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Class of 2020 MS & PhD Thesis Titles

Master's Thesis

The NEVRland Platform: An Immersive Virtual Reality Experimentation Platform for Research in Neuroergonomics

Optimizing Stability of Engineered Anti-RAS bioPROTAC for Rapid Degradation of Undruggable Proteins

MicroTraitLLM: A Microbial-focused Large Language Model for Researchers

TGF-β Dominant Negative Receptor Equipped CAR-iT and iNK Cells for Enhanced Killing in Bladder Cancer Tumor Microenvironment

Development and Optimization of GelMA Hydrogels for Controlled Dual-Drug Release in Chronic Wound Healing

Development of CF-PEKK Composite Bone Plates via 3D Printing and Pressing for Void Reduction and Improved Mechanical Strength

Point-of-Care Additive Fused Filament Manufacturing of Patient-Specific Triflange Acetabular (TA) Reconstruction Implants

Magnetically Levitated Axial Flow Blood Pump for Pediatric Total Artificial Heart

Statistical Shape Modeling of Pelvic Anatomy: Design Envelope for Future Acetabular Implant Reconstructions and Statistical Shape Model Based on 15th-90th Percentile Ranges of Male and Female CT Scans

Identifying Neurophysiological Biomarkers Derived From fNIRS To Quantify Cognitive Workload During a UAS Mission

Investigating Eye Tracking Features in a Machine Learning Classifier To Assess Cognitive Workload During Simulation Based Training

3D-Printing at the Point-of-Care: Patient-Specific PEKK Ankle Fusion Implants for Diabetic Patients

Development of Finite Element Models of Maternal Pelvis, Fetus and Brachial Plexus

Using Supramolecular Chemistry To Develop Injectable Hydrogel Composites for Multi-Drug Delivery

Design of “Armored” Lipid-Based Nanoparticles for Prolonged Drug Circulation via Complement Pathway Attenuation

Aqueous CdSe Quantum Dot Molecular Beacon for RNA Detection

Exploring Biokinetics of Metal-Ion Release in Total Knee Arthroplasty: A Modeling Approach

Characterizing Aware and Unaware Vehicle Occupant Responses During Sled-Simulated Evasive Swerving: The Effect of Age and Maneuver Duration

Developing Mutant KRAS Targeted Vaccines for Pancreatic Cancer Interception

Combining Systems Biology Markup Language (SBML) Models in the Context of Cellular Aging Mechanisms

Mitochondrial Sequencing and Single-Cell RNA Sequencing Combination: A Promising Technique To Effectively Understand the Cell Dynamics in Breast Cancer

Hydrogel Scaffold for Neural Stem Cell Transplantation in Spinal Cord Injuries

Evaluation of Cognitive Function Using Time-Domain Optical Neuroimaging

Prediction of ADHD in Adolescents Utilizing fMRI-Based Individual Cortical Thickness Measurements

Development of a Finite Element Model of the Thoracic and Lumbar Spine with Ribs for Idiopathic Early Onset Scoliosis (EOS)

Acoustic Coupling Pads for the Control of Ultrasound Neuromodulation Exposure

Development and Characterization of Covalently Crosslinked Hydrogels for Use in Geometrically Tunable Blood Shunts

Local Delivery of Polycations From a Hydrogel Scaffold for Treating Spinal Cord Injury

A Pipeline for the Creation of Biophysically Realistic Multicompartment Models of Drosophila Melanogaster Descending Neurons (MDN)

Implementation of a Home-Use Virtual Environment Brain-Computer Interface (BCI) for People with ALS Using Different Facial Stimuli

Quantifying Lung, Diaphragm, and Thoracospinal Radiographic Parameters to Predict Lung Volume and Function in Pediatric Normative and Early Onset Scoliosis Subjects

Simeon Kofman, Master’s Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisors:
Liang Oscar Qiang, MD, PhD
Assistant Professor
Department of Neurobiology and Anatomy
Drexel University College of Medicine

