Digital Commons Network^™

Automated, High-Throughput Platform To Generate A High-Reliability, Comprehensive Rectal Cancer Database, Neal Bhutiani, Mahmoud M G Yousef, Abdelrahman Yousef, Mohammad Zeineddine, Mark Knafl, Olivia Ratliff, Uditha P Fernando, Anastasia Turin, Fadl A Zeineddine, Jeff Jin, Kristin Alfaro-Munoz, Drew Goldstein, George J Chang, Scott Kopetz, John Paul Shen, Abhineet Uppal

Faculty, Staff and Student Publications

Purpose: Dynamic operations platforms allow for cross-platform data extraction, integration, and analysis, although application of these platforms to large-scale oncology enterprises has not been described. This study presents a pipeline for automated, high-fidelity extraction, integration, and validation of cross-platform oncology data in patients undergoing treatment for rectal cancer at a single, high-volume institution.

Methods: A dynamic operations platform was used to identify patients with rectal cancer treated at MD Anderson Cancer Center between 2016 and 2022 who had magnetic resonance imaging (MRI) imaging and preoperative treatment details available in the electronic health record (EHR). Demographic, clinicopathologic, tumor mutation, radiographic, and …

Genomic Landscape Of Lynch Syndrome Colorectal Neoplasia Identifies Shared Mutated Neoantigens For Immunoprevention, Ana M Bolivar, Fahriye Duzagac, Nan Deng, Laura Reyes-Uribe, Kyle Chang, Wenhui Wu, Charles M Bowen, Melissa W Taggart, Selvi Thirumurthi, Patrick M Lynch, Y Nancy You, Jesus Rodriguez-Pascual, Steven M Lipkin, Scott Kopetz, Paul Scheet, Gregory A Lizee, Alexandre Reuben, Krishna M Sinha, Eduardo Vilar

Faculty, Staff and Student Publications

Background & aims: Lynch syndrome (LS) carriers develop mismatch repair-deficient neoplasia with high neoantigen (neoAg) rates. No detailed information on targetable neoAgs from LS precancers exists, which is crucial for vaccine development and immune-interception strategies. We report a focused somatic mutation and frameshift-neoAg landscape of microsatellite loci from colorectal polyps without malignant potential (PWOMP), precancers, and early-stage cancers in LS carriers.

Methods: We generated paired whole-exome and transcriptomic sequencing data from 8 colorectal PWOMP, 41 precancers, 8 advanced precancers, and 12 early-stage cancers of 43 LS carriers. A computational pipeline was developed to predict, rank, and prioritize the top 100 …

Transfer-Learning-Enhanced Regression Generative Adversarial Networks For Optimal Evtol Takeoff Trajectory Prediction, Shuan Tai Yeh, Xiaosong Du

Mechanical and Aerospace Engineering Faculty Research & Creative Works

Electric vertical takeoff and landing (eVTOL) aircraft represent a crucial aviation technology to transform future transportation systems. The unique characteristics of eVTOL aircraft include reduced noise, low pollutant emission, efficient operating cost, and flexible maneuverability, which in the meantime pose critical challenges to advanced power retention techniques. Thus, optimal takeoff trajectory design is essential due to immense power demands during eVTOL takeoffs. Conventional design optimizations, however, adopt high-fidelity simulation models in an iterative manner resulting in a computationally intensive mechanism. In this work, we implement a surrogate-enabled inverse mapping optimization architecture, i.e., directly predicting optimal designs from design requirements (including …

Conversion Of Microcrystalline Cellulose To Hexane Using Hydrogenated Metal Oxides At Low Temperature And Pressure, Mubarak Osman

Electronic Theses and Dissertations

Increasing global energy demand and environmental concerns have fueled the exploration of sustainable and efficient methods for renewable fuel production. The conversion of cellulosic waste to hydrocarbon fuels using hydrogenated metal oxides presents a novel and eco-friendly approach to sustainably address energy demand. In this study, hydrogenated metal oxides were used as catalysts in a relatively low-temperature and atmospheric-pressure environment to facilitate the conversion of cellulosic waste into hydrocarbon fuels. Hydrogenated metal oxides have been introduced as potential hydrogen transfer catalysts. The expected result is the selective conversion of cellulose to hexane at relatively low temperatures, which significantly reduces energy …

The Role Of The Speech-Language Pathologist With Survivors Of Traumatic Brain Injury From Intimate Partner Violence And Providers’ Knowledge Of This Role, Nicolle Mcadams

Electronic Theses and Dissertations

Intimate partner violence occurs globally at alarming rates. Many experience adverse health impacts such as traumatic brain injury. Healthcare providers do not know the role of the speech-language pathologist, or the rehabilitation needs of survivors.

