Biomedical Engineering and Bioengineering Commons^™

Regulation Of Tgf-Β1–Induced Epithelial–Mesenchymal Transition By Integrin Inhibition, Wesam Elhawabri

Theses and Dissertations

Epithelial–mesenchymal transition (EMT) is a critical process underlying cancer progression, fibrosis, and tissue remodeling, characterized by coordinated changes in cell morphology, nuclear structure, and extracellular matrix (ECM) organization. Transforming growth factor beta 1 (TGF-β1) is a primary inducer of EMT; however, the extent to which integrin-mediated signaling and ECM remodeling regulate these structural changes remains incompletely understood. In this study, we quantitatively investigated EMT-associated remodeling in A549 lung carcinoma cells and MCF10A epithelial cells following TGF-β1 stimulation. Cells were cultured on ECM-coated substrates and treated with TGF-β1 in the presence or absence of integrin-targeting inhibitors (ATN-161, 28-G11, and STX-100). Im …

Empirical Dynamical Modeling Of Cortico-Hippocampal Information Transfer During Memory Encoding, Sam Y. Cole

Theses and Dissertations

Understanding how brain dynamics support successful memory formation remains a central challenge in neuroscience. This dissertation applies tools from empirical dynamical systems theory to investigate the neural mechanisms underlying episodic encoding, with a focus on cortico-hippocampal interactions. Using stereoelectroencephalography (sEEG) data recorded during a delayed free recall of word lists task, this work reveals nonlinear, state-dependent shifts in directed information flow between cortex and hippocampus that distinguish successful from unsuccessful encoding. To further characterize these dynamics, state-space trajectories are reconstructed using time-delay embedding and recurrence-based methods, and features derived from these trajectories are used to classify memory outcomes. By integrating …

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 …

Evaluating The Brain-Muscle Connectivity Of Cyclic Ankle Pedaling Movement In A Clinical Setting, Matthew K. Shanosky

Graduate Studies Theses and Dissertations 2026

Clinical neurorehabilitation requires objective biomarkers to accurately detect and monitor neuromotor impairments. While traditional metrics are favored for their efficiency and minimal equipment demands, they typically rely on subjective observation and lack physiological resolution. High-resolution electrophysiological technologies, such as electroencephalography (EEG) and electromyography (EMG), offer objective insights into nervous system dynamics; however, prolonged data acquisition times have hindered their translation into frontline clinics. To bridge this translational gap, this study developed a time-efficient experimental paradigm designed for rapid clinical deployment. Healthy participants completed two initial resting baseline trials before performing an externally paced, dynamic, cyclic ankle movement task utilizing simulation …

Mathematical Modeling And Characterization Of A Variable Stiffness Ankle-Foot-Orthosis, David E.L. Richards

Graduate Studies Theses and Dissertations 2026

Conventional ankle–foot orthoses (AFOs) typically employ static stiffness profiles that do not replicate the dynamic quasi-stiffness of the human ankle during gait. Variable stiffness mechanisms (VSMs) offer a promising alternative solution for gait pathologies, such as foot drop and post-stroke hemiparesis; however, their implementation is limited by the lack of accurate mathematical models capable of predicting force and stiffness characteristics. The objective of this thesis is to develop and validate comprehensive mathematical models describing the kinematics and kinetics of a novel variable stiffness ankle–foot orthosis (VS-AFO). This study derives governing equations to characterize how mechanical adjustments influence the force transmission …

Integrated Optical Probes For Confocal Scanning Imaging And Adjustable Coherent-Gated Dynamic Sensing, Yonglin Huang

Graduate Studies Theses and Dissertations 2026

Optics and photonics have been one of the most important sciences and technologies that impact modern human life in a big way. For example, fiber-optics for communications and artificial intelligence. Optical probes are critical components for optical imaging and optical sensing technologies that have been actively researched and developed in the past decades. Advanced fiber-optic sensor probes with smaller size, better performance, lower noise, higher photon efficiency, rapid sensing time, and lower cost are needed in many applications, such as nanoscale material science, chemistry, and biomedical fields, etc.  In this project, new fiber-optic sensor probe technologies and integrated micro-optic devices …

Evaluating The Impact Of Cognitive Distraction On Spaceflight-Relevant Task Performance Using Surface Electromyography And Motion Capture, Allyson K. Mitchell

