VictorJuiz/thesis huggingface dataset:
A Tasteful Study of the Drosophila Mushroom Body

Learning to distinguish ‘good’ from ‘bad’ is essential to an animal’s survival. Taste compounds have intrinsic value to animal survival and serve as innate rewards and punishments. From humans to flies, nutritious substances like sugar are intrinsically positive and promote acceptance behavior, whereas potentially toxic bitter substances like quinine, for example, are met with disgust and aversion. Yet, even the strongest instinctual behavioral drives such as feeding can be modified by prior associations. How does this learning happen? Using the model organism Drosophila Melanogaster, I investigated how the inputs and outputs of a learning center can modulate feeding behavior./nIn the first part of this dissertation, I investigated the modulation of proboscis extension by inputs and outputs of the learning center (mushroom body, MB) in the fly brain. I identified 10 split-Gal4 lines that cover 7 different cell types of MB output neurons (MBONs) that decrease the probability of proboscis extension when activated. Silencing these neurons had modest effects on proboscis extension. Additionally, I found 3 split-Gal4 lines labeling dopaminergic neurons (DANs) that decrease proboscis extension to sucrose, upon activation. I also found that the MBONs which suppress proboscis extension upon activation do not respond to sucrose. Lastly, I describe areas for putative neurons that are downstream of MBONs./nIn the second part of this dissertation, I outline the methods I developed for a large-scale calcium imaging experiment to track neuronal changes during an aversive taste conditioning paradigm. While this set of experiments was ultimately inconclusive because we lacked a good positive control and behavioral readout to determine successful learning in our in vivo prep, we believe that outlining the experimental methods and analysis pipeline may be useful and applicable for more general analysis of large-scale calcium imaging endeavors to answer questions about neuronal changes during a behavior./nOverall, my thesis research investigated how the activity of MB inputs and outputs impinges on feeding behavior by characterizing mushroom body neurons that antagonize feeding behavior and examining how they alter activity in feeding circuits. The work described in this thesis provides insight into how the mushroom body flexibly alters the response to taste compounds and modifies feeding decisions.

Advisor: Scott, Kristin
Modular Syntheses and Applications of Functionalized Graphene Nanoribbons

Laterally confining graphene into 1D strips known as graphene nanoribbons (GNRs) opens up a tunable bandgap dependent on width, edge structure, and dopant atoms, while still preserving the exceptional physical and electronic properties associated with graphene. As a result, GNRs have been heralded as materials for post-silicon electronics development and recently have become promising candidates as catalytic support materials. Deterministic bottom up synthesis is key to accessing atomically precise GNRs and has the powerful capability of “writing-in” selective properties by controlling the structure. The solution synthesis of these materials enables large scale production of GNRs; however, their integration into organic electronic devices is hampered by their visualization and localization on the surface by scanning probe microscopies and the functionalities that can be installed must survive the harsh parameters of synthesis. To this end, we have developed an azide functionalized GNR to enable late stage modification via copper-catalyzed click-chemistry (Chapter 2). “Clicking” on Cy5 fluorescent dyes gives rise to GNRs decorated along the edges with fluorescent tags detectable by optical microscopy and thus can be more efficiently visualized and localized by super resolution imaging. Bandgap engineering by tuning the width and edge structure of GNRs, as well as global alignment of GNRs is also required for their integration into next generation electronic devices (Chapter 4). Furthermore, bulk GNRs are proven to have practical applications beyond functioning as channel materials for electronic devices as tunable catalytic support materials (Chapter 3).

Advisor: Fischer, Felix R
Growing Environmental Literacy: On small-scale farms, in the urban agroecosystem, and in school garden classrooms

Food systems in the United States are in need of transformation. The current globalized, mechanized, chemical-based, fossil fuel-powered food system causes negative impacts on ecology, human health, social justice, and local economies. This dissertation explores places where alternatives to the dominant food system are being advanced, and investigates how such alternatives could be scaled up, better supported, or reinforced through food systems education. The crisis of global climate change intersects with the challenge of sustainably (and nutritiously) feeding a growing global population, leading to synergistic opportunities to engage in integrated food systems and climate education. As branches of environmental literacy, which is increasingly promoted in new state standards for K-12 education, food and climate literacy offer opportunities to educate young people while building a climate resilient, equitable local food system. How to build food, climate, and environmental literacy effectively remains a question requiring further action-research. The following chapters address this question through case studies of relocalized food system transitions in Lopez Island, WA and the East Bay region of California’s San Francisco Bay Area. Lessons from these two case studies inform a food and climate change curriculum, a work in progress presented in Chapter 4 alongside an overarching analysis of effective, experiential climate change education pedagogy. Ultimately, efforts to reform our food system with the realities of climate change in mind will require young people partnering with allies in older generations to create and scale alternative production, distribution, and consumption practices. Education has a critical role to play in enabling food system transitions and climate solutions, implemented at a community scale but integrated in a global network of climate-friendly food system transformation.

