Digital Commons Network^™

Identification And Characterization Of An Interferon Stimulated Gene That Restricts Alphavirus Infection And Pathogenesis, Subhajit Poddar

Arts & Sciences Graduate Student Theses and Dissertations

Viral infection of host cells induces the Type I interferon (IFN) response, which ischaracterized by the production of hundreds of IFN-stimulated genes (ISGs). Altogether, theseISGs function to induce an antiviral state, hindering or blocking various steps of the virallifecycle. Many individual ISGs have potent and broad antiviral functions. However eliminationof a single ISG does not completely abrogate protection, suggesting that other ISGs, althoughmoderate or moderate when considered alone, must work cooperatively to provide optimalantiviral activity.In order to identify and characterize novel ISGs, an attenuated strain of the alphaviruschikungunya (CHIKV-181/25) was tested against an shRNA library of 243 curated murine genesupregulated …

Designing Epigenome Editing Tools To Understand The Functional Role Of Dna Methylation Changes In Cancer, James Mcdonald

Arts & Sciences Graduate Student Theses and Dissertations

DNA methylation is known to silence gene expression in the context of imprinting, X-chromosome inactivation, and retrotransposon silencing. However, the role of DNA methylation in silencing gene expression outside of these contexts is not fully understood. This is especially true in diseases such as cancer, where normal DNA methylation patterns are significantly altered. In breast cancer as well as nearly all cancer types, most of the genome loses DNA methylation while small regions of the genome gain methylation. DNA methylation generally correlates with decreased gene expression when present at a gene promoter. Therefore, these regions of hypo- and hyper-methylation may …

Native Roots And Foreign Grafts: The Spiritual Quest Of Uchimura Kanzō, Christopher Andrew Born

Arts & Sciences Graduate Student Theses and Dissertations

Between 1875 and 1890, Japanese academics, writers, legal experts, and intellectuals discussed and debated a host of new ideas and programs in the rapidly-expanding national media. Of great consequence were the 1890 Imperial Rescript on Education and the Meiji Constitution. The first sought to establish a strong nativist basis for a Japanese identity under the aegis of an imperial hegemon. The second sought to create a structure for modern citizenship based on Western notions of law and social contract. These seemingly antithetical documents came to symbolize the problematical status of the individual in Meiji Japan. They would become the touchstone …

Mental Health And Academic Outcomes Among Adolescents In South Korean Orphanages, Hollee Ann Mcginnis

Arts & Sciences Graduate Student Theses and Dissertations

Research conducted over the past 100 years in Western nations support the adverse effects of orphanages on children’s emotional, developmental, and social well-being as well as economic costs to society (Save the Children UK, 2009; Bakermans-Kranenburg, Van IJzendoorn & Juffer, 2008; Williams & Greenberg, 2010). Globally, the number of orphaned and abandoned children is conservatively estimated to be around 143 million, of whom the majority reside in Asia, followed by Sub-Saharan Africa (UNICEF, UNAIDS, & USAID, 2004). South Korea (hereafter “Korea”) is an exemplary nation for study because it has a well-established child welfare system, including family-based alternatives (domestic and …

Efficiently And Transparently Maintaining High Simd Occupancy In The Presence Of Wavefront Irregularity, Stephen V. Cole

McKelvey School of Engineering Graduate Student Theses & Dissertations

Demand is increasing for high throughput processing of irregular streaming applications; examples of such applications from scientific and engineering domains include biological sequence alignment, network packet filtering, automated face detection, and big graph algorithms. With wide SIMD, lightweight threads, and low-cost thread-context switching, wide-SIMD architectures such as GPUs allow considerable flexibility in the way application work is assigned to threads. However, irregular applications are challenging to map efficiently onto wide SIMD because data-dependent filtering or replication of items creates an unpredictable data wavefront of items ready for further processing. Straightforward implementations of irregular applications on a wide-SIMD architecture are prone …

Robust Odorant Recognition In Biological And Artificial Olfaction, Nalin Katta

McKelvey School of Engineering Graduate Student Theses & Dissertations

Accurate detection and identification of gases pose a number of challenges for chemical sensory systems. The stimulus space is enormous; volatile compounds vary in size, charge, functional groups, and isomerization among others. Furthermore, variability arises from intrinsic (poisoning of the sensors or degradation due to aging) and extrinsic (environmental: humidity, temperature, flow patterns) sources. Nonetheless, biological olfactory systems have been refined over time to overcome these challenges. The main objective of this work is to understand how the biological olfactory system deals with these challenges, and translate them to artificial olfaction to achieve comparable capabilities. In particular, this thesis focuses …

