Digital Commons Network^™

Using Natural Language Processing Techniques To Inform Research On Nanotechnology, Nastassja A. Lewinski, Bridget T. Mcinnes

Chemical and Life Science Engineering Publications

Literature in the field of nanotechnology is exponentially increasing with more and more engineered nanomaterials being created, characterized, and tested for performance and safety. With the deluge of published data, there is a need for natural language processing approaches to semi-automate the cataloguing of engineered nanomaterials and their associated physico-chemical properties, performance, exposure scenarios, and biological effects. In this paper, we review the different informatics methods that have been applied to patent mining, nanomaterial/device characterization, nanomedicine, and environmental risk assessment. Nine natural language processing (NLP)-based tools were identified: NanoPort, NanoMapper, TechPerceptor, a Text Mining Framework, a Nanodevice Analyzer, a Clinical …

Waterpipe Smoking And Regulation In The United States: A Comprehensive Review Of The Literature, Linda Haddad, Omar El-Shahawy, Roula Ghadban, Tracey E. Barnett, Emily Johnson

Social and Behavioral Sciences Publications

Background: Researchers in tobacco control are concerned about the increasing prevalence of waterpipe smoking in the United States, which may pose similar risks as cigarette smoking. This review explores the prevalence of waterpipe smoking in the United States as well as the shortcomings of current U.S. policy for waterpipe control and regulation. Methods: Researchers conducted a literature review for waterpipe articles dated between 2004 and 2015 using five online databases: MEDLINE, CINHAHL, ScienceDirect, PMC, and Cochrane Library. Results: To date, few studies have explored the marketing and regulation of waterpipe smoking in the U.S., which has increased …

Upward Communication About Cancer Screening—Adolescent Daughter To Mother, Maghboeba Mosavel, Katie A. Ports

Social and Behavioral Sciences Publications

Substantial breast and cervical cancer disparities exist in the United States, particularly among African American women with low social economic status. There is considerable potential for discussions about cancer prevention between mothers and daughters. However, upward communication, from child to parent, remains a relatively novel research area, and it remains unclear how receptive mothers would be to messages from their daughter about cancer, a topic that may be considered culturally inappropriate for daughters to initiate. In this study, we simulated cancer message delivery to daughters and then conducted direct observation of daughters as they recalled and shared the message with …

Proceedings Of The 2015 Midsouth Computational Biology And Bioinformatics Society (Mcbios) Conference, Jonathan D. Wren, Shraddha Thakkar, Ramin Homayouni, Donald J. Johann, Mikhail G. Dozmorov

Biostatistics Publications

No abstract provided.

Penalized Ordinal Regression Methods For Predicting Stage Of Cancer In High-Dimensional Covariate Spaces, Amanda Elswick Gentry, Colleen K. Jackson-Cook, Debra E. Lyon, Kellie J. Archer

Biostatistics Publications

The pathological description of the stage of a tumor is an important clinical designation and is considered, like many other forms of biomedical data, an ordinal outcome. Currently, statistical methods for predicting an ordinal outcome using clinical, demographic, and high-dimensional correlated features are lacking. In this paper, we propose a method that fits an ordinal response model to predict an ordinal outcome for high-dimensional covariate spaces. Our method penalizes some covariates (high-throughput genomic features) without penalizing others (such as demographic and/or clinical covariates). We demonstrate the application of our method to predict the stage of breast cancer. In our model, …

Generalized Monotone Incremental Forward Stagewise Method For Modeling Count Data: Application Predicting Micronuclei Frequency, Mateusz Makowski, Kellie J. Archer

Biostatistics Publications

The cytokinesis-block micronucleus (CBMN) assay can be used to quantify micronucleus (MN) formation, the outcome measured being MN frequency. MN frequency has been shown to be both an accurate measure of chromosomal instability/DNA damage and a risk factor for cancer. Similarly, the Agilent 4×44k human oligonucleotide microarray can be used to quantify gene expression changes. Despite the existence of accepted methodologies to quantify both MN frequency and gene expression, very little is known about the association between the two. In modeling our count outcome (MN frequency) using gene expression levels from the high-throughput assay as our predictor variables, there are …

