Digital Commons Network^™

Sequence-Based Bioinformatics Approaches To Predict Virus–Host Relationships In Archaea And Eukaryotes, Yingshan Li

School of Computing: Dissertations, Theses, and Student Research

Viral metagenomics is independent of lab culturing and capable of investigating viromes of virtually any given environmental niches. While numerous sequences of viral genomes have been assembled from metagenomic studies over the past years, the natural hosts for the majority of these viral contigs have not been determined. Different computational approaches have been developed to predict hosts of bacteria phages. Nevertheless, little progress has been made in the virus-host prediction, especially for viruses that infect eukaryotes and archaea. In this study, by analyzing all documented viruses with known eukaryotic and archaeal hosts, we assessed the predictive power of four computational …

A Study On Interactions Between Metal-Organic Frameworks And Biological Materials, Josh Phipps

Graduate Theses and Dissertations

Metal-organic frameworks or MOFs are an extremely useful tool in many areas of applications. Their popularity in recent years has arisen from their high efficiency in catalytic chemical reactions. This is made possible due to their porous interior and the ability of the MOFs components to be functionalized. These same traits make MOFs excellent for use in protein encapsulation or immobilization and have the potential to become excellent drug carriers. Their development in this utilization has been limited dramatically compared to MOFs chemical applications. This is due in part to the nature of biological processes taking longer to study, but …

The Role Of Generative Adversarial Networks In Bioimage Analysis And Computational Diagnostics., Ahmed Naglah

Electronic Theses and Dissertations

Computational technologies can contribute to the modeling and simulation of the biological environments and activities towards achieving better interpretations, analysis, and understanding. With the emergence of digital pathology, we can observe an increasing demand for more innovative, effective, and efficient computational models. Under the umbrella of artificial intelligence, deep learning mimics the brain’s way in learn complex relationships through data and experiences. In the field of bioimage analysis, models usually comprise discriminative approaches such as classification and segmentation tasks. In this thesis, we study how we can use generative AI models to improve bioimage analysis tasks using Generative Adversarial Networks …

Fabrication And Characterization Of Force Spun Polymeric Nanofiber For Drug Delivery And Tissue Engineering Applications, Salahuddin Ahmed

Theses and Dissertations

This study focuses on the development and characterization of polymeric nanofiber for drug delivery and tissue engineering applications. In this study, poly(lactic-co-glycolic) acid (PLGA), Poly-vinyl alcohol (PVA), and Pullulan(PL) were used as the base polymers to develop the nanofiber. Bioactive components Oleanolic acid(OA), Oxymatrine(OM), and Salvianolic Acid(SA) were incorporated in PLGA, PVA, and PL, respectively, via solution mixing. The nano fiber systems were developed using the Forcespinning® method. Morphological, thermo-physical, and biological properties of the fiber mats were analyzed. The composite fiber system containing OA showed a very high drug loading efficiency. The composite fiber system containing high concentration of …

An Exploration Into The Design Of A Portable Music Player For People With Alzheimer’S And Dementia, Jaxon V. Silva

Liberal Arts and Engineering Studies

An exploration into the design of a portable music player for people with Alzheimer's and dementia.

Novelty Ice Cream Assembly Prototype, Mason Sylvester, Logan Williamson, Alvaro Martinez, Adin Gilman-Cohen

Mechanical Engineering

Cool Beans USA is a novelty ice cream startup company founded by Keith Zachow. In the winter of 2022, our team began working with Mr. Zachow to develop a machine to automate parts of the production process for his product. This product consists of two hemispherical ice-cream cone shell halves filled with soft serve ice cream and pressed together. The assembled pods are around the size and shape of a small walnut and are intended to be sold in stores as a frozen finger food. At the time of project inception, this product was in its early stages and was …

The Bridge Newsletter Winter 2022, Missouri University Of Science And Technology

The Bridge Newsletter

-Missouri S&T CO2 research is rock solid
-Bringing circular economy to construction projects
-Ph.D. graduate wins Fellowship for solar farm protection research
-Rockne presents 2022 Mathes Lecture on ways to evolve engineering education
-Missouri S&T Ph.D. graduate wins $70,000 Laegeler Fellowship for solar farm protection research

