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Protein Language Models-Based Representation For Post-Translational Modification Prediction, Suresh Pokharel Jul 2025

Protein Language Models-Based Representation For Post-Translational Modification Prediction, Suresh Pokharel

Theses

Post-translational modifications (PTMs) are chemical changes that occur after translation and play a key role in regulating protein function and cellular processes. Their dysregulation is associated with various diseases, making accurate prediction of PTM sites essential for understanding cellular mechanisms and informing therapeutic strategies. This work focuses on the computational prediction of two biologically significant PTMs, namely succinylation and O-GlcNAcylation, utilizing recent advances in protein language models (pLMs). Drawing an analogy to natural languages, amino acids are treated as words and sequences as sentences, allowing pLMs to capture contextual dependencies within protein sequences. One of the earliest contributions of this …

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Dynamic Defenses To Systematically Secure Exposed Attack Surfaces In Wireless Systems, Naureen Hoque Jul 2025

Dynamic Defenses To Systematically Secure Exposed Attack Surfaces In Wireless Systems, Naureen Hoque

Theses

While modern wireless systems rely on strong encryption, this alone does not secure the entire attack surface, including exposed signal attributes, pre-authentication exchanges, and protocol metadata. This dissertation challenges the assumption that existing cryptographic protections are sufficient to protect these vulnerabilities. Signal attributes, including phase and amplitude variations due to modulation, are physical-layer characteristics of encrypted data communication that remain observable and exploitable for attacks like traffic analysis. The pre-authentication phase—during which session keys are negotiated and installed—is vulnerable to spoofing and denial-of-service attacks. Protocol metadata, such as operating channel, sender’s address and location, and timestamps, is unencrypted and can …

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Consumer Behavior Of Gen Z In Kosovo: Purchasing Preferences And Brand Engagement, Sara Dumani Jul 2025

Consumer Behavior Of Gen Z In Kosovo: Purchasing Preferences And Brand Engagement, Sara Dumani

Theses

This capstone project examines the consumer behavior of Generation Z in Kosovo by analyzing their purchasing preferences and brand engagement. The Generation Z demographic, which includes individuals born between 1996 and 2010, is the focus of this study. This generation is characterized by digital savviness and a significant influence from social media platforms, shaping their purchasing decisions and brand engagement. Generation Z’s behavior is often marked by a preference for online shopping, collaborative marketing approaches, and sustainability, making it essential to understand these factors in the context of Kosovo. The data for analyzing Generation Z’s consumer behavior were collected through …

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Investigating Spectral Rendering Techniques To Improve Colour Matching In Virtual Production, Vlad Simion Jul 2025

Investigating Spectral Rendering Techniques To Improve Colour Matching In Virtual Production, Vlad Simion

Theses

As rendering engines become increasingly important in film and television, with their use in virtual production (VP) to display rendered imagery, some underlying issues become more apparent. This thesis aims to investigate how we can improve asset color matching of VP elements with real-life objects found on sets. Experiments were conducted in which objects were exposed to various types of lighting setups, and digital twins were rendered using traditional computer graphics techniques. The renderings occurred in both classic RGB spaces and the spectral domain. Additionally, data reduction techniques were used for the spectral renderings to determine if any of them …

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Identifying Underspecifications In Security Requirements Using A Formal Reasoning Approach, Viktoria Koscinski Jul 2025

Identifying Underspecifications In Security Requirements Using A Formal Reasoning Approach, Viktoria Koscinski

Theses

Within requirements engineering, software requirements specifications tend to prioritize functional needs, potentially failing to capture critical security aspects and adequate security requirements. Security requirements engineering is a manual and error-prone activity often neglected due to the knowledge gap between cybersecurity professionals and software requirements engineers. Consequently, security requirements are especially prone to being underspecified, a condition where they lack a complete set of feature-values and are thus open to multiple interpretations. Underspecified security requirements can lead to incorrect assumptions and missing security properties, often remaining undiscovered until system deployment, thereby leaving the system vulnerable to exploitation. Furthermore, even individually well-written …

