Digital Commons Network^™

Design Of Complex Engineered Systems And The Effectiveness Of Organizational Networks, Bryan Still

Open Access Dissertations

Cost and schedule overruns have become increasingly common in projects that set out to design and deliver complex engineered systems. Noting the well-established relationship between products and the organizations that design them, this study evaluates the effectiveness of different organizational networks at designing complex engineered systems using agent-based modeling. Specifically, it compares matrix and military staff organizational networks to random and multiscale networks, modeling design as an activity that requires organizations to create design artifacts and share information. It examines the nature of design, the role of product architecture, the nature of complexity and how it affects projects, and the …

Analysis Of Band Pair Formation In Elasmobranch Vertebrae With Implications For Fisheries Management, Kelsey James

Open Access Dissertations

Sharks, skates, and rays are particularly sensitive to over-exploitation due to their life history traits (slow growth, late age at maturity, small litter size, and extended longevity). It is important to know the age of sharks, skates, and rays because it has implications for our ability to assess the status of populations and to manage fisheries. They are aged most often using the concentric bands that alternate in appearance: opaque and translucent in their vertebral centra. An opaque and translucent band together (a band pair) is assumed to represent one year of growth and is counted to estimate an individual’s …

A Multiphysics Computational Framework For Understanding Cell And Microtissue Morphogenesis, Bahador Marzban

Open Access Dissertations

A sophisticated computational model is developed to consider different interactive parts between cells and its components and their local microenvironment. The present work is mainly focused on the modeling of the coupling of the stress and concentration of the signaling proteins within the cell domain. In this research, the fundamental aspects and details of a coupled Contraction-Reaction-Diffusion (CRD), is presented. The model accounts for diffusion of the proteins and mechanical equilibrium of the cells simultaneously while considering different subunits which are affecting the cell migration. For instance, cell-cell interaction, nucleus effects, focal adhesion distribution, anisotropic stress fiber formation, membrane tension, …

Eastern Oyster Larval Transcriptomes In Response To Probiotic And Pathogenic Bacteria, Tejashree Modak

Open Access Dissertations

Oysters are described as keystone species serving an important ecological role. As filter-feeders they help in maintaining water quality. Oyster reefs provide refuge and support to different organisms. The eastern oyster, Crassostrea virginica, native to the East Coast of United States and Gulf of Mexico is a part of the rapidly growing aquaculture industry. Aquaculture production depends on a healthy and constant supply of oyster larvae that are provided by hatcheries. Several hatcheries on the east coast that provide C. virginica seed to oyster farms face significant losses owing to Vibrio infections causing massive larval mortalities. Use of antibiotics …

Compassion: Can Service Learning Make A Difference, And If So, How?, Edward Goldberg

Open Access Dissertations

The future of education is often framed in terms of bringing education into the second half of the 21^st century. Technology and along with it, faster and better ways to bring content to our students are important topics for discussion; but how our students treat each other and other members of their community is equally, if not more, important.

This study takes a look at how we may be able to encourage and foster compassion among our students. I wanted to know how compassionate thoughts and feelings develop following a service-learning experience focused on compassionate behavior. In this qualitative …

Analysis Of Atp-Dependent Chaperone Protein Interactions With Misfolded Proteins, Amyloids, And Aggregated Proteins, Shannon May

Open Access Dissertations

Protein aggregation occurs when proteins adopt non-native conformations, exposing hydrophobic surfaces due to misfolding. The exposed regions of two or more proteins associate to form amorphous deposits or highly ordered, stable fibrillar structures called amyloid aggregates. Within the cell, a robust network of proteins safeguard against protein misfolding and aggregation. This network is referred to as the proteostasis network and includes molecular chaperone proteins, co-chaperone proteins, and the ubiquitin proteasome system. Molecular chaperone proteins function in various cellular processes including intracellular transport, oligomeric assembly, and efficient protein folding. Moreover, molecular chaperones are required for folding denatured, misfolded, and de novo …

Widening The Sphere: Mid-To-Late Victorian Popular Fiction, Gender Representation, And Canonicity, Anna J. Brecke

Open Access Dissertations

When Victorian fiction entered academic study in the mid-twentieth century, the texts that were considered essential had been influenced by a small group of scholars primarily concerned with studying the novel form across periods rather than studying literature of the Victorian Era. The collection of authors that became "the" Victorian canon included Dickens, Thackeray, Hardy, the Brontës, Trollope, Henry James and George Eliot, limiting the Victorian novel to realist fiction. The choices of these critics did not accurately represent the diverse range of authors and genres in fiction published during the period. Particularly absent from this canon are the popular …

