Biomedical Engineering and Bioengineering Commons^™

Machine-Learning-Based Approach To Decoding Physiological And Neural Signals, Elnaz Lashgari

Computational and Data Sciences (PhD) Dissertations

In recent years, machine learning algorithms have been developing rapidly, becoming increasingly powerful tools in decoding physiological and neural signals. The aim of this dissertation is to develop computational tools, and especially machine learning techniques, to identify the most effective methods for feature extraction and classification of these signals. This is particularly challenging due to the highly non-linear, non-stationery, and artifact- and noise-prone nature of these signals.

Among basic human-control tasks, reaching and grasping are ubiquitous in everyday life. I investigated different linear and non-linear dimensionality reduction techniques for feature extraction and classification of electromyography (EMG) during a reach-grasp-lift task. …

Tissue Engineering And The Effect Of Volumetric Muscle Loss On Muscle Performance, Alex Pemberton

Biomedical Engineering Undergraduate Honors Theses

Trauma, for so many people, creates life altering injuries. One of the major injuries that results from trauma is volumetric muscle loss (VML), which is the loss of muscle tissue that cannot be naturally regenerated and results in chronic loss of function. When a small amount of damage is done to a muscle, but the underlying extracellular matrix of the cell is still intact, the muscle can regenerate much of its volume and function. If the injury damages the extracellular matrix, the injury site is instead filled with scar tissue, which cannot regenerate muscle mass or function. Seen widely in …

Siderophore-Mediated Zinc Acquisition Enhances Enterobacterial Colonization Of The Inflamed Gut, Judith Behnsen, Hui Zhi, Allegra T. Aron, Venkateswaran Subramanian, William Santus, Michael H. Lee, Romana R. Gerner, Daniel Petras, Janet Z. Liu, Keith D. Green, Sarah L. Price, Jose Camacho, Hannah Hillman, Joshua Tjokrosurjo, Nicola P. Montaldo, Evelyn M. Hoover, Sean Treacy-Abarca, Benjamin A. Gilston, Eric P. Skaar, Walter J. Chazin, Sylvie Garneau-Tsodikova, Matthew B Lawrenz, Robert D Perry, Sean-Paul Nuccio, Pieter C. Dorrestein, Manuela Raffatellu

Pharmacy Nuclear Magnetic Resonance Center Faculty Publications

Zinc is an essential cofactor for bacterial metabolism, and many Enterobacteriaceae express the zinc transporters ZnuABC and ZupT to acquire this metal in the host. However, the probiotic bacterium Escherichia coli Nissle 1917 (or “Nissle”) exhibits appreciable growth in zinc-limited media even when these transporters are deleted. Here, we show that Nissle utilizes the siderophore yersiniabactin as a zincophore, enabling Nissle to grow in zinc-limited media, to tolerate calprotectin-mediated zinc sequestration, and to thrive in the inflamed gut. We also show that yersiniabactin’s affinity for iron or zinc changes in a pH-dependent manner, with increased relative zinc binding as the …

Investigation On Effects Of Lactate Adaptation Using Metabolic Indicators And Amino Acids To Explore Cell Metabolism, Lisa Uy

All Theses

Biopharmaceutical products are drugs that are made from living cells. One protein type of high importance to biopharmaceuticals is monoclonal antibodies. Monoclonal antibodies allow for highly specific, targeted treatment of diseases and detection of molecules related to diseases. With major roles in detecting and/or treating diseases like human immunodeficiency virus (HIV), coronavirus disease 2019 (COVID-19), and some cancers, monoclonal antibodies are in demand. This demand has led to a need for efficient cell culture systems to produce high yields of protein with minimal waste. The most commonly used cell culture system for these high-value proteins is Chinese hamster ovary (CHO) …

Design Of Miniaturized Antipodal Vivaldi Antennas And A Microwave Head Imaging System For The Detection Of Blood Clots In The Brain, Farhana Parveen

