Characterizing Genetic Drivers of Lymphoma through High-Throughput Sequencing

The advent of next-generation sequencing, now nearing a decade in age, has enabled, among other capabilities, measurement of genome-wide sequence features at unprecedented scale and resolution.

In this dissertation, I describe work to understand the genetic underpinnings of non-Hodgkin’s lymphoma through exploration of the epigenetics of its cell of origin, initial characterization and interpretation of driver mutations, and finally, a larger-scale, population-level study that incorporates mutation interpretation with clinical outcome.

In the first research chapter, I describe genomic characteristics of lymphomas through the lens of their cells of origin. Just as many other cancers, such as breast cancer or lung cancer, are categorized based on their cell of origin, lymphoma subtypes can be examined through the context of their normal B Cells of origin, Naïve, Germinal Center, and post-Germinal Center. By applying integrative analysis of the epigenetics of normal B Cells of origin through chromatin-immunoprecipitation sequencing, we find that differences in normal B Cell subtypes are reflected in the mutational landscapes of the cancers that arise from them, namely Mantle Cell, Burkitt, and Diffuse Large B-Cell Lymphoma.

In the next research chapter, I describe our first endeavor into understanding the genetic heterogeneity of Diffuse Large B Cell Lymphoma, the most common form of non-Hodgkin’s lymphoma, which affects 100,000 patients in the world. Through whole-genome sequencing of 1 case as well as whole-exome sequencing of 94 cases, we characterize the most recurrent genetic features of DLBCL and lay the groundwork for a larger study.

In the last research chapter, I describe work to characterize and interpret the whole exomes of 1001 cases of DLBCL in the largest single-cancer study to date. This highly-powered study enabled sub-gene, gene-level, and gene-network level understanding of driver mutations within DLBCL. Moreover, matched genomic and clinical data enabled the connection of these driver mutations to clinical features such as treatment response or overall survival. As sequencing costs continue to drop, whole-exome sequencing will become a routine clinical assay, and another diagnostic dimension in addition to existing methods such as histology. However, to unlock the full utility of sequencing data, we must be able to interpret it. This study undertakes a first step in developing the understanding necessary to uncover the genomic signals of DLBCL hidden within its exomes. However, beyond the scope of this one disease, the experimental and analytical methods can be readily applied to other cancer sequencing studies.

Thus, this dissertation leverages next-generation sequencing analysis to understand the genetic underpinnings of lymphoma, both by examining its normal cells of origin as well as through a large-scale study to sensitively identify recurrently mutated genes and their relationship to clinical outcome.

Chemistry and grain-size distribution of terrigenous sediments deposited at Site GeoB9501

The Sahara Desert is the largest source of mineral dust in the world. Emissions of African dust increased sharply in the early 1970s, a change that has been attributed mainly to drought in the Sahara/Sahel region caused by changes in the global distribution of sea surface temperature. The human contribution to land degradation and dust mobilization in this region remains poorly understood, owing to the paucity of data that would allow the identification of long-term trends in desertification. Direct measurements of airborne African dust concentrations only became available in the mid-1960s from a station on Barbados and subsequently from satellite imagery since the late 1970s: they do not cover the onset of commercial agriculture in the Sahel region ~170 years ago. Here we construct a 3,200-year record of dust deposition off northwest Africa by investigating the chemistry and grain-size distribution of terrigenous sediments deposited at a marine site located directly under the West African dust plume. With the help of our dust record and a proxy record for West African precipitation we find that, on the century scale, dust deposition is related to precipitation in tropical West Africa until the seventeenth century. At the beginning of the nineteenth century, a sharp increase in dust deposition parallels the advent of commercial agriculture in the Sahel region. Our findings suggest that human-induced dust emissions from the Sahel region have contributed to the atmospheric dust load for about 200 years.

