Biomedical Engineering and Bioengineering Commons^™

Toward Precision Medicine With Nanopore Technology, Trang Andrea Vu

Theses and Dissertations

Currently, when patients are diagnosed with cancer, they often receive a treatment based on the type and stage of the tumor. However, different patients may respond to the same treatment differently, due to the variation in their genomic alteration profile. Thus, it is essential to understand the effect of genomic alterations on cancer drug efficiency and engineer devices to monitor these changes for therapeutic response prediction. Nanopore-based detection technology features devices containing a nanometer-scale pore embedded in a thin membrane that can be utilized for DNA sequencing, biosensing, and detection of biological or chemical modifications on single molecules. Overall, this …

Non-Invasive Peripheral Venous And Arterial Line Air Detector For Embolization Prevention, Alexandria Kwong, Kevin Shu, Dylan Meinster

Biomedical Engineering

The scope of this project includes designing a non-invasive bubble detector for peripheral venous and arterial lines. For minimally invasive cardiac procedures, arterial and venous access is necessary for these procedures as is constant flow through the tubing to prevent clotting and to administer drugs. Air bubbles are common in these lines and can be consequential if enough air is introduced into the human system. Air embolisms are the most common and relevant issues during these procedures. The goal of this device is to create an attachable detector for air bubbles in saline that can also terminate flow and alert …

Brain Structure Changes Over Time In Normal And Mildly Impaired Aged Persons, Charles D. Smith, Linda J. Van Eldik, Gregory A. Jicha, Frederick A. Schmitt, Peter T. Nelson, Erin L. Abner, Richard J. Kryscio, Richard R. Murphy, Anders H. Andersen

Neurology Faculty Publications

Structural brain changes in aging are known to occur even in the absence of dementia, but the magnitudes and regions involved vary between studies. To further characterize these changes, we analyzed paired MRI images acquired with identical protocols and scanner over a median 5.8-year interval. The normal study group comprised 78 elders (25M 53F, baseline age range 70-78 years) who underwent an annual standardized expert assessment of cognition and health and who maintained normal cognition for the duration of the study. We found a longitudinal grey matter (GM) loss rate of 2.56 ± 0.07 ml/year (0.20 ± 0.04%/year) and a …

Screening And Characterization Of A Pan-Gtpase Inhibitor, Leyla Akhadov

Biomedical Engineering ETDs

Abnormal functioning of small GTPases is implicated in a variety of diseases, ranging from neurological and developmental diseases to cancer. In fact, mutant GTPases are found in up to 30% of cancers. Thus, small GTPases are a highly relevant target in drug discovery and development. High-throughput targeted screening of small molecules is the most productive method of discovering compounds that can give insights into drug development. This thesis describes improvements made to a high-throughput GTPase-targeted screening method to minimize confounding systematic error. It also describes the follow-up characterization of a compound that was identified in a high-throughput screen. The compound …

Development Of Fluorescent Hyaluronic Acid Nanoparticles For Intraoperative Tumor Detection, Nicholas E. Wojtynek

Theses & Dissertations

Surgical resection remains to be the primary treatment for the majority of solid tumors, including breast cancer. The complete removal of the primary tumor, local metastases, and metastatic lymph nodes dramatically improve a patient’s treatment outcome and prognosis. Nevertheless, surgeons are limited to tactile and visual cues in distinguishing malignant and healthy tissue. This can result in a positive surgical margin (PSM), which occurs when tumor goes undetected and is left behind in the surgical cavity. PSMs decreases a patient’s prognosis and necessitate additional treatment in the form of surgery, radiation, and chemotherapy. An emerging imaging modality, known as fluorescence-guided …

Implementation Of A Computer-Vision System As A Supportive Diagnostic Tool For Parkinson’S Disease, Diego Machado Reyes

Honors Theses

Parkinson’s disease is the second most common neurodegenerative disorder, affecting nearly 1 million people in the US and it is predicted that the number will keep increasing. Parkinson’s disease is difficult to diagnose due to its similarity with other diseases that share the parkinsonian symptoms and the subjectivity of its assessment, thus increasing the probabilities of misdiagnosis. Therefore, it is relevant to develop diagnostic tools that are quantitatively based and monitoring tools to improve the patient’s quality of life. Computer-based assessment systems have shown to be successful in this field through diverse approaches that can be classified into two main …

Ml-Medic: A Preliminary Study Of An Interactive Visual Analysis Tool Facilitating Clinical Applications Of Machine Learning For Precision Medicine, Laura Stevens, David Kao, Jennifer Hall, Carsten Görg, Kaitlyn Abdo, Erik Linstead

