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Engineered Nucleic-Acid Binding Intrinsically Disordered Proteins For Biomedical Applications, Telmo Diez Perez

Biomedical Engineering ETDs

This dissertation explores the use of intrinsically disorder proteins (IDPs) in biomedical applications related to the detection and biosensing of nucleic-acid species. We engineer several low critical solution temperature (LCST) nucleic-acid binding elastin-like polypeptides (ELPs) as model IDPs and study their potential in biomedical application via interactions with short single-stranded (ss) DNA, tRNA and viral RNAs. First, we engineer a simple polycationic ELP capable of recruiting DNA on demand in a DNA-protein-rich condensate via LLPS. Moreover, we develop a modified Flory-Huggins theory to quantify the partitioning of DNA and protein upon coacervate formation with and without salts. We then design …

The Role Of Sensing Modalities In Shaping Collective Motion And Group Behavior, Poorendra P. Ramlall

Doctoral Dissertations and Master's Theses

Collective behavior refers to the coordinated movements that emerge from simple interactions between individuals within a group. Traditionally, researchers have modeled these interactions assuming individuals can sense their surroundings in all directions, like having eyes all around their heads. While this is a useful simplification, it does not capture the diverse ways animals actually sense the world. In this thesis, we take inspiration from the natural world, particularly from animals like bats and dolphins that use a combination of hearing and sight to navigate their environments. We explore how combining these sensory cues in a three-dimensional space affects the way …

Energy Safety Management: A Training Model To Improve Flight Safety, Juan R. Merkt, Matthijs H. J. Amelink, David G. Sizoo

Journal of Aviation Technology and Engineering

Failing to properly manage an airplane’s energy state can be unforgiving. Mismanagement of mechanical energy (altitude and/or airspeed) is a contributing factor to three common types of fatal accidents in aviation: loss of control in flight, approach and landing accidents, and controlled flight into terrain. Recognizing the importance of energy management, the Federal Aviation Administration has incorporated new elements into the Airman Certification Standards, emphasizing knowledge of energy management concepts and the consequences of mishandling an airplane’s energy state. Unfortunately, no adequate guidance has been available in terms of defining key energy management concepts or suggesting how these should be …

Differentiating Dynamic System Outcomes In Cam Photosynthesis Through Sonification, Duncan Turley

Civil and Environmental Engineering Undergraduate Honors Theses

Sonification is a powerful tool that is harnessed by modern engineers to represent information through audio, and is beginning to be used to interpret more complex data sets. Sonification can be used to facilitate the listeners' ability to grasp microscopic or complex changes in the state of a system. This study uses the assigning of sound patterns to model outputs that indicate chaotic or non-chaotic systems in Crassulacean acid metabolism photosynthesis. Using sound allows the interpretation of chaotic data without the more time intensive processes typically used, such as of Fast Fourier Transformations. Based on past research, it is known …

Analysis Of Wingtip Vortex Structure Generated By Bio-Inspired Winglets, D'Zahn A. Smith

Doctoral Dissertations and Master's Theses

Bio-inspired winglets were studied with the goal of better understanding the structure of the wingtip vortices they generate. Measurements of the tip vortex were previously carried out using stereoscopic particle image velocimetry (sPIV). The bio-inspired winglet was tested on a rectangular NACA 0012 wing section at a 5-degree angle of attack and at a chord Reynolds number of 900,000. Velocity field measurements were recorded at 0.7 and 2 chord lengths aft of the wing’s trailing edge. Compared to the wing with no attachment and a traditional blended winglet, the bio-inspired winglet’s vortex exhibited significantly less intense flow field properties. These …

Development And Characterization Of A Low Intensity Vibrational System For Microgravity Studies, Omor Khan

Boise State University Theses and Dissertations

The advent of extended-duration human spaceflight demands a better comprehension of the physiological impacts of microgravity. One primary concern is the adverse impact on the musculoskeletal system, including muscle atrophy and bone density reduction. Ground-based microgravity simulations have provided insights, with vibrational bioreactors emerging as potential mitigators of these negative effects. Despite the potential they have, the adaptation of vibrational bioreactors for space remains unfulfilled, resulting in a significant gap in microgravity research. This paper introduces the first automated low-intensity vibrational (LIV) bioreactor designed specifically for the International Space Station (ISS) environment. Our research covers the bioreactor's design and characterization, …

Effect Of Lunar Magnetic Field And Lunar Regolith Simulant On The Growth And Bioactive Compounds Production Of Chlorella Vulgaris Microalgae, Jeries Philip Butros Abedrabbo

