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Two Systems For User Control On The Modern Web, Caleb Malchik Jan 2025

Two Systems For User Control On The Modern Web, Caleb Malchik

Yale Graduate School of Arts and Sciences Dissertations

Providers of web services and content are compelled to offer value in order to attract users, but they are also increasingly incentivized to abuse their users in order to maximize revenue. Interfaces that monitor, distract, manipulate, and addict users are commonplace, and means of resistance are largely individualized and dependent on technical proficiency. This dissertation advocates a collective approach to empowering users in their relationship to the web services that they use, centered on an organizational form known as the data co-op. We describe two software systems that pair naturally with data co-ops and are designed to improve users’ control …

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Vaccine-Induced Immunity: Insights Into Sars-Cov-2 And Orthopoxvirus, Valter Monteiro Jan 2025

Vaccine-Induced Immunity: Insights Into Sars-Cov-2 And Orthopoxvirus, Valter Monteiro

Yale Graduate School of Arts and Sciences Dissertations

Emerging infectious diseases like SARS-CoV-2 and re-emergent pathogens such asmpox (formally known as monkeypox) have posed substantial challenges to global health, often due to immune escape and antigenic variability. My research addresses these challenges by evaluating and designing vaccine strategies to enhance immune responses and cross-protection, focusing on SARS-CoV-2 variants and members of the Orthopoxvirus family. The central aim of my research is to understand and overcome limitations in immune responses to antigenically variable pathogens. My studies focus on humoral responses to SARS-CoV-2 variants through targeted booster regimens, exploring cross-protective immunity in Orthopoxvirus vaccines, and testing new mRNA vaccines to …

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Epicurus’S Ethics: Pleasure, Deliberation, And The Goal, Max Duboff Jan 2025

Epicurus’S Ethics: Pleasure, Deliberation, And The Goal, Max Duboff

Yale Graduate School of Arts and Sciences Dissertations

Although Epicurus was a highly systematic thinker, most discussion of his ethics has had too narrow a focus. To address this problem, I propose a unified account of pleasure, the absence of pain, and deliberation in Epicurus's ethics. I explain three puzzles which have plagued Epicureanism since Cicero and even before: why the absence of pain is called pleasure; why the absence of pain is the greatest good; and how the absence of pain governs deliberation, including about death. I develop a new view of Epicurean pleasure, and I argue against the standard framing of Epicurus's ethics as a "hedonistic …

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Building Certified Systems With Compositional Semantics, Yu Zhang Jan 2025

Building Certified Systems With Compositional Semantics, Yu Zhang

Yale Graduate School of Arts and Sciences Dissertations

Formal verification has emerged as the most rigorous approach for building reliable computer systems. Certified systems, in particular, are accompanied by a formal specification and a machine-checkable proof of correctness, enabling independent verification by third parties. However, verifying large-scale, heterogeneous systems presents significant challenges that current techniques cannot adequately address. Such systems require compositional methods that can flexibly integrate diverse verification approaches, including program logic, certified compilation, and data abstraction. While compositional semantics offers a promising foundation, existing frameworks are typically built on specialized operational models that resist integration with one another. This dissertation presents a three-dimensional algebraic compositional structure …

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Neurocognition In Youth With Prediabetes, Jade Ivey Quillian Jan 2025

Neurocognition In Youth With Prediabetes, Jade Ivey Quillian

Yale Graduate School of Arts and Sciences Dissertations

The association between type 2 diabetes (T2D) and cognitive impairment has been well established. This is critical because T2D is a key risk factor for Alzheimer’s disease. However, these studies often fail to account for adiposity and other co-morbid conditions that accompany T2D in older adults. As a result, the mechanisms linking connecting T2D and cognitive impairment consequently remain unclear. The overall aim of this dissertation is to understand the precise effects of dysfunctional glucose metabolism on neurocognition. To do this I capitalized on a unique opportunity to study dysregulated glucose in youth from the Pathogenesis of Youth Onset Diabetes …

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Understanding The Double-Itcz Bias: From Ocean-Atmosphere Interactions To Future Climate Projections, Zhiyuan Li Jan 2025

