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Quantifying Components Of Protein Translation And Metabolite Heterogeneity In Isogenic Microbial Populations, Alexander Schmitz

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cell-to-cell variation in gene expression and metabolite levels have a significant impact on ensemble productivity of microbial bioproduction. New metabolic engineering tools and approaches are needed that consider cell cultures as an amalgam of uniquely behaving individuals to improve the slow commercialization of metabolically engineered systems. Stochastic cellular process including gene expression, metabolism, and growth lead to phenotypic variation between genetically identical cells. Understanding and the ability to control microbial phenotypic variation is key to improving microbial bioproduction metrics. During protein translation, codon usage strongly influences ensemble gene expression but the effect on the variation of gene expression was not …

Plasmonically-Enhanced Dna-Rna Hybrid-Based Bioassay For Amplification-Free Quantification Of Sars-Cov-2, Yuxiong Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Corona Virus Disease 2019 (COIVD-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a highly infectious respiratory illness. Within just a few months, it spread around the whole world and became a global pandemic. Real-time reverse-transcription polymerase chain reaction (RT-PCR) works as a gold standard method diagnosing COVID-19 with high sensitivity and specificity. But due to the programs of RT-PCR, it usually takes more than 24 hours to get the results while specialized devices are also required. False-negative results can happen as well using RT-PCR which increase the risk of spreading coronavirus. To promote quicker detection of COVID-19, …

Effects Of Tendon Viscoelasticity On The Distribution Of Forces Across Sutures In A Model Tendon-To-Bone Repair, Yuxuan Huang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Tears to the rotator cuff often require surgical repair. These repairs often culminate in re-tearing when sutures break through the tendon in the weeks following repair. Numerous studies have been performed to identify suturing strategies that reduce this risk by balancing forces across sutures. However, the structural engineering basis for these approaches is still emerging, and the effects of tendon mechanics on load balancing is still unclear. Specifically, the effects of the viscoelastic nature of tendon on load sharing have not been established. With the aim of providing insight into this problem, this thesis studies how tendon viscoelasticity, tendon stiffness, …

Revised Semiempirical Approach To Predict The Occurrence Of Twinning In Titanium Alloys, Chirag Dhirajlal Rabadia, Syed Faraz Jawed, Jincheng Wang, Milind Siddhpura, Arti Siddhpura

Research outputs 2014 to 2021

A revised semiempirical approach, considering the average values of the valence electron to atom ratio (e/a̅) and a difference in atomic radii of alloying element/s and the base element (Δr¯), is proposed to predict the twin formation in titanium alloys. The revised e/ā versus Δr¯ diagram is plotted, considering the reported results of 90 titanium alloys fabricated using various processing methods. A new twin/slip boundary has been plotted and recommended based on the revised e/ā versus Δr¯ diagram. The conventional maximum limit reported for the twinning in titanium alloys is e/ā = 4.20; however, it has been found that twinning …

Pertumbuhan Dan Hasil Dua Kultivar Bayam Pada Sistem Budidaya Hidroponik Untuk Lahan Sempit, Syariful Mubarok, Asyifa Mardatillah, Anne Nuraini

Jurnal Kultivasi

Hidroponik merupakan salah satu teknik sistem budidaya yang biasa digunakan di lahan sempit seperti di perkotaan. Tujuan dari penelitian ini adalah untuk menentukan sistem budidaya bayam yang paling baik untuk diterapkan pada sistem urban farming pada lahan sempit, misalnya di kawasan pemukiman padat penduduk di bagian timur Jakarta. Rancangan Acak Kelompok Lengkap yang digunakan dalam penelitian ini terdiri dari dua kultivar bayam dan tiga sistem budidaya yaitu budidaya konvensional, sistem hidroponik Wick dan NFT. Hasil penelitian menunjukkan bahwa sistem NFT menghasilkan pertumbuhan dan hasil terbaik yang ditunjukkan oleh jumlah daun, diameter batang, luas daun, panjang akar, volume akar dan berat …

Polymeric Nanofibers Supported Metal Oxides For Electrochemical Energy Storage Devices, Rutul Patel

Electronic Theses & Dissertations

With increasing demand for energy, there is an increased need to find effective ways to store the available energy to sustain current and future generations. Thus, the research investigates whether polymetric nanofibers support metal oxide are a good solution to store energy. The materials used for synthesis includes N-dimethylformamide, nickel nitrate, cobalt nitrate and polyacrylonitrile.

