Physical Sciences and Mathematics Commons^™

Accurate And Integrative Detection Of Copy Number Variants With High-Throughput Data, Xizhi Luo

Theses and Dissertations

Copy number variation, as a major source of genetic variation in the human genome, are gains or losses of the DNA segments. Copy number variation has gained considerable interest as it plays important roles in human complex diseases. Therefore, accurate detection of CNVs with data generated by modern genotyping technologies, such as SNP array and whole-exome sequencing (WES), comprises a critical step toward a better understanding of disease etiology. However, current statistical methodologies for CNV detection still face analytical challenges due to numerous genetic and technological factors that may lead to spurious findings. First, existing methods assume the independent observations …

Developing And Understanding Catalysts For Organic Synthesis, Shelby Dickerson

Theses and Dissertations

Organic synthesis relies on improving catalyst designs and understanding reaction mechanisms for the advancement of the field. This dissertation will describe projects in both of these areas. First it will cover new photocatalysts in the aim of maintaining reactivity while increasing solubility in less polar solvents, and second understanding the importance of intermolecular interactions between new nucleophilic catalysts and substrates.

Photocatalysis has become a major focus as a sustainable pathway for chemical reactions with visible light photocatalysts performing a large range of reactions such as redox reactions, cyclization reactions, and energy transfer reactions. Chapter 1 will discuss classes of organic …

Exploration Of Vase As An Extraction Method For Emerging Disinfection By-Products And Acidic Methanol As A Safe And Effective Derivatization Method For Haloacids, Madison Leigh Kilpatrick

Theses and Dissertations

This project aims to create an environmentally friendly, robust, and efficient extraction and preconcentration method in both the detection and quantification of various disinfection by-products (DBPs). Vacuum assisted sorbent extraction (VASE) is a newly developed method in the extraction of both volatile organic compounds (VOCs) and semi-volatile organic compounds (SVOCs). This extraction method is paired with a Thermo Scientific TSQ Quantum Triple Quadrupole GC-MS system for the quantification of DBPs. VASE outperforms current DBP extraction methods, with liquid-liquid extraction (LLE) being the most used alternative, because of its minimal use of solvent, high level of automation, and over-all ease of …

Characterization Of Ph – Responsive Nanocage Based On The Ferritin Iron Storage Protein, Satyam Singh

Theses and Dissertations

The iron-storage protein ferritin (Ftn) assembles into a protein cage structure with 24 subunits and octahedral (4-fold, 3-fold, 2-fold) symmetry. Each monomeric subunit contains a robust four-helix bundle fold. The fully assembled Ftn structure has a high degree of thermal stability (up to 100°C), a mono dispersed size (12 nm in diameter), and a large central cavity (7-8 nm in diameter). The central cavity stores ferric iron in phylogenetically diverse group of organisms, including humans. The central cavity has been used for encapsulation of cargoes such as other metals, contrast agents for imaging, small molecule drugs for therapy, …

Colloidal Semiconductor Quantum Dots: Solution Processing And Heterostructure-Based Optoelectronics, Mathew L. Kelley

Theses and Dissertations

Colloidal semiconductor quantum dots (QDs) are attractive candidates for high-efficiency solar cells and uncooled multiplexed photodetectors due to their favorable characteristics including large absorption cross-sections, size-tunable bandgap energies spanning the ultraviolet (UV) to short wave infrared, and solution processability. These QD-based optoelectronic devices operate on the basis of efficient photogenerated charge migration within QD solids and charge separation and recombination at electrical junctions, underscoring the need for (1) processing strategies that facilitate charge transport and (2) characterization techniques that robustly interrogate charge separation at QD interfaces. Here, my work on the post-synthetic processing and surface modifications of several semiconductor QDs, …

Plasmonic Metallic And Semiconductor Nanomaterials, Mengqi Sun

Theses and Dissertations

The earliest account of localized surface plasmon resonance (LSPR) has to date back to the ancient age of Rome in 400 A.D. The famous glass of Lycurgus cup told the story of unique light-and-matter interaction at the nanoscale that confines the electromagnetic field resonance at its surface and therefore allows LSPR feature to noticeably arise. The conventional metallic LSPR nanomaterials, like Au and Ag nanoparticles attract constant attentions due to their synthetic simplicity, chemical robustness, and visible spectral response. Its ability to generate sensitive dielectric sensing of the surroundings, strong electromagnetic field and active charge carriers upon optical excitation triggered …

