Engineering Commons^™

Assesment Of Structure, Function, And Microevolutionary Dynamics Of Extrachromosomal Circular Dna In Chinese Hamster Ovary Cells, Dylan Chitwood

All Dissertations

Chinese hamster ovary (CHO) cell lines are among the most popular expression hosts used in biopharmaceutical manufacturing due to relative ease of culture, capacity to perform human-like post-translational modifications, and non-susceptibility to viruses. However, the intrinsic plasticity of the CHO genome can lead to undesired genetic rearrangements, phenotypic shifts, reduced product quality, and early culture termination that prevents continuous biomanufacturing. A characteristic of plastic and unstable genomes that is poorly understood in CHO cells is extrachromosomal circular DNA (eccDNA). EccDNAs are focal amplifications of the genome that reside in the extranuclear space. These plasmid-like entities are structurally complex and are …

A Deep-Learning Framework For Spray Pattern Segmentation And Estimation In Agricultural Spraying Systems, Praneel Acharya, Travis Burgers, Kim-Doang Nguyen

Mechanical Engineering Faculty Publications

This work focuses on leveraging deep learning for agricultural applications, especially for spray pattern segmentation and spray cone angle estimation. These two characteristics are important to understanding the sprayer system such as nozzles used in agriculture. The core of this work includes three deep-learning convolution-based models. These models are trained and their performances are compared. After the best model is selected based on its performance, it is used for spray region segmentation and spray cone angle estimation. The output from the selected model provides a binary image representing the spray region. This binary image is further processed using image processing …

E-Cadherin Force Transmission And Stiffness Sensing, Mazen Mezher

Mechanical & Aerospace Engineering Theses & Dissertations

E-cadherin is the chief mediator of cell-cell adhesion between epithelial cells and is a known mechanosensor. Force transmission and stiffness sensing are two crucial aspects of E-cadherin mechanobiology.

E-cadherin has an extracellular adhesive region, a transmembrane region and an intracellular region that binds to adhesion-associated proteins. Here, we assessed how different factors affect the level of force transmission (i) from inside the cell such as adhesion-associated proteins, (ii) on the cell membrane, such as growth factor receptors and (iii) outside the cell, such as different binding partners in adhesion. To study the level of force transmission inside the cell, we …

Cardiac Ablation And Stimulation With Nanosecond Pulsed Electric Fields (Nspefs), Federica Serra

Biomedical Engineering Theses & Dissertations

Surgical ablation of cardiac tissue is the definitive treatment for the most common arrhythmia, atrial fibrillation. In current medical practice, myocardial tissue is often ablated by the application of radiofrequency (RF) currents which are delivered through an electrode to create lesions that block the electrical pathways that sustain reentrant arrhythmias and restore the normal heart rhythm. An alternative to RF is cryoablation, during which the endocardial or epicardial tissue is brought in contact with a cryoprobe. Both RF ablation and cryoablation have significant limitations. In RF ablation, tissue is heated in order to ablate it, but it is an open …

Trace Dna Detection Using Diamond Dye: A Recovery Technique To Yield More Dna, Leah Davis

Master's Theses

This study aspires to find a new screening approach to trace DNA recovery techniques to yield a higher quantity of trace DNA from larger items of evidence. It takes the path of visualizing trace DNA on items of evidence with potential DNA so analysts can swab a more localized area rather than attempting to recover trace DNA through the general swabbing technique currently used for trace DNA recovery. The first and second parts consisted of observing trace DNA interaction with Diamond Dye on porous and non-porous surfaces.

