On pattern oriented software architecture for the grid

Precision, sophistication and economic factors in many areas of scientific research that demand very high magnitude of compute power is the order of the day. Thus advance research in the area of high performance computing is getting inevitable. The basic principle of sharing and collaborative work by geographically separated computers is known by several names such as metacomputing, scalable computing, cluster computing, internet computing and this has today metamorphosed into a new term known as grid computing. This paper gives an overview of grid computing and compares various grid architectures. We show the role that patterns can play in architecting complex systems, and provide a very pragmatic reference to a set of well-engineered patterns that the practicing developer can apply to crafting his or her own specific applications. We are not aware of pattern-oriented approach being applied to develop and deploy a grid. There are many grid frameworks that are built or are in the process of being functional. All these grids differ in some functionality or the other, though the basic principle over which the grids are built is the same. Despite this there are no standard requirements listed for building a grid. The grid being a very complex system, it is mandatory to have a standard Software Architecture Specification (SAS). We attempt to develop the same for use by any grid user or developer. Specifically, we analyze the grid using an object oriented approach and presenting the architecture using UML. This paper will propose the usage of patterns at all levels (analysis. design and architectural) of the grid development.

Selective double quantum resolved correlation experiment for the complete separation of entire proton NMR spectra of enantiomers

The present study reports a two dimensional NMR experiment which separates single quantum spectra of enantiomers from that of a racemic mixture. This is a blend of selective double quantum refocusing, for resolving couplings and chemical shift interactions along two dimensions followed by correlation of the selectively excited protons to the entire coupled spin network. The concept is solely based on the presence of distinct intra methyl dipolar couplings of different enantiomers when dissolved in chiral orienting media. The analysis of single enantiomer spectrum obtained from respective F-2 cross sections yield all the spectral information. (C) 2011 Elsevier Inc. All rights reserved.

Review of correlations between SPT N and shear modulus: A new correlation applicable to any region

A low strain shear modulus plays a fundamental role in earthquake geotechnical engineering to estimate the ground response parameters for seismic microzonation. A large number of site response studies are being carried out using the standard penetration test (SPT) data, considering the existing correlation between SPT N values and shear modulus. The purpose of this paper is to review the available empirical correlations between shear modulus and SPT N values and to generate a new correlation by combining the new data obtained by the author and the old available data. The review shows that only few authors have used measured density and shear wave velocity to estimate shear modulus, which were related to the SPT N values. Others have assumed a constant density for all the shear wave velocities to estimate the shear modulus. Many authors used the SPT N values of less than 1 and more than 100 to generate the correlation by extrapolation or assumption, but practically these N values have limited applications, as measuring of the SPT N values of less than 1 is not possible and more than 100 is not carried out. Most of the existing correlations were developed based on the studies carried out in Japan, where N values are measured with a hammer energy of 78%, which may not be directly applicable for other regions because of the variation in SPT hammer energy. A new correlation has been generated using the measured values in Japan and in India by eliminating the assumed and extrapolated data. This correlation has higher regression coefficient and lower standard error. Finally modification factors are suggested for other regions, where the hammer energy is different from 78%. Crown Copyright (C) 2012 Published by Elsevier Ltd. All rights reserved.

Pattern recognition and cellular immune responses to novel Mycobacterium tuberculosis-antigens in individuals from Belarus

