Digital Commons Network^™

Plat: A Web Based Protein Local Alignment Tool, Stephen H. Jaegle

Open Access Master's Theses

Protein structure largely determines functionality; three-dimensional structural alignment is thus important to analysis and prediction of protein function. Protein Local Alignment Tool (PLAT) is an implementation of a web-based tool with a graphic interface that performs local protein structure alignment based on user-selected amino acids. Global alignment compares entire structures; local alignment compares parts of structures. Given input from the user and the RCSB Protein Data Bank, PLAT determines an optimal translation and rotation that minimizes the distance between the structures defined by the selected inputs.

Use Of Ground-Penetrating Radar For Monitoring Bridge Scour And The Identification Of Shallow Bedrock, Moritz Kanter

Open Access Master's Theses

Ground-penetrating radar (GPR) is increasingly being used in transportation projects to monitor the performance of roadways and bridges and to identify buried structures. The objective of this thesis was to evaluate the use of GPR for the identification of bridge scour and to estimate the depth of shallow rock for geotechnical site investigations. The ability to understand and predict scour at bridges is a requirement for safe, economical foundation design and is important for the development of feasible scour monitoring systems. Accurate assessment of the depth to rock is essential for designing and constructing foundations for buildings and transportation infrastructure. …

Flavin-Containing Monooxygenase-3 And 5: Tissue Distribution, Age-Related Expression And Regulation By Endoplasmic Reticulum Stress, Zhen Xu

Open Access Master's Theses

Background Flavin-containing monooxygenases (FMO) constitute a class of oxidative enzymes. FMO3 and FMO5 are two major FMOs that are highly expressed in the liver. The study was performed to determine regulated expression of both enzymes by age, fructose, therapeutic agents and endoplasmic reticulum (ER) stressors. The expression of both enzymes in 33 extrahepatic tissues was determined as well.

Methods The tissue distribution of FMO3 and FMO5 was determined by immunohistochemistry. For age-related expression, livers were collected and divided into 5 age groups: I (< 31 days), II (35-70 days), III (89-119 days), IV (123-198 days), and V (>18 years of age). These samples were analyzed for the expression of FMO3 and FMO5 by …

Circadian Rhythm: A Functional Connection Between Shp And Dec1 Transcription Factor, Marek Matczynski Marczak

Open Access Master's Theses

Circadian rhythms ensure physiological processes to be coordinated with daily changes of the surrounding. Circadian rhythm misalignment has been increasingly recognized to pose health risk for a wide range of diseases, particularly metabolic disorders. The liver maintains metabolic homeostasis and express many circadian genes, such as the genes encoding differentiated embryo chondrocyte-1 (DEC1) and small heterodimer partner (SHP). DEC1 is established to repress transcription through class B E-box elements, and SHP belongs to the superfamily of nuclear receptors and has multiple Ebox elements in its promoter. Importantly, DEC1 and SHP are expressed in an inverse oscillating manner. The present study …

Epidemiology Of Browser-Based Malware, Sindhura Jaladhanki

Open Access Master's Theses

The presence of personal financial data, intellectual property, and classified documents on University computer systems makes them particularly attractive to hackers, but not well prepared for their attacks. The University of Rhode Island (URI) is one of the few institutions collecting network traffic data (NetFlow) for inference and analysis of normal and potentially malicious activity. This research focuses on web-based traffic with client-server architecture and adopts simple probability-based transmission models to explore the vulnerability of the URI web-network to anticipated threats. The fact that the URI firewall captures only traffic data in- and out- of URI necessitates the modeling of …

Assessment Of Activity Of Bacteria In Integrated Fixed Film Activated Sludge, Hannes Behrmann

Open Access Master's Theses

In this study, the feasibility of a manometric batch test method to measure biological activity of Integrated Fixed Film Activated Sludge (IFAS) microbial aerobic and anaerobic communities was investigated. Additionally, the substrate consumption ratio, the N₂O emissions from the biological activity of the different microbial populations and the inhibitory effect of stormwater pollutants on the activity and N₂O production were investigated as well.

