Digital Commons Network^™

Modeling Intercellular And Intracellular Organization And Dynamics Of The Bacteria Escherichia Coli : From Population Dynamics In The Gut Microbiome, To Condensate Formation In Starved Cells, Alberto Alonso

Theses

Escherichia coli is a predominantly non-pathogenic species of bacteria present in the gut of most healthy adults. It plays a critical role in the health of the gut microbiome and is also widely used as a model organism in microbiology and synthetic biology studies. This thesis discusses results from two ongoing projects on E. Coli organization and emergent biophysical properties at two very distinct length scales. The first project focuses on using genetically modified engineered E. coli bacteria for early detection and intervention in colorectal cancer (CRC), a significant public health issue in the US. The success of these engineered …

Stimuli-Responsive Chemotherapy For Glioblastoma: Sequence-Dependent Synergy Of Cold Atmospheric Plasma And Ultrasound With Cationic Lipo-Doxo, Alessandro Cazzolla

Theses

Glioblastoma (GBM) is an aggressive, infiltrative astrocytic tumour in which pharmacotherapy remains constrained by the blood-brain barrier (BBB) and the heterogeneously altered blood brain tumour barrier, with additional limitations imposed by active efflux and the complexity of the tumour microenvironment. In this setting, externally addressable strategies that modulate transport and uptake at the site of disease are required. A stimuli-responsive chemotherapy platform was developed in which Lipo-DOXO was combined with two non-invasive physical modalities, low-frequency ultrasound (US) and cold atmospheric plasma (CAP), to enhance intratumoural delivery while limiting off-target effects. Liposomes were produced by thin-film hydration followed by a controlled, …

Generation And Detection Of Photo-Thermal And Photo-Acoustic Waves In Solids For Advanced Near-Field Ir Imaging, Yide Zhang

Theses

Atomic force microscopy-infrared (AFM-IR) spectroscopy has become an essential tool for nanoscale chemical imaging, offering spatial resolution beyond the diffraction limit of conventional infrared spectroscopy. A typical AFM-IR setup directs a pulsed IR laser onto the sample, precisely at the tip of an AFM cantilever, detecting local absorption indirectly as photothermal expansion via the tip. This combination of AFM’s high spatial resolution and infrared spectroscopy’s chemical specificity enables detailed studies of a wide range of materials, from polymers and biological tissues to nanomaterials. However, the factors influencing AFM-IR signal generation and spatial resolution-especially in complex and inhomogeneous samples-remain challenging to …

Pd Chlorin-Based Molecμlar Imaging Probes For Breast Cancer, Yoonjung Cho

Theses

Breast cancer (BrCa) is the second most common cancer and the second leading cause of cancer death among women in the U.S. This highlights the necessity of developing effective therapeutic agents to aid in the treatment of BrCa. A promising new method of treatment is photodynamic therapy (PDT), a clinically approved therapeutic procedure that uses a porphyrin-based photosensitizer (PS) dye to kill cancer cells upon excitation with a light source. It has been observed that chelation of a metal ion into the porphyrin increases the therapeutic efficacy. We have developed a synthetic route incorporating the palladized analogue of the PS …

Holistic Correlation Measure For Enhanced Encapsulation Of Trait Heterogeneity And Discovery Of Co-Expression, Zachary Valleroy

Theses

Large-scale, high-dimensional data analyses can be computationally prohibitive due to combinatorial explosion of the search space for finding complex patterns; a viable alternative is network modeling for abstraction and quantifying intrinsic data associations. Prominent network analysis methods furnish frameworks for model synthesis and validation but rely on standard correlation measures impaired by semi-supervised biases, latent heterogeneity, and uneven discretization techniques. Here we investigate a holistic measure for encapsulating data heterogeneity for enhanced efficacy of revealing complex patterns through network analysis. Our unique correlation metric, K-medoids Utility for Duo Original Similarities (Kudos), exhaustively factors real-valued analyte data to compute …

Studies On The Corrosion Of Bronze Artifacts From Sarouq Al-Hadid And Al-Qusais Archeological Sites In Dubai, Uae, Zainab Ali Salmin

