Engineering Commons^™

Identifying Novel Molecular Targets To Induce Ferroptosis In Drug-Tolerant Cancer Cells Through Computational Modeling, Haris J. Rana

Biological Sciences Undergraduate Honors Theses

Ferroptosis is an iron-dependent, reactive oxygen species (ROS)-driven form of regulated cell death in which the cell membrane is degraded by lipid peroxidation. It is regulated by multiple enzymes, such as glutathione peroxidase 4 (GPX4), which prevents membrane degradation by reducing lipid peroxides and protecting cells from oxidative damage. When inhibitors like RSL3 target GPX4, lipid peroxides build up, and toxic ROS compromises membrane integrity. Traditional anticancer treatments, such as most chemotherapies, aim to eliminate tumor cells by damaging DNA and triggering apoptosis. However, resistance to apoptosis is a “hallmark of cancer,” often resulting in treatment failure. As a distinct …

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, …

Multi-Domain Machine Learning For Biological Classification: Mallard Classification And Protein Function Prediction, Tolulope Samuel Adeyina

Open Access Theses & Dissertations

Multi-domain machine learning applications have revolutionized how we understand and predict complex biological phenomena. This dissertation presents novel computational methodologies addressing two critical problems: mallard classification using single-nucleotide polymorphisms (SNPs), and protein function prediction via interpretable topic-aware peptide embeddings. The research focuses on distinguishing mallard populations through SNP data, which are inherently characterized by ultra-high dimensionality. The research uses advanced feature-selection and dimensionality-reduction strategies alongside machine learning classification algorithms to identify minimal, yet highly predictive SNP sets crucial for accurate breed differentiation. This framework demonstrates robust performance with optimal computational efficiency, significantly aiding conservation and breed management efforts. Furthermore, the …

Design And Optimization Of Aquaculture Gear: Development Of A Cage-Integrated Reeling Mechanism For Oyster Farming, Felicity Bryant

Honors Theses

This project encompasses the design, fabrication, and testing of a cage-integrated reeling system aimed at reducing the physical labor required in oyster aquaculture at Bama Bay Oyster Farm, the last operational oyster farm in Mobile Bay. The proposed system includes two primary components: lightweight, modular oyster cages and a dual-winch reeling device for automated retrieval. Three cage prototypes—rectangular, oval, and hexagonal—were evaluated for structural performance and fabrication feasibility. The oval design was ultimately excluded due to practical fabrication limitations. The rectangular and hexagonal designs were fabricated using recycled materials and tested under the most extreme environmental conditions derived from years …

Metabolic Responses Of Adipose-Derived Stem Cells In Collagen I Hydrogels, Caroline R. King

Biological Sciences Undergraduate Honors Theses

Peripheral nerve injury affects approximately 44 in 1 million people in the United States every year and can lead to incomplete nerve recovery and loss of motor and sensory function. A significant amount of energy is required for nerve injury repair. A lack of energy allocation to the injury site hinders repair. Current treatments include hollow nerve guidance conduits, decellularized nerve grafts, and autografts. However, they are limited by factors such as donor site morbidity and sustained immunosuppressive treatments. Using three-dimensional collagen I hydrogels laden with adipose-derived stem cells (ASCs) can assist in neural regeneration. Three-dimensional collagen scaffolds aim to …

Ghosts In Glass: Ghost Crabs As Judges Of Glass Sand For Coastal Restoration, Emily Parrish

Honors Theses

Over 60% of the Gulf of Mexico coastline is actively eroding, which has resulted in thousands of miles of lost coastline over the last 100 years. This drastic loss of coastal land highlights the dire need for coastal restoration across the entirety of the Gulf Coast. A vital aspect of restoring these eroded areas is replenishing eroded substrate, traditionally conducted through offshore dredging of substrates which comes with high economic and ecological costs. Recycled glass sand may be able to fill this role and reduce our reliance on dredging while lowering the amount of glass waste entering landfills each year. …

A Case Study On Readiness Of Engineers In Agricultural Technology Start-Ups, Katie Marie Mowat

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

This dissertation explores the perceptions of practicing engineers regarding the skills necessary to be workforce-ready at agricultural technology (ag-tech) start-ups in the Midwestern United States. A qualitative case study methodology is leveraged, combining both interview and job description data. Given their uniqueness, the study divides the ag-tech start-up industry into two subcases: livestock and cropping systems. The Work Readiness Integrated Competence Model (WRICM) is used as the theoretical framework for this study and informs the conceptual framework and analysis processes. The study identified skills that fit into thirteen distinct categories, which are further grouped into four overarching resource groups. Skills …

