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Learning from high-dimensional measurements
No full textThis thesis considers the problems of distilling and quantifying information in high-dimensional measurements, with a focus on applications in biology. First, we explore the idea that underlying low-dimensional structure in high-dimensional data can be exploited to circumvent the curse of dimensionality in mutual information estimation. We develop a method that we call latent MI (LMI) approximation, which applies a nonparametric MI estimator to low-dimensional representations learned by a simple, theoretically-motivated model architecture. Using several benchmarks, we show that unlike existing techniques, LMI can approximate MI well for variables with dimensions when their dependence structure has low intrinsic dimensionality. Second, we study how measurement noise in data affects the quality of representation learning models. Using an information-theoretic metric of representation quality, we show that model performance scales predictably with molecular undersampling noise in single-cell genomic data. We show that the form of this relationship can be recovered from a simple Gaussian noise model, which provides an intuitive interpretation of the law. Finally, we show that the same scaling relationship emerges in image classification problems, suggesting that noise scaling may be a general phenomenon.Systems Biolog
Automatic Enrollment with a 12% Default Contribution Rate
No full textWe study a retirement savings plan with a default contribution rate of 12% of income, which is much higher than previously studied defaults. Twenty-five percent of employees had not opted out of this default 12 months after hire; a literature review finds that the corresponding fraction in plans with lower defaults is approximately one-half. Because only contributions above 12% were matched by the employer, 12% was likely to be a suboptimal contribution rate for employees. Employees who remained at the 12% default contribution rate had average income that was approximately one-third lower than would be predicted from the relationship between salaries and contribution rates among employees who were not at 12%. Defaults may influence low-income employees more strongly in part because these employees face higher psychological barriers to active decision making.Author's Origina
Scientific distinctions between coca and cocaine support policy reform
No full textCoca is not cocaine—it is an ancient, safe, and culturally vital crop now under renewed scrutiny by the World Health Organization, whose review could prompt revision of United Nations drug policy rooted in colonialist bias and begin to repair decades of social injustice, while affirming scientific evidence and cultural sovereignty.Organismic and Evolutionary BiologyAccepted Manuscrip
Formation, integration, and control of semiconductor spin-defects in electronic and photonic devices
No full textCan we identify new techniques to better create, control, and understand quantum systems? This is the central question of my thesis, which I explore by focusing on a particular class of quantum system--semiconductor-hosted spin-defects, namely the silicon monovacancy in silicon carbide, and the G center and T center in silicon. In this thesis, I investigate laser-mediated local defect formation in nanophotonics (create - Ch. 3), electrical manipulation of telecom defects in a silicon lateral PIN-diode (control - Ch. 4), and defect-enabled mapping of carrier phase transitions revealing negative differential resistance in silicon (understand - Ch. 5). Together, these results underpin the wealth of insight to be probed at the intersection of semiconductor physics and quantum science, as decades-old solid-state theories can be rediscovered in emergent quantum networking candidates.
Detailed:
In the recent decade, the ideas of quantum information science (QIS) have begun to become realized through the rapid development of technology which directly rely upon the principles of quantum mechanics such as superposition and entanglement. Computing, sensing, and communications are the three principal modalities which quantum technology is re-imagining, enabling enhanced capabilities unrivaled by their classical counterparts such as information theoretic security and efficient simulation of quantum phenomena. Fundamentally, a quantum technology platform is constituted by an isolated quantum two-level system (qubit) in which information can be controllably stored, manipulated, and accessed. However, each candidate offers vastly different advantages and challenges toward experimental implementation. The great promise of these technologies has motivated an intense study of quantum engineering to realize platforms ideally suited to their respective QIS task. While atoms, ions, superconducting Josephson-junctions, and photons are all compelling candidate qubits, a class of quantum systems known as solid-state spin-defects (color centers) are particularly exciting due to their natural environmental coupling (quantum sensing) and inherent spin-photon interface with facile deployment in nanofabricated devices which enhance their performance (quantum communications and networking).