Theses

This thesis compares the status of bronze artefacts from two archaeological sites in Dubai (UAE): the Sarouq Al-Hadid site (Stone Age to Early Islamic Period) and the Al- Qusais site (Late Bronze Age to Early Iron Age). The main objective of this research is to understand the two sites' environment and their influence on the corrosion of archaeological bronze artifacts found at the sites. This study uses mCed methods to comprehensively understand the corrosion behavior of bronze objects, depending on their burial environment. The two different sites presented different soil types and rates of corrosivity on the buried bronze artifacts, …

The Cumulative Incidence And Site Of Recurrent Metastatic Breast Cancer And Post-Metastasis Survival Of Females With An Initial Diagnosis Of Non-Metastatic Breast Cancer In New South Wales, Sarah Jane Lord

Theses

This dissertation aimed to investigate the population-level incidence, site, and survival of recurrent metastatic breast cancer (rMBC) occurring after stage I−III breast cancer, and changes over time. Breast cancer mortality has declined over the last 30 years due to advances in screening, diagnosis, and treatment. However, the impact of improved cancer care on rMBC is not yet well understood because cancer registries do not routinely report on cancer recurrence (Chapter 1). A systematic review of 20 population-based studies provided evidence of improvements in survival for people with de novo metastatic breast cancer (stage IV at diagnosis) since 1995 in high-income …

New Treatment Modality For Metastatic Cancer By Targeting The Endothelin Type A Receptor (Etar), Elbara Fathelrahman Abdelmoula

Theses

Ambrisentan, an FDA-approved selective antagonist of the Endothelin Type A Receptor (ETAR) for pulmonary arterial hypertension, has shown potential in limiting cancer growth and metastasis. While effective treatment options for melanoma remain elusive, this study investigates the effects of Ambrisentan on invasive, metastatic B16F10 melanoma using a syngeneic mouse model, aiming to assess Ambrisentan’s impact on tumor growth, metastasis, and overall host survival in B16F10 melanoma, along with gaining mechanistic insights into ETAR antagonism. C57Bl/6 mice were divided into two groups, receiving either dH2O or Ambrisentan orally. Treatments commenced prior to tumor implantation and continued post-implantation. Luciferase-expressing B16F10 cells facilitated …

An Ontology Based System For Cancer Diseases Knowledge Mining, Shinead Casey

Theses

National cancer registries play an important role in understanding the patterns and trends of cancer diseases, prevention methods, and treatment management. However, issues arising from data silos and an inability to link heterogeneous data sources have led to problems within the healthcare industry. This became apparent in Ireland in 2018 when Dr Scally’s scoping inquiry into the CervicalCheck controversy highlighted patient safety issues relating to disjointed data and an inability to link datasets.

Worldwide, semantic technologies are being utilised for their ability to link diverse data and enhance analytical capabilities. Therefore, this thesis will examine the use of a knowledge …

Biomimetic Aerosol Exposure System For In Vitro Human Airway Exposure Studies, Samantha Emma Sarles

Theses

Tobacco use remains the number one cause of preventable death in the United States, disproportionately affecting residents of rural areas, people who are financially disadvantaged, and adults who identify as gay, lesbian, or bisexual. The impact that electronic cigarettes will have on public health is not yet fully understood. Combinations of electronic cigarette products, human airway geometries, and user behaviors create barriers to understanding products’ interaction with the human airway and their health effects. Current in vitro emissions systems, also called smoking robots, lack biomimicry, use unrealistic flow conditions, produce unrealistic aerosol dose, and provide inaccurate bio-mechanical cues to cell …

Understanding Environmental Art: A Case Study Of Jason Decaires Taylor's Coral Greenhouse (2019), Laura Dean Hinson

Theses

This thesis highlights the need for a new way to analyze environmental art. In the past, environmental artwork has been discussed in terms of the abstract concepts that drove their creation and the role they played in moving artists outside of the gallery space in the1960s and 70s. However, in recent years environmental artists are increasingly driven by themes of environmental conservation and preservation, using scientific research as the basis of their designs. Because of the shift in focus, developing a new way to discuss environmental art that takes into consideration the influence scientific research has on art production and …

A Patent-Based Approach To Understanding The Role Of University, Company, And Government Collaboration In Biotechnological Innovation, Rachel Strader