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Online And Offline Multi-Variate Time Series Forecasting With Neuroevolution Based Neural Architecture Search, Zimeng Lyu Jul 2025

Online And Offline Multi-Variate Time Series Forecasting With Neuroevolution Based Neural Architecture Search, Zimeng Lyu

Theses

Time series forecasting plays a crucial role in various fields, ranging from financial markets and predictive maintenance in industrial settings to healthcare analytics. Traditionally, statistical approaches were employed primarily for univariate forecasting tasks, but modern applications often require robust solutions capable of handling complex, multivariate, noisy, and non-stationary data. Current state-of-the-art solutions predominantly utilize transformer-based models, which demand significant computational resources, limiting their practicality, especially in resource-constrained environments. This dissertation introduces novel and efficient approaches to multivariate time series forecasting, leveraging NeuroEvolution-based Neural Architecture Search (NAS) methodologies. Specifically, two robust algorithms---Evolutionary eXploration of Augmenting Memory Models (EXAMM) for offline forecasting …

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Comprehensive Investigation Of The Torsional Behavior Of Triply Periodic Minimal Surface (Tpms) Inspired Structures, Mikhail Skibar Jul 2025

Comprehensive Investigation Of The Torsional Behavior Of Triply Periodic Minimal Surface (Tpms) Inspired Structures, Mikhail Skibar

Theses

This work is concentrated on research of torsion properties of TPMS structures, numerically and experimentally. Currently, there are not many works that concentrate on studying torsion properties of TPMS structures. Most of them are concentrated on structures for biomedical applications and structures, printed of Ti6Al4V titanium alloy. In other areas, such as aerospace, automotive, etc. TPMS structures may also find applications. In this work, shear modulus, shear strength and resilience are tested, depending of the following conditions: cell geometries Diamond, Gyroid and Primitive, with relative densities of 30%, 50% and 70%, and unit cell sizes of 10 mm, 15 mm …

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Characterizing Tcap Set-Ups For Effective Separation On Hydrogen Isotope Species, James R. Hanby Jul 2025

Characterizing Tcap Set-Ups For Effective Separation On Hydrogen Isotope Species, James R. Hanby

Theses

Hydrogen isotope separation was investigated using a series of thermal cycling absorption process (TCAP) experiments. Pulse tests were conducted using deuterium injected into a protium flow over a range of superficial velocities, temperatures, particle sizes, and column diameters to quantify the efficiency of this process for a palladium on kieselguhr catalyst. The resulting response curves, obtained from residual gas analysis, were used to calculate the height equivalent to a theoretical plate (HETP) in each case. These values were then fit with van Deemter curves to illustrate the change in HETP over gas velocity. A strong positive correlation with temperature was …

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Exploring Kosovo's Need For A Technology-Driven Offset Strategy, Alba Cikaqi Jul 2025

Exploring Kosovo's Need For A Technology-Driven Offset Strategy, Alba Cikaqi

Theses

At a time where technological innovation is redefining national security, Kosovo risks falling behind by failing to adopt emerging technologies for defense and security. This research addresses that vulnerability by exploring the need for a dedicated national strategy as a solution. Drawing on global best practices, including the United States Offset Strategy, NATO frameworks, and innovation models from the Baltic countries, the study outlines a potential path forward. Additionally, through qualitative analysis, including interviews with key stakeholders across public, private, and academic sectors, this study looks into the opportunities and challenges of developing a context-specific strategy for integrating emerging technologies …

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A Strategic Approach For Space-Based Solar Power Implementation In The Uae, Salamah Alhajeri Jul 2025

A Strategic Approach For Space-Based Solar Power Implementation In The Uae, Salamah Alhajeri

Theses

This thesis investigates the strategic potential of Space-Based Solar Power (SBSP) as a transformative clean energy solution for the United Arab Emirates (UAE). Set against the UAE’s Energy Strategy 2050 and increasing global climate pressures, this study explores how the UAE can take a leadership position in orbital solar energy through foresight-based planning, technological innovation, and policy integration. The research is guided by the following four questions: 1. What trends and uncertainties shape the future of space-based solar power in the UAE? 2. How can strategic foresight methodologies be used to develop a flexible SBSP strategy for the UAE? 3. …

