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.

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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Class of 2020 MS & PhD Thesis Titles

Master's Thesis

PhD Thesis