Engineering Faculty Articles and Research

Accessible interactive tools that integrate machine learning methods with clinical research and reduce the programming experience required are needed to move science forward. Here, we present Machine Learning for Medical Exploration and Data-Inspired Care (ML-MEDIC), a point-and-click, interactive tool with a visual interface for facilitating machine learning and statistical analyses in clinical research. We deployed ML-MEDIC in the American Heart Association (AHA) Precision Medicine Platform to provide secure internet access and facilitate collaboration. ML-MEDIC’s efficacy for facilitating the adoption of machine learning was evaluated through two case studies in collaboration with clinical domain experts. A domain expert review was also …

Pilot Study Exploring The Effect Of Targeted Cox-2 Inhibition In Macrophages Responding To Neuronal Injury; Promoting Enhanced Axonal Regeneration, Alyssa Brauckmann

Electronic Theses and Dissertations

Celecoxib nanoemulsion (CXB-NE) has been developed as a macrophage targeted analgesics by Dr. Janjic and her team at Duquesne University, (Janjic et al, 2018; Liu et al, 2020; Saleem et al, 2019b; Vasudeva et al, 2014). The CXB-NE nanoemulsion carrying a Nonsteroidal Anti-inflammatory (NSAID) inhibitor of COX-2 activity result in a reduction in PGE2 expression in macrophages. Using CXB-NE in rats that have peripheral nerve injury constricting the sciatic nerve relieves hypersensitivity, a pain-like behavior. The treatment also decreases inflammation associated with this chronic constriction injury (Janjic et al, 2018; Saleem et al, 2019b; Stevens et al, 2019). In this …

Redesign And Quantitative Assessment Of An Accelerated Venous Valve Fatigue Apparatus, Megan Kueh

Biomedical Engineering Undergraduate Honors Theses

Chronic venous insufficiency (CVI) is a form of cardiovascular disease that is caused when valves in the leg become incompetent. Current treatment methods serve to manage symptoms, but there are currently no ways to treat the underlying cause of CVI. A venous valve prosthetic made from a xenograft of a bovine jugular vein is one possible treatment method currently in the research phase. Prosthetic valves must be tested with an accelerated wear tester prior to approval for clinical testing. Although such testers exist for heart valves, physiological differences between heart and venous valves restrict the use those testers on venous …

Modified Stent Design For A Coronary Bifurcation Lesion, Abigail Nowell

Biological Sciences Undergraduate Honors Theses

Currently, 18.2 million adults aged 20 and older are diagnosed with Coronary Artery Disease (CAD) (Benjamin et al., 2019). Stenosis is the most common intervention. However, when a patient has a bifurcated artery, treatment becomes more difficult and is often unsuccessful. This project created a new stent and balloon complex that was tested in vitro using a gel phantom artery model. Two separate prototypes have been created and tested so far, with improvements made upon each. Testing is still underway with Prototype 2.

A Reinforcement Learning Based Control Approach For Propofol-Induced Burst Suppression, Jason C. Huang, Scott C. Tadler, Brian J. Mickey, Keith Jones

Utah Space Grant Consortium

High-dose propofol is being investigated for its potential antidepressant effect. Propofol is titrated to induce burst suppression, a specific EEG pattern. However, propofol is difficult to dose due to uncertainty in each patient’s pharmacokinetics (PK) and pharmacodynamics (PD), and the lack of a commercially available monitor of propofol concentration. Clinicians currently infer the proper drug dose after observing the EEG response to the given dose. In this report we share our development of an automated controller to optimally administer propofol-induced burst suppression. We designed a deep deterministic policy gradient (DDPG) algorithm, which includes two deep neural networks and relates a …

Development Of Fully Balanced Ssfp And Computer Vision Applications For Mri-Assisted Radiosurgery (Mars), Jeremiah Sanders

Dissertations and Theses (Open Access)

Prostate cancer is the second most common cancer in men and the second-leading cause of cancer death in men. Brachytherapy is a highly effective treatment option for prostate cancer, and is the most cost-effective initial treatment among all other therapeutic options for low to intermediate risk patients of prostate cancer. In low-dose-rate (LDR) brachytherapy, verifying the location of the radioactive seeds within the prostate and in relation to critical normal structures after seed implantation is essential to ensuring positive treatment outcomes.

One current gap in knowledge is how to simultaneously image the prostate, surrounding anatomy, and radioactive seeds within the …

Evaluation Of Tracing Techniques In The Rat Spinal Cord Using A Custom Matlab Application., Rachel M. Zalla

Electronic Theses and Dissertations

The objective of this research project is to evaluate the efficiency of traditional chemical tracing compared to dual-viral tracing for labeling long ascending propriospinal neurons (LAPNs) in the uninjured rat spinal cord, and to develop a MATLAB program which will accurately quantify this labeling.