Photodynamic Therapy: Agents And Mechanisms, Rebecca Claire Gilson

McKelvey School of Engineering Graduate Student Theses & Dissertations

Despite enormous efforts, cancer remains a leading cause of morbidity and mortality world-wide. The main challenges currently facing cancer therapy include lack of adequate tumor targeting, failure to treat hypoxic tumor cells, and induction therapy resistant tumors. A solution to these limitations can be found in photodynamic therapy (PDT) which combines light and light activatable compounds, photosensitizers (PSs), to produce cytotoxic reactive oxygen species (ROS) to damage tumor tissue. This creates a spatiotemporal therapeutic effect, where cell damage only occurs at the intersection of the PS and light. PDT can treat tumors through unique mechanisms which reduce induction of tumor …

Development Of High Resolution Tools For Investigating Cardiac Arrhythmia Dynamics, Christopher Reed Gloschat

McKelvey School of Engineering Graduate Student Theses & Dissertations

Every year 300,000 Americans die due to sudden cardiac death. There are many pathologies, acquired and genetic, that can lead to sudden cardiac death. Regardless of the underlying pathology, death is frequently the result of ventricular tachycardia and/or fibrillation (VT/VF). Despite decades of research, the mechanisms of ventricular arrhythmia initiation and maintenance are still incompletely understood.

A contributing factor to this lack of understanding is the limitations of the investigative tools used to study VT/VF. Arrhythmias are organ level phenomena that are governed by cellular interactions and as such, near cellular levels of resolution are needed to tease out their …

Novel Pet Systems And Image Reconstruction With Actively Controlled Geometry, Ke Li

McKelvey School of Engineering Graduate Student Theses & Dissertations

Positron Emission Tomography (PET) provides in vivo measurement of imaging ligands that are labeled with positron emitting radionuclide. Since its invention, most PET scanners have been designed to have a group of gamma ray detectors arranged in a ring geometry, accommodating the whole patient body. Virtual Pinhole PET incorporates higher resolution detectors being placed close to the Region-of-Interest (ROI) within the imaging Field-of-View (FOV) of the whole-body scanner, providing better image resolution and contrast recover. To further adapt this technology to a wider range of diseases, we proposed a second generation of virtual pinhole PET using actively controlled high resolution …

Designing Metabolite Biosensors And Engineering Genetic Circuits To Regulate Metabolic Pathways, Di Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Microbial production of chemicals has provided an attractive alternative to chemical synthesis. A key to make this technology economically viable is to improve titers, productivities, and strain robustness. However, pathway productivities and yields are often limited by metabolic imbalances that inhibit cell growth and chemical production. In contrast, natural metabolic pathways are dynamically regulated according to cellular metabolic status. Dynamic regulation allows cells to adjust metabolite concentrations to optimal levels and avoid wasting carbon and energy. Inspired by nature, synthetic regulatory circuits have shown great promise in improving titers and productivities, because they can balance the metabolism by dynamically adjusting …

Composition-Dependent Mechanisms Of Multiscale Tendon Mechanics, Fei Fang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Tendons serve as an integral part of the musculoskeletal system by transferring loads from muscle to bone and providing joint mobility and stability. From the physiologically-loading perspective, while progress has been made in evaluating mechanical behavior of different types of tendons in tension, further work is needed to relate tendon mechanics to compositional and microstructural properties, particularly under non-tensile loading modalities (i.e., shear, compression). This information is vital to explore mechanisms of how mechanical signals lead to changes in tendon structure and composition to enable these tissues to function properly, including in in vivo multiaxial loading conditions. From the structural …

Hollow And Porous Plasmonic Nanostructures For Highly Efficient Chemical And Biological Sensing, Keng-Ku Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Localized surface plasmon resonance (LSPR) involves the collective and coherent oscillation of dielectrically confined conduction electrons. The LSPR wavelength of noble metal nanoparticles (such as gold, silver and copper), which falls into the visible and near infrared range of the electromagnetic spectrum, is sensitive to the composition, size, shape, dielectric properties of the surrounding medium, and proximity to other nanostructures (plasmon coupling). Based on the sensitivity of the surface plasmon resonance to the changes in the dielectric properties of the surrounding medium and the enhancement of the electromagnetic (EM) field in proximity of metal nanostructures, two important classes of plasmonic …

Mechanism Of Apoptosis Inhibition To Squamous Cell Carcinoma Of Oral Cancer In Cisplatin Treatment, R Marjono Dwi Wibowo, David S Perdanakusuma, Eddy Herman Tanggo

