Digital Commons Network^™

Assessing Inter-Rater Agreement For Compositional Data, Ningning Chen

Open Access Dissertations

Compositional data are non-negative vectors whose elements sum to one (e.g., [0.1, 0.5, 0.4]). This type of data occurs in many research areas where the relative magnitudes between the vector’s elements are of primary interest. In this dissertation we propose novel methodology for assessing inter-rate agreement based on compositional data. This is needed because existing agreement measures either involve converting the vector to a univariate value, thereby losing information, or they fail to account for the sum-to-one restriction. We propose a novel Bayesian approach, enabled by Markov chain Monte Carlo, to investigate differences in the pattern of compositional vector scores. …

Signal Enhancement And Data Mining For Biological And Chemical Samples Using Mass Spectrometry, Yuezhi Du

Open Access Dissertations

Mass spectrometry has been actively involved in the areas of healthcare, pharmaceutics, environmental analysis, food industry and forensics due to its ability to provide molecular information at trace levels. Recently, because of the complexity of chemical and biological samples, computer-assisted mass spectra analysis, including signal enhancement, statistics and machine learning, has been drawn more and more attention especially for researches in biomarker identification, sample classification and omics-related areas where high volume of data is generated.

Evaluation Of In Vitro Anti-Inflammatory, Anti-Diabetic And Anti-Lipogenic Activity Of Natural Polyphenolic Extracts And Their Pure Constituents, Pragati P. Nahar

Open Access Dissertations

The long-term goals and objectives of our group are to identify bioactive natural products relevant to human disease prevention and health promotion. To attain this goal, the objective of this thesis was to demonstrate that bioactive polyphenol-rich extracts or preparations exert positive health benefits beyond basic nutrition, thus impacting overall health and wellness. We believe that this project has immense scientific merit from a human health perspective and will be of great public impact given that consumers are seeking natural and organic choices for improving health. In this investigation, we have focused our attention on investigating the biological activities of …

Probabilistic Uncertainty Quantification And Experiment Design For Nonlinear Models: Applications In Systems Biology, Vu Cao Duy Thien Dinh

Open Access Dissertations

Despite the ever-increasing interest in understanding biology at the system level, there are several factors that hinder studies and analyses of biological systems. First, unlike systems from other applied fields whose parameters can be effectively identified, biological systems are usually unidentifiable, even in the ideal case when all possible system outputs are known with high accuracy. Second, the presence of multivariate bifurcations often leads the system to behaviors that are completely different in nature. In such cases, system outputs (as function of parameters/inputs) are usually discontinuous or have sharp transitions across domains with different behaviors. Finally, models from systems biology …

Identification Of Genomic Factors Using Family-Based Association Studies, Libo Wang

Open Access Dissertations

Genome-wide association studies become increasingly popular and important for detecting genetic associations of complex traits. However, it is well known that spurious associations could arise from statistical analysis without proper consideration of genetic relatedness of samples. Many methods have been proposed to guard against these spurious associations. Here we focus on multi-locus association studies of quantitative traits and the case-control status, and propose algorithms that take into consideration of genetic related samples to address possible confounding issues. As supervised dimension reduction methods, these algorithms performs well to conduct association studies with a large number of biomarkers but a relative small …

Phytochemical Investigation Of The Traditional Botanical Medicine Iresine Celosia, Caroline Grace Killian

Open Access Dissertations

Iresine celosia L. is a traditional medicine used by the indigenous Mayan people for a variety of ailments. It is also the sole active ingredient in the Odyliresin™ formulation currently marketed to humans worldwide as an antioxidant and for the promotion of prostate health. However, Odyliresin™ has not been characterized phytochemically, or evaluated biologically for its intended use. This work represents the first comprehensive phytochemical investigation of the Odyliresin™ formulation botanical extract. To better understand its constitutive phytochemistry, a tailored isolation scheme was developed, using various chromatography resins (silica gel, LH-20), separation and purification techniques. In all, eleven compounds were …

Altered Cholesterol Metabolism In Human Cancers Unraveled By Label-Free Spectroscopic Imaging, Shuhua Yue

Open Access Dissertations

Despite tremendous scientific achievements, cancer remains the second leading cause of death in the United States. Metabolic reprogramming has been increasingly recognized as a core hallmark of cancer. My dissertation work identified novel diagnostic markers and therapeutic targets for human cancers through the study of cholesterol in cancer cells.

