Physical Sciences and Mathematics Commons^™

Positron Emission Tomography In Oncology And Environmental Science, Samantha Delaney

Dissertations, Theses, and Capstone Projects

The last half century has played witness to the onset of molecular imaging for the clinical assessment of physiological targets. While several medical imaging modalities allow for the visualization of the functional and anatomical properties of humans and living systems, few offer accurate quantitation and the ability to detect biochemical processes with low-administered drug mass doses. This limits how physicians and scientists may diagnose and treat medical issues, such as cancer, disease, and foreign agents.

A promising alternative to extant invasive procedures and suboptimal imaging modalities to assess the nature of a biological environment is the use of positron emission …

Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave

Dissertations, Theses, and Capstone Projects

The challenge of establishing a sustainable and circular economy for materials in medicine and technology necessitates bioinspired design. Nature's intricate machinery, forged through evolution, relies on a finite set of biomolecular building blocks with through-bond and through-space interactions. Repurposing these molecular building blocks requires a seamless integration of computational modeling, design, and experimental validation. The tools and concepts developed in this thesis pioneer new directions in peptide-materials design, grounded in fundamental principles of physical chemistry. We present a synergistic approach that integrates experimental designs and computational methods, specifically molecular dynamics simulations, to gain in-depth molecular insights crucial for advancing the …

Towards Sociobiogeochemistry: Critical Perspectives On Anthropogenic Alterations To Soil Nitrogen Chemistry Via U.S. Urban And Suburban Development, Christopher D. Ryan

Dissertations, Theses, and Capstone Projects

The ecological impacts of changes to land use are relevant to concerns about climate change, eutrophication of waterbodies, and reductions in biodiversity. As a foundational component of ecosystem functioning, changes to soil biogeochemistry have significant effects on overall ecosystem health. With cities continuing to grow and develop in extent, the impacts of urbanization and suburbanization on soils are of particular concern. Despite a wide range of natural climatic and geologic conditions, several factors have driven similar patterns of land transformation and management across the United States. In particular, federal initiatives including the Home Owners Loan Corporation, the Federal Housing Administration, …

A Causal Inference Approach For Spike Train Interactions, Zach Saccomano

Dissertations, Theses, and Capstone Projects

Since the 1960s, neuroscientists have worked on the problem of estimating synaptic properties, such as connectivity and strength, from simultaneously recorded spike trains. Recent years have seen renewed interest in the problem coinciding with rapid advances in experimental technologies, including an approximate exponential increase in the number of neurons that can be recorded in parallel and perturbation techniques such as optogenetics that can be used to calibrate and validate causal hypotheses about functional connectivity. This thesis presents a mathematical examination of synaptic inference from two perspectives: (1) using in vivo data and biophysical models, we ask in what cases the …

Optimization And Application Of Graph Neural Networks, Shuo Zhang

Dissertations, Theses, and Capstone Projects

Graph Neural Networks (GNNs) are widely recognized for their potential in learning from graph-structured data and solving complex problems. However, optimal performance and applicability of GNNs have been an open-ended challenge. This dissertation presents a series of substantial advances addressing this problem. First, we investigate attention-based GNNs, revealing a critical shortcoming: their ignorance of cardinality information that impacts their discriminative power. To rectify this, we propose Cardinality Preserved Attention (CPA) models that can be applied to any attention-based GNNs, which exhibit a marked improvement in performance. Next, we introduce the Directional Node Pair (DNP) descriptor and the Robust Molecular Graph …

Out-Of-Distribution Generalization Of Deep Learning To Illuminate Dark Protein Functional Space, Tian Cai

Dissertations, Theses, and Capstone Projects

Dark protein illumination is a fundamental challenge in drug discovery where majority human proteins are understudied, i.e. with only known protein sequence but no known small molecule binder. It's a major road block to enable drug discovery paradigm shift from single-targeted which looks to identify a single target and design drug to regulate the single target to multi-targeted in a Systems Pharmacology perspective. Diseases such as Alzheimer's and Opioid-Use-Disorder plaguing millions of patients call for effective multi-targeted approach involving dark proteins. Using limited protein data to predict dark protein property requires deep learning systems with OOD generalization capacity. Out-of-Distribution (OOD) …