Folia Medica Indonesiana

This study was to approve the increased secretion of Hsp 70, DNA damage, and inhibitor apoptosis protein in cisplatin therapy which influence apoptosis of oral cancer cell and to know mechanism of molecular pathology. This study was an in vitro experimental laboratory using Randomized Block Design. Cell culture of oral cancer divided from cisplatin resistance cancer cell and cancer cell never induce cisplatin. Two group of cancer cell would be given cisplatin therapy. Secretion of Hsp 70, DNA damage, Inhibitor of apoptosis protein, and apoptosis index would be examined. Cisplatin resistance cancer cell group showed lower apoptosis than never induce …

Effect Of Mindfullness Meditation On Stress Level And Coping Mechanism In Cancer Patients, Yesiana Dwi Wahyu Werdani

Folia Medica Indonesiana

Cancer patients have a tendency to experience mental disorders, because the physical changes cause frustration and despair. It impacts on anxiety, depression, and social isolation. The purpose of this study was to analyze the influence of mindfullness meditation to stress levels and coping mechanisms in cancer patients. This study used pre experimental approach with one group pre-test post-test design. Samples were 32 cancer patients with composmentis condition in Indonesian Cancer Foundation East Java Branch, taken by total sampling. The instrument was Perceived Stress Scale and Coping Strategies Inventory. Statistics was verified with Wilcoxon Sign Rank Test and Paired T-test P < 0.05. Results showed the effect of Mindfulness Meditation on the level of stress p = 0.001, the adaptive of coping mechanisms p = 0.001 and maldaptive p = 0.003. In conclusion, Mindfulness meditation can cause the respondent to concentrate and focus on themselves, and also strengthen brain regions at the center of attention and executive function, interoception and mental flexibility.

Identification Of Antiretroviral Mutation In Protease And Reverse Trancriptase Inhibitor In Human Immunodeficiency Virus-1 Of Hiv/Aids Patients In Mimika Regency, Papua, Mirna Widiyanti, Eva Fitriana, Evi Iriani Natalia, Irawati Wike

Folia Medica Indonesiana

Treatment with RT Inhibitors has been used as first line program in Mimika. Regular use of antiretroviral drugs can lower the amount of the virus, but after that HIV can become resistant to the drugs given. Viral resistance to the drugs can occur because of a mutation. If the resistance-associated mutations occur in the DNA of the virus, then the ARV provided will no longer be effective. The aim of this study was to identify the presence of resistance-associated mutations in DNA fragment that encodes the protease and reverse transcriptase. This study used cross sectional design with 84 subjects who …

Posttranscriptional Upregulation Of Idh1 By Hur Establishes A Powerful Survival Phenotype In Pancreatic Cancer Cells., Mahsa Zarei, Shruti Lal, Seth J. Parker, Avinoam Nevler, Ali Vaziri-Gohar, Katerina Dukleska, Nicole C. Mambelli-Lisboa, Cynthia Moffat, Fernando F Blanco, Saswati N. Chand, Masaya Jimbo, Joseph A. Cozzitorto, Wei Jiang, Charles J. Yeo, Eric R. Londin, Erin L. Seifert, Christian M. Metallo, Jonathan R. Brody, Jordan M. Winter

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Cancer aggressiveness may result from the selective pressure of a harsh nutrient-deprived microenvironment. Here we illustrate how such conditions promote chemotherapy resistance in pancreatic ductal adenocarcinoma (PDAC). Glucose or glutamine withdrawal resulted in a 5- to 10-fold protective effect with chemotherapy treatment. PDAC xenografts were less sensitive to gemcitabine in hypoglycemic mice compared with hyperglycemic mice. Consistent with this observation, patients receiving adjuvant gemcitabine (n = 107) with elevated serum glucose levels (HgbA1C > 6.5%) exhibited improved survival. We identified enhanced antioxidant defense as a driver of chemoresistance in this setting. ROS levels were doubled in vitro by either nutrient withdrawal …

Information Theoretic Study Of Gaussian Graphical Models And Their Applications, Ali Moharrer

LSU Doctoral Dissertations

In many problems we are dealing with characterizing a behavior of a complex stochastic system or its response to a set of particular inputs. Such problems span over several topics such as machine learning, complex networks, e.g., social or communication networks; biology, etc. Probabilistic graphical models (PGMs) are powerful tools that offer a compact modeling of complex systems. They are designed to capture the random behavior, i.e., the joint distribution of the system to the best possible accuracy. Our goal is to study certain algebraic and topological properties of a special class of graphical models, known as Gaussian graphs. First, …

