Biomedical Engineering and Bioengineering Commons^™

Non-Ribosomal In Vivo Protein Ligation, Sarah Desautel, Kenneth Joseph, Victorino Miguel Francisco

Bioengineering Senior Theses

Protein ligation is a process integral to many biomedical applications, however the current industry standard, expressed protein ligation (EPL), is highly error prone and time-and-cost inefficient. Our team sought to improve this integral process by proving the efficacy of a new method of protein ligation using the transpeptidase Sortase A. Sortase A is known to efficiently bind two peptide fragments so long as they are attached to LPXTG motifs, which signal and activate the enzyme’s ligation abilities. Previous studies affirm Sortase A’s binding ability and efficacy in in vitro situations, however none have yet confirmed its abilities in vivo. Operating …

Classifying Common Knee Rehabilitation Exercise Mistakes Using Imu Data, Fedor Myagkov

Dartmouth College Undergraduate Theses

Physical therapy following major surgeries is a branch of medicine that has seen its fair share of technologically inspired advances. One important facet of physical therapy, the “at-home exercises” patients are prescribed to do, is still somewhat of a “black box” to many physical therapists (PTs). PTs have no way of knowing (1) whether the patient is doing the home exercises, or (2) whether the patient is doing the exercises in the correct and healthy manner. This lack of awareness makes it difficult for the PT to guide the patient, which can often lead to prolonged rehabilitation periods or (sometimes) …

Patella Resection In Total Knee Arthroplasty: An Analytical Comparison Of Three Techniques, Kelsey Cushway

Medical Engineering Theses

Patella resection, as a routine component of TKA, can be both difficult to plan and difficult to execute. The primary purpose of this study was to evaluate the repeatability of three unique patellar resection techniques used in total knee arthroplasty. The secondary purpose of this study was to establish whether different surgical techniques were able to reproduce preoperative plans made by each surgeon. We used radiographic measurements to evaluate patellar thickness and patellar cut angle preoperatively and postoperatively. Three techniques (45 cases in total) were evaluated, revealing qualitative differences between surgical techniques and significant quantitative differences between average patellar thickness …

Development Of Novel Deep Learning Models In The Detection Of Breast Cancer And Brain Aneurysm, Pradnya Patel

Bioengineering Master's Theses

Three deep learning models using convolutional neural network (CNN) were developed for the early detection of breast cancer and brain aneurysm. Model 1 was built for the detection of breast mass; it consists of 20 total layers including 5 convolutional layers, 5 maxpool layers with Rectifier Linear Unit as the activation function for feature extraction, one flatten layer, 4 batch normalization with fully connected layers, and one output layer. This CNN model was trained and validated on an open-source breast ultrasound dataset that contains a total of 830 images categorized into three classes: normal (133 images), benign (487 images), and …

Predictive Model For Design Of A 3d Developmental Neurotoxicity Platform, Emma Barrett-Catton, Murial Ross, Cameron Read

Bioengineering Senior Theses

Exposure to developmental toxins during gestation have been shown to be linked to neurological disorders such as epilepsy, schizophrenia, and dyslexia [1] . In this report we describe efforts that represent the ground work to develop a predictive neurotoxicity model to test developmental toxicity on early neuronal differentiation from drugs and toxins for human consumption or exposure. Developmental toxins are toxins that prevent stem cell differentiation into neurons by impacting neural development [2] . Currency technologies used to evaluate a compound's potential as a developmental toxin are centered around culturing stem cells in a two-dimensional environment or exposing animal models …

Classifying Brainwaves For Brain-Computer Interface Technology, Derrick Wang, Brendan Lawler

Bioengineering Senior Theses

The intention of this project is to develop a brainwave classification system that will help restore the independence of those with severe motor function impairments. While current brain computer interface (BCI) technology offers a means of control for those with limited mobility, severely motor disabled individuals represent a population in need of methods to restore independent motor control. Thus, the objective of our project is to utilize neural signals from electroencephalogram (EEG) recordings to develop a machine learning classifier. Since our specific goal is to help those with limited mobility, we are focusing on motion imagery tasks which elicit a …

Flow Visualization Of Bolus Microcapsule Delivery Through 3d Printed Microneedles, Sophie Quisling, Leana Vestal, Alexis Enstrom

Bioengineering Senior Theses

Microneedle arrays are an emerging technology that offers a novel drug delivery system to treat a variety of skin wounds and diseases. The needles deliver therapeutics to the epidermis layer of the skin and therefore establish advantageous qualities over the standard hypodermic needle as they are non-invasive, efficient in biologic absorption, and can be self-administered. This project investigates a custom 3D-printed hollow microneedle device created by a Santa Clara University Senior Design team in 2018 for microencapsulated cell extrusion to be applied for accelerated wound healing. The goal of our project is to operate in the therapeutic range for flowrate …

