Engineering Commons^™

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, …

Uta Datathon 2025 Challenges (Archive), Rubab Shahzad, Srinivasa Sai Abhijit Challapalli, Ghanbarian Behzad, Mei Yang, Clivin Geju, Zecil Yogeshkumar Jain, Jay Mahavirkumar Shah, Sai Nikhitha Chandana

2025 Datathon Challenges-Archive

Timed and Model Challenges from the UTA Datathon 2025

04.21.2025 Ored Connect, Liz Williamson

ORED Newsletter

ORED Stakeholder Meetings

SEC Travel Grants

Acoustic Filter For Biopharmacy, Nicholas Rivet

Three Minute Thesis (3MT)

The design and development of a novel flow induced acoustically tuned “filterless” filter is proposed. The proposed research is on developing two or more prototypes that function as a cell retention device for perfusion cell cultures used in continuous manufacturing of monoclonal antibodies and recombinant proteins. This research will provide a non-invasive, cost-effective, flexible, and robust cell retention device for sustainable manufacturing of biologics.

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

Securing Biometric Data, Alyssa F. Carroll

Cybersecurity Undergraduate Research Showcase

Biometric data has been widely adopted across various sectors, including digital identity, artificial intelligence (AI), border control, digital wallets, and national identification systems. While biometric identifiers—such as fingerprints, retina scans, and facial recognition—offer reliable and convenient authentication, they also raise significant concerns regarding privacy and security. This paper examines how biometric data is stored, the vulnerabilities it faces, and the most effective methods for safeguarding it. By highlighting the critical importance of biometric data protection, this study reviews current research on approaches, strategies, and policies that enhance security while preserving the functionality and efficiency of biometric systems.

Examining Physiological Responses To Misophonic Triggers, Christian O'Reilly, Xuan Yang, Sewon Oh, Doug Wedell, Svetlana Shinkareva

Faculty Publications

We collected and analyzed an array of biosignals (face electromyogram, skin electrodermal activity, peripheral temperature, and electrocardiogram) in 60 participants with and without misophonia, a condition characterized by decreased tolerance to innocuous sounds. Our goal was to objectively characterize the physiological response to misophonia triggering sounds. We found that misophonic responses can be objectively identified in some cases through atypical physiological reactions to triggering stimuli, though not all participants exhibited this response. Our analyses suggest a large interindividual variability in response to misophonic triggers and highlights the need for methodological adjustments in future experiments to increase the detectability of misophonic …

04.07.2025 Ored Connect, Liz Williamson

ORED Newsletter

New ORED Website Goes Live

Oxford Pitch Competition

Hughes Miller, Strategic Partnerships

Determining The Wound Closure Capabilities Of A Biological Engineered Blood Vessel For Hd Access, Brianna Regan, Alex Dumitru, Mai Lam

Medical Student Research Symposium

End stage renal disease (ESRD) is a prominent chronic condition with dialysis as a primary treatment option. Dialysis necessitates implementation of an access point, with the gold standard being an AV fistula which possesses multiple shortcomings. Alternative access points, namely synthetic grafts, do not allow wound healing characteristics. This work aims to explore how a tissue engineered vascular graft (TEVG) may be able to address these issues by allowing a long-term access point for HD that can close puncture wounds.

The effects of growth factors on our cells were tested preliminarily by means of a scratch assay on plates of …

Limbgod(Pat. Pending): Wearable Garment For Amputation Prevention, Naomi Choi Dpm, Mba, Phuc An Dinh Bs, Ms, Eric Lee Bs, Francois M. Lokenye Dpm

Posters

Approximately 1.6 million people in the U.S. have lower limb amputations, which is expected to double by 2050 (Wong et al.). Socio-economic factors: income, education, rural residency & race, impact amputation risk (Okesina et al.), with Black Americans 70% are more likely to undergo major lower limb amputations than white Americans, even after adjusting for care access & comorbidities (Feinglass et al., Holman et al., Regenbogen et al.). Within 5 years, up to 50% of first-time amputees require another amputation (Dilingham et al., Glaser et al.) & those with comorbidities face a 77% five-year mortality rate (Fortington et al.).

2025- The Twenty-Ninth Annual Symposium Of Student Scholars

Symposium of Student Scholars Program Books

The full program book from the 29th Annual Symposium of Student Scholars, held on April 16-18, 2025. Includes abstracts from the presentations and posters.

