VictorJuiz/thesis huggingface dataset:
Up in the Sound: Form and Voice in Jazz and Post-War American Poetry

In this study, I build a case for redrawing the conceptual lines of American post-war poetry and music. My overall argument is that the post-war American and African American poets who engaged with jazz most profoundly were those who heard the music not simply as a set of sounds, but as an ongoing argument about the nature of aesthetic form. These poets responded to the conceptual innovations of jazz by thinking in new ways about the body, and about how a body of sound could relate to the body of the poet. In setting lyric's material limits against its trans-medial aspirations, I show, jazz empowered poets to rethink the very nature of poetic activity, and in turn to construct a powerful new model of race-inflected aesthetics./nThe dissertation is divided into two sections, each of which pairs music and poetry to outline a larger historical or theoretical argument. In this it leverages the many years I have spent as a practicing jazz musician. In the first section, I use musicological analysis to develop a new account of jazz-inspired lyric based in Charlie Parker's approach to musical narrative. What Parker's music offers, I argue in Chapter One, is not only a set of imitable sounds, but an improvisational organization of those sounds that resists their being heard as "telling a story," and instead turns musical form into a multi-layered, dialectical phenomenon. In Chapter Two, I use Langston Hughes' 1951 sequence Montage of a Dream Deferred and the poetry and poetics of Charles Olson to establish the poetic resonances of this account, articulating a theory of poetic musicality in which poetry's music becomes a matter less of how a poem sounds than how effectively it translates the structure of hermeneutic opacity that Parker's solos put in place. In the second section, the music of Miles Davis' mid-60's band anchors my excavation of a powerful but overlooked model of (African) American avant-garde performance. Davis' key aesthetic move, I argue, is to play sensuous presence against intellectual reception, so oversaturating notes and rhythms with potential meaning that pinning any of them down to a single implication becomes constitutively impossible. Chapter Four pairs Langston Hughes' 1961 poem Ask Your Mama with the work of Robert Creeley to push this aesthetic into the realm of language, detailing a theory of poetic representation in which language's inherent falsehoods forge identity as a permanently dispersed condition. The dissertation's final chapter extends this model in the work of two contemporary poets, Harryette Mullen and Ed Roberson, who unsettle traditional aesthetics of "blackness" by teasing apart the multiple sensory registers upon which the concept usually rests.

Advisor: Silverman, Kaja
Pervasive Health Monitoring

Pervasive health monitoring is the application of non-invasive ambulatory monitoring technologies towards continuous physiologic monitoring. These technologies can be used for the detection of sudden, acute, health problems and the management of chronic disease. For people at risk for specific incidents, such as a heart attack in an individual with heart disease or a fall from an elderly individual, being able to detect a potentially life threatening incident and alerting a care provider can mean the difference between life and death. Likewise, individuals who have chronic health conditions, such as congestive heart failure, can benefit from tracking the progress of their disease. Feedback provided from an ambulatory monitor can be used to help manage the treatment of the disease with the goal of keeping the individual out of the hospital. Currently, people wait until a health problem manifests itself in a way which necessitates a visit to a doctor or a hospital. This type of management is the antithesis of early detection. Often, many conditions have simpler, more effective, and less costly treatments if detected and diagnosed at an early stage. Not only does this result in a better quality of life, but can help to by reducing the costs to the healthcare system. In 2010, U.S. healthcare costs were $2.6 trillion, and it is expected to grow to an incredible $4.6 trillion by 2020./nIn order to enable a wide range of pervasive monitoring applications, a highly integrated ambulatory physiologic monitor was developed and used in a number of studies. The hardware platform is called The Berkeley Tricorder, and is capable of acquiring a high resolution data from a number of physiologic sensors including an electrocardiograph, an electromyography, a photoplethysmograph, a bioimpedance spectrometer, and an accelerometer. In addition, The Berkeley Tricorder is capable of storing data on an SD memory card, or transmitting it wirelessly over Bluetooth to a local target, or to a remote target using the dial-up-networking Bluetooth profile and a mobile phone. The latest version of the hardware measures 1.4"x1.85"./nThe first chapter explores a number of acute and chronic health conditions to better understand which physiologic monitors are of the most value in an ambulatory system. Next, the physiologic basis of the biosignals are examined, along with the technology which enables their measurement. Based on the methodology used to measure the biosignals, a detailed set of requirements for the implementation of the ambulatory monitor is derived. The requirements are then translated into a physical implementation along with a set of lessons learned along the way. The hardware is then examined to see how it compares to the original design and to quantify its signal quality. Finally, a study used to explore the physiology of stress is using the ambulatory monitor is discussed.

