Digital Commons Network^™

Research & Innovation For 2012-2013, University Of Rhode Island

Publications (Research and Economic Development)

The 2012-2013 issue of Research & Innovation, a periodical focused on research at the University of Rhode Island.

Epigenetics In Research And Practice, Debra E. Lyon, Susan G. Dorsey, Leorey Saligan

School of Nursing Publications

This special issue focused on the intersection of epigenetics with nursing research and practice. The first paper in this series addresses the role of epigenetic modifications in pain and analgesia response, highlighting the need for future research on epigenomic modification in the development of chronic pain, and summarizes the therapeutic potential to alter epigenetic processes to improve health outcomes. The second studies the epigenetic alterations and an increased frequency of micronuclei in women with fibromyalgia, highlighting a difference in an epigenetic biomarker in participants versus controls. The third paper explored the role of epigenetics in critical illness and the need …

Recruiting For Epigenetic Research: Facilitating The Informed Consent Process, Nancy Jallo, Debra E. Lyon, Patricia Anne Kinser, Debra Lynch Kelly, Victoria Menzies, Colleen Jackson-Cook

School of Nursing Publications

Because the effects of epigenetic (gene-environment interaction) changes have been associated with numerous adverse health states, the study of epigenetic measures provides exciting research opportunities for biobehavioral scientists. However, recruitment for studies focusing on any aspect of genetics poses challenges. Multiple factors, including lack of knowledge regarding a research study, have been identified as barriers to recruitment. Strengthening the informed consent process through extended discussion has been found to be effective in recruiting for research studies in general, yet there is a paucity of information that focused on such a recruitment strategy for epigenetic studies. In this paper, we share …

Psychoneuroimmunology-Based Stress Management During Adjuvant Chemotherapy For Early Breast Cancer, Jo Lynne W. Robins, Nancy L. Mccain, R. K. Elswick Jr., Jeanne M. Walter, D. Patricia Gray, Inez Tuck

School of Nursing Publications

Objective. In a randomized trial of women with early stage breast cancer undergoing adjuvant chemotherapy, two stress management interventions, tai chi training and spiritual growth groups, were compared to a usual care control group, to evaluate psychosocial functioning, quality of life (QOL), and biological markers thought to reflect cancer- and treatment-specific mechanisms. Method. The sample consisted of 145 women aged 27–75 years; 75% were Caucasian and 25% African American. A total of 109 participants completed the study, yielding a 75% retention rate. Grounded in a psychoneuroimmunology framework, the overarching hypothesis was that both interventions would reduce perceived stress, enhance QOL …

Epigenetic Alterations And An Increased Frequency Of Micronuclei In Women With Fibromyalgia, Victoria Menzies, Debra E. Lyon, Kellie J. Archer, Kimberly Jones, Guimin Gao, Timothy P. York, Colleen Jackson-Cook

School of Nursing Publications

Fibromyalgia (FM), characterized by chronic widespread pain, fatigue, and cognitive/mood disturbances, leads to reduced workplace productivity and increased healthcare expenses. To determine if acquired epigenetic/genetic changes are associated with FM, we compared the frequency of spontaneously occurring micronuclei (MN) and genome-wide methylation patterns in women with FM () to those seen in comparably aged healthy controls ( (MN); (methylation)). The mean (sd) MN frequency of women with FM (51.4 (21.9)) was significantly higher than that of controls (15.8 (8.5)) (; df = 1; ). Significant differences ( sites) in methylation patterns were observed between cases and controls considering a 5% …

Hypothermic Machine Perfusion Preservation Of The Dcd Kidney: Machine Effects, Susanne L. Lindell, Heather Muir, John Brassil, Martin J. Mangino

