Digital Commons Network^™

Variation In Growth And Developmental Responses To Supraoptimal Temperatures Near Latitudinal Range Limits Of Gypsy Moth Lymantria Dispar (L.), An Expanding Invasive Species, Lily M. Thompson, Trevor M. Faske, Nana Banahene, Dominique Grim, Salvatore J. Agosta, Dylan Parry, Patrick C. Tobin, Derek M. Johnson, Kristine L. Grayson

Biology Publications

Variation in thermal performance within and between populations provides the potential for adaptive responses to increasing temperatures associated with climate change. Organisms experiencing temperatures above their optimum on a thermal performance curve exhibit rapid declines in function and these supraoptimal temperatures can be a critical physiological component of range limits. The gypsy moth, Lymantria dispar (L.) (Lepidoptera: Erebidae), is one of the best-documented biological invasions and factors driving its spatial spread are of significant ecological and economic interest. The present study examines gypsy moth sourced from different latitudes across its North American range for sensitivity to high temperature in constant …

Genetic Differentiation Of Spring-Spawning And Fall-Spawning Male Atlantic Sturgeon In The James River, Virginia, Matthew T. Balazik, Daniel J. Farrae, Tanya L. Darden, Greg C. Garman

Biology Publications

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) populations are currently at severely depleted levels due to historic overfishing, habitat loss, and pollution. The importance of biologically correct stock structure for effective conservation and management efforts is well known. Recent improvements in our understanding of Atlantic sturgeon migrations, movement, and the occurrence of putative dual spawning groups leads to questions regarding the true stock structure of this endangered species. In the James River, VA specifically, captures of spawning Atlantic sturgeon and accompanying telemetry data suggest there are two discrete spawning groups of Atlantic sturgeon. The two putative spawning groups were …

Immediate Effects Of Microclimate Modification Enhance Native Shrub Encroachment, Joseph A. Thompson, Julie C. Zinnert, Donald R. Young

Biology Publications

Shrubs have become more dense and expanded beyond their range all over the world for a variety of reasons including increased temperatures, overgrazing, and alteration of historical fire regime. Native shrubs have been encroaching on Virginia barrier island grasslands for over half a century for unknown reasons. Species composition, soil nutrients, leaf area index (LAI), and ground and air temperature were recorded across the shrub to grass transition and at free-standing shrubs in a coastal grassland in order to determine the effect of shrub encroachment on plant community and microclimate. Species richness was significantly lower inside shrub thickets. Soil water …

Directed Evolution Provides Insight Into Conformational Substrate Sampling By Srta, Muna Suliman, Vishaka Santosh, Tom C. M. Seegar, Annamarie C. Dalton, Kathryn M. Schultz, Candice S. Klug, William A. Barton

Biochemistry and Molecular Biology Publications

The Sortase family of transpeptidases are found in numerous gram-positive bacteria and involved in divergent physiological processes including anchoring of surface proteins to the cell wall as well as pili assembly. As essential proteins, sortase enzymes have been the focus of considerable interest for the development of novel anti-microbials, however, more recently their function as unique transpeptidases has been exploited for the synthesis of novel bio-conjugates. Yet, for synthetic purposes, SrtA-mediated conjugation suffers from the enzyme's inherently poor catalytic efficiency. Therefore, to identify SrtA variants with improved catalytic efficiency, we used directed evolution to select a catalytically enhanced SrtA enzyme. …

Differential Response Of Barrier Island Dune Grasses To Species Interactions And Burial, April Harris, Julie C. Zinnert, Donald R. Young

Biology Publications

Barrier islands are at the forefront of storms and sea-level rise. High disturbance regimes and sediment mobility make these systems sensitive and dynamic. Island foredunes are protective structures against storm-induced overwash that are integrally tied to dune grasses via biogeomorphic feedbacks. Shifts in dune grass dominance could influence dune morphology and susceptibility to overwash, altering island stability. In a glasshouse study, two dune grasses, Ammophila breviligulata and Uniola paniculata, were planted together and subjected to a 20 cm burial to quantify morphological and physiological responses. Burial had positive effects on both plants as indicated by increased electron transport rate and …