These fibers are developed three phases. First, a homogenous mixture is prepared, followed by electrospinning of the mixture. Next, calcination of the prepared nanofibers was done to generate the 1D nanofibers embedded with metal oxides. The samples are primarily tested for supercapacitor applications, hydrogen evolution …

Gis-Based Volunteer Cotton Habitat Prediction And Plant-Level Detection With Uav Remote Sensing, Tianyi Wang, Xiaohan Mei, J. Alex Thomasson, Chenghai Yang, Xiongzhe Han, Pappu Kumar Yadav, Yeyin Shi

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Volunteer cotton plants germinate and grow at unwanted locations like transport routes and can serve as hosts for a harmful cotton pests called cotton boll weevils. The main objective of this study was to develop a geographic information system (GIS) framework to efficiently locate volunteer cotton plants in the cotton production regions in southern Texas, thus reducing time and economic cost for their removal. A GIS network analysis tool was applied to estimate the most likely routes for cotton transportation, and a GIS model was created to identify and visualize potential areas of volunteer cotton growth. The GIS model indicated …

Hydrogen Peroxide Vapor Decontamination Of Polylactic Acid Fibers, Alexandra Craig

Mechanical Engineering Theses

Electrospun fibers have attracted attentions in topical drug delivery due to the ability to modulate drug release at high drug loading. While the pharmaceutical properties of these drug-eluting fibers were reported elsewhere, the compatibility of these fibers with hydrogen peroxide vapor, an effective decontaminant, is not fully established. In this work, polylactic acid (PLA) microfibers loaded with acetylsalicylic acid (ASA) were electrospun to examine their compatibility with hydrogen peroxide vapor. Results suggested a strengthening effect of the PLA/ASA fibers due to intermolecular interactions of ASA with PLA, which modulated the in vitro drug release rates. After exposing PLA/ASA fibers to …

Effects Of Bonding Pressure And Lamina Thickness On Mechanical Properties Of Clt Composed Of Southern Yellow Pine, Cody S. Bates

Theses and Dissertations

This study produced cross-laminated timber panels at a range of four lamina thickness (5/8, 1, 1 1/8, and 1 1/4 inch) and three bonding pressures (50, 125, 200 psi), producing a total of 12 panels for mechanical testing. The goal of this study is to observe how the thickness and pressure trends affect the mechanical properties of CLT. Tests include flatwise bending, flatwise shear, internal-bond, and delamination. Results showed that bending MOE decreases as the panel thickness increases while bonding pressure had no significance. Bending MOR was less significant for the thickness and more significant for pressure compared to the …

A Dual Perspective Towards Building Resilience In Manufacturing Organizations, Steven A. Fazio

Theses and Dissertations

Modern manufacturing organizations exist in the most complex and competitive environment the world has ever known. This environment consists of demanding customers, enabling, but resource intensive Industry 4.0 technology, dynamic regulations, geopolitical perturbations, and innovative, ever-expanding global competition. Successful manufacturing organizations must excel in this environment while facing emergent disruptions generated as biproducts of complex man-made and natural systems. The research presented in this thesis provides a novel two-sided approach to the creation of resilience in the modern manufacturing organization. First, the systems engineering method is demonstrated as the qualitative framework for building literature-derived organizational resilience factors into organizational structures …

Hydrology And Water Quality Analysis In The Big Black River Watershed, Mississippi, Moniba Shabbir

