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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 …

Dietary Nitrate Increases Exercise Tolerance In Patients With Non-Ischemic, Dilated Cardiomyopathy-A Double-Blind, Randomized, Placebo-Controlled, Crossover Trial., Conor Kerley, James O'Neill, Venu Reddy Bijjam, Ciara Blaine, Philip James, Liam Cormican

Articles

No abstract provided.

Collective Timekeeping Among Cells Of The Master Circadian Clock, Jennifer A. Evans

Biomedical Sciences Faculty Research and Publications

The suprachiasmatic nucleus (SCN) of the anterior hypothalamus is the master circadian clock that coordinates daily rhythms in behavior and physiology in mammals. Like other hypothalamic nuclei, the SCN displays an impressive array of distinct cell types characterized by differences in neurotransmitter and neuropeptide expression. Individual SCN neurons and glia are able to display self-sustained circadian rhythms in cellular function that are regulated at the molecular level by a 24h transcriptional–translational feedback loop. Remarkably, SCN cells are able to harmonize with one another to sustain coherent rhythms at the tissue level. Mechanisms of cellular communication in the SCN network are …

The Concerted Regulation Of Intracellular Signaling By Amyloid Precursor Protein And Aβ Peptide, Lisa Kirouac

USF Tampa Graduate Theses and Dissertations

It is widely accepted that A-beta (Aβ) generated from amyloid precursor protein (APP) oligomerizes and fibrillizes to form neuritic plaques in the Alzheimer’s disease (AD) brain, yet little is known about the contribution of APP preceding AD pathogenesis. Our data presented here suggest that APP has a functional role in cell cycle regulation and proliferation. First, we demonstrat that APP is pathologically phosphorylated at Thr₆₆₈ and that P-APP localizes to the centrosomes. Furthermore, P-APP is proteolytically processed in a cell cycle -dependent manner to generate its pathogenic metabolites. Using Stable Isotope Labeling by Amino Acids in Culture (SILAC) and …

The Future Is In The Numbers: The Power Of Predictive Analysis In The Biomedical Educational Environment, Charles A. Gullo Phd

Biochemistry and Microbiology

Biomedical programs have a potential treasure trove of data they can mine to assist admissions committees in identification of students who are likely to do well and help educational committees in the identification of students who are likely to do poorly on standardized national exams and who may need remediation. In this article, we provide a step-by-step approach that schools can utilize to generate data that are useful when predicting the future performance of current students in any given program. We discuss the use of linear regression analysis as the means of generating that data and highlight some of the …

Type Iv Pili Promote Early Biofilm Formation By Clostridium Difficile, Grace A. Maldarelli, Kurt H. Piepenbrink, Alison J. Scott, Jeffrey A. Freiberg, Yang Song, Yvonee Achermann, Robert K. Ernst, Mark E. Shirtliff, Eric J. Sundberg, Michael S. Donnenberg, Erik C. Von Rosenvinge

Food for Health: Publications

Increasing morbidity and mortality from Clostridium difficile infection (CDI) present an enormous challenge to healthcare systems. Clostridium difficile express type IV pili (T4P), but their function remains unclear. Many chronic and recurrent bacterial infections result from biofilms, surface-associated bacterial communities embedded in an extracellular matrix. CDI may be biofilm mediated; T4P are important for biofilm formation in a number of organisms. We evaluate the role of T4P in C. difficile biofilm formation using RNA sequencing, mutagenesis and complementation of the gene encoding the major pilin pilA1, and microscopy. RNA sequencing demonstrates that, in comparison to other growth phenotypes, C. difficile …

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 …

Carbonylation Modification Regulates Na/K-At Pasesignaling And Salt Sensitivity: A Review And A Hypothesis, Preeya Shah Phd, Rebecca Martin, Yanling Yan, Joseph I. Shapiro Md, Jiang Liu

Biochemistry and Microbiology

Na/K-ATPase signaling has been implicated in different physiological and pathophysiological conditions. Accumulating evidence indicates that oxidative stress not only regulates the Na/K-ATPase enzymatic activity, but also regulates its signaling and other functions. While cardiotonic steroids (CTS)-induced increase in reactive oxygen species (ROS) generation is an intermediate step in CTS-mediated Na/K-ATPase signaling, increase in ROS alone also stimulates Na/K-ATPase signaling. Based on literature and our observations, we hypothesize that ROS have biphasic effects on Na/K-ATPase signaling, transcellular sodium transport, and urinary sodium excretion. Oxidative modulation, in particular site specific carbonylation of the Na/K-ATPase α1 subunit, is a critical step in proximal …

