Digital Commons Network^™

B-Spline Representations For Hyperspectral Inverse Rendering, Rachel Liang

Computer Science Theses

This work explores the use of a B-spline-based approach for hyperspectral inverse rendering from RGB images, experimenting on both spectral and geometric reconstruction. While the B-spline method is less accurate than brute-force optimization, it offers significant improvements in computational efficiency- reducing both runtime and memory usage.

Our experiments show that the B-spline representation can approximate smooth spectral data effectively but struggles with sharper spectral features unless more knots are introduced. Notably, wavelengths near the edges of the visible spectrum (around 400 nm and 700 nm) were less stable during optimization, reflecting lower convergence reliability. Despite these challenges, the final RGB …

Setting Up Students For Success: Analysis Of Effectiveness Of Mathematics Placement, Jeff Carvell, Jason Ho, David Klanderman, Sarah Klanderman

University Faculty Publications and Creative Works

How do we e!ectively and equitably place students into math classes in a way that provides them the best chance of success? As many higher education institutions veer away from placement based on standardized testing, many departments are seeking placement alternatives that will properly support students. Additionally, math placement determines not only a student’s mathematics courses but also influences their progress in related fields, including physics, chemistry, engineering, and more. This paper will describe three di!erent existing placement systems at each of our liberal arts institutions as well as the a!ordances and constraints of each approach. Further, we analyze data …

Human Endogenous Retroviruses (Hervs) Associated With Glioblastoma Risk And Prognosis, Harun Mazumder, Hui Yi Lin, Melody Baddoo, Wojciech Gałan, Diana Polania-Villanueva, Chindo Hicks, David Otohinoyi, Francesca Peruzzi, Zbigniew Madeja, Victoria P. Belancio, Erik K. Flemington, Krzysztof Reiss, Monika Rak

School of Medicine Faculty Publications

Emerging evidence suggests expression from human endogenous retrovirus (HERV) loci likely contributes to, or is a biomarker of, glioblastoma multiforme (GBM) disease progression. However, the relationship between HERV expression and GBM malignant phenotype is unclear. Applying several in silico analyses based on data from The Cancer Genome Atlas (TCGA), we derived a locus-specific HERV transcriptome for glioma that revealed 211 HERVs significantly dysregulated in the comparisons of GBM vs. normal brain (NB), GBM vs. low-grade glioma (LGG), and LGG vs. NB. Our analysis supported development of a unique HERV scoring algorithm that segregated GBM, LGG, and NB. Interestingly, lower HERV …

Sequence Conservation Of Suppressor Of Ikk Epsilon Phosphorylation Sites, Kaydence M. Isaacs

Undergraduate Honors Theses

Suppressor of IKK epsilon (SIKE) is a protein that is implicated in immune response signaling pathways. SIKE interaction networks suggest roles in cell motility and macromolecular complexes mediating kinase/phosphatase activity. In this project, we aim to better understand the function of SIKE by analyzing amino acid sequences across different species. In human SIKE, viral infection leads to phosphorylation of SIKE at defined serine residues. Comparing SIKE sequences, and specifically these phosphorylation sites, allows us to discover its ancestral connections to innate immune function. This has particular applications in bridging the evolutionary gap between fungi and metazoa SIKE sequences. Multiple sequence …

Decarbonized Shipping: Is It The Best Sustainable Shipping Solution?, Olivia Akers

Sustainable Supply Chain Management

In the era of globalization and the fourth industrial revolution, the maritime shipping industry has grown exponentially in the twenty-first century. In fact, 90% of today’s goods travel across the ocean before reaching the end consumer, meaning that ocean transportation of goods contributes significantly to overall environmental impacts on the ocean. Awareness of this impact has increased as humans strive to eliminate unsustainable practices in an effort to protect the long term health of our planet. Decarbonized shipping has been proposed as a possible solution for unsustainable shipping practices, and the goal of this chapter is to evaluate this solution …

Asymmetric, Carboxy And Ester Functionalized Fluorophthalocyanines: Synthesis, Adsorption, And Reactivity, Sean J. Scally

Seton Hall University Dissertations and Theses (ETDs)

