Digital Commons Network^™

Compartmental Disaggregation: Bridging Simulation And Sampling Methods For Synthetic Population Data Generation, Dylan Mack

McKelvey School of Engineering Graduate Student Theses & Dissertations

As agent-based models (ABMs) grow increasingly widespread in public health, their associated challenges have become all the more significant. Lauded for their ability to capture population heterogeneity, nonlinear dynamics, and emergent behaviors, disease ABMs are also computationally expensive and often require detailed inputs that describe each agent at the individual-level, known as synthetic population data. Current approaches for synthetic population data generation generally fall into one of two categories: sampling or simulation. These methods are both feasible only under restricted conditions and suffer from challenges surrounding data availability and computing power. This thesis proposes compartmental disaggregation, an intermediate method for …

Predicting Which Genes Will Respond To Transcription Factor Perturbation, Eric L. Jia

McKelvey School of Engineering Graduate Student Theses & Dissertations

A fundamental issue in mapping regulatory networks between transcription factors and their target genes is the poor overlap between the set of genes bound by a given transcription factor (TF), and the set of genes that are differentially expressed after knocking out or overexpressing the same TF. We began with the hypothesis that to predict whether a gene will respond to perturbation of a TF, it is important to not only consider whether that TF is bound at the gene’s promoter, but also whether other TFs bind at the same promoter.

In this work, we propose a novel modeling procedure …

Locked Dimerized Cxcl12 Exerts Radiosensitizing Effects In Head And Neck Cancer, Oscar Villarreal Espinosa, Musaddiq Awan, Abdullah A. Memon, Anne Frei, Jamie Foeckler, Rachel Kuehn, Jennifer Bruening, Becky Massey, Stuart J. Wong, Monica Shukla, Julia Kasprzak, Amit Joshi, Michael B. Dwinell, Heather A. Himburg, Joseph Zenga

Biomedical Engineering Faculty Research and Publications

Background

Head and neck squamous cell carcinoma (HNSCC) presents significant treatment challenges, particularly in cases unrelated to human papillomavirus (HPV). The chemokine receptor CXCR4, interacting with its ligand CXCL12, plays a crucial role in tumor proliferation, metastasis, and treatment resistance. This study explores the therapeutic potential of engineered monomeric and dimerized CXCL12 variants (CXCL121 and CXCL122, respectively) in HNSCC and evaluates potential additive effects when combined with radiation therapy.

Methods

Clinical HNSCC biopsies were evaluated for CXCR4 expression in both previously untreated and radiorecurrent disease. HNSCC cell lines were then treated with combinations of CXCL12 variants and radiotherapy and interrogated …

Trends In And Factors Associated With Science Achievement Among Eighth Graders In Saudi Arabia: A Secondary Analysis Of Timss Data, Roba Alzahrani

Theses and Dissertations

This secondary analysis examined trends in and factors influencing science achievement among eighth-grade students in Saudi Arabia, using data from the Trends in International Mathematics and Science Study (TIMSS). However, Saudi Arabia's performance on the TIMSS science assessments fell below the international average, from 2003 through 2019. In addition, gender differences in science achievement have been observed, with female students outperforming male students by 30 or more points. This study addresses two problems: factors associated with the lower performance of Saudi students on TIMSS science assessments compared to global standards, and the small number of studies which explored factors which …

Game Changing Education: Empowering High School Stem Teachers To Teach Engineering Using Games, Leslie Brown

All Graduate Theses and Dissertations, Fall 2023 to Present

In response to the Next Generation Science Standards (NGSS) released in 2013, there was a nationwide push for K-12 schools to include engineering concepts in science classrooms. However, there is an overall lack of teacher preparedness and training towards engineering topics as shown by common engineering misconceptions. To improve this issue, I initiated a qualitative study to describe the strategies and attitudes of high school science, technology, engineering, and mathematics (STEM) teachers that have implemented game-based, engineering activities into their classroom. Game-based learning is an instructional framework that utilizes game-like elements in a classroom and was used in this study …

Strategies For Increasing Methane Removal In Methanotroph Bench-Scale Systems For The Production Of Ectoine, Jaden Storrer

All Graduate Theses and Dissertations, Fall 2023 to Present

Anthropogenic methane emissions contribute to the greenhouse gas profile which is the chief cause of climate change. One significant source of methane emissions is biogas produced from bacteria in wastewater facilities and landfills. Methane rich biogas has the potential to be valorized into high value bioproducts by using methanotrophs (microbes that use methane as their primary carbon source). Methylotuvimicrobium alcaliphilum 20Z was selected for this study as it can generate ectoine when grown in highly saline environments. Ectoine has been proven to have many benefits such as it prevents protein denaturation, it has hydration properties, and is a UV protectant. …

