Mean Squared Residue Based Biclustering Algorithms for the Analysis of Gene Expression Data

Computational Biology is the research are that contributes to the analysis of biological data through the development of algorithms which will address significant research problems.The data from molecular biology includes DNA,RNA ,Protein and Gene expression data.Gene Expression Data provides the expression level of genes under different conditions.Gene expression is the process of transcribing the DNA sequence of a gene into mRNA sequences which in turn are later translated into proteins.The number of copies of mRNA produced is called the expression level of a gene.Gene expression data is organized in the form of a matrix. Rows in the matrix represent genes and columns in the matrix represent experimental conditions.Experimental conditions can be different tissue types or time points.Entries in the gene expression matrix are real values.Through the analysis of gene expression data it is possible to determine the behavioral patterns of genes such as similarity of their behavior,nature of their interaction,their respective contribution to the same pathways and so on. Similar expression patterns are exhibited by the genes participating in the same biological process.These patterns have immense relevance and application in bioinformatics and clinical research.Theses patterns are used in the medical domain for aid in more accurate diagnosis,prognosis,treatment planning.drug discovery and protein network analysis.To identify various patterns from gene expression data,data mining techniques are essential.Clustering is an important data mining technique for the analysis of gene expression data.To overcome the problems associated with clustering,biclustering is introduced.Biclustering refers to simultaneous clustering of both rows and columns of a data matrix. Clustering is a global whereas biclustering is a local model.Discovering local expression patterns is essential for identfying many genetic pathways that are not apparent otherwise.It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.A biclusters is a submatrix of the gene expression data matrix.The rows and columns in the submatrix need not be contiguous as in the gene expression data matrix.Biclusters are not disjoint.Computation of biclusters is costly because one will have to consider all the combinations of columans and rows in order to find out all the biclusters.The search space for the biclustering problem is 2 m+n where m and n are the number of genes and conditions respectively.Usually m+n is more than 3000.The biclustering problem is NP-hard.Biclustering is a powerful analytical tool for the biologist.The research reported in this thesis addresses the problem of biclustering.Ten algorithms are developed for the identification of coherent biclusters from gene expression data.All these algorithms are making use of a measure called mean squared residue to search for biclusters.The objective here is to identify the biclusters of maximum size with the mean squared residue lower than a given threshold. All these algorithms begin the search from tightly coregulated submatrices called the seeds.These seeds are generated by K-Means clustering algorithm.The algorithms developed can be classified as constraint based,greedy and metaheuristic.Constarint based algorithms uses one or more of the various constaints namely the MSR threshold and the MSR difference threshold.The greedy approach makes a locally optimal choice at each stage with the objective of finding the global optimum.In metaheuristic approaches particle Swarm Optimization(PSO) and variants of Greedy Randomized Adaptive Search Procedure(GRASP) are used for the identification of biclusters.These algorithms are implemented on the Yeast and Lymphoma datasets.Biologically relevant and statistically significant biclusters are identified by all these algorithms which are validated by Gene Ontology database.All these algorithms are compared with some other biclustering algorithms.Algorithms developed in this work overcome some of the problems associated with the already existing algorithms.With the help of some of the algorithms which are developed in this work biclusters with very high row variance,which is higher than the row variance of any other algorithm using mean squared residue, are identified from both Yeast and Lymphoma data sets.Such biclusters which make significant change in the expression level are highly relevant biologically.

Development of Free Space Method for Material Characterisation and GPR Study & A Case Study on Biological Samples

