Biomedical Engineering and Bioengineering Commons^™

Development Of Standard Criteria To Evaluate The Effectiveness Of Helmets At Decreasing The Risk Of Concussions, Daniel Y. Shyu, Goutham N. Sankaran, Kevin G. Mciver, Nicolas Leiva, Eric A. Nauman

The Summer Undergraduate Research Fellowship (SURF) Symposium

In many sports, such as American football, accumulations of mild traumatic brain injuries have been suggested as a possible link to neurodegeneration and future mental disorders. With head impacts occurring at all levels of competition and in different sports, it is critical to develop an accurate method for quantifying the effects of head impacts and determining the efficacy of helmets. This study examines the derivation of different dimensionless numbers and ascertains the critical factors needed to predict the effects of head impacts, specifically the resulting accelerations from an impact. Given a known force of impact, parameters such as peak translation …

Stimuli Responsive Fluidics Controls On A Paper-Based Bacterial Detection Platform, Siyu Zhao, Elizabeth Phillips, Jacqueline Linnes

The Summer Undergraduate Research Fellowship (SURF) Symposium

Infectious diseases are the leading causes of death around the world. Point-of-care devices using nucleic acid amplification are sensitive enough to diagnose these diseases, however, often require complex and time-intensive sample preparation steps that are not integrated with the detection process. A rapid, sensitive, and integrated sample-to-result diagnostic device will permit disease treatment planning at the point-of-care. Paper-based detection assays are a promising platform to integrate the sample preparation and detection, with minimal infrastructure, equipment, and user involvement. To integrate sample preparation with detection on paper-based assays, timing and delivery of sample fluid flow needs to be controlled. Here we …

Lysis And Amplifciation Of Neonatal Sepsis Causing Pathogens, Gregory Berglund, Elizabeth A. Phillips, Jacqueline C. Linnes

The Summer Undergraduate Research Fellowship (SURF) Symposium

Neonatal sepsis, resulting from a bloodstream infection within the first few weeks of life, is the leading cause of newborn deaths worldwide. The gold standard of neonatal sepsis diagnosis requires a blood culture to identify the infecting bacteria, however require days of incubation, expensive equipment, and expertise. Any delay in diagnosis is critical, as the condition can be treated easily if appropriate antibiotics are administered promptly. A low-cost, rapid, and sensitive diagnostic test would enable more timely treatment and lead to better patient outcomes with fewer required resources. Point-of-care, nucleic acid amplification assays are a promising alternative to blood culture …

Measurement Of Hydrogen Peroxide Influx Into Cells: Preparation For Measurement Using On-Chip Microelectrode Array, Hannah R. Kriscovich, Sarah M. Libring, Siddarth V. Sridharan, James K. Nolan, Jose F. Rivera, Jenna L. Rickus, David B. Janes

The Summer Undergraduate Research Fellowship (SURF) Symposium

Hydrogen peroxide (H₂O₂) is commonly known as a toxic reactive oxidative species (ROS) for cells. Recent studies have found evidence that H₂O₂ is also an important cellular signalling molecule. Quantifying cellular influx of H₂O₂ will contribute to researchers’ understanding of the role H₂O₂ plays in healthy cells and cells involved in the progression of cancers and degenerative diseases. This work utilizes an assay kit and fluorescence techniques to evaluate cell lines and conditions to create a model biological system for measuring cellular H₂O₂ consumption. …

Optical Dosimetry Tools And Monte Carlo Based Methods For Applications In Image Guided Optical Therapy In The Brain, Akshay N Prabhu Verleker

Open Access Dissertations

Purpose: The long-term goal of this research is to determine the feasibility of using near infra-red light to stimulate drug release in metastatic lesions within the brain. In this work, we focused on developing the tools needed to quantify and verify photon fluence distribution in biological tissue. To accomplish this task, an optical dosimetry probe and Monte Carlo based simulation code were fabricated, calibrated and developed to predict light transport in heterogeneous tissue phantoms of the skull and brain. Empirical model (EM) of photon transport using CT images as input were devised to provide real-time calculations capable of being translated …

The Role Of Mechanical Loading In Chondrocyte Signaling Pathways, Qiaoqiao Wan

Open Access Dissertations

Chondrocytes are a predominant cell type present in articular cartilage, whose integrity is jeopardized in joint degenerative diseases such as osteoarthritis (OA). In the chondrocytes of patients with OA, the elevated levels of inflammatory cytokines such as interleukin 1β (IL1β) and tumor necrosis factor α (TNFα) have been reported. These cytokines contribute to degradation of cartilage matrix by increasing activities of proteolytic enzymes. In addition to their contribution to proteolytic enzymes, these cytokines adversely affect anabolic activity of chondrocytes by inhibiting the production of proteoglycans and type II collagen. Therefore, blocking the action of these cytokines is a potential strategy …