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Unique Architecture: In Praise Of Paradox Persistence, Odaly Plancarte Jul 2025

Unique Architecture: In Praise Of Paradox Persistence, Odaly Plancarte

Theses

This thesis explores how bold and unconventional architectural designs are first rejected and later embraced by the public. Through a comparative study of the Sydney Opera House, the Louvre Pyramid, and the Walt Disney Concert Hall, it examines how public opinion shifts over time. Using media reports, interviews, and public comments, the study tracks emotional responses (positive, neutral, or negative) assigned a score to measure change over the years. The research applies Everett Rogers’ Diffusion of Innovation Theory to explain this shift in five stages: knowledge, persuasion, decision, implementation, and confirmation. Each building faced early backlash, but eventually became a …

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Network And Tree-Based Approaches To Data-Driven Modeling Of Complex Climate Systems, Adam M. Giammarese Jul 2025

Network And Tree-Based Approaches To Data-Driven Modeling Of Complex Climate Systems, Adam M. Giammarese

Theses

The guiding thread throughout this thesis work is data-driven modeling of Earth's climate. We investigate a variety of settings within the field of complex climate systems, such as gridded, high-resolution reanalysis data, lower-resolution climate indices, and incomplete paleoclimate records with missing values. We begin with reanalysis data of high spatial and temporal resolution, and use climate network analysis to uncover hidden trends in the data in regards to the Amazon rainforest and its changing role in the global climate system. We introduce a novel formulation of k-nearest neighbors climate networks to study changing trends at a local level, and apply …

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Utilizing Natural Language Processing To Optimize Business Processes, Olt Kondirolli Jul 2025

Utilizing Natural Language Processing To Optimize Business Processes, Olt Kondirolli

Theses

This Capstone project explores the potential of Natural Language Processing (NLP) techniques in optimizing decision-making and organizational workflows across various domains. The Capstone project uses three case studies to demonstrate how sentiment analysis, frequency analysis, and topic modeling can analyze unstructured textual data to provide insightful findings. The first case study evaluates employee satisfaction using sentiment analysis, uncovering trends across departments and roles to guide targeted organizational interventions. The second case study focuses on student feedback at a higher education institution, using sentiment and frequency analyses to identify key areas for improvement in academic programs and services. The third case …

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Development Of Nanopocket Membranes For The Isolation And Purification Of Extracellular Vesicles, Munther Alsudais Jul 2025

Development Of Nanopocket Membranes For The Isolation And Purification Of Extracellular Vesicles, Munther Alsudais

Theses

Extracellular vesicles (EVs) play a crucial role in intercellular communication and serve as significant biomarkers for various diseases. EVs carry biomolecules such as lipids, proteins, DNA, and RNA, which reflect the physiological state of their cells of origin, making them promising tools for non-invasive diagnostics and therapeutic applications. Effective isolation of EVs is essential for advancing scientific understanding of their biological roles and unlocking their clinical potential. Porous membranes have been widely used for the purification of various biological species from biological fluids. While membranes have prove highly effective for general size-based separation, recent innovations have focused on structurally refined …

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An Investigation Of Water-Based Cutting Fluids: Choline Amino Acid Protic Ionic Liquids As A Potential Sustainable Additive, Moni I. Chavez-Padilla Jun 2025

An Investigation Of Water-Based Cutting Fluids: Choline Amino Acid Protic Ionic Liquids As A Potential Sustainable Additive, Moni I. Chavez-Padilla

Theses

This comprehensive investigation examines the use of choline amino acid protic ionic liquids (CHAAPILs) as environmentally friendly additives for water-based cutting fluids (WBCFs) and showed a significant improvement in both friction and wear compared to traditional cutting fluids. Notably, water alone is ineffective as a boundary lubricant for aluminum machining promoting cyclic hydrolysis that generates brittle Al(OH)3 films while generating friction above dry sliding. As traditional petroleum-based lubricants are increasingly recognized for their detrimental environmental impact, the development of sustainable alternatives has become essential in the tribology community. CHAAPILs derived from renewable amino acids and choline sources were specifically formulated …