Aggregate Stability And Water Retention Near Saturation Characteristics As Affected By Soil Texture, Aggregate Size And Polyacrylamide Application, Amrakh I. Mamedov, Chi-Hua Huang, Fazil A. Aliev, Guy J. Levy

Biology Publications

Understanding the effects of soil intrinsic properties and extrinsic conditions on aggregate stability is essential for the development of effective soil and water conservation practices. Our objective was to evaluate the combined role of soil texture, aggregate size and application of a stabilizing agent on aggregate and structure stability indices (composite structure index [SI], the and n parameters of the VG model and the S-index) by employing the high energy (0-5.0 J kg(-1)) moisture characteristic (HEMC) method. We used aggregates of three sizes (0.25-0.5, 0.5-1.0 and 1.0-2.0 mm) from four semi-arid soils treated with polyacrylamide (PAM). An increase in SI …

Functional Traits Of Expanding, Thicket-Forming Shrubs: Contrasting Strategies Between Exotic And Native Species, Sheri A. Shiflett, Julie C. Zinnert, Donald R. Young

Biology Publications

Woody expansion has been documented for decades in many different systems globally, often yielding vast changes in ecosystem functioning. While causes and consequences of woody expansion have been well documented, few studies have addressed plant functional traits that promote dramatic and rapid expansion in range. Our objectives were to investigate plant functional traits that contribute to the colonization, rapid expansion, and thicket formation of an invasive, N-fixing shrub, Elaeagnus umbellata Thunb. (Elaeagnaceae), and a native, N-fixing shrub Morella cerifera (L.) Small (Myricaceae) and compare to native, sympatric, non-expanding shrub species. Quantified functional traits included morphological (e.g., specific leaf area, leaf …

Minion™ Nanopore Sequencing Of Environmental Metagenomes: A Synthetic Approach, Bonnie L. Brown, Mick Watson, Samuel S. Minot, Maria C. Rivera, Rima B. Franklin

Biology Publications

Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: …

Targeting Hepatocellular Carcinoma Through Tgf-Β Pathway E3 Ligases, Kazufumi Ohshiro, Jian Chen, Shulin Li, Jon White, Asif Rashid, Lopa Mishra

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

The Role Of Uridine-Cytidine Kinase 2 In The Development Of Hepatocellular Carcinoma, Dehai Wu, Song Tao, Keunsoo Ahn, Nicha Wongjarupong, Lewis Roberts

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Ibrutinib In Combination With Sorafenib Synergistically Inhibits Proliferation And Survival Of Hepatocellular Carcinoma Cells By Targeting Egfr Signaling Pathway, Cho-Hao Lin, Nissar Wani, Khadija Elkholy, Kalpana Ghoshal

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Commonly Used H1 And H2 Histamine Receptor (Hr) Blockers Decrease Cholangiocarcinoma Xenograft Tumor Growth, Angiogenesis And Emt, Lindsey Kennedy, Laura Hargrove, Jennifer Demieville, Walker Karstens, Steven Smith, Heather Francis

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Perfluorocarbon Emulsions Radiosensitise Brain Tumors In Carbogen Breathing Mice With Orthotopic Gl261 Gliomas, Lisa A. Feldman, Marie-Sophie Fabre, Carole Grasso, Dana Reid, William C. Broaddus, Gregory M. Lanza, Bruce D. Spiess, Joel R. Garbow, Melanie J. Mcconnell, Patries M. Herst

Neurosurgery Publications

Background

Tumour hypoxia limits the effectiveness of radiation therapy. Delivering normobaric or hyperbaric oxygen therapy elevates pO2 in both tumour and normal brain tissue. However, pO2 levels return to baseline within 15 minutes of stopping therapy.

Aim

To investigate the effect of perfluorocarbon (PFC) emulsions on hypoxia in subcutaneous and intracranial mouse gliomas and their radiosensitising effect in orthotopic gliomas in mice breathing carbogen (95%O2 and 5%CO2).