Strong electron-deficient compounds, fluorinated metal phthalocyanines (F_xPcM), exhibit enhanced photosensitizing properties, making them optimal candidates for photocatalytic studies. Perfluoroalkyl-substituted phthalocyanines are notably thermally robust materials that are chemically inert and resistant to electrophilic, nucleophilic, and radical, including reactive oxygen species (ROS) attacks. These properties can be attributed to their ‘Teflon-like’ inert organic shield that surrounds a reactive metal center, as well as their complete (x = 16, 40, 64), or almost complete (x = 48) lack of C-H bonds. Third-generation, functionalized, asymmetric phthalocyanines are of interest due to their ability to bind to oxidic supports via a carboxyl …

Complementary Design Of Optical And Photochemical Systems, Joshua Plank

Chemistry Theses and Dissertations

The ability to manipulate chemical systems has been prized through history as the bridge between the macroscopic and microscopic worlds. As an example, the camera obscura has arguably existed since the earliest days of humanity; however, it was the discovery of early silver halide chemistry that lead to the ability to fix these images into the earliest photographs. In modern photolithography employed in electronics manufacturing, the primary resolution limits arise not from the chemistry of the molecules involved, but from the limits of the systems used to project light. Thus, as much as photochemistry advances, optical imaging and projection techniques …

Quantum Chemical Methods And Multiscale Modeling In Computer-Aided Drug Design, Hunter W. La Force

Chemistry Theses and Dissertations

Computer-Aided Drug Design (CADD) leverages a diverse toolkit of computational methods to accelerate the discovery and development of novel therapeutics. Among these, quantum chemical calculations provide unparalleled accuracy in understanding molecular interactions, albeit at a higher computational cost. This accuracy is crucial for identifying and quantifying fundamental interactions that dictate drug efficacy and selectivity, as exemplified by our investigation of ruthenium polypyridyl complexes. These metal-based compounds are model systems for studying covalent coordination bonds between ruthenium and its ligands and noncovalent interactions with DNA and protein targets. Local Mode Vibrational Theory emerges as a powerful lens within this framework, enabling …

Hybrid Graph-Recurrent Architecture For Citation Recommendation Via Future Embedding Forecasting, Mohammad Ausaf Ali Haqqani

Computer Science and Engineering Theses and Dissertations

The rapid expansion of scientific literature has intensified the challenge of identifying relevant citations, particularly for newly published or under-cited papers. Traditional citation recommendation systems typically model static relationships or respond to past citation activity, offering limited predictive power for emerging works. In response, this thesis presents a temporal modeling framework for citation recommendation that anticipates future scholarly relevance by forecasting the latent representations of academic papers.

Building on prior work that utilized Temporal Graph Networks (TGNs) to model dynamic citation flows, we propose Graph-Time, a hybrid architecture that integrates a Graph Transformer with a GRU-based time series predictor. The …

Noise-Embedded Image Processing Based On Quantum Data Encodings, Yayu Mo

Multidisciplinary Studies Theses and Dissertations

Advancements in quantum information have significantly impacted the field of image processing, although challenges remain. Especially in the edge detection and image encoding area, distorted feature and noises would affect the further classification or super resolution tasks. In our work, we conduct researches on two stages to both evaluate the potential of Quantum-based Convolutional Structure in extracting distorted feature and further explore the effects of quantum noise channels on quantum image encodings.

In the first stage, we propose a method to extract distorted edge features by applying shallow layers in quantum convolutional neural networks (QCNN). By combining the advantages of …

A Computational Method For Detecting Compound Promiscuity In Early-Stage Pharmaceutical Discovery, John Allen Ringer

Computer Science ETDs

Modern drug discovery and chemical biology research relies heavily on analyzing bioassay data. One of the many challenges in bioassay data analysis is identifying false trails, i.e., chemical compounds which initially appear to have desirable activity but are found to be problematic upon further investigation. Badapple (the BioAssay-Data Associative Promiscuity Pattern Learning Engine) was created over ten years ago to help researchers identify promiscuous compounds and thus avoid a common source of these false trails. Through an effort involving software engineering, cheminformatics, and biomedical data science we have developed Badapple 2.0, which incorporates updated assay records and expanded data semantics. …

Investigating The Microbial Communities In Freshwaters Of Northern Sweden, Maizy Wilcox

