“Reconstruction of Gene Regulatory Network from Expression Profile of Plasma RNA Data of Colorectal Cancer Patients using Soft Computing Techniques”

Microarray data analysis is one of data mining tool which is used to extract meaningful information hidden in biological data. One of the major focuses on microarray data analysis is the reconstruction of gene regulatory network that may be used to provide a broader understanding on the functioning of complex cellular systems. Since cancer is a genetic disease arising from the abnormal gene function, the identification of cancerous genes and the regulatory pathways they control will provide a better platform for understanding the tumor formation and development. The major focus of this thesis is to understand the regulation of genes responsible for the development of cancer, particularly colorectal cancer by analyzing the microarray expression data. In this thesis, four computational algorithms namely fuzzy logic algorithm, modified genetic algorithm, dynamic neural fuzzy network and Takagi Sugeno Kang-type recurrent neural fuzzy network are used to extract cancer specific gene regulatory network from plasma RNA dataset of colorectal cancer patients. Plasma RNA is highly attractive for cancer analysis since it requires a collection of small amount of blood and it can be obtained at any time in repetitive fashion allowing the analysis of disease progression and treatment response.

Cooperative Caching Framework for Mobile Cloud Computing

Due to the advancement in mobile devices and wireless networks mobile cloud computing, which combines mobile computing and cloud computing has gained momentum since 2009. The characteristics of mobile devices and wireless network makes the implementation of mobile cloud computing more complicated than for fixed clouds. This section lists some of the major issues in Mobile Cloud Computing. One of the key issues in mobile cloud computing is the end to end delay in servicing a request. Data caching is one of the techniques widely used in wired and wireless networks to improve data access efficiency. In this paper we explore the possibility of a cooperative caching approach to enhance data access efficiency in mobile cloud computing. The proposed approach is based on cloudlets, one of the architecture designed for mobile cloud computing.

Channel Adaptive MAC Protocol with Traffic-Aware Distributed Power Management in Wireless Sensor Networks-Some Performance Issues

In Wireless Sensor Networks (WSN), neglecting the effects of varying channel quality can lead to an unnecessary wastage of precious battery resources and in turn can result in the rapid depletion of sensor energy and the partitioning of the network. Fairness is a critical issue when accessing a shared wireless channel and fair scheduling must be employed to provide the proper flow of information in a WSN. In this paper, we develop a channel adaptive MAC protocol with a traffic-aware dynamic power management algorithm for efficient packet scheduling and queuing in a sensor network, with time varying characteristics of the wireless channel also taken into consideration. The proposed protocol calculates a combined weight value based on the channel state and link quality. Then transmission is allowed only for those nodes with weights greater than a minimum quality threshold and nodes attempting to access the wireless medium with a low weight will be allowed to transmit only when their weight becomes high. This results in many poor quality nodes being deprived of transmission for a considerable amount of time. To avoid the buffer overflow and to achieve fairness for the poor quality nodes, we design a Load prediction algorithm. We also design a traffic aware dynamic power management scheme to minimize the energy consumption by continuously turning off the radio interface of all the unnecessary nodes that are not included in the routing path. By Simulation results, we show that our proposed protocol achieves a higher throughput and fairness besides reducing the delay

Intelligent Agent-based Multilingual Information Retrieval System

The goal of this work is to develop an Open Agent Architecture for Multilingual information retrieval from Relational Database. The query for information retrieval can be given in plain Hindi or Malayalam; two prominent regional languages of India. The system supports distributed processing of user requests through collaborating agents. Natural language processing techniques are used for meaning extraction from the plain query and information is given back to the user in his/ her native language. The system architecture is designed in a structured way so that it can be adapted to other regional languages of India

A Generic Software Architecture for a Domain Specific Distributed Embedded System

In this paper, we have evolved a generic software architecture for a domain specific distributed embedded system. The system under consideration belongs to the Command, Control and Communication systems domain. The systems in such domain have very long operational lifetime. The quality attributes of these systems are equally important as the functional requirements. The main guiding principle followed in this paper for evolving the software architecture has been functional independence of the modules. The quality attributes considered most important for the system are maintainability and modifiability. Architectural styles best suited for the functionally independent modules are proposed with focus on these quality attributes. The software architecture for the system is envisioned as a collection of architecture styles of the functionally independent modules identified