Identifying Molecular Features Associated With Psychoneurological Symptoms In Women With Breast Cancer Using Multivariate Mixed Models, Qing Zhou, Colleen Jackson-Cook, Debra Lyon, Robert Perera, Kellie Archer

Biostatistics Publications

Breast cancer (BC) is the second most common cancer among women. Research shows many women with BC experience anxiety, depression, and stress (ADS). Epigenetics has recently emerged as a potential mechanism for the development of depression.1 Although there are growing numbers of research studies indicating that epigenetic changes are associated with ADS, there is currently no evidence that this association is present in women with BC. The goal of this study was to identify high-throughput methylation sites (CpG sites) that are associated with three psychoneurological symptoms (ADS) in women with BC. Traditionally, univariate models have been used to examine …

Computer Simulation, Bioinformatics, And Statistical Analysis Of Cancer Data And Processes, Kellie J. Archer, Kevin Dobbin, Swati Biswas, Roger S. Day, David C. Wheeler, Hao Wu

Biostatistics Publications

No abstract provided.

Pdgfrα Signaling Drives Adipose Tissue Fibrosis By Targeting Progenitor Cell Plasticity, Tomoaki Iwayama, Cameron Steele, Longbiao Yao, Mikhail G. Dozmorov, Dimitris Karamichos, Jonathan D. Wren, Lorin E. Olson

Biostatistics Publications

Fibrosis is a common disease process in which profibrotic cells disturb organ function by secreting disorganized extracellular matrix (ECM). Adipose tissue fibrosis occurs during obesity and is associated with metabolic dysfunction, but how profibrotic cells originate is still being elucidated. Here, we use a developmental model to investigate perivascular cells in white adipose tissue (WAT) and their potential to cause organ fibrosis. We show that a Nestin-Cre transgene targets perivascular cells (adventitial cells and pericyte-like cells) in WAT, and Nestin-GFP specifically labels pericyte-like cells. Activation of PDGFRα signaling in perivascular cells causes them to transition into ECM-synthesizing profibrotic cells. Before …

Analysis Of Environmental Chemical Mixtures And Non-Hodgkin Lymphoma Risk In The Nci-Seer Nhl Study, Jenna Czarnota, Chris Gennings, Joanne S. Colt, Anneclaire J. De Roos, James R. Cerhan, Richard K. Severson, Patricia Hartge, Mary H. Ward, David C. Wheeler

Biostatistics Publications

Background: There are several suspected environmental risk factors for non-Hodgkin lymphoma (NHL). The associations between NHL and environmental chemical exposures have typically been evaluated for individual chemicals (i.e., one-by-one).

Objectives: We determined the association between a mixture of 27 correlated chemicals measured in house dust and NHL risk.

Methods: We conducted a population-based case–control study of NHL in four National Cancer Institute–Surveillance, Epidemiology, and End Results centers—Detroit, Michigan; Iowa; Los Angeles County, California; and Seattle, Washington—from 1998 to 2000. We used weighted quantile sum (WQS) regression to model the association of a mixture of chemicals and risk of NHL. The …

B-Cell And Monocyte Contribution To Systemic Lupus Erythematosus Identified By Cell-Type-Specific Differential Expression Analysis In Rna-Seq Data, Mikhail G. Dozmorov, Nicolas Dominguez, Krista Bean, Susan R. Macwana, Virginia Roberts, Edmund Glass, Judith A. James, Joel M. Guthridge

Biostatistics Publications

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by complex interplay among immune cell types. SLE activity is experimentally assessed by several blood tests, including gene expression profiling of heterogeneous populations of cells in peripheral blood. To better understand the contribution of different cell types in SLE pathogenesis, we applied the two methods in cell-type-specific differential expression analysis, csSAM and DSection, to identify cell-type-specific gene expression differences in heterogeneous gene expression measures obtained using RNA-seq technology. We identified B-cell-, monocyte-, and neutrophil-specific gene expression differences. Immunoglobulin-coding gene expression was altered in B-cells, while a ribosomal signature was prominent in …

Diabetes Management Before And After Cancer Diagnosis: Missed Opportunity, Nengliang Yao, Fabian T. Camacho, Askar S. Chukmaitov, Steven T. Fleming, Roger T. Anderson

Health Policy Publications

Background

Few studies have examined the management of comorbidities in cancer patients. This study used population-based data to estimate the guideline concordance rates for diabetes management before and after cancer diagnosis and examined if diabetes management services among cancer patients was associated with characteristics of the hospital where the patient was treated.

