Biological Engineering Commons^™

Comparative Performance Of Physiological Vital-Sign Forecasting Under Random And Patient-Wise Splitting Using Deep Learning, Lavanya Vasavi Chittem Reddy

Theses and Dissertations

Physiological vital-sign forecasting estimates future measurements based on recent temporal patterns and can support analysis of continuously recorded monitoring data. This study comparatively evaluated deep feedforward, recurrent, bidirectional recurrent, long short-term memory, and bidirectional long short-term memory architectures for one-step-ahead forecasting of peripheral oxygen saturation, heart rate, and pulse rate. Each model received consecutive observations of peripheral oxygen saturation, heart rate, pulse rate, respiratory rate, and age, while separate single-output models predicted the next value of the selected target.

Random and patient-wise data splitting were compared using identical input definitions, preprocessing procedures, model architectures, and training hyperparameters. The strongest architecture …

Probe Cytotoxic And Oxidative Stress Effects Of Nanoplastics On Caco-2 Cells: Insights From Raman Spectroscopy And Machine Learning, Bryan Gustafson, Negar Kosari, Emily Brothersen, Morgan Mosher, Anhong Zhou

Biological Engineering Student Research

Nanoplastics and microplastics have become an increasing ecological and health concern due to their widespread presence in the environment and food chain. In this study, Caco-2 cells were used as an in vitro model of the human intestinal epithelium to investigate the cytotoxic effects of polystyrene nanoparticles and microparticles of varying sizes, concentrations, and surface modification. Oxidative stress and apoptosis were evaluated following particle exposure. Raman spectroscopy, combined with machine learning analysis, was employed to detect and characterize biochemical alterations in the cells. Several peak ratios were selected to cluster data depending on size. A correlation between apoptosis and both …

Enhancing Algae Biofilm Quantity And Value Through Controlled Light Intensity For Treatment Of Municipal Anaerobic Digestor Effluent, Joshua D. Wintch, Ronald C. Sims

Biological Engineering Student Research

Rotating algae biofilm reactors (RABRs) have been shown to remove nutrients from wastewater and to cultivate algae for bioproducts. Another key variable in RABR technology for cultivating microalgae biomass is light intensity. The goal of this study was to address a gap in the design and operation of algae biofilm reactors by analyzing the effects of light intensity on biomass quality and quantity, chemical precipitation of phosphorus, and phosphorus uptake into biomass. This study utilized a triplicate laboratory-scale experiment with PAR intensities from 10 to 2000 µmol m⁻²·s⁻¹. Municipal wastewater anaerobic digester effluent (ADE) was utilized …

A Functional Ultrasound Imaging (Fusi) Pipeline For Investigating Brain-Wide Hemodynamics During Torpor-Like Hypothermia, Owen J. Culver

McKelvey School of Engineering Graduate Student Theses & Dissertations

Torpor is a regulated state of reduced metabolic demand that enables animals to conserve energy under unfavorable environmental conditions. The controlled induction of a similar state, termed synthetic torpor, has potential applications in ischemic protection, organ preservation, cancer treatment, radiation protection, and long-term spaceflight. Although neuronal populations within the preoptic hypothalamus have been shown to initiate hypothermic and hypometabolic states, the distributed cerebral hemodynamic dynamics accompanying their induction and maintenance remain poorly understood. In this thesis, we developed an accessible functional ultrasound imaging (fUSI) acquisition and analysis pipeline and applied it to investigate cerebral hemodynamics during chemogenetic activation of the …

Isolation, Identification, And Enzymatic Screening Of Fungi From Utah Dryland Soils For Industrial And Waste Valorization Applications, Jessica Lorena Silva Cuero

All Graduate Reports and Creative Projects, Fall 2023 to Present

Agricultural waste accumulation presents environmental challenges but also opportunities for biological valorization into value-added products. Fungi are particularly well-suited for this purpose due to their capacity to produce extracellular enzymes involved in the degradation of complex organic substrates. Dryland ecosystems represent a promising source for bioprospecting microbes capable of producing such enzymes. Drylands harbor a high diversity of extremophilic microorganisms that can withstand harsh conditions, extreme heat, UV, and low nutrients using unique adaptations. This suggests that these microbes are resilient and capable of surviving under varying conditions and still produce enzymes for biotransformation. The objective of this study was …

Cadmium Biosorption By Fusarium Venenatum And Its Application In Functional Permeable Materials For Metal Removal, Bradley Lawson

All Graduate Theses and Dissertations, Fall 2023 to Present

Heavy metals are pollutants of increasing concern as continued industrialization and urbanization have escalated the discharge of these toxins into aquatic environments. Cadmium (Cd) is a metal of particular concern due to its acute toxicity and high mobility in aquatic ecosystems. Given these characteristics Cd poses significant health risks to both humans and aquatic ecosystems. The continued development of sustainable, low-cost remediation technology is imperative to manage metal pollution.