Understanding The Double-Itcz Bias: From Ocean-Atmosphere Interactions To Future Climate Projections, Zhiyuan Li

Yale Graduate School of Arts and Sciences Dissertations

The double-ITCZ bias is one of the most persistent and long-standing model deficiencies in General Circulation Models (GCMs), affecting simulations of tropical precipitation patterns and future climate projections. This bias manifests as an unrealistic secondary Intertropical Convergence Zone (ITCZ) forming south of the equator, particularly in coupled ocean-atmosphere models. Since the ITCZ plays a crucial role in shaping global precipitation patterns, addressing this bias is essential for improving climate model reliability. CMIP6 projections indicate that the double-ITCZ feature may become more pronounced under global warming, raising the question of whether this enhancement represents a true climate change response or a …

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Unwanted Transitions Of A Superconducting Qubit Induced By Microwave Drives, Pavel Kurilovich Jan 2025

Unwanted Transitions Of A Superconducting Qubit Induced By Microwave Drives, Pavel Kurilovich

Yale Graduate School of Arts and Sciences Dissertations

Quantum bits built from microwave superconducting circuit components such as capacitors, inductors, and tunnel junctions are one of the leading platforms for realizing a fault-tolerant quantum computer. A roadblock towards this goal is the insufficient fidelity of operations -- single-qubit gates, two-qubit gates, and readout measurements -- performed on the quantum bits via microwave pulses. The main limitation of operation fidelity comes from decoherence. If the operation is performed too slowly compared to the decoherence time, a qubit error will happen. Usually, it is possible to speed up the operations by increasing the power of the microwave pulse. However, reducing …

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Light Sheet Microscopy For 3d Nanoscale Imaging, Hannahmariam Mekbib Jan 2025

Light Sheet Microscopy For 3d Nanoscale Imaging, Hannahmariam Mekbib

Yale Graduate School of Arts and Sciences Dissertations

Advances in expansion microscopy, a super resolution microscopy technique in which samplesare expanded up to ~8,000 times their original volume, require new microscope modalities to image the large sample sizes. These new techniques should be suitable for imaging large sample volumes, yet need to maintain the high 3D resolution of 250-500 nm of high-end confocal microscopy to provide the maximum level of detail and thereby reveal nanoscale cellular ultrastructure. Axially Swept Light Sheet Microscopy (ASLM) has emerged as a promising technique for generating high-resolution images at high-throughput. However, current designs struggle with the trade-off between limited resolution and field-of-view (FOV) …

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Programming Cell States With Emage And Engineered Allosteric Crispr Effectors In Saccharomyces Cerevisiae, Peter Ciaccia Jan 2025

Programming Cell States With Emage And Engineered Allosteric Crispr Effectors In Saccharomyces Cerevisiae, Peter Ciaccia

Yale Graduate School of Arts and Sciences Dissertations

Cells are self-replicating information processing systems that maintain control of internal state by gathering and expending chemical energy. Programming these cellular states requires complementary technological paradigms: genome editing methods define the phase space of possible cellular behaviors by modifying an underlying genetic blueprint, and transcriptional and allosteric control systems enable precise navigation within that defined space through spatiotemporal and environmentally responsive regulation. In this sense, genome editing and gene regulation tools work synergistically to expand ability to perturb, control, and monitor cellular function. No single genome editing or control paradigm optimally addresses all applications: eukaryotic MAGE (eMAGE) excels at generating …

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Circuit And Cell Class Specific Effects Of Psilocybin And Serotonergic Psychedelics, Pasha Davoudian Jan 2025

Circuit And Cell Class Specific Effects Of Psilocybin And Serotonergic Psychedelics, Pasha Davoudian

Yale Graduate School of Arts and Sciences Dissertations

Psychedelics are compounds that can alter perception and cognition and are being explored as treatments for depression, anxiety, and substance-use disorders. Yet, the mechanisms by which they reshape brain function remain poorly understood. This dissertation presents four studies in rodent models examining how psychedelics act across synapses, microcircuits, and whole-brain networks. Chapter 1 shows that a single dose of psilocybin promotes plasticity in the frontal cortex. Chapter 2 maps brain-wide activity induced by psilocybin and ketamine, linking shared and distinct effects to gene expression. Chapter 3 extends this approach to multiple psychiatric drugs, using machine learning to classify drug-specific circuit …

