Digital Commons Network^™

Snpredict: A Machine Learning Approach For Detecting Low Frequency Variants In Cancer, Vatsal Mehra

Master's Theses (2009 -)

Cancer is a genetic disease caused by the accumulation of DNA variants such as single nucleotide changes or insertions/deletions in DNA. DNA variants can cause silencing of tumor suppressor genes or increase the activity of oncogenes. In order to come up with successful therapies for cancer patients, these DNA variants need to be identified accurately. DNA variants can be identified by comparing DNA sequence of tumor tissue to a non-tumor tissue by using Next Generation Sequencing (NGS) technology. But the problem of detecting variants in cancer is hard because many of these variant occurs only in a small subpopulation of …

Static And Dynamic Spectral Acuity In Cochlear Implant Listeners For Simple And Speech-Like Stimuli, Benjamin Anderson Russell

USF Tampa Graduate Theses and Dissertations

For cochlear implant (CI) listeners, poorer than normal speech recognition abilities are typically attributed to degraded spectral acuity. However, estimates of spectral acuity have most often been obtained using simple (tonal) stimuli, presented directly to the implanted electrodes, rather than through the speech processor as occurs in everyday listening. Further, little is known about spectral acuity for dynamic stimuli, as compared to static stimuli, even though the perception of dynamic spectral cues is important for speech perception.

The primary goal of the current study was to examine spectral acuity in CI listeners, and a comparison group of normal hearing (NH) …

The Influence Of Motivational Salience On Attention Selection: An Erp Investigation, Constanza De Dios

USF Tampa Graduate Theses and Dissertations

The current study used event-related potentials (ERPs) to investigate how motivational salience in the form of expectation violation influences spatial attention. The medial frontal negativity (MFN) ERP indexes expected value, being negative to unexpected punishments and positive to unexpected rewards. The P1 and N1 ERPs index spatial attention, being larger to stimuli in attended locations. This design attached motivational value to locations by making one visual hemifield economically rewarding (greater probability of a rewarding outcome) and the other punishing (greater probability of a punishing outcome). Keypresses to a dot probe following a reward-signifying stimulus were awarded money if correct, and …

Can Gait Signatures Provide Quantitative Measures For Aiding Clinical Decision-Making? A Systematic Meta-Analysis Of Gait Variability Behavior In Patients With Parkinson’S Disease, Niklas König Ignasiak

Physical Therapy Faculty Articles and Research

A disturbed, inconsistent walking pattern is a common feature of patients with Parkinson's disease (PwPD). Such extreme variability in both temporal and spatial parameters of gait has been associated with unstable walking and an elevated prevalence of falls. However, despite their ability to discretise healthy from pathological function, normative variability values for key gait parameters are still missing. Furthermore, an understanding of each parameter's response to pathology, as well as the inter-parameter relationships, has received little attention. The aim of this systematic literature review and meta-analysis was therefore to define threshold levels for pathological gait variability as well as to …

Combining Real-Time Fmri Neurofeedback Training Of The Dlpfc With N-Back Practice Results In Neuroplastic Effects Confined To The Neurofeedback Target Region, Matthew Sherwood, Michael P. Weisend, Jessica H. Kane, Jason G. Parker

Neuroscience, Cell Biology & Physiology Faculty Publications

In traditional fMRI, individuals respond to exogenous stimuli and are naïve to the effects of the stimuli on their neural activity patterns. Changes arising in the fMRI signal are analyzed post-hoc to elucidate the spatial and temporal activation of brain regions associated with the tasks performed. The advent of real-time fMRI has enabled a new method to systematically alter brain activity across space and time using neurofeedback training (NFT), providing a new tool to study internally-driven processes such as neuroplasticity. In this work, we combined n-back practice with fMRI-NFT of the left dorsolateral prefrontal cortex (DLPFC) to better understand the …

A Cell Cycle-Regulated Toxoplasma Deubiquitinase, Tgotud3a, Targets Polyubiquitins With Specific Lysine Linkages, Animesh Dhara, Anthony P. Sinai

