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Hearing The Tonality In Microtonality, Michael Bruschi Apr 2021

Hearing The Tonality In Microtonality, Michael Bruschi

Yale Graduate School of Arts and Sciences Dissertations

In the late 1970s and 1980s, composer-pianist Easley Blackwood wrote a series of microtonal compositions exploring the tonal and modal behavior of a dozen non–twelve-tone equal temperaments, ranging from 13 to 24 tones per octave. This dissertation investigates a central paradox of Blackwood’s microtonal music: that despite being full of intervals most Western listeners have never heard before, it still seems to “make sense” in nontrivial ways. Much of this has to do with the music’s idiosyncratic approach to tonality, which I define as a regime of culturally conditioned expectations that guides one’s attentional processing of music’s gravitational qualities over …

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Intuitive And Accurate Material Appearance Design And Editing, Weiqi Shi Apr 2021

Intuitive And Accurate Material Appearance Design And Editing, Weiqi Shi

Yale Graduate School of Arts and Sciences Dissertations

Creating and editing high-quality materials for photorealistic rendering can be a difficult task due to the diversity and complexity of material appearance. Material design is the process by which artists specify the reflectance properties of a surface, such as its diffuse color and specular roughness. Even with the support of commercial software packages, material design can be a time-consuming trial-and-error task due to the counter-intuitive nature of the complex reflectance models. Moreover, many material design tasks require the physical realization of virtually designed materials as the final step, which makes the process even more challenging due to rendering artifacts and …

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Motive-Directed Meter, Daniel Nathan Cox Apr 2021

Motive-Directed Meter, Daniel Nathan Cox

Yale Graduate School of Arts and Sciences Dissertations

This dissertation isolates, defines, and explores the phenomenon of Motive-Directed Meter (MDM), which has hitherto received little scholarly attention. MDM is a listening experience evoked by music that is temporally regular enough to encourage metric listening and prediction, but irregular enough to frustrate these behaviors. MDM arises when recurring musical motives suggest parallel metric hearings, but shifting durational spans make metrical parallelism difficult to achieve. Listeners are therefore caught in a state of expectational limbo, urged to continually revise predictions that are recurrently thwarted. To approach this phenomenon, Chapter 1 describes the model of musical meter that undergirds this project, …

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Analyzing The Role Of Er Membrane Biogenesis In Mitotic Fidelity, Holly Elizabeth Merta Apr 2021

Analyzing The Role Of Er Membrane Biogenesis In Mitotic Fidelity, Holly Elizabeth Merta

Yale Graduate School of Arts and Sciences Dissertations

In cell division, chromosomes align and attach to the mitotic spindle with high fidelity in order to limit missegregation of chromosomes that form individual nuclei, termed micronuclei. During cell division, membrane-bound organelles are cleared to the periphery of the cell; lack of clearance of membranes from chromosomes leads to chromosome missegregation. Cells regulate the biogenesis of their membranes throughout the cell cycle. Cancer cells frequently have upregulation of membrane lipid synthesis and micronuclei, but a connection between membrane biogenesis and chromosome missegregation leading to formation of micronuclei has not been established. In my thesis work, I show that the protein …

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Co-Transcriptional Splicing In Murine Erythroblasts, Kirsten Reimer Apr 2021

Co-Transcriptional Splicing In Murine Erythroblasts, Kirsten Reimer

Yale Graduate School of Arts and Sciences Dissertations

Eukaryotic genes contain non-coding sequences called introns. The removal ofintrons from pre-mRNAs, termed splicing, is carried out by the spliceosome, a multi-megadalton molecular complex of proteins and RNAs. Splicing occurs cotranscriptionally across multiple cell types and species. The Neugebauer lab has developed single molecule nascent RNA sequencing methods—including single molecule intron tracking (SMIT) and long-read sequencing (LRS) of nascentRNA— to visualize the precursors, intermediates, and products of transcription and splicing in budding and fission yeasts. Using these methods, the lab was able to estimate the kinetics of single intron removal in both yeasts by relating the 30 end of nascent …

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Improving Risk Factor Identification Of Human Complex Traits In Omics Data, Weimiao Wu Apr 2021

Improving Risk Factor Identification Of Human Complex Traits In Omics Data, Weimiao Wu

