Space and time efficient parallel algorithms and software for EST clustering

Expressed sequence tags, abbreviated as ESTs, are DNA molecules experimentally derived from expressed portions of genes. Clustering of ESTs is essential for gene recognition and for understanding important genetic variations such as those resulting in diseases. We present the algorithmic foundations and implementation of PaCE, a parallel software system we developed for large-scale EST clustering. The novel features of our approach include 1) design of space-efficient algorithms to limit the space required to linear in the size of the input data set, 2) a combination of algorithmic techniques to reduce the total work without sacrificing the quality of EST clustering, and 3) use of parallel processing to reduce runtime and facilitate clustering of large data sets. Using a combination of these techniques, we report the clustering of 327,632 rat ESTs in 47 minutes, and 420,694 Triticum aestivum ESTs in 3 hours and 15 minutes, using a 60-processor IBM xSeries cluster. These problems are well beyond the capabilities of state-of-the-art sequential software. We also present thorough experimental evaluation of our software including quality assessment using benchmark Arabidopsis EST data.     

An experimental study of non-newtonian fluid flow in fluidized beds: minimum fluidization velocity and bed expansion characteristics

In this work, new experimental measurements of the minimum fluidization velocity and velocity-voidage characteristics are reported for a variety of liquid-particle systems in glass columns of two different diameters. Three types of liquids, namely, Newtonian, visco-inelastic, and visco-elastic fluids, were used to fluidize the beds of glass particles of four different sizes (1.27–15.8 mm). The results obtained with Newtonian liquids conform to the expected behaviour. The applicability of a variety of equations has been examined with a view to predicting the values of the minimum fluidization velocity and fluidization index for non-Newtonian systems. The experimental results reported herein embrace the following ranges of conditions: 1.27 < D_p < 15.8 mm; D_T = 50.8 and 101.6 mm, and 0.382 n 1.00.     

Reevaluation of Cl-/HCO3- exchange in cultured bovine corneal endothelial cells

PURPOSE: To determine the apical versus basolateral polarity of the putative anion exchanger in cultured bovine corneal endothelial cells (BCECs) and to examine the influence of Cl--dependent membrane potential (Em) changes on HCO3- transport. METHODS: BCECs grown on permeable supports were used for independent perfusion of apical and basolateral surfaces. Intracellular pH (pHi) was measured using the fluorescent dye BCECF. Relative changes in Em were measured using the fluorescent dye bis-oxonol. Western blot analysis was used to detect immunoreactivity against the anion exchanger (AE1 or AE2). RESULTS: Cl- removal from apical and basolateral surfaces produced cellular alkalinization (apical side, 0.07 pH units; basolateral side, 0.06 pH units; both sides, 0.20 pH units). Application of 100 microM H2-4,4'-diisothiocyanatodihydrostilbene-2,2'-disulfonic acid (DIDS), an anion exchange inhibitor, on the apical side produced an alkalinization (0.02 pH units) followed by acidification (-0.05 pH units), whereas basolateral H2DIDS caused a substantial acidification (-0.16 pH units). In the absence of Na+, Cl- removal from the apical side caused a transient alkalinization (0.03 pH units) followed by a return to baseline; Cl- removal from the basolateral side caused a small (-0.03) acidification. In Na+-free Ringer, apical H2DIDS produced a transient alkalinization (0.02 pH units), whereas basolateral exposure had no effect. 5-Nitro-2-(3-phenylpropylamino)benzoic acid (NPPB), N-phenylanthranilic acid (DPC), and niflumic acid (50-200 microM), known Cl- channel blockers, produced cellular acidification in control Ringer. Niflumic acid hyperpolarized Em and inhibited depolarization after Cl- removal. Western blot analysis failed to detect AE2 expression in cultured BCECs. However, fresh BCECs produced a trace response. CONCLUSIONS: Physiological activity of an apical anion exchanger is weak in cultured BCECs. Cultured BCECs have significant Cl- conductance. Thus, cellular alkalinization after Cl- removal is caused primarily by depolarization of Em, which drives HCO3- influx through the basolateral electrogenic Na+:nHCO3- cotransporter. In contrast with cultured BCECs, AE2 may be present in fresh cells.     

Robust multidisciplinary UAS design optimisation

There are many applications in aeronautical/aerospace engineering where some values of the design parameters/states cannot be provided or determined accurately. These values can be related to the geometry (wingspan, length, angles) and or to operational flight conditions that vary due to the presence of uncertainty parameters (Mach, angle of attack, air density and temperature, etc.). These uncertainty design parameters cannot be ignored in engineering design and must be taken into the optimisation task to produce more realistic and reliable solutions. In this paper, a robust/uncertainty design method with statistical constraints is introduced to produce a set of reliable solutions which have high performance and low sensitivity. Robust design concept coupled with Multi-Objective Evolutionary Algorithms (MOEAs) is defined by applying two statistical sampling formulas; mean and variance/standard deviation associated with the optimisation fitness/objective functions. The methodology is based on a canonical evolution strategy and incorporates the concepts of hierarchical topology, parallel computing and asynchronous evaluation. It is implemented for two practical Unmanned Aerial System (UAS) design problems; the first case considers robust multi-objective (single-disciplinary: aerodynamics) design optimisation and the second considers a robust multidisciplinary (aero-structures) design optimisation. Numerical results show that the solutions obtained by the robust design method with statistical constraints have a more reliable performance and sensitivity in both aerodynamics and structures when compared to the baseline design.     