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The contribution of ubiquitin-mediated mechanisms in the regulation of the Toxoplasma gondii cell cycle has remained largely unexplored. Here, we describe the functional characterization of a T. gondii deubiquitinase (TGGT1_258780) of the ovarian-tumor domain-containing (OTU) family, which, based on its structural homology to the human OTUD3 clade, has been designated TgOTUD3A. The TgOTUD3A protein is expressed in a cell cycle-dependent manner mimicking its mRNA expression, indicating that it is regulated primarily at the transcriptional level. TgOTUD3A, which was found in the cytoplasm at low levels in G₁ parasites, increased in abundance with the progression of the …

N-Acetyl Cysteine May Support Dopamine Neurons In Parkinson's Disease: Preliminary Clinical And Cell Line Data., Daniel A. Monti, George Zabrecky, Daniel Kremens, Tsao-Wei Liang, Nancy A. Wintering, Jingli Cai, Xiatao Wei, Anthony J. Bazzan, Li Zhong, Brendan Bowen, Charles Intenzo, Lorraine Iacovitti, Andrew B. Newberg

Marcus Institute of Integrative Health Faculty Papers

BACKGOUND: The purpose of this study was to assess the biological and clinical effects of n-acetyl-cysteine (NAC) in Parkinson's disease (PD).

METHODS: The overarching goal of this pilot study was to generate additional data about potentially protective properties of NAC in PD, using an in vitro and in vivo approach. In preparation for the clinical study we performed a cell tissue culture study with human embryonic stem cell (hESC)-derived midbrain dopamine (mDA) neurons that were treated with rotenone as a model for PD. The primary outcome in the cell tissue cultures was the number of cells that survived the insult …

Pruning Or Tuning? Maturational Profiles Of Face Specialization During Typical Development, Xun Zhu, Ramesh S. Bhatt, Jane E. Joseph

Psychology Faculty Publications

Introduction: Face processing undergoes significant developmental change with age. Two kinds of developmental changes in face specialization were examined in this study: specialized maturation, or the continued tuning of a region to faces but little change in the tuning to other categories; and competitive interactions, or the continued tuning to faces accompanied by decreased tuning to nonfaces (i.e., pruning). Methods: Using fMRI, in regions where adults showed a face preference, a face- and object-specialization index were computed for younger children (5-8 years), older children (9-12 years) and adults (18-45 years). The specialization index was scaled to each subject's maximum activation …

Ramadan & Pregnancy, Omar Rizvi

Celebration of Learning

Fasting during Ramadan, the ninth month of the Muslim calendar, is one of the five pillars of Islam and is fard (obligatory) for all Muslims physically and mentally capable of doing so. In the Qur’an, it is made abundantly clear that religion and its acts of worship are not meant to pose undue difficulty or hardship (Qur’an 22:78, 5:6, 2:185). My paper explores the Islamic definitions for “unnecessary difficulty” and “physically capable” specifically in regards to pregnant women. At what point does fasting incur significant, if any, damage to the fetus that it should prevent the mother from participating in …

Communication-Microelectrode Detection Of Cholesterol Efflux From The Human Buccel Mucosa, Xiaochun Yu, Thomas J. Kelley, Hillel J. Chiel, James D. Burgess

Faculty Scholarship

It has previously demonstrated that cholesterol efflux from the cell plasma membrane is increased in a mouse model of cystic fibrosis (CF) compared to a wild-type control. A noninvasive means of characterizing plasma membrane cholesterol efflux at the surface of airway tissue of CF patients is needed to extend the trends found in animal models of CF to the human disease state. Microelectrode-induced cholesterol efflux from the plasma membrane of cells at the surface of tissue is proposed as a strategy to demonstrate increased cholesterol efflux for CF in human subjects. Data demonstrating detection of cholesterol efflux from the human …

The Effects Of Cognitive Training Among Individuals With Neurodegenerative Diseases, Elise Gabriela Valdes

USF Tampa Graduate Theses and Dissertations

With the growing older adult population, neurodegenerative diseases common in old age such as mild cognitive impairment (MCI) or Parkinson’s disease (PD) are becoming increasingly germane areas of research. Pharmacological treatments have thus far been unsuccessful in treating cognitive decline associated with these neurodegenerative disorders. Alternative interventions, such as cognitive training programs, have shown promise. The current dissertation contains three papers examining cognitive interventions in neurodegenerative diseases. The first paper examined the longitudinal effects of cognitive speed of processing training (SPT) among those with PD. Results showed that training gains seen at initial post-test were maintained three months later. The …

Role Of Protein Kinase G In Regulating Vascular Tone In Hypoxic Ovine Cerebral Arteries, Richard Burdette Thorpe

