Digital Commons Network^™

Modeling And Analysis Of Intracellular Signaling Networks And Cellular Decisions, Mustafa Ozen

Dissertations

Developing molecular network analysis methods is important due to their applications on complex biological systems such as target discovery, development of drugs, discovering drug effects, and finding treatments for many complex diseases, e.g., cancer, autoimmune, and mental disorders. An example of analysis techniques is the fault diagnosis analysis, in which the purpose is to quantify how much vulnerable the entire network is to dysfunction of one or multiple molecules. Such analysis can be done after proper network models are implemented, trained, and tested against the experimental data. In this dissertation, a Boolean modeling framework is implemented and methods to train …

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. …

Analyzing The Effects Of E-Hook Peptides On Kinesin-1, Ashton Ward Murrah, Baylee Hope Howard

Honors Theses

Cancer is the second leading cause of death in the United States. Cancerous growth is a result of oncogenes, or mutated genes that increase the rate of cell division in an uncontrolled manner. Cell division, which consists of mitosis and cytokinesis phases, is dependent upon the active movement of kinesin motor proteins along microtubules to rearrange the cytoskeleton for equitable distribution of genetic material to daughter cells. As kinesins are vital to this process, if we could prevent kinesin from binding to the microtubules, cell division would cease.

The goal of this study is to develop a method to prevent …

Engineering Cardiac Tissues With Three-Dimensional Bioprinting For Biomedical Applications, Matthew Alonzo

Open Access Theses & Dissertations

The role of a biomedical engineer is to solve unmet health-related needs that face society. For the past couple of decades, heart disease (HD) has remained the leading cause of mortality and morbidity worldwide. The disease is characterized by various pathologies that affect the heart. Indeed, malfunction of one of the bodyâ??s most vital organs is bound to manifest poor health and even death in patients. Despite advances in medicine and technology, heart disease continues to be prevalent and diminishes the quality of life for many around the world. Certainly, there exists a need for developing new tools to better …

Differentiating Human Embryonic Stem Cells In Micropatterns To Study Cell Fate Specification And Morphogenetic Events During Gastrulation, Kyaw Thu Minn

McKelvey School of Engineering Graduate Student Theses & Dissertations

During mammalian embryogenesis, the first major lineage segregation occurs when embryonic epiblast, and extraembryonic trophectoderm and hypoblast arise in the blastocyst. In the next fundamental and conserved phase of animal embryogenesis known as gastrulation, extraembryonic cells provide signals to epiblast to instruct embryonic patterning, and epiblast gives rise to germ layers ectoderm, mesoderm, and endoderm, that will establish all embryonic tissues. Proper specification and morphogenesis of germ layers during gastrulation is vital for correct embryonic development. Due to ethical and legal restrictions limiting human embryo studies, human gastrulation is poorly understood. Our knowledge of human gastrulation has largely been derived …

Multi-Functional Fluorescence Microscopy Via Psf Engineering For High-Throughput Super-Resolution Imaging, Jinhan Ren

Electronic Theses and Dissertations, 2020-2023

Image-based single cell analysis is essential to study gene expression levels and subcellular functions with preserving the native spatial locations of biomolecules. However, its low throughput has prevented its wide use to fundamental biology and biomedical applications which require large cellular populations in a rapid and efficient fashion. Here, we report a 2.5D microcopy (2.5DM) that significantly improves the image acquisition rate while maintaining high-resolution and single molecule sensitivity. Unlike serial z-scanning in conventional approaches, volumetric information is simultaneously projected onto a 2D image plane in a single shot by engineering the fluorescence light using a novel phase pattern. The …

Development Of Chemical Methods For Oligonucleotide Purification, Paramagnetic Labeling And Synthesis Of Dna-Based Advanced Materials, Muhan He

Legacy Theses & Dissertations (2009 - 2024)

This thesis describes a chemical method for alternative oligonucleotide purification that is non-chromatographic and gel-free and allows to routinely synthesize and purify long functional RNA strands. The purification of long RNAs is based on the bio-orthogonal inverse electron demand Diels-Alder (IEDDA) chemistry between trans-cyclooctene (TCO) and tetrazine (Tz). Target oligonucleotide strands are selectively tagged with Tz and can be captured and purified from the failure sequences with immobilized TCO. RNA strands are synthesized on solid support through a photolabile linker to avoid the loss of Tz tag. Purity of the isolated oligonucleotides was evaluated using gel electrophoresis, HPLC and mass …

Sample Mislabeling Detection And Correction In Bioinformatics Experimental Data, Soon Jye Kho

