VictorJuiz/thesis huggingface dataset:
Applications of optics in PET [electronic resource] : fast timing, multiplexing, and PET/MRI
Keywords: Bioengineering.

This thesis presents the development and experimental evaluation of promising new PET (positron emission tomography) techniques which are made possible through the use of optical technologies. The large number of detector channels in modern PET scanners poses a challenge in terms of readout electronics complexity, and the preservation of fast timing information is especially important for time-of-flight (ToF) PET. A new multiplexing scheme based on encoding detector interaction events using a series of extremely fast overlapping optical pulses with precise delays has been developed. Encoding events in this way potentially allows many detector channels to be simultaneously encoded onto a single optical fiber that is then read out by a single digitizer. A two channel SiPM-based prototype utilizing this optical delay encoding technique along with a new circuit that implements dual threshold time-over-threshold is demonstrated. This prototype optical encoding and multiplexing system achieves a coincidence time resolution of 160 ps FWHM and an energy resolution of 13.1% FWHM at 511 keV with 3×3×5 mm³ LYSO crystals. All interaction information for both detectors, including timing, energy, and channel identification is encoded onto a single optical fiber with little degradation. Optical delay encoding and multiplexing technology could lead to ToF PET scanners with reduced electronics complexity and simplified data acquisition systems. Additionally, a brain sized RF (radio frequency)-penetrable PET insert has been designed for simultaneous operation within whole body MRI (magnetic resonance imaging) scanners. This system takes advantage of electro-optical coupling and battery power to enable the PET detector to electrically float relative to the MRI ground, permitting RF signals to be transmitted and received through the PET ring. The PET insert uses non-magnetic silicon photomultipliers (SiPMs) in conjunction with a compressed sensing signal multiplexing scheme and telecommunications lasers coupled to optical fibers to transmit analog PET detector signals out of the MRI room to a custom data acquisition system for decoding, processing, and reconstruction. The PET insert was placed within a 3T whole body MRI, and PET phantom images were successfully acquired under continuous pulsing from different MR imaging sequences. MR phantom images were successfully acquired from RF signals transmitted through the RF-penetrable PET ring using only the built in MR body coil, suggesting that simultaneous imaging is possible without significant mutual interference. These results show promise for this technology as an alternative to costly fully integrated PET/MR scanners, as a PET insert that is compatible with any existing clinical MRI system could greatly expand the availability of combined PET/MR. The performance of a commercial whole body ToF integrated PET/MR scanner was also evaluated.
Applying genomic approaches to address ecological, evolutionary, and clinical questions [electronic resource]
Keywords: Biology.

Technological developments in genomics over the past two decades have allowed biologists to address long-standing questions in ecology, evolutionary biology, and medicine, but also pose a substantial challenge for analysis and interpretation. This thesis addresses these challenges by developing and testing novel genomic tools and resources as well as leveraging them to address basic biological questions. The thesis chapters are united in their focus on the origin and maintenance of natural genetic variation as well as its influence on phenotypic variation. The first introductory chapter expands upon the unifying themes and briefly outlines the history of the study of genetic variation, with a specific focus on aneuploidy. The second chapter focuses on reference genome assembly by identifying advantages and limitations of a new synthetic long-read technology for de novo genome reconstruction. The third chapter introduces a low-cost method to survey genetic variation in non-model species by simultaneously building a transcriptome reference and discovering expressed single nucleotide polymorphisms from a population sample. These genomic data are then used to infer the demographic history of an introduced checkerspot butterfly, achieving parameter estimates that are consistent with the known population history. The final two chapters focus on application of high-throughput genomic technologies in a clinical setting, specifically in the context of preimplantation genetic screening (PGS) during in vitro fertilization. PGS data are then analyzed to study variation in chromosome copy number (i.e. aneuploidy) which is prevalent in early human development, but rarely survives to live birth. The fourth chapter contrasts the incidences of various forms of aneuploidy at different stages of preimplantation development, demonstrating that mitotic-origin aneuploidies are strongly selected against at the onset of zygotic genome activation. The final chapter provides evidence that a maternal genetic variant influences aneuploidy risk, identifying a promising candidate gene in the region. Together, these dissertation chapters develop and apply novel genomic approaches to achieve new biological insights and pave the way for future genomic studies.
Aristotle on virtue and understanding [electronic resource] : how his theory is intellectualist and why it matters for contemporary education
Keywords: Philosophy.