Fred Allen, PhD
Teaching Professor
Associate Dean for Undergraduate Education
School of Biomedical Engineering, Science and Health Systems
Drexel University

Development of a Next Generation Human Induced Pluripotent Stem Cell-derived CNS Model for the Study of Tauopathy

Emma Katherine MacNeil, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Kurtulus Izzetoglu, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Investigating the Performance of Sensor-driven Biometrics in the Assessment of Cognitive Workload

Pratishtha Guckhool, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Catherine von Reyn, PhD
Assistant Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

The Role of DIPs and Dprs in Synaptic Connection Specificity

Jillian Clare Saunders, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisors:
Catherine von Reyn, PhD
Assistant Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Denise Garcia, PhD
Associate Professor
Department of Biology
College of Arts and Sciences
Drexel University

Identification of Astrocyte Subtypes in the Drosophila Melanogaster Visual System

Joy Anita Iaconianni, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisors:
Sriram Balasubramanian, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Anita Singh, PhD
Chair of Biomedical Engineering
Associate Professor
Department of Biomedical Engineering
School of Engineering
Widener University

Mathematical Dynamic Modeling (MADYMO) of Shoulder Dystocia and Delivery Maneuvers

Victor Mishin, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisors:
Christopher B. Rodell, PhD
Assistant Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Amy L. Throckmorton, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Photoresponsive Hydrogels Enable Geometrically Tunable Blood Shunts for Pediatric Use

Virginia Orozco, PhD Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisors:
Sriram Balasubramanian, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Anita Singh, PhD
Chair of Biomedical Engineering
Associate Professor
Department of Biomedical Engineering
School of Engineering
Widener University

Investigating Biomechanical Properties and Structural Changes Post-Stretch in Neonatal Brachial Plexus

Alison Kane, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisors:
Janarthanan (Janar) Sathananthan, BHB, MBChB, MPH, FRACP
Interventional and Structural Cardiologist
University of British Columbia (UBC)
St Paul’s Hospital and Vancouver General Hospital

Amy Throckmorton, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Exploring the Responses of Acute Aortic Regurgitation (AR) Through the Design of a Novel Benchtop Physiological Model

Benchtop physiological modeling using a flow loop is a necessary requirement for medical device manufacturers both for the development and the commercial approval of devices. Custom models are frequently created to meet these needs regarding specific anatomical and hemodynamic parameters required to the test cardiovascular devices. Since response to aortic regurgitation (AR) in humans cannot be ethically studied, animal models can be used as a surrogate; however, the expense of these models raises a need for a benchtop model capable of mimicking specific responses. This custom model has been designed for an end user to respond appropriately to acute AR while remaining compliant with certain standards governing traditional benchtop testers.

Kevt’her Hoxha, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Lin Han, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Poroelasticity of Fibrocartilage is Governed by the Collagen Fibrillar Structure and Proteoglycan Content of the Extracellular Matrix

The synovial joint of the knee is essential for shock absorption and joint lubrication during locomotion. For high frequency activities, such as running and jumping, the shock absorption function is governed by the fluid flow-induced poroelasticity of cartilage, in which, the interstitial fluid pressurization arises due to the densely packed, highly negatively charged aggrecan in the cartilage extracellular matrix (ECM). The meniscus acts as a key functional unit of the knee joint, enhancing congruency, providing direct load transmission to cartilage, and increasing joint stability.

