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Machine Learning For Tau Leptons And The Search For The Associated Production Of A Higgs Boson With A Vector Boson, With The Higgs Boson Decaying To A Tau Pair At Atlas, Emma Grace Castiglia Apr 2022

Machine Learning For Tau Leptons And The Search For The Associated Production Of A Higgs Boson With A Vector Boson, With The Higgs Boson Decaying To A Tau Pair At Atlas, Emma Grace Castiglia

Yale Graduate School of Arts and Sciences Dissertations

After the discovery of the Higgs boson in 2012, many particle physicists have focused on measuring its various production methods and decay modes. One channel that has previously only been measured at well below the observation threshold is the associated production of a Higgs boson with a vector boson, where the Higgs boson decays to a pair of taus. In this thesis, I describe an ongoing search for that channel using data from proton-proton collisions taken during Run 2 at the Large Hadron Collider with the ATLAS detector (2015-2018), with a recorded integrated luminosity of 139fb^-1 at a center of …

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Does Soil Carbon Support Climate Resilient Agricultural Systems? Searching For Evidence And Developing New Measurement Tools, Daniel Kane Apr 2022

Does Soil Carbon Support Climate Resilient Agricultural Systems? Searching For Evidence And Developing New Measurement Tools, Daniel Kane

Yale Graduate School of Arts and Sciences Dissertations

2022Increasing soil organic carbon (SOC) is frequently promoted as a “win-win” strategy for agricultural management in the face of a changing climate. This framing is based on the notion that building SOC both reduces yield losses/variability by improving soil water dynamics, and that building SOC can contribute to climate change mitigation by reducing atmospheric carbon. While this framing may be useful, relationships between SOC and such outcomes are often poorly described and not quantitative. That is, it’s unclear how much of an improvement to SOC is needed to reduce yield losses, whether or not that effect translates across soil types …

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Stresses Within The Actin Meshwork Control The Turnover Of Fimbrin During Clathrin-Mediated Endocytosis, Xiaobai Li Apr 2022

Stresses Within The Actin Meshwork Control The Turnover Of Fimbrin During Clathrin-Mediated Endocytosis, Xiaobai Li

Yale Graduate School of Arts and Sciences Dissertations

In this dissertation, I investigated the molecular mechanism of clathrin-mediated endocytosis (CME) in fission yeast with a sparse labeling strategy to track endocytic proteins at the single molecule level. CME is involved in a variety of biological processes, such as nutrient internalization and receptor recycling. CME is also a well-conserved biological process from yeast to mammalian cells. During clathrin-mediated endocytosis, about 60 different endocytic proteins are recruited to the endocytic site in a highly reproducible order. During the endocytic event, endocytic proteins assemble into endocytic structures, contributing to membrane invagination and endocytic vesicle formation. Based on the single molecule endocytic …

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Essays In Corruption And Capture, Trevor Incerti Apr 2022

Essays In Corruption And Capture, Trevor Incerti

Yale Graduate School of Arts and Sciences Dissertations

Corruption is commonly defined as the abuse of public office for private gain. However, private gain can be extracted from political processes or connections in ways that often do not constitute "abuse" or meet legal definitions of corruption. This volume explores some of the myriad ways private and public actors use political decisions to extract private gains—legal or extralegal—as well as explores potential mechanisms to reduce these actions. The first two chapters examine the degree to which individual citizens can reduce extraction of private gain from public office through participation in politics. The first chapter examines the average electoral cost …

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Modulating Innate Immunity Via Cd40-Based Myeloid Targeting Can Overcome Anti-Pd1 Therapy Resistance, Irina Krykbaeva Apr 2022

Modulating Innate Immunity Via Cd40-Based Myeloid Targeting Can Overcome Anti-Pd1 Therapy Resistance, Irina Krykbaeva

Yale Graduate School of Arts and Sciences Dissertations

Melanoma is the most aggressive skin cancer and is estimated to have caused 7180 deaths in the United States in 2021. Immune checkpoint inhibitors have revolutionized melanoma treatment over the past decade and dual therapy with anti-PD-1 and anti-CTLA4 inhibitors is currently the standard of care for advanced melanoma. Despite the success of this treatment regimen, resistance remains a significant clinical challenge. Many tumors either do not respond to checkpoint inhibition or develop resistance and ultimately patients experience disease progression. Options for these patients are limited and there is a critical need for new therapies to adequately treat anti-PD1 non-responders. …