Aerobic Biodegradation Of Algae-Derived Bioplastics Under Controlled Composting Conditions, Clayton J. Lords

All Graduate Theses and Dissertations, Fall 2023 to Present

Plastics are versatile polymers that have become critically important materials in many industries. Although plastics are important and useful materials, they account for vast amounts of environmental pollution and climate change contribution. Sustainable bioproducts are becoming increasingly important in the effort to mitigate the impacts of pollution and climate change. The scale of environmental damage caused by plastic pollution highlights the need to implement sustainably sourced biodegradable plastics within the global economy. Bioplastics are materials that may be manufactured from biological materials or can biodegrade under certain conditions. Algae are microorganisms that can be grown using nutrient-rich municipal wastewater; the …

Analyzing Microalgae-Bacteria Population Changes In Response To Environmental Parameters For Improved Wastewater Treatment, Amanda M. Moravek

All Graduate Theses and Dissertations, Fall 2023 to Present

Microalgae are incredible organisms that have a variety of uses such as wastewater treatment, fertilizer, livestock feed, and bio-compound production. Microalgae require a light source and minimal nutrients space to proliferate, making them an environmentally friendly and sustainable option for such processes. The Sustainable Wastes-to-Bioproducts Engineering Center at Utah State University is developing and implementing a Rotating Algae Biofilm Reactor (RABR) to remove total nitrogen and phosphorous from the Central Valley Wastewater Reclamation Facility wastewater effluent. Harmful compounds such as nitrates and phosphates are metabolized by the microalgae and converted into useful bioproducts, resulting in a circular economy. These RABRs …

Water Use By Irrigated Turfgrass And Connections To Climate And Biophysical Processes, Karem Meza

All Graduate Theses and Dissertations, Fall 2023 to Present

Urbanization and limited water supply and storage result in imbalanced urban water budgets. Quantification of water use becomes important in urban landscapes because urban turfgrass requires a significant amount of water and competes with other urban requirements. Evapotranspiration (ET) plays a crucial role in determining irrigation needs. Credible measurements and spatial estimates of urban turfgrass ET are needed for urban water management. However, these have not been addressed in urban landscapes in arid and semiarid regions. Despite estimating spatial urban turfgrass ET, turfgrass quality linked to ET has not been widely evaluated. Due to different environmental conditions, the driving forces …

Effects Of Light Intensity On Algae Biofilms In Rotating Algae Biofilm Reactors (Rabr), Joshua D. Wintch

All Graduate Theses and Dissertations, Fall 2023 to Present

There is a growing need for economically and ecologically friendly wastewater treatment processes. Utilizing natural algae biofilms to remediate excess nitrogen and phosphorus from municipal wastewater is a treatment technique of academic interest. Utilizing natural algae in rotating algae biofilm reactors (RABR) is a potential engineering application of algae biofilms for municipal wastewater anaerobic digestor effluent treatment. The ideal reactor operation would use sunlight as the light source for algae growth, however, there is little academic research on algae biofilm growth productivity across natural sunlight light intensity ranges. This research seeks to understand the relationship between rotating algae biofilm reactor …

Uv-A Light And Heat-Activated Antimicrobial And Biodegradable Materials For Food Packaging And Preservation, Michael J. Bodily

All Graduate Theses and Dissertations, Fall 2023 to Present

Current food packaging materials are often non-biodegradable and harmful for ingestion, which poses a threat to the environment and public health. Thus far, the dangers of microbial contamination of food on human health have outweighed the risks associated with using these conventional packaging plastics. A possible solution to these issues is to use a combination of innovative materials and microbial inactivation methods that can potentially both reduce plastic waste and combat harmful microorganisms. In this study, two antimicrobial, biodegradable composites were developed and tested for their ability to inactivate two types of bacterium, Escherichia coli K12 and Listeria innocua, …

Critical Analysis Of Coursework And Internship Experience In Relation To Biological Engineering At The University Of Arkansas, Samantha Wheat

Biological and Agricultural Engineering Undergraduate Honors Theses

My internship allowed me to gain important experience about a possible future career path with a biological engineering degree. Not only did this experience apply knowledge learned in the classroom from classes taken, I was also able to use my critical thinking skills gained from biological engineering coursework and teaching style to learn new skills and efficiently complete tasks given to me. This internship allowed me to try out a possible career path that interested me, and through my internship experience I was able to learn more about what kind of career path I was interested in after graduation. Additionally, …

Effects Of Sensor Separation On Flux Calculations In The Eddy Covariance Method., Maria D. Vergara Murillo

