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Dynamical Mechanisms Of Neural Computation, Frederick Michael Berl

Yale Graduate School of Arts and Sciences Dissertations

The brain is one of the most complex dynamical systems in the universe and despite our everyday familiarity with it, the intricacies of how it functions remain a mystery to us. It is enormously powerful, continuously learning, and able to perform computations flexibly and adapt to novel situations. Although science presently has an understanding of how individual neurons work and a general idea of what the functions of each region in the brain are, how the computations of each neuron are modulated by context and how the various regions work together to produce behavior are unclear. Here, we explore the …

A Possible Mechanism Of Miwi2-Mediated Dna Methylation By De Novo Dna Methyltransferases, Tianshu Liu

Yale Graduate School of Arts and Sciences Dissertations

Epigenetic information refers to inheritable information that is not directly encoded in the genomic locus. Among various epigenetic mechanisms, DNA methylation play a crucial role in development and homeostasis and undergoes dynamic remodeling during mouse embryogenesis. In the mouse germline, primordial germ cells experience a global erasure of DNA methylation, a process important for the re-establishment of parent-specific methyl-imprint in the late stage of gametogenesis. However, how DNA methylation occurs at specific genomic loci remains an open question. Miwi2, one of three murine PIWI proteins, has been implicated in guiding de novo DNA methylation, yet the molecular machinery of Miwi2-mediated …

Adaptation Of Learning Dynamics And Feature Representations Via The Neural Kernel, Lianghui Peng

Yale Graduate School of Arts and Sciences Dissertations

The ability to learn from experience is essential for both biological and artificial agents. To learn efficiently in complex, high-dimensional environments, agents must generalize strategically from limited data by focusing on features relevant for the task. The generalization strategy, known as inductive bias, shapes the dynamics of learning. Previous works have established the theory of neural tangent kernels that describes the learning dynamics of artificial neural networks. However, a comparable framework for understanding and quantifying inductive bias in biological systems performing behavioral tasks remains underdeveloped. Here, we introduce a neural kernel framework to characterize inductive biases of humans and artificial …

Exploring Squamate Evolution Through Focused Taxonomic And Anatomic Lenses: A Taxon-Character Approach To A Taxon-Character Problem, Dalton Meyer

Yale Graduate School of Arts and Sciences Dissertations

Among the living terrestrial vertebrates, the greatest diversity of verifiable species is seenamong the squamates, the group which contains the lizards and snakes. With a global distribution limited only by their general intolerance to long periods of cold temperatures, they are a ubiquitous component of modern ecosystems. Furthermore, over their roughly 180-million-year evolutionary history they have achieved tremendous morphological disparity and a range of body sizes that spans three orders of magnitude. However, our understanding of the origins and early evolution of squamates remains obscured due to persistent conflict in hypotheses generated from morphological and molecular data. This discordance is …

A Second Wave Of Notch Signaling Diversifies The Intestinal Secretory Lineage, Eleanor Zagoren

Yale Graduate School of Arts and Sciences Dissertations

The small intestine is well known for its nutrient-absorbing enterocytes; yet equally crucial for homeostasis is a diverse set of secretory cells, all presumed to originate from the same intestinal stem cell. Despite their major roles in intestinal function and health, understanding how the full spectrum of secretory cell types arises remains a longstanding challenge, largely due to their comparative rarity. Here, I investigate the specification of a rare population of small intestinal epithelial cells found in rats and humans but not mice: CFTR high expressers (CHEs). Using pseudotime trajectory analysis of single-cell RNA-sequencing data from rat jejunum, I provide …

Valuing Cheap: Constructing, Consuming, And Contesting The Dollar Store Economy, Frances Evelyn Barrett

Yale Graduate School of Arts and Sciences Dissertations

In Valuing Cheap, Barrett traces the histories of Dollar General, Family Dollar, and Dollar Tree from the firms’ twentieth century origins in three distinct southern locales into corporate behemoths with more stores than McDonald’s or Walmart. Valuing Cheap provides an important chapter of the late twentieth century history of racial capitalism, detailing how dollar stores at once “served” local communities while capitalizing on existing spatialized, racialized, classed, and gendered inequalities. This history illuminates the interwovenness of business, consumer, and labor histories, emphasizing the fundamental entanglements of power, material and cultural production, and consumption. The dollar store industry’s cheap goods, low-wage …