Theses and Dissertations

Evaluating hydrology and water quality for the Big Black River Watershed in Mississippi was accomplished by using the Better Assessment Science Integrating Point and Nonpoint Source (BASINS 4.5), Loading Simulation Program in C++ (LSPC), and Water Quality Analysis Simulation Program (WASP) models. The watershed model calibration was originally accomplished by using historical data collected from U.S. Geological Survey (USGS). The watershed model was calibrated using data from 2000 through 2018 in order to quantify stream flow and point source discharges under a variety of hydrologic conditions. The model predicted response of hydrology was consistent with the observed data range. The …

Methods For Inference And Analysis Of Gene Networks From Rna Sequencing Data, Himangi Srivastava

Theses and Dissertations

RNA (Ribonuceic Acid) sequencing technology is a powerful technology used to give re- searchers essential information about the functionality of genes. The transcriptomic study and downstream analysis highlight the functioning of the genes associated with a specific biological process/treatment. In practice, differentially expressed genes associated with a particular treatment or genotype are subjected to downstream analysis to find some critical set of genes. This critical set of genes/ genes pathways infers the effect of the treatment in a cell or tissue. This disserta- tion describes the multiple stages framework of finding these critical sets of genes using different analysis methodologies …

Uncertainty-Aware Deep Learning For Prediction Of Remaining Useful Life Of Mechanical Systems, Samuel J. Cornelius

Theses and Dissertations

Remaining useful life (RUL) prediction is a problem that researchers in the prognostics and health management (PHM) community have been studying for decades. Both physics-based and data-driven methods have been investigated, and in recent years, deep learning has gained significant attention. When sufficiently large and diverse datasets are available, deep neural networks can achieve state-of-the-art performance in RUL prediction for a variety of systems. However, for end users to trust the results of these models, especially as they are integrated into safety-critical systems, RUL prediction uncertainty must be captured. This work explores an approach for estimating both epistemic and heteroscedastic …

The Development Of Authentic Virtual Reality Scenarios To Measure Individuals’ Level Of Systems Thinking Skills And Learning Abilities, Vidanelage L. Dayarathna

Theses and Dissertations

This dissertation develops virtual reality modules to capture individuals’ learning abilities and systems thinking skills in dynamic environments. In the first chapter, an immersive queuing theory teaching module is developed using virtual reality technology. The objective of the study is to present systems engineering concepts in a more sophisticated environment and measure students learning abilities. Furthermore, the study explores the performance gaps between male and female students in manufacturing systems concepts. To investigate the gender biases toward the performance of developed VR module, three efficacy measures (simulation sickness questionnaire, systems usability scale, and presence questionnaire) and two effectiveness measures (NASA …

Development Of A Bioinspired Nugalbot For Precision Seeding Of Rice, Harsa Dhani

Theses and Dissertations

Many people around the world live in islands with mountainous lands. These people plant upland rice for their staple food. However, farming in these disadvantageous farms requires high input and gains low yield. One possible solution for improving productivity is by utilizing precision seeding. This study is focused on developing a robot for precision seeding of rice that is suitable for farming in rough terrain. A bioinspired human arm robot for picking seeds and making a hole on the ground was developed in accordance with Aalborg method for bioinspired design. Development of a mobile platform to carry the robot arm …

Design Of Plastic Contaminant Eliminator In Seed Cotton, Joshua H. Tandio

Theses and Dissertations

Plastic contamination in cotton is a problem in cotton industry and researchers have worked on this problem with different approaches. This thesis documents the design of mechanical and electronic real-time systems for detecting and removing plastic contaminants. The mechanical system was designed to expose plastic embedded inside the seed cotton to the sensor and to separate plastic contaminated cotton from the process stream. The detection system consisted of an embedded computer interfaced with a USB camera and Neural Network (NN) software running in it. Two NN models were tested, a transfer learning model and a built-from-scratch original model. The original …

