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The Manifold Of Neural Responses Informs Physiological Circuits In The Visual System, Luciano Dyballa Apr 2021

The Manifold Of Neural Responses Informs Physiological Circuits In The Visual System, Luciano Dyballa

Yale Graduate School of Arts and Sciences Dissertations

The rapid development of multi-electrode and imaging techniques is leading to a data explosion in neuroscience, opening the possibility of truly understanding the organization and functionality of our visual systems. Furthermore, the need for more natural visual stimuli greatly increases the complexity of the data. Together, these create a challenge for machine learning. Our goal in this thesis is to develop one such technique. The central pillar of our contribution is designing a manifold of neurons, and providing an algorithmic approach to inferring it. This manifold is functional, in the sense that nearby neurons on the manifold respond similarly (in …

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Non-State Superpowers, Transnational Challenges, And 21st Century Global Order: Private Sector Climate Action In An Age Of State Inaction, Charlotte Jude Hulme Apr 2021

Non-State Superpowers, Transnational Challenges, And 21st Century Global Order: Private Sector Climate Action In An Age Of State Inaction, Charlotte Jude Hulme

Yale Graduate School of Arts and Sciences Dissertations

This project explores the new actors, issues, and dynamics that are reshaping the land-scape and context in which states will have to advance their interests in the 21st century. Examining the case study of private sector climate action, it demonstrates that select transnational actors have not just the capacity to alter relationships between govern-ments, as scholars like Nye and Keohane anticipated in the 1970s, but the ability and, increasingly, the ambition to address non-traditional issues that states cannot address independently. Focusing on 34 of the world’s largest companies, representing four in-dustry groups (energy-intensive, automotive, technology, and finance) and three main …

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A Constitution Contested: Governors, Assemblies, And Imperial Politics In Jamaica And New York, 1675-1730, Winston Sinclair Hill Apr 2021

A Constitution Contested: Governors, Assemblies, And Imperial Politics In Jamaica And New York, 1675-1730, Winston Sinclair Hill

Yale Graduate School of Arts and Sciences Dissertations

This dissertation focuses on the constitutional politics of England, and then Britain’s, transatlantic empire in the seventeenth and eighteenth centuries, through the lens of Jamaica and New York. In those two colonies, as in the rest of the Atlantic empire, colonial elites and imperial authorities were in perpetual political conflict. In this dissertation, I explain why the conflict persisted without resolution. Historians, though they rarely answer this question, have described fundamental transatlantic clashes of interests, and I take these as my starting point. I argue that each side’s ideological and material interests interwove with and sustained one another, and were …

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Animating Heritage: Affective Experiences, Institutional Networks, And Themed Consumption In The Japanese Cultural Industries, Heidi K. Lam Apr 2021

Animating Heritage: Affective Experiences, Institutional Networks, And Themed Consumption In The Japanese Cultural Industries, Heidi K. Lam

Yale Graduate School of Arts and Sciences Dissertations

This dissertation ethnographically examines a Japanese historical themed park to illuminate the cultural industries’ role in shaping Japanese identity through creative labor, consumption, and institutional relationships. It argues that cultural heritage is animated through embodied experiences (taiken) with performative elements and contingent contexts that take place around a central organization’s selective interpretation and staging of the past. This dissertation is based on 15 months of fieldwork in 2015-2017 at and around “Edo Town,” the pseudonym for a historical themed park in Japan that evokes the Edo or Tokugawa period (1603-1867) in Japan’s history. I explore the creative labor, institutional networks, …

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Living And Judging: Studies In Pragmatic Reasoning In Philosophy, Literature, And Law, Tobias Kuehne Apr 2021

Living And Judging: Studies In Pragmatic Reasoning In Philosophy, Literature, And Law, Tobias Kuehne

Yale Graduate School of Arts and Sciences Dissertations

This dissertation presents five studies on the problem of formalization. Every body of knowledge—whether it be scientific, philosophical, literary, practical, or personal—has its own conventions by which that knowledge is generated, arranged, reworked, presented, and defended. But formalization is rarely without its blind spots or glitches. Sometimes, a body of knowledge seeks to mask its techniques of formalization to cover up its own contingency or lack of ultimate answers. In this process, rhetoric plays an elusive dual role. Rhetoric sometimes contributes to formalization, while sometimes undermining it. Studying the rhetoric of a body of knowledge thus serves as an access …

