Using the PGAS Programming Paradigm for Biological Sequence Alignment on a Chip Multi-Threading Architecture

The Partitioned Global Address Space (PGAS) programming paradigm offers ease-of-use in expressing parallelism through a global shared address space while emphasizing performance by providing locality awareness through the partitioning of this address space. Therefore, the interest in PGAS programming languages is growing and many new languages have emerged and are becoming ubiquitously available on nearly all modern parallel architectures. Recently, new parallel machines with multiple cores are designed for targeting high performance applications. Most of the efforts have gone into benchmarking but there are a few examples of real high performance applications running on multicore machines. In this paper, we present and evaluate a parallelization technique for implementing a local DNA sequence alignment algorithm using a PGAS based language, UPC (Unified Parallel C) on a chip multithreading architecture, the UltraSPARC T1.

Development of a Brain Glutamate Microbiosensor

This work attempts to improve the permselectivity of poly-ortho-phenylenediamine (PPD) coating for glutamate biosensor applications on Pt microelectrode, using constant potential amperometry and cyclic voltammetry. Percentage permeability of the modified PPD microelectrode was carried out towards hydrogen peroxide (H2O2) and ascorbic acid (AA) whereas permselectivity represents the percentage interference by AA in H2O2 detection. The 50-μm diameter Pt disk microelectrode showed a good permeability value toward H2O2 (95%) and selectivity against AA (0.01%) compared to other sizes of electrode studied here. The electrode was further modified with glutamate oxidase (GluOx) that was immobilized and cross linked with glutaraldehyde (GA, 0.125%), resulting in Pt/PPD/GluOx-GA electrode design. The maximum current density Jmax and apparent Michaelis constant, KM, obtained on Pt/PPD/GluOx-GA electrodes were 48 μA cm-2 and 50 μM, respectively. The linear region slope (LRS) was 0.96 μA cm-2 mM-1. The detection limit (LOD) for glutamate was 3.0 ± 0.6 μM. This study shows a promising glutamate microbiosensor for brain glutamate detection. 

A Compact Pi Network for Reducing Bit Error Rate in Dispersive FIR Channel Noise Model

During signal transmission, the combined effect of the transmitter filter, the transmission medium, and additive white Gaussian noise (AWGN) are included in the channel which distort and add noise to the signal. This causes the well defined signal constellation to spread causing errors in bit detection. A compact pi neural network with minimum number of nodes is proposed. The replacement of summation at each node by multiplication results in more powerful mapping. The resultant pi network is tested on six different channels.

Enhancement of Biogas Production from Bakery Waste by Pseudomonas aeruginosa

Production of biogas from bakery waste was enhanced by additional bacterial cell. This study was divided into 2 steps. First step, grease waste from bakery industry-s grease trap was initially degraded by Pseudomonas aeruginosa. The concentration of byproduct, especially glycerol, was determined and found that glycerol concentration increased from 12.83% to 48.10%. Secondary step, 3 biodigesters were set up in 3 different substrates: non-degraded waste as substrate in first biodigester, degraded waste as substrate in secondary biodigester, and degraded waste mixed with swine manure in ratio 1:1 as substrate in third biodigester. The highest concentration of biogas was found in third biodigester that was 44.33% of methane and 63.71% of carbon dioxide. The lower concentration at 24.90% of methane and 18.98% of carbon dioxide was exhibited in secondary biodigester whereas the lowest was found in non-degraded waste biodigester. It was demonstrated that the biogas production was greatly increased with the initial grease waste degradation by Pseudomonas aeruginosa.

Comprehensive Characteristics of the Municipal Solid Waste Generated in the Faculty of Engineering, UKM

The main aims in this research are to study the solid waste generation in the Faculty of Engineering and Built Environment in the UKM and at the same time to determine composition and some of the waste characteristics likewise: moisture content, density, pH and C/N ratio. For this purpose multiple campaigns were conducted to collect the wastes produced in all hostels, faculties, offices and so on, during 24th of February till 2nd of March 2009, measure and investigate them with regard to both physical and chemical characteristics leading to highlight the necessary management policies. Research locations are Faculty of Engineering and the Canteen nearby that. From the result gained, the most suitable solid waste management solution will be proposed to UKM. The average solid waste generation rate in UKM is 203.38 kg/day. The composition of solid waste generated are glass, plastic, metal, aluminum, organic and inorganic waste and others waste. From the laboratory result, the average moisture content, density, pH and C/N ratio values from the solid waste generated are 49.74%, 165.1 kg/m3, 5.3, and 7:1 respectively. Since, the food waste (organic waste) were the most dominant component, around 62% from the total waste generated hence, the most suitable solid waste management solution is composting.

