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Copper Complexes For Water Oxidation Electrocatalysis And Strong Bond Activation, Claire C. Cody Oct 2023

Copper Complexes For Water Oxidation Electrocatalysis And Strong Bond Activation, Claire C. Cody

Yale Graduate School of Arts and Sciences Dissertations

In order to meet rising global energy and material demands while mitigating negative effects on our climate, renewable energy sources must offer a competitive alternative to fossil fuels. Understanding chemical activation of small molecules such as water can provide a basis for leveraging electrocatalytic reactions using electricity from photovoltaics paired with catalysts for chemical transformations. For an efficient and widely applicable system, catalysts should be robust and use cheap, earth-abundant elements. This thesis investigates Cu-based complexes for electrocatalytic transformations, structural studies, and bond activation. First, we investigate the influence of ligand structure on water oxidation electrocatalysis. In comparison to the …

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Optimization And Sequential Decision Making: Implicit Loss Functions And Variance-Aware Reinforcement Learning, Ruitu Xu Oct 2023

Optimization And Sequential Decision Making: Implicit Loss Functions And Variance-Aware Reinforcement Learning, Ruitu Xu

Yale Graduate School of Arts and Sciences Dissertations

Machine learning, as a transformative tool, has demonstrated remarkable efficacy across diverse applications. This dissertation delves into a selection of learning algorithms, analyzing their learning dynamics and providing theoretical guarantees on their performance. First, we scrutinize a novel neural network learning paradigm, leveraging a set of random weights that represent more biologically plausible neural connections during the back-propagation training process. Our research establishes a theoretical framework, illustrating both the convergence of the training loss and the mechanism of alignment between the forward-propagated network weights and the randomized backward-propagated weights. Subsequently, we venture into the realm of model-agnostic meta-learning, examining an …

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Semi-Inclusive Measurement Of The Shared Groomed Momentum Fraction Of Jets In Au+Au Collisions At Star, Daniel B. Nemes Oct 2023

Semi-Inclusive Measurement Of The Shared Groomed Momentum Fraction Of Jets In Au+Au Collisions At Star, Daniel B. Nemes

Yale Graduate School of Arts and Sciences Dissertations

Jet quenching is one of the main signals used to investigate the properties of a quark-gluon plasma (QGP). Besides energy loss, jet quenching can also manifest itself in the modification of jet substructure. This thesis focuses on using STAR data to measure the substructure observable zg, a result of SoftDrop grooming, which probes the physics of the first hard splitting of a hard-scattered parton. As opposed to previous measurements, this thesis explores employing a semi-inclusive approach to measure zg, selecting candi- date jets found within the recoil region of a high transverse momentum trigger particle. Requiring a high transverse momentum …

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Antiviral Hiv-1 Serinc Restriction Factors Disrupt Virus Membrane Asymmetry, Ziwei Yang Oct 2023

Antiviral Hiv-1 Serinc Restriction Factors Disrupt Virus Membrane Asymmetry, Ziwei Yang

Yale Graduate School of Arts and Sciences Dissertations

The human immunodeficiency virus 1 (HIV-1), which is the causative agent responsible for Acquired Immunodeficiency Syndrome (AIDS), is a retrovirus that primarily infects CD4+ T lymphocytes. When left untreated, HIV replication results in progressive CD4+ T cell loss and leads to a myriad of immunological abnormalities in the host, escalating the risk of infections as well as oncological complications. To combat the progression of HIV-1, host cells have evolved to produce proteins known as restriction factors, which are crucial elements of the innate immune system, to inhibit the HIV-1 infection by disrupting various stages of viral replication. Such factors include …

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Statistical Methods In High-Throughput Biomedical Data With Application To Precision Medicine, Yunqing Liu Oct 2023

Statistical Methods In High-Throughput Biomedical Data With Application To Precision Medicine, Yunqing Liu