Advisor: Iles, Alastair
Emplacing White Possessive Logics: Socializing Latinx Youth into Relations with Land, Community, and Success

This dissertation examines the logics and relations that Latinx youth are socialized into via a college preparation program from a settler colonial studies perspective. An ethnographic project drawing upon critical place inquiry and language socialization approaches, it features data from pláticas and interviews, participant observation, and a multi-sited place project, building upon youths’ and educators’ readings and navigations of their social worlds. It contends that white possessive logics (Moreton-Robinson, 2015) were enacted through a series of classificatory technologies of control which shifted in response to efforts by local educators to employ educational structures and practices that countered them. Further, it examines the navigation of the settler-native-slave triad by Latinx youth, as their status as exogenous others positioned them as not-quite-yet determined within this structure. This dissertation argues that the precarity and tenuousness of life shaped by racialized and gendered vulnerabilities made aspiring towards normative visions of success a (non)option for those given the opportunity to do so. Finally, it describes the complex and at times conflicting relations with Land, community, and success that Bridge Program youth were socialized into, arguing that, ultimately, the relations embedded therein limit the potential for such a program to produce significant changes to the structural inequities of the U.S. nation-state. In all, this dissertation underscores that college-going pathways and the attainment of higher education are always embedded within the white supremacist, settler colonial nation-state, and cannot be the primary strategy for racialized peoples’ liberation, despite its championing by liberal multicultural approaches to social change.

Advisor: Baquedano-López, Patricia
Evaluating RNA-based gene regulation across different systems

Ribonucleic acid (RNA) is an essential biomolecule that is commonly recognized as the template for protein synthesis across different classes of life. Aside from this well-known function, RNA plays many diverse roles within the cell and is directly involved in several processes that control gene expression. Different forms of RNA, spanning a range of lengths and structures, interact with the cellular machinery either alone or in complex with proteins and other nucleic acids to regulate how and when genes are expressed. In the past sixty years, the RNA field has grown at an astounding rate, and our understanding of this pervasive molecule is ever-expanding. However, in addition to its function as a gene regulator, RNA can also be engineered for use as a tool to probe cellular processes. We present here our efforts towards employing RNA in three different roles – targeting device, gene repressor, and sensor – to study fundamental processes in bacteria and eukaryotes.

Advisor: Hammond, Ming C
Quantum feedback for measurement and control

The standard quantum formalism introduced at the undergraduate level treats measurement as an instantaneous collapse. In reality however, no physical process can occur over a truly infinitesimal time interval. A more subtle investigation of open quantum systems lead to the theory of continuous measurement and quantum trajectories, in which wave function collapse occurs over a finite time scale associated with an interaction. Within this formalism, it becomes possible to ask many new questions that would be trivial or even ill-defined in the context of the more basic measurement model. In this thesis, we investigate both theoretically and experimentally what fundamentally new capabilities arise when an experimental apparatus can resolve the continuous dynamics of a measurement. Theoretically, we show that when one can perform feedback operations on the timescale of the measurement process, the resulting tools provide significantly more control over entanglement generation, and in some settings can generate it optimally. Experimentally, we show that continuous measurement allows one to observe the dynamics of a system undergoing simultaneous non-commuting measurements, which provides a reinterpretation of the Heisenberg uncertainty principle. Finally, we combine the theoretical focus on quantum feedback with the experimental capabilities of superconducting circuits to implement a feedback controlled quantum amplifier. The resulting system is capable of adaptive measurement, which we use to perform the first canonical phase measurement.