Undergraduate University Honors Capstones

Climate change is shifting the stability of sensitive ecosystems in the Arctic region due to global warming, with widespread impacts on permafrost regions, including the Stordalen Mire region of Sweden. Due to climate change, the Stordalen Mire is composed of thawing permafrost shifting into a wetland (V onk et al., 2015). As permafrost thaws, the landscape transforms due to changing water environmental conditions, causing lower pH changes and higher temperatures in the water, impacting the underlying soil chemistry and biology, vegetation, and microbial communities (Webb et al., 2022). The increased temperature can enhance methanogenic microbial growth by expanding the groundwater …

Aerial Robotic Studies Of Volcanic Co2 Emissions, John Ericksen

Computer Science ETDs

Volcanic systems are inherently complex, involving dynamic interactions among magma flow, gas emissions, and atmospheric dispersion. This dissertation focuses on developing and analyzing autonomous UAS algorithms for efficiently surveying volcanic CO2 plumes, introducing several novel methods: the LoCUS algorithm, a swarm coordination and self-healing algorithm that supports gradient-based plume tracking, a transect-based technique that employs a 2D Gaussian fit to calculate CO2 plume flux, and the Sketch algorithm for rapid plume boundary tracing. By treating multiple UAS as a single scientific instrument, these methods leverage swarm algorithms to use in-situ data in ways impossible with individual drones. Validated through simulations …

A Roadmap For Greywater Reuse At The University Of San Francisco Hilltop Campus: A Financial, Regulatory, And Technical Feasibility Study, Apama'bo Anand Oszkar

Master's Projects and Capstones

Abstract

Water scarcity is increasing in California, so we need strategies to reduce potable water demand. Decentralized greywater systems offer promising solutions to this problem. This study provides a roadmap for successfully implementing greywater reuse at the University of San Francisco (USF) by addressing financial, technical, and regulatory considerations. By deploying a mixed-methods approach that combines qualitative expert interviews and quantitative water usage analysis, policy review, cost analysis, and case studies, this study established USF’s annual recycled water demand as 8 million gallons, with two primary uses: irrigation, which accounts for 67% of the demand, and toilet-urinal flushing, which represents …

Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel

Electronic Theses & Dissertations

The growing demand for sustainable materials, driven by environmental concerns and the rapid depletion of fossil fuels, has garnered significant attention in the fabrication of bio-based epoxy thermosets as renewable alternatives to petroleum-derived thermosetting polymers. The present study focuses on the synthesis and characterization of epoxy prepolymer resins derived from limonene and geraniol via a two-step process, followed by the fabrication of thermally cross-linked flexible epoxy thermoset films using various traditional aliphatic diamine curing agents, namely 1,2-ethylenediamine (EDA), 1,4-butylenediamine (BDA), and 1,6-hexamethylenediamine (HDA). Additionally, the incorporation of cystamine, a disulfide-containing diamine, enabled the formation of a covalent adaptable network through …

Zn–Assisted Synthesis Of M (Mn/Fe/Co/Ni)-N-C Catalysts For Multifunctional Electrochemical Activity, Kemila A. Chaudhary

Electronic Theses & Dissertations

The design and development of atomically dispersed M-N-C catalysts (metal (M) supported on an nitrogen-carbon (NC) matrix with high multifunctional electrocatalytic performance is desirable but proved to be very challenging. Herein, we synthesized M-N-C catalysts (M = Fe, Co, Mn, and Ni) using Zn-assisted high temperature treatment and characterized using various techniques. The prepared catalysts were tested for their electrocatalytic performance towards oxygen and hydrogen evolution reaction (OER and HER) as well as oxygen reduction reaction (ORR) in alkaline media. The results indicated that Mn-N-C catalyst showed higher performance towards both the ORR (E_1/2 = 0.90 V) and …

Effectiveness Of Urban Composting And Waste Management In The San Francisco Bay Area, Elijah Ashiagbor

Master's Projects and Capstones

The increasing food waste epidemic contributes to environmental degradation through amplified GHG emissions, notably CH4, from MSW landfills. Addressing this challenge is essential for public health and environmental sustainability. This research reviews municipal composting initiatives within the San Francisco Bay Area, evaluating effectiveness, efficiency, and sustainability. Utilizing data from CalRecycle and local municipalities, this study analyzes different composting processes, regulatory compliance with California’s Senate Bill 1383, and factors affecting waste diversion rates. Key discoveries indicate that in-vessel composting shows better efficiency and compost quality compared to windrow methods, particularly suitable for urban counties with space limitations. However, participation rates in …