Biological and Agricultural Engineering Undergraduate Honors Theses

Rice production contributes approximately 8% of global anthropogenic methane emissions. Methane (CH₄) is a powerful greenhouse gas with a global warming potential 28 times greater than carbon dioxide (CO₂) which makes it important to monitor for understanding and mitigating its contribution to climate change. The Eddy Covariance (EC) method is used to monitor greenhouse gas emissions such as CO₂, CH₄, etc. As part of the EC method, the instruments on the EC towers are used to record the gas concentrations in the atmosphere; these concentrations are then run in the EddyPro software …

Flowermd: A Flexible Library Of Organic Workflows And Extensible Recipes For Molecular Dynamics And Machine-Learned Coarse-Grained Simulations Of Isotropic And Anisotropic Systems, Marjan Albooyeh

Boise State University Theses and Dissertations

Molecular dynamics (MD) simulations are essential tools for understanding and predicting material behavior at the atomic and molecular scale. While numerous open-source software packages exist for different stages of MD simulations, assembling a seamless, end-to-end workflow for complex multi-step simulations remains a significant challenge. In this work, we develop FlowerMD, a flexible and extensible Python-based software package that automates molecular simulation workflows, improving both reproducibility and ease of use.

FlowerMD provides modular components that simplify the end-to-end execution of MD workflows, from system initialization and force field application to simulation execution. It also automates multi-step simulation workflows through Recipes—predefined, modular …

Influence Of Terrain Model Resolution On Rockfall Dispersion And Tortuosity Of Rockfall Paths, Lucas Jason Arsenith

Boise State University Theses and Dissertations

The geology of the Snake River Plain region of southwestern Idaho contains terraces formed from downcutting of the Boise River and columnar jointed basalt cliffs from lava flows. Within the city limits of Boise, Idaho, rockfall events originate from these columnar jointed basalt cliffs. Whitney Terrace, a rockfall-prone location in southwestern Boise, was chosen as the study site. Site-specific LiDAR data was used to create a bare earth terrain model, and rockfall boulders were geolocated and measured to be used as inputs into rockfall models. The slope below the cliff face was divided into four distinct slope zones, each with …

Development And Application Of Computational Tools For Organic Molecular Structure Prediction From Small Molecule Crystal Structure Determination To Polymer Persistence Length, Madilyn E. Paul

Boise State University Theses and Dissertations

This dissertation utilized two areas of computational simulations for organic molecular structure prediction. First, we investigate the possible polymorphism of both barbituric acid dihydrate (BTADH) and violuric acid monohydrate (VAMH) using density functional theory. Crystalline structures that exhibit polymorphism have an increased level of uncertainty in predicting their chemical and physical properties. BTADH was previously thought to undergo a subtle phase transition from P2₁/n to planar Pnma at 217 K. We conclude that barbituric acid dihydrate exhibits crystalline disorder in which the molecules are crystallized in a non-merohedrally twinned P2₁/n configuration below …

Flexible Microelectrode-Based Impedance Immunosensor For Rapid Detection Of E. Coli O157:H7, Sonatan Kumar Biswas

Graduate Theses and Dissertations

Abstract Food contamination poses a significant threat to public health, the economy, and human health worldwide, occurring at any stage of the food supply chain, from farm to fork. Escherichia coli 0157:H7, recognized as one of the principal causes of foodborne illness, poses a considerable risk to food safety. The primary objective of this investigation is to devise a flexible microelectrode-based immunosensor capable of swiftly identifying E. coli O157:H7 cells without the need for incubation in a pure culture environment. In the development of the biosensor, the gold electrode (composed of 50% Au) underwent an initial coating process involving 2-aminoethanethiol/cysteamine, …

Exploration Of Polymorphic Gate-Based Watermarking In Asynchronous Circuits, Stephanie Stock

Graduate Theses and Dissertations

With the increasing demand for new state-of-the-art integrated circuits (ICs), intellectual property (IP) reuse has become more commonplace to both accelerate the design process and lessen the non-recurring engineering costs of a design. Reuseable IP poses significant security risks, not only to the creator of the IP, but also to the consumer purchasing the IP. For an IP vendor, this risk can come from illegal distribution, cloning, or overuse. For the purchaser, counterfeit IPs may be purchased from an unvetted vendor, leading to a substandard design, malfunctions, IP infringement, or security vulnerabilities. Hardware watermarking is a method to protect designers …

Using Deep Learning And Two-Photon Excitation Fluorescence Microscopy To Predict Breast Cancer Recurrence And Response To Chemotherapy, Nicholas Powell

