Physical Sciences and Mathematics Commons^™

Chicken Keypoint Estimation, Rohit Kala

Computer Science and Computer Engineering Undergraduate Honors Theses

Poultry is an important food source across the world. To facilitate the growth of the global population, we must also improve methods to oversee poultry with new and emerging technologies to improve the efficiency of poultry farms as well as the welfare of the birds. The technology we explore is Deep Learning methods and Computer Vision to help automate chicken monitoring using technologies such as Mask R-CNN to detect the posture of the chicken from an RGB camera. We use Meta Research's Detectron 2 to implement the Mask R-CNN model to train on our dataset created on videos of chickens …

A Survey And Comparative Study On Vulnerability Scanning Tools, Cassidy Khounborine

Computer Science and Computer Engineering Undergraduate Honors Theses

Vulnerability scanners are a tool used by many organizations and developers as part of their vulnerability management. These scanners aid in the security of applications, databases, networks, etc. There are many different options available for vulnerability scanners that vary in the analysis method they encompass or target for which they scan, among many other features. This thesis explores the different types of scanners available and aims to ease the burden of selecting the ideal vulnerability scanner for one’s needs by conducting a survey and comparative analysis of vulnerability scanners. Before diving into the vulnerability scanners available, background information is provided …

Developing A Multi-Platform Application To Facilitate Internal Campus Hiring, Carissa Patton

Computer Science and Computer Engineering Undergraduate Honors Theses

Undergraduate research has proven to be highly beneficial to students, yet there are many students who do not know how to get involved or who are too timid to approach professors to inquire about potential research opportunities. Our hypothesis is that a cross-platform application has the potential to bridge the gap and help more students get involved in undergraduate research by providing them information about open positions and the faculty or staff members who are mentoring the projects. The key focus of this thesis is to develop an application that provides details about participating faculty or staff including their research …

Characterization Of 2d Quantum Materials Using Ai And Large-Scale Quantum Data Collection, Apoorva Bisht

Computer Science and Computer Engineering Undergraduate Honors Theses

2D materials like hexagonal boron nitride, graphene, and tungsten diselenide are widely utilized for studying their unique mechanical and opto-electronic properties to exploit them to make transistors and fabricating a variety of other devices. All these applications require that the 2D materials used be of specific uniform thickness. Until very recently, this process has been largely manual and tedious. However, few applications exploit the characteristic color-to-thickness correspondence of these near-transparent materials. To continue this effort, in this work we create a large-scale dataset for three different materials (hBN, graphene, and WSe$_2$) to train and test an image segmentation model along …

Universal Computation Using Self-Assembling, Crisscross Dna Slats, Jackson S. Bullard

Computer Science and Computer Engineering Undergraduate Honors Theses

I first give a brief introduction to formal models of computation. I then present three different approaches for computation in the aTAM. I later detail generating systems of crisscross slats given an arbitrary algorithm encoded in the form of a Turing machine. Crisscross slats show potential due to their high levels of cooperativity, so it is hoped that implementations utilizing slats are more robust to various growth errors compared to the aTAM. Finally, my software converts arbitrary crisscross slat systems into various physical representations that assist in analyzing their potential to be realized in experiments.

Testing The Interaction Between A Substellar Companion And A Debris Disk In The Hr 2562 System, Stella Yimiao Zhang, Gaspard Duchêne, Robert J. De Rosa, Megan Ansdell, Quinn Konopacky, Thomas Esposito, Eugene Chiang, Malena Rice, Brenda Matthews, Paul Kalas, Bruce Macintosh, Franck Marchis, Stan Metchev, Jenny Patience, Julien Rameau, Kimberly Ward-Duong, Schuyler Wolff, Michael P. Fitzgerald, Vanessa P. Bailey, Travis S. Barman, Joanna Bulger, Christine H. Chen, Jeffrey K. Chilcotte, Tara Cotten, René Doyon, Katherine B. Follette, Benjamin L. Gerard, Stephen Goodsell, James R. Graham, Alexandra Z. Greenbaum, Pascale Hibon, Li Wei Hung

Astronomy: Faculty Publications

The HR 2562 system is a rare case where a brown dwarf companion resides in a cleared inner hole of a debris disk, offering invaluable opportunities to study the dynamical interaction between a substellar companion and a dusty disk. We present the first ALMA observation of the system as well as the continued Gemini Planet Imager monitoring of the companion's orbit with six new epochs from 2016 to 2018. We update the orbital fit, and in combination with absolute astrometry from GAIA, place a 3σ upper limit of 18.5 M J on the companion's mass. To interpret the ALMA observations, …