Simulation Of Pituitary Organogenesis In Two Dimensions, Chace E. Covington

Theses and Dissertations

The pituitary gland is a vital part of the endocrine system found in all vertebrates and is responsible for the production of hormones that influence many physiological processes in the organism’s body. Although much has been learned of pituitary organogenesis, studying the dynamics of the cells in the developing pituitary gland is difficult. Pituitary organogenesis has been studied through “snapshots” of a developing pituitary gland by removing and viewing the pituitary glands of different specimens. Thus, how the individual cells in the developing pituitary gland behave and interact with one another is not fully understood. To aid in understanding pituitary …

Alkyne Cyclization Involving A Zwitterionic Hexaruthenium Carbido Carbonyl Complex And The Synthesis Of The First-Nitrido Heterometallic Carbonyl Cluster Complexes, Nutan Damodhar Wakdikar

Theses and Dissertations

Chapter 1 introduces two related topics with the primary focus on the background of zwitterions and the conceptual understanding of a metal-complexed zwitterion. It also discusses the potential of a metal-complexed zwitterion for a carbon-carbon bond formation reaction. Synthesis of the metal carbonyl cluster, Ru6(µ6-C)(µ-CO)(CO)16, is also discussed in detail. Then, the background with the importance of heterometallic cluster complexes is discussed with the help of various examples used for catalysis.

The reaction of hexaruthenium carbido carbonyl cluster, Ru6(µ6-C)(µ-CO)(CO)16, with C2H2 and Me3NO yielding first examples of two new zwitterionic complexes, Ru6C(CO)15(μ−η2−C2H2NMe3), 2.2, and Ru6C(CO)14(μ3−η4−C4H4NMe3), 2.3, are presented in Chapter …

Large-NC Constraints For One- And Two-Nucleon Currents In Effective Field Theory, Thomas Richardson

Theses and Dissertations

There is a long-standing goal of understanding nuclear physics in terms of quarks and gluons, the constituent particles of nucleons. However, the underlying theory is strongly coupled at the scales relevant for nuclear physics; therefore, this goal can only be achieved through nonperturbative calculations. Additionally, nuclear targets are employed in a variety of experiments ranging from electroweak processes to Beyond the Standard Model physics. Thus, it is important to have a strong theoretical foundation for nuclear physics in the presence of external fields in order to interpret experimental results. Effective field theory (EFT) for nuclear physics constitutes a systematic and …

Carbon Storage Via Mineral Bonding In Subsoils A Review Of Soil Processes, Kiele Goins

Theses and Dissertations

Soil is an important but often poorly understood portion of the carbon cycle. Soil can store more carbon than twice today’s atmosphere, but the factors that control carbon storage are often unclear. Carbon enters the soil through input of organic matter, erosion, and aerosol deposition and is lost mostly via microbial decomposition. Carbon loss in soil is impacted by the chemical composition of organic compounds, environmental factors, and human activities. Furthermore, as climate changes soil, carbon storage may be vulnerable. Although carbon can be stored throughout soil, carbon storage varies with depth. In topsoil, carbon is stored for short periods …

Two Aspects Of Magnetic Nanoparticle Self-Assembly On Thin-Film Multilayers: Custom Media Properties And Accurate Determination Of Nanoparticle Anisotropy Constant, Sara L. Fitzgerald

Theses and Dissertations

ZFC/FC moment versus temperature measurements are a common technique to determine magnetic properties of nanoparticles. In this work, I varied both applied field strength and nanoparticle concentration to study resulting changes in blocking temperature, T_B, and anisotropy constant, K. T_B and K values were obtained using both existing and new analytic methods. Accurate determination of these parameters helps researchers optimize the use of magnetic nanoparticles for a variety of applications, including magnetic heating, drug delivery, and magnetic field-directed self-assembly. For magnetic self-assembly particularly, not only nanoparticle properties, but also the magnetic properties of the substrate alter …

Characterization Of A High Affinity Glutathione Transporter And Its Impact On Glutathione Depleted Saccharomyces Cerevisiae, Tirthankar Bandyopadhyay

