Digital Commons Network^™

Design And Development Of A Perfusable Hydrogel Platform With Bioprinted Human-Endothelialized Microvascular Channels, Calvin A. Chernyatinskiy

All Theses

We developed an integrated bioprinting and perfusion platform to generate vascularized hydrogel constructs that support perfusable microchannel networks. Multiple hydrogel formulations, sacrificial ink systems, device geometries, and perfusion conditions were systematically evaluated to optimize print fidelity, mechanical stability, and cellular compatibility. Internally gelling alginate–calcium carbonate hydrogels were identified as a robust matrix, providing tunable gelation kinetics and structural stability during embedded printing. In parallel, Pluronic F-127 fugitive ink enabled reliable fabrication of continuous hollow channels due to its shear-thinning behavior and efficient post-print removal.

The finalized platform integrates stereolithographically fabricated perfusion chambers with extrusion-based bioprinting to produce three-dimensional, perfusable vascular …

Bio-Payload Senior Design Report, Connor Bishop, Oliver Goodall, Marcus Kirk, Gabby Robles, Anish Shanmuganathan

Interdisciplinary Design Senior Theses

This project focuses on the design and development of an autonomous experimental platform capable of conducting cellular biology experiments in a well plate within a CubeSat environment. The system integrates microfluidics, robotics, and onboard sensors to remotely initiate experiments, monitor them, and collect data without human intervention. The objective is to create a platform for automated biological experimentation in microgravity, while reducing reliance on ground-based control and increasing mission efficiency and reproducibility. The team used Saccharomyces cerevisiae to assess the biocompatibility of the well plate and monitor changes in cell culture, including optical density and cell viability.

Volumetric Fluorescence Microscopy For High-Throughput And High-Sensitivity Imaging: From Single Molecules To Tissues, Le-Mei Wang

Graduate Studies Theses and Dissertations 2026

Fluorescence microscopy is an indispensable tool in the biological sciences, enabling researchers to investigate intricate subcellular structures, particularly for volumetric studies. However, conventional optical microscopy for volumetric imaging remains fundamentally constrained by imaging speed and throughput. To bypass traditional serial z-scanning, we introduce an axially scan-free method using a phase layer cake to modulate the system's point spread function. This approach projects volumetric information onto a 2D plane in a single shot, offering high flexibility in tuning axial depth alongside simultaneous multicolor imaging with high spatial resolution and sensitivity. This dissertation divides these technical advancements into cellular and tissue imaging …

2d-Nanosilicate Carriers For Sustained Delivery Of Vaccine Components, Chih Yun Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Laponite® 2D Nanosilicates (NS) are disc-shaped platelets (~30 nm diameter, ~1 nm thick) with positively charged edges and negatively charged faces, capable of loading proteins, drugs, and nucleic acids via electrostatic interactions to form a house-of-cards gel that sequesters cargo. Here, we evaluated NS for sustained delivery of antigens and Toll-like receptor (TLR) agonists to extend germinal center duration and enhance antibody quality. The model antigen ovalbumin (OVA) was adsorbed onto NS at acidic pH in a ~1:1 ratio, with partial unfolding that remained stable at physiological pH. NS-OVA complexes were efficiently internalized by dendritic cells, with uptake driven primarily …

G2pdeep-V2: A Web-Based Deep-Learning Framework For Phenotype Prediction And Biomarker Discovery For All Organisms Using Multi-Omics Data, Shuai Zeng, Trinath Adusumilli, Sania Zafar Awan, Manish Sridhar Immadi, Dong Xu, Trupti Joshi

Biomedical Sciences

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm …

Developing A Metabolic Engineering Chassis From A Metabolically Versatile Organism, Rhodopseudomonas Palustris Cga009, Mark William Kathol

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

Metabolic engineering has made it possible to develop biological processes that were once considered economically unfeasible or uncompetitive. This field has enabled both a robust niche market, whereby products, such as pharmaceutical substances like monoclonal antibodies, are produced exclusively through biological means, as well as an emerging commodity production market. Nonetheless, significant challenges remain in harnessing the unique metabolic capabilities of genetically non-tractable organisms. This dissertation focuses on Rhodopseudomonas palustris CGA009 as a potential chassis for metabolic engineering. To address the issue of genetic intractability, a synthetic biology toolkit was developed to facilitate the expression of heterologous proteins in R …

Design And Development Of A Standalone Digital Holographic Microscope Employing Phase-Driven Reconstruction And Classification For Biomedical Imaging And Optical Diagnostics, Charlotte Kyeremah

