Other Biomedical Engineering and Bioengineering Commons^™

Convergence Properties Of Solutions Of A Length-Structured Density-Dependent Model For Fish, Geigh Zollicoffer

Rose-Hulman Undergraduate Mathematics Journal

We numerically study solutions to a length-structured matrix model for fish populations in which the probability that a fish grows into the next length class is a decreasing nonlinear function of the total biomass of the population. We make conjectures about the convergence properties of solutions to this equation, and give numerical simulations which support these conjectures. We also study the distribution of biomass in the different age classes as a function of the total biomass.

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 …

Dimensionality Reduction For Classification Of Object Weight From Electromyography, Elnaz Lashgari, Uri Maoz

Psychology Faculty Articles and Research

Electromyography (EMG) is a simple, non-invasive, and cost-effective technology for measuring muscle activity. However, multi-muscle EMG is also a noisy, complex, and high-dimensional signal. It has nevertheless been widely used in a host of human-machine-interface applications (electrical wheelchairs, virtual computer mice, prosthesis, robotic fingers, etc.) and, in particular, to measure the reach-and-grasp motions of the human hand. Here, we developed an automated pipeline to predict object weight in a reach-grasp-lift task from an open dataset, relying only on EMG data. In doing so, we shifted the focus from manual feature-engineering to automated feature-extraction by using pre-processed EMG signals and thus …

Understanding The Effect Of Adaptive Mutations On The Three-Dimensional Structure Of Rna, Justin Cook

Undergraduate Research and Scholarship Symposium

Single-nucleotide polymorphisms (SNPs) are variations in the genome where one base pair can differ between individuals.¹ SNPs occur throughout the genome and can correlate to a disease-state if they occur in a functional region of DNA.¹According to the central dogma of molecular biology, any variation in the DNA sequence will have a direct effect on the RNA sequence and will potentially alter the identity or conformation of a protein product. A single RNA molecule, due to intramolecular base pairing, can acquire a plethora of 3-D conformations that are described by its structural ensemble. One SNP, rs12477830, which …

Primer Payload System For Higher-Order Multiplex Lamp: Design And Development Of Unit Processes, Tochukwu Dubem Anyaduba

KGI Theses and Dissertations

Design and Development of Platforms for the Application of Loop-mediated Isothermal Nucleic Acid Amplification, LAMP, in the Diagnosis of Polymicrobial Diseases

Tochukwu Dubem Anyaduba, Travis Schlappi (PI)

For the past two decades, several isothermal nucleic acid amplification technologies have emerged. These are mostly in response to the need for robust molecular diagnostic tools amenable to point-of-care and limited-resource settings. Of these, loop-mediated isothermal amplification, LAMP, stands out as a highly specific and rapid alternative to the polymerase chain reaction, PCR. One of LAMP's significant characteristics involves using four essential and two loop (rate increasing) primers to recognize six to eight …

Development Of Light Actuated Chemical Delivery Platform On A 2-D Array Of Micropore Structure, Hojjat Rostami Azmand, Hojjat Rostami Azmand

Dissertations and Theses

Localized chemical delivery plays an essential role in the fundamental information transfers within biological systems. Thus, the ability to mimic the natural chemical signal modulation would provide significant contributions to understand the functional signaling pathway of biological cells and develop new prosthetic devices for neurological disorders. In this paper, we demonstrate a light-controlled hydrogel platform that can be used for localized chemical delivery in a high spatial resolution. By utilizing the photothermal behavior of graphene-hydrogel composites confined within micron-sized fluidic channels, patterned light illumination creates the parallel and independent actuation of chemical release in a group of fluidic ports. The …

Impact Of Hemodynamic Vortex Spatial And Temporal Characteristics On Analysis Of Intracranial Aneurysms, Kevin W. Sunderland

Dissertations, Master's Theses and Master's Reports

Subarachnoid hemorrhage is a potentially devastating pathological condition in which bleeding occurs into the space surrounding the brain. One of the prominent sources of subarachnoid hemorrhage are intracranial aneurysms (IA): degenerative, irregular expansions of area(s) of the cerebral vasculature. In the event of IA rupture, the resultant subarachnoid hemorrhage ends in patient mortality occurring in ~50% of cases, with survivors enduring significant neurological damage with physical or cognitive impairment. The seriousness of IA rupture drives a degree of clinical interest in understanding these conditions that promote both the development and possible rupture of the vascular malformations. Current metrics for the …

Modeling Residence Time Distribution Of Chromatographic Perfusion Resin For Large Biopharmaceutical Molecules: A Computational Fluid Dynamic Study, Kevin Vehar