Assessing Sleep Quality In A Preclinical Model Of Low Back Pain Through Novel Noninvasive Methods, Lydia C. Saltz

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Chronic low back pain (LBP) has widespread negative impacts on quality of life. Current treatments for chronic LBP fail to provide long-term efficacy and motivate the need to understand key drivers of poor patient outcomes. Mounting evidence indicates that sleep disturbances and chronic LBP have a strong reciprocal relationship. Women may be particularly vulnerable to the negative impacts of the sleep-pain axis, exhibiting greater prevalence in both conditions. However, the relationship between sleep, pain, and sex remains understudied. Preclinical models can be used to parse out characteristic sleep features that degrade with pain, which can be further broken out by …

Sustainable Agriculture Through Data-Driven Land And Soil Management For Rural Farming Communities, Peggy Clareece Discenza

Open Access Theses & Dissertations

This thesis aims to investigate sustainable farming practices by utilizing a database containing soil, weather, and water data. Additionally, it evaluates cropping strategies using a system that incorporates nutrient dynamics and environmental values. The objective is to monitor, develop predictive models, and assess the impact of both controlled and uncontrolled nutrient variables. This is achieved through the development of an algorithm that provides information on soil health based on datasets and land use, with a particular focus on residual values after harvesting for deeper analytical insights and interpretation. This study focuses on key nutrients, including pH levels, water availability, and …

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 …

A Neuroimmune Circuit Mediates Chemo Brain Pathology, Daniel Ahmadi

McKelvey School of Engineering Graduate Student Theses & Dissertations

Chemotherapeutic agents, while effective in targeting malignant tumors, often reduce the patients’ quality of life by inducing fatigue, pain, and motivational deficits. These symptoms are collectively referred to as “chemo brain.” The mechanisms underlying these adverse effects, and specifically whether fatigue and motivational impairments share a common etiology, remain poorly understood. The neural–immune substrates of these symptoms remain obscure, in part because standard preclinical regimens either bypass key systemic signals or introduce local toxicity confounds. Here, I establish and validate a three‑day, low‑dose intravenous cisplatin protocol that avoids peritoneal inflammation and severe renal injury yet produces robust, reversible fatigue and …

Mechanistic Investigation Of Ring-Opening Polymerization Of Polycaprolactone Using Tin(Ii) Catalysts: Ligand Effects And Biomedical Applications, Eva-Larue M. Barber

Honors Scholar Theses

This research explores the mechanistic aspects of ring-opening polymerization (ROP) of ε-caprolactone (CL) to produce polycaprolactone (PCL), a biodegradable polymer widely used in biomedical applications. The study investigates how light exposure and catalyst concentration influence polymerization efficiency, using tin(II) 2-ethylhexanoate [Sn(Oct)₂] as the catalyst in a non-polar toluene solvent at 90 °C. Reactions were conducted under either ambient light or black light bulb (BLB) illumination, with monomer-to-catalyst ratios of 1:1 and 200:1.

Proton nuclear magnetic resonance (¹H NMR) spectroscopy was used to analyze conversion efficiency by tracking the disappearance of monomer signals and appearance of characteristic PCL peaks. Results revealed …

Impact Of Shear Flow On Marine Biofilms Using Hyperspectral Imaging, Shantanu Mahesh Kore

All Theses

Various microbial communities in marine biofilms cause biofouling on submerged surfaces, posing challenges to marine industries. Despite their ecological and economic importance, biofilms' biomechanical and biochemical responses to hydrodynamic shear stress are insufficiently understood, particularly in dynamic flow conditions. To fill this gap, our study uses an innovative fiber-optic hyperspectral imaging (HSI) system and a supercontinuum laser source to examine marine biofilms' structure, composition, and detachment behavior at different shear stress levels.

To detect spectral and spatial heterogeneity in live biofilms without labeling, we created a custom imaging pipeline that captures reflectance spectra in the 600-850 nm range, targeting microbial …

Berm-Leveling Machine For Peach Orchards: Incorporation Of Tree-Sensing Feature And Profitability Study, Shubham Singh

All Theses

Root collar excavation extends the productive life of peach trees in Armillaria root rot-infested soil, but the process requires trees to be planted on berms. Berm-planted peach orchards restrict the mobility of workers and machinery and can lead to increased erosion in furrows on either side of the berms. The current inter-tree berm-leveling machine depends on the driver's command to dodge the peach trees. The objectives of this thesis were to (1) integrate the feeler, infrared, and LiDAR-based tree sensing systems in the berm-leveling machine to make the soil excavating head's movement independent, (2) measure the impact of finger weeder-based …