Loma Linda University Electronic Theses, Dissertations & Projects

Nitric oxide (NO) and its precursors have been used clinically to induce vasorelaxation long before the specific mechanism of how this operates was understood. With the discovery in 1977 of the influence of NO on guanylate cyclase, and the subsequent elucidation of the NO pathway, the role of cyclic guanidine monophosphate (cGMP)-dependent protein kinase (PKG) has been shown to be the main mediator of NO-induced vasorelaxation. Less well understood is the behavior of this pathway in conditions of long term hypoxia (LTH). It was later shown that LTH attenuates the ability of PKG to mediate vasorelaxation. How this operates is …

Effects Of Neonatal Dexamethasone On The Maturation And Endowment Of Cardiomyocytes, Maresha Gay

Loma Linda University Electronic Theses, Dissertations & Projects

Each year 1 in 9 infants are born preterm in the United States. Preterm infants have a host of complications associated with prematurity, including respiratory distress syndrome. Dexamethasone, a synthetic glucocorticoid is the ‘gold standard’ intervention in the treatment of preterm infants and mothers at risk of preterm birth because it promotes organ maturation, particularly the lungs and aids in surfactant production. However, a growing body of evidence suggests perinatal dexamethasone exposure is associated with health consequences later in life including increased risk of cardiovascular disease. Cardiomyocytes are the functional unit of the heart and are unique in that they …

Gene Delivery Using Calcium Phosphate Nanoparticles: Optimization Of The Transfection Process And The Effects Of Citrate And Poly(L-Lysine) As Additives, Mohammed A. Khan, Victoria M. Wu, Shreya Ghosh, Vuk Uskoković

Pharmacy Faculty Articles and Research

Despite the long history of nanoparticulate calcium phosphate (CaP) as a non-viral transfection agent, there has been limited success in attempts to optimize its properties for transfection comparable in efficiency to that of viral vectors. Here we focus on the optimization of: (a) CaP nanoparticle precipitation conditions, predominantly supersaturation and Ca/P molar ratios; (b) transfection conditions, mainly the concentrations of the carrier and plasmid DNA; (c) the presence of surface additives, including citrate anion and cationic poly(l-lysine) (PLL). CaP nanoparticles significantly improved transfection with plasmid DNA encoding enhanced green fluorescent protein (eGFP) in pre-osteoblastic MC3T3-E1 cells compared to a commercial …

The Relationship Between Lexical Performance And Regional Gray Matter Volumes: A Longitudinal Study Of Cognitively Healthy Elderly, Jungmoon Hyun

Dissertations, Theses, and Capstone Projects

This study investigated the longitudinal relationship among aging, performance on lexical tasks, and regional gray matter volumes over 2-7 years. A total of 137 older participants who remained cognitively normal were administered four lexical tasks at each time point: the Boston Naming Test (BNT), Vocabulary Test, Semantic- and Phonemic-Fluency task. In addition, they underwent repeated magnetic resonance imaging (MRI) scanning acquired within two months of the lexical tasks. The average interval between time points was 2.36 years (range 1.50-7.64) and the average number of time points was 2.65 times (range 2-5).

Results indicated that age differentially affects lexical task performance …

Membrane Insertion For The Detection Of Lipopolysaccharides: Exploring The Dynamics Of Amphiphile-In-Lipid Assays, Loreen R. Stromberg, Nicolas W. Hengartner, Kirstie L. Swingle, Rodney A. Moxley, Steven W. Graves, Gabriel A. Montaño, Harshini Mukundan

School of Veterinary and Biomedical Sciences: Faculty Publications

Shiga toxin-producing Escherichia coli is an important cause of foodborne illness, with cases attributable to beef, fresh produce and other sources. Many serotypes of the pathogen cause disease, and differentiating one serotype from another requires specific identification of the O antigen located on the lipopolysaccharide (LPS) molecule. The amphiphilic structure of LPS poses a challenge when using classical detection methods, which do not take into account its lipoglycan biochemistry. Typically, detection of LPS requires heat or chemical treatment of samples and relies on bioactivity assays for the conserved lipid A portion of the molecule. Our goal was to develop assays …

Development Of A Course-Based Undergraduate Research Experience To Introduce Drug-Receptor Concepts, Hollie I. Swanson, Ok-Kyong Park-Sarge, Thushani Rodrigo-Peiris, Lin Xiang, Vincent M. Cassone

