VictorJuiz/thesis huggingface dataset:
Complex-valued Deep Learning with Applications to Magnetic Resonance Image Synthesis

Magnetic resonance imaging (MRI) has the ability to produce a series of images that each have different visual contrast between tissues, allowing clinicians to qualitatively assess pathologies that may be visible in one contrast-weighted image but not others. Unfortunately, these standard contrast-weighted images do not contain quantitative values, producing challenges for post-processing, assessment, and longitudinal studies. MR fingerprinting is a recent technique that produces quantitative tissue maps from a single pseudorandom acquisition, but it relies on computationally heavy nearest neighbor algorithms to solve the associated nonlinear inverse problem. In this dissertation, we present our deep learning methods to speed up quantitative MR fingerprinting and synthesize the standard contrast-weighted images directly from the same MR fingerprinting scan./nAdapting deep learning methodologies to MR image synthesis presents two specific challenges: 1) complex-valued data and 2) the presence of noise while undersampling./nMRI signals are inherently complex-valued, as they are measurements of rotating magnetization within the body. However, modern neural networks are not designed to support complex values. As an example, the pervasive ReLU activation function is undefined for complex numbers. This limitation curtails the impact of deep learning for complex data applications, such as MRI, radio frequency modulation identification, and target recognition in synthetic-aperture radar images. In this dissertation, we discuss the motivation for complex-valued networks, the changes that we have made to implement complex backpropagation, and our new complex cardioid activation function that made it possible to outperform real-valued networks for MR fingerprinting image synthesis./nIn Fourier-based medical imaging, undersampling results in an underdetermined system, in which a linear reconstruction will exhibit artifacts. Another consequence is lower signal-to-noise ratio (SNR) because of fewer acquired measurements. The coupled effects of low SNR and underdetermined system during reconstruction makes it difficult to model the signal and analyze image reconstruction algorithms. We demonstrate that neural networks trained only with a Gaussian noise model fail to process in vivo MR fingerprinting data, while our proposed empirical noise model allows neural networks to successfully synthesize quantitative images. Additionally, to better understand the impact of noise on undersampled imaging systems, we present an image quality prediction process that reconstructs fully sampled, fully determined data with noise added to simulate the SNR loss induced by a given undersampling pattern. The resulting prediction image empirically shows the effects of noise in undersampled image reconstruction without any effect from an underdetermined system, allowing MR pulse sequence and reconstruction developers to determine if low SNR, rather than the underdetermined system, is the limiting factor for a successful reconstruction.

Advisor: Lustig, Michael
Yu, Stella X
The arithmetic Hodge-index theorem and rigidity of algebraic dynamical systems over function fields

In one of the fundamental results of Arakelov’s arithmetic intersection theory, Faltings and Hriljac (independently) proved the Hodge-index theorem for arithmetic surfaces by relating the intersection pairing to the negative of the Neron-Tate height pairing. More recently, Moriwaki and Yuan–Zhang generalized this to higher dimension. In this work, we extend these results to projective varieties over transcendence degree one function fields. The new challenge is dealing with non-constant but numerically trivial line bundles coming from the constant field via Chow’s K/k-image functor./nAs an application of the Hodge-index theorem to heights defined by intersections of adelic metrized line bundles, we also prove a rigidity theorem for the set height zero points of polarized algebraic dynamical systems over function fields. In the special case of a global field, this gives a rigidity theorem for preperiodic points, generalizing previous work of Mimar, Baker–DeMarco, and Yuan–Zhang.

