Digital Commons Network^™

Integrating Mrna And Mirna Weighted Gene Co-Expression Networks With Eqtls In The Nucleus Accumbens Of Subjects With Alcohol Dependence, Mohammed Mamdani, Vernell Williamson, Gowon O. Mcmichael, Tana Blevins, Fazil Aliev, Amy Adkins, Laura Hack, Tim Bigdeli, Andrew D. Van Der Vaart, Bradley Todd Webb, Silviu-Alin Bacanu, Gursharan Kalsi, Coga Consortium, Kenneth S. Kendler, Michael F. Miles, Danielle Dick, Brien P. Riley, Catherine Dumur, Vladimir I. Vladimirov

Psychology Publications

Alcohol consumption is known to lead to gene expression changes in the brain. After performing weighted gene co-expression network analyses (WGCNA) on genome-wide mRNA and microRNA (miRNA) expression in Nucleus Accumbens (NAc) of subjects with alcohol dependence (AD; N = 18) and of matched controls (N = 18), six mRNA and three miRNA modules significantly correlated with AD were identified (Bonferoni-adj. p≤ 0.05). Cell-type-specific transcriptome analyses revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four mRNA modules were enriched for astrocyte and microglial specific marker genes and …

A Disproportionate Burden Of Care: Gender Differences In Mental Health, Health-Related Quality Of Life, And Social Support In Mexican Multiple Sclerosis Caregivers, Paul B. Perrin, Ivan Panyavin, Alejandra Morlett Paredes, Adriana Aguayo, Miguel Angel Macias, Brenda Rabago, Sandra J. Fulton Picot, Juan Carlos Arango-Lasprilla

Psychology Publications

Background. Multiple sclerosis (MS) rates in Latin America are increasing, and caregivers there experience reduced mental and physical health. Based on rigid gender roles in Latin America, women more often assume caregiving duties, yet the differential impact on women of these duties is unknown. Methods. This study examined gender differences in mental health (Patient Health Questionnaire-9, Satisfaction with Life Scale, Rosenberg Self-Esteem Scale, State-Trait Anxiety Inventory, and Zarit Burden Inventory), health-related quality of life (HRQOL; Short Form-36), and social support (Interpersonal Support Evaluation List-12) in 81 (66.7% women) Mexican MS caregivers. Results. As compared to men caregivers, women had lower …

Electronic Cigarettes And Nicotine Dependence: Evolving Products, Evolving Problems, Caroline O. Cobb, Peter S. Hendricks, Thomas Eissenberg

Psychology Publications

Electronic cigarettes (ECIGs) use an electric heater to aerosolize a liquid that usually contains propylene glycol, vegetable glycerin, flavorants, and the dependence-producing drug nicotine. ECIG-induced nicotine dependence has become an important concern, as some ECIGs deliver very little nicotine while some may exceed the nicotine delivery profile of a tobacco cigarette. This variability is relevant to tobacco cigarette smokers who try to switch to ECIGs. Products with very low nicotine delivery may not substitute for tobacco cigarettes, so that ECIG use is accompanied by little reduced risk of cigarette-caused disease. Products with very high nicotine delivery may make quitting ECIGs …

Patterns Of Substance Use Across The First Year Of College And Associated Risk Factors, Seung Bin Cho, Danielle C. Llaneza, Amy E. Adkins, Megan Cooke, Kenneth S. Kendler, Shaunna L. Clark, Danielle M. Dick

Psychology Publications

Starting college is a major life transition. This study aims to characterize patterns of substance use across a variety of substances across the first year of college and identify associated factors. We used data from the first cohort (N = 2056, 1240 females) of the “Spit for Science” sample, a study of incoming freshmen at a large urban university. Latent transition analysis was applied to alcohol, tobacco, cannabis, and other illicit drug uses measured at the beginning of the fall semester and midway through the spring semester. Covariates across multiple domains – including personality, drinking motivations and expectancy, high …

Genome-Wide Association Data Suggest Abcb1 And Immune-Related Gene Sets May Be Involved In Adult Antisocial Behavior, J E. Salvatore, A. C. Edwards, J. N. Mcclintik, T. B. Bigdeli, A. Adkins, F. Aliev, H. J. Edenburg, T. Foroud, V. Hesselbrock, J. Kramer, J. I. Nurnberger, M. Schuckit, J. A. Tischfield, X. Xuei, D. M. Dick

Psychiatry Publications

Adult antisocial behavior (AAB) is moderately heritable, relatively common and has adverse consequences for individuals and society. We examined the molecular genetic basis of AAB in 1379 participants from a case–control study in which the cases met criteria for alcohol dependence. We also examined whether genes of interest were expressed in human brain. AAB was measured using a count of the number of Antisocial Personality Disorder criteria endorsed under criterion A from the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV). Participants were genotyped on the Illumina Human 1M BeadChip. In total, all single-nucleotide polymorphisms (SNPs) accounted for …

Developmental Changes In Genetic And Shared Environmental Contributions To Smoking Initiation And Subsequent Smoking Quantity In Adolescence And Young Adulthood, Cristina B. Bares, Kenneth S. Kendler, Hermine H. Maes

Psychiatry Publications

Background

Few studies examining the genetic architecture of cigarette smoking have focused on adolescents or examined developmental changes in additive genetic, shared environment and unique environmental influences on liability to initiate cigarette smoking and quantity of cigarettes smoked. The aim of this study is to add to the literature on liability to initiate and use cigarettes during adolescence using a nationally representative sample.