Random Matrices And Statistical Inference With Correlated Structures, Haoyu Wang

Yale Graduate School of Arts and Sciences Dissertations

Random matrices play a central role in modern probability theory and high-dimensionalstatistics, both as fundamental mathematical objects and as powerful tools for inference. This dissertation presents several works on random matrix theory and its connections to statistical inference with correlated structures in high dimensions. On the random matrix side, we investigate the spectral properties of sample covariancematrices. Our approach is built upon the resolvent method, and we utilize local laws for various spectral analyses. Specifically, our contributions are three-fold: (1) we attain the first explicit rate of convergence for the largest eigenvalue of sample covariance matrices; (2) we derive the …

Russian Forms: Race, Sex, And The Making Of Russian Literature, Fiona Bell

Yale Graduate School of Arts and Sciences Dissertations

This dissertation argues that the elaboration of Russian racial imaginaries was coterminous with the construction of the Russian literary canon and Russian literary theory. Beginning with the global debates concerning the abolition of slavery and serfdom in the 1850s and concluding with the first wave of emigration from the Soviet Union in the 1920s, the dissertation demonstrates how canonical Russian authors—Ivan Turgenev, Fyodor Dostoevsky, Viktor Shklovsky, and others—wrote fiction that, in mobilizing the racial implications of intimacy, kinship, and heredity, articulated arguments about racial difference and the conceptual “fit” of “race” for the Russian Empire. Literary authors make arguments about …

Bridging Behavior And Neural Activity: Neural Dynamics Leading To Self-Initiated And Task-Driven Movements, Yongxu Zhang

Yale Graduate School of Arts and Sciences Dissertations

Understanding how populations of neurons generate behavior remains a fundamental question in neuroscience. While single-neuron analyses have provided valuable insights, behavior emerges from the coordinated dynamics of large neural ensembles that evolve over time and across states. A major difficulty is that neural population activity is non-stationary: it exhibits temporal distributional shifts, transitions between distinct dynamical regimes, and modulation by external or inter-regional inputs. Advances in artificial intelligence offer new opportunities to address this challenge. Yet, conventional models, such as standard recurrent neural networks, often fail to capture such complexity, limiting both predictive performance and mechanistic interpretability. This motivates the …

(1+1)D Topological Phases Enriched With Fusion Category Symmetries, Xinping Yang

Yale Graduate School of Arts and Sciences Dissertations

Symmetry and its anomaly constrain a system's dynamics and provide a universal characterization of its behaviors. It serves as a powerful tool to understand exotic phases of matter, especially symmetry-protected topological (SPT) orders. The notion of generalized symmetries requires extending our previous understanding of topological phases to those enriched by fusion category symmetries, yet new mathematical formalism is needed to apply unitary fusion category symmetries to a microscopic system. This thesis starts with a model-independent description of an abstract spin chain viewed as a net of C*-algebras. From a microscopic SymTFT, categorical structures describing symmetry and symmetry charges can be …

Outside The Workshop: Alternative Spaces Of U.S. Printmaking, 1935–1977, Michelle Donnelly

Yale Graduate School of Arts and Sciences Dissertations

The studio, the land, the camp, and the home are vital locations of print production. Yet scholars have overwhelmingly focused on prints made in the workshop, or an institutional facility stocked with specialized equipment and overseen by “master printers.” This dissertation investigates how women artists and artists of color expanded the parameters of printmaking outside the traditional site of the workshop from 1935 to 1977 in the United States. Each spatially organized chapter centers on one artist: David Hammons, Sari Dienes, Matsusaburo “George” Hibi, and Ruth Asawa. All four artists practiced what I call emplaced printmaking: an engagement with the …

Real-Time Minimum-Weight Parity Factor Decoders For Quantum Error Correction, Yue Wu

Yale Graduate School of Arts and Sciences Dissertations

Quantum error correction (QEC) is essential for fault-tolerant quantum computing, but its practical deployment is limited by the complexity of decoding. Most-Likely-Error (MLE) decoding offers near-optimal accuracy but is computationally challenging, especially for general quantum Low-Density Parity-Check (qLDPC) codes. This dissertation develops a family of Minimum-Weight Parity Factor (MWPF) decoders that accelerate MLE decoding by exploiting the locality and parallelism inherent in the decoding problem. We first improve locality by designing decoders that operate on the sparse decoding hypergraph rather than the dense syndrome graph. This leads to an almost-linear average runtime and enables a generalization to hypergraphs with certifying …

Incorporating Environmental Information Into Genetic Studies Of Psychiatric Disorders, Yue Hu

