Biomedical Engineering and Bioengineering Commons^™

Wearable Hearing Accessory Technology, Tyler Cindea, Jaime Alcorn, Brooke Draper, Kyle Glascott, Ben Hanna, Robert Thoerner

Williams Honors College, Honors Research Projects

We set out in August 2017 to develop an active noise suppressing device that would be usable both in military and civilian activities. Due to constraints in knowledge and time, we decided our best course of action was to divide the project into two equal projects with the hope to be able to combine them into a single project at the end of the allotted time. This consisted of an active noise suppression device and a passive noise suppression device. The passive device would have no electronic components and the active device would be pure circuitry with no housing. This …

Identification Of Streptococcus Pyogenes Using Raman Spectroscopy, Ehsan Majidi

Wayne State University Dissertations

Despite the attention that Raman Spectroscopy has gained recently in the area of pathogen identification, the spectra analyses techniques are not well developed. In most scenarios, they rely on expert intervention to detect and assign the peaks of the spectra to specific molecular vibration. Although some investigators have used machine-learning techniques to classify pathogens, these studies are usually limited to a specific application, and the generalization of these techniques is not clear. Also, a wide range of algorithms have been developed for classification problems, however, there is less insight to applying such methods on Raman spectra. Furthermore, analyzing the Raman …

The Impact Of Gallium Content On Degradation, Bioactivity, And Antibacterial Potency Of Zinc Borate Bioactive Glass, Alireza Rahimnejad Yazdi, Lawrence Torkan, Wendy Stone, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Zinc borate glasses with increasing gallium content (0, 2.5, 5, 10, and 15 Wt % Ga) were synthesized and their degradation, bioactivity in simulated body fluid (SBF), and antibacterial properties were investigated. ICP measurements showed that increased gallium content in the glass resulted in increased gallium ion release and decreased release of other ions. Degradability declined with the addition of gallium, indicating the formation of more symmetric BO₃ units with three bridging oxygens and asymmetric BO₃ units with two bridging oxygens in the glass network as the gallium content in the series increased. The formation of amorphous Ca-P …

Molded Features In Pdms For Fabricating Bacterial Cellulose For Various Geometries, Mitchell Habegger

Williams Honors College, Honors Research Projects

The purpose of producing features on bacterial cellulose (BC) is to facilitate the elongation and alignment for cells, in this case Normal Human Dermal Fibroblast (NHDF) cells. The elongated cells have applications in wound healing, tissue engineering, disease diagnostics, and many other fields. Experiments were run to test the effectiveness of transferring features to BC sheets from features induced by fracturing on polydimethylsiloxane (PDMS) and those duplicated from molds with existing features. The features were duplicated to BC sheets by either air drying or Guided Assembly-Based Biolithography (GAB). The research results showed that fracture inducing on PDMS produced very small …

Modification Of Bacterial Cellulose Using Organosilanes To Enhance Cell Adhesion And Growth, Kristi Ferrato

Williams Honors College, Honors Research Projects

In this project, drying bacterial cellulose (BC) to maintain its structural integrity, and treating BC with organosilanes 3-aminopropyltriethoxysilane (APTES) and (3-Mercaptopropyl)trimethoxysilane (MPTMS) as well as with various concentration of gelatin to increase the cells per area was studied. Drying BC with hexamethyldisilazane (HMDS) by soaking the BC in ascending concentrations of ethanol and HMDS did not protect the structural integrity of the BC grown in lab but did for the BC grown in Dr. Siriporn Taokaew’s lab. Freeze drying also did not fully protect the structural integrity as the BC was placed in a freezer for several hours at -20oC …

A Novel Approach For Cancer Characterization Using Latent Dirichlet Allocation And Disease-Specific Genomic Analysis, Hima Bindu Yalamanchili