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Investigating Human Expertise In Manufacturing To Enhance Knowledge Preservation And Transfer Practices, Krzysztof Kamil Jarosz Jun 2025

Investigating Human Expertise In Manufacturing To Enhance Knowledge Preservation And Transfer Practices, Krzysztof Kamil Jarosz

Theses

In the US, the machining industry is a vital part of the economy, employing over 290,000 skilled machinists and over 89,000 mechanical engineers. Whilst employment figures for engineers in this crucial sector has been fairly steady, a rapid decline in machinist workforce has been observed in the last decade, along with retirement of aging expert machinists and engineers, creating workforce shortages and loss of valuable manufacturing knowledge inherent to those highly skilled and experienced individuals. As engineering design and manufacturing knowledge are closely intertwined, so is the knowledge pertaining to practical aspects of machining and design of components that are …

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Crispr-Dcas9 Genomic Engineering For Boosting The Therapeutic Potential Of Extracellular Vesicles, Iker Martinez Zalbidea Jun 2025

Crispr-Dcas9 Genomic Engineering For Boosting The Therapeutic Potential Of Extracellular Vesicles, Iker Martinez Zalbidea

Theses

Degenerative disc disease is a major contributor to low back pain, characterized by inflammation of the intervertebral disc (IVD), degradation of the extracellular matrix, loss of hydration, and cell death. Current therapies fail to address these underlying mechanisms, underscoring the need for regenerative strategies. Mesenchymal stem cells (MSCs) exhibit immunomodulatory and regenerative potential, but their efficacy is hampered by the harsh microenvironment of the degenerated IVD. Acellular MSC-derived extracellular vesicles (EVs) have shown therapeutic potential and offer a promising alternative for IVD regeneration. Here, we explore CRISPR-dCas9 mediated activation of TSG6 and STEAP3 to boost the therapeutic potency and biogenesis …

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Engineering Microphysiological Systems To Investigate Cellular Responses To Biophysical Cues In Human Tissue Microenvironments, Mehran Mansouri Jun 2025

Engineering Microphysiological Systems To Investigate Cellular Responses To Biophysical Cues In Human Tissue Microenvironments, Mehran Mansouri

Theses

Cells constantly sense and respond to biophysical cues in their microenvironment. Understanding how they interpret these mechanical signals is essential for advancing tissue modeling, studying disease mechanisms, and developing more predictive in vitro platforms. This dissertation presents a series of engineered microphysiological systems (MPS) designed to investigate how mechanical stimuli shape cellular behavior in distinct human tissue microenvironments. In Aim 1, I developed a reconfigurable microfluidic platform that mimics key features of human vascular barriers. This system supports the integration of porous membranes, 3D hydrogels, and flow channels, enabling precise control over both mechanical and biochemical cues. The modularity of …

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Modeling Femtosecond Laser Interaction With Glass For Optical Fabrication, Nathan Klein Jun 2025

Modeling Femtosecond Laser Interaction With Glass For Optical Fabrication, Nathan Klein

Theses

The fabrication of precision optics is critical for a wide range of applications, including biosensors, virtual and augmented reality, medical imaging, and micro-electronics. However, it is challenging to meet the demands of these applications with conventional chemical and mechanical fabrication methods, as they can introduce chemical waste, mid-spatial-frequency errors, and subsurface damage that degrades image quality. Femtosecond lasers have emerged as a promising alternative, offering fast, non-contact, and chemical-free machining with single digit nanometer precision. This thesis presents a computational model designed to investigate the interaction process between a high-intensity femtosecond laser pulse and dielectric material. A pulse propagation model …

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Mechanisms For Oxygen Vacancy Defect Migration In Srtio3/Nio Heterostructures, Anish Rajesh More Jun 2025

Mechanisms For Oxygen Vacancy Defect Migration In Srtio3/Nio Heterostructures, Anish Rajesh More