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 …

Cyclic Di-Gmp-Regulated Periplasmic Proteolysis Of A Pseudomonas Aeruginosa Type Vb Secretion System Substrate, Richard B. Cooley, T. Jarrod Smith, Wilfred Leung, Valerie Tierney, Bradley Borlee, George A. O'Toole, Holger Sondermann

Dartmouth Scholarship

We previously identified a second-messenger-regulated signaling system in the environmental bacterium Pseudomonas fluorescens which controls biofilm formation in response to levels of environmental inorganic phosphate. This system contains the transmembrane cyclic di-GMP (c-di-GMP) receptor LapD and the periplasmic protease LapG. LapD regulates LapG and controls the ability of this protease to process a large cell surface adhesin protein, LapA. While LapDG orthologs can be identified in diverse

Week Of June 20, 2016, New York Medical College

InTouch

• Victor T. Madubuko Is Named Diversity and Inclusion Officer
• Department of Family and Community Medicine Hosts Annual Faculty Appreciation Dinner
• NYMC Honors Preceptors and Seminar Leaders at Annual Dinner
• School of Medicine Joins Ranks of AAMC Te4Q Sites

Glial Cell Involvement In Early Alzheimer's Disease, Rachel Y. De La Torre

PSU McNair Scholars Online Journal

Glial cells, the resident immune cells of the brain, are important for brain health as they represent a critical function both in brain injury as well as in brain development and maintenance. Following brain injury, glia quickly respond by cleaning up neuronal and synaptic debris. In addition to their role as the cleaning cell of the brain, recent research has shown that during development, glia also shape and fine-tune neural connections by eliminating weak synapses fated for removal. However, whether glial cells also continue to remodel synaptic architecture in the adult brain is unclear. Moreover, synaptic pruning and loss are …

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 …

Inhibiting The Interaction Between Grp94 And Myocilin To Treat Primary Open-Angle Glaucoma, Andrew Stothert

USF Tampa Graduate Theses and Dissertations

Glaucoma is a neurodegenerative protein misfolding disorder classified by increases in IOP, damage to retinal ganglion cells (RGCs), optic nerve (ON) head damage, and progressive irreversible blindness. Primary open-angle glaucoma (POAG) is the most common form of glaucoma, constituting over 90% of clinical cases. POAG is observed in patients where normal outflow channels, mainly the trabecular meshwork (TM), are exposed at the angle formed by the iris and cornea. However, due to TM cellular dysfunction, aqueous outflow resistance is increased preventing normal circulation of aqueous humor. Recent studies have shown that in 2-4% of POAG cases, increased intracellular levels of …

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 Pseudomonas Aeruginosa Efflux Pump Mexghi-Opmd Transports A Natural Phenazine That Controls Gene Expression And Biofilm Development, Hassan Sakhtah, Leslie Koyama, Yihan Zhang, Diana K. Morales, Blanche Fields, Alexa Price-Whelan, Deborah Hogan

Dartmouth Scholarship

Redox-cycling compounds, including endogenously produced phenazine antibiotics, induce expression of the efflux pump MexGHI-OpmD in the opportunistic pathogen Pseudomonas aeruginosa Previous studies of P. aeruginosa virulence, physiology, and biofilm development have focused on the blue phenazine pyocyanin and the yellow phenazine-1-carboxylic acid (PCA). In P. aeruginosa phenazine biosynthesis, conversion of PCA to pyocyanin is presumed to proceed through the intermediate 5-methylphenazine-1-carboxylate (5-Me-PCA), a reactive compound that has eluded detection in most laboratory samples. Here, we apply electrochemical methods to directly detect 5-Me-PCA and find that it is transported by MexGHI-OpmD in P. aeruginosa strain PA14 planktonic and biofilm cells. We …

1st Place Research Paper: The Effectiveness Of Yoga Therapy On An Adult, Post-Stroke Population: A Systematic Review, Baylor E. Hogan

Kevin and Tam Ross Undergraduate Research Prize

Objectives: The objectives of this paper are to (1) give a brief overview of stroke pathophysiology (2) outline yoga as a therapeutic strategy (3) present the current research on yoga rehabilitation for stroke (4) discuss the efficacy of yoga for chronic stroke.