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Development Of A Synthetic Strategy To Access Novel And Structurally-Diverse Pleuromutilins, Olivia Francis Goethe Apr 2022

Development Of A Synthetic Strategy To Access Novel And Structurally-Diverse Pleuromutilins, Olivia Francis Goethe

Yale Graduate School of Arts and Sciences Dissertations

In this thesis, I describe how we built upon the foundation of our previous totalsynthesis of (+)-pleuromutilin (1) and its C12 epimer (125) in order to produce a new, scalable, and generalizable route to novel pleuromutilins. (+)-Pleuromutilin (1), the namesake of this antibiotic class, has been extensively developed by semisynthesis, and several semisynthetic derivatives are in clinical use for the treatment of Gram-positive infections. Pleuromutilins are associated with slow rates of resistance development, and limited cross-resistance with existing agents. Thus, they hold promise to combat the growing problem of antibiotic resistance. The utility of many semisynthetic pleuromutilins is hindered by …

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Essays In Financial Economics, Canyao Liu Apr 2022

Essays In Financial Economics, Canyao Liu

Yale Graduate School of Arts and Sciences Dissertations

In my dissertation, I dive into three specific areas in financial economics. Chapter 1 of my Ph.D. dissertation studies how the boom in off-exchange trading at the market close affects the close price discovery. In recent years, investment banks like Goldman Sachs have started a "guaranteed close" business where investors looking to buy or sell shares of a certain stock can get a guarantee from the bank to execute their orders at the close price set on the primary exchange. Using the TAQ data and a quasi-experimental shock from NYSE fee cut, we find that when the fraction of trades …

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Synthesis And Transport Properties Of Topological Crystalline Insulator Snte Nanowires, Pengzi Liu Apr 2022

Synthesis And Transport Properties Of Topological Crystalline Insulator Snte Nanowires, Pengzi Liu

Yale Graduate School of Arts and Sciences Dissertations

Over the last decade, significant progress has been made in studying topological materials whose wavefunctions possess a distinct topological invariant signature barring adiabatic deformation from a trivial phase to a non-trivial phase. There has been mounting experimental evidence for the presence of topological nature in nanomaterials due to their favorable surface-to-volume ratio and phase-coherent confinement. Considering that the material synthesis and transport measurement challenges must be overcome before topological nanomaterials can be used in next-generation electronic devices, in my dissertation, I focus on improving crystal quality and controlling dimensions of topological crystalline insulator SnTe in nanoscale as it provides a …

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Essays In Inference For Nonparametric Regression Models, Koohyun Kwon Apr 2022

Essays In Inference For Nonparametric Regression Models, Koohyun Kwon

Yale Graduate School of Arts and Sciences Dissertations

This dissertation presents three essays in inference for nonparametric regression models. The first chapter, “Bias-Aware Inference for Conditional Average Treatment Effect Functions,” proposes a new method to construct a confidence band for the conditional treatment average treatment effect (CATE), as a function of a continuous covariate in a randomized controlled trial. My confidence band is bias-aware, taking into account the maximum smoothing bias of the nonparametric estimators used to construct the confidence band. I provide a computationally simple procedure to obtain a bias-aware confidence band whose half-length at each evaluation point is asymptotically shortest uniformly over the domain of the …

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Neural Graph Transfer Learning In Natural Language Processing Tasks, Irene Li Apr 2022

Neural Graph Transfer Learning In Natural Language Processing Tasks, Irene Li

Yale Graduate School of Arts and Sciences Dissertations

Natural language is essential in our daily lives as we rely on languages to communicate and exchange information. A fundamental goal for natural language processing (NLP) is to let the machine understand natural language to help or replace human experts to mine knowledge and complete tasks. Many NLP tasks deal with sequential data. For example, a sentence is considered as a sequence of works. Very recently, deep learning-based language models (i.e.,BERT \citep{devlin2018bert}) achieved significant improvement in many existing tasks, including text classification and natural language inference. However, not all tasks can be formulated using sequence models. Specifically, graph-structured data is …

