Digital Commons Network^™

A Bayesian Zero-Inflated Generalized Growth Mixture Model For Adolescent Health Risk Behaviors, Si Yang

Open Access Master's Theses

Using longitudinal data to model change patterns of behaviors is a major interest in the field of developmental psychology and behavioral science. As het- erogeneity often exists in the population, researchers are more and more interested in a topological representation of the growth trajectories. That is, to identify distinct trajectories depending on their individual characteristics. Latent class models(LCM) are flexible methods of modeling unobserved heterogeneity in a population and it has been recently extended to analyzing longitudinal data. Latent class growth models(LCGM) assume individuals come from a finite number of latent classes and individuals share the same growth trajectory within …

Winter Vertical Distributions Of Antarctic Krill As Seen Through A New Stereo Camera System, Mary Kane

Open Access Master's Theses

A new stereo camera system, encompassing a Sonde, acoustic Doppler current profiler (ADCP), and high-resolution-imaging cameras, was developed to improve our understanding of in situ Antarctic krill behaviors and distribution. Krill were observed on 18 deployments in 3 bays in the Western Antarctic Peninsula from May-June 2013. Observation conditions varied, including time of day, clear to stormy surface conditions, temperatures (-1.2ºC to 0.8ºC) and salinities (33.5ppt to 34.8ppt). Krill were observed in 61% of profiles. Krill distributions were found in two distinct profiles with regards to where highest abundances occurred: Type I profiles had maxima in the middle of the …

Human Tau Gene Expression In A Transgenic Animal Model Altered By Developmental Pb Exposure, Miriam Erline Dash

Open Access Master's Theses

Alzheimer’s Disease (AD), the sixth leading cause of death in the United States, is a neurodegenerative disease characterized by a decline in memory and cognitive function. Demographics show that more than 90% of patients are first diagnosed with AD after the age of 65, classified as Late Onset AD (LOAD). The remaining 10% are said to have Early Onset AD. Research has shown that no mutation is linked to LOAD. Thus we hypothesize that environmental and/or epigenetic factors may be playing a major role in LOAD. AD traits coincide with the presence of two pathological hallmarks found in the brain: …

Estimating Daily Primary Production And Nighttime Respiration In Estuaries By An In Situ Carbon Method, Catherine M. Coupland

Open Access Master's Theses

A Dawn Dusk Dawn Carbon method was developed to estimate daily primary productivity and respiration in Narragansett Bay at 9 Narragansett Bay Fixed Site Monitoring Network stations. The method utilizes YSI temperature, salinity, and pH measurements and measured alkalinity values. The method was compared to a previously verified Dawn Dusk Dawn Oxygen method for Narragansett Bay developed by Smith (2011). The methods compared well with correlations coefficients between 0.69 - 0.96 for all four categories (surface production, surface respiration, bottom production, and bottom respiration) and both summers. In all categories, 2014 comparisons were more highly correlated than 2013.

Metabolic rate …

Emerging Persistent Organic Pollutants (Pops) In The Western South Atlantic And Antarctic Biota, Erin Markham

Open Access Master's Theses

Persistent organic pollutants (POPs) are largely synthetically produced chemicals that are known to persist in the environment, bioaccumulate, have the potential to be transported long distances, and cause adverse effects. There are legacy POPs that have been around for decades and have either been banned or strictly regulated, but are still found in the environment; and there are emerging POPs that are either not yet or are very newly regulated. This research focuses on contributions to the global dataset of emerging POPs by investigating hydrophilic perfluoroalkyl substances (PFAS) in surface waters and at depth of the Western South Atlantic; as …

Investigating The Intraspecific Effect Of Cell Concentration In Mediating Oxyrrhis Marina Swimming Behaviors, Michael Warren Fong

Open Access Master's Theses

Heterotrophic protists are known to respond to a multitude of abiotic and biotic stimuli which confers a strong selective advantage in marine environments that are frequently dilute and heterogeneously distributed. In this laboratory study, we investigated the role of intraspecific signals in mediating Oxyrrhis marina swimming behavior that could be utilized to enhance dispersive behaviors and reduce competition between intraspecific predators. Using video and image analysis, three-dimensional movement behaviors of O. marina (on scales of micrometers and seconds) were simultaneously quantified with population-scale vertical distributions (on scales of centimeters and hours) and used in dispersal and encounter rate estimates. Three …

Training And Source Code Generation For Artificial Neural Networks, Brandon Winrich

Open Access Master's Theses

he ideas and technology behind artificial neural networks have advanced considerably since their introduction in 1943 by Warren McCulloch and Walter Pitts. However, the complexity of large networks means that it may not be computationally feasible to retrain a network during the execution of another program, or to store a network in such a form that it can be traversed node by node. The purpose of this project is to design and implement a program that would train an artificial neural network and export source code for it so that the network may be used in other projects.