Surgery Publications

Purpose. Kidneys from DCD donors represent a significant pool, but preservation problems exist. The study objective was to test the importance of machine type for hypothermic preservation of DCD kidneys.Methods. Adult Beagle dog kidneys underwent 45 minutes of warm in situ ischemia followed by hypothermic perfusion for 24 hours (Belzer-MPS Solution) on either an ORS LifePort or a Waters RM3 using standard perfusion protocols. Kidneys were then autotransplanted, and renal function was assessed over 7 days following contralateral nephrectomy. Results. Renal vascular resistance was not different between the two pumps. After 24 hours, the oxygen partial pressure and oxygen delivery …

Improving The Diagnosis Of Meningitis Due To Enterovirus And Herpes Simplex Virus I And Ii In A Tertiary Care Hospital, Eduardo Casaroto, Alexandre R. Marra, Fernando Morgadinho S. Coelho, Joao Renato Rebello Pinho, Roberta Sitnik, Fernando Colombari, Elivane Silva Victor, Nair Hideko Muto, Carlos Senne, Oscar Fernando Pavão Dos Santos, Michael B. Edmond

Internal Medicine Publications

Background Enterovirus and herpes simplex viruses are common causes of lymphocytic meningitis. The purpose of this study was to analyse the impact of the use molecular testing for Enteroviruses and Herpes simplex viruses I and II in all suspected cases of viral meningitis.

Methods From November 18, 2008 to November 17, 2009 (phase II, intervention), all patients admitted with suspected viral meningitis (with pleocytosis) had a CSF sample tested using a nucleic acid amplification test (NAAT). Data collected during this period were compared to those from the previous one-year period, i.e. November 18, 2007 to November 17, 2008 (phase I, …

Htert Promoter Polymorphism, -1327c>T, Is Associated With The Risk Of Epithelial Cancer, Toshihiko Iizuka, Motoji Sawabe, Kaiyo Takubo, Miao Liu, Yukio Homma, Motofumi Suzuki, Tomio Arai

Internal Medicine Publications

Telomeres are repetitive nucleotide sequences that cap the end of eukaryotic chromosomes. Attrition of these structures has been associated with carcinogenesis in many tissues, and therefore, they are essential for chromosome stabilization. Telomeres are maintained by telomerase complexes, of which human telomerase reverse transcriptase (hTERT) is an essential component. A functional polymorphism, -1327C>T (rs2735940), located in the promoter of the hTERT gene is associated with telomere length in peripheral blood leukocytes. We hypothesized that this polymorphism might affect susceptibility to various epithelial malignancies. The -1327C>T polymorphism was examined in 1,551 consecutive autopsy cases (mean age, 80.3 years), and …

Fenretinide Causes Emphysema, Which Is Prevented By Sphingosine 1-Phoshate, Masanori Yasuo, Shiro Mizuno, Jeremy Allegood, Donatas Kraskauskas, Harm J. Bogaard, Sarah Spiegel, Norbert F. Voelkel

Internal Medicine Publications

Sphingolipids play a role in the development of emphysema and ceramide levels are increased in experimental models of emphysema; however, the mechanisms of ceramide-related pulmonary emphysema are not fully understood. Here we examine mechanisms of ceramide-induced pulmonary emphysema. Male Sprague-Dawley rats were treated with fenretinide (20 mg/kg BW), a synthetic derivative of retinoic acid that causes the formation of ceramide, and we postulated that the effects of fenretinide could be offset by administering sphingosine 1-phosphate (S1P) (100 µg/kg BW). Lung tissues were analyzed and mean alveolar airspace area, total length of the alveolar perimeter and the number of caspase-3 positive …

Multi-Snp Analysis Of Gwas Data Identifies Pathways Associated With Nonalcoholic Fatty Liver Disease, Qing-Rong Chen, Rosemary Braun, Ying Hu, Chunhua Yan, Elizabeth M. Brunt, Daoud Meerzaman, Arun J. Sanyal, Kenneth Buetow