Babbitt Casting and Babbitt Spraying Processes Case Study

In this paper, the babbitting of a bearing in boiler feed pump of an electromotor has been studied. These bearings have an important role in reducing the shut down times in the pumps, compressors and turbines. The most conventional method in babbitting is casting as a melting method. The comparison between thermal spray and casting methods in babbitting shows that the thermal spraying babbitt layer has better performance and tribological behavior. The metallurgical and tribological analysis such as SEM, EDS and wet chemical analysis has been made in the Babbitt alloys and worn surfaces. Two type of babbitt materials: tinbase and lead-base babbitt was used. The benefits of thermally sprayed babbitt layers are completely clear especially in large bearings.

The Experimental and Numerical Analysis of a Lightpipe using a Simulation Software

A lightpipe is an about 99 percent specular reflective mirror pipe or duct that is used for the transmission of the daylight from the outside into a building. The lightpipes are usually used in the daylighting buildings, in the residential, industrial and commercial sectors. This paper is about the performances of a lightpipe installed in a laboratory (3 m x 2.6 m x 3 m) without windows. The aim is to analyse the luminous intensity distribution for several sky/sun conditions. The lightpipe was monitored during the year 2006. The lightpipe is 1 m long and the diameter of the top collector and of the internal diffuser device is 0.25 m. In the laboratory there are seven illuminance sensors: one external is located on the roof of the laboratory and six internal sensors are connected to a data acquisition system. The internal sensors are positioned under the internal diffusive device at an height of 0.85 m from the floor to simulate a working plane. The numerical data are obtained through a simulation software. This paper shows the comparison between the experimental and numerical results concerning the behavior of the lightpipe.

Synthesis and Characterization of Cu-NanoWire Arrays by EMD Using ITO-Template

Nanowire arrays of copper with uniform diameters have been synthesized by potentiostatic electrochemical metal deposition (EMD) of copper sulphate and potassium chloride solution within the nano-channels of porous Indium-Tin Oxide (ITO), also known as Tin doped Indium Oxide templates. The nanowires developed were fairly continuous with diameters ranging from 110-140 nm along the entire length. Single as well as poly-crystalline copper wires have been prepared by application of appropriate potential during the EMD process. Scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM), small angle electron diffraction (SAED) and atomic force microscopy (AFM) were used to characterize the synthesized nano wires at room temperature. The electrochemical response of synthesized products was evaluated by cyclic voltammetry while surface energy analysis was carried out using a Goniometer.

Integral Tracking Control for a Piezoelectric Actuator System

We propose an integral tracking control method for a piezoelectric actuator system. The proposed method achieves the output tracking without requiring any hysteresis observer or schemes to compensate the hysteresis effect. With the proposed control law, the system is converted into the standard singularly perturbed model. Using Tikhonov-s theorem, we guarantee that the tracking error can be reduced to arbitrarily small bound. A numerical example is given to illustrate the effectiveness of our proposed method.

Effect of Transmission Codes on Hybrid SC/MRC Diversity Reception MQAM system over Rayleigh Fading Channels

In this paper, the effect of transmission codes on the performance of coherent square M-ary quadrature amplitude modulation (CSMQAM) under hybrid selection/maximal-ratio combining (H-S/MRC) diversity is analysed. The fading channels are modeled as frequency non-selective slow independent and identically distributed Rayleigh fading channels corrupted by additive white Gaussian noise (AWGN). The results for coded MQAM are computed numerically for the case of (24,12) extended Golay code and compared with uncoded MQAM under H-S/MRC diversity by plotting error probabilities versus average signal to noise ratio (SNR) for various values L and N in order to examine the improvement in the performance of the digital communications system as the number of selected diversity branches is increased. The results for no diversity, conventional SC and Lth order MRC schemes are also plotted for comparison. Closed form analytical results derived in this paper are sufficiently simple and therefore can be computed numerically without any approximations. The analytical results presented in this paper are expected to provide useful information needed for design and analysis of digital communication systems over wireless fading channels.

Effect of Bentonite on the Properties of Liquid Insulating Oil

Bentonitic material from South Aswan, Egypt was evaluated in terms of mineral-ogy and chemical composition as bleaching clay in refining of transformer oil before and after acid activation and thermal treatment followed by acid leaching using HCl and H2SO4 for different contact times. Structural modification and refining power of bento-nite were investigated during modification by means of X-ray diffraction and infrared spectroscopy. The results revealed that the activated bentonite could be used for refining of transformer oil. The oil parameters such as; dielectric strength, viscosity and flash point had been improved. The dielectric breakdown strength of used oil increased from 29 kV for used oil treated with unactivated bentonite to 74 kV after treatment with activated bentonite. Kinematic Viscosity changed from 19 to 11 mm2 /s after treatment with activated bentonite. However, flash point achieved 149 ºC.