Construction And Performance Optimization Of Bioconjugated Nanosensors For Early Detection Of Breast Cancer And Pro-Inflammatory Diseases, Pooja Gaikwad

Dissertations, Theses, and Capstone Projects

In recent years, nanosensors have emerged as a tool with strong potential in medical diagnostics. Single-walled carbon nanotube (SWCNT) based optical nanosensors have notably garnered interest due to the unique characteristics of their near-infrared fluorescence emission, including tissue transparency, photostability, and various chiralities with discrete absorption and fluorescence emission bands. Additionally, the optoelectronic properties of SWCNT are sensitive to the surrounding environment, which makes them suitable for in vitro and in vivo biosensing. Single-stranded (ss) DNA-wrapped SWCNTs have been reported as optical nanosensors for cancers and metabolic diseases. Breast cancer and cardiovascular diseases are the most common causes of death …

Characterization Of Boreal-Arctic Vegetation Growth Phases And Active Soil Layer Dynamics In The High-Latitudes Of North America: A Study Combining Multi-Year In Situ And Satellite-Based Observations, Michael G. Brown

Dissertations, Theses, and Capstone Projects

This dissertation examined the seasonal freeze/thaw activity in boreal-Arctic soils and vegetation physiology in Alaska, USA and Alberta, Canada, using in situ environmental measurements and passive microwave satellite observations. The boreal-Arctic high-latitudes have been experiencing ecosystem changes more rapidly in comparison to the rest of Earth due to the presently warming climatic conditions having a magnified effect over Polar Regions. Currently, the boreal-Arctic is a carbon sink; however, recent studies indicate a shift over the next century to become a carbon source. High-latitude vegetation and cold soil dynamics are influenced by climatic shifts and are largely responsible for the regions …

Statistical And Biological Analyses Of Acoustic Signals In Estrildid Finches, Moises Rivera

Dissertations, Theses, and Capstone Projects

Acoustic communication is a process that involves auditory perception and signal processing. Discrimination and recognition further require cognitive processes and supporting mechanisms in order to successfully identify and appropriately respond to signal senders. Although acoustic communication is common across birds, classical research has largely disregarded the perceptual abilities of perinatal altricial taxa. Chapter 1 reviews the literature of perinatal acoustic stimulation in birds, highlighting the disproportionate focus on precocial birds (e.g., chickens, ducks, quails). The long-held belief that altricial birds were incapable of acoustic perception in ovo was only recently overturned, as researchers began to find behavioral and physiological evidence …

The Development Of Novel Radioimmunoconjugates For The Pet Imaging And Radioimmunotherapy Of Cancer, Samantha M. Sarrett

Dissertations, Theses, and Capstone Projects

Antibodies have long played a vital role in nuclear medicine for both the diagnosis and therapy of various malignancies. The role and development of antibodies in nuclear medicine can be broadly separated into three different categories: 1) bioconjugation strategies, 2) immunoPET imaging, and 3) radioimmunotherapy. This dissertation will attempt to comprehensively cover each of these categories through a series of studies, protocols, and reviews. For the bioconjugation strategies, we will describe the development of a novel site-selective bioconjugation strategy using an innovative lysine-targeting reagent, PFP-bisN₃, to prepare [⁸⁹Zr]Zr-^SSKDFO-pertuzumab for visualizing HER2+ breast cancer. Further, …

Fine Characterization Of Leafing Phenology In The Brazilian Atlantic Forest By Optical And Microwave Remote Sensing, James B. Bell