Yale Graduate School of Arts and Sciences Dissertations

With recent advances in various high throughput technologies, the rise of omics data offers a promise of personalized health care with its potential to expand both the depth and the width of the identification of risk factors that are associated with human complex traits. In genomics, the introduction of repeated measures and the increased sequencing depth provides an opportunity for deeper investigation of disease dynamics for patients. In transcriptomics, high throughput single-cell assays provide cellular level gene expression depicting cell-to-cell heterogeneity. The cell-level resolution of gene expression data brought the opportunities to promote our understanding of cell function, disease pathogenesis, …

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Diffusion-Based Approaches To Visualization And Exploration Of High-Dimensional Data, Scott Anthony Gigante Apr 2021

Diffusion-Based Approaches To Visualization And Exploration Of High-Dimensional Data, Scott Anthony Gigante

Yale Graduate School of Arts and Sciences Dissertations

In recent years, modern technologies have enabled the collection of exponentially larger quantities of data in the biomedical domain and elsewhere. In particular, the advent of single-cell genomics has allowed for the collection of datasets containing hundreds of thousands of cells measured in tens of thousands of dimensions. This rapid expansion of common datasets beyond the possibility of manual annotation brings forth the need for large-scale exploratory data analysis. In this thesis, we will explore the problem of dimensionality reduction for visualization of high-dimensional datasets. Visualization of high-dimensional data is an essential task in exploratory data analysis, as the low-dimensional …

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Latent Factor Analysis Of High-Dimensional Brain Imaging Data, Siyuan Gao Apr 2021

Latent Factor Analysis Of High-Dimensional Brain Imaging Data, Siyuan Gao

Yale Graduate School of Arts and Sciences Dissertations

Recent advances in neuroimaging study, especially functional magnetic resonance imaging (fMRI), has become an important tool in understanding the human brain. Human cognitive functions can be mapped with the brain functional organization through the high-resolution fMRI scans. However, the high-dimensional data with the increasing number of scanning tasks and subjects pose a challenge to existing methods that wasn’t optimized for high-dimensional imaging data. In this thesis, I develop advanced data-driven methods to help utilize more available sources of information in order to reveal more robust brain-behavior relationship. In the first chapter, I provide an overview of the current related research …

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Polybrominated Diphenyl Ethers, Thyroid Hormones, And Risk Of Papillary Thyroid Cancer, Huang Huang Apr 2021

Polybrominated Diphenyl Ethers, Thyroid Hormones, And Risk Of Papillary Thyroid Cancer, Huang Huang

Yale Graduate School of Arts and Sciences Dissertations

Thyroid cancer is the most common cancer of the endocrine system. The incidence of thyroid cancer has increased worldwide for decades in the general populations and in the US military personnel. Although emerging evidence indicates that exposure to polybrominated diphenyl ethers (PBDEs) is related to disruption of thyroid hormone homeostasis, the association between exposure to PBDEs and risk of thyroid cancer is still unclear. Additionally, mutations in genes coding for enzymes involved in regulation, metabolism, or functional activation of PBDEs and thyroid hormones could modify the PBDEs and thyroid hormones related risk of thyroid carcinogenesis. Using data from a nested …

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Rethinking Aesthetic Humanism: Schiller After Agamben And Rancière, Thiti Owlarn Apr 2021

Rethinking Aesthetic Humanism: Schiller After Agamben And Rancière, Thiti Owlarn

Yale Graduate School of Arts and Sciences Dissertations

Since de Man, aesthetic humanism is often thought of as an ideology that valorizes the arts and their capacity to improve humanity. This study argues that something more important is at stake in Schiller’s aesthetics. Following Rancière, I argue that aesthetic experience is inherently meaning-disruptive and therefore not utilizable as means to an end. The fact that the aesthetic has this means-without-end structure allows us to reconceive of humanity, like Agamben, not as a rational animal or an end-setting subject, but as a figure of surplus potential, a life that gives itself form without being reducible to a specific way …

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Prototypical Arm Motions From Human Demonstration For Upper-Limb Prosthetic Device Control, Yuri Gloumakov Apr 2021

