Efficient String Graph Construction Algorithm

In the field of genome assembly research where assemblers are dominated by de Bruijn graph-based approaches, string graph-based assembly approach is getting more attention because of its ability to losslessly retain information from sequence data. Despite the advantages provided by a string graph in repeat detection and in maintaining read coherence, the high computational cost for constructing a string graph hinders its usability for genome assembly. Even though different algorithms have been proposed over the last decade for string graph construction, efficiency is still a challenge due to the demand for processing a large amount of sequence data generated by NGS technologies. Therefore, in this thesis, we provide a novel, linear time and alphabet-size-independent algorithm SOF which uses the property of irreducible edges and transitive edges to efficiently construct string graph from an overlap graph. Experimental results show that SOF is at least 2 times faster than the string graph construction algorithm provided in SGA, one of the most popular string graph-based assembler, while maintaining almost the same memory footprint as SGA. Moreover, the availability of SOF as a subprogram in the SGA assembly pipeline will give user facilities to access the preprocessing and postprocessing steps for genome assembly provided in SGA

Dynamic modelling of Heat Exchanger fouling in multistage flash (MSF) desalination

YesFouling on heat transfer surfaces due to scale formation is the most concerned item in thermal desalination industry. Here, a dynamic fouling model is developed and incorporated into the MSF dynamic process model to predict fouling at high temperature and high velocity. The proposed dynamic model considers the attachment and removal mechanisms in the fouling phenomena with more relaxation of the assumptions such as the density of the fouling layer and salinity of the recycle brine. While calcium sulphate might precipitate at very high temperature, only the crystallization of calcium carbonate and magnesium hydroxide are considered in this work. Though the model is applied in a 24 stages brine recycle MSF plant, only the heat recovery section (21 stages) is considered under this study. The effect of flow velocity and surface temperature are investigated. By including both diffusion and reaction mechanism in the fouling model, the results of the fouling prediction model are in good agreement with most recent studies in the literature. The deposition of magnesium hydroxide increases with the increase in surface temperature and flow velocity while calcium carbonate deposition increases with the increase in the surface temperature and decreases with the increase in the flow velocity

Generic Model Control (GMC) in Multistage Flash (MSF) Desalination

YesMultistage Flash Desalination (MSF) is currently facing an enormous challenge in cutting of the cost: within the last few years, the MSF experienced a gradual decline in investment compared to other techniques of desalting water and thus, a significant improvement is required to remain attractive for capital investors. Improved process control is a cost effective approach to energy conservation and increased process profitability. In this work, a dynamic model is presented using gPROMS model builder to optimize and control MSF process. The Proportional Integral Derivative Controller (PID) and Generic Model Control (GMC) are used successfully to control the Top Brine Temperature (TBT) and the Brine Level (BL) in the last stage at different times of the year. The objectives of this study are: firstly, to obtain optimum TBT and BL profiles for four different seasons throughout the year by minimizing the Total Seasonal Operating Cost (TSOC); secondly, to track the optimum TBT and BL profiles using PID and GMC controllers with and without the presence of constraints; thirdly, to examine how both types of controllers handle the disturbances which occur in the plant. The results are promising and show that GMC controller provides better performance over conventional PID controller to handle a nonlinear system

Financial Market Integration: Empirical Evidence from the Economic Cooperation of India and Pakistan

The aim of this study was to explore the integration between financial markets of India and Pakistan with the help of economic cooperation among them. Monthly data from the period of January 2002 to December 2012, was applied for this stud, the data of Monthly stock price index and Trade was used. The results highlighted that there is cointegration between the two stock markets in short run, and as we have used 11 years data it is not appropriate to conclude the long run relationship on this basis, although the Johansen Cointegration test proves the presence of two cointegrating vectors. Therefore we may conclude that there is direct cause and effect relationship between stock markets of India and Pakistan with respect to trade and if the hindrances in trade are removed the financial markets will perform much better than now. Trade between India and Pakistan is of great importance for the development of both the nations as well as the regional development. There are ample opportunities available for the investors as well, they can reduce risk and earn higher returns by investing in each other’s markets. Key Terms: Financial Markets, Financial Markets Integration, Economic Cooperation, Cooperation versus Integratio

Effect of Hydrogen Peroxide Concentration on 100% Cotton Knit Fabric Bleaching

This paper focuses on the effect of different concentration of hydrogen peroxide (an oxidizing bleaching agent) on 100% single jersey cotton knit fabric. Five different concentrations (25%, 30%, 35%, 40% and 45%) of hydrogen peroxide solution (5% stock solution) were adopted for this experiment. For each individual concentration, bleaching was performed in three different quantities (6gm/L, 8gm/L and 10gm/L) at the same temperature (100˚C) and same time (60 minute) cycle. 5gm samples were taken where 1:10 material and liquor ratio was maintained in each operation. Spectrophotometer (data color 650) was used to test the reflectance of all bleached samples, and their bursting strengths were measured by an Auto burst instrument following ISO 13938-1 method. The effects of hydrogen peroxide concentration on various physical properties such as weight loss, absorbency, GSM, bursting strength, and whiteness was studied to minimize the cost of bleaching process by optimizing the concentration of hydrogen peroxide. As majority of industries have concerned to alineate the production cost with maximum quality assurance which has been obtained through bleaching at 30% concentration

Physiological studies on Ascochyta rabiei (Pass.) Lab.

