VictorJuiz/thesis huggingface dataset:
Programming Abstractions and Synthesis-Aided Compilation for Emerging Computing Platforms

Today's cutting-edge applications, ranging from wearable devices and embedded medical sensors to high-performance data centers, put new demands on computer architectures. Those demands include more computation capability, a tight power budget, low latency, high throughput, and many more. To meet these requirements, specialized architectures with low energy consumption are becoming more prevalent. Many of these architectures trade off programmability features for gains in energy efficiency and performance. Hence, programmability challenges are inevitable as applications continue to evolve and make new demands on computing architectures./nI propose key principles for improving programmability intended for application writers as well as compiler developers and language designers. First, I address programmability issues by providing a programming model that hides low-level details but sufficiently exposes essential details for application writers to control. Second, to compile and optimize programs, I apply a new compilation methodology based on synthesis. Unlike a classical compiler's transformation, synthesis obtains a correct and optimal solution by searching for an optimal candidate that is semantically equivalent to a specification program. This search helps compilers generate efficient code without deriving a program via a sequence of transformations, which are challenging for compiler developers to design for new unconventional architectures./nIn this thesis, I demonstrate the key principles in three projects: Chlorophyll, a language and compiler for low-power spatial architectures; Floem, a programming system for NIC-accelerated data center applications; and GreenThumb, a framework for building a superoptimizer (an assembly program optimizer based on synthesis).

Advisor: Bodik, Rastislav
Yelick, Katherine
Wearable Medical Sensors Enabled by Printed Bioelectronics and Biophotonics

Wearable medical sensors that can monitor biosignals have the potential to transform healthcare - they encourage healthy living by providing individuals feedback on personal vital signs and enable facile implementation of both in-hospital and in-home health monitoring. To date, fabrication of wearable medical sensors heavily relies on conventional semiconductor vacuum-processing, which is expensive and has limited large-area scalability. Taking advantage of the unique manufacturing capabilities of printed electronics, we can now design wearables that are soft, lightweight, and skin-like. These soft and conformable sensors significantly improve the signal-to-noise ratio (SNR) by establishing high-fidelity sensor-skin interfaces./nThis thesis presents a review of existing literature on flexible and wearable health monitoring devices, discusses different printing techniques for fabricating wearable medical sensors, and highlights two sensing modalities: bioelectronic and biophotonic. For bioelectronic sensing, the design and fabrication of flexible and inkjet-printed gold electrode arrays are demonstrated, which are implemented in a smart bandage for early-detection of pressure ulcers. Also, the efficacy of the electrodes is demonstrated on conformal surfaces and on the skin to record electrocardiography (ECG) and electromyography (EMG) signals. For biophotonic sensing, an all-organic optoelectronic sensor is demonstrated for transmission-mode pulse oximetry, which accurately measures pulse rate and oxygenation. Since transmission-mode pulse oximetry can only be performed at the extremities of the body and requires a pulsatile arterial blood signal - printed, organic, reflection-mode oximeters are reported. The design, sensing methodology, and fabrication of a flexible and printed sensor array composed of organic light-emitting diodes (OLEDs) and organic photodiodes (OPDs) are shown, which senses reflected light from tissue to determine the oxygen saturation. The sensor is implemented to measure oxygen saturation on different parts of the body and to create 2D oxygenation maps of adult forearms under pressure-cuff-induced ischemia. Finally, a key enabling technology for wearables - flexible hybrid electronics (FHE) is presented. The implementation of FHE in an integrated multi-sensor platform is discussed, where soft sensors are interfaced with hard silicon-based integrated circuits for wearable health monitoring.

Advisor: Arias, Ana C
Alternative Tobacco Product Use among Adolescents and Young Adults

