Physical Sciences and Mathematics Commons^™

Investigation Of Neonatal Pulmonary Structure And Function Via Proton And Hyperpolarized Gas Magnetic Resonance Imaging, Nara Savoye Higano

Arts & Sciences Electronic Theses and Dissertations

Magnetic resonance imaging (MRI) is a modality that utilizes the phenomenon of nuclear magnetic resonance (NMR) to yield tomographic images of the body. Proton (1H) MRI has historically been successful in soft tissues but has suffered in the lung due to a variety of technical challenges, such as the low proton-density, rapid T2* relaxation time of the lung parenchymal tissue, and inherent physiological motion in the chest. Recent developments in radial ultrashort echo time (UTE) MRI have in part overcome these issues. In addition, there has been much progress in techniques for hyperpolarization of noble gases (3He and 129Xe) out …

Structured Illumination Diffuse Optical Tomography For Mouse Brain Imaging, Matthew Reisman

Arts & Sciences Electronic Theses and Dissertations

As advances in functional magnetic resonance imaging (fMRI) have transformed the study of human brain function, they have also widened the divide between standard research techniques used in humans and those used in mice, where high quality images are difficult to obtain using fMRI given the small volume of the mouse brain. Optical imaging techniques have been developed to study mouse brain networks, which are highly valuable given the ability to study brain disease treatments or development in a controlled environment. A planar imaging technique known as optical intrinsic signal (OIS) imaging has been a powerful tool for capturing functional …

New Ventures In Amidine-Based Catalyst Design, Nicholas Alan Ahlemeyer

Arts & Sciences Electronic Theses and Dissertations

Two new cascade transformations of α,β-unsaturated thioesters catalyzed by amidine-based catalysts have been developed. First, a reagent-free transformation of o-formylaryl cinnamoyl thioesters catalyzed by HBTM-2 to produce 2-substituted thiochromenes achieved high enantioselectivities and yields while forming carbon dioxide as the only byproduct. Second, a highly diastereo- and enantioselective tandem rearrangement of less reactive enone thioesters into tricyclic thiochromanes in the presence of electron-rich amidine-based catalysts was developed. These catalysts were designed with the help of DFT calculations. H-PIP, the first chiral amidine-based catalyst synthesized in our group, performed the best overall in the thiochromane synthesis.

The second chapter of this …

Fast Monte Carlo Simulations For Quality Assurance In Radiation Therapy, Yuhe Wang

Arts & Sciences Electronic Theses and Dissertations

Monte Carlo (MC) simulation is generally considered to be the most accurate method for dose calculation in radiation therapy. However, it suffers from the low simulation efficiency (hours to days) and complex configuration, which impede its applications in clinical studies. The recent rise of MRI-guided radiation platform (e.g. ViewRay’s MRIdian system) brings urgent need of fast MC algorithms because the introduced strong magnetic field may cause big errors to other algorithms. My dissertation focuses on resolving the conflict between accuracy and efficiency of MC simulations through 4 different approaches: (1) GPU parallel computation, (2) Transport mechanism simplification, (3) Variance reduction, …

Knowledge Driven Approaches And Machine Learning Improve The Identification Of Clinically Relevant Somatic Mutations In Cancer Genomics, Benjamin John Ainscough

Arts & Sciences Electronic Theses and Dissertations

For cancer genomics to fully expand its utility from research discovery to clinical adoption, somatic variant detection pipelines must be optimized and standardized to ensure identification of clinically relevant mutations and to reduce laborious and error-prone post-processing steps. To address the need for improved catalogues of clinically and biologically important somatic mutations, we developed DoCM, a Database of Curated Mutations in Cancer (http://docm.info), as described in Chapter 2. DoCM is an open source, openly licensed resource to enable the cancer research community to aggregate, store and track biologically and clinically important cancer variants. DoCM is currently comprised of 1,364 variants …

The Chemistry And Biology Of Iron-Scavenging Natural Products From Pathogenic Acinetobacter Baumannii, Justin Shapiro

Arts & Sciences Electronic Theses and Dissertations

Multidrug resistant (MDR) Gram-negative bacteria represent a global health crisis. Traditional antibiotics create selective pressure and breed resistance, making our current drugs less and less effective. Targeting of bacterial virulence factors has gained interest as an alternative strategy to potentially circumvent this problem. Virulent Acinetobacter baumannii synthesize and secrete pre-acinetobactin, a small molecule metal chelator that scavenges life-sustaining iron and is critical for establishing infection. The work described herein sheds light on the unusual properties of a non-enzymatic isomerization from pre-acinetobactin to acinetobactin and proposes a siderophore-swapping mechanism by which A. baumannii expands its pH window for virulence. Knowledge from …

