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.

The (t) property of some classes of graphs

In this note,the (t) properties of five class are studied. We proved that the classes of cographs and clique perfect graphs without isolated vertices satisfy the (2) property and the (3) property, but do not satisfy the (t) property for tis greater than equal to 4. The (t) properties of the planar graphs and the perfect graphss are also studied . we obtain a necessary and suffieient conditions for the trestled graph of index K to satisfy the (2) property

Median graphs, the remoteness function, periphery transversals, and geodetic number two

A periphery transversal of a median graph G is introduced as a set of vertices that meets all the peripheral subgraphs of G. Using this concept, median graphs with geodetic number 2 are characterized in two ways. They are precisely the median graphs that contain a periphery transversal of order 2 as well as the median graphs for which there exists a profile such that the remoteness function is constant on G. Moreover, an algorithm is presented that decides in O(mlog n) time whether a given graph G with n vertices and m edges is a median graph with geodetic number 2. Several additional structural properties of the remoteness function on hypercubes and median graphs are obtained and some problems listed

Starved Extrusion for the Improvement of Mechanical Properties of Rubber Vulcanizates

Filled compounds of natural rubber, isobutylene-isoprene rubber and styrene-butadiene rubber compounds were extruded through a laboratory extruder by varying the feeding rate at different temperatures and revolutions per minute. The extruded compounds were vulcanized up to their optimum cure times and the mechanical properties of the vulcanizates were determined. The properties suggest that there is a particular feeding rate in the starved fed region which results in maximum mechanical properties. The study shows that running the extruder at a slightly starved condition is an attractive means of improving the physical properties.

Starved Feeding for Improving the Mechanical Properties of Styrene-Butadiene Rubber Vulcanizates

Gum and filled compounds of styrene-butadiene rubber are extruded through a laboratory extruder by varying the feeding rase at different temperatures and screw speed (rpm). The extruded compounds are vulcanized up4o their optimum cure times and the mechanical properties of the vulcanizates are determined. From the properties data obtained it Is concluded that there is a specific feeding rate wit in the starved fed region, which results In maximum Improved mechanical properties . The enhancement In properties is found to be due to better thermal and shear homogeneity.

The effect of dopants on the microwave dielectric properties of Ba( Mgo.33Ta0.67)03 ceramics

The effect of dopants with different valencies and ionic radii on the densification, structural ordering, and microwave dielectric properties of Ba(Mg1t3Tazt3)O3 (BMT) is investigated. It is found that dopants such as Sb,05, MnO, ZrO,, WO1, and ZnO improve the microwave dielectric properties of BMT. Addition of trivalent dopants is detrimental to the cation ordering and dielectric properties of BMT. A correlation between the microwave dielectric properties of BMT and ionic radii of the dopant has been established. The variation of the dielectric properties of pure and doped BMT at cryogenic temperatures is also discussed

Influence of sulphate content on the physico-chemical properties and catalytic activity of some sulphated zirconia systems

The present work attempts a systematic examination of the effect of sulphate content on the physico-chemical properties and catalytic activity of sulphated zirconia and iron promoted sulphated zirconia systems. Sulphate content is estimated by EDX analysis. The amount of sulphate incorporated has been found to influence the surface area, crystal structure and the acid strength distribution. Ammonia TPD and adsorption studies using perylene have enabled the determination of surface acidic properties. The results are supported by the thermodesorption studies using pyridine and 2,6-dimethylpyridine. The catalytic activity towards benzoylation reaction has been correlated with the surface acidity of the systems.

Studies on grain refinement and alloying additions on the microstructure and mechanical properties of Mg-8Zn-4Al alloy