After discussing …

"A Great And Terrible Event": Historical Evidence For The 551 Ce Tsunami At Akko, Israel, Emma Heidtman

Open Access Master's Theses

In 2001, the Old City of Akko in northern Israel was declared a UNESCO World Heritage site. This designation was based on the Old City's well-preserved Ottoman and Islamic-era town and the partly subterranean ruins of the once-thriving Crusader port. Five years of excavation, from 2009 to 2014, have uncovered more of Akko's history as a strategic naval outpost for several iterations of Mediterranean Sea power, particularly during the Hellenistic Age. However, evidence for Akko's harbor operations during the Byzantine period is still being uncovered. In light of recent discoveries in geoarchaeology, scientists have learned that part of Akko's Byzantine …

Synthesis Of 2-Amino-Α-Carboline And Analogues Relevant For Structural Investigations Of The Corresponding Dna Adducts, Matthew S. Blake

Open Access Master's Theses

In rational drug design, the most effective targets are identified when a mechanism-based understanding of a disease state’s proliferation and persistence is available. 2-amino-α-carboline (2-AαC) is a heterocyclic aromatic amine (HAA), which upon metabolic activation in vivo, can covalently bind to the C8-position of guanine. This modification elicits a response from the Nucleotide Excision Repair (NER) system but, if left unrepaired, may result in mutations. The metabolites of 2-AαC are significantly more reactive towards adduct formation than those of 4-aminobiphenyl (4-ABP), a confirmed human bladder carcinogen. Furthermore, 2-AαC is found in cigarette smoke at concentrations 1000 times greater than …

The Effects Of Environmental Education On The Public's Attitudes And Level Of Policy Support For Habitat Restoration In Narragansett Bay, Castine Elizabeth Audette

Open Access Master's Theses

This research aims to address how to increase support and understanding for coastal and marine policy as well as coastal habitat restoration in Narragansett Bay, Rhode Island. More specifically, the objective is to determine both the influences of environmental education on public attitudes and how environmental education influences the public's support for habitat restoration and protection policies. From this research one can discern whether environmental education plays a significant role in attitude formation, which can prove to be important for public support of policy. Research was conducted at and near an environmental education facility, the Save the Bay Aquarium in …

Functional Site Based Protein Structure Analysis With Self-Organizing Maps, Seonjoo Lim

Open Access Master's Theses

The exponential growth of proteome databases has increased the demand for methodologies that can reveal the structural relationships between proteins. In general, large protein families need to be approached on several different levels in order to be fully understood. In such families, key characteristics and relationships are hidden under their sophisticated structures. While similarities in the primary sequences of two proteins give basic clues about their relationship, three-dimensional structural information provides crucial details needed for determining protein functionality.

As such, powerful and efficient computational analytic methods are becoming all the more essential. In the case of proteins, functionalities are most …

Epidemiology Of Puffy Snout Syndrome In Tuna, Taylor M. Voorhees

Open Access Master's Theses

The domestication of tuna species has proven to be one of the most challenging endeavours in aquaculture. Among the issues yet unresolved is the occurrence of ‘puffy snout syndrome,’ a condition in which tumor-like growths form on the head. Ultimately, vision and feeding are impaired and long-term afflictions typically result in mortality. Though few mentions of puffy snout exist in the literature, evidence suggests that it is not uncommon among facilities that hold tunas in captivity. The specific aims of this study were to: a) describe pathological features of puffy snout, and b) investigate its etiology through the evaluation of …

Understanding The Barrier And Facilitators Of Lifestyle Intervention Programs For Preventing Diabetes In High Risk Hispanic Adults, Lisa Adorno Dimaria