Analyzing Ballast Water Treatments, Invasive Species, And Pathogens, And A Decade-Long Analysis On The San Francisco And Baltimore Ports, Jasmin Ibarra-Cortes

Master's Projects and Capstones

Installation of advanced technologies to treat ballast water on ships is necessary to meet current ballast water management standards and reduce the secondary spread of invasive species during intracoastal voyages. This research includes a literature review on non-native aquatic species, particularly diapausing eggs, and available treatment methods for installation. A comparative analysis from 2014 - 2024 on bulker, tanker, and container vessels arriving coastwise to the ports of San Francisco and Baltimore was performed to evaluate treatment installation trends, traffic patterns, and the effectiveness of treatment(s) on targeting diapausing eggs. Use of ultraviolet (UV) radiation combined with filtration has increased …

Synthetic Data Augmentation For Retinoblastoma Using Diffusion, Andrew Thompson

Theses and Dissertations

Many AI models rely on large and high quality datasets for optimal training. In certain cases, data can be difficult or expensive to obtain, making training difficult. Rare medical conditions are one of these cases. Datasets for retinoblastoma are severely lacking in quantity. Diffusion has been used to create synthetic data in the industrial, medical, and financial domains. By applying the latest Diffusion methods to retinoblastoma, this work seeks to improve predictive model performance on identifying retinoblastoma.

Global Attractivity Of Positive Solutions Of Higher Order Nonlinear Difference Equations And Its Applications, Abdulaziz Almaslokh

Theses and Dissertations

Difference equations play an effective role in many mathematical models that represent some phenomena in different fields such as physics, economics, engineering and biology. From this perspective, studying and analyzing such equations are interesting issues for the advancement of scientific research. In particular, studying the asymptotic behavior of positive solutions of some population models that are a system of difference equations has become a necessity. In this dissertation, we examine the global attractivity of positive solutions of certain higher order nonlinear difference equations and apply these results to some population models.

A Framework For Modular Knowledge Composition In Network Intrusion Detection Systems, Patrick L. Day

Theses and Dissertations

Autonomic Intrusion Detection Systems (AIDS) are sophisticated software systems designed to autonomously and adaptively identify and respond to security threats and intrusions in computer networks or systems. One of the fundamental challenges in intrusion detection research lies in the limited availability and scope of publicly available datasets. The proposed research aims to address data-related gaps with autonomic and traditional intrusion detection systems by describing a comprehensive approach to investigate the impact and potential of data augmentation. The goal is to explore various data augmentation techniques, assess their effectiveness in introducing variability, and evaluate their impact on the performance of neural-based …

Assessment Of Water Quality And Remediation Of Heavy Metals In A Coastal System, Christiana Fumnanya Eziashi

Theses and Dissertations

This research focuses on a three-part study to assess water quality in a coastal system and evaluate the absorption capacity of modified biochar and algae to remediate cadmium (Cd). The first chapter introduces the hypothesis and objectives, and the second chapter provides a detailed literature review. The third chapter focuses on the first study, where surface water samples and water quality data collected from a manned boat and a novel autonomous surface vessel (ASV) in the Western Mississippi Sound (WMS) in the summer of 2021 and 2022 were analyzed and the interrelationship between the nutrient, trace metals, salinity, and chlorophyll-a …

From Tree Rings To Streamflow: Reconstructing The Hydroclimatic History Of The Mississippi River Basin Over The Past Millennia, Brandon Mcdaniel

Theses and Dissertations

The Mississippi River Basin (MRB), the largest watershed in the United States, plays a central role in shaping regional hydroclimate. This study reconstructs streamflow variability in the MRB from the year 1200 to 2005 by applying principal component regression to streamflow data from 51 gauges and the North American Drought Atlas (NADA), a tree-ring-based reconstruction of the summer self-calibrating Palmer Drought Severity Index. Verification statistics indicated strong predictive skill across the domain. These findings provide critical insight into long-term hydroclimatic variability in the MRB and underscore the value of paleoclimate records for improving water resource assessments.