Computing median and antimedian sets in median graphs

The median (antimedian) set of a profile π = (u1, . . . , uk) of vertices of a graphG is the set of vertices x that minimize (maximize) the remoteness i d(x,ui ). Two algorithms for median graphs G of complexity O(nidim(G)) are designed, where n is the order and idim(G) the isometric dimension of G. The first algorithm computes median sets of profiles and will be in practice often faster than the other algorithm which in addition computes antimedian sets and remoteness functions and works in all partial cubes

Soft Computing Approach for Optimization of siRNA Efficiency Prediction for Post-transcriptional Gene Silencing

Post-transcriptional gene silencing by RNA interference is mediated by small interfering RNA called siRNA. This gene silencing mechanism can be exploited therapeutically to a wide variety of disease-associated targets, especially in AIDS, neurodegenerative diseases, cholesterol and cancer on mice with the hope of extending these approaches to treat humans. Over the recent past, a significant amount of work has been undertaken to understand the gene silencing mediated by exogenous siRNA. The design of efficient exogenous siRNA sequences is challenging because of many issues related to siRNA. While designing efficient siRNA, target mRNAs must be selected such that their corresponding siRNAs are likely to be efficient against that target and unlikely to accidentally silence other transcripts due to sequence similarity. So before doing gene silencing by siRNAs, it is essential to analyze their off-target effects in addition to their inhibition efficiency against a particular target. Hence designing exogenous siRNA with good knock-down efficiency and target specificity is an area of concern to be addressed. Some methods have been developed already by considering both inhibition efficiency and off-target possibility of siRNA against agene. Out of these methods, only a few have achieved good inhibition efficiency, specificity and sensitivity. The main focus of this thesis is to develop computational methods to optimize the efficiency of siRNA in terms of “inhibition capacity and off-target possibility” against target mRNAs with improved efficacy, which may be useful in the area of gene silencing and drug design for tumor development. This study aims to investigate the currently available siRNA prediction approaches and to devise a better computational approach to tackle the problem of siRNA efficacy by inhibition capacity and off-target possibility. The strength and limitations of the available approaches are investigated and taken into consideration for making improved solution. Thus the approaches proposed in this study extend some of the good scoring previous state of the art techniques by incorporating machine learning and statistical approaches and thermodynamic features like whole stacking energy to improve the prediction accuracy, inhibition efficiency, sensitivity and specificity. Here, we propose one Support Vector Machine (SVM) model, and two Artificial Neural Network (ANN) models for siRNA efficiency prediction. In SVM model, the classification property is used to classify whether the siRNA is efficient or inefficient in silencing a target gene. The first ANNmodel, named siRNA Designer, is used for optimizing the inhibition efficiency of siRNA against target genes. The second ANN model, named Optimized siRNA Designer, OpsiD, produces efficient siRNAs with high inhibition efficiency to degrade target genes with improved sensitivity-specificity, and identifies the off-target knockdown possibility of siRNA against non-target genes. The models are trained and tested against a large data set of siRNA sequences. The validations are conducted using Pearson Correlation Coefficient, Mathews Correlation Coefficient, Receiver Operating Characteristic analysis, Accuracy of prediction, Sensitivity and Specificity. It is found that the approach, OpsiD, is capable of predicting the inhibition capacity of siRNA against a target mRNA with improved results over the state of the art techniques. Also we are able to understand the influence of whole stacking energy on efficiency of siRNA. The model is further improved by including the ability to identify the “off-target possibility” of predicted siRNA on non-target genes. Thus the proposed model, OpsiD, can predict optimized siRNA by considering both “inhibition efficiency on target genes and off-target possibility on non-target genes”, with improved inhibition efficiency, specificity and sensitivity. Since we have taken efforts to optimize the siRNA efficacy in terms of “inhibition efficiency and offtarget possibility”, we hope that the risk of “off-target effect” while doing gene silencing in various bioinformatics fields can be overcome to a great extent. These findings may provide new insights into cancer diagnosis, prognosis and therapy by gene silencing. The approach may be found useful for designing exogenous siRNA for therapeutic applications and gene silencing techniques in different areas of bioinformatics.

Study on Microcredit in Kerala with Special Reference to Employment and Income Generation through Microenterprises and Livelihood Projects

This study aimed to study the evolution and substance of microfinance as a major tool for combating poverty at the global and national level. The development of micro finance in Kerala is briefly discussed. It also indicates the importance and role of microcredit in bringing the poor up in the society through entrepreneurial initiatives. The current trends in the field are also discussed, leading to the need of the present research.