Advisor: Canny, John F
Negative feedback confers mutational robustness in yeast transcription factor regulation

Organismal fitness depends on the ability of gene networks to function robustly in the face of environmental and genetic perturbations. Understanding the mechanisms of this stability is one of the key aims of modern systems biology. Dissecting the basis of robustness to mutation has proven a particular challenge, with most experimental models relying on artificial DNA sequence variants engineered in the laboratory. In this work, we hypothesized that negative regulatory feedback could stabilize gene expression against the disruptions that arise from natural genetic variation. We screened yeast transcription factors for feedback, and used the results to establish the hypoxia regulator Rox1 as a model system for the study of feedback in circuit behaviors and its impact across genetically heterogeneous populations. Mutagenesis experiments revealed the mechanism of Rox1 as a direct transcriptional repressor at its own gene, enabling a regulatory program of rapid induction during environmental change that reached a plateau of moderate steady-­‐state expression. Additionally, in a given environmental condition, Rox1 levels varied widely across genetically distinct strains; the ROX1 feedback loop regulated this variation, as the range of expression levels across genetic backgrounds showed greater spread in ROX1 feedback mutants than among strains with the ROX1 feedback loop intact. Our findings indicate that the ROX1 feedback circuit is tuned to respond to perturbations arising from natural genetic variation, in addition to its role in induction behavior. We suggest that regulatory feedback may be an important element of the network architectures that confer mutational robustness across biology.

Advisor: Brem, Rachel
Intellectual Property and Academic Science

Academia's usage of intellectual property (IP) has occasioned passionate debates on both sides. Supporters argue that it speeds the transfer of scientific discoveries to the private sector, and have advocated policies such as the Bayh-Dole Act to promote it. Detractors worry about the collision between the norms of science and the norms of commerce. They fear that the exclusionary rights of patents and licenses may fence off areas of research, making the costs to science outweigh the benefits from increased technology transfer. This dissertation addresses this empirically by testing whether the issuance of a license increases or decreases the flow of knowledge on that discovery, using citations to the focal publication(s) as a measure of knowledge flows./nIn order to address this question, this dissertation first develops two intermediate results. The first is a primer on material transfer agreements which shows that they can be used as a proxy for research tools - an area where the conflict between scientific and commercial norms may be more significant. The second is to show that inventor-based matching, a new, automated methodology for matching intellectual property to its underlying scientific publication(s), can be used to construct a large dataset for this analysis./nUsing these intermediate results and a non-parametric method for building a convincing control group, this dissertation finds two important results. First, it finds that, for most discoveries, licensing increases the flow of knowledge on that discovery. This is consistent with the license providing a positive signal about the discovery that benefits the underlying science. In contrast, this paper also finds that for research tools, licensing decreases the flow of knowledge on that discovery. This may indicate that licensed materials are being shared less widely amongst scientists, raising concerns about science progressing more slowly in these areas.

Advisor: Mowery, David C
From lab to life: Concordance between laboratory and caregiver assessment of emotion in dementia

In recent years, laboratory methodologies for assessing emotional functioning have been applied to the study of dementia. These in-laboratory assessments have provided a number of insights into domains of loss, as well as preservation, of emotional functioning for different neurological illnesses. However, such laboratory tests of emotion have yet to be compared to measures assessing dementia patients' daily emotional lives. In clinical practice, family and spousal caregivers are often called upon to provide this real-world perspective. The current study tested concordance between a laboratory assessment of emotional functioning in dementia with the perspective of caregivers and informants on patients' and controls' emotion in daily life. Specifically, two domains of emotional functioning -- emotional reactivity and empathic accuracy -- were assessed for three emotion types -- negative, positive, and self-conscious emotion -- in patients diagnosed with a neurodegenerative illness, as well as in neurologically healthy controls. Patients' and controls' emotional functioning was assessed two ways: in the laboratory, using dynamic audiovisual stimuli, and via questionnaire, completed by informants (i.e., caregivers of dementia patients and family members of controls, reporting on patients' or controls' emotional functioning, respectively). The laboratory tasks measured reactivity through participants' physiological arousal, facial behavior, and self-reported experience to emotion-eliciting films; empathic accuracy was measured via participants' correct identification of target emotions expressed by characters in a second set of films. Participants' performance on the laboratory tasks was used to predict the ratings their informants made on the questionnaire for each emotion category. To account for possible bias in informant report due to the effects of caregiver burden, analyses controlled for informants' levels of depression and anxiety symptoms./nResults indicated that overall, laboratory assessments of emotional reactivity and empathic accuracy were in accord with informant-reported emotional functioning. Specific analyses of each emotion type, however, indicated that participants' self-conscious reactivity in the laboratory was not in concordance with their self-conscious reactivity according to informants. The findings indicate that, broadly speaking, an assessment of emotional functioning conducted in a laboratory using dynamic measures, and the report of caregivers on dementia patients' emotion in daily life, are each tracking the same constructs: ostensibly, representing the true emotional experiences and empathic understanding of dementia patients. However, these results also raise questions concerning the measurement of self-conscious reactivity. This work has important implications in refining the assessment of emotional functioning in clinical settings through the use of more comprehensive tools to systematically capture emotional changes in dementia.