There is a changing landscape of tobacco use among adolescents and young adults in the United States. Non-cigarette, alternative tobacco product (ATP) use such as such as electronic cigarettes (e-cigarettes), smokeless tobacco (chewing tobacco, dissolvable or dipping tobacco, moist snuff, and snus), tobacco pipes, cigars (traditional, filtered, and cigarillos or little cigars), and hookah (water pipes) has increased in the past decade among AYAs. This changing tobacco landscape threatens decades of public health campaigns and gains in tobacco control dedicated to denomormilize smoking and lowering rates of tobacco use. Research shows positive relationships among marketing receptivity through ownership of tobacco promotional items, tobacco retail environment, and risk and benefit perceptions with cigarette use among adults. Limited studies have assessed these relationships with ATP use among adolescents and young adults./nThis dissertation aims to illustrate the relationships between marketing receptivity and ATP initiation, identify a hierarchical relationship between individual-level, neighborhood-level, and school-level covariates and ATP initiation; and assess the relationship between risk and benefit perceptions with cigarette or ATP switching. These aims were examined using a prospective longitudinal cohort study of adolescents and young adults from California designed to assess adolescents’ use and perceptions of a variety of tobacco products. This dissertation further analyzes data from this longitudinal cohort, linked with the Census Bureau’s American Community Survey, the state retailer-licensing database maintained by California’s Board of Equalization, and school-level data from the California Department of Education./nThese findings suggest marketing receptivity, tobacco retail environment, and risk and benefit perceptions may predict individual ATP use among adolescents and young adults. Results of this dissertation indicate adolescents and young adults with increased marketing receptivity, who reside in neighborhoods with increased retail access to ATPs, and who have lower ATP risk perceptions and greater benefit perceptions exhibit greater ATP initiation, product switching, and use over time. These findings may help inform the Food and Drug Administration’s regulations of new and emerging tobacco products by regulating marketing efforts, informing health campaigns, and regulating the tobacco retail environment.

Advisor: Bradshaw, Patrick T
THE MECHANICS OF DYNEIN STEPPING AND DIRECTIONALITY

The ability of cytoskeletal motors to move unidirectionally along linear tracks is central to their cellular roles. While kinesin and myosin motor families have members that move in opposite directions, all dyneins studied to date exclusively move towards the microtubule minus-end. The source of dynein’s directionality remains as the central unresolved question about the mechanism of its motility. In my doctoral work, I focused on understanding the underlying mechanism of dynein’s directional motility along the microtubules in three dimensions. I used a protein engineering approach, guided by all-atom molecular dynamics simulations and high-resolution cryoEM imaging, along with the tools of single-molecule biophysics to dissect the elements of dynein motility. We successfully engineered a plus-end-directed dynein for the first time and revealed the mechanism of its directionality. This work has three major outcomes. First, by altering the length of the coiled-coil stalk that connects the dynein motor domain to the microtubule, we controlled the handedness of the helical motility of dynein around the circumference of the microtubule. This experiment showed that the stalk length of native dynein is critical for restricting sideways movement and directing dynein motility along the microtubule axis. Second, we altered the angle and length of dynein’s stalk. Remarkably, these modifications reversed the direction by which the linker swings relative to the microtubule and directed the motility towards the plus-end. Finally, similar to native dynein, the plus-end directed mutant maintains its preference to release from the microtubule when pulled towards the minus-end by an optical trap. Our results provide direct evidence for the linker swing model in which the direction the linker swings determines the direction of dynein motility. Our results also rule out the asymmetric release model that the directionality is proposed to be determined by the direction dynein favors for release from the microtubule under tension. Two critical features of dynein’s stalk, the length of its antiparallel coiled-coils and two proline residues located at its base, control the directionality by directing the linker swing towards the MT minus-end. Because both features of the stalk are fully conserved in cytoplasmic and ciliary dyneins across species, this mechanism explains the minus-end directionality of all dyneins.

Advisor: Yildiz, Ahmet
Engineering microbial pectin utilization for renewable chemical production

Production of renewable chemicals for industrial, energy and consumer applications represents an important economic and societal challenge. Metabolic engineering is a promising route for producing chemicals by environmentally-friendly, sustainable fermentations using modified microbial biocatalysts. However, feedstock costs (usually refined sugar) drive which products can be economically produced by fermentation. Pectin-rich agricultural byproducts from fruit and vegetable processing represent plant biomass not currently utilized in fermentations, but are attractive due to their ease of hydrolysis to component monosaccharides and low current market value. Furthermore, these byproducts are produced consistently each year at high volumes, with over 10 million tons of citrus peel and 70 million tons of sugar beet pulp produced worldwide from the citrus juice and sugar industries, respectively. This thesis describes the use of D-galacturonic acid (D-galUA) present in these byproducts for microbial fermentations and renewable chemical production. The identification of a novel eukaryotic D-galUA transporter, GAT-1, from N. crassa is described. GAT-1 and related transporter from A. niger, GatA, demonstrate utility in S. cerevisiae for bioconversions to L-galactonate and meso-galactarate. Importantly, GatA allows for co-consumption of D-galUA and D-glucose in S. cerevisiae, which are present in high concentration in pectin-rich hydrolysates. We additionally characterize the D-galUA catabolic elements of the basidiomycete yeast, R. toruloidies, a highly efficient D-galUA utilizing organism and potential host for D-galUA bioconversions. Lastly, the commercial potential for meso-galactaric acid fermentations by S. cerevisiae is discussed.