Fault tolerance in multiprocessor systems

Multiprocessor systems which afford a high degree of parallelism are used in a variety of applications. The extremely stringent reliability requirement has made the provision of fault-tolerance an important aspect in the design of such systems. This paper presents a review of the various approaches towards tolerating hardware faults in multiprocessor systems. It emphasizes the basic concepts of fault tolerant design and the various problems to be taken care of by the designer. An indepth survey of the various models, techniques and methods for fault diagnosis is given. Further, we consider the strategies for fault-tolerance in specialized multiprocessor architectures which have the ability of dynamic reconfiguration and are suited tovlsi implementation. An analysis of the state-of-the-art is given which points out the major aspects of fault-tolerance in such architectures.     

A Scenario Based Impact Assessment of Trace Metals on Ecosystem of River Ganges Using Multivariate Analysis Coupled with Fuzzy Decision-Making Approach

The growing consciousness about the health risks associated with environmental pollutants has brought a major shift in global concern towards prevention of hazardous/trace metals discharge in water bodies. Majority of these trace metals gets accumulated in the body of aquatic lives, which are considered as potential indicators of hazardous content. This results in an ecological imbalance in the form of poisoning, diseases and even death of fish and other aquatic lives, and ultimately affect humans through food chain. Trace metals such as Cd, Cr, Cu, Mn, Ni, Pb and Zn originated from various industrial operations containing metallic solutions and agricultural practices, have been contributing significantly to cause aquatic pollution. The present study develops a novel approach of expressing sustainability of river’s ecosystem based on health of the fish by coupling fuzzy sensitivity analysis into multivariate analysis. A systematic methodology has been developed by generating monoplot, two dimensional biplot and rotated component matrix (using ‘Analyze it’ and ‘SPSS’ software), which can simultaneously identify critical trace metals and their industrial sources, critical sampling stations, and adversely affected fish species along with their interrelationships. A case study of assessing the impact of trace metals on the aquatic life of river Ganges, India has also been presented to demonstrate effectiveness of the model. The clusters pertaining to various water quality parameters have been identified using Principal Component Analysis (PCA) to determine actual sources of pollutants and their impact on aquatic life. The fuzzy sensitivity analysis reveals the cause-effect relationship of these critical parameters. The study suggests pollution control agencies to enforce appropriate regulations on the wastewater dischargers responsible for polluting river streams with a particular kind of trace metal(s).     

A Stochastic Optimization Model to Reduce Expected Post-Disaster Response Time Through Pre-Disaster Investment Decisions

This paper seeks to enhance network survivability under a disaster and reduce the expected post-disaster response time for transportation networks through pre-disaster investment decisions. The planning focuses on determining the links of the network to strengthen through investment under two types of uncertainties: the disaster characteristics, and the surviving network under each disaster. A bi-level stochastic optimization model is proposed for this problem, in which link investment decisions are made at the upper level to enhance the network survivability subject to a budget constraint such that the expected post-disaster response time is minimized at the lower level. A two-stage heuristic algorithm is proposed to obtain effective solutions efficiently. The numerical experiments indicate that the proposed heuristic algorithm converges to a fixed point representing a feasible solution, within an acceptable tolerance level, of the bi-level stochastic optimization model which is an effective solution under disasters of moderate severity. Parametric and sensitivity analyses reinforce the need for a holistic approach that integrates multiple relevant considerations to determine the link investment decisions.     

Synthesis of Polycarbonate Precursors over Titanosilicate Molecular Sieves

A novel catalytic application of titanosilicate molecular sieves (TS-1 and TiMCM-41), in the synthesis of polycarbonate precursors like cyclic carbonates and dimethyl and diphenyl carbonates, avoiding toxic chemicals like phosgene or CO, is reported. Cyclic carbonates were prepared, over TS-1 and TiMCM-41, in high yields, by cycloaddition of CO₂ to epoxides, like epichlorohydrin, propylene oxide and styrene oxide, at low temperatures and pressures. Further, transesterification of the cyclic carbonates with methanol and phenol, over TiMCM-41, yielded other polycarbonate precursors like dimethyl carbonate (DMC) and diphenyl carbonate (DPC). The cyclic carbonates could also be synthesized from the olefins in the same reactor by reacting the olefins, in the presence of TiMCM-41, with a mixture of an epoxidizing agent (like H₂O₂ or tert-butyl hydroperoxide) and CO₂.     

Adaptive PSODV algorithm for OPF with non-smooth cost functions and statistical analysis

This paper presents a particle swarm optimization with differentially perturbed velocity hybrid algorithm with adaptive acceleration coefficient (APSO-DV) for solving the optimal power flow problem with non-smooth and non-convex generator fuel cost characteristics. The APSO-DV employs differentially perturbed velocity with adaptive acceleration coefficient for updating the positions of particles for the particle swarm optimization. The feasibility of the proposed approach was tested on IEEE 30-bus and IEEE 118-bus systems with three different objective functions. Several cases were investigated to test and validate the robustness of the proposed method in finding the optimal solution. The effectiveness of the proposed approach was tested including contingency also. Simulation results demonstrate that the APSO-DV provides superior results compared to classical DE, PSO, PSO-DV and other methods recently reported in the literature. An innovative statistical analysis based on central tendency measures and dispersion measures was carried out on the bus voltage profiles and voltage stability indices.