Trace Dna Detection Using Diamond Dye: A Recovery Technique To Yield More Dna, Leah Davis

Master's Theses

This study aspires to find a new screening approach to trace DNA recovery techniques to yield a higher quantity of trace DNA from larger items of evidence. It takes the path of visualizing trace DNA on items of evidence with potential DNA so analysts can swab a more localized area rather than attempting to recover trace DNA through the general swabbing technique currently used for trace DNA recovery. The first and second parts consisted of observing trace DNA interaction with Diamond Dye on porous and non-porous surfaces.

The third part involved applying the Diamond Dye solution by spraying it onto …

Partitioning And Microdosimetry Of Plutonium-239 And 55-Iron In Environmental Bacteria Grown In Liquid Cultures, Lisa Manglass

All Dissertations

The work presented herein provides quantitative data related to bacteria exposed in situ to two radionuclides relevant to nuclear sensing: plutonium-239 (²³⁹Pu) and iron-55 (⁵⁵Fe). Originally motivated by the fundamental science underlying biosensing, liquid cultures of Pseudomonas putida and Escherichia coli were exposed to radionuclides over the course of 15-day experimental periods with the intent of gaining insight into the response of these bacteria. An essential component of characterizing or utilizing this response in a meaningful way is an understanding of the dose leading to that response. This dissertation narrows the knowledge gap associated with dose-response …

Characterizing Metabolic Activity Of Fish Liver Microsomes Towards Fluoxetine In Four Fish Species Using Michaelis-Menten Enzyme Kinetics, Morgan Steiner

Honors College Theses

Discharge of pharmaceuticals into the environment is of emergent concern due to the unknown long-term effects on aquatic organisms. Wastewater treatment plants are not effective in completely removing pharmaceuticals, allowing them to be discharged into aquatic systems. To investigate the potential effects of fluoxetine, a common antidepressant, on aquatic species, the potential of four freshwater fish species to metabolize this drug was investigated. Livers from redbreast sunfish, bluegill, striped jumprock and bluehead chub were collected, homogenized, and centrifuged to collect the microsomes. These microsomes were used in an assay to determine the in vitro hepatic metabolism of fluoxetine by cytochrome …

Music Mentor, Jacob Webb

Honors College Theses

Extra-curricular learning is on the rise, and many are interested in expanding their current knowledge by utilizing the recent increase in educational technology. While many forms of educational technology exist, there are few interactive and engaging platforms that teach music theory. Apps such as Perfect Ear and MyMusicTheory are great for becoming familiar with reading music and recognizing pitches, however, they often become dry with repetition and repeated tasks. By combining existing technologies that can complete real time conversions from raw audio to MIDI, our goal was to gather information such as harmonies, key and compatible chords from the user’s …

Long-Time Stability For An Imex Discretization Of The 1d Fujita Equation, Victoria Luongo

Honors College Theses

We study an efficient time-stepping scheme for the 1D Fujita equation that is implicit for the linear terms but explicit for the nonlinear terms. We analyze the long-time stability of the scheme for varying parameter values, which reveal parameter value regimes in which the method is stable. We provide numerical results that illustrate the theory and show the analytically derived stability conditions are sufficient to achieve long-time stability results.

Building Community Resiliency Against Disasters, Zachary L. Doering

Undergraduate Honors Thesis Collection

Disasters impact people in many different places around the world. The impact to communities by disasters is shaped by their constructed vulnerability. The goal of this research project was to better understand how the vulnerability and resiliency of different communities was shaped at six different sites across the U.S. and to construct a collection of best practices to raise the resiliency of populations and locations in the face of many different forms of possible disasters in the future. These concepts and conclusions were drawn from internet research of the chosen sites. Phase 1 of the research determined noteworthy sites and …

Design, Modeling, And Simulation Of Secure X.509 Certificate Revocation, Sai Medury