Background: Tuberculosis (TB) is an enduring health problem worldwide and the emerging threat of multidrug resistant (MDR) TB and extensively drug resistant (XDR) TB is of particular concern. A better understanding of biomarkers associated with TB will aid to guide the development of better targets for TB diagnosis and for the development of improved TB vaccines. Methods: Recombinant proteins (n = 7) and peptide pools (n = 14) from M. tuberculosis (M.tb) antigens associated with M.tb pathogenicity, modification of cell lipids or cellular metabolism, were used to compare T cell immune responses defined by IFN-gamma production using a whole blood assay (WBA) from i) patients with TB, ii) individuals recovered from TB and iii) individuals exposed to TB without evidence of clinical TB infection from Minsk, Belarus. Results: We identified differences in M.tb target peptide recognition between the test groups, i.e. a frequent recognition of antigens associated with lipid metabolism, e.g. cyclopropane fatty acyl phospholipid synthase. The pattern of peptide recognition was broader in blood from healthy individuals and those recovered from TB as compared to individuals suffering from pulmonary TB. Detection of biologically relevant M.tb targets was confirmed by staining for intracellular cytokines (IL-2, TNF-alpha and IFN-gamma) in T cells from non-human primates (NHPs) after BCG vaccination. Conclusions: PBMCs from healthy individuals and those recovered from TB recognized a broader spectrum of M.tb antigens as compared to patients with TB. The nature of the pattern recognition of a broad panel of M.tb antigens will devise better strategies to identify improved diagnostics gauging previous exposure to M.tb; it may also guide the development of improved TB-vaccines.

PAMAM Dendrimer-Drug Interactions: Effect of pH on the Binding and Release Pattern

Understanding the dendrimer-drug interaction is of great importance to design and optimize the dendrimer-based drug delivery system. Using atomistic molecular dynamics (MD) simulations, we have analyzed the release pattern of four ligands (two soluble drugs, namely, salicylic acid (Sal), L-alanine (Ala), and two insoluble drugs, namely, phenylbutazone (Pbz) and primidone (Prim)), which were initially encapsulated inside the ethylenediamine (EDA) cored polyamidoamine (PAMAM) dendrimer using the docking method. We have computed the potential of mean force (PMF) variation with generation 5 (G5)-PAMAM dendrimer complexed with drug molecules using umbrella sampling. From our calculated PMF values, we observe that soluble drugs (Sal and Ala) have lower energy barriers than insoluble drugs (Pbz and Prim). The order of ease of release pattern for these drugs from G5 protonated PAMAM dendrimer was found to be Ala > Sal > Prim > Pbz. In the case of insoluble drugs (Prim and Pbz), because of larger size, we observe much nonpolar contribution, and thus, their larger energy barriers can be reasoned to van der Waals contribution. From the hydrogen bonding analysis of the four PAMAM drug complexes under study, we found intermolecular hydrogen bonding to show less significant contribution to the free energy barrier. Another interesting feature appears while calculating the PMF profile of G5NP (nonprotonated)-PAMAM Pbz and G5NP (nonprotonated)-PAMAM-Sal complex. The PMF was found to be less when the drug is bound to nonprotonated dendrimer compared to the protonated dendrimer. Our results suggest that encapsulation of the drug molecule into the host PAMAM dendrimer should be carried out at higher pH values (near pH 10). When such complex enters the human body, the pH is around 7.4 and at that physiological pH, the dendrimer holds the drug tightly. Hence the release of drug can occur at a controlled rate into the bloodstream. Thus, our findings provide a microscopic picture of the encapsulation and controlled release of drugs in the case of dendrimer-based host-guest systems.

Structure and deformation correlation of closed-cell aluminium foam subject to uniaxial compression

We report the results of an experimental and numerical study conducted on a closed-cell aluminium foam that was subjected to uniaxial compression with lateral constraint. X-ray computed tomography was utilized to gain access into the three-dimensional (3-D) structure of the foam and some aspects of the deformation mechanisms. A series of advanced 3-D image analyses are conducted on the 3-D images aimed at characterizing the strain localization regions. We identify the morphological/geometrical features that are responsible for the collapse of the cells and the strain localization. A novel mathematical approach based on a Minkowski tensor analysis along with the mean intercept length technique were utilized to search for signatures of anisotropy across the foam sample and its evolution as a function of loading. Our results show that regions with higher degrees of anisotropy in the undeformed foam have a tendency to initiate the onset of cell collapse. Furthermore, we show that strain hardening occurs predominantly in regions with large cells and high anisotropy. We combine the finite element method with the tomographic images to simulate the mechanical response of the foam. We predict further deformation in regions where the foam is already deformed. Crown Copyright (C) 2012 Published by Elsevier Ltd. on behalf of Acta Materialia Inc. All rights reserved.

