Genetic association studies under the population stratification, family pedigree and application to genome-wide association studies

This dissertation has three separate parts: the first part deals with the general pedigree association testing incorporating continuous covariates; the second part deals with the association tests under population stratification using the conditional likelihood tests; the third part deals with the genome-wide association studies based on the real rheumatoid arthritis (RA) disease data sets from Genetic Analysis Workshop 16 (GAW16) problem 1. Many statistical tests are developed to test the linkage and association using either case-control status or phenotype covariates for family data structure, separately. Those univariate analyses might not use all the information coming from the family members in practical studies. On the other hand, the human complex disease do not have a clear inheritance pattern, there might exist the gene interactions or act independently. In part I, the new proposed approach MPDT is focused on how to use both the case control information as well as the phenotype covariates. This approach can be applied to detect multiple marker effects. Based on the two existing popular statistics in family studies for case-control and quantitative traits respectively, the new approach could be used in the simple family structure data set as well as general pedigree structure. The combined statistics are calculated using the two statistics; A permutation procedure is applied for assessing the p-value with adjustment from the Bonferroni for the multiple markers. We use simulation studies to evaluate the type I error rates and the powers of the proposed approach. Our results show that the combined test using both case-control information and phenotype covariates not only has the correct type I error rates but also is more powerful than the other existing methods. For multiple marker interactions, our proposed method is also very powerful. Selective genotyping is an economical strategy in detecting and mapping quantitative trait loci in the genetic dissection of complex disease. When the samples arise from different ethnic groups or an admixture population, all the existing selective genotyping methods may result in spurious association due to different ancestry distributions. The problem can be more serious when the sample size is large, a general requirement to obtain sufficient power to detect modest genetic effects for most complex traits. In part II, I describe a useful strategy in selective genotyping while population stratification is present. Our procedure used a principal component based approach to eliminate any effect of population stratification. The paper evaluates the performance of our procedure using both simulated data from an early study data sets and also the HapMap data sets in a variety of population admixture models generated from empirical data. There are one binary trait and two continuous traits in the rheumatoid arthritis dataset of Problem 1 in the Genetic Analysis Workshop 16 (GAW16): RA status, AntiCCP and IgM. To allow multiple traits, we suggest a set of SNP-level F statistics by the concept of multiple-correlation to measure the genetic association between multiple trait values and SNP-specific genotypic scores and obtain their null distributions. Hereby, we perform 6 genome-wide association analyses using the novel one- and two-stage approaches which are based on single, double and triple traits. Incorporating all these 6 analyses, we successfully validate the SNPs which have been identified to be responsible for rheumatoid arthritis in the literature and detect more disease susceptibility SNPs for follow-up studies in the future. Except for chromosome 13 and 18, each of the others is found to harbour susceptible genetic regions for rheumatoid arthritis or related diseases, i.e., lupus erythematosus. This topic is discussed in part III.

AN ASSESSMENT OF FLOW REGIME MAPS AND A NUMERICAL HEAT TRANSFER CORRELATION FOR THE STRATIFIED/ANNULAR REGIME OF SHEAR-DRIVEN INTERNAL CONDENSING FLOWS

Several modern-day cooling applications require the incorporation of mini/micro-channel shear-driven flow condensers. There are several design challenges that need to be overcome in order to meet those requirements. The difficulty in developing effective design tools for shear-driven flow condensers is exacerbated due to the lack of a bridge between the physics-based modelling of condensing flows and the current, popular approach based on semi-empirical heat transfer correlations. One of the primary contributors of this disconnect is a lack of understanding caused by the fact that typical heat transfer correlations eliminate the dependence of the heat transfer coefficient on the method of cooling employed on the condenser surface when it may very well not be the case. This is in direct contrast to direct physics-based modeling approaches where the thermal boundary conditions have a direct and huge impact on the heat transfer coefficient values. Typical heat transfer correlations instead introduce vapor quality as one of the variables on which the value of the heat transfer coefficient depends. This study shows how, under certain conditions, a heat transfer correlation from direct physics-based modeling can be equivalent to typical engineering heat transfer correlations without making the same apriori assumptions. Another huge factor that raises doubts on the validity of the heat-transfer correlations is the opacity associated with the application of flow regime maps for internal condensing flows. It is well known that flow regimes influence heat transfer rates strongly. However, several heat transfer correlations ignore flow regimes entirely and present a single heat transfer correlation for all flow regimes. This is believed to be inaccurate since one would expect significant differences in the heat transfer correlations for different flow regimes. Several other studies present a heat transfer correlation for a particular flow regime - however, they ignore the method by which extents of the flow regime is established. This thesis provides a definitive answer (in the context of stratified/annular flows) to: (i) whether a heat transfer correlation can always be independent of the thermal boundary condition and represented as a function of vapor quality, and (ii) whether a heat transfer correlation can be independently obtained for a flow regime without knowing the flow regime boundary (even if the flow regime boundary is represented through a separate and independent correlation). To obtain the results required to arrive at an answer to these questions, this study uses two numerical simulation tools - the approximate but highly efficient Quasi-1D simulation tool and the exact but more expensive 2D Steady Simulation tool. Using these tools and the approximate values of flow regime transitions, a deeper understanding of the current state of knowledge in flow regime maps and heat transfer correlations in shear-driven internal condensing flows is obtained. The ideas presented here can be extended for other flow regimes of shear-driven flows as well. Analogous correlations can also be obtained for internal condensers in the gravity-driven and mixed-driven configuration.