Yale Graduate School of Arts and Sciences Dissertations

Precision medicine has emerged as a critical approach in healthcare due to its potential to revolutionize patient care. Traditional medical practices often adopt a one-size-fits-all approach, treating patients based on generalized guidelines. However, individuals exhibit significant variations in their genetic makeup, lifestyle factors, and environmental exposures. Precision medicine recognizes and leverages these differences to deliver personalized treatment plans tailored to each patient's unique characteristics. Recent technological advancements have facilitated the generation of high-throughput data, such as single-cell RNA sequencing (scRNA-seq) data, spatial transcriptomics (ST) data, locomotor activity assays measuring behavior, which offers the potential to the development of precision medicine. …

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Bacterial Cell Surface Characterization By Phage Display Coupled To High-Throughput Sequencing, Casey Grun Oct 2023

Bacterial Cell Surface Characterization By Phage Display Coupled To High-Throughput Sequencing, Casey Grun

Yale Graduate School of Arts and Sciences Dissertations

Antimicrobial resistance is a looming threat that reflects the remarkable capacity of bacteria to adapt and change in response to selective pressures. The versatile pathogen P. aeruginosa is a model case---already intrinsically resistant to many antibiotics, it can establish decades-long chronic infections, during which it evolves to survive antimicrobial treatment and evade host defenses. Many changes occur on its cell surface, a key location for both virulence and antibiotic resistance, but our technologies for studying these adaptive phenotypes are limited. Here we combined phage display with high-throughput DNA sequencing to create a high throughput, highly multiplexed technology for surveying bacterial …

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Beyond Bias: Three Papers On Bias In Social Networks And Mitigating Bias In Social Science Research, Jeffrey K. Sachs Oct 2023

Beyond Bias: Three Papers On Bias In Social Networks And Mitigating Bias In Social Science Research, Jeffrey K. Sachs

Yale Graduate School of Arts and Sciences Dissertations

The dissertation consists of three relational-based approaches to analyzing bias in socialnetworks and social data. The first study introduces two group fairness metrics that incorporate network structure, revealing its substantial impact on fairness outcomes, which is often overlooked by traditional metrics. The second study investigates information diffusion processes, highlighting the potential for inequality generated by conventional seeding strategies. It focuses on designing equitable network interventions, considering each group’s relative influence. I calibrate the diffusion models to actual diffusion processes to assess various network influence measures and their likelihood of producing equitable outcomes under a set of fairness constraints. The analysis …

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Chromatin Expansion Microscopy Reveals Nanoscale Organization Of Transcription And Chromatin, Mark Pownall Oct 2023

Chromatin Expansion Microscopy Reveals Nanoscale Organization Of Transcription And Chromatin, Mark Pownall

Yale Graduate School of Arts and Sciences Dissertations

Nanoscale chromatin organization regulates gene expression. While chromatin is dramatically reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. Here, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA Polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed …

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Nutrient Acquisition And Plant-Microbe Interactions In Savanna Trees, Arielle Biro Oct 2023

Nutrient Acquisition And Plant-Microbe Interactions In Savanna Trees, Arielle Biro

Yale Graduate School of Arts and Sciences Dissertations

Ecosystem productivity is often constrained by the availability of essential macronutrients. Ecosystem processes that are vital to nutrient acquisition like nutrient cycling and microbial activity are expected to change under global warming, but prediction accuracy in the face of global change is challenging, as prediction requires a thorough mechanistic understanding of how plants acquire nutrients from their environments. These strategies include exploration by roots for resources like nutrients or water, releasing enzymes that decompose organic matter into plant available forms, or forming symbioses with soil bacteria or mycorrhizal fungi, which can have downstream impacts on ecosystem nutrient budgets, nutrient cycling, …

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Methods And Complexity In Phage-Bacteria Ecology And Evolution, Michael Blazanin Oct 2023

Methods And Complexity In Phage-Bacteria Ecology And Evolution, Michael Blazanin

Yale Graduate School of Arts and Sciences Dissertations

Chapter I:Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights. However, existing tools are limited. Many use parametric analyses that require mathematical assumptions about the microbial growth characteristics. Those that use non-parametric or model-free analyses often can only quantify a few traits of interest, and none are capable of importing and reshaping all known growth curve data formats. To address this gap, here I present a newly-developed R package: gcplyr. gcplyr can flexibly …