The thesis mainly focuses on material characterization in different environments: freely available samples taken in planar fonn, biological samples available in small quantities and buried objects.Free space method, finds many applications in the fields of industry, medicine and communication. As it is a non-contact method, it can be employed for monitoring the electrical properties of materials moving through a conveyor belt in real time. Also, measurement on such systems at high temperature is possible. NID theory can be applied to the characterization of thin films. Dielectric properties of thin films deposited on any dielectric substrate can be determined. ln chemical industry, the stages of a chemical reaction can be monitored online. Online monitoring will be more efficient as it saves time and avoids risk of sample collection.Dielectric contrast is one of the main factors, which decides the detectability of a system. lt could be noted that the two dielectric objects of same dielectric constant 3.2 (s, of plastic mine) placed in a medium of dielectric constant 2.56 (er of sand) could even be detected employing the time domain analysis of the reflected signal. This type of detection finds strategic importance as it provides solution to the problem of clearance of non-metallic mines. The demining of these mines using the conventional techniques had been proved futile. The studies on the detection of voids and leakage in pipes find many applications.The determined electrical properties of tissues can be used for numerical modeling of cells, microwave imaging, SAR test etc. All these techniques need the accurate determination of dielectric constant. ln the modem world, the use of cellular and other wireless communication systems is booming up. At the same time people are concemed about the hazardous effects of microwaves on living cells. The effect is usually studied on human phantom models. The construction of the models requires the knowledge of the dielectric parameters of the various body tissues. lt is in this context that the present study gains significance. The case study on biological samples shows that the properties of normal and infected body tissues are different. Even though the change in the dielectric properties of infected samples from that of normal one may not be a clear evidence of an ailment, it is an indication of some disorder.ln medical field, the free space method may be adapted for imaging the biological samples. This method can also be used in wireless technology. Evaluation of electrical properties and attenuation of obstacles in the path of RF waves can be done using free waves. An intelligent system for controlling the power output or frequency depending on the feed back values of the attenuation may be developed.The simulation employed in GPR can be extended for the exploration of the effects due to the factors such as the different proportion of water content in the soil, the level and roughness of the soil etc on the reflected signal. This may find applications in geological explorations. ln the detection of mines, a state-of-the art technique for scanning and imaging an active mine field can be developed using GPR. The probing antenna can be attached to a robotic arm capable of three degrees of rotation and the whole detecting system can be housed in a military vehicle. In industry, a system based on the GPR principle can be developed for monitoring liquid or gas through a pipe, as pipe with and without the sample gives different reflection responses. lt may also be implemented for the online monitoring of different stages of extraction and purification of crude petroleum in a plant.Since biological samples show fluctuation in the dielectric nature with time and other physiological conditions, more investigation in this direction should be done. The infected cells at various stages of advancement and the normal cells should be analysed. The results from these comparative studies can be utilized for the detection of the onset of such diseases. Studying the properties of infected tissues at different stages, the threshold of detectability of infected cells can be determined.

Educational rights of the minorities under article 30 of the Indian Constitution

This thesis entitled “ Educational rights of the minorities under article 30 of the indian constitution.The study is divided into nine chapters.The object of the present study is to explore whether the judiciary has been successful in balancing the conflicting rights of the minorities and the state. The study also seeks to bring forth those judicial principles which have governed the operation of these rights and determined the limits of their application. Article 30 confers a special right on minorities to establish educational institutions of their own choice.This is an expression of the liberal and tolerent culture of our nation which is reflected in the Constitution. The idea is to foster unity' in diversity, ea unique characteristic of the Indian way of life.This study suggested that where a minority is a minority’ in the historical or national context and its claim is based on religion it must be defined and ascertained in terms of the population of the whole country irrespective of its being a numerical majority' in any particular State and the minority status. of linguistic group has to be ascertained in terms of the population of any particular State irrespective of its being a numerical minority in terms of the population of the whole country.A religious denomination also can be treated as a religion within the meaning of Article 30(1) provided it is having a separate organisation with doctrines and tenets and rites and practices of its own.

Bayesian Inference in Exponential and Pareto populations in the presence of Outliers

This thesis Entitled Bayesian inference in Exponential and pareto populations in the presence of outliers. The main theme of the present thesis is focussed on various estimation problems using the Bayesian appraoch, falling under the general category of accommodation procedures for analysing Pareto data containing outlier. In Chapter II. the problem of estimation of parameters in the classical Pareto distribution specified by the density function. In Chapter IV. we discuss the estimation of (1.19) when the sample contain a known number of outliers under three different data generating mechanisms, viz. the exchangeable model. Chapter V the prediction of a future observation based on a random sample that contains one contaminant. Chapter VI is devoted to the study of estimation problems concerning the exponential parameters under a k-outlier model.

Seasonal and interannual variability of sea level and associated surface meteorological parameters at Cochin

This thesis entitled seasonal and interannual variability of sea level and associated surface meteorological parameters at cochin.The interesting aspect of studying sea level variability on different time scales can be attributed to the diversity of its applications.Study of tides could perhaps be the oldest branch of physical oceanography.The thesis is presented in seven chapters. The first chapter gives, apart from a general introduction, a survey of literature on sea level variability on different time scales - tidal, seasonal and interannual (geological scales excluded), with particular emphasis on the work carried out in the Indian waters. The second chapter is devoted to the study of observed tides at Cochin on seasonal and interannual time scales using hourly water level data for the period 1988-1993. The third chapter describes the long-term climatology of some important surface oceanographic and meteorological parameters (at Cochin) which are supposed to affect the sea level. The fourth chapter addresses the problem of seasonal forecasting of the meteorological and oceanographic parameters at Cochin using autoregressive, sinusoidal and exponentially weighted moving average techniques and testing their accuracy with the observed data for the period 1991-1993. The fifth chapter describes the seasonal cycles of sea level and the driving forces at 16 stations along the Indian subcontinent. It also addresses the observed interannual variability of sea level at 15 stations using available multi-annual data sets. The sixth chapter deals with the problem of coastal trapped waves between Cochin and Beypore off the Kerala coast using sea level and atmospheric pressure data sets for the year 1977. The seventh and the last chapter contains the summary and conclusions and future outlook based on this study.