Evaluating The Role Of Electrostatic Forces In The Adsorption Of Perfluoroalkyl Substances To Granular Activated Carbon, Thomas A. Mccall

All Theses

In response to new drinking water regulations announced by the EPA in 2024, many municipalities will need to monitor concentrations and implement new treatments to address PFAS, a class of anthropogenic organic contaminants. A leading technology for this application is GAC adsorption due to its familiarity and availability. The adsorption of four PFAS species (PFBA, PFBS, PFOA and PFOS) to Calgon Filtrasorb400 (F400) was evaluated for a range of pH and ionic strength conditions to investigate the role of electrostatic interactions in adsorption capacity. These PFAS are all strong acids, so pH was used as a control for GAC surface …

Exploring Veto Activity: Dnam-1-Cd155 Axis In Overcoming Nk Cell-Mediated Allo-Rejection And Applications For Car-T Cell Therapy, Wei-Hsin Liu

Dissertations and Theses (Open Access)

As Miller et al. defined veto activity, it enables cells to target host cytotoxic T lymphocyte (CTL) precursors specific to veto cells' antigens, selectively eliminating anti- donor T cell clones without inducing rejection. By leveraging this unique immune property, two key research aims were proposed: “Exploration of the Impact of Veto Activity on Natural Killer (NK) Cell-Mediated Allo-rejection” and “Development of Off-the- shelf Chimeric Antigen Receptor (CAR)-T Therapy: Engineering Anti-Viral Veto CD8+ T Cells”. As demonstrated in our previous research, in a murine model with mild conditioning, anti-third-party central memory CD8+ veto T cells (veto Tcm) can prevent T cell- …

Toward The Application Of Natural Language Processing In Electronic Health Record Analysis For Taxonomy Development, Latoya Mcdonald

All Dissertations

Electronic health records (EHRs) are pivotal resources for nurse practice because they increase the timeliness and reliability of patient information at the point of care and support access by multiple healthcare providers and the individual patients themselves. However, it is widely recognized that data extraction from EHRs is challenging due to the variability in the language used in clinical care notes and the lack of standardized terminology across healthcare systems. The broad objective of this dissertation is to develop taxonomy-based classification models for nursing care by applying feature engineering approaches to EHRs that include nursing care of ostomy patients following …

A System And Method For Measuring Spatially Varying Surface Appearances With A Study Of Feathers, Jessica Baron-Lis

All Dissertations

Real-world materials, particularly biological structures such as feathers exhibit complex appearances that vary spatially across their surfaces. The field of computer graphics provides a means of understanding such surfaces through material modeling which uses both analytical models and data acquired from light-surface interactions. There are many efforts within the past decade in measuring materials for graphics, but common limitations in these works include not accounting for spatially varying properties and reliance on neural networks and synthetic datasets.

Feathers from modern birds present diverse appearances due to how light interacts with their unique hierarchical microstructures. Variations in those structures lead to …

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. …

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 …

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, …

Investigating The Effects Of Hepatocyte Growth Factor On Primary Myoblast Proliferation, Grace Heller

Biomedical Engineering

Peripheral artery occlusive disease (PAOD) is a progressive vascular condition that affects over 200 million people worldwide and approximately 8 million in the United States. It is characterized by atherosclerotic narrowing of peripheral arteries, leading to reduced blood flow, ischemia, and, in severe cases, tissue loss and limb amputation. Although surgical revascularization is the gold standard, many patients—particularly those with comorbidities like diabetes— continue to experience poor outcomes, emphasizing the need for alternative therapies. One promising strategy is to enhance collateral arteriogenesis, the remodeling and enlargement of collateral arterioles that naturally bypass occluded vessels. Satellite cells (SCs), which give rise …

Sustainable Smart Farming Device With Leafit Adaptive Growth Technology, Saville Atkins, Anthony Iwejuo, Julian Pitts, Luis Mercado, Rachnicha Rojjhanarittikorn, Sandip Das, Hai Ho

Symposium of Student Scholars

For farmers, gardeners, and horticulture enthusiasts worldwide, one immutable reality is that maintaining a consistent physical presence to care for plants is not always feasible. In addition, different plants have unique needs for watering, nutrients, and environmental conditions to thrive. Failing to meet these specific needs can result in poor plant health, reduced yields, and inefficient resource usage. In this research project, we have designed and developed ‘LeaFit’ – a cutting-edge Internet of Things (IoT) device that offers a sophisticated and sustainable smart farming and gardening solution. Equipped with intelligent soil moisture, ambient temperature, humidity, and light sensors, LeaFit autonomously …