Yale Graduate School of Arts and Sciences Dissertations

Psychiatric disorders are among the most common diseases of humans, affecting a large number of individuals worldwide and contributing to a considerable burden of disease and disability. With a lifetime prevalence ranging from 5% to 17%, depression – characterized by a persistent low mood or loss of interest in activities for extended periods – is prominent amongst psychiatric disorders. Despite the availability of new medications developed over the past decade to treat depression, long-term treatment response remains disappointing; the risk of death by suicide is over 8-times national averages. Depression is multifactorial with both genetic and environmental factors, including demographic …

Warm Life, Cold Stones: The Effigial Tomb In Late Medieval English Literature, Maia Ruth Béar

Yale Graduate School of Arts and Sciences Dissertations

The effigial tomb is one of the defining features of Gothic sacred art. Tombs topped with grand effigies populated the churches, cathedrals, and chapels of late medieval England and many survive to this day. This dissertation explores the encounter with these tombs as represented in the literature of the period, in particular hagiography, romance, and narrative poetry. Although it literally demarcates the boundary between dead and living, the tomb is a powerful site of boundary-breaking in these texts at which the distinctions between life and death, flesh, and natural and artistic bodies are tested and often complicated. I consider various …

Advancing Neuroimaging Brain-Behavior Machine Learning Biomarkers, Brendan Adkinson

Yale Graduate School of Arts and Sciences Dissertations

Machine learning models trained on human neuroimaging data are increasingly used as tools for predicting individual behavioral phenotypes and enhancing precision medicine. However, multiple limitations hinder their current scientific and future clinical utility. In this dissertation, I address key challenges surrounding "brain-behavior" predictive model interpretability, generalization, and bias. In Chapters 2 and 3, I show that prevalent feature selection practices overlook features that are meaningful for both prediction and neurobiological interpretation. This suggests that prevailing approaches lead to feature overinterpretation and a misrepresentation of the neurobiological bases of brain-behavior associations. In Chapters 4 and 5, I demonstrate that brain-behavior predictions …

Distrust Of Psychotherapy For Biologically Explained Mental Disorders: A Validation Of Beliefs Underlying This Distrust And Interventions To Mitigate This Distrust, Annalise Perricone

Yale Graduate School of Arts and Sciences Dissertations

Lay and scientific communities alike increasingly attribute mental disorders to biological causes (e.g., genetic risk or neurobiological abnormalities). Biological explanations of mental disorders have some beneficial consequences, including reduced personal blame of individuals affected by such disorders. One adverse consequence, however, is that upon learning that a mental disorder has a biological etiology, people tend to show reduced trust in the effectiveness of psychotherapy. Given that the combination of psychotherapy and pharmacotherapy is often optimal for many mental disorders, reduced trust of psychotherapy could result in poorer clinical outcomes, if people elect not to receive such treatment. Although this distrust …

Bosonization And Fermionization Of Categorical Symmetries, Karan Bhatia

Yale Graduate School of Arts and Sciences Dissertations

The thesis investigates the processes of bosonization and fermionization within the framework of fusion category symmetries, which serve as the mathematical language for understanding topological phases of matter. We show that all fermionic fusion categories can be bosonized via a minimal braiding construction, providing a systematic method to relate fermionic and bosonic topological orders. Conversely, certain bosonic fusion categories that contain a Z_2 symmetry object can be fermionized using the same construction. However, a concrete obstruction arises when attempting to fermionize the remaining bosonic fusion categories, specifically those whose fusion rules involve two fixed points fusing into an odd number …

Investigation Of How Long Noncoding Rna Pvt1 Regulates Myc Expression, Qiao Li

Yale Graduate School of Arts and Sciences Dissertations

Long noncoding RNAs (lncRNAs) play essential roles in both physiological processes and disease, including cancer. A growing body of evidence positions lncRNAs as key regulators and biomarkers in tumorigenesis. Mechanistically, functional lncRNAs can regulate gene expression through epigenetic and transcriptional pathways, acting either via scaffold-like motifs that recruit regulatory complexes or through their abundance, which contributes to RNA-mediated feedback that modulates transcriptional condensates. Within the Plasmacytoma variant translocation 1 (Pvt1) locus, two alternative transcription start site isoforms have been identified: the constitutively expressed Pvt1a and the stress-inducible Pvt1b. While the precise functions of Pvt1a were not well understood, previous studies …

Two Paradigms Of Research And Their Influence On The Study Of Animal Behaviour, David Fraser

General - Animal Cognition and Behavior

Taxonomist Roy Crowson identified a fundamental difference among sciences. What he called “natural history” is exemplified by classical biology; it begins by observing, describing and classifying phenomena in the real world, then seeks patterns and concepts that help to synthesize and explain the observations, and proceeds to measurement and experimentation grounded in that framework. What he called “natural philosophy” is exemplified by classical physics; it postulates fundamental principles or concepts that are thought to apply universally, and the research proceeds more directly to measurement and experimentation directed at these principles or concepts. The study of animal behaviour has been influenced …

