Digital Commons Network^™

Hierarchical Multi-Label Classification: Going Beyond Generalization Trees, Peerapon Vateekul

Open Access Dissertations

Traditional approach to automated classification assumes that each object should be assigned to only one out of two or more classes. However, some real-world applications digress from this generic scenario in two important ways. First, each example can belong to several classes simultaneously (multi-label classification). Second, the classes can be hierarchically ordered in the sense that some are more specific versions of others (hierarchical classification). Seeking to address both of these issues, the presented work deals with “hierarchical multi-label classification”. In non-hierarchical multi-label classification, literature survey indicates that good performance is achieved when a Support Vector Machine (SVM) is used …

Molecular Ecology And Evolution Of Reef Corals And Their Algal Symbionts, Herman H. Wirshing

Open Access Dissertations

Molecular approaches to the fields of taxonomy, systematics and population genetics are imperative in order to better understand the evolutionary history and ecological interactions among organisms. This dissertation utilized genetic techniques to address evolutionary and ecological questions in corals and octocorals at different levels of resolution, from ancient phylogenetic relationships to the relatively recent population dynamics of individuals within species in both the coral host and its algal endosymbionts (genus Symbiodinium). Collectively, this work: (1) demonstrates a novel use of genes involved in the calcification process to test hypotheses of morphological convergence in scleractinian corals; (2) helps reconcile contrasting morphological …

The Comparison Of Body Composition, Eating Habits, Exercise Habits, And High Risk Behaviors In A Tri-Racial Group Of Division I Collegiate Female Athletes, Yi-Tzu Kuo

Open Access Dissertations

Given the increased participation in competitive sports and athletics among women, there is a greater number of issues related to body weight concerns, eating and exercise habits, as well as high risk behaviors, which are particularly evident in female athletes. There are also many more minority women participating in competitive sports, presenting a greater need to examine these issues among a more diverse population of competitive female athletes. Hispanic American (HA) athletes in particular, represent a growing segment of the athletic population that is in need of more information regarding their exercise-related behaviors. The aim of this study was to …

Astroglial Nf-Κb: A Critical Pathway In Retinal Ischemia Reperfusion Injury, David J. Barakat

Open Access Dissertations

Astrocytes are a critical cell type of the retina which support ganglion cell axons and maintain the blood retinal barrier. Upon ischemia reperfusion (IR) injury, astrocytes undergo rapid activation, which has been characterized by hypertrophy, proliferation and global changes in gene expression. The failure of these cells to support neurons after ischemia is thought to promote secondary injury response and retinal ganglion cell apoptosis. Therefore, promoting survival and proper function of astrocytes is critical for protecting the inner retina to ischemic injury. The activation of astrocytes and changes in gene expression in retinal IR injury has been linked to the …

Molecular Pathways Of Cell Death And Regulation By Jnk-1 And Bnip3 During Ischemia-Reperfusion Injury, Weiwen Wang

Open Access Dissertations

The c-Jun N-terminal kinase-1 (JNK-1) is rapidly induced by reactive oxygen species generated when the heart is reperfused during acute myocardial infarction (AMI). However, the role of JNK-1 activation in reperfusion injury has remained controversial because different groups have reported both protective and injurious consequences. My thesis work has resolved much of this controversy. I have demonstrated that JNK-1 switches from a pro-survival role when the period of ischemia is brief to become injurious when the period of ischemia is extended. My results further show that this switch in function is driven by dynamic changes in the metabolic state of …

Modulation Of Peripheral Taste Function By Glial-Like Taste Cells, Michael S. Sinclair

Open Access Dissertations

Taste is detected by cells of taste buds in the oral cavity. Mammalian taste buds contain three types of cells: receptor, presynaptic, and glial-like. Of these three, glial-like cells are the least studied. Their only known function is that they clear neurotransmitters from the extracellular space. The present work describes two previously undocumented properties of glial-like cells. First, Oxytocin receptor (OXTR) mRNA was detected by RT-PCR in taste tissue of mice. In the taste buds of Oxtr-YFP knockin mice, YFP was seen in glial-like taste cells and other cells immediately outside the taste bud, but no other cells in oral …

The Molecular Machinery Critical To The Degradation Of Cellular Rna, Brad J. Schmier