Advisor: Yuan, Xinyi
Mechanical Evaluation of Polycarbonate Polyurethane for Long-Term Orthopedic Implant Applications

There are currently over 2 million total joint replacement procedures completed every/nyear worldwide. The number of total joint replacement procedures is predicted to grow. At/nthe same time, the percentage of younger, more active patients undergoing joint replacement/nprocedures is also predicted to increase. Such predictions motivate a need for joint replacements to last longer and perform better in more active patients. The greatest challenge for current joint replacement device designs is wear-related failures. One potential solution to/nimprove wear performance is to use alternative materials with superior wear performance./nPolycarbonate polyurethane (PCU) has been proposed as an alternative material to improve/nthe performance of joint replacements. It is softer and more elastomeric than the current/nstandard polymer, ultra-high molecular weight polyethylene. It has been hypothesized that,/ndue to its lower elastic modulus, PCU will have improved lubrication performance, reducing/nwear. Historically, improvement to ultra-high molecular weight polyethylene wear performance/nhas come at the expense of fracture resistance. Therefore, in the highly cyclic loading/nenvironment of a total joint replacement, the fatigue and fracture properties are also important/nto consider./nThis thesis evaluated the long-term mechanical performance of PCU in orthopedic implant/napplications. First, we characterized the fatigue crack growth mechanisms in PCU/nas a function of loading, frequency, hydration, and thermal annealing treatment. We found/nhighly time-dependent behavior as mechanisms of crack growth and failure changed with/nloading regime. Second, we looked at changes in the structural organization of PCU as a/nfunction of thermal treatments and strain. We found trends of increasing ductility with/nincreasing annealing temperature and increasing hydrogen bonding in the ordered hard domain. The amount of hydrogen bonding decreased with increasing strain. Finally, we used an 3D-transient elastohydrodynamic lubrication model to characterize the lubrication regimes in PCU during a simulated gait cycle. Our model contradicts the optimistic predictions/nof 1D-steady state modeling and may explain the disconnect between early modeling and/nthe experimental wear results for PCU. Moving forward, this work serves as a foundation/nfor many questions that still need to be answered to understand the fatigue, fracture, and/ntribological performance of this complex material in long-term clinical implant applications.

Advisor: Pruitt, Lisa
Spatial and Color Vision in the Absence of Retinal Motion

Abstract/nSpatial and Color Vision in the Absence of Retinal Motion/nby/nAlexandra Elizabeth Boehm/nDoctor of Philosophy in Vision Science/nUniversity of California, Berkeley/nProfessor Austin Roorda, Chair/nIn the mid-19th century, Johannes Peter Müller first proposed what has become known as the law of specific nerve energies, where sensory perception is understood in the context of underlying physiological mechanisms which create an internal representation of an external stimulus. In the Handbuch der Physiologie des Menschen für Vorlesungen he wrote, “Sensation is not the conduction of a quality of state of external bodies to consciousness, but the conduction of a quality or state of our nerves to consciousness, excited by an external cause,” (translated by Clarke & O’Malley, 1996). While it has long been appreciated that visual perception and the underlying physiology are inextricably linked, scientific research has been limited in its ability to provide direct comparisons between the two. Perception is the culmination of multiple levels of neural processing involving millions of cells, but physiological models are often limited to data from a single or few cells in nonhuman primates. In contrast, what we know about perception has largely been gathered from psychophysical experiments performed in humans, where behavior is quantified and related to controlled differences in external stimuli, but the underlying physiological mechanisms can only be inferred./nFor vision, this is further complicated by the fact that the eye is constantly in motion. Even when fixated, the eye makes microscopic eye movements which cause light from a stationary stimulus to be moved across many light-sensitive cells on the retina, and consequently across many receptive fields of downstream neurons. Recent advances in optics and eye tracking technology have made it possible to perform psychophysical experiments in human observers with cellular resolution where stimuli are fixed on the retina even in the presence of eye motion. This has brought about a new generation of experiments attempting to unify physiology and behavior. The work described here utilizes and expands upon these methodologies toward a better understanding of color and spatial vision in the absence of retinal motion. Chapter 1 provides a background on the origins of color and spatial vision in the retina, in addition to a review of the methodology. Chapter 2 explores the spatial extent of desensitization to stabilized stimuli and compares this to the known constraints to spatial vision imposed by anatomy and physiology. Chapter 3 expands upon previous work, looking at the contribution of individual cone photoreceptors to color vision, toward the construction of physiologically relevant color space from multiple cone-targeted stimulation. Finally, Chapter 4 demonstrates novel methodology to compensate for stimulus motion on the retina that is due to dynamic changes in transverse chromatic aberration.