Internal Medicine Publications

Non-alcoholic fatty liver disease (NAFLD) is a common liver disease; the histological spectrum of which ranges from steatosis to steatohepatitis. Nonalcoholic steatohepatitis (NASH) often leads to cirrhosis and development of hepatocellular carcinoma. To better understand pathogenesis of NAFLD, we performed the pathway of distinction analysis (PoDA) on a genome-wide association study dataset of 250 non-Hispanic white female adult patients with NAFLD, who were enrolled in the NASH Clinical Research Network (CRN) Database Study, to investigate whether biologic process variation measured through genomic variation of genes within these pathways was related to the development of steatohepatitis or cirrhosis. Pathways such as …

Modulation Of The Metabiome By Rifaximin In Patients With Cirrhosis And Minimal Hepatic Encephalopathy, Jasmohan S. Bajaj, Douglas M. Heuman, Arun J. Sanyal, Phillip B. Hylemon, Richard K. Sterling, R. Todd Stravitz, Michael Fuchs, Jason M. Ridlon, Kalyani Daita, Pamela Monteith, Nicole A. Noble, Melanie B. White, Andmorgan Fisher, Masoumeh Sikaroodi, Huzefa Rangwala, Patrick M. Gillevet

Internal Medicine Publications

Hepatic encephalopathy (HE) represents a dysfunctional gut-liver-brain axis in cirrhosis which can negatively impact outcomes. This altered gut-brain relationship has been treated using gut-selective antibiotics such as rifaximin, that improve cognitive function in HE, especially its subclinical form, minimal HE (MHE). However, the precise mechanism of the action of rifaximin in MHE is unclear. We hypothesized that modulation of gut microbiota and their end-products by rifaximin would affect the gut-brain axis and improve cognitive performance in cirrhosis. Aim To perform a systems biology analysis of the microbiome, metabolome and cognitive change after rifaximin in MHE.

Methods

Twenty cirrhotics with MHE …

Regulation Of Antigenic Variation In Trypanosoma Brucei, Imaan A. Benmerzouga

ETD Archive

Trypanosoma brucei is a protozoan parasite that causes sleeping sickness in humans and nagana in cattle. When inside the mammalian host, T. brucei cells stay in extracellular spaces and regularly switch their surface antigen, Variant Surface Glycoprotein (VSG), to escape the host's immune responses. To ensure the effectiveness of VSG switching, T. brucei expresses a single type of VSG at any time exclusively from one of 20 identical VSG expression sites located next to the telomere. Monoallelic expression of VSG and VSG switching are important for T. brucei's pathogenesis. Our major goal is to understand the mechanisms of antigenic variation …

A Meta-Analysis Of The Effectiveness Of Stem-Programs In The United States, Dayoung An

ETD Archive

The federal government has been spending a large amount of funds on STEM programs. It is important to examine the effectiveness of such spending. Much research has been conducted in the past 30 years for this particular purpose however, the results of such evaluations have not painted a clear picture of the effectiveness of STEM programs. The goal of this meta-analysis is to investigate whether STEM programs are successful in the outcomes they claim to achieve. Such a meta-analysis must integrate all of the empirical studies which reported their effort in evaluating the effectiveness of STEM programs, based on measures …

Genome-Wide Angiotensin Ii Regulated Microrna Expression Profiling ; A Smooth Muscle-Specific Microrna Signature, Jacqueline R. Kemp

ETD Archive

Renin-angiotensin system (RAS) activation and phenotypic modulation of vascular smooth muscle cells (VSMCs) are common characteristics associated with human diseases, such as pulmonary hypertension, atherosclerosis and stroke. While elevation of the RAS hormone product, angiotensin II (AngII) is a well-established risk in these diseases the mechanism of activation of RAS and modulation of VSMC phenotype by AngII is vague, suggesting that novel global regulators may mediate the risk by AngII. MicroRNAs (miRNAs) represent one such class of potential global regulators. MiRNAs are small (╠â22 nt), endogenous, non-coding RNAs that act as post-transcriptional regulators of physiological processes. MiRNAs primarily function by …

The Role Of School And Motivational Factors In Mathematics Achievement And Self-Efficacy : A Multi-Level Analysis, Enock Obuba Meshack