Development Of A Fluidic Mixing Nozzle For 3d Bioprinting, Will Hoggatt

Open Access Theses

3D bioprinting is a relatively new and very promising field that uses conventional 3D printing techniques and adapts them to print biological materials that are suited for use with cells. These bioprinters can be used to print cells encapsulated within biological "ink" (bio-ink) to create and customize complex three-dimensional tissues and organs. Our work has focused on developing a new bioprinter nozzle that addresses critical gaps with present-day bioprinters, namely, the lack of standardized, physiologically-relevant biomaterials, and their one nozzle per composition printing capacity. These shortcomings preclude printing a range of cellular and biomaterial compositions (including gradients of cells and …

Development Of Orthogonally Crosslinked Thiol-Ene Hydrogels For Encapsulation Of Pancreatic Beta-Cells, Han Shih

Open Access Dissertations

Type I diabetes mellitus (T1DM) is an autoimmune disease caused by auto-reactive T-cell-mediated destruction of insulin-producing β-cells. Effective encapsulation strategies can protect the transplanted islets from direct attack by host immune cells while maintaining insulin secretion. To achieve this goal, I have developed a hydrogel conformal coating using a visible light-mediated interfacial thiol-ene photopolymerization. Unlike conventional chain-growth visible light polymerizations, no additional cytotoxic co-initiator or co-monomer was required in thiol-ene gelation scheme for rapid gelation. More importantly, islets coated with thiol-ene gel maintained their viability and function in vitro. In addition to microencapsulate β-cells, the second objective of my …

Can Neuromorphic Computer Vision Inform Vision Science? Disparity Estimation As A Case Study, Guido Maiello, Manuela Chessa, Peter J. Bex, Fabio Solari

MODVIS Workshop

The primate visual system efficiently and effectively solves a multitude of tasks from orientation detection to motion detection. The Computer Vision community is therefore beginning to implement algorithms that mimic the processing hierarchies present in the primate visual system in the hope of achieving flexible and robust artificial vision systems. Here, we reappropriate the neuroscience “borrowed” by the Computer Vision community and ask whether neuromorphic computer vision solutions may give us insight into the functioning of the primate visual system. Specifically, we implement a neuromorphic algorithm for disparity estimation and compare its performance against that of human observers. The algorithm …

Modelling Short-Latency Disparity-Vergence Eye Movements Under Dichoptic Unbalanced Stimulation, Agostino Gibaldi, Guido Maiello, Peter J. Bex, Silvio P. Sabatini

MODVIS Workshop

Vergence eye movements align the optical axes of our two eyes onto an object of interest, thus facilitating the binocular summation of the images projected onto the left and the right retinae into a single percept. Both the computational substrate and the functional behaviour of binocular vergence eye movements have been the topic of in depth investigation. Here, we attempt to bring together what is known about computation and function of vergence mechanism. To this aim, we evaluated of a biologically inspired model of horizontal and vertical vergence control, based on a network of V1 simple and complex cells. The …

Measuring And Modeling Shared Visual Attention, Jeffrey B. Mulligan, Patrick Gontar

MODVIS Workshop

Multi-person teams are sometimes responsible for critical tasks, such as flying an airliner. Here we present a method using gaze tracking data to assess shared visual attention, a term we use to describe the situation where team members are attending to a common set of elements in the environment. Gaze data are quantized with respect to a set of N areas of interest (AOIs); these are then used to construct a time series of N dimensional vectors, with each vector component representing one of the AOIs, all set to 0 except for the component corresponding to the currently fixated …

Consonant Discrimination In The Inferior Colliculus Of Young And Aged Rats, Christopher S. Soverns

Open Access Theses

Complex acoustic stimuli are thoroughly encoded and processed along the primary auditory pathway to give reliable and relevant information about the environment, and elucidating the neural coding mechanisms is essential to informing clinical attempts to combat auditory dysfuntion. Receiving a uniquely diverse set of ascending and descending inputs, the inferior colliculus (IC) is a site of intricate temporal processing. In this work, natural and modified human speech is used to investigate discrimination of voice onset time (VOT) in the spiking output of IC neurons. A template-matching classification model is proposed in which single stimulus presentation responses are correlated with aggregate …