Browse all Theses and Dissertations

Two challenging problems in the clinical study of cancer are the characterization of cancer subtypes and the classification of individual patients according to those subtypes. Further, understanding the role of differential gene expression in the development of and molecular response to cancer is a complex problem that remains challenging, in part due to the sheer number of genes and gene products involved. Traditional statistical approaches addressing these problems are hindered by within-class heterogeneity and challenges inherent in data integration across high-dimensional data. In addition, many current machine learning methods do not lend themselves to biological interpretation. We have developed a …

M1 To M2 Macrophage Induction Using Retinoic Acid And Mesenchymal Stem Cells Loaded On An Electrospun Pullulan/Gelatin Scaffold To Promote Healing Of Chronic Wounds, Kaivon Assani

Browse all Theses and Dissertations

Modulation of macrophage polarization is required for effective tissue repair and regenerative therapies. Conversion of macrophages from inflammatory M1 to fibrotic M2 phenotype could help in diseases such as chronic wound which are stuck in inflammatory state. During the inflammatory phase, macrophages are of the inflammatory phenotype (M1) and distribute pro-inflammatory cytokines including TNF-a and IL1[beta] which are microbicidal and recruit/activate cells. In normal wound healing macrophages then switch to a fibrotic phenotype (M2) promoting wound closure by angiogenesis, and matrix deposition. Chronic wounds are a major biological and financial burden to both patients and the health care system, costing …

Effect Of Dimensionality On In Vitro Growth Environment And Mesenchymal Stem Cell Function, Fatema Tuj Zohora

Browse all Theses and Dissertations

The use of the standard two dimensional (2D) cell culture has laid down the fundamentals of molecular and cell biology. However, recent advances in cell-based regenerative medicine raises the concern on deconstructing cellular behaviors in more physiologically relevant three dimensional (3D) microenvironments. Differences in cell response in 2D versus 3D systems arise from the perturbations in gene expression patterns that stem from how cells sense their underlying 2D or surrounding 3D matrices and adjust their phenotypes accordingly. Thus, cells are no longer considered as a solitary entity of genome but a context arises from a combinatorial interactions of cell-ECM, cell-cell, …

Novel Auto-Calibrating Neural Motor Decoder For Robust Prosthetic Control, Andrew Earl Montgomery

Browse all Theses and Dissertations

The overarching goal of this project is to develop novel neural motor decoders for prosthetic control. EMG decoders measure the activity from an intact but non-target muscle. Neural motor decoders transform the signal measured from the severed motor axons of the target muscle. A multi-scale, highly-realistic computer model of a spinal motor pool was developed (Allen & Elbasiouny, 2018) to serve as a computational platform for decoder development and testing. A firing rate-based algorithm was developed to transform the aggregate discharge of the motor pool into a command signal to control the simulated prosthetic MuJoCo hand. This algorithm was informed …

Development Of Novel Models To Study Deep Brain Effects Of Cortical Transcranial Magnetic Stimulation, Farheen Syeda

Theses and Dissertations

Neurological disorders require varying types and degrees of treatments depending on the symptoms and underlying causes of the disease. Patients suffering from medication-refractory symptoms often undergo further treatment in the form of brain stimulation, e.g. electroconvulsive therapy (ECT), transcranial direct current stimulation (tDCS), deep brain stimulation (DBS), or transcranial magnetic stimulation (TMS). These treatments are popular and have been shown to relieve various symptoms for patients with neurological conditions. However, the underlying effects of the stimulation, and subsequently the causes of symptom-relief, are not very well understood. In particular, TMS is a non-invasive brain stimulation therapy which uses time-varying magnetic …

Non-Targeted Colonization By The Endomycorrhizal Fungus, Serendipita Vermifera, In Three Weeds Typically Co-Occurring With Switchgrass, Prasun Ray, Yingqing Guo, Jaydeep Kolape

Nebraska Center for Biotechnology: Faculty and Staff Publications

Serendipita vermifera (=Sebacina vermifera; isolate MAFF305830) is a mycorrhizal fungus originally isolated from the roots of an Australian orchid that we have previously shown to be beneficial in enhancing biomass yield and drought tolerance in switchgrass, an important bioenergy crop for cellulosic ethanol production in the United States. However, almost nothing is known about how this root-associated fungus proliferates and grows through the soil matrix. Such information is critical to evaluate the possibility of non-target effects, such as unintended spread to weedy plants growing near a colonized switchgrass plant in a field environment. A microcosm experiment was conducted …