Aristotle's understanding of the moral psychology and decision-making of the morally good person is more intellectualist than commentators tend to think. The morally good person must have a complete understanding of the value and structure of virtue. Drawing on a number of under-studied texts and concepts in Aristotle's corpus, I argue that this intellectualism lies at the heart of his ethical theory and cannot be excised with ease. Recognizing the centrality of moral intellectualism to Aristotle's theory of practical wisdom has direct consequences for contemporary theorists who wish to defend an Aristotelian theory of ethics or civic education.
Art confiscations and cultural diplomacy [electronic resource] : the Ming (1368-1644) imperial inventory system at work
Keywords: Art and Art History.

This dissertation explores the role inventory systems played in mapping, defining, and legitimizing the imperial power of the Ming dynasty (1368-1644). It contributes to comparative studies of legal histories and inventory practices in the early modern world at large. The inventory marks take two different forms: half-seals and half-codes that appear on 201 canonical 6th-14th century Chinese paintings and calligraphies. Although undetected by art historians, these half-marks help to unravel violent history of imperial art confiscations. I argue that these inventory half-marks indicate property confiscations perpetrated by Emperors Hongwu (r. 1368-1398), Jiajing (r. 1522-1566), and Wanli (r. 1573-1620). When facing the state's financial crisis, the Ming emperors dismissed their prime ministers and took their property, because the ministers' power and wealth irritated the emperors. I further prove that the confiscation law at the time required every seized item to be marked with half-character credentials. Halves of the marks were stamped on the art, whereas the other halves were printed on official ledgers, and the emperors kept the ledgers. Functioning similarly to contemporary barcodes on merchandise, the half-seals and half-codes recorded on the ledgers allowed the Ming emperors to track down the forfeited treasures. In contrast to previous scholarship which highlights positive aspects of art collecting, I instead explore the darker side of art collecting culture. In this way, my dissertation takes a new approach to look at the after-life of art objects, which includes the ownership, censorship, and imperial competition with prime ministers over art collections. Interestingly, half marks occurred not only in Ming Chinese inventory accounts, but also on Asian trade permits. I further place the Ming inventory system in the wider context of a globalizing world by exploring how the system proliferated throughout Asia. The Ming founding emperor Hongwu issued limited inventory codes as trade permits to other Asian countries, in order to establish a Sinocentric world view and to control international trade. I show how Korean, Japanese, Thai, and Javanese kingdoms assimilated the Ming inventory systems, and then modified them to create their own methods of codification. The logic of transforming objects into formulaic inventory codes illuminates the ways in which the emperors mapped out their political landscapes. Drawing upon a diverse array of inventory codes, I demonstrate how China and its neighbors used such codes to negotiate space, claim ownership of marked items, and assert hegemony over the empire.
The ascetic lifestyle in the early Indian buddhist monastery [electronic resource] : a study of the Dhūtaguna practices in the Vinaya tradition
Keywords: Religious Studies.

This study examines the role played by the set of ascetic precepts known as the dhutagunas in early Indian Buddhist monastic communities. Although there are numerous references to the dhutagunas found throughout the monastic discourses which comprise the Buddhist Vinaya (law codes), modern scholarship has largely rejected the notion that the dhutagunas could have been regarded by members of the monastic community as anything other than vestigial ideals received from the non-Buddhist ascetic milieu. This dissertation challenges the premise that the dhutagunas were merely vestiges from non-Buddhist communities, arguing instead that the editors of the Vinaya viewed the ascetic precepts as practices common to the lifestyle of the early Buddhist monk.
Asymptotics for large stochastic systems [electronic resource]
Keywords: Management Science and Engineering.

Large, interacting stochastic systems appear in many facets of today's world and are of broad importance. Examples include the banking system, financial markets, electric power grids, engineering systems, health care, and social networks. Due to their scale, complexity, and large amounts of data, analyzing such systems is inherently challenging. This dissertation develops computational methods for simulation and optimization for such large systems. The computational methods are built upon weak convergence results which can be used to approximate a large system. An ecient Monte Carlo approximation for the fast simulation of large systems is developed. The Monte Carlo approximation is built upon a dynamic law of large numbers and dynamic central limit theorem. This same approximation is used to approximate optimization problems for large stochastic systems. The solution to the approximate optimization problem, called the "asymptotically optimal portfolio", yields accurate and computationally cheap solutions to large-scale optimization problems for such systems. In particular, the work in this dissertation is motivated by the modeling of large pools of financial loans. Financial institutions, government-sponsored enterprises such as Fannie Mae, and asset-backed security investors are often exposed to delinquency and prepayment risk from large numbers of loans. Examples include mortgages, credit cards, auto, commercial, real estate, student, and small business loans. Due to the size of such loan pools and the potentially long maturities of their cashflows, the measurement and management of these exposures are computationally expensive. This dissertation develops and tests ecient numerical methods for the risk analysis and optimization of large pools of loans. The methods are extensively tested using actual loan data sets. The computational methods proposed here can potentially provide financial institutions and regulators with ecient data-driven methods to manage and estimate risk in large pools of loans.
Atomic layer deposition of earth abundant electrocatalysts for the oxygen evolution reaction [electronic resource]
Keywords: Chemical Engineering.