Browse all Theses and Dissertations

Sample mislabeling or incorrect annotation has been a long-standing problem in biomedical research and contributes to irreproducible results and invalid conclusions. These problems are especially prevalent in multi-omics studies in which a large set of biological samples are characterized by multiple types of omics platforms at different times or different labs. While multi-omics studies have demonstrated tremendous value in understanding disease biology and improving patient outcomes, the complexity of these studies may increase opportunities for human error. Fortunately, the interrelated nature of the data collected in multi-omics studies can be exploited to facilitate the identification and, in some cases, correction …

3d Cell Culture: Techniques, Applications In Healthcare, And Future Challenges, Mukunthan K S

Manipal Journal of Science and Technology

Two-dimensional (2D) cell cultures have been the most commonly used technique since cell culture was first introduced. However, these cultures do not accurately represent animal physiology as many factors that play an important role in the growth of animal cells are overlooked. Three-dimensional (3D) cell culture techniques provide higher accuracy in recreating the microenvironment of native tissues. But, 2D cell culture techniques are still preferred for the majority of animal cell cultures as these are well established and relatively inexpensive. Various techniques have been developed for 3D cell culture but these systems are highly complex as the number of parameters …

Point-Of-Care Devices For Therapeutic, Medical And Environmental Applications, Alisha Prasad

LSU Doctoral Dissertations

Point-of-care testing (POCT) or Point-of-use (POU) devices or technologies are defined as testing aids that are capable for onsite use or testing. The key advantages of POCT are low sample volume, quick onsite diagnosis, high accuracy, and cost-effectiveness. POCT has the potential and the benefits to facilitate better health care management by rapid routine diagnosis and monitoring. To reach this goal, several researchers as well as the healthcare industry over a few years have conducted cutting edge research to bring science to technology by developing smart diagnostic devices capable of performing as per patient profiles and make personalized health care …

Development Of Plant Extract-Based Composite Fibers And Aerogels, Raul C. Barbosa

Theses and Dissertations

The aim of this study is to use the solid templating process of pullulan nanofibers in order to produce biocompatible, biodegradable, and antibacterial aerogels. The developed aerogels were produced using cross-linked pullulan nanofibers, which provide a water-stable structure allowing them to be used as wound dressing material. The morphology, thermal properties, water solubility, and thermal and physical properties of the nanofibers and aerogels were characterized. Furthermore, the antibacterial effect against gram-negative bacteria, Escherichia coli, and the biocompatibility using mouse embryonic fibroblasts (NIH 3T3) were investigated.

Biomaterials For Bone Regeneration: Tunable Structural And Mechanical Characteristics, Anwer Mhanawee

Theses and Dissertations

Tissue engineering is a promising alternative treatment for damaged tissues. In bone regeneration, bone graft replacements can be made from different biomaterials (basically ceramic and polymer) and used for different treatment purposes. In the first section of this dissertation, the Compression test results showed that its modulus of elasticity depends on its porosity. Also, we developed a testing method to measure the swelling force of the material during expansion due to liquid absorption. The maximum swelling force was found to be proportional to the material modulus. In the second part, we successfully design, fabricate and characterize a novel expandable bone …

Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse

Publications and Research

A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways along which information can be transmitted in the network. In this representation, we find remarkable symmetries in the input trees that deconstruct the network into functional building blocks called fibers. Nodes in a fiber have isomorphic input trees and thus process equivalent dynamics and synchronize their activity. Each …

Space And Defense – Volume Nine – Number One – Spring 2016, Space And Defense Journal

Space and Defense

No abstract provided.

Preparation, Characterization And Biological Activity Of Novel Schiff Base Complexes Based On La, Er And Yb Metal Ions, Hoda Ahmed, Walaa H. Mahmoud, Islam M. Al-Akraa Dr, Gehad G. Mohamed

Chemical Engineering

The tridentate [HL, (4-[(2-(2-quinolinoimino)-3, 5-dibromobenzyl) amino] cyclohexanol)]Schiff base ligand was prepared from the condensation reaction of 2-quinoline carbaldehyde with the drug ambroxol. The prepared HL ligand was further used in the preparation of some new complexes via the reaction with La(III), Er(III) and Yb(III) metal ions. The geometry of the prepared complexes was proposed from elemental analysis, FT-IR, 1H NMR, thermal and magnetic susceptibility. 1H NMR showed that the three nitrogen atoms of the ligand were responsible for the complex formation. The thermal analysis technique provided a clear prospect about the decomposition steps of the Schiff base ligand and its …