KGI Theses and Dissertations

The need for production processes of large biotherapeutic particles, such as virus-based particles and extracellular vesicles, has risen due to increased demand in the development of vaccinations, gene therapies, and cancer treatments. Liquid chromatography plays a significant role in the purification process and is routinely used with therapeutic protein production. However, performance with larger macromolecules is often inconsistent, and parameter estimation for process development can be extremely time- and resource-intensive. This thesis aimed to utilize advances in computational fluid dynamic (CFD) modeling to generate a first-principle model of the chromatographic process while minimizing model parameter estimation's physical resource demand. Specifically, …

The Investigation Of Surface Structures On Various Pathogens And Their Interactions With The Human Immune System, Carmen M. Villalobos

Biomedical Engineering ETDs

The cell surface is the first interface the host immune system encounters and

its investigation has led to a better understanding of cellular biology and types of

pathways that pathogens target in a host cell. The cell surface has evolved to include

many functions such as manipulation of the cytoskeleton, cell signaling, membrane

trafficking, adhesion, and integration into host tissue. The pathogens of interest are

the pathogenic fungus, Candida albicans, and the parasite, Giardia lamblia and we

investigate the consequences of drug treatments on the cell surface, leading to

promising new targets.

The Impact Of Aging And Mechanical Injury On Alveolar Epithelial And Macrophage Responses In Acute Lung Injury And Inflammation, Michael S. Valentine

Theses and Dissertations

Patients with severe lung pathologies, such as Acute Respiratory Distress Syndrome (ARDS), often require mechanical ventilation as a clinical intervention; however, this procedure frequently exacerbates the original pulmonary issue and produces an exaggerated inflammatory response that potentially leads to sepsis, multisystem organ failure, and mortality. This acute lung injury (ALI) condition has been termed Ventilator-Induced Lung Injury (VILI). Alveolar overdistension, cyclic atelectasis, and biotrauma are the primary injury mechanisms in VILI that lead to the loss of alveolar barrier integrity and pulmonary inflammation. Stress and strains during mechanical ventilation are believed to initiate alveolar epithelial mechanotransduction signaling mechanisms that contribute …

Age Dependent Regulation Of Cardiac Sodium Channel Gain Of Function, Madison Nowak, David Ryan King, Steven Poelzing, Seth Weinberg

Biology and Medicine Through Mathematics Conference

No abstract provided.

Development Of A Sonically Powered Biodegradable Nanogenerator For Bone Regeneration, Avi S. Patel

University Scholar Projects

Background: Reconstruction of bone fractures and defects remains a big challenge in orthopedic surgery. While regenerative engineering has advanced the field greatly using a combination of biomaterial scaffolds and stem cells, one matter of difficulty is inducing osteogenesis in these cells. Recent works have shown electricity’s ability to promote osteogenesis in stem cell lines when seeded in bone scaffolds; however, typical electrical stimulators are either (a) externally housed and require overcomplex percutaneous wires be connected to the implanted scaffold or (b) implanted non-degradable devices which contain toxic batteries and require invasive removal surgeries.

Objective: Here, we establish a biodegradable, piezoelectric …

Development Of A Sonically Powered Biodegradable Nanogenerator For Bone Regeneration, Avi Patel

Honors Scholar Theses

Background: Reconstruction of bone fractures and defects remains a big challenge in orthopedic surgery. While regenerative engineering has advanced the field greatly using a combination of biomaterial scaffolds and stem cells, one matter of difficulty is inducing osteogenesis in these cells. Recent works have shown electricity’s ability to promote osteogenesis in stem cell lines when seeded in bone scaffolds; however, typical electrical stimulators are either (a) externally housed and require overcomplex percutaneous wires be connected to the implanted scaffold or (b) implanted non-degradable devices which contain toxic batteries and require invasive removal surgeries.

Objective: Here, we establish a biodegradable, piezoelectric …

The Role Of Gene Expression Noise In Mammalian Cell Survival, Kevin Farquhar

Dissertations and Theses (Open Access)

Drug resistance and metastasis remain obstacles to effective cancer treatment. A major challenge contributing to this problem is cellular heterogeneity. Even in the same environment, cells with identical genomes can display cell-to-cell differences in gene expression, also known as gene expression noise. Gene expression noise can vary in magnitude in a population or in fluctuation time scales, which is influenced by gene regulatory networks.

Currently, it is unclear how gene expression noise from gene regulatory networks contributes to drug survival outcomes in mammalian cells. An isogenic cell line with a noise-modulating genetic system tuned to the same mean is required. …

Aptamer Functionalized Zinc Oxide Field Effect Transistors For Odor Detection, Michael D. Aldridge

Graduate Theses, Dissertations, and Problem Reports (ETD)

Odor detection and identification are complex processes, and tasks that currently only animals do well. There is a pressing need for an electronic nose, or eNose, with good sensitivity, selectivity, and speed that mimics that ability. Food quality control operations, environmental sensing, occupational safety, and the defense sectors all require systems that can rapidly and reliably detect trace levels of volatile organic compounds. The goal of this work is to create a biologically inspired device which can accurately detect and identify odors at concentrations consistent with the most sensitive biological systems.