Intelligent Autonomous Inspections Using Deep Learning And Detection Markers, Alejandro Martinez Acosta

Open Access Theses & Dissertations

Inspection of industrial and scientific facilities is a crucial task that must be performed regularly. These inspections tasks ensure that the facilityâ??s structure is in safe operational conditions for humans. Furthermore,the safe operation of industrial machinery, is dependent on the conditions of the environment. For safety reasons, inspections for both structural integrity and equipment is often manually performed by operators or technicians. Naturally, this is often a tedious and laborious task. Additionally, buildings and structures frequently contain hard to reach or dangerous areas, which leads to the harm, injury or death of humans. Autonomous robotic systems offer an attractive solution …

Hybrid Machine Learning And Physics-Based Modeling Approaches For Process Control And Optimization, Junho Park

Theses and Dissertations

Transformer neural networks have made a significant impact on natural language processing. The Transformer network self-attention mechanism effectively addresses the vanishing gradient problem that limits a network learning capability, especially when the time series gets longer or the size of the network gets deeper. This dissertation examines the usage of the Transformer model for time-series forecasting and customizes it for a simultaneous multistep-ahead prediction model in a surrogate model predictive control (MPC) application. The proposed method demonstrates enhanced control performance and computation efficiency compared to the Long-short term memory (LSTM)-based MPC and one-step-ahead prediction model structures for both LSTM and …

Immobilized Algae For Produced Water Treatment And Desalination, Shibin Nadersha, Ashraf Aly Hassan

Department of Civil and Environmental Engineering: Faculty Publications

Produced water (PW) is the effluent generated during oil mining and extraction. On average, for every barrel of oil, 4-5 barrels of PW are generated worldwide. The presence of various contaminants in PW makes it toxic. Disposal of untreated PW into oceans and water bodies can cause adverse effects on human health and the environment. Taking into account the large volumes of it being generated, and its effects on the environment, proper treatment is required before reuse or disposal. Microalgal treatment is an effective method for the bioremediation and biodesalination of produced water when acclimatized algal biomass is used for …

Establishing The Efficacy Of Non-Cellular Components Of Adipose-Derived Stromal Vascular Fraction In Promoting Angiogenesis., Daniel Benson

Electronic Theses and Dissertations

Microvascular disease is hallmarked by pathophysiological conditions such as endothelial senescence, intimal thickening which impairs vasodilation, and regression of the capillary beds causing tissue ischemia in the myocardium or in peripheral vascular networks. Adipose-derived stromal vascular fraction (SVF) has previously demonstrated the ability to revascularize tissue. Increasing evidence shows that regenerative cells elicit their therapeutic benefit by paracrine mechanisms, leaving open extracellular vesicles (EVs) as a potential crux of the cell therapy paradigm. To test this idea, three types of gelatin methacrylate hydrogels were employed: SVF gels, EV gels derived from SVF, and blank control gels, which were used in-vitro …

Deep Learning Of Microstructures, Amir Abbas Kazemzadeh Farizhandi

Boise State University Theses and Dissertations

The internal structure of materials also called the microstructure plays a critical role in the properties and performance of materials. The chemical element composition is one of the most critical factors in changing the structure of materials. However, the chemical composition alone is not the determining factor, and a change in the production process can also significantly alter the materials' structure. Therefore, many efforts have been made to discover and improve production methods to optimize the functional properties of materials. The most critical challenge in finding materials with enhanced properties is to understand and define the salient features of the …

Direct Ink Writing Of Flexible Piezoelectric Sensors, Amanda M. White

Boise State University Theses and Dissertations

Piezoelectric poly(vinylidene fluoride-co-trifluoroethylene), or PVDF-trFE, builds up significant electrical charges on its surface when stressed. By correlating the mechanical force with the resulting electrical charges or voltages, researchers have developed flexible, broadband, and biocompatible force sensors. PVDF-trFE force sensors are traditionally fabricated via spin coating or solvent casting, which result in large waste production and experience difficulties in forming complex geometries. To tackle these challenges, I leveraged a commercial direct ink writing system (nScrypt microdispenser) to additively manufacture PVDF-trFE force sensors. I first synthesized an unprecedented piezoelectric ink that is compatible with a commercial ink writing system at Boise State …

