Digital Commons Network^™

Fit To Predict? Ecoinformatics For Predicting The Catchability Of A Pelagic Fish In Near Real-Time, Kylie L. Scales, Elliot L. Hazen, Sara M. Maxwell, Heidi Dewar, Suzanne Kohin, Michael G. Jacox, Christopher A. Edwards, Dana K. Briscoe, Larry B. Crowder, Rebecca L. Lewison, Steven J. Bograd

Biological Sciences Faculty Publications

The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing ecoinformatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 years (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of …

Experimental Evaluation Of Several Key Factors Affecting Root Biomass Estimation By 1500 Mhz Ground-Penetrating Radar, John C. Bain, Frank P. Day, John R. Butnor

Biological Sciences Faculty Publications

Accurate quantification of coarse roots without disturbance represents a gap in our understanding of belowground ecology. Ground penetrating radar (GPR) has shown significant promise for coarse root detection and measurement, however root orientation relative to scanning transect direction, the difficulty identifying dead root mass, and the effects of root shadowing are all key factors affecting biomass estimation that require additional research. Specifically, many aspects of GPR applicability for coarse root measurement have not been tested with a full range of antenna frequencies. We tested the effects of multiple scanning directions, root crossover, and root versus soil moisture content in a …

Rapid Adaptive Responses To Climate Change In Corals, Gergely Torda, Jennifer M. Donelson, Manuel Aranda, Daniel J. Barshis, Line Bay, Michael L. Berumen, David G. Bourne, Neal Cantin, Sylvain Foret, Mikhail Matz

Biological Sciences Faculty Publications

Pivotal to projecting the fate of coral reefs is the capacity of reef-building corals to acclimatize and adapt to climate change. Transgenerational plasticity may enable some marine organisms to acclimatize over several generations and it has been hypothesized that epigenetic processes and microbial associations might facilitate adaptive responses. However, current evidence is equivocal and understanding of the underlying processes is limited. Here, we discuss prospects for observing transgenerational plasticity in corals and the mechanisms that could enable adaptive plasticity in the coral holobiont, including the potential role of epigenetics and coral-associated microbes. Well-designed and strictly controlled experiments are needed to …

Reproductive Competency And Mitochondrial Variation In Aged Syrian Hamster Oocytes, Fang Li, Frank J. Castora, Wentia Ford, Khalid Alarid, Howard W. Jones Jr., R. James Swanson

Biological Sciences Faculty Publications

The hamster is a useful model of human reproductive biology because its oocytes are similar to those in humans in terms of size and structural stability. In the present study we evaluated fecundity rate, ovarian follicular numbers, ova production, mitochondrial number, structure and function, and cytoplasmic lamellae (CL) in young (2–4 months) and old (12–18 months) Syrian hamsters (Mesocricetus auratus). Young hamsters had higher fertilisation rates and larger litters than old hamsters (100 vs 50% and 9.3 +/- 0.6 vs 5.5 +/- 0.6, respectively). Ovarian tissue from superovulated animals showed a 46% decrease in preantral follicles in old …

The Conservation Status Of Marine Bony Shorefishes Of The Greater Caribbean, Kent E. Carptenter, Christi Linardich, Gina Ralph, N. Cox, D. R. Robertson, H. Harwell, A. Acero P., W. Anderson Jr., F. Barthelat, J. -L. Bouchereau, J. J. Brown, J. Buchanan, D. Buddo, B. Collette, M. Comeros-Raynal, M. Craig, M. Curtis, T. Defex, J. Dooley, W. Driggers Iii, C. Elfes Livsey, T. Fraser, R. Gilmore Jr., L. Grijalba Bendeck, A. Hines, R. Kishore, K. Lindeman, J. -P. Maréchal, J. Mceachran, R. Mcmanus, J. Moore, T. Munroe, H. Oxenford, F. Pezold, F. Pina Amargós, A. Polanco Fernandez, B. Polidoro, C. Pollock, R. Robins, B. Russell, C. Sayer, S. Williams

Biological Sciences Faculty Publications

The greater Caribbean biogeographic region covered in this report (representing 38 countries and territories) encompasses an outstanding marine bony shorefish richness of approximately 1,360 species, with many (53%) being endemic. This report provides an overview of the conservation status of greater Caribbean shorefishes, with detailed information available through the IUCN Red List, and gives recommendations.