Theses

Perovskite-based oxide heterostructures display promising properties resulting from interface phenomena, making them good candidates for next-generation solid oxide fuel cell electrolytes. Amongst the different features exhibited by these interfaces, misfit dislocations play an important role in influencing ionic transport, yet their role remains poorly understood, which is the case in rock salt-perovskite interfaces too. In SrTiO3/NiO heterostructures, to comprehend interface ionic transport, we investigate oxygen vacancy migration near misfit dislocations. To this end, we developed a high-throughput framework that integrates atomistic simulations with nudged elastic band method to predict migration energy barriers across disparate interface atomic environments. By comprehensively mapping …

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Performance Comparison Of Learning With Errors Cryptosystems, Gabriel Johnson Jun 2025

Performance Comparison Of Learning With Errors Cryptosystems, Gabriel Johnson

Theses

Due to recent advancements in quantum computing, there has been great interest in finding quantum-resistant public key encryption algorithms. Much focus has been given to lattice-based cryptosystems, as certain lattice problems appear difficult even in the quantum setting. In particular, the Learning with Errors (LWE) problem, introduced by Regev, gives a means for constructing numerous public key cryptosystems with very strong proofs of security based on the hardness of finding a short vector in a lattice. We analyze and compare the performance, in terms of memory usage and speed, of four different Learning with Errors cryptosystems: basic LWE, normal-form LWE, …

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Parsing Of Math Formulas And Chemical Diagrams Using Graph-Based Representation And Attention Models, Ayush Kumar Shah Jun 2025

Parsing Of Math Formulas And Chemical Diagrams Using Graph-Based Representation And Attention Models, Ayush Kumar Shah

Theses

Mathematical formulas and chemical diagrams appear frequently in scientific documents but are often embedded as visual content, either rasterized or vector-based images, limiting their accessibility and automated analysis. This thesis aims to bridge this gap by presenting a graph-based visual parsing framework that recognizes and parses these notations from both vector and raster image inputs in digital documents. For mathematical formulas in born-digital PDFs, we construct Symbol Layout Trees (SLTs) using a graph defined over vector-based primitives, capturing spatial relationships, avoiding relying on OCR. For born-digital chemical diagrams, we introduce a Minimum Spanning Tree (MST)-based technique that extracts molecular structure …

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Fixed Points In Linear Regression, David L. Farnsworth Jun 2025

Fixed Points In Linear Regression, David L. Farnsworth

Articles

There is a set of points in the plane whose elements correspond to the observations that are used to generate a simple least-squares regression line. Each value of the independent variable in the observations matches up with one of these points, which are called pivot or fixed points. The coordinates of the fixed points are derived, and the properties of the points are explored. All points in the plane that yield each of the fixed points are found. The role that fixed points play in regression diagnostics is investigated. A new mechanical device that uses linkages to model the role …

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Using Predictive Analytics To Reduce Small Business Cost Estimation Error, Diana Solt May 2025

Using Predictive Analytics To Reduce Small Business Cost Estimation Error, Diana Solt

Journal of Applied Packaging Research

Small and medium packaging companies generally employ the use of custom-developed quoting programs to bid goods and services. Custom bid programs (e.g. Excel) are used to capture the company-specific costs of production. The inputs of variable costs, such as machine rate and scrap rate, are critical to get correct; however, companies often rely on educated guesses and industry expertise to quote packaging products to end-users. Due to the guesswork involved there can be a financial difference between the quoted costs and actual costs. This variance is often the cause of significant lost dollars. Price, if not determined correctly, could negatively …

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Hybrid Sentiment Analysis Of Police Social Media: Managing Big Data Impact On Youth, Alunood Yousuf Alamiri May 2025

Hybrid Sentiment Analysis Of Police Social Media: Managing Big Data Impact On Youth, Alunood Yousuf Alamiri

Theses

The pervasive influence of social media has reshaped public communication, particularly for institutions like law enforcement agencies that rely on these platforms to engage with the community. As police departments increasingly utilize social media to disseminate information, interact with the public, and manage public relations, the need for effective sentiment analysis becomes crucial. Understanding how police messages are received by the public, especially by the youth, who are among the most active and impressionable users of social media, is essential for maintaining public trust and ensuring effective communication. This thesis, seeks to develop a comprehensive solution for this challenge. The …