ETD Archive

Mathematics performance in the U.S., relative to other developed countries remains unsatisfactory despite the emphasis on teacher training, rigor in teaching, and provision of physical resources, adjustments in curriculum and utilization of modern technology. Psychological aspects such as motivation and self-efficacy, which are known to have significant relationships to academic outcomes, have not been sufficiently and exhaustively studied in relation to mathematics achievement. This study used the Educational Longitudinal Survey of 2002 (ELS-2002) data available from the National Center for Educational Statistics (NCES) to explore the relationship between the students’ psychological attributes and their mathematics achievement. The ELS-2002 was a …

Design, Synthesis And Characterization Of Chain-End Functionalized Glyco-Polymer For Efficient Proteomic Analysis, Satya Nandana Narla

ETD Archive

No abstract provided.

Activated Neutrophils Mediate Kim-1 Shedding And Renal Remodelling, Shreyas Lingadahalli

ETD Archive

Kidney performs a complex task of concentrating the urine, retention of salts and protein and excretion of metabolic toxins and by the virtue of its function, is always under the chemical stress and subject to constant tissue damage. Post injury, nephrons have the ability to regain their function by remodeling including, clearing of apoptotic and necrotic debris. Kidney Injury Molecule-1(KIM-1/TIM-1/HAVCR-1) is a phosphatidylserine receptor that recognizes the apoptotic bodies and directs them to the lysosomal degradation. KIM-1 a type I transmembrane glycoprotein, although not constitutively expressed, is expressed in injured epithelial cells. It is known that the extracellular domain is …

Influence Of Earthworms On Plant And Soil Invertebrate Communities Of The Cleveland Metroparks, Anton F. Schermaier

ETD Archive

No native earthworms exist in the Great Lakes region of Ohio. All earthworms found in previously glaciated areas of the United States either migrated from unglaciated areas or were introduced as a result of human activities such as agriculture and sport fishing. Non-native earthworms may facilitate dramatic changes in structure and function of plant and invertebrate communities of forest ecosystems. This study examined how the presence of non-native earthworms within the Cleveland Metroparks may correspond with plant and soil invertebrate communities. Special attention was given to the Asian earthworm, Amynthas spp., a recent arrival to northeastern Ohio and a particularly …

Saline Adaptation Of The Microalga Scenedesmus Dimorphus: From Fresh Water To Brackish Water, Bethany Marie Gigante

ETD Archive

The fresh water microalga Scenedesmus dimorphus is of interest in the microalgae to biofuel field. With a 26 dry weight as lipid content and a potential doubling time of 60-70 hours, it is a viable candidate for biofuel production. Recent studies have focused on optimizing the growth rate and lipid content of S. dimorphus by finding ideal light, carbon-dioxide flow rates, nutrient composition of media, pH, temperature, and implementation of various stresses in the growth environment. Adaptation of S. dimorphus to a saline environment would make it a viable biofuel stock world-wide. This saline adaptation experiment was conducted in two …

Othering, Mirroring, And Identity In John Edgar Wideman's Brothers And Keepers, James E. Walker

ETD Archive

Jacques Lacan's notion of the mirror stage of human development, formulated from the theories of Sigmund Freud, lies at the core of psychoanalytic theory. Fundamental components of the mirror stage include the concepts of Otherness and Identity. This examination proffers a critical reading of John Edgar Wideman's Brothers and Keepers, through a psychoanalytic matrix and contemporary constructions of Othering, Mirroring, and Identity. To that end, this examination traces the evolution of the ways subsequent scholars have understood, applied, and expanded Lacan's classical mirror stage, and its components. Nancy VanDerHeide transforms the solitary, individual, experience of Lacan's mirror stage into a …

Development, Disease, And Regeneration Of Tissues In The Dental-Craniofacial Complex, Brian L. Foster, Yong-Hee P. Chun, Erica L. Scheller, Zhao Lin, Chad M. Novince, Avina Paranjpe

Periodontics Publications

This article has no abstract.