UNF Graduate Theses and Dissertations

Cognitive distraction poses a risk to astronaut performance during complex, multitasking operations in spaceflight environments. This study examined the effects of cognitive load on neuromuscular coordination and task execution using surface electromyography (sEMG) and motion capture. Thirteen participants performed spaceflight-relevant tasks under undistracted and distracted conditions, with distraction induced through verbal questioning. EMG signals from eight upper-extremity muscles were processed using envelope filtering, peak normalization, and time normalization to enable inter-subject comparison, and group-level mean activation with standard deviation was analyzed. While overall muscle activation was similar between conditions, phase-dependent differences were observed, with undistracted trials showing higher activation during …

Preventing G/J Tube Dislodgement: A Device And Communication Innovation, Sarah Clark

2026

The Problem
G/J tube dislodgement is a frequent complication in pediatric patients
Leads to:

• Emergency department visits
• Hospital admissions
• Delays in nutrition/medication

Impact on Patients & Families:

• IV placement (traumatic)
• Radiation exposure
• Overnight hospital stays

Impact on Nurses & System:

• Increased workload (admissions, coordination)
• Occupied inpatient beds for stable patients
• Inefficient care processes

Aims/Objectives
Aim: Reduce unplanned G/J tube dislodgements and related hospital utilization.
Objectives: Develop a breakaway connector prototype

Implementation and Evaluation
Setting: Pediatric inpatient & outpatient system
Participants: Nurses (bedside, GI, IR), caregiver, innovation team
Process:
Roundtable discussions → identified workflow gaps
Communication/workflow audit
Developed device …

Privacy-Preserving Federated Learning With Optimized Ensemble Weighting And Knowledge Distillation For Covid-19 Detection From Non-Iid Medical Imaging Data, Richard Annan, Hong Qin, Robert Newman, Madhuri Siddula, Letu Qingge

Computer Science Faculty Publications

Medical imaging enables rapid and accurate diagnosis of COVID-19, with CT scans proving especially effective. However, data privacy concerns limit collaborative model development across hospitals. To address this issue, we introduce a novel federated learning framework. It is referred to as Independent Knowledge Distillation with post-Ensemble Federated Learning (IKDEFL). Differential Privacy (DP) is integrated into the framework to improve privacy guarantees. Three DP mechanisms are evaluated. These include Fixed Gaussian, Gaussian Adaptive, and Tree Adaptive. The evaluation has been conducted on heterogeneous and Non-Independent and Identically Distributed (Non-IID) datasets. These datasets reflect real-world hospital scenarios. Results show that IKDEFL significantly …

Isotropic Shrinkage Of Patterned Vacancies Enables Three-Dimensional Nanoprecise Metastructures For Visible Light Applications, Quansan Yang, Gaojie Yang, Takahiro Nambara, Hiroyuki Kusaka, Yuichiro Kunai, Alex C. Matlock, Corban Swain, Brett Pryor, Yannick Salamin, Daniel Oran, Hasindu Kariyawasam, Ramith Hettiarachchi, Dushan Wadduwage, Marin Soljačić, Peter T. C. Soflaei, Edward S. Boyden

Computer Science Faculty Publications

Three-dimensional metastructures with nanoscale feature sizes exhibit unique properties compared with structures with larger feature sizes, but are difficult to fabricate. Here we introduce implosion carving (ImpCarv), a method for photopatterning vacancies of complex geometry throughout materials, followed by isotropic shrinkage (>10-fold). ImpCarv works by photoactivating sensitizers to generate reactive oxygen species that cleave a swollen hydrogel at defined points, followed by controlled shrinkage via dehydration. ImpCarv creates three-dimensional metastructures where the refractive index of each point throughout a material can be specified with nanoscale precision via material presence or absence. By leveraging refractive index programmability for precise phase …

Memebuddy: Dialog-Style Audio Representations For Engaging Non-Visual Meme Experiences, Chirag Bhansali, Vikas Ashok, Hae-Na Lee