Theses and Dissertations

Thiol-disulfide redox homeostasis is integral for maintaining the redox status of proteins and other thiol-containing molecules within the cell. Among the many antioxidants and detoxifying enzymes and small peptides, glutathione (GSH) has proven to be critical for the preservation of function and structural integrity of the cell due to its functionality in areas like oxidative protein folding, thiol redox control, reactive oxygen species (ROS) and xenobiotics removal as well as iron regulation and Fe-S cluster biogenesis. Therefore, our studies are aimed at elucidating the factors that control GSH trafficking and metabolism in the model eukaryote Saccharomyces cerevisiae (baker’s yeast). Using …

Groundwater Discharge From Passive Continental Margins: Rethinking Marine Chemical Budgets, Andrew William Osborne

Theses and Dissertations

Geothermal convection and sediment compaction drive large-scale flow in continental shelves. We suggest that this flow is an overlooked control on the major ion chemistry of the ocean. Conventional ocean chemical budgets are constructed using river discharge, axial mid-ocean ridge (MOR) convection and CaCO3 production, but these budgets are still poorly quantified. We synthesized data from 17 passive continental margin basins to calculate a range of estimated groundwater and chemical fluxes from continental shelves, considering five major ions (Ca2+, Na+, K+, Mg2+, and Cl-). When extrapolated globally, volumetric groundwater flux estimates were comparable to those for MOR axial circulation, and …

Π+Π- Electroproduction Off Protons In Deuterium: Measurements Of Quasi-Free Cross Sections And Kinematic Probing Of Final State Interactions, Iuliia Skorodumina

Theses and Dissertations

In this study, the process of π⁺π^- electroproduction off protons bound in deuterium nuclei is explored. The exploration is performed through the analysis of experimental data on electron scattering off the deuteron target, collected in Hall B at Jefferson Lab with the CLAS detector. As a main result, the set of integrated and single-differential cross sections of the reaction $\gamma_{v}p(n) \rightarrow p' (n')\pi^{+}\pi^{-}$ is obtained. The cross sections are extracted in the quasi-free regime, which implies that only events not affected by final state interactions are subject to selection. The measurements are performed in the kinematic region …

Groundwater Flow And Transport At The Forest-Marsh Boundary: A Modeling Study, Sophia Chason Sanders

Theses and Dissertations

The forest-marsh boundary, where tidally influenced salt marshes meet a forested upland, is hydrologically complex due to its multiple water inputs. Groundwater flow and salinity transport at this boundary are not well understood. In order to make predictions about salinity at this boundary as it responds to climatic factors, a two-dimensional model was built to simulate groundwater flow and solute transport at a salt marsh on Sapelo Island, Georgia. After calibration based on observed data from wells at the study site, the model can be used to identify patterns in groundwater movement and solute transport that may influence the vegetation …

Regression Methods For Group Testing Data, Michael Stutz

Theses and Dissertations

Group testing is an efficient method of disease screening, whereby individual specimens (e.g., blood, urine, etc.) are pooled together and tested as a whole for the presence of disease. A common goal is to use data arising from these testing protocols to better understand the relationship between disease status and potential risk factors (e.g., age, symptom status, etc.). Numerous statistical methodologies have been developed for this purpose, most of which are built within the framework of a generalized linear model. Recent authors have suggested the inadequacy of such regression methods to capture the true functional relationships when nonlinear effects are …

Comparing Dietary Score Associations With Lipoprotein Particle Subclass Profiles: A Cross-Sectional Analysis Of A Middle-To Older-Aged Population, Seán R. Millar, Pilar Navarro, Janas M. Harrington, Nitin Shivappa Mbbs, Mph, Ph.D., James Hébert Scd, Ivan J. Perry, Catherine M. Phillips

Faculty Publications

Background and objectives: Lipoprotein particle concentrations and size are associated with increased risk for atherosclerosis and premature cardiovascular disease. Studies also suggest that certain dietary behaviours may be cardioprotective. Limited comparative data regarding any dietary score/index-lipoprotein particle subclass associations exist. Thus, our objective was to assess relationships between the Dietary Approaches to Stop Hypertension (DASH), Health Eating Index-2015 (HEI-2015), Mediterranean Diet (MD) and Energy-adjusted Dietary Inflammatory Index (E-DII™) scores and plasma lipids and lipoprotein profiles to test the hypothesis that healthier diet (better quality and more anti-inflammatory) would be associated with a more favourable lipoprotein profile.

