VictorJuiz/thesis huggingface dataset:
Design of Low Profile, Modular Lower Extremity Exoskeletons

Studies have shown that walking for as little as 30 minutes of a day can improve overall health. However, more than 250,000 people in the United States are paralyzed due to spinal cord injuries (SCI), and can no longer walk without support. Most of the SCI patients rely on wheelchairs after their injuries, and suffer from secondary injuries caused by prolonged sitting. Moreover, the patients' reduced mobility often brings negative effects to their independence and social life./nThe primary research objective is to develop practical and effective exoskeleton technology that enables paralyzed individuals to achieve mobility and gain independence in their daily lives. In this dissertation, I discuss designs of low profile and modular exoskeletons, with an emphasis on different design attributes that increase device usability./nA minimally-actuated medical exoskeleton was developed with powered hip joints and passive knee joints. The low profile actuation units used for this exoskeleton's hip actuation allowed the wearer to achieve propulsion and walk through narrow passageways. In fact, this exoskeleton became the first powered medical exoskeleton that weighs less than twenty pounds. This exoskeleton continued to evolve into a system with increased modularity that meets various user needs based on different physical conditions. The modular design allows easy customization via its versatile support level configurations for different individuals. As a part of this research, comprehensive user studies of these devices and the user interface were conducted to create a positive user experience and a comfortable link between the user and the exoskeleton./nParalyzed patients who participated in this study corroborated that the compact and lightweight design of the system enhances their mobility and maneuverability. The modularity in design opens assistive opportunities to various people, such as the elderly and other people with intact mobility. I expect that assistive exoskeleton technology will continue to advance and enhance the quality of life for a wide spectrum of communities in our aging society.

Advisor: KAZEROONI, HOMAYOON
Exact tensor network ansatz for strongly interacting systems

It appears that the tensor network ansatz, while not quite complete, is an efficient coordinate system for the tiny subset of a many-body Hilbert space which can be realized as a low energy state of a local Hamiltonian./nHowever, we don't fully understand precisely which phases are captured by the tensor network ansatz, how to compute their physical observables (even numerically), or how to compute a tensor network representation for a ground state given a microscopic Hamiltonian. These questions are algorithmic in nature, but their resolution is intimately related to understanding the nature of quantum entanglement in many-body systems./nFor this reason it is useful to compute the tensor network representation of various `model' wavefunctions representative of different phases of matter; this allows us to understand how the entanglement properties of each phase are expressed in the tensor network ansatz, and can serve as test cases for algorithm development./nCondensed matter physics has many illuminating model wavefunctions, such as Laughlin's celebrated wave function for the fractional quantum Hall effect, the Bardeen-Cooper-Schrieffer wave function for superconductivity, and Anderson's resonating valence bond ansatz for spin liquids./nThis thesis presents some results on exact tensor network representations of these model wavefunctions./nIn addition, a tensor network representation is given for the time evolution operator of a long-range one-dimensional Hamiltonian, which allows one to numerically simulate the time evolution of power-law interacting spin chains as well as two-dimensional strips and cylinders.

Advisor: Moore, Joel E
Mechanisms underlying spontaneous glutamatergic activity in developing mouse retina

Throughout the developing nervous system, spontaneous oscillatory patterns of activity have been observed. The developing murine retina is no exception, where spontaneous activity manifests as spatially correlated waves of depolarizations. These retinal waves propagate between neighboring neurons within retinal layers during the two postnatal weeks just prior to eye-opening and development of the light response. Waves are necessary for the normal patterning of connections of the retinal projections to their primary targets in the brain, indicating they contribute to a general self-organizing principal of neural development./nThere are three distinct circuits that mediate these waves at different developmental stages: gap junction mediated waves that occur around birth, acetylcholine-receptor mediated that occur during the first postnatal week, and glutamate-receptor mediated that occur between postnatal day 10 (P10) and P13. At this age, retinal circuitry appears adult-like such that excitatory synapses connect neurons across layers but inhibitory synapses connect neurons within layers. Thus it remains a mystery as to how depolarization propagates between neighboring within-layer neurons during waves./nThis dissertation addresses the cellular and synaptic basis underlying the initiation and propagation of glutamatergic retinal waves. Using a combination of multielectrode array recording and two-photon calcium imaging, I identified a role for electrical coupling, diffuse release of glutamate, and inhibitory circuits in the retinal wave generation. In addition, I studied the role of endogenous copper in modulating retinal waves. This research represents a near-complete description of the intraretinal circuits that underlie the spatial and temporal properties of glutamatergic retinal waves.