Association Between Mechanics And Biology In Vascular Graft Remodeling, David Andrew Prim

Theses and Dissertations

Coronary artery bypass grafting (CABG) restores myocardial perfusion in patients with severe coronary artery disease by utilizing autografts – usually at least one of the internal thoracic artery (ITA), radial artery (RA), and great saphenous vein (GSV) – to bypass stenosed regions of coronary arteries. While decades of research and clinical improvements have made CABG an indispensable procedure, tens of thousands of grafts fail each year, which is due, at least in part, to an inability of the source vessels to adapt to the altered stimuli of the coronary circulation. In this dissertation, we first quantify and compare the mechanical …

A Comprehensive Reengineering Of The Hospital Emergency Triage System, Nicholas D. Boltin

Theses and Dissertations

Hospital emergency triage and specifically Mass Casualty Incidents (MCIs) are of major concern with regard to treatment and patient outcomes. Traditional emergency department triage models are oversimplified and often lead to over/under triaging of patients. Furthermore, triage models do not account for the full spectrum of different types of MCIs which often results in misclassification. In this thesis, we begin by looking at traditional triage models currently being used in hospital systems and identify several shortcomings of using these models within the context of a chemical related MCI. I will then move to describe a new approach to creating a …

Changes Of Dispersal Ability In An Isolated Population, Connor Bacon

Theses and Dissertations

Dispersal is a core mechanism in the maintenance of metapopulations. It maintains genetic diversity by connecting subpopulations and generates new populations to replace those that die out. However, as populations become more isolated, as occurs in habitat fragmentation, dispersal becomes more difficult. This should lead to selective pressure against dispersive individuals, causing a reduction in dispersal traits. Over time, this can lead to variation in dispersal traits among populations. We examine this idea using an extreme case of isolation in Euphydryas gillettii, a population that has remained completely isolated for forty years. By comparing this population to a baseline established …

Modulation Of Amyloid-Β Aggregation Via Small Molecules And Glycine Zipper Alterations, Steven Zebulon Vance

Theses and Dissertations

Alzheimer’s disease (AD) is the most common form of neurodegenerative disease. Nationally, AD is the 6th leading cause of death and the only top 10 killer of Americans that cannot be slowed, cured, or prevented. AD is characterized by the deposition of extracellular plaques of aggregated amyloid-β protein (Aβ). Aβ originates from the amyloid precursor protein (APP), a transmembrane protein that is cleaved to form a short and inert protein fragment called Aβ. However, Aβ undergoes a nucleation process wherein aggregates from soluble oligomers to insoluble fibrils are formed. While uncertainty remains as to the exact mechanism, studies have associated …

Screening Of Novel Active Salicylic Acid Analogs And Identification Of A Bacterial Effector Targeting Key Proteins Involved In Salicylic Acid-Mediated Defense, Ian Palmer

Theses and Dissertations

The master regulator of salicylic acid (SA)-mediated plant defense, NPR1 (NONEXPRESSER OF PR GENES 1), and its paralogs NPR3 and NPR4 act as SA receptors. After the perception of a pathogen, plant cells produce SA in the chloroplast. In the presence of SA, NPR1 protein is reduced from oligomers to monomers, and translocated into the nucleus. There, NPR1 binds to TGA and WRKY transcription factors to induce expression of plant defense genes. EDS1 and PBS3 are two key proteins involved in SA biosynthesis. Previous research has shown that several plant pathogens produce SA hydroxylases. These pathogen-produced hydroxylases act to degrade …