Prototypical Arm Motions From Human Demonstration For Upper-Limb Prosthetic Device Control, Yuri Gloumakov

Yale Graduate School of Arts and Sciences Dissertations

Controlling a complex upper limb prosthesis, akin to a healthy arm, is still an open challenge due to the inadequate number of inputs available to amputees. Designs have therefore largely focused on a limited number of controllable degrees of freedom, developing a complex hand and grasp functionality rather than the wrist. This thesis investigates joint coordination based on human demonstrations that aims to vastly simplify the controls of wrist, elbow-wrist, and shoulder-elbow wrist devices.The wide range of motions performed by the human arm during daily tasks makes it desirable to find representative subsets to reduce the dimensionality of these movements …

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Hardware Architectures For Post-Quantum Cryptography, Wen Wang Apr 2021

Hardware Architectures For Post-Quantum Cryptography, Wen Wang

Yale Graduate School of Arts and Sciences Dissertations

The rapid development of quantum computers poses severe threats to many commonly-used cryptographic algorithms that are embedded in different hardware devices to ensure the security and privacy of data and communication. Seeking for new solutions that are potentially resistant against attacks from quantum computers, a new research field called Post-Quantum Cryptography (PQC) has emerged, that is, cryptosystems deployed in classical computers conjectured to be secure against attacks utilizing large-scale quantum computers. In order to secure data during storage or communication, and many other applications in the future, this dissertation focuses on the design, implementation, and evaluation of efficient PQC schemes …

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Environmental Assessments Of Capital-Intensive Product Systems, Travis Reed Miller Apr 2021

Environmental Assessments Of Capital-Intensive Product Systems, Travis Reed Miller

Yale Graduate School of Arts and Sciences Dissertations

The UN Sustainable Development Goals (SDGs) set out a bold vision to advance global society on multiple dimensions by the year 2030. The 17 SDGs tackle key issues of human wellbeing in part by building infrastructure, industrializing, and growing economies. The SDGs simultaneously aim to prevent climate change and conserve the natural environment. There are synergies between many of the goals, but clear tradeoffs as well. Investments in capital assets like buildings, roads, equipment, vehicles, and information technology come at an environmental cost. Innovative strategies are needed to grapple with these tradeoffs and optimize paths toward sustainable development. Innovative tools …

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Mechanisms Of Resource Competition With Intraspecific Variation, Erica Marie Holdridge Apr 2021

Mechanisms Of Resource Competition With Intraspecific Variation, Erica Marie Holdridge

Yale Graduate School of Arts and Sciences Dissertations

Intraspecific trait variation occurs in nearly all species and is found in a variety of traits, including morphological, behavioral, and physiological traits. Unlike fields such as evolutionary biology and behavioral ecology which have long recognized the importance of intraspecific trait variation (ITV), community ecologists have historically viewed ITV as “noise” that obscures broader population- and community-level patterns of interest. However, recent work has demonstrated that ITV can profoundly affect ecological interactions and processes through a variety of mechanisms (other earlier paper, Bolnick et al. 2011). Of particular interest is the effect of ITV on competition and coexistence. Empirical work has …

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Exoplanet Measurement To The Extreme: Novel Methods Of Instrumentation And Data Extraction For Radial-Velocity Spectrographs, Ryan Richard Petersburg Apr 2021

Exoplanet Measurement To The Extreme: Novel Methods Of Instrumentation And Data Extraction For Radial-Velocity Spectrographs, Ryan Richard Petersburg

Yale Graduate School of Arts and Sciences Dissertations

The current generation of radial-velocity spectrographs are at the precipice of discovering the first Earth-like exoplanets orbiting in the habitable zones of nearby stars. Such detections require Doppler precision of approximately 10 cm/s, an order of magnitude better than the typical best-case measurement from the previous generation of instruments. Therefore, the radial-velocity community requires research and innovation from all angles to push our technology over the brink. This thesis presents multiple contributions to this field---ranging from the development of precision laser equipment to the implementation of advanced statistical data analysis algorithms---all in support of the EXtreme PREcision Spectrograph (EXPRES) with …

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Genetically Encoded Biomaterials: Design, Characterization, And Applications For Functionalizing Biological Therapeutics, Koen Vanderschuren Apr 2021