Earth Analogue Analysis Of Volcanic/Tectonic Interactions With Applications To Venusian Stresses, Michael Ortigoza

Theses and Dissertations

Venus shares many geological similarities with Earth, yet its tectonic processes and magma injection mechanisms remain poorly understood. A key question in planetary geology is how effusive volcanism persists despite the intense horizontal compression terrestrial bodies experience over time. To explore these issues, we examine the Spanish Peaks dike swarm in Colorado which serves as an ideal site for investigating magma intrusion under compressive stress conditions. Through field mapping, orientation measurements, and structural analysis, we identify a strong relationship between pre-existing joints and dike orientations, suggesting that these fractures serve as critical magma pathways in compressive regimes. Additionally, evidence of …

Enhancing Chemical Synthesis For Sustainability And Process Monitoring Utilizing Group Ten Metal Catalysis, Amanda M. Perkins

Theses and Dissertations

This thesis explores two sustainable methodologies by modifying established catalytic processes using group ten metal complexes from nickel and palladium. Efforts were made to provide alternatives for processes that often do not follow the principles of green chemistry. In the first project, a nickel(II) N-heterocyclic carbene complex was used to perform catalytic hydrogenation of 2-acetylpyridine under mild conditions. The complex was synthesized and characterized with techniques including mass spectrometry and 1H-NMR. Following this, the reactions were carried out to optimize conditions and yield moderate conversions. For the second project, the Suzuki-Miyaura cross coupling of 7-chlorotryptophan occurred utilizing a palladium complex …

Climate Change Impacts On Drinking Water Security: A Comparative Study In Australia’S Remote Central Australia And Torres Strait Islands, Nina Lansbury, Julia Bradford, Sandra J. Creamer, Geoffrey Evans

Journal of the Australian Indigenous HealthInfoNet

Aboriginal and Torres Strait Islander communities are well adapted to the many different environments in which they have lived for thousands of years. However, their environments and communities are highly vulnerable to impacts of anthropogenic climate change, including increasing threats to the security of drinking water supplies. Climate change is intensifying the significant social and economic disadvantage Australia’s Aboriginal and Torres Strait Islander communities face from poverty, poor housing, and poor health including high exposure to infectious and other diseases. Lack of sufficient safe, clean, drinking water could force Aboriginal and Torres Strait Islander people to leave their homelands, adding …

Adverse Cognitions: The Effects Of Childhood Trauma On Brain Development, Faith Salamone

The Confluence

The effect of adverse experiences in childhood have been known to create lasting difficulties, even in adulthood. While it can be hard to determine the effects of childhood trauma on the brain, many studies have identified areas that appear to be negatively impacted by these adverse childhood experiences. This paper is a meta-analysis of eight articles that have attempted to investigate the effects of childhood trauma on the developing brain. These articles are specifically investigating the effects of childhood physical and/or sexual abuse. The areas that will be discussed in this paper are the prefrontal cortex, corpus callosum, the limbic …

Creating A Shade Tree Commission For Shamokin, Skye Sunderhauf, Beth Williams, Marques Owens, Olivia Follansbee

Final Reports in ENST 411: Environmental Community Projects

Final Project for ENST411 Environmental Community Projects

Turtle Creek Tree Restoration Project, Rebecca Beneroff, Risa Kanefsky, Max Dicerbo, Pj Newhart, Amanda Mitchell

Final Reports in ENST 411: Environmental Community Projects

Over the course of this project our group members Rebecca, Max, PJ, Amanda, and Risa worked closely with Jim Knight and Brian Auman from Turtle Creek Park to help research, plan, and execute a tree transplanting event that would be efficiently implemented and environmentally sound. This work involved extensive preparatory work in the park including soil testing, bare leaf tree identification, tree and shrub species characterization, and recommendation. The entire process was rooted in the most up to date literature and scientific practices surrounding bare root tree nurseries, existing land management plans, invasive species and public park management, ecological succession, …

Climate Change And Hydropower Development Impacts In The Lower Mekong Basin, Nudthawud Homtong

UNLV Theses, Dissertations, Professional Papers, and Capstones

The Mekong River Basin is vital to East and Southeast Asia, supporting over 60 million people and sustaining critical ecological systems. However, the basin faces dual threats from climate change and hydropower development, jeopardizing its ecological balance, hydrological patterns, and resource reliability. This research focuses on the Lower Mekong Basin (LMB), where aggressive hydropower expansion and climate variability have intensified concerns about sustainable water management. The study is divided into three interconnected parts. Part I examines spatial and temporal precipitation patterns in the Chi-Mun Basin (CMB) and Lower Mekong River (LMR) from 1950 to 2008, using linear regression and Mann-Kendall …