Advisor: Roorda, Austin
Small Victories: Indigenous Proprietors Across Empires in North America, 1763-1891

Across North America, small Indigenous nations seized the unique legal conditions created by imperial transitions to defend territory as state-sanctioned property. The 1763 Treaty of Paris, the 1803 Louisiana Purchase, and the 1848 Treaty of Guadalupe Hidalgo transferred sovereignty from French, Spanish, and Mexican regimes that incorporated forms of indigenous landholding to British and U.S. regimes that sought to exclude them. Yet these treaties also required new administrations to uphold pre-existing property in newly acquired territories. Through three case studies—Abenakis and Sokokis in British Quebec after 1763, Tunicas and Chitimachas in American Louisiana after 1803, and Tongva and Tataviam peoples in U.S. California after 1848—this dissertation demonstrates how small Native polities used settler property processes not only to protect portions of their territories, but to insist on their on-going existence as political communities. Chapter One explores the contested and flexible bureaucratic processes of land tenure transition after imperial cessions. Chapters Two, Three and Four present case studies detailing the efforts of Native peoples in Quebec, Louisiana, and California to exploit these transitional legal structures. Chapter Five explores how Indigenous proprietors inscribed their territories onto official state maps in surprisingly complex and ambivalent ways./nThis dissertation makes three major interventions. First, by focusing on small polities, rather than the large Native nations that dominate eighteenth and nineteenth-century historiography, it offers an alternative to familiar narratives of military conquest, land cession treaties, and reservation confinement. Small polities often faced erasure and benign neglect instead of targeted colonialism. They transformed settler legal processes into the diplomatic channels they lacked to defend land and articulate political authority. Second, it reconceptualizes the development of territorial state sovereignty in North America as a process of accommodation and negotiation, in which multiple imperial legal regimes continued to play unpredictable roles long after geographic borderlands disappeared. Third and finally, it casts property ownership itself as a malleable and diffuse set of practices across the eighteenth and nineteenth centuries. Rather than a self-evident and stable legal entity, property was a highly local and deeply social set of negotiations. During imperial transitions, it was contested, exploited, and ultimately transformed by Indigenous peoples.

Advisor: DeLay, Brian
The Critical Tradition of Byzantine Botanical Illustration in the Alphabetical Dioscorides

This dissertation recovers the history of Byzantine botanical illustration in the Alphabetical Dioscorides from its origins in the Hellenistic Period to its integration with early modern botanical illustration in the fifteenth century. Chapter 1 examines Pliny the Elder’s Naturalis/nhistoria to establish how botanical illustration differed from descriptions and specimens as a way to create visual knowledge. It also connects the emergence of botanical illustration to Hellenistic rulers' study of botany. Chapter 2 delineates the different ways ancient botanical illustrations selectively depict plants. Chapter 3 assesses the relationship between illustration and text copying, in order to show how the makers of early illustrated herbals ensured and even emphasized the transmission of visual knowledge. Chapter 4 reconstructs Middle Byzantine (ca. 843-1204 CE) modes of botanical inquiry through a close study of the Morgan Dioscorides (New York, Morgan Library, MS M 652). It demonstrates the critical and innovative dimensions of the Byzantine botanical illustration, including the comparison and compilation of earlier pictures and the ex novo illustration of plants through direct observation of nature. Chapter 5 considers the continuation of this critical tradition and how it disseminated in the wider Mediterranean world in the Late Byzantine period (1204-1453 CE). Chapter 6 finally outlines contemporaries' shifting attitudes towards botanical illustration through close study of the frontispieces of the Vienna Dioscorides (Vienna, Österreichische Nationalbibliothek, med. gr. 1)./nThis study upsets the common scholarly view that Byzantine art and science were unconcerned with observation of the natural world. Botanical illustrations played a central role in the Byzantine botanical tradition by enabling the creation of visual knowledge. The study further characterizes Byzantine contemporaries' approaches to botanical study through the priorities expressed in their depictions of the natural world. Although researchers have routinely typified Byzantine art by its lack of natural forms and its artists’ seeming unwillingness to depict the natural world through direct observation, evidence for detailed, “from life” depictions of plants in botanical manuscripts shows that Byzantine artists were capable of looking to nature. Byzantine conceptions of the natural world were not based on received classical texts and images, but also in direct experience of the natural environments within which Byzantine people worked and lived.