To evaluate chemical tracing, Fluoro-Ruby (FR) was injected at the level of the axon terminals, and the number of ipsilateral labeled cell bodies at lumbar level was quantified. Similarly, two dual-viral systems were evaluated, by either injecting retro-AAV-Cre or HiRet-Lenti-Cre unilaterally in combination with a Cre-dependent adeno-associated virus. The HiRet-Lenti and FR groups labeled significantly greater …

Artifact Identification For Blood Pressure And Photoplethysmography Signals In An Unsupervised Environment, Pooi Khoon Lim

Student Works (2020-2029)

Physiological signals play a significant role in clinical diagnosis, it always acts as a major input of a decision support system. However, the physiological signal is easily corrupted by different factors especially motion artifacts. Several research works have been tried to recover the underlying physiological signal by suppressing the artifact. However, not much attention has been paid to situation where the artifact is too extreme and the artifact suppression is not possible. In this situation, physiological signal quality must be evaluated before any further assessment. In this study, an automated artifact detection algorithm was developed for Blood Pressure and PPG …

Relative Contribution Of Arms And Legs Through Repetitive Assisted Sit-To-Stand Motion In Individuals With Incomplete Spinal Cord Injury, Abd Aziz Musfirah

Student Works (2020-2029)

Sit-To-Stand (SitTS) exercise is one of important prerequisites to achieve some functional independence goals in everyday life especially for individuals undergoing rehabilitation In general, the execution of SitTS in spinal cord injury (SCI) patients involves motor function in both upper and lower extremities. The use of arm support in particular is a very significant element while executing SitTS movement for SCI population. In addition, application of functional electrical stimulation (FES) onto the quadriceps muscles is one of the prescribed management for incomplete SCI to improve muscle action for simple lower limb movements. However, the relative contribution of upper and lower …

Designing An Antibiotic Eluting Trauma Screw To Reduce Short Term Infection In Bone Fractures, Dominic Lincoln

Honors Theses

Orthopedic infection in the United States is one of the most common and severe health risks faced by trauma patients. The most prevalent infection is orthopedic and trauma device-related infection (ORDI) and often occurs in long bones at the fracture site. The purpose of this paper is to explore this infection, its causes, and solutions currently on the market while providing novel solutions to the problem. The designs proposed will be evaluated for their effectiveness and value, while attempting to keep costs low for all stakeholders. The feasibility of patenting these ideas will also be considered, as will the testing …

Biomimetic Gold Nanoshell-Loaded Macrophage For Photothermal Biomedicine, Sung Hun Kang, Yong Kyu Lee, Il Seok Park, In-Kyu Park, Seok Min Hong, Soon Young Kwon, Young Hee Choi, Steen J. Madsen, Henry Hirschberg, Seok Jin Hong

Integrated Health Sciences Faculty Research

The purpose of this study was to investigate the effect of photothermal treatment (PTT) with gold nanoshell (ANS) using a macrophage-mediated delivery system in a head and neck squamous cell carcinoma (HNSCC) cell line. To achieve this, ANS-loaded rat macrophages (ANS-MAs) were prepared via the coculture method with ANS. The human HNSCC (FaDu cell) and macrophage (rat macrophage; NR8383 cell) hybrid spheroid models were generated by the centrifugation method to determine the possibility of using ANS-MAs as a cancer therapy. These ANS-MAs were set into the tumor and macrophage hybrid spheroid model to measure PTT efficacy. Kinetic analysis of the …

Walking Kinematics In Young Children With Limb Loss Using Early Versus Traditional Prosthetic Knee Prescription Protocols, Mark Daniel Geil, Zahra Safaeepour, Brian Giavedoni, Colleen Coulter

Faculty Articles

The traditional treatment protocol for young children with congenital or acquired amputations at or proximal to the knee prescribes a prosthesis without a working knee joint, based in part on the assumption that a child learning to walk cannot properly utilize a passively flexing prosthetic knee component. An alternative to this Traditional Knee (TK) protocol is an “Early Knee” (EK) protocol, which prescribes an articulating prosthetic knee in the child’s first prosthesis, during development of crawling and transitioning into and out of upright positions. To date, no study has compared samples of children with limb loss at or proximal to …