Deep Learning Approach To Speech Recognition: A Signal Extractor & Producer For Artificial General Intelligence, Ahmad Zuhair S. Hasanain

Theses and Dissertations

The efficient use of a communication bandwidth starts with the data source. The features of the speech signals can be extracted and reconstructed to lower the Internet traffic of the acoustic artificial agents and to increase the quality of the automatic speech recognition systems. The Speech Quefrency Transform (SQT) is hereby introduced in the work to enrich the communication space between the artificial agents and mankind. We describe the motivation, methodology, and deep learning approach in detail as we apply the SQT technology to several applications: sharp pitch track extraction, real-time speech communications, and emotion recognition. The results were excellent. …

Development Of Vegetable Oil-Based Nano-Lubricants Using Ag, H-Bn And Mgo Nanoparticles As Lubricant Additives, Kollol Sarker Jogesh

Theses and Dissertations

Because of the harmful impact of petroleum-based lubricant on the environment and human body, vegetable oil-based lubricant with eco-friendly nanoparticles has a great potential to be an alternative lubricant if it possesses proper lubricating properties. In this study, thermal conductivity, viscosity and tribological properties (wear scar diameter and coefficient of friction) of vegetable oil-based nanolubricant, developed from soybean oil and sunflower oil, modified with Ag, h-BN and MgO nanoparticles as lubricant additives, were evaluated. For thermal conductivity evaluation, a line heat source method was used with KD2 Pro-Thermal Property Analyzer. For viscosity evaluation, Haake Mars 40-rheometer was used to evaluate …

Mango Surface Color Features Measurement Using Digital Image Processing, Md Towfiqur Rahman, Goutom Kumar, Md Abdul Momin

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Summary

Postharvest processing of agricultural produce is still done the conventional way in Bangladesh. Manual grading of agricultural produce, especially fruits and vegetables, is laborious and costly due to acute shortage of labor during the peak season, as well as difficulty maintaining the product quality. Machine vision system (MVS) applications are widely used nowadays as a non-destructive and cost-effective technology for automatically grading and sorting large volumes of produce in the packing house according to size, shape, color, texture, and surface defects. In this study, a simple MVS was constructed measuring different color features of mango fruit surface as a …

Framework For The Use Of Extended Reality Modalities In Aec Education, Barbara Oliveira Spitzer, Jae Hoon Ma, Ece Erdogmus, Ben Kreimer, Erica Ryherd, Heidi Diefes-Dux

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The educational applications of extended reality (XR) modalities, including virtual reality (VR), augmented reality (AR), and mixed reality (MR), have increased significantly over the last ten years. Many educators within the Architecture, Engineering, and Construction (AEC) related degree programs see student benefits that could be derived from bringing these modalities into classrooms, which include but are not limited to: a better understanding of each of the subdisciplines and the coordination necessary between them, visualizing oneself as a professional in AEC, and visualization of difficult concepts to increase engagement, self-efficacy, and learning. These benefits, in turn, help recruitment and retention efforts …

High Throughput And Highly Controllable Methods For In Vitro Intracellular Delivery, Justin Brooks, Grayson Minnick, Prithvijit Mukherjee, Arian Jaberi, Lingqian Chang, Horacio D. Espinosa, Ruiguo Yang

Department of Mechanical and Materials Engineering: Faculty Publications

In vitro and ex vivo intracellular delivery methods hold the key for releasing the full potential of tissue engineering, drug development, and many other applications. In recent years, there has been significant progress in the design and implementation of intracellular delivery systems capable of delivery at the same scale as viral transfection and bulk electroporation but offering fewer adverse outcomes. This review strives to examine a variety of methods for in vitro and ex vivo intracellular delivery such as flow-through microfluidics, engineered substrates, and automated probe-based systems from the perspective of throughput and control. Special attention is paid to a …