Electronic Theses and Dissertations, 2020-2023

Traditional brain imaging modalities, for example, MRI, CT scan, X-ray, etc. can provide precise and high-resolution images of the brain for diagnosing lesions, tumors or clots inside the brain. However, these modalities require bulky and expensive test setups accessible only at specialized diagnostic centers, and hence may not be suitable or affordable to many patients. Furthermore, the inherent health risks limit the usability of these modalities for frequent monitoring. Microwave imaging is deemed a promising alternative due to its being cost-effective, portable, non-ionizing, non-intrusive. Therefore, this work aims to design an effective microwave head imaging system for the detection of …

3d Printing In Cardiology: A Review Of Applications And Roles For Advanced Cardiac Imaging, Ellen M. Lindquist, Jordan M. Gosnell, Sana K. Khan, John L. Byl, Weihua Zhou, Jingfeng Jiang, Et. Al.

Michigan Tech Publications, Part 1

With the rate of cardiovascular diseases in the U.S increasing throughout the years, there is a need for developing more advanced treatment plans that can be tailored to specific patients and scenarios. The development of 3D printing is rapidly gaining acceptance into clinical cardiology.

In this review, key technologies used in 3D printing are briefly summarized, particularly, the use of artificial intelligence (AI), open-source tools like MeshLab and MeshMixer, and 3D printing techniques such as fused deposition molding (FDM) and polyjet are reviewed. The combination of 3D printing, multiple image integration, and augmented reality may greatly enhance data visualization …

Effect Of Hydrogen Peroxide On Algae And Microcystin In Control And Lake Waters, Tatiana Castillo Hernandez

Biological and Agricultural Engineering Undergraduate Honors Theses

Cyanobacteria are photo-autotrophic organisms with a worldwide distribution, which can result in Harmful Algal Blooms (HABs) producing toxins. One of the most common strains of cyanobacteria is Microcystis, which produces the most abundant cyanotoxin, microcystin. In this study, we analyzed the effect of H₂O₂ on algae and microcystin using both lake and reagent grade water. The first objective was to determine the effect of H₂O₂ on algae and cyanobacteria in lake water that was nutrient enriched. The second objective was to detect the effect of H₂O₂ at oxidizing microcystin in …

Tailoring Of The Left Ventricular Assist Device Cannula Implantation Using Coupled Multi-Scale Multi-Objective Patient Specific Optimization., Abubakar Dankano

Electronic Theses and Dissertations, 2020-2023

Despite advancements in device design and anti-coagulation treatments, there are numerous adverse events that may occur following implantation of LVADs. The most devastating involves the embolization of thrombus into the brain causing a stroke, with incidence of up to 14-47% over a 6–12-month period. This study aims to elucidate ways to reduce this risk by surgical maneuvers guided by a multi-scale computational fluid dynamics analysis wrapped around a multi-objective shape optimization scheme which optimizes the anastomosis location of the VAD outflow graft (OG) along the ascending aorta to minimize the incidence of thrombi reaching the cerebral vessels and reduce particle …

Subtalar Joint Definition In Biomechanical Models, Julia Noginova

Biomedical Engineering Theses & Dissertations

The effect of including a subtalar joint in a dynamic musculoskeletal model has not been fully explored or validated. The subtalar joint is often modeled as a one DOF hinge with the tri-planar axis defined as a combination of inclination and deviation angles measured from the ground and midline of the foot, respectively. The overall purposes of this dissertation were to explore how the inclusion of the subtalar joint and the definition of origin location and axis orientation affect the kinematics, joint kinetics, and muscle activations of the knee, ankle, and subtalar joint during dynamic tasks of walking and running …

Effects Of Aging On Mouse Rotator Cuff Tendon Biomechanics, Chinmay Sagar Patwardhan

