Biomedical Engineering and Bioengineering Commons^™

Early Detection And Objective Assessment Of Neonatal Hypoxic-Ischemic Encephalopathy Severity, Soheila Norasteh

Bioengineering Dissertations

Hypoxic–ischemic encephalopathy (HIE) is a neonatal brain injury caused by reduced oxygen and blood flow to the brain around the time of birth. It remains a major cause of neonatal mortality and long-term neurodevelopmental impairment worldwide. Therapeutic hypothermia is the standard treatment for moderate-to severe HIE and improves outcomes when initiated within the first six hours of life. Therefore, accurate assessment of injury severity during this period is essential. Cur rently, HIE severity is determined primarily through neurological examination and classified as mild, moderate, or severe. However, these examinations are subjective, cannot provide continuous monitoring of brain function, and may …

Peculiarities Of Phosphatidylserine Externalization By Nano- And Microsecond Electric Pulses, Mantas Silkunas, Alayna Enos, Iurii Semenov, Giedre Silkuniene, Eleni Zivla, Olga N. Pakhomova, Andrei G. Pakhomov

Bioelectrics Publications

Phosphatidylserine (PS) externalization is a hallmark of apoptosis but can also be triggered within seconds by pulsed electric fields (PEFs). Whether PS reaches the outer leaflet by lateral migration through electropores or indirectly through Ca²⁺-dependent signaling and scramblase activation remains debated. We used total internal reflection fluorescence (TIRF) microscopy with Annexin V-Alexa Fluor 568 and/or bovine lactadherin-FITC to resolve PS externalization in HEK293 cells placed on an indium tin oxide (ITO) transparent electrode. PEF exposures produced discrete PS-positive puncta ("freckles") within ~ 10 s after a 20-µs pulse (1.2-2.5 kV/cm) or with a ~ 1-min delay after a …

Noninvasive Optical Assessment Of Tissue Hemodynamics In Preterm Infants And Mastectomy Skin Flaps, Samaneh Rabienia Haratbar

Theses and Dissertations--Biomedical Engineering

Adequate tissue blood flow and oxygenation are essential for maintaining cellular viability and normal organ function. Disruptions in microvascular perfusion and oxygen delivery contribute to ischemia- and hypoxia-related diseases, including stroke, cancer, retinopathy of prematurity (ROP), and mastectomy skin flap necrosis. Reliable, noninvasive approaches for assessing tissue hemodynamics are therefore critical for improving diagnosis and therapeutic decision-making, particularly in settings where conventional methods are limited. This dissertation investigates the clinical and physiological importance of measuring tissue blood flow and oxygenation across neonatal and surgical applications using both clinical monitoring and advanced optical imaging techniques. In the first study, high-speed pulse …

Nanosecond Electric Pulses As A Novel In Situ Vaccination Strategy For Cancer Treatment: Mechanisms, Challenges And Prospects, Siqi Guo

Bioelectrics Publications

Nanosecond electric pulses (nsEPs) are an emerging pulsed-power technology with unique bioelectric characteristics distinct from conventional long-pulse electroporation. As a tunable physical modality, nsEPs can modulate intracellular structures, membrane dynamics, and signaling pathways. Increasing evidence supports nsEPs as a promising non-thermal tumor ablation approach due to their high spatial precision, preservation of critical tissue structures, and minimal adverse effects. One of the most significant discoveries associated with nsEP tumor ablation is the induction of potent systemic antitumor immunity, particularly in situ vaccination (ISV) effects and, in some cases, abscopal effects against distant untreated tumors. Substantial evidence demonstrates that nsEPs can …

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 …

Using Network Models To Understand Biological Signaling Architecture, Russ White, Emily Brown Reeves, Gerald L. Fudge

Faculty Publications

Engineers have developed abstract network models to better understand the recurring problems faced by communication systems. This paper argues that these models can be generalized to describe biological communications systems given that they share many requirements with human-designed systems, including functional requirements and physical constraints. Leveraging collaboration, biologists and engineers can work together to use well-understood communication systems, designed to carry data across a computer network, as a model for analyzing less well-understood biological communication systems in order to make predictions and uncover previously unknown functionalities. To illustrate this approach, we apply the Recursive Internet Network Architecture model (RINA) to …

Adversarial Robustness In Biomedical Time-Series Models, Rohan Tiwari

Bioengineering Theses

This study investigates adversarial vulnerabilities in deep learning models for biomedical time-series classification across two clinically important modalities: electrocardiography (ECG) and electroencephalography (EEG). Using the MIT-BIH Arrhythmia and CHB-MIT seizure datasets, I evaluate time-domain attacks (FGSM, PGD), Fourier-domain constrained attacks, and learned spectral perturbations designed to reveal modality-specific sensitivity patterns. Across both tasks, a consistent trend emerges low-frequency components (0–5 Hz) constitute a dominant axis of adversarial vulnerability, with perturbations in this range producing the steepest degradation in classification performance. In ECG models, protecting the physiologically relevant QRS band (5–20 Hz) significantly improves robustness, whereas EEG models remain highly sensitive …