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Tumor Cell Migration And Interaction With Ecm And Stroma In 3d Tissue Models, Chang Liu Apr 2022

Tumor Cell Migration And Interaction With Ecm And Stroma In 3d Tissue Models, Chang Liu

Yale Graduate School of Arts and Sciences Dissertations

Tumors are often described as ”wounds that do not heal”. Tumor progression and woundhealing both feature sustained proliferative signaling, evasion from immune destruction, cell death resistance, inflammation, angiogenesis, extracellular matrix(ECM) remodeling, and activated cell migration. Unlike normal wound healing which often ends up with restored tissue homeostasis, pathological ECM remodeling is frequently implicated in fibrotic diseases and solid tumors. In addition, the dysregulated ECM signatures are directly associated with poor prognosis and also immunotherapy failure in certain types of cancers. In this dissertation, we used 3D in vitro cocultures to understand how tumor cells co-op with stromal/immune components, how ECM …

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System Abstractions For Scalable Application Development At The Edge, Bo Hu Apr 2022

System Abstractions For Scalable Application Development At The Edge, Bo Hu

Yale Graduate School of Arts and Sciences Dissertations

Recent years have witnessed an explosive growth of Internet of Things (IoT) devices, which collect or generate huge amounts of data. Given diverse device capabilities and application requirements, data processing takes place across a range of settings, from on-device to a nearby edge server/cloud and remote cloud. Consequently, edge-cloud coordination has been studied extensively from the perspectives of job placement, scheduling and joint optimization. Typical approaches focus on performance optimization for individual applications. This often requires domain knowledge of the applications, but also leads to application-specific solutions. Application development and deployment over diverse scenarios thus incur repetitive manual efforts. There …

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Essays On Information Economics, Weicheng Min Apr 2022

Essays On Information Economics, Weicheng Min

Yale Graduate School of Arts and Sciences Dissertations

This dissertation consists of three independent essays that examine how to improveinformation transmission and how to incentivize learning. In Chapter 2, I study the role of a recommender’s career concerns in his relation-ship with a consumer when the recommender has a private type in expertise. An informed type has valuable expertise for the consumer, whereas an uninformed type does not. The uninformed type cannot mimic the informed type, suggesting that the informed type can build a reputation for competence. However, I find that the relationship breaks down completely if the recommender is sufficiently patient. In Chapter 3, which is co-authored …

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An Intellectual History Of Black Literary Discourse 1910-1956, Shayne Mcgregor Apr 2022

An Intellectual History Of Black Literary Discourse 1910-1956, Shayne Mcgregor

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines the first forty-six years of black literary discourse in the American twentieth century. Beginning with Benjamin Brawley’s The Negro in Literature and Art (1910), I begin the dissertation by identifying black literary discourse’s original goal. In the parlance of the time, the goal of black literary discourse was to solve the “Negro Problem.” I then discuss how further into the twentieth century other critics and artists like James Weldon Johnson and Sterling Brown expanded on Brawley’s ideas in ways that attempted to get at the underlying philosophical thought that underpinned the Problem. By the 1930s a competing …

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Identification And Characterization Of Legionella Pneumophila Effector Proteins Important For In Vivo Pathogenesis And Persistence, Luying Liu Apr 2022

Identification And Characterization Of Legionella Pneumophila Effector Proteins Important For In Vivo Pathogenesis And Persistence, Luying Liu

Yale Graduate School of Arts and Sciences Dissertations

Legionella pneumophila is a natural pathogen of freshwater protozoa and an opportunistic pathogen of humans. Legionella is the causative agent of Legionnaires’ disease, a potentially fatal atypical pneumonia. This bacteria lives a unique intracellular lifestyle that involves internalization via phagocytosis, rapid avoidance of endocytic degradation, and subversion of host pathways to decorate its compartment into an ER-like, replication-permissive vacuole called the Legionella-Containing Vacuole (LCV). This process is largely mediated by a special secretion machinery called the Dot/Icm type IVb secretion system. This system is predicted to secrete over 300 effector proteins into the host cytosol during intracellular infection and is …

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Investigating The Impact Of Maternal Antiviral Responses On Pregnancy And Fetal Development, Alice Lu-Culligan Apr 2022

Investigating The Impact Of Maternal Antiviral Responses On Pregnancy And Fetal Development, Alice Lu-Culligan