Using A Systemic Skills Model To Build An Effective 21st Century Workforce: Factors That Impact The Ability To Navigate Complex Systems, Morteza Nagahi

Theses and Dissertations

The growth of technology and the proliferation of information made modern complex systems more fragile and vulnerable. As a result, competitive advantage is no longer achieved exclusively through strategic planning but by developing an influential cadre of technical people who can efficiently manage and navigate modern complex systems. The dissertation aims to provide educators, practitioners, and organizations with a model that helps to measure individuals’ systems thinking skills, complex problem solving, personality traits, and the impacting demographic factors such as managerial and work experience, current occupation type, organizational ownership structure, and education level. The intent is to study how these …

Pan Variant Sars-Cov-2 Common Interactions And Drug Candidates, Kolton Hauck

Fall Student Research Symposium 2021

As the SARS-CoV-2 virus has spread, multiple strains have appeared. Research has investigated potential drug candidates for COVID-19, but without consideration for the multiple variants of SARS-CoV-2. A domain-based and interolog-based method were implemented to predict protein-protein interactions (PPIs) between the SARS-CoV-2 variants and human proteins. A common set (conserved among all strains) and a unique set (distinct for each strain) of interactions were made. These sets of interactions were characterized via subcellular localization, tissue expression, pathway enrichment and gene ontology. Lastly, drug candidates were identified for the common set. The combined domain and interolog methods resulted in 8963 predicted …

Establishing A Framework Of Nitrogen Acquisition For Martian Agriculture, Tyler Wallentine

Fall Student Research Symposium 2021

Nitrogen (N) forms a crucial part of DNA, proteins, and other biomolecules and is an essential element to life. Luckily, N is abundant in Earth’s and Mars’ atmospheres in its atmospheric form (N₂); however, plants and humans are unable to metabolize it in this state. N₂ gas is only able to be consumed by undergoing nitrogen fixation, an intensive process that breaks the extremely-stable N ≡ N bond in order to form bioavailable ammonia (NH₃). Many prokaryotes are capable of nitrogen fixation. Plants may uptake fixed N from these, which are then consumed by other …

A Computational Model Of Angiogenesis In Wet Age-Related Macular Degeneration, Brandon Pace

Fall Student Research Symposium 2021

Age-related macular degeneration (AMD) is a chronic disease which causes central blindness in the eye. This progressive disease is thought to affect 1 of every 4 people over the age of 80 living in developed countries, including America. There is no cure and the only treatments to halt disease progression involve biweekly eye injections for the rest of the patient’s life. Clearly there is a great need to understand AMD and find better treatment for the many afflicted. It is known that harmful capillary growth (angiogenesis) contributes to AMD. By learning more about retinal angiogenesis, we can understand AMD in …

Effectiveness Of Cannabidiol And Resveratrol Against Diesel Exhaust Particle-Induced Lung Cell Cytotoxicity, Emily Brothersen

Fall Student Research Symposium 2021

Environmental air pollution poses a significant health risk to individuals across the world. Diesel exhaust particles (DEPs), a major component of air pollution, have been shown to cause lung damage leading to cancer, respiratory infections, and premature death. Antioxidants, such as resveratrol, have previously demonstrated protective properties against DEP-induced cytotoxicity and reactive oxygen species. Cannabinoids extracted from hemp species have also been found to have powerful antioxidant properties, though these properties have not been thoroughly explored. In this study, A549 human lung carcinoma cells were used as a cellular model to determine the effectiveness of cannabinoids’ antioxidant properties against DEP-induced …

Smooth Muscle Cells Affect Differential Nanoparticle Accumulation In Disturbed Blood Flow-Induced Murine Atherosclerosis, Hunter Miller, Morgan A. Schake, Badrul Alam Bony, Evan T. Curtis, Conner C. Gee, Ian Mccue, Thomas J. Ripperda Jr., Yiannis S. Chatzizisis, Forrest Kievit, Ryan M. Pedrigi

