Biomedical Engineering and Bioengineering Commons^™

Predicting Depression Progression Rates In Radiotherapy Patients, Ardella Phoa, Joshua Vincent, Shani Williams

Bioengineering Senior Theses

Cancer is a highly prevalent disease that affects millions of people worldwide. In addition to the physiological effects of the disease, cancer patients are more likely to be diagnosed with Major Depressive Disorder (MDD). Unfortunately, prior research has shown that MDD can also decrease the efficacy of radiotherapy cancer treatments. Currently, there is no way to predict, prevent, or mitigate this comorbidity, preventing physicians from administering supplemental therapies. In this paper, we propose a low-cost and efficient computational tool that can be utilized to quantify a patient’s likelihood of developing depression. To do so, we used PET images and a …

In Vivo Non-Ribosomal Protein Synthesis In Mammalian Cells, Akhil Choppa

Bioengineering Master's Theses

The mechanism of Sortase A substrate specificity has been widely studied and applied to many approaches to bioconjugation. Current research includes transpeptidation between peptide nucleotide acids, polypeptides, viruses, or antibodies. These applications help improve drug targeting and delivery. Scientists have performed Sortase A-mediated protein ligation in vitro. This project proposes an in vivo protein ligation method with Sortase A. In this design, Sortase A acts as a catalyst to initiate bioconjugation between the LPETG motif and pentaglycine (Gly5) chain to express GFP. This technique bypasses the ribosome and offers an alternative way to synthesize protein in mammalian cells. Three recombinant …

Microfluidic Liquid Biopsy For Cancer Prognosis, Brendan Heap, Anthony Ramirez Guerrero, Sam Nichols

Bioengineering Senior Theses

Leukemia is a deadly and common cancer, especially in children and adolescents. The misdiagnosis and unexpected complications during the treatment are some factors that increase the mortality rate of leukemia. The goal of our project was to create a device that would quickly and accurately assess these complications. While there are existing tests that can perform a single test for either metastasis or sepsis, there are none that can test for both simultaneously and rapidly. We propose to modify and combine some of these existing microfluidic designs as well as create a new component to perform a combinatorial assessment. While …

Developing A Skin Phantom For The Testing Of Biowearables, Tawni Henderson, Ju Young Lee, Matthew Placide, Kiran Sutaria

Interdisciplinary Design Senior Theses

There is a demonstrated need in the biowearables industry for a benchtop model that can accurately emulate the perspiration mechanism and corresponding impedance vs. frequency spectra of skin. This model, or skin phantom, could increase the efficiency and accuracy of early-stage testing of biowearables, as well as minimize animal, human, and cadaver testing.

The objective of this project is to develop a skin phantom that can emulate the perspiration mechanism and impedance spectrum behavior of human skin for the testing of biowearables in the 2,000 - 20,000 Hz range. We also endeavored to create computer-simulated models to aid in the …

Sustainable, Alginate-Based Sensor For Detection Of Escherichia Coli In Human Breast Milk, Nicholas Kikuchi, Margaret May, Matthew Zweber, Jerard Madamba, Craig M. Stephens, Unyoung Kim, Maryam Mobed-Miremadi

Bioengineering

There are no existing affordable diagnostics for sensitive, rapid, and on-site detection of pathogens in milk. To this end, an on-site colorimetric-based sustainable assay has been developed and optimized using an L₁₆ (5⁴) Taguchi design to obtain results in hours without PCR amplification. To determine the level of Escherichia coli (E. coli) contamination, after induction with 150 µL of breast milk, the B-Per bacterial protein extraction kit was added to a solution containing an alginate-based microcapsule assay. Within this 3 mm spherical novel sensor design, X-Gal (5-Bromo-4-Chloro-3-Indolyl β-_D-Galactopyranoside) was entrapped at a concentration of 2 …

Role Of Nanoparticle–Polymer Interactions On The Development Of Double-Network Hydrogel Nanocomposites With High Mechanical Strength, Andrew Chang, Nasim Babhadiashar, Emma Barrett-Catton, Prashanth Asuri

Bioengineering

Extensive experimental and theoretical research over the past several decades has pursued strategies to develop hydrogels with high mechanical strength. Our study investigated the effect of combining two approaches, addition of nanoparticles and crosslinking two different polymers (to create double-network hydrogels), on the mechanical properties of hydrogels. Our experimental analyses revealed that these orthogonal approaches may be combined to synthesize hydrogel composites with enhanced mechanical properties. However, the enhancement in double network hydrogel elastic modulus due to incorporation of nanoparticles is limited by the ability of the nanoparticles to strongly interact with the polymers in the network. Moreover, double-network hydrogel …