Evaluation of Radiation Synthesized β-Glucan Hydrogel Wound Dressing using Rat Models

In this study, hydrogels consisted of polyvinyl alcohol, propylene glycol and β-glucan were developed by radiation technique for wound dressing. The prepared hydrogels were characterized by examining of physical properties such as gel fraction and absorption ratio. The gel fraction and absorption ratio were dependent on the crosslinking density. On observing the wound healing of rat skin, the resulting hydrogels accelerated the wound healing comparing to cotton gauze. Therefore, the PVA/propylene glycol/β-glucan blended hydrogels can greatly accelerate the healing without causing irritation.

Dynamics of Functional Composition of a Brazilian Tropical Forest in Response to Drought Stress

The aim of this study was to examine the dynamics of functional composition of a non flooded Amazonian forest in response to drought stress in terms of diameter growth, recruitment and mortality. The survey was carried out in the continuous forest of the Biological dynamics of forest fragments project 90 km outside the city of Manaus, state of Amazonas Brazil. All stems >10 cm dbh where identified to species level and monitored in 18 one hectare permanent sample plots from 1981 to 2004.For statistical analysis all species where aggregated in three ecological guilds. Two distinct drought events occurred in 1983 and 1997. Results showed that more early successional species performed better than later successional ones. Response was significant for both events but for the 1997 event this was more pronounced possibly because of the fact that the event was in the middle of the dry rather than the wet period as was the 1983 one.

Experimental Investigation on the Effect of CO2 and WAG Injection on Permeability Reduction Induced by Asphaltene Precipitation in Light Oil

Permeability reduction induced by asphaltene precipitation during gas injection is one of the serious problems in the oil industry. This problem can lead to formation damage and decrease the oil production rate. In this work, Malaysian light oil sample has been used to investigate the effect CO2 injection and Water Alternating Gas (WAG) injection on permeability reduction. In this work, dynamic core flooding experiments were conducted to study the effect of CO2 and WAG injection on the amount of asphaltene precipitated. Core properties after displacement were inspected for any permeability reduction to study the effect of asphaltene precipitation on rock properties. The results showed that WAG injection gave less asphaltene precipitation and formation damage compared to CO2 injection. The study suggested that WAG injection can be one of the important factors of managing asphaltene precipitation.

Treatment of Biowaste (Generated in Biodiesel Process) - A New Strategy for Green Environment and Horticulture Crop

Recent research on seeds of bio-diesel plants like Jatropha curcas, constituting 40-50% bio-crude oil indicates its potential as one of the most promising alternatives to conventional sources of energy. Also, limited studies on utilization of de-oiled cake have revealed that Jatropha bio-waste has good potential to be used as organic fertilizers produced via aerobic and anaerobic treatment. However, their commercial exploitation has not yet been possible. The present study aims at developing appropriate bio-processes and formulations utilizing Jatropha seed cake as organic fertilizer, for improving the growth of Polianthes tuberose L. (Tuberose). Pot experiments were carried out by growing tuberose plants on soil treated with composted formulations of Jatropha de-oiled cake, Farm Yard Manure (FYM) and inorganic fertilizers were also blended in soil. The treatment was carried out through soil amendment as well as foliar spray. The growth and morphological parameters were monitored for entire crop cycle. The growth Length and number of leaves, spike length, rachis length, number of bulb per plant and earliness of sprouting of bulb and yield enhancement were comparable to that achieved under inorganic fertilizer. Furthermore, performance of inorganic fertilizer also showed an improvement when blended with composted bio-waste. These findings would open new avenues for Jatropha based bio-wastes to be composted and used as organic fertilizers for commercial floriculture.

Highly Efficient White Light-emitting Diodes Based on Layered Quantum Dot-Phosphor Nanocomposites as Converting Materials

This paper reports on the enhanced photoluminescence (PL) of nanocomposites through the layered structuring of phosphor and quantum dot (QD). Green phosphor of Sr2SiO4:Eu, red QDs of CdSe/CdS/CdZnS/ZnS core-multishell, and thermo-curable resin were used for this study. Two kinds of composite (layered and mixed) were prepared, and the schemes for optical energy transfer between QD and phosphor were suggested and investigated based on PL decay characteristics. It was found that the layered structure is more effective than the mixed one in the respects of PL intensity, PL decay and thermal loss. When this layered nanocomposite (QDs on phosphor) is used to make white light emitting diode (LED), the brightness is increased by 37 %, and the color rendering index (CRI) value is raised to 88.4 compared to the mixed case of 80.4.

