Digital Commons Network^™

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 …

The Role Of Glutamate In The Medial Prefrontal Cortex In The Acquistion And Expression Of Conditioned Approach, Rudolf Nisanov

Dissertations, Theses, and Capstone Projects

A series of experiments were conducted to assess the role of glutamatergic stimulation in the dorsal and ventral regions of the medial prefrontal cortex (mPFC) in both the acquisition and expression of reward-related learning using a Pavlovian conditioning paradigm, the conditioned-approach paradigm. Rats with surgically implanted cannulas were exposed to Pavlovian conditioning sessions that occurred on three alternative days (acquisition) or seven consecutive days (expression). These 60-min conditioning sessions consisted of 30 pairings of light (CS) and food pellets (US) presented under a random time schedule. After a two-day break, rats underwent a session with no CS or US and …

Studying Lake Surface Temperature Variabilities At Regional And Global Scales Using Remote Sensing And In-Situ Observations, Abdou Rachid Bah

Dissertations, Theses, and Capstone Projects

Surface temperature changes can be effectively monitored by employing remote sensing thermal infrared (TIR) data, offering advantages such as improved spatial and temporal coverage. Notably, this approach enables observation without disturbing the studied object and overcomes accessibility challenges in the study regions. The study utilizes remotely sensed data from Landsat 8, Geostationary Operational Environmental Satellites-R series (GOES-R), and the Moderate Resolution Imaging Spectroradiometer (MODIS) thermal infrared bands. These satellite TIR data are instrumental in model development and understanding patterns and processes in environmental systems. In my dissertation, I employed remote sensing tools, specifically Landsat 8, GOES-R, and MODIS Aqua temperature …

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 …

Protein-Protein Interactions In Cell Cycle Proteins: An In Silico Investigation Of Two Important Players, Andriele Eichner

Dissertations, Theses, and Capstone Projects

The examination of the cell cycle carries significant implications for the biology, health, and overall existence of all living things. These implications span from the development and growth of these organisms to the aging process and cancer, as well as the potential of stem cell therapies to repair diseases and injuries. Numerous proteins of the cell cycle are essential for cellular division and proliferation and are widely conserved over the course of evolution. In this work, we aimed to investigate the molecular processes of protein-protein interactions in cell cycle proteins, centering on two key players: Cdc6 in budding yeast and …

The Effect Of Alpha Binaural Beats On Virtual Reality Experiences, Andronikki C. Gerohristodoulos

Dissertations, Theses, and Capstone Projects

Visually induced motion sickness (VIMS), a subset of motion sickness, has been a long-term obstacle preventing comfortable experiences in virtual reality (VR). There is a growing body of research showing that binaural beats (BBs) have been effective to influence aspects of cognition. The goal of this experiment was to investigate the possible effects of attending to BBs and any changes to the severity of VIMS symptoms following immersion in a virtual reality environment (VRE). To validate our hypothesis a repeated-measures, between-subjects experiment was designed (n=16) and an alpha (10Hz) frequency BB and a control audio were created. Participants were split …

Stereospecific Cross-Coupling Reactions Of Enantioenriched Secondary Alkyltricyclohexyltin Nucleophiles, Meruyert Binayeva

Dissertations, Theses, and Capstone Projects

Transition metal-catalyzed cross-coupling reactions have evolved into a remarkable instrument for the formation of new bonds, and have significantly impacted how we approach to access complex organic molecules. Palladium is currently one of the most popular elements for catalytic applications due to its ability to facilitate powerful carbon-carbon and carbon-heteroatom couplings. Traditional Pd-catalyzed cross-coupling reactions have primarily concentrated on C(sp2)-C(sp2) cross-couplings, yielding planar products. Considering the use of C(sp3) nucleophiles would offer a viable control of the three dimensional arrangement in molecules. Herein, the first chapter details the history and development of Pd-catalyzed Stille cross-coupling reactions. The use of configurationally …

Targeting Strategies To Optimize The Therapeutic Potential Of Gold Compounds Against Her2-Positive Breast Cancers, Afruja Ahad