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Essays On Panel And Network Modeling, Ming Li Apr 2021

Essays On Panel And Network Modeling, Ming Li

Yale Graduate School of Arts and Sciences Dissertations

This dissertation studies identification and estimation in panel and network models. Panel models have long been a workhorse in empirical research. In the first two chapters, we analyze random coefficient linear panel model and panel multinomial choice model, respectively, where we incorporate features such as time-varying endogeneity and unobserved heterogeneity that are prevalent in real life into the models. We present new identification results and provide consistent estimators based on the identification strategy. Then, we apply the estimation procedures to panel data and obtain economically convincing results. The study of networks is a fast-growing area of economic research thanks to …

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Essays On Robust Methods In Econometrics, Soonwoo Kwon Apr 2021

Essays On Robust Methods In Econometrics, Soonwoo Kwon

Yale Graduate School of Arts and Sciences Dissertations

This dissertation presents four essays on robust methods in econometrics. The first chapter, "Optimal Shrinkage Estimation of Fixed Effects in Linear Panel Data Models," proposes a shrinkage estimator for the fixed effects in linear panel data models whose risk properties are robust against violations of the distributional assumptions that are commonly imposed. Shrinkage methods are frequently used to estimate fixed effects. However, the risk properties of existing estimators are fragile to violations of the underlying distributional assumptions. I develop an estimator for the fixed effects that obtains the best possible mean squared error (MSE) within a class of shrinkage estimators. …

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Elucidation Of Vps13 And Pikfyve Proteins Functioning In The Regulation Of Eukaryotic Lipid Homeostasis, Peiqi Li Apr 2021

Elucidation Of Vps13 And Pikfyve Proteins Functioning In The Regulation Of Eukaryotic Lipid Homeostasis, Peiqi Li

Yale Graduate School of Arts and Sciences Dissertations

In eukaryotic cells, organelles are surrounded by membranes, which act as barriers to the cytosolic environment. Each subcellular membrane has a distinct lipid composition that is required for its unique organellar function, and is therefore is fundamental for cellular physiology. The unique distributions of organellar lipids result from highly regulated lipid transport networks and the activity of lipid metabolizing enzymes. Most phospholipids are initially synthesized in the ER and transferred to different organelles via vesicular or non-vesicular lipid transport pathways. Lipid transfer proteins (LTPs) localized at membrane contact sites mediate non-vesicular lipid transport. They contain a hydrophobic cavity to solubilize …

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Development, Implementation And Evaluation Of Medical Decision Support Systems Based On Mortality Prediction Algorithms From An Operations Research Perspective., Junchao Ma Apr 2021

Development, Implementation And Evaluation Of Medical Decision Support Systems Based On Mortality Prediction Algorithms From An Operations Research Perspective., Junchao Ma

Yale Graduate School of Arts and Sciences Dissertations

Wide implementation of electronic health record systems provides rich data for personalized medicine. One topic of great interest is to develop methods to assist physicians in prognosis for example mortality. While many studies have reported on various new prediction models and algorithms there is relatively little literature on if and how these new prediction methods translate into actual benefits. My dissertation consists of three theses that aims at filling this gap between prognostic predictions and clinical decisions in end-of-life care and intensive care settings. In the first thesis, we develop an approach to using temporal trends in physiologic data as …

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Effects Of Social Context On Women’S Political Engagement: Evidence From Focus Group Experiments In Tanzania, Elizabeth Kay Mcguire Apr 2021

Effects Of Social Context On Women’S Political Engagement: Evidence From Focus Group Experiments In Tanzania, Elizabeth Kay Mcguire

Yale Graduate School of Arts and Sciences Dissertations

Both theory and policy experts have sought to understand how norms around women’s political participation may shift. This dissertation provides evidence that the engagement of women can be affected by social contexts at the micro-level. Through two randomized field experiments, I show that the social referents who are present during a discussion about women and gender culture in Tanzania have a significant impact, not only in how those topics are discussed, but also on the behavior of the subjects with regards to women’s political participation. Between these two experiments, I conducted over 400 total focus groups in both rural and …