Methods

We linked 2005-2009 Medicare claims data to information on 2,707 breast and colorectal cancers patients in state cancer registry files. Multivariate logistic regression models examined hospital characteristics associated with receipt of diabetes management care after cancer diagnosis.

Results

The rates of HbAlc testing, LDL-C testing, and retinal …

The “Aha!” Moment: Library Support For The Cognitive Process Of Creativity, Carla-Mae Crookendale

VCU Libraries Faculty and Staff Presentations

Research on creativity in the field of cognitive psychology suggests that creativity is a process, and therefore success in creativity is less about talent or temperament than about the ability to manage that process. Creativity is necessary for all disciplines, though those in art and design fields tend to be more focused on it as an everyday practice.

This poster gives an overview of a session on creativity designed for “Advance Your Research,” a workshop provided by VCU Libraries for graduate students and advanced researchers. Through the in-person session and following webinar the visual arts librarian sought to familiarize attendees …

Contribution Of Nrf2 To Atherogenic Phenotype Switching Of Coronary Arterial Smooth Muscle Cells Lacking Cd38 Gene, Ming Xu, Xiao-Xue Li, Lei Wang, Mi Wang, Yang Zhang, Pin-Lan Li

Pharmacology and Toxicology Publications

Background/Aims: Recent studies have indicated that CD38 gene deficiency results in dedifferentiation or transdifferentiation of arterial smooth muscle cells upon atherogenic stimulations. However, the molecular mechanisms mediating this vascular smooth muscle (SMC) phenotypic switching remain unknown. Methods & Results: In the present study, we first characterized the phenotypic change in the primary cultures of coronary arterial myocytes (CAMs) from CD38-/- mice. It was shown that CD38 deficiency decreased the expression of contractile marker calponin, SM22α and α-SMA but increased the expression of SMC dedifferentiation marker, vimentin, which was accompanied by enhanced cell proliferation. This phenotypic change in CD38-/- CAMs was …

Concentration-Dependent Diversification Effects Of Free Cholesterol Loading On Macrophage Viability And Polarization, Xiaoyang Xu, Aolin Zhang, Ningjun Li, Pin-Lan Li, Fan Zhang

Pharmacology and Toxicology Publications

Background/Aims: The accumulation of free cholesterol in atherosclerotic lesions has been well documented in both animals and humans. In studying the relevance of free cholesterol buildup in atherosclerosis, contradictory results have been generated, indicating that free cholesterol produces both pro- and anti-atherosclerosis effects in macrophages. This inconsistency might stem from the examination of only select concentrations of free cholesterol. In the present study, we sought to investigate the implication of excess free cholesterol loading in the pathophysiology of atherosclerosis across a broad concentration range from (in µg/ml) 0 to 60. Methods:Macrophage viability was determined by measuring formazan formation and …

The Induction Of Emt And Activation Of Adipose Stem Cells In Correlation With The Secretion Of Ltbp-1 In Mammary Cells, Roshni Malik, Lauren Griggs, Dr. Christopher Lemmon Phd

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

This work is part of an ongoing study that investigates the upregulation of LTBP-1 in mammary epithelial cells as well as the differentiation of breast adipose stem cells (BASCs) in the presence of TGF-β1. Through immunofluorescence imaging, LTBP-1 is shown to co-localize with fibronectin fibrils in adipose stem cells. Previous work from our lab has shown that blocking fibronectin fibril formation can inhibit Epithelial-Mesenchymal Transition. Thus, targeting of fibronectin assembly could be a potent new therapeutic in cancer treatment. In the current work, we focus on the pharmacodynamics of a FN assembly inhibitor derived from the protein Adhesin F1 (refered …