Method

Data for this study came from adolescent and young adult twin pairs (ages 14-33) from the National Longitudinal Study of Adolescent to Adult Health. We ran a series of developmental causal-contingent-common pathway models to examine whether …

Genetic Network Properties Of The Human Cortex Based On Regional Thickness And Surface Area Measures, Anna R. Docherty, Chelsea K. Sawyers, Matthew S. Panizzon, Michael C. Neale, Lisa T. Eyler, Christine Fennema-Notestine, Carol E. Franz, Chi-Hua Chen, Linda K. Mcevoy, Brad Verhulst, Ming T. Tsuang, William S. Kremen

Psychiatry Publications

We examined network properties of genetic covariance between average cortical thickness (CT) and surface area (SA) within genetically-identified cortical parcellations that we previously derived from human cortical genetic maps using vertex-wise fuzzy clustering analysis with high spatial resolution. There were 24 hierarchical parcellations based on vertex-wise CT and 24 based on vertex-wise SA expansion/contraction; in both cases the 12 parcellations per hemisphere were largely symmetrical. We utilized three techniques—biometrical genetic modeling, cluster analysis, and graph theory—to examine genetic relationships and network properties within and between the 48 parcellation measures. Biometrical modeling indicated significant shared genetic covariance between size of several …

Political Attitudes Develop Independently Of Personality Traits, Peter K. Hatemi, Brad Verhulst

Psychiatry Publications

The primary assumption within the recent personality and political orientations literature is that personality traits cause people to develop political attitudes. In contrast, research relying on traditional psychological and developmental theories suggests the relationship between most personality dimensions and political orientations are either not significant or weak. Research from behavioral genetics suggests the covariance between personality and political preferences is not causal, but due to a common, latent genetic factor that mutually influences both. The contradictory assumptions and findings from these research streams have yet to be resolved. This is in part due to the reliance on cross-sectional data and …

Genome-Wide Association Data Suggest Abcb1 And Immune-Related Gene Sets May Be Involved In Adult Antisocial Behavior, J E. Salvatore, A C. Edwards, J N. Mcclintick, T B. Bidgeli, A Adkins, F Aliev, H J. Edenberg, T Foround, V Hesselbrock, J Kramer, J I. Nurnberger, M Schuckit, J A. Tischfield, X Xuei, D Dick

Psychiatry Publications

Adult antisocial behavior (AAB) is moderately heritable, relatively common and has adverse consequences for individuals and society. We examined the molecular genetic basis of AAB in 1379 participants from a case–control study in which the cases met criteria for alcohol dependence. We also examined whether genes of interest were expressed in human brain. AAB was measured using a count of the number of Antisocial Personality Disorder criteria endorsed under criterion A from the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV). Participants were genotyped on the Illumina Human 1M BeadChip. In total, all single-nucleotide polymorphisms (SNPs) accounted for …

Who Are Those “Risk-Taking Adolescents”? Individual Differences In Developmental Neuroimaging Research, James M. Bjork, Dustin A. Pardini

Psychiatry Publications

Functional magnetic resonance imaging (fMRI) has illuminated the development of human brain function. Some of this work in typically-developing youth has ostensibly captured neural underpinnings of adolescent behavior which is characterized by risk-seeking propensity, according to psychometric questionnaires and a wealth of anecdote. Notably, cross-sectional comparisons have revealed age-dependent differences between adolescents and other age groups in regional brain responsiveness to prospective or experienced rewards (usually greater in adolescents) or penalties (usually diminished in adolescents). These differences have been interpreted as reflecting an imbalance between motivational drive and behavioral control mechanisms, especially in mid-adolescence, thus promoting greater risk-taking. While intriguing, …

Respiratory Motion Variability Of Primary Tumors And Lymph Nodes During Radiotherapy Of Locally Advanced Non-Small-Cell Lung Cancers, Nuzhat Jan, Geoffrey D. Hugo, Nitai Mukhopadhyay, Elisabeth Weiss

Radiation Oncology Publications

Background and purpose

The need for target adjustment due to respiratory motion variation and the value of carina as a motion surrogate is evaluated for locally advanced non-small-cell lung cancer.