Aims: This scoping review aims to identify speech-language pathology services for survivors of intimate partner violence with a resulting traumatic brain injury, and knowledge of healthcare providers on the rehabilitation needs of this population. A search was completed in May to October 2023, resulting in a total of 13 articles reviewed.

Main contributions: Speech-language pathologists lack knowledge to provide services to intimate partner violence survivors …

Beyond The Screen: Understanding College Students’ Perspectives On Cyberstalking, Gabrielle Jackson

Electronic Theses and Dissertations

Previous research regarding the victimization of college students is primarily geared toward physical or sexual encounters. There is a limited scope of research regarding the online victimization of college students, specifically those involved in Greek life organizations. Furthermore, there is a misinterpretation of the definition of cyberstalking among college students, as many students are unaware that they have been personally victimized (Cass, 2011). This study seeks to examine college students’ perceptions of online victimization and how they may vary. The different student impressions and the prevalence of online victimization were examined using self-reported data from students enrolled in a university …

The Effects Of Text-Based Gaming On Reading Comprehension For Students With Intellectual Disability, Faith Ihrig

Electronic Theses and Dissertations

Since the COVID-19 Pandemic, reading comprehension and reading engagement have decreased in the United States. Our world is also becoming increasingly technological, and a large percentage of individuals in the United States, specifically children, are playing video games. There are increasing amounts of video games that target educational skills, such as reading and math, and video games that have been created strictly for entertainment. This study examined the potential effects of playing text-based video games on the comprehension and engagement of 6-8 grade students with intellectual disabilities. A Multiple Baseline Across Participants single case design was used to measure the …

Interpreting Shift Encoders As State Space Models For Stationary Time Series, Patrick Donkoh

Electronic Theses and Dissertations

Time series analysis is a statistical technique used to analyze sequential data points collected or recorded over time. While traditional models such as autoregressive models and moving average models have performed sufficiently for time series analysis, the advent of artificial neural networks has provided models that have suggested improved performance. In this research, we provide a custom neural network; a shift encoder that can capture the intricate temporal patterns of time series data. We then compare the sparse matrix of the shift encoder to the parameters of the autoregressive model and observe the similarities. We further explore how we can …

Magnetic Properties Of Zgnrs With Nitrogen And Fluorine Adsorbates, A Computational Study, Justin Petit

Electronic Theses and Dissertations

Imposing dimensional restrictions on graphene sheets and adding impurities can give rise to carbon nanostructures with magnetic properties. In this work, zigzag graphene nanoribbons, zGNRs, with nitrogen and fluorine adatoms are investigated for magnetic properties of interest for spin devices. Geometry optimizations were done determining which position along a zGNR electrode that N and F would favorably attach to. Edge positions were determined as the most stable attachment site. M-cell zGNR electrodes (M = 1-3) edge-functionalized by N and F adatoms were investigated with respect to their band structures and spin densities in antiferromagnetic and ferromagnetic, AFM and FM, configurations. …

Exploring The Correlates And Predictors Of Covid-19 Vaccine Hesitancy And Uptake Among People Living With Hiv/Aids In Tennessee, Charles Olomofe

Electronic Theses and Dissertations

Background

The administration of the COVID-19 vaccines has met with resistance and hesitance from different population groups including people living with HIV/AIDS (PLWHA). It is concerning to know that PLWHAs are showing a higher rate of COVID-19 vaccine hesitancy than the general population. The objective of this study is to synthesize the literature and determine the correlates and predictors of COVID-19 vaccine hesitancy among PLWHA using primary and secondary data.