Lamin A/C Is Dispensable To Mechanical Repression Of Adipogenesis, Matthew Goelzer, Gunes Uzer

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Mesenchymal stem cells (MSCs) maintain the musculoskeletal system by differentiating into multiple lineages, including osteoblasts and adipocytes. Mechanical signals, including strain and low-intensity vibration (LIV), are important regulators of MSC differentiation via control exerted through the cell structure. Lamin A/C is a protein vital to the nuclear architecture that supports chromatin organization and differentiation and contributes to the mechanical integrity of the nucleus. We investigated whether lamin A/C and mechanoresponsiveness are functionally coupled during adipogenesis in MSCs. siRNA depletion of lamin A/C increased the nuclear area, height, and volume and decreased the circularity and stiffness. Lamin A/C depletion significantly decreased …

Portable Ventilator, Bradley C. Weeks, Jack W. Brewer, Sanders Sanabria

Electrical Engineering

The current COVID-19 pandemic has heavily impacted the healthcare system in the United States and elsewhere. The need for patients to have access to a hospital with a ventilator along with a shortage of ventilators for recovery and at-home care as a result of minimal hospital vacancy for patients has been greatly stressed. The presented problem is both an unmet demand and supply of portable and effective ventilators. Existing ventilators have many shortcomings that should be addressed: size, weight, cost, and complexity of current ventilators confines users to stay in a medical facility whilst being monitored by professionals. This both …

Flywheel Fanny Pack Balance Assist, Ella Joy Mahood, Jason Scott Provol, Raymond Ming Tseng

Biomedical Engineering

The aim of this project is to develop a wearable device that will provide support to a balance impaired individual. The device will be predicated on the principle of gyroscopes. It will include a rapidly spinning flywheel, which will resist any changes to spatial orientation.

Handheld Transvaginal Probe For Pap Smear Exams, Kim Knollenberg, Taeah Truong

Biomedical Engineering

This project aims to discard the use of the speculum in pap smear exams. A pap smear is a procedure that tests for cervical cancer in individuals assigned female at birth (AFAB) by screening cells collected from the cervix. Speculums are utilized in these examinations, as well as other gynecologic examinations and procedures. Due to the stigma and racist and misogynistic history of the speculum, we moved to design a device that removes the need for specula in pap smear exams. This device will aim to decrease the cervical cancer mortality rate and reduce the stigma around pap smear exams.

3-D Positioning System For Trackable Adjustments Of Papillary Muscles, Ryan Michael Winters, Micaela Andrea Bataclan, Christine Do, Giselle Morales

Biomedical Engineering

Redacted.

Hand Strength And Dexterity Enhancer, Julia Ann Denison, Autumn B. Rexford, Melissa A. Kurani, Christina K. Fong

Biomedical Engineering

Good Grips created the hand strength and dexterity enhancer project to meet the challenge presented by Bill Phelps. He has Inclusion Body Myositis (IBM), an inflammatory muscle disease characterized by progressive muscle weakness and atrophy. Bill has limited strength in both hands and lost the ability to bend his fingers, making it difficult to grip anything. He needed a device that would help with everyday tasks such as writing, lifting, and holding various objects.

Our team consists of four engineering students attending Cal Poly, San Luis Obispo. We researched, designed, manufactured, and tested a device that would fulfill the problem …

Automatic Tourniquet For Military Emergencies, Arshia Nazerani Houshmand, Marina Felt, Blake Juett

Biomedical Engineering

This document contains the progress and development of an automated tourniquet that would be intended for use within the United States military. The project was student-led and sponsored. Coordination and confirmation of our device was provided by Dr. John F. Kragh, who is part of the U.S. Army Institute of Surgical Research. The document will outline the research conducted on tourniquets, specification development of the tourniquet, morphology process, and final design production of the automatic tourniquet.

Evaluation Of Blood Vessel Mimic Scaffold Biocompatibility, Nicole M. Abraham

Master's Theses

The Tissue Engineering Research Lab at California Polytechnic State University, San Luis Obispo focuses on creating tissue-engineered blood vessel mimics (BVMs) for use in preclinical testing of vascular devices. These BVMs are composed of electrospun scaffolds made of an assortment of polymers that are seeded with different cell types. This integration of polymers with cells leads to the need for biocompatibility testing of the polymer scaffolds. Many of the lab’s newest scaffolds have not been fully characterized for biologic interactions. Therefore, the first aim of this thesis developed methods for in vitro cytotoxicity testing of polymers used in the fabrication …

Microfluidic Electrical Impedance Spectroscopy System Automation And Characterization, Keaton Frahmann