Masters Theses and Doctoral Dissertations

TLS communication over the internet has risen rapidly in the last seven years (2015--2022), and there were over 156M active SSL certificates in 2022. The state-of-the-art Public Key Infrastructure (PKI), encompassing protocols, computational resources, and digital certificates, has evolved for 24 years to become the de-facto choice for encrypted communication over the Internet even on newer platforms such as mobile devices and Internet-of-Things (IoT) (despite being low powered with computational constraints). However, certificate revocation is one sub-protocol in TLS communication that fails to meet the rising scalability demands and remains open to exploitation. In this dissertation, the standard for X.509 …

Numerical Evaluation Of Wavenumbers Of The Acoustic Waves Propagating In An Ice-Covered Ocean, Mohammad Khan

Masters Theses and Doctoral Dissertations

We consider acoustic wave propagation in a layered ocean waveguide covered by thick ice. The standard method of separation of variables leads to a Sturm-Liouville problem in the crosssection of the waveguide. We are specifically interested in the two leading modes, the separated solutions for the maximal eigenvalues. We first consider the homogeneous waveguide. We prove the differentiability of the eigenvalues with respect to the frequency, the monotonicity of the eigenvalues with respect to the frequency, and the existence of the cut-off frequency. We compare these eigenvalues with the eigenvalues for the case of a waveguide with a free surface. …

Representations Of Time In Time-Based Media: An Exploration Of The Human Experience Of Temporality In Film And Tv, Nelea Fong

Honors Thesis

Time is an aspect of the human experience that fascinates us but eludes our understanding. Humans have turned to science, philosophy, and theology in our endeavor to understand time, but our shared love and history of storytelling drives us to explore temporality through visual medias that have a structural foundation in time. Expanding our understanding of the human experience of time through time-based media such as movies and TV can point us toward comprehending various forms of time and how each person can perceive said time differently. Using film and TV theory, informed by scientific and philosophical explorations in the …

Caspi: Collaborative Photon Processing For Active Single-Photon Imaging, Jongho Lee, Atul Ingle, Jenu V. Chacko, Kevin W. Eliceiri, Mohit Gupta

Computer Science Faculty Publications and Presentations

Image sensors capable of capturing individual photons have made tremendous progress in recent years. However, this technology faces a major limitation. Because they capture scene information at the individual photon level, the raw data is sparse and noisy. Here we propose CASPI: Collaborative Photon Processing for Active Single-Photon Imaging, a technology-agnostic, application-agnostic, and training-free photon processing pipeline for emerging high-resolution single-photon cameras. By collaboratively exploiting both local and non-local correlations in the spatio-temporal photon data cubes, CASPI estimates scene properties reliably even under very challenging lighting conditions. We demonstrate the versatility of CASPI with two applications: LiDAR imaging over a …

Toward Digital Phenotyping: Human Activity Representation For Embodied Cognition Assessment, Mohammad Zakizadehghariehali

Computer Science and Engineering Dissertations

Cognition is the mental process of acquiring knowledge and understanding through thought, experience and senses. Based on Embodied Cognition theory, physical activities are an important manifestation of cognitive functions. As a result, they can be employed to both assess and train cognitive skills. In order to assess various cognitive measures, the ATEC system has been proposed. It consists of physical exercises with different variations and difficulty levels, designed to provide assessment of executive and motor functions. This thesis focuses on obtaining human activity representation from recorded videos of ATEC tasks in order to automatically assess embodied cognition performance. Representation learning …

Treatment Planning Automation For Rectal Cancer Radiotherapy, Kai Huang

Dissertations & Theses (Open Access)

Background

Rectal cancer is a common type of cancer. There is an acute health disparity across the globe where a significant population of the world lack adequate access to radiotherapy treatments which is a part of the standard of care for rectal cancers. Safe radiotherapy treatments require specialized planning expertise and are time-consuming and labor-intensive to produce.

Purpose:

To alleviate the health disparity and promote the safe and quality use of radiotherapy in treating rectal cancers, the entire treatment planning process needs to be automated. The purpose of this project is to develop automated solutions for the treatment planning process …

Nitroalkane Oxidase Inspired No-Transfer Agents, No Sensors, And The Computational Design Of Fluorescent Sensors, Thanh Thuy Thi Vuong

Chemistry & Biochemistry Dissertations

Flavin adenine dinucleotide and flavin mononucleotide are co-enzymes with biologically relevant redox potentials. They are involved in many chemical transformation processes in the biological system, such as one-electron and two-electron transfer reactions, dehydrogenase reactions, and intramolecular electron transfer reactions critical to cellular function. Their ability to be reoxidized under aerobic conditions has inspired us to investigate biomimetic transformations with their derivatives, especially in converting NO2 to NO. Besides that, a series of biosensors was designed and investigated to detect NO in the aqueous system. NO sensors were achieved with computational DFT calculations correctly predicting the fluorescence response.