Advisor: Dueber, John
Epistemic Institutions: Law’s Encounters with Knowledge

This dissertation examines the construction of “legal knowledge”—the finding of facts to which legal norms are to be applied in the adjudication of disputes—from an interdisciplinary perspective emphasizing epistemology, the sociology of scientific knowledge, political theory, and cognitive psychology. While the construction of legal knowledge is an essential component of the legal process and the principal task of American trial courts, the process remains fraught with practical and theoretical challenges that complicate simplistic conceptions of factfinding as a transparent process of veridical reconstruction of past events. Legal epistemic agents, like all epistemic agents, lack direct access to past events; thus, legal knowledge cannot perceive the past directly, but can only interpret it. The process of legal factfinding inevitably creates distortions and is subject to systemic biases in its effort to create a veridical construct of past events giving rise to a legal dispute./nAlthough this dissertation cannot address every under-explored problem concerning the legitimacy and reliability of legal knowledge construction, its principal contribution is to bring interdisciplinary insights to bear on several of the more salient unresolved problems around the law’s engagement with knowledge claims and the construction of legal knowledge through the adversarial process. The dissertation examines both practical and normative concerns regarding the construction of legal knowledge and its legitimacy as state-backed orthodoxy. It first asks whether judges’ performance as factfinders is consistent with courts’ claims of superlative judicial competence and objectivity vis-à-vis jurors. Second, the dissertation examines one area in which legal factfinders, both judges and jurors, have a notoriously poor record of reliable knowledge construction: the interpretation and application of scientific expert testimony to the resolution of legal disputes. Finally, the dissertation examines the legitimacy of legal factfinding in a liberal democratic society characterized by entrenched disagreement concerning matters of empirical fact through the lens of John Rawls’s work on political liberalism./nThe dissertation concludes that legal factfinding faces myriad practical and normative challenges that defy simple solutions, but that progress can be made toward the law’s epistemic goals by applying relevant insights from the social sciences, philosophy, and political theory. It finds that three themes cut across all of the law’s epistemic difficulties—the epistemic limitations of human decision makers, the social entrenchment of empirical disagreement, and the promise and limitations of systems-based reforms to improving the veridicality of legal knowledge—and suggests further engagement with these themes as the foundation of a new research agenda applying interdisciplinary insights to problems in the construction of legal knowledge.

Advisor: Feeley, Malcolm
High-order Solution Transfer between Curved Meshes and Ill-conditioned Bézier Curve Intersection

The problem of solution transfer between meshes arises frequently in computational physics, e.g. in Lagrangian methods where remeshing occurs. The interpolation process must be conservative, i.e. it must conserve physical properties, such as mass. We extend previous works --- which described the solution transfer process for straight sided unstructured meshes --- by considering high-order isoparametric meshes with curved elements. The implementation is highly reliant on accurate computational geometry routines for evaluating points on and intersecting Bézier curves and triangles./nTwo ill-conditioned problems that occur evaluating points on and intersecting Bézier curves are then explored. This work presents a family of compensated algorithms to accurately evaluate a polynomial in Bernstein form with floating point coefficients. The principle is to apply error-free transformations to improve the traditional de Casteljau algorithm. The resulting output is as accurate as the de Casteljau algorithm performed in K times the working precision. After compensated evaluation is considered, a compensated Newton's method is described, both for root-finding for polynomials in the Bernstein basis and for Bézier curve intersection.

Advisor: Persson, Per-Olof
Boom, Bust, Repeat: Commitments to Insecure Work in the Oil and Tech Industries

Work is increasingly characterized by flexibility, instability, and precarity. How do workers make sense of these changes, and how do they maintain commitments in such conditions? To explore these questions, this project examines the experiences of workers in two industries that epitomize these trends: oil and tech. Despite clear cultural differences between them, both of these industries have seen similar increases in contingent work arrangements in recent decades. Based on 212 interviews with workers and ethnographic observations of worksites, I observed workers in both these industries develop narratives of insecurity that allow them to see their work as a symbolic response to the perceived root cause of insecurity./nIn the oil and gas industry, the common account of insecurity roots it in global geopolitics: dictatorial regimes in the Middle East disrupt the global market, causing drops in prices that are felt through lay-offs and reductions. The solution to this insecurity, according to these workers, is a strong domestic oil industry. The connection they describe between their work and this goal is symbolic rather than material. Work allows them to enact American patriotism, freedom, and individuality that they see as a moral response to the fluctuating global market. Although these workers understand that this response does not have a material impact, they extract from it a sense of symbolic agency that bolsters their commitments./nIn the tech industry, the perceived root of insecurity is outdated, rigid, and overregulated business models that present obstacles to natural, inevitable, and positive technological advancement. The solution to insecurity under this narrative is to pursue disruption and innovation, to break from established models of business and organization. Daily work in the tech industry allows workers to enact these goals. Like in the oil industry, working toward these goals holds meaning beyond any tangible effect on job security and bolsters commitment./nThe narratives of insecurity and symbolic agency in these industries parallel one another, and reflect a new form of psychological commitment to work. Although each is unique to its industry, in both, the insecurity experienced at work becomes the basis of a narrative that allows work to be seen as a moral response to insecurity, intensifying commitment to these contingent work arrangements. This pattern of commitment forms a new, neoliberal spirit of capitalism: one that reflects global narratives, is not dependent on particular firms, and is centered on individualized symbolic contributions.