Automatic Image Processing And Conversion To Tactile Graphics, Tyler Ferro

Theses and Dissertations

Graphical information has become a critical method for portraying information for education, work and personal tasks and decisions. Unfortunately there are currently limited means of providing this information to individuals who are blind or visually impaired: alternate text is frequently missing, and accessible tactile diagrams tend to be time consuming to make and require expertise in order for them to be interpretable (which may be costly to the user and/or impossible to get). The aim of this project is to provide an accessible system to automatically generate tactile graphics for those who need to interpret information contained in visual images. …

Nuclear Rupture In Progeria Expressing Cells, Kranthidhar Bathula

Theses and Dissertations

Cells regularly take on various types of force in the body. They have structures that are able to mediate, transfer and respond to the forces. A mutation in force regulating proteins such as lamin in the nucleus or the KASH domain which connects the nucleus to the cytoskeleton of the cell can cause catastrophic events to occur. The aims of this study were to better understand the response of the nucleus when structural proteins are mutated or are not present while under force. Progeria, a rare disease where an additional farnesyl group is attached to lamin was used in this …

Fibronectin Mechanics And Signaling In Tgf-Β1-Induced Epithelial To Mesenchymal Transition, Lauren Griggs

Theses and Dissertations

Epithelial to Mesenchymal Transition (EMT) is a dynamic process by which a distinct change in the phenotype and function of epithelial cells render them as mesenchymal cells. Characteristics of mesenchymal cells include the ability to invade, increased migratory kinetics and heightened resistance to apoptosis. Therefore, there is a strong need to fully understand the mechanism for the induction of EMT in pathological conditions such as carcinoma progression. Recent advances highlight two pivotal contributors, soluble growth factor (gf) signals, and mechanical signals, in the process. However, to date, no clear mechanism exists linking the two in epithelial transdifferentiation. Transforming Growth Factor-β1 …

Decellularized Matrices Effect On The Adaptive Immune Response, Kegan Sowers

Theses and Dissertations

Decellularized extracellular matrices have been a growing area of interest in the biomedical engineering fields of tissue engineering and regenerative medicine.As these materials move toward clinical applications, the immune response to these materials will be a driving force toward their success in clinical approaches. Fully digested decellularized matrix constructs derived from porcine liver, muscle and lung were created to test the adaptive immune response. Hydrogel characterization ensured that the materials had relatively similar stiffness levels to reduce variability, and in vitro studies were conducted. Each individual construct as well as a gelatin control were plated with a co-culture of macrophages …

Matrix Stiffness Modulates Mesenchymal Stem Cell Sensitivity To Geometric Asymmetry Signals, Maria Eugenia Piroli

Theses and Dissertations

Human stem cells hold significant potential for the treatment of various diseases. However, their use as a therapy is hampered by the limited understanding of the mechanisms by which stem cells respond to environmental stimuli. Efforts to understand extracellular biophysical cues have demonstrated the critical roles of geometric and mechanical signals in determining the fate of stem cells. The goal of this study was to explore the interplay between cell polarity and matrix stiffness in stem cell lineage specification. We hypothesize that confining cells to asymmetric extracellular matrix (ECM) islands will impart polarity at a single-cell level and result in …

Plants As Biofactories To Produce Mammalian Tumor Suppressor Micrornas, John Lachlan Macarthur

Theses and Dissertations

MicroRNAs (miRNAs) are small noncoding single stranded RNAs that are considered master regulators of gene expression. They are also an emerging class of therapeutic agents with significant potential for the prevention and treatment of many diseases, including cancer. Many different forms of cancer are associated with loss or reduced accumulation of one or more miRNAs that function as tumor suppressors. In animal models, restoration of missing tumor suppressor miRNAs prevents the initiation, progression and/or spread of the disease. However, the current absence of an efficient method for delivery of therapeutic miRNAs is a critical barrier to their use. The research …

Effects Of Protein-Coated Nanofibers On Conformation Of Gingival Fibroblast Spheroids: Potential Utility For Connective Tissue Regeneration, Gili Kaufman, Ryan A. Whitescarver, Laiz Nunes, Xavier-Lewis Palmer, Drago Skrtic, Wojtek Tutak