Methods

A scoping review was conducted to identify and summarize studies on COVID-19 vaccine hesitancy among PLWHA using the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) Extension for …

Landslide Susceptibility And Tree Ring Eccentricity Analysis Along Unstable Slopes Of The New River Watershed, Anderson And Morgan Counties, Tn, Megan Palmer

Electronic Theses and Dissertations

Landslides are mass movements that affect infrastructure across East Tennessee, causing problems for the Tennessee Department of Transportation (TDOT). An assessment of conditions and locations of unstable slopes can aid TDOT in infrastructure management. Landslide susceptibility was evaluated for Anderson and Morgan counties, TN, off State Route 116 in the New River watershed. Susceptibility maps used a landslide inventory and six factors: elevation, slope, geology, distance from stream, rainfall, and curvature, input in forest-based classification and logistic regression models. Additionally, affected trees along these unstable slopes in Anderson and Morgan counties were cored to analyze mass movement impacts on tree …

Caring For The Aging In The Twenty-First Century: A Principlist Approach To Psychiatric Care For Geriatric Patients, Gabriella Agostaro

Electronic Theses and Dissertations

As the field of psychiatry continues to expand, the importance of equitable care continues to remain apparent. Geriatric patients with psychiatric conditions experience a heightened rate of discrimination in care facilities and psychiatric symptoms are often left untreated or individuals are forcibly treated against their will. While these patients typically present with a handful of physical comorbidities, gaps in care typically result from a lack of resources delegated to the aging population and an extreme lack of education for clinicians dealing with psychiatric patients.

Clinicians and additional members of the medical team have typically prioritized a paternalistic approach to the …

Creating A Unified Brand Identity For United Way Chapters In New York, Sarah Dejoy

Theses

Consistent and effective web design plays a role in enhancing the online presence and supporting the mission of nonprofit organizations (NPOs), which utilize online spaces to provide information to their constituents and the general public. This study centers on the web presence of United Way, presenting an analysis of the official websites of chapters in New York State. Visual rhetoric was used as the conceptual framework orienting the analysis, considering websites typically include written and visual texts intended to appeal to various audiences. The Brand Standards & Guidelines provided by United Way Worldwide were utilized to identify various website characteristics. …

Neural Network Characterization Methods For Noisy Quantum Hardware Results, Daniel Richard Breslawski

Theses

As the nascent quantum computing paradigm matures and quantum devices become widely available, discrete "eras" are emerging which characterize evolving quantum computing technologies, much like semiconductor technology node classifications. The current period has been coined the Noisy Intermediate-Scale Quantum (NISQ) era, as devices above 50 qubits in size exist but computations using these devices accumulate error quickly from classical interference sources and state decoherence. NISQ machines may surpass the capabilities of modern classical computers in ideal circumstances, but the accumulation of error from physical noise limits the size and implementability of reliable quantum algorithms. Because of these limitations, strategies are …

Exploring The Phase Space Of Binary Neutron Star Simulations And Photon Geodesics In The Presence Of Black Holes, Ben Fisler

Theses

Here, we investigate the use of the Lorene code to generate quasi-equilibrium initial data for close binary neutron star configurations. The code has been widely used throughout the field of numerical relativity, and is capable of generating initial data for a wide range of neutron star equations of state and binary mass ratios. We also explore the ranges of parameter space for which the code can generate accurate initial data, and the nature of the instabilities that arise when the code is asked to produce data outside this range. This work should aid other groups performing merger simulations of binary …

Uvm Verification Of A Dtmf Receiver Core, Clayton Koppi

Theses

Integrated circuits grow more complex as digital designers implement more features on a project. All modern integrated circuits require some form of testing in order to prove that their functionality matches the design requirements. As the complexity of a design increases, the number of potential bugs increases dramatically. The need for a testbench that is reusable, modular, and organized is apparent for modern integrated circuits. Verification is the process of proving the design matches its requirements, and discovering bugs in simulation. The business motivation behind verification is ensuring the product will work before starting the costly and long fabrication process. …

New Trigger Board Design For An Inductive Adder Topology Circuit, Htet A. Kyaw

Theses

After working at Laboratory for Laser Energetics for about 10 months, I was assigned in doing the research for replacing the obsolete parts on the trigger board of the high voltage and high current system. After studying the system, it was noticed that the circuit topology used was part of the pulse power system. Hence, the pulse power system was studied further to understand how it was used and its advantages. The inductive adder topology was studied thoroughly so that the trigger board design would meet the requirements. The components such as MOSFETs and Gate Drivers were studied and compared …