Investigating Core Shale Depositional Environments Of Late Pennsylvanian Cyclothems Utilizing Geochemical Proxies To Test The Superestuarine Model, Bryce A. Mathis

LSU Master's Theses

The Late Paleozoic Midcontinent Sea (LPMS) inundated vast areas of the North American interior during glacio-eustatic transgressions, depositing widespread black shales facies within the core shale intervals of major cyclothems. These black shale deposits are unique because no modern analogs can adequately explain the depositional environments and model for organic matter preservation across such vast ancient epicontinental settings. One possible explanation is that a superestuarine circulation system developed across the LPMS during humid interglacial phases, which promoted strong water column stratification and benthic anoxia.

The goal of this research was to test the validity of the superestuarine estuarine model and …

Impacts Of Coastal Acidification On Louisiana Plankton, Amy Mallozzi

LSU Master's Theses

Anthropogenic input of carbon dioxide (CO₂) has an increasingly acidifying effect on the world’s oceans with the potential to impact biogeochemical cycles and food web dynamics. Coastal Louisiana is an area highly vulnerable to changing climate, but the unique local water chemistry created by input from the Mississippi and Atchafalaya Rivers makes the manifestation of elevated CO₂ and its biological implications difficult to predict. Louisiana estuaries are highly productive and support a large commercial market for the eastern oyster, Crassostrea virginica. This study explores the use of experimental microcosms to expose natural phytoplankton assemblages and larval …

Review Of Training Principles For Flight Training In Aircraft Or Simulator, Stefan Kleinke

National Training Aircraft Symposium (NTAS)

In human-performance-driven fields such as the social and behavioral sciences and education, there is a particular risk for a disconnect between current research and applied practice. Often, new findings require policy changes and workforce re-education before being applied in a meaningful way. Therefore, a continuous need for practitioner professional development and continuation training exists to ensure informed practices. This presentation is motivated by these needs and aims to help flight training professionals to make informed decisions when designing and conducting flight training events. Based on a conceptual framework of cognitive and behavioral theories in learning, a variety of common training …

Energy Safety Management: Mitigating Loss Of Control Inflight, Juan Merkt

National Training Aircraft Symposium (NTAS)

Under the new Airman Certification Standards (ACS), the Federal Aviation Administration (FAA) has mandated for the first time that private and commercial pilot candidates demonstrate understanding of energy management in several areas of operation. Recognition by the FAA of the importance of energy management is a welcome development, given the potential lethal consequences of mishandling the airplane’s energy state. Poor management of the energy associated with vertical flight path and/or airspeed is a significant factor in loss of control in flight and runway excursions during landing, two leading causes of fatal accidents in aviation. While most pilots are familiar with …

September 14, 2017, James Madison University

The Breeze, 2010-2019

The Breeze is the student newspaper of James Madison University in Harrisonburg, Virginia.

Eyitayo Coauthors Article On Seminatural Grasslands And Powerline Clearings, Ohio University College Of Arts & Sciences

All Forum Articles

No abstract provided.

Carotid Body-Mediated Chemoreflex Drive In The Setting Of Low And High Output Heart Failure., Rodrigo Del Rio, David C. Andrade, Camilo Toledo, Hugo S. Diaz, Claudia Lucero, Alexis Arce-Alvarez, Noah J. Marcus, Harold D. Schultz

Journal Articles: Cellular & Integrative Physiology

Enhanced carotid body (CB) chemoreflex function is strongly related to cardiorespiratory disorders and disease progression in heart failure (HF). The mechanisms underlying CB sensitization during HF are not fully understood, however previous work indicates blood flow per se can affect CB function. Then, we hypothesized that the CB-mediated chemoreflex drive will be enhanced only in low output HF but not in high output HF. Myocardial infarcted rats and aorto-caval fistulated rats were used as a low output HF model (MI-CHF) and as a high output HF model (AV-CHF), respectively. Blood flow supply to the CB region was decreased only in …

Unh Researchers Aim To Re-Domesticate Quinoa For Northern New England, Lori Tyler Gula

Media Relations

No abstract provided.