Open Access Dissertations

Exoribonucleases are indispensable for cellular RNA metabolism. RNA processing, end-turnover, and degradation all require the concerted action of exoribonucleases. In this thesis, two families of exoribonucleases that act in the final steps of RNA decay pathways are explored. The first of these is the RNR superfamily of processive 3’→5’ RNases with major roles in both mRNA and stable RNA degradation. The initial focus of this work is the structural and enzymatic characterization of an unusual RNR family enzyme from the radiation-resistant bacterium Deinococcus radiodurans. This enzyme is demonstrated biochemically to be an RNase II-type enzyme (DrII), based on its sensitivity …

Molecular Mechanisms Of Ampk- And Akt-Dependent Survival Of Glucose-Starved Cardiac Myocytes, Ines Chopra

Open Access Dissertations

Muscle may experience hypoglycemia during ischemia or insulin infusion. During severe hypoglycemia energy production is blocked and an increase in AMP:ATP activates the energy sensor and putative insulin-sensitizer AMP-dependent protein kinase (AMPK). AMPK promotes energy conservation and survival by shutting down anabolism and activating catabolic pathways. We investigated the molecular mechanism of a unique glucose stress defense pathway involving AMPK-dependent, insulin-independent activation of the insulin signaling pathway. Results from my work showed that the central insulin signaling pathway is rapidly activated when cardiac and skeletal myocytes are subjected to conditions of glucose starvation. The effect occurred independently of insulin receptor …

Engineering Of Nanoparticles For Luminescence Switching, Stefania Impellizzeri

Open Access Dissertations

Fluorescence microscopy offers the opportunity to image biological samples noninvasively in real time and has become an essential analytical tool in the biomedical laboratory. Nonetheless, the phenomenon of diffraction imposes stringent limitations on the resolving power of conventional microscopes, preventing the spatial resolution of fluorescent species co-localized within areas of nanoscaled dimensions. Time, however, can be exploited to distinguish fluorophores within the same subdiffraction area, if their fluorescence can be switched independently, and reconstruct sequentially their spatial distribution. In this context, photolytic reactions and photochromic transformations can be invoked to switch fluorescence under optical control. Fluorescent units, such as inorganic …

Insights Into The Roles Of Mss51 In The Biogenesis Of Mitochondrial Cox1, Iliana C. Soto

Open Access Dissertations

In eukaryotic cells, energy is produced by the coordinated action of the mitochondrial respiratory chain (MRC) and the oxidative phosphorylation system (OXPHOS). Cytochrome c oxidase (COX) is the fourth enzyme of the MRC. COX catalytic activity is mediated by prosthetic groups located in subunits 1 (Cox1) and 2. More than twenty nuclear encoded factors are required for the assembly of the functional enzyme. Cox1 is the center of a regulatory mechanism in which its protein levels depend on the availability of its assembly partners. A key element in the regulatory pathway is the nuclear encoded factor Mss51, a protein essential …

The Role Of Mitochondrial Dysfunction In Neurodegenerative Proteinopathies And Aging., Alejandro Ocampo

Open Access Dissertations

Age-related neurodegenerative proteinophaties, including polyglutamine (polyQ) diseases such as Huntington’s disease, are a group of disorders in which a single protein or a set of proteins misfold and aggregate resulting in a progressive and selective loss of anatomically or physiologically related neuronal systems. Despite evidence showing a clear relationship between mitochondrial dysfunction, aging and neurodegenerative proteinophaties, the extent of the mitochondrial respiratory chain deficits, the involvement of mitochondrial dysfunction and the mechanisms responsible for these processes are largely unknown. Using yeast models of cellular aging and polyQ disorders we show that mitochondrial dysfunction is an important contributor to the process …

Hormonal And Pheromonal Effects Of 20-Hydroxyecdysone In The American Lobster, Homarus Americanus, Michael W. Sipala

Open Access Dissertations

20-hydroxyecdysone (20E), the active principle of the molting hormone in the American lobster has significant effects on the animals’ agonistic behavior and has been shown to influence the outcome of agonistic interactions. Animals injected with 20E are significantly more aggressive than saline-injected control animals, and premolt animals, which have high circulating levels of 20E in their hemolymph, are more successful than intermolt animals in agonistic interactions. 20E has been shown to act as an internal modulator of neuromuscular physiology: there is an increase in the amplitude of excitatory post-synaptic potentials in the claw opener muscle and a decrease of them …