Yale Graduate School of Arts and Sciences Dissertations

The maternal-fetal interface during pregnancy is an underexplored environment rich in immunological factors that must propel developmental processes while simultaneously providing protection from invading pathogens such as viruses. Almost half of all cells in the maternal decidua in pregnancy are leukocytes, which are required for successful pregnancy, and the placenta has increasingly become recognized as an immunological organ. Viral infections during pregnancy are associated with significant mortality and morbidity, both for the pregnant female and the developing fetus. Notably, impacts on fetal development have typically been attributed to direct viral damage to cells and tissues during the course of infection, …

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Characterizing The Neural Signatures Of Individual Differences In Memory Across The Lifespan, Qi Lin Apr 2022

Characterizing The Neural Signatures Of Individual Differences In Memory Across The Lifespan, Qi Lin

Yale Graduate School of Arts and Sciences Dissertations

One of the mind's most fundamental and fascinating facets is memory. We rely on memory to learn about the world around us and adapt to the environment we live in. Yet there are considerable individual differences in memory abilities. Moreover, memory abilities also change across the lifespan. Here, across three studies, each focusing on a distinct developmental stage (youth, young adulthood and aging), I demonstrate that individual differences in aspects of memory performance can be predicted from functional brain connectivity. Importantly, beyond capturing individual differences, I present approaches to dissociate different cognitive processes and their corresponding brain networks as well …

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Calibration Instrumentation For The Hydrogen Intensity And Real-Time Analysis Experiment, Emily Rita Kuhn Apr 2022

Calibration Instrumentation For The Hydrogen Intensity And Real-Time Analysis Experiment, Emily Rita Kuhn

Yale Graduate School of Arts and Sciences Dissertations

The Hydrogen Intensity and Real-time Analysis eXperiment (HIRAX) is a 21 cm neutral hydrogen intensity mapping experiment to be deployed in the Karoo Desert in South Africa. It aims to improve constraints on the dark energy equation of state through measurements of large-scale structure at high redshift, while doubling as a state-of-the-art fast radio burst (FRB) detector. This dissertation focuses on two aspects of the HIRAX instrument characterization: (1) optimizing the signal-to-noise of antennas, through the design and implementation of a custom test-bed for determining the noise temperature of radio antennas operating between 400-800MHz, and (2) mapping the HIRAX telescope …

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Spectroscopic Characterization Of Microhydration: Studying Molecular Properties, Acidity And Solvation In Ionic Water Clusters Using Cryogenic Infrared Vibrational Predissociation Spectroscopy, Sayoni Mitra Apr 2022

Spectroscopic Characterization Of Microhydration: Studying Molecular Properties, Acidity And Solvation In Ionic Water Clusters Using Cryogenic Infrared Vibrational Predissociation Spectroscopy, Sayoni Mitra

Yale Graduate School of Arts and Sciences Dissertations

Molecular level interactions give rise to the macroscopic chemical and physical properties of bulk electrolyte systems. A fundamental knowledge of these interactions facilitates understanding of this behavior and enables rational manipulation of the system at the molecular level. Among the experimental techniques, vibrational spectroscopy is widely used in several variations including linear absorption spectroscopy, ultrafast multidimensional spectroscopy, and interface specific spectroscopy. The advantage of using vibrational spectroscopy to study systems at the molecular level is its sensitivity towards structural information as well as relatively high time resolution. Standard solution phase and surface-sensitive spectroscopies, however, suffer from the drawback that the …

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4pi Single-Molecule Switching Nanoscopy For Live-Cell Imaging, Kevin Hu Apr 2022

4pi Single-Molecule Switching Nanoscopy For Live-Cell Imaging, Kevin Hu

Yale Graduate School of Arts and Sciences Dissertations

plays a critical role in cell biology due to its ability tovisualize molecules of interest inside living cells with high specificity and contrast. However, diffraction of light limits spatial resolution to ~250 nm. Super-resolution microscopy bypasses this physical limit to achieve resolutions of ~10 nm, which is nearly the size of many biological macromolecules. Notably, 4Pi single-molecule switching nanoscopy achieves this resolution in all three spatial dimensions, finally making it possible to resolve specific proteins within convoluted structures like the Golgi. However, the current implementation is only compatible with dead or fixed cell samples, restricting experimental design. To explore the …