Results

PFC emulsions completely abrogated hypoxia in both subcutaneous and intracranial GL261 models and conferred a significant survival advantage orthotopically (Mantel Cox: p = 0.048) in carbogen breathing mice injected intravenously (IV) with …

Management Of Invasive Allee Species, David Chan, C. M. Kent, D. M. Johnson

Mathematics and Applied Mathematics Publications

In this study, we use a discrete, two-patch population model of an Allee species to examine different methods in managing invasions. We first analytically examine the model to show the presence of the strong Allee effect, and then we numerically explore the model to test the effectiveness of different management strategies. As expected invasion is facilitated by lower Allee thresholds, greater carrying capacities and greater proportions of dispersers. These effects are interacting, however, and moderated by population growth rate. Using the gypsy moth as an example species, we demonstrate that the effectiveness of different invasion management strategies is context-dependent, combining …

Aldh2*2 And Peer Drinking In East Asian College Students, Karen G. Chartier, Taryl O'Shea, Nathaniel Thomas, Bradley Todd Webb, Danielle M. Dick, Kenneth S. Kendler

Social Work Publications

Background: The ALDH2*2 allele (A-allele) at rs671 is more commonly carried by Asians and is associated with alcohol-related flushing, a strong adverse reaction to alcohol that is protective against drinking. Social factors, such as having friends who binge drink, also contribute to drinking in Asian youth. Objectives: This study examined the interplay between ALDH2*2, peer drinking, and alcohol consumption in college students. We hypothesized that the relationship between ALDH2*2 and standard grams of ethanol per month would vary based on the level of peer drinking. Methods: Subjects (N = 318, 63.25% female) were East Asian …

Code For "Noise-Enhanced Coding In Phasic Neuron Spike Trains", Cheng Ly, Brent D. Doiron

Statistical Sciences and Operations Research Data

This zip file contains Matlab scripts and ode (XPP) files to calculate the statistics of the models in "Noise-Enhanced Coding in Phasic Neuron Spike Trains". This article is published in PLoS ONE.

When Do Correlations Increase With Firing Rates In Recurrent Networks?, Andrea K. Barreiro, Cheng Ly

Statistical Sciences and Operations Research Publications

A central question in neuroscience is to understand how noisy firing patterns are used to transmit information. Because neural spiking is noisy, spiking patterns are often quantified via pairwise correlations, or the probability that two cells will spike coincidentally, above and beyond their baseline firing rate. One observation frequently made in experiments, is that correlations can increase systematically with firing rate. Theoretical studies have determined that stimulus-dependent correlations that increase with firing rate can have beneficial effects on information coding; however, we still have an incomplete understanding of what circuit mechanisms do, or do not, produce this correlation-firing rate relationship. …

Biophysical Drivers Of Carbon Dioxide And Methane Fluxes In A Restored Tidal Freshwater Wetland, Ellen Stuart-Haëntjens, Scott C. Neubauer, William Shuart, Christopher M. Gough

Rice Rivers Center Research Symposium

Wetlands store large amounts of carbon (C) in biomass and soils, playing a crucial role in offsetting greenhouse gas (GHG) emissions; however, they also account for 30% of global yearly CH4 emissions. Anthropogenic disturbance has led to the decline of natural wetlands throughout the United States, with a corresponding increase in created and restored wetlands. Studies characterizing biogeochemical processes in restored forested wetlands, particularly those that are both tidal and freshwater, are lacking but essential for informing science- based carbon management.

Identifying Biotic Determinants Of Historic American Eel (Anguilla Rostrata) Distributions, Taylor E. Woods, Daniel J. Mcgarvey

Rice Rivers Center Research Symposium

Traditionally, ecologists studying large scale patterns in species distributions emphasize abiotic variables over biotic interactions. Noting that both abiotic & biotic variables likely determine distributions of all organisms, many ecologists now aim for a more comprehensive view of species distributions, inclusive of both abiotic and biotic components (Soberón 2007).