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In Terms Of Theory, Samuel Steinmetz Jan 2025

In Terms Of Theory, Samuel Steinmetz

Yale Graduate School of Arts and Sciences Dissertations

In Terms of Theory attends to theory in relation to the eighteenth-century novel and to early twentieth-century film, primarily as the taking account of the possibility of form—of the novel, of film, and of theory. The overarching argument of the dissertation, developed in chapter 1, is that the novel and film, as modern forms unknown to classical aesthetics, present particularly rich cases for exploring what theory does, what it looks like, how it relates to its subject, and what kind of knowledge it offers. The rest of the dissertation presents independent case studies: chapter 2 analyzes and contextualizes the style …

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Moral Uncertainty And Bargaining, Harry Reginald Lloyd Jan 2025

Moral Uncertainty And Bargaining, Harry Reginald Lloyd

Yale Graduate School of Arts and Sciences Dissertations

I develop and defend an original answer to the problem of moral uncertainty - the question of how to behave when one has at least some credence in more than one moral theory. My marketplace response to this problem models the moral theories in which one has credence using "theory representatives," who bargain with each other to determine how the morally uncertain decision maker is to behave. This marketplace approach gives plausible recommendations in a wide range of cases, and also escapes the various objections that have been levelled against other proposed solutions to the problem of moral uncertainty.

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Trade Unions And The Challenge Of Technological Displacement, Alexander Trubowitz Jan 2025

Trade Unions And The Challenge Of Technological Displacement, Alexander Trubowitz

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines trade unions' responses to the employment risks generated by labor-saving technological change in British and West German manufacturing during the third quarter of the twentieth century, an era of rapid technological advance and the period during which British manufacturing fell behind the German competition. Drawing on previously untapped archival evidence from both countries, this dissertation challenges existing views in comparative political economy and economic history regarding unions' attitudes toward technological change and the welfare state as well as received contrasts between coordinated capitalism in West Germany and its supposed opposite in Britain. Focusing on the engineering industry, …

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Roles For The Planar Cell Polarity Pathway In Postnatal Intestinal Patterning And Architecture, Rebecca Frances Lee Jan 2025

Roles For The Planar Cell Polarity Pathway In Postnatal Intestinal Patterning And Architecture, Rebecca Frances Lee

Yale Graduate School of Arts and Sciences Dissertations

The coordination and patterning of cells required for proper tissue architecture play a critical role in organ development and function. This process is especially important in the small intestine, which relies heavily on its unique architecture of “hills” (villi) and “valleys” (crypts) to maximize nutrient absorption. Stem cells from a single crypt generate daughter cells that migrate up the villus in a linear ribbon pattern to form villus ribbons, while progressively differentiating into zonated cell states. This differentiation is tightly correlated to distinct digestive functions through compartmentalized expression of nutrient transporters. Despite the implicit reliance of intestinal tissue physiology on …

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Cross-Stack Design Space Exploration For Energy-Efficient Ai Systems, Abhishek Moitra Jan 2025

Cross-Stack Design Space Exploration For Energy-Efficient Ai Systems, Abhishek Moitra

Yale Graduate School of Arts and Sciences Dissertations

The growing complexity of neural networks—from spiking neural networks (SNNs) to vision transformers (ViTs) and large language models (LLMs)—has posed major challenges for deployment on edge devices with limited compute and memory resources. This thesis addresses these challenges by proposing a suite of co-optimization strategies that span device, circuit, architecture, and algorithm layers to enable efficient AI inference on both analog and digital compute-in-memory (CiM) platforms. The first contribution, SpikeSim, presents an end-to-end simulation framework for evaluating SNNs on CiM hardware, uncovering key tradeoffs in neuronal memory, latency, and crossbar mapping. XPert introduces a differentiable co-search framework that jointly optimizes …

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Inference Of Somatic Selection In Cancer: Methods And Applications, Jeffrey Mandell Jan 2025

Inference Of Somatic Selection In Cancer: Methods And Applications, Jeffrey Mandell