The effect of culture media, carbon and nitrogen sources, pH levels and temperature were studied on mycelial growth of Ascochyta rabiei. Maximum growth of the fungus was found on chickpea extract agar medium. Glucose was found to be the best source of carbon while potassium nitrate and sodium nitrate were better sources of nitrogen. The most suitable pH level for growth of the fungus was 7.0 and 7.5. Growth of A. rabiei was maximum at 250 C after 15 days of inoculation while it is not significantly different from that of 200C after 21 days of inoculation. The growth was reduced drastically below 100C and above 300C

Response of Chickpea Lines to Ascochyta rabiei at Two Growing Stages

During winter 2004 and 2005, two field and glasshouse experiments were conducted to evaluate the response of 471 chickpea genotypes to Ascochyta rabiei, as Ascochyta blight (AB) disease in Chickpea (Cicer aurietimum). Frequent rainfall at flowering and pod formation stages made favorite conditions conducive for the infection and symptoms expression. So, the genotypes with high level of tolerance at seedling stage proved response to the pathogen under field condition. Disease at seedling and adult plant stage exhibited high association, although level of infection was higher at adult plant stage. In glasshouse 65 genotypes at seedling stage and in field experiment 14 genotypes at pod formation stage were resistant to the pathogen. Following green house and field screening methods, six genotypes FLIP98-229C, FLIP82-150C,NCS 950204, NCS 950219, NCS 9903 and PaidarxParbat from NARC and six lines (FLIP 00-20C, FLIP 02-18C, FLIP 02-44C, FLIP 97-120C, FLIP 02-39C and FLIP 97-102C) from ICARDA found resistant for multilocational / agronomic evaluation and use as resistant parent trials for high yielding AB resistance breeding varieties

Physiological studies on Macrophomina phaseolina (Tassi) Goid

In vitro physiological studies on mycelial growth of Macrophomina phaseolina (Tassi) Goid revealed that the fungus grew best on cornmeal agar out of five culture media that were tried. All the carbon sources were found to be more or less equally good while peptone was the best among the nitrogen sources. Growth of M. phaseolina was maximum at 300 C after 7 days of inoculation, which was reduced significantly below 200 C and above 350 C. All the tested pH levels (6.0 to 8.0) were found equally suitable for growth of fungus.&nbsp

Resistance in Mungbean to bacterial leaf spot disease

Fifty-eight mungbean genotypes/cultivars of indigenous as well as exotic origin were screened against natural infection of bacterial leaf spot disease under field conditions at National Agriculture Research Centre, Islamabad during Kharif season of 2002. Two genotypes exhibited highly resistant reaction, 10 displayed resistant reaction and 18 were tolerant, while the rest were either susceptible or highly susceptible against the disease. Identified resistant sources may be exploited for the development of high yielding disease resistant cultivars of mungbean by using in hybridization programme.&nbsp

Correlation between human ether-a-go-go-related gene channel inhibition and action potential prolongation

Background and Purpose: Human ether-a-go-go-related gene (hERG; Kv11.1) channel inhibition is a widely accepted predictor of cardiac arrhythmia. hERG channel inhibition alone is often insufficient to predict pro-arrhythmic drug effects. This study used a library of dofetilide derivatives to investigate the relationship between standard measures of hERG current block in an expression system and changes in action potential duration (APD) in human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). The interference from accompanying block of Cav1.2 and Nav1.5 channels was investigated along with an in silico AP model. Experimental Approach: Drug-induced changes in APD were assessed in hiPSC-CMs using voltage-sensitive dyes. The IC50 values for dofetilide and 13 derivatives on hERG current were estimated in an HEK293 expression system. The relative potency of each drug on APD was estimated by calculating the dose (D150) required to prolong the APD at 90% (APD90) repolarization by 50%. Key Results: The D150 in hiPSC-CMs was linearly correlated with IC50 of hERG current. In silico simulations supported this finding. Three derivatives inhibited hERG without prolonging APD, and these compounds also inhibited Cav1.2 and/or Nav1.5 in a channel state-dependent manner. Adding Cav1.2 and Nav1.2 block to the in silico model recapitulated the direction but not the extent of the APD change. Conclusions and Implications: Potency of hERG current inhibition correlates linearly with an index of APD in hiPSC-CMs. The compounds that do not correlate have additional effects including concomitant block of Cav1.2 and/or Nav1.5 channels. In silico simulations of hiPSC-CMs APs confirm the principle of the multiple ion channel effects