Enhanced And Interpretable Prediction Of Multiple Cancer Types Using A Stacking Ensemble Approach With Shap Analysis, Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Zhongming Zhao

Faculty, Staff and Student Publications

Background: Cancer is a leading cause of death worldwide, and its early detection is crucial for improving patient outcomes. This study aimed to develop and evaluate ensemble learning models, specifically stacking, for the accurate prediction of lung, breast, and cervical cancers using lifestyle and clinical data.

Methods: 12 base learners were trained on datasets for lung, breast, and cervical cancer. Stacking ensemble models were then developed using these base learners. The models were evaluated for accuracy, precision, recall, F1-score, AUC-ROC, MCC, and kappa. An explainable AI technique, SHAP, was used to interpret model predictions.

Results: The stacking …

Analysis Of Differentially Expressed Genes (Deg) And Upstream Regulator Proteins Indicates That Inhibition Of Transforming Growth Factor Beta 1 (Tgfb1) Is A Potential Target For Acne Inversa, Weri Veranita, Siva Fauziah, Siti Nurbaya

Indonesian Journal of Medical Chemistry and Bioinformatics

Acne inversa (AI) is a chronic inflammatory skin disease characterized by painful nodules, abscesses, and scarring, primarily in intertriginous areas. This study aims to identify potential therapeutic targets for managing acne inversa based on the analysis of differentially expressed genes (DEG). The expression targets of these genes were then validated for their potential as biomarkers, and upstream regulator proteins (URPs) were identified from the resulting DEG. DEG analysis on the GEO dataset GSE122592 (acne inversa vs. healthy donor skin) revealed five DEG that can serve as biomarkers for acne inversa, with a sensitivity and specificity of (100%). These DEG—IL10, GZMB, …

04.21.2025 Ored Connect, Liz Williamson

ORED Newsletter

ORED Stakeholder Meetings

SEC Travel Grants

Field Calibration Of A Time Domain Reflectometry Sensor For Water Content Measurement In Soils With Low Content Of Coarse Fragments, Rehnuma Maisha, Dean Steele, Aaron L. M. Daigh, Derek M. Heeren, Trenton E. Franz

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Comparison of soil water sensors for irrigation scheduling requires an accurate reference measurement. An Acclima TDR-310H soil water content sensor was calibrated and validated for sand, loamy sand, clay loam, sandy clay loam, and sandy loam soils. In 2021, sensor readings and soil samples were collected in the same sensor volume at depths of 15 and 46 cm at three irrigated field sites with five stations each. Gravimetric water content, bulk density, and volumetric water content (θv) were determined in the lab. The root mean square error was 0.032 cm³ cm⁻³, which was within acceptable limits. The …

Durability And Steel Corrosion Resistance Of Fly Ash Concrete Exposed To Groundwater, Mohamed Ahmed Bayomy, Khaled M. Osman, Hala Emad Elden Fouad

Mansoura Engineering Journal

This article proposes replacing Ordinary Portland Cement (OPC) with a fly ash (FA)-based geopolymer (GP) material, activated by a chemical activator, as the binding material. A 90-day study was conducted to evaluate the performance of fly ash geopolymer concrete (GPC) in a corrosive environment (groundwater). Scanning electron microscopy (SEM), compression testing, and energy-dispersive X-ray spectroscopy (EDX) were used to assess the toughness of the samples. Additionally, the linear polarization resistance (LPR) method was employed to measure the corrosion of steel embedded in the concrete structures. The comparison shows that increasing the fly ash (FA) content in geopolymer concrete (GPC) enhances …

Research Week 2025, Michael Schueth

Research Week

Welcome to Undergraduate Research Week at Collin College!

This week celebrates the innovative research and scholarly work of our undergraduate students across all disciplines. From our informative webinars to Cultivating Scholars, our student poster presentation, the week offers opportunities to explore new ideas, share discoveries, and connect with fellow researchers and faculty mentors.

We invite all students, faculty, and staff to participate in these events designed to highlight the importance of undergraduate research in academic and professional development. Whether you're presenting your work or simply curious about your peers' projects, your engagement helps foster our college's culture of inquiry and …

04.14.2025 Ored Connect, Liz Williamson

ORED Newsletter

Updated CITI Training Courses

Science Celebration

IHL Prepayment Approval