Yale Graduate School of Arts and Sciences Dissertations

Cancers are predominantly understood as diseases in which somatic tissue lineagesacquire genetic or epigenetic alterations that confer traits which lead to aberrant cell growth. Such phenotypes include maintenance of proliferative signaling, resistance of apoptotic signaling, and immune suppression. In a microcosm of classical evolution, which progresses via random genetic drift and natural selection, somatic cells accumulate mutations throughout the life course. The small subset of mutations (or other heritable alterations) that provide proliferative advantages to the cells in which they occur tend to gain prevalence in subsequent generations, which may eventually lead to clonal evolution of cancer cell traits. While …

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United States Trade Policy Brief, Sylvie Nomeny Jan 2025

United States Trade Policy Brief, Sylvie Nomeny

Journal of Statesmanship & Public Policy: Briefs and Commentaries

No abstract provided.

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Unveiling The Spatial Cellular Dynamics And Regulatory Network In Glioblastoma, Shuozhen Bao Jan 2025

Unveiling The Spatial Cellular Dynamics And Regulatory Network In Glioblastoma, Shuozhen Bao

Yale Graduate School of Arts and Sciences Dissertations

Glioblastoma (GBM) is a grade IV astrocytoma, the most common malignant brain tumor in adults, which has a poor prognosis and high recurrence. To better understand the disease's fundamental mechanism, tremendous effort has been made to investigate the molecular and cellular interactions between malignant cells and the tumor microenvironment using single-cell technology. However, the spatial intra-tumoral information of GBM, including the disease progression regulatory network and cellular dynamics, has yet to be widely constructed. Our investigation undertakes a novel approach to address the challenges. Specifically, we employ different spatial omics technologies at all levels from epigenetics, transcriptomics, post-transcriptomics, and proteomics, …

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Extending And Improving The Study Of Gene Expression Regulatory Mechanisms, Isaac William Vock Jan 2025

Extending And Improving The Study Of Gene Expression Regulatory Mechanisms, Isaac William Vock

Yale Graduate School of Arts and Sciences Dissertations

Gene expression levels are a product of RNA synthesis and degradation kinetics. In addition, the bulk rates of RNA synthesis and decay are a function of the rates of several highly regulated biochemical steps, from transcription initiation, productive elongation, RNA processing, export from the nucleus, and degradation in either the cytoplasm or nucleus. When gene expression levels need to be regulated, cells can tune any combination of these kinetic parameters to achieve the desired change. If one only studies the levels of mature RNA and their fluctuations, one misses out on understanding the intricate kinetic regulation underlying gene expression. Because …

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Discovery Of Direct-Acting Small-Molecule Rig-I Agonists Through Creation Of A Selective Card Activation Platform, Rong Guo Jan 2025

Discovery Of Direct-Acting Small-Molecule Rig-I Agonists Through Creation Of A Selective Card Activation Platform, Rong Guo

Yale Graduate School of Arts and Sciences Dissertations

Retinoic acid-inducible gene I (RIG-I) is a human pattern recognition receptor (PRR) that plays a key role in the innate immune response against RNA viruses, including influenza viruses, coronaviruses, and flaviviruses. As a ubiquitously expressed protein in nearly all nucleated cells, RIG-I resides primarily in the cytoplasm, where it detects foreign RNA. Although RIG-I can bind to a variety of RNA molecules, it is selectively activated by viral RNAs that have specific structural features—such as blunt-ended double-stranded regions and 5′-triphosphates. Beyond its antiviral role, RIG-I has emerged as a promising target in cancer immunotherapy, largely due to its ability to …

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Cræft-Ing The Assembly: Political Vision In The Age Of Alfred, Megan Renz Perry Jan 2025

Cræft-Ing The Assembly: Political Vision In The Age Of Alfred, Megan Renz Perry

Yale Graduate School of Arts and Sciences Dissertations

This dissertation presents an early medieval vision of pastoral education and its desired political effects through analysis of the Old English Pastoral Care, which was translated from Latin in the ninth-century Alfredian educational revival. My study is grounded in the educational formation of the clerics whom Alfred recruited in the decade prior to the initiative: men of letters from neighboring Wales, Mercia, and Francia. These grammarian-translators envisioned forming vernacular readers in prudentia, that is, practical wisdom. I read Latin and Old English sources in light of the educational (chs. I- III), linguistic (ch. IV), philosophical (ch. V), and political (ch. …