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Mechanisms Of Resistance Against B Cell Targeting Treatments For Myasthenia Gravis, Ruoyi Jiang Apr 2021

Mechanisms Of Resistance Against B Cell Targeting Treatments For Myasthenia Gravis, Ruoyi Jiang

Yale Graduate School of Arts and Sciences Dissertations

Myasthenia gravis (MG) is an autoimmune neuromuscular disorder caused by autoantibodies that disrupt neuromuscular transmission by targeting components of neuromuscular junctions, such as the acetylcholine receptor (AChR, 90% of patients) and muscle specific kinase (MuSK, 10% of patients). Treatments that address the underlying causes of MG target the cells responsible for producing these autoantibodies. Two such treatment strategies are predominantly used: (1) surgical resection of the thymus (a reservoir for auto-antigen specific B cells in patients with AChR MG) and (2) systemic therapy targeting subsets of autoantibody-producing B cells. The thymus is a known anatomic reservoir for B cells that …

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Computational Studies Of Proteins:\\ Void Analyses, Nmr And X-Ray Structures, Fluctuations In Protein Structure Measured Using Molecular Dynamics Simulations, Zhe Mei Apr 2021

Computational Studies Of Proteins:\\ Void Analyses, Nmr And X-Ray Structures, Fluctuations In Protein Structure Measured Using Molecular Dynamics Simulations, Zhe Mei

Yale Graduate School of Arts and Sciences Dissertations

Although the amount of experimental and theoretical protein studies have grown exponentially in recent years, we still do not have enough knowledge about the folding dynamics and structural properties of proteins to fold a protein from its primary sequence. The hydrophobic effect of protein cores is a dominant driving force of the protein folding process. In my work, I utilize high-quality X-ray crystallography and solution NMR structures, along with an atomistic model of proteins, to study the structural properties and fluctuations of protein cores. This thesis presents three computational and theoretical studies of proteins and their core regions. In the …

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Sampling From The Greedy Mixture Posterior, Dylan Potter O'Connell Apr 2021

Sampling From The Greedy Mixture Posterior, Dylan Potter O'Connell

Yale Graduate School of Arts and Sciences Dissertations

Mixtures of distributions provide a flexible model for heterogeneous data, but this versatility is concomitant with computational difficulty. We study the task of generating samples from the "greedy'' gaussian mixture posterior. While it is widely known that Gibbs sampling can be slow to converge, concrete results quantifying this behavior are scarce. In this dissertation, we establish conditions under which the number of steps required by the Gibbs sampler is exponential in the separation of the data clusters. Further, we analyze the efficacy of potential solutions. The simulated tempering algorithm uses an auxiliary temperature variable to flatten the target density (reducing …

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Developing Tradition: A History Of Intercultural Health Governance In Mexico, 1940-2000, Joshua Mentanko Apr 2021

Developing Tradition: A History Of Intercultural Health Governance In Mexico, 1940-2000, Joshua Mentanko

Yale Graduate School of Arts and Sciences Dissertations

This is an intellectual and social history of efforts by the Mexican state to order and transform medical pluralism for developmentalist ends in the highlands of Chiapas state between 1940 and 2000. Focusing on state employees, bilingual and indigenous doctors and midwives, and Mexican and foreign anthropologists, it grounds the emergence of “interculturalidad” – or the project of integrating indigenous traditional medicine into state and non-state health institutions – in a broader history of economic development and modernization and indigenous resistance to and negotiation of capitalist and national integration projects. It shows how efforts to integrate traditional medicine have not …

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Macrophage Mechanosensing Of The Tissue Environment And Signal Integration Through The Cytoskeleton, Matthew Lowell Meizlish Apr 2021

Macrophage Mechanosensing Of The Tissue Environment And Signal Integration Through The Cytoskeleton, Matthew Lowell Meizlish