The third part involved applying the Diamond Dye solution by spraying it onto …

Program And Proceedings: Nebraska Academy Of Sciences 1880–2023, 143rd Anniversary Year, One Hundred-Thirty-Third Annual Meeting, April 21, 2023

Nebraska Academy of Sciences: Programs and Proceedings

Program

Aeronautics and Space Science

Humans Past and Present

Applied Science and Technology Section

Biology

Biomedical Sciences

Chemistry

Earth Sciences

Environmental Science

Physics

Science Education

2023 Maiben Lecture: Jason Bartz

2023 Friend of Science Award: Ray Ward and Jim Lewis

Comprehensive Long- And Short- Read Sequencing Approaches To Screen The Mutational Landscape After Therapeutic Crispr-Editing For Duchenne Muscular Dystrophy, Mary Jia, Made Harumi Padmaswari, Landon Burcham, Shilpi Agrawal, Alexis Ivy, Abbey Bryan, Christopher E. Nelson

Biomedical Engineering Undergraduate Honors Theses

Duchenne muscular dystrophy (DMD) is an X-linked muscle wasting disease caused by mutations in the Dmd gene resulting in non-functional dystrophin. Adeno-associated virus (AAV)-mediated delivery of classical CRISPR systems resulting in double-stranded breaks (DSBs) has yielded promise as a curative DMD therapeutic. However, the consequences of AAV-CRISPR require more thorough characterization. PCR-enriched short-read amplicon sequencing at cut sites is the most common method of sequencing CRISPR editing, but PCR bias results in unreliable quantification of on-target edits. We analyze orthogonal long- and short-read sequencing approaches to screen the outcomes of CRISPR technologies at the DNA and RNA-level for DMD. We …

Development Of A Computational Model To Investigate Pathways And The Effects Of Treatment In Fanconi Anemia, Sabrina Kellett

Biological Sciences Undergraduate Honors Theses

Fanconi Anemia (FA) is a rare type of anemia that is not easily studied and can have very detrimental effects. This disease compromises the bone marrow, resulting in decreased hemopoiesis. Symptoms of FA also include abnormalities in the brain and spinal cord, incorrect formation of the kidneys, abnormal formation of the heart and lungs, and a dramatically increased risk of developing cancer. FA can be caused by various mutations in any of the 22 genes that encode for proteins involved in what is called the FA DNA repair pathway. In healthy individuals, this pathway specifically repairs interstrand cross-links (ICLs) recognized …

Mitral Valve Imaging And Biomechanics: A Workflow Towards Computational Modeling And Validation, Sam Stephens

Graduate Theses and Dissertations

The mitral valve serves a critical role in healthy cardiac function by ensuring the unidirectional flow of oxygenated blood from the left atrium into the left ventricle. It experiences the highest pressures found within the heart and its closure is the result of a complex interaction of several different structures that, furthermore, are unique to each individual. Despite the valve’s vital role however, the specific function of these constituent structures is not fully understood. This, confounded by its asymmetric, personalized nature, make surgical interventions for the mitral valve far less effective than for its neighboring aortic valve. Efforts to overcome …

Irrigation-As-A-Service For Smallholder Farmers, Ishani Lal

Department of Agricultural Economics: Dissertations, Theses, and Student Research

Irrigation is a crucial management practice that can help increase food security among smallholders globally while mitigating climate change impacts. High-efficiency irrigation technologies such as drip kits and sprinkler systems are relatively expensive and smallholder farmers cannot afford them to buffer crop yields against low precipitation. In many developing countries, farmers participate in robust informal markets for renting and sharing of irrigation equipment. Such services may be operated by farmers or via a third party such as irrigation start-ups, water user associations, non-governmental organizations, or even government agencies. These services are referred to collectively as Irrigation-as-a-Service (IaaS).

The objective of …

Opensim-Based Musculoskeletal Modeling: Foundation For Interactive Obstetric Simulator, Bahador Dodge

Electrical & Computer Engineering Theses & Dissertations

The use of mathematical and computational models to understand complex biological systems, such as the human birth process, is a rapidly growing field in medicine. These models can be used to optimize and personalize medical treatments for individual patients, enhance training, and aid in educational efforts. While recent advancements in healthcare, particularly in obstetrics, have improved care for mothers and babies, studies and government reports indicate a rising rate of maternal mortality in the United States.