‘Reliability Concepts in Quantile-based Analysis of Lifetime Data

Reliability analysis is a well established branch of statistics that deals with the statistical study of different aspects of lifetimes of a system of components. As we pointed out earlier that major part of the theory and applications in connection with reliability analysis were discussed based on the measures in terms of distribution function. In the beginning chapters of the thesis, we have described some attractive features of quantile functions and the relevance of its use in reliability analysis. Motivated by the works of Parzen (1979), Freimer et al. (1988) and Gilchrist (2000), who indicated the scope of quantile functions in reliability analysis and as a follow up of the systematic study in this connection by Nair and Sankaran (2009), in the present work we tried to extend their ideas to develop necessary theoretical framework for lifetime data analysis. In Chapter 1, we have given the relevance and scope of the study and a brief outline of the work we have carried out. Chapter 2 of this thesis is devoted to the presentation of various concepts and their brief reviews, which were useful for the discussions in the subsequent chapters .In the introduction of Chapter 4, we have pointed out the role of ageing concepts in reliability analysis and in identifying life distributions .In Chapter 6, we have studied the first two L-moments of residual life and their relevance in various applications of reliability analysis. We have shown that the first L-moment of residual function is equivalent to the vitality function, which have been widely discussed in the literature .In Chapter 7, we have defined percentile residual life in reversed time (RPRL) and derived its relationship with reversed hazard rate (RHR). We have discussed the characterization problem of RPRL and demonstrated with an example that the RPRL for given does not determine the distribution uniquely

Impact of Gulf Money with Particular Reference to Chowghat, Trichur District,Kerala

The problems associated with emigration, inward remittances and economic development of Herala have not received ample attention. Kerala depends much on the inward remittances sent by Keralites employed abroad. It is a State that experience chronic unemployment problem. Emigration cannot provide a lasting solution to the problem of unemployment since its direction is governed mainly by the social, political and ecnonomic factors of the host countries. The present study is an attempt to focus attention on the major problems associated with emigration from Kerala. It also tries to deal with the issues involved in diverting the inward remittances to the development of the state which has some vital policy implications The problems associated with emigration, inward remittances and economic development of Herala have not received ample attention. Kerala depends much on the inward remittances sent by Keralites employed abroad. It is a State that experience chronic unemployment problem. Emigration cannot provide a lasting solution to the problem of unemployment since its direction is governed mainly by the social, political and ecnonomic factors of the host countries. The present study is an attempt to focus attention on the major problems associated with emigration from Kerala. It also tries to deal with the issues involved in diverting the inward remittances to the development of the state which has some vital policy implications Investment proepect of non~resident Keralites is the theme oi Chapter VIII. It examines the various measures taken to promote industrial development by attracting non~resident investment tc industrial ventures. Chapter IX diecusses the future of emigration from Kerale especially in the light of declining international oil prices. It also deals with the role o¥ emigration as a safety valve t: the chronic problem of unemployment in Kerala. The last Chapter presents the summary and conclusions of the study

The impact of sterilisation on family relationships

The major objective of the researcher was to assess the gains or losses in relationship between spouses after sterilization of the wife. The second objective was to gauge the impact of sterilisation upon parent—child relationships. Factors that were responsible in motivating women to accept sterilization were subjected to enquiry with the conviction that the information would give insight into the inadequacies of the official Family Planning Programme, offering prospects for feasible and salutary changes. The report is arranged under six chapters. The first chapter, Introduction, has three parts. The global and natural dimension of the problem of population is considered in Part I; The Importance of the topic studied namely sterilisation is discussed in the second Part: and Part III explains the background and methodology %f the study. The second chapter is a description of tubecto~ mized women who were the respondents. Their personal and family data, economic, social, educational and demographic profilesform its contents. The direct and indirect influences that were-responsible to make women decide in favour of sterilization are dealt with in the Third chapter. The Fourth Chapter is an analysis of the interspouse relations pre and post—operatively and an assessment of gains and losses in the area subsequent to sterilisation. How children have benefitted physically and emotionally as a consequence of improved care/attention from parents post~operatively constitutes the analysis attempted in the Fifth chapter.

Quantum decay of metastable states in small magnetic particles

We present an imaginary-time path-integral study of the problem of quantum decay of a metastable state of a uniaxial magnetic particle placed in the magnetic field at an arbitrary angle. Our findings agree with earlier results of Zaslavskii obtained by mapping the spin Hamiltonian onto a particle Hamiltonian. In the limit of low barrier, weak dependence of the decay rate on the angle is found, except for the field which is almost normal to the anisotropy axis, where the rate is sharply peaked, and for the field approaching the parallel orientation, where the rate rapidly goes to zero. This distinct angular dependence, together with the dependence of the rate on the field strength, provides an independent test for macroscopic spin tunneling.