Open Access Dissertations

Since the Diabetes Prevention Program Research Group (2002) concluded that type 2 diabetes can be prevented or delayed in pre-diabetic individuals, translation of the study's intensive lifestyle intervention has been a research priority. Translational research conducted with the high risk Hispanic population is in its infancy. In general, the needs of this population have been neglected in the development and refinement of interventions to prevent T2D. This qualitative study explored intervention components and the perceived facilitators and barriers to making and sustaining dietary and physical activity behavior changes within the context of a lifestyle intervention program designed for a high …

A Numerical Study Of The Circulation, Ecology And Biogeochemistry On The Southern New England Shelf, Shuwen Zhang

Open Access Dissertations

This Ph.D. dissertation presents a process-oriented study with two primary objectives: 1) to obtain a physical understanding of the impacts of local and remote forcing, including basin-scale natural climate variability, on the interannual variability of along-shelf transport and water properties of the Middle Atlantic Bight (Chapter 1); 2) to explore the impacts of physical processes on the seasonal variation of phytoplankton biomass in Rhode Island coastal waters (Chapter 2). To achieve the two objectives, we apply a numerical modeling approach employed by the Regional Ocean Modeling System (ROMS) together with substantive analyses of both in-situ and remote observations.

Chapter 1 …

Regioselective Carbon-Nitrogen Bond Formation Via Oxidative Transition Metal Catalysis, Louis Marchetti

Open Access Dissertations

The synthesis of carbon-nitrogen (C-N) bonds is an area of research that has garnered significant interest due to the ubiquity of C-N bonds in pharmaceuticals and natural products. Various methods exist for forming C-N bonds, most recognizably Buchwald-Hartwig amination, but these reactions typically require functionalization of either the C-H or N-H bond resulting in the formation of harmful byproducts. As a result, the need to explore alternative means for synthesizing C-N bonds merits consideration. An alternative means for achieving C-N bond formation lies in the oxidative cross coupling of carbon-hydrogen (C-H) and nitrogen-hydrogen (N-H) bonds. While this approach eliminates the …

Bridging The Soft-Skill Gap From Education To Employment Through Internships, Kim Stack Washor

Open Access Dissertations

Employers express a growing concern that recent college graduates do not possess the necessary soft-skills to transition into entry level positions seamlessly. Educators are asked by employers and policy makers to provide instruction which would develop student skills in both the “hard” (academic and technical) and “soft” (personality traits and habits) skills required to be workplace-ready. The research study was designed to understand the degree to which internships enhance student soft-skill development, specifically in the areas of communication, teamwork, initiative, and, analytical thinking. Researcher-designed pre-post retrospective surveys were administered to students and one to corresponding supervisors to measure change in …

Development Of New Tools For Study Of Tumor Microenvironment, Michael D. Anderson

Open Access Dissertations

Solid tumors have a microenvironment that is inherently acidic and hypoxic. Hypoxia is caused by leaky blood vessels and large diffusion distances from cells to them. It is heterogeneous throughout the tumor and while all solid tumors are hypoxic to a degree, it is difficult to predict invasiveness based on it. However, acidity is a near ubiquitous characteristic of tumors with more aggressive tumors producing greater acidity. It is important to measure pH in diseased tissue with accuracy and precision, since acidity is associated with the development of various pathological states including tumors. In this work we focus on the …

Examining Health Professional Students’ Attitudes On Interprofessional Education, Suzanne Carr

Open Access Dissertations

There is a growing need for healthcare teams to effectively collaborate and communicate to improve patient outcomes. The need to improve patient care has been well established and cited by the Institute of Medicine’s (IOM) Committee on Quality Health Care in America landmark report, To Err Is Human: Building a Safer Health System (IOM, 1999; Kohn, Corrigan, & Donaldson, 2000). Health educational programs are known to be a gateway to changing behaviors of health professionals to impact practice and direct patient care. Interprofessional Education (IPE) has been identified as a viable mechanism to increase the collaboration and communication of health …

Evaluation And Management Implications Of Uncertainty In A Multispecies Size‐Structured Model Of Population And Community Responses To Fishing, Robert B. Thorpe, Will J. F. Le Quesne, Fay Luxford, Jeremy S. Collie, Simon Jennings

Graduate School of Oceanography Faculty Publications

1. Implementation of an ecosystem approach to fisheries requires advice on trade‐offs among fished species and between fisheries yields and biodiversity or food web properties. However, the lack of explicit representation, analysis and consideration of uncertainty in most multispecies models has limited their application in analyses that could support management advice.