Mechanical & Aerospace Engineering Theses & Dissertations

Since humans last went to the moon on the Apollo missions, there has been a fascination with inhabiting and colonizing other planetary objects, starting with the Earth’s Moon, Mars, and recently Jupiter’s moon, Europa. However, there is still lack of knowledge and science behind many of the extraterrestrial environmental effects on biological organisms living on Earth. Therefore, there is a need to study how such environments would affect these organisms. Moreover, how can we attain sustainable living in such environments as well through self-providing life support systems (LSS), without the need to provide for additional necessities back and forth from …

The Quest For A Sensitive And Accurate Flash Radiation Model: Whole Abdominal Irradiation And Real Time Dosimetry, Noah J G Daniel

Dartmouth College Master’s Theses

Cancer remains the second leading cause of death in the US, and more than 50% of all cancer patients receive radiation therapy (RT), often in combination with surgery, chemotherapy and/or immunotherapy. However, the fundamental limit on radiotherapy treatment efficacy is normal tissue tolerance. One potential way to overcome this limitation is through ultra-high dose rate radiation (FLASH RT). Compared to conventional radiotherapy (CONV RT), FLASH RT has been shown to be just as damaging to cancerous tissue but far more sparing of healthy tissue.

However, clinical translation of FLASH research has been obstructed by the failure of many labs to …

Selective Targeting Of Microglia By Quantum Dots And Green Synthesis Of Metal Organic Biohybrids; Applications In Dynamic Cell And Assay Systems, Navya Uppu

Doctoral Dissertations

Neurological disorders are the leading cause of physical and cognitive disability across the globe, currently affecting approximately 15% of the worldwide population. Part of the glioma microenvironment are microglia, resident immune cells of the CNS that were thought to be involved in the pathogenesis of diverse neurodegenerative diseases. Though it remains uncertain what triggers microglial activation in these disorders, targeting and tracking microglial functions using nanotools like Quantum Dots (QDs) could help us elucidate them in such neurological diseases. This research focuses on the comparative study of different QDs formulations and their selective uptake by brain microglia in primary cultures …

Geographical Variation In Songs Of Bachman’S Sparrow (Peucaea Aestivalis), L. Nguyen, K. Doñas, J. Jackson, R. Kannan

Journal of the Arkansas Academy of Science

We present an analysis of geographic variation in primary song components of the Near Threatened North American endemic, Bachman’s Sparrow (Peucaea aestivalis). These songs have 2 distinct portions: an introductory tweet we call the "whistle" and a more complex second portion that we call the "trill". We analyzed 327 songs from 111 recordings downloaded from eBird.org from the entire current range of the species. We grouped the recordings into 3 distinct geographic clusters, East, Central, and West. The data measured from spectrograms suggest a significant statistical difference among groups for 3 measured characteristics: frequency range of trill, number of horizontal …

Optimizing Large Language Models And Multimodal Approaches For Biomedical Publication And Satellite Imagery, Youngsun Jang

Electronic Theses and Dissertations

This dissertation comprises two main sections: the first focuses on natural language processing (NLP) for extracting key information from scientific literature using large language models (LLMs), and the second addresses remote sensing for detecting natural disasters, such as floods, from satellite imagery using a multimodal approach. The first section investigates methods to enhance Transformer-based models in classifying and extracting information from biomedical scientific publications. Key contributions include the development of a custom dataset for classification and Question and Answering (Q&A) tasks, fine-tuning Transformer models like the Bidirectional Encoder Representations from Transformers (BERT) and addressing multi-span answer issues with the TAg-based …

Computational Characterization Of Extracellular Electro-Osmotic Flow During Tissue Repair, Ashley Jorgensen-Blocker

Electronic Theses and Dissertations

Electrical stimulation (ES) therapy promotes the healing of chronic epidermal wounds and suppresses the degeneration of articular cartilage. Despite the success of ES therapy, the underlying mechanisms by which ES promotes tissue repair are largely unknown, preventing the standardization and optimization of treatments. One proposed mechanism involves electro-osmotic flow (EOF), electrically driven water flow generated within close proximity to the cell surface. EOF induces the transport of macromolecules and removes metabolic wastes and inflammatory molecules from these dense tissues through interstitial flow. This dissertation investigates the application of weak electric fields (EFs) to non-excitable cells and the generation of EOF …

A Computational Exploration: Docking Analysis Of Compounds From Foeniculum Vulgare As Potential Aromatase Inhibitors For Endometriosis Candidate Therapy, Dwi Anita Suryandari, Puji Sari, Hadi Sunaryo, Khaerunissa Anbar Istiadi