The Natural Historian’S Guide To The Ct Galaxy: Step-By-Step Instructions For Preparing And Analyzing Computed Tomographic (Ct) Data Using Cross-Platform, Open Access Software, T. J. Buser, O. F. Boyd, A. Cortés, Cassandra M. Donatelli, M. A. Kolmann, J. L. Luparell, J. A. Pfeiffenberger, B. L. Sidlauskas, A. P. Summers

Engineering Faculty Articles and Research

The decreasing cost of acquiring computed tomographic (CT) data has fueled a global effort to digitize the anatomy of museum specimens. This effort has produced a wealth of open access digital three-dimensional (3D) models of anatomy available to anyone with access to the Internet. The potential applications of these data are broad, ranging from 3D printing for purely educational purposes to the development of highly advanced biomechanical models of anatomical structures. However, while virtually anyone can access these digital data, relatively few have the training to easily derive a desirable product (e.g., a 3D visualization of an anatomical structure) from …

Hybrid Electro-Plasmonic Stimulation Of Primary Neurons, Ratka Damnjanovic

USF Tampa Graduate Theses and Dissertations

Biomedical prosthetics utilizing electrical stimulation have limited, effective spatial resolution due to spread of electrical currents to surrounding tissue, causing nonselective stimulation. So, precise spatial resolution is not possible for traditional neural prosthetic devices, such as cochlear implants. More recently, alternative methods utilize optical stimulation, mainly infrared, sometimes paired with nanotechnology for stimulating action potentials, which has its own drawbacks, as it may heat surrounding tissue. Recently, we employed plasmonic stimulation methods utilizing gold nanoparticle-coated nanoelectrodes to convert visible light pulses into localized surface plasmon resonance transduction for stimulation of electrically excitable cells, which had limited success. Here, we report …

Computational Approach To Correcting Joint Instability In Patients With Recurrent Patellar Dislocation, Oliver Alvarez, Robert N. Steensen, Paul J. Rullkoetter, Clare K. Fitzpatrick

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Patellar dislocation is a debilitating injury common in active adolescents and young adults. Conservative treatment after initial dislocation is often recommended, but almost half of these patients continue to suffer from recurrent dislocation. The objective of this study was to compare preoperative patellofemoral joint stability with stability after a series of simulated procedures, including restorative surgery to correct to pre-injury state, generic tibial tubercle osteotomy, patient-specific reconstructive surgery to correct anatomic abnormality, less invasive patient-specific surgery, and equivalent healthy controls. Three-dimensional, subject-specific finite element models of the patellofemoral joint were developed for 28 patients with recurrent patellar dislocation. A …

How Do Surgeon Preferences And Technique Variances Affect Outcome?, Anastasia Axiopoulou, Caroline G. L. Cao, Katherine Lin Md, Keith Watson Md

Celebration of Undergraduate & Graduate Research, Scholarship, and Creative Activities Materials

The goal of the research project is to create a blue-print of a robot-assisted hysterectomy procedure to support design and evaluation of technology to enhance system performance. To create this blue-print, we will conduct a task analysis, model the cognitive task flow and decision making, and develop a simulation of the hysterectomy procedure. The surgical simulation will be used as a platform to train surgeons on robotic-assisted hysterectomies, as well as to assess learning and performance. Additionally, it will be used to design and develop techniques and novel technology to support surgeons in their performance of the surgery. Current research …

Impedance Analysis Of Tissues In Nspef Treatment For Cancer Therapy, Edwin Ayobami Oshin

Biomedical Engineering Theses & Dissertations

Nanosecond pulsed electric field (nsPEF) for cancer therapy is characterized by applications of high voltage pulses with low pulsed energy to induce non-thermal effects on tissues such as tumor ablation. It nonthermally treats tissues via electroporation. Electroporation is the increase in permeabilization of a cell membrane due to the application of high pulsed electric field. The objective of this study was to investigate the effect of nsPEF on tissue by monitoring the tissue’s impedance in real-time. Potato slices (both untreated and electroporated), and tumors extracted from female BALBc mice were studied. 100ns, 1-10kV pulses were applied to the tissues using …

Transcutaneous Auricular Vagus Nerve Stimulation-Paired Rehabilitation For Oromotor Feeding Problems In Newborns: An Open-Label Pilot Study, Bashar W. Badran, Dorothea D. Jenkins, Daniel Cook, Sean Thompson, Morgan Darcy, William H. Devries, Georgia Mappin, Philipp Summers, Marom Bikson, Mark S. George