Informing Marine Protected Area Designation And Management For Nesting Olive Ridley Sea Turtles Using Satellite Tracking, Tiffany M. Dawson, Angela Formia, Pierre D. Agamboué, Georges M. Asseko, François Boussamba, Floriane Cardiec, Emmanuel Chartrain, Philip D. Doherty, J. Michael Fay, Brendan J. Godley, Francis Lambert, Brice D. Koumba Mabert, Jean C. Manfoumbi, Kristian Metcalfe, Gianna Minton, Ivan Ndanga, Jacob Nzegoue, Carmen K. Kouerey Oliwina, Philippe Du Plessis, Guy-Philippe Sounguet, Dominic Tilley, Matthew J. Witt, Sara M. Maxwell

Biological Sciences Faculty Publications

Understanding the horizontal and vertical habitat of olive ridley sea turtles (Lepidochelys olivacea), a threatened species, is critical for determining regions for protection and relevant gear modifications that may effectively reduce bycatch, the largest threat to this species. Satellite transmitters were used to determine the movement and dive behavior of 21 female olive ridley turtles tagged in Pongara National Park, Gabon during the 2012, 2013, and 2015 nesting seasons. A switching state-space model was used to filter the tracking data and categorize the internesting and post-nesting movements. Gridded utilization distribution (UD) home range analysis of tracking data revealed …

Frontiers In Otolith Chemistry: Insights, Advances And Applications, B. D. Walther, K. E. Limburg, C. M. Jones, J. J. Schaffler

OES Faculty Publications

The rapid proliferation of publications employing chemical assays of fish hard parts, and otoliths in particular, has led to many novel insights into the migration patterns, life history strategies and mixed stock dynamics of fishes across the globe (Campana et al., 2000; Elsdon et al., 2008; Walther & Limburg, 2012). These insights include uncovering diverse migratory strategies within species and populations (Kerr et al., 2009; Hogan et al., 2014; Schoen et al., 2016), quantifying rates of mixing among stocks across management boundaries (Rooker et al., 2008; Walther & Thorrold, 2010) and estimating the relative …

Dna Methylation Patterns In Cord Blood Of Neonates Across Gestational Age Association With Cell-Type Proportions, Susan M. Braid, Kwame Okrah, Amol Shetty, Hector Corrada Bravo

Ellmer School of Nursing Faculty Publications

Background: A statistical methodology is available to estimate the proportion of cell types (cellular heterogeneity) in adult whole blood specimens used in epigenome-wide association studies (EWAS). However, there is no methodology to estimate the proportion of cell types in umbilical cord blood (also a heterogeneous tissue) used in EWAS.

Objectives: The objectives of this study were to determine whether differences in DNA methylation (DNAm) patterns in umbilical cord blood are the result of blood cell type proportion changes that typically occur across gestational age and to demonstrate the effect of cell type proportion confounding by comparing preterm infants exposed and …

Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ά-helices can be detected from density maps at 5-8 angstrom resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 angstrom-8.25 angstrom resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands …

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He

Computer Science Faculty Publications

A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to compute the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, the computational problem becomes more complex. We present an efficient method that addresses the secondary structure placement problem in presence of multiple secondary structure predictions and computes the optimal mapping. We tested the method using 12 simulated images from alpha-proteins and …

Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He

Computer Science Faculty Publications

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM …

Homeomorphic Tetrahedral Tessellation For Biomedical Images, Jing Xu, Andrey N. Chernikov

Computer Science Faculty Publications

We present a novel algorithm for generating three-dimensional unstructured tetrahedral meshes for biomedical images. The method uses an octree as the background grid from which to build the final graded conforming meshes. The algorithm is fast and robust. It produces meshes with high quality since it provides dihedral angle lower bound for the output tetrahedra. Moreover, the mesh boundary is a geometrically and topologically accurate approximation of the object surface in the sense that it allows for guaranteed bounds on the two-sided Hausdorff distance and the homeomorphism between the boundaries of the mesh and the boundaries of the materials. The …

An Iterative Bézier Method For Fitting Beta-Sheet Component Of A Cryo-Em Density Map, Michael Poteat, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic structures when the resolution of density maps is not sufficiently high. Geometrical shape representation of secondary structural components in a medium-resolution density map enhances modeling of atomic structures. We compare two methods in producing surface representation of the β-sheet component of a density map. Given a 3-dimensional volume of β-sheet that is segmented from a density map, the performance of a polynomial fitting was compared with that …

Simulations Of Coherent Synchrotron Radiation On Parallel Hybrid Gpu/Cpu Platform, B. Terzić, K. Arumugam, D. Duffin, A. Godunov, T. Islam, D. Ranjan, S. Sangam, Mohammad Zubair

