some minor modifications to the vacuum system of the commercial quadrupole ion trap but most of the modifications are external to the mass spectrometer. Two applications of this interface are described: differentiation between two phosphoglucose positional isomers and detection of a phosphopeptide in a peptide mixture. Both applications are using the reactivity of trimethoxyborate towards a phosphate moiety in the negative ion mode. The detection of phosphopeptides hinges on our findings that non-phosphorylated peptide anions do not react with trimethoxyborate. This LC/MS detection can be easily visualized in terms of selected reaction monitoring. Copyright © 2008 John Wiley & Sons, Ltd. [source] A simplified protein precipitation/mixed-mode cation-exchange solid-phase extraction, followed by high-speed liquid chromatography/mass spectrometry, for the determination of a basic drug in human plasmaRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 18 2006Y.-J. Xue A simplified protein precipitation/mixed-mode cation-exchange solid-phase extraction (PPT/SPE) procedure has been investigated. A mixture of acetonitrile and methanol along with formic acid was used to precipitate plasma proteins prior to selectively extracting the basic drug. After vortexing and centrifugation, the supernatants were directly loaded onto an unconditioned Oasis® MCX µElution 96-well extraction plate, where the protonated drug was retained on the negatively charged sorbent while interfering neutral lipids, steroids or other endogenous materials were washed away. Normal wash steps were deemed unnecessary and not used before sample elution. The sample extracts were analyzed under both conventional and high-speed liquid chromatography/tandem mass spectrometry (LC/MS/MS) conditions to examine the feasibility of the PPT/SPE procedure for human plasma sample clean-up. For the conventional LC/MS/MS method, chromatographic separation was achieved on a C18, 2.1,×,50,mm column with gradient elution (k,,=,5.5). The mobile phase contained 0.1% formic acid in water and 0.1% formic acid in acetonitrile. For the high-speed LC/MS/MS method, chromatographic separation was achieved on a C18, 2.1,×,10,mm guard column with gradient elution (k,,=,2.2, Rt,=,0.26,min). The mobile phase contained 0.1% formic acid in water and 0.001% trifluoroacetic acid in acetonitrile. Detection for both conventional and high-speed LC/MS/MS methods was by positive ion electrospray tandem mass spectrometry on a ThermoElectron Finnigan TSQ Quantum Ultra, where enhanced resolution (RP 2000; 0.2,amu) was used for high-speed LC/MS/MS. The standard curve, ranging from 0.5 to 100,ng/mL, was fitted to a 1/x weighted quadratic regression model. This combined PPT/SPE procedure effectively eliminated time-consuming sorbent conditioning and wash steps, which are essential for a conventional mixed-mode SPE procedure, but retained the advantages of both PPT (removal of plasma proteins) and mixed-mode SPE (analyte selectivity). The validation results demonstrated that this PPT/SPE procedure was well suited for both conventional and high-speed LC/MS/MS analyses. In comparison with a conventional mixed-mode SPE procedure, the simplified PPT/SPE process provided comparable sample extract purity. This simple sample clean-up procedure can be applied to other basic compounds with minor modifications of PPT solvents. Copyright © 2006 John Wiley & Sons, Ltd. [source] Polymorphism of microcrystalline urate oxidase from Aspergillus flavusACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Ines Collings Different polymorphs of rasburicase, a recombinant urate oxidase enzyme (Uox) from Aspergillus flavus, were obtained as a series of polycrystalline precipitates. Different crystallization protocols were followed in which the salt type, pH and polyethylene glycol 8000 (PEG 8000) concentration were varied. The related crystalline phases were characterized by means of high-resolution synchrotron X-ray powder diffraction. In all cases, Uox complexed with the inhibitor 8-azaxanthine (AZA) was not altered from its robust orthorhombic I222 phase by variation of any of the factors listed above. However, in the absence of AZA during crystallization ligand-free Uox was significantly affected by the type of salt, resulting in different crystal forms for the four salts tested: sodium chloride, potassium chloride, ammonium chloride and ammonium sulfate. Remarkable alterations of some of these phases were observed upon gradual increase of the exposure time of the sample to the synchrotron beam in addition to variation of the PEG 8000 concentration. When Uox was crystallized in Tris buffer or pure water in the absence of salt, a distinct polymorph of orthorhombic symmetry (P21212) was obtained that was associated with significantly altered lattice dimensions in comparison to a previously reported isosymmetrical structure. The latter form of Uox exhibits enhanced stability to variation of pH and PEG 8000 concentration accompanied by minor modifications of the unit-cell dimensions in the ranges under study. Accurate lattice parameters were extracted for all crystalline phases. This study reveals the rich phase diagram of Uox, a protein of high pharmaceutical importance, which is associated with an enhanced degree of polymorphism. The outcome of our analysis verifies previously reported results as well as demonstrating polymorphs that have altered unit-cell dimensions with respect to known structural models. [source] A Semiparametric Estimate of Treatment Effects with Censored DataBIOMETRICS, Issue 3 2001Ronghui Xu Summary. A semiparametric estimate of an average regression effect with right-censored failure time data has recently been proposed under the Cox-type model where the regression effect ,(t) is allowed to vary with time. In this article, we derive a simple algebraic relationship between this average regression effect and a measurement of group differences in K -sample transformation models when the random error belongs to the Gp family of Harrington and Fleming (1982, Biometrika69, 553,566), the latter being equivalent to the conditional regression effect in a gamma frailty model. The models considered here are suitable for the attenuating hazard ratios that often arise in practice. The results reveal an interesting connection among the above three classes of models as alternatives to the proportional hazards assumption and add to our understanding of the behavior of the partial likelihood estimate under nonproportional hazards. The algebraic relationship provides a simple estimator under the transformation model. We develop a variance estimator based on the empirical influence function that is much easier to compute than the previously suggested resampling methods. When there is truncation in the right tail of the failure times, we propose a method of bias correction to improve the coverage properties of the confidence intervals. The estimate, its estimated variance, and the bias correction term can all be calculated with minor modifications to standard software for proportional hazards regression. [source] | ||||||||||||||||