Yale Graduate School of Arts and Sciences Dissertations

The extracellular matrix (ECM) is an organized assembly of proteins and polysaccharides that is produced by cells and forms the physical environment in which cells reside. Together, diverse cell types and their surrounding extracellular matrix form units of organization known as tissues, which make up organs. The ECM gives rise to the particular architecture and mechanical properties of each organ. During tissue repair, cells known as myofibroblasts deposit large quantities of ECM, in order to reconstruct the injured tissue. In normal tissue repair, that reparative phase is followed by a resolution phase, in which cells such as macrophages degrade and …

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In Between Dār Al-Islām And The ‘Lands Of The Christians’: Three Christian Arabic Travel Narratives From The Early Modern/Ottoman Period (Mid-17th-Early 18th Centuries), Iraj Sheidaee Apr 2021

In Between Dār Al-Islām And The ‘Lands Of The Christians’: Three Christian Arabic Travel Narratives From The Early Modern/Ottoman Period (Mid-17th-Early 18th Centuries), Iraj Sheidaee

Yale Graduate School of Arts and Sciences Dissertations

This study analyzes closely the Arabic travel narratives of three Christians from the Ottoman Levant and Near East, who travelled to what they called the ‘lands of the Christians’—ie. Europe. Paul of Aleppo (Būluṣ al-Ḥalabī), a deacon of the Orthodox Church, travelled from 1652 to 1659 to Southeastern and Eastern Europe: the Danubian Principalities (modern Romania), the ‘lands of the Cossacks’ (Ukraine), and Muscovite Russia. Paul’s travels were part of an Arab Orthodox ecclesial mission in the company of this father, Patriarch Makarios III ibn al-Zaʿīm of the see of Antioch. He recorded his travel experiences in one of the …

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Urban Dreams And Agrarian Renovations: Examining The Politics And Practices Of Peri-Urban Land Conversion In Hanoi, Vietnam, Emily Nguyen Apr 2021

Urban Dreams And Agrarian Renovations: Examining The Politics And Practices Of Peri-Urban Land Conversion In Hanoi, Vietnam, Emily Nguyen

Yale Graduate School of Arts and Sciences Dissertations

In Mễ Trì village on the Western peri-urban edge of Hanoi, Vietnam, landless rice farmers no longer tend to rice paddy fields. Instead, many have converted 40 square meters of their residential space into a small factory for producing an artisanal rice product called cốm (young rice). This small village-based industry has garnered national demand for the product, drawing the attention of central policymakers who want to preserve the craft as a cultural relic of Hanoi. But without land to cultivate the rice inputs, young rice production is largely driven by the outsourcing of grains, the use of inventive new …

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Essays On Geography And Firm Dynamics, Marcos Ribeiro Frazao Apr 2021

Essays On Geography And Firm Dynamics, Marcos Ribeiro Frazao

Yale Graduate School of Arts and Sciences Dissertations

In this dissertation, I study the effects of geography on firm dynamics. I do so from three different perspectives. The first two chapters explore how geography affects sales of branded retail products in the United States. Chapter 1 focuses on the spread of sales over time and space. It describes each component of sales and discusses the potential role of word-of-mouth in the growth of brands. Chapter 2 studies the cross-section relation of brand sales and distance. The chapter analyses how physical trade frictions and information frictions interact and generate the observed reduction in customer base as distance increases. Chapter …

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Essays In Asset Pricing And Financial Intermediation, Sharon Yin Ross Apr 2021

Essays In Asset Pricing And Financial Intermediation, Sharon Yin Ross

Yale Graduate School of Arts and Sciences Dissertations

This dissertation consists of three essays on the topics of asset pricing, financial intermediation, and macrofinance. The first essay shows the role of government risk in asset prices. Firms that depend on the government—either through implicit guarantees or direct sales—face a special risk: government risk. I show that this risk is priced and is not spanned by other factors. I study four cases: U.S. banks, U.S. auto companies, U.S. government suppliers, and Japanese zombie firms. The U.S. cases involve direct exposure to government risk, and a U.S. government risk factor prices portfolios formed from government-dependent firms. Japanese zombies rely on …

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Essays On Dynamic Games, Io Kuan Vong Apr 2021