Genomic consequences of mating system evolution in the Pacific coastal dune endemic, Abronia umbellata (Nyctaginaceae)

The advent of next-generation sequencing has significantly reduced the cost of obtaining large-scale genetic resources, opening the door for genomic studies of non-model but ecologically interesting species. The shift in mating system, from outcrossing to selfing, has occurred thousands of times in angiosperms and is accompanied by profound changes in the population genetics and ecology of a species. A large body of work has been devoted to understanding why the shift occurs and the impact of the shift on the genetics of the resulting selfing populations, however, the causes and consequences of the transition to selfing involve a complicated interaction of genetic and demographic factors which are difficult to untangle. Abronia umbellata is a Pacific coastal dune endemic which displays a striking shift in mating system across its geographic range, with large-flowered outcrossing populations south of San Francisco and small-flowered selfing populations to the north. Abronia umbellata is an attractive model system for the study of mating system transitions because the shift appears to be recent and therefore less obscured by post-shift processes, it has a near one-dimensional geographic range which simplifies analysis and interpretation, and demographic data has been collected for many of the populations. In this study, we generated transcriptome-level data for 12 plants including individuals from both subspecies, along with a resequencing study of 48 individuals from populations across the range. The genetic analysis revealed a recent transition to selfing involving a drastic reduction in genetic diversity in the selfing lineage, potentially indicative of a recent population bottleneck and a transition to selfing due to reproductive assurance. Interestingly, the genetic structure of the populations was not coincident with the current subspecies demarcation, and two large-flowered populations were classified with the selfing subspecies, suggesting a potential need for re-evaluation of the current subspecies classification. Our finding of low diversity in selfing populations may also have implications for the conservation value of the threatened selfing subspecies.

A State of Minds : Canada in the Information Era (Working Paper 10)

Globalization and the knowledge/ information revolution are signalling the advent of a new societal order, one with profound and pervasive implications for citizens, for markets, for governments and, therefore, for public policy. This new global order is a truly remarkable watershed in the annals of human history and, as is the case with all such great transformations, it carries with it both enormous opportunities and daunting challenges. Building on my 1999 Mabel Timlin Lecture at the University of Saskatchewan, I want to share with you my perspectives on the nature of some of these opportunities and challenges, with an eye toward drawing out the implications for the evolution of the Canadian society and economy.

Tailoring Magnetic, Mechanical and Dielectric Properties of Magnetorheological Elastomers based on Natural Rubber and Iron by Magnetic Field Assisted Curing for Possible Applications

If magnetism is universal in nature, magnetic materials are ubiquitous. A life without magnetism is unthinkable and a day without the influence of a magnetic material is unimaginable. They find innumerable applications in the form of many passive and active devices namely, compass, electric motor, generator, microphone, loud speaker, maglev train, magnetic resonance imaging, data recording and reading, hadron collider etc. The list is endless. Such is the influence of magnetism and magnetic materials in ones day to day life. With the advent of nanoscience and nanotechnology, along with the emergence of new areas/fields such as spintronics, multiferroics and magnetic refrigeration, the importance of magnetism is ever increasing and attracting the attention of researchers worldwide. The search for a fluid which exhibits magnetism has been on for quite some time. However nature has not bestowed us with a magnetic fluid and hence it has been the dream of many researchers to synthesize a magnetic fluid which is thought to revolutionize many applications based on magnetism. The discovery of a magnetic fluid by Jacob Rabinow in the year 1952 paved the way for a new branch of Physics/Engineering which later became magnetic fluids. This gave birth to a new class of material called magnetorheological materials. Magnetorheological materials are considered superior to electrorheological materials in that magnetorheology is a contactless operation and often inexpensive.Most of the studies in the past on magnetorheological materials were based on magnetic fluids. Recently the focus has been on the solid state analogue of magnetic fluids which are called Magnetorheological Elastomers (MREs). The very word magnetorheological elastomer implies that the rheological properties of these materials can be altered by the influence of an external applied magnetic field and this process is reversible. If the application of an external magnetic field modifies the viscosity of a magnetic fluid, the effect of external magnetic stimuli on a magnetorheological elastomer is in the modification of its stiffness. They are reversible too. Magnetorheological materials exhibit variable stiffness and find applications in adaptive structures of aerospace, automotive civil and electrical engineering applications. The major advantage of MRE is that the particles are not able to settle with time and hence there is no need of a vessel to hold it. The possibility of hazardous waste leakage is no more with a solid MRE. Moreover, the particles in a solid MRE will not affect the performance and durability of the equipment. Usually MR solids work only in the pre yield region while MR fluids, typically work in the post yield state. The application of an external magnetic field modifies the stiffness constant, shear modulus and loss modulus which are complex quantities. In viscoelastic materials a part of the input energy is stored and released during each cycle and a part is dissipated as heat. The storage modulus G′ represents the capacity of the material to store energy of deformation, which contribute to material stiffness. The loss modulusG′′ represents the ability of the material to dissipate the energy of deformation. Such materials can find applications in the form of adaptive vibration absorbers (ATVAs), stiffness tunable mounts and variable impedance surfaces. MREs are an important material for automobile giants and became the focus of this research for eventual automatic vibration control, sound isolation, brakes, clutches and suspension systems