MAGNESIUM ALLOYS have strong potential for weight reduction in a wide range of technical applications because of their low density compared to other structural metallic materials. Therefore, an extensive growth of magnesium alloys usage in the automobile sector is expected in the coming years to enhance the fuel efficiency through mass reduction. The drawback associated with the use of commercially cheaper Mg-Al based alloys, such as AZ91, AM60 and AM50 are their inferior creep properties above 100ºC due to the presence of discontinuous Mg17A112 phases at the grain boundaries. Although rare earth-based magnesium alloys show better mechanical properties, it is not economically viable to use these alloys in auto industries. Recently, many new Mg-Al based alloy systems have been developed for high temperature applications, which do not contain the Mg17Al12 phase. It has been proved that the addition of a high percentage of zinc (which depends upon the percentage of Al) to binary Mg-Al alloys also ensures the complete removal of the Mg17Al12 phase and hence exhibits superior high temperature properties.ZA84 alloy is one such system, which has 8%Zn in it (Mg-8Zn-4Al-0.2Mn, all are in wt %) and shows superior creep resistance compared to AZ and AM series alloys. These alloys are mostly used in die casting industries. However, there are certain large and heavy components, made up of this alloy by sand castings that show lower mechanical properties because of their coarse microstructure. Moreover, further improvement in their high temperature behaviour through microstructural modification is also an essential task to make this alloy suitable for the replacement of high strength aluminium alloys used in automobile industry. Grain refinement is an effective way to improve the tensile behaviour of engineering alloys. In fact, grain refinement of Mg-Al based alloys is well documented in literature. However, there is no grain refiner commercially available in the market for Mg-Al alloys. It is also reported in the literature that the microstructure of AZ91 alloy is modified through the minor elemental additions such as Sb, Si, Sr, Ca, etc., which enhance its high temperature properties because of the formation of new stable intermetallics. The same strategy can be used with the ZA84 alloy system to improve its high temperature properties further without sacrificing the other properties. The primary objective of the present research work, “Studies on grain refinement and alloying additions on the microstructure and mechanical properties of Mg-8Zn-4Al alloy” is twofold: 1. To investigate the role of individual and combined additions of Sb and Ca on the microstructure and mechanical properties of ZA84 alloy. 2. To synthesis a novel Mg-1wt%Al4C3 master alloy for grain refinement of ZA84 alloy and investigate its effects on mechanical properties.

Optimisation of the Mechanical Properties of HDPE/PP Blends and Their Recyclable Composites

This study was undertaken in order to upgrade blends of HDPE and PP, two of the most widely used standard plastics so as to widen their application spectrum. Dicumyl peroxide was used as the modifier for the upgradation. Optimum concentration of dicumyl peroxide required for modification was detennined by measurement of mechanical, rheological, thermal and morphological properties. Selected blends were used to prepare recyclable composites with nylon clothes by compression moulding. The composites were characterized by measurement of mechanical and thermal properties. The composites were recycled and the mechanical propertics of the recycled material were determined.

Equal opportunity networks, distance-balanced graphs, and Wiener game

Given a graph G and a set X ⊆ V(G), the relative Wiener index of X in G is defined as WX (G) = {u,v}∈X 2  dG(u, v) . The graphs G (of even order) in which for every partition V(G) = V1 +V2 of the vertex set V(G) such that |V1| = |V2| we haveWV1 (G) = WV2 (G) are called equal opportunity graphs. In this note we prove that a graph G of even order is an equal opportunity graph if and only if it is a distance-balanced graph. The latter graphs are known by several characteristic properties, for instance, they are precisely the graphs G in which all vertices u ∈ V(G) have the same total distance DG(u) = v∈V(G) dG(u, v). Some related problems are posed along the way, and the so-called Wiener game is introduced.

Effect of Carbon Black on the Mechanical and Dielectric Properties of Rubber Ferrite Composites Containing Barium Ferrite

Fine particles of barium ferrite (BaFe12O19) were synthesized by the conventional ceramic technique. These materials were then characterized by the X-ray diffraction method and incorporated in the natural rubber matrix according to a specific receipe for various loadings of ferrite. The rubber ferrite composites (RFC) thus obtained have several applications, and have the advantage of molding into complex shapes. For applications such as microwave absorbers, these composites should have an appropriate dielectric strength with the required mechanical and magnetic properties. The N330 (HAF) carbon black has been added to these RFCs for various loadings to modify the dielectric and mechanical properties. In this article we report the effect of carbon black on the mechanical and dielectric properties of these RFCs. Both the mechanical and dielectric properties can be enhanced by the addition of an appropriate amount of carbon black

Investigations on the structural, optical and magnetic properties of nanostructured cerium oxide in pure and doped forms and its polymer nanocomposites