Graduate Theses and Dissertations

Accurate prediction of breast cancer recurrence plays a critical role in guiding treatment decisions, particularly regarding the use of systemic therapy for patients. While genomic assays such as the Oncotype DX Recurrence Score offer valuable prognostic information, they are limited in accessibility and application. The work presented in this thesis explores an imaging-based approach for the prediction of breast cancer recurrence that combines multiphoton microscopy (MPM) with deep learning to classify individual breast cancer biopsy samples by risk of recurrence. Genomic differences in tumors with different recurrence potentials may translate to distinct optical and structural information that can be captured …

Involvement Of Long Non-Coding Rna (Lncrna) Malat1 In Shear Stress Regulated Adipocyte Differentiation, Justin Caron, Marjan Ghanbariabdolmaleki, Madison Marino, Chong Qiu, Bo Wang, Michael Mak, Shue Wang

Biomedical Engineering Faculty Research and Publications

Adipocyte differentiation plays an important role in bone remodeling due to secretory factors that can directly modulate osteoblast and osteoclast, thus affecting overall bone mass and skeletal integrity. Excessive adipocyte differentiation within the bone marrow microenvironment can lead to decreased bone mass, eventually causing osteoporosis. The mechanical microenvironment of bone marrow, including fluid shear, maintains the balance of adipocyte and osteoblast differentiation during bone remodeling. However, how mechanical cues interact with long noncoding RNA (lncRNA) and regulate adipocyte differentiation remains unexplored. In this study, we investigated the mechanosensitive role of lncRNA MALAT1 during mesenchymal stem cells (MSCs) adipocyte differentiation. By …

Kinetic Growth Rate Analysis Of Coelastrella Sp. In Aquaculture Wastewater., Rob Skarvan

Master of Engineering Theses

The demand for sustainable food and energy production continues to rapidly rise. Utilizing aquaculture wastewater as microalgae growth medium is a potential opportunity for nutrient recycling and industrial symbiosis, but more research is required to understand how best to design and scale-up a dual-purpose facility. This study investigates the growth of Coelastrella sp. in aquaculture wastewater compared to industry-standard growth medium BG-11 and modified tap water as controls. Though cell size and pigment density varied throughout media, aquaculture wastewater performed very comparably to BG-11 as a microalgae culture broth.

The Monod equation can model Coelastrella sp. growth based …

Minimizing Secondary Spinal Cord Injuries With Hypertonic Saline., Francisco A. Cortez-Thomas

Master of Engineering Theses

Spinal cord injury (SCI) disrupts white matter, causing periaxonal swelling, axonal degeneration, and impaired function. To examine vascular edema’s role, we developed a 3Dprinted dual-compartment imaging chamber to mimic and manipulate interstitial and vascular fluid dynamics in real time. We hypothesized that hypertonic saline (HTS) in the "vascular" chamber would osmotically shift fluid from the periaxonal space and preserve myelinated fibers after SCI. Using two-photon excitation microscopy, we imaged myelin and axons ex vivo in Thy1^YFP+ transgenic mice following C5 contusive SCI and assessed three clinically relevant HTS concentrations versus normal saline for their effectiveness in mitigating periaxonal swelling …

Fabrication And In Vitro Biocompatibility Assessment Of Composite-Coated Magnesium Materials, Bryce Williams

Biomedical Engineering Undergraduate Honors Theses

This study provides a comparative assessment of the corrosion, morphology, and biological properties of four of the most promising coating methods for magnesium in biomedical applications, namely micro-arc oxidation (MAO), graphene oxide (GO)-containing MAO coating, MAO/sol-gel composite coating, and MAO/polycaprolactone (PCL) polymer dip coating approaches. Despite the abundance of research focused on these promising approaches, there is a notable lack of comparative studies evaluating their properties. To this end, the investigated composite coatings are ZK60+MAO, ZK60+MAO/GO, ZK60+MAO/Sol-gel, and ZK60+MAO/PCL composite coating. Several tests were used to assess various properties of the prepared groups such as in vitro corrosion characteristics, surface …

In Vitro Investigation Of Macrophage Functional And Metabolic Modulation, Shelby Nicole Bess

Graduate Theses and Dissertations

Macrophages are a subset of immune cells with a variety of functions that are abundant in numerous tumor types such as colorectal and breast cancer. It has been suggested that macrophages may serve an important function as immune mediators in tumor behavior; however, macrophage activity is complex and remains not completely understood. The overall goal of this dissertation was to explore and exploit tumor-associated macrophage phagocytic function and the changes in their interactions with cancer cells in an in vitro mouse model and in 2D and 3D in vitro culture models. First, we wanted to better understand macrophage behavior under …