Advisor: Siddiqi, Irfan
Whaley, K. Birgitta
Mycelium Materials

Mycelium materials are made of fungi. By digesting waste to create a bio-composite of mycelium and the feedstock, they are becoming a sustainable material option. Fungi are nature’s recyclers, with millions of species that can digest everything from cellulose to polymers. By selecting specific species to digest industrial waste such as sawdust, bio-composites can be grown that can be disposed of after use by composting. Composting reduces their environmental impact in comparison to synthetic composites. As part of an academic-industry collaboration, bio-composites were explored made of Ganoderma lucidum fungi. The findings provide researchers and commercial developers with information on the properties, performance and suitable applications of these novel materials. The material was characterized from a physical, mechanical, thermal, and manufacturing standpoint using American Society of Testing and Materials standards./nThe ultimate tensile strength was 176 kPa, with a tensile modulus of 1.3 MPa, and an ultimate compressive strength of 490 kPa. These properties are comparable to brittle, cellular materials such as expanded polymer foams. The values for the thermal resistance and thermal conductivity ranged from 0.0014 to 0.0019 m2 K/W and 0.053 to 0.077 W/m K respectively, which are comparable to current natural insulator materials such as balsa wood and natural cork. The average maximum use temperature was found to be 390 ºC (734ºF). These properties are comparable to polymer foams such as expanded polystyrene foam, suiting the material to non-structural applications such as packaging and insulation. Combining a mycelium material core with carbon fiber and bamboo laminate skins improved the flexural strength. The core shear ultimate stress was 36.2 kPa for the mycelium material alone, rising to 63.3 kPa with bamboo skins and 76.6 kPa with carbon fiber skins. The large improvement in strength suggests that with development mycelium materials could be suited to higher-performance applications such as interior wall panels and construction bricks. Methods were tested to manufacture mycelium materials, finding the material could be shaped with drilling, milling, sanding, and that laser cutting can form features of ~3mm./nFinally, current and future applications were considered using three use case studies: as packaging, as fabrics, and as a sanitation solution to digest human waste to create useful products. Overall, mycelium materials show great promise for further development as a bio-composite that can digest waste to create useful materials.

Advisor: Agogino, Alice M
Constructive Formal Control Synthesis through Abstraction and Decomposition

Control synthesis is the problem of automatically constructing a control strategy that induces a system to exhibit a declared behavior. Synthesis algorithms vary widely across different classes of system dynamics and specifications./nWhile continuous optimization has traditionally been used to construct stabilizing controllers for physical systems modeled with differential equations, temporal logic synthesis for finite state machines heavily leverages discrete algorithms and data structures./nHybrid systems are a class of systems that exhibit both continuous and discrete behaviors, which are necessary to capture phenomena such as impacts for legged robots and congestion shockwaves in freeways. Tractable control synthesis remains elusive because hybrid systems violate many of the fundamental topological assumptions made by prior algorithms for purely continuous or discrete systems./nThis thesis exploits compositionality and system structure to provide a suite of algorithmic and theoretical techniques to tackle acute computational bottlenecks in hybrid control synthesis./nThe first half of this thesis provides a framework for engineers to model control systems and construct algorithmic pipelines for control synthesis./nBy explicitly capturing system structure, this framework gives users the flexibility to rapidly iterate over and leverage a library of optimizations for control synthesis./nWe demonstrate this framework in the context of abstraction-based control, a synthesis workflow that translates continuous systems into finite state machines by throwing away high precision information. Different optimization techniques such as multi-scale grids, lazy abstraction, and decomposed synthesis, can all be expressed as modifications to a computational pipeline. We demonstrate computational gains while synthesizing safe motion primitives for numerous robotic examples./nThe second half addresses distributed control synthesis where multiple controllers act as agents that seek to jointly satisfy a specification and are restricted by some communication topology. We introduce parametric assume-guarantee contracts as a formalism to derive guarantees about the closed loop behavior of a collection of interacting components. Dynamic contracts allow contract parameters to change at runtime and enable coordination of multiple interacting sub-systems./nThese results are demonstrated in the context of a freeway ramp meter and an adjacent arterial network.

Advisor: Arcak, Murat
Seshia, Sanjit A
Utilizing Chemoproteomics to Discover Novel Druggable Hotspots Targeted by Natural Products

It is estimated that over 1.7 million people will be diagnosed with cancer and 600,000 people will die from cancer in 2019. The need for new therapeutics against cancer is therefore imperative. Natural product based drug discovery has provided a multitude of effective answers to many diseases, however difficulties in synthesizing natural products, isolating them, and deciphering their mechanism of action can limit translating more natural products into the clinic. Coupling natural product based drug discovery with chemical genetics and with powerful chemoproteomic strategies can allow for new questions to be asked and potentially new therapeutics to be developed even from formerly well-characterized molecules./nParthenolide, a natural product from the feverfew plant and member of the large family of sesquiterpene lactones, exerts multiple biological and therapeutic activities including anti-inflammatory and anti-cancer effects. Herein, we further study parthenolide mechanism of action using activity-based protein profiling (ABPP)-based chemoproteomic platforms to map additional covalent targets engaged by parthenolide in human breast cancer cells. We find that parthenolide, as well as other related exocyclic methylene lactone-containing sesquiterpenes, covalently modify cysteine 427 (C427) of focal adhesion kinase 1 (FAK1) leading to impairment of FAK1-dependent signaling pathways and breast cancer cell proliferation, survival, and motility. These studies reveal a novel functional target exploited by members of a large family of anticancer natural products.