In order to mimic a natural olfactory system, we …

Direct Quantification Of Deubiquitinating Enzyme Activity In Single Intact Cells, Nora Safabakhsh

LSU Doctoral Dissertations

Challenges in drug efficacy occur during the treatment of most types of cancer due to the heterogeneity of the tumor microenvironment. This has led to the development of personalized medicine. Due to the clinical success of the proteasome inhibitors Bortezomib and Carfilzomib in treatment of multiple myeloma, interest has shifted towards molecularly-targeted chemotherapeutics for ubiquitin-proteasome system (UPS). Deubiquitinating enzymes (DUBs) are an essential part of this pathway which have been found to promote Bortezomib resistance in multiple myeloma patients. Unfortunately, there is a lack of specific, high throughput biochemical assays to characterize DUB activity in patient samples before and after …

Evaluation Of Drug-Loaded Gold Nanoparticle Cytotoxicity As A Function Of Tumor Tissue Heterogeneity., Hunter Allan Miller

Electronic Theses and Dissertations

The inherent heterogeneity of tumor tissue presents a major challenge to nanoparticle-medicated drug delivery. This heterogeneity spans from the molecular to the cellular (cell types) and to the tissue (vasculature, extra-cellular matrix) scales. Here we employ computational modeling to evaluate therapeutic response as a function of vascular-induced tumor tissue heterogeneity. Using data with three-layered gold nanoparticles loaded with cisplatin, nanotherapy is simulated with different levels of tissue heterogeneity, and the treatment response is measured in terms of tumor regression. The results show that tumor vascular density non-trivially influences the nanoparticle uptake and washout, and the associated tissue response. The drug …

Preparation And Characterization Of Functionalized Heparin-Loaded Poly-Ɛ-Caprolactone Fibrous Mats To Prevent Infection With Human Papillomaviruses, Daniela Gonzalez, Jorge Ragusa, Peter C. Angeletti, Gustavo F. Larsen

Department of Chemical and Biomolecular Engineering: Faculty Publications

In this study, heparin-loaded poly-ε-caprolactone (PCL) fibrous mats were prepared and characterized based on their physical, cytotoxic, thermal, and biological properties. The main objective of the work described here was to test the hypothesis that incorporation of heparin into a PCL carrier could serve as bio-compatible material capable of inhibiting Human Papillomavirus (HPV) infection. The idea of firmly anchoring heparin to capture soluble virus, vs. a slow heparin release to inhibit a virus in solution was tested. Thus, one material was produced via conventional heparin matrix encapsulation and electrohydrodynamic fiber processing in one step. A second type of material was …

Comparative Analysis Of Physiological Measurements And Environmental Metrics On Predicting Heat Stress Related Events, Mckenzie Lee Barlow

Master's Theses

Exposure to high heat and humidity can lead to serious health risks, including heat exhaustion and heat stroke. Wet Bulb Globe Temperature (WBGT) and heat index have historically been used to predict heat stress events, but individualized factors are not included in the measurement. It has been shown that there is a relationship between cardiovascular measurements and heat stress, which could be used to measure heat stress risk on an individual level. Research has been done to find relationships between cardiovascular metrics in a workplace environment, however the study did not include the use of a controlled environment as a …

Investigating Smoke Exposure And Chronic Obstructive Pulmonary Disease (Copd) With A Calibrated Agent Based Model (Abm) Of In Vitro Fibroblast Wound Healing., J Alex Ratti, Angela Reynolds, Rebecca L. Heise

Biology and Medicine Through Mathematics Conference

No abstract provided.

Analytical Cpg Model Driven By Limb Velocity Input Generates Accurate Temporal Locomotor Dynamics, Sergiy Yakovenko, Anton Sobinov, Valeriya Gritsenko

Faculty & Staff Scholarship

The ability of vertebrates to generate rhythm within their spinal neural networks is essential for walking, running, and other rhythmic behaviors. The central pattern generator (CPG) network responsible for these behaviors is well-characterized with experimental and theoretical studies, and it can be formulated as a nonlinear dynam- ical system. The underlying mechanism responsible for locomotor behavior can be expressed as the process of leaky integration with resetting states generating appropriate phases for changing body velocity. The low-dimensional input to the CPG model generates the bilateral pattern of swing and stance modulation for each limb and is consistent with the desired …