Cure Newsletter Volume 4 Issue 2, Department Of Oncology

Cancer Updates Research & Education (CURE) Archives

• Message from the Chair
• Conferences & Workshops
• Conferences & Workshops
• Invited Talk
• Events and Celebrations
• Umeed Parr
• Awards and Achievements
• Oncology Social Media
• Oncology CPSP
• Residents & Fellows
• Spotlight on Faculty Contributions
• Nursing Oncology
• Nursing Awards Oncology Appreciation Evening 2024
• Upcoming Events Oncology
• Appointments
• Promotions
• Publications

Cure Newsletter Volume 4 Issue 3, Department Of Oncology

Cancer Updates Research & Education (CURE) Archives

• Message from the Chair
• Advancing Oncology Through Education & Exchange
• Clinical Conversations & Collaborations
• Voices from Oncology “Invited Perspectives”
• Spotlight on Achievements
• Workshops Spotlight: Nurturing Clinical Excellence
• Moments That Matter "Celebrating Together”
• Umeed Parr
• Social Media Spotlight
• Oncology at CPSP “The Academic Contributions”
• Resident Reflections "Future Leaders in Oncology"
• Nursing Highlights
• The upcoming Event at Oncology
• Clinical Wisdom Shared via Grand Rounds
• Welcoming New Colleagues, “New Strengths”
• “Climbing Higher”, Promotions at Oncology
• “Where Research Meets Impact” Oncology Publications

Description’S Displacements: Writing Experience In Musil, Benjamin, And Bachmann, Aida Feng

Yale Graduate School of Arts and Sciences Dissertations

This dissertation unfolds the ways in which description emerged as an active site for reconfiguring human experience in the writing experiments of the 20th century. Description, as a procedure for presenting and arranging the phenomena of reality, typically constructs an epistemological realm of experience that progresses toward comprehension and internal consistency. Understood in this way, description mediates one kind of experiential reality while foreclosing others. This project enlarges description’s operative capabilities toward a presentational mode that does not merely re-describe the phenomenal objects in this reality. To do so, it foregrounds writers and thinkers who conversed directly with philosophical traditions …

Aligning Water And Carbon Goals In Sustainable Transitions To Clean Energy, Yan Du

Yale Graduate School of Arts and Sciences Dissertations

As the global energy sector transitions toward cleaner and more sustainable sources, understanding the interdependencies between energy production and water resources becomes increasingly critical. Water is an essential input across a wide range of energy technologies – both conventional and renewable – impacting not only power generation efficiency but also broader dimensions of environmental sustainability, climate resilience, and resource equity. These interdependencies are central to the water-energy nexus, where decisions about one resource inevitably affect the other. In this context, assessing water-use efficiencies across diverse energy systems offers valuable insights into how societies can optimize resource allocation, minimize ecological impacts, …

Development And Mechanistic Investigation Of First-Row Transition Metal-Catalyzed Alkene Functionalization Reactions, Juan Serviano

Yale Graduate School of Arts and Sciences Dissertations

This thesis describes the discovery and mechanistic studies of cobalt- and iron-catalyzed alkene hydrofunctionalization reactions. Chapter 1 introduces the fields of alkene hydrofunctionalization via metal-catalyzed hydrogen atom transfer (MHAT) and first-row transition metal-catalyzed alkene dicarbofunctionalization. Chapter 2 describes a method for intermolecular hydroalkoxylation and hydrocarboxylation of 2-azadienes using oxidative cobalt-catalyzed hydrogen atom transfer. The method generates 2-azaallyl cation equivalents under mild conditions to yield hemiaminal ethers and esters, and is chemoselective for 2-azadienes in the presence of other C=C double bonds. Chapter 3 describes the synthesis, characterization, and reactivity of an isolable alkylcobalt complex that models an intermediate proposed in …

Functional Roles Of Subcellularly Localized Glycolytic Isoforms Of Glucose 6-Phosphate Isomerase, Ian Joseph Gonzalez