Advisor: Feller, Marla B
Substantive Truth and Knowledge of Meaning

Deflationists have been hard at work convincing us that the concept of truth is far less interesting, and therefore far less mysterious, than long-lasting debates as to its true nature have made it seem. By denying that there is a substantive notion of truth expressed by our uses of the word `true,' deflationism promises to dissolve a number of explanatory hurdles./nDonald Davidson rejected deflationism. He grew increasingly sceptical of attempts to assimilate our understanding of truth to any definition or schema, and came to see his own approach to meaning as crucially dependent on a substantive notion of truth./nExactly how, and where, does Davidson's approach to meaning depend on the availability of a substantive notion of truth? One of my goals is to answer this question. Another is to explain why it has proved so hard to answer it. A third goal is to bring to light what it would really be like to be a deflationist--in particular, what linguistic competence would look like if we took deflationism seriously./nIn Chapter 1, I clarify Davidson's proposal to use truth theories as meaning theories. I explain this proposal as rooted in a certain conception of a meaning theory as an account of a speaker's understanding of her own sentences, and of this understanding as at least partly consisting in the speaker's knowledge of the truth-conditions of her sentences. In Chapter 2, I argue that deflationism does not allow us to describe competent speakers as knowing the truth-conditions of their sentences. If this is right, deflationism is incompatible with Davidson's conception of truth theories as theories of linguistic competence, but not for the reason usually given. That is, it is not because deflationism explains knowledge of truth-conditions as a trivial by-product of linguistic competence rather than being constitutive of it, since deflationism does not even allow us to ascribe such knowledge to speakers./nIn Chapter 3, I argue against the widespread assumption that Davidson's proposal concerning the form to be taken by a meaning theory is primarily an answer to the question: what knowledge would enable us to interpret any utterance in a given language? This assumption underlies recent attempts to exhibit Davidson's approach to meaning as hospitable to a deflationary account of truth. However, as I explain, it undermines the distinction Davidson insists on between meaning theories and translation manuals, and thus cannot be right. Chapter 4 further argues that the methodology of radical interpretation does not, by itself, explain the need for a substantive notion of truth, contrary to what some (including Davidson) have suggested. Finally, in Chapter 5, I highlight some consequences of these results for both our understanding of Davidson's philosophy of language, and our understanding of deflationism.

Advisor: Stroud, Barry
MacFarlane, John
General signaling properties of small noncoding RNAs in Escherichia coli

Bacterial survival depends on the ability of cells to rapidly adapt to diverse environments, stress and pathogenesis. Many of these adaptive pathways involve regulation by small non-coding RNAs (sRNAs) that act in trans by binding to the 5' untranslated region of target mRNAs to form sRNA-target mRNA duplexes that alter mRNA translation and/or degradation. This dissertation examines the regulation of gene expression by sRNAs using synthetic gene circuits in Escherichia coli to understand their regulatory properties and to gain insight into why sRNAs may have evolved as critical regulators of bacterial stress responses./nIn the first chapter, we characterize the regulatory properties of sRNAs in vivo and compare them to that of transcription factors. Specifically, we examine the dose response curves and dynamics of regulating gene expression with sRNAs and transcription factors and find that the primary advantage of sRNAs are that their activity can be rapidly turned off. This can provide an advantage for cells needing to signal and reprogram gene expression rapidly in response to environmental stress. In the second chapter, we examine sRNA regulation in the context of a network controlled by competition for the Hfq protein, which mediates the activity of most sRNAs. The role of Hfq is critical in bacterial stress responses because it allows efficient gene regulation by sRNAs in response to cellular stress including during starvation, and shifts in optimal pH, osmolarity, and temperature. We show that physiological levels of Hfq are low and that this can lead to reduced activity of sRNAs and cross-talk between different sRNAs and target mRNAs due to competition for Hfq. We further show that this competition can be at least partly relieved when the sRNAs and target mRNAs are co-transcribed, which would allow more efficient duplex formation. In the third chapter, we characterized sRNA regulation using the fluorescent in situ hybridization (RNA FISH) technique. We showed that RNA FISH can allow rapid and broad characterization of a large number of sRNA-target mRNA pairs and that thereby provide information (such as the localization, cell-to-cell variation, and intracellular variation of sRNAs and target mRNAs) that cannot be obtained by other techniques. Together, the three chapters provide insight into the roles of sRNAs and their networks during bacterial stress responses, and suggest paths for future exploration.