Epimeric Peptides In Alzheimer’S Disease: Implications For Liquid Chromatography-Mass Spectrometry And Immunotherapies, Elizabeth Readel

Chemistry & Biochemistry Dissertations

Evidence has shown that the extracellular deposition of amyloid-beta (Aβ) peptide is a contributing factor of Alzheimer’s disease. Further, modifications to Aβ peptides may enhance the deposition of Aβ plaques and/or contribute to the neurodegeneration in AD patients. These aberrations include the isomerization and epimerization of L-Asp and D-Ser residues to form D-Asp, L/D-iso-Asp, and D-Ser residues, respectively. Therefore, considerable effort has been expended to create effective methods to distinguish such aberrant Aβ peptides from wild type. A useful technique to extract aberrant Aβ peptides in AD patients is by immunotherapies, or antibodies. A few immunotherapies are thought to provide …

An Investigation Of Peak Shape Models In Chiral Separations, Ryan Jacob Burk

Chemistry & Biochemistry Theses

The use of superficially porous particles in chromatography has led to significant improvements in separation efficiency. However, peak asymmetry in enantiomeric separations causes performance comparisons across particle types a challenge. In this study, we screened 28 pharmaceutically relevant compounds and developed practical methods to reduce peak asymmetry in normal phase chiral chromatography. The use of additives was found to be effective in reducing peak tailing for all compounds, including neutrals. Additionally, we observed that solvent mismatch with the eluent can cause system peak interference, which can be managed by reducing injection volumes. To more accurately assess the performance of the …

Differentiating Biotic Vs. Abiotic Co2 In The Formation Of Pedogenic Carbonate In Agriculture And Natural Dryland Soils, Valeria Isabel Molina

Open Access Theses & Dissertations

Drylands, characterized by low and sporadic precipitation, require irrigation for crop growth. However, irrigation practices can lead to salt accumulation in soil due to high evaporation rates and reduced leaching. In addition to loading salts to soil, irrigation promotes the accumulation of secondary calcite. In natural systems, the formation of pedogenic carbonate (secondary calcite, CaCO3) is critical, impacting the soil properties hydrologically and biogeochemically, and modifying the global carbon cycle over geological time, albeit at a lower rate. In agricultural sites, irrigation water supplies HCO3- and Ca2+, accelerating the rates of CaCO3 formation and releasing abiotic CO2. This study investigated …

Incorporating Community Science In Improving Environmental Data Quality Through Model Based Reasoning Techniques, John Gilbert Olgin

Open Access Theses & Dissertations

This dissertation will address the questions: In what ways can MBR theory be applied to designtraining that will improve the capacity of Citizen scientists to collect and analyze high quality scientific data? To what degree does this training impact their ability to formulate complex understandings of environmental problems in their Citizen? The project will be comprised of three research objectives focused in three sections, carried out with NASAâ??s GLOBE Observer Citizen Science Program:

Section 1: An analysis of existing GLOBE data will be conducted, identifying whereerrors in data collection originate. At least three principal errors will be selected from this …

Analyzing Software Maintenance Through Machine Learning And Mining Software Repositories Approaches, Sayed Mohsin Reza

Open Access Theses & Dissertations

The rapid growth of software systems demands meticulous planning and maintenance to accommodate the evolution of the code base over extended periods. Without maintenance, software systems will become more complex, low in quality, and hence unsustainable. Software engineers who perform maintenance often strive to optimize code quality or minimize code smells in a timely manner. Several techniques have been used to detect code quality or code smells as a part of software maintenance. Most of these techniques are based on heuristics, which create detection rules using a few metrics. These approaches have reasonable accuracy but do not work in cross-project …

Modeling And Predicting Emerging Threats Using Disparate Data, Ismael Villanueva Miranda

Open Access Theses & Dissertations

Early detection is crucial to mitigate the impact of emerging threats. This work proposes four innovative frameworks that build machine learning and deterministic epidemiological models using multiple domain-specific datasets to detect the onset of emerging threats in two domains: infectious diseases and cybersecurity. Our models are designed to detect infectious disease outbreaks, model their spread, detect malware activity, and analyze the relationship between software/hardware weaknesses and attack techniques.