Genetically Encoded Biomaterials: Design, Characterization, And Applications For Functionalizing Biological Therapeutics, Koen Vanderschuren

Yale Graduate School of Arts and Sciences Dissertations

Engineering of the translation apparatus has permitted site-specific incorporation of nonstandard amino acids (nsAAs) into proteins, thereby expanding the genetic code of organisms. Recent work in genome engineering has enabled whole genome recoding, in which codons removed from the genetic code can be repurposed as new sense codons dedicated for incorporation of nsAAs. This work describes our vision of how synthetic biology and genetic code expansion will allow the development of genetically encoded biomaterials -- a new class of biomaterials that marries the sequence-defined production, fidelity and processivity of ribosomal protein expression, with the vast molecular and structural diversity of …

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Infant Fmri: A Model System For Cognitive Neuroscience, Cameron Thomas Ellis Apr 2021

Infant Fmri: A Model System For Cognitive Neuroscience, Cameron Thomas Ellis

Yale Graduate School of Arts and Sciences Dissertations

Studying the infant mind and brain promises to benefit three distinct fields of science in critical ways. In developmental science, understanding infancy is necessary for appreciating the foundations of the human life and determining what changes with development. In cognitive science, revelations about infant cognitive capacities can constrain theories by limiting the possible explanations of how those capacities emerge. In neuroscience, infants offer the unique possibility to study large-scale neural change in humans, while also revealing principles that underlie the optimization of neural circuitry. Yet, there are limits on the kinds of questions that can be asked by the methods …

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Tracking Single Cell Lineages In Saccharomyces Cerevisiae, Guste Urbonaite Apr 2021

Tracking Single Cell Lineages In Saccharomyces Cerevisiae, Guste Urbonaite

Yale Graduate School of Arts and Sciences Dissertations

The ability to measure the number of gene-specific mRNA molecules in individual mammalian cells has transformed the transcriptomics field. Among the key technologies enabling single-cell mRNA sequencing has been Droplet Sequencing (Drop-Seq). While this method works efficiently for mammalian cells, its direct application to yeast cells has been problematic due to cell-type specific differences such as size, doublet formation rate, and cell wall. Here we introduce yeast DropSeq, a single-cell RNA sequencing method for the study of transcriptomics in yeast. I modified and optimized the original Drop-Seq method to address the issues that emerged from smaller cell sizes and the …

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Three Essays On Political Responses To Opioid Use In The United States, Lilla Orr Apr 2021

Three Essays On Political Responses To Opioid Use In The United States, Lilla Orr

Yale Graduate School of Arts and Sciences Dissertations

In the first two decades of the 21st century, opioid use in the United States has grown to unprecedented levels. Approximately half of the U.S. adult population has been prescribed an opioid based pain reliever, 1.7 million people have an opioid use disorder, and nearly 50,000 people die of opioid related overdoses each year. Public attitudes and drug policy have transformed in the wake of this staggering loss of life. These changes are often attributed to the racial, socioeconomic, and geographic profile of those most affected by the overdose and addiction epidemic, as well as the perceived culpability of physicians, …

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Entangled Revolutions: Cuba, Nicaragua, And The United States In The Cold War Caribbean, 1979-1990, Emily Snyder Apr 2021

Entangled Revolutions: Cuba, Nicaragua, And The United States In The Cold War Caribbean, 1979-1990, Emily Snyder

Yale Graduate School of Arts and Sciences Dissertations

“Entangled Revolutions” examines Cuba and Nicaragua’s revolutionary relationship with a sustained lens on institutions, ideology, gender, and local and international frames. My analysis first demonstrates how each revolution’s relationship with the other demanded, and produced, profound domestic and international effects. Nicaragua relied on Cuba for material support and technical expertise; Cuba looked to Nicaragua as a source of revolutionary radicalization. The United States crafted public diplomacy campaigns alongside the Contra insurgency in Nicaragua as it attempted to prevent “another Cuba.” Second, Cuban and Nicaraguan experiences of collaboration were heavily gendered. Though both revolutionary states sought to impose gendered logics on …

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Neurite Placement And Synapse Formation In Layered Neuropils, Titas Sengupta Apr 2021