Gendered Patterns In High Achievement In Mathematics For Grades 4, 6, And 8, Laura J. Falvey

Open Access Dissertations

The issue of underrepresentation of women in science, technology, engineering, and mathematics (STEM) careers is especially important to the future of the United States in current times when STEM careers play an increasingly important role in the global economy (Toulmin & Groome, 2007; United States Department of Labor, 2007). The pool of students who enter careers in science, technology, engineering, or mathematics first appear in elementary school and overwhelmingly come from those with high achievement in mathematics (Berryman, 1983; Tai, Liu, Maltese, & Fan, 2006).

This study examined mathematics achievement data for students in grades 4, 6, and 8 in …

Beyond The Black Horizon: Perspectives Of African American Collegians Who Studied Abroad, Aaron Ian Bruce

Open Access Dissertations

Although U.S. colleges and universities continue to discuss creative ways to increase the number of African American collegians participating in study abroad, this research is limited when revealing the unique perspectives of African American collegians who have studied abroad. Traditionally an emphasis on program success has been placed on the quantity of study abroad participants rather than the quality of African American student support and engagement; the personal reflections through the lens of African American race and identity are often overlooked. A series of culturally responsive, guided interviews were conducted with African American collegians from a variety of institutions across …

Transport And Partitioning Of Organochlorine Pollutants In The Open Oceans, Lin Zhang

Open Access Dissertations

Remote open oceans were traditionally considered as sinks of persistent organic pollutants (POPs) such as industrial chemicals (PCBs) and organochlorine pesticides (OCPs). In the context of reduced primary emissions as well as global warming, previous polluted reservoirs such as soil, large water bodies, and glaciers may act as secondary sources returning these POPs back to the atmosphere and ocean. It was also hypothesized that biogeochemical activities associated with phytoplankton in the water column would lead to the coupling of air-plankton systems to draw down the lipophilic POPs from the overlying atmosphere, similar to the biological pump taking up CO_{2 …}

Relationships Between Gender, Socioeconomic Status, Math Attitudes, And Math Achievement: An International Investigation, Sunny R. Duerr

Open Access Dissertations

Investigations into the factors related to math achievement have traditionally been studied within individual countries, despite the existence of large international data sets available for analysis. This dissertation investigated the relationships among gender, socioeconomic status, math attitudes, and math achievement based on information from 50 participating countries in the Trends in International Mathematics and Science Study (TIMSS).

Countries were grouped into clusters using hierarchical cluster analysis. Six cluster solutions were investigated based on average mathematics scores, average science scores, and average math attitude. The clusters were then validated on a separate sample using discriminant function analysis. The validation process utilized …

Quantifying The Effects Of Tidal Restrictions And Plant Invasions On Resident Fish In Atlantic Coast Salt Marshes, Kimberly Lellis Dibble

Open Access Dissertations

This research investigates the combined effects of tidal restriction and Phragmites australis invasion on habitat quality for marsh fauna across a large geographic area while evaluating the reversal of those effects through ecological restoration. We used meta-analytic tools and published literature to examine differences in the quantity, condition, and diversity of fauna in invaded and restored marshes relative to uninvaded (reference) marshes in the mid-Atlantic and in New England. In addition, we collected data for two projects designed to move beyond the collection of community data (e.g., density, richness, as included in the meta-analysis) to assess the functional response of …

Brain Penetration Of Tolfenamic Acid And Its Ability To Enhance The Cognitive Functions And To Lower Amyloid Pathology In Animal Models Of Alzheimer's Disease, Gehad Mohammed Subaiea

Open Access Dissertations

Alzheimer’s disease (AD) is a neurodegenerative disease that is responsible for up to 80% of all dementia cases. Hallmarks of AD include the presence of beta-amyloid (Aβ) deposits and twisted strands of abnormal hyperphosphorylated tau forming neurofibrillary tangles (NFT_s), which ultimately lead to damage and death of nerve cells in the brain. Symptoms of the disease include impairments in cognitive and functional abilities that gradually worsen as the disease progress. Finally, in advanced AD, patients become unable to perform basic daily activities, become more susceptible to infections, and ultimately die. Only five drugs are FDA-approved for use in …