Optimization Of Wireless Power Networks For Biomedical Applications, Kyle A. Thackston

Open Access Theses

Successful physiological integration of electronics will open the doors to new methods of treatment and diagnoses. One of the key challenges of this integration is designing devices as small as possible while still maintaining high functionality, such as bio-signal recording, processing, telemetry, and stimulation. Wireless power transfer (WPT) can help shrink a device’s footprint by removing the need for bulky batteries. While many modalities of WPT exist for biomedical applications, the optimal power transfer efficiency (PTE) is seldom achieved due to improper impedance matching. Existing methods for determining the optimal impedance matching conditions tend to be application specific and make …

Densified Collagen-Fibril Biomaterials For Bone Tissue Engineering, Lauren E. Watkins

Open Access Theses

Millions of craniofacial bone defects occur annually as a result of trauma, congenital defects, disease, or tooth extraction. When present in the oral cavity, these defects are associated with adverse impacts on speech, mastication, and aesthetics. Thus, there is a clinical need for interventional strategies to restore and preserve alveolar bone mass to improve the success of future treatment options intended to reestablish functionality and aesthetics. Guided bone regeneration using bone grafts and a membrane represent the current standard of care for repairing alveolar bone defects, but face a number of limitations related to resorption time and structural integrity. Improvements …

Improving The Mechanistic Study Of Neuromuscular Diseases Through The Development Of A Fully Wireless And Implantable Recording Device, Rebecca A. Bercich

Open Access Dissertations

Neuromuscular diseases manifest by a handful of known phenotypes affecting the peripheral nerves, skeletal muscle fibers, and neuromuscular junction. Common signs of these diseases include demyelination, myasthenia, atrophy, and aberrant muscle activity—all of which may be tracked over time using one or more electrophysiological markers. Mice, which are the predominant mammalian model for most human diseases, have been used to study congenital neuromuscular diseases for decades. However, our understanding of the mechanisms underlying these pathologies is still incomplete. This is in part due to the lack of instrumentation available to easily collect longitudinal, in vivo electrophysiological activity from mice. There …

Influence Of The 3d Microenvironment On Glioblastoma Migration And Drug Response, Ruth Marisol Herrera Perez

Open Access Dissertations

Glioblastoma (GBM) is a highly invasive brain cancer characterized by poor prognosis. Despite significant efforts by the basic and clinical research community our understanding of GBM progression and recurrence has been incremental. Improvements in therapeutic response have been dismal, and GBM continues to be the deadliest tumor of the central nervous system, with patient average survival rate of 12 months. Synergistic relationships that the tumor cells establish with the brain microenvironment have been proven fundamental for successful tumor progression and maintenance. Yet, many in vitro GBM studies are performed in formats that fail to recapitulate the most essential component of …

Coupled Resonator Based Wireless Power Transfer For Bioelectronics, Henry Mei

Open Access Dissertations

Implantable and wearable bioelectronics provide the ability to monitor and modulate physiological processes. They represent a promising set of technologies that can provide new treatment for patients or new tools for scientific discovery, such as in long-term studies involving small animals. As these technologies advance, two trends are clear, miniaturization and increased sophistication i.e. multiple channels, wireless bi-directional communication, and responsiveness (closed-loop devices). One primary challenge in realizing miniaturized and sophisticated bioelectronics is powering. Integration and development of wireless power transfer (WPT) technology, however, can overcome this challenge.

In this dissertation, I propose the use of coupled resonator WPT for …

Direct Drug Screening And Lipid Profiling Using Ambient Mass Spectrometry, Yuan Su

Open Access Dissertations

Mass spectrometry (MS) stands in an outstanding position in analysis of biological specimens owing to its abundant structural information, high accuracy, incomparable sensitivity, high speed, and the large variety of its applications. The ion source, an instrumental part for converting the analyte into ions, has played an important role in analyzing biological specimens by MS. However, the performance of conventional spray-based ionization methods always suffers from chemical interferences derived from complex biological matrices. A series of sample extraction, purification, and separation steps is required before the ionization, so as to ensure excellent performance of MS analysis. In order to simplify …

Advancing Multiple Model-Based Control Of Complex Biological Systems: Applications In T Cell Biology, Jeffrey P. Perley

Open Access Dissertations

Activated CD4+ T cells are important regulators of the adaptive immune response against invading pathogens and cancerous host cells. The process of activation is mediated by the T cell receptor and a vast network of intracellular signal transduction pathways, which recognize and interpret antigenic signals to determine the cell's response. The critical role of these early signaling events in normal cell function and the pathogenesis of disease ultimately make them attractive therapeutic targets for numerous autoimmune diseases and cancers.

