Digital Commons Network^™

A Multi-Organ Maize Metabolic Model Connects Temperature Stress With Energy Production And Reducing Power Generation, Niaz Bahar Chowdhury, Margaret Simons- Senftle, Berengere Decouard, Isabelle Quillere, Martine Rigault, Karuna Anna Sajeevan, Bibek Acharya, Ratul Chowdhury, Bertrand Hirel, Alia Dellagi, Costas Maranas, Rajib Saha

Department of Chemical and Biomolecular Engineering: Faculty Publications

Climate change has adversely affected maize productivity. Thereby, a holistic understanding of metabolic crosstalk among its organs is important to address this issue. Thus, we reconstructed the first multi-organ maize metabolicmodel, iZMA6517, and contextualized itwith heat and cold stress transcriptomics data using expression distributed reaction flux measurement (EXTREAM) algorithm. Furthermore, implementing metabolic bottleneck analysis on contextualized models revealed differences between these stresses. While both stresses had reducing power bottlenecks, heat stress had additional energy generation bottlenecks.We also performed thermodynamic driving force analysis, revealing thermodynamics-reducing power-energy generation axis dictating the nature of temperature stress responses. Thus, a temperaturetolerant maize ideotype can …

Optimal Inverter-Based Resource Installation To Minimize Technical Energy Losses In Distribution Systems, Felipe B. Dantas, Damasio Fernandes, Washington L.A. Neves, Alana K.X.B. Branco, Flavio Costa

Michigan Tech Publications

This paper proposes an algorithm for the optimal installation of inverter-based resources (IBR) composed of wind energy conversion systems, photovoltaic systems, and battery energy storage systems in distribution systems using genetic algorithm (GA) and the cuckoo search (CS) as optimization techniques. The OpenDSS software is used to calculate the power flow in the distribution system with different penetration levels of IBRs. It is used a standard load shape of the IEEE 123 bus system programmed in OpenDSS and irradiance, temperature, and wind speed curves from Brazil. The proposed algorithm, using a genetic algorithm and cuckoo search, was able to define …

A Novel Application Of Spinning Disk Technology To Collect Plasma From Whole Blood Prior To Quantifying Plasma Rna, Naomi Rapier-Sharman, Mae-Lynn L. Hutchinson, Carlos M. Moreno, Abraham Quaye, Brian D. Poole, K. Scott Weber, William G. Pitt, Brett E. Pickett

Faculty Publications

The spinning disk technology has previously been utilized to isolate bacterial components from blood in hours instead of days. We hypothesized that this platform could be applied as an alternative approach to isolating plasma RNA from a whole blood sample. We consequently tested the efficacy of the spinning disk technology to extract plasma from whole blood upstream of RNA isolation and analysis. To do so, we collected plasma using either the spinning disk or the typical two-spin centrifuge method. We found that the spinning disk method results in significantly more hemolysis during collection than the conventional two-spin centrifuge method. However, …

Integrated Periphyton Biofilters In Marine Recirculating Aquaculture Systems, Adam N. Bell

USF Tampa Graduate Theses and Dissertations

Marine aquaculture is a growing industry that has the potential to reduce eutrophication, overfishing, and loss of biodiversity. Recirculating aquaculture systems (RAS) are a type of aquaculture system that decreases discharge, raises biological control, and conserves water; however, RAS are challenged due to high energy cost, low biodiversity, water quality control, and waste nutrients. Periphyton biofilters are a new technology that allows for feed production, water quality control, microbial diversity, and resource recovery in marine aquaculture systems. The overarching question that this dissertation investigates is, how can periphyton biofilters be integrated into RAS to address the challenges of modern sustainable …

Research Outreach Interdisciplinary Activity To Classify Olive Oil Blends Integrating Multicolor Imaging, Image Processing, And Machine Learning, Allan Abraham, Kameshwaran Balachandran

Undergraduate Research (Journal)

This outreach undergraduate research project presents a low-cost method to distinguish the quality of different olive oils. The proposed method is based on an indirect measurement of the chlorophyll molecules present when a green laser diode illuminates the oil sample. Oil blends can be classified into five classes (no olive oil, light olive oil, medium olive oil, olive oil, and extra virgin olive oil) by quantifying the ratio of the red channel versus the green channel along the laser illumination path from a color image. After labeling each oil blend, a convolutional neural network has been implemented and trained to …

S-Net: A Multiple Cross Aggregation Convolutional Architecture For Automatic Segmentation Of Small/Thin Structures For Cardiovascular Applications, Nan Mu, Zonghan Lyu, Mostafa Rezaeitaleshmahalleh, Cassie Bonifas, Jordan Gosnell, Marcus Haw, Joseph Vettukattil, Jingfeng Jiang