2. We assessed the consequences of parameter uncertainty by developing 78 125 multispecies size‐structured fish community models, with all combinations of parameters drawn from ranges that spanned parameter values estimated from data and literature. This unfiltered ensemble was reduced to 188 plausible models, the filtered ensemble (FE), by screening …

Automated Essay Evaluation And The Computational Paradigm: Machine Scoring Enters The Classroom, Catherine M. Barrett

Open Access Dissertations

Grading papers is a "tedious, repetitive, and time-consuming" undertaking, one that invites the sort of sympathies one might receive upon the "death of a pet' (Baker, 2014, p. 36). Perhaps, though, the only thing more distasteful for an English professor than having to grade hundreds of essays each semester is having to hand the job over to the likes of a mindless software program. Automated Essay Evaluation (AEE), the process of scoring essays by computer, was developed in the 1960s but has mostly aroused suspicion and derogation from the composition community.

The parable of the blindfolded villagers describing the same …

Factor Graphs And Submap Simultaneous Localization And Mapping For Microbathymetry, James Ian Vaughn

Open Access Dissertations

The utility of high-resolution bathymetric surveys important to many problems in oceanography is often limited by the poor navigation options available to Unmanned Underwater Vehicles. This thesis presents a novel method to integrate conventional dead-reckoning navigation with recent advances in factor graph Simultaneous Localization and Mapping (SLAM) algorithms. Dead-reckoning is represented in the factor graph as a new type of factor using a linearized state transition model derived from the Extended Kalman Filter commonly used for dead reckoning. The new factor graph submap-SLAM is faster and more scalable than prior methods and is shown to properly represent navigation uncertainty. This …

Phonosys: Mobile Phonocardiography Diagnostic System For Newborns, Amir Mohammad Amiri, Giuliano Armano, Amir Mohammad Rahmani, Kunal Mankodiya

Electrical, Computer, and Biomedical Engineering Faculty Publications

Heart murmurs have been found to be a life threatening condition for the newborns who are born with cardiac abnormalities. The first sign of pathological changes of heart valves appears in phonocardiogram which contains very useful information about cardiovascular system. It is a challenging venture to distinguish pathological murmurs from innocent ones. In this paper we have developed a diagnostic algorithm called PhonoSys to analyze PCG using random forest. PhonoSys algorithm will run on mobile devices for remote PCG analysis. We recorded PCG signals from 120 newborns who are either healthy or with cardiac abnormalities. Eventually, in this study, 97.6% …

Modeling Onsite Wastewater Treatment System Contaminants In Current And Climate Changing Conditions, Ivan Morales Parra

Open Access Dissertations

The use of onsite wastewater treatment system (OWTS) is a common practice in the U.S., especially in rural areas where the access to centralized wastewater treatment systems is limited. Onsite wastewater treatment systems include a soil treatment area or drainfield where contaminants are removed or attenuated. Ineffective OWTS are a source of microbial pathogens (bacteria and viruses), biological oxygen demand (BOD) and nutrients, which are among the major causes of contamination and water quality impairments in surface water in the U.S. The main objective of this research was to model the different chemical, physical processes, and removal mechanisms that influence …

Casimir Effect Modified Surface Energy Of A Nanocavity In Homogeneous Media, Yi Zheng, Arvind Narayanaswamy

Mechanical, Industrial & Systems Engineering Faculty Publications

We determine the regularized van der Waals contribution to pressure within a spherical cavity of vapor in a homogeneous, isotropic, infinite medium. The spherical Hamaker function, , has been defined, for the first time, in contrast to the conventional Hamaker function for planar surfaces, . For the materials under consideration, the pressure inside the cavity varies as , where a is the radius of the cavity. For radii below a transition radius, the surface energy (or surface tension) becomes size dependent and could have important implications for homogeneous nucleation of nanosized bubbles in liquids, as well as cavitation of bubbles.