Somatic Symptom Disorder In Dermatology, James L. Levenson, Aditi A. Sharma, Alex G. Ortega-Loayza

Psychiatry Publications

Somatic symptom disorder (SSD) is defined by the prominence of somatic symptoms associated with abnormal thoughts, feelings, and behaviors related to the symptoms, resulting in significant distress and impairment. Individuals with these disorders are more commonly encountered in primary care and other medical settings, including dermatology practice, than in psychiatric and other mental health settings. What defines the thoughts, feelings, and behaviors as abnormal is that they are excessive, that is, out of proportion to other patients with similar somatic symptoms, and that they result in significant distress and impairment. SSD may occur with or without the presence of a …

Molecular Genetic Influences On Normative And Problematic Alcohol Use In A Population-Based Sample Of College Students, Bradley T. Webb, Alexis C. Edwards, Aaron R. Wolen, Jessica E. Salvatore, Fazil Aliev, Brien P. Riley, Cuie Sun, Vernell S. Williamson, James N. Kitchens, Kimberly Pedersen, Amy Adkins, Megan E. Cooke, Jeanne E. Savage, Zoe Neale, Seung B. Cho, Danielle M. Dick, Kenneth S. Kendler

Psychiatry Publications

Background: Genetic factors impact alcohol use behaviors and these factors may become increasingly evident during emerging adulthood. Examination of the effects of individual variants as well as aggregate genetic variation can clarify mechanisms underlying risk.

Methods: We conducted genome-wide association studies (GWAS) in an ethnically diverse sample of college students for three quantitative outcomes including typical monthly alcohol consumption, alcohol problems, and maximum number of drinks in 24 h. Heritability based on common genetic variants (h2SNP) was assessed. We also evaluated whether risk variants in aggregate were associated with alcohol use outcomes in an independent sample of young …

Electroconvulsive Therapy In Geriatric Patients: A Literature Review And Program Report From Virginia Commonwealth University, Richmond, Virginia, Usa, Andrew D. Snyder, Vasu Venkatachalam, Ananda Pandurangi

Psychiatry Publications

Electroconvulsive therapy (ECT) is an effective therapeutic intervention in the elderly patients with major depression, especially those with psychosis, suicidality, catatonia, nutritional compromise, and resistance to medications. Response rates can be as high as 80%. We present an extensive review of the relevant literature, provide a description of the ECT program at Virginia Commonwealth University in Richmond, Virginia, USA, and present results of our experience with ECT in fifty elderly patients. The treatments were safe, well tolerated, and produced high response rates, variably between 68% and 84%. Patients in the long‑term maintenance ECT program continue to show sustained benefits from …

An Annotated Corpus With Nanomedicine And Pharmacokinetic Parameters, Nastassja Lewinski, Ivan Jimenez, Bridget Mcinnes

Chemical and Life Science Engineering Publications

A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP) approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP) efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration’s Drugs@FDA online database. In this work, we present the development of the Engineered Nanomedicine Database corpus to support the …

Quadmutex: Quadratic Driver Mutation Explorer, Bokhari Yahya, Tomasz Jakub Arodz

Computer Science Publications

Background

Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accumulate in the DNA of cancer cells. An ongoing problem is to figure out which mutations are drivers - play a role in oncogenesis, and which are passengers - do not play a role. One way of addressing this question is through inspection of somatic mutations in DNA of cancer samples from a cohort of patients and detection of patterns that differentiate driver from passenger mutations. …

An Integrative In-Silico Approach For Therapeutic Target Identification In The Human Pathogen Corynebacterium Diphtheriae, Syed Babar Jamal, Syed Shah Hassan, Sandeep Tiwari, Marcus V. Viana, Leandro De Jesus Benevides, Asad Ullah, Adrián G. Turjanski, Debmalya Barh, Preetam Ghosh, Daniela Arruda Costa, Artur Silva, Richard Röttger, Jan Baumbach, Vasco A.C. Azevedo