Dissertations, Theses, and Capstone Projects

The overexpression of HER2 accounts for 20-30% of breast cancer tumors and not only serves as a marker for poor predictive clinical outcomes but also as a target for treatment. Antibody-drug conjugates (ADCs) combine the selectivity of monoclonal antibodies (mAbs) with the efficacy of chemotherapeutic drugs to provide targeted treatment without toxicity to normal tissue. Most of the ADCs currently in the clinic for cancer chemotherapy are based on complex organic molecules. In contrast, the conjugation of metallodrugs to mAbs has been overlooked when there is enormous potential in this area with the resurgence of metal-based drugs as prospective cancer …

Methamphetamine-Induced Dna Double-Stranded Breaks: The Impact Of The Dopamine Transporter And Insights Into The Mechanisms Of Dna Damage In Mouse Neuro 2a Cells, Lizette Couto

Dissertations, Theses, and Capstone Projects

Methamphetamine (METH) abuse remains a global health concern, with emerging evidence highlighting its genotoxic potential. In the central nervous system METH enters dopaminergic cells primarily through the dopamine transporter (DAT), which controls the dynamics of dopamine (DA) neurotransmission by driving the reuptake of extracellular DA into the presynaptic neuronal cell. Additional effects of METH on the storage of DA in synaptic vesicles lead to the dysregulated cytosolic accumulation of DA. Previous studies have shown that after METH disrupts intracellular vesicular stores of DA, the excess DA in the cytosol is rapidly oxidized. This generates an abundance of reactive oxygen species …

Effects Of Transcranial Direct Current Stimulation On Metamemory Vary By Task Difficulty, Tiffanie T. Li

Dissertations, Theses, and Capstone Projects

Metamemory is broadly defined as the awareness of one’s memory and consists, in part, of a process referred to as monitoring, where one is assessing the contents of their memory. Feeling of knowing (FOK) is one metamemory monitoring judgment where one rates how strongly they believe they will remember a currently unrecalled item. Prior work has shown that HighDefinition Transcranial Direct Current Stimulation (HD-tDCS) over the dorsal lateral prefrontal cortex (DLPFC) led to greater metamemory accuracy and that HD-tDCS over the anterior temporal lobe (ATL) led to better recall for medium difficulty questions. Other work has also shown that effects …

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, …

The Divided Self: Internal Conflict In Literature, Philosophy, Psychology, And Neuroscience, Yulia Greyman

Dissertations, Theses, and Capstone Projects

This thematic project examines the notion of self-division, particularly in terms of the conflict between cognition and metacognition, across the fields of philosophy, psychology, and, most recently, the cognitive and neurosciences. The project offers a historic overview of models of self-division, as well as analyses of the various problems presented in theoretical models to date. This work explores how self-division has been depicted in the literary works of Edgar Allan Poe, Don DeLillo, and Mary Shelley. It examines the ways in which artistic renderings alternately assimilate, resist, and/or critique dominant philosophical, psychological, and scientific discourses about the self and its …

Comparative Animal Mucomics, Antonio R. Cerullo

Dissertations, Theses, and Capstone Projects

Mucus is one of Nature’s most abundant and versatile biomaterials. These secretions are present in all animals, from the lowly garden snail to the great blue whale, and fulfill a multitude of functions, acting as antimicrobial barriers, moisturizers, adhesive glues, surface lubricants, and mineralizing agents. Despite their importance, very little is known about mucus compositions or properties. The largest challenge precluding the greater understanding of mucus function is its complexity; a single mucus contains complex mixtures of proteins, glycans, and ions that all have important roles in function. Therefore, understanding mucus function necessitates analysis that compares different mucus from one …

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 …

Neurochemical Signaling Of Reward-Based Learning In Ventral Tegmental Area Dopamine Neurons, Kyla F. Wholley

Dissertations, Theses, and Capstone Projects

Ventral tegmental area (VTA) dopamine neurons signal and participate in reward-related learning. Specifically, dopamine is postulated to encode reward-related environmental stimuli to compute reward prediction errors (RPEs). It is through the computation and maintenance of RPEs that learning occurs. However, little is known about the neural mechanisms that underlie how dopamine neurons compute RPEs and facilitate reward-related learning. The present study utilized fiber photometry in conjunction with a Pavlovian reward-based task to identify how GABA inputs to VTA dopamine neurons contribute to the computation of RPEs and reward-based behavior. Activity of GABA inputs to VTA dopamine neurons increased for reward-predicting …