Benchmarking Of Matrix Multiplication Acceleration Methods, Ashish Tondwalkar

Theses

With the advent of artificial intelligence (AI), performance and model runtime feasibility poses a challenge to the advancement of AI technology. Novel methods of accelerating the core mathematical functions of AI applications are being explored. The crux of AI computations that would benefit from hardware acceleration is matrix multiplication. This thesis explores the acceleration of matrix multiplication using systolic arrays and the strassen algorithm, methods known for enhancing computational efficiency through parallel processing. The research focuses on the design, implementation, and comprehensive testing of these architectures to expedite matrix multiplication tasks, crucial for applications in deep learning and signal processing. …

If The Last Petals Fall, Soomin Kim

Theses

During the Spring of 2023, I visited my mother in Los Angeles. I unpacked my belongings and sat down for a light snack with her. Watching her cut fruits, I noticed for the first time that her face had aged significantly. If The Last Petals Fall is a photographic series that delves into the concept of memory. With the handful amount of what’s left of my family archives, I have accepted the fact that I can no longer contribute to my past but rebuild the missing in-between moments. These photos represent my childhood, adulthood, and everything in between. Through this …

Enola, Justin Gibson

Theses

Enola, is a photographic collection of visual fragments without a beginning or end. These moments reflect on my inner psychological landscape, translated from pieces of stories, dreams, recollections. My project, inspired heavily by the town that I once called home, Enola, Pennsylvania, acts as a cultural origin point for my photographs. This work highlights aspects of the uncanny, the quiet, and the unfamiliar tendencies of life. These formulations usually manifest as dreamlike scenes. My work weaves these disconnected pieces into a cohesive reflection.

Methodology For Volumetric Estimation Of Condensed Water Vapor Plumes From Remotely Sensed Imagery, Ryan J. Connal

Theses

In recent years, technological developments have advanced the capabilities of computer vision techniques, including those leveraged toward 3D reconstruction with Structure-from-Motion. This process allows for the generation of accurate 3D models from sets of 2D imagery. With accurate feature detectors and matchers, Structure-from-Motion remains a widely used technique. However, the reconstruction of 3D structure is heavily dependent on the spatial characteristics of the object of interest. Fast-moving, featureless, and dynamic objects suffer from this latter issue, where standard or advanced feature detectors cannot derive any information on the object's surface. With the goal of producing three-dimensional geometric reconstructions of condensed …

Defect Detection Of Photovoltaic Panels By Image Processing, Hamad Almarzooqi

Theses

A key component of the transition towards cleaner and more sustainable power sources, driven by the global demand for such energy, has been the fast improvement in the installation of solar photovoltaic (PV) plants. Ensuring the dependability of photovoltaic panels becomes crucially important when solar installations develop in scale. Photovoltaic panels have flaws that reduce their effectiveness and shorten their lifespan, but they are durable and long-lasting otherwise. Solar plants need to work as efficiently as possible with low downtime and to want solar energy to be viable in the long run, the issues shall be fined a fixed promptly. …

Improvements To Testing And Packaging Technology For Silicon Photonics Research And Development, Eric Thornton

Theses

Silicon photonics is an emerging field that aims to integrate traditional digital CMOS logic with micro scale optical components made using silicon onto the same chip in order to overcome recent bottlenecks related to information transfer through copper interconnects. The end goal of silicon photonics is to use optical links, integrated together with modulators (devices that translate between the electrical and optical systems) controlled by traditional CMOS logic, packaged in familiar form factors, and interfaced using traditional digital serial protocols. However, groups involved in the research and development of silicon optical components do not work with these fully integrated designs …

Leveraging Machine Learning For Enhanced Lead Quality Prediction: A Case Study Of Vam Consulting, Huthayfa Nawafleh

Theses

In today's data-driven business landscape, companies are increasingly leveraging data analytics and machine learning to optimize their lead management processes and enhance customer acquisition strategies. This research focuses on the application of data analytics and the CRISP-DM methodology to improve lead quality prediction and streamline the sales funnel for VAM Consulting, a company specializing in marketing and business technology solutions. VAM Consulting has been developing customer acquisition processes and digital marketing strategies since 2016, amassing a diverse portfolio of over 300 client projects. Despite their extensive experience and utilization of various technologies, the company faces challenges in optimizing lead generation …