Materials and methods: This …

Evaluation Of Circulating Levels Of Interleukin-10 And Interleukin-16 And Dietary Inflammatory Index In Lebanese Knee Osteoarthritis Patients, Zeina El-Ali, Germine El-Kassas, Fouad M. Ziade, Nitin Shivappa Mbbs, Mph, Ph.D., James Hébert Scd, Nisrine Bissar

Faculty Publications

Objectives

To investigate plasma concentrations of Interleukin-16 (IL-16) and Interleukin-10 (IL-10) in Lebanese knee osteoarthritis (KOA) patients and to examine the association between the diet-associated inflammation and increased risk for KOA.

Methods

A total of 208 study participants were assigned to one of the 3 groups: Diagnosed Knee Osteoarthritis group (DKOA) (N = 78); Undiagnosed Knee Osteoarthritis group (UKOA) (N = 60) and controls matched on age, sex and sociodemographic characteristics (N = 70). UKOA represents KOA features before they are altered by therapeutic intervention and lifestyle modifications that follow the diagnosis. Energy-adjusted dietary inflammatory index (E-DII™) scores were calculated …

Free Three-Dimensional Carborane Carbanions, H.D.A. Zzzchathumal Jayaweera, Md. Mamdudur Rahman, Perry J. Pellechia, Mark D. Smith, Dmitry V. Peryshkov

Faculty Publications

Carbon atom functionalization via generation of carbanions is the cornerstone of carborane chemistry. In this work, we report the synthesis and structural characterization of free ortho-carboranyl [C₂B₁₀H₁₁]⁻, a three-dimensional inorganic analog of the elusive phenyl anion that features a “naked” carbanion center. The first example of a stable, discrete C(H)-deprotonated carborane anion was isolated as a completely separated ion pair with a crown ether-encapsulated potassium cation. An analogous approach led to the isolation and structural characterization of a doubly deprotonated 1,1′-bis(o-carborane) anion [C₂B₁₀H₁₀] …

Concentrations, Ratios, And Sinking Fluxes Of Major Bioelements At Ocean Station Papa, Montserrat Roca-Martí

Faculty Publications

Fluxes of major bioelements associated with sinking particles were quantified in late summer 2018 as part of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign near Ocean Station Papa in the subarctic northeast Pacific. The thorium-234 method was used in conjunction with size-fractionated (1–5, 5–51, and >51 μm) concentrations of particulate nitrogen (PN), total particulate phosphorus (TPP), biogenic silica (bSi), and particulate inorganic carbon (PIC) collected using large volume filtration via in situ pumps. We build upon recent work quantifying POC fluxes during EXPORTS. Similar remineralization length scales were observed for both POC and PN across …

Review Of The Analysis Of 234Th In Small Volume (2–4 L) Seawater Samples: Improvements And Recommendations, Samantha J. Clevenger, Claudia Benitez-Nelson, Jessica Drysdale, Steven Pike, Viena Puigcorbé, Ken O. Buesseler

Faculty Publications

Schools may be one important context where adolescents learn and shape the behaviors necessary for promoting global inclusivity in adulthood. Given the importance of bystanders in halting bullying and peer aggression, the focus of this study is on both moral judgments regarding one type of bullying, social exclusion, and factors that are associated with bystander intervention. The study includes 896 adolescents, who were 6th (N = 450, M_age = 11.73), and 9th (N = 446, M_age = 14.82) graders, approximately evenly divided by gender. Participants were primarily European–American (63.3%). Results revealed that girls and participants who …

Biogenic Sinking Particle Fluxes And Sediment Trap Collection Efficiency At Ocean Station Papa, Margaret Estapa, Ken Buesseler, Collen A. Durkin, Melissa Omand, Claudia Benitez-Nelson, Montserrat Rocca-Martí, Elly Breves, R. P. Kelly, Steve Pike

Faculty Publications

Comprehensive field observations characterizing the biological carbon pump (BCP) provide the foundation needed to constrain mechanistic models of downward particulate organic carbon (POC) flux in the ocean. Sediment traps were deployed three times during the EXport Processes in the Ocean from RemoTe Sensing campaign at Ocean Station Papa in August–September 2018. We propose a new method to correct sediment trap sample contamination by zooplankton “swimmers.” We consider the advantages of polyacrylamide gel collectors to constrain swimmer influence and estimate the magnitude of possible trap biases. Measured sediment trap fluxes of thorium-234 are compared to water column measurements to assess trap …