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Predicting Patient No-Show Rate In Healthcare To Improve Operational Excellence, Saeed Ahmed Al Wari May 2025

Predicting Patient No-Show Rate In Healthcare To Improve Operational Excellence, Saeed Ahmed Al Wari

Theses

The challenge of integrating no-show predictive models into healthcare environments is complex and multifaceted, extending far beyond the distinct technical challenge of building accurate models. This thesis will discuss more on the subject of incorporating machine learning into healthcare. While algorithmic accuracy and model validation are critical, they are a mere sub-system of a much larger operational, technological, ethical, legal and human ecosystem. Predictive models face mass deployment in healthcare systems which are complex networks of stakeholders across strict regulatory frameworks and deeply embedded workflows (AlMuhaideb et al., 2019). However, for these models to result in long term and real …

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Predicting Customer Churn In E-Commerce, Hind Tawfiq Kazim May 2025

Predicting Customer Churn In E-Commerce, Hind Tawfiq Kazim

Theses

Customer retention has become a critical focus for businesses seeking to sustain growth and profitability in an increasingly competitive market. In this thesis, advanced machine learning techniques are used to develop a data-driven churn prediction model for Majid Al Futtaim's customer base. In an e-commerce environment, the research focuses on identifying the key transactional and behavioral factors that influence customer churn, based on customer relationship management theory. The study is contextualized in the context of increased digital consumer engagement and high customer acquisition costs, which make retaining existing customers more cost- effective than acquiring new ones. Our primary research questions …

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Transmit And Deceive: Addressing The Insider Threat To Beacon Security, Noah Troy May 2025

Transmit And Deceive: Addressing The Insider Threat To Beacon Security, Noah Troy

Theses

IEEE 802.11 Beacon frames exist at the forefront of modern Wi-Fi networks and facilitate a wide array of essential network functionality, from discovery to time synchronization and even transmit power control. However, the central role Beacon frames play in initial network advertisement comes at the price of incomplete security guarantees, leaving these frames historically vulnerable to forgery and granting significant leverage over proximal wireless devices to a malicious actor that can effectively spoof them. With the publication of IEEE Std 802.11-2020, beacon protection was introduced to enable the authentication of received Beacon frames, placating most concerns. However, beacon protection is …

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The Role Of Digitalization Technologies In Enhancing Supply Chain Performance In The Service Industry: A Framework For Decision-Makers, Laith Hiasat May 2025

The Role Of Digitalization Technologies In Enhancing Supply Chain Performance In The Service Industry: A Framework For Decision-Makers, Laith Hiasat

Theses

Digitalization technologies are proving to be effective in many different situations across the service industry. Technologies such as AI, blockchain, big data, IoT, IoE, 6G, digital twin, and cobots are showing positive effects when implemented in different types of companies. This research highlights the important role of digitalization technologies in enhancing supply chain performance within the service industry. Despite their adoption across sectors, limited research examines their specific impact on service supply chains. A comprehensive search of 3 academic databases identified 429 peer-reviewed studies published since 2019. PRISMA was implemented, resulting in a final dataset of 66 studies. A survey …

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On The Use Of Nonlinear Electrophoresis For Separating Particles And Cells In Insulator-Based Electrokinetic Systems, Alaleh Vaghef-Koodehi May 2025

On The Use Of Nonlinear Electrophoresis For Separating Particles And Cells In Insulator-Based Electrokinetic Systems, Alaleh Vaghef-Koodehi

Theses

The increasing demand for efficient separation processes of micron-sized particles, including microorganisms, highlights the importance of developing low-cost, non-labor-intensive, and time-efficient techniques. Insulator-based electrokinetic (iEK) systems have proven to be a practical alternative to bench-scale methodologies such as centrifugation and membrane filtration. Several studies have reported the separation of microparticles by employing direct current (DC) voltages. However, all of them have overlooked the phenomenon of nonlinear electrophoresis (EPNL) and its role in the electrokinetic migration of particles. This study combines mathematical modeling and experiments to extend the capabilities of iEK systems. This dissertation has four aims: (1) to separate microparticles …

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