Despite this rising trend, there is a lack of detailed studies concerning the use of modeling and simulation to develop an interactive obstetrics simulator …

Rattus Norvegicus As A Biological Detector Of Clandestine Remains And The Use Of Ultrasonic Vocalizations As A Locating Mechanism, Gabrielle M. Johnston

Master's Theses

In investigations, locating missing persons and clandestine remains are imperative. One way that first responder and police agencies can search for the remains is by using cadaver dogs as biological detectors. Cadaver dogs are typically used due to their olfactory sensitivity and ability to detect low concentrations of volatile organic compounds produced by biological remains. Cadaver dogs are typically chosen for their stamina, agility, and olfactory sensitivity. However, what is not taken into account often is the size of the animal and the expense of maintaining and training the animal. Cadaver dogs are typically large breeds that cannot fit in …

Laser Inscribed Graphene Aptasensor For Detection Of Apple Stem Pitting Virus, Yifan Tang

All Theses

Apple stem pitting virus (ASPV) is a latent RNA virus that could cause significant loss to apple production; early-stage field diagnosis could reduce the economic loss caused by ASPV infection. Biosensor is a promising user-friendly detection tool that could transduce biological or chemical interactions into electric signals. Among various types of biosensors, aptasensor, which use aptamers as recognition elements show potential as a high throughput, in-field test. The goal of this thesis is to develop an electrochemical aptasensor testing system for ASPV detection. The quality control study of laser inscribed graphene (LIG) based working electrode of the biosensor was conducted …

Nanosecond Pulsed Electric Field Modulates Electron Transport And Mitochondrial Structure And Function, Lucas Nelson Potter

Biomedical Engineering Theses & Dissertations

Pulsed power treatment has been used to induce regulated cell death (RCD) in cells or ablate tumors in animals. A subset of pulsed power as electroporation with high voltage and pulse duration of milliseconds is used for biomedical treatment to induce pores in the plasma membrane of cells. Nanosecond Pulsed Electric Fields (nsPEFs)– an extension of electroporation, uses waveforms with pulse durations on the order of 10-900 nanoseconds. nsPEF treatment has demonstrated intracellular effects for potential biomedical applications. In this work, nsPEF treatment is used to demonstrate changes that affect viability, plasma membrane permeability ROS (Reactive Oxygen Species) in the …

Wearable Sensor Gait Analysis For Fall Detection Using Deep Learning Methods, Haben Girmay Yhdego

Electrical & Computer Engineering Theses & Dissertations

World Health Organization (WHO) data show that around 684,000 people die from falls yearly, making it the second-highest mortality rate after traffic accidents [1]. Early detection of falls, followed by pneumatic protection, is one of the most effective means of ensuring the safety of the elderly. In light of the recent widespread adoption of wearable sensors, it has become increasingly critical that fall detection models are developed that can effectively process large and sequential sensor signal data. Several researchers have recently developed fall detection algorithms based on wearable sensor data. However, real-time fall detection remains challenging because of the wide …

Case Study: Modeling A Grain Bin For Safe Entry Retrofit, Michael Dyer, Serap Gorucu, Randall Bock, Roderick Thomas, Jude Liu, Linda Fetzer

Office of Research Faculty and Staff Publications

All new grain bins produced after 2018 are recommended to have anchor points capable of handling a 2000 lb loading for attachment of bin entry lifeline systems. This study aims to assess the feasibility of a safe entry anchor point retrofit by using finite element analysis (FEA). We used a grain bin owned by Penn State for 3D FEA modeling in SolidWorks. To validate the model results from the FEA model, first strain and then deflection measurements were conducted on the grain. Strain gauges were applied to the grain bin in five locations and strain values were obtained after applying …

Mechanical Properties And Morphological Alterations In Fiber-Based Scaffolds Affecting Tissue Engineering Outcomes, James Dolgin, Samerender Nagam Hanumantharao, Stephen Farias, Carl G. Simon, Smitha Rao