Spatial And Temporal Patterns In Nutrient Standing Stock And Mass-Balance In Response To Load Reductions In A Temperate Estuary, Jason Seth Krumholz

Open Access Dissertations

The addition of excess organic matter into a system, commonly referred to as eutrophication (Nixon, 1995), is a widespread problem in estuaries throughout much of the world. To combat this trend, many management agencies are imposing regulations limiting the amount of nutrients (nitrogen and phosphorus) which can be discharged into coastal waters through wastewater treatment and agriculture. In 2005, the Rhode Island Department of Environmental Management (RIDEM) enacted legislation mandating that wastewater treatment facilities (WWTF) discharging their effluent into Narragansett Bay and its tributaries reduce the concentration of nitrogen in their effluent. This legislation will reduce wastewater nitrogen loading to …

Age-Structured Multispecies Model Of The Georges Bank Fish Community, Kiersten Lynn Curti

Open Access Dissertations

Georges Bank has exhibited marked changes in ecosystem structure over the last half century. The community once dominated by groundfish and other finfish is now primarily composed of pelagic and elasmobranch species. Community dynamics are profoundly influenced by species interactions such as predation. The focus of this dissertation is to estimate the trophic interactions among fish species on Georges Bank. These species interactions are estimated by developing a multispecies, statistical catch-atage model of the Georges Bank fish community that explicitly quantifies the mortality due to predation.

Manuscript I: A submodel was developed for three important fish species on Georges Bank: …

Cultural Sites As Platforms For Environmental Characterization Of Marine Landscapes, Michael Lee Brennan

Open Access Dissertations

Our ability to understand and interpret archaeological data collected from the excavation of an archaeological site is constrained by our capacity to investigate it. This is often limited by our understanding of the surrounding environment and the modern landscape. This dissertation is composed of three separate studies, each of which examines the environmental and oceanographic contexts of archaeological sites using geophysical and geochemical analyses. The focus of these case studies is to initiate the process of determining the oceanographic and geological histories of the modern sites. Viewing sites from their abandonment to the present day provides an understanding of the …

Impacts Of Marine Invasive Species On Subtidal And Intertidal Food Web Dynamics, Nicole Rohr

Open Access Dissertations

Invasive species can have a variety of impacts on food web structure and interspecific interactions. They can impact recruitment rates of associated marine species, influence behavior of potential prey items, and alter predator-prey relationships. This research is designed to assess 1) the relationship between the recruitment of Lacuna vincta and two species of algal epiphytes, the native Ceramium virgatum and the invasive Neosiphonia harveyi, in the shallow subtidal zone; 2) the spatial and temporal distribution of the invasive Hemigrapsus sanguineus in the intertidal zone of cobble beaches; and 3) the top-down effects and predator-prey interactions of H. sanguineus.

Through manipulative …

Comparison Of Impairments, Activity Limitations, Physical Activity, And Self-Efficacy Among Healthy Weight, Overweight And Obese Minority Middle School Children, Annabel Nunez-Gaunaurd

Open Access Dissertations

The feasibility and outcomes of a 12-week extracurricular family-based intervention led by physical therapists that was designed to increase physical activity (PA) in three Hispanic male middle-school children was examined. This intervention has limited feasibility and may increase physical activity levels for overweight Hispanic middle school children. In a second study, differences in motor proficiency, strength, endurance, and PA among healthy weight, overweight and obese children were examined, and correlations between BMI and physical impairments were explored. Obese children demonstrated impairments in motor proficiency, strength, and endurance when compared to healthy weight children. Among overweight children, higher BMI was associated …

Web-Based Medical Imaging Simulation System For Education And Research, Xiping Li

Open Access Dissertations

In this work, a major effort has been made to establish an Internet accessible system for medical imaging simulation as a convenient service under the cloud computing environment. First, an Internet accessible, medical imaging education platform has been developed. It includes teaching and dynamic assessment tracking system for five commonly used imaging modalities. The system is integrated by the open source MySQL database software that manages updating materials and also tracks students’ learning engagements, which allow the reliability and appropriateness of the on-line teaching material and assessment methods to be optimized. The evaluation results have shown increased learning gains promisingly. …

Micrornas As Effectors For Acetyltransferase P300 In Cardiac Hypertrophy, Salil Sharma

