Digital Commons Network^™

Semi-Supervised Learning For Annotation And Representation Of Single-Cell Rna Sequencing And Spatial Transcriptomics Data, Haoran Liu

Dissertations

Semi-supervised learning has emerged as a powerful paradigm for analyzing single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data, where full annotation is often costly or impractical. scRNA-seq technologies measure the expression of thousands of genes across tens of thousands of cells, whereas ST additionally captures the spatial coordinates of gene expression within intact tissue sections. Annotation is a key step in both scRNA-seq and ST analysis pipelines, aiming to identify cell types, spatial domains, and latent biological structures. However, most existing annotation approaches rely on separate clustering methods that are typically fully unsupervised and fail to leverage side information …

Computational Methods For Single-Cell And Multi-Omic Data Integration And Regulatory Network Inference, Jianlan Ren

Dissertations

Single-cell and multi-omic technologies have transformed the dissection of cellular heterogeneity and regulatory dynamics in health and disease. However, the high dimensionality, technical variability, and biological complexity of these datasets present significant challenges for integration, annotation, and interpretation. In this dissertation, a suite of computational approaches is introduced to address key problems in single-cell and multi-omic data analysis through model-based innovations and applied statistical frameworks.

First, a constrained deep learning framework for single-cell data integration, label transfer, and clustering is proposed. By incorporating biologically motivated constraints into the training process, robust performance is achieved across simulated and benchmark datasets spanning …

The Malonate Template: The Key To Unlocking Novel Amino Acids, Thomas Owens

Dissertations

The “Malonate Template” provides access to various amino acids, all from a common intermediate. Herein, demonstrates the use of the malonate template to establish a synthetic route to both 2-thiohistidine and 2-thio-3-N-methyl-histidine from a benzyl methyl malonate derived intermediate. Furthermore, efforts exploiting the applicability of the malonate template for the of both 2-thiohistidine and 2-thio-3-N-methyl-histidine as a suitable alternative to methods previously described by Erdelmeier are described.

The method presented incorporates modifications to the biomimetic pathway described by Erdelmeier for the synthesis of 2-thiohisidine. By exploiting the biomimetic formation of 2-thiohisitidne’s mechanism via mass spectrometry, we …

Bodipy-Based Photocages For The Controlled Release Of Hydrogen Sulfide And Persulfides, Yanmei Li

Dissertations

Reactive sulfur species (RSS) such as hydrogen sulfide (H2S) and hydropersulfides (RSSH) are crucial mediators in a variety of physiological and pathological processes. Their regulatory roles span from maintaining cellular redox balance to influencing signaling pathways critical for homeostasis and stress responses. This dissertation investigates H2S and RSSH as biologically important molecules and explores the development of boron-dipyrromethene (BODIPY)-based photocages for its controlled, light-triggered release. Given H2S and RSSH's critical role in redox regulation and cellular protection, achieving spatiotemporal control over its delivery is essential for both therapeutic and research applications. BODIPY scaffolds offer favorable photophysical properties, including visible-light activation …

A Constructivist Grounded Theory Exploration Of Intergenerational Trauma Among Lgbtq+ Bipoc Individuals, Satveer Kler

Dissertations

Many scholars have argued that existing conceptualizations of trauma such as the Diagnostic and Statistical Manual of Mental Disorders (5th Ed.; DSM-5) conceptualization are inapplicable for individuals of marginalized communities. Individuals of marginalized communities may experience historical trauma, racial trauma, identity-related trauma, or collective trauma. Moreover, the effects of these forms of trauma may persist throughout different generations via biological transmission (e.g., epigenetics) or via interpersonal transmission (e.g., emotion socialization, cultural socialization, attachment, communication styles, behavioral socialization). The generational effects of these forms of trauma are referred to as intergenerational trauma. There has been a paucity of empirical explorations of …

"Operation Motivation" - Samuel Shepard Jr., Nicalee Stephens-Wilson

Dissertations

African-American students have often faced systemic oppression and racial inequities as learners in the United States. Public schools in their communities lacked the resources to offer full access to a fair and equitable education. For years, human rights activists fought for radical changes in public schools. Finally, in 1954, the U. S. Supreme Court in Brown v. Board of Education ruled segregation in public schools unconstitutional. The Brown decision did not have the power to eliminate the long-established segregation practices. Nor did it grant access to educational equity for children of color. Dr. Samuel Shepard Jr. began his work in …