Advisor: Lim, Han N.
The Death of Myth on Roman Sarcophagi

A perplexing development sweeps over Roman sarcophagi in the middle of the third century: the unexpected Entmythologisierung or "demythologization" of their imagery. These lavishly carved coffins, often sculpted with figural scenes of the most astonishing workmanship, had featured bold mythological characters since the very beginning of their mainstream production in the early second century, when inhumation had replaced cremation as the favored means for disposing of the dead. Evocative testament to Rome's ongoing love affair with classical Greek culture, they derived visual force from their resonance with an artistic tradition centuries old while providing catharsis and consolation to those still living. How then to make sense of this imagery's peculiar withering and subsequent abandonment on later sarcophagi, as mythological narratives were truncated, gods and heroes were excised, and genres featuring no mythic content whatsoever -- such as the late third century's endless procession of sarcophagi featuring bucolic shepherds and studious philosophers -- came to the fore? That it must represent a major shift of some kind in the cultural values of the Late Empire is usually taken for granted, given the central position occupied by sarcophagi in the Roman visual imagination of the third century. But no consensus exists regarding its precise significance; and most explanations proposed for the shift groan and collapse under the weight of other evidence./nThis enigmatic phenomenon -- the extinction of mythological imagery on Roman sarcophagi -- is what this dissertation decisively reframes. For critical traction it turns to both archaeological and textual evidence, examining the altered spatial relationships between house and tomb that came to dominate in the Late Empire. This reveals what was at stake in sarcophagi's demythologization: new demands among the living, manifested across all social registers, for greater proximity to their dead. The dissertation thus integrates recent archaeological findings, social-scientific analysis of religious change, and analysis of hundreds of Roman metropolitan sarcophagi with a humanist's eye for shifts in cultural values as refracted through funerary art. The results will be of interest to Classicists, Archaeologists, and Art Historians as well as scholars of religious history and early Christianity.

Advisor: Hallett, Christopher H.
High Pressure Xenon Detectors for Rare Physics Searches

High pressure xenon gas detectors have the potential to significantly contribute to searches for rare physics processes such as neutrinoless double beta (0νββ) decay and interactions of dark matter with ordinary matter. We summarize the physics and implications of these two phenomena and discuss experimental developments conducted with an electroluminescent high pressure xenon time projection chamber (TPC)./nThe detector was constructed as a prototype for the NEXT experiment - Neutrino Experiment with a Xenon TPC - and was intended to demonstrate an ability to detect electron recoils with an energy resolution sufficient for a strong neutrinoless double beta decay search. Using the low-gain ionization signal amplification process of electroluminescence, we are able to obtain an energy resolution of approximately 1% FWHM in the detection of 662 keV gamma rays. In addition, we demonstrate basic particle tracking capabilities using a silicon photomultiplier-based tracking plane, a technique also relevant to the NEXT approach in searching for 0νββ decay./nTo investigate the possibility of a gaseous xenon dark matter detector, we also characterize the ionization and scintillation signals produced by nuclear recoils in the TPC and compare them to the corresponding signals produced by electron recoils. The nuclear recoils are produced using radioisotope neutron sources. Our measurements demonstrate the ability to discriminate between electron and nuclear recoils using the ratio of ionization to scintillation produced on an event-by-event basis and provide an estimate of the ionization and scintillation yields of nuclear recoils in gaseous xenon./nWe end with a discussion of the physical principles behind another approach to obtaining nearly-intrinsic energy resolution in a noble gas detector. This approach, called negative ion drift, consists of drifting negative ions produced by intentionally introducing impurities into a gaseous medium that capture ionization electrons. These negative ions are then counted individually by detaching and amplifying the electron they carry. We develop a basic formalism in an attempt to understand the ion drift and detachment processes that are critical to the implementation of this technique.

Advisor: Siegrist, James
Electronic and vibrational properties of two-dimensional materials constructed from graphene and molecular components

In the first part of this dissertation, We study the effects of electron-phonon coupling on the electronic properties of two-dimensional graphene-based materials and molecular lattices. We develop a theoretical model of magneto-phonon resonances in graphene under high magnetic fields, for phonons at both Gamma and K points. Multiphonon excitations in molecular lattices are treated within the cumulant expansion, leading to an accurate description of phonon satellite structures in tunneling experiments. The second half of this dissertation deals with the electronic structure of graphene-based materials and two-dimensional electron gases under external long wavelength potential variations. We show how a graphene-like electronic structure can be created in molecular lattices self-assembled on metal surfaces. We show how velocity renormalization, new Dirac points, and band gap openings can occur when modulated electric and magnetic fields are applied to graphene or bilayer graphene.