Pharmacology and Nutritional Sciences Faculty Publications

Course-based research experiences (CUREs) are currently of high interest due to their potential for engaging undergraduate students in authentic research and maintaining their interest in science, technology, engineering, and mathematics (STEM) majors. As part of a campuswide initiative called STEMCats, which is a living learning program offered to freshman STEM majors at the University of Kentucky funded by a grant from Howard Hughes Medical Institute, we have developed a CURE for freshmen interested in pursuing health care careers. Our course, entitled “Drug–Drug Interactions in Breast Cancer,” utilized a semester-long, in-class authentic research project and instructor-led discussions to engage students in …

Modulation Of Nitric Oxide Synthase I Transcription By Tau And Alpha-Synuclein And Its Relevance To Alzheimer's And Parkinson's Diseases, Taelor A. Weaver, Alexandra L. Deal

Senior Honors Projects, 2010-2019

Alzheimer's Disease (AD) and Parkinson's Disease (PD) are both progressive neurodegenerative disorders that affect millions of Americans and for which there are no cures. AD can significantly impair the ability to think, remember, communicate, and carry out daily activities, while PD can affect motor functions such as balance, coordination, and the ability to speak. Intracellular protein aggregation is a hallmark of both diseases, with AD being characterized by the build up of neurofibrillary tangles composed of misfolded tau protein and PD being characterized by Lewy bodies composed of alpha-synuclein. Both normal tau and alpha-synuclein can localize to the nucleus; however, …

Gross Anatomy Dissection Videos: Effect On Student Dissection Confidence And Laboratory Examination Scores, Kevin J. Selting

Theses & Dissertations

As medical colleges across the world experience cadaver shortages, faculty shortages, and decreased time allotted to teaching gross anatomy, a need for different teaching modalities has emerged. New ways of teaching are being studied to optimize efficiency and to acquire the same, or better, student outcomes as before the previously mentioned variables became prevalent. This was the stimulus for our research. Dissection videos were made, closely adhering to the dissections performed by Physician Assistant, Physical therapy, and Medical students at the University of Nebraska Medical Center (UNMC). The current Gross Anatomy course at UNMC involves four written examinations covering material …

Molecular Basis And Consequences Of The Cytochrome C-Trna Interaction., Cuiping Liu, Aaron J Stonestrom, Thomas Christian, Jeongsik Yong, Ryuichi Takase, Ya-Ming Hou, Xiaolu Yang

Department of Biochemistry and Molecular Biology Faculty Papers

The intrinsic apoptosis pathway occurs through the release of mitochondrial cytochrome c to the cytosol, where it promotes activation of the caspase family of proteases. The observation that tRNA binds to cytochrome c revealed a previously unexpected mode of apoptotic regulation. However, the molecular characteristics of this interaction, and its impact on each interaction partner, are not well understood. Using a novel fluorescence assay, we show here that cytochrome c binds to tRNA with an affinity comparable with other tRNA-protein binding interactions and with a molecular ratio of ∼3:1. Cytochrome c recognizes the tertiary structural features of tRNA, particularly in …

White Blood Cell Count Versus Temperature As Predictors Of Pediatric Bacteremia, Ashley Ashby, Loren Moscinski

Physician Assistant Capstones, 2016 to 2019

Introduction: Although the prevalence of bacteremia has largely declined with the development of the Haemophilus Influenza Type b (Hib) and pneumococcal vaccines, it continues to be a leading cause of morbidity and mortality in children. Thus, it is crucial to differentiate bacteremia from other illnesses via the clinical picture and laboratory test results. Objective: The purpose of this research was to determine whether there is a clinically significant difference between temperature and white blood cell (WBC) count as determinants of bacteremia in the pediatric population. Methods: A PubMed search was conducted utilizing the following terms and filters: temperature, WBC, pediatrics, …

Comparing Direct Factor Xa Inhibitors And Warfarin In The Prevention Of Stroke In Patients With Atrial Fibrillation, Alessandra Lof, Stephanie Pillai

