Biological Engineering Commons^™

Multiscale 3d Whole Joint Cellular And Molecular Mapping Reveals Disease-Specific Neurovascular Plasticity Underlying The Structure-Pain Relationship, Peng Chen, Jiaxin Chai, Abirami Soundararajan, R. Glenn Hepfer, Benjamin Kheyfets, Jiaxin Hu, Ishraq Alshanqiti, Swarnalakshmi Raman, Ikue Tosa, Jun Tae Huh, Matthew Yee, Brooke J. Damon, Shangping Wang, Yu Shin Kim, Man-Kyo Chung, Mildred C. Embree, Janice S. Lee, Tong Ye, Hai Yao

Publications

Understanding musculoskeletal joints from a 3D multiscale perspective, from molecular to anatomical levels, is essential for resolving the confounding relationships between structure and pain, elucidating mechanisms regulating joint health and diseases, and developing new treatment strategies. Here, a musculoskeletal joint immunostaining and clearing (MUSIC) method specifically developed to overcome key challenges of immunostaining and optical clearing of intact joints are introduced. Coupled with large-field light sheet microscopy, this approach achieves 3D high-resolution, microscale neurovascular mapping within the context of whole-joint anatomy without the need for image coregistration across various joints, including temporomandibular joints, knees, and spines, and multiple species, including …

Strategies For Increasing Methane Removal In Methanotroph Stirred-Tank Reactors For The Production Of Ectoine, Jaden Storrer, Tansley M. Mazurkiewicz, Bodee Hancock, Ronald C. Sims

Biological Engineering Student Research

Methane is a potent greenhouse gas that requires its emissions to be mitigated. A significant source for methane emissions is in the form of the biogas that is produced from anaerobic digestion in wastewater reclamation and landfill facilities. Biogas has a high valorization potential in the form of its bioconversion into ectoines, an active ingredient in skin care products, by halotolerant alkaliphilic methanotrophs. Cultures of Methylotuvimicrobium alcaliphilum 20Z were grown in bench scale stirred-tank reactors to determine factors to improve methane uptake and removal. Tangential flow filtration was also implemented for a bio-milking method to recover ectoine from culture media. …

Capacity Of Microbial Strains And Communities To Degrade Sewerage Fats, Oils, And Grease Clog Deposits, Allondra M. Woods, Catherine J. Pettinger, Catherine Harris, Tanya Soule, Garth Farley, Erica L.-W. Majumder

Biological Engineering Student Research

Fats, oils, and grease (FOG) deposits are hardened, sticky, insoluble solids that accumulate in sewage systems globally. These deposits contribute to pipe blockages and sanitary sewer overflows, releasing pathogens and pollutants into the environment, posing significant environmental and public health risks. Current removal methods are labor-intensive and costly, emphasizing the need for alternatives. While biological strategies offer a viable alternative, the microbial breakdown of FOG is poorly understood. In this study, we evaluated the potential of individual microbial strains and synthetic microbial communities to biodegrade wastewater-derived FOG deposit samples. These biological agents were applied to a range of FOG samples, …

Multi-Material Printer Development, Jessica Hu, Phoebe Eplett

College of Engineering Summer Undergraduate Research Program

Surgeons require pre-surgical models to practice procedures and improve success rates. However, the current process of creating physical models for practice using 3D printing is limited to producing homogeneous mimics of the human body, while the human body is a heterogeneous structure composed of multiple materials with varying properties, including bones, muscles, and skin. Additive manufacturing methods cannot easily print multiple materials simultaneously, as current AM machines only print homogeneous material, unlike the human body. In this proposal, we aim to develop a multi-material additive manufacturing system, from software to hardware, to manufacture pre-surgical models. We will investigate multi-material AM …

Analysis Of Modifications To An Outdoor Field-Scale Rotating Algal Biofilm Reactor With A Focus On Biomass Productivity And Power Usage, Davis R. Haag, Phillip E. Heck, Ronald C. Sims

Biological Engineering Student Research

Filtrate from dewatering anaerobically digested biosolids is a side-stream of wastewater treatment that contains high concentrations of nitrogen and phosphorus compounds that can serve as nutrients for cultivating microalgae biomass as biofilms for bioproduct production at Water Resource Recovery Facilities (WRRFs). One system used to cultivate attached microalgae biofilms is the rotating algal biofilm reactor (RABR). A pilot RABR with 72 m² growth surface area, 11.5 m² footprint area, and a liquid volume of 11,500 L was operated in an outdoor environment at the largest WRRF in Utah, U.S.A, the Central Valley Water Reclamation Facility (CVWRF). The configuration …

Bioresources And Bioproducts: A New Open Access Journal, Ronald C. Sims

Biological Engineering Faculty Publications

Greetings to the bioresource and bioproducts community! I will serve as the Editor-in-Chief to collaborate with you as we promote the aims and scope of this new MDPI journal [1], with the help of its distinguished Editorial Board, by publishing Special Issues, Topics, Topical Collections, and Editorials, and by providing high-impact scholarship through the outstanding published work of each of our contributors.