Analysis Of Proposed Active Radiation Shielding Design Concept For Spacecraft, Claire Mechmann

Theses and Dissertations

A need exists to protect the crew of interplanetary spacecraft from lethal doses of Galactic Cosmic Radiation (GCR) and Solar Energetic Particles (SEPs). As plans progress to send humans beyond lower Earth orbit (LEO) and outside of Earth’s protective magnetosphere, agencies involved in this endeavor find themselves confronted with the obstacle of shielding the crew from this harmful radiation. A proposed active shielding concept design has been suggested, utilizing charged dielectric capacitors to deflect incoming charged particles. This analysis will examine the feasibility of the proposed design and offer potential materials useful for application. The results should prove informative for …

Examining The Effects Of Payload Type And Framing On Weather-Related Decision-Making In A Simulated Urban Air Mobility (Uam) Environment, Maria Chaparro Osman

Theses and Dissertations

The purpose of the current research study was two-fold. First, the study examined the effect of payload type on the riskiness of weather-related decision-making in a simulated urban air mobility (UAM) environment. Second, the current study examined whether framing information using prospect theory (Kahneman & Tversky, 1979) could influence the riskiness of weather-related decision-making in a simulated UAM environment. In the context of the current study, riskiness referred to the risk associated with the decision outcome, specifically whether participants selected a risk-averse decision outcome (return to the departure site) or risk-seeking decision outcome (continue to the destination site) based on …

Importance Of Light Activation For Plant Cryptochrome And Antibacterial Drug Delivery Strategies, Merfat Ahmed Hammad

Theses and Dissertations

The goal of this project is to investigate the benefits of applying light in different systems. In the first part, the magnetoreception process that occurs in the light activated cryptochrome of Arabidopsis Thaliana was investigated. In the second part, photo-carbon monoxide releasing molecules (photo-CORMs) were investigated for their antibacterial effect to develop biomedical strategies. Overall, this has been achieved in three different studies. The first study investigated if the forward lightdriven reaction is involved in the magnetoreception process or not in cryptochrome (CRY). To accomplish this, the plant seedlings were tested for 90 minutes as follows: 5 minutes in the …

Investigating The Role Of Cryptochrome Activity In Arabidopsis Plant And Blue Light Exposure In Saos-2 Cell-Mediated Mineralization, Maria Nijr Albaqami

Theses and Dissertations

Cryptochromes (CRYs) are flavoproteins that absorb blue light and are associated with the perception of electromagnetic stimuli in a variety of organisms including animals and plants. When exposed to blue light, CRYs undergo flavin redox cycles and form radical pairs intermediates that are assumed to be magnetically sensitive as predicted by the radical-pair hypothesis. However, it is unknown if CRYs fulfill the criteria to act as biological magnetosensors. In the first aim, Arabidopsis thaliana seedlings were exposed to blue light and a time-dependent weak magnetic field at radiofrequency (RF) of 7 MHz as a diagnostic tool to test the radical-pair …

Tympanostomy Tubes In Children: A Fem Study Of Adverse Effects, Manuel Nicolas Jaramillo Bucheli

Theses and Dissertations

Background: The current study investigates if tympanic (myringotomy) tubes affect hearing by comparing the harmonic displacement response to sound excitation within the hearing frequency range for healthy vs. surgically-treated pediatric tympanic membranes. The use of ear myringotomy tubes has proven an effective method for combating recurrent ear infections in infants and children. These tubes are placed in the tympanic membrane through an incision and connect the middle ear to the external ear, thereby allowing fluid drainage and middle-ear ventilation. While this treatment has been proven beneficial in alleviating urgent pus accumulation in the middle ear, recent research shows that it …

The Effect Of Zonation, Biofouling, And Corrosion Products On Cathodic Protection Design For Offshore Monopiles, Caglar Erdogan