Spin-defects are imperfections in an otherwise perfect crystal lattice, whereby an electronic structure is localized in the bandgap via the removal or addition of atoms in the crystal, leaving behind some isolated electron system. While imperfections exist in every crystal, their utility toward quantum technology varies drastically--reliant on features such as their possession of: microwave-controllable spin, optically-active charge state, robust spin-photon interface, and host material quality. Considering all of these traits, the current leading solid-state spin defect qubits are the Silicon Vacancy (SiV) and Nitrogen Vacancy (NV) in diamond. However more recently, there has been great interest in evaluating emergent spin defects which may exist in other crystal hosts and offer inherent unique benefits not possessed by these leading diamond candidates. For instance, quantum-grade diamond is highly-specialized and hard to fabricate, the NV and SiV visible-photon emission exhibits tremendous loss in conventional telecom fiber, and the SiV spin requires milliKelvin temperatures to utilize.
In contrast, silicon (Si) and silicon carbide (SiC) are ubiquitous commercial semiconductors with nearly a century of development in growth, material purity, and nanofabrication techniques--therefore, quantum technology stands to benefit greatly by leveraging the wealth of research and development of semicondcutor hosts. Furthermore, a class of carbon-related color centers in Si have been recently re-discovered which emit photons in the low propagation loss (0.3dB/km) telecommuncations O-Band (1260-1360nm) of the optical fiber which circles the globe for classical internet, and which possess an optically-addressable spin. The immense practical advantages of material host and emission frequency for these semiconductor spin-defects renders them exciting candidates for scalable quantum networking, however their nascency requires significant investigation to compete with existing leading systems in diamond.
In this thesis, I present work on the investigation and device engineering of semiconductor-hosted spin-defects, focusing on the silicon monovacancy (VSi) in silicon carbide (SiC) and the G and T centers in silicon. I first introduce the relevant background information to support this thesis in Chapter 1, from QIS theory to the varied platforms which enable it. In Chapter 2 I introduce solid-state spin defects, analyze the leading host materials and defect qubit trade-offs, then describe the intersection of defect integration with quanutum photonics, electronics, acoustics, and nanofabrication techniques. At the conclusion of this section I detail the thin-film SiC platform our group has developed for device nanofabrication of SiC defects. In Chapter 3 I develop a laser-based approach for controllably forming silicon vacancy defects (VSi) within these fabricated nanophotonic crystal cavities in SiC. Chapters 4 and 5 then focus on electrical integration, characterization, and control of silicon color centers in lateral PIN-diodes. Using these principles, chapter 4 presents stark tuning and optical charge state control of a G center ensemble, and chapter 5 reports direct optical observation of carrier phase transitions characteristic of negative differential resistance through the coupling of electrical nonlinearities to a T center ensemble. Finally Chapter 6 describes the outlook for semiconductor spin-defects, detailing the remaining challenges faced by VSi, G centers, and T centers, and discussing exciting new opportunities with color centers such as Vanadium.Engineering and Applied Sciences - Applied Physic
Integrative statistical methods for human biology, from biobanks to perturbation atlases
No full textSince the human genome project, many new types of rich biological data have empowered new insight into basic biological science and human disease. Among these are genetic association studies, which characterize many genetic variants in large numbers of individuals, and perturbation atlases, which profile how genetic perturbations shape the expression of thousands of transcripts. However, statistical methods for answering basic questions about these data (How much signal is in each experiment? What is the relationship between experiments? How many discoveries will we make at massive sample size?) lag behind. This thesis presents a suite of novel statistical approaches for the analysis of rich biological data. Our analyses clarify several integrative questions about human biology, ranging from the contribution of rare genetic variation to common diseases, to the consistency of gene perturbation effects across cell types, among others. Looking forward, these methods contribute to the creation of a harmonized analysis toolbox to facilitate replicable characterization and comparison of high-throughput biological experiments.Biomedical Informatic
Unveiling the Factors Influencing Effective Water, Sanitation and Hygiene Response in Filipino Schools
No full textOver the past few decades, the Philippines has made significant progress in improving the health and wellbeing of its children and adolescents, leading to reduced infant and child mortality and a decline in adolescent pregnancies. However, despite these advancements, challenges remain, particularly in providing universal access to water, sanitation, and hygiene (WASH) facilities. This study investigates the factors influencing the effective and equitable implementation of the National Water, Sanitation and Hygiene in Schools (WinS) Program. Despite operating under the same governmental structure, health inequities in program implementation across schools highlight areas that warrant further investigation, suggesting the presence of influential but less obvious factors. Utilizing a qualitative research design with a multiple case study approach, the study uncovers not only the direct factors impacting implementation but also explores the underlying drivers and strategic responses needed to address them. Findings emphasize the importance of adaptive local strategies and transformative leadership to effectively navigate these challenges, enhancing both the sustainability and effectiveness of the program. Recommendations are provided to guide policymakers and stakeholders in refining these strategies, informed by an understanding of the broader social determinants of health that shape educational and health outcomes.Public Healt
The role of novel long non-coding RNA TRIDENT in non-small cell lung cancer
No full textNon-small cell lung cancer (NSCLC) continues to be the leading cause of cancer mortality. While significant advancements have been made in its treatment and management, it remains incurable due to tumor recurrence. The molecular mechanisms driving NSCLC involving protein-coding genes have been extensively studied. However, systematically identifying and characterizing the regulatory factors involved in NSCLC can also provide invaluable insight into the pathways involved and aid in developing novel therapeutic and diagnostic strategies. Long non-coding RNAs (lncRNAs) are a class of non-coding regulatory RNAs that have been implicated in many human diseases. These RNAs, primarily through their secondary structure, employ diverse mechanisms to regulate most processes important for cell survival. Due to bioinformatic and technical limitations and a nascent understanding of functional RNA domains, most of these RNA molecules remain uncharacterized.