Theses

The biotechnology industry has shifted in recent years in corporate policy from a more traditional, closed research and development (R&D) model to an open innovation (OI) model, leading to increased collaboration between companies and academic institutions. The literature has reinforced this shift by demonstrating the role these collaborative relationships play in contributing to high-quality innovations. In this study, I use a unique dataset composed of biotechnology patents granted in the United States from 2000-2020 to examine the relationship between patent assignee and patent quality. Specifically, I measure patent quality using the number of forward citations and patent family size and …

Identifying Psychological Mental Disorders Through Machine Learning, Mohammad Al Abdooli

Theses

Psychology is the Study of Human Behavior and the various ways of thinking in it’s both consciousness and unconsciousness mind as this field is still growing to various fields such as Sports, Criminal and even Administrative Psychology through, Furthermore, This Study aims to shape and accommodate both fields of Sciences together, There are very few Scholars and Researches done on Medical Mental Health from a Data Analytics perspective, examining the datasets of the patients ICD-11 or DSM-5 scores and correlating it with the patients well-being, family medical history or any accident the patient have been through, so the current study …

Studying Neurotoxic Effects Of Three Synthetic Insecticides And Two Herbal Infusions On The Nervous System Of The Fruit Fly Drosophila Melanogaster, Sara Khamis Obaid Hamarain Al Dhaheri

Theses

Pesticides applied on plants and animals can reach the human diet once they enter food chains. Insecticides are neurotoxic agents; they have the potential of causing damage to the nervous system in people. The damage could induce or promote neurodegenerative diseases such as the Parkinson’s and Alzheimer's. It is well-documented that the exposure to the insecticide chlorpyrifos (CPF) stimulate the Parkinson disease in humans and experimental animals. Thus, this research project will study effect of three synthetic insecticides pirimicarb, tefluthrin, and CPF on the nervous system of Drosophila melanogaster as a model organism. In addition, the project will evaluate the …

Material Engagement Theory And Extensive Enactivism Within The 4e Cognitive Debate: A Phenomenological Approach To Material Agency And Application To Current Technology, Israel Quirit

Theses

4E Cognition is a fairly new field of study within cognitive science, cognitive psychology, and cognitive philosophy. The various approaches to cognition namely embodied, embedded, extended and enacted cognition; provide multi-faceted approaches to cognition. A common claim of these approaches is that cognition may have various contributing factors such as the role of the brain, body and its environments. Thus challenges the traditional idea that cognition exists purely mentally within the confines of the brain and skull. However, even within the 4E Cognition family, some nuanced arguments are hotly debated, particularly among the proponents of Embedded Theories (EmT) and Extended …

Design Of A Comprehensive Modeling, Characterization, Rupture Risk Assessment And Visualization Pipeline For Abdominal Aortic Aneurysms, Golnaz Jalalahmadi

Theses

Abdominal aortic aneurysms (AAA) is a dilation of the abdominal aorta, typically within the infra-renal segment of the vessel that cause an expansion of at least 1.5 times the normal vessel diameter. It is becoming a leading cause of death in the United States and around the world, and consequentially, in 2009, the Society for Vascular Surgery (SVS) practice guidelines expressed the critical need to further investigate the factors associated with the risk of AAA rupture, along with potential treatment methods. For decades, the maximum diameter (Dmax) was introduced as the main parameter used to assess AAA behavior and its …

Determination Of Vitamin D Metabolites And Their Epimers In Obese Emirati Population, Bashar Hiatham Alzohily

Theses

Vitamin D deficiency is a global issue, and despite all-year-round sunshine, it is a big problem in the UAE. Obesity or overweight refers to an accumulation of excessive fat that may harm health so, it is considered a worldwide health concern. The accurate measurement of vitamin D active forms is a problematic issue. This study aimed to develop and validate a UHPLC-MS/MS method for the new method for determining vitamin D levels in the obese Emirati population. The vitamin D epimers and other metabolites were determined by UHPLC-MS/MS system, model 8060. The methods include the collection of blood samples from …

Investigating The Molecular Pathology Of Dupuytren’S Disease, Robert Pearce

Theses

The eponymous progressive palmar fibromatosis described by Guillaume Dupuytren in 1831 is a common and debilitating disease with limited treatment options and high rates of recurrence after intervention. Dupuytren’s disease has been generally accepted as predominantly affecting Northern European individuals; Dupuytren’s disease is sometimes referred to as “Vikings Disease” as an attribution to this ethnic origin. Its familial occurrence in all communities is suggestive of Mendelian inheritance as an autosomal dominant disease with incomplete penetrance. The genetic and molecular basis of Dupuytren’s disease (DD) has been the focus of many studies, with increasingly sophisticated approaches since the sequencing of the …