Physician Assistant Capstones, 2016 to 2019

Objective: To evaluate the overall efficacy, advantages, and disadvantages of treatment with direct factor Xa inhibitors as compared to warfarin in the prevention of stroke in patients with atrial fibrillation. Methods: A quantitative meta-analysis was performed on three separate studies, each of which evaluated the efficacy and safety outcomes of a direct factor Xa inhibitor versus warfarin in preventing stroke in patients with atrial fibrillation. The direct factor Xa inhibitors that were evaluated included apixaban, edoxaban, and rivaroxaban. Results: The direct factor Xa inhibitors were found to be as effective, and in some cases more effective, than …

Porphyromonas Gingivalis Gingipains Induce A Pro-Inflammatory Extracellular Microenvironment : The Role Of Par-2 And Fibronectin., Jeffrey S. Marschall

Electronic Theses and Dissertations

Periodontitis is a chronic inflammatory disease that is characterized by severe tissue destruction of the gingiva and other tooth supporting structures; if left untreated, tooth loss and disintegration of the alveolar bone occurs. This chronic inflammatory state has been linked to other systemic diseases such as cardiovascular disease, diabetes, rheumatoid arthritis, and Alzheimer’s disease. Porphyromonas gingivalis is the major pathogenic microbe in periodontitis. The main virulence factors of P. gingivalis are the Arg-aa and Lys-aa gingipains, which are proteolytic enzymes implicated in a plethora of activities that allow P. gingivalis to subvert the human immune system in the oral cavity …

Characterization Of The Skeletal Phenotype In Idua-W392x Knock-In Mice: Bone Metabolism Biomarkers, Christina J. Owensby

Graduate Theses/Dissertations

Mucopolysaccharidosis Type I (MPS I, Hurlers Syndrome) is a lysosomal storage disease caused by a deficiency of alpha-L-iduronidase (IDUA). IDUA catalyzes the degradation of the two glycosaminoglycans (GAGs); heparin sulfate (HS) and demantan sulfate (DS). The accumulation of HS and DS makes MPS I progressive with inevitable degeneration of multiple organ systems. Accumulated excess of GAGs on the skeletal system causes dysostosis multiplex, atlantoaxial instability, thoracolumbar kyphosis, genu valgum, acetabular dysplasia, and short stature. Skeletal biomarkers of bone formation and bone resorption were compared in wild-type, heterozygous, and IDUAW392X mice. To investigate osteoblast activity, levels of the bone formation marker …

Micellular Electrokinetic Chromatography For Studying Amyloid Beta Oligomer Membrane Affinity, Andrew Bryson

Biomedical Engineering Undergraduate Honors Theses

Amyloid Beta (Aβ) was the major focus of this study. It is a peptide that is present in the brain with a high tendency to self-aggregate. When this protein aggregates, it forms oligomers and protofibrils which in turn are deposited as senile plaques in the brain. The reason for the concern with these plaques is their association with the neurological disorder Alzheimer’s disease. It has been found that the most dangerous oligomers are formed in a portion of the plasma membrane known as lipid rafts. The purpose of this study was to understand how micelles affect the aggregation properties of …

Ethnic Identity And Teratogenic Risk Perceptions, Katie M. Chan

Dissertations and Theses (Open Access)

Elevated perceptions of teratogenic risk can cause anxiety and confusion among pregnant women. To assess whether ethnic identity and demographic factors can influence teratogenic risk perceptions, 194 pregnant women in Houston were surveyed using the Multigroup Ethnic Identity Measure (MEIM) and visual analog scales to quantify perceptions of teratogenic risk for common exposures during pregnancy. Overall, participants estimated an elevated baseline risk of 25% for birth defects among the general population. In addition, participants overestimated birth defect risks for specific exposures, such as alcohol and marijuana. Based on the MEIM scores, ethnic identity was not significantly associated with teratogenic risk …

Validation Of The Use Of Doubly Labeled Water For Measuring Metabolic Rate In Timber Rattlesnakes (Crotalus Horridus), Caitlin Hirsh

Biological Sciences Undergraduate Honors Theses

The doubly labeled water method is an isotopic technique for measuring field metabolic rate and water flux rates of free-living animals. We present a validation of the use doubly labeled water for measuring metabolic rate and water loss in Timber Rattlesnakes (Crotalus horridus). For this study seven animals of varying body size were used with masses ranging from 148 to 650 grams. Prior to dosing, blood samples were taken to establish background isotope levels for each animal. Snakes were injected with water enriched with isotopes of oxygen (18O) and hydrogen (2H, deuterium). The injected isotopes were then allowed to equilibrate …