Co-Existence Of Microbial Ecology In A Chemostat Using A Robust Feedback, Hector Puebla, Mariana Rodriguez-Jara, Margarita M. Gonzalez-Brambila, Eliseo Hernandez-Martinez, Alejandra Velasco-Perez, Ennio Piceno-Diaz

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Food Web Control And Synchronization Using A Robust Feedback, Hector Puebla, Mariana Rodriguez-Jara, Cesar S. Lopez-Monsalvo, Eliseo Hernandez-Martinez, Alejandra Velasco-Perez

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Rice Hull Bioreactor For Recirculating Aquaculture, Marlon A. Greensword

LSU Doctoral Dissertations

The engineering of floating media biofilters has been optimized over the years. The backwashing process has made them more energy and water efficient. Likewise, moving bed bioreactors (MBBR) are gaining interest and popularity because they are relatively affordable to build. Yet, developing countries’ aquaculture production remains largely excluded from the advances made in recirculating aquaculture systems (RAS). This discrepancy is partially driven by the high costs of media such plastic beads and Kaldnes (KMT) media, commonly used in MBBR.

This dissertation evaluates the usability and profitability of rice hulls (RH), an abundant by-product in many developing nations, as a sinking …

A Multiscale Modeling Study Of The Mammary Gland, Joseph D. Butner

Biomedical Engineering ETDs

Multiscale, hybrid computer modeling has emerged as a valuable tool in the fields of computational systems biology and mathematical oncology. In this work, we present an overview of the motivations for, and development and implementation of, three hybrid multiscale models of the mammary gland system and early stage ductal carcinoma in situ (DCIS) in the gland. Pubertal mammary gland development was described first using a two-dimensional, lattice-based hybrid agent-based model description of the mammary terminal end bud (TEB), and then with a three-dimensional lattice-free TEB model. Both models implement a discrete, agent-based description of the cell scale, and a continuum, …

Characterization Of Murine Breast Cancer Cell Lines For Anti-Cancer Vaccine, Haven N. Frazier

Biological Sciences Undergraduate Honors Theses

Breast cancer is the most commonly diagnosed cancer in women and the second leading cause of cancer death among women in the United States (1). While treatments involving radiation and chemotherapy currently exist, disease must be detected early in order for the treatments to be somewhat effective, and there is no effective treatment after metastasis occurs (2). Additionally, current therapies do not mitigate tumor immunosuppression. Decreasing the tumor-associated immunosuppressive conditions while activating antitumor immunity could prevent recurrence and metastasis, possibly leading to an effective treatment for cancer (3). Tumor cell vaccines could possibly address this issue and have become a …

Optimizing A Standard Fasting Time For 2-Nbdg Uptake Studies In Murine Breast Cancers, Andrew C. Briley

Biomedical Engineering Undergraduate Honors Theses

Recently, there has been a larger use of 2-NBDG, a fluorescent glucose analog, to study glucose uptake in different cell types. These cell types have ranged anywhere from bacteria to human cancer cells. However, there has yet to be a standard procedure and practice for using 2-NBDG. In this study, our goal is to create a standard fasting time for the cells before introducing 2-NBDG to them. This study uses 4T07 cells, a murine breast cancer cell line, to help optimize this fasting time. These cells were fasted at different time points in order to find the ideal fasting time. …

Improvement Of Fluorescence-Based Microfluidic Dna Analyzers, Collin Tranter

Doctoral Dissertations

A tremendous effort continues in the development of micro-total-analysis-systems; in support of this, many chemical passivation methods have been developed to enhance the biocompatibility of such microfluidic systems. However, the suitability of these passivation techniques to many fluorescence-based assays still remains inconsistent. This part of this work is focused on the performance of a third generation intercalating DNA dye when used within microfluidic devices treated with a select variety of passivating coatings. The results of these tests indicate that passivation coatings which are intended to shed DNA based on electrostatic repulsion will in fact imbibe the fluorescent DNA intercalating dye …

Serum Comp And The Inflammatory Environment Of The Knee Before And After Exercise-Induced Load, Alyssa Evans, Robert D. Hyldahl, Sarah T. Ridge, Sunku Kwon, Ty J. Hopkins, Eric R. Robinson, Matthew K. Seeley

Biomedical Engineering Western Regional Conference

The purpose of this study was to determine how accurately serum COMP represents inflammatory cytokine levels, within the knee, before and after exercise.

Cytokines included: GM-CSF, IFNa2, IL-10, IL-12p40, IL-13, IL-15, IL-1ra, IL1b, IL1a, IL-4, IL-6, IL-8, IP-10, MCP-1, MIP-1a, MIP-1b and IL-17.

Engineering Fret Biosensors For Microrna Presence/Absence Analysis, Nicholas E. Larkey, Sean M. Burrows

Biomedical Engineering Western Regional Conference

No abstract provided.