Neurite Placement And Synapse Formation In Layered Neuropils, Titas Sengupta

Yale Graduate School of Arts and Sciences Dissertations

A fundamental design principle of nervous systems is the grouping of neuronal contacts into layers within nerve bundles. The layered arrangement of neurites requires nanoscale precision in their placement within bundles, and this precision, which cannot be exclusively explained by simple tip-directed outgrowth dynamics, underpins synaptic specificity and circuit architecture. For my thesis work, I implemented novel dynamic imaging methods and analyses and constructed fluorescent labeling tools to document the specific placement of single neurites during the assembly of the C. elegans nerve ring. We uncover a zippering mechanism that controls precise placement of neurites onto specific layer subdomains. Through …

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Where Do We Go When We Go Off-The-Grid?, Andrey Tolstoy Apr 2021

Where Do We Go When We Go Off-The-Grid?, Andrey Tolstoy

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines how the idea of going off-the-grid has affected the epistemology of documentary film, particularly three of its variants: romantic ethnography, observational cinema, and the essay film. The grid is understood to be a graphic design that is fundamental to modern cultural techniques, especially those involving the organization of objects and data, administration and governance. The grid as an organizational principle has been a definitive feature of modernity, particularly in so-called “disciplinary societies,” where its use intensified as a system of social control during industrialization and increasing urbanization. The expansion of the grid has resulted in a certain …

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Time As A Bridge From Brain To Behavior, Maxwell Shinn Apr 2021

Time As A Bridge From Brain To Behavior, Maxwell Shinn

Yale Graduate School of Arts and Sciences Dissertations

Time has mystified philosophers, artists, and scientists for centuries, but only recently has it become possible to study the neurobiology of time. Time is critical for cognition, and the mechanisms through which it impacts neural processes, such as those for decision-making, are starting to be better understood. Standard mathematical models for decision-making are not suited to studying stimuli or strategies which change over time, so we construct a generalization of a standard model as well as an efficient computational framework, providing insight at both the behavioral and the neural level. We use this framework to understand behavior and single-neuron recordings …

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Fraternité, Liberté, Égalité: Sophie De Grouchy, Moral Republicanism, And The History Of Liberalism, 1785-1815, Kathleen Theodora Mccrudden Apr 2021

Fraternité, Liberté, Égalité: Sophie De Grouchy, Moral Republicanism, And The History Of Liberalism, 1785-1815, Kathleen Theodora Mccrudden

Yale Graduate School of Arts and Sciences Dissertations

This thesis explores the political thought and activities of Sophie de Grouchy (1763-1822), author of Letters on Sympathy (1798) and wife of the philosophe and French Revolutionary the marquis de Condorcet. The chapters proceed chronologically and thematically. I begin by forwarding a new and earlier date for the drafting of Grouchy’s major treatise, Letters on Sympathy, and thus an original interpretation of this text. I argue that the central tenets of Grouchy’s philosophy, in particular her key argument that founds a knowledge of natural rights on the proper combination of sympathy and reason, were developed in response to her interest …

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Genomic Analysis Of 11,555 Probands Provides A Framework For Congenital Heart Disease Genetics, Michael Sierant Apr 2021

Genomic Analysis Of 11,555 Probands Provides A Framework For Congenital Heart Disease Genetics, Michael Sierant

Yale Graduate School of Arts and Sciences Dissertations

This dissertation presents the results from a genomic analysis of 11,555 congenital heart disease (CHD) probands with deep clinical phenotyping using a custom Molecular Inversion Probe Sequencing (MIPS) gene panel in order to further elucidate the genetic etiology of human CHD. CHD is a structural defect in the heart arising during development and afflicting ~1% of live newborns. CHD is a phenotypically complex and genetically heterogenous disease that frequently presents with congenital extracardiac abnormalities (EC) and neurodevelopmental deficits (NDD). The etiology for a majority of CHD cases is unknown and genotype-phenotype correlation is rare. Although hundreds of genes have been …

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Uncovering Novel Roles For Glia In Neurodegenerative Diseases, Leon Lall Tejwani Apr 2021