Michigan Tech Publications

With the success of U-Net or its variants in automatic medical image segmentation, building a fully convolutional network (FCN) based on an encoder-decoder structure has become an effective end-to-end learning approach. However, the intrinsic property of FCNs is that as the encoder deepens, higher-level features are learned, and the receptive field size of the network increases, which results in unsatisfactory performance for detecting low-level small/thin structures such as atrial walls and small arteries. To address this issue, we propose to keep the different encoding layer features at their original sizes to constrain the receptive field from increasing as the network …

Biological Seawater Desalination Using Green Algae And Cyanobacteria, Abdul Mannan Zafar

Thesis/ Dissertation Defenses

Water shortage in many coastal parts of the world is reaching alarming situation, including the United Arab Emirates. Urbanization and rapid population growth are generating critical water demands with an increase in per capita consumption. Seawater is usually treated by membrane processes such as reverse osmosis (RO). However, this technology is energy intensive and generates excessive brine as a waste. The solution to this problem can be found in natural remediation techniques that can reduce salt concentration from seawater, such as halophytes. A salt-tolerant species can consume Na+ and Clions and increase cellular growth which is termed biological desalination or …

Novel Method Of The Quantification Of Turbulent Fluid Flow In Silicone Artery Phantoms Using Acoustic Analysis, Julia Wong

Master's Theses

Cardiovascular disease is the leading cause of death globally and is responsible for taking 17.9 million lives per year. Despite the use of clinical treatments and detection methods, there remains a large population of individuals that suffer from CVD whose symptoms are left undetected and untreated prior to a life-threatening cardiac event. This highlights a need for an early detection method that can prevent the manifestation and worsening of the disease as well as address limitations of current early detection methods. An area of interest for early detection of CVD is subclinical atherosclerosis, which is the long, early, asymptomatic stage …

Development Of An Angiogenic Tissue-On-A-Chip Microenvironment, Eric Stuehr

Master's Theses

Preclinical testing is necessary to investigate the safety and efficacy of novel therapeutics before moving to clinical trials, yet approximately 90% of these therapies fail once tested in humans. This has led to increased interest in developing robust preclinical models that accurately mimic the complex human in vivo physiology. Microfluidic devices that can introduce dynamic conditions to 3D cell/organoid cultures, also known as tissue-on-a-chip, have emerged as physiologically relevant in vitro preclinical models that can achieve high throughput screening of therapeutics. The research presented here aimed to develop an angiogenic environment within a novel microfluidic device to stimulate formation of …

Quantitative, Photocurrent Multidimensional Coherent Spectroscopy, Adam Halaoui

Electronic Theses and Dissertations

Multidimensional coherent spectroscopy (MDCS) is a quickly growing field that has a lot of advantages over more conventional forms of spectroscopy. These advantages all come from the fact that MDCS allows us to get time resolved correlated emission and absorption spectra using very precisely chosen interactions between the density matrix and the excitation laser. MDCS spectra gives the researcher a lot of information that can be extracted purely through qualitative analysis. This is possible because state couplings are entirely separated on the spectra, and once we know how to read the data, we can see how carriers transport in the …

Pedicle Screw Placement Accuracy In Robot-Assisted Spinal Fusion In A Multicenter Study, Victoria L. Volk, Keegan A. Steele, Mia Cinello‑Smith, Richard V. Chua, John Pollina, Gregory Poulter, Eiman Shafa, Peter Busselberg, Clare K. Fitzpatrick

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Pedicle screw fixation is a spinal fusion technique that involves the implantation of screws into vertebral pedicles to restrict movement between those vertebrae. The objective of this research is to measure pedicle screw placement accuracy using a novel automated measurement system that directly compares the implanted screw location to the planned target in all three anatomical views. Preoperative CT scans were used to plan the screw trajectories in 122 patients across four surgical centers. Postoperative scans were fused to the preoperative plan to quantify placement accuracy using an automated measurement algorithm. The mean medial–lateral and superior–inferior deviations in the pedicle …

Permeable Concrete Barriers To Control Water Pollution: A Review, Rehab O. Abdel Rahman, Ahmed M. El-Kamash, Yung-Tse Hung

Civil and Environmental Engineering Faculty Publications

Permeable concrete is a class of materials that has long been tested and implemented to control water pollution. Its application in low-impact development practices has proved its efficiency in mitigating some of the impacts of urbanization on the environment, including urban heat islands, attenuation of flashfloods, and reduction of transportation-related noise. Additionally, several research efforts have been directed at the dissemination of these materials for controlling pollution via their use as permeable reactive barriers, as well as their use in the treatment of waste water and water purification. This work is focused on the potential use of these materials as …