Enabled by label-free Raman spectromicroscopy, we performed the first quantitative analysis of lipogenesis at single cell level in human patient cancerous tissues. Our imaging data revealed an unexpected, aberrant accumulation of esterified cholesterol in lipid droplets of high-grade prostate cancer and metastases, but not in normal prostate, benign prostatic hyperplasia, or …

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 …

Growth, Reproductive Life-History Traits And Energy Allocation In Epinephelus Guttatus (Red Hind),E. Striatus (Nassau Grouper), And Mycteroperca Venenosa (Yellowfin Grouper) (Family Serranidae, Subfamily Epinephelinae), Nicolle Marie Cushion

Open Access Dissertations

Fish populations are regulated by both external environmental factors, e.g., water quality parameters and habitat, and internal reproductive biology and physiology processes. For many species and populations there is often ample external information, while critical internal, i.e., life-history trait (LHT), information is not available. For this study, I determined LHTs and energy allocation patterns for Epinephelus guttatus (red hind), E. striatus (Nassau grouper), and Mycteroperca venenosa (yellowfin grouper) harvested from The Bahamas. I determined age ranges, and how growth patterns and rates differed among the study species. The maximum ages were: 17, E. guttatus; 22, E. striatus; and 13, M. …

A Transdiagnostic Model Of Suicidal Ideation And Suicide Attempts, Lori R. Eisner

Open Access Dissertations

Suicide is one of the most tragic issues in mental health. Suicide has traditionally been studied as an outcome of specific psychiatric disorders. The goal of this study was to consider whether there might be underlying dimensions across psychiatric disorders that are related to suicidality. This study proposed a transdiagnostic model of suicidality. Psychiatric symptoms were hypothesized to load onto three factors: Negative Mood, Impulsivity, and Arousal. Factors were then examined as predictors of suicidal ideation and suicide attempts. Data were drawn from the National Comorbidity Survey-Replication Study (NCS-R). Structured interviews were conducted in two parts using the Composite International …

Physical And Chemical Interactions Between Marine Phytoplankton And Particle-Colonizing Bacteria, Jason Robert Graff

Open Access Dissertations

It is inherently difficult to study the direct interactions between marine microbes due to the size of the organisms and microscale environments in which they exist. Recent evidence suggests that the direct associations between marine phytoplankton and particle-colonizing bacteria can influence marine microbial community succession, microalgal primary production, toxin production by marine phytoplankton, and have potential implications for human health. The goal of this dissertation was to elucidate some of the physical and chemical mechanisms that regulate microbial interactions, particularly the colonization of phytoplankton and other marine particles by bacteria. To accomplish these goals, I used a creative and multi-disciplinary …

Lipid Bilayer-Nanoparticle Interactions In Nanotoxicology And Nanomedicine, Yanjing Chen

Open Access Dissertations

Nanoparticle (NP) interactions that may destabilize cell membranes and cause toxicity can also be used to design and control therapeutic assemblies. Fundamentally examining interactions between NPs and cell membranes is crucial to understanding NP toxicity mechanisms and the development of safe and non-toxic NP-based commercial and therapeutic applications. In this dissertation it is demonstrated that self-assembled lipid bilayers can be employed as model membranes to determine NP interact ions. First, protocols were developed for examining hydrophobic and hydrophilic NP-bilayer interactions using lipid bilayer vesicles or liposomes. Second, interactions between liposomes and NPs were characterized by examining changes in liposome structure, …

Incorporating Recreational And Artisanal Fishing Fleets In Atlantic Billfish Management, Ayeisha A. Brinson

Open Access Dissertations

Atlantic billfish include sailfish (Istiophorus platypterus), blue marlin (Makaira nigricans), white marlin (Kajikia albida, formerly Tetrapturus albidus) and the spearfishes (Tetrapturus); these fishes are found in tropical and subtropical waters. The spearfishes include the longbill spearfish (T. pfluegeri), the Mediterranean spearfish (T. belone) and the roundscale spearfish (T. georgii). The International Commission for the Conservation of Atlantic Tunas (ICCAT) is the regional fishery management organization that conducts research to determine the condition of tuna and billfish resources and supports international cooperative management. ICCAT has determined that blue marlin and white marlin are overfished; the status of sailfish and spearfish are …

Assessment Of The Rhode Island Coastal Lagoon Ecosystem, Kathryn Hale Ford

Open Access Dissertations

The health of the Rhode Island coastal lagoon ecosystem is of importance due to its critical role as a wildlife habitat and recreation destination. As human population continues to expand along the coast, this ecosystem will receive increasing pressure from contaminants. By examining how the lagoons have changed in the past, we can postulate what variables are linked to change. Current conditions need to be thoroughly studied to provide a baseline with which to study future change, as well as to determine areas of concern in the lagoons. In order to understand how the ecosystem responds to such pressures, a …

Fish Landmarks For Chromosome 11 Of Bombyx Mori: An In Situ Analysis, Charles Eugene Mcgovern