Graduate Doctoral Dissertations

Access to advanced biomedical imaging technologies remains a significant challenge in resource-limited settings, especially for early disease detection and monitoring of diseases such as malaria, HIV, and other blood-borne diseases. Although point-of-care (POC) devices have gained popularity in global health, many rely on antibody-based tests, lateral flow strips, or optical readouts that often lack quantitative capabilities, sensitivity to early infections, or versatility in different diagnostic targets. In addition, these systems are typically dependent on disposable reagents or manual interpretation, which limits their effectiveness in remote areas. Digital Holographic Microscopy (DHM) presents a promising alternative as a label-free imaging method capable …

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 …

Mechanistic Insights Into The Flash Effect: The Role Of Oxygen And Radiation Chemistry In Ultra-High Dose Rate Radiation Therapy, Jacob Pierce Sunnerberg

Dartmouth College Ph.D Dissertations

The development of new cancer therapies focuses on widening the therapeutic ratio between tumor control and normal tissue toxicity. Over the last decade, ultra-high dose rate (UHDR) radiation therapy, commonly known as FLASH radiotherapy (FLASH-RT), has shown promising potential to reduce normal tissue toxicity while maintaining tumor control. However, the underlying mechanisms of the FLASH effect remain poorly understood. This thesis explores the radiation-chemical basis of FLASH-RT, focusing on the role of oxygen and reactive oxygen species in modulating biological outcomes.

A comprehensive set of in vitro studies demonstrated that UHDR delivery significantly alters radiation chemistry compared to conventional dose …

Advances In Bone And Orthopedics 2025 – 5th Edition, Jean-Philippe Berteau, Laurent Pujo-Menjouet, Hélène Follet, Aurélie Levillain

Publications and Research

This volume brings together selected works from the 2025 Bone and Orthopedics Interdisciplinary Symposium (BONITOS), underscoring our community’s ongoing commitment to advancing research in biomechanics, bone health, and orthopedic science. The symposium unites leading experts from around the world, fostering collaboration and the exchange of ideas across disciplines. Organized in partnership with the French-speaking Society of Biomechanics, the French National Institute of Health and Medical Research (INSERM), the University of Lyon, the College of Staten Island of the City University of New York (CUNY), and the American Association of Physical Therapists (APTA) – Brooklyn Staten Island Chapter, BONITOS 2025 represents …

Nanosecond Pulsed Electric Field And Plasma Jets For Cancer Therapy, Edwin Ayobami Oshin

Biomedical Engineering Theses & Dissertations

Nanosecond pulsed electric field (nsPEF) employs nanosecond-duration, high voltage pulses to induce oxidative stress, leading to temporary or permanent damage to cells or tissue (also known as reversible and irreversible electroporation), and has been considered a promising approach for cancer therapy. In parallel to this, nanosecond pulsed atmospheric pressure plasma jets (ns-APPJs) have also shown to be effective in inactivating cancer cells or increasing sensitivity of cells to electric fields. ns-APPJs are known to generate reactive chemical agents, including reactive oxygen and nitrogen species (RONS) which induces oxidative stress resulting in cell proliferation, apoptosis, and necrosis. In this dissertation, a …

Decoding Tattoo And Permanent Makeup Pigments: Linking Physicochemical Properties To Absorption, Distribution, Metabolism, And Elimination Profiles Using Quantitative Structure-Activity Relationship (Qsar)-Based New Approach Methodologies (Nams), Girija Bansod, Ajay Vikram Singh, Preeti Bhardwaj, Tulika Rai, Sweta Vijay Nakhale, Amruta Shelar, Rajendra Patil, Peter Laux, Andreas Luch, Christopher J. Osgood, Michael W. Stacey

Biological Sciences Faculty Publications

The safety and quality of tattoo and permanent makeup (PMU) pigments are subject to increased scrutiny due to their potential to cause adverse effects like anaphylaxis, photoallergic responses, and long-term toxicity. These undesirable reactions governed by their chemical structure possess varied physicochemical properties and absorption, distribution, metabolism, and elimination (ADME) characteristics. These properties control the pigment behavior during application, stability, and interaction with human tissue. The correlation between these physicochemical characteristics and ADME parameters of tattoo/PMU pigments remain under-explored despite the current advances in toxicology. Our study aims to address and bridge the gap by leveraging open-access QSAR computational toxicology …