In Vitro Drug Metabolism And Population Pharmacokinetics As Tools For Elucidating Pharmacokinetic Variability, Enoch Cobbina

Open Access Dissertations

Pharmacokinetic variability is an important consideration in pharmacotherapy to ensure safety and efficacy of medications, thus the understanding of the sources of variability in drug concentrations in the body is imperative. The goals of this dissertation were: (1) To use in vitro drug metabolism tools to characterize the influence of non-alcoholic fatty liver disease (NAFLD) on Cytochrome P450 2B6 (CYP2B6)-mediated hydroxylation of bupropion in human liver microsomes; and (2) To use population pharmacokinetics to characterize the pharmacokinetics of PF-5190457, an inverse agonist of the growth hormone secretagogue receptor (hGHSR1a). This work has been organized in two parts. Part one is …

Use Of Radiation To Kill Cancer By Nanoparticles And In A Biodosimeter Using Gene Expression Analysis, Samana Shrestha

Open Access Dissertations

The use of radiation is broad in biological systems, in different areas of research mostly in health.

Radiation is used to kill cancer. In radiation therapy proper calculation is done so that a maximum dose is delivered to the cancer. Inspite of this precaution, radiation effects healthy tissue. This effect is especially dangerous when the tumor is located near important organs. Thus in radiation therapy, it is important to reduce the dose and the damage to the healthy tissues and organs. The damage on the healthy tissues due to radiation therapy in cancer could be reduced by reducing the radiation …

Impacts Of Urbanization And Invasive Species On Foraging Behavior And Body Size In Anolis Sagrei, Zachary Chejanovski

Open Access Dissertations

Urbanization dramatically alters the abiotic and biotic environment of cities, favoring species that are pre-adapted or are able to adapt (e.g. through phenotypic plasticity or evolutionary mechanisms) to these novel conditions. While urbanization is widely considered one of the greatest threats to biodiversity worldwide, we still lack a general understanding of the mechanisms underlying organismal responses to human-induced rapid environmental change. The focus of this thesis was to examine how urbanization-induced changes in the abiotic and biotic environment influence the foraging behavior and body size of the brown anole, Anolis sagrei. In Chapter 1, we presented anoles from habitats …

Regulation Of Ubiquitin Specific Peptidase 2 Expression By Farnesoid X Receptor In Hepatocellular Carcinoma, Christina Nadolny

Open Access Dissertations

Liver cancer is in the ten leading cancer types for estimated new cases and deaths in the United States in 2018, and is often detected at late stages when it is rapidly fatal. Of the types of liver cancers in humans, hepatocellular carcinoma (HCC) is the most lethal and prevalent. An important factor in the development of HCC is Farnesoid X Receptor (FXR). FXR acts as master regulator of bile acid homeostasis, and is involved in lipid, cholesterol, and glucose homeostasis. In addition, it plays a protective role against HCC, the precise mechanisms of which has yet to be identified. …

Characterizing The Functional Role And Regulated Assembly Of Protein Polymers Mind And Ftsa During Escherichia Coli Cell Division, Joseph Jake Conti

Open Access Dissertations

It is an immense undertaking for any organism, including a bacterium, to self-replicate. Accurate and rapid division is essential for bacteria to proliferate and produce progeny, especially in environments where there is competition for resources. The nucleoid, the region of the cell that contains the DNA, harbors the genetic information required to achieve robust division, but it is the assembly of the cell division machinery, collectively referred to as the divisome, that produces and coordinates the mechanical force necessary to divide a cell. The hallmark of prokaryotic cell division is the formation of a protein super-structure, called the Z-ring, which …

Conformations, Energetics, And Kinetics Of Peptides In Membrane Environment, Ganga P. Sharma

Open Access Dissertations

Chapter 1: We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an α-helix conformation. The polypeptide is assumed to be adsorbed to the interface between a polar and a non-polar environment such as realized by water and the lipid bilayer of a membrane. The interfacial coil-helix transformation is the first stage in the folding process of helical membrane proteins. Depending on the values of model parameters, the conformation changes as a crossover, a discontinuous transition, or a continuous transition with helicity in the role of …