This research explores the use of fungal-based remediation systems to remove Cd from contaminated water. Living biomass of the filamentous fungus Fusarium venenatum was evaluated as a biosorbent material for Cd …

Fluorescence Cryotomography For Preclinical Validation: Applications In Gene Therapy And Fluorescence-Guided Surgery, Caleb Y. J. Kwon

Dartmouth College Ph.D Dissertations

Fluorescence imaging has become a powerful tool in biomedical research and clinical practice, offering molecular specificity and high sensitivity for visualizing biological processes in real time, However, the successful translation of novel fluorescent probes or medicines from preclinical development to clinical applications requires rigorous validation of their biodistribution and target specificity. Traditional methods for assessing performance, such as bulk excised organ analysis or two-dimensional histology, provide limited information as they cannot capture the complete, organism-wide distribution of these probes or medicines. This thesis aims to improve this analysis pipeline through the application and optimization of fluorescence cryotomography for quantitative, high-resolution …

A Computational Micropatterning Approach To Study Caveolae And Protein Localization In Vascular Biology, Andrew B. Grespin

Electronic Theses and Dissertations

Caveolae are specialized, flask-shaped membrane invaginations highly expressed in endothelium and dysregulated in atherosclerosis. Caveolae play a central role in buffering membrane tension, yet the principles governing their spatial organization remain elusive. Thus, we sought to generate the most comprehensive and systematic analysis of blood vessel caveolar spatial organization. However, cell culturing, the backbone of human-focused biological research, does not standardly do well to model physiologically relevant cell behaviors such as migration or polarity-based tissue formation, particularly for punctate proteins and structures like caveolae. Micropatterns are cell-adhesive shapes that biophysically confine cell(s) to a user defined geometry which stereotype organelle …

Design And Characterization Of A Pulsed Electric Field Chamber For Microalgae Lysis, Connor Strutin

Electrical Engineering

Microalgae are a promising renewable source of biofuel due to their high lipid content and rapid growth rates; however, algae cells must be electroporated (lysed) to release these lipids. The system developed in this project applies short (40 μs–10 ms), high-intensity (up to 33 kV/cm) pulsed electric fields (PEF) across cell membranes to enable electroporation.

Our lab-scale PEF chamber generates uniform, high-intensity electric fields using parallel-plate electrodes with sub-millimeter spacing. The system is designed to efficiently lyse microalgae cells for lipid extraction and biofuel production.

High-Throughput Robotic Ethanol Inhibition Assays For Engineered Thermophilic Biofuel Strains, Kevin He, Daniel Olson, Marybeth Maloney, Anthony Lanahan

Wetterhahn Science Symposium Posters

Ethanol stress assays are commonly used to evaluate microbial tolerance, metabolic adaptation, and fermentation performance. However, manual liquid handling introduces variability across replicate wells and small-volume pipetting steps, limiting reproducibility and throughput. This study developed an automated OT-2 robotic workflow to generate replicated ethanol concentration gradients for high-throughput inhibition assays in engineered thermophilic biofuel strains. Kinetic plate-reader measurements were used to quantify ethanol-dependent growth responses under anaerobic fermentation conditions. The reasearch question is: How do engineered thermophilic biofuel strains differ in ethanol-dependent growth inhibition under anaerobic fermentation conditions, and can automated robotic assays improve the reproducibility of these measurements? Can …

Characterizing Stiffness Dynamics Of Normal And Malignant Breast Spheroids Using Brillouin Microscopy, Razanne Rafat Zaghloul, Karlin Hilai, Chenjun Shi, Jitao Zhang

Medical Student Research Symposium

Background: Breast cancer progression and metastasis are closely linked to alterations in the mechanical properties of tumor cells and their microenvironment. Softer, more deformable cells are often associated with higher metastatic potential. While atomic force microscopy (AFM) is the current gold standard for mechanical characterization, it is limited to surface measurements and can damage 3D cultures. It remains unclear how the mechanical properties evolve over time in normal versus malignant spheroids. This study utilizes Brillouin light-scattering microscopy, a non-contact and label-free optical technique, to assess stiffness changes in normal and malignant breast epithelial spheroids over time. Understanding these mechanical signatures …

Agentic Scientific Machine Learning For Autonomous Model Discovery In Systems Pharmacology, Nazanin Ahmadi, George Karniadakis

Biology and Medicine Through Mathematics Conference

No abstract provided.