Advisor: Angelova, Diliana
Fricke, Beate
Listening Through and Against Ma’lūf: Place, Power, and Practice in Post-2011 Tunisia

Ma’lūf – Tunisian music of Arab-Andalusian origin – has been emblematic of the emerging nation since 1930s, but today many Tunisians can hardly afford the cost of attending a performance. In the fallout of Tunisia’s second revolution (2011-), I ask: to whom does ma’lūf still sound “familiar?” Whereas previous music research in Tunisia has focused on modernization and nationalism, anxiety over loss of tradition, and expert musical masters, I theorize ma’lūf listening practices – and the acoustemologies (“acoustic epistemologies”) that frame them – as a contested site for State and social elite control (which I term “listening through”) and for acts of critique, reclamation, and inclusion (i.e., “listening against”)./nFurthering initiatives of my Tunisian interlocutors, I re-situate ma’lūf as part of the “Andalusī way of life,” by studying listening (1) as historically-informed, learned socio-cultural practices, (2) as emplaced within built environments, (3) as richly inter- and multi-sensory embodied experiences, and (4) as enmeshed in dynamic political and ethical discourses. In these regards, my effort is a post-colonial and post-authoritarian (post-2011) intervention that recognizes Tunisians’ recent re-centering of sound knowledge and cultural reclamation and renewal, especially among younger generations, amateur music enthusiasts, and musicians who operate outside of institutional spheres or outside of the capital city. Amid complex power struggles in a locale defined for millennia as a crossroads of cultural contact, I investigate the mapping of “affective orientations” onto geographic places and identity categories. Ultimately, this dissertation argues that music listening plays a significant role in the structuring and disruption of social class and hegemonies of cultural normativity.

Advisor: Brinner, Benjamin
Equatorial Magnetic Waves in the Stratified Ocean of Earth's Core

Earth’s global magnetic field envelops us all, protecting us from cosmic rays, aiding our navigation, and shielding our oxygen-rich atmosphere. Yet details about its origin, operation, and future remain unknown. Recent space-based magnetic observatories let us observe the field more precisely than ever before, and we can use these measurements to study the deep interior of the Earth and illuminate a region of our planet previously observed mainly by listening to the echoes of earthquakes. In this thesis, I use observations of changes in Earth’s magnetic field to study the structure and processes occurring near the top of Earth’s core. In particular, I examine the long-debated question of whether a stratified layer of fluid, termed by some as the stratified ocean of the core or SOC (Braginsky, 1998), lies at the top of Earth’s outer core. I first implement a model to simulate fluid motions in the SOC, which I describe in chapter two. Then, I derive the properties of a class of eastward-propagating equatorially trapped magnetic waves I term eMAC waves in chapter three and develop a statistical threshold to detect these waves in chapter four. In chapter five, I apply my statistical test to observations of Earth’s geomagnetic field and find evidence for these waves in Earth’s core. Finally, in chapter six, I propose a 20-40 km thick SOC with buoyancy strength of N ≥ 10 Ω to support the observed eMAC wave modes. I then discuss the implications of this layer, propose a double-layer SOC as a way to reconcile eMAC signals with previous observations, and enumerate possible future avenues of investigation.