Synthesis, Characterization, And Biological Activity Of Spherical Nucleic Acid (Sna) Constructs For Cancer Therapy And Imaging, Colin Calabrese

Arts & Sciences Electronic Theses and Dissertations

This dissertation focuses on the development of biocompatible oligonucleotide-based nanomaterials, known as spherical nucleic acids (SNAs), as therapeutic and diagnostic agents for intracellular gene regulation and in vivo cancer imaging by positron emission tomography (PET). SNAs consist of a nanoparticle core functionalized with a dense shell of oligonucleotides such as deoxyribonucleic acid (DNA). Detailed synthetic procedures and characterization of novel SNAs with purpose-built biocompatible core materials are described. The SNAs exhibit comparable chemical, physical and biological properties regardless of core composition. The functionalities of the SNAs were further tailored by deliberate design and chemical modification of their oligonucleotide sequences.

The …

Effects Of Nucleosome Structure On Dna Photoproduct Formation And Deamination, Kesai Wang

Arts & Sciences Electronic Theses and Dissertations

Cyclobutane pyrimidine dimers (CPDs) are DNA photoproducts linked to skin cancer, whose mutagenicity depends in part on their frequency of formation and deamination. Nucleosomes modulate CPD formation, favoring outside facing sites, and disfavoring inward facing sites. A similar pattern of CPD formation in protein-free DNA loops suggest that DNA bending causes the modulation of photoproduct formation in nucleosomes. To systematically study the cause and effect of nucleosome structure on CPD formation and deamination, we had developed a circular permutation synthesis strategy for positioning a target sequence at different superhelix locations (SHLs) across a nucleosome in which the DNA has been …

Effects Of Regolith Properties On Uv/Vis Spectra And Implications For Lunar Remote Sensing, Ecaterina Ioana Coman

Arts & Sciences Electronic Theses and Dissertations

Lunar regolith chemistry, mineralogy, various maturation factors, and grain size dominate the reflectance of the lunar surface at ultraviolet (UV) to visible (VIS) wavelengths. These regolith properties leave unique fingerprints on reflectance spectra in the form of varied spectral shapes, reflectance intensity values, and absorption bands. With the addition of returned lunar soils from the Apollo and Luna missions as ground truth, these spectral fingerprints can be used to derive maps of global lunar chemistry or mineralogy to analyze the range of basalt types on the Moon, their spatial distribution, and source regions for clues to lunar formation history and …

Genetic And Biological Studies On Solanum Plants: Insights Into The Leaf Wax Alkane Paleoclimate Proxy, Amanda Lorraine Dorothy Bender

Arts & Sciences Electronic Theses and Dissertations

The hydrogen isotopic composition (δ2H) of precipitation records fluxes of water in the hydrological cycle, and can reflect climatic variables such as temperature and humidity. Leaf wax n-alkanes can record δ2H of precipitation; consequently, n-alkanes extracted from sedimentary archives are commonly used as proxies for paleoenvironmental reconstruction. However, the utility of the leaf wax paleoclimate proxy is modulated by uncertainty about how physiological processes affect hydrogen isotopic compositions during alkane biosynthesis. This work aims to improve our understanding of the leaf wax paleoclimate proxy by examining biological and environmental sources of variability on cuticular leaf waxes. We used Solanum (tomato) …

Electronic And Thermal Properties Of Puckered Orthorhombic Materials, Ruixiang Fei

Arts & Sciences Electronic Theses and Dissertations

Puckered orthorhombic crystals, such as black phosphorus and group IV monochalcogenides, are attracting tremendous attention because of their new exotic properties, which are of great interests for fundamental science and novel applications. Unlike those well studied layered hexagonal materials such as graphene and transition metal dichalcogenides, the puckered orthorhombic crystals possess highly asymmetrical in-plane crystal structures. Understanding the unique properties emerginge from their low symmetries is an intriguing and useful process, which gives insight into experimental observation and sheds light on manipulating their properties. In this thesis, we study and predict various properties of orthorhombic materials by using appropriate theoretical …

Physics-Inspired Replica Approaches To Computer Science Problems, Bo Sun

Arts & Sciences Electronic Theses and Dissertations

We study machine learning class classification problems and combinatorial optimization problems using physics inspired replica approaches. In the current work, we focus on the traveling salesman problem which is one of the most famous problems in the entire field of combinatorial optimization. Our approach is specifically motivated by the desire to avoid trapping in metastable local minima-a common occurrence in hard problems with multiple extrema. Our method involves (i) coupling otherwise independent simulations of a system (“replicas”) via geometrical distances as well as (ii) probabilistic inference applied to the solutions found by individual replicas. In particular, we apply our method …