Synthetic Amphiphiles As Antibiotic Potentiators, Helena Spikes

Dissertations

Antibiotic resistance has become a massive threat to modern medicine. Bacteria acquire resistance either through genetic mutations or mobile genetic elements, such as plasmids. The growing resistance crisis is exacerbated by over-prescription of antibiotics and improper use. As antimicrobial resistance becomes more widespread, superbugs (bacteria resistant to more than one class of drug) have evolved. Since few new drugs reach clinical trials and even fewer are approved by the FDA, we must find a way to make existing drugs more potent. One technique to accomplish this is by using combination therapy. By administering two or more drugs at a time, …

Flaxseed’S Paradoxical Role In Extending Lifespan And Reproductive Capacity In White Leghorn Laying Hens; And The Effect Of Polyunsaturated Fatty Acids (Pufas) On Lipid Metabolism, Mitochondrial Bioenergetics And E-Cadherin Expression In Laying Hen Ovarian Tumors, William Christopher Weston

Dissertations

We are the first lab to report the occurrence of a diet-induced transsulfuration (TS) blockade associating with elevated S-adenosylmethionine (i.e. SAM) synthesis, enhanced lifespan and enhanced reproductive capacity, in a vertebrate animal model. In this paradoxical study, we used LC-MS/MS-derived metabolomics data to report the effects of flaxseed (Linum Usitatissimum) on one-carbon metabolism in White Leghorn laying hens (Gallus gallus). Flaxseed contains a vitamin B6-antagonizing molecule called ‘linatine’ that is particularly effective at reducing vitamin B6 levels in small rodents and poultry. Linatine reduces TS flux through its inhibition of the vitamin B6-dependent enzymes cystathionine beta synthase (CBS) and cystathionine …

Controlled Reduction Of Graphene Oxide And Graphene Oxide-Carbon Nanotube Hybrids And Their Applications, Samar Azizighannad

Dissertations

Graphene and graphene derivatives are widely used in diverse research and industrial applications. Graphene production on a large scale is carried out by exfoliating graphite oxide and producing graphene oxide (GO), which comprises of graphene sheets with different oxygen-containing functional groups such as hydroxyl, carboxyl, and carbonyl. GO is reduced to reduced graphene oxide (rGO), which has properties that are closer to graphene. Properties of GO and rGO depend upon the oxygen content, and the effect of reducing oxygen content on the aqueous behavior of rGOs is not well understood.

In an effort to understand how properties of rGO change …

Modeling And Analysis Of Intracellular Signaling Networks And Cellular Decisions, Mustafa Ozen

Dissertations

Developing molecular network analysis methods is important due to their applications on complex biological systems such as target discovery, development of drugs, discovering drug effects, and finding treatments for many complex diseases, e.g., cancer, autoimmune, and mental disorders. An example of analysis techniques is the fault diagnosis analysis, in which the purpose is to quantify how much vulnerable the entire network is to dysfunction of one or multiple molecules. Such analysis can be done after proper network models are implemented, trained, and tested against the experimental data. In this dissertation, a Boolean modeling framework is implemented and methods to train …

Bio-Inspired Learning And Hardware Acceleration With Emerging Memories, Shruti R. Kulkarni

Dissertations

Machine Learning has permeated many aspects of engineering, ranging from the Internet of Things (IoT) applications to big data analytics. While computing resources available to implement these algorithms have become more powerful, both in terms of the complexity of problems that can be solved and the overall computing speed, the huge energy costs involved remains a significant challenge. The human brain, which has evolved over millions of years, is widely accepted as the most efficient control and cognitive processing platform. Neuro-biological studies have established that information processing in the human brain relies on impulse like signals emitted by neurons called …

Amyloid Proteins And Fibrils Stability, Farbod Mahmoudinobar

Dissertations

Compared to globular proteins that have a stable native structure, intrinsically disordered peptides (IDP) sample an ensemble of structures without folding into a native conformation.One example of IDP is the amyloid-beta(Abeta) protein which is the main constituent of senile plaques in the brain of Alzheimer's patients.Understanding the process by which IDPs undergo structural changes to form oligomers that eventually aggregate into senile plaques/amyloid fibrils may significantly advance the development of novel therapeutic methods to treat neurodegenerative diseases, for which there is no cure to date. This dissertation has two main objectives. The first one is to investigate and identify structural …