Bioengineering Theses - Archive

Rotator cuff tendon injuries and tear are caused by overuse, falling, or other accidents, and are often associated with old age. The severe injuries and tear can be debilitating and require nonsurgical treatment for partial tear and arthroscopic surgery for complete tear. The frequent location of injuries and tear are at the enthesis region, the interface where the tendon tissue gradually hardens and merges into the bone. Although aging has been identified as an important factor for rotator cuff tendon injuries and tear, how the mechanical properties of the bone-tendon complex evolve along with age is still a knowledge gap. …

Antibody-Drug Nanoparticle Induces Synergistic Treatment Efficacies In Her2 Positive Breast Cancer Cells, Muhammad Raisul Abedin, Kaitlyne Powers, Rachel Aiardo, Dibbya Barua, Sutapa Barua

Chemical and Biochemical Engineering Faculty Research & Creative Works

Chemotherapeutic drugs suffer from non-specific binding, undesired toxicity, and poor blood circulation which contribute to poor therapeutic efficacy. In this study, antibody–drug nanoparticles (ADNs) are engineered by synthesizing pure anti-cancer drug nanorods (NRs) in the core of nanoparticles with a therapeutic monoclonal antibody, Trastuzumab on the surface of NRs for specific targeting and synergistic treatments of human epidermal growth factor receptor 2 (HER2) positive breast cancer cells. ADNs were designed by first synthesizing ~ 95 nm diameter × ~ 500 nm long paclitaxel (PTX) NRs using the nanoprecipitation method. The surface of PTXNRs was functionalized at 2′ OH nucleophilic site …

Role Of The Nuclear Envelope In The Mechanoregulation Adipogenesis, Matthew H. Goelzer

Boise State University Theses and Dissertations

Mechanical signals are known regulators of mesenchymal stem cell (MSC) fate, regulating their differentiation into osteoblasts, chondrocytes, and adipocytes. These relevant mechanical signals reach to nucleus through nuclear envelope proteins such as Lamin A/C and the Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes. Within the context of bone, clinically relevant mutations of Lamin A/C and the LINC complexes have been shown to alter adipogenic and osteogenic MSC differentiation patterns, suggesting that that nucleo-cytoskeletal connectivity provided by nuclear envelope is important in regulating MSC fate. Using MSC adipogenesis as a model of MSC mechanical regulation, the goal of this work …

Effects Of Il-10 On Local Cell Populations And Functional Recovery Following Vml Injury, Zain Blackwell

Biomedical Engineering Undergraduate Honors Theses

Volumetric muscle loss (VML) injuries are prevalent in both military personnel suffering from battlefield related incidents, and civilians following severe motor accidents. Despite its prevalence, VML has no pro-regenerative clinical treatments in place to recover some of the functional capabilities of the damaged muscle. Free flap grafting, debridement of damaged tissue, and physical therapy are the only clinical standards available that offer little functional recovery benefits, even after years of consistent treatment. In this study, anti-inflammatory cytokine interleukin-10 in conjunction with autologous minced muscle was assessed as a possible treatment for VML injuries and its influences on cellular behavior within …

Classifying Electrocardiogram With Machine Learning Techniques, Hillal Jarrar

Master's Theses

Classifying the electrocardiogram is of clinical importance because classification can be used to diagnose patients with cardiac arrhythmias. Many industries utilize machine learning techniques that consist of feature extraction methods followed by Naive- Bayesian classification in order to detect faults within machinery. Machine learning techniques that analyze vibrational machine data in a mechanical application may be used to analyze electrical data in a physiological application. Three of the most common feature extraction methods used to prepare machine vibration data for Naive-Bayesian classification are the Fourier transform, the Hilbert transform, and the Wavelet Packet transform. Each machine learning technique consists of …

Characterizing Direction Specific Ganglion Cell Receptor Activation Using A Perturbation Based Decomposition Method, Camila Paola Monchini Moline

Master's Theses

Characterizing postsynaptic current signals in the retina by neuroreceptor activation frequency is important for studying the mechanism of action behind phototransduction of varied visual stimuli. A better understanding could in turn lead to the creation of methods for early detection and prevention of debilitating optical neuropathies, such as glaucoma, age-related macular degeneration, and retinitis pigmentosa. More recent in-vitro and in-vivo studies have aimed to differentiate the effects of various neurotransmitters, such as acetylcholine, GABA, and glutamate, on receiving and processing different types of visual stimuli from the retina into the visual cortex.