Fabrication, Optical Analysis and Photonic Applications of Certain Metallic Nanostructure-Integrated Dye Doped Polymer Optical Fibers” submitted by Ms. Suneetha Sebastian

Polymer Optical Fibers have occupied historically a place for large core flexible fibers operating in short distances. In addition to their practical passive application in short-haul communication they constitute a potential research field as active devices with organic dopants. Organic dyes are preferred as dopants over organic semiconductors due to their higher optical cross section. Thus organic dyes as gain media in a polymer fiber is used to develop efficient and narrow laser sources with a tunability throughout the visible region or optical amplifier with high gain. Dyes incorporated in fiber form has added advantage over other solid state forms such as films since the pump power required to excite the molecules in the core of the fiber is less thereby utilising the pump power effectively. In 1987, Muto et.al investigated a dye doped step index polymer fiber laser. Afterwards, numerous researches have been carried out in this area demonstrating laser emission from step index, graded index and hollow optical fibers incorporating various dyes. Among various dyes, Rhodamine6G is the most widely and commonly used laser dye for the last four decades. Rhodamine6G has many desirable optical properties which make it preferable over other organic dyes such as Coumarin, Nile Blue, Curcumin etc. The research focus on the implementation of efficient fiber lasers and amplifiers for short fiber distances. Developing efficient plastic lasers with electrical pumping can be a new proposal in this field which demands lowest possible threshold pump energy of the gain medium in the cavity as an important parameter. One way of improving the efficiency of the lasers, through low threshold pump energy, is by modifying the gain of the amplifiers in the resonator/cavity. Success in the field of Radiative Decay Engineering can pave way to this problem. Laser gain media consisting of dye-nanoparticle composites can improve the efficiency by lowering the lasing threshold and enhancing the photostability. The electric field confined near the surface of metal nanoparticles due to Localized Surface Plasmon Resonance can be very effective for the excitation of active centers to impart high optical gain for lasing. Since the Surface Plasmon Resonance of nanoparticles of gold and silver lies in the visible range, it can affect the spectral emission characteristics of organic dyes such as Rhodamine6G through plasmon field generated by the particles. The change in emission of the dye placed near metal nanoparticles depend on plasmon field strength which in turn depends on the type of metal, size of nanoparticle, surface modification of the particle and the wavelength of incident light. Progress in fabrication of different types of nanostructures lead to the advent of nanospheres, nanoalloys, core-shell and nanowires to name a few. The thesis deals with the fabrication and characterisation of polymer optical fibers with various metallic and bimetallic nanostructures incorporated in the gain media for efficient fiber lasers with low threshold and improved photostability.

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.

Towards an Asynchronous Cinema: how can the asynchronous use of sound in artists' moving image underpin the creation of dialectic tension between the audio, the visual and the audience?