Advisor: Levenson, Robert W
(Dis)Claiming Mestizofilia: Chicana/os Disarticulating Euromestizaje

This dissertation investigates the development and contradictions of the discourse of mestizaje in its key Mexican ideologues and its revision by Mexican American or Chicana/o intellectuals. Great attention is given to tracing Mexico's dominant conceptions of racial mixing, from Spanish colonization to Mexico's post-Revolutionary period. Although mestizaje continues to be a constant point of reference in U.S. Latino/a discourse, not enough attention has been given to how this ideology has been complicit with white supremacy and the exclusion of indigenous people./nMestizofilia, the dominant mestizaje ideology formulated by white and mestizo elites after Mexico's independence, proposed that racial mixing could be used as a way to "whiten" and homogenize the Mexican population, two characteristics deemed necessary for the creation of a strong national identity conducive to national progress. Mexican intellectuals like Vicente Riva Palacio, Andrés Molina Enríquez, José Vasconcelos and Manuel Gamio proposed the remaking of the Mexican population through state sponsored European immigration, racial mixing for indigenous people, and the implementation of public education as a way to assimilate the population into European culture. I argue that although Mexican Americans inherited this Eurocentric formulation of mestizaje, by the mid-1960s their specific social position as a negatively racialized and economically exploited population in the United States allowed self-identified Chicana/o activists and intellectuals to depart significantly from, and in some cases, clearly critique inherited Eurocentric conceptions of racial mixing and racist views of indigenous people./nChicano/a discourse of mestizaje and indigeneity is not an uncritical reproduction of dominant Mexican mestizofilia and indigenismo, it is a collective, and sometimes deeply personal, exploration of mixed race ancestry that sought to recuperate, and in some cases, center the indigenous. Chicano/as' historical and practical context made some of their claims to indigeneity, including those dealing with spirituality, not only oppositional, but also decolonizing. Through an interdisciplinary approach grounded in Chicano/a studies, this study critically examines a broad array of texts by Mexican and Chicana/o intellectuals, including political speeches, historical texts, and literature.

Advisor: Pérez, Laura E
Advances in Zero-Field Nuclear Magnetic Resonance Spectroscopy

In the course of the last century, Nuclear magnetic resonance (NMR) has become a powerful and ubiquitous analytical tool for the determination of molecular identity, structure, and function. Traditionally, the great analytical power of NMR comes at the cost of mobility and large expenses for cryogenic cooling. This thesis presents how zero-field NMR detected with an atomic magnetometer is emerging as a new, potentially portable and cost-effective modality of NMR with the ability of providing information-rich and high-resolution spectra. A detailed description of the zero-field NMR spectrometer and its operation is provided. The thesis details how the acquired zero-field NMR spectra result from the electron mediated scalar interaction (J-coupling) of nuclear spins in an analyte. Simple rules of addition of angular momenta are introduced for the prediction of the observed spectral lines overcoming the need for numerical simulations and enabling unambiguous assignment of peaks to different molecules. Additional information can be obtained in the near zero field regime, where the Zeeman interaction can be treated as a perturbation to the J-coupling. The presence of small magnetic fields results in splitting of the zero-field NMR lines, imparting additional information to the pure zero-field spectra. In addition to the utilization of the atomic magnetometers for enhanced sensitivity, hyperpolarization schemes can be implemented. This thesis shows that chemically specific zero-field NMR spectra can be recorded using hydrogenative and non-hydrogenative parahydrogen induced polarization (PHIP, NH-PHIP), enabling high-resolution NMR. The increased sensitivity enables detection of compounds with 13C or 15N in natural abundance. Since PHIP and NH-PHIP operate in situ, and eliminate the need for a prepolarizing magnet, they broaden the analytical capabilities of zero-field NMR. Lastly, this thesis gives insight into the PHIP and NH-PHIP mechanism by developing an appropriate theoretical framework.