Department of Mechanical and Materials Engineering: Faculty Publications

Atherosclerosis is a lipid-driven chronic inflammatory disease that leads to the formation of plaques in the inner lining of arteries. Plaques form over a range of phenotypes, the most severe of which is vulnerable to rupture and causes most of the clinically significant events. In this study, we evaluated the efficacy of nanoparticles (NPs) to differentiate between two plaque phenotypes based on accumulation kinetics in a mouse model of atherosclerosis. This model uses a perivascular cuff to induce two regions of disturbed wall shear stress (WSS) on the inner lining of the instrumented artery, low (upstream) and multidirectional (downstream), which, …

Pd Doped Sno2 Resistive Film As A Non-Enzymatic Glucose Sensor, Salim F. Bamsaoud, Sandhya Rani, R. N. Karekar Prof., S. W. Gosavi

Hadhramout University Journal of Natural & Applied Sciences

A new sugar sensor based on metal oxide is presented here. The variation on the sensor resistance is studied against different glucose and fructose concentrations (1 - 360 mg/dl). The study is done for three different resistive films (i) pristine palladium oxide (PdOx); (ii) tin oxide (SnO2) and (iii) palladium doped tin oxide (Pd-SnO2). The chemical reactions of glucose and fructose with surface species were studied. Pd-SnO2 films show an excellent and reliable response to glucose and fructose solution in comparison with the bare films (PdOx and SnO2). Sensor performance was checked for the blood of normal (120 mg/d) and …

Evaluating And Enhancing Iron Removal Via Filterable Iron Precipitates Formation During Coal-Waste Bioleaching, Prasenjit Podder, Zongliang Zhang, Rick Q. Honaker, Michael L. Free, Prashant K. Sarswat

Mining Engineering Faculty Publications

Iron removal via jarosite precipitate formation is a commonly used technique in various hydrometallurgical processes. Excess iron removal often becomes essential to an overall metal recovery circuit. This is particularly important to processes involving iron-bearing minerals. A technique, which involved the use of pyrite to generate acid for leaching, for iron removal is critical to enabling the process. Iron removal using CaO or similar reagents is expensive and often results in lost product. In the present study, various compounds that facilitate jarosite formation, namely Na₂SO₄, NH₄OH, KCl, and KOH, were utilized and their effect …

Microfabricated Platforms To Investigate Cell Mechanical Properties, Amir M. Esfahani, Grayson Minnick, Jordan Rosenbohm, Haiwei Zhai, Xiaowei Jin, Bahareh Tajvidi Safa, Justin Brooks, Ruiguo Yang

Department of Mechanical and Materials Engineering: Faculty Publications

Mechanical stimulation has been imposed on living cells using several approaches. Most early investigations were conducted on groups of cells, utilizing techniques such as substrate deformation and flow-induced shear. To investigate the properties of cells individually, many conventional techniques were utilized, such as AFM, optical traps/optical tweezers, magnetic beads, and micropipette aspiration. In specific mechanical interrogations, microelectro- mechanical systems (MEMS) have been designed to probe single cells in different interrogation modes. To exert loads on the cells, these devices often comprise piezo-electric driven actuators that attach directly to the cell or move a structure on which cells are attached. Uniaxial …

Injectable Decellularized Nucleus Pulposus Tissue Exhibits Neuroinhibitory Properties, Logan M. Piening, David J. Lillyman, Fei San Lee, Alvaro Moreno Lozano, Jeremy R. Miles, Rebecca A. Wachs

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: Chronic low back pain (LBP) is a leading cause of disability, but treatments for LBP are limited. Degeneration of the intervertebral disc due to loss of neuroinhibitory sulfated glycosaminoglycans (sGAGs) allows nerves from dorsal root ganglia to grow into the core of the disc. Treatment with a decellularized tissue hydrogel that contains sGAGs may inhibit nerve growth and prevent discassociated LBP.