Engineering Technology Faculty Publications

Deep wounds in the gingiva caused bytrauma or surgery require a rapid and robust healing of connective tissues. Wepropose utilizing gas-brushed nanofibers coated with collagen and fibrin for that purpose. Our hypotheses are that protein-coated nanofibers will: (i) attract and mobilize cells in various spatial orientations, and (ii) regulate the expression levels ofspecific extracellular matrix (ECM)-associated proteins, determining the initial conformational nature ofdense and soft connective tissues. Gingival fibroblast monolayers and3D spheroids were cultured onECMsubstrate and covered with gas-blown poly-(DL-lactide-co-glycolide)(PLGA) nanofibers (uncoated/coated with collagen and fibrin). Cell attraction and rearrangement was followed byF-actin staining and confocal microscopy. Thicknesses ofthe cell …

Knockdown Of Heparan Sulfate Via Ndst1 Knockout Does Not Inhibit Mouse Aortic Endothelial Cell Alignment In-Vivo, John Diaz De Leon Iii

Dissertations and Theses

Atherosclerotic plaque localizes in predictable areas such as arches and bifurcations which are characterized by disturbed flow patterns and the resulting damage and dysfunction to the endothelium. Endothelial cells (ECs) under sustained laminar flow align in the direction of flow; however, under disturbed flow conditions, ECs sustain damage to their glycocalyx (GCX) which results in unaligned and rounder cells. An investigation into the role of NDST1 sulfation of heparan sulfate (HS), a key component of many proteoglycans which make up the GCX, was conducted. The descending aortas (DAs) of transgenic mice with conditional knockouts (KOs) of NDST1 in vascular ECs …

Developing A 3d In Vitro Model By Microfluidics, Hung-Ta Chien

Dissertations and Theses

In vitro tissue models play an important role in providing a platform that mimics the realistic tissue microenvironment for stimulating and characterizing the cellular behavior. In particular, the hydrogel-based 3D in vitro models allow the cells to grow and interact with their surroundings in all directions, thus better mimicking in vivo than their 2D counterparts. The objective of this thesis is to establish a 3D in vitro model that mimics the anatomical and functional complexity of the realistic cancer microenvironment for conveniently studying the transport coupling in porous tissue structures. We pack uniform-sized PEGDA-GelMA microgels in a microfluidic chip to …

Collective Chemotaxis Of Retinal Neural Cells From Drosophila Melanogaster In Controlled Microenvironments, Stephanie Zhang

Dissertations and Theses

More than 172 million people are influenced by a retinal disorder that stems from either age-related or developmental causes. Of those, 1.5 million people endure a developmental retinal disorder. In the developing retina, neural cells undergo a series of highly complicated differentiation and migration process. A main cause of these diseases is abnormal collective migration of neural progenitors hindering the retinogenesis process. However, our grasp of collective migration and signaling molecules, critical to the developing retina, is incompletely understood. Understanding the molecular mechanisms, such as the fibroblast growth factor pathway, that regulate glial and neuronal migration provides decisive insights in …

Mechanical And Material Characterization Of Advanced Materials For Tissue Regeneration, Bailey Kylara Ricketts Jackson

Theses and Dissertations

In natural disasters and military deployment operations, injury to long bone can cause extensive damage and be difficult to treat and heal quickly. Explosive devices and trauma often produce long-bone (>2-cm length) wounds that are more complicated than common fractures. Due to the size and complexity of these injuries, they can be difficult to treat in a battlefield environment and take a long time to heal completely and properly. Even after the long healing period, these injuries often require rehabilitation to strengthen the muscles that have weakened in the wounded limb. For military applications especially, these effects can put …

Biom 3110: Medical Physiology (Syllabus), Bradford D. Pendley

Biomedical Engineering Syllabi Archive

Course Description: Basic principles of human physiology and how these are applied in medicine and biomedical engineering problem and devices; physiological principles using appropriate mathematical and engineering models to construct an understanding of how the body works as an integrated system.