Computer Simulation Of Tooth Mobility Using Varying Material Properties, Allison R. Beckmann, Lena Unterberg, Stefan Raith, Horst Fischer

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Tooth mobility is the major cause of stress on a tooth implant or partial denture and often results in the damage of the device. For many prosthetic devices like dental bridges, a partial denture used for a person who is missing a tooth to give the appearance and function of a tooth, mobility can cause up to double the amount of stress in comparison to a fixed model. Creating a computer simulation of tooth mobility using Finite Element Analysis allows one to understand and predict this movement in order to improve future dental prosthetic devices. The main cause of tooth …

Neuronal Migration: How Do You Build A Brain?, Sravya Uppalapati

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Senior biology major Alex Burkard is working in the Walsh Neurodevelopment Laboratory at VCU to help answer the question, ‘How do you build a brain?’ Burkard is researching neuronal migration in Zebrafish and how cellular polarity affects hindbrain development.

Immortal Mortals, Sterling Giles

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Junior Information Systems and Bioinformatics major Michael Kiflezghi focuses his research interests on an organism’s lifespan and gut microbial communities.

Molecular Overlap In The Regulation Of Sk Channels By Small Molecules And Phosphoinositides, Miao Zhang, Xuan-Yu Meng, Ji-Fang Zhang, Meng Cui, Diomedes E. Logothetis

Physiology and Biophysics Publications and Presentations

Phosphatidylinositol 4,5-bisphosphate (PIP2) directly interacts with the small-conductance Ca2+-activated K+2-a (SK2-a) channel/calmodulin complex, serving as a critical element in the regulation of channel activity. We report that changes of protein conformation in close proximity to the PIP2 binding site induced by a small-molecule SK channel modulator, NS309, can effectively enhance the interaction between the protein and PIP2 to potentiate channel activity. This novel modulation of PIP2 sensitivity by small-molecule drugs is likely not to be limited in its application to SK channels, representing an intriguing strategy to develop drugs controlling the activity of the large number of PIP2-dependent proteins.

Impact Of V-Ets Erythroblastosis Virus E26 Oncogene Homolog 1 Gene Polymorphisms Upon Susceptibility To Autoimmune Diseases, Ye Zhou, Miao Liu, Jun Li, Fiza Hashmi, Zhi Mao, Ning Zhang, Liang Zhou, Weiran Lv, Jingwei Zheng, Xiaoli Nie, Changzheng Li

Physiology and Biophysics Publications and Presentations

V-ets erythroblastosis virus E26 oncogene homolog 1 (ETS1) is recognized as a gene of risk to autoimmune diseases (ADs). Two single nucleotide polymorphisms (SNPs) in ETS1 (rs1128334 G>A and rs10893872 T>C) were considered associated with ADs risk. However, the results remain conflicting.

We performed a meta-analysis to evaluate more precise estimations of any relationship. We searched PubMed, OvidSP, and Chinese National Knowledge Infrastructure databases (papers published prior to September 12, 2014) and extracted data from eligible studies. Meta-analysis was performed using the STATA 12.0 software. Random effect model or fixed effect model were chosen according to …

Editorial: Phosphoinositides And Their Phosphatases: Linking Electrical And Chemical Signals In Biological Processes, Susy C. Kohout, Carlos A. Villalba-Galea

Physiology and Biophysics Publications and Presentations

The voltage-sensing phosphatase (VSP) has changed the way we think about both cellular electrical activity and PIPs (phosphatidylinositol phosphates). Originally discovered in 1999 (Chen et al., 1999), these proteins were not recognized as electrically-controlled enzymes until 2005 (Murata et al., 2005). They constitute the first, and so far the only, example of an enzyme linking electrical signals at the plasma membrane to the catalysis of PIPs (Murata et al., 2005), a ubiquitous family of intracellular signaling molecules (Di Paolo and De Camilli, 2006; Balla, 2013). Before the discovery of VSP, there were no known direct links between the two. Textbook …