Chemical Investigation Of Candidate Probiotics In Aquaculture And Formulation Of A Probiotic Agent For Oyster Larviculure, Christine Anh Dao

Open Access Dissertations

Aquaculture is a multi-billion dollar industry worldwide. The United States is a significant consumer to both fresh and marine aquaculture products. Aquaculture sales in Rhode Island have dramatically increased in the last 20 years. In Rhode Island nearly 4.3 million oysters were produced via aquaculture in 2012. Currently, hatcheries and nurseries in the United States produce large amounts of a variety of species of oysters, clams and scallops. Oysters are filter feeders and are exposed to many microbes in the hatchery. Infectious diseases from bacterial pathogens in the hatcheries can have serious impacts on production. Vibrio species are often responsible …

Predatory Behavior And Physiological Response Of Chinese Mantids To Toxic And Non-Toxic Lepidopteran Prey, Jamie L. Rafter

Open Access Dissertations

Prey have evolved a number of defenses against predation, and predators have developed means of countering these protective measures. Monarch caterpillars, Danaus plexippus, for example, feed on milkweed plants in the genus Asclepias and sequester cardenolides as an anti-predator defense. However, some predators are able to consume this otherwise unpalatable prey. The observation of a Chinese mantid, Tenodera sinensis, consuming the body tissue of a monarch caterpillar while ‘gutting’ the prey (i.e., removing the gut and associated internal organs) without any apparent ill-effects prompted this research. In a series of behavioral trials we explored how adult T. sinensis …

An Investigation Of The Fisheries Ecosystem Dynamics In Rhode Island's Nearshore Waters, Anna Malek

Open Access Dissertations

This research was developed in response to recent interest in offshore wind energy development and the ongoing need for ecosystem-based spatial management planning in Rhode Island’s nearshore waters. Despite heavy use and close proximity to a number of marine science institutions, Rhode Island and Block Island Sounds have been neglected in terms of scientific research, resulting in a poor understanding of the fisheries ecosystem in this area. This research aimed to address this knowledge gap by assessing the biogeography, trophic dynamics and habitat associations of the fish and invertebrate communities in this region. Specifically, the goals of this research were …

Goal Representation Adaptive Dynamic Programming For Machine Intelligence, Zhen Ni

Open Access Dissertations

This dissertation is focused on a general purpose new framework for machine intelligence based on adaptive dynamic programming (ADP) design. This research is significantly important for developing self-adaptive intelligent system that is highly robust and fault-tolerant to uncertain and unstructured environments. Generally, there are two key components toward building truly self-adaptive systems: fundamental understanding of brain intelligence and complex engineering designs. This dissertation will focus on general purpose computational intelligence methodologies from a biological inspired perspective, and develop a new self-learning machine intelligent system online over time. Furthermore, this new approach will also be explored on wide critical engineering applications. …

The Stigma Of Obesity: Examining The Relationship Between Bmi And The Treatment Of Pain In Surgery Patients, Dennis H. Sewchuk Jr.

Open Access Dissertations

There is a growing epidemic of obesity in the United States and a corresponding increase in the number of morbidly obese patients receiving healthcare. Despite the increasing focus and research on obesity over the years, the prevalence of obesity in the United States has continued to worsen. A stigma against obesity exists in the general public including among healthcare professionals. Attitudes and bias of healthcare professionals against obesity can negatively affect judgment and choices related to the enactment of care, affecting both the quality of healthcare delivered and patient outcomes. Studies have shown that stigmatization against groups of patients such …

Role Of Nuclear Factor E2 Related Factor 2 (Nrf2) In Environmental Chemical Induced Steatosis And Adipogenesis, Prajakta Shimpi

Open Access Dissertations

Prevalence of non-alcoholic fatty liver disease (NAFLD) and obesity both in the young and adult population is increasing at an alarming rate globally. Along with traditional risk factors, such as diet and sedentary life style, exposure of environmental chemicals is suspected to be a risk factor for metabolic disruption. Moreover, the ‘fetal basis of adult disease’ hypothesis implicates that early life exposure to environmental chemicals is more impactful in causing lipid homeostasis disturbances than exposure in maturity. Nuclear factor E2 related factor 2 (Nrf2) is a cytoprotective transcription factor known to combat oxidative stress. The contribution of Nrf2 to other …