IONIC LIQUID EXTRACTION UNVEILS PREVIOUSLY OCCLUDED HUMICBOUND IRON IN PEAT POREWATER

Extracellular iron reduction has been suggested as a candidate metabolic pathway that may explain a large proportion of carbon respiration in temperate peatlands. However, the o-phenanthroline colorimetric method commonly employed to quantitate iron and partition between redox species is known to be unreliable in the presence of humic and fulvic acids, both of which represent a considerable proportion of peatland dissolved organic matter. We propose ionic liquid extraction as a more accurate iron quantitation and redox speciation method in humic-rich peat porewater. We evaluated both o-phenanthroline and ionic liquid extraction in four distinct peatland systems spanning a gradient of physico-chemical conditions to compare total iron recovery and Fe2+:Fe3+ ratios determined by each method. Ionic liquid extraction was found to provide more accurate iron quantitation and speciation in the presence of dissolved organic matter. A multivariate approach utilizing fluorescence- and UV-Vis spectroscopy was used to identify dissolved organic matter characteristics in peat porewater that lead to poor performance of the o-phenanthroline method. Where these interferences are present, we offer an empirical correction factor for total iron quantitation by o-phenanthroline, as verified by ionic liquid extraction. The written work presented in this thesis is in preparation for submission to Soil Biology and Biochemisrty by T.J. Veverica, E.S. Kane, A.M. Marcarelli, and S.A. Green.

Electrospun chitosan nanofibers for virus removal

Electrospinning uses electrostatic forces to create nanofibers that are far smaller than conventional fiber spinning process. Nanofibers made with chitosan were created and techniques to control fibers diameter and were well developed. However, the adsorption of porcine parvovirus (PPV) was low. PPV is a small, nonenveloped virus that is difficult to remove due to its size, 18-26 nm in diameter, and its chemical stability. To improve virus adsorption, we functionalized the nanofibers with a quaternized amine, forming N-[(2-hydroxy-3-trimethylammonium) propyl] chitosan chloride (HTCC). This was blended with additives to increase the ability to form HTCC nanofibers. The additives changed the viscosity and conductivity of the electrospinning solution. We have successfully synthesized and functionalized HTCC nanofibers that absorb PPV. HTCC blend with graphene have the ability to remove a minimum of 99% of PPV present in solution.

Place for video games : a theoretical and pedagogical framework for multiliteracies learning in English studies

Students are now involved in a vastly different textual landscape than many English scholars, one that relies on the “reading” and interpretation of multiple channels of simultaneous information. As a response to these new kinds of literate practices, my dissertation adds to the growing body of research on multimodal literacies, narratology in new media, and rhetoric through an examination of the place of video games in English teaching and research. I describe in this dissertation a hybridized theoretical basis for incorporating video games in English classrooms. This framework for textual analysis includes elements from narrative theory in literary study, rhetorical theory, and literacy theory, and when combined to account for the multiple modalities and complexities of gaming, can provide new insights about those theories and practices across all kinds of media, whether in written texts, films, or video games. In creating this framework, I hope to encourage students to view texts from a meta-level perspective, encompassing textual construction, use, and interpretation. In order to foster meta-level learning in an English course, I use specific theoretical frameworks from the fields of literary studies, narratology, film theory, aural theory, reader-response criticism, game studies, and multiliteracies theory to analyze a particular video game: World of Goo. These theoretical frameworks inform pedagogical practices used in the classroom for textual analysis of multiple media. Examining a video game from these perspectives, I use analytical methods from each, including close reading, explication, textual analysis, and individual elements of multiliteracies theory and pedagogy. In undertaking an in-depth analysis of World of Goo, I demonstrate the possibilities for classroom instruction with a complex blend of theories and pedagogies in English courses. This blend of theories and practices is meant to foster literacy learning across media, helping students develop metaknowledge of their own literate practices in multiple modes. Finally, I outline a design for a multiliteracies course that would allow English scholars to use video games along with other texts to interrogate texts as systems of information. In doing so, students can hopefully view and transform systems in their own lives as audiences, citizens, and workers.