Comparison Of Seldm Simulated Total-Phosphorus Concentrations With Ecological Impervious-Area Criteria, Lillian C. Jeznach, Gregory E. Granato

Engineering, Computing & Construction Management Faculty Publications

Ecological studies indicate that impervious cover (IC) greater than approximately 5%–20% may have adverse effects on receiving-stream ecology. It is difficult to separate the effects of runoff quality from other effects of urbanization on receiving streams. This study presents the results of a numerical experiment to assess the effects of increasing IC on water quality using the Stochastic Empirical Loading and Dilution Model (SELDM). Hydrologic and physiographic variables representative of southern New England were used to simulate receiving water quality in a basin with IC ranging from 0.1% to 30%. Simulation results mirror the results of ecological studies; event mean …

Development Of 3d Porous Chitosan-Based Platform For In Vitro Culture, Kailei Xu

Electronic Theses and Dissertations, 2020-2023

Three-dimensional (3D) cell cultures have been widely used in biological research since two-dimensional (2D) cultures have many limitations including alteration of cell morphology, metabolic pathways and gene expression. Therefore, the application of 2D cell cultures in pharmaceutical companies for drug screening causes reproducibility issues in animal studies, which strongly influences the efficiency of drug development. The aim of my studies is to develop 3D cell culture models to better mimic the extracellular matrix (ECM) in tumor microenvironment, not only for deeper understanding of interaction between cells and ECM, but also for the application in drug screening. Three different compositions of …

Fluorescence Microscopy With Tailored Illumination Light, Jialei Tang

Electronic Theses and Dissertations, 2020-2023

Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from single molecule imaging to long-term observation of living organisms. While numerous fluorescence imaging techniques have been developed over the past decades, there is always an inevitable tradeoff among the spatial resolution, imaging speed, contrast, photodamage and the total cost when it comes to choose the appropriate microscope. A main goal of my dissertation research is to develop state-of-the-art microscope systems that exhibit unprecedented performance in …

Assessment Of Heat Stress For Outdoor Work Conditions In Saudi Arabia, Jamal Alanazi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Outdoor workers have an increased risk of heat stress in Saudi Arabia since it is one of the hottest places in the Middle East. Recently, the government decided to limit outdoor work hours during the months of June, July, and August every year, and banned working under the direct sunlight from 12:00 to 03:00 p.m., although outdoor workers in the petroleum, natural gas, or emergency maintenance work industries are exempt from this prohibition. Traditionally, the efforts by safety and health professionals to mitigate work-related heat injury has been directed toward the assessment of environmental heat stress (e.g., wet-bulb globe temperature), …

Application Of A Brain-Inspired Spiking Neural Network Architecture To Odor Data Classification, Anup Vanarse, Josafath Israel Espinosa-Ramos, Adam Osseiran, Alexander Rassau, Nikola Kasabov

Research outputs 2014 to 2021

Existing methods in neuromorphic olfaction mainly focus on implementing the data transformation based on the neurobiological architecture of the olfactory pathway. While the transformation is pivotal for the sparse spike-based representation of odor data, classification techniques based on the bio-computations of the higher brain areas, which process the spiking data for identification of odor, remain largely unexplored. This paper argues that brain-inspired spiking neural networks constitute a promising approach for the next generation of machine intelligence for odor data processing. Inspired by principles of brain information processing, here we propose the first spiking neural network method and associated deep machine …

Development Of An Integrated Microfluidic System For Cell Sorting And Trapping—Considering Sorting Efficacy And Cell Viability, Thammawit Suwannaphan

Chulalongkorn University Theses and Dissertations (Chula ETD)

This study is divided into two phases. The first phase is about the investigation of cell viability and damage of white blood cells after sorting in both a spiral microchannel and contraction and expansion array (CEA) at appropriate flow rates for cell separation. Three techniques such as Trypan Blue staining, Scanning Electron Microscopy (SEM) and Wright-Giemsa staining are employed in the experiments. After flowing the sample through a whole setup of spiral microchannel at 2 ml/min, 85% of cells are viable while 30% of cells are significantly deformed and 2% of cells are seriously damaged in their intracellular structures. In …

Bio-Inspired Learning And Hardware Acceleration With Emerging Memories, Shruti R. Kulkarni

Dissertations

Machine Learning has permeated many aspects of engineering, ranging from the Internet of Things (IoT) applications to big data analytics. While computing resources available to implement these algorithms have become more powerful, both in terms of the complexity of problems that can be solved and the overall computing speed, the huge energy costs involved remains a significant challenge. The human brain, which has evolved over millions of years, is widely accepted as the most efficient control and cognitive processing platform. Neuro-biological studies have established that information processing in the human brain relies on impulse like signals emitted by neurons called …