Computer Science Faculty Publications

Image memes are a pervasive form of online communication, widely used to convey humor, opinions, and cultural references. Prior work has explored making memes accessible to blind users, primarily through auto-generated descriptive captions. While these approaches improve comprehensibility and sometimes incorporate prosodic or emotional cues, they often fail to capture the humor, narrative structure, and contextual nuances that make memes engaging. We present MemeBuddy, a system that models memes as dialog, generating structured, multi-turn audio representations using role-based speakers. MemeBuddy reinterprets a meme as a conversation between two speakers, integrating extracted meme text with contextual knowledge implicitly inferred by a …

Susceptibility To High-Fidelity Misinformation: An Eye-Tracking Analysis, Yasasi Abeysinghe, Gavindya Jayawardena, Enkelejda Kasneci, Sampath Jayarathna

Computer Science Faculty Publications

With the rise of online misinformation and AI-generated text, understanding human perception of news truthfulness is critical. In this study, we examine visual attention and cognitive processing using eye-tracking measures as individuals read fake and real news articles sharing nearly identical structure and imagery, differing only in subtle textual changes. Using the public FakeNewsPerception dataset, we analyze advanced gaze measures, including scanpaths, AOI transitions, and luminance-corrected pupil measures, beyond basic gaze features, in relation to news truthfulness and perceived believability. Results show that, given the high fidelity of the fake news, readers exhibited comparable visual scanning patterns, attention allocation across …

Untrained Position-Encoded Multilayer Perceptron Network For Structured Illumination Microscopy Reconstruction, Sahil Sharma, Leonidas Zimianitis, Krishnendu Samanta, Balpreet Singh Ahluwalia, Joby Joseph, Dushan N. Wadduwage

Computer Science Faculty Publications

Structured Illumination Microscopy (SIM) enables super-resolution imaging by encoding high-frequency spatial information through patterned light. While traditional Fourier-based reconstruction methods are prone to artifacts under suboptimal conditions, recent deep learning approaches often require large training datasets and lack adaptability across different imaging setups. In this work, we present Position Encoded Multi-Layer Perceptron (PEM) network that leverages implicit neural representations (INRs) and SIM forward-model-driven modeling to reconstruct super-resolved images without any training data. PEM-SIM represents each spatial coordinate as a combination of sinusoidal functions across multiple frequencies, enabling rich encoding of fine spatial detail. A forward model grounded in SIM image …

Adaptive Self-Attention For Enhanced Segmentation Of Adult Gliomas In Multi-Modal Mri, Evan P. Savaria, Jiangwen Sun

Computer Science Faculty Publications

Every year there are an estimated 80,000–90,000 new glioma cases, highlighting the need for reliable imaging-based decision support. Although deep learning has improved tumor sub-region segmentation, many state-of-the-art models fail to fully capture complementary information across T1, T1Gd, T2, and FLAIR MRI modalities and often operate as “black boxes,” limiting physician trust when precise delineation is critical for surgical planning, radiation targeting, and treatment monitoring. To address these limitations, we propose AIMS, an Adaptive Integrated Multi-Modal Segmentation framework that maintains modality-specific feature streams and employs adaptive self-attention within a hierarchical CNN-Transformer architecture to prioritize and fuse multi-modal MRI features. We …

Effect Of Local Steel Slag Incorporation On The Mechanical Properties Of Concrete, Ahmed Safaa Tariq Karmah, Wissam Khadum Alsaraj, Luma A. Zghair

Al-Esraa University College Journal for Engineering Sciences

The increasing interest in the production of concrete through the utilization of inexpensive materials has caused a rise in the number of studies concerning the use of materials with cementitious properties, such as Silica Fume, Slag, Fly Ash and other pozzolanic materials. Moreover, the increasing amounts of Steel Slag being produced from local factories that are being deposited without an available method of disposal provides an opportunity to harness the Slag in the production of an inexpensive, and possibly better concrete. Slag has been used as both an addition and substitution of the cement and fine aggregate. The mixtures included …

Decoding Climate Change: A Comprehensive Statistical Insight Into Temperature Anomalies In Iraq And Its Neighboring Countries, Jameel T. Al-Naffakha, Mohammed R. Al-Qassabanda, Israa Jafar