Development Of Highly Sensitive & Selective Sensor, Megha Shinde

Biomedical Engineering Theses & Dissertations

This work presents the development of innovative electrochemical sensors for selective and sensitive dopamine (DA) detection using flexible laser-induced graphene (LIG) electrodes modified with advanced nanocomposites. An LIG electrode synthesized from pyralux film was functionalized with Nb₄C₃Tx MXene and silver nanoparticles (AgNPs), significantly enhancing its electrochemical performance. The modified electrode exhibited a peak anodic current increase from 150 μA to 330.4 μA and demonstrated a wide linear detection range (100 nM to 10 μM) with a low detection limit of 1 nM and high sensitivity (160.96 μA/nM cm ^-2). It also displayed excellent selectivity against …

Graduate School Blog - April 2025 Volume 1, Cynthia Haynes

UofM Grad School Blog

The April 2025 UofM Graduate School Blog highlights a month full of events, stories, and celebrations, beginning with Dr. Deborah Tollefsen’s personal graduate school journey, shared during the “Is Graduate School Right for Me?” virtual workshop an inspiring narrative of resilience, mentorship, and finding purpose through education. This edition also spotlights Graduate Student Appreciation Week, featuring a robust lineup of events such as a virtual town hall, resume and job market workshop, student social and awards ceremony, study session, and social dinners all designed to support, celebrate, and connect the UofM graduate student community. With opportunities to hear from …

The Interplay Between Endothelial Glycocalyx Maturity And Both The Toxicity And Intracellular Uptake Of Charged Nanoparticles, Claire A. Bridges, Lu Fu, Jonathan Yeow, Xiaojing Huang, Miriam Jackson, Rhiannon P. Kuchel, James D. Sterling, Shenda M. Baker, Megan S. Lord

Business and Information Technology Faculty Research & Creative Works

Nanoparticles are widely studied for delivering treatments to target tissues, but few have reached clinical use. Most nanoparticles encounter blood vessels on their way to target tissues. The inner surface of these vessels is lined with endothelial cells covered by a glycocalyx, an extracellular matrix rich in anionic glycans. The role of the glycocalyx in nanoparticle interactions is not well understood. Here, we demonstrate that endothelial cells need extended culture times to synthesize a mature glycocalyx. Our research shows that branched polyethyleneimine functionalized gold nanoparticles bind to endothelial cells expressing either a developing or mature glycocalyx, with the interaction involving …

Nanosecond Pulsed Electric Field And Plasma Jets For Cancer Therapy, Edwin Ayobami Oshin

Biomedical Engineering Theses & Dissertations

Nanosecond pulsed electric field (nsPEF) employs nanosecond-duration, high voltage pulses to induce oxidative stress, leading to temporary or permanent damage to cells or tissue (also known as reversible and irreversible electroporation), and has been considered a promising approach for cancer therapy. In parallel to this, nanosecond pulsed atmospheric pressure plasma jets (ns-APPJs) have also shown to be effective in inactivating cancer cells or increasing sensitivity of cells to electric fields. ns-APPJs are known to generate reactive chemical agents, including reactive oxygen and nitrogen species (RONS) which induces oxidative stress resulting in cell proliferation, apoptosis, and necrosis. In this dissertation, a …

Development And Analysis Of The Kinematic-Dynamic Model Of The Rehabilitation Exoskeleton System, Umidjon Abdumutalipovich Takabaev, Zafar Botirovich Juraev

Technical science and innovation

Designing modern rehabilitation exoskeleton systems requires a comprehensive study of human-machine interactions. In this process, creating kinematic and dynamic mathematical models of the system is extremely important. In this paper, we develop mathematical models that describe rehabilitation exoskeleton systems' kinematic and dynamic properties. Based on the Denavit-Hartenberg method we construct kinematic model of the exoskeleton system. The method gave us to determine the coordinate system for each joint. Furthermore, we also study the motion range of joints of the exoskeleton. Modeling the dynamic properties of the system performed with the second-order Lagrange equation. The exoskeleton construction consisting of knee, thigh, …

03.31.2025 Ored Connect, Liz Williamson

ORED Newsletter

Indirect Cost Rate Agreement

NIH Transition to Common Forms

NIH Implementation of New Initiatives and Policies

Automated Data Analysis For Concussion Patient Records: A Flutter-Based Desktop Application, Fhaheem Tadamarry

USF Tampa Graduate Theses and Dissertations

Concussions are a prevalent and complex medical condition requiring careful clinical assessment and data-driven insights for effective management. This thesis presents the development of an automated data analysis system for concussion patient records, integrating Flutter-based desktop application development with SQL-driven data processing. The system provides a streamlined, interactive interface for clincians and researchers to upload, visualize, and analyze patient data efficiently.