Optimizing Beer Fermentation Through Intelligent Control, Azizbek Nodirbekovich Yusupbekov, Mirjalol Yusupov

Chemical Technology, Control and Management

This paper presents an intelligent control approach for optimizing the beer fermentation process using fuzzy logic and adaptive neuro-fuzzy inference systems. By incorporating multivariable inputs—temperature error and pH deviation—the proposed system effectively handles the nonlinear dynamics and biological variability inherent in fermentation. Simulation results demonstrate improved control accuracy, responsiveness, and robustness compared to conventional methods, making the approach suitable for integration in modern brewery automation systems.

Influence Of Obesity On Knee Joint Mechanics: A Subject-Specific Musculoskeletal Modeling Approach, Ryan C. Knowles

Electronic Theses and Dissertations

Obesity has been consistently linked to knee osteoarthritis (KOA), a debilitating joint disease. While prior work has shown that obese individuals often walk with altered biomechanics compared to normal-weight (NW) individuals, which may accelerate KOA progression, less is known about how these mechanics affect load distribution between the medial and lateral tibiofemoral (TF) compartments, particularly during higher-demand activities. This study developed subject-specific musculoskeletal models of five obese and five NW individuals, incorporating CT-based bone measurements and individualized joint contact points. Simulations were driven by six degree-of-freedom (6DOF) kinematics obtained from high-speed stereo radiography (HSSR) to predict TF loading and associated …

Optimization And Utilization Of Microbial Electrolysis Cells In Waste To Product Applications, Hayden Harrison

All Graduate Theses and Dissertations, Fall 2023 to Present

As the world searches for cleaner and more sustainable energy solutions, turning waste into fuel is an increasingly attractive strategy. This research focuses on microbial electrolysis cells, a new technology that uses bacteria and a small amount of electricity to convert organic waste—like food scraps or wastewater—into useful gases such as hydrogen and methane. These gases can be used as energy sources to reduce dependency on more traditional fuels.

This thesis tackles two key challenges that limit the real-world use of microbial electrolysis systems. First, it introduces a simpler and more effective method to stop hydrogen losses in single-chamber cells. …

Population Analysis Of Cyanobacteria In Rotating Algal Biofilm Reactors, Eric H. Matthews

All Graduate Theses and Dissertations, Fall 2023 to Present

Algal biofilms have numerous applications in wastewater treatment and bioproduct production. The Sustainable Waste-to-Bioproducts Engineering Center at Utah State University is working to develop rotating algal biofilm reactors (RABRs) to remove excess nitrogen and phosphorus from wastewater effluent while producing biomass for downstream production.

Genetic analysis of algal biofilms on various RABRs was performed to gain improved understanding of the biofilm populations. This analysis focuses on a pilot-scale RABR and how it compares to several other RABRs. Additionally, old methods of genetic analysis filtered out important cyanobacterial populations. A new method was developed to identify the cyanobacteria within the biofilms. …

Advancements In Microarray Manufacturing Enable Emerging Technologies, Kendall Hoff

Biomedical Engineering ETDs

Significant advances in manufacturing technologies have enabled the production of new DNA microarrays for use in emergent technology. Photolithography, wafer scale manufacturing, and improvements in synthesis chemistry and design enable high-throughput production of extremely high-quality arrays. These new arrays offer extremely high oligonucleotide densities, in the range of tens of thousands of oligonucleotides per square micron. They also offer smaller features sizes, with millions of features per square centimeter. Furthermore, they can be manufactured with the DNA tethered at either end to the surface, leaving either the 5’ or 3’ end free and available for use in enzymatic reactions; and …

Harnessing Environmentally Healthy Approaches For Plastic Degradation: A Review And Future Perspectives, Marc Chojnacki

Beyond: Undergraduate Research Journal

In the face of escalating plastic pollution, innovative degradation strategies, such as enzymatic degradation, smokeless incineration technology, and biodegradable plastics, are gaining traction. This paper collates comprehensive research on these methods, assessing their environmental impact and operational feasibility. A special focus is placed on the role of technology and its capacity to spark advancements in these degradation strategies as well as to draw on specific research to understand the economic implications of these methods. At the core of this study is the exploration of potential new, inventive degradation methodologies. Through examining methods of green plastic degradation, the study aims to …

Characterization Of Lactobacilli-Containing Catheter Segments Developed By Using Selective Laser Sintered Mold., Caden Maners

Master of Engineering Theses

Catheter-associated urinary tract infections (CAUTIs) are a major healthcare burden with current prevention strategies offering limited success. This study presents a novel, self-coating biomaterial approach using a silicone-based bioink embedded with thermally sensitive probiotic strains (L. crispatus, L. rhamnosus, and L. reuteri). Catheter segments were fabricated via bio-injection molding using 3D-printed CAD molds. These Lactobacilli, selected for their probiotic and antimicrobial potential, serve as a non- antibiotic strategy to reduce infection risk. These segments were evaluated for mechanical strength (Shore A hardness), thermal stability (TGA/DSC), porosity and bacterial presence (SEM), biofilm formation (crystal-violet assay), as well as mass retention in …

A Smart System For Detecting Anatomic And Histological Symptoms Of Diseased Agricultural Plants, Rustam Baratov, Himola Sunnatillayeva, Alimardon Mamatovich Mustafoqulov