Scale Optimization Of Milkguard Biosensor For Detecting E. Coli In Human Breast Milk, Jerard Roniel Del Rosario Madamba

Bioengineering Master's Theses

Milkguard is an alginate-based biosensor developed to detect E. coli in human breast milk via the metabolism of X-gal (5-Bromo-4-Chloro-3-Indolyl β-D-Galactopyranoside) by β-galactosidase. In order to deconvolute metabolic reproducibility from scaling laws, the commercial enzyme β-galactosidase was used to mimic the biological function of the bacterial lac operon. Downscaling was explored as an optimization of the biosensor design based on numerical solutions to Fickian-based diffusion models. The characterization of large capsules (d ≅ 3 mm) and atomized microcapsules (d ≅ 300 ± 60 μm) yielded size-specific Michaelis-Menten constants. Small capsules (K_m = 3.6 x 10^-4 M; Vmax ’’ …

Epic: Examining Patch Impedance Characteristics, Shane Buck, Jyotsna Gopinath, Kyle Markfield

Interdisciplinary Design Senior Theses

In the United States, approximately one in 4 adults have at least one chronic illness, making up approximately 84% of US Healthcare Spending. Unfortunately, 50% of patients with chronic diseases do not take their medication properly and as such spend more money trying to get better – approximately $100 billion in annual preventable costs. One solution to this issue is digital medicine as it allows for the monitoring of patient medicine consumption.

Our industry partner has developed a three-part digital medicine system with the aim of allowing patients with chronic health issues to better reach their health goals through monitoring …

Justrun - Social Gps Running Game, Riley Bergin, Maggie Cai, Simran Judge, Grace Ling

Interdisciplinary Design Senior Theses

With advances in technology allowing people to live more sedentary lives, more and more people are struggling to live a healthy active lifestyle. In the efforts to combat unhealthy styles of living, we wish to introduce a mobile app that takes advantage of motivational game mechanics to motivate players will make go on runs regularly.

Anti-Infective Mechanism-Based Drug Discovery Via Sortase A, Huong Chau, Alice Matsuda, Leepakshi Johar

Bioengineering Senior Theses

Sortase A is a transmembrane protein prominent in gram-negative bacterial strains. It is a virulence factor that anchors other proteins, which facilitate MRSA infections. In the long term, we plan to utilize this protein to create anti-infective drugs as antibiotic resistance continues to become a global health issue. Starting with five NIH drug candidates, we decided to first study Sortase A with B12 due to its historical past of ancient civilizations using natural sources of B12 to treat infections. Our senior design is further centered around understanding how vitamin B12 interacts with Sortase A in vitro, particularly the binding affinity …

Effects Of Glycation On Blood Protein Interactions With Nanomaterials: A Biophysical And Cytotoxicity Study, Karl Baumgartner, Madeline Eiken

Bioengineering Senior Theses

When engineered nanoparticles (NPs) enter into a biological system, the proteins and biomolecules in the system adsorb to the NP surface to form a “protein corona” (PC). The PC greatly influences NP transformations, biological interactions, and cell response. Further complicating the development of NPs for biomedical applications, disease states alter the population of proteins and changes the biophysical features of individual proteins through posttranslational modifications. Here-in, we aim to understand how glycation of the PC, as in uncontrolled diabetes, alters the NP-PC interaction and toxicity by conducting biochemistry and cell toxicity experiments. We focus upon 40 and 80 nm citrate-coated …

Cervis: Cervical Cancer Early Response Visual Identification System, Julia Lanoha, Claire Hultquist, Rosie Mcdonagh, Hallie Mcnamara

Bioengineering Senior Theses

The goal of CERVIS is to make a substantial, positive impact in the cervical cancer screening space through the development of a minimally invasive, cost effective solution that enables women in low-resource settings to test for cervical cancer on a frugal and effective platform. In the developed world, there are a variety of options that can aid in early detection, including Pap smears. However, due to the high cost and laboratory requirements that accompany this procedure, women in low-resource settings rarely have access to this preventative care or regular screenings for cervical cancer. Using new research about the changes in …

Microfluidic Chip For High Efficiency Microinjection Of Caenorhabditis Elegans, Delaney Gray, Alex Hadsell, Jessica Talamantes