This PhD by publication examines selected practice-based audio-visual works made by the author over a ten-year period, placing them in a critical context. Central to the publications, and the focus of the thesis, is an exploration of the role of sound in the creation of dialectic tension between the audio, the visual and the audience. By first analysing a number of texts (films/videos and key writings) the thesis locates the principal issues and debates around the use of audio in artists’ moving image practice. From this it is argued that asynchronism, first advocated in 1929 by Pudovkin as a response to the advent of synchronised sound, can be used to articulate audio-visual relationships. Central to asynchronism’s application in this paper is a recognition of the propensity for sound and image to adhere, and in visual music for there to be a literal equation of audio with the visual, often married with a quest for the synaesthetic. These elements can either be used in an illusionist fashion, or employed as part of an anti-illusionist strategy for realising dialectic. Using this as a theoretical basis, the paper examines how the publications implement asynchronism, including digital mapping to facilitate innovative reciprocal sound and image combinations, and the asynchronous use of ‘found sound’ from a range of online sources to reframe the moving image. The synthesis of publications and practice demonstrates that asynchronism can both underpin the creation of dialectic, and be an integral component in an audio-visual anti-illusionist methodology.

Digital accessibility challenges: the impact of locality, usability and technology

Abstract: It is estimated that 1 in 5 will, at some point in their lives, experience a long-term illness or disability that will impact their day to day lives. Access to digital information and technologies can be life changing and a necessity to fully participate in education, work and society. Specialist assistive technologies, such as screen readers, have been available for many years and are now built-into operating systems and devices. In addition, web accessibility standards have been compiled and published since the advent of the World Wide Web over two decades ago. However, internet use by people with disabilities continues to lag significantly behind those with no disability and use of assistive technologies remains lower than should be the case with tools often abandoned. In this seminar we will talk about our work to identify digital accessibility challenges; the barriers experienced by those with disabilities and how computer scientists can play a part in removing obstacles to access and ease of use. We will discuss some of our projects focussing on: • Development of assistive technologies for niche groups of users, • improving accessibility standards to cover a wider range of disabilities, • creating accessibility training resources for developers and stakeholders • embedding accessibility practice within development projects.

Measuring the geographic distribution of maternal education in Africa

Thesis (Master's)--University of Washington, 2016-08

The Meanings of New Money: Social Constructions of Value in the Rise of Digital Currencies

Thesis (Ph.D.)--University of Washington, 2016-07

Guiding Monte Carlo tree searches with neural networks in the game of go

A dissertation submitted in fulfillment of the requirements to the degree of Master in Computer Science and Computer Engineering

A study of computational methods to analyze gene expression data

The recent advent of new technologies has led to huge amounts of genomic data. With these data come new opportunities to understand biological cellular processes underlying hidden regulation mechanisms and to identify disease related biomarkers for informative diagnostics. However, extracting biological insights from the immense amounts of genomic data is a challenging task. Therefore, effective and efficient computational techniques are needed to analyze and interpret genomic data. In this thesis, novel computational methods are proposed to address such challenges: a Bayesian mixture model, an extended Bayesian mixture model, and an Eigen-brain approach. The Bayesian mixture framework involves integration of the Bayesian network and the Gaussian mixture model. Based on the proposed framework and its conjunction with K-means clustering and principal component analysis (PCA), biological insights are derived such as context specific/dependent relationships and nested structures within microarray where biological replicates are encapsulated. The Bayesian mixture framework is then extended to explore posterior distributions of network space by incorporating a Markov chain Monte Carlo (MCMC) model. The extended Bayesian mixture model summarizes the sampled network structures by extracting biologically meaningful features. Finally, an Eigen-brain approach is proposed to analyze in situ hybridization data for the identification of the cell-type specific genes, which can be useful for informative blood diagnostics. Computational results with region-based clustering reveals the critical evidence for the consistency with brain anatomical structure.

CONCERNS REGARDING THE PROTECTION OF COPYRIGHT IN THE INTERNET

The advent of the World Network(Net) Internet and the use of the technology in the digital environment raised new challenges to the author's copyright. These worries were considered in the last international agreements, so that the warning is not true of those who postulate that the Internet is a " territory of nobody ", where the works are unprotected completely. To educate on the topic of the protection of the author's copyright and to provide with resources the instances(authorities) in charge of the observance of these rights looks like an ineluctable task.