Aakankschit Nandkeolyar, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Hasan Ayaz, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

A Computational Approach To Explore the Link Between Serum Biomarkers and Clinical Outcomes in Psoriasis

Psoriasis is a chronic autoimmune skin disease that affects nearly 2% of the world’s population. It is characterized by the formation of red plaques on the skin. Such plaques can cause irritation and pain to patients, not to mention the plaques are a major source of anxiety related to appearance for patients, making psoriasis a disease with high morbidity. While there are currently no cures for psoriasis, anti-inflammatory pharmaceuticals can be used to treat psoriasis by reducing the severity of the symptoms. The efficacy of treatments for psoriasis is measured by improvement in clinical outcomes, the most popular of which is Psoriasis Area Severity Index Score (PASI). These scores are provided by a dermatologist to quantify the severity of psoriasis in a patient. Quantitative Systems Pharmacology (QSP) is a new field in the area of computational disease modeling that allows for quantification and prediction of disease serum biomarkers in virtual patient models. Such prediction can potentially be correlated with clinical outcomes, such as PASI scores, to allow a scientist to predict clinical outcomes in virtual patients. The current study proposes the use of machine learning algorithms to bridge the gap between QSP simulation data for serum biomarkers and clinical outcome measures to predict PASI scores post-treatment to potentially reduce cost and time for clinical trials.

Kimtee Dahari Ramsagur, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Kurtulus Izzetoglu, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Personalized Rebreathing Device for Hypercapnia Administration

Cerebrovascular reactivity (CVR) is the ability of cerebral vessels to dilate or constrict in response to vasoactive challenges. CVR has been shown to be an important biomarker for diagnosing and monitoring neurological disorders. Assessment of CVR commonly requires a hypercapnic challenge, which is the elevation of the partial arterial carbon dioxide (CO2) level or end-tidal CO2 level (EtCO2). Current methods used to induce hypercapnia consist of breath holding, fractional inspired CO2, or sequential gas delivery. Limitations of the existing systems are that they are either not portable, require manual operations, take a long time to set-up, or do not induce an accurate and precise hypercapnic stimulus. Therefore, there is a need to develop a personalized, portable, and automated gas delivery system that induces hypercapnia in a controlled manner.

Raj Patel, MS Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Margaret A. Wheatley, PhD
John M. Reid Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Development of a Co-loaded Lonidamine and Paclitaxel Ultrasound Contrast Agent for Treatment of Multi-Drug Resistant Tumors

Multi-drug resistance (MDR) is a condition often found in breast cancer that significantly reduces the efficacy of chemotherapy. Many factors contribute to this, including tumor hypoxia, which further serves to increase the resistance of tumors to radiotherapy. Combination therapy has been shown to be effective at reversing the effects of MDR through the combined effects of various therapeutics targeting different mechanisms of the tumor. One such combination involves the co-delivery of lonidamine (LND) and paclitaxel (PTX), which has shown greater efficiency in treating and reversing MDR tumors than the delivery of single drug alone. Multimodal therapy takes this principle a step further, and employs combinations of chemotherapy, radiotherapy, surgery, and phototherapy to treat cancer, and has shown greater survival rates in patients than monomodal therapy alone. Currently, our group has developed a LND loaded D-α-Tocopherol polyethylene glycol 1000 succinate (TPGS) and sorbitan monostearate surfactant stabilized microbubble (LND-SE61 MBs) with an oxygen core for the application of sensitizing hypoxic tumors to radiotherapy. This MB also doubles as an ultrasound contrast agent (UCA), allowing for enhanced ultrasound imaging. The aim of this proof-of-principle study was to further leverage the LND-SE61 MB to include PTX within its surfactant shell in an effort to expand its capability to treat MDR tumors using chemotherapy, as well as to make the tumor more sensitive to radiotherapy, through a multimodal approach.

Marina Korinne Lilieholm, MS Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Alessandro Fatatis, MD, PhD
Professor
Department of Pharmacology and Physiology
College of Medicine
Drexel University