Igfbp-3 Inhibits Cytokine-Induced Insulin Resistance And Early Manifestations Of Atherosclerosis, Lathika Mohanraj, Ho-Seong Kim, Wei Li, Qing Cai, Ki E. Kim, Hye-Jung Shin, Yong-Jae Lee, Woo J. Lee, Jung H. Kim, Youngman Oh

Pathology Publications

Metabolic syndrome is associated with visceral obesity, insulin resistance and an increased risk of cardiovascular diseases. Visceral fat tissue primarily consists of adipocytes that secrete cytokines leading to a state of systemic inflammation in obese conditions. One of the IGF-independent functions of IGFBP-3 is its role as an anti-inflammatory molecule. Our study in obese adolescents show a decrease in total IGFBP-3 levels and increase in proteolyzed IGFBP-3 in circulation when compared to their normal counterparts and establishes a positive correlation between IGFBP-3 proteolysis and adiposity parameters as well as insulin resistance. In human adipocytes, we show that IGFBP-3 inhibits TNF-α-induced …

Ennet: Inferring Large Gene Regulatory Networks From Expression Data Using Gradient Boosting, Janusz Slawek, Tomasz Arodź

Computer Science Publications

Background

The regulation of gene expression by transcription factors is a key determinant of cellular phenotypes. Deciphering genome-wide networks that capture which transcription factors regulate which genes is one of the major efforts towards understanding and accurate modeling of living systems. However, reverse-engineering the network from gene expression profiles remains a challenge, because the data are noisy, high dimensional and sparse, and the regulation is often obscured by indirect connections.

Results

We introduce a gene regulatory network inference algorithm ENNET, which reverse-engineers networks of transcriptional regulation from a variety of expression profiles with a superior accuracy compared to the state-of-the-art …

Biomedical Informatics For Computer-Aided Decision Support Systems: A Survey, Ashwin Belle, Mark A. Kon, Kayvan Najarian

Computer Science Publications

The volumes of current patient data as well as their complexity make clinical decision making more challenging than ever for physicians and other care givers. This situation calls for the use of biomedical informatics methods to process data and form recommendations and/or predictions to assist such decision makers. The design, implementation, and use of biomedical informatics systems in the form of computer-aided decision support have become essential and widely used over the last two decades. This paper provides a brief review of such systems, their application protocols and methodologies, and the future challenges and directions they suggest.

An Entropy-Based Automated Cell Nuclei Segmentation And Quantification: Application In Analysis Of Wound Healing Process, Varun Oswal, Ashwin Belle, Robert Diegelmann, Kayvan Najarian

Computer Science Publications

The segmentation and quantification of cell nuclei are two very significant tasks in the analysis of histological images. Accurate results of cell nuclei segmentation are often adapted to a variety of applications such as the detection of cancerous cell nuclei and the observation of overlapping cellular events occurring during wound healing process in the human body. In this paper, an automated entropy-based thresholding system for segmentation and quantification of cell nuclei from histologically stained images has been presented. The proposed translational computation system aims to integrate clinical insight and computational analysis by identifying and segmenting objects of interest within histological …

Natural Plasmodium Infection In Monkeys In The State Of Rondônia (Brazilian Western Amazon), Maisa S. Araújo, Mariluce R. Messias, Marivaldo R . Figueiró, Luiz Herman S. Gil, Christian M. Probst, Newton M. Vidal, Tony H. Katsuragawa, Luiz H. Pereira Da Silva, Luiz S. Ozaki

Study of Biological Complexity Publications

Background

Simian malaria is still an open question concerning the species of Plasmodium parasites and species of New World monkeys susceptible to the parasites. In addition, the lingering question as to whether these animals are reservoirs for human malaria might become important especially in a scenario of eradication of the disease. To aid in the answers to these questions, monkeys were surveyed for malaria parasite natural infection in the Amazonian state of Rondônia, Brazil, a state with intense environmental alterations due to human activities, which facilitated sampling of the animals.