Open Access Dissertations

Myocardial transcriptional response to stress is critically dependent on availability of the histone acetyltransferase p300. p300 is a transcription coactivator which is rapidly induced by hemodynamic stress in the myocardium. This induction is both necessary and sufficient to drive myocardial hypertrophy in vivo. Although short-term elevation of p300 may be adaptive, sustained elevation of p300 increases the risk of heart failure. The mechanism of p300 induction during stress is unknown. The downstream effectors of p300 have been only incompletely elucidated. In this context, the role of microRNAs in regulating p300-driven cardiac hypertrophy can be of potential interest. MicroRNAs are short …

P27 And Metastatic Progression: Molecular Mechanisms Underlying Bone Metastasis, Seth A. Wander

Open Access Dissertations

The complex PI3K/mTOR pathway regulates tumor progression via effects on cellular proliferation, apoptosis, autophagy, and motility. New drugs that inhibit the catalytic site of both PI3K and mTOR have shown promise in clinical trials. Here, we report the first use of a novel, dual PI3K/mTOR catalytic site inhibitor (PF-04691502, PF1502) in a xenograft model of breast cancer metastasis to bone. Metastatic MDA-MB-1833 cells showed PI3K/mTOR activation relative to parental MDA-MB-231. Low-dose PF1502 significantly impaired tumor cell motility and invasion in vitro without causing cell cycle arrest, apoptosis, or reduced proliferation. Pre-treatment of tumor cells at this dose reduced bone metastatic …

Mouse Models Of Menopause And Ovarian Cancer Risks, Ying Wang

Open Access Dissertations

Epithelial ovarian cancer (EOC) is the leading cause of death from gynecological malignancy in Western countries. A better understanding of the etiology and risk factors associated with this disease is crucial for the development of early detection protocols as well as more effective therapies. Epidemiological data has shown that the risks of EOC are highest among peri- or post- menopause women, while increased parity or the use of oral contraceptives is preventive. These data suggest that alterations in reproductive factors are associated with ovarian cancer risks; however, the molecular mechanisms underlying such a link remain to be understood. For decades, …

Psychological Distress, Social Support And Substance Use In Women With Hiv In Substance Use Recovery, Brian E. Mccabe

Open Access Dissertations

The purpose of this study was to investigate concurrent and prospective relationships between psychological distress and social support and substance abuse in a convenience sample of predominantly minority women with HIV in substance use recovery. This study involved a secondary analysis of data from a randomized controlled trial comparing a family therapy intervention and a group health intervention. Participants completed the Hamilton Depression and Anxiety Scales (psychological distress) and the Social Support Questionnaire (social support) at baseline and 4 months, 8 months, and 12 months post-baseline. Substance use over a 30-day period was measured by the Addiction Severity Index Lite, …

Nuclear Factor-Κb Activation In Schwann Cells Regulates Regeneration And Re-Myelination, Paul D. Morton

Open Access Dissertations

Schwann cells (SCs) are crucial for peripheral nerve development and regeneration; however, the intrinsic regulatory mechanisms governing post-injury responses are poorly understood. Activation and deacetylation of nuclear factor-κB (NF- κB) in SCs have been implicated as prerequisites for peripheral nerve myelination. Using GFAP-IκBα-dn mice, in which NF- κB transcriptional activation is inhibited in SCs, we found no discernable differences in the quantity or structure of myelinated axons in adult facial nerves. Following crush injury, axonal regeneration was impaired at 31 days and greatly improved at 65 days in GFAP-IκBα-dn mutants. Compact re-myelination and sensory fiber organization were significantly compromised at …

Checking The Walls For Cracks: Race/Ethnic Differences In Age-Related Arterial Changes, And The Relevance Of Carotid Ultrasound For Subclinical Neurovascular Disease, Matthew Scott Markert

Open Access Dissertations

Despite advances, stroke remains the largest cause of disability and fourth leading cause of death in the United States. The relationship between changes in human vasculature (atherosclerosis and arteriosclerosis) prior to clinical incident, and other risk factors for stroke remains unclear. This dissertation represents work towards the identification of imaging biomarkers for vascular change, focusing on ultrasound to characterize persons at risk, including differences among race/ethnic groups. This research contained three distinct projects. The first goal was to determine if changes within ultrasonographic measures of carotid vasculature could be found across race/ethnic groups after adjustment for risk factors. The second …