Dissertations and Theses

Tropical forests provide important ecosystem functions in the global biosphere, but they remain among the most poorly understood elements of land surface models, especially with regard to their seasonal dynamics. For instance, in seasonally dry forests, the pattern of the annual green-up in their canopies closely follows annual patterns of rainfall. The same, however, does not occur in wet forest canopies which are dominated by evergreen trees. In the latter, water is not scarce enough to limit leaf photosynthetic function. Canopy leafing phenology in these forests is therefore poorly characterized by optical remote sensing methods which are not sensitive to …

Methods For Drone Trajectory Analysis Of Bottlenose Dolphins (Tursiops Truncatus), Jillian D. Bliss

Theses and Dissertations

With the increase in the use of UAS (Unmanned Aerial Systems) for marine mammal research, there is a need for the development of methods of analysis to transform UAS high resolution video into quantitative data. This study sought to develop a preliminary method of analysis that would quantify and present a way to visualize the dynamics and relative spatial distribution and changes in distribution of bottlenose dolphins (Tursiops truncatus) in the waters of Turneffe Atoll, Belize. This approach employs a previously developed video tracking program ‘Keypoint Tracking’ that enables manual tracking of individual dolphins and the creation of …

Nutrient Dynamics And Ecosystem Development Of Urban Forests, Gisselle A. Mejía

Dissertations, Theses, and Capstone Projects

Urban growth and expansion are a major component of global environmental change, with impacts on climate, air and water quality, biodiversity, and human well-being. Forests embedded in urban landscapes are critical in mitigating these impacts at local, regional, and continental scales. However, assessing urban forests is difficult because cities are heterogenous in physical, chemical, biological, and social dimensions. This heterogeneity has constrained how urban forests are defined, and therefore, how they are studied. The objective of this dissertation is to determine how these biophysical and social factors drive ecological processes in urban forests and will address three outstanding challenges in …

Conformation Of The U12-U6atac Snrna Complex Of The Minor Spliceosome And Binding By Ntc-Related Protein Rbm22, Joanna Ciavarella

Dissertations, Theses, and Capstone Projects

Splicing of precursor messenger (pre-m)RNA is a critical process in eukaryotes in which the non-coding regions, called introns, are removed and coding regions, or exons, are ligated to form a mature mRNA. This process is catalyzed by the spliceosome, a multi-mega Dalton ribonucleoprotein complex assembled from five small nuclear ribonucleoproteins (snRNP) in the form of small nuclear (sn)RNA-protein complexes (U1, U2, U4, U5 and U6) and >100 proteins. snRNA components catalyze the two transesterification reactions while proteins perform critical roles in assembly and rearrangement. U2 and U6 snRNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA. …

The Microscopical Evidence Traces Analysis Of Household Dust And Its Statistical Significance As A Definitive Identification Technique, Stephanie Polifroni

Dissertations, Theses, and Capstone Projects

Evidence found at crime scenes is used to assist in creating a link the suspect, the victim, and the scene. As stated by the Locard’s Principle, every contact leaves a trace, that evidence can be used to link together an investigation. Traces are collected in hopes that they can be identified and associated to an individual or individuals to help solve that particular crime. However, the strongest conclusion for evidence traces is an association to a source, and unless a physical match of some kind is found, an individualization cannot be established even when known sample is available. However, having …

Quantifying Aboveground Biomass In A Tropical Forest Using A Lidar Waveform Weighted Allometric Model, Alejandro Rojas

Theses and Dissertations

Our knowledge of the distribution and amount of terrestrial above ground biomass (AGB) has increased using lidar technology. Recent advancements in satellite lidar has enabled global mapping of forest biomass and structure. However, there are large biases in satellite lidar estimates which impacts our understanding of carbon dynamics, particularly in tropical forests.

Ni-Meister et al. (2022) developed a lidar full waveform weighted height-based allometric model which produced very good results in temperate deciduous/conifer forest in the continental US. The purpose of this study was to evaluate this biomass model in an African tropical forest using the Land Vegetation and Ice …

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

The Significance Of Sonic Branding To Strategically Stimulate Consumer Behavior: Content Analysis Of Four Interviews From Jeanna Isham’S “Sound In Marketing” Podcast, Ina Beilina

Student Theses and Dissertations

Purpose:
Sonic branding is not just about composing jingles like McDonald’s “I’m Lovin’ It.” Sonic branding is an industry that strategically designs a cohesive auditory component of a brand’s corporate identity. This paper examines the psychological impact of music and sound on consumer behavior reviewing studies from the past 40 years and investigates the significance of stimulating auditory perception by infusing sound in consumer experience in the modern 2020s.