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Identifying Quantitative Trait Loci Of Genetically Regulated Molecules To Reveal Biological Mechanisms In Complex Traits, Chen Lin Jan 2025

Identifying Quantitative Trait Loci Of Genetically Regulated Molecules To Reveal Biological Mechanisms In Complex Traits, Chen Lin

Yale Graduate School of Arts and Sciences Dissertations

Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases, but most of these variants reside in non-coding regions, making their biological functions challenging to study and interpret. To investigate the potential roles of these variants, expression quantitative trait locus (eQTL) analyses associate genetic variants with gene expression, providing insights into their regulatory roles. Integrating eQTL results with GWAS summary statistics has motivated transcriptome-wide association studies (TWAS), which focus on testing associations between imputed genetically regulated gene expression (GReX) and complex traits, offering a powerful gene-level view of genetic contributions to disease. Despite substantial …

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Exploration Of The Mechanisms Regulating Genomic Stability In Plants, Wenxin Yuan Jan 2025

Exploration Of The Mechanisms Regulating Genomic Stability In Plants, Wenxin Yuan

Yale Graduate School of Arts and Sciences Dissertations

Genomic stability is a cornerstone of cellular integrity, with implications spanning genetic engineering, epigenetic regulation, and disease modeling. However, most studies rely on yeast or mammalian models, leaving significant gaps in our understanding of plant chromatin biology and genome stability mechanisms. Exploring the conserved and divergent processes regulating genome stability in plants has become increasingly important, especially as global climate change threatens crop yields and biodiversity. Furthermore, the developmental resilience of plants provides a unique opportunity to study genes essential in mammals, offering translational insights for agriculture and human health. This dissertation investigates the molecular and genetic mechanisms underpinning T-DNA …

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Scalable Real-Time Decoding System For Quantum Error Correction, Namitha Godawatte Liyanage Jan 2025

Scalable Real-Time Decoding System For Quantum Error Correction, Namitha Godawatte Liyanage

Yale Graduate School of Arts and Sciences Dissertations

A real-time decoder capable of meeting the stringent requirements for accuracy, latency, and throughput is essential for fault-tolerant quantum computing. While prior work has demonstrated progress in decoding isolated logical qubits, scaling to interacting logical qubits introduces significantly greater challenges, as all logical qubits in the system must be decoded collectively. This thesis addresses these challenges through the design and implementation of DECOARC, a vertex-level parallel decoding architecture based on the decoding graph abstraction. DECOARC organizes parallel computing resources using a hybrid tree-grid topology. We instantiate DECOARC in this work through two complementary systems: HELIOS, for single logical qubits, and …

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Investigating The Seasonal And Interannual Evolution Of Dissolved Oxygen In The Arctic Ocean’S Canada Basin, Ashley Arroyo Jan 2025

Investigating The Seasonal And Interannual Evolution Of Dissolved Oxygen In The Arctic Ocean’S Canada Basin, Ashley Arroyo

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines the evolution of dissolved oxygen in the waters of the Arctic Ocean's Canada Basin. Dissolved oxygen concentrations in the ocean are initially set at the surface through air-sea exchange and subsequently modified by physical and biogeochemical processes as waters circulate and mix. The variability of dissolved oxygen in the Arctic Ocean across seasonal and interannual timescales provides valuable insight into the broader evolution of water masses in the Arctic Ocean. As dissolved oxygen concentrations are gradually depleted in deeper waters via biological consumption, and only replenished when waters return to the surface, their distribution provides a valuable …

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Learning Randomized Reductions For Security, Privacy, And Side-Channel Resilience, Ferhat Erata Jan 2025

Learning Randomized Reductions For Security, Privacy, And Side-Channel Resilience, Ferhat Erata