Weak Measurement And Quantum Smoothing Of A Superconducting Qubit, Dian Tan

Arts & Sciences Electronic Theses and Dissertations

In quantum mechanics, the measurement outcome of an observable in a quantum system is intrinsically random, yielding a probability distribution. The state of the quantum system can be described by a density matrix (t), which depends on the information accumulated until time t, and represents our knowledge about the system. The density matrix (t) gives probabilities for the outcomes of measurements at time t. Further probing of the quantum system allows us to refine our prediction in hindsight. In this thesis, we experimentally examine a quantum smoothing theory in a superconducting qubit by introducing an auxiliary matrix E(t) which is …

Sequence Determinants Of The Individual And Collective Behaviour Of Intrinsically Disordered Proteins, Alexander S. Holehouse

Arts & Sciences Electronic Theses and Dissertations

Intrinsically disordered proteins and protein regions (IDPs) represent around thirty percent of the eukaryotic proteome. IDPs do not fold into a set three dimensional structure, but instead exist in an ensemble of inter-converting states. Despite being disordered, IDPs are decidedly not random; well-defined - albeit transient - local and long-range interactions give rise to an ensemble with distinct statistical biases over many length-scales. Among a variety of cellular roles, IDPs drive and modulate the formation of phase separated intracellular condensates, non-stoichiometric assemblies of protein and nucleic acid that serve many functions. In this work, we have explored how the amino …

Determining The Molecular Mechanisms Of Huntington’S Disease Through Multi-Scale Modeling, Kiersten Ruff

Arts & Sciences Electronic Theses and Dissertations

Huntington’s disease (HD) is associated with a mutational CAG repeat expansion within exon 1 of the huntingtin (Htt) gene. Post-transcriptional processing leads to the generation of N-terminal Htt protein fragments (Htt-NTFs), including those that encompass exon 1 (Httex1). Within Httex1, the CAG-repeat encoded polyglutamine (polyQ) tract is flanked N-terminally by a 17-residue amphipathic stretch (N17) and C-terminally by a 50-residue proline rich (PR) domain. Htt-NTFs, including Httex1, are among the smallest fragments that recapitulate HD pathology in mouse models. However, the direct link between Htt-NTFs with polyQ expansions and neurodegeneration that leads to HD remains unresolved. Despite being a monogenic …

Topics In Qcd At Nonzero Temperature And Density, Kamal Pangeni

Arts & Sciences Electronic Theses and Dissertations

Understanding the behavior of matter at ultra-high density such as neutron stars require the knowledge of ground state properties of Quantum chromodynamics (QCD) at finite chemical potential. However, this task has turned out to be very difficult because of two main reasons: 1) QCD may still be strongly coupled at those regimes making perturbative calculations unreliable and 2) QCD at finite density suffers from the sign problem that makes the use of lattice simulation problematic and it even affects phenomenological models. In the first part of this thesis, we show that the sign problem in analytical calculations of finite density …

Participation In Governance And Well-Being In The Yukon Flats, Jessica Charlene Black

Arts & Sciences Electronic Theses and Dissertations

This dissertation explains the relationship between participation in governance and well-being in the Yukon Flats. To garner a deeper understanding of this relationship, definitions of governance and well-being are sought from the participants, thus providing holistic, Indigenous definitions of these concepts. Both formal and informal governance are also explored to understand the important institutions that underpin these larger relationships. Lastly, this dissertation investigates the relationship between participation in traditional hunting, fishing, and gathering and well-being in the Yukon Flats. Qualitative methods, including semi-structured interviews, observations, and photographs are all used to document these relationships. Applied thematic analysis is used due …

Studies Of Magic-Size Ii-Vi Nanoclusters And Surface Exchange On Flat Colloidal Nanocrystals, Yang Zhou

Arts & Sciences Electronic Theses and Dissertations

This dissertation presents the isolation, characterization and reactivity of two magic size clusters, (ZnSe)34 and (CdTe)34, as well as the L-, Z- and X-type ligand exchange on the CdSe QBs or CdS QP surface.