Master's Theses

In this work, a novel microfluidic cell culture platform capable of automated electrical impedance measurements and immunofluorescence and brightfield microscopy was developed for further in-vitro cellular research intended to optimize cell culture conditions. The microfluidic system design, fabrication, automation, and design verification testing are described. Electrical and optical measurements of the 16 parallel cell culture chambers were automated via a custom LabView interface. A proposed design change will enable gas diffusion, removing the need for an environmental enclosure and allow long-term cell culture experiments. This "lab on a chip" system miniaturizes and automates experiments improving testing throughput and accuracy while …

The Impact Of Myoblast Transplantation On Collateral Capillary Arteriogenesis And Macrophage Phenotype, Christine Hue Do

Biomedical Engineering

Gangrene, pain, loss of limb function, amputation, and death are only few of the grievous consequences associated with peripheral arterial disease (PAD), a vascular disease caused by an obstruction that narrows the blood vessels. Since some patients have collateral vessels that can re-route blood to its downstream destination, much focus has been spotlighted upon discovering the mechanism of this process, termed arteriogenesis, as well as cell therapies to increase arterial diameter of collateral vessels. Since some patients do not have native pre-existing collateral vessels, another method to re-route blood is through arterialized collateral capillaries (ACC), which is the conversion of …

Calibrated Tensioner For Total Knee Arthroplasty Gap Balancer, Lauren Henigman, Jaypreet Dhanota, Corey Catuara

Biomedical Engineering

The purpose of this project was to design a device that interfaces with the previously created gap balancer to simultaneously measure the gap between the femur and tibia and measure the tension in the ligaments of the knee. First, we met with Dr. Delagrammaticas to outline the key customer requirements: we wanted the device to be precise, sterilizable, reliable, and compatible with the gap balancer. Based on the customer requirements, we outlined the specifications that would drive our design and testing, which included precision, ease of use, size, and material properties. The design process began by using a morphology to …

Stair Wagon To Heaven, Maria Cristina Solis Andrade, Nick Ryan Dion, Alexander Pham

Biomedical Engineering

Our design process began with developing a list of questions for our sponsor based on the problem statement we were provided. We took these questions to interview our sponsor. From this interview, we derived a series of customer requirements, which were then used to develop our more specific engineering specifications (Table 8.1). We used these engineering specifications to develop a design morphology. Each of our group mates used the concepts from our design morphology to develop their own full concept sketches. We used Pugh charts to compare the different aspects of each design. The designs were compared based off their …

Label-Free Multiphoton Microscopy For The Detection And Monitoring Of Calcific Aortic Valve Disease, Ishita Tandon, Kyle P. Quinn, Kartik Balachandran

Biomedical Engineering Faculty Publications and Presentations

Calcific aortic valve disease (CAVD) is the most common valvular heart disease. CAVD results in a considerable socio-economic burden, especially considering the aging population in Europe and North America. The only treatment standard is surgical valve replacement as early diagnostic, mitigation, and drug strategies remain underdeveloped. Novel diagnostic techniques and biomarkers for early detection and monitoring of CAVD progression are thus a pressing need. Additionally, non-destructive tools are required for longitudinal in vitro and in vivo assessment of CAVD initiation and progression that can be translated into clinical practice in the future. Multiphoton microscopy (MPM) facilitates label-free and non-destructive imaging …

A Gallium-Doped Cement For The Treatment Of Bone Cancers. The Effect Of Zno ↔ Ga2o3substitution Of An Ionomeric Glass Series On The Rheological, Mechanical, Ph And Ion-Eluting Properties Of Their Corresponding Glass Polyalkenoate Cements, Sunjeev Phull, Alireza Rahimnejad Yazdi, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

The primary treatment for patients suffering from bone cancers is resection of the tumor followed by reconstruction of the damaged bone. Despite the administration of post-operative chemotherapy, tumor recurrence continues to present itself as a severe complication leading to re-operation. Attempts to incorporate chemotherapeutic drugs into bone cements elicits local toxic effects on healthy bone, which could compromise implant fixation. Alternatively, the local administration of gallium (Ga) may prove to be more effective. This report considers the development of a Ga ionomeric glass series (0.48SiO₂-0.355ZnO-0.06CaO-0.08SrO-0.02P₂O₅-0.005Ta₂O₅, with 0.01-0.05 mol% substitution for …

Development Of Deep Learning Neural Network For Ecological And Medical Images, Shaobo Liu

Dissertations

Deep learning in computer vision and image processing has attracted attentions from various fields including ecology and medical image. Ecologists are interested in finding an effective model structure to classify different species. Tradition deep learning model use a convolutional neural network, such as LeNet, AlexNet, VGG models, residual neural network, and inception models, are first used on classifying bee wing and butterfly datasets. However, insufficient data sample and unbalanced samples in each class have caused a poor accuracy. To make improvement the test accuracy, data augmentation and transfer learning are applied. Recently developed deep learning framework based on mathematical morphology …