Motif-Cluster: A Spatial Clustering Package For Repetitive Motif Binding Patterns, Mengyuan Zhou

School of Computing: Dissertations, Theses, and Student Research

Previous efforts in using genome-wide analysis of transcription factor binding sites (TFBSs) have overlooked the importance of ranking potential significant regulatory regions, especially those with repetitive binding within a local region. Identifying these homogenous binding sites is critical because they have the potential to amplify the binding affinity and regulation activity of transcription factors, impacting gene expression and cellular functions. To address this issue, we developed an open-source tool Motif-Cluster that prioritizes and visualizes transcription factor regulatory regions by incorporating the idea of local motif clusters. Motif-Cluster can rank the significant transcription factor regulatory regions without the need for experimental …

Novel Castor Oil/Water/Ethanol Pickering Emulsions Stabilized By Magnetic Nanoparticles And Magnetically Controllable Demulsification, Mohammad J. Hasan, Peng Chen, Neithan Dominick, Erick S. Vasquez, Esteban E. Ureña-Benavides

Chemical and Materials Engineering Faculty Publications

A novel castor oil/water/ethanol Pickering emulsion, stabilized by magnetic nanoparticles (NPs), was developed to allow on-demand demulsification by an external magnetic field for the extraction of ethanol from aqueous solution using the castor oil. The emulsion was stabilized by Fe3O4-coated cellulose nanocrystals (CNC@Fe3O4) and lignin-coated Fe3O4 NPs (lignin@Fe3O4). The stability of the emulsions was investigated at various castor oil to ethanol-water ratios (50/50 and 70/30), various NP concentrations, and ethanol concentrations in the aqueous phase. The magnetically controlled demulsification ability of the emulsions was investigated by using a permanent magnet. The results showed that the 70/30 emulsions were more stable …

Continuous Time Recurrent Network For Human Activity Detection, Abdallah Al Zubi

Durham School of Architectural Engineering and Construction: Dissertations, Theses, and Student Research

Human activity detection is crucial to personalize the control of the building environment. For example, understanding certain human activities (e.g., walking, sitting, etc.) for an occupant in a building helps provide the proper thermal comfort control. However, these applications require large-scale neural networks that are challenging to implement and train.

In this thesis, we implemented a continuous-time recurrent neural network implementation (CTRNN) network that can solve real-time human activity detection with a smaller-size network. The CTRNN uses differential equations with a time constant to describe the neuron equations. It was implemented and trained for the first time using TensorFlow. Specifically, …

Deficient Aeronautical Decision-Making Contributions To Fatal General Aviation Accidents, Douglas D. Boyd, Mark Scharf Phd

Publications

INTRODUCTION: General aviation (GA), mainly comprised of light (≤12,500 lb) aircraft, maintains an inferior safety record compared with air carriers. To improve safety, aeronautical decision-making (ADM) practices have been advocated to GA pilots since 1991. Herein, we determined the extent to which GA pilots disregard such practices. METHODS: Fatal accidents (1991–2019) involving private pilots (PPLs) in single-engine airplanes were identified (N = 1481) from the National Transportation Safety Board AccessR database. Of these, deficient go/no-go and in-flight ADM-related mishaps were scored using the PAVE (pilot, aircraft, environment, external pressure)/IMSAFE (illness, medicine, stress, alcohol, fatigue, eating) and PPP (perceive, process, …

Design Guidance For Wetland-Road Crossings To Reduce Blanding’S Turtle Mortality Risk, Thomas P. Ballestero, Lauren E. White, Sandra Houghton, David Burdick, Josh Megyesy

Faculty Publications

Road mortality is a leading threat to freshwater turtles, particularly the Blanding’s turtle (Emydoidea blandingii), an endangered species in New Hampshire. Wildlife wetland-crossing structures, such as culverts and/or fences, have proven effective in reducing wildlife road mortality while retaining habitat connectivity. Funding for adequate wetland-crossing creation or restoration is limited, so prioritizing areas of high mortality risk is essential to ensuring that the resources spent are impactful. A research team of professionals from the New Hampshire Department of Environmental Services, New Hampshire Fish and Game, University of New Hampshire, and other organizations formed to create a model capable …

Electrophertic Deposition And Characterization Of Molybdenum Disulfide On Silicon Substrates, Alex J. Young