Bioengineering Senior Theses

The terrestrial nematode, Caenorhabditis elegans, is an invaluable model organism for the study of molecular and cellular processes due to their small size, rapid generation time, easy cultivation, and invariant cell number. Additionally, 40% of genes known to be associated with human disease have clear orthologs in the C. elegans genome. In C. elegans genetics research, microinjection of genetic material into the worms is critical. Although an established technique, manual microinjection is tedious, low-throughput, and requires an expert researcher. This thesis details a novel microfluidic device designed to perform high-throughput microinjection. This two-layer, PDMS-based chip integrates microfluidic elements to …

Automated Atrial Fibrillation Detection From Electrocardiogram, Senbao Lu

Bioengineering Master's Theses

In this study, a novel Atrial Fibrillation (AFib) detection algorithm is presented based on Electrocardiography (ECG) signals. In particular, the spectrogram of ECG signal is used as an input to a Convolutional Neural Network (CNN) to classify normal and AFib ECG signals. This model is shown to perform well with an accuracy of 92.91% and a value of 0.9789 for the area under the ROC curve (AUC). This study demonstrated the potential of using image classification methods and CNN model to detect abnormal biosignals with noise.

Machine Learning Solution To Organ-At-Risk Segmentation For Radiation Treatment Planning, Brie Goo, Katrina May, Haobo Zhang, James Olivas

Interdisciplinary Design Senior Theses

In the treatment of cancer using ionizing radiation, it is important to design a treatment plan such that dose to normal, healthy organs is sufficiently low. Today, segmentation requires a trained human to carefully outline, or segment, organs on each slice of a treatment planning computed tomography (CT) scan but it is laborious, time-consuming, and contains intra- and inter-rater variability. Currently, existing clinical automation technology relies on atlas-based automation, which has limited segmentation accuracy. Thus the auto-segmentations require post process editing by an expert. In this paper, we propose a machine learning solution that shortens the segmentation time of organs-at-risk …

Human-Centered Electric Prosthetic (Help) Hand, Jamie Ferris, Shiyin Lim, Michael Mehta, Evan Misuraca

Interdisciplinary Design Senior Theses

Through a partnership with Indian non-profit Bhagwan Mahaveer Viklang Sahayata Samiti, we designed a functional, robust, and and low cost electrically powered prosthetic hand that communicates with unilateral, transradial, urban Indian amputees through a biointerface. The device uses compliant tendon actuation, a small linear servo, and a wearable garment outfitted with flex sensors to produce a device that, once placed inside a prosthetic glove, is anthropomorphic in both look and feel. The prosthesis was developed such that future groups can design for manufacturing and distribution in India.

Assessment Of Hand Gestures Using Wearable Sensors And Fuzzy Logic, Angel Cardenas, Ryan Messersmith, Will Newcomb

Bioengineering Senior Theses

Hand dexterity and motor control are critical in our everyday lives because a significant portion of the daily motions we perform are with our hands and require some degree of repetition and skill. Therefore, development of technologies for hand and extremity rehabilitation is a significant area of research that will directly help patients recovering from hand debilities sustained from causes ranging from stroke and Parkinson’s disease to trauma and common injuries. Cyclic activity recognition and assessment is appropriate for hand and extremity rehabilitation because a majority of our essential motions are cyclic in their nature. For a patient on the …

Nebuflask: Advancing Usability Of Nebulizers To Increase Patient Compliance, Murray Bartho, Michael Breshock, Megan Nolte

Bioengineering Senior Theses

Nebulizers are ubiquitous in the world of medicine. Any patient diagnosed with asthma, pneumonia, cystic fibrosis, chronic obstructive pulmonary disorder (COPD), or any other severe lung disease often use a nebulizer in order to deliver medication to the lungs. Although these technologies are quite common, they are surprisingly outdated. The most commonly used nebulizers today are bulky, loud, awkward to carry around, and must be plugged into an outlet. These aspects of the nebulizer make it a nuisance to use in general and almost impossible to use outside of the home or clinic. The ultrasonic and mesh nebulizers do address …

High-Throughput, Portable Microfluidic Aptamer Assay, Atticus Mccoy, Matthew Curtin