Al-Esraa University College Journal for Engineering Sciences

This study applies advanced statistical techniques, including the Mann-Kendall Trend Test and ARIMA forecasting, to validate and predict temperature anomalies across Iraq and its neighboring countries (2014–2024). Findings confirm a statistically significant warming trend (p < 0.00000005) across all nations, with Syria (1.02°C) and Turkey (0.97°C) experiencing the highest anomalies. GIS-based spatial analysis highlights regional disparities, identifying climate-vulnerable zones. The persistent rise in temperature anomalies correlates with worsening water scarcity, desertification, and extreme weather events, including prolonged droughts and heatwaves. Iraq’s peak anomaly (1.48°C) has exacerbated heat stress, agricultural decline, and reduced river inflows, while Kuwait and Saudi Arabia struggle to maintain critical infrastructure under record-breaking temperatures exceeding 50°C. These climate shifts pose severe risks to water availability, food security, and energy demand, necessitating urgent policy interventions. Key recommendations include enhanced water resource management, climate-adaptive agriculture, and renewable energy expansion. If left unaddressed, rising temperatures could destabilize the region, increasing socio-economic vulnerabilities and escalating resource conflicts. This study underscores the need for cross-border collaboration and sustainable adaptation policies to mitigate the long-term impacts of climate change in the Middle East.

Optimal Power Flow Control In The Iraqi Power Grid Using Artificial Intelligence Algorithms For Carbon Emission Reduction, Mohammed Shakir Juber

Al-Esraa University College Journal for Engineering Sciences

Iraq’s power sector remains in a protracted and severe crisis characterized by a significant mismatch between supply and demand, high levels of losses during transmission and distribution, as well as an increasing challenge to the resources base being largely unfavourably. These inefficiencies impose heavy costs on the national economy in excess of 40 billion annually and they also reinforce greenhouse gas emissions, and exacerbate environmental issues. To deal with these problems, we proposed in this paper that a new hybrid AI tool should be developed for the solution of multi-objective optimization problem based on purpose Genetic Algorithm (GA) merger with …

Applying Machine Learning Techniques For Early Detection Of Cyber Attacks On Iot Devices, Noor Adnan Allamy

Al-Esraa University College Journal for Engineering Sciences

This research designs, implements, and evaluates a machine learning-based framework for the early detection of cyber attacks targeting Internet of Things (IoT) devices, with a specific focus on the context and challenges present in Iraq. The study conducts a comparative analysis of three supervised learning algorithms—Support Vector Machine (SVM), Random Forest (RF), and Deep Neural Networks (DNN)—using a combination of benchmark datasets (NSL-KDD, CIC-IDS-2017, Bot-IoT) and a synthesized dataset adapted to simulate the Iraqi threat landscape. Key performance metrics, including accuracy, precision, recall, and F1-score, were used for evaluation. The proposed Random Forest model demonstrated superior performance, achieving an accuracy …

Ai-Enhanced Heat Transfer Optimization In Magnetic Bio-Nanofluids, Hasan Attyah Shaboot

Al-Esraa University College Journal for Engineering Sciences

This study presents a hybrid Artificial Intelligence–Computational Fluid Dynamics (AI-CFD) framework for optimizing heat transfer in magnetic bio-nanofluids subjected to external magnetic fields. Magnetic bio-nanofluids, composed of biocompatible base fluids containing superparamagnetic nanoparticles, exhibit tunable thermal and flow behavior, making them promising for biomedical and micro-cooling applications. Conventional optimization methods based on experiments or brute-force CFD are computationally expensive and limited in exploring the full design space. To overcome these challenges, an Artificial Neural Network (ANN) surrogate model was developed to predict two key performance indicators, the Nusselt number and the friction factor, with high accuracy (R² > 0.997). The surrogate …

Hybrid Experimental–Computational Study On The Energy Absorption Of Graphene Nanoplatelet-Reinforced Sandwich Structures, Hamdan Yousif Hamdan

Al-Esraa University College Journal for Engineering Sciences

Background: Sandwich composites are widely used in aerospace, automotive, and marine applications because of their lightweight, stiffness, and strength, but they remain prone to out-of-plane impacts and barely visible impact damage (BVID). Graphene Nanoplatelets (GNPs) have shown strong potential to improve fracture toughness and impact resistance. However, hybrid experimental–computational studies applying such reinforcement are still lacking in developing contexts like Iraq, where practical and accessible solutions are essential. Aims: The study investigates the effect of GNP reinforcement on the low-velocity impact behavior and energy absorption of glass fiber/epoxy sandwich panels with PVC foam and balsa wood cores. Objectives include fabricating …