Quantitative Detection Of Levofloxacin Hydrochloride By Differential Pulse Stripping Voltammetry With Electrodeposited Bismuth Film Electrodes, Zi-Ying Guo, Zuo-Peng Li, Jiang Li, Jian-Guo Zhao, Feng Feng

Journal of Electrochemistry

In this study, differential pulse stripping voltammetry was developed for the quantitative detection of levofloxacin hydrochloride indirectly. Levofloxacin hydrochloride contains organic amine, which can be precipitated upon interaction with Zn(SCN)₄^2-. By means of differential pulse stripping voltammetry, the concentration of Zn²⁺ can be determined using an in-situ formed bismuth film electrode, which allows determining indirectly the amount of levofloxacine hydrochloride. The linearity equation, I = 1.1401c - 0.5309 with the correlative coefficient R = 0.9979, was presented in the experiment. The results showed that this approach is very sensitive, having a limitation of detection of 3.18 …

Localized Dielectric Loss Heating In Dielectrophoresis Devices, Tae Joon Kwak, Imtiaz Hossen, Rashid Bashir, Woo-Jin Chang, Chung-Hoon Lee

Electrical and Computer Engineering Faculty Research and Publications

Temperature increases during dielectrophoresis (DEP) can affect the response of biological entities, and ignoring the effect can result in misleading analysis. The heating mechanism of a DEP device is typically considered to be the result of Joule heating and is overlooked without an appropriate analysis. Our experiment and analysis indicate that the heating mechanism is due to the dielectric loss (Debye relaxation). A temperature increase between interdigitated electrodes (IDEs) has been measured with an integrated micro temperature sensor between IDEs to be as high as 70 °C at 1.5 MHz with a 30 V_pp applied voltage to our ultra-low …

Modeling The Effects Of Distribution System Topology On Water Quality, Chun-Ying Chao

McKelvey School of Engineering Graduate Student Theses & Dissertations

Inadequate treatment of drinking water causes the formation of disinfection by-products and the regrowth of harmful microbial species. Various studies have addressed the problem of water quality monitoring, but very few have employed topological analysis, a valuable mathematical tool widely applied in biological, business, and social research. This thesis examines the relationship between the topological properties of water distribution systems and water-quality models. In particular, the research proposes a novel framework for mapping network topological attributes to water-quality models. This research adopts topological metrics to assess the accuracy of the predictions of chlorine concentrations in dead ends. It examines four …

Magnetocaloric Effect Near Room Temperature In Quintenary And Sextenary Heusler Alloys, Benjamin D. White, R. I. Barabash, O. M. Barabash, I. Jeon, M. B. Maple

All Faculty Scholarship for the College of the Sciences

An inverse magnetocaloric effect is studied in Ni₂Mn_1+xX_1-x-type Heusler alloys. Principally known for their shape-memory properties, these alloys also exhibit significant entropy and temperature changes (ΔS and ΔT_Ad, respectively) under adiabatic conditions when a modest magnetic field is applied. We investigated the impact on magnetocaloric properties of introducing substantial chemical disorder on the X-site (X = Si, Ga, In), of replacing Ni with nonmagnetic Ag, and of replacing a small amount of Mn with Gd. While a reduction in ΔS is observed in the first two cases, we observe a significant enhancement …

Sequencing Heparan Sulfate Using Hilic Lc-Netd-Ms/Ms, Jiandong Wu, Juan Wei, Pradeep Chopra, Geert Jan Boons, Cheng Lin, Joseph Zaia

Chemical and Biochemical Engineering Faculty Research & Creative Works

Heparan Sulfate (HS) Mediates a Wide Range of Protein Binding Interactions Key to Normal and Pathological Physiology. Though Liquid Chromatography Coupled with Mass Spectrometry (LC-MS) based Disaccharide Composition Analysis is Able to Profile Changes in HS Composition, the Heterogeneity of Modifications and the Labile Sulfate Group Present Major Challenges for Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Sequencing of the HS Oligosaccharides that Represent Protein Binding Determinants. Here, We Report Online LC-MS/MS Sequencing of HS Oligosaccharides using Hydrophilic Interaction Liquid Chromatography (HILIC) and Negative Electron Transfer Dissociation (NETD). a Series of Synthetic HS Oligosaccharides Varying in Chain Length (Tetramers and Hexamers), …