Indonesian Journal of Medical Chemistry and Bioinformatics

Aromatase inhibitors (AI) have controlling symptoms and size of endometriotic implants, making them a promising second-line therapy for endometriosis treatment.pretreatment with letrozole, an AI, combined with leuprolide acetate and resveratrol has been found to improve in vitro fertilization (IVF) outcomes in women mild endometriosis.in this study we screening and analysis of ten phenolic compounds from Foeniculum vulgare using molecular docking with Mcole server.from this results showed that three phenolic trans resveratrol (TR), caempherol coumaril (CC) have low gibbs energy compare with resveratrol (R). The binding modalities of compound TR and compound R were hydrogen-bonding between the hydroxyl and oxygen atom …

Feminist Pedagogy In Stem: The Intersection Of Stem Pedagogy And Feminist Theory, Lesley-Ann Giddings, Candice R. Price

Feminist Pedagogy

No abstract provided.

Effect Of The Homogenization Process On Titanium Oxide-Reinforced Nanocellulose Composite Membranes, Taufiq Mahsuli, Aisyah Larasati, Aminnudin Aminnudin, Jibril Maulana

Journal of Mechanical Engineering Science and Technology (JMEST)

Indonesian pineapple production can reach 200 tons per day; however, pineapples generate a significant amount of waste. Pineapple peel waste can be used to make membranes. Composite membranes containing TiO2 have dense properties, low porosity, and increase the mechanical strength of the cellulose sheet. This research uses various ultrasonic homogenizers to homogenize the distribution of nanocellulose and TiO2 (50% and 100% power with 30, 60, and 90 minutes). The casting method is used to shape the membrane. The SEM test shows that the higher the power used and the longer the sonication time, the less agglomeration of about 1.63%/ cm2 …

Attack On The Brain: Neurowars And Neurowarfare, Armin Krishnan

Space and Defense

Is neurotechnology leading nation-states toward a new domain of war? Neuroscience is on the verge of deciphering the human brain. As a result, brains will become a part of the battlefield against which attacks will be directed. As neuroscientist James Giordano argued: “the brain is the next battlespace.” It is foreseeable that this will have tremendous implications for warfare and could amount to a true military revolution in the sense of military historian Williamson Murray: it would completely change the characteristics of conflict, as well as transform state and society.

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 …

Simultaneous 3d Construction And Imaging Of Plant Cells Using Plasmonic Nanoprobe-Assisted Multimodal Nonlinear Optical Microscopy, Kun Liu, Yutian Lei, Dawei Li

Department of Civil and Environmental Engineering: Faculty Publications

Nonlinear optical (NLO) imaging has emerged as a promising plant cell imaging technique due to its large optical penetration, inherent 3D spatial resolution, and reduced photodamage; exogenous nanoprobes are usually needed for nonsignal target cell analysis. Here, we report in vivo, simultaneous 3D labeling and imaging of potato cell structures using plasmonic nanoprobe-assisted multimodal NLO microscopy. Experimental results show that the complete cell structure can be imaged via the combination of second-harmonic generation (SHG) and two-photon luminescence (TPL) when noble metal silver or gold ions are added. In contrast, without the noble metal ion solution, no NLO signals from the …

Simultaneous 3d Construction And Imaging Of Plant Cells Using Plasmonic Nanoprobe-Assisted Multimodal Nonlinear Optical Microscopy, Kun Liu, Yutian Lei, Dawei Li

Department of Civil and Environmental Engineering: Faculty Publications

Nonlinear optical (NLO) imaging has emerged as a promising plant cell imaging technique due to its large optical penetration, inherent 3D spatial resolution, and reduced photodamage; exogenous nanoprobes are usually needed for nonsignal target cell analysis. Here, we report in vivo, simultaneous 3D labeling and imaging of potato cell structures using plasmonic nanoprobe-assisted multimodal NLO microscopy. Experimental results show that the complete cell structure can be imaged via the combination of second-harmonic generation (SHG) and two-photon luminescence (TPL) when noble metal silver or gold ions are added. In contrast, without the noble metal ion solution, no NLO signals from the …

Integrating Glycolysis, Citric Acid Cycle, Pentose Phosphate Pathway, And Fatty Acid Beta‑Oxidation Into A Single Computational Model, Sylwester M. Kloska, Krzysztof Pałczyński, Tomasz Marciniak, Tomasz Talaśka, Beata J. Wysocki, Paul H. Davis, Tadeusz A. Wysocki