Scientists increasingly rely on predictive mathematical models and control-theoretic tools to design effective strategies to manipulate cellular processes for the advancement …

Supervised Learning-Based Explicit Nonlinear Model Predictive Control And Unknown Input Estimation In Biomedical Systems, Ankush Chakrabarty

Open Access Dissertations

Application of nonlinear control theory to biomedical systems involves tackling some unique and challenging problems. The mathematical models that describe biomedical systems are typically large and nonlinear. In addition, biological systems exhibit dynamics which are not reflected in the model (so-called 'un-modeled dynamics') and hard constraints on the states and control actions, which exacerbate the difficulties in designing model-based controllers or observers.

This thesis investigates the design of scalable fast explicit nonlinear model predictive controllers (ENMPCs). The design involves (i) the estimation of a feasible region using Lyapunov stability methods and support vector machines; and (ii) within the estimated feasible …

Β-Aminopropionitrile-Induced Reduction In Enzymatic Crosslinking Causes In Vitro Changes In Collagen Morphology And Molecular Composition, Silvia P. Canelón, Joseph M. Wallace

Weldon School of Biomedical Engineering Graduate Student Publications

Type I collagen morphology can be characterized using fibril D-spacing, a metric which describes the periodicity of repeating bands of gap and overlap regions of collagen molecules arranged into collagen fibrils. This fibrillar structure is stabilized by enzymatic crosslinks initiated by lysyl oxidase (LOX), a step which can be disrupted using β-aminopropionitrile (BAPN). Murine in vivo studies have confirmed effects of BAPN on collagen nanostructure and the objective of this study was to evaluate the mechanism of these effects in vitro by measuring D-spacing, evaluating the ratio of mature to immature crosslinks, and quantifying gene expression of type I collagen …

Biomechanics Of Retinal Venous Pulsations As Indicators Of Intracranial Pressure, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Working Papers

The origin of retinal venous pulsations remains an open problem in physiology and medicine; so too, their exact relationship to intracranial pressure. This study takes a mathematical modeling approach to explore details of blood flow through the eye to reveal the mechanism of pulsations. The intravaginal, intraneural, and intraocular segments of the retinal arteries and veins are modeled as connected resistive-capacitive segments. The analysis incorporates two critical mechanical properties of these small blood vessels, not heretofore studied, which become significant under conditions of negative transmural pressures: (1) dramatically reduced compliance during flattening and (2) cross-sectional shape change as internal volume …

A Potential New Technique To Estimate The Origins Of Focal Atrial Tachycardias From 12-Lead Electrocardiograms, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Publications

Background: This brief report presents a potential new technique for locating the sites of origin of focal atrial tachycardias from standard 12-lead electrocardiograms. Methods: Estimated P wave vector coordinates are derived from leads I, aVF, V1 and V2, and mapped to a three dimensional coordinate system in space. A simple graphical method is used to find the back projection of the P wave vector onto the surface of atrial muscle to estimate the most likely site of origin of the tachycardia. Results: Graphical back projection correctly identified foci of atrial tachycardias in 19 of 19 cases described in the most …

An Implantable Device To Regulate Urination Through Deep Brain Stimulation, Jesse E. Bucksot, Muhammad A. Arafat, Pedro Irazoqui

The Summer Undergraduate Research Fellowship (SURF) Symposium

Urinary Incontinence (UI) is a disease in which patients lose control of their bladder. It is particularly common in elderly women having a prevalence of as much as 30% to 50% [1]. Many of these patients are left without successful treatment. A recent study has shown a new option for treatment that consists of deep brain stimulation (DBS) at a site known as the periaqueductal gray (PAG) [2, 3]. To test the effectiveness of this treatment, chronic stimulation of the PAG should be used in animals to see if it can reliably prevent micturition in the long term. A device …

Simulating Low-Frequency Sonic Pulsations To Achieve Thrombolysis, Joseph C. Muskat, Matthew C. Pharris, Charles F. Babbs