Due to its intermittent nature, large-scale adoption of solar energy requires new technological advancements to efficiently store and distribute energy. The photoelectrochemical (PEC) splitting of water is a promising way to capture solar energy and store it in the form of chemical bonds. We look at leveraging the advantages of ALD, a technique well known in the microelectronics industry, to address some of the most pressing issues in PEC water splitting. In particular, the focus of our studies is the development of catalysts to drive the oxygen evolution reaction (OER), a reaction typically associated with high overpotentials and sluggish kinetics. We first investigate known active transition metal oxide catalysts, exploring how to enhance their activity with higher surface area and through electronic effects. We create highly active electrocatalysts of both MnOx and NiOx, and discuss some of the advantages and limitations of using ALD to deposit these films. Next, we focus on using ALD to manage charge transport limitations in semiconducting oxide thin films. We demonstrate the sensitivity of semiconducing thin films to film thickness using ALD TiO2 as a model material. We then show how ALD can be used to explore new semiconducting oxide catalysts, focusing on a Ti-Mn oxide system. We also discuss the integration of these catalysts into PEC devices, with an emphasis on the role of stability, oxidation, and surface area in enhancing the OER activity for photoanodes.
Automated construction of order parameters for analyzing simulations of protein folding and water dynamics [electronic resource]
Keywords: Chemistry.

This thesis discusses the role of analysis in the application of molecular dynamics (MD) simulations for studying phenomena at an atomic level of detail. Many interesting questions can be asked of the physical world: How do proteins fold? Are there two liquid phases of supercooled water? How does a drug inhibit an enzyme? Many of these questions, however, are not quantitatively specific, meaning that the answers depend on scientists' interpretation. Researchers tend to describe these phenomena through hand-chosen functions, or order parameters, that are based on physical intuition. However, there is an immense amount of information contained in a large-scale simulation that is typically not used. Here, we attempt to illustrate the usefulness of data-driven analysis in the study of physical phenomena with MD. In all cases, the strategy begins by reformulating the nebulous physical questions into a specific and quantitative question, which can be used to derive an appropriate unsupervised learning method for the given problem. This strategy rests on physical intuition, because the problem formulation must be done in a physically meaningful way, but the advantage is that the specific solutions are driven by the data itself, allowing for interesting phenomena to be discovered rather than required to be known a priori.
Band-engineered germanium for CMOS-compatible light emission [electronic resource]
Keywords: Electrical Engineering.

Modern electronics has advanced at a tremendous pace over the course of the last half century due to transistor scaling. However, while scaling a complementary metal oxide semiconductor (CMOS) transistor to smaller dimensions increases speed and reduces power consumption, the opposite is true for scaling down the copper interconnects that link these transistors. CMOS-compatible on- and off-chip optical interconnects offer a promising solution to this new performance bottleneck and several key components such as waveguides, detectors and modulators have already been demonstrated. However, a practical silicon CMOS-compatible light source remains elusive. Germanium has been proposed as a laser gain material due to its inherent compatibility with CMOS technology, but this requires overcoming the limitations imposed by germanium's indirect bandgap. Several techniques had been proposed to overcome this limitation such as n-type doping and band engineering through tensile strain. However, there was limited information about how effective each of these two techniques would be. There was also no truly CMOS-compatible technique for engineering large tensile strains in germanium for optimal band engineering. In this work we present theoretical and experimental answers to these problems. We begin with a theoretical investigation of the relative merits of n-type doping and band engineering through tensile strain to determine which is more useful. We then show theoretically that while n-type doping is of limited benefit, using a large tensile strain can result in an efficient low-threshold germanium laser. From there we present new CMOS-compatible techniques for engineering large tensile strains in germanium. Firstly, we improve upon an existing microbridge technique to achieve up to 5.7% uniaxial tensile strain in germanium. This is the highest such strain ever reported and is sufficient to turn germanium into a direct bandgap semiconductor. Secondly, we present a completely new technique for engineering up to 1.1% biaxial strain in germanium microdisks. This is the largest CMOS-compatible biaxial strain ever reported in germanium, and we further demonstrate an optical cavity integrated with our biaxially strained germanium structure. Finally, we discuss the implications of these theoretical and experimental achievements toward creating an efficient low-threshold germanium laser for use in CMOS-compatible on-chip light emission.
Batteries for efficient energy recovery from wastewater [electronic resource]
Keywords: Civil and Environmental Engineering.