The obtained results from the aerobic tests showed qualitative correspondence with trends described in the literature, but differed greatly in quantitative terms (1 to 2 orders of magnitude). The anoxic test did not …

The Physiological Glucagon Receptor In Rat Heart, Kevin Agostinucci

Open Access Master's Theses

The actions of glucagon have been extensively studied for many years. In heart, it is well established that glucagon is capable of causing inotropy. This action is mediated by glucagon binding to a G-protein coupled receptor (GPCR) which activates adenylate cyclase, increasing the intracellular concentrations of cAMP. The studies that were able to show this effect used concentrations of glucagon that were considered to be much higher than what is normally found in blood. A recent report, by Harney and Rodgers (2008), described the actions and signaling mechanisms of physiological concentrations of glucagon (<10^-10 M) on perfused rat hearts. …

Metatranscriptomic Analysis Of Co-Occurring Phytoplankton Species In The Ross Sea Polynya, Sylvia Minjee Kim

Open Access Master's Theses

Primary production (PP) of the Ross Sea Polynya (RSP) contributes a significant proportion of the total PP of the Southern Ocean. As a result, the photosynthetic activities of phytoplankton communities in the RSP play important roles in the overall biochemical cycling of carbon and nutrients and structuring the marine food-web. Environmental change, especially in light and iron regimes, regulates variations in PP and affects the phytoplankton community dynamics. Since individual phytoplankton species have unique nutrient requirements, the limited resources impact these algal taxa in different ways. In this study, we used metatranscriptomic analysis to examine how the algal taxa Fragilariopsis …

Conformational Insights Into Aminobiphenyl-Modified Dna: Implications For Mutation And Repair, Ang Cai

Open Access Dissertations

Cancer is a major public health problem worldwide. An estimated 1.6 million new cases of cancer will be diagnosed in the United States in 2017. Most cancers are assumed to develop from the initiation of chemically induced DNA damages. Chemical carcinogens are genotoxic and they undergo enzymatic activation into reactive electrophilic species to form covalent bonds with the electron-rich DNA that form adducts. Aromatic amines are one of the most examined chemical carcinogens, and once activated, these amines attack the C-8 position of guanine to form C8-dG adducts (ABP [N-(2′-deoxyguanosin-8-yl)-2-aminobiphenyl], AF [N-(2′-deoxyguanosin-8-yl)-2-aminofluorene], and AAF [N-(2′-deoxyguanosin-8-yl)-2 acetylaminofluorene]); these formations result in …

Modeling Gas Budgets In Marginal Sea Ice Zones, Arash Bigdeli

Open Access Dissertations

Biogeochemical gas budgets at high-latitude regions and sea ice zones are a source of uncertainty in climate models. The four main processes that regulate these budgets include advection, ventilation, mixing, and accumulation/release from sea ice. Considering the scarcity of data in sea ice zones, specifically during winter time, the environment is too poorly sampled to constrain these processes through direct measurements; hence we proposed models to systematically investigate these processes. The models proposed in this dissertation consist of regional numerical ice-ocean models, 1D forward and inversion numerical models, and analytical models.

Manuscript I of this dissertation focuses on a 3D …

Bifurcations Of Some Planar Discrete Dynamical Systems With Applications, Toufik Khyat

Open Access Dissertations

The focus of this thesis is on some contemporary problems in the field of difference equations and discrete dynamical systems. The problems that I worked on range global attractivity results to all types of bifurcations for systems of difference equations in the plane.

The major goal was to investigate the impact of nonlinear perturbation and the introduction of quadratic terms on linear fractional difference equations such as the Beverton-Holt as well as the Sigmoid Beverton-Holt Model with delay that describes the growth or decay of single species.

The first Manuscript was on the study of the following equation:

[Mathematical equations …

Novel Methods For Delivering And Promoting The Endosomal Escape Of Nucleic Acid Based Drugs: Chiral Polyamines And Hydrophobic Nanoparticle-Containing Liposomes, Ruchi Verma

Open Access Dissertations

Nucleic acid based drugs such as plasmid DNA (pDNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), micro RNA (miRNA), and both antisense and antigene oligonucleotides, are potentially potent and specific compounds for therapeutic applications. Many major life threatening ailments might be treated using these molecules, and many polynucleotide products are currently in advanced clinical development. However, their successful therapeutic application is hindered due to limited delivery to their site of action in either the cytosol or the nucleus of a cell. Some of the barriers in the path of successful delivery of these biomolecules to their site of action …

Teaching Writing With Play: A Study Of Community-Based Science Education In A National Park, Jamie Remillard