Monitoring Salt Marsh Condition And Change With Satellite Remote Sensing, Anthony Daniel Campbell

Open Access Dissertations

Salt marshes are a frontline of climate change providing a bulwark against sea level rise, an interface between aquatic and terrestrial habitat, important nursery grounds for many species, a buffer against extreme storm impacts, and vast blue carbon repositories. Since the 1700s salt marshes have been in flux due to anthropogenic actions, such as reclamation for development causing loss and an influx of sediment from land clearing leading to marsh expansion. The Clean Water Act of 1972 provides legal protections for wetlands, limiting wetland reclamation and requiring that impacts be offset. However, salt marshes continue to change rapidly due to …

High Resolution Data Acquisition System For Brain Imaging, Seyed Hadi Nasrollaholhosseini

Open Access Dissertations

The U.S. has 12.3% disabled people based on the American Community Survey (ACS) in 2012. According to this survey, more than half of the disabled population suffers from ambulatory disabilities. Therefore, a system which enables people with disabilities to control their environments is crucially important. Moreover, ubiquitous physiological monitoring will be a key driving force in the upcoming medical revolution. Cardiac and brain signals in the form of electrocardiograms (ECGs) and electroencephalograms (EEGs) are two critical health indicators that directly benefit from long-term monitoring.

Brain-computer interfaces (BCIs) are systems that detect changes in brain signals related to human intentions, typically …

Brain-Body Sensory Fusion: Merging Fnirs/Eeg Neuroimaging And Full-Body Motion Capture, Mohammadreza Abtahi

Open Access Dissertations

Functional connectivity between the brain and body kinematics has not been largely investigated due to the requirement of being motionless in neuroimaging techniques such as functional magnetic resonance imaging (fMRI). The importance of investigating this connectivity arises from the fact that the connectivity is disrupted in many neurodegenerative disorders such as Parkinson’s Disease (PD). PD is a neurological progressive disorder characterized by movement symptoms including slowness of movement, stiffness, tremors at rest, and walking and standing instability.

Body kinematics are generally divided into two categories of fine and gross motor tasks. Fine motor movements are referred to small range kinematics …

Benthic Habitat Mapping And Its Applications To Coastal Resource Management, Monique Lafrance Bartley

Open Access Dissertations

This dissertation is comprised of three chapters focused on benthic habitat mapping of coastal waters within northeast region of the United States to support science-based regulatory and management strategies. The first chapter is entitled: Shallow water benthic habitat mapping utilizing the Coastal and Marine Ecological Classification Standard (CMECS) to establish baseline conditions post-Hurricane Sandy at Fire Island National Seashore, New York. In response to Hurricane Sandy, a benthic habitat mapping study was conducted at Fire Island National Seashore (FIIS), New York, representing one of the first comprehensive mapping efforts undertaken by the National Park Service. FIIS was of particular interest …

After “Being Thrown In The Classroom”: The Development Of Pedagogical Skills In Veteran Adjunct Faculty Teaching In The Natural Sciences, Heather Shannon Miceli

Open Access Dissertations

The postsecondary landscape has changed drastically in the past 40 years, with one of the most obvious changes being the increased reliance on adjunct or part-time faculty. Approximately 50% of the current faculty employed by postsecondary institutions are categorized as part-time faculty, up from approximately 25% in 1975 (American Association of University Professors, 2017; Snyder, de Bray, & Dillow, 2016). While there is literature surrounding the impacts of this phenomenon, the majority of studies are entrenched in a positivist framework, utilize quantitative methods, and many use large datasets to distill down whether students are more or less successful when taught …

Experimental And Numerical Simulations For Fluid Body Interaction Problems, Amin Mivehchi

Open Access Dissertations

This dissertation focuses on the experimental and numerical modelling of fluid structure interaction (FSI) problems. The main objective of this work was to develop state-of-art experimental and numerical tools to investigate a variety of Fluid-Structure Interaction problems. This topic is of critical importance to Naval Hydrodynamics and offshore applications, such as in ship design, floating offshore wind platforms and offshore ocean energy systems.