Advisor: Burawoy, Michael
(Re)Figuring the World of General Chemistry: Possibilities for Participation, Learning, and Identity

Scholars have called for the design of alternative educational spaces that counter dominant narratives about who is capable of learning science (Nasir et al., 2013) and what it means to be “good” at science (Carlone et al., 2011). This design-based research study examines possibilities for learning and identity in CHEM 101B, an undergraduate general chemistry course re-designed to dismantle racialized, gendered, and classed hierarchies of competence in chemistry and provide broad access to rich chemistry learning and identities of competence for students. Specifically, this study sought to understand: 1) shifts in students’ conceptions of chemistry, chemical competence, and themselves; 2) shifts in students’ participation in chemistry learning; and 3) how course design was organized to support these shifts. Classroom video, fieldnotes, student artifacts, and written course reflections were collected and interviews were conducted with students. Analysis was carried out through close examination of students’ participation in groups, and through analyzing students’ meaning making about competent participation in chemistry learning and their chemical identities./nFindings indicate that developing more authentic conceptions of chemistry as a social practice supported students to reject the notion that being good at chemistry requires innate intelligence. Giving students opportunities to participate in ways aligned with notions of authentic chemical practice supported students to both develop identities as competent participants in chemical thinking and learning, and engage in rich and rigorous chemistry learning./nThis study found that supporting rich and authentic participation in and conceptions of chemistry learning required a significant restructuring of the classroom systems around: (1) coherent content connected to core ideas, (2) engagement in collective investigation of big scientific ideas and relationships, (3) opportunities for students to be scientists as themselves and connect science to their lives, and (4) reflection that creates awareness of tensions between common sense notions and new conceptions of science. This dissertation has implications for institutions of higher education, course designers and instructors committed to constructing learning settings that deconstruct and disrupt hegemonic narratives in science and build more productive counter narratives in their place.

Advisor: Stacy, Angelica M
Beauty, Art and Testimony: Subjectivity and Objectivity in Aesthetics

We acquire beliefs on the basis of what others tell us all the time. If you tell me that your house is painted red, chances are that I will simply believe you without question; and if someone asks me what color your house is, I will simply tell her that it is red. Yet we do not seem to accept others’ testimony about beauty and art in the same way. If you tell me that the Taj Mahal is beautiful, or that Middlemarch is a great novel, it would be strange for me simply to adopt your view, even if I have a lot of confidence in your judgment. In order for me to be in a position to believe or to claim that the Taj Mahal is beautiful, or that Middlemarch is a great novel, I must experience these things myself—by going to Agra, or by reading the book./nMy dissertation explains this apparent resistance to aesthetic testimony. I argue that aesthetic claims carry what is known in linguistics as ‘evidential’ information, to the effect that they are made on the basis of the subject’s firsthand experience. I locate aesthetic claims amongst a slew of other kinds of claims—including personal taste claims, perceptual appearance claims and moral claims—that all carry evidential information of this kind. These claims are loosely connected by having content that is essentially subjective or perspectival in some way, even when, as in the aesthetic and moral cases, there is also some claim to objectivity in play. I offer a detailed explanation in the aesthetic case—specifically for claims about beauty—of how their content comprises both subjective and objective elements. I argue that the evidential information carried by aesthetic claims and the other ‘perspectival’ claims I mention is communicated as conversational implicature, in spite of initial appearances to the contrary. Our apparent resistance to aesthetic testimony thus turns out to be an artifact of the evidential implications of aesthetic language: we often do accept aesthetic testimony, but we must describe our beliefs in a way that does not convey misleading evidential information.

Advisor: Ginsborg, Hannah
Stroud, Barry