Correlation of Calcification on Excised Aortic Valves by Micro-Computed Tomography with Severity of Aortic Stenosis

Background and aim of the study: The quantification of incidentally found aortic valve calcification on computed tomography (CT) is not performed routinely, as data relating to the accuracy of aortic valve calcium for estimating the severity of aortic stenosis (AS) is neither consistent nor validated. As aortic valve calcium quantification by CT is confounded by wall and coronary ostial calcification, as well as motion artifact, the ex-vivo micro-computed tomography (micro-CT) of stenotic aortic valves allows a precise measurement of the amounts of calcium present. The study aim, using excised aortic valves from patients with confirmed AS, was to determine if the amount of calcium on micro-CT correlated with the severity of AS. Methods: Each of 35 aortic valves that had been excised from patients during surgical valve replacement were examined using micro-CT imaging. The amount of calcium present was determined by absolute and proportional values of calcium volume in the specimen. Subsequently, the correlation between calcium volume and preoperative mean aortic valve gradient (MAVG), peak transaortic velocity (V-max), and aortic valve area (AVA) on echocardiography, was evaluated. Results: The mean calcium volume across all valves was 603.2 +/- 398.5 mm(3), and the mean ratio of calcium volume to total valve volume was 0.36 +/- 0.16. The mean aortic valve gradient correlated positively with both calcium volume and ratio (r = 0.72, p <0.001). V-max also correlated positively with the calcium volume and ratio (r = 0.69 and 0.76 respectively; p <0.001). A logarithmic curvilinear model proved to be the best fit to the correlation. A calcium volume of 480 mm(3) showed sensitivity and specificity of 0.76 and 0.83, respectively, for a diagnosis of severe AS, while a calcium ratio of 0.37 yielded sensitivity and specificity of 0.82 and 0.94, respectively. Conclusion: A radiological estimation of calcium amount by volume, and its proportion to the total valve volume, were shown to serve as good predictive parameters for severe AS. An estimation of the calcium volume may serve as a complementary measure for determining the severity of AS when aortic valve calcification is identified on CT imaging. The Journal of Heart Valve Disease 2012;21:320-327

How good are the simulations of tropical SST-rainfall relationship by IPCC AR4 atmospheric and coupled models?

The failure of atmospheric general circulation models (AGCMs) forced by prescribed SST to simulate and predict the interannual variability of Indian/Asian monsoon has been widely attributed to their inability to reproduce the actual sea surface temperature (SST)-rainfall relationship in the warm Indo-Pacific oceans. This assessment is based on a comparison of the observed and simulated correlation between the rainfall and local SST. However, the observed SSTconvection/rainfall relationship is nonlinear and for this a linear measure such as the correlation is not an appropriate measure. We show that the SST-rainfall relationship simulated by atmospheric and coupled general circulation models in IPCC AR4 is nonlinear, as observed, and realistic over the tropical West Pacific (WPO) and the Indian Ocean (IO). The SST-rainfall pattern simulated by the coupled versions of these models is rather similar to that from the corresponding atmospheric one, except for a shift of the entire pattern to colder/warmer SSTs when there is a cold/warm bias in the coupled version.

A study of epileptogenic network structures in rat hippocampal cultures using first spike latencies during synchronization events

Study of hypersynchronous activity is of prime importance for combating epilepsy. Studies on network structure typically reconstruct the network by measuring various aspects of the interaction between neurons and subsequently measure the properties of the reconstructed network. In sub-sampled networks such methods lead to significant errors in reconstruction. Using rat hippocampal neurons cultured on a multi-electrode array dish and a glutamate injury model of epilepsy in vitro, we studied synchronous activity in neuronal networks. Using the first spike latencies in various neurons during a network burst, we extract various recurring spatio-temporal onset patterns in the networks. Comparing the patterns seen in control and injured networks, we observe that injured networks express a wide diversity in their foci (origin) and activation pattern, while control networks show limited diversity. Furthermore, we note that onset patterns in glutamate injured networks show a positive correlation between synchronization delay and physical distance between neurons, while control networks do not.

Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences

Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

A study of epileptogenic network structures in rat hippocampal cultures using first spike latencies during synchronization events

Study of hypersynchronous activity is of prime importance for combating epilepsy. Studies on network structure typically reconstruct the network by measuring various aspects of the interaction between neurons and subsequently measure the properties of the reconstructed network. In sub-sampled networks such methods lead to significant errors in reconstruction. Using rat hippocampal neurons cultured on a multi-electrode array dish and a glutamate injury model of epilepsy in vitro, we studied synchronous activity in neuronal networks. Using the first spike latencies in various neurons during a network burst, we extract various recurring spatio-temporal onset patterns in the networks. Comparing the patterns seen in control and injured networks, we observe that injured networks express a wide diversity in their foci (origin) and activation pattern, while control networks show limited diversity. Furthermore, we note that onset patterns in glutamate injured networks show a positive correlation between synchronization delay and physical distance between neurons, while control networks do not.

Activation of Lattice Oxygen of TiO2 by Pd2+ Ion: Correlation of Low-Temperature CO and Hydrocarbon Oxidation with Structure of Ti1-xPdxO2-x (x=0.01-0.03)

Lattice oxygen of TiO2 is activated by the substitution of Pd ion in its lattice. Ti1-xPdxO2-x (x = 0.01-0.03) have been synthesized by solution combustion method crystallizing in anatase TiO2 structure. Pd is in +2 oxidation state and Ti is in +4 oxidation state in the catalyst. Pd is more ionic in TiO2 lattice compared to Pd in PdO. Oxygen storage capacity defined by ``amount of oxygen that is used reversibly to oxidize CO'' is as high as 5100 mu mol/g of Ti0.97Pd0.03O1.97. Oxygen is extracted by CO to CO2 in absence of feed oxygen even at room temperature which is more than 20 times compared to pure TiO2. Rate of CO oxidation is 2.75 mu mol g(-1) s(-1) at 60 degrees C over Ti0.97Pd0.03O1.97 and C2H2 gets oxidized to CO2 and H2O at room temperature. Catalyst is not poisoned on long time operation of the reactor. Such high catalytic activity is due to activated lattice oxygen created by the substitution of Pd ion as seen from first-principles density functional theory (DFT) calculations with 96 atom supercells of Ti32O64, Ti31Pd1O63, Ti30Pd2O62, and Ti29Pd3O61. The compounds crystallize in anatase TiO2 structure with Pd2+ ion in nearly square planar geometry and TiO6 octahedra are distorted by the creation of weakly bound oxygens. Structural analysis of Ti31Pd1O63 which is close to 3% Pd ion substituted TiO2 shows that oxygens associated with both Ti and Pd ions in the lattice show bond valence sum of 1.87, a low value characteristic of weak oxygen in the lattice compared to oxygens with valence 2 and above in the same lattice. Exact positions of activated oxygens have been identified in the lattice from DFT calculations.

A high precision instrument to measure angular and binocular deviation introduced by aircraft windscreens by using a shadow casting technique

Objects viewed through transparent sheets with residual non-parallelism and irregularity appear shifted and distorted. This distortion is measured in terms of angular and binocular deviation of an object viewed through the transparent sheet. The angular and binocular deviations introduced are particularly important in the context of aircraft windscreens and canopies as they can interfere with decision making of pilots especially while landing, leading to accidents. In this work, we have developed an instrument to measure both the angular and binocular deviations introduced by transparent sheets. This instrument is especially useful in the qualification of aircraft windscreens and canopies. It measures the deviation in the geometrical shadow cast by a periodic dot pattern trans-illuminated by the distorted light beam from the transparent test specimen compared to the reference pattern. Accurate quantification of the shift in the pattern is obtained by cross-correlating the reference shadow pattern with the specimen shadow pattern and measuring the location of the correlation peak. The developed instrument is handy to use and computes both angular and binocular deviation with an accuracy of less than +/- 0.1 mrad (approximate to 0.036 mrad) and has an excellent repeatability with an error of less than 2%. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4769756]