LSU Doctoral Dissertations

The electrical characteristics of 2D materials such as high electron mobility and current density are of great interest to various fields from optoelectronics to renewable energy. Researchers have focused their efforts on transition metal dichalcogenides (TMDCs) due to their direct energy band gap. One such TMDC that has garnered much attention is molybdenum disulfide (MoS2). MoS2 has electrical properties comparable to graphene and is a TMDC with characteristics amenable to applications such as solar cells and sensors. Commonly deposited through time-consuming and complex deposition methods such as chemical vapor deposition (CVD), the viability of MoS2 as an electronic material will …

A Consortium Of Microalgae And Wastewater Activated Sludge To Generate Biohydrogen, Muhammad Asad Javed

Dissertations

Hydrogen is a clean source and carbon-free source of energy that can be generated photobiologically using green microalgae with 122 kJ/g of energy output which is 2.75 times that of hydrocarbon-based fuels. However, challenges, such as presence of molecular oxygen (O₂) within the cells, hinder their practical application. Molecular O₂, emanating from the activity of photosynthesis, acts as a powerful and effective switch that turns off bioH₂ production activity. The objective of this research was to develop an innovative approach to increase the yield and sustain bioH₂ photoproduction. For this purpose, a consortium of …

Biomimetic Approach To Elucidate The Role Of Microenvironment In Regulating Cell Communications In Liver Diseases, Youra Moeun

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Liver is a complex organ but often underappreciated for its functions to remove toxins and fight infection in the body. Despite the ongoing prevalence of patients contracting chronic liver diseases, coupled with a global healthcare investment of approximately $70 billion, there is still no effective treatment for chronic liver diseases including alcoholic liver disease. The purpose of this dissertation was to understand the interactions of parenchymal and non-parenchymal liver cells in physiological and pathological like environments. This allowed us to recreate a healthy and the diseased microenvironments to observe the stages of the liver diseases development and apply appropriate treatments …

Modeling Overdraft-Driven Nitrate Transport In Shallow Wells For Mitigation And Scenario Planning, Jonathan Cronk

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

In Nebraska, average nitrate concentrations in groundwater have doubled since 1974, making water quality management more important than ever. As droughts, heat waves, and floods become more common climate events, understanding their impacts will be necessary to make informed management decisions. Emerging literature describes that drought correlates to an increase in the concentration of nitrate-N at domestic and irrigation wells, however the relative contributions of the mechanisms thought to be responsible is currently unknown.

This research assessed the impact of recharge and pumping rate changes as two mechanisms affecting nitrate-N concentration during drought, assessed the relationship between well depth and …

Examining The Externalities Of Highway Capacity Expansions In California: An Analysis Of Land Use And Land Cover (Lulc) Using Remote Sensing Technology, Serena E. Alexander, Bo Yang, Owen Hussey, Derek Hicks

Mineta Transportation Institute

There are over 590,000 bridges dispersed across the roadway network that stretches across the United States alone. Each bridge with a length of 20 feet or greater must be inspected at least once every 24 months, according to the Federal Highway Act (FHWA) of 1968. This research developed an artificial intelligence (AI)-based framework for bridge and road inspection using drones with multiple sensors collecting capabilities. It is not sufficient to conduct inspections of bridges and roads using cameras alone, so the research team utilized an infrared (IR) camera along with a high-resolution optical camera. In many instances, the IR camera …

Selection Of Natural Surfactants For Possible Use In Improving Oil Recovery Of Carbonate Oil Reservoirs, Hiba Hachem Limam

Theses

Middle East petroleum industry is currently searching for the most suitable enhanced oil technique to improve the oil recovery from local oil reservoirs. The biggest challenge for the application of enhanced oil recovery (EOR) in the Middle East is the harsh environment (high salinity and temperature). Surfactant (synthetic or natural) is one of the EOR major players considered for application in the Middle East. However, synthetic surfactants have several drawbacks, such as economically unattractive and environmental impacts. This study investigated the possible use of natural surfactant extracted from the leaves of three types of plants, namely Aloe Vera, Tetraena qatarensis, …

Development Of Popcorn Thermal Insulation Panels, Yonis Hussein Mohamud

Theses

The research and development of sustainable and renewable materials that can take the place of conventional plastics derived from petroleum has attracted increasing attention in recent years. Polylactic acid (PLA) and Polyhydroxy butyrate (PHB) are viable alternatives biopolymers due to their biodegradability. Also, the enhancement of material properties can be achieved through the incorporation of fillers. In this study, the utilization of popcorn in developing of insulation materials has been employed in two distinct methodologies. The first involves the coating of popcorn with varying percentages of PLA using the solvent casting method, while the second involves the integration of popcorn …