Bioengineering Senior Theses

Aptamer-based assays are a powerful platform for sensing a wide variety of biochemical targets, including drugs, disease biomarker, and biomolecules. However, aptamer assays often lack rapid identification and high-throughput screening. Performing an aptamer-based assay on a microfluidic device is a promising solution to increase throughput, portability, and sensitivity. In this paper, we present a microfluidic device capable of running aptamer-based assays. Our device utilizes normally-closed valves and a central micropump to move fluids throughout the chip. One chip could theoretically be scaled up to run multiple assays, and multiple of these microfluidic devices could be run in parallel to increase …

Noninvasive Screening Of A Fecal Biomarker For Human Necrotizing Enterocolitis (Nec), Daniela Campa, Kyle Sullivan

Bioengineering Senior Theses

Necrotizing enterocolitis (NEC) is a disease that predominantly affects preterm infants. Of the 10% of preterm neonates that develop NEC, about one in four cases results in death. The pathophysiology presents as inflammation of intestinal epithelial cell lining and subsequent tissue death, sometimes resulting in intestinal perforations. The underlying mechanisms have yet to be comprehensively identified. Diagnosis--the rate limiting step in reducing critical disease-onset-to-treatment time--is based on relatively nonspecific signs, impeding early and accurate diagnosis. This project, a collaborative effort between Santa Clara and Stanford Universities, aims to improve current diagnostic methods by identifying the first verifiable and useful fecal …

Exploring The Role Of Nanoparticles In Enhancing Mechanical Properties Of Hydrogel Nanocomposites, Josergio Zaragoza, Scott Fukuoka, Marcus Kraus, James Thomin, Prashanth Asuri

Bioengineering

Over the past few decades, research studies have established that the mechanical properties of hydrogels can be largely impacted by the addition of nanoparticles. However, the exact mechanisms behind such enhancements are not yet fully understood. To further explore the role of nanoparticles on the enhanced mechanical properties of hydrogel nanocomposites, we used chemically crosslinked polyacrylamide hydrogels incorporating silica nanoparticles as the model system. Rheological measurements indicate that nanoparticle-mediated increases in hydrogel elastic modulus can exceed the maximum modulus that can be obtained through purely chemical crosslinking. Moreover, the data reveal that nanoparticle, monomer, and chemical crosslinker concentrations can all …

Three-Dimensional (3d) Printed Microneedles For Microencapsulated Cell Extrusion, Chantell Farias, Roman Lyman, Cecilia Hemingway, Huong Chau, Anne Mahacek, Evangelia Bouzos, Maryam Mobed-Miremadi

Bioengineering

Cell-hydrogel based therapies offer great promise for wound healing. The specific aim of this study was to assess the viability of human hepatocellular carcinoma (HepG2) cells immobilized in atomized alginate capsules (3.5% (w/v) alginate, d = 225 µm ± 24.5 µm) post-extrusion through a three-dimensional (3D) printed methacrylate-based custom hollow microneedle assembly (circular array of 13 conical frusta) fabricated using stereolithography. With a jetting reliability of 80%, the solvent-sterilized device with a root mean square roughness of 158 nm at the extrusion nozzle tip (d = 325 μm) was operated at a flowrate of 12 mL/min. There was no significant …

Production Of Living Nanoparticles For Blood Cancer Therapy, Michael Pierotti, Matthew Piro, Peter Mitchell

Bioengineering Senior Theses

Current cancer therapies leave much to be desired because they are very harmful to the patient and cause a significant decrease in quality of life. Chimeric Antigen Receptors (CAR) are a promising novel approach for treating specific types of leukemia due to their binding affinity for proteins expressed solely on leukemia B cells. This approach increases specificity of how cells receive treatment, thus allowing for the destruction of cancerous cells while leaving the healthy cells unharmed. In this experiment, we show that production of CAR expressing exosomes (liposome like vesicles produced naturally by human cells) is possible through cell transfection. …

Influence Of Macromolecular Crowding And Confinement On Enzyme Activity And Structure Under Native And Denaturing Conditions, Steven Long, Jeffrey Kunkel, Prashanth Asuri

Bioengineering

It is now well appreciated that both crowding and confinement influence enzyme structure and function due to excluded volume effects; however, the relative efficacies of these environments on protein fates remain unclear due to a lack of direct comparison studies. In this study, we explore the use of the biopolymer alginate to develop an in vitro platform to investigate the effects of both crowding and confinement on the behavior of two model enzymes - horseradish peroxidase and β-galactosidase. Alginate, in its solution phase, can be used as a crowding agent and, in its gel phase by crosslinking using divalent cations, …