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Essays On Information Economics, Weicheng Min Apr 2022

Essays On Information Economics, Weicheng Min

Yale Graduate School of Arts and Sciences Dissertations

This dissertation consists of three independent essays that examine how to improveinformation transmission and how to incentivize learning. In Chapter 2, I study the role of a recommender’s career concerns in his relation-ship with a consumer when the recommender has a private type in expertise. An informed type has valuable expertise for the consumer, whereas an uninformed type does not. The uninformed type cannot mimic the informed type, suggesting that the informed type can build a reputation for competence. However, I find that the relationship breaks down completely if the recommender is sufficiently patient. In Chapter 3, which is co-authored …

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Light Microscopy Of Proteins In Their Ultrastructural Context, Ons M'Saad Apr 2022

Light Microscopy Of Proteins In Their Ultrastructural Context, Ons M'Saad

Yale Graduate School of Arts and Sciences Dissertations

Fluorescence light microscopy is an essential tool in biomedical research. In immunofluorescence, fluorophore-conjugated antibodies are used to detect specific proteins of interest in a fixed biological sample. With recently developed nanoscopy techniques, whole cells can be imaged at an isotropic spatial resolution of ~10 nm, revealing accurate protein distributions on the nanoscale. However, most localized proteins are imaged against a dark background, which forbids seeing the overall subcellular compartments (ultrastructural context) that encompass them. Electron microscopy (EM), on the other hand, offers a complete cellular overview on the scale of a few nanometers. However, EM fails to reliably detect specific …

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Some Are Guilty, All Are Responsible': A Theory And Ethics Of Prophetic Citizenship, Alex Ozar Apr 2022

Some Are Guilty, All Are Responsible': A Theory And Ethics Of Prophetic Citizenship, Alex Ozar

Yale Graduate School of Arts and Sciences Dissertations

When it comes to injustices in free societies, Abraham Joshua Heschel says, “some are guilty, but all are responsible.” This dissertation asks what responsibility individuals in fact bear for societal injustices of which they are not guilty, and offers a construction of the prophetic vocation as the answer. We are each responsible for caring about (those suffering under) injustice, and we are each responsible for holding each other responsible for so caring. We effectively address demands to others to care by manifestly caring ourselves, which turns out to require the assumption of some measure of cost, risk, or sacrifice in …

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Network Approaches To The Study Of Genomic Variation In Cancer, Hussein Mohsen Apr 2022

Network Approaches To The Study Of Genomic Variation In Cancer, Hussein Mohsen

Yale Graduate School of Arts and Sciences Dissertations

Advances in genomic sequencing technologies opened the door for a wider study of cancer etiology. By analyzing datasets with thousands of exomes (or genomes), researchers gained a better understanding of the genomic alterations that confer a selective advantage towards cancerous growth. A predominant narrative in the field has been based on a dichotomy of alterations that confer a strong selective advantage, called cancer drivers, and the bulk of other alterations assumed to have a neutral effect, called passengers. Yet, a series of studies questioned this narrative and assigned potential roles to passengers, be it in terms of facilitating tumorigenesis or …

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The Role Of Metabolism In Embryonic Development: Mitochondria Determine The Fate Of The Spemann-Mangold Organizer, Alexandra Elizaberth Maccoll Garfinkel Apr 2022

The Role Of Metabolism In Embryonic Development: Mitochondria Determine The Fate Of The Spemann-Mangold Organizer, Alexandra Elizaberth Maccoll Garfinkel

Yale Graduate School of Arts and Sciences Dissertations

Carbon metabolism is critical for complex multicellular life. Therefore, mitochondria, and the aerobic metabolism that they perform, have long been a focus of developmental biologists. The discovery of the Spemann-Mangold Organizer, a powerful embryonic patterning center in the dorsal region of the vertebrate embryo, first inspired the idea that embryonic patterning and aerobic metabolism may be connected almost 100 years ago. However, the advent of modern molecular genetics overshadowed this work, and metabolism in development has only recently resurfaced as a focus in the field. A permissive role for mitochondria has been well studied in development. However, it remains unclear …