Material and methods

Using weekly 4D CTs (with audio-visual biofeedback) of 12 patients, respiratory motion variation of primary tumors (PT), lymph nodes (LN) and carina (C) were determined.

Results

Mean (SD) 3D respiratory motion ranges of PT, LN and C were 4 (3), 5 (3) and 5 (3) mm. PT and LN (p = 0.003), and LN and C motion range were correlated (p = 0.03). Only 20 …

Spag17 Deficiency Results In Skeletal Malformations And Bone Abnormalities, Maria Eugenia Teves, Gobalakrishnan Sundaresan, David J. Cohen, Sharon L. Hyzy, Illya Kajan, Melissa Maczis, Zhibing Zhang, Richard M. Costanzo, Jamal Zweit, Zvi Schwartz, Barbara` D. Boyan, Jerome F. Strauss Iii

Obstetrics and Gynecology Publications

Height is the result of many growth and development processes. Most of the genes associated with height are known to play a role in skeletal development. Single-nucleotide polymorphisms in the SPAG17 gene have been associated with human height. However, it is not clear how this gene influences linear growth. Here we show that a targeted mutation in Spag17 leads to skeletal malformations. Hind limb length in mutants was significantly shorter than in wild-type mice. Studies revealed differences in maturation of femur and tibia suggesting alterations in limb patterning. Morphometric studies showed increased bone formation evidenced by increased trabecular bone area …

Sperm Associated Antigen 6 (Spag6) Regulates Fibroblast Cell Growth, Morphology, Migration And Ciliogenesis, Wei Li, Abir Mukherjee, Jinhua Wu, Ling Zhang, Maria E. Teves, Hongfei Li, Shanti Nambiar, Scott C. Henderson, Alan R. Horwitz, Jerome F. Strauss Iii, Xianjun Fang, Zhibing Zhang

Obstetrics and Gynecology Publications

Mammalian Spag6 is the orthologue of Chlamydomonas PF16, which encodes a protein localized in the axoneme central apparatus, and regulates flagella/cilia motility. Most Spag6-deficient mice are smaller in size than their littermates. Because SPAG6 decorates microtubules, we hypothesized that SPAG6 has other roles related to microtubule function besides regulating flagellar/cilia motility. Mouse embryonic fibroblasts (MEFs) were isolated from Spag6-deficient and wild-type embryos for these studies. Both primary and immortalizedSpag6-deficient MEFs proliferated at a much slower rate than the wild-type MEFs, and they had a larger surface area. Re-expression of SPAG6 in the Spag6-deficient MEFs …

Screening And Surveillance Ct Abdomen/Pelvis For Metastases In Patients With Soft-Tissue Sarcoma Of The Extremity, M. J. Thompson, J. Ross, G. Domson, W. Foster

Orthopaedic Surgery Publications

Objectives The clinical utility of routine cross sectional imaging of the abdomen and pelvis in the screening and surveillance of patients with primary soft-tissue sarcoma of the extremities for metastatic disease is controversial, based on its questionable yield paired with concerns regarding the risks of radiation exposure, cost, and morbidity resulting from false positive findings.

Methods Through retrospective review of 140 patients of all ages (mean 53 years; 2 to 88) diagnosed with soft-tissue sarcoma of the extremity with a mean follow-up of 33 months (0 to 291), we sought to determine the overall incidence of isolated abdominopelvic metastases, their …

Quality Control Material For The Detection Of Somatic Mutations In Fixed Clinical Specimens By Next-Generation Sequencing, Catherine I. Dumur, Jorge A. Almenara, Celeste N. Powers, Andrea Ferreira-Gonzalez

Pathology Publications

Background

Targeted next generation sequencing (NGS) technology to assess the mutational status of multiple genes on formalin-fixed, paraffin embedded (FFPE) tumors is rapidly being adopted in clinical settings, where quality control (QC) practices are required. Establishing reliable FFPE QC materials for NGS can be challenging and/or expensive. Here, we established a reliable and cost-effective FFPE QC material for routine utilization in the Ion AmpliSeq™ Cancer Hotspot Panel v2 (CHP2) assay.

Methods

The performance characteristics of the CHP2 assay were determined by sequencing various cell line mixtures and 55 different FFPE tumors on the Ion Torrent PGM platform. A FFPE QC …

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 …

Measuring & Monitoring Impact Of Community Engagement At Virginia Commonwealth University, Valerie Holton, Jennifer Jettner

Division of Community Engagement Resources

This report provides a summary of existing and developing enterprise data mechanisms that track and assess Virginia Commonwealth University’s engagement with our communities. The activities included here are limited to those efforts with which the DCE is actively involved.

The Division of Community Engagement (DCE) undertook this effort and published the original document in fall 2014. This 2015 report has been updated to reflect progress that has been made during the 14-15 academic year.