Methods: Relevant terms were searched in PubMed, Web of Science, Academic OneFile, ScienceDirect, and Google Scholar electronic databases. Studies were excluded if they contained pediatric stroke, non-stroke neurological diseases, or subjects with comorbidities. Statistically significant data was extracted for the primary measures of nine trials.

Results: Four studies measured statistically significant outcomes (p<0.05). These included improvements in balance, independence, endurance, trait anxiety, fear of falling, self-efficacy, pain, strength, range of motion (ROM), activity, participation, and quality of life (QoL). Discussion: Lack of statistical significance in post-stroke depression (PSD) measures may be due to inadequate intervention length or a psychosocial cause of depression. Improvements in balance, flexibility, and strength from yoga participation permitted progress in disability and functionality. Finally, overall health-related quality of life (HRQL) is affected by the severity of mental disorders and physical disability. Yoga can have a positive effect in both domains and therefore, may improve HRQL.

Conclusion: …

Role Of Histidine 547 Of Human Dopamine Transporter In Molecular Interaction With Hiv-1 Tat And Dopamine Uptake, Yaxia Yuan, Pamela M. Quizon, Wei-Lun Sun, Jianzhuang Yao, Jun Zhu, Chang-Guo Zhan

Molecular Modeling and Biopharmaceutical Center Faculty Publications

HIV-1 Tat plays an important role in HIV-associated neurocognitive disorders (HAND) by disrupting neurotransmission including dopamine uptake by human dopamine transporter (hDAT). Previous studies have demonstrated that HIV-1 Tat directly binds to hDAT and some amino-acid mutations that attenuate the hDAT-Tat binding also significantly decreased dopamine uptake activity of hDAT. This combined computational-experimental study demonstrates that histidine-547 (H547) of hDAT plays a crucial role in the hDAT-Tat binding and dopamine uptake by hDAT, and that the H547A mutation can not only considerably attenuate Tat-induced inhibition of dopamine uptake, but also significantly increase the V_max of hDAT for dopamine uptake. …

Targeting Tau Degradation By Small Molecule Inhibitors For Treatment Of Tauopathies, Mackenzie Martin

USF Tampa Graduate Theses and Dissertations

Tauopathies are neurodegenerative diseases that affect millions of people around the world. Tauopathies include more than 20 neurodegenerative diseases. Some of the most common tauopathies are Alzheimer’s disease (AD), frontotemporal dementia (FTD), chronic traumatic encephalopathy (CTE), Pick’s disease, corticobasal degeneration, progressive supranuclear palsy (PSP), agyrophillic grain disease, and amyotrophic lateral sclerosis (ALS). These diseases can cause significant memory loss, behavioral changes, motor deficits and speech impairments. Tauopathies stem from accumulation of the microtubule associated protein tau (MAPT). Tau stabilizes microtubules and helps with axonal transport. In a disease state tau becomes hyperphosphorylated and truncated leading to its aggregation. More recently …

Theaflavin-3, 3'-Digallate Induces Apoptosis And G2 Cell Cycle Arrest Through The Akt/Mdm2/P53 Pathway In Cisplatin-Resistant Ovarian Cancer A2780/Cp70 Cells, Youying Tu, Eunhye Kim, Ying Gao, Gary O. Rankin, Bo Li, Yi Charlie Chen

Pharmacology, Physiology and Toxicology

Ovarian cancer is the most lethal gynecological cancer among women worldwide. Adverse side effects and acquired resistance to conventional platinum based chemotherapy are major impediments in ovarian cancer treatment, and drive the development of more selective anticancer drugs that target cancer-specific defects. In this study, theaflavin-3, 3'-digallate (TF3), the major theaflavin monomer in black tea, exhibited a potent growth inhibitory effect on the cisplatinresistant ovarian cancer A2780/CP70 cells (IC50, 23.81 μM), and was less cytotoxic to a normal ovarian IOSE‑364 cells (IC50, 59.58 μM) than to the cancer cells. Flow cytometry analysis indicated that TF3 induced preferential apoptosis and G2 …

Oligodendrocyte Ablation As A Tool To Study Demyelinating Diseases, Ahdeah Pajoohesh-Ganji, Robert H. Miller

Anatomy and Regenerative Biology Faculty Publications

Multiple sclerosis (MS) is an autoimmune mediated neurodegenerative disease characterized by demyelination and oligodendrocyte (OL) loss in the central nervous system and accompanied by local inflammation and infiltration of peripheral immune cells. Although many risk factors and symptoms have been identified in MS, the pathology is complicated and the cause remains unknown. It is also unclear whether OL apoptosis precedes the inflammation or whether the local inflammation is the cause of OL death and demyelination. This review briefly discusses several models that have been developed to specifically ablate oligodendrocytes in an effort to separate the effects of demyelination from inflammation.