Performance Effectiveness Of Bank Managers: A Study Of Psycho-Social Correlates

The present study by the researcher focuses attention on the problem of performance effectiveness among managers operating in one of the critical and socially important sectors of our economy namely commercial banking. The banking sector is selected for the study due to two reasons. Firstly, commercial banking plays an important role in the country's development. Secondly, for improving the efficiency of the banking system, we need to know more about the performance dynamics of the executives in our banking organizations

Detection of Flock Movement in Spatio-Temporal Database using Clustering Techniques - an Experience

In this paper, moving flock patterns are mined from spatio- temporal datasets by incorporating a clustering algorithm. A flock is defined as the set of data that move together for a certain continuous amount of time. Finding out moving flock patterns using clustering algorithms is a potential method to find out frequent patterns of movement in large trajectory datasets. In this approach, SPatial clusteRing algoRithm thrOugh sWarm intelligence (SPARROW) is the clustering algorithm used. The advantage of using SPARROW algorithm is that it can effectively discover clusters of widely varying sizes and shapes from large databases. Variations of the proposed method are addressed and also the experimental results show that the problem of scalability and duplicate pattern formation is addressed. This method also reduces the number of patterns produced

Analytical Study of Typographical Errors in OPACS and Corrective Measures

The present study is an attempt to highlight the problem of typographical errors in OPACS. The errors made while typing catalogue entries as well as importing bibliographical records from other libraries exist unnoticed by librarians resulting the non-retrieval of available records and affecting the quality of OPACs. This paper follows previous research on the topic mainly by Jeffrey Beall and Terry Ballard. The word “management” was chosen from the list of likely to be misspelled words identified by previous research. It was found that the word is wrongly entered in several forms in local, national and international OPACs justifying the observations of Ballard that typos occur in almost everywhere. Though there are lots of corrective measures proposed and are in use, the study asserts the fact that human effort is needed to get rid of the problem. The paper is also an invitation to the library professionals and system designers to construct a strategy to solve the issue

Analytical Study of Typographical Errors in OPACS and Corrective Measures

The present study is an attempt to highlight the problem of typographical errors in OPACS. The errors made while typing catalogue entries as well as importing bibliographical records from other libraries exist unnoticed by librarians resulting the non-retrieval of available records and affecting the quality of OPACs. This paper follows previous research on the topic mainly by Jeffrey Beall and Terry Ballard. The word “management” was chosen from the list of likely to be misspelled words identified by previous research. It was found that the word is wrongly entered in several forms in local, national and international OPACs justifying the observations of Ballard that typos occur in almost everywhere. Though there are lots of corrective measures proposed and are in use, the study asserts the fact that human effort is needed to get rid of the problem. The paper is also an invitation to the library professionals and system designers to construct a strategy to solve the issue

Reinforcement Learning Solution for Unit Commitment Problem Considering Minimum Start Up and Shut Down Times

Unit Commitment Problem (UCP) in power system refers to the problem of determining the on/ off status of generating units that minimize the operating cost during a given time horizon. Since various system and generation constraints are to be satisfied while finding the optimum schedule, UCP turns to be a constrained optimization problem in power system scheduling. Numerical solutions developed are limited for small systems and heuristic methodologies find difficulty in handling stochastic cost functions associated with practical systems. This paper models Unit Commitment as a multi stage decision making task and an efficient Reinforcement Learning solution is formulated considering minimum up time /down time constraints. The correctness and efficiency of the developed solutions are verified for standard test systems

Performance of hybrid rebars as longitudinal reinforcement in normal strength concrete

A/though steel is most commonly used as a reinforcing material in concrete due to its competitive cost and favorable mechanical properties, the problem of corrosion of steel rebars leads to a reduction in life span of the structure and adds to maintenance costs. Many techniques have been developed in recent past to reduce corrosion (galvanizing, epoxy coating, etc.) but none of the solutions seem to be viable as an adequate solution to the corrosion problem. Apart from the use of fiber reinforced polymer (FRP) rebars, hybrid rebars consisting of both FRP and steel are also being tried to overcome the problem of steel corrosion. This paper evaluates the performance of hybrid rebars as longitudinal reinforcement in normal strength concrete beams. Hybrid rebars used in this study essentially consist of glass fiber reinforced polymer (GFRP) strands of 2 mm diameter wound helically on a mild steel core of 6 mm diameter. GFRP stirrups have been used as shear reinforcement. An attempt has been made to evaluate the flexural and shear performance of beams having hybrid rebars in normal strength concrete with and without polypropylene fibers added to the concrete matrix