The proposed solution automates data cleaning, preprocessing, and statistical analysis, ensuring robust and reliable insights into demographic, clinical, and recovery-related factors. Key analyses include sex-based differences injury mechanisms, prior head injury impact, mood disorder correlations, and time-to-treatment variations. The …

Multimodal Ai-Driven Biomarker For Early Detection Of Cancer Cachexia, Sabeen Ahmed

USF Tampa Graduate Theses and Dissertations

Cancer cachexia is a metabolic syndrome characterized by substantial skeletal muscle loss, impacting cancer patients' survival and quality of life. Despite its clinical significance, early detection remains a challenge due to the lack of standardized diagnostic criteria and the reliance on indirect markers. This work presents an AI-driven approach to enhance cachexia detection and monitoring by integrating multiple deep learning methodologies. We explore transformer architectures for time-series analysis to model sequential medical data, enabling disease prediction and progression modeling. To ensure robust and reliable decision-making in clinical settings, we explore Bayesian deep neural networks for uncertainty estimation. Additionally, we introduce …

Role Of Eye-Tracking Technology And Software Algorithms In Enhancing Adhd Detection And Diagnosis: A Systematic Literature Review, Lauren E. Perkins

Honors College Theses

This systematic literature review explores the role of eye-tracking technology and software algorithms in enhancing the detection and diagnosis of ADHD. ADHD, a neurodevelopmental disorder affecting both children and adults, is traditionally diagnosed through behavioral assessments, which may lack objectivity. Recent studies suggest that eye-tracking, specifically focusing on saccades, fixations, and blink rates, offers the potential for more accurate and objective measures of ADHD. The review examines clinical trials, observational studies, and machine learning research to assess the correlation between ADHD and eye movement patterns. Results indicate that individuals with ADHD exhibit distinct eye movement patterns, which can be quantified …

03.17.2025 Ored Connect, Liz Williamson

ORED Newsletter

SPA director Andrea Rich

ARC Nomination Deadline Extended

Tannic Acid-Stabilized Liposomal Platform For Microrna Delivery In Endometriosis, Victoria Herrera, Rahul Tiwari, Bridgette Lozano Lozano, Subhash Chauhan, Murali Yallapu

Research Symposium

Background: Endometriosis is defined as the presence of endometrial-type mucosa outside the uterine cavity. It affects about 6.5 million women of reproductive age in the United States. It is a leading cause of infertility, impacting up to 50% of women with difficulty conceiving, and is prevalent in as many as 90% of individuals experiencing severe, chronic pelvic pain. Women with endometriosis had 4.2-fold higher ovarian cancer risk than those without endometriosis. Within this work, a range of liposomal formulations was investigated for endometriosis. Recent studies confirmed the role of miR-205-5p as a potential suppressor of ectopic endometriotic progression. Clinical translation …

Fabrication Of Docetaxel Loaded Pcl/Plga Electrospun Nanofibers For Lung Cancer Therapy, Rahul Tiwari, Fnu Pranav, Eswara N. Hanuma Kumar Ghali, Subhash Chauhan, Murali Yallapu, Luis Chavez

Research Symposium

Background: Electrospinning is a commonly employed method in tissue engineering due to its ability to produce nano-/microscale fibrous materials with mechanical and functional properties that mimic the extracellular matrix of living tissues. The general interest in electrospun fibrous matrices has recently expanded to cancer research both as scaffolds for in vitro cancer modeling and as patches for in vivo therapeutic delivery. This research aims to investigate the efficient delivery of anticancer drug in lung cancer treatment.