Department of Electrical and Computer Engineering: Faculty Publications

The metabolic network of a living cell is highly intricate and involves complex interactions between various pathways. In this study, we propose a computational model that integrates glycolysis, the pentose phosphate pathway (PPP), the fatty acids beta-oxidation, and the tricarboxylic acid cycle (TCA cycle) using queueing theory. The model utilizes literature data on metabolite concentrations and enzyme kinetic constants to calculate the probabilities of individual reactions occurring on a microscopic scale, which can be viewed as the reaction rates on a macroscopic scale. However, it should be noted that the model has some limitations, including not accounting for all the …

Design, Synthesis, And Characterization Of Peptide Amphiphile Biomaterials, Huihua Xing

Theses & Dissertations

Self-assembled peptide amphiphiles (PAs) have gained significant attention in recent years due to their ability to form various supramolecular nanostructures with unique physical and chemical properties. These amphiphilic molecules consist of a hydrophobic tail and a peptide domain, allowing for the formation of nanoscale assemblies in aqueous environments. The PA supramolecular structures have a wide range of potential applications, including drug delivery, tissue engineering, and regenerative medicine.

By manipulating the driving forces (e.g., hydrophobic interactions, hydrogen bonds, and electrostatic interactions) involved in the self-assembly, researchers can tune the self- assembly properties (size, shape, stability, and surface character) and, consequently, the …

Site-Specific Glyco-Engineering Of Recombinant Thrombomodulin, Joseph M. Keil

ETD Archive

Thrombomodulin (TM), a membrane glycoprotein predominately expressed on endothelium, plays essential roles in regulating local hemostatic balance. Particularly, TM modulates the activity of thrombin from a procoagulant to an anticoagulant protease. When bound to TM, thrombin activates plasma protein C, which selectively inactivates coagulation factors Va and VIIIa. At the same time, TM-bound thrombin is unable to cleave fibrinogen or to activate platelets diminishing its procoagulant activity. recombinant TM456 is a promising anticoagulant candidate, but it has a very short half-life. TM is a proteoglycan and its O-linked glycosaminoglycan (GAG), chondroitin sulfate (CS), on the D3 domain contributes to TM’s …

3d Printed Poly Lactic Acid Structures For Cell Growth And Nanoparticle Transport-Simulation And Experimental Validation, Shrikrushna Vinayak Sonawane

Masters Theses

In today's world, 3D printing or additive manufacturing (AM) is being widely used in various fields due to its benefits such as rapid prototyping, reduced material waste and energy usage, lower cost, and more. Even the tissue engineering field is utilizing this technology. This study focused on examining the compatibility of 3D printed Lab-on-a-Chip structures made of Poly Lactic Acid (PLA) for in-vitro applications. In this research, the Lab-on-a-Chip structures were designed and created using 3D printing. To achieve the required bio-functionality scaffold surface was customized by post-printing processes such as mechanical polishing, hydrolysis (Wet Chemical Etching), and ultraviolet light …

Mitochondrial Complex Iii Bypass Complex I To Induce Ros In Gpr17 Signaling Activation In Gbm, Sana Kari, Jeyalakshmi Kandhavelu, Akshaya Murugesan, Ramesh Thiyagarajan, Srivatsan Kidambi, Meenakshisundaram Kandhavelu

Department of Chemical and Biomolecular Engineering: Faculty Publications

Guanine nucleotide binding protein (G protein) coupled receptor 17 (GPR17) plays crucial role in Glioblastoma multiforme (GBM) cell signaling and is primarily associated with reactive oxidative species (ROS) production and cell death. However, the underlying mechanisms by which GPR17 regulates ROS level and mitochondrial electron transport chain (ETC) complexes are still unknown. Here, we investigate the novel link between the GPR17 receptor and ETC complex I and III in regulating level of intracellular ROS (ROSi) in GBM using pharmacological inhibitors and gene expression profiling. Incubation of 1321N1 GBM cells with ETC I inhibitor and GPR17 agonist decreased the ROS level, …

Reflect To Connect, Sophia Rae Guzules

Liberal Arts and Engineering Studies

Engineering statics is an important course and a prerequisite for many subsequent courses for many engineering majors. It is often students’ first exposure to technical engineering sciences. Most statics concepts are addressed in ways disconnected from students’ prior experiences and interests. Utility Value Interventions (UVIs) have been employed in fields like biology and chemistry to help students connect concepts in class and their lives outside the classroom. However, UVI usage in engineering so far has been limited. In this Senior Project paper, I will describe the process that the team Critical Research in Engineering and Technology Education (CREATE) and I …