Wastewater treatment is an energy intensive process, consuming ~ 3% of U.S. electricity production. This is despite the fact that considerable energy in wastewater is potentially recoverable. This energy includes the chemical energy in reduced organics and nitrogen, and, at coastal treatment plants, the energy of the salinity-gradient between wastewater effluent and seawater. This thesis focuses on development of two battery technologies, the "mixing entropy battery" (MEB) and the "microbial battery" (MB), to enable efficient recovery of energy from salinity gradients and the organics in wastewater, respectively. In initial studies, the MEB is evaluated with wastewater effluent as the source of freshwater and different operational parameters are investigated. The MEB flushed with wastewater effluent achieved an energy recovery efficiency comparable to that of a MEB with river water flushes. With 12 cells in series, an energy recovery efficiency of 68% was achieved. Two operational trade-offs were identified: (1) energy recovery efficiency and capital investment, and (2) power output and energy recovery efficiency. In follow-up studies, new electrode materials are evaluated for the MEB. Prussian Blue (PB) and polypyrrole (PPy) were employed as the cationic electrode and the anionic electrode, respectively. Both materials are low cost (
/kg for PPy) and showed desirable electrochemical properties, including redox reactivity with Na+ or Cl-, rapid potential response to the salinity change, excellent cycling performance, and stability in aqueous environments. These novel electrode materials also enabled another significant breakthrough. Because the potential range of the PB electrode and the PPy electrode are similar, the MEB can be operated without the charge step. The charge-free MEB requires no additional energy investment and produces energy during both wastewater effluent and seawater flushes. The voltage efficiency of the charge-free MEB was similar to that of the original MEB that required a charge step and used inferior electrode materials (89.5% and 97.6% voltage ratio). Moreover, the MEB was stable for 50 cycles with less than 7% loss in energy production. In a set of final experiments, use of PB is evaluated in a MB as a low-cost cathode material to replace Ag/Ag2O. Regeneration of the PB electrode was straightforward and required no energy input. By exposing the PB electrode in air for 100 min, 80% of the original capacity was restored. The process was rapid; the PB electrode discharged in a MB for 8 min after exposing in air for only 5 min. The energy recovery efficiency of the MB with a PB cathode was comparable to that of the original MB with Ag/Ag2O cathode (18% to 33%, depending upon operating conditions) with stable power output for 20 cycles.
Beauty and the bestiary [electronic resource] : animal art and humane thought in the Gilded Age
Keywords: Art and Art History.

This project investigates how American artists contended with the problems and exploited the possibilities of representing animals during the final decades of the nineteenth century. Thanks to the precipitous rise of Darwinism, the anti-cruelty movement, zoological parks, and conservationism, as well as the emergence of modern forms of taxidermy, pet breeding, and pet keeping, this period witnessed a wholesale reevaluation of human and animal alike. Fascinated by these transformations, Americans voraciously sought out new opportunities to encounter animals, both in life and in art. "Beauty and the Bestiary" focuses on four turn-of-the century American artists—James Henry Beard, Winslow Homer, Astley D. M. Cooper, and Albert Laessle—who actively engaged with animal subjects during this transformative time. Their work not only reflected but actively participated in the development of in humane thought, an interdisciplinary field of inquiry which, much like contemporary animal studies, grappled with the ethical, epistemological and ontological ramifications of human un-exceptionalism. In their sculptures and paintings of animals, these artists charted the shifting boundary between the human and the nonhuman, thoughtfully interrogating the personal and political meaning of our relations with other species. Revisiting and reconsidering their unruly visions is imperative, not only to nuance our understanding of American art, but to fully grasp how its evolution has shaped our present-day commitments to the natural world.