Plant-Derived Extracellular Matrix Mimetic Scaffolds For Bone Repair Applications, Jessica Cardenas Turner

Dissertations

Autologous and allogeneic bone grafts are currently used to treat large bone defects or fractures that will not heal. However, for patients with osteoporosis or other conditions that impair the natural bone healing process, such as diabetes, smoking, bed rest, aging, autologous bone graft, which is the patient's own bone, is limited in quantity and its healing potential may be compromised. Allograft bone, or donated bone, lacks the necessary biological activity and has poor integration into defect. There is an urgent need for constructs/grafts capable of promoting bone cell function in fracture healing and large bone defects where the endogenous …

Using Fnirs As An Objective Measure Of Susceptibility To Informational Masking, Min Zhang

Dissertations

Resolving complicated auditory scenes is crucial for daily communication where background sound is often present. However, most hearing aid (HA) and cochlear implant (CI) users have difficulties understanding speech when competing sound sources are present, resulting in reduced job opportunities and increased risk for social isolation. Perceptual interference from background sound is called auditory masking. At least two distinct masking phenomena exist, called energetic and informational masking (EM and IM).

In the first masking phenomenon, EM, target and masker energies coincide at the same time and frequency. Computational and physiological models of cochlear auditory processing can reliably predict listeners' performances …

Heparan Sulfate Proteoglycan Glypican‑1 And Pecam‑1 Cooperate In Shear‑Induced Endothelial Nitric Oxide Production, Anne Marie W. Bartosch, Rick Mathews, Marwa M. Mahmoud, Limary M. Cancel, Zahin S. Haq, John M. Tarbell

Publications and Research

This study aimed to clarify the role of glypican-1 and PECAM-1 in shear-induced nitric oxide production in endothelial cells. Atomic force microscopy pulling was used to apply force to glypican-1 and PECAM-1 on the surface of human umbilical vein endothelial cells and nitric oxide was measured using a fluorescent reporter dye. Glypican-1 pulling for 30 min stimulated nitric oxide production while PECAM-1 pulling did not. However, PECAM-1 downstream activation was necessary for the glypican-1 force-induced response. Glypican-1 knockout mice exhibited impaired flow-induced phosphorylation of eNOS without changes to PECAM-1 expression. A cooperation mechanism for the mechanotransduction of fluid shear stress …

Real Time Analysis Of Eye Movements Using Computer Aided Software, Farhan Ahmad

Theses

Eye movement analysis is a slow and tasking job that require a trained vision analyst to sift through hundreds of eye movements. The difficulty of the task increases when a subject has undiagnosed eye related disorders. One such disorder is Convergence insufficiency (CI) which affects nearly 12 million people in the US. Convergence insufficiency occurs when the eyes are unable to coordinate simultaneous inward movement for near focal tracking. Individuals with CI are unable to coordinate eye movements this can result in many symptoms such as double vision, blurred vision, headaches, vision strain, and fatigue. A diagnosis for CI relies …

The Effects Of Design Parameters On The Neural Recordings With Micro-Ecog Arrays, Manan Amish Sethia

Theses

In the field of neural prosthetics, electro-cortico-graph (ECoG) arrays are commonly used to record neural activity of the brain cortex both in animal and human subjects. A finite element model (FEM) was developed to simulate the electric field generated by a single neuron in the rat brain cortex and a micro ECoG array (µECoG) placed on the pia surface for recording the neural signal. The neuron was simulated as a dipole current source with a magnitude of 1µA and placed at three different depths in the motor cortex corresponding to different layers under the µECoG array. The array design was …

Reu Site: Stem For Plant Health, David W. Britt

Funded Research Records

No abstract provided.

Harnessing The Physicochemical Properties Of Dna As A Multifunctional Biomaterial For Biomedical And Other Applications, Aishik Chakraborty, Shruthi Polla Ravi, Yasmeen Shamiya, Caroline Cui, Arghya Paul

Chemical and Biochemical Engineering Publications

The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions …

Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale, Nandhini Rajagopal

Dissertations - ALL

Biological barriers in the human body are one of the most crucial interfaces perfected through evolution for diverse and unique functions. Of the wide range of barriers, the paracellular protein interfaces of epithelial and endothelial cells called tight junctions with high molecular specificities are vital for homeostasis and to maintain proper health. While the breakdown of these barriers is associated with serious pathological consequences, their intact presence also poses a challenge to effective delivery of therapeutic drugs. Complimenting a rigorous combination of in vitro and in vivo approaches to establishing the fundamental biological construct, in addition to elucidating pathological implications …