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The Role Of Dietary Fats In Driving Atherosclerosis, Zenan Wang Oct 2023

The Role Of Dietary Fats In Driving Atherosclerosis, Zenan Wang

Yale Graduate School of Arts and Sciences Dissertations

Cardiovascular diseases (CVDs) are the number one killer of people worldwide, of which coronary heart disease, which is mainly due to atherosclerosis, is the main contributor to death. Nonetheless, the etiology of atherosclerosis remains poorly understood. It is universally accepted that dietary fat influences atherosclerosis, however, the role of specific fats is not well-understood. Despite the widely-held perception that saturated fats drive atherosclerotic CVDs while monounsaturated fats are protective, there have been numerous studies from human and mice that do not fit with this prevailing narrative. Thus, despite the importance of dietary fats in CVDs, the exact effects remain controversial …

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Modifying The Surface Topography Of Pegylated Nanoparticles Based On Bottlebrush Block Copolymer For Drug Delivery Applications, Julian Grundler Oct 2023

Modifying The Surface Topography Of Pegylated Nanoparticles Based On Bottlebrush Block Copolymer For Drug Delivery Applications, Julian Grundler

Yale Graduate School of Arts and Sciences Dissertations

The clinical translation of nanomedicines has been closely tied to the development ofnovel drug delivery techniques. In particular, nanoparticle formulations promise to improve the pharmacokinetics, selective accumulation at the target site, and intracellular delivery of therapeutics. Extensive research efforts have identified structure-function relationships between nanoparticle physicochemical properties (e.g. size, charge, surface functionalization) and biological fate. However, studying the biological impact of nanoparticle surface topography still remains a challenge due to the limited spatial control of conventional nanoparticle surface coatings based on hydrophilic linear polymers including poly(ethylene glycol) (PEG). In this dissertation, we investigated a novel method to precisely control the …

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Many-Body Physics With A Ultracold Uniform Fermi Gas, Yunpeng Ji Oct 2023

Many-Body Physics With A Ultracold Uniform Fermi Gas, Yunpeng Ji

Yale Graduate School of Arts and Sciences Dissertations

Ultracold atomic gases, traditionally produced in harmonic traps, have been a successful platform in studying many-body problems. In recent years, the realization of homogeneous quantum gases in optical box potentials has opened up new opportunities to study complex problems without the complications arising from the density inhomogeneity, and allows for more direct comparisons with theories. In this thesis, we present the production and the study of a homogeneous Fermi gas consisting of Lithium-6 atoms. We begin by examining the experimental setup for cooling and trapping atoms, with a particular emphasis on how the box trapping potential is implemented. We then …

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Computational Study Of The Mechanism Of Attention In Cortical Information Coding, Xiang Wang Oct 2023

Computational Study Of The Mechanism Of Attention In Cortical Information Coding, Xiang Wang

Yale Graduate School of Arts and Sciences Dissertations

The animals’ visual perception of natural scenes is influenced by both the external condi-tions of the environment and the internal states. External conditions include the contrast of the stimulus, the crowding of distractors and the complexity of visual features. Internal states include the level of arousal, the deployment of attention, and the goal of behavior. An important and extensively studied internal state is selective attention, which is thought to be critical in solving visual perception problems by increasing the saliency of the attended ob-jects against the background. Electrophysiological studies have indicated attentional modu-lation of single neurons along the hierarchy of …

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A New View Of Galaxy Morphology, Timothy Blake Miller Oct 2023

A New View Of Galaxy Morphology, Timothy Blake Miller

Yale Graduate School of Arts and Sciences Dissertations

A galaxy’s morphology provides crucial constraints on its formation history. Most studies rely on forward modeling procedure utilizing the S\ersic profile to measure morphological parameters and focus on the half-light radius of galaxies measured at optical wavelength. In this P.hD I investigated how common assumptions made when measuring galaxy structure bias the interpretation. First I consider the size-mass distribution using the radii that contain 20% and 80% of the light, as opposed to the traditional half-light radius. We find qualitatively different relations and suggest that the 20% radius is related to the star-formation history of galaxies while the 80% radius …