Optical Methods For Time-Resolved Dosimetry And Oximetry Of Ultra-High Dose Rate Radiation Therapy, Megan A. Clark

Dartmouth College Ph.D Dissertations

Radiotherapy (RT) is a cornerstone method used to treat over 50% of the 2 million new cancer diagnoses each year in the United States. The success of RT directly relies on an optimal balance between maximizing the dose to the tumor while minimizing dose to surrounding normal tissues. Achieving this balance is often challenging due to underlying radiation transport and the presence of anatomical constraints that limit the beam delivery geometry. In turn, minimizing healthy tissue toxicity prevents use of a more aggressive tumor killing approach, and even in curative cases may decrease the patient’s quality of life due to …

In-House Polydimethylsiloxane Microfluidic Device On Single Cell Trapping And Culturing Of Leukemia Cell Line: Comparison Between Conventional And Conventional With Centrifugal Methods, Alongkorn Pimpin, Sudchaya Bhanpattanakul, Tepparit Wongpakham, Chomkwan Tawatcharaporn, Thanawit Siha-Umphai, Mookdapa Sinsiriphan, Atikan Chalermchuang, Tewan Tongmanee, Attawut Thanomsridetchai, Thammawit Suwannaphan, Witsaroot Sripumkhaie, Pattaraluck Pattamang, Mayuree Chanasakulniyom, Praprudee Piyaviriyakul, Wutthinun Jeamsaksiri, Achariya Sailasuta, Theerawat Tharasanit, Theerayuth Kaewamatawong

The Thai Journal of Veterinary Medicine

To develop a suitable model to study biological and characterization of Cancer stem cells (CSCs), single cell trapping and culturing using microfluidic techniques have become a high-through put system that can manage and control microenvironment and practical intracellular analysis. The aim of this study was to develop and validate a microfluidic device for single cell trapping and culturing using the leukemia cell line as a cell model. Comparison between conventional and conventional with centrifugal methods was also analyzed. To compare trapping efficacy between these 2 methods, leukemia cell concentration of 1.5×106 cells/ml was loaded with a flow rate of 0.25 …

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 …

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 …

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 …

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 …

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, …

Exploring Ph Gradient Phenomena In Non-Linear Electrokinetic Microfluidic Devices, Azade Tahmasebi

Dissertations, Master's Theses and Master's Reports

Electrokinetic microfluidics is a versatile technology utilized within lab on a chip (LOC) devices for diagnostic and analytical applications; advantages include reduced resource demands, flexibility, and simplicity of use. Dielectrophoresis (DEP) is a precision nonlinear electrokinetic tool utilized within microfluidic microdevices to induce polarization and control bioparticle motions for applications that range from hemoglobin separations to cancer cell isolation and detection. Despite promising results, undesired side phenomena can occur in electrokinetic systems which impede reproducibility and accuracy. These unfavorable phenomena have not been comprehensively explored in the literature. Prior preliminary research suggests the fundamental phenomena originate from microelectrodes utilized in …

An Experimental Study On The Mechanical Properties And Chemical Composition Of Lcd 3d Printed Specimens, Sebastian Gomez

College of Graduate Studies: Theses & Dissertations

Additive manufacturing technologies have been enhanced throughout the years yet have surprised the manufacturing industry due to their high-end surface finish and dimensional accuracy. Different experiments have been done to identify a specific phenomenon known in the vat-polymerization field. Distortion and dimensional inaccuracy tend to affect the overall properties of the process, either physical or chemical. This approach allows the understanding of how the physical properties have been affected and how to study the chemical properties to avoid this type of phenomenon. The chemical reaction between polymer and UV light has been studied and experimented with to the point that …

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

Theses and Dissertations

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

Advancing The Portability, Field Of View, And Spatiotemporal Resolution Of Multi-Parametric Photoacoustic Microscopy, Fenghe Zhong

McKelvey School of Engineering Graduate Student Theses & Dissertations

Capable of structural, functional, molecular, and metabolic imaging with high spatial resolution in vivo, photoacoustic microscopy (PAM) is an emerging tool in biomedical research. Further, recent advances in multi-parametric acquisition and analysis make PAM uniquely capable of simultaneously mapping the total concentration of hemoglobin (CHb), oxygen saturation of hemoglobin (sO2), and blood flow speed. However, there are multiple major limitations, including, the large footprint, low imaging speed, limited imaging contrast, and insufficient axial resolution, which impedance its applications in basic and translational research. In this dissertation, I presented potential solutions to overcome the limitations above.In the first part of this …