Open Access Dissertations

Teaching Writing with Play: A Study of Community-Based Science Education in a National Park is a rhetorical ethnography designed to bring the lessons of community-based science education and science communication practices to bear on the university writing classroom. I examined how park rangers use engaged, playful methods to educate people about scientific and technical issues that affect coastal communities. Through three years of ethnographic field research and collaborative writing with the National Park Service, I investigated evolving public outreach programs at Fire Island National Seashore (FIIS) in New York during a time when heightened public contention about science-based decision-making created …

Evidence For Environmental And Ecological Selection In A Microbe With No Geographic Limits To Gene Flow, Kerry A. Whittaker, Tatiana A. Rynearson

Graduate School of Oceanography Faculty Publications

The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than …

Aquatic Global Passive Sampling (Aqua-Gaps) Revisited – First Steps Towards A Network Of Networks For Organic Contaminants In The Aquatic Environment, Rainer Lohmann, Derek Muir, Eddy Y. Zeng, Lian-Jun Bao, Ian J. Allan, Kenneth Arinaitwe, Kees Booij, Paul Helm, Sarit Kaserzon, Jochen F. Mueller, Yasukuki Shibata, Foppe Smedes, Manolis Tsapakis, Charles S. Wong, Jing You

Graduate School of Oceanography Faculty Publications

Organic contaminants, in particular persistent organic pollutants (POPs), adversely affect water quality and aquatic food webs across the globe. As of now, there is no globally consistent information available on concentrations of dissolved POPs in water bodies. The advance of passive sampling techniques has made it possible to establish a global monitoring program for these compounds in the waters of the world, which we call the Aquatic Global Passive Sampling (AQUA-GAPS) network. A recent expert meeting discussed the background, motivations, and strategic approaches of AQUA-GAPS, and its implementation as a network of networks for monitoring organic contaminants (e.g., POPs and …

Spatial Distribution, Air-Water Exchange, And Toxicity Of Organic Pollutants Using Passive Samplers, Carrie A. Mcdonough

Open Access Dissertations

Thousands of hydrophobic organic contaminants (HOCs) are present in air and water worldwide, yet we know little about how these chemicals’ concentrations vary spatially and temporally, or what biological effects they have in concert. The first four studies described in this dissertation present data from a sampling campaign in which passive polyethylene samplers (PEs) deployed throughout the lower Great Lakes region (Lake Erie and Lake Ontario) from 2011 to 2014. Results were used to deduce air-water fluxes and analyze spatial trends of the truly gaseous and dissolved fraction of three distinct groups of HOCs: polycyclic aromatic hydrocarbons (PAHs), polycyclic musks …

Anthelmintic Efficacy Of Bioactive Compounds Within Cranberry Vine And Birdsfoot Trefoil, Carly Barone

Open Access Dissertations

With the growth of resistance to commercial dewormers in small ruminant gastrointestinal nematodes (GIN), alternative methods are needed for GIN control. It has been shown that plants containing certain secondary compounds (SC) suppress GIN infection, but there is a lack of knowledge concerning the mechanism behind this anthelmintic activity, as well as a lack of viable alternatives to commercial dewormers in the northeastern United States. Secondary compounds, such as proanthocyanidin (PAC), have complex chemical structures that vary between plant species, while SC concentrations can vary between different varieties of the same species. The relationship between specific SC and anti-parasitic efficacy …

Identity, Awareness, Action: A Study Of White Anti-Racist Faculty Praxis At Two Predominantly White Institutions, David Brian Hayes

Open Access Dissertations

Despite decades of research into the racial construct known as whiteness (e.g., Roediger, 1991; Frankenberg, 1993; Leonardo, 2002), as well as on white privilege and racism within predominantly white institutions (PWIs) (e.g., Harper & Hurtado, 2007), little research exists exploring the work of white faculty who confront racism in teaching, research, or service. In this study, I applied a Critical White Studies (Delgado & Stefancic, 1997) analytical frame to a Constructivist Grounded Theory (Charmaz, 2006) study of white anti-racist faculty in two predominantly white institutions within a state higher education system. The study used interviews with 11 white faculty members …

Biotransformation And Pharmacokinetic Evaluation Of Pf-5190457, A Novel Drug Candidate For Alcoholism, Sravani Adusumalli