Civilian And Military Civil Engineer Mission In The Space Domain, Linda E. Kuster

Theses and Dissertations

Military and civil interest in space-based operations has increased dramatically in recent years due to the discovery of life sustaining properties such as water on Mars and advancements in cyber technology. Civilian sector discussions and research have centered on the establishment of permanent extraterrestrial infrastructure, while discussions from the military perspective have focused on providing reliable, resilient infrastructure, capable of withstanding cyber-based and kinetic attacks. Both perspectives account for known threats and sustainment methods required to ensure success in the space domain. With the existence of threats for the military and civilian missions, civil engineers will undoubtedly be critical to …

Multifunctional Microgel-Based Cream Hydrogels For Postoperative Abdominal Adhesion Prevention, Bo Liu, Yunfan Kong, Olawale A. Alimi, Mitchell Kuss, Huiyin Tu, Wenfeng Hu, Abu Rafay, Kumar Vikas, Wen Shi, Megan Lerner, William L. Berry, Yulong Li, Mark A. Carlson, Bin Duan

Department of Mechanical and Materials Engineering: Faculty Publications

Postoperative abdominal adhesions are a common problem after surgery and can produce serious complications. Current anti-adhesive strategies focus mostly on physical barriers and are unsatisfactory and inefficient. In this study, we designed and synthesized advanced injectable cream-like hydrogels with multiple functionalities, including rapid gelation, self-healing, anti-oxidation, anti-inflammation, and anti-cellular adhesion. The multifunctional hydrogels were facilely formed by the conjugation reaction of epigallocatechin gallate (EGCG) and hyaluronic acid (HA)-based microgels and polyvinyl alcohol (PVA) based on the dynamic boronic ester bond. The physicochemical properties of the hydrogels including anti-oxidative and anti-inflammatory activities were systematically characterized. A mouse cecum-abdominal wall adhesion model …

Histomorphology Of The Distal Urogenital Ducts In The Male Northern Crawfish Frog, Rana Areolata Circulosa (Anura: Ranidae), S.E. Trauth, R.G. Neal

Journal of the Arkansas Academy of Science

We examined the microanatomy of the distal urogenital ducts in the male Northern Crawfish Frog (Rana areolata circulosa) from a small sample (n = 5) collected in February and March from central Arkansas over a 5-year period (2017–2022). Specifically, we sought information on the following structures: (1) the paired Wolffian (urogenital) ducts caudally from the kidneys to their merging with the urodeum of the cloaca, (2) the paired seminal vesicles (sperm storage structures), and (3) the paired Müllerian ducts and glands. This study provides new information on these urogenital ducts and promotes a clearer understanding of this anatomical region for …

No Sperm Morphometric Differences Between Two Snapping Turtle Species, J.D. Konvalina, S.E. Trauth

Journal of the Arkansas Academy of Science

We examined sperm morphometrics between Chelydra serpentina and Macrochelys temminckii. When both species are combined, we found significant correlations between total sperm length and sperm head length as well as sperm tail length and sperm head length. In addition, we observed significant correlations between total sperm length and sperm tail length. T-tests revealed no significant differences in any of the sperm morphometrics between the two species. Both snapping turtle species had greater values for every sperm morphometric when compared to another freshwater turtle. The strong correlation between total sperm length and sperm tail length is concurrent with what has previously …

Occurrence Of Predation Of Juvenile Chum Salmon (Oncorhynchus Keta) By Chub Mackerel (Scomber Japonicus) And Spotted Mackerel (Scomber Australasicus) In Miyako Bay, Iwate Prefecture, Japan, Kei Sasaki, Miwa Yatsuya, Daisuke Shimizu, Daisuke Ojima, Shinji Komatsu

Journal of Marine Science and Technology–Taiwan

In recent years, chub mackerel (Scomber japonicus) and spotted mackerel (Scomber australasicus) have started migrating to the coastal areas off Iwate Prefecture earlier than they did previously, resulting in a geographic overlap between hatchery-bred juvenile chum salmon (Oncorhynchus keta) released at sea and the occurrence of predatory mackerel. To clarify whether the mackerels prey on the juvenile chum salmon, we captured adult mackerels by angling during the period when these species overlap in Miyako Bay, Iwate Prefecture. After capture, the stomach contents of the mackerel were examined using a combination of visual examinations and DNA metabarcoding analysis. As a result, …