Yale Graduate School of Arts and Sciences Dissertations

While metabolic pathways are largely conserved across cells and organisms, tissues exhibit metabolic heterogeneity that tailors metabolism to their physiological demands. How the conserved pathways of metabolism achieve metabolic heterogeneity is incompletely understood, particularly in vivo. In this dissertation, I investigate the genetic requirement of glucose 6-phosphate isomerase (GPI-1), a conserved glycolytic enzyme that also regulates the pentose phosphate pathway (PPP). Using CRISPR-Cas9 genome editing, I found that gpi-1 knockout animals display germline defects consistent with impaired PPP, and somatic defects consistent with impaired glycolysis. I discovered that GPI-1 isoforms are differentially expressed and localized: GPI-1A is cytosolic in all …

Epidemiologic And Immunologic Characterization Of The Post-Acute Sequelae Of Covid-19, Christine Marie Miller

Yale Graduate School of Arts and Sciences Dissertations

Since its emergence in late 2019, SARS-CoV-2 has infected over 15 million people—and the number continues to rise. The global impact of this novel coronavirus has been profound, reshaping not only public health infrastructure but also our understanding of human biology. The full extent of the virus’s effects on the immune system remains incompletely understood and will likely take years to fully unravel. What is already evident, however, is that SARS-CoV-2 uniquely modulates both innate and adaptive immunity, with consequences that span the developmental spectrum—from fetal and pediatric stages through adulthood. While many individuals recover without overt clinical sequelae, an …

Glycolysis-Induced Acidification Links Mitochondrial Deficiency To Axon Degeneration, Hadas Dabas

Yale Graduate School of Arts and Sciences Dissertations

Axons extend far from the neuronal soma and depend on local energy metabolism to sustain signaling and structural integrity. Mitochondria are normally abundant in axons, where they provide numerous utilities. In many neurodegenerative diseases, however, mitochondrial function or trafficking is impaired, but the mechanisms linking mitochondrial loss to axon degeneration remain unclear.In this dissertation, I use C. elegans mitochondrial trafficking mutants, in which axons completely lack mitochondria, to define the metabolic basis of degeneration. I find that glycolysis, typically viewed as a protective energy source, unexpectedly promotes axon breakdown. Elevated glycolytic flux in axons without mitochondria leads to accumulation of …

Advanced Spectroscopic Techniques For Probing The Photophysical Properties Of Metal Halide Perovskites, Shunran Li

Yale Graduate School of Arts and Sciences Dissertations

Metal halide perovskites (MHPs) have emerged as a versatile class of semiconductors with exceptional optoelectronic properties, yet their performance is intricately linked to their structural, dynamical, and photophysical characteristics. This dissertation presents a comprehensive investigation of MHPs—spanning three-dimensional, low-dimensional, and lead-free double perovskite compositions—using advanced spectroscopic techniques from the mid-infrared to X-rays. Steady-state optical spectroscopies are employed to probe ground-state properties and structure–property relationships, with emphasis on chiral 2D hybrid perovskites. A reflection-based methodology is developed to determine the intrinsic circular-polarization-dependent complex refractive index of single crystals, enabling quantitative separation of circular dichroism and birefringence. The formation of distinct spherulitic …

Associations Between Mental Health Conditions And Adverse Pregnancy Outcomes Among Active-Duty Servicewomen, Laura Manzo

Yale Graduate School of Arts and Sciences Dissertations

Active duty servicewomen (ADSW) have increased risk for mental health conditions compared to civilian women. Civilian research demonstrates that women with mental health conditions experience serious pregnancy complications at rates 50% higher than those without mental health conditions. Although mental health conditions are the leading underlying cause of maternal mortality, there is limited research on the prevalence of perinatal mental health conditions among active duty servicewomen (ADSWs) or their association with adverse pregnancy outcomes. This study aimed to explore associations of mental health conditions and adverse pregnancy outcomes in a population of ADSW. Methods Department of Defense Birth and Infant …

‘Soñando En Un Futuro Mejor’: U.S. Empire, Racial Capitalism, And Garífuna And Afro-Caribbean Radicalism In Caribbean Honduras, 1920-1963, Cristian Jose Padilla Romero

Yale Graduate School of Arts and Sciences Dissertations

This dissertation argues that Afro-Caribbean and Garífuna radicals in 20th-century Honduras forged, at different times, radical, race-conscious, and sometimes anti-imperialist and nationalist politics that contested both U.S. corporate domination and the racialized exclusions of the U.S and Honduran nation-state. Focusing on the period between 1920 and 1963, it traces struggles across the Caribbean coastal cities of La Ceiba, Trujillo, Puerto Cortés, and Tela. By foregrounding Black and Indigenous working-class actors, like Centeno García and Alfonso Lacayo, it highlights how racial capitalism, labor radicalism, and anti-Black state and corporate repression intersected in Honduras’ banana economy. The stories of individuals like Centeno …