Central Pattern Generator Test Bench Report, Stephanie Wing-Yee Lee, Dustin Wong, Joseph Hernandez

Electrical Engineering

The project presents the design, fabrication, and implementation of a PCB test bench that interfaces with a custom VLSI chip designed to emulate the neural activity of a Central Pattern Generator (CPG). The test bench provides a precise and reliable platform for supporting signal operations and validating neuromorphic functionality. The design integrates both analog and digital circuitry to provide stable biasing, signal routing, and measurement access for chip characterization. The incorporation of op-amp buffers and adjustable potentiometers enables precise voltage tuning, resulting in controlled neuron-like behavior within the custom IC. The two-layer PCB supports modular interfacing with standard laboratory instruments …

Developing Warning Signage For Harmful Algal Blooms At Lake Fayetteville, Abigail R. Evans

Biological Sciences Undergraduate Honors Theses

The presence of harmful algal blooms (HABs) poses many risk factors for human health, and once microcystin concentration has reached a certain level, that water source will be closed for the duration of the bloom. Agencies tend to use static signage with limited information to inform the public about the current status of the water, but a sign similar to the one used by the National Fire Danger Rating System can allow for constant updates detailing specific risk levels for the public. Using previously reported data on Lake Fayetteville, thresholds for risk factors that are easily measurable were determined. The …

Beyond Local Pathology: Exploring The Role Of Gut Microbiota In Chronic Low Back Pain Using An Integrated Behavioral And Microbiological Approach, Adan L. Redwine

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

Chronic low back pain (LBP) affects millions worldwide, often originating from intervertebral disc (IVD) degeneration. While the gut microbiome modulates musculoskeletal pain, prior studies of the gut-disc axis have focused entirely on structural changes. This leaves a critical gap: does the microbiome influence the experience of discogenic pain? To answer this, an integrated approach using longitudinal gut microbiome profiling, machine learning-based behavioral phenotyping, and structural disc assessments in a rat model of discogenic LBP was utilized.

Female Sprague Dawley rats underwent one of four conditions: sham surgery, IVD injury, antibiotic-mediated microbiome depletion + IVD injury, or IVD injury + treatment …

Fluorescence-Based Quantification Of Hepatic Ldl Uptake And Donor Hepatocyte Engraftment Using Atto 700–Labeled Ldl, Victor Agustin Cortes Flores

All Theses

Familial hypercholesterolemia (FH) is an inherited disorder characterized by elevated low-density lipoprotein cholesterol (LDL-C) that increases the risk of premature atherosclerotic cardiovascular disease. In severe FH, including low-density lipoprotein receptor (LDLR), hepatic LDL clearance is profoundly impaired and many lipid lowering treatment strategies have limited effectiveness. Current advances in ex vivo CRISPR–Cas9 hepatocyte gene editing in vivo and ex vivo approaches for treatment of FH are under development.

However, a central barrier to translation is the ability to quantitatively measure the percentage of healthy gen edited hepatocytes in the liver while simultaneously assessing functional hepatic LDL handling. This thesis establishes …

Retrospective Analysis Of Implemented Project Management Within A Small-Scale Student Engineering Project: Beng Fountain Wars Team Case Study, Holli E. Jenkins

Biological and Agricultural Engineering Undergraduate Honors Theses

This honors thesis provides a retrospective analysis of how the 2025 inaugural University of Arkansas’s ASABE Fountain Wars Student Team could be improved through project management. Project commitment, early stakeholder influence, rich communication, and a detailed project plan are all attributes of successful projects, and the team’s strengths and weaknesses within these categories were determined through a team poll. After the poll was conducted, three methodologies, Agile, Hybrid, and Waterfall, were assessed to determine how they would effectively address the team’s weaknesses. A weighted objectives table was created to compare each methodology’s effectiveness across the management categories. The analysis revealed …

Monitoring Streambank Morphology Using Iphone Lidar Technology, Lily C. Stitt

Biological and Agricultural Engineering Undergraduate Honors Theses

Monitoring stream morphology is crucial for maintaining the health and safety of fluvial environments, particularly as these naturally dynamic systems are shifted out of equilibrium due to climate and land-use change. Quantifying changes in stream geometry are useful for infrastructure design, water quality assessment, water resource management, and stream restoration, among other applications. Traditional stream surveying methods contain numerous cost limitations that inhibit affordable and accessible stream surveying needed for evaluating stream geometry with high accuracy and larger spatial scales (>100s of ). In recent years, several advancements have been made in the use of Light Detection and Ranging …