Computer Science Publications

Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms. In this study, our contributions include the prediction of modelome of 13 C. diphtheriae strains, using the MHOLline workflow. A set of 463 conserved proteins were identified by combining the results of pangenomics …

Quantifying Variation In Gait Features From Wearable Inertial Sensors Using Mixed Effects Models, Kellen Garrison Cresswell, Yongyun Shin, Shanshan Chen

Biostatistics Publications

The emerging technology of wearable inertial sensors has shown its advantages in collecting continuous longitudinal gait data outside laboratories. This freedom also presents challenges in collecting high-fidelity gait data. In the free-living environment, without constant supervision from researchers, sensor-based gait features are susceptible to variation from confounding factors such as gait speed and mounting uncertainty, which are challenging to control or estimate. This paper is one of the first attempts in the field to tackle such challenges using statistical modeling. By accepting the uncertainties and variation associated with wearable sensor-based gait data, we shift our efforts from detecting and correcting …

Comorbidity, Pain, Utilization, And Psychosocial Outcomes In Older Versus Younger Sickle Cell Adults: The Pisces Project, Donna K. Mcclish, Wally R. Smith, James L. Levenson, Imoigele P. Aisiku, John D. Roberts, Susan D. Roseff, Viktor E. Bovbjerg

Biostatistics Publications

Background. Patients with SCD now usually live well into adulthood. Whereas transitions into adulthood are now often studied, little is published about aging beyond the transition period. We therefore studied age-associated SCD differences in utilization, pain, and psychosocial variables. Methods. Subjects were 232 adults in the Pain in Sickle Cell Epidemiology Study (PiSCES). Data included demographics, comorbidity, and psychosocial measures. SCD-related pain and health care utilization were recorded in diaries. We compared 3 age groups: 16–25 (transition), 26–36 (younger adults), and 37–64 (older adults) years. Results. Compared to the 2 adult groups, the transition group reported fewer …

Factors Distinguishing Positive Deviance Among Low-Income African American Women: A Qualitative Study On Infant Feeding, Cecilia E. Barbosa, Saba W. Masho, Kellie E. Carlyle, Maghboeba Mosavel

School of Nursing Publications

Background: Positive deviant individuals practice beneficial behaviors in spite of having qualities characterizing them as high risk for unhealthy behaviors.

Objective: This study aimed to identify and understand factors distinguishing low-income African American women who breastfeed the longest (positive deviants) from those who breastfeed for a shorter duration or do not breastfeed.

Methods: Seven mini-focus groups on infant-feeding attitudes and experiences were conducted with 25 low-income African American women, grouped by infant-feeding practice. Positive deviants, who had breastfed for 4 months or more, were compared with formula-feeding participants who had only formula fed their babies and short-term breastfeeding participants who …

The Scope, The Scope

The Scope

Collection of all 2016 articles from The Scope.

About The Scope

This magazine was produced by students in Science Journalism (MASC 491-005), which was taught during the Fall 2016 semester by Jeff South, an associate professor in the Robertson School of Media and Culture at Virginia Commonwealth University, and Sara Williams, head of academic outreach for VCU Libraries.

The course, VCU’s first focusing exclusively on science reporting, was supported by a grant that funds projects aligned with VCU’s strategic plan, called Quest for Distinction. VCU selected the Science Journalism course as a “disruptively innovative idea” and as a way …

Colonialism's Role In The Success Of The Filipino Skin Whitening Industry, Francine Singson

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

In the Philippines and other developing countries, the skin whitening industry is prolific and expanding among native populations. However, this desire for white skin has dire health repercussions, both physical and psychological. Many researchers in the field of Filipino-American psychology attribute this desire for whiter skin to the American colonial rule of the Philippines, which began in 1898 and lasted for nearly fifty years. Historians often characterize the American occupation as cruel and demeaning, leading to colonial mentality that has continued into the post-colonial era. As a result, in order to ameliorate this dilemma, one must explore how the internalized …