Essays On Dynamic Games, Io Kuan Vong

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines several economic questions related to dynamic incentives. In the first chapter, I study a dynamic game in which a careerist expert advises a sequence of principals on their actions to match a hidden, randomly evolving state. The expert privately knows her competence. The principals learn about the state and the expert's competence from past advice and past action outcomes, both publicly observable. I find that the equilibrium can feature a ``crisis of expertise,'' in which principals dismiss a competent expert's correct advice, and rely only on public information. Notably, the crisis happens precisely when the quality of …

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Representations Of Time In Late-Medieval Music, Philippa Ovenden Apr 2021

Representations Of Time In Late-Medieval Music, Philippa Ovenden

Yale Graduate School of Arts and Sciences Dissertations

The late-medieval style that is characterized by complexity of rhythm, notation, and pitch is commonly referred to as the ars subtilior, the “more subtle art,” a term coined by Ursula Günther in 1963. Along with its stylistic attributes, the scope of this repertory has been defined chronologically and geographically, associated with Southern France and Northern Italy during the period c. 1380–1420. In recent years, scholars such as David Catalunya, David Fallows, Karl Kügle, Jason Stoessel, Anne Stone, and Anna Zayaruznaya have argued that the so-called ars subtilior style should be expanded to incorporate a wider chronological and geographical purview. Responding …

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Driving Emissions Down: Whole-Supply-Chain Mitigation Of Greenhouse Gases From Passenger Vehicles, Paul Wolfram Apr 2021

Driving Emissions Down: Whole-Supply-Chain Mitigation Of Greenhouse Gases From Passenger Vehicles, Paul Wolfram

Yale Graduate School of Arts and Sciences Dissertations

Greenhouse-gas emitting human activities have caused the warming of the earth surface temperature by 0.97°C relative to pre-industrial levels. In order to prevent the most catastrophic consequences of climate change, most countries are committed to pursue action to limit global warming to well below 2°C under the Paris Agreement. Global transportation is the single largest user of energy as well as the largest carbon-dioxide emitting end-use sector, chiefly driven by passenger vehicles. Emissions caused by vehicles do not only occur at the vehicle tailpipe though. Pollutants are released along the entire vehicle supply chain, ranging from electric power plant discharges …

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Essays In Financial Economics, Kevin Zhao Apr 2021

Essays In Financial Economics, Kevin Zhao

Yale Graduate School of Arts and Sciences Dissertations

My dissertation consists of three chapters. In the first chapter, I show across three different settings that an individual's history of experiencing persistent processes can impact their beliefs. First, I examine analyst forecasts of earnings and show that forecasters who have covered firms with more autocorrelated earnings in the past are more extrapolative relative to their peers: they are relatively optimistic after high past earnings and relatively pessimistic after low past earnings. This generates predictable errors: after a good announcement in the previous period, firms that are covered by more extrapolative analysts on average will tend to have negative earnings …

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Learning To Map Natural Language To Executable Programs Over Databases, Tao Yu Apr 2021

Learning To Map Natural Language To Executable Programs Over Databases, Tao Yu

Yale Graduate School of Arts and Sciences Dissertations

Natural language is a fundamental form of information and communication and is becoming the next frontier in computer interfaces. As the amount of data available online has increased exponentially, so has the need for Natural Language Interfaces (NLIs, which is not used for natural language inference in this thesis) to connect the data and the user by easily using natural language, significantly promoting the possibility and efficiency of information access for many users besides data experts. All consumer-facing software will one day have a dialogue interface, and this is the next vital leap in the evolution of search engines. Such …

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Spatial And Temporal Variability Of Trace Metal Concentrations And Speciation In Connecticut Surface Waters, Zhemin Xuan Apr 2021

Spatial And Temporal Variability Of Trace Metal Concentrations And Speciation In Connecticut Surface Waters, Zhemin Xuan

Yale Graduate School of Arts and Sciences Dissertations

In this research, two studies were conducted to investigate the spatial distribution and seasonal variation of trace metal concentrations and speciation in Connecticut surface waters. In the first part, along with the monthly vertical profile of background biogeochemistry parameters (pH, Temperature, Dissolved oxygen, Major ions, Total dissolved solids, Nutrients, Acid neutralizing capacity, dissolved organic carbon), competitive ligand exchange – adsorptive cathodic stripping voltammetry was used to determine cobalt speciation in Linsley Pond, North Branford. Vitamin B12 (VB12) via enzyme-linked immunosorbent assay (ELISA) was measured in an American stratified lake for the very first time. During summer stratification, the patterns of …