Methods

Parasites were detected and identified in DNA from blood …

Whole Brain And Brain Regional Coexpression Network Interactions Associated With Predisposition To Alcohol Consumption, Lauren A. Vanderlinden, Laura M. Saba, Katerina Kechris, Michael F. Miles, Paula L. Hoffman, Boris Tabakoff

Study of Biological Complexity Publications

To identify brain transcriptional networks that may predispose an animal to consume alcohol, we used weighted gene coexpression network analysis (WGCNA). Candidate coexpression modules are those with an eigengene expression level that correlates significantly with the level of alcohol consumption across a panel of BXD recombinant inbred mouse strains, and that share a genomic region that regulates the module transcript expression levels (mQTL) with a genomic region that regulates alcohol consumption (bQTL). To address a controversy regarding utility of gene expression profiles from whole brain, vs specific brain regions, as indicators of the relationship of gene expression to phenotype, we …

Intracellular Function Of Interleukin-1 Receptor Antagonist In Ischemic Cardiomyocytes, Elena Vecile, Aldo Dobrina, Fadi N. Salloum, Benjamin W. Van Tassell, Antonella Falcione, Edorado Gustini, Samuele Secchiero, Sergio Crovella, Gianfranco Sinagra, Nicoletta Finato, Martin J. Nicklin, Antonio Abbate

VCU Health Publications

Background

Loss of cardiac myocytes due to apoptosis is a relevant feature of ischemic heart disease. It has been described in infarct and peri-infarct regions of the myocardium in coronary syndromes and in ischemia-linked heart remodeling. Previous studies have provided protection against ischemia-induced cardiomyocyte apoptosis by the anti-inflammatory cytokine interleukin-1 receptor-antagonist (IL-1Ra). Mitochondria triggering of caspases plays a central role in ischemia-induced apoptosis. We examined the production of IL-1Ra in the ischemic heart and, based on dual intra/extracellular function of some other interleukins, we hypothesized that IL-1Ra may also directly inhibit mitochondria-activated caspases and cardiomyocyte apoptosis.

Methodology/Principal Findings

Synthesis of …

Superlinear Increase Of Photoluminescence With Excitation Intensity In Zn-Doped Gan, Michael A. Reshchikov, Anita J. Olsen, Marilyn F. Bishop, Tom Mcmullen

Physics Publications

We have observed a superlinear increase of photoluminescence (PL) intensity in a narrow range of excitation intensities for Zn-doped GaN. The characteristic intensity at which the abrupt increase occurs increases with increasing temperature. This is unlike the usual observations for defects in semiconductors in which the PL intensity increases linearly with excitation intensity, saturating at high intensity because defects become saturated with photogenerated charge carriers. The observed phenomenon is attributed to a redirection of electron and hole flow from nonradiative centers at low excitation intensity to a recombination path via the Zn-Ga acceptor at high excitation intensity. This is the …

Subcutaneous Administration Of D-Luciferin Is An Effective Alternative To Intraperitoneal Injection In Bioluminescence Imaging Of Xenograft Tumors In Nude Mice, Ashraf A. Khalil, Mark J. Jameson, William C. Broaddus, Theodore D. Chung, Sarah E. Golding, Seth M. Dever, Elisabeth Rosenberg, Kristoffer Valerie

Otolaryngology Publications

Currently, intraperitoneal (IP) injection of D-luciferin is the preferred method of providing substrate for bioluminescence imaging (BLI); however it has a failure rate of 3–10% due to accidental intestinal injection. The present study evaluates the quality of BLI after subcutaneous (SC) injection of D-luciferin and demonstrates the effectiveness of SC injection in anatomically disparate tumor models. Mice bearing luciferase-expressing tumors underwent BLI after SC or IP injection of D-luciferin. The average time to maximal luminescence was 6 min (range 5–9 min) after SC injection and 8 min (range 5–8 min) after IP injection. Within 7 minutes of injection, SC and …