Development Of Multimodal Measurements And Analysis For Early Detection Of Alzheimer’S Disease, Fiza Saeed

Bioengineering Dissertations

Alzheimer's disease (AD) is the leading cause of dementia, and existing diagnostic methods such as PET scans, cerebrospinal fluid sampling and biomarker quantification, and gene sequencing are all either invasive, costly, or not sensitive enough for early detection. This dissertation introduces three different studies that develop a novel multimodal, non-invasive approach to diagnosing AD at its early stages by combining broad band near infrared spectroscopy (bbNIRS) and electroencephalography (EEG) technologies.

The first study showed cerebrovascular-cerebrospinal fluid coupling (CBV-CSF), which is measured by using 2-channel bbNIRS as an indicator of brain aging and early AD. Linear correlations between total blood (Δ[HbT]) …

Orchestrating Bone Healing: Biomaterial-Driven Immunoengineering Of The Bone Microenvironment For Advanced Regenerative Therapies, Ah Joung Rachel Yu, Mohammad Reza Zare, Edikan Ogunnaike, Mostafa Yazdi

Chemical and Biochemical Engineering Faculty Research & Creative Works

Bone regeneration is a multistage and tightly regulated process driven by coordinated interactions between the immune and skeletal systems. While inflammation is essential for initiating repair, its dysregulation contributes to delayed union, nonunion, and impaired healing commonly seen in trauma, chronic disease, and aging. Traditional interventions, including autografts and inert biomaterials, provide structural support but fail to engage or modulate the immune microenvironment that governs successful regeneration. Emerging research in osteoimmunology has revealed the centrality of immune cell populations such as macrophages, T regulatory cells, dendritic cells, and myeloid-derived suppressor cells in directing osteogenesis, angiogenesis, and the resolution of inflammation. …

Combining Haptic Feedback With Electromyography To Study Knee Injury In Stationary Cycling, Christopher Kirby

Honors Theses

Patellofemoral Pain Syndrome (PFPS) is the most prevalent overuse injury in cycling, often linked to altered neuromuscular activation patterns of the quadriceps and hamstrings. While sensory feedback has successfully modified cyclists posture, there is a critical lack of evidence-based interventions targeting the underlying muscle activation imbalances associated with chronic knee pain. This study aimed to develop and validate a novel, real-time biofeedback system that utilizes electromyography (EMG) to trigger vibrotactile cues, aiming to shift muscle onset timing earlier in the pedal stroke to mitigate PFPS-related imbalances. A closed-loop system was engineered by integrating a Delsys EMG system with a SageMotion …

Training A Cellpose Model For T-Cell Cytoplasm And Nucleus Segmentation, William Laws, Matthew Lindley, Irene Georgakoudi

Wetterhahn Science Symposium Posters

Accurate single-cell segmentation of cytoplasm from nucleus in autofluorescence images is critical for quantifying cellular metabolism using the optical redox ratio (FAD / FAD+NAD(P)H). However, automated cytoplasmic segmentation of T cell two-photon excitation fluorescence images remains challenging due to low signal-to-noise ratio, small cell size, and variability in cell brightness across imaging conditions. Here, we present a pipeline combining a custom-trained Cellpose-SAM model with an adapted cytoplasmic post-processing algorithm (CPPA) for automated single-cell metabolic analysis of T cell NAD(P)H autofluorescence images. Raw 2048×2048 pixel images were spatially binned 4×4 in MATLAB to improve signal-to-noise ratio and reduce processing time. A …

Fiber-Reinforced Composites For Vaginal Tissue Engineering Applications, Samyuktha S. Kolluru, Abir Hamdaoui, Annabella M. Mascot, Siobhan S. Sutcliffe, Jerry L. Lowder, Michelle L. Oyen, Samantha G. Zambuto

Mechanical Engineering Faculty Publications

The vagina is a fibromuscular tube-shaped organ that plays critical roles in menstruation, pregnancy, and female sexual health. Vaginal tissue constituents, including cells and extracellular matrix components, contribute to tissue structure, function, and prevention of injury and pathology. However, much microstructural function remains unknown, including how the fiber-cell and cell–cell interactions influence macromechanical properties. A deeper understanding of these interactions will provide critical information needed to reduce and prevent vaginal pathologies. Our objective for this work is to design a novel tissue-mimicking biomaterial for vaginal tissue engineering, and characterize its biological and mechanical performance in the vaginal microenvironment. We successfully …