In Vivo Raman Spectroscopy For Biochemical Monitoring Of The Human Cervix Throughout Pregnancy, Christine M. O'Brien, Elizabeth Vargis, Amy Rudin, James C. Slaughter, Giju Thomas, J. Michael Newton, Jeff Reese, Kelly A. Bennett, Anita Mahadevan-Jansen

Biological Engineering Faculty Publications

Background

The cervix must undergo significant biochemical remodeling to allow for successful parturition. This process is not fully understood, especially in instances of spontaneous preterm birth. In vivo Raman spectroscopy is an optical technique that can be used to investigate the biochemical composition of tissue longitudinally and noninvasively in human beings, and has been utilized to measure physiology and disease states in a variety of medical applications.

Objective

The purpose of this study is to measure in vivo Raman spectra of the cervix throughout pregnancy in women, and to identify biochemical markers that change with the preparation for delivery and …

การพัฒนาระบบตรวจวัดแคลเซียมออกซาเลตในปัสสาวะเพื่อการคัดกรองโรคนิ่วไต, พิชญุตม์ ฤกษนันทน์

Chulalongkorn University Theses and Dissertations (Chula ETD)

วิทยานิพนธ์นี้ได้ทำการพัฒนาระบบตรวจคัดกรองผู้ที่มีโอกาสเสี่ยงต่อโรคนิ่วไต (Kidney stone disease) โดยใช้วิธี Indole Calcium Oxalate Crystalization Index : iCOCI ซึ่งเป็นการตรวจวัดความเข้มสีที่เกิดจากปฏิกิริยาระหว่างออกซาเลตในปัสสาวะกับสาร Indole reagent โดยได้ทำการศึกษาถึงตัวแปรต่าง ๆ ที่มีผลต่อการวัดเพื่อปรับปรุงประสิทธิภาพของวิธี iCOCI ซึ่งพบว่าสามารถลดเวลาในขั้นตอนการบ่มปัสสาวะได้เหลือเพียง 10 นาที และการใช้ Indole reagent ที่ความเข้มข้น 2.5 mg/ml สามารถให้ความแยกชัดในการตรวจคัดกรองได้สูงที่สุด จากนั้นได้ทำการทดสอบประสิทธิภาพของการตรวจคัดกรองโดยนำตัวอย่างปัสสาวะของกลุ่มผู้ที่มีสุขภาพดีและกลุ่มผู้ป่วยโรคนิ่วไต กลุ่มล่ะ 60 ตัวอย่างมาทำการตรวจวัดโดยใช้วิธี iCOCI ร่วมกับระบบวัดทางแสงที่พัฒนาขึ้นโดยใช้เซนเซอร์อาเรย์ที่ตอบสนองต่อแสงที่ความยาวคลื่นต่าง ๆ ซึ่งพบว่าการใช้ค่าการดูดกลืนแสงของสารตัวอย่างที่ความยาวคลื่น 600 nm จะสามารถให้ประสิทธิภาพของการตรวจคัดกรองได้สูงสุดคือได้ค่าความไวและความจำเพาะในการตรวจคัดกรองมากกว่า 70% ซึ่งเพียงพอต่อการนำไปใช้งานเพื่อตรวจคัดกรองในทางคลีนิค นอกจากนี้ยังได้ทำการพัฒนาระบบผสมและนำส่งสาร และระบบแปลและแสดงผลการตรวจคัดกรองเพื่อทดสอบความเป็นไปได้ในการนำไปพัฒนาเป็นระบบแบบอัตโนมัติโดยใช้ไมโครคอนโทรลเลอร์ในการควบคุม ซึ่งจากการทดสอบพบว่าระบบทั้งหมดที่พัฒนาขึ้นสามารถนำไปใช้ในการตรวจวัดที่ใกล้เคียงกับการนำไปใช้งานจริงนอกสถานพยาบาลได้อย่างเหมาะสม จึงทำให้มีความเป็นไปได้ในการนำระบบที่ได้พัฒนาขึ้นนี้ไปใช้ในการตรวจคัดกรองโรคนิ้วไตแบบไม่รุกล้า (Non-invasive) ได้ต่อไป