Methods: A protocol to decellularize porcine nucleus pulposus (NP) was adapted from previous methods. DNA, sGAG, α-gal antigen, and collagen content were analyzed before and after decellularization. The decellularized tissue was then enzymatically modified to be …

Global Analysis Of Differential Gene Expression Within The Porcine Conceptus Transcriptome As It Transitions Through Spherical, Ovoid, And Tubular Morphologies During The Initiation Of Elongation, Sophie C. Walsh, Jeremy R. Miles, Brittney N. Keel, Lea A. Rempel, Elane C. Wright‐Johnson, Amanda K. Lindholm‐Perry, William T. Oliver, Angela K. Pannier

Department of Agricultural and Biological Systems Engineering: Faculty Publications

This study aimed to identify transcriptome differences between distinct or transitional stage spherical, ovoid, and tubular porcine blastocysts throughout the initiation of elongation. We performed a global transcriptome analysis of differential gene expression using RNA‐Seq with high temporal resolution between spherical, ovoid, and tubular stage blastocysts at specific sequential stages of development from litters containing conceptus populations of distinct or transitional blastocysts. After RNA‐Seq analysis, significant differentially expressed genes (DEGs) and pathways were identified between distinct morphologies or sequential development stages. Overall, 1898 significant DEGs were identified between distinct spherical and ovoid morphologies, with 311 total DEGs between developmental stages …

A Survey Of Stainless Steel In Medical And Surgical Application, Noah Slack, Clint Balch

ME 4133/6133 Mechanical Metallurgy

Stainless steels can be separated into four families based on the microstructure of the material: Austenitic, Ferritic, Martensitic, and Duplex. Each family provides a specific set of advantages and disadvantages, and material selection should be based on the specific application the material will be used for. For this study, the processing, microstructure, and performance of the four families of stainless steels will be compared in the context of medical device applications. The most important factors in medical device materials are biocompatibility, surface properties, mechanical properties and life span/corrosion resistance. This study will focus on medical devices that will be permanently …

A Highly Versatile Fungal Glucosyltransferase For Specific Production Of Quercetin-7-O-Β-D-Glucoside And Quercetin-3-O-Β-D-Glucoside In Different Hosts, Jie Ren, Wenzhu Tang, Caleb Don Barton, Owen M. Price, Mark Wayne Mortensen, Alexandra Phillips, Banner Wald, Simon Elgin Hulme, Logan Powell Stanley, Joan Hevel, Jixun Zhan

Biological Engineering Faculty Publications

Glycosylation is an effective way to improve the water solubility of natural products. In this work, a novel glycosyltransferase gene (BbGT) was discovered from Beauveria bassiana ATCC 7159 and heterologously expressed in Escherichia coli. The purified enzyme was functionally characterized through in vitro enzymatic reactions as a UDP-glucosyltransferase, converting quercetin to five monoglucosylated and one diglucosylated products. The optimal pH and temperature for BbGT are 35 ℃ and 8.0, respectively. The activity of BbGT was stimulated by Ca2+, Mg2+, and Mn2+, but inhibited by Zn2+. BbGT enzyme is flexible and can glycosylate a variety of substrates such as curcumin, …

Irrigation Systems Management, Dean Eisenhauer, Derrel L. Martin, Derek M. Heeren, Glenn J. Hoffman

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Management of irrigation systems should be based on the desired objectives or outcomes consistent with economic, energy, environmental, labor, water, and resource constraints. Goals can vary from maximizing profit, producing a contracted yield, optimizing water resource use, maintaining the quality of produce, or assuring an attractive landscape. Managers cannot achieve these goals without considering the performance of the irrigation system. This chapter discusses the basic characteristics of various irrigation systems, defines terms that quantify performance, describes basic requirements all systems must provide, gives a range of attributes for systems, and discusses how water supply requirements are governed by ET and …