Advisor: Louie, Steven G
Glycoengineered Antibodies and Fluorogenic Sulfatase Probes

Sulfatases hydrolyze sulfate esters and are critical for regulating the sulfation state of biological systems. The active site of type I sulfatases contains an aldehyde-bearing formylglycine (fGly) residue required for catalytic activity; fGly is installed after the formylglycine-generating enzyme (FGE) recognizes the consensus CxPxR sequence and oxidizes the cysteine to fGly./nOur lab developed an approach to site-selectively modify proteins by installing the CxPxR motif onto proteins. The technique, called the aldehyde tag, involves cloning a variation of the consensus sequence, such as LCTPSR, into genes. Subsequently, fGly is incorporated site-specifically onto proteins of interest following conversion of Cys to fGly by FGE. The introduced aldehyde can then be used for protein modification using aldehyde selective chemistries./nChapter One provides an overview of the aldehyde tag technique and the various technologies advanced by this protein modification method. Chapter Two reports the development of a platform to chemoselectively and site-specifically modify the crystallizable fragment (Fc) of IgG1. The natural Fc N-glycosylation sequon was replaced with a small aldehyde tag. Successful installation of fGly within the structured region required in vitro treatment with M. tuberculosis FGE; this internal aldehyde can then be chemically elaborated with various moieties to produce modified Fcs./nChapter Three describes the synthesis of oxime-linked Fc glycoconjugates. Aldehyde tagged Fc was conjugated to aminooxy N-acetylglucosamine followed by chemoenzymatic transfer of complex glycan oxazolines by a glycosynthase, and the generated oxime-linked glycoconjugates emulate the structure of the natively glycosylated Fc. Fc glycans contribute to the overall structure and modulate Fc receptor binding; however, the Fc domain typically exists as a mixture of different glycoforms. Using this platform, homogeneous Fc glycoforms can be readily produced from numerous glycans to elucidate the role specific glycans have on antibody effector function./nFinally, Chapter Four presents two new fluorogenic sulfatase-activated probes, 3-O-methylfluorescein-sulfate and resorufin-sulfate. Both probes were validated with commercial sulfatases and employed to reveal species-specific sulfatase activity in mycobacterial lysates using a gel-based assay. Sulfatases are genetically conserved across many mycobacterial pathogens; however, their mechanism and function are not fully understood. These enzyme-activated probes can help clarify substrate specificity of sulfatases.

Advisor: Bertozzi, Carolyn R
Mousike and Mythos: The Role of Choral Performance in Later Euripidean Tragedy

This dissertation takes a new approach to the study of Greek theater by examining the dramatic function of mousike (music, song, dance) in the plays of Euripides. Previous scholarship has tended to see the many references to mousike in his later work only in connection with the "New Music" (the changes in musical style, language, and instruments in fifth-century Athens), and to disregard their place within the plays themselves, often deeming especially meta-musical choral odes to be irrelevant to the surrounding drama. In contrast, I explore the dynamics of choreia (choral song and dance) and the sociocultural meanings of different musical images in four plays to show how mousike plays a vital role in directing and complementing the movement of the plot. I demonstrate how Euripides uses traditional as well as new images of mousike, and argue that this combination of musical motifs is essential to an understanding of each play's dramatic structure./nThe dissertation is divided into four studies of individual plays, which span roughly the last fifteen years of Euripides' career. The first chapter focuses on Electra, the earliest extant tragedy to include multiple, extended descriptions of mousike. I argue that choreia both frames our understanding of Electra and has a generative power, anticipating and even enacting pivotal moments of the plot. In Chapter Two I examine how Hecuba and the chorus in Troades create the illusion of an absence of choreia, even while they sing and dance on stage, and liken this to the concept of "embodied absence" within Performance Studies. I also argue that the chorus' proclamation in the first stasimon that they will sing "new songs" refers not only to Euripides' experimentation at this point in his career, but to musical change within the drama itself. Chapter Three explores patterns of mousike and choreia in Helen, showing how the dominance of such imagery in the play's choral odes shapes the audience's understanding of Helen's relationship with the chorus. I suggest that the play's mousike creates an aetiology not only of Helen's cult in Sparta, but also of the Dionysiac performance of the chorus of Athenian citizens in the theater. Chapter Four examines the dynamics of chorality and monody in Iphigenia in Aulis, showing how, through the performance of mousike, the audience's attention is directed away from the panhellenic choreia of the parodos and toward the sacrifice of Iphigenia. I also explore how representations of instrumental mimesis provide a poignantly vivid impression of pastoral calm before the beginning of the Trojan War, and argue for the authenticity of contested lines at the end of the tragedy on the basis of their style of musical performance. Throughout the dissertation, my methodology centers on the idea that a complex interaction between described and performed mousike encourages the audience to see and hear a performance in a particular way--a form of aesthetic suggestion through choreia.

Advisor: Griffith, Mark
Kurke, Leslie