A Rapid In Vivo Screen For Pancreatic Ductal Adenocarcinoma Therapeutics, Ozhan Ocal, Victor Pashkov, Rahul K. Kollipara, Yalda Zolghadri, Victoria H. Cruz, Michael A. Hale, Blake R. Heath, Alex B. Artyukhin, Alana L. Christie, Pantelis Tsoulfas, James B. Lorens, Galvin H. Swift, Rolf A. Brekken, Thomas M. Wilkie

Physiology and Biophysics Publications and Presentations

Pancreatic ductal adenocarcinoma (PDA) is the fourth leading cause of cancer-related deaths in the United States, and is projected to be second by 2025. It has the worst survival rate among all major cancers. Two pressing needs for extending life expectancy of affected individuals are the development of new approaches to identify improved therapeutics, addressed herein, and the identification of early markers. PDA advances through a complex series of intercellular and physiological interactions that drive cancer progression in response to organ stress, organ failure, malnutrition, and infiltrating immune and stromal cells. Candidate drugs identified in organ culture or cell-based screens …

Starvation-Induced Collective Behavior In C. Elegans, Alexander B. Artyukhin, Virginia Commonwealth University J. Yim, Mi Cheong Cheong, Leon Avery

Physiology and Biophysics Publications and Presentations

We describe a new type of collective behavior in C. elegans nematodes, aggregation of starved L1 larvae. Shortly after hatching in the absence of food, L1 larvae arrest their development and disperse in search for food. In contrast, after two or more days without food, the worms change their behavior—they start to aggregate. The aggregation requires a small amount of ethanol or acetate in the environment. In the case of ethanol, it has to be metabolized, which requires functional alcohol dehydrogenase sodh-1. The resulting acetate is used in de novo fatty acid synthesis, and some of the newly made fatty …

A Multilaboratory Comparison Of Calibration Accuracy And The Performance Of External References In Analytical Ultracentrifugation, Huaying Zhao, Rodolfo Ghirlando, Carlos Alfonso, Fumio Arisaka, Ilan Attali, David L. Bain, Marina M. Bakhtina, Donald F. Becker, Gregory J. Bedwell, Ahmet Bekdemir, Tabot M. D. Besong, Catherine Birck, Chad A. Brautigam, William Brennerman, Olwyn Byron, Agnieszka Bzowska, Jonathan B. Chaires, Catherine T. Chaton, Helmut Cölfen, Keith D. Connaghan, Kimberly A. Crowley, Ute Curth, Tina Daviter, William L. Dean, Ana I. Díez, Christine Ebel, Debra M. Eckert, Leslie E. Eisele, Edward Eisenstein, Patrick England, Carlos Escalante, Jeffrey A. Fagan, Robert Fairman, Ron M. Finn, Wolfgang Fischle, José García De La Torre, Jayesh Gor, Henning Gustafsson, Damien Hall, Stephen E. Harding, José G. Hernández Cifre, Andrew B. Herr, Elizabeth E. Howell, Richard S. Isaac, Shu-Chuan Jao, Davis Jose, Soon-Jong Kim, Bashkim Kokona, Jack A. Kornblatt, Dalibor Kosek, Elena Krayukhina, Daniel Krzizike, Eric A. Kusznir, Hyewon Kwon, Adam Larson, Thomas M. Laue, Aline Le Roy, Andrew P. Leech, Hauke Lilie, Karolin Lugar, Juan R. Luque-Ortega, Jia Ma, Carrie A. May, Ernest L. Maynard, Anna Modrak-Wojcik, Yee-Foong Mok, Norbert Mücke, Luitgard Nagel-Steger, Geeta J. Narlikar, Masanori Noda, Amanda Nourse, Tomas Obsil, Chad K. Park, Jin-Ku Park, Peter D. Pawelek, Erby E. Perdue, Stephen J. Perkins, Matthew A. Perugini, Craig L. Peterson, Martin G. Peverelli, Grzegorz Piszczek, Gali Prag, Peter E. Prevelige, Bertrand D. E. Raynal, Lenka Rezabkova, Klaus Richter, Alison E. Ringel, Rose Rosenberg, Arthur J. Rowe, Arne C. Rufer, David J. Scott, Javier G. Seravalli, Alexandra S. Solovyova, Renjie Song, David Staunton, Catlin Stoddard, Katherine Stott, Holger M. Strauss, Werner W. Streicher, John P. Sumida, Sarah G. Swygert, Roman H. Szczepanowski, Ingrid Tessmer, Ronald T. Toth Iv., Ashutosh Tripathy, Susumu Uchiyama, Stephen F. W. Uebel, Satoru Unzai, Anna Vitlin Gruber, Peter H. Von Hippel, Christine Wandrey, Szu-Huan Wang, Steven E. Weitzel, Beata Wielgus-Kutrowska, Cynthia Wolberger, Martin Wolff, Edward Wright, Yu-Sung Wu, Jacinta M. Wubben, Peter Schuck