Application Of The Picoloyl Group In Carbohydrate Chemistry, Michael Mannino

Dissertations

Stereocontrol of glycosylation reactions is a constant struggle in the field of synthetic carbohydrate chemistry. The application of the picoloyl (Pico) substituent can offer numerous stereocontrolling avenues. The most popular application is the Hydrogen-bond-mediated Aglycone Delivery (HAD) method that provides excellent selectivity in the glycosylation of a variety of sugar substrates. The HAD method relies on the formation of an intermolecular hydrogen bond between the nitrogen atom of the Pico substituent on the glycosyl donor with the hydroxyl group of the glycosyl acceptor. This interaction provides a facial preference for the nucleophilic attack and hence provides powerful stereocontrol for the …

High-Performance Reductive Strategies For Big Data From Lc-Ms/Ms Proteomics, Muaaz Gul Awan

Dissertations

Mass Spectrometry (MS)-based proteomics utilizes high performance liquid chromatography in tandem with high-throughput mass spectrometers. These experiments can produce MS data sets with astonishing speed and volume that can easily reach peta-scale level, creating storage and computational problems for large-scale systems biology studies. Each spectrum output by a mass spectrometer may consist of thousands of peaks, which must all be processed to deduce the corresponding peptide. However, only a small percentage of peaks in a spectrum are useful for further processing, as most of the peaks are either noise or are not useful. Our experiments have shown that 90 to …

Streaming Feature Grouping And Selection (Sfgs) For Big Data Classification, Noura Helal Hamad Al Nuaimi

Dissertations

Real-time data has always been an essential element for organizations when the quickness of data delivery is critical to their businesses. Today, organizations understand the importance of real-time data analysis to maintain benefits from their generated data. Real-time data analysis is also known as real-time analytics, streaming analytics, real-time streaming analytics, and event processing. Stream processing is the key to getting results in real-time. It allows us to process the data stream in real-time as it arrives. The concept of streaming data means the data are generated dynamically, and the full stream is unknown or even infinite. This data becomes …

Determination Of Transforming Growth Factor-Β Signaling Targets In Activated T Cells, Ramiah Jacks

Dissertations

T lymphocytes are a critical component of the adaptive immune system and their responses in pathogenic and steady state conditions require strict regulation. One mechanism involved in this regulation is Transforming Growth Factor-β (TGF-β) signaling. TGF-β can act on activated T cells to facilitate the differentiation of TGF-β dependent T helper subsets or the suppression of T cell activation and proliferation. However, the molecular mechanism(s) by which TGF-β signaling controls T cell differentiation vs T cell suppression remain poorly understood.TGF-β signaling is propagated by initially binding to the TGF-β type II receptor, which subsequently activates TGF-β type I receptor (TGF-βRI) …

Shame, Aggression, And Self-Compassion In At-Risk Adolescents, Sara Ashline Hofmann

Dissertations

Prior research has identified a strong link between experiences of shame and aggressive behavior in at-risk and offender populations but the mechanisms of this relationship are unclear. One potential interrupter of this relationship is self-compassion, a teachable emotional regulation skill. The purpose of this study was to investigate whether nonoffender at-risk youth differed significantly in levels of self-compassion, shame, and aggression from nonviolent offender and violent offender youth with the goal of evaluating these relationships to aid in the future development of more tailored and effective interventions for court-involved youth. One hundred and six at-risk adolescents in the Rocky Mountain …

The Association Of Kangaroo Mother Care, Energy Conservation, And Bonding In Preterm Neonates, Dorothy Forde

Dissertations

Purpose:To examine the association of kangaroo mother care (KMC) on energy utilization and bonding as evidenced by reduced biochemical markers of adenosine triphosphate (ATP) degradation, hypoxanthine (Hx), xanthine (Xa), and uric acid (UA), and (allantoin), a measure of oxidative stress in preterm infants 24-36 weeks gestation. A secondary objective was to compare specific physiological parameters using bedside monitoring and perfusion and oxygenation of the gut using near-infrared spectroscopy (NIRS) during 1 hour of KMC compared to incubator care.