Cyclic automorphic graph decompositions

Chapter 1 introduces the tools and mechanics necessary for this report. Basic definitions and topics of graph theory which pertain to the report and discussion of automorphic decompositions will be covered in brief detail. An automorphic decomposition D of a graph H by a graph G is a G-decomposition of H such that the intersection of graph (D) @H. H is called the automorhpic host, and G is the automorphic divisor. We seek to find classes of graphs that are automorphic divisors, specifically ones generated cyclically. Chapter 2 discusses the previous work done mainly by Beeler. It also discusses and gives in more detail examples of automorphic decompositions of graphs. Chapter 2 also discusses labelings and their direct relation to cyclic automorphic decompositions. We show basic classes of graphs, such as cycles, that are known to have certain labelings, and show that they also are automorphic divisors. In Chapter 3, we are concerned with 2-regular graphs, in particular rCm, r copies of the m-cycle. We seek to show that rCm has a ρ-labeling, and thus is an automorphic divisor for all r and m. we discuss methods including Skolem type difference sets to create cycle systems and their correlation to automorphic decompositions. In the Appendix, we give classes of graphs known to be graceful and our java code to generate ρ-labelings on rCm.

Synthesis, structure, and stability of metal-organic frameworks

Metal-organic frameworks (MOFs) obtained much attention because of their unusual structures and properties as well as their potential applications. This dissertation research was focused on (1) the effects of synthesis conditions on the structures of MOFs, (2) the thermal stability of MOFs, (3) pressure-induced amorphization, and (4) the effect of high-valent ions on the structure of a MOF. This research demonstrated that the crystal structure of MOF-5 could be controlled by drying solvents. If the vacuum solvent is dimethylformamide (DMF), the crystal structure of MOF-5 is tetragonal. In contrast, if the DMF is displaced by CH2Cl2 before the vacuum, the obtained MOF-5 occupies a cubic structure. Furthermore, it was found that the tetragonal MOF-5 exhibited a mediate surface area (300-1000 m2/g). The surface area of tetragonal MOF-5 is also dependent on Zn(NO3)2/H2BDC (H2BDC: terephthalic acid) molar ratios used for its synthesis. The optimum ratio is 1.38, at which synthesized tetragonal MOF-5 exhibits the highest crystallinity and surface area (1297 m2/g). The thermal stability and decomposition of MOF-5 were systematically investigated. The thermal decomposition of cubic and tetragonal MOF-5s resulted in the same products: CO2, benzene, amorphous carbon, and crystal ZnO. The thermal decomposition is due to breaking carboxylic bridges between benzene rings and Zn4O clusters. Identifying structural relationships between crystalline and noncrystalline states is of fundamental interest in materials research. Currently, amorphization of solid materials at ambient temperature requires an ultra-high pressure (several GPa). However, this research demonstrated that MOF-5 and IRMOF-8 can be irreversibly amorphized at ambient temperature by employing a low compressing pressure of 3.5 MPa, which is 100 times lower than that required for amorphization of other solids. Furthermore, the pressure-induced amorphization (PIA) of MOFs is strongly dependent on the changeability of bond angles. If the geometric structure of a MOF can allow bond angles to be changed without breaking bonds, it can easily be amorphized by compression. This can explain why MOF-5 and IRMOF-8 can easily be amorphized via compression than Cu-BTC. It is generally recognized that zeolitic imidazolate frameworks (ZIFs) occupy much higher stability than other types of MOFs. The representative of ZIFs is Zn(2-methylimidazole)2 (ZIF-8) exhibiting high-decomposition temperature and high chemical resistance to various solvents. However, so far, it is still unknown whether the high stability of ZIF-8 can be challenged by ions, which is important for its modification by doping ions. In this research, we performed aqueous salt solution treatment on ZIF-8, and the results showed that anions (Cl¯ and NO3¯) in a solution exhibited no effect on the crystal structure of ZIF-8. However, the effect of cations (in a solution) on structure of ZIF-8 strongly depends on the cation valences. The univalent metal cations showed no effect on the structure of ZIF-8, whereas the bivalent or higher-valent metal cations caused the collapse of ZIF-8 crystal structure. Therefore, structure stability of ZIF-8 is considered when it is subjected to the application, in which high-valent metal cations are involved.