Fabrication of a Novel Filtration Device for Circulating Tumor Cells

More than 90% of cancer-related deaths are caused by metastasis, which is caused by circulating tumor cells (CTCs). CTCs are shed by the primary tumor, enter the systemic blood circulation before lodging in distant organs, where they seed secondary colonies. Of all tumor cells that disseminate, only a few possess the genetic profile to initiate colonization. Enumeration and molecular analysis of these rare cell populations collected through liquid biopsy possesses inherent clinical relevance and yields insight into the biology of metastasis. However, enrichment of CTCs from whole blood is encumbered by their rarity (approximately 1 CTC for every 105 to 106 peripheral blood mononuclear cells (PBMCs)) and limited to antibody-dependent and independent capture techniques. Antibody-independent methods are preferred because they capture CTCs in an unbiased fashion; however, these methods deliver excessively diluted cell suspensions, with a few hundred cells in five to ten mL of fluid. Recovery of these cells by centrifugation is lengthy, induces cell damage, is overall incompatible with systematic investigation and has so far prevented full integration of CTC analysis into clinical practice. For these reasons, over the last two decades, CTCs evaluation has been dominated by antibody-dependent staining on chip, significantly limiting our breadth of knowledge. Herein we describe the design and production of a device capable of collecting CTCs from diluted suspensions and re-eluting them into a 10-fold smaller volume, thus allowing to bridge the technological gap between CTC capture from blood and downstream molecular analyses.

Roze Alzabey, MS Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Catherine von Reyn, PhD
Assistant Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

A Comparison of Drosophila Melanogaster RNA-seq Data Sets

RNA sequencing (RNA-seq) has been established as a high throughput sequencing method that provides gene expression profiling. However, with the vast amount of data generated through RNA-seq, it remains a challenge to extract meaningful interpretations of the data. In addition, RNA-seq library preparation requires multiple steps, and there remains to be differences in techniques at various levels of the process, and a lack of standardized methods to compare across different datasets.

Andrew G. Dai, PhD Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Hasan Ayaz, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

NeuroHub Fog: Wireless Network Time Synchronization Device for Multimodal Brain Imaging and Hyperscanning Research

Brain computer interfaces have a variety of applications including but not limited to neuroscience, engineering, computer science, psychology, and rehabilitation. With a wide range of disciplines and advancing technologies, there is a growing interest, especially in using multiple systems concurrently in multimodal/hybrid configurations to extract complimentary aspects of brain activity, and in measuring multiple brains using hyperscanning configurations to investigate brain activities in social interactions. The use of functional neuroimaging in brain computer interface protocols such as functional near infrared spectroscopy (fNIRS) and electroencephalography (EEG) require precise time synchronized transmission of experimental events and acquired data for proper analysis and interpretation. A scalable, portable device that can act as a bridge between multiple monitoring systems with different communication protocols is required for ensuring practicality of these experimental setups. A challenge is presented with the complexity of having multiple brain and body sensors and providing a proper timing of event markers and data acquisition. The original NeuroHub device, developed at Drexel University, offered time synchronization capabilities through four serial ports, a TTL port, and a parallel port. The following generation of NeuroHub was designed as a modular expansion to the original device in order to offer wireless communications to accommodate for modern computing systems with more complex options.

PhD Thesis

Improved Methods for Detection and Prioritization of Structural Variants from Long-read Sequencing Data

Role of Dopaminergic Descending Neurons in the Control of Locomotion in Drosophila

Characterization of Genomic Regions for Improved Reference Genomes Using Optical Mapping (OM) and Sequencing Technologies

Development and Clinical Application of an Arduino-based Functional Near Infrared Spectroscopy (fNIRS)

Regulatory Roles of Fibril-Forming Collagens in Cartilaginous Tissue Biomechanics and Mechanobiology

Debra V. Klopfenstein, PhD Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Will Dampier, PhD
Assistant Professor
Department of Microbiology and Immunology
College of Medicine
Drexel University

Protein-coding Hotspots in the Human Genome: Annotation, Significance, and Their Conservation in Animal Models

Uncovering understudied genes that are not yet associated with disease, but that have common functions with nearby genes that are not in the same gene family, can lead towards further understanding of these molecular mechanisms and may reveal novel drug targets. Previous studies of utilizing population genetics approaches did not focus on the chromosomal topology of a large number of major diseases on the human genome.

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