Design/methodology/approach:
Qualitative content analysis of audio media was used to test two hypotheses. Four archival oral interview recordings from Jeanna Isham’s podcast “Sound in Marketing” featuring the sonic branding experts …

Water-Based Lead Generation, Brian Olson

Dissertations, Theses, and Capstone Projects

Water-based Lead Generation. The opioid epidemic and the SARS-CoV-2 pandemic are current serious challenges whose devastating effects could be assuaged through the development of new drugs. Opioids that are functional painkillers, that are less likely to cause overdose, and small molecule drugs that could inhibit the life cycle of SARS-CoV-2 would be useful. The work herein investigated the use of water molecules for lead generation in drug development against opioid receptors and SARS-CoV-2 viral proteins. In opioid receptor binding sites, purported bridging waters were obtained from crystal waters or from molecular dynamics simulations, as Hydration Site Analysis was used to …

Don't Sell Them Short, There's More To Bacterial Natural Products Than Antibiotics, Alison Clare Domzalski

Dissertations, Theses, and Capstone Projects

Recent genomic studies of microbiomes have revealed an overwhelming number of biosynthetic genes of unknown function. Most of these “cryptic” biosynthetic genes are not expressed in laboratory monocultures of individual microbes. Thus, there remains tremendous untapped potential for natural products discovery. Here we employ mixed microbial culture (MMC) as a simple yet powerful approach to awaken cryptic biosynthetic gene clusters. Our preliminary studies demonstrated that arrays of metabolites could be induced in MMCs upon environmental cues, such as surface adhesion. Using this system, we have screened, identified, and isolated bioactive bacterial metabolites, which were characterized structurally and biologically. Of the …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Connecting Communities To Coastal Resilience: Enhancing Sustainability Through Public Participation In Salt Marsh Management And Restoration In Suffolk County, Ny, Jennifer L. Mcgivern

Dissertations, Theses, and Capstone Projects

Coastal resiliency is becoming significantly more critical to the livelihood of coastal communities as the frequency and intensity of storm events increases and is exacerbated by rising sea levels due to climate change. In October 2012 Superstorm Sandy impacted the New York-New Jersey area costing over $70 billion in storm damages and 147 lives lost, as storm surges surpassed record highs for the region. Protruding more than 100 miles into the Atlantic Ocean with over 1,000 miles of shoreline, Long Island is particularly vulnerable to the increasingly ferocious and numerous storms as well as the rising sea levels that climate …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Design, Synthesis And Evaluation Of Molecules With Selective And Poly-Pharmacological Actions At D1r, D3r And Sigma Receptors, Pierpaolo Cordone

Dissertations, Theses, and Capstone Projects

The dopamine D3 receptor (D3R) is one of the most studied receptors involved in drug addiction. One of the most common strategies to treat substance use disorders is via D3R antagonism. The majority of the D3R antagonists synthesized so far have poor pharmacokinetic properties and/or lack selectivity toward D3R. In this thesis, the design, synthesis and biological evaluation of novel molecules that target the dopamine D1 receptor (D1R), D3R and the serendipitous discovery of molecules that target s receptors will be described.