Yale Graduate School of Arts and Sciences Dissertations

Modern computing systems face multifaceted challenges in security, privacy, and leakage resilience. This dissertation makes four key contributions to addressing these challenges through novel combinations of symbolic reasoning, machine learning, and neurosymbolic techniques. First, it develops symbolic AI techniques for analyzing side-channel vulnerabilities in low-level code and quantum computers. I introduce novel symbolic register analyses to automatically detect power side-channel vulnerabilities in constant-time cryptographic implementations. Additionally, I demonstrate an algebraic reconstruction method using Mixed-Integer Linear Programming (MILP) optimization to reverse-engineer quantum circuits from power traces, enabling extraction of proprietary circuit information. Second, my research pioneers automated learning of randomized self-reductions …

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The Recruitment, Retention, And Motivation Of Black Male Teachers In K-12 Schools: A Perception Study, Ann M. Brame Jan 2025

The Recruitment, Retention, And Motivation Of Black Male Teachers In K-12 Schools: A Perception Study, Ann M. Brame

Doctor of Education Dissertations

Black male teachers have been underrepresented in K–12 classrooms since integration in the United States. This mixed methods exploratory sequential study investigated the recruitment, retention, and motivation of Black male teachers. The foundation of Maslow’s (1943) Hierarchy of Needs, Herzberg’s (1959) Two-Factor Theory, and Bell’s (1980) Critical Race Theory guided the investigation of the psychological, structural, and social-cultural variables that affect the experiences and retention of Black males in education. The quantitative phase examined survey data to determine patterns aligned with job satisfaction, motivation, and retention. Subsequently, the qualitative phase explored the individuals lived experiences through interviews that offered insights …

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A Qualitative Study On The Perspective Of Instructional Coaching Through The Lens Of Teachers, Coaches, And Administrators, Lamonica D. Mcnair Jan 2025

A Qualitative Study On The Perspective Of Instructional Coaching Through The Lens Of Teachers, Coaches, And Administrators, Lamonica D. Mcnair

Doctor of Education Dissertations

Instructional coaching can be a key puzzle piece in teacher improvement and the academic success of students. This qualitative study examined the perspectives of administrators, teachers, and instructional coaches on the role that instructional coaches play in education and how the process of instructional coaching works. Further, the study sought to determine the perceptions of specific supports and barriers to effective coaching, and to examine the effectiveness of coaching through the experiences of both the coach and the teacher. It also examined the role of the school leader in an effective coaching program. Knight’s (2022c) The Definitive Guide to Instructional …

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The Impact Of High-Stakes Summative Reading Outcome Measures On Student Self-Efficacy, Hayley M. Johnson Jan 2025

The Impact Of High-Stakes Summative Reading Outcome Measures On Student Self-Efficacy, Hayley M. Johnson

Doctor of Education Dissertations

The purpose of this mixed methods study was to explore the influence of high-stakes reading tests on student self-efficacy, or confidence, as readers. The study focused on sixth-grade students who had taken the reading end-of-grade (EOG) test in Grades 3, 4, and 5. I analyzed their third-grade reading EOG scores to determine if that score was predictive of the fourth-grade reading EOG score and repeated the same analysis to see if fourth-grade reading EOG scores were predictive of fifth-grade scores. Then, those sixth-grade students' reading self-efficacies, as measured by the Butz and Usher (2015) Self-Efficacy Survey, were compared to their …

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The Influence Of Letrs Volume 1 On Elementary Teachers’ Perceptions And Practices Around Systematic Phonics Instruction In A Rural School In North Carolina, Katherine P. Wise Jan 2025

The Influence Of Letrs Volume 1 On Elementary Teachers’ Perceptions And Practices Around Systematic Phonics Instruction In A Rural School In North Carolina, Katherine P. Wise

Doctor of Education Dissertations

This dissertation is a mixed methods study that examined the influence Language Essentials for Teachers of Reading and Spelling (LETRS) Volume 1 had on elementary educators’ perceptions and practices around systematic phonics instruction in a rural, Title I elementary school in North Carolina. Adult learning theory was the theoretical framework used to ground this study. A sequential explanatory design was used: Quantitative data were collected through surveys, and qualitative data gathered through interviews were used to help frame and explain the quantitative data. Both data sources overwhelmingly supported that the completion of this professional learning positively influenced teachers’ perceptions of …

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