Open Access Dissertations

Alcohol use disorder is a chronic condition characterized by an inability to control alcohol intake. Recent research has shown that appetite-regulating hormones, ghrelin, and leptin, may play a role in alcohol craving. In addition, it is known that food and alcohol craving have overlapping receptors in the brain reward system. Ghrelin, a naturally occurring hormone in the human body, is produced mainly by ghrelinergic cells of the gastric mucosa. Once the hormone crosses the blood-brain barrier, it binds to growth hormone secretagogue receptor (ghrelin receptor) in the hypothalamus and stimulates the appetite and food intake. Leptin, a hormone produced from …

Atlantic Mackerel (Scomber Scombrus) Population And Habitat Trends In The Northwest Atlantic, Michael Conor Mcmanus

Open Access Dissertations

Atlantic mackerel (Scomber scombrus) has long been a significant marine resource in the northwest Atlantic, supporting commercial and recreational fisheries over two centuries. As a small pelagic fish feeding on planktonic organisms, mackerel serve a critical role in the marine food web as prey for higher trophic level species, including large predatory fish, marine mammals, and sea birds. Significant harvest pressure and recent low abundances and landings have led to questioning whether such removals have jeopardized the fishery and ecosystem’s sustainability. Further complicating management, mackerel populations throughout the North Atlantic have been significantly influenced by climate change, represented …

Towards Fog-Driven Iot Ehealth: Promises And Challenges Of Iot In Medicine And Healthcare, Bahar Farahani, Farshad Firouzi, Victor Chang, Mustafa Badaroglu, Nicholas Constant, Kunal Mankodiya

Electrical, Computer, and Biomedical Engineering Faculty Publications

Internet of Things (IoT) offers a seamless platform to connect people and objects to one another for enriching and making our lives easier. This vision carries us from compute-based centralized schemes to a more distributed environment offering a vast amount of applications such as smart wearables, smart home, smart mobility, and smart cities. In this paper we discuss applicability of IoT in healthcare and medicine by presenting a holistic architecture of IoT eHealth ecosystem. Healthcare is becoming increasingly difficult to manage due to insufficient and less effective healthcare services to meet the increasing demands of rising aging population with chronic …

Magicsox: An E-Textile Iot System To Quantify Gait Abnormalities, Mohammadreza Abtahi, Joshua V. Gyllinsky, Brandon Paesang, Scott Barlow, Matthew Constant, Nicholas Gomes, Oliver Tully, Susan E. D'Andrea, Kunal Mankodiya

Electrical, Computer, and Biomedical Engineering Faculty Publications

The global society is increasingly facing the challenges that reduce mobility, quality of life, and independence. Gait disorders are often both a result of, and predictor of further issues, tied to the 15 million stroke patients annually worldwide. These individuals face a number of gait abnormalities including drop foot that is a pathological condition, limiting patients' ability to lift the foot from the ground during the swing phase of walking. In this research work, we introduce a novel smart textile system, MagicSox that is woven with multiple sensors distributed over the surface of the foot. The overarching goal of MagicSox …

Detection Of Diffuse Seafloor Venting Using A Structured Light Laser Sensor: 2. Evaluation Of Detection Sensitivity And Limitations, Clara Smart, Chris Roman

Ocean Engineering Faculty Publications

Algorithms to detect diffuse hydrothermal vent fluids using the structured light laser sensor have proven to be successful. However, potential limitations due to survey parameters, including altitude and vehicle heading, have not been explored and are the focus of this study. Data from 12 surveys conducted over a single hydrothermal vent at three different altitudes (2.7 m, 4.2 m, and 6.2 m) and four different headings are analyzed. Increasing survey altitude decreases the resolution and intensity of the imaged laser line; therefore, range-dependent processing considerations to maintain detection sensitivity are presented. Analysis of these surveys suggests minimal degradation of vent …

Detection Of Diffuse Seafloor Venting Using A Structured Light Laser Sensor: 1. Development Of A Classification Based Detection Method, Clara Smart, Chris Roman, Steven Carey

Ocean Engineering Faculty Publications

Systematic and remote detection of diffuse hydrothermal venting is complex yet necessary to establish a comprehensive understanding the distribution, contribution, and context of fluid flow within hydrothermal systems. Diffuse flow is characterized by both low temperature and low flow rates and cannot be consistently distinguished during extensive systematic surveys using current vehicle-mounted visual, acoustic, or environmental sensors. The remotely operated vehicle-mounted structured light laser sensor is sensitive to fluid density anomalies and seafloor characteristics. Presented advancements to the detection algorithm include the development and implementation of intensity normalization routines and a support vector machine classification algorithm. The resulting comprehensive maps …