Michigan Tech Publications, Part 1

Electrospinning is a versatile tool used to produce highly customizable nonwoven nanofiber mats of various fiber diameters, pore sizes, and alignment. It is possible to create electrospun mats from synthetic polymers, biobased polymers, and combinations thereof. The post-processing of the end products can occur in many ways, such as cross-linking, enzyme linking, and thermal curing, to achieve enhanced chemical and physical properties. Such multi-factor tunability is very promising in applications such as tissue engineering, 3D organs/organoids, and cell differentiation. While the established methods involve the use of soluble small molecules, growth factors, stereolithography, and micro-patterning, electrospinning involves an inexpensive, labor …

What If Plants Compute?, Jordi Vallverdú

Animal Sentience

The unexpended cognitive capacities of plants suggest the possibility of combining them with advances in computation. It is important to explore such a new field of research despite the incompleteness of the empirical support for it.

The Santa Clara, 2023-04-21, Santa Clara University

The Santa Clara

No abstract provided.

Air Pre-Heat System Optimization For Flash Dryers, Sophia Louden

Honors Theses

Primient, a leading producer of food and industrial ingredients made from plant-based, renewable sources is the industrial sponsor for this project. The company is currently using Plate & Frame Heat exchangers to heat up a 40% by-weight glycol and water solution that is then used to preheat the incoming ambient air. Glycol is being added to reduce the risks of freezing in the system during the winter season. It is important to highlight that this fact affects the heat transfer properties of the liquid overall. Since air heating is a highly energy-demanding process, an outlet stream of hot water produced …

Deficit Irrigation Management For Irrigated Corn In Nebraska: Economically Viable?, Lia Nogueira, Cory Walters, Emily O'Donnell, E. Wesley F. Peterson, Suat Irmak

Cornhusker Economics

In this study we determine the economic value of deficit irrigation management using both technological and methodological advancements. The use of soil moisture probes represents the technological improvement. We provide improvements in the methodology as follows. Regarding data, we employ a field-size study, instead of plots, where the irrigation decision is determined by the moisture level in the soil measured through a soil moisture probe. Regarding the understanding of the yield response to water, although we examine the commonly used quadratic function, we improve upon this specification by also examining an alternative response function, the linear response stochastic plateau. Our …

Glycosylation Of Anti-Tb Agent Chlorflavonin For Combating Mycobacterium Tuberculosis, Jie Ren

Student Research Symposium

More than two billion people were infected by the bacterial pathogen Mycobacterium tuberculosis (Mtb) in 2020. However, during the past 50 years, the first-line (isoniazid, delamanid, and rifampicin) and second-line (capreomycin, streptomycin, and cycloserine) therapies have remained unchanged with disadvantages such as long treatment periods and severe side effects. The slow development of anti-TB drugs cannot combat the fast development of drug resistant M. tuberculosis strains from multidrug-resistant (MDR) into extensively drug resistant (XDR), which further hinders the World Health Organization’s goal to end the global TB pandemic by the year 2035. Flavonoids are a type of natural product with …

Does Diet Effect The Brain?, Janna Hart

Student Research Symposium

Short-chain fatty acids are biomolecules produced from bacterial fermentation of dietary fiber in the gut. Short-chain fatty acids are used in the gut to supply energy and reduce inflammation but are also believed to have effects on the brain. While we do not know how short-chain fatty acids affect the brain and behavior, recent research has led to the idea of using dietary changes as a treatment for mental health disorders. In my research, we aimed to visualize where short-chain fatty acids act in the brain with a particular focus on neural immune cells called microglia and the neurons that …

"Challenging The Known." 16th Annual Research Week: Event Proceedings, University Of The Incarnate Word

Excellence Summit (Research Week) Archived Proceedings

Presentations of completed and ongoing research activity conducted by graduate students, undergraduate students, and faculty at University of the Incarnate Word. Includes poster, podium, visual arts, interactive demo, and creative and performing arts presentations. Coordinated and presented by the Office of Research and Graduate Studies.