Landsat Based Sargassum Coverage In The Northern Gulf Of Mexico, 2010, Chuanmin Hu, Lian Feng

C-IMAGE data

This dataset contains the sargassum coverage in the northeastern Gulf of Mexico detected using both Landsat remote sensing images and airborne AVIRIS data. The mean Sargassum coverage during the four quarters of 2010 for the study region are also provided. Dataset results are provided in Excel format and correspond to the the publication: Hu, C.; Hardy, R.; Ruder, E.; Geggel, A.; Feng, L.; Powers, S.; Hernandez, F.; Graettinger, G.; Bodnar, J.; McDonald, T. (2016). Sargassum coverage in the northeastern Gulf of Mexico during 2010 from Landsat and airborne observations: Implications for the Deepwater Horizon oil spill impact assessment. Marine Pollution …

The Mechanism Of Alpha Lipoic Acid On Reducing The Mda Level And Mcp-1 Expression In Endothelial Dysfunction Of Hypercholesterolemia Rat (Rattus Norvegicus) Model, Dewi Perwito Sari, Imam Susilo, Junaidi Khotib

Folia Medica Indonesiana

Endothelial dysfunction is an initial condition of atherosclerosis and other vascular diseases where one of the risk factors is hypercholesterolemia. Blood cholesterol levels is associated with an increase in the production of reactive oxygen species (ROS). The increasing of ROS production can cause increased oxidative stress which in turn resulting in endothelial dysfunction. Alpha lipoic acid (ALA) is one of the antioxidant compound that has been developed and studied. In this study we found that the use of ALA in Rattus norvegicus rats signifficantly lower the total cholesterol levels at dose 60 mg/kgBW (p=0.020). ALA also inhibit the expression of …

Integrative Analysis Identifies Four Molecular And Clinical Subsets In Uveal Melanoma., A Gordon Robertson, Juliann Shih, Christina Yau, Ewan A Gibb, Junna Oba, Karen L Mungall, Julian M Hess, Vladislav Uzunangelov, Vonn Walter, Ludmila Danilova, Tara M Lichtenberg, Melanie Kucherlapati, Patrick K Kimes, Ming Tang, Alexander Penson, Ozgun Babur, Rehan Akbani, Christopher A Bristow, Katherine A Hoadley, Lisa Iype, Matthew T Chang, Andrew D Cherniack, Christopher Benz, Gordon B Mills, Roel G W Verhaak, Klaus G Griewank, Ina Felau, Jean C Zenklusen, Jeffrey E Gershenwald, Lynn Schoenfield, Alexander J Lazar, Mohamed H Abdel-Rahman, Sergio Roman-Roman, Marc-Henri Stern, Colleen M Cebulla, Michelle D Williams, Martine J Jager, Sarah E Coupland, Bita Esmaeli, Cyriac Kandoth, Scott E Woodman

Articles, Abstracts, and Reports

Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis monosomy 3 (M3) and two with better-prognosis disomy 3 (D3). We show that BAP1 loss follows M3 occurrence and correlates with a global DNA methylation state that is distinct from D3-UM. Poor-prognosis M3-UM divide into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. We report change-of-function SRSF2 mutations. Within D3-UM, EIF1AX- and SRSF2/SF3B1-mutant tumors have distinct somatic copy number alterations and DNA methylation profiles, providing insight into the biology of these low- versus intermediate-risk clinical mutation subtypes.

Increasing Serum Cholesterol Level Among Sri Lankan Adult Obese Patients Admitted To Medical Wards: A Cross-Sectional Study, Dioso R. (Ii) P., Shalina K., Judenimal K.

ASEAN Journal on Science and Technology for Development

This research identifid the factors affcting the widespread of the level of serum cholestrol among adult obese patients admitted to government hospitals in the easternpart of Sri Lanka, and identifie the number of adults obese patients with increasing serum cholesterollevel. A descriptive cross-sectional studydesign was used. Convenience sampling technique helped select 150 patients in medical wards and clinics of two government hospitals in the easternprovince of Sri Lanka, and Questionnaireswere distributedfor data analysis. Overall findingsof 150 obese patients regarding increasing serum cholestrol level admitted in the medical wards and follow-up at medical clinics had 59% in moderate risk, 36% with …

Reevaluating The Occurrence And Phylogeny Of The Pigtoe Unionid Mussels Fusconaia Askewi, Fusconaia Lananensis, Fusconaia Flava, And Pleurobema Riddelli In Texas, Charles J. Pratt

Biology Theses

The recent development of DNA-based species classification methods has led to the revision of many morphology-based species designations as genetic data has provided new information for species delineation. Analysis of standardized DNA ‘barcoding’ gene regions has proven particularly effective in resolving the taxonomic status of taxa that display phenotypic and habitat overlap.

Freshwater Unionid and Margaritiferid mussels comprise one of the most diverse aquatic taxa in North America, but are also among the most threatened, with over 70% of the approximately 300 native species considered at-risk or in decline. Although mussels face extensive threats from anthropogenic activity, conservation efforts have …