Chemical Technology, Control and Management

This study describes a novel agricultural plant disease detecting smart system, capable of handling measured plant body parameters and images received by high resolution camera at the same time. The proposed plant disease detection method is based on evaluation of the signals received by measured and controlled plant body physical parameters like resistance, temperature and capacitance of the plant stem and image processing. An analogue plant model based on an electrical circuit with distributed parameters was developed. In addition, in the article the block diagram of the smart system for the early detection of plant diseases, the circuit diagram, its …

Computational Fluid Dynamics And Fluid Structure Interaction Modeling In Healthy Vertebral Arteries: A Comparative Study, Bryce Clinkenbeard

Electronic Theses and Dissertations

Cerebral perfusion is critical for maintaining proper brain function, with each cerebrovascular artery playing an integral role in the overall cerebrovascular system. When these arteries become damaged or develop plaque, cardiovascular disease (CVDs) such as atherosclerosis can arise, leading to conditions like arterial stenosis. While CVDs are most prevalent in older individuals, they are also observed in young adults, particularly those engaged in high-endurance occupations such as military service. Diagnosis and prediction of CVDs often rely on imaging modalities supported by computational fluid dynamics (CFD) which account for low resolution in fluid flow. CFD models assume rigid arterial walls, which …

A Hybrid Ai-Based Framework For Real-Time Epileptic Seizure Detection In Intracranial Eeg Signals Using Brain-Computer Interfaces, Ahmed, M. Salaheldin Dr., Manal Abdel Wahed Prof., Neven Saleh

Future Engineering Journal

Epilepsy is a serious neurological disorder that can significantly impact an individual's quality of life. This study proposes a novel method for the detection and mitigation of epileptic seizures through the integration of artificial intelligence (AI) and a brain-computer interface (BCI) system. Statistical features were extracted from intracranial electroencephalography (IEEG) signals using a multi-resolution decomposition technique and used to train five classification algorithms: support vector machines (SVM), k-nearest neighbors (KNN), Naïve Bayes (NB), artificial neural networks (ANN), and long short-term memory (LSTM). The model demonstrated strong performance, achieving classification accuracies of 98.28% (SVM), 93.88% (KNN), 95.73% (NB), 95.73% (ANN), and …

Alterations And Improvements Of The Photoacoustic Flow Cytometry Method, Nicholas J. Taylor

Electronic Theses and Dissertations

The emergence and proliferation of antibiotic-resistant bacteria present a significant and growing challenge to global public health, with the potential to render many existing antibiotics ineffective. Infections caused by these resistant pathogens are difficult to treat, resulting in higher morbidity, mortality, and healthcare costs. A major obstacle in combating these infections is the slow pace of traditional diagnostic methods, such as blood cultures, which typically take 2-3 days to identify the causative bacteria and determine their antibiotic resistance profiles. This delay in diagnosis hinders timely interventions and appropriate treatment, further contributing to the spread of resistant infections. As such, there …

Fundus Retinal Images And Glaucoma Detection, Lama Alsabban, Malak Alnahdi, Nema Salem

Effat Undergraduate Research Journal

Abstract. Glaucoma is a severe eye disease that has no symptoms and, globally, it is the second cause of blindness. Glaucoma causes structural changes in the retina that make ophthalmologists detecting the disease in early stage and thus provide the suitable treatment. Fundus camera is an imaging technique that provides the fundus image showing the internal structure of retina. Our project provides an automated system for early detection of Glaucoma. The proposed system based MATLAB starts by acquiring the fundus image, followed by preprocessing stage, going through noise removal, enhancement, segmentation, feature extraction and ends up by the classification stage. …

Development Of Translational Microscale Systems To Interrogate How Biophysical And Biochemical Cues Alter The Phenotype Of Hormone Positive Breast Cancer, Braulio Ortega Quesada

All Dissertations

Cancer is a complicated disease and one in every three diagnoses are women with breast cancer. Recent research shows that the progression of cancer depends strongly on interactions with other non-cancerous cells and non-cellular components. Metastasis, the spread of cancer to other parts of the body, is a key step in cancer progression and makes treatment harder, leading to poor response to treatments culminating in death in ~90% of patients. This dissertation focused on creating a series of microdevices as novel pre-clinical models of breast cancer. Two different devices were fabricated to (1) study how exposing cancer cells to the …

Aerobic Biodegradation Of Algae-Derived Bioplastics Under Controlled Composting Conditions, Clayton J. Lords

All Graduate Theses and Dissertations, Fall 2023 to Present

Plastics are versatile polymers that have become critically important materials in many industries. Although plastics are important and useful materials, they account for vast amounts of environmental pollution and climate change contribution. Sustainable bioproducts are becoming increasingly important in the effort to mitigate the impacts of pollution and climate change. The scale of environmental damage caused by plastic pollution highlights the need to implement sustainably sourced biodegradable plastics within the global economy. Bioplastics are materials that may be manufactured from biological materials or can biodegrade under certain conditions. Algae are microorganisms that can be grown using nutrient-rich municipal wastewater; the …