Biological Seawater Desalination Using Green Algae And Cyanobacteria, Abdul Mannan Zafar

Dissertations

Water shortage in many coastal parts of the world is reaching alarming situation, including the United Arab Emirates. Urbanization and rapid population growth are generating critical water demands with an increase in per capita consumption. Seawater is usually treated by membrane processes such as Reverse Osmosis (RO). However, this technology is energy intensive and generates excessive brine as a waste. The solution to this problem can be found in natural remediation techniques that can reduce salt concentration from seawater, such as halophytes. A salt-tolerant species can consume Na⁺ and Cl^- ions and increase cellular growth which is termed …

Control Methods For Maximizing Power Absorption And Grid Integration In Point Absorber Wave Energy Converters, Abdin Yousif Elamin

Dissertations

Wave energy is an emerging renewable energy source with great potential attributable to its consistent availability and high energy density. Technologies responsible for harnessing this form of energy are referred to as wave energy converters (WECs), among which point absorbers (PAs) are a notable subcategory. Unfortunately, the unpredictable and variable nature of waves, coupled with their complex hydrodynamics, has hindered PAs from achieving maximum wave energy absorption. Moreover, the inherent variability in wave energy leads to fluctuations in the power output of PAs. These power fluctuations pose challenges for grid integration, which requires power quality compatible with grid code standards. …

Microbial Glycosylation Of Antitubercular Agent Chlorflavonin, Jie Ren, Jixun Zhan

Biological Engineering Faculty Publications

Flavonoids have shown health-benefiting properties, such as antioxidative and anti-inflammatory activities, and are commonly used as nutraceuticals and pharmaceuticals. Although flavonoids are predominantly identified from plants, several filamentous fungal species have also been reported to produce bioactive flavonoids, including chlorflavonin from Aspergillus candidus, a novel halogenated flavonoid with potent antifungal and antitubercular (anti-TB) activities. Unfortunately, the low water-solubility of this molecule may hinder its bioavailability. Glycosylation is an effective method to enhance the polarity of natural products and alter their physicochemical properties. This work focuses on the development of novel water-soluble chlorflavonin derivatives to combat the threat of drug-resistant …

Multicolor Dye-Based Flow Structure Visualization For Seal-Whisker Geometry Characterized By Computer Vision, Ondřej Ferčák, Kathleen Lyons, Christin T. Murphy, Kristina M. Kamensky, Raul Bayoan Cal

Mechanical and Materials Engineering Faculty Publications and Presentations

Pinniped vibrissae possess a unique and complex three-dimensional topography, which has beneficial fluid flow characteristics such as substantial reductions in drag, lift, and vortex induced vibration. To understand and leverage these effects, the downstream vortex dynamics must be studied. Dye visualization is a traditional qualitative method of capturing these downstream effects, specifically in comparative biological investigations where complex equipment can be prohibitive. High-fidelity numerical simulations or experimental particle image velocimetry (PIV) are commonplace for quantitative high-resolution flow measurements, but are computationally expensive, require costly equipment, and can have limited measurement windows. This study establishes a method for extracting quantitative data …

Analysis Of Bombyx Mori Silk And Polyimide Nanofibers, Sabrina Leseul

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

This thesis presents a study on the properties of Bombyx Mori silk nanofibers and polyimide (PI) nanofibers. Firstly, a Bombyx Mori silk solution has been created with degummed silkworm cocoons in order to separate the fibroin and the sericin, the two main proteins of the silk. The fibroin was then centrifuged to remove insoluble particles and stored and 4°C before mixing with hexafluoroisopropanol (HFIP). On the second part, a polyimide solution, made with shavings of polyimide and N,N-dimethylformamide (DMF). Both solutions are then electrospun. Electrospinning parameters are studied. In this way, a part of my thesis has been dedicated to …

Hydroxyapatite-Based Coatings On Silicon Wafers And Printed Zirconia, Antoine Chauvin

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Dental surgery needs a naturally attract implant design that can ensure both osseointegration and soft tissue integration. Hydroxyapatite (HAp), the main mineral constituent of dentine and tooth enamel, is commonly used as a coating component, notably for overlaying titanium– or ceramics–based implants. This thesis aims to investigate the behavior of a HAp-based coating, specifically designed to be compatible with a porous substrate. Coating layers are made by sol–gel dip coating by immersion of porous substrates made by additive manufacturing into solutions of HAp, having been mixed with polyethyleneimine (PEI), to improve the adhesion of HAp on the substrate. First, the …