Open Access Dissertations

Fluorescence in situ hybridization (FISH) has been used to simultaneously identify the positions of the ribosomal DNA and the Sericin genes on chromosome 11 of Bombyx mori. The ribosomal DNA genes were detected using biotin labeled plasmid pBmR 161 and avidin-Texas Red and the Sericin 2 gene was detected using digoxigenin labeled plasmid 2002 and anti-digoxigenin-fluorescein. The position of the Sericin 1 gene was identified using the ribosomal DNA genes as a chromosomal landmark. Sericin 1 was detected using digoxigenin labeled bacterial artificial chromosome 9HJD and anti-digoxigenin-fluorescein. The chromosomal spreads were counterstained with diamindino-phenyl-indole (DAPI). The signals from the sericin …

Remote Sensing Of Bio-Optical Water Types, Phytoplankton Seasonality, And Algal Pigments In Ocean Margin Waters, Paula Susan Bontempi

Open Access Dissertations

A frontal edge detection algorithm was applied to remotely sensed ocean color satellite data to identify incorrect retrievals of phytoplankton chl a concentrations, and refine estimates of primary producer abundance in bio-optically complex ocean margin waters. Improvement of the remotely sensed biological signal will facilitate establishment of more accurate daily to decadal phytoplankton spatial patterns in these waters, and enable prediction of phytoplankton blooms or features from space. Spatial patterns of chlorophyll a (chl a) and water-leaving radiance (Lwn) from 1998 SeaWiFS (Sea-Viewing Wide Field-of-View Sensor) images were examined from ocean margin waters off the southeastern continental United States (SEC). …

A General And Facile Synthesis Of Beta-And Gamma-Hydroxyphosphonates From Epoxides: Application In Phospholipid Synthesis, Zhengong Li

Open Access Dissertations

No abstract provided.

Development Of Chromatographic Methods And Analysis Of Metal Ions In Environmental And Biological System, Zhen Yi

Open Access Dissertations

No abstract provided.

Optimization Strategies For Reverse-Phase Liquid Chromatographic Separations Of Deoxyribonucleotides, Deoxyribonucleosides, And Dideoxyribonucleosides, Nan-In Jang

Open Access Dissertations

No abstract provided.

Chemical Synthesis And Purification Of Biologically Active Phosphonolipids: Pulmonary Surfactant Analogs, Winnie Hui Chiun Lin

Open Access Dissertations

No abstract provided.

Foraging Behavior Of American White Pelicans Pelecanus Erythrorhyncos In Western Nevada, John Guy Thomas Anderson

Open Access Dissertations

No abstract provided.

Purification And Characterization Of A New Class Of Dna Topoisomerase From Pearl Millet Mitochondria, Yong Pyo Lim

Open Access Dissertations

No abstract provided.

Foraging Behavior Of American White Pelicans Pelecanus Erythrorhyncos, John Guy Thomas Anderson

Open Access Dissertations

Foraging behavior by American White Pelicans (Pelecanus erythrorhyncos was studied in the Lahontan Basin in western Nevada. Pelicans engaged in cooperative fish herding and in kleptoparasitism upon Double Crested cormorants (Phalacrocorax auritus). Pelicans in groups of size 2 through 6 caught more fish than single birds. Mean strike number increased initially with increasing flock size but leveled off at a flock size of between 3 and 4. strike efficiency (captures/bird/strike) declined with flock size, reaching an asymptote at a flock size of 4. Analysis of the regurgitate of young birds revealed that the pelicans' primary food source …

Population Dynamics Of The American Lobster (Homarus Americanus) (Stock Assessment, Yield Model, Time Series Analysis, Production), Michael J. Fogarty

Open Access Dissertations

No abstract provided.

Comparative Evaluation Of Aerial And Shipboard Sampling Techniques For Estimating The Abundance Of Humpback Whales (Megaptera Novaeangliae), Gerald Preston Scott Jr.

Open Access Dissertations

No abstract provided.

A Study Of Biological And Physical Controls On The Trace Metal Content Of Calcite And Aragonite, Robert Bruce Lorens

Open Access Dissertations

No abstract provided.

Locomotor Activity Of Adult-Sized American Eels (Anguilla Rostrata Lesueur): Effects Of Shelter Availability, Induced Maturation And Sensory Impairment, Richard Kenneth Edel

Open Access Dissertations

No abstract provided.

Effect Of The Browning Reaction On Quality, Digestion And Absorption Of Protein, Munehiko Tanaka

Open Access Dissertations

No abstract provided.

Feeding Habits Of The Sand Shrimp, Crangon Septemspinosa (Crustacea, Decapoda, Natantia), J. Ross Wilcox

Open Access Dissertations

No abstract provided.

The Metabolic Expenditures Of The American Eel (Anguilla Rostrata) On Itsmigration To The Sargasso Sea, William Bruce Hunter

Open Access Dissertations

No abstract provided.