Double Polarisation Observable G For Single Pion Photoproduction From The Proton, N. Zachariou, D. P. Watts, J. Mcandrew, L. Zana, M. Bashkanov, I. I. Strakovsky, R. Workman, A. V. Sarantsev, V. Nikonov, K. P. Adhikari, S. Adhikari, M. J. Amaryan, G. Angelini, W. R. Armstrong, H. Atac, N. A. Baltzell, L. Barion, M. Battaglieri, I. Bedlinskiy, F. Benmokhtar, Steffen Strauch, Et. Al.

Faculty Publications

We report measurements of π⁺ and π⁰ meson photoproduction from longitudinally spin-polarised protons by an energy tagged (0.73-2.3 GeV) and linearly polarised photon beam. A close to complete solid angle coverage for the reaction products was provided by the CEBAF Large Acceptance Spectrometer at Jefferson Laboratory. The double-polarisation observable G is extracted from Maximum Likelihood fits to the data, enabling the first accurate determination for the reaction γ p → π⁺n, while also significantly extending the kinematic coverage for γ p → π⁰ p. This large data set provides an important constraint on the properties …

Measurement Of Branching Fractions And Cp Asymmetries For D + S K+ (Η,Π) And D D + S → Π+(Η,Π) Decays At Belle Decays At Belle, Y. Guan, A.J. Schwartz, K. Kinoshita, I. Adachi, H. Aihara, S. Al Said, D. M. Asner, H. Atmacan, V. Aulchenko, T. Aushev, R. Ayad, V. Babu, P. Behera, J. Bennett, M. Bessner, V. Bhardwaj, B. Bhuyan, T. Bilka, Milind Purohit, Et. Al.

Faculty Publications

We report measurements of the branching fractions and CP asymmetries for D ⁺ _S → K⁺η, D ⁺ _S → K⁺π⁰, and D ⁺ _S → π+η decays, and the branching fraction for D ⁺ _S → π⁺π⁰. Our results are based on a data sample corresponding to an integrated luminosity of 921 fb⁻¹ collected by the Belle detector at the KEKB e⁺e⁻ asymmetric-energy collider. Our measurements of CP asymmetries in these decays are the most precise to date; no evidence for CP …

Measurement Of Branching Fractions And Cp Asymmetries For D+S → D + S → K+ (Η,Π;0) And D + S →Π + (Η;Π0) Decays At Belle, Y. Guan, A.J. Schwartz, K. Kinoshita, I. Adachi, H. Aihara, S. Al Said, D. M. Asner, H. Atmacan, V. Aulchenko, T. Aushev, R. Ayad, V. Babu, P. Behera, J. Bennett, M. Bessner, V. Bhardwaj, B. Bhuyan, T. Bilka, J. Biswal, Milind Purohit, Et. Al.

Faculty Publications

We report measurements of the branching fractions and CP asymmetries for D⁺ _s → Kþη, Dþ s → K⁺π⁰, and D⁺ _s → πþη decays, and the branching fraction for Dþ s → π⁺π⁰. Our results are based on a data sample corresponding to an integrated luminosity of 921 fb⁻¹ collected by the Belle detector at the KEKB e⁺e⁻ asymmetric-energy collider. Our measurements of CP asymmetries in these decays are the most precise to date; no evidence for CP violation is found.

Tailored Porous Carbons Enabled By Persistent Micelles With Glassy Cores, Eric R. Williams, Paige L. Mcmahon, Joseph E. Reynolds Iii, Jonathan L. Snider, Vitalie Stavila, Mark Allendorf, Morgan Stefik

Faculty Publications

Porous nanoscale carbonaceous materials are widely employed for catalysis, separations, and electrochemical devices where device performance often relies upon specific and well-defined regular feature sizes. The use of block polymers as templates has enabled affordable and scalable production of diverse porous carbons. However, popular carbon preparations use equilibrating micelles which can change dimensions in response to the processing environment. Thus, polymer methods have not yet demonstrated carbon nanomaterials with constant average template diameter and tailored wall thickness. In contrast, persistent micelle templates (PMTs) use kinetic control to preserve constant micelle template diameters, and thus PMT has enabled constant pore diameter …