Automatic Analysis Of The Frequency, Vigor, And Complexity Of Spontaneous Locomotion Bouts Of Mice With Loss And Gain Of Function Of The G Protein-Coupled Receptor Smoothened In Cholinergic Neurons, Aleksandra Feshchenko

Dissertations, Theses, and Capstone Projects

Locomotion, a fundamental behavior, is classically assessed using simple metrics of velocity and total distance moved in an open field. This behavior however offers rich data about the organization and breadth of actions an animal can take while only facing limitations due to the bio-mechanical constraints of the organism. Importantly, these actions are not biased towards a particular task-solution space imposed by many behavioral paradigms. Here, to analyze motor complexity in freely ambulating mice, we developed a method for the automatic and unbiased identification of locomotor bouts which we call Bout Finder (BF). This analysis utilizes Open Feld data to …

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 …

Electrophysiological Signatures Of Stress Adaptability In The Bnst-Vta Pathway, Yuka Miura

Dissertations, Theses, and Capstone Projects

Chronic stress has detrimental effects on psychological and physiological health. Incapability to adapt to chronic stress can lead to depression, anxiety disorders, and addiction. The brain regions critical for reward processing share diverse physiological and molecular changes linked to depressive-like behaviors as a result of chronic stress. Cumulative evidence shows that counteraction or prevention of these alterations in neurons, occasionally in a projection-specific manner, can enhance stress adaptation or resilience.

Chronic stress induces various changes in the brain, including in the bed nucleus of the stria terminalis (BNST) and the ventral tegmental area (VTA). The neural projections from the BNST …

Characterization Of Pathological Tau Mutants, Charles J. Mcdonald

Dissertations, Theses, and Capstone Projects

Tau is a protein expressed exclusively in glia and neurons in the central nervous system and implicated in several neurogenerative diseases called “tauopathies”. Among all the tauopathies, one third is characterized by the presence of genetic mutations leading to the synthesis of tau proteins with single amino acid substitutions at specific locations and affecting protein function. While most of the initial studies have emphasize the functional role of tau as modulator of the axonal cytoskeleton, it has recently been well accepted that tau is also an intrinsically disordered protein that tends to form membraneless organelles called coacervates, due to a …

Examining Metacognitive Access To Low-Level Ensemble Representations, Vladimir Mudragel

Dissertations, Theses, and Capstone Projects

Ensemble perception is a process that allows our sensory systems to rapidly extract summary information about the stimuli in the environment. For example, we are able to get a sense of the average number of items in a group of similar items (Burr & Ross, 2008; Halberda, Sires, & Feigenson, 2006) or the average size of a group of similar shapes of different sizes (Ariely, 2001). It is theorized that the qualitative result of ensemble perception is that it provides a gist impression of the current environment, which then enables attentional processes in the brain to determine which parts of …

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) …

Brainwaves, Memory, And Reward, Rebecca Mccune

Dissertations, Theses, and Capstone Projects

The development of effective educational curricula for enhancing learning involves the crucial consideration of effort and rewards. In the realm of education, teachers commonly employ rewards as motivational tools. Traditionally, these rewards are given to students as a recognition of their successful performance. However, a thought-provoking idea emerges: What if we were to extend rewards to students not solely based on accurate answers, but also on the effort they invest, even in cases where their actual response might be incorrect? Our study explores the potential impact of this approach on the way information is absorbed and subsequently retained, specifically focusing …

You Hurt My Feelings: Autonomic And Behavioral Responses To Social Exclusion And The Moderating Effect Of Psychopathic Traits, Liat Kofler

Dissertations, Theses, and Capstone Projects

Humans have a fundamental need to form and maintain social connections, and thus experiencing social exclusion is extremely distressing as it threatens this basic human need. Individuals who are socially excluded often respond aggressively, not only towards their ostracizers but also towards innocent bystanders, with ostracism being implicated in extreme acts of violence such as school shootings. However, individual differences in behavior exist within the context of social exclusion as not everyone responds aggressively after being ostracized. Identifying risk factors for retaliatory aggressive behavior following experiences of social exclusion may facilitate the development of targeted interventions aimed at mitigating such …

Population Genomics, Ecology And Conservation Of Asterias Sea Stars In The North Atlantic, Melenia I. Giakoumis

Dissertations, Theses, and Capstone Projects

Uncovering how species respond to environmental change is a central question in biology (Ehrlén & Morris 2015; Habibullah et al. 2022). It is the key to elucidating the past, understanding the present and predicting the future of species’ population dynamics. This dissertation investigates the influence of environmental change on intertidal species’ distributions and genomics at several timescales, with implications for conservation.