Study design: A randomized controlled trial (RCT) examining the effects of 1-hour of KMC or 1-hour incubator care on urinary markers …

Exploring Churn And Alignment Between Retention And Occupational Culture As Perceived By Professional Truck Drivers, Catherine M. Cole

Dissertations

Despite advances in logistics software and increased driver pay, the trucking industry continues a historic wave of human capital risks in the form of driver turnover and driver shortages. Previous efforts to understand the phenomenon of driver turnover rely heavily on supply chain, transportation, and logistics based disciplines. The current study provides a human capital ontology towards understanding professional truck driver perceptions. Within the interpretive framework of pragmatism, the study applied a simultaneous ethnographic and phenomenological research design to explore the phenomenon of churn and professional truck driver perceptions of environmental alignment between trucking industry retention strategies and the occupational …

Longitudinal Stratified Structure As Tunable Platform Using Liquid Crystal At Terahertz Regime, Abubaker Mustafa Tareki

Dissertations

In recent years, the terahertz (THz) band of the electromagnetic spectrum has received considerable attention. The THz region falls above the RF (radio frequency- gigahertz frequencies) engineering and falls below IR (infrared frequencies). The region has been referred to as the terahertz gap because it has been highly underutilized in spite of the fact that THz waves have unique properties that provide advantages in medical and defense applications. The increase in THz research has been a result of the significant advances in THz sources and detectors. To continue the advancement of THz technology, component research that can actively manage the …

Anna He Purnabramha: Deorukhe Women’S Agency In The Making Of Bodies, Cuisines, And Culture In Maharashtra, India, Gauri Anilkumar Pitale

Dissertations

The world is changing. India is changing. Food is changing. Bodies are changing. What does this mean for the women of Maharashtra, India? Globalization and modernity manifest in new and interesting ways the world over. As people establish networks of global commodity, capital, and human circulation, anthropologists raise pertinent concerns. While some are apprehensive about cultural loss and western cultural imperialism, others make a case for the rise of glocalization. While some espouse the positives of a free market economy, others are critical of the nutrition transition in developing countries and what this means for the health of the people …

Fast Estimation Model Of Pressure-Temperature Response For Planning Focused Ultrasound Surgery, Tariq Mohammad Arif

Dissertations

High Intensity Focused Ultrasound (HIFU) is becoming a widely accepted modality for extracorporeal non-invasive hyperthermia and surgical procedures. Since ultrasonic transducers need to operate in various challenging body locations, the arrangement of their array elements can be optimized to improve the capability of controlling focus intensity. In the first part of this dissertation, patterns of pressure field variations with several selected design variables (kerf, transducer element’s number and element’s width-height) are studied. These patterns indicate that there is a more suitable shape and arrangement of transducer elements in a specified area to achieve highest possible pressure. In order to obtain …

Synthetic Ion Channels: A New Class Of Membrane Disruptor And Efflux Pump Inhibitor For The Recovery Of Antibiotic Potency, Mohit Bharatkumar Patel

Dissertations

Antibiotic resistance has become a world-wide health care crisis. In 2013 there were 50,000 deaths in U.S. and EU, associated with hospital acquired bacterial infections. This problem is exacerbated by the lack of new antibiotics in development. Here, we report that synthetic amphiphiles represent a new class of adjuvants that rescue antibiotic potency against multidrug resistant bacteria. Hydraphiles are amphiphiles, designed and synthesized in Gokel lab, that show many of the same properties as protein ion channels. Hydraphiles were previously shown to have antimicrobial activity against Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae. Here, we report that hydraphiles recover the …

Synthesis And Characterization Of Amphiphiles For Mammalian Cell Transfection And Antimicrobial Activity, Joseph William Meisel

Dissertations

Amphiphiles are molecules that contain both water-soluble and water-insoluble components. The dual nature of these molecules engenders remarkable properties including the ability to self-assemble into ordered structures. Cell membranes are composed of amphiphilic phospholipids that organize into a bilayer motif. Synthetic amphiphiles can interact with natural membranes and influence the transport of molecules across the cell membrane. The work elaborated in this report employs amphiphiles to co-assemble with DNA and transport the genetic material across cell membranes. First, a simplified method for interacting DNA with amphiphiles was developed. Second, a series of known ion-transporting compounds were assayed for their interaction …