On the experimental modelling of FSI, this dissertation includes detailed of state-of-art hydrodynamic testing tank system for studying biomimetic fluid-structure interaction problems. This system was employed to study unsteady ground effect for pitching and heaving flapping foil …

High Through-Put Analysis Reveals Novel Maternal Germline Rnas Critical For Pgc Survival, Migration, And Differentiation, Dawn Owens

Open Access Dissertations

Xenopus laevis embryonic development requires the selective localization of maternal RNAs to the animal or vegetal pole. These RNAs include somatic and germline determinants, essential in establishing the embryo’s body plan. Such determinants are involved in primary germ layer formation and organization, dorsal/ventral axis specification, anterior/posterior axis specification, and germline development. In Xenopus laevis, germline development requires maternally inherited germplasm, a vegetally localized material that both specifies and protects primordial germ cells (PGCs) from adopting somatic fates throughout embryogenesis. The germline is unique in its ability to maintain heritable genetic material for many metazoans, including humans. It is, therefore, of …

Nearshore Salinity And Juvenile Pink Shrimp (Farfantepenaeus Duorarum): Integrating Field Observations, Laboratory Trials, And Habitat Suitability Simulations, Ian C. Zink

Open Access Dissertations

The pink shrimp Farfantepenaeus duorarum is one ecological indicator of the Biscayne Bay Coastal Wetlands (BBCW) project, which intends to increase mesohaline and oligohaline areal extent along southwestern Biscayne Bay nearshore areas. These changes were anticipated to benefit pink shrimp abundances. My dissertation tested whether increased mesohaline and oligohaline area within a 50-m strip of shallow-water shoreline area likely would increase pink shrimp densities. First, I carried out a comprehensive literature review that revealed polyhaline and/or euhaline salinity regimes generally maximized pink shrimp occurrence, abundance, growth, and survival. Next, I analyzed 10 yrs of pink shrimp density and habitat observations …

Ecological And Evolutionary Genomics: Differential Variability Of Gene Expression And Fine-Scale Adaptive Divergence Among Microhabitats Of Large Fundulus Heteroclitus Populations, Dominique Neitzel Wagner

Open Access Dissertations

Adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation from standing genetic variation is polygenic – does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation is not resolved. To investigate this process, the gene expression and genetic divergence of a teleost fish, Fundulus heteroclitus, was explored. Among nearby (< 200m) microhabitats in three separate saltmarshes, and over the course of a season (spring to fall), thousands of single-nucleotide polymorphisms (SNPs) were analyzed. Among these SNPs, 1.3-2.3% have large and highly significant differences among microhabitats (mean FST = 0.15; false discovery rate (FDR) ≤ 1%), and 1.8-5.7% are significantly different between seasons (mean FST = 0.077 to 0.597; FDR ≤ 1%). The divergence among microhabitats and between seasons for these SNPs is larger than that among populations, exceeds neutral expectation, and indicates surprising population structure among microhabitats. These data suggest that polygenic selection is surprisingly effective in altering allele frequencies over very small geographic distances.

Mems Scale Integrated Lab-On-A-Chip System For Detection And Analysis Of Human Tumor Cells, Rajapaksha Waththegedara Randil Lalinda Gajasinghe

Open Access Dissertations

Detection and analysis of circulating tumor cells (CTCs) present in human blood is gaining attention as a reliable technique for obtaining information that are vital for diagnostic and research procedures. Only a limited number of semi-automated commercial tools capable of single cell detection and analysis exist; they are expensive and bulky instruments that require highly trained operators. Micro-electromechanical systems (MEMS) are ideal for the application due to their inherent advantages. A method for immobilizing target CTCs at MEMS scale regions of interest was developed. Developed MEMS device utilized superparamagnetic micro beads and micro electromagnets to immobilize MCF-7 cells flowing in …

Deposition And Diagenesis Of Subtropical Microbial Carbonates, Chelsea L. Pederson

Open Access Dissertations

The primary objective of this dissertation is to characterize freshwater microbial palustrine deposits, and assess how their textures and geochemical characteristics change over various stages of early burial and diagenesis in order to assess their recognition and preservation in the geologic record. A detailed study of sediments, microbial communities, and chemical environments was carried out for a sequence of cored Holocene deposits, from the modern surficial freshwater environment and seaward to those similar sediments buried during the Holocene transgression in the Florida Everglades (mainly terrestrial) and Florida Bay (full marine). In addition, the early diagenesis of microbial lime mud is …

Effects Of Probiotics On The Aquaculture Performance Of Cobia (Rachycentron Canadum) And Yellowfin Tuna (Thunnus Albacares), Juan Felipe Sierra De La Rosa