Advisor: Pines, Alexander
Intratidal Transport and Mixing Processes at the Shoal-Channel Interface in a Partially-Stratified Estuary

This work addresses transport and mixing processes at work during each tide across the shoal-channel interface. These are fundamental to long-term, large-scale, salt, sediment and biomass budgets yet remain poorly characterized and understood. Most of the analyses presented here are based on field observations collected in South San Francisco Bay, CA, during winter 2009./nHorizontal transport across the interface is governed by the transverse flow, which is predominantly characterized by the presence of one or two lateral circulation cells. This study reveals that these circulation cells can evolve more rapidly than previously thought, reversing multiple times during a single ebb tide. The formation of convergence fronts is found to be sensitive to the direction of the lateral circulation and is therefore marked by a similar intratidal variability. It is hypothesized that these intratidal variations are the result of competing lateral density gradients which are the main forcing mechanism for transverse flows. The outcome of this competition depends strongly on vertical mixing conditions on the slope./nVertical mixing on the slope is driven for the most part by turbulence generated in the bottom boundary layer, except for occasional late-ebb bursts generated by internal vertical shears. These internal shears result from the destabilizing straining of lateral shear by the lateral circulation which overcomes in this case the stabilizing straining of lateral density gradients./nHorizontal mixing across the interface is quantified indirectly and is found to be driven mostly by lateral shear instabilities, but is also affected by lateral dynamics. As a result, transverse mixing also displays significant intratidal variability. This result poses a challenge to existing parametrization developed for steady shear layers.

Advisor: Stacey, Mark T
Two probabilistic models of competition

In this thesis we introduce and study two probabilistic models of competition and their applications. The first model is a particular contact process, and is intended to simulate propagation dynamics in real social networks. The second one stems from game theory and is of more theoretical value, as it is used to prove the existence of solutions to a certain non-linear partial differential equation./nThe first model consists of two competing first passage percolation processes started from uniformly chosen subsets of a random regular graph on N vertices. The processes are allowed to spread with different rates, start from vertex subsets of different sizes or at different times. We obtain tight results regarding the sizes of the vertex sets occupied by each process, showing that in the generic situation one process will occupy Theta(1)N^α vertices, for some 0 < α < 1. The value of α is calculated in terms of the relative rates of the processes, as well as the sizes of the initial vertex sets and the possible time advantage of one process./nThe second model is a version of the stochastic "Tug-of-War" game, played on graphs and smooth domains, with the empty set of terminal states. We prove that, when the running payoff function is shifted by an appropriate constant, the values of the game after n steps converge in the continuous case and the case of finite graphs with loops. Using this we prove the existence of solutions to the infinity Laplace equation with vanishing Neumann boundary condition.

Advisor: Chatterjee, Sourav
Peres, Yuval
Dissecting neuronal specification in the Drosophila taste system

Establishing a complex brain and nervous system requires a wide array of neurons with diverse forms, functions, and characteristics. Developing nervous systems employ many strategies to create this neuronal diversity, and these strategies remain the subject of ongoing investigations in developmental neuroscience./nNeuronal diversity in the taste system of Drosophila melanogaster is important for the appropriate detection of chemosensory signals in the fly's environment. Drosophila can distinguish sweet substances, bitter compounds, pheromones, and pure water using distinct populations of taste neurons. The correct detection of such substances is critical for correct ingestion of nutritive foods, avoidance of toxins, recognition of appropriate mates, and hydration, all of which are essential for the survival and propagation of the fly. The first part of this thesis focuses on the developmental relationship between these classes of neurons and the signaling pathways used to diversify them. Mosaic analysis revealed at least two stereotyped lineages for taste neurons innervating bristles on the proboscis of the fly. Furthermore, mutant mosaic studies showed that Numb inheritance or lack thereof is necessary for correct cell fate decisions. The involvement of Numb strongly indicates that Notch signaling is the key player in establishing taste neuron diversity./nThe second part of this thesis describes an expression screen for transcription factors with specific expression patterns in subsets of taste neurons. The transcription factors activated in each cell type ultimately establish that cell's unique identity by activating expression of appropriate receptors, axon guidance cues, neurotransmitters, and more. The screen identified two transcription factors, knot and Lim3, with specific expression in bitter-sensing neurons. Results of loss-of-function and gain-of-function studies with each gene indicate that neither one alone is necessary or sufficient to specify the full bitter neuron fate, but it remains possible that each could play a role in subsets of the bitter neuron's identity not observed by these analyses.

Advisor: Scott, Kristin
Computational and Experimental Investigations of the Principles of Eukaryotic Transcriptional Regulation Before, During, and After Open Complex Formation

In this work, I describe my doctoral work studying the regulation of transcription with both computational and experimental methods before, during, and after recruitment of RNA Polymerase II and the formation of the open complex at gene promoters. This works spans investigation of the combinatorial binding of sequence specific distal enhancer binding proteins in the developing fly embryo the role of the yeast AAA-ATPase YTA7 in reorganizing the nucleosome positioning at the highly transcribed loci, and the role of the AFF scaffold-associated members of the human super elongation complex.

Advisor: Eisen, Michael B