Methods: Three different biocompatible polymeric nanofibers (i.e. PCL fibers, PCL-PLGA mixed fibers, and PCL-PLGA tetra-layered fibers) loaded with docetaxel, were prepared using electrospinning technique. …

The Interplay Between Endothelial Glycocalyx Maturity And Both The Toxicity And Intracellular Uptake Of Charged Nanoparticles, Claire A. Bridges, Lu D. Fu, Jonathan A. Yeow, Xiaojing D. Huang, Miriam D. Jackson, Rhiannon P. Kuchel, James D. Sterling, Shenda M. Baker, Megan S. Lord

Business and Information Technology Faculty Research & Creative Works

Nanoparticles are widely studied for delivering treatments to target tissues, but few have reached clinical use. Most nanoparticles encounter blood vessels on their way to target tissues. The inner surface of these vessels is lined with endothelial cells covered by a glycocalyx, an extracellular matrix rich in anionic glycans. The role of the glycocalyx in nanoparticle interactions is not well understood. Here, we demonstrate that endothelial cells need extended culture times to synthesize a mature glycocalyx. Our research shows that branched polyethyleneimine functionalized gold nanoparticles bind to endothelial cells expressing either a developing or mature glycocalyx, with the interaction involving …

Effect Of Walking Speed And Asymmetric Loading On Human Gait, Dumitru I. Caruntu, Alfirio Trejo, Eric Rodriguez, Camila T. Alvarez Barriga

Research Symposium

Background: Human gait is influenced by factors such as walking speed and carrying heavy objects asymmetrically. Understanding these effects enhances rehabilitation research for individuals recovering from leg injuries. Clinical angles of the knee, derived from experimental data, provide insights into movement patterns, revealing abnormalities or compensations. Calculating these angles requires a joint coordinate system (JCS) for the knee joint.

Methods: This study employed the VICON motion analysis system with ten infrared cameras arranged circularly for comprehensive gait analysis. Reflective markers placed on anatomical landmarks facilitated motion capture, recorded at 100 Hz. Data processing included filtering, establishing a JCS, …

Muscle Force Analysis In Patients With Forefoot Amputees And Healthy Subjects During Walking, Anthony Melgar, Dumitru Caruntu, Javier La Fontaine, Luis Venegas, Hafizur Rahman

Research Symposium

Forefoot amputation, a type of partial foot amputation, involves the surgical disarticulation of either the interphalangeal or metatarsophalangeal joints. This procedure not only removes critical joint structures but also alters the positioning of associated muscles. Forefoot amputations significantly affect gait patterns and redistribute plantar pressure maps across the plantar surface of the foot. The phalanges are crucial in absorbing and redistributing plantar pressure during the gait cycle. The absence of phalanges and the loss of metatarsophalangeal joints alter the normal pressure distribution maps, possibly shifting peak pressure from one local foot region to another region of the foot. This research …

Analysis Of Systematic Trade-Offs Between Military And Healthcare Expenditure Alongside Gdp Growth Of Select Asian And Western Exporting Economies In The 21st Century, Rahul Balamurugan, Carlos Gershenson, Preethi Nanjundan, Hiroki Sayama

Northeast Journal of Complex Systems (NEJCS)

This study explores the complexity in the trade-offs between military expenditure, healthcare expenditure, and GDP growth across select Asian nations and major weapon-exporting countries, examining how nations allocate finite resources between national security and human well-being over the past two decades. Using a systems science approach, the research integrates Granger causality testing to analyze temporal and directional relationships among GDP growth, military expenditure, and healthcare expenditure, uncovering their dynamic interdependencies. The methodology includes trend and slope analysis, Granger causality testing, outlier detection, and clustering to identify heterogeneity in resource allocation strategies. Developed, weapon-exporting nations exhibit complementary trends, with strong causality …

Analysis Of Nuclear Security And Safety Integration Using Survey Responses And Pairwise Comparison Methods, Sheila V. Gbormittah, Theodore A. Thomas, Jason Timothy Harris

International Journal of Nuclear Security

Integrating nuclear security and safety is important for implementing and sustaining nuclear technology because it promises improved and effective management. This integration is an ongoing effort to ensure that both work together with minimal conflicts. This research aimed to determine the preferred level at which nuclear security and nuclear safety integrate by using the pairwise comparison methods of decision-making. This methodology used survey responses from women nuclear professionals to identify the most-desired criteria at three levels: strategic, operational, and cultural. The strategic level includes actions that government officials and regulators can take. The operational level encompasses actions that deliver the …