Ecological And Phenotypic Factors Influencing The Movement Dynamics Of The Blackspotted Topminnow, Fundulus Olivaceus, Scott Richard Clark

Dissertations

Movement of individuals throughout a landscape is a complex behavior that has important consequences on numerous ecological and evolutionary processes. Perhaps most notably is the relationship between movement and reproduction, as this has implicit ramifications on individual fitness and consequently, population level processes. Although this relationship has been theoretically and empirically demonstrated across a number of animal taxa, its role in fishes remains understudied and largely unknown. Using a series of outdoor mesocosms, in combination with a field study, I employed passive integrated transponder (PIT) tags to experimentally assess the sex-specific movement dynamics of a small-bodied, sexually-dimorphic stream fish, the …

Studies On Purification And Functionalization Of Carbon Nanotubes And Their Aqueous Phase Behavior, Zheqiong Wu

Dissertations

Carbon nanotubes (CNTs) are known to have unique mechanical, thermal and electrical properties which make them attractive for a wide range of applications ranging from batteries to sensors. CNTs are rolled up graphene sheets where the single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) are classified according to the number of concentric rings. In this dissertation, the focus is on several different aspects of MWCNTs. These include purification, functionalization and colloidal behavior.

MWCNTs are insoluble in solvents and therefore some degree of functionalization is required prior to their real-world applications. Oxidation debris is generated during carboxylation which is usually the first …

Influence Of Maternal Prior Life Adversity On The Psycho-Neuroendocrine-Immune Profile During Pregnancy, Karen J. Kotz

Dissertations

Pregnancy is accompanied by a multitude of physical and psychological changes. Adaptation to these changes through reduced anxiety and attenuated stress responsiveness is necessary across gestation and into the postpartum period for optimal maternal-infant health. In contrast, exposure to higher amounts of stressors during pregnancy can disrupt neuroendocrine-immune processes required for successful pregnancy outcomes. Evolving evidence demonstrates that exposure to adversity early in life has long-lasting effects on stress response systems that alter stress reactivity during adulthood. Given this evidence, it is posited that women who experience greater pre-pregnancy adversity during their childhood are at greater risk for negative maternal-infant …

Understanding The Impact Of Adolescent Attachment On Academic Success, Cristina Cortesi

Dissertations

In recent years, studies are citing an increase in adolescent mental health diagnoses and symptomotology related to AD/HD, Bipolar Disorder, Depression, Anxiety, and Conduct Disorders. While the associated behaviors may be the result of several variables, recent neurobiological studies combined with Attachment Theory have pointed to a possible link to attachment issues. Because of the developmental stage of adolescents, these behaviors have been observed in both home and school environments. Schools, in general in the United States, have been experiencing significant struggles in terms of lack of adequate educational success which prompted the implementation of legislation commonly known as No …

Exercise Alters Glial Cell Line-Derived Neurotrophic Factor (Gdnf) Protein Content In The Spinal Cord, Monica Janine Mccullough

Dissertations

Neurotrophic factors may play a role in exercise-induced neuroprotective effects; however, it is not known if exercise mediates changes in glial cell line-derived neurotrophic factor (GDNF) protein levels in the spinal cord. The aim of the studies described herein was to determine if exercise alters GDNF protein expression in the lumbar spinal cord of healthy and diseased animals. The lumbar spinal cord was analyzed from adult rats aged 6-, 12-, 18- and 24-months, and from transgenic amyotrophic lateral sclerosis (ALS) mice and wild-type mice aged 3 months. Animals had undergone either forced wheel running, voluntary wheel running or swimming for …

Effect Of Doping On Β-Tricalcium Phosphate Bioresorbable Bulk Material And Thin Film Coatings, Suhaila Abdalla

Dissertations

Magnesium has emerged as a revolutionary biodegradable metal for use as an orthopedic material, it has several advantages over the permanent metallic materials currently in use, including eliminating the effects of stress shielding, improving biocompatibility and degradation properties, thus removing the requirement of a second surgery for implant removal. Due to the rapid degradation of magnesium, it is necessary to control the corrosion rates of the materials to match the rates of bone healing. This dissertation reports on the effect of doping on the properties of β-tricalcium phosphate (β-TCP). It also reports on its application as a thin film coating …