Lysosomal Delivery Of Bioactive Proteins To Living Human Cells Via Engineered Exosomes, Daniel Levy

Bioengineering Master's Theses

Exosomes are naturally secreted nanovesicles derived from mammalian cells that are used for intercellular communication in vivo. As a result, they can potentially be used for intracellular delivery of therapeutics for disease treatment. We have developed an exosome pseudotyping approach using vesicular stomatitis virus glycoprotein (VSVG) to produce protein chimeras that optimize production of modified exosomes containing protein therapeutics and facilitate effective delivery to their target cells. To the VSVG transmembrane scaffold, we have fused both fluorescent and luminescent reporters for exosome tracking/visualization and quantification of activity respectively. Through our design, we have shown the biogenesis of VSVG modified exosomes …

Engineering Nanoscale Exosomes For Lysosomal Delivery Of Bioactive Enzymes, Mai Anh Do

Bioengineering Master's Theses

There are at least 50 lysosomal storage diseases that are caused by accumulation of a substrate due to a defective enzyme. Although some treatment options are available, low efficacy, high cost, and immunogenicity are main challenges of current treatments. To overcome those limitations, we use cell-derived nanoparticles to deliver biologically active cargos into lysosomes. Naturally produced exosomes can deliver proteins without triggering an immune response. Additionally, exosome have an intrinsic ability to cross blood brain barrier benefiting patients at a late disease stage that affects the brain. After fusing either Gaussia luciferase (gLuc) or puromycin resistant protein (puro) onto a …

Active Auxetic Heel Support For Achilles Tendon Therapy, Anna Hinrichs, Kseniya Malukhina, Ishaan Sharma, Micaela Vierra

Bioengineering Senior Theses

The Achilles tendon, which stretches from the calf to the ankle, can be injured due to repeated daily activities or overstretching. In severe cases a tear in the tendon can prevent athletes from performing in games as well as individuals from completing their daily tasks. Achilles tendon injuries affect millions of people. The severe pain that occurs upon injury can take months to improve and for the Achilles tendon to heal. Our goal is to design an auxetic support to provide comfort, help heal the tendon, and allow the individual to continue to be active through the natural healing process. …

Modifying The Size Of Nanopores Of Alginate Microcapsules, Andrea Filler, Jordan Levine, Jerard Roniel Madamba, Natalie Ploof

Bioengineering Senior Theses

Alginate hydrogels provide desirable biocompatibility and material properties for various biomedical applications, but are limited by the polymer's natural pore size. With the rise of nanotechnology, the desired crosslinked pore size range of 30 nm to 100 nm has not yet been achieved. This project aimed to develop a method to increase the pore size of alginate-based hydrogels in a reproducible manner without compromising their structural integrity. Experimental methods included altering alginate composition using carboxymethyl cellulose or gelatin and inducing conformational changes via Mach-1TM mechanical compression. Fluorescence microscopy was used to visualize the diffusion of FITC-dextran weight markers and fluorescent …

Powering A Biosensor Using Wearable Thermoelectric Technology, Anneliese Bals, Noah Barnes, Rafael Bravo, Nicolas Garcia, Joseph O'Bryan, Dylan Santana

Interdisciplinary Design Senior Theses

Wearable medical devices such as insulin pumps, glucose monitors, hearing aids, and electrocardiograms provide necessary medical aid and monitoring to millions of users worldwide. These battery powered devices require battery replacement and frequent charging that reduces the freedom and peace of mind of users. Additionally, the significant portion of the world without access to electricity is unable to use these medical devices as they have no means to power them constantly. Wearable thermoelectric power generation aims to charge these medical device batteries without a need for grid power.

Our team has developing a wristband prototype that uses body heat, ambient …

Urinalysis Screening For Rural Communities, Dana Bren-Cardali, Lilian Dao, Jeffrey Destruel, Ryan Fernandez

Interdisciplinary Design Senior Theses

Access to medical care and health screenings is a necessity for patients around the globe, but it can be difficult to provide this without screenings becoming costly or convoluted. In rural and underdeveloped areas, patients are often disadvantaged when it comes to finding reliable and affordable healthcare. The isolation provided by their location and the rising costs of physicians makes it impossible for most impoverished communities to attain personalized care. Because of this, treatable diseases often go unaddressed, allowing diseases to progress to a critical condition. Mortality rates have shown to be higher in communities located in rural areas and …