Open Access Dissertations

Effects of probiotics pulse-supplementation on cobia were assessed over two experimental trials carried out with larval and juvenile stages using a commercial blend of Bacillus subtilis, B. lincheniformis, B. magaterium, and Brevibacillus laterosporus. The first trial evaluated the effects of probiotic-enriched live feeds (7x106 and 10x106 colony-forming units (CFU) L-1 for rotifers and Artemia sp., respectively) on the growth and survival of fingerlings during a commercial larval rearing run. The second trial assessed the effects of probiotics supplementation in dry feeds (109 CFU kg-1) on the survival, growth, feed conversion ratio (FCR), ammonia excretion of cobia juveniles (58 g to …

Wildlife Policy And Conservation: An Interdisciplinary Historical Perspective, Catherine C. Macdonald

Open Access Dissertations

It is widely recognized that historical data about human interactions with the natural world is critical to understanding anthropogenic environmental change over time (McNeill, 2001). However, the potential contribution of interdisciplinary historical perspectives to wildlife conservation problems remains largely unexplored. Human-wildlife interactions are informed by a variety of factors, including the scientific and ecological literacy of human populations, human values, the availability of habitat and resources for human and animal populations, and the types of resource conflicts taking place (or likely to take place) (Treves et al., 2006). The role of historical interactions in shaping present attitudes and conflicts can …

The Evolution Of The Krüppel-Like Factor Gene Family And Their Function During Embryonic Development In The Ctenophore Mnemiopsis Leidyi, Jason Scott Presnell

Open Access Dissertations

How modifications during development influence large-scale evolutionary changes is a major emphasis in the field of evolutionary developmental biology (evo-devo). Comparing the underlying cellular and molecular basis of development in diverse organisms can provide insight into how alterations of these processes contribute to morphological diversity. Ctenophores, or comb jellies, are a phylum of marine invertebrates and, due to their unique phylogenetic position as one of the earliest branching lineages of extant animals, are an ideal system for investigating the origin and evolution of metazoan character traits. For example, the animal through-gut is thought to have originated in the metazoan stem …

Intestinal Exposure To Pcb 153 Induces Inflammation Via The Atm/Nemo Pathway, Matthew C. Phillips

Open Access Dissertations

Polychlorinated biphenyls (PCBs) are persistent organic pollutants that adversely affect human health. Although production of PCBs has stopped, they remain a pressing environmental problem due to their slow biodegradation and high lipophilicity. These properties enable PCBs to bio-accumulate in food chains leading to high levels of PCBs in the tissues of foodstuffs, especially fish. Despite dietary exposure being one of the main routes of exposure to PCBs, the gut has been widely ignored when studying the effects of PCBs. We set out to investigate the effects of PCB 153, the most environmentally prevalent PCB, on the gut, looking specifically for …

Bioluminescent Sensing Systems For Cytokines And Cancer Biomarker Detection, Xiaowen Yu

Open Access Dissertations

Bioluminescence is the generation of light through a natural oxidation chemical reaction, thus eliminating the need for an external light source which eliminates background fluorescence. This results in higher signal-to-noise ratio when compared to fluorescence, making it suitable for use as a label in ultra-sensitive detection applications. Herein, a multiplexed assay to measure three analytes simultaneously in a single solution by employing the variants of the photoprotein aequorin (AEQ) has been demonstrated. Aequorin, natively found in jellyfish Aequorea victoria, can emit a flash-type light at 469 nm with a half-life around 0.5-1 s after the binding of calcium ions (Ca2+). …

Role Of An Upwelled Coastal Area In Northeastern Colombia In The Distribution, Population Dynamics And Genetic Diversity Of The Migratory Habitat-Shifting Chelonia Mydas, Catalina Vasquez Carrillo

Open Access Dissertations

The Caribbean is generally an oligotrophic sea; however, in the southern portion between Venezuela and Colombia, a yearly, moderate, coastal upwelling fuels a very productive marine ecosystem, the Southern Caribbean Upwelling System. Extensive submerged aquatic vegetation (SAV) ecosystems are found in the Colombian side of the system, by La Guajira peninsula. SAV ecosystems constitute key habitat for multiple marine fauna species, specially at juvenile/larval stages. La Guajira’s SAV unique, upwelled ecosystems are hypothesized as important foraging and developmental habitat for the endangered, migratory sea turtle Chelonia mydas. The complex habitat-shifting behavior and very long-lasting juvenile stage traits of the species …