Predicting Student Attrition In Higher Education Institutions In The Uae Using Machine Learning, Dezzil M. Castelino

Theses

UAE has made significant progress in the field of education, including Higher Education, by attracting students from all around the world to various colleges and universities. Student dropout or attrition is a major issue that is faced by Higher Education Institutions (HEI). Hence, we need effective techniques to identify student data that affects attrition. This research aims to explore the use of machine learning algorithms to predict student attrition at Rochester Institute of Technology- Dubai (RIT Dubai). In this research, the CRISP-DM (Cross-Industry Standard Process for Data Mining) methodology was used as it is widely used in projects based on …

An Analysis Of Machine Learning Hardware From Tenstorrent, Matthew Stephen Doerner

Theses

Machine learning is growing at an exponential rate in industry today, with contemporary machine learning models having parameter counts in the high hundred millions to trillions paired with a huge computing requirement. As the field continues to grow and the models get larger and more computationally expensive, there is a greater need for specialized hardware that can accelerate the inference and training computations that are required of these machine learning models. The design of a custom hardware device specifically made to accelerate machine learning models is very intricate, with software and hardware development that needs to work together at the …

Assessment Of Culture Media Conditions For Bacteria/Macrophages Co-Cultures, Sage M. Luebbert

Chemistry & Biochemistry Undergraduate Honors Theses

Co-cultures are utilized as a tool in biology to measure immune responses to pathogens. This method involves a coordinated reaction between two populations, a bacterial biofilm of S.aureus and macrophages derived from THP-1 cells. The current state of the art prevents the continuous supply of nutrients and removal of waste products which causes macrophage death. This limits the time to collect samples and therefore the ability to measure proteins within the innate immune response. The time constraint is a major issue for long term co-culturing. This thesis aims to optimize the co-culturing process by developing a two-pump system to …

Evaluating An Integrated Science, Technology, Engineering, And Math/Computational Thinking Professional Development Program For Elementary Level Paraprofessional Educators, Aubrey A. Rogowski

All Graduate Theses and Dissertations, Fall 2023 to Present

For my dissertation, I looked at a training program one Utah school district used to teach paraprofessional educators science, technology, engineering, math, and computational thinking. Specifically, the program taught them about what computational thinking is and how they could use it when teaching science, technology, engineering, and math to students from kindergarten to sixth grade. While reviewing this program, I evaluated 1) The experiences the paraprofessionals had with the program, 2) Whether the paraprofessionals understood computational thinking, and 3) Whether the program prepared them to teach computational thinking to K-6 students.

I worked with eight paraprofessionals who participated in this …

Water Data Science: Data Driven Techniques, Training, And Tools For Improved Management Of High Frequency Water Resources Data, Amber Spackman Jones

All Graduate Theses and Dissertations, Fall 2023 to Present

Electronic sensors can measure water and climate conditions at high frequency and generate large quantities of observed data. This work addresses data management challenges associated with the volume and complexity of high frequency water data. We developed techniques for automatically reviewing data, created materials for training water data managers, and explored existing and emerging technologies for sensor data management.

Data collected by sensors often include errors due to sensor failure or environmental conditions that need to be removed, labeled, or corrected before the data can be used for analysis. Manual review and correction of these data can be tedious and …

Experimental Nonnative Wood Addition Enhances Instream Habitat For Native Fishes And Investigating Dryland River Alterations, Benjamin J. Miller

All Graduate Theses and Dissertations, Fall 2023 to Present

The rivers of the Colorado River Basin (CRB) have been degraded by human activities such flow regulation, water overallocation, and the introduction of invasive riparian vegetation (primarily tamarisk tamarix spp. and Russian olive Elaeagnus angustifolia). These stressors have resulted in widespread habitat loss and simplification, which is a major contributor to the endangerment of native fishes in the CRB.

The objectives of this study were to 1) assess the effectiveness of enhancing native fish habitat by experimentally adding cut wood from nonnative Russian olive to the San Juan River, a highly degraded dryland river, and 2) determine the …