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Multi-Scale Gene Regulation Analysis With Chip-Seq And Beyond, Jiahao Gao Oct 2023

Multi-Scale Gene Regulation Analysis With Chip-Seq And Beyond, Jiahao Gao

Yale Graduate School of Arts and Sciences Dissertations

Regulation of gene expression is one of the most important and fundamental aspects of biological systems. The intricate regulation could be observed in different aspects, including the variations in individual genes, dynamic interactions between multiple genes, and complicated regulatory relationships between expression and other properties such as methylation level. Therefore, studying gene regulation at all these multiple scales is crucial. Transcription factors (TFs) are a special group of proteins that recognize specific DNA sequences and control gene expression by DNA binding. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) had been developed to identify genome-wide protein–DNA interactions. It has become the standard …

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Probing Diverse Biological Systems And Their Hydration Shells By Modeling Chiral Sum Frequency Generation Spectroscopy, Daniel Konstantinovsky Oct 2023

Probing Diverse Biological Systems And Their Hydration Shells By Modeling Chiral Sum Frequency Generation Spectroscopy, Daniel Konstantinovsky

Yale Graduate School of Arts and Sciences Dissertations

All biological processes occur in aqueous solution. Water dictates biomolecular structure, is responsible for a large portion of the free energy of ligand binding, and participates structurally in protein-protein interactions. However, few experimental techniques can probe the biomolecular hydration shell and its diverse environments. Chirality-sensitive vibrational sum frequency generation spectroscopy (chiral SFG) is a powerful technique that probes hydration shell water. The work presented here clarifies the conditions required for a chiral SFG signal to emerge, identifies the water immediately neighboring a biomolecule as the source of the aqueous chiral SFG signal, and investigates the interaction between biomolecules and their …

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Outbreak Dynamics Of Emerging Sars-Cov-2 Variants In Human And Animal Populations, Rebecca Lynn Earnest Oct 2023

Outbreak Dynamics Of Emerging Sars-Cov-2 Variants In Human And Animal Populations, Rebecca Lynn Earnest

Yale Graduate School of Arts and Sciences Dissertations

The COVID-19 pandemic is characterized by cycles of SARS-CoV-2 viral variant emergence followed by surges of infections and deaths. In the United States, the most notable variants to date are Alpha (B.1.1.7), Delta (B.1.617.2 and AY.x sub-lineages), and Omicron (BA.1, BA.2, BA.4, BA.5, and various sub-lineages). Pandemic response evolved along with the virus, raising three overarching research questions with each new variant that correspond to the chapters of this dissertation. When a new variant emerges, how is it different from the previously dominant variant(s) in circulation? The set of mutations that define a SARS-CoV-2 variant can affect viral properties such …

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Exploiting Dna Repair Deficiencies In Cancer To Develop And Characterize Novel Therapeutics, Sateja Paradkar Oct 2023

Exploiting Dna Repair Deficiencies In Cancer To Develop And Characterize Novel Therapeutics, Sateja Paradkar

Yale Graduate School of Arts and Sciences Dissertations

Genomic instability is one of the hallmarks of cancer, which underlies cancer development and progression. This DNA repair vulnerability presents cancer researchers with a therapeutic opportunity. Targeted therapies designed to overwhelm DNA repair pathways in cancer have proven largely effective as anti-cancer treatments. However, there are currently three major issues with their widespread use in cancer. Firstly, for cancers such as glioblastomas (GBMs), there have been no targeted therapies approved for decades. Secondly, for most targeted therapies there is an incomplete understanding of their precise mechanism of action, which limits their clinical utility. Thirdly, cancers develop resistance to most targeted …

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Mind Perception In Moral Judgment, Madeline G. Reinecke Oct 2023