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Harnessing The Masses: International Conflict And Chinese Public Opinion, Jiahua Yue Apr 2021

Harnessing The Masses: International Conflict And Chinese Public Opinion, Jiahua Yue

Yale Graduate School of Arts and Sciences Dissertations

My dissertation project (``Harnessing the Masses: International Conflict and Chinese Public Opinion") examines the interaction between Chinese foreign policy and public opinion. It comprises three empirical papers. I generalize theories of international relations and political economy developed under democratic settings and explore the role of domestic audiences in Chinese foreign policymaking. My main findings are two-fold. On the one hand, the state holds considerable political resources and plays an influential role in setting the political agenda. It has the power to mobilize popular nationalism in support of hawkish policies under favorable circumstances (e.g., territorial disputes). On the other hand, blind …

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Error-Corrected Quantum Metrology, Sisi Zhou Apr 2021

Error-Corrected Quantum Metrology, Sisi Zhou

Yale Graduate School of Arts and Sciences Dissertations

Quantum metrology, which studies parameter estimation in quantum systems, has many applications in science and technology ranging from frequency spectroscopy to gravitational wave detection. Quantum mechanics imposes a fundamental limit on the estimation precision, called the Heisenberg limit (HL), which bears a quadratic enhancement over the standard quantum limit (SQL) determined by classical statistics. The HL is achievable in ideal quantum devices, but is not always achievable in presence of noise. Quantum error correction (QEC), as a standard tool in quantum information science to combat the effect of noise, was considered as a candidate to enhance quantum metrology in noisy …

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Dna-Origami-Based Fluorescence Brightness Standards For Convenient And Fast Protein Counting In Live Cells, Nathan David Williams Apr 2021

Dna-Origami-Based Fluorescence Brightness Standards For Convenient And Fast Protein Counting In Live Cells, Nathan David Williams

Yale Graduate School of Arts and Sciences Dissertations

Fluorescence microscopy has been one of the most discovery-rich methods in biology. In the digital age, the discipline is becoming increasingly quantitative. Virtually all biological laboratories have access to fluorescence microscopes, but abilities to quantify biomolecule copy numbers are limited by the complexity and sophistication associated with current quantification methods. Here, we present DNA-origami-based fluorescence brightness standards for counting 5–300 copies of proteins in bacterial and mammalian cells, tagged with fluorescent proteins or membrane-permeable organic dyes. Compared to conventional quantification techniques, our brightness standards are robust, straightforward to use, and compatible with nearly all fluorescence imaging applications, thereby providing a …

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Statistical Methods For Gene-Environment Interactions, Yaqing Xu Apr 2021

Statistical Methods For Gene-Environment Interactions, Yaqing Xu

Yale Graduate School of Arts and Sciences Dissertations

Despite significant main effects of genetic and environmental risk factors have been found, the interactions between them can play critical roles and demonstrate important implications in medical genetics and epidemiology. Although many important gene-environment (G-E) interactions have been identified, the existing findings are still insufficient and there exists a strong need to develop statistical methods for analyzing G-E interactions. In this dissertation, we propose four statistical methodologies and computational algorithms for detecting G-E interactions and one application to imaging data. Extensive simulation studies are conducted in comparison with multiple advanced alternatives. In the analyses of The Cancer Genome Atlas datasets …

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Interdisciplinary Machine Learning Methods For Particle Physics, Mariel Pettee Apr 2021

Interdisciplinary Machine Learning Methods For Particle Physics, Mariel Pettee

Yale Graduate School of Arts and Sciences Dissertations

Following the discovery of a Higgs boson-like particle in the summer of 2012 at the Large Hadron Collider (LHC) at CERN, the high-energy particle physics community has prioritized its thorough study. As part of a comprehensive plan to investigate the many combinations of production and decay of the Standard Model Higgs boson, this thesis describes a continued search for this particle produced in association with a leptonically-decaying vector boson (i.e. a W or Z boson) and decaying into a pair of tau leptons. In Run 1 at the LHC, ATLAS researchers were able to set an upper constraint on the …

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