The dissertation first reports the spectroscopically observed magic-size nanoclusters (ZnSe)34 and (CdTe)34 are isolable as amine derivatives. The nanoclusters [(ZnSe)34(n-octylamine)29±6(di-n-octylamine)5±4] and [(CdTe)34(n-octylamine)4±3(di-n-pentylamine)13±3] are fully characterized by UV-visible spectroscopy, IR spectroscopy, elemental analysis, and mass spectrometry. Amine derivatives of both (ZnSe)34 and (CdTe)34 are observed to convert to the corresponding (ZnSe)13 and (CdTe)13 derivatives, indicating that the former are kinetic products and the latter thermodynamic products, under …

Understanding Household, Network, And Organizational Drivers Of Adoption Of Cleaner Cooking Fuels In Rural India, Praveen Kumar

Arts & Sciences Electronic Theses and Dissertations

Adoption of evidence-based cleaner cooking systems such as Liquefied Petroleum Gas (LPG) is a crucial first step in eventually providing a sustainable solution for household air pollution. To promote adoption of LPG in below poverty line households, we require evidence-based implementation strategies. For these strategies to be feasible and scalable, they need to be grounded in a thorough understanding of the household, network, and organizational level drivers of LPG adoption. However, systematic research on adoption of LPG by poor communities is still lacking.

The overall objective of the study was to develop a better understanding about new insights on the …

Mri In Cancer: Improving Methodology For Measuring Vascular Properties And Assessing Radiation Treatment Effects In Brain, Chong Duan

Arts & Sciences Electronic Theses and Dissertations

Tumors cannot survive, progress and metastasize without recruiting new blood vessels. Vascular properties, including perfusion and permeability, provide valuable information for characterizing cancers and assessing therapeutic outcomes. Dynamic contrast-enhanced (DCE) MRI is a non-invasive imaging technique that affords quantitative parameters describing the underlying vascular structure of tissue. To date, the clinical application of DCE-MRI has been hampered by the lack of standardized and validated quantitative modeling approaches for data analysis.

From a therapeutic perspective, radiation therapy is a central component of the standard treatment for patients with cancer. Besides killing cancer cells, radiation also induces parenchymal and stromal changes in …

Mass Spectrometry-Based Structural Proteomics: Methodology And Application Of Fast Photochemical Oxidation Of Proteins (Fpop), Ben Niu

Arts & Sciences Electronic Theses and Dissertations

The dissertation will be solely focused on using mass spectrometry to characterize protein high order structures (HOS), it emphasizes the use of hydroxyl radical footprinting (FPOP) coupled to bottom-up MS approach. A detailed background information about FPOP, and the corresponding method developments as well as applications will be covered.

The first chapter will be a comprehensive review regarding the FPOP. Following this, chapter 2, 3, and 4 will be focused on the method developments. Chapter 2 describes an isotope dilution GC-MS method to quantitate OH radicals in FPOP; chapter 3 describes the incorporation of Leu-enkephalin as reporter peptide for a …

Mortgage Transition Model Based On Loanperformance Data, Shuyao Yang

Arts & Sciences Electronic Theses and Dissertations

The unexpected increase in loan default on the mortgage market is widely considered to be one of the main cause behind the economic crisis. To provide some insight on loan delinquency and default, I analyze the mortgage performance data from Fannie Mae website and investigate how economic factors and individual loan and borrower information affect the events of default and prepaid. Various delinquency status including default and prepaid are treated as discrete states of a Markov chain. One-step transition probabilities are estimated via multinomial logistic models. We find that in general current loan-to-value ratio, credit score, unemployment rate, and interest …

How Do Environmental Changes And Shared Cultural Experiences Impact The Health Of Indigenous Peoples In South Louisiana?, Shanondora M. Billiot

Arts & Sciences Electronic Theses and Dissertations

Global environmental change is an ongoing and complex social problem that will continue to permeate all spheres of life on earth (Moran, 2010). Not all communities experience social and economic consequences of environmental change at the same level (Adger, 2006a; Cutter, Boruff, & Shirley, 2003; Gillespie, 2010; Nicholls et al., 2007; Vogel, Moser, Kasperson, & Dabelko, 2007). The variability of vulnerability, or potential for exposure or harm, stems from proximity to fragile ecosystems as well as social and economic differences across communities (Boruff, Emrich, & Cutter, 2005). Additionally, environmental changes are projected to have adverse impacts on marginalized populations through …

Stellar And Interstellar Origins Of Meteoritic Nanodiamonds, Josiah Lewis

Arts & Sciences Electronic Theses and Dissertations

In 1987 presolar grains were first isolated from meteorites, opening up a new line of data about the stars that produced them. Based on anomalies in isotopic ratios, identification and classification of presolar grains has borne great fruit in understanding nucleosynthesis, stellar evolution, and mass loss from the stellar objects in which these grains originated: primarily, but not exclusively, supernovae and asymptotic giant branch stars.Meteoritic nanodiamonds were the first type of presolar grain identified, but more than three decades later, their origins remain unclear. Anomalies in the ratios of Xe isotopes carried by the nanodiamonds suggest the nanodiamonds formed from …