Mind Perception In Moral Judgment, Madeline G. Reinecke

Yale Graduate School of Arts and Sciences Dissertations

Humans face a series of moral puzzles. We have to determine who (or what) matters, morally speaking. Of all the potential creatures we could care about, who should we care about? Some such judgments come easily: Babies and young children, for example, seem obvious candidates for having moral rights and deserving our protection from harm. Family and friends also seem to enjoy special moral value. Yet other determinations seem less obvious. Does an unborn fetus have the same value as a two-year-old? Does the family dog count just as much as a human relative—or is it true that humans always …

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Mechanisms That Control Lipid Synthesis At The Endoplasmic Reticulum And Nuclear Envelope, Jake Williams Carrasquillo Rodriguez Oct 2023

Mechanisms That Control Lipid Synthesis At The Endoplasmic Reticulum And Nuclear Envelope, Jake Williams Carrasquillo Rodriguez

Yale Graduate School of Arts and Sciences Dissertations

The endoplasmic reticulum (ER) is the largest membrane bound organelle in most cells. The ER is made up of distinct structural and functional domains, which include the nuclear envelope (NE) and peripheral ER sheets and tubules. The nuclear envelope surrounds and protects the genome, while the peripheral ER is essential for protein and de novo lipid synthesis. Lipids synthesized at the ER are either retained or shuttled to other membrane bound organelles through membrane contact sites or vesicular trafficking. As such, regulation of ER lipid synthesis is a tightly controlled process carried out by a subset of enzymes that are …

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Error Detection In Bosonic Circuit Quantum Electrodynamics, James David Teoh Oct 2023

Error Detection In Bosonic Circuit Quantum Electrodynamics, James David Teoh

Yale Graduate School of Arts and Sciences Dissertations

Any useful quantum computer must be robust to errors on the individual qubits. This means a quantum algorithm can still reliably give the correct answer despite the qubits suffering from decoherence. Quantum error correction provides a means for achieving this, by encoding logical qubits redundantly in many additional physical qubits and/or additional energy levels. In the presence of errors the logical information is still preserved, but this remains a monumentally difficult task to achieve in practice. But what can we do with quantum error detection? Rather than trying to recover from a quantum error we instead reset qubits that are …

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Yale Medicine Magazine Autumn 2023, Issue 171, Yale University. School Of Medicine Oct 2023

Yale Medicine Magazine Autumn 2023, Issue 171, Yale University. School Of Medicine

Yale Medicine Magazine - alumni bulletin and magazine

This is the Autumn 2023 issue of Yale Medicine Magazine, issue 171. Prepared in cooperation with the alumni and development offices at the School of Medicine. Earlier volumes are called Yale School of Medicine alumni bulletins, dating from v.1 (1953) through v.13 (1965) and Yale Medicine: alumni bulletin of the School of Medicine, v.1 (1965) through v. 52, no.1. (Autumn 2017).

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Commercial Bank Examination Manual: Section 3300.1, Federal Reserve System: Board Of Governors Oct 2023

Commercial Bank Examination Manual: Section 3300.1, Federal Reserve System: Board Of Governors

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No abstract provided.

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Transdniestria, Encyclopedia Britannica Sep 2023

Transdniestria, Encyclopedia Britannica

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No abstract provided.

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Caixabank Capital Distribution, Caixabank Sep 2023

Caixabank Capital Distribution, Caixabank

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No abstract provided.

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Programme Timeline For Cyprus, European Stability Mechanism Sep 2023

Programme Timeline For Cyprus, European Stability Mechanism

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No abstract provided.

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Recapitalisation Through Bail-In And Resolution Exit Bank Of Cyprus Announcement, The Bank Of Cyprus Sep 2023

Recapitalisation Through Bail-In And Resolution Exit Bank Of Cyprus Announcement, The Bank Of Cyprus

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No abstract provided.

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Debt Relief: What Was The Private Sector Debt Restructuring In March 2012?, European Stability Mechanism Sep 2023

Debt Relief: What Was The Private Sector Debt Restructuring In March 2012?, European Stability Mechanism

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No abstract provided.

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Hellenic Financial Stability Fund Selection Panel, Hellenic Financial Stability Fund Sep 2023

Hellenic Financial Stability Fund Selection Panel, Hellenic Financial Stability Fund

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No abstract provided.

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