Uncovering Novel Roles For Glia In Neurodegenerative Diseases, Leon Lall Tejwani

Yale Graduate School of Arts and Sciences Dissertations

The complexity of the central nervous system poses a tremendous challenge for understanding the intricate interplay between the myriad cell types that comprise the brain and spinal cord. Understanding these interactions becomes especially challenging when examining dynamic processes, such as aging or disease. In genetic disorders, an additional layer of complexity emerges when multiple cell types express the disease-causing or disease-associated proteins, as this expression can contribute to pathophysiology through primary, cell autonomous effects and secondary, non-cell autonomous mechanisms. Identifying these cell type-specific changes and interpreting them in the overall context of the disease have remained difficult, especially in the …

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High-Throughput Experimental Strategies: The Highway To New Complex Alloys And Understanding Complex Phenomena, Sebastian Alexander Kube Apr 2021

High-Throughput Experimental Strategies: The Highway To New Complex Alloys And Understanding Complex Phenomena, Sebastian Alexander Kube

Yale Graduate School of Arts and Sciences Dissertations

Metallurgical research is struggling to build a satisfactory understanding of various complex alloy classes and phenomena. For many of these problems, such as glass formation, single phase solid solution formation, or supercooled melt viscosities, computational approaches are overwhelmed. Experiments, by contrast, can directly evaluate real materials systems to generate valuable data. Unfortunately, experiments remain costly and time consuming, severely restricting the progress of materials discovery. This dissertation pushes to overcome this obstacle through a comprehensive high-throughput research strategy: The experimental approach is centered around combinatorial co-sputtering and rapid characterization, investigating hundreds of alloys at a time while maintaining highest sample …

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Investigations Of Novel Mechanisms Of Epigenetic Regulation On Chromatin, William J. Lu-Culligan Apr 2021

Investigations Of Novel Mechanisms Of Epigenetic Regulation On Chromatin, William J. Lu-Culligan

Yale Graduate School of Arts and Sciences Dissertations

The epigenetic regulation of gene expression, mediated by chromatin, is a critical component of eukaryotic cellular function. Chromatin regulates gene expression through a variety of mechanisms including histone post-translational modifications, chromatin remodeling, and recruitment of non-coding RNAs. Together, the chromatin states enable cells to organize the genome and efficiently carry out cellular functions. Given the implications of chromatin regulation in normal, developmental, and disease states, an understanding of the mechanisms of chromatin regulation is of critical importance. In this dissertation, I describe three projects towards furthering the field’s understanding of the mechanisms of chromatin regulation.First, I propose Kacme, a novel …

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Development Of Mechanically Complex Dna Nanodevices And A Diverse Dna Origami Toolkit For Cryo-Em Imaging, John Taylor Powell Apr 2021

Development Of Mechanically Complex Dna Nanodevices And A Diverse Dna Origami Toolkit For Cryo-Em Imaging, John Taylor Powell

Yale Graduate School of Arts and Sciences Dissertations

Mechanically interlocked supramolecular assemblies are appealing building blocks for creating functional nanodevices. Here we describe the multi-step assembly of massive DNA origami rotaxanes that are capable of programmable structural switching. We validated the topology and structural integrity of these rotaxanes by analyzing the intermediate and final products of various assembly routes using electrophoresis and electron microscopy. Additionally, we explore the use of various other DNA origami nanodevices as support structures for improved cryoEM imaging of proteins of interest. Namely, we demonstrate progress toward several DNA nanodevice-based solutions to artifacts stemming from air-water interface interactions and other freezing effects.

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Blurred Boundaries: Iberian Representations Of The Spanish Civil War, Sarah Glenski Apr 2021

Blurred Boundaries: Iberian Representations Of The Spanish Civil War, Sarah Glenski

Yale Graduate School of Arts and Sciences Dissertations

In my dissertation, “Blurred Boundaries: Iberian Representations of the Spanish Civil War,” I reconceptualize the Spanish Civil War, which has been understood to have national and international significance, as an Iberian conflict of multicultural importance. To understand the war as Iberian, I work with 20th-century narrative and film from the Basque Country, Catalonia, Galicia, and Portugal that portray the time before, during, and/or after Spain’s war. With “blurred boundaries,” I refer to how I remap the ways in which the war has traditionally been viewed. In doing so, I bring the question of region to the forefront of my analysis, …

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