Chapter 1 presents a survey of the fundamental pharmacology of D1R, D3R and s receptors and the therapeutic …

Computational Modeling Of Water And Proteins In Drug Discovery, Anthony Cruz Balberdy

Dissertations, Theses, and Capstone Projects

This thesis aims to improve how structural and thermodynamic properties of water on protein surfaces can be exploited to aid early stage drug discovery and lead optimization. We first discuss our development of SSTMap, a public domain software suite that maps out the properties of water on biomolecular surfaces. We then show the utility of these maps in describing differences in binding affinities between congeneric pairs of ligands. We then discuss our use of solvation maps in the prospective discovery of novel binders to cytochrome C peroxidase. Finally, we present our creation and validation of a homology model of Interleukin-24 …

Third Harmonic Generation: A Method For Visualizing Myelin In The Murine Cerebral Cortex, Michael Redlich

Dissertations, Theses, and Capstone Projects

Here we present the use of Third Harmonic Generation (THG) for the label-free imaging of myelinated axons in the murine cerebral cortex. Myelin plays an important role in the processes of learning and disease. However, much of the myelin biology research thus far has focused on white matter tracts where myelin is more visible. Much is still unknown, particularly with regard to myelin in gray matter. First, we engage in THG microscopy using an optical parametric oscillator pumped by a titanium-sapphire laser to demonstrate the utility of the technique for imaging myelin in vivo. Second, we investigate the use of …

The C. Neoformans Cell Wall: A Scaffold For Virulence, Christine Chrissian

Dissertations, Theses, and Capstone Projects

Cryptococcus neoformans is a globally distributed opportunistic fungal pathogen and the causative agent of life threatening cryptococcal meningoencephalitis in immunocompromised individuals, resulting in ~180,000 deaths each year worldwide. A primary virulence-associated trait of this organism is the production of melanin. Melanins are a class of diverse pigments produced via the oxidation and polymerization of aromatic ring compounds that have a characteristically complex, heterogenous, and amorphous structure. They are synthesized by representatives of all biological kingdoms and share a multitude of remarkable properties such as the ability to absorb ultraviolet (UV) light and protect against ionizing radiation. Melanin production in fungi …

Using The Marcus Inverted Region And Artificial Cofactors To Create A Charge Separated State In De Novo Designed Proteins, Eskil Me Andersen

Dissertations, Theses, and Capstone Projects

To create an efficient de novo photosynthetic protein it is important to create long lived charge separated states. Achieving stable charge separation leads to an increase in the efficiency of the photosynthetic reaction which in turn leads to higher yields of end products, such as biofuels, electrical charge, or synthetic chemicals. In an attempt to create charge separated states in de novo proteins we hypothesized that we could engineer the free energy gaps in the proteins from excited primary donor (PD) to acceptor (A), and A back to ground state PD such that the forward electron transfer (ET) would be …

A New Mathematical Theory For The Dynamics Of Large Tumor Populations, A Potential Mechanism For Cancer Dormancy & Recurrence And Experimental Observation Of Melanoma Progression In Zebrafish, Adeyinka A. Lesi

Dissertations and Theses

Cancer, a family of over a hundred disease varieties, results in 600,000 deaths in the U.S. alone. Yet, improvements in imaging technology to detect disease earlier, pharmaceutical developments to shrink or eliminate tumors, and modeling of biological interactions to guide treatment have prevented millions of deaths. Cancer patients with initially similar disease can experience vastly different outcomes, including sustained recovery, refractory disease or, remarkably, recurrence years after apparently successful treatment. The current understanding of such recurrences is that they depend on the random occurrence of critical mutations. Clearly, these biological changes appear to be sufficient for recurrence, but are they …

Long Term Nutrient And Chlorophyll A Dynamics Across Long Island Sound And Impacts On Dissolved Oxygen Conditions Within The Western Sound (1991-2019), Sherry Perreira

Dissertations and Theses

Nitrogen overload, eutrophication, and hypoxia have been challenging and persistent water quality problems in Long Island Sound (LIS) over the past decades with major impacts on commercial industries, ecology, and recreational activities in the region. Recognizing these problems, the EPA enforced three phases of the Clean Water Act (CWA) to reduce nitrogen loads in an effort to improve this important estuary. This study examines how nitrogen (NH₃, NO_x & TDN), chlorophyll a (CHLA), and dissolved oxygen (DO) concentrations changed in LIS over the past 30 years, in response to water quality regulations as well as changes in …