Study Of Y-Chromosome Str Markers In United Arab Emirates Population, Tareq Zeyad Mohammed Ahmed

Theses

The recently introduced 6-dye Yfiler Plus multiplex which includes 27 Y-STR loci (DYS576, DYS389I, DYS635, DYS389II, DYS627, DYS460, DYS458, DYS19, YGATAH4, DYS448, DYS391, DYS456, DYS390, DYS438, DYS392, DYS518, DYS570, DYS437, DYS385 a/b, DYS449, DYS393, DYS439, DYS481, DYF387S1a/b and DYS533) has been used to study 343 UAE Arab male individuals using Yfiler Plus® amplification kit. This set includes seven rapidly mutating loci (RM Y-STRs). These RM Y-STRs are useful for discriminating between closely related and unrelated males.. According to measures of genetic diversity the highest diversity were observed at loci DYS385=(0.94984), DYF387S1=(0.930523) and DYS449=(0.895402). Therefore, these loci should be considered the …

Network Exploration Of Correlated Multivariate Protein Data For Alzheimer's Disease Association, Matthew J. Lane

Theses

Alzheimer Disease (AD) is difficult to diagnose by using genetic testing or other traditional methods. Unlike diseases with simple genetic risk components, there exists no single marker determining as to whether someone will develop AD. Furthermore, AD is highly heterogeneous and different subgroups of individuals develop the disease due to differing factors. Traditional diagnostic methods using perceivable cognitive deficiencies are often too little too late due to the brain having suffered damage from decades of disease progression. In order to observe AD at early stages prior to the observation of cognitive deficiencies, biomarkers with greater accuracy are required. By using …

The Influences Of Different Socioeconomic Scenarios In Bioinformatics And Biotechnology Research: The Ethical Issues Arising From Technological Advances, Marcia Miki Sato

Theses

In the last couple decades, we could see the combination of technology and biology taking large steps in science. As new fields, bioinformatics and biotechnology also led to important discussions between excited scientists and social thinkers. The divergent opinions argue about the amazing possibilities of human advances and the social issues that follow the progress. This paper discusses ethical matters of new developments and compares policy choices with respect to research and use of biotechnology and bioinformatics in different countries. Even though the world is increasingly globalized, the comparisons suggest that different cultures have different ethical responses and public policies …

Study Of The Seasonal And Interannual Variability Of Phytoplankton Bloom In Arabian Gulf Using Modisdata, Malik Mutasim Malik Gasim

Theses

The Arabian Gulf is a semi enclosed large water body that experiences seasonal

variations and reversal of it water currents flow circulation. The Gulf waters are characterized by having high primary productivity and strong phytoplankton blooms at particular seasons within the year. Phytoplankton is a base of the food chain for marine species, providing an essential food resource for aquatic life. Marine phytoplankton affects the diversity of any marine ecosystem and drives its functioning and is strongly correlated with fishery yields. The primary

objectives of this research study are to answer key research questions related to phytoplankton blooms in the …

Killing Two Birds With One Stone: The Concurrent Development Of The Novel Alignment Free Tree Building Method, Scrawkov-Phy, And The Extensible Phyloinformatics Utility, Emu-Phy., J. Nick Fisk

Theses

Many components of phylogenetic inference belong to the most computationally challenging and complex domain of problems. To further escalate the challenge, the genomics revolution has exponentially increased the amount of data available for analysis. This, combined with the foundational nature of phylogenetic analysis, has prompted the development of novel methods for managing and analyzing phylogenomic data, as well as improving or intelligently utilizing current ones. In this study, a novel alignment tree building algorithm using Quasi-Hidden Markov Models (QHMMs), Scrawkov-Phy, is introduced. Additionally, exploratory work in the design and implementation of an extensible phyloinformatics tool, EMU-Phy, is described. Lastly, features …