Computational Methods For Identification Of Molecular Signatures, Weijun Yi

Graduate Theses, Dissertations, and Problem Reports (ETD)

This work develops computational methods for identifying molecular signatures from high-throughput genomic data and for modeling long non-coding RNA (lncRNA) sub-cellular localization. The response of multiple myeloma to CB-6644, a selective RUVBL1/2 complex inhibitor with potential anti-tumor activity, is analyzed to identify drug-responsive pathways and molecular signatures. Conventional gene set enrichment analysis (GSEA) often excludes low-expression genes. Here, phenotype comparison is reformulated as a supervised machine learning problem: genes most informative for discrimination are first selected using a machine learning approach, and GSEA is then applied to these machine-learning derived gene sets. This framework improves detection of CB-6644-associated pathways. For …

Ambulatory Monitoring Of Biomarkers For Enhanced Recovery, Lucas Abrahamian, Gurman Dhami

Bioengineering Senior Theses

Oxidative stress, an imbalance of reactive oxygen species and antioxidants, serves as both a marker and progressor of several chronic and degenerative diseases. These conditions create a major global health burden, accounting for significant cost and deaths. The prevalence of oxidative stress–driven diseases highlights the need for improved strategies to detect the imbalance before irreversible damage occurs. However, despite its major role in disease progression, oxidative stress is typically assessed using static, invasive, or laboratory methods. These approaches are poorly suited for continuous monitoring and fail to serve high-risk groups, such as patients with a family history of disease or …

Development Of In Vitro Hydrogel Blood Clots, Xiomara Garcia, Jasmine Urbina, Sapna Wolf

Bioengineering Senior Theses

Deep Vein Thrombosis (DVT) affects up to almost one million individuals in the United States annually and can lead to life-threatening complications, such as a pulmonary embolism. DVT occurs when a thrombus composed of platelets and fibrin forms within deep veins, obstructing blood flow. Current treatments include anticoagulants, thrombolytics, inferior vena cava filters, and balloon catheter procedures. However, the development and testing of these medical devices heavily rely on animal blood models due to physiological similarities in coagulation, raising ethical concerns and limitations related to cost, scalability, and sustainability. This project proposes a synthetic, in vitro alternative using agarose and …

Rapid Skin Stapler, Emma J. Patterson, Allison M. Milligan, Morgan E. Dunlap

Williams Honors College, Honors Research Projects

Severe burn injuries frequently require split-thickness skin grafts, with metal surgical staples serving as the current standard for fixation. While staples provide rapid and secure placement of graft material, they also introduce significant challenges. Removal is painful, time-consuming, and often requires sedation in pediatric patients, leading to added risk, resource strain, and poor patient experience. These drawbacks highlight the need for improved fixation methods that maintain graft stability while reducing procedural burden. This project applies the engineering design process to address these challenges through identification of user needs, translation into design inputs, risk assessment, and development of a prototype aimed …

Breech Baby, Madison Kaufman, Cassidy Allen, Lilian Mills

Williams Honors College, Honors Research Projects

Our project aims to develop a non-invasive device to assist in turning breech babies to a head down position before delivery. Pregnant women facing breech presentations often need safe and effective solutions, yet current options like external cephalic version (ECV), maternal positioning techniques, and cesarean sections can present challenges. Key barriers include variability in maternal and fetal anatomy, patient comfort, compliance, and training for healthcare providers, along with cost and insurance concerns.

Our innovative device will address these issues by providing clear guidance and support throughout the process. It will prioritize minimizing discomfort and risk, ensuring adaptability for various stages …

The Development And Implementation Of A Computational Framework To Simulate Patellofemoral Joint Mechanics, Mahmood Rashedi

Master’s Theses

Anterior knee pain affects approximately 25% of adults and is associated with altered joint mechanics. Patellofemoral joint (PFJ) models vary widely in complexity, with no established gold standard. Musculoskeletal models efficiently estimate joint loading but do not capture tissue-level mechanics, whereas finite element (FE) models provide tissue-level predictions at greater computational cost. This thesis developed a workflow to evaluate relationships between musculoskeletal model-predicted PFJ loads and FE-predicted cartilage mechanics, examined the impact of altered quadriceps activation, and introduced improved computational models.

Marker trajectories and ground reaction forces were collected from four adults (2 male, 2 female) during walking and squatting. …

Quantifying Hemodynamics In Implantable Cardiac And Renal Support Devices Using Computational Modeling, Alexander D. De Oliveira

Summer Research Program Abstracts

No abstract provided.