Physiology and Biophysics Publications and Presentations

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy …

An Opioid-Like System Regulating Feeding Behavior In C. Elegans, Mi Cheong Cheong, Alexander B. Artyukhin, Yong-Jai You, Leon Avery

Physiology and Biophysics Publications and Presentations

Neuropeptides are essential for the regulation of appetite. Here we show that neuropeptides could regulate feeding in mutants that lack neurotransmission from the motor neurons that stimulate feeding muscles. We identified nlp-24 by an RNAi screen of 115 neuropeptide genes, testing whether they affected growth. NLP-24 peptides have a conserved YGGXX sequence, similar to mammalian opioid neuropeptides. In addition, morphine and naloxone respectively stimulated and inhibited feeding in starved worms, but not in worms lacking NPR-17, which encodes a protein with sequence similarity to opioid receptors. Opioid agonists activated heterologously expressed NPR-17, as did at least one NLP-24 peptide. Worms …

Let's Talk Tobacco: African American Parent-Adolescent Communication About Tobacco Use Within The Context Of Parental Smoking, Michell Pope

Theses and Dissertations

Tobacco use and the associated health risks are a major public health concern. Research suggests that parents’ own tobacco use, caregiver-adolescent antismoking communication, and parenting practices (e.g., prompting, parental monitoring) may work to influence adolescents’ tobacco-related attitudes and behavioral outcomes (e.g., refusal efficacy, intentions to use and actual use). Although historically African American adolescents have exhibited lower rates of tobacco use than their racial/ethnic counterparts, there is growing evidence to suggest that this may be changing because of increased use of tobacco products and/or underreporting of the use of alternative tobacco products or ATPs (e.g., cigars, cigarillos), among this population. …

Finding Unfound_Graphic Hybridity, Yaeyoung Park

Theses and Dissertations

Hybridity is the result when visual form, color or tools interact. While not every combination of multiple elements result in success, I believe creativity, intuition and serendipity determines the successful hybridity. This is the documentation of my journey to develop a personal definition of successful hybridity in graphic design.

Proof-Of-Concept Of Environmental Dna Tools For Atlantic Sturgeon Management, Jameson Hinkle

Theses and Dissertations

Abstract

The Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus, Mitchell) is an anadromous species that spawns in tidal freshwater rivers from Canada to Florida. Overfishing, river sedimentation and alteration of the river bottom have decreased Atlantic Sturgeon populations, and NOAA lists the species as endangered. Ecologists sometimes find it difficult to locate individuals of a species that is rare, endangered or invasive. The need for methods less invasive that can create more resolution of cryptic species presence is necessary. Environmental DNA (eDNA) is a non-invasive means of detecting rare, endangered, or invasive species by isolating nuclear or mitochondrial DNA (mtDNA) from the …

The Influence Of Executive Functions And Emotion Regulation On Teacher-Rated Social Behaviors In Middle Childhood, Tennisha N. Riley

Theses and Dissertations

Early social interactions are important to developing and maintaining positive social relationships in childhood. It is well understood that the social development is dependent on a number of developmental changes in both cognition and emotion. While most research has focused on cognitive and emotional models of social behaviors separately, a consideration for research investigating social behaviors is to examine cognitive processing and emotional processing concurrently. The current work focuses on the relationship between the executive processes involved in cognition and emotion regulation, and the influence on adaptive (social skills) and maladaptive (aggressive behavior) social behaviors. Specifically, the reformulated social behavioral …