Collaborative Curiosity: A Connected-Learning Course On Designing Community-Engaged Research, Valerie Holton, Tessa Mckenzie

Division of Community Engagement Resources

This was presented at the IARSLCE annual meeting in Boston, MA in November 2015.

Urban Biking Meets Community-Engaged Research And Service-Learning, Tessa Mckenzie

Division of Community Engagement Resources

No abstract provided.

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 …

Identifying Regional Priorities And Opportunities, Valerie Holton, Jennifer Jettner

Division of Community Engagement Resources

During 2014-2105, the Division of Community Engagement collected and reviewed publicly available community assessments to gain a better understanding of community-identified priorities. Twenty-four (24) reports from the past 10 years (2005-2015) were reviewed for their geographical focus, explicit population of interest, data collection methods and stated priorities. The common priorities that emerged from this review are included here, along with the associated recommendations from the assessments. This effort was not intended to replace other assessments, rather as a means to understand the overarching priorities that have been identified through these various community assessments.

The University Next Door: Developing A Centralized Unit That Strategically Cultivates Community Engagement At Urban Universities, Catherine Howard, Valerie Holton

Division of Community Engagement Resources

This presentation is from the Coalition for Urban and Metropolitan Universities Conference in Omaha, Nebraska on October 13, 2015.

Understanding Cognition Across Modalities For The Assessment Of Digital Resources, Valeriana Colon

Teaching and Learning Publications

Drawing from the theories of the cognitive process, this paper explores the transmission, retention and transformation of information across oral, written, and digital modes of communication and how these concepts can be used to examine the assessment of digital resource tools. The exploration of interactions across modes of communication is used to gain an understanding of the interaction between the student, digital resource and teacher. Cognitive theory is considered as a basis for the assessment of digital resource tools. Lastly, principles for the assessment of digital resource tools are presented along with how assessment can be incorporated in the educational …

Detrimental Effects Of Duplicate Reads And Low Complexity Regions On Rna- And Chip-Seq Data, Mikhail G. Dozmorov, Indra Adrianto, Cory B. Giles, Edmund Glass, Stuart B. Glenn, Courtney Montgomery, Kathy L. Sivils, Lorin E. Olson, Tomoaki Iwayama, Willard M. Freeman, Christopher J. Lessard, Jonathan D. Wren

Biostatistics Publications

Background

Adapter trimming and removal of duplicate reads are common practices in next-generation sequencing pipelines. Sequencing reads ambiguously mapped to repetitive and low complexity regions can also be problematic for accurate assessment of the biological signal, yet their impact on sequencing data has not received much attention. We investigate how trimming the adapters, removing duplicates, and filtering out reads overlapping low complexity regions influence the significance of biological signal in RNA- and ChIP-seq experiments.

Methods

We assessed the effect of data processing steps on the alignment statistics and the functional enrichment analysis results of RNA- and ChIP-seq data. We compared …

Catchment Area Analysis Using Bayesian Regression Modeling, Aobo Wang, David C. Wheeler

Biostatistics Publications

A catchment area (CA) is the geographic area and population from which a cancer center draws patients. Defining a CA allows a cancer center to describe its primary patient population and assess how well it meets the needs of cancer patients within the CA. A CA definition is required for cancer centers applying for National Cancer Institute (NCI)-designated cancer center status. In this research, we constructed both diagnosis and diagnosis/treatment CAs for the Massey Cancer Center (MCC) at Virginia Commonwealth University. We constructed diagnosis CAs for all cancers based on Virginia state cancer registry data and Bayesian hierarchical logistic regression …

Evaluation Of The Performance Of Smoothing Functions In Generalized Additive Models For Spatial Variation In Disease, Umaporn Siangphoe, David C. Wheeler

Biostatistics Publications

Generalized additive models (GAMs) with bivariate smoothing functions have been applied to estimate spatial variation in risk for many types of cancers. Only a handful of studies have evaluated the performance of smoothing functions applied in GAMs with regard to different geographical areas of elevated risk and different risk levels. This study evaluates the ability of different smoothing functions to detect overall spatial variation of risk and elevated risk in diverse geographical areas at various risk levels using a simulation study. We created five scenarios with different true risk area shapes (circle, triangle, linear) in a square study region. We …

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.

Assessment Of Residential History Generation Using A Public-Record Database, David C. Wheeler, Aobo Wang

Biostatistics Publications

In studies of disease with potential environmental risk factors, residential location is often used as a surrogate for unknown environmental exposures or as a basis for assigning environmental exposures. These studies most typically use the residential location at the time of diagnosis due to ease of collection. However, previous residential locations may be more useful for risk analysis because of population mobility and disease latency. When residential histories have not been collected in a study, it may be possible to generate them through public-record databases. In this study, we evaluated the ability of a public-records database from LexisNexis to provide …

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, …