Study of Coupled Lateral-Torsional Free Vibrations of Laminated Composite Beam: Analytical Approach

In this paper, an analytical approach is used to study the coupled lateral-torsional vibrations of laminated composite beam. It is known that in such structures due to the fibers orientation in various layers, any lateral displacement will produce a twisting moment. This phenomenon is modeled by the bending-twisting material coupling rigidity and its main feature is the coupling of lateral and torsional vibrations. In addition to the material coupling, the effects of shear deformation and rotary inertia are taken into account in the definition of the potential and kinetic energies. Then, the governing differential equations are derived using the Hamilton-s principle and the mathematical model matches the Timoshenko beam model when neglecting the effect of bending-twisting rigidity. The equations of motion which form a system of three coupled PDEs are solved analytically to study the free vibrations of the beam in lateral and rotational modes due to the bending, as well as the torsional mode caused by twisting. The analytic solution is carried out in three steps: 1) assuming synchronous motion for the kinematic variables which are the lateral, rotational and torsional displacements, 2) solving the ensuing eigenvalue problem which contains three coupled second order ODEs and 3) imposing different boundary conditions related to combinations of simply, clamped and free end conditions. The resulting natural frequencies and mode shapes are compared with similar results in the literature and good agreement is achieved.

A New Face Detection Technique using 2D DCT and Self Organizing Feature Map

This paper presents a new technique for detection of human faces within color images. The approach relies on image segmentation based on skin color, features extracted from the two-dimensional discrete cosine transform (DCT), and self-organizing maps (SOM). After candidate skin regions are extracted, feature vectors are constructed using DCT coefficients computed from those regions. A supervised SOM training session is used to cluster feature vectors into groups, and to assign “face" or “non-face" labels to those clusters. Evaluation was performed using a new image database of 286 images, containing 1027 faces. After training, our detection technique achieved a detection rate of 77.94% during subsequent tests, with a false positive rate of 5.14%. To our knowledge, the proposed technique is the first to combine DCT-based feature extraction with a SOM for detecting human faces within color images. It is also one of a few attempts to combine a feature-invariant approach, such as color-based skin segmentation, together with appearance-based face detection. The main advantage of the new technique is its low computational requirements, in terms of both processing speed and memory utilization.

Numerical Simulation of Wall Treatment Effects on the Micro-Scale Combustion

To understand working features of a micro combustor, a computer code has been developed to study combustion of hydrogen–air mixture in a series of chambers with same shape aspect ratio but various dimensions from millimeter to micrometer level. The prepared algorithm and the computer code are capable of modeling mixture effects in different fluid flows including chemical reactions, viscous and mass diffusion effects. The effect of various heat transfer conditions at chamber wall, e.g. adiabatic wall, with heat loss and heat conduction within the wall, on the combustion is analyzed. These thermal conditions have strong effects on the combustion especially when the chamber dimension goes smaller and the ratio of surface area to volume becomes larger. Both factors, such as larger heat loss through the chamber wall and smaller chamber dimension size, may lead to the thermal quenching of micro-scale combustion. Through such systematic numerical analysis, a proper operation space for the micro-combustor is suggested, which may be used as the guideline for microcombustor design. In addition, the results reported in this paper illustrate that the numerical simulation can be one of the most powerful and beneficial tools for the micro-combustor design, optimization and performance analysis.

Identification of Differentially Expressed Gene(DEG) in Atherosclerotic Lesion by Annealing Control Primer (ACP)-Based Genefishing™ PCR

Atherosclerosis was identified as a chronic inflammatory process resulting from interactions between plasma lipoproteins, cellular components (monocyte, macrophages, T lymphocytes, endothelial cells and smooth muscle cells) and the extracellular matrix of the arterial wall. Several types of genes were known to express during formation of atherosclerosis. This study is carried out to identify unknown differentially expressed gene (DEG) in atherogenesis. Rabbit’s aorta tissues were stained by H&E for histomorphology. GeneFishing™ PCR analysis was performed from total RNA extracted from the aorta tissues. The DNA fragment from DEG was cloned, sequenced and validated by Real-time PCR. Histomorphology showed intimal thickening in the aorta. DEG detected from ACP-41 was identified as cathepsin B gene and showed upregulation at week-8 and week-12 of atherogenesis. Therefore, ACP-based GeneFishing™ PCR facilitated identification of cathepsin B gene which was differentially expressed during development of atherosclerosis.