During my dissertation, I sought to use existing RNAseq databases to identify and characterize novel lncRNAs that show differential regulation in NSCLC. Through our screen, we identified several lncRNAs that have been previously described and some not. We focused on the novel lncRNAs and utilized online tools to filter out lncRNAs whose expression was significantly associated with patient prognosis. Next, we employed CRISPRi and antisense oligos (ASOs) to knock them down in cellular models of NSCLC to assess the effect on classical cancer phenotypes such as proliferation, invasion, and migration. Our analysis revealed several lncRNAs, yet uncharacterized, that significantly alter cancer phenotypes when their levels are perturbed. We delved deeper into the mechanism of one such lncRNA - RP11-462G12.1 or TRIDENT. We found that TRIDENT expression was significantly induced upon EGFR activation. Perturbing levels of TRIDENT highlighted its role in cell proliferation and drug resistance. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to the accumulation of DNA damage in cancer cells via decrease TRIM28 phosphorylation. Altogether, our results reveal a novel molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance.
My work highlights the critical roles lncRNAs can play in modulating disease mechanisms and response to treatments. Their effect, though subtle, can have implications for treatment strategies for patients and aid in the development of better therapeutic targetsMedical Science
Voyage of Injustice: The Socioeconomic Exploitation in the Cruise Industry and a Call for Action
No full textBehind the glamour of the cruise ship industry lies a dark reality of systemic
exploitation that requires public awareness and urgent action to facilitate reform. This
thesis unveils the dark side of the cruise ship industry and explores the question: "How
does the existing international legal architecture enable exploitation in the cruise ship
industry and what are the pathways forward for reform?”
This thesis delves into the cruise ship industry’s employment practices, and unfair
treatment of its workers. It explores the phenomenon of exploitation on the high seas and
examines the legal architecture that permits it. It highlights the critical role of flags of
convenience in facilitating and perpetuating exploitation. It addresses prior attempts for
reform that have been unsuccessful and, in some instances, met with lobbying efforts by
the cruise line industry. It illustrates the industry’s absolute refusal to voluntarily act in a
moral and ethical manner that respects the rights of its workers. It advocates for reform
and illustrates the need for multinational efforts. It finds that consumers putting direct
bilateral pressure on domestic governments, flag states and the cruise industry are
required. This thesis urges a call to action and concludes that consumers have the power
to create change, recommending a boycott as one of the most powerful and effective
actions to drive change in the cruise ship industry.