Nonlinear Optical Microscopy Assessment Of Tissue Structure And Chondrocyte Viability Of Articular Cartilage, Michael Le

All Theses

Articular cartilage functions to protect the ends of bones by providing a surface that can withstand compressive forces and minimize friction during movement. Collagen fibers form the organizational backbone of the extracellular matrix (ECM) in cartilage. Proteoglycans within the ECM function to retain water and provide the tissue with the swelling pressure needed to withstand compressional forces. Chondrocytes, the only type of cell found in articular cartilage, produces these collagen fibers and proteoglycans to maintain the tissue structure and function. Significant injuries to articular cartilage can damage the chondrocytes and disrupt their ability to maintain homeostasis in the tissue. Therefore, …

Computer Vision And Machine Learning Applications In Cellular Images And Clinical Data, Guochang Ye

Theses and Dissertations

With the progressive development of artificial intelligence (AI), automated analysis has been explored for substituting tedious manual methods in cellular image analysis. Additionally, medical information not included in the conventional statistical methods is now being reconsidered with AI-based personalized medicine. The adaptivity and flexibility of AI ensure its efficiency and accuracy. In this work, computer vision and machine learning (ML) methods under the scope of AI are explicitly investigated and applied to cellular images and clinical data for cytological analysis and to provide diagnosis-based assistance/predictions. Firstly, novel computer vision algorithms achieve cell detection and differentiation estimation on phase-contact microscopic images …

Multi-Organs-On-Chips For Testing Small-Molecule Drugs: Challenges And Perspectives., Berivan Cecen, Christina Karavasili, Mubashir Nazir, Anant Bhusal, Elvan Dogan, Fatemeh Shahriyari, Sedef Tamburaci, Melda Buyukoz, Leyla Didem Kozaci, Amir K Miri

Henry M. Rowan College of Engineering Departmental Research

Organ-on-a-chip technology has been used in testing small-molecule drugs for screening potential therapeutics and regulatory protocols. The technology is expected to boost the development of novel therapies and accelerate the discovery of drug combinations in the coming years. This has led to the development of multi-organ-on-a-chip (MOC) for recapitulating various organs involved in the drug-body interactions. In this review, we discuss the current MOCs used in screening small-molecule drugs and then focus on the dynamic process of drug absorption, distribution, metabolism, and excretion. We also address appropriate materials used for MOCs at low cost and scale-up capacity suitable for high-performance …

Reu Site: Stem For Plant Health, David W. Britt

Funded Research Records

No abstract provided.

Quantum Chemistry Calculations For Metabolomics, Susanta K. Das, Ricardo M. Borges, Sean M. Colby, Arthur S. Edison, Oliver Fiehn, Tobias Kind, Jesi Lee, Amy T. Merrill, Kenneth M. Merz Jr., Thomas O. Metz, Jamie R. Nunez, Dean J. Tantillo, Lee-Ping Wang, Shunyang Wang, Ryan S. Renslow

Mechanical Engineering Publications

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building …

Tuning Radiation And Microgravity Exposure For Human Brain Organoids, Bailey Mcfarland

Utah Space Grant Consortium

The environment of space, specifically radiation and microgravity, poses a substantial threat to astronauts' brain health. Understanding the damage mechanism and therefore paving the way to finding potential remedies is critical to protect astronauts during space flight. Current models are insufficient at representing the human brain, and insufficient research has been conducted on the effect of radiation and microgravity on the higher structures of the human brain. This ongoing research aims to use brain organoids, a tissue-engineered model that recapitulates the human brain's anatomy and structure and investigate the effects of radiation and microgravity on the brain. At the current …

3d Printable And Computational Models Of The Bone Marrow Mechanical Environment, Alexander Regner

Boise State University Theses and Dissertations

Aged individuals and astronauts experience bone loss despite rigorous physical activity. Bone mechanoresponse is in part regulated by mesenchymal stem cells (MSCs). We reported that daily low intensity vibration (LIV) restores MSC proliferation in senescence and simulated microgravity models, suggesting reduced mechanical signal delivery to MSCs likely contributes to declining bone mechanoresponse. To this end, we have developed a 3D bone marrow analog which controls trabecular geometry, marrow mechanics and external stimuli.

Finite element (FE) models of hydrogels, representing bone marrow, were generated using instantaneous compression (1000% strain/s, 20% strain) and relaxation experiments (100s) of both gelatin and hyaluronin-based hydrogels. …