In recent years, nanoscience and nanotechnology has emerged as one of the most important and exciting frontier areas of research interest in almost all fields of science and technology. This technology provides the path of many breakthrough changes in the near future in many areas of advanced technological applications. Nanotechnology is an interdisciplinary area of research and development. The advent of nanotechnology in the modern times and the beginning of its systematic study can be thought of to have begun with a lecture by the famous physicist Richard Feynman. In 1960 he presented a visionary and prophetic lecture at the meeting of the American Physical Society entitled “there is plenty of room at the bottom” where he speculated on the possibility and potential of nanosized materials. Synthesis of nanomaterials and nanostructures are the essential aspects of nanotechnology. Studies on new physical properties and applications of nanomaterials are possible only when materials are made available with desired size, morphology, crystal structure and chemical composition. Cerium oxide (ceria) is one of the important functional materials with high mechanical strength, thermal stability, excellent optical properties, appreciable oxygen ion conductivity and oxygen storage capacity. Ceria finds a variety of applications in mechanical polishing of microelectronic devices, as catalysts for three-way automatic exhaust systems and as additives in ceramics and phosphors. The doped ceria usually has enhanced catalytic and electrical properties, which depend on a series of factors such as the particle size, the structural characteristics, morphology etc. Ceria based solid solutions have been widely identified as promising electrolytes for intermediate temperature solid oxide fuel cells (SOFC). The success of many promising device technologies depends on the suitable powder synthesis techniques. The challenge for introducing new nanopowder synthesis techniques is to preserve high material quality while attaining the desired composition. The method adopted should give reproducible powder properties, high yield and must be time and energy effective. The use of a variety of new materials in many technological applications has been realized through the use of thin films of these materials. Thus the development of any new material will have good application potential if it can be deposited in thin film form with the same properties. The advantageous properties of thin films include the possibility of tailoring the properties according to film thickness, small mass of the materials involved and high surface to volume ratio. The synthesis of polymer nanocomposites is an integral aspect of polymer nanotechnology. By inserting the nanometric inorganic compounds, the properties of polymers can be improved and this has a lot of applications depending upon the inorganic filler material present in the polymer.

Clique Irreducibility of Some Iterative Classes of Graphs

In this paper, two notions, the clique irreducibility and clique vertex irreducibility are discussed. A graph G is clique irreducible if every clique in G of size at least two, has an edge which does not lie in any other clique of G and it is clique vertex irreducible if every clique in G has a vertex which does not lie in any other clique of G. It is proved that L(G) is clique irreducible if and only if every triangle in G has a vertex of degree two. The conditions for the iterations of line graph, the Gallai graphs, the anti-Gallai graphs and its iterations to be clique irreducible and clique vertex irreducible are also obtained.

Significance of Feeding Rate in the Extrusion of Filled and Gum 11R Vulcanizates

Filled and gum compounds of Isobutylene-Isoprene rubber were extruded through a laboratory extruder at various feeding rates, different temperatures and revolutions per minute. The extruded compounds were vulcanized up to their optimum cure times and the mechanical properties of the vulcanizates were determined. The properties suggest that there is a particular feeding rate in the starved fed region, which results in maximum mechanical properties. The study shows that running the extruder at a slightly starved condition is an attractive means of improving the physical properties.

Effect of Silane Coupling Agent on Cure Characteristics and Mechanical Properties of Nitrile Rubber/Reclaimed Rubber Blend

Blends of nitrile rubber and reclaimed rubber containing different levels of a coupling agent, Si 69 (bis(3- triethoxysilyl propyl)(tetrasulphide) were prepared and the cure characteristic's and mechanical properties were studied. Optimum loading of Si-69 was found to be a function of blend ratio. 3 phi- of Si 69 in a 70:30. Blend was found to be the optimum combination with respect to the mechanical properties. The rate and state of cure were also affected bv the conp/ing agent. Tensile strength, tear strength and abrasion resistance were improved in the presence of coupling agent. While the state of cure improved, the cure rate and scorch time decreased with increasing silane content. Ageing studies showed that the blends containing the coupling agent were inferior to the unmodified blends.