Preclinical Development Of Genome Editing To Treat Duchenne Muscular Dystrophy By Exon Skipping, Made Harumi Padmaswari, Shilpi Agrawal, Christopher E. Nelson

Biomedical Engineering Faculty Publications and Presentations

Duchenne muscular dystrophy (DMD) is caused by loss-of-function mutations to the gene encoding dystrophin. Restoring the reading frame of dystrophin by removing internal out-of-frame exons may address symptoms of DMD. Therefore, the principle of exon skipping has been at the center stage in drug development for Duchenne muscular dystrophy (DMD) over the past two decades. Antisense oligonucleotides (AONs) have proven effective in modulating splicing sites for exon skipping, resulting in the FDA approval of several drugs using this technique in recent years. However, due to the temporary nature of AON, researchers are actively exploring genome editing as a potential long-term, …

Enhancing Patient Safety: Exploring Virtual Sitters' Role In Fall Prevention Through Remote Virtual Monitoring, Adama Diallo, Awatef Ergai Dr., Leeanna Spiva Dr., Meriel Mccollum Dr.

Symposium of Student Scholars

Remote Virtual Monitoring (RVM) technology enhances safety for both patients and care teams by reducing falls, improving the efficiency and effectiveness of continuous patient observation, and lowering costs associated with falls and staff support. The success of fall reduction efforts largely depends on the role of virtual sitters, individuals who remotely monitor high-risk patients to prevent falls. This study aims to explore the experiences of virtual sitters, identifying key themes, challenges, and opportunities to improve the intervention. Specifically, the research investigates how technology, work shifts, and institutional support impact the effectiveness and job satisfaction of virtual sitters.

Investigating The Impact Of Waterhead, Time And Temperature On Dam Displacement: Application Of Computer Aided Models, Maaz Abdullah

AUIQ Technical Engineering Science

Dam displacement is a crucial indicator for assessing the safety of a concrete dam through structural health monitoring. Since the displacement data exhibits a non-linear and complex relationship with influencing factors like waterhead, time and temperature, machine learning models are deployed to accurately predict dam displacement. Furthermore, the limited availability of monitored data in the majority of the dams renders the studies conducted with a large number of observations valueless. In order to address the aforementioned issues, this study proposes a feature selection approach to predict dam displacement by examining the ability of four ensemble machine learning models on different …

Surface Urban Heat Island Effects Analysis In The Most Populated City In Thailand: Towards Sustainable Urban Development, Abdul Maulud Khairul Nizam, Muhammad Noor, Zafar Iqbal

AUIQ Technical Engineering Science

The fast and unprecedented urban growth process may violate cities' responsibilities by causing an urban heat island (UHI) and increasing the public's risk of heat-related illnesses due to vegetative area reduction and urban area inclination. The Bangkok Metropolitan Area (BMA)'s variations in Land Use Land Cover (LULC), Land Surface Temperature (LST), UHI, and several geospatial indicators, as well as the daytime and nighttime LST, are the main subjects of the study. Between 2015 and 2021, the highest Daytime LST (DLST) rose consistently from 36.77°C to 38.14°C, then slightly decreased to 37.22°C in 2023. There is a general increase in the …

A Comprehensive Review Of Advancements In Materials And Manufacturing For 3d Knee Implants, Huda Ali Hashim, Ghaidaa A. Khalid

AUIQ Technical Engineering Science

Over the past three decades, knee implant design has significantly advanced to address the challenges of replacing damaged knee joint bone with durable and efficient prosthetics. The aim of this review explore key developments in materials and manufacturing processes, focusing on biocompatible options such as zirconium, titanium alloys, UHMWP, and smart materials, as well as coatings designed for metal-sensitive patients. The study examines the mechanical forces acting on implants during daily activities, highlighting wear and infection risks, and evaluates the role of innovative manufacturing techniques in improving implant precision, cost-efficiency, and durability. Simulation methods, including Finite Element Analysis (FEA), are …

Wide Band Single-Mode Optical Fiber Design For Decreasing Bending Loss, Zahraa M. Kassem Alasady, Ahmed Al-Amiery

AUIQ Technical Engineering Science

Radiation loss due to fiber curving or bending is a major challenge in advanced technical applications like fiber-optic sensing or biomedical applications. This study focuses on the basic features that characterize a single-mode fiber (SMF) and its critical parameters in view of the recent improvements made. The planned design of SMF is, however, intended to resolve these problems by proposing minimizing bend loss by adopting a five-layer fiber structure designed to keep the optical field within the fiber core. The proposed SMF design exhibit ultra-low bending sensitivity, with estimated bending loss of 2×10-3 dB/turn for bending radius of 5 mm. …