Visual Detection And Tracking Methods For E. Superba (Antarctic Krill), Regina R. Yopak

Open Access Master's Theses

Antarctic krill are a keystone species of the Southern Ocean. They have been well documented over large spatial scales but generally not quantfiably at the scale of single individuals in the open water column. It is important to study how individuals behave in their natural environment in order to further understand how they interact within dense krill aggregations. Using a pair of calibrated grayscale stereo cameras mounted on a towed instrument sled, krill were imaged in situ at 10Hz in the bays along the western Antarctic Peninsula during austral winter 2013. Krill were identified and tracked through the images …

Global Dynamics And Boundedness Of Discrete Population Models, David T. Mcardle

Open Access Dissertations

Discrete dynamical systems are widely used in biological and entomological applications to model interacting populations. The manuscripts included in this thesis present global dynamic results for three different population models. Manuscript 1 presents basic concepts and definitions for general systems of difference equations in order to lay the theoretical foundation for the remaining sections.

Manuscript 2 discusses competitive systems of difference equations with the form

[Mathematical equations can not be displayed here, refer to PDF]

where the parameters b₁, b₂ are positive real numbers and α₁, α₂, c₁, c₂ and …

Stress, Coping, Emotional Intelligence, Emotional Health And Cortisol In Premature Infants, At Age 23, Joyce Ellen Hickey

Open Access Dissertations

Little is known about the psychobiological processes of adults, at age 23 who were born prematurely. Compared to infants born at term, premature infants face additional obstacles of immature body systems, more neonatal stress and are at risk for developmental delay and possible parental overprotective patterns. The Developmental Origins of Health and Disease theory asserts that early prenatal and neonatal stress disturbs hypothalamic-pituitary-adrenal (HPA) axis function, which in the long run, affects later health and behavior. The purpose of this secondary analysis is to examine neonatal stress of prematurity on coping, emotional intelligence, physiological responses, developmental milestones and emotional health …

Investigating And Comparing The Mechanisms Of Behavior Change To Prevent Smoking Acquisition In Middle School Students, Allie W. Scott

Open Access Dissertations

The disease consequences of smoking such as high blood pressure, heart disease, and lung cancer, are well documented (U.S. Department of Health and Human Services, 1964, 1989, and 2010). One clear finding from epidemiological studies is that the early uptake of smoking during adolescence can lead to addiction in adulthood. A recent study by the Centers for Disease Control (CDC) found nearly 9 out of 10 adult cigarette smokers tried their first cigarette as minors and 99% tried smoking by age 26 (CDC, 2017). To mitigate smoking incidence and reduce the harm caused by smoking, a number of primary prevention …

Ces Involved Inhibition And Regulation, Yuanjun Shen

Open Access Dissertations

Sofosbuvir has been widely adopted for Hepatitis C Virus (HCV) infection therapies through its effect as HCV non-structured protein 5B (NS5B) inhibitor, which is essential for HCV particle assembly. Sofosbuvir, as a prodrug, is activated through the hydrolysis by carboxylesterase 1 (CES1) and is reported to have limited interactions with cytochrome P450 enzymes (CYP450) and p-glycoprotein, which results in less clinical drug-drug interactions. However, reports showed fatal or nephrotoxic cases that utilized a co-therapy of Sofosbuvir with an anti-Human Immunodeficiency virus (HIV) agent, tenofovir disoproxil fumarate (TDF). This study was designed to give one explanation for these case reports. Interestingly, …

Genetic, Demographic And Ecological Factors Contributing To The Evolution Of Anolis Lizard Populations, Johanna E. Wegener

Open Access Dissertations

Geographic and environmental factors can be catalysts of evolutionary processes and central drivers of genetic and phenotypic differentiation. Characteristic patterns of genetic and phenotypic variation elucidate whether predominately adaptive or non-adaptive processes are involved in shaping variation among populations. Such genetic and phenotypic signatures can provide insight in how specific extrinsic factors relate to adaptive and non-adaptive processes. This dissertation aims to investigate whether and how disturbance events, intraspecific competition and secondary contact after a species introduction contribute to genetic and phenotypic differentiation among populations of Anolis lizard.

In chapter 1, I tested whether patterns of genetic diversity and differentiation …