The aim of this thesis is to raise awareness about the negative treatment inflicted
upon cruise ship employees in hope that it will ignite public outcry and force positive
change, accountability and reform
Nourishing Nostalgia: Modern Ex-Soviet Expatriates and their Foodways in the UAE
No full textOn a busy street in one of Dubai’s colorful neighborhoods, a vibrant Uzbek restaurant opens its doors to international customers interested in trying a new cuisine or who have longed for their childhood memories. Often, these customers, known in the UAE as expatriates, appear to be of Commonwealth of Independent States (CIS) origin and engagingly speak Russian among themselves. On the other side of the road, a modest CIS food store has taken a permanent location, bringing CIS foods to often the same customers of the Uzbek place. Why do CIS expatriates keep coming back to CIS restaurants and supermarkets in Dubai, and what do they look for there? What does it mean for them to maintain ties with “home”? How does Dubai’s internationality as a host affect this meaning? And how strong is intergenerational cultural knowledge transmission in the state of expatriation? As a CIS expatriate myself, I have long asked these questions. Now, it is time to find out what brings us back again and again and how we understand ourselves through our ethnic roots and cultural foods while being abroad. This exploratory qualitative project draws on phenomenological and ethnographic methods to study the day-to-day lives of CIS expatriates in Dubai through conducting unstructured interviews, supportive modes of field observations, and online ethnography of food blogs. The results of this research help fill the gap in understanding former Soviet people abroad and their constructed ethnic identity through food in the unique environment of the UAE, an exceptional country with nearly zero assimilation. In
addition, through the insights gathered from expatriates and while juxtaposing those with an online ethnography of food stores’ social media accounts, utilizing linguistic anthropology of images, supplementary insights were produced as implications and suggestions for these supermarkets. Overall, I expect this endeavor to support future studies on migrants’ ethnic construction and migrant cultures. I build on previous studies of ex-Soviet migrants in other European countries, the US, Israel, and Japan, and from broader studies on migration vs expatriation, ethnicity, nationalism, food, and social identity theory, which provides the necessary frame of sociocultural exposure with own attitudes towards other expatriates with shared ethnicity. Here, I try to understand how expatriate communities make sense of their ongoing and changing experiences as “expatriates” and uncover meanings expatriates assign to their experiences through “home” food abroad
Dignity and Indignation, Ancient and Modern: Plato’s Thumos and Rousseau’s Amour-propre
No full textThis dissertation is a study of a forgotten part of the human psyche, a part at the core of our political nature. Thumos was originally conceived by Plato as a third principle of the mind distinct from reason and desire, a principle responsible for the attachment to justice and courage. This principle was later reconceived and subjected to probing criticism by Jean-Jacques Rousseau under the name of amour-propre. Most simply, thumos and amour-propre are responsible for three related concerns: the desire to be honored or esteemed by others, the pride that reflects our own esteem for our comparative worth or dignity, and the indignation or anger that defends such dignity. These passions and their education pose fundamental problems for any political regime: for Rousseau, amour-propre was responsible for “what is best and worst among men,” for the “virtues” that make us political beings and for the most pathological of our “vices.”
The project has two aims. The first is to recover an understanding of this psychic principle through two thinkers who examined it in greatest depth and to offer an account of why it is widely neglected in contemporary political science. The second is to explain why Rousseau turned to Plato in his critique of the 18th-century Enlightenment: why is Plato the philosopher Rousseau cites the most throughout his writings? I argue that Rousseau recovered and repurposed the thought of Plato in his effort to understand what was pathological about the amour-propre of the “bourgeois,” the human type promoted by the modern Enlightenment. Rousseau drew from Plato a conception of the natural human being as an ideal or standard from which to judge political life and its pathologies. This standard for both thinkers was characterized by the undivided unity or wholeness of the human psyche. Rousseau criticized Enlightenment efforts to ground morality on a form of public esteem that placed individuals in contradiction with themselves, preventing the unity of the mind.
The project is focused on Rousseau’s Emile, or On Education (1762) and its response to Plato’s Republic. I situate these in a broader study of each thinker’s other political writings and their contexts, from the treatment of thumos in the poetry of Homer to the critique of amour-propre in the 17th-century French Augustinians who first adopted the term. On the whole, Plato proves to be a greater critic of thumos, and Rousseau a greater optimist about amour-propre, than they are widely taken to be. Plato’s apparent promotion of thumos as a motive for civic virtue is in fact accompanied by a critique of its tendency to divide the mind: thumos gives rise to contradictory opinions on morality that are only fully resolved in the Socratic vision of the philosophic life, the rare perfection or end of human nature. Conversely, Rousseau’s influential critique of bourgeois amour-propre is in fact accompanied by a characteristically Enlightenment optimism about the possibility of reshaping the passion, on the basis not of any highest end but of its simplest and most elemental roots, toward a form of morality that would avoid setting ordinary minds in contradiction with themselves. For Rousseau this unity of mind was the precondition for genuine self-rule in any individual. Rousseau’s optimism about the educable character of amour-propre is thus a neglected theoretical foundation for the democratic political theory that he took to a new height in the Enlightenment in spite of his return to the ancient Greeks.Governmen