Application Of Microbial Fuel Cells For Leachate Bioremediation: The Effects Of Nutrient Nourishment, Umi Sholikah, Fidela Chosta, Tegar Palyus Fiqar, Eka Masrifatus Anifah, Riza Hudayarizka, Tadashi Hibino

Makara Journal of Science

Leachate contains a high organic content, which can cause environmental pollution. The organic content in leachate can be removed through bioremediation using microbial fuel cell (MFC) systems to remediate pollutants and generate bioelectricity. Organic matter is important to the MFC process as both a substrate and a nutrient source. This study investigated the effects of glucose and sodium phosphate buffer nourishment on BOD, COD, and TSS removal and bioelectricity generation. This study used leachate as a substrate and a graphite rod with a surface area of about 32.98 cm² as an electrode. The reactor uses plastic blocks with a …

The Impact Of Human Myoblasts On Macrophage Polarization In A Coculture Model, Elisabeth Ann Stodola

Biomedical Engineering

Peripheral Artery Disease (PAD) is characterized by the buildup of atherosclerotic plaque in the lower extremities that occludes blood flow, and affects over 200 million people worldwide. Without effective treatment, PAD can lead to claudication, ischemia, ulcers, and gangrene. PAD causes more amputations in the United States than any other condition, and for severe cases that require revascularization, procedures benefit fewer than 50% of patients. This demonstrates a clear need for alternative therapies. Potential therapies for PAD target expansion of collateral blood vessels around the area of occlusion – a process called arteriogenesis to compensate for loss of blood flow …

Design And Validation Of A Wearable Respiratory Protection System For Wildland Firefighters, Oliver Pilon

Master's Theses

Wildland and Wildland–Urban Interface firefighters are routinely exposed to hazardous smoke with fine particulate matter, carbon monoxide, volatile organic compounds, and other toxic combustion products. Existing protective gear has significant limitations and shortcomings for these conditions. Respirators with tight-fitting facepieces make it difficult to breathe and speak. On the other hand, self-contained breathing apparatuses are too heavy, have a limited duration of use, and do not work well with long wildland fire scenes, while smaller protective equipment like N-95’s and gaiters provide very little protection. These constraints contribute to low adoption rates and prolonged occupational exposure.

This thesis presents the …

Jaundease Phototherapy Vest Test Plan, Sujay Panthulu, Jasdev Banwait, Gwynn Moss, Solomon M. Fernandez

Biomedical Engineering

Neonatal hyperbilirubinemia is a common condition affecting more than 60% of newborns, caused by an excess buildup of bilirubin in the blood due to the liver’s limited ability to process it efficiently [1]. The standard treatment involves hospital-based phototherapy, where infants are placed in incubators under blue light to break down bilirubin in the skin. Although effective, this approach requires infants to remain under the lights for 12–18 hours per day, often with eye protection, and separated from their parents—disrupting early bonding and potentially contributing to toxic stress that can impact neurological and emotional development [2]. While at-home phototherapy solutions …

Raw Data Files Contributing To "Changes In Apoe And Timp-1 Expression Correlate With Outer Blood-Retinal Barrier Disruption In An In Vitro Model Of Retinal Aging", Elizabeth Vargis

Browse all Datasets

Age-related macular degeneration (AMD) is a leading cause of blindness worldwide. Unfortunately, the early stages of this disease are poorly understood, which has led to limited treatment options. Investigating normal changes in tissues eventually affected by AMD can further elucidate the mechanisms of disease progression and lead to novel therapeutic targets. The primary cell layer affected in AMD is the retinal pigment epithelium (RPE), which forms the outer blood-retinal barrier (oBRB). Beneath the RPE lies Bruch’s membrane, a proteinaceous layer that naturally thickens and stiffens with age. These changes to Bruch’s membrane are also implicated in RPE dysfunction and AMD …

Stentrx, Emma Barna, Minuthi Cooray, Bruce Newlands, Joseph A. Sabetta

Williams Honors College, Honors Research Projects

This project aims to develop a biodegradable, drug-eluting biliary stent for the treatment of biliary cancers. Current metal stents that restore bile flow bit are non-degradable, prone to migration, and unable to deliver drugs locally. The proposed stent will be biocompatible, biodegradable, and capable of controlled drug release to both maintain bile flow and treat tumors. The end goal is to produce a functional prototype that can be deployed via a minimally invasive catheter and maintain bile duct patency for at least three months. The project is expected to be involved in the NEOMED Bench-to-Bedside competition and provisionally patented.

Bioprinted Scaffolds For Investigating Fibroblast Alignment, Lillian Thro, Daeha Joung Ph.D.