Mapping Analyte-Signal Relations In Lc-Ms Based Untargeted Metabolomics, Nathaniel Guy Mahieu

Arts & Sciences Electronic Theses and Dissertations

The goal of untargeted metabolomics is to profile metabolism by measuring as many metabolites as possible. A major advantage of the untargeted approach is the detection of unexpected or unknown metabolites. These metabolites have chemical structures, metabolic pathways, or cellular functions that have not been previously described. Hence, they represent exciting opportunities to advance our understanding of biology. This beneficial approach, however, also adds considerable complexity to the analysis of metabolomics data - an individual signal cannot be readily identified as a unique metabolite. As such, a major challenge faced by the untargeted metabolomic workflow is extracting the analyte content …

Connectivity Bounds And S-Partitions For Triangulated Manifolds, Alexandru Ilarian Papiu

Arts & Sciences Electronic Theses and Dissertations

Two of the fundamental results in the theory of convex polytopes are Balinski’s Theorem on connectivity and Bruggesser and Mani’s theorem on shellability. Here we present results that attempt to generalize both results to triangulated manifolds. We obtain new connectivity bounds for complexes with certain missing faces and introduce a way to measure how far a manifold is from being shellable using S-partitions and the Stanley-Reisner Ring.

Environmentalism And The Music Of Sir Peter Maxwell Davies, Karen Olson

Arts & Sciences Electronic Theses and Dissertations

Music critics and scholars frequently present British composer Sir Peter Maxwell Davies (1934-2016) as a green composer, but little work has been done to determine the kinds of environmentalism his music supports. This dissertation focuses on the relationship between Davies’s music and British environmentalism, both as protest music and as government policy. Drawing on such diverse fields as philosophy of the environment, British political history, and environmental aesthetics, I examine how Davies’s music responded to the political climate of its times, and how its reception changed as certain environmental models, such as sustainable development, gained political relevance. Over the course …

Evolution Of Olivine Crystallographic Preferred Orientation In The Upper Mantle -- Implications For The Interpretation Of Seismic Anisotropy, Yuval Boneh

Arts & Sciences Electronic Theses and Dissertations

Earth’s plate tectonics is the outermost manifestation of mantle convection. Understanding plate tectonics at the global scale requires understanding of regional processes near plate boundaries. Flow patterns in the upper mantle are generally inferred from observations of anisotropy of seismic wave speed. In plate interiors, where flow patterns are assumed to be simple, interpretation of seismic anisotropy is straightforward. However, near plate boundaries, where flow patterns are complex, different strategies for interpreting seismic anisotropy may be required. This dissertation examines, using experimental and numerical tools, the effects of complex flow patterns on the evolution of olivine crystallographic preferred orientation (CPO). …

Disordered Proteins: Connecting Sequences To Emergent Properties, Tyler Scott Harmon

Arts & Sciences Electronic Theses and Dissertations

Many IDPs participate in coupled folding and binding reactions and form alpha helical structures in their bound complexes. Alanine, glycine, or proline scanning mutagenesis approaches are often used to dissect the contributions of intrinsic helicities to coupled folding and binding. These experiments can yield confounding results because the mutagenesis strategy changes the amino acid compositions of IDPs. Therefore, an important next step in mutagenesis-based approaches to mechanistic studies of coupled folding and binding is the design of sequences that satisfy three major constraints. These are (i) achieving a target intrinsic alpha helicity profile; (ii) fixing the positions of residues corresponding …

Coexistence Of Confamilial, Folivorous Indriids, Propithecus Diadema And Indri Indri, At Betampona Strict Nature Reserve, Madagascar, Lana Kerker Oliver

Arts & Sciences Electronic Theses and Dissertations

In this dissertation, I examine how two confamilial and ecologically similar indriids, indri (Indri indri), and diademed sifakas (Propithecus diadema) maintain coexistence in Betampona Nature Reserve (BNR), an eastern lowland rainforest in Madagascar. These two species occur sympatrically throughout much of their species ranges and are similarly-sized folivorous primates. As anatomic folivores, they present an opportunity to investigate how niche differentiation and resource partitioning allow two sympatric primate species with similar feeding patterns to coexist. I examined coexistence strategies and the general behavioral ecology of each species by examining their activity patterns, dietary profiles, home range use, and daily path …