Environmental changes have occurred throughout history, on a geological scale, and have shaped the global patterns of species’ distributions and population sizes. Biologists have long studied how geological history has shaped species distributions (Sanmartín 2012) in both terrestrial (Liu …

Drug Repurposing Using Gene Expression Data Mining, Yue Qiu

Dissertations, Theses, and Capstone Projects

The conventional drug discovery process that employs the "one disease, one target, one drug'' paradigm is expensive, time-consuming, and has a high rate of failure for multi-genic complex diseases. An alternative approach to drug discovery is to repurpose an existing drug that has been used to treat some medical conditions. Drug repurposing is considered a promising method due to its accelerated the process of drug discovery and lower overall cost and risk.

Drug-perturbed gene expression profiles are powerful phenotype readouts of biological systems, and they have been widely used in drug repurposing studies. However, the existing drug-perturbed gene expression datasets …

Magnetically-Driven Therapeutic Agents Delivery System Using Iron Oxide Nanocages And Enhancement Of Exosome Secretion, A Potential Biological Drug Delivery Carrier, Min A Kang

Dissertations, Theses, and Capstone Projects

Nano-scale particles have attracted research attention due to their differences in properties such as penetration, circulation, and toxicity compared to bulk materials. This thesis mainly focused on using 20 nm iron oxide nanoparticles as siRNA delivery carriers under the alternating magnetic field and the development of a method to amplify the secretion of 150 nm exosomes from the cells, which could potentially use as a biological drug carrier.

Chapter 2 discusses a magnetically driven nanoparticle therapeutic agent delivery system, which efficiently modified the gene expression post-transcriptionally. In this work, we examined whether the caged-shaped 20nm iron oxide nanoparticles (IO-nanocages) can …

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 The Conformational Binding Of N-Methyl Mesoporphyrin Ix With Dna Model Telomeric G-Quadruplex Forming Sequences, Jessica Desamero

Dissertations, Theses, and Capstone Projects

DNA G-quadruplexes are alternative secondary structures formed from guanine rich DNA sequences. G-quadruplexes are found most abundantly at the ends of chromosomes called telomeres, where they can ultimately prevent further tumor growth and progression. Thus, quadruplex interactive agents, or ligands that can bind to and stabilize DNA G-quadruplex structures, are of high interest for their potential chemotherapeutic abilities. One quadruplex interactive agent is the porphyrin N-methyl mesoporphyrin IX (NMM), which has high binding selectivity for quadruplex structures. While the NMM-quadruplex complex in crystallized form has been greatly studied, this complex in solution form is not as well studied. Through circular …

Illuminating The Drivers Of Genomic Diversification In Lamprologine Cichlids Of The Lower Congo River, Naoko P. Kurata

Dissertations, Theses, and Capstone Projects

Freshwater fishes are extraordinarily diverse, considering their available habitats represent a tiny proportion of the earth’s surface. Rivers connect heterogeneous habitats in a linear form and provide excellent simplified models to understand how aquatic biodiversity evolves. In particular, the lower Congo River (LCR) in west Central Africa consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and morphological and ecological specialization. This system is thus an excellent natural laboratory for understanding complex speciation and population diversification processes. In my research, I explore various drivers of diversification, and adaptive evolution in rheophilic lamprologine cichlids endemic to the LCR, including Lamprologus …

Transcranial Direct Current Stimulation Studies Investigating The Role Of The Dlpfc In Memory And Metamemory, Casey M. Imperio

Dissertations, Theses, and Capstone Projects

Metamemory, broadly defined as knowledge about one’s own memory, is thought to consist of two separate processes, monitoring, the ability to assess the contents of your own memory, and control, altering behavior in service of memory, that work together to aide in encoding and retrieval processes. Prior work has shown that metamemory monitoring accuracy can be improved in a semantic memory task via high-definition transcranial direct current stimulation (HD-tDCS), a form of non-invasive brain stimulation, over the left dorsolateral prefrontal cortex (DLPFC). Over three experiments, the current dissertation sought to replicate and extend this work by: 1) testing the effects …