Advisor: Nomura, Daniel
Towards Scalable Community Networks

Over 400 million people live without access to basic communication services, largely in rural areas. Community-based networks, and particularly community cellular networks, can sustainably support services even in these extremely rural areas where traditional commercial network operators cannot. However, community cellular networks face a variety of technical, business, and regulatory challenges that hamper their proliferation./nIn this thesis, we aim to develop approaches to enable scale within and across community cellular networks. Through a mixed-methods study of more than 80 rural wireless Internet service providers, a related class of network operators, we identify key scaling challenges rural network operators face. We next present two approaches for addressing these challenges in the context of community cellular networks. The first, GSM Whitespaces, demonstrates that rural community cellular networks can safely share spectrum in bands occupied by incumbent mobile network operators, removing a key barrier to independent operation. The second, CCM, shows how community networks and incumbent mobile network operators can cooperate to share resources to extend service. We will explore each of these approaches through practical systems and longitudinal deployments of community cellular networks in Southeast Asia that provide service to thousands of rural people.

Advisor: Brewer, Eric
Agency and Market Efficiency in the U.S. Health Care Industry

This dissertation studies the role of principal-agent problems as a barrier to market efficiency in the U.S. health care industry. The rise of health care as a percent of U.S. gross domestic product, as well as the documented dispersion in the productivity and price of health care, demand a policy response. In this dissertation I ask how demand-side (Chapter 1) and supply-side (Chapter 2) incentives can work to increase or decrease competitive forces and affect the efficient functioning of the market./nThe first chapter, coauthored with Amitabh Chandra, Benjamin Handel, and Jonathan Kolstad, studies the role of principal-agent problems on the demand side. We study a large U.S. employer that changed their health insurance benefits from a comprehensive plan with no employee cost-sharing to a high-deductible health plan with significant cost-sharing, effectively increasing the price of health care to those employees. We find that, although employees do reduce their health care spending in response to this change, they do so in suboptimal ways. We find that (i) they reduce high-value care in similar proportion to low-value care; (ii) that reductions in spending come from reductions in utilization rather than substitution of care to lower-priced providers; and (iii) that employees do not understand the dynamic incentives embedded in high-deductible plans, so that even those employees whose effective marginal price of care has not changed cut back spending in response to deductibles. Our results suggest that although demand-side policies may reduce spending, they do so in highly inefficient ways, and may not solve the underlying causes of high U.S. health care spending growth./nThe second chapter studies the role of principal-agent issues on the supply-side in determining the productivity of the U.S. health care industry. I document extensive vertical integration between primary care physicians (PCPs) and orthopedic joint surgeons. Using a stylized model, I show that this integration can increase productivity through technical production efficiencies, or lower productivity by distorting where PCPs refer their patients. I estimate that both of these effects are present, but that which effect dominates depends critically on the identities of the integrating parties. Echoing my first chapter, I find that demand is insensitive to price, lowering the potential distortionary effects of vertical integration on demand. I do find that the use of `global budget' capitation contracts, which make PCPs share the cost of patient care, do induce the reallocation of patients towards lower-cost orthopedists. This suggests that supply-side remedies may be more effective for future policy than demand-side remedies.

Advisor: Handel, Benjamin
Tune-out measurement in lukewarm lithium with phase-patterned atom interferometry

Atom interferometry deploys atoms as sensors, delivering precision measurements that span the gamut of physics. Laser-cooled samples simplify uniform detection strategies and allow meticulous control over degrees of freedom and systematic effects. Advanced cooling and interferometry techniques do apply readily to a few atomic species, but they leave behind a large class of species otherwise suited for precision sensing. This thesis describes atom interferometry with a sample of lukewarm $^7$Li, near the Doppler temperature. High thermal speeds demand rapid atom optics and complicate detection. We nevertheless develop interferometer techniques that considerably relax cooling requirements, including a recoil-sensitive scheme capable of measuring the fine-structure constant that takes advantage of $^7$Li's low mass. We also establish a phase-patterning protocol to inscribe and sense spatially-varying phases with matter-wave interferometers whose sample sizes exceed the arm separation. Phase patterning forms the basis of the first precision measurement of $^7$Li's red tune-out wavelength, the wavelength where AC Stark shifts from the $D$-line transitions cancel and the polarizability vanishes. Our measurement registers a 3-$\sigma$ tension with \emph{ab initio} atomic theory regarding the tensor-shifted tune-out wavelength and a 2-$\sigma$ tension regarding the size of the tensor shift, but agrees with theory regarding the scalar tune-out wavelength. These results motivate further work on lithium's polarizability, enable direct measurements of hyperpolarizability, and empower an assortment of future applications of phase patterning in matter-wave interferometry.

Advisor: Mueller, Holger