Homology Based Motif Generation, Cameron Baker

Theses

Generating motifs from known active sites and matching those motifs to an uncharacterized protein is a classic way of determining protein function. Until now, the generation of motifs has been based purely on enzymatic function. This approach does not account for situations where highly different active sites can arrive at the same function by processes like convergent evolution. As such, a secondary metric on which to base the generation of motifs is necessary. This metric exists in the form of UniProt designation for homologous proteins on a global scale or PFam for designation of homologous proteins at the active site …

Fabrication Of Multibore Carbon Nanopipettes Using A Template-Based Nanomanufacturing Process, Ayomipo Arowosola

Theses

Currently, cancer accounts for nearly 1 of every 4 deaths in the United States which rates it as the second most common cause of death in the US, exceeded only by heart diseases. The detection, prevention and treatment of these death-causing diseases have necessitated and led to the development of novel tools for interfacing with single live cells –intracellular cell physiology. A major challenge, preventing the realization of effective and efficient intracellular physiology, is the lack of minimally invasive, nanoscale electrodes capable of probing cells without causing cell damage or death. Previous studies have succeeded in fabricating single nanoscale electrodes …

Bilingualism, Executive Function, And Attention Deficit/Hyperactivity Disorder, Carina Ann Beck

Theses

In an era where the diagnosis of attention deficit/hyperactivity disorder (ADHD) is as high as 7% in school-aged children, the search for causes and preventions has never been more important. Current research indicates a positive relationship between bilingualism, particularly native bilingualism, and executive function in normally developing individuals. This study served to examine the potential relationship between bilingual education in a public school setting and the presence of ADHD symptoms in that school's students. This was a comparative analysis of students in a South Florida School District's two-way immersion program with the national average in terms of frequency of ADHD …

Study The Quality Of Groundwater Of Al-Zoroup Area In Mahdah State, The Sultanate Of Oman, Fahad Khalifa Rashid Al-Shidi

Theses

The groundwater is the most important source of water in the Sultanate of Oman. Accordingly, the Oman Government has paid great attention commensurate with the importance of water resource in terms of their sources, quality, and ways to rationalize consumption to remain under the term of sustainability and validity of present and future generations. This study was conducted in Al Buraymi at Mahdah State in Al-Zoroub area targete a groundwater quality for 20 wells in private farms. The water samples were taken from these wells and subjected to analysis for microbial and geochemical aspects. For this analysis, the assorted devices …

Responsive Website Design For First Unitarian Church And Louis Kahn, Chen Zhang

Theses

Responsive Website Design for First Unitarian Church and Louis Kahn is a thesis project for Master Degree of Fine Arts in Computer Graphics Design program at the Rochester Institute of Technology. This thesis project is to design a responsive website for the First Unitarian Church, a website which has three user experiences: a desktop site, tablet site and a mobile site. The website audience is architecture or design students, professors, and enthusiasts. There are three objectives in this thesis project: first, to design a responsive website for cross-platform experience for users; second, to provide users a real digital visiting experience …

Synthesis Of Biodiesel From Animal Fat And Polymerization Of Glycerin, Zixu Zhang

Theses

Biodiesel was synthesized using raw beef fat using esterification and transesterification reaction. The obtained biodiesel-glycerin mixture was tested using Fourier transform infrared resonance (FT-IR) and compared with the FT-IR of raw beef fat, glycerin, biodiesel made from vegetable oil and commercial biodiesel. The FT-IR spectrum of the synthesized biodiesel was identical to that of biodiesel made from vegetable oil. Poly-glycerin was synthesized from glycerin by water elimination reaction, where solid NaOH was used as a catalyst under a stream of nitrogen gas. The water-elimination reaction obeys the "N-1" rule. "N-1" is the degree of polymerization and "N" is the number …

Alzheimer's Disease Literacy In The African American Community, Angel Mckenzie Watson

Theses

Alzheimer's disease (AD) is a public health crisis in the African American (AA) community, as evidenced by both increased prevalence and familial risk among African Americans. African Americans are two times as likely to suffer with this disease, are diagnosed later in the disease process, and are considered to have less factual information about AD when compared to their white counterparts. Late diagnosis has been associated with significantly higher dementia-related morbidity and health care costs. Moreover, studies have shown that patients with increased health literacy have better health outcomes. Therefore, we want to assess how well African Americans understand Alzheimer's …