Undergraduate Research Posters

Fibroblasts play a vital role in tissue repair, ECM remodeling, and maintaining structural integrity in human tissues. However, their behavior in engineered 3D microenvironments remains poorly understood. Traditional 2D cultures fail to capture the complex cell-cell and cell-matrix interactions that govern fibroblast alignment, migration, and proliferation in vivo. To address this gap, this project uses bioprinted scaffolds that mimic native ECM structures and provide a platform for studying fibroblast behavior in controlled microenvironments. The project focuses on varying scaffold channel properties—such as width, depth, and geometry—to investigate how physical cues influence fibroblast organization and collective migration. A biodegradable gelatin-based ECM …

The Role Of Laminin Isoforms In Glioblastoma Migration, Aseel Ahmed, Faezeh Ghobadi, Hanna Devillier, Qi Cai

Distinguished Undergraduate Researcher Program

Glioblastoma (GBM) remains the most prevalent and lethal invasive brain tumor, denoted by a median survival of 12-15 months despite standard procedures such as safe surgical resection, radiotherapy, and chemotherapy. This limited effectiveness largely arises from the infiltrative nature of GBM cells, which interact with the brain’s extracellular matrix (ECM) by migrating along blood vessels and axonal pathways. The ECM contains the interstitial matrix (IM) and the
basement membrane (BM) made up of proteins and glycans which interact with the malignant cells. While research has mainly been focused on understanding how GBM cells interact with IM components, our knowledge about …

The Healing Power Of Nanoparticles: Bioengineering Gelatin Films With Lignin-Graft-Plga Nanoparticles For Enhanced Tissue Repair, Marie Howe, Cristina Sabliov, Thanida Chuacharoen, Willyam Nikiema

Distinguished Undergraduate Researcher Program

Fish gelatin, a biocompatible material, can be methacrylated to enable its photo-crosslinking and formation of hydrogels for tissue-repair applications (1). This study investigated the incorporation of lignin-grafted PLGA nanoparticles (LNPs) into 3D-printed fGelMA hydrogels as controlled drug delivery systems. Lignin has UV absorbing properties, which could potentially interfere with photocrosslinking of fGelMA (2). These LNPs possess hydrophobic PLGA core and hydrophilic lignin forming the shell providing ample opportunities for delivery of drugs of different chemistries (3). Fluorescent LNPs (FLNPs) were engineered by covalently bonding a fluorophore to the shell prior to nanoparticle synthesis to allow for fluorophore tracking. The understanding …

Probing Proficiency-Related Neural Representations With Pca And Ica, Onila R. Narayana Mudalige Don

Graduate Student Theses, Dissertations, & Professional Papers

How proficiency-related information is represented in task fMRI depends not only on the data themselves, but on the representational lens used to summarize them. This thesis examines second-language (L2) proficiency as a problem of representational organization rather than as a simple classification exercise. Using task fMRI from adult language learners performing semantic animacy judgments in their native language (L1) and second language (L2), I derive shared low-dimensional network representations with principal component analysis (PCA) and independent component analysis (ICA), then evaluate those representations under matched leakage-controlled decoding pipelines.

Across analyses, the central comparison is between representational frameworks rather than between …

De Novo Protein Binding To Zinc Oxide Through Biomineralization Pathways, Jean-Mark A. Francis

Theses and Dissertations

De novo proteins are structurally distinct from proteins found in nature and thus capable of having their amino acid sequence modified to accomplish tasks such as increasing protein-nanoparticle binding without unfolding or decomposing. Zinc Oxide nanoparticles are functionally distinct from their bulk counterparts and are widely used as semiconductors in a variety of fields such as medicine and agriculture. With demand for these nanoparticles increasing, environmentally sustainable methods of Zinc Oxide nanoparticle synthesis are being investigated as an eco-friendly alternative to currently utilized but environmentally hazardous chemical and physical techniques. This research investigates the binding characteristics between Zinc Oxide nanoparticles …

Design And Validation Of A Novel Patterned Microfluidic Culture Platform For Hipsc-Cm Maturation, Anisia Gabriela Țiplea

Dartmouth College Master’s Theses

Adult cardiomyocytes (CMs) are among the most challenging cells to culture in vitro, given their poor adherence to plastic culture wells and poor maturation outside the native extracellular matrix (Narkar et al., 2022). Human induced pluripotent stem cell-derived CMs (hiPSC-CMs) offer a viable alternative to study heart development and disease progression. While not comparable to adult CMs in their maturity (Narkar et al., 2022), they mimic the clinical phenotypes of heart failure and are more feasible to culture. Nevertheless, hiPSC-CMs require specialized culture conditions that cannot be achieved with 2D static culturing, which fail to replicate native tissue environments (X. …