A Review Of The Implications Of The Love Canal Disaster And The Subsequent Actions Of The State And Federal Government, Hannah Albright, Brooklyn Hurtt, Douglas Mock

2023 Celebration of Student Scholarship - Poster Presentations

There is much literature written about environmental law and policy. The one focused on in this poster presentation is “Love Canal: A Toxic History from Colonial Times to the Present” by Richard S. Newman. The novel focuses on the Love Canal tragedy in upstate New York, where a chemical plant caused housewives to turn into activists after their neighbors, friends, and even their own families became extremely ill or succumbed because of the toxic waste. The tragedy at Love Canal was the precursor to grassroots movements across the United States.

Enhancing Telomerase Activity In Saccharomyces Cerevisiae Through A Genetic Screen For Gain-Of-Function Mutations, Keenan Conley, Hailey Rietz, Mackenzie Neal, Melissa Mefford

2023 Celebration of Student Scholarship - Poster Presentations

Telomeres are located at the ends of eukaryotic linear chromosomes and are composed of repeated nucleotide sequences. The main function of telomeres is to protect chromosomal ends. However, telomeres cannot be copied entirely during DNA replication leading to a gradual shortening known as the “end-replication problem”. To counteract this problem, the RNA-dependent enzyme complex telomerase works to extend telomeres and maintain the chromosomal ends which helps to prevent senescence. Understanding the structure and function of telomerase could have important implications for the development of anti-cancer therapeutics, since telomerase is over-active in >85% of all human cancers. While the general role …

Collapse: The History Of How We Fail, And What We Can Do To Save Ourselves, David Ace, Grace Funke, Aj Abdel-Rahman, Nate Floccare, Kristen Russell, Madison Ingram, Douglas Mock

2023 Celebration of Student Scholarship - Poster Presentations

Using Diamond's Five point framework for how societies have collapsed in the past allow us in the present to recognize these signs in modern societies. We have the gift of hindsight in which we now know that factors such as climate change, impact on the environment, decline on friendly contact, increase in hostile contact, and a conservative outlook have all contributed to past societies' collapse. We now recognize these issues in modern societies such as China, Australia, Rwanda, and Haiti. This allows these societies to reevaluate their current environmental standards on whether they are compatible with their survival or collapse. …

The Impact Of Nursing Skill Competency On Patient Outcomes: A Quality Improvement Project, Abby Blair, Riley Boling, Natalie Crace, Jascie Greene, Peyton Kennedy, Andrew Morris, Joseph Sewell, Abigail Wesselkamper, Suzi White

2023 Celebration of Student Scholarship - Poster Presentations

45 out of 50 facilities that implemented continued education saw improved patient outcomes. This presentation focuses on the importance of nurse participation in continued professional development programs because it is a shortcoming that we noticed in clinical practice.

The Diversity Of Life By E.O. Wilson, Emma Collins, Matthew Grace, Brady Lawson, Michelle Lopez, Zane Rousey, Douglas Mock

2023 Celebration of Student Scholarship - Poster Presentations

In The Diversity of Life, E. O. Wilson tells a tale about how our earth is on track for another extinction event and humans are at fault. Wilson discusses various topics such as environmental preservation, biodiversity and its importance, and how life has evolved over time. Wilson views biodiversity differently than many as he focuses on all species found in the ecosystem rather than narrowing his focus on one. He mentions how new species can be created by groups evolving and developing new skills or existing in new environments. Species are going extinct and being created constantly; these extinctions don't …

Age And Growth Of The Highland Shiner (Notropis Micropteryx) In Rockcastle County, Kentucky, Caitlyn Senters, Zoe Baker, Shelbie Black, Jared Vise, David J. Eisenhour

2023 Celebration of Student Scholarship - Poster Presentations

Notropis micropteryx, the Highland Shiner, is common in small to large streams of the Cumberland, Tennessee, and upper Green River drainages. It usually inhabits rocky riffles (Eisenhour and Eisenhour 2004)). While their population size was assessed as stable by the IUCN in 2012, little is known about the age and growth of this minnow species. Despite being a small fish, attention must be given to the health of its population as it serves an ecological niche and impact on the surrounding ecosystem.