Theses and Dissertations

Cathodic protection (CP) is required to prevent corrosion of the submerged steel for offshore wind monopile foundations in the marine environment. The design of these systems depends on the environmental conditions, including temperature, salinity, pH, dissolved oxygen, depth, micro- and macro-organisms, and water flow rates. The standards utilized to design cathodic protection systems consider only some of these conditions. This research identified the gaps in knowledge for the design of corrosion prevention systems for offshore wind monopile foundations and investigated the changes in cathodic current densities due to macro-galvanic cells, fouling communities and corrosion products established on uncoated vertical steel …

Color Resolved Cherenkov Imaging Allows For Differential Signal Detection In Blood And Melanin Content, Vihan A. Wickramasinghe

Dartmouth College Master’s Theses

Cherenkov imaging in radiation therapy allows a video display of the irradiation beam on the patient’s tissue, for visualization of the treatment. High energy radiation from a linear accelerator (Linac) results in the production of spectrally-continuous broadband light inside tissue due to the Cherenkov effect; this light is then attenuated by tissue features from transport and exits from the delivery site. Progress with the development of color Cherenkov imaging has opened the possibility for some level of spectroscopic imaging of the light-tissue interaction and interpretation of the specific nature of the tissue being irradiated. Generally, there is a linear relationship …

Evaluating The Viscoelastic Properties Of Alligator Skin Gelatin, Alligel, Compared To Mammalian And Fish Gelatins, Sarah E. Jimenez

Honors Capstones

No abstract provided.

Highly Adherent Antimicrobial Coatings For Orthopedic Implants, Mikhail Bredikhin

All Dissertations

Fracture-related infections (FRIs) are the most devasting sort of complications associated with fracture fixation devices, as they lead to patients’ morbidity, prolonged hospitalization, amputations, and even death.External fixators additionally suffer from pin site infections (PSIs), which initiate at the skin entry points of the skin-metallic pin interface present in the external fixation of the damaged bones, often causing deep tissue infection and osteomyelitis. Small percutaneous pins, commonly known as Kirschner wires (K-wires), are used to treat complex fractures and deformities.They are drilled inside the diseased bone for the healing period and are left protruding outside the skin for fixation adjustments …

Metabolic Engineering Of Yarrowia Lipolytica For Enhanced Peroxisomal Production Of Polyhydroxyalkanoates, Michael Spagnuolo

All Dissertations

Traditional chemical processes are made inefficient by the generation of side products and reactions that fail to reach completion. Bioprocesses, on the other hand, lose product potential due to the necessity of growing the organism required to produce the desired compounds. The field of metabolic engineering often seeks to alter this balance between product formation and cell growth to generate more product from the same quantity of feed (reagent). In addition to balance, such organisms may also be engineered to produce the desired products from nontraditional substrates, such as waste compounds. In resource-poor environments, the ability to produce a wanted …

Ligand-Promoted Dissolution Of Uranyl Phosphate Across Scales, Brennan Ferguson

All Dissertations

The formation of uranyl phosphate precipitate is a remediation strategy because the low solubility of uranyl phosphate minerals, like chernikovite, limits the mobility of uranium in contaminated soils. However, organic ligands can complex with aqueous metal cations to form more soluble species. For example, citrate is a commonly occurring organic ligand produced by plants and microbes that increases the solubility of uranium and therefore the dissolution of uranyl phosphate minerals in the uranyl phosphate-citrate system. This effect is an important control on the mobility of uranium in organic-rich, and near-surface vegetated environments. Nevertheless, key aspects of the citrate-uranyl phosphate system …

Seeing The Big Picture: System Architecture Trends In Endoscopy And Led-Based Hyperspectral Subsystem Intergration, Craig M. Browning

Graduate Theses and Dissertations (2019 - present)

Early-stage colorectal lesions remain difficult to detect. Early development of neoplasia tends to be small (less than 10 mm) and flat and difficult to distinguish from surrounding mucosa. Additionally, optical diagnosis of neoplasia as benign or malignant is problematic. Low rates of detection of these lesions allow for continued growth in the colorectum and increased risk of cancer formation. Therefore, it is crucial to detect neoplasia and other non-neoplastic lesions to determine risk and guide future treatment. Technology for detection needs to enhance contrast of subtle tissue differences in the colorectum and track multiple biomarkers simultaneously. This work implements one …