Publications and Research

Neonates born premature or who suffer brain injury at birth often have oral feeding dysfunction and do not meet oral intake requirements needed for discharge. Low oral intake volumes result in extended stays in the hospital (>2 months) and can lead to surgical implant and explant of a gastrostomy tube (G-tube). Prior work suggests pairing vagus nerve stimulation (VNS) with motor activity accelerates functional improvements after stroke, and transcutaneous auricular VNS (taVNS) has emerged as promising noninvasive form of VNS. Pairing taVNS with bottle-feeding rehabilitation may improve oromotor coordination and lead to improved oral intake volumes, ultimately avoiding the …

Total Knee Arthroplasty Gap Balancer, Christina Grigorian, Andrew Beckley, Alexandra Rockett

Biomedical Engineering

California Polytechnic State University’s Biomedical Engineering Department worked in conjunction with local San Luis Obispo orthopedic surgeon Dr. Dimitri Delagrammaticas. The goal of the project was to create a surgical tool that assists a surgeon in measuring knee gap distance and balancing collateral ligament tension during a total knee arthroplasty (TKA) surgery. The final product of this project was completed in five months and initially began with understanding our sponsor’s expectations for the device. A portion of time was devoted to conducting research to understand the process of a knee replacement surgery, the requirements of the device, and the limitations …

Left Atrial Appendage Printing Process, Areli Reyes, Brandon James Mukai, Mia Noelle Von Knorring

Biomedical Engineering

The left atrial appendage senior design team aims to assist in closing off the left atrial appendage that is susceptible to coagulation due to non-valvular atrial fibrillation. Coagulation in the left atrial appendage (LAA) can be life threatening as it can lead to a stroke. Dr. Chris Porterfield performs a procedure that uses the Boston Scientific Watchman to close the appendage. He finds that sizing the Watchman properly is difficult with limited visuals from live CT scans. He proposed converting the CT scans into a 3D printed model of the left atrial appendage and left atrium so he can visually …

Gesea Biosciences - Core Shell Pellet Manufacturing Device, Claire Edelman, Maria Medrano, Rachel Longoria

Biomedical Engineering

No abstract provided.

Barn-Raising On The Digital Frontier: The L.A.U.N.C.H. Collaborative, Bradford W. Hesse, David Ahern, Michele Ellison, Eliah Aronoff-Spencer, Robin C. Vanderpool, Karen Onyeije, Michael C. Gibbons, Timothy W. Mullett, Ming-Yuan Chih, Victoria Attencio, Grant Patterson, Jessica Boten, Christopher Hartshorn, Ben Bartolome, Katie Gorscak, Melanie Mccomsey, Alexandra Hubenko, Bin Huang, Corey Baker, Don Norman

Journal of Appalachian Health

A meta-analysis of oncology papers from around the world revealed that cancer patients who lived more than 50 miles away from hospital centers routinely presented with more advanced stages of disease at diagnosis, exhibited lower adherence to prescribed treatments, presented with poorer diagnoses, and reported a lower quality of life than patients who lived nearer to care facilities. Connected health approaches—or the use of broadband and telecommunications technologies to evaluate, diagnose, and monitor patients beyond the clinic—are becoming an indispensable tool in medicine to overcome the obstacle of distance.

Experimental And Computational Tools For Single Cell Analysis In Cancer Diagnostics, Manibarathi Vaithiyanathan

LSU Doctoral Dissertations

Substantial evidence shows that cellular heterogeneity commonly exists within an isogenic or clonal population. Whether in isolation or caused through a combination of the above events, cellular heterogeneity can dramatically influence cellular decision making and cell fate, however, this can be masked by the average response from a population. One approach to solve this issue is to analyze a population at the individual cell level. The goal of this work is to develop high-throughput experimental and computational platforms to screen and quantify single cancer cells for specific intracellular enzyme activities. An interdisciplinary approach was taken to 1) better understand the …

Investigation Of Physiochemical Properties And Biocompatibility Of Amourphos Calcium Polyphosphate Hydrogel Doped With Antibiotics And Injectable Polymeric Dicalcium Phosphate Dihydrate Bone Cement, Yasaman Chehreghanianzabi

Wayne State University Dissertations

Amorphous calcium polyphosphate (ACPP) is an inorganic polymer ceramic. Here we use a simple method of preparing ACPP hydrogel in the presence of excess volume of water. Essentially, water availability to polyphosphate chains accelerates water molecule ingress and microstructural transformation of ACPP hydrogels. Antibiotic delivery capacity of ACPP hydrogel increases by the specific mixing and molding method, where the VCM has higher antibiotic encapsulation efficiency with the small burst release for the compressed discs. In part of this study, we investigate impact of ACPP hydrogel replacement by monomeric calcium phosphate on the quality of final product (dicalcium phosphate dihydrates (DCPD) …