Reversibility Of Apixaban Anticoagulation With A Four-Factor Prothrombin Complex Concentrate In Healthy Volunteers., S Nagalla, Lynda Thomson, Y Oppong, B Bachman, I Chervoneva, Walter K. Kraft

Department of Pharmacology and Experimental Therapeutics Faculty Papers

It was hypothesized that the four-factor prothrombin complex concentrate (4F-PCC) Kcentra 25 unit/kg would reverse impairment of thrombin generation in healthy volunteers dosed with apixaban to steady state. In this randomized, two-period crossover, assessor-blinded trial, 12 healthy subjects received 5 mg apixaban every 12 h. Three h after the fifth dose, four-factor prothrombin complex concentrate (4F-PCC) 25 unit/kg or saline were infused. Serial blood samples were assessed for thrombin generation using PPP-reagent and PPP-reagent low, anti-Xa, PT, and PTT assays. Geometric mean ratio was calculated at 30 min postinfusion, and at 24, 48, and 72 h. Peak thrombin generation was …

Activation Of Target Gene Expression In Neurons By The C. Elegans Rfx Transcription Factor, Daf-19, Katherine P. Mueller

Lawrence University Honors Projects

DAF-19, the only RFX transcription factor found in C. elegans, is required for the formation of neuronal sensory cilia. Four isoforms of the DAF-19 protein have been reported, and the m86 nonsense (null) mutation affecting all four isoforms has been shown to prevent cilia formation. Transcriptome analyses employing microarrays of L1 and adult stage worms were completed using RNA from daf-19(m86) worms and an isogenic wild type strain to identify additional putative DAF-19 target genes. Using transcriptional fusions with GFP, we compared the expression patterns of several potential gene targets using fluorescence confocal microscopy. Expression patterns were characterized in …

Proteomic Profiling Of Serum Derived Exosomes From Prostate Cancer Patients, David Turay

Loma Linda University Electronic Theses, Dissertations & Projects

Touted among the major achievements in the diagnosis and management of Prostate cancer (PCa) in the past few decades has been, the dramatic decline of men with advanced/metastatic PCa at diagnosis coupled with a significant improvement ( >90%) in the five and ten year survival rates of the disease. Non-palpable PCa (potentially clinically treatable disease) now accounts for 70-80% of all newly diagnosed cases of PCa. Preceding these changes by about a decade was the introduction of Prostatic Specific Antigen (PSA) into clinical practice; first as biomarker for monitoring response to therapy and subsequently as a complementary screening tool. It …

Mechanism Of Chimeric Vaccine Mediated Immune Suppression Of Human Dendritic Cells, Jacques Christian Mbongue

Loma Linda University Electronic Theses, Dissertations & Projects

Type 1 diabetes mellitus is a chronic inflammatory disease in which insulin producing β-cells of the pancreatic islets are killed by autoreactive cells of the immune system in response to a loss of tolerance. Dendritic cells (DC) interact predominantly with naïve T cells to regulate the delicate balance between immunity and tolerance required to maintain immunological homeostasis. In this dissertation, immature human dendritic cells (iDC) were inoculated with a chimeric fusion protein vaccine containing the pancreatic β-cell auto-antigen proinsulin linked to a mucosal adjuvant the cholera toxin B subunit (CTB-INS). Proteomic analysis of vaccine inoculated DCs revealed strong up-regulation of …

The Role Of Collagen Interacting Proteins In The Pathogenesis Of Filifactor Alocis, Ozioma Salomey Chioma

Loma Linda University Electronic Theses, Dissertations & Projects

Filifactor alocis is a Gram-positive, asaccharolytic; obligate anaerobe that has emerged as a potential periodontal pathogen due to its presence in high numbers in patients who have periodontal disease and least detection in healthy individuals (Kumar et al., 2003, Kumar et al., 2006, Wade, 2011). There is compelling evidence in the literature that demonstrates that F. alocis has virulence properties that may play an important role in infection-induced periodontitis (Abusleme et al., 2013, Griffen et al., 2012, Hutter et al., 2003, Khader et al., 2006, Siqueira and Rocas, 2003, Siqueira et al., 2009). However, there is a gap in our …

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 …

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 …