The Summer Undergraduate Research Fellowship (SURF) Symposium

Cardiovascular thrombosis may result in critical ischemia to a range of anatomical regions, constituting a leading cause of death in the United States. Current invasive treatments for such arterial blockages often yield blood clot recurrence, resulting in repeated hospitalization of patients. This research aims to show how internally introduced pressure oscillations may be used to initiate thrombolysis. We present a novel computational model for determining the resonant frequency and corresponding deformation of an idealized thrombus. Sinusoidal pressure differences across the thrombus induce axial displacements of frequency dependent amplitude. The maximum peak displacement occurs at a resonant frequency of 73 Hz …

Cold Atmospheric Plasma: An Inside Look Through Optical Diagnostics For Biomedical Applications, Liesl Krause, Ahmed Hassanein, Prasoon Diwakar

The Summer Undergraduate Research Fellowship (SURF) Symposium

An emerging technology for medical applications is cold atmospheric plasma (CAP). CAP is generated using various gasses in a “pen” to create room temperature plasma and then carry the effluents and species. Success has been shown when cold atmospheric plasma is applied to oncology treatments, accelerated wound healing, pathogen disinfection, and various material-changing effects. However, the mechanisms behind these effects are still speculative. This study uses multiple diagnostic techniques including fast photography, two wavelength emission spectroscopy and optical emission spectroscopy to characterize the plasma properties and eventually further test the plasma’s interaction with biological samples. The plume dynamics are observed …

An Investigation Of The Applicability Of Sugar And Wax Valves For Rapid Molecular Diagnostics, Rui Shen, Jacqueline C. Linnes

The Summer Undergraduate Research Fellowship (SURF) Symposium

Paper-based Loop-mediated Isothermal Amplification (LAMP) of nucleic acids is a low-cost molecular diagnostic method to detect biological pathogens and has been successfully combined with lateral flow devices. This invention is a low-cost visual detection technique of various disease. However, existing assays require multiple user-activated steps and are relatively complicated to use at the point of care due to steps like the heating process. This project aimed to investigate an ideal valve for integrating LAMP onto the lateral flow assay. An ideal valve needs to be able to stop the fluid flow for 20-60 minutes under 65 degree to complete the …

Indentation Probing Of In Vitro Bovine Articular Cartilage: Effects On Chondrocyte Viability And Tissue Biomechanics, Pablo F. Argote, Alan Poon, Xin Xu Ph.D, Corey P. Neu Ph.D.

The Summer Undergraduate Research Fellowship (SURF) Symposium

Osteoarthritis (OA) consists of a degenerative disease on articular cartilage, which is prone to excessive mechanical loading and frictional resistance that leads to the wear and tear of the tissue. These factors result in the progressive and incurable disease that affects millions of people worldwide. The goal is to characterize chondrocyte viability and the in vitro biomechanical properties of articular cartilage in two confined indentation studies. One study looks at the chondrocyte viability over seven days. The second compares the immediate effects of strain rates on chondrocyte viability and tissue biomechanics. Bovine cartilage explants are harvested, cultured, and then 40% …

Bioengineered Cell Niche For Skeletal Muscle Regeneration, Nicole M. Whittern, Naagarajan Narayanan, Chunhui Jiang, Owen Jones, Jay Gilbert, Michael Whittern, Shihuan Kuang, Meng Deng

The Summer Undergraduate Research Fellowship (SURF) Symposium

Skeletal muscles can self-repair minor strains, lacerations, and contusions; however, in cases of volumetric muscle lossand muscle degenerative diseases, tissue fails to regenerate. Current cell-based therapies, such as myoblast transplantation, have significant drawbacks of low survival rates and engraftment efficacy, mainly due to the absence of supportive cell microenvironment. Scaffolds that mimic the natural cell microenvironment provide a robust platform to support cell adhesion, migration, proliferation, and differentiation. Electrospinning is a versatile technology platform used for fabricating the fiber scaffold that mimics the extracellular matrix. Thus, we aim to reconstitute the cell microenvironment through development of aligned fiber scaffolds by …

Angiotensin Ii-Induced Hypertension In Apolipoprotein E-Deficient Rats, Sydney N. Gorman, Craig J. Goergen, A Nicole Blaize

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal aortic aneurysms (AAAs) are characterized by a weakened vessel wall and a diameter 50% greater than normal. AAA are usually asymptomatic until they are near rupturing, which can be fatal if not treated immediately. Apolipoprotein E-deficient (ApoE) mice are commonly used as a model to study aneurysm growth. Our lab has created a similar model using rats, which are more similar to humans. This study focuses on the analysis of blood pressures collected from ApoE rats for comparison with a known mouse model. Five ApoE rats (1 female, 4 males) received subcutaneous implants of osmotic mini pumps that released …