Advisor: Buffett, Bruce
Development of bioluminescent sensors for interrogating cyclic di-nucleotide signaling

Bioluminescence is the spectacular natural phenomenon in which living organisms produce and emit light. Natural bioluminescent protein systems have been discovered and characterized in over 30 species, ranging from fireflies to fungi and bacteria. Significant effort has been put towards engineering and improving these natural systems so that they may be used as tools for interrogating biological processes. As opposed to fluorescence, because bioluminescence requires no excitation light to produce a signal, it has proven extremely useful for imaging in highly autofluorescent samples, such as within deep tissues of whole organisms. To date, however, most bioluminescent imaging systems have been developed solely for the study of eukaryotic systems, and few have focused on the study of bacteria. Bacteria naturally colonize highly diverse and complex environments, from gastrointestinal tracts to soil and plant surfaces, that have proven difficult to study with currently available fluorescent tools. To allow for the study of bacterial signaling within these complex environments, new bioluminescent sensors developed specifically for bacterial signaling are needed./nHere, we describe the development and application of bioluminescent sensors for the bacterial cyclic di-nucleotide (CDN) signaling molecule cyclic di-GMP. Cyclic di-GMP is nearly ubiquitous in bacteria and plays a key role in the controlling motility and biofilm formation. As a first-generation bioluminescent sensor system, we developed intensity-based bioluminescent sensors for cyclic di-GMP. These sensors proved useful as in vitro tools for studying cyclic di-GMP, however were not amenable to live cell imaging. To move beyond purely in vitro systems, we developed next-generation ratiometric bioluminescent sensors for cyclic di-GMP. This next-generation system led to significantly improved sensor properties and allowed for the imaging of small numbers of live bacterial cells in an animal tissue-like model system. Finally, to expand these sensor systems to CDNs other than cyclic di-GMP, we applied a novel directed evolution approach to find sensors that respond to cyclic GMP-AMP. The first round of directed evolution was not successful, but work is ongoing on this front. Collectively, the work presented here lays the groundwork for using bioluminescent sensor systems to interrogate signaling in bacteria in their natural environments, which was previously not possible.

Advisor: Hammond, Ming C
Francis, Matthew B
Ultrafast Dynamics in Condensed Matter Studied with Attosecond Extreme Ultraviolet Transient Reflectivity

The advent of attosecond pulse duration light sources has enabled the study of fundamental light-matter interactions. Condensed matter systems are of particular interest, as they are often significantly impacted by many body interactions, and thus provide a natural environment for the observation and study of such interactions in the time domain. In this dissertation, an apparatus for extreme ultraviolet (XUV) transient reflectivity is described, and several studies on ultrafast dynamics in solids are performed. In the first chapter, background on ultrafast spectroscopy, light matter interaction, and reflection from surfaces is provided, giving the necessary underpinnings for the subsequent discussion. In the second chapter, the development and capabilities of the constructed XUV transient reflection apparatus are reviewed. Additionally, the static refractive index of germanium (a commonly employed semiconductor), is recovered from multi angle reflection measurements. In the third chapter, femtosecond dynamics in germanium are studied by XUV transient reflection. The results are analyzed and interpreted in the context of the existing optical literature. In the fourth chapter, preliminary attosecond resolved measurements in germanium are presented, and the results are tentatively interpreted in the context of light dressed states. In the fifth chapter, attosecond dynamics of core excitons in magnesium oxide (MgO) are studied. The results are analyzed and interpreted as a light induced modification of excitonic coherence. This body of work is intended to establish XUV transient reflectivity as a technique for study of solid-state systems and to provide example studies in two representative systems, a semiconductor and an insulator.

Advisor: Leone, Stephen R
Neumark, Daniel M