The focus of this work will be to …

Assessing The Effects Of Oxaliplatin On An In Vitro Three-Dimensional Human Colorectal Cancer Model, Sabrina Nelson

Master's Theses

Colorectal cancer is the third most common cancer in the United States with a 5-year late-stage survival rate of only 14%. Due to the lack of translation between animal models and clinical trials as well as the inefficacy of many chemotherapeutics in initial clinical trials, researchers are turning to in vitro drug screening models in an effort to mimic the conditions in vivo. This research project aimed to validate an in vitro tumor culture model within a microfluidic device using a clinically relevant chemotherapy drug. The first experiment consisted of a cell density and drug concentration study to determine …

Nuclear Envelope Mechanobiology: Linking The Nuclear Structure And Function, Matthew Goelzer, Julianna Goelzer, Matthew L. Ferguson, Corey P. Neu, Gunes Uzer

Mechanical and Biomedical Engineering Faculty Publications and Presentations

The nucleus, central to cellular activity, relies on both direct mechanical input as well as its molecular transducers to sense external stimuli and respond by regulating intra-nuclear chromatin organization that determines cell function and fate. In mesenchymal stem cells of musculoskeletal tissues, changes in nuclear structures are emerging as a key modulator of their differentiation and proliferation programs. In this review we will first introduce the structural elements of the nucleoskeleton and discuss the current literature on how nuclear structure and signaling are altered in relation to environmental and tissue level mechanical cues. We will focus on state-of-the-art techniques to …

Time-Lapse Observation Of Sarcomeric Addition In Hypertrophic Models Based On A Tissue Like Cardiomyocyte Culture, Ailin Wei

All Dissertations

Cardiac hypertrophy is the response of the heart to increased mechanical stress exerted on the heart. In a hypertrophic heart, the muscles elongate or/and thicken with cardiomyocytes growing sizes. It is assumed that cardiomyocytes elongate by adding sarcomeres in series; the cardiomyocytes thicken with the addition of sarcomeres in the parallel position.

In this study, a tissue-like culture model was achieved with step-like ICDs. Uniaxial static stretch has been applied to our unique culture model for studying mechanical-load-induced cardiac hypertrophy. Hypertrophic responses of these cardiomyocytes have been confirmed on transcriptional and translational levels in our tissue-like model. The two-photon excitation …

Evapotranspiration In Mid-South Rice Production, Colby Wade Reavis

Graduate Theses and Dissertations

Rice provides much needed sustenance to a large portion of the global population, particularly in the developing world. With stress placed on food production systems under the reality of climate change and an increasing global population, rice production systems require solutions to a number of issues, including a limited water supply. As producers explore new strategies for conserving local water resources to continue to maintain yields, new irrigation strategies and technologies are being developed and validated for use at commercial production scales. Alternate wetting and drying (AWD) is an irrigation practice that provides water savings through the capture of rainfall …

Greenhouse Tomatoes: Process Simulation, Juan Gabriel Marin Jr.

Graduate Theses and Dissertations

Growing population demand and challenges brought on by climate change have spurred the need for more resilient fruit and vegetable supply chains. One agricultural technology of significant interest is the use of greenhouses for food production. Greenhouses create a stable and adaptable environment for crops such as tomatoes to grow year-round. Fresh tomatoes are the second most consumed vegetable per capita in U.S. diets, currently averaging 20.7 pounds. The growing consumption of fresh tomatoes has been the result of increasing cultural diversity in the United States.

To meet the growing demand, Venlo-type greenhouses have been frequently used by growers. It …