First, we present a novel framework to detect multiple infectious disease outbreaks by integrating standardized disease-specific domain knowledge and public search trend data. Our framework showed high performance in identifying infectious disease …

Recursive Forms For Determinant Of K-Tridiagonal Toeplitz Matrices, Eugene Agyei-Kodie

Open Access Theses & Dissertations

Toeplitz matrices have garnered renewed interest in recent years due to their practical applications in engineering and computational sciences. Additionally, research has shown their connection to other matrices and their significance in matrix theory. For example, one study demonstrated that any matrix can be expressed as the product of Toeplitz matrices \citep{ye2016every}, while another showed that any square matrix is similar to a Toeplitz matrix \citep{mackey1999every}.

Numerous studies have examined various properties of Toeplitz matrices, including ideals of lower triangular Toeplitz matrices \citep{dogan9some}, matrix power computation with band Toeplitz structures \citep{dogan2017matrix}, and norms of Toeplitz matrices. Moreover, the use of …

Likelihood Inference For Flexible Cure Models With Interval Censored Data, Jodi Treszoks

Mathematics Dissertations

Models for survival data with a surviving fraction, known as cure rate models, play a vital role in survival analysis. Due to the improvement of intervening methodologies, some subjects are seen to be immune permanently. While cure rate models have been studied extensively in the recent literature with a standard assumption of right-censored data, in many applied settings, such as recidivism studies or medical studies where the event of interest is not immediately harmful, continuous observation of a subject is impracticable. We call lifetime data generated with discrete follow-up times as interval-censored. In this thesis, we extend several existing cure …

Another Shipment Of Six Short-Period Giant Planets From Tess, Joseph E. Rodriguez, Samuel N. Quinn, Andrew Vanderburg, George Zhou, Jason D. Eastman, Erica Thygesen, Bryson Cale, David R. Ciardi, Phillip A. Reed, Ryan J. Oelkers

Physics and Astronomy Faculty Publications and Presentations

We present the discovery and characterization of six short-period, transiting giant planets from NASA’s Transiting Exoplanet Survey Satellite (TESS) -- TOI-1811 (TIC 376524552), TOI-2025 (TIC 394050135), TOI-2145 (TIC 88992642), TOI-2152 (TIC 395393265), TOI-2154 (TIC 428787891), and TOI-2497 (TIC 97568467). All six planets orbit bright host stars (8.9 <G < 11.8, 7.7 <K < 10.1). Using a combination of time-series photometric and spectroscopic follow-up observations from the TESS Follow-up Observing Program Working Group, we have determined that the planets are Jovian-sized (R_P = 0.99--1.45 R_J), have masses ranging from 0.92 to 5.26 M_J, and orbit F, G, and K stars (4766 ≤ T_eff ≤ 7360 K). We detect a significant orbital …

Self-Consistent Effects Of The Recirculating Plasmapshere On The Development Of Storm Time Dynamics In The Inner Magnetosphere., Christian-Andrew Bagby-Wright

Physics Dissertations

The near Earth space environment is a highly coupled system. The Interplanetary Magnetic Field (IMF) interacts with the magnetosphere in myriad ways depend on the orientation of the IMF to the magnetosphere. The magnetic fields of the magnetosphere and the IMF trap plasma and carry the plasma with it as both magnetic fields evolve over time. This plasma can in turn interact with other plasmas, carried by other field lines, affecting the dynamics of the other population and the magnetic field lines of both populations. The nature, frequency, and importance of interactions between different plasma, or magnetic fields, varies greatly …

Boundaries And Currents Of The Dayside Magnetosphere: Mhd Simulations And Observations, Pauline Marie Dredger

Physics Dissertations

The solar wind streams through space at supersonic speeds, carrying plasma and the interplanetary magnetic field (IMF) from the sun. Earth’s magnetosphere presents a magnetosonic obstacle to the solar wind flow, which slows down suddenly, creating a bow shock. Between the bow shock and Earth’s magnetic field is the region of space called the magnetosheath, which contains the dense plasma and turbulent IMF of the shocked solar wind. The magnetopause is the boundary between the magnetosheath and the region of near-Earth space dominated by the terrestrial magnetic field; its location is determined by the competing pressures of the plasma in …