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Religion And Contested Cultural Heritage: The Rotunda And Hagia Sophia As Church, Mosque, And Museum, Stephanie Machabee Apr 2022

Religion And Contested Cultural Heritage: The Rotunda And Hagia Sophia As Church, Mosque, And Museum, Stephanie Machabee

Yale Graduate School of Arts and Sciences Dissertations

This project uses the fourth-century Rotunda in Thessaloniki, Greece and the sixth-century Hagia Sophia in Istanbul, Turkey as case study sites for exploring conflicts over religious heritage. These two sites have a shared history of repurposing, from pre-Christian sites, to churches, to mosques, to museums, and to hybrid religious/heritage spaces today. These transformations are the outcome of shifting political powers and changing religious priorities over the centuries. As a result of these complex histories, the Rotunda and Hagia Sophia are notable examples of “dissonant heritage” (Tunbridge and Ashworth 1996). That is, they are loci of competing narratives and public representations …

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Structural Analysis Of Complex Bacterial Secretion Systems, Donghyun Park Apr 2022

Structural Analysis Of Complex Bacterial Secretion Systems, Donghyun Park

Yale Graduate School of Arts and Sciences Dissertations

From the moment Anton van Leeuwenhoek saw bacteria for the first time to the modern era of the ‘resolution revolution’ by the Nobel prize-winning method single particle cryo-electron microscopy (EM), advances in microscopy have led to visual observations that enhance our understanding of life at a wide range of scales, from millimeters to angstroms. The increasingly popular imaging technique cryo-electron tomography (cryo-ET) is uniquely suited for visualizing protein complexes and cellular features at high resolution in their native environment. This technology presents great potential for visualizing host-pathogen interactions. The work within this dissertation utilizes cutting-edge cryo-ET technologies to visualize different …

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Nonhistory: Slavery And The Black Historical Imagination, Xavier Lee Apr 2022

Nonhistory: Slavery And The Black Historical Imagination, Xavier Lee

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines the theoretical significance of slavery in contemporary novels by black writers of English and French expression. I contend that black authors like Gayl Jones, Edouard Glissant, Léonora Miano, Sherley Anne Williams, Jean Métellus, and Fred D’Aguiar use literature to revise historical narratives and generate new histories of slavery. By reading novels as historical texts, I theorize nonhistory as a critique of the epistemological limitations of historiography. I argue that Black Francophone and Anglophone Atlantic writers of the postcolonial and post-Jim Crow era narrate the past as a nonhistory whose discursive and aesthetic afterimages expose the disjointed experience …

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Fern Ecophysiology: Linking Photosynthesis, Water Relations, And Stomatal Dynamics In Ferns, Kyra Alexandra Prats Apr 2022

Fern Ecophysiology: Linking Photosynthesis, Water Relations, And Stomatal Dynamics In Ferns, Kyra Alexandra Prats

Yale Graduate School of Arts and Sciences Dissertations

Ferns are the second-most diverse major clade of green, vascular plants, and yet, they have been historically excluded from ecophysiology, ecology, and evolution studies. Ferns were once the dominant vegetation making up forested ecosystems, and while the fern lineage predates seed plants (gymnosperms and angiosperms), the majority of extant ferns diversified alongside and even after angiosperms, the flowering plants. The theory that ferns were literally overtopped by angiosperms includes the hypothesis that over evolutionary time ferns had to adapt to new ecological niches that are less desirable, such as shaded understories or bright and dry tree canopies growing on branches …

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Applications Of Dynamic Modeling And Statistical Analysis To Infectious Diseases, Alyssa Sholeh Parpia Apr 2022

Applications Of Dynamic Modeling And Statistical Analysis To Infectious Diseases, Alyssa Sholeh Parpia

Yale Graduate School of Arts and Sciences Dissertations

In this dissertation, I explore the disproportionate burden of infectious disease outbreaks, epidemics, and pandemics and the projected impact of interventions for mitigating their harm on populations in Cameroon and the United States. The spatial heterogeneity in vaccination coverage and access to care in Cameroon creates areas that are highly susceptible to measles transmission. In the US, the HIV epidemic is increasingly concentrated in the southern states in addition to larger cities with variable levels of prevention and linkage to sustained treatment. Disparities in COVID-19 burden exist by race and geography across Michigan, in part due to systemic racism and …

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