Host–Guest Interactions In A Metal–Organic Framework Isoreticular Series For Molecular Photocatalytic Co2 Reduction, Philip M. Stanley, Johanna Haimerl, Christopher Thomas, Alexander Urstoeger, Michael Schuster Prof. Dr., Natalia B. Shustova Prof. Dr., Angela Casini Prof. Dr., Bernhard Rieger Prof. Dr., Julien Warnan Dr., Roland A. Fischer Prof. Dr.

Faculty Publications

A strategy to improve homogeneous molecular catalyst stability, efficiency, and selectivity is the immobilization on supporting surfaces or within host matrices. Herein, we examine the co-immobilization of a CO2 reduction catalyst [ReBr(CO)3(4,4′-dcbpy)] and a photosensitizer [Ru(bpy)2(5,5′-dcbpy)]Cl2 using the isoreticular series of metal–organic frameworks (MOFs) UiO-66, -67, and -68. Specific host pore size choice enables distinct catalyst and photosensitizer spatial location—either at the outer MOF particle surface or inside the MOF cavities—affecting catalyst stability, electronic communication between reaction center and photosensitizer, and consequently the apparent catalytic rates. These results allow for a rational understanding of an optimized supramolecular layout of catalyst, …

Supernova Neutrino Burst Detection With The Deep Underground Neutrino Experiment, B. Abi, R. Acciarri, M. A. Acero, G. Adamov, D. Adams, M. Adinolfi, Z. Ahmad, J. Ahmed, T. Alion, S. Alonso Monslave, C. Alt, J. Anderson, C. Andreopoulos, M. P. Andrews, F. Andrianala, S. Andringa, A. Ankowski, M. Antonova, S. Antusch, A. Aranda-Fernadez, Roberto Petti

Faculty Publications

The Deep Underground Neutrino Experiment (DUNE), a 40-kton underground liquid argon time projection chamber experiment, will be sensitive to the electronneutrino flavor component of the burst of neutrinos expected from the next Galactic core-collapse supernova. Such an observation will bring unique insight into the astrophysics of core collapse as well as into the properties of neutrinos. The general capabilities of DUNE for neutrino detection in the relevant few- to few-tens-of-MeV neutrino energy range will be described. As an example, DUNE’s ability to constrain the ν_e spectral parameters of the neutrino burst will be considered.

Differences In ​The Proportion Of Children Meeting Behavior Guidelines ​Between Summer ​And School By Socioeconomic Status And Race, Ethan T. Hunt, Lauren Von Klinggraeff, Alexis Jones, Sarah Burkart, Roddrick Dugger, Bridget Armstrong Ph.D., Michael Beets Ph.D., Gabrielle Turner-Mcgrievy Ph.D., Rd, Marco Geraci, Robert Glenn Weaver Med, Phd

Faculty Publications

Objective

Children who fail to meet activity, sleep, and screen-time guidelines are at increased risk for obesity. Further, children who are Black are more likely to have obesity when compared to children who are White, and children from low-income households are at increased risk for obesity when compared to children from higher-income households. The objective of this study was to evaluate the proportion of days meeting obesogenic behavior guidelines during the school year compared to summer vacation by race and free/reduced priced lunch (FRPL) eligibility.

Methods

Mixed-effects linear and logistic regressions estimated the proportion of days participants met activity, sleep, …

Ocean-Atmosphere Interactions During Hurricanes Marco And Laura (2020), Emily N. Eley, Bulusu Subrahmanyam, Corinne B. Trott

Faculty Publications

During August of the 2020 Atlantic Hurricane Season, the Gulf of Mexico (GoM) was affected by two subsequent storms, Hurricanes Marco and Laura. Hurricane Marco entered the GoM first (22 August) and was briefly promoted to a Category 1 storm. Hurricane Laura followed Marco closely (25 August) and attained Category 4 status after a period of rapid intensification. Typically, hurricanes do not form this close together; this study aims to explain the existence of both hurricanes through the analysis of air-sea fluxes, local thermodynamics, and upper-level circulation. The GoM and its quality of warm, high ocean heat content waters proved …