Physics Faculty Publications

Coherent synchrotron radiation (CSR) is an effect of self-interaction of an electron bunch as it traverses a curved path. It can cause a significant emittance degradation, as well as fragmentation and microbunching. Numerical simulations of the 2D/3D CSR effects have been extremely challenging due to computational bottlenecks associated with calculating retarded potentials via integrating over the history of the bunch. We present a new high-performance 2D, particle-in-cell code which uses massively parallel multicore GPU/GPU platforms to alleviate computational bottlenecks. The code formulates the CSR problem from first principles by using the retarded scalar and vector potentials to compute the self-interaction …

Back-Flow Prevention Strategies For Stormwater Lines, Ron Evins

September 29, 2016: Adaptive Structures and Innovative Solutions

No abstract provided.

Plasma Processes And Polymers Third Special Issue On Plasma And Cancer, Mounir Laroussi, Annemie Bogaerts, Nazir Barekzi

Electrical & Computer Engineering Faculty Publications

(First paragraph) This issue of Plasma Processes and Polymers is the third in a series on the applications of low temperature plasma (LTP) against cancer, or “plasma oncology.” The papers in this issue are inspired from the talks given at the third International Workshop on Plasma for Cancer Treatment (IWPCT) which took place on April 11–12, 2016 in Washington, DC, USA. IWPCT is an international workshop that was created in 2014 as a venue to share cutting edge plasma oncology research. The first IWPCT was held in Washington DC, under the co-chairmanship of Prof. Mounir Laroussi (Old Dominion University) and …

Alcohol Use Variability In A Community-Based Sample Of Nonstudent Emerging Adult Heavy Drinkers, Cathy Lau-Barraco, Abbly L. Braitman, Amy L. Stamates, Ashley N. Linden-Carmichael

Psychology Faculty Publications

BACKGROUND: While nonstudent emerging adults are at elevated risk for experiencing alcohol-related problems, there remains a paucity of research devoted specifically to addressing drinking in this group.

OBJECTIVES: The present study sought to offer unique insights into nonstudent drinking by examining drinking variability across 30 days using a retrospective diary method. Specific aims were to: (1) compare within- and between-person variability in alcohol use across 30 days, and (2) determine the extent to which central social-cognitive between-person factors (i.e., social expectancies, perceived drinking norms, social drinking motivations) predict between-person alcohol use as well as within-person variability in drinking.

METHODS: Participants …

Graduate News, Odu Graduate School, Old Dominion University

Graduate News

October 2016 issue of Graduate News from the ODU Graduate School.

Circulation, Vol. 22, No. 1, Center For Coastal Physical Oceanography, Old Dominion University, Mike Dinniman

CCPO Circulation

Fall 2016 issue of CCPO Circulation featuring article "I have to Do What to the Model? How Did I Get Here, Part ll" by Mike Dinniman.

Thermo-Mechanical System Identification Of A Shape Memory Alloy Actuated Mechanism, Cody Alexander Wright

Mechanical & Aerospace Engineering Theses & Dissertations

Shape memory alloy (SMA) actuators paired in an antagonistic arrangement can be used to produce mechanisms that replicate human biomechanics. To investigate this proposal, the biomechanical articulation of the elbow by means of the biceps brachii muscle is compared with that of a SMA actuated arm. This is accomplished by parametric analysis of a crank-slider kinematic mechanism actuated, first, with an experimentally characterized SMA wire and then an idealized musculotendon actuator based on actuation properties of muscles published in the literature. Next, equations of motion for the system dynamics of the SMA actuated mechanism are derived and phase portrait analysis …

Design Of Drug Nano-Carriers For Study Of Multidrug Resistance In Single Live Cells, Pavan Kumar Cherukuri

Chemistry & Biochemistry Theses & Dissertations

Multidrug resistance (MDR) exists in both prokaryotic and eukaryotic cells. MDR is responsible for ineffective treatment of a wide range of diseases, such as infections and cancer. The ATP-binding cassette (ABC) membrane transporters (efflux pumps) are one of the largest and most diverse super-families of membrane proteins found in all living organisms, ranging from bacteria to humans. All ABC transporters share a common structure of four core domains; two transmembrane domains (TMD) with variable sequence and topology and two nucleotide-binding domains (NBD) with conserved sequences. Conventional methods for the study of the efflux functions are radioactively labeled substrates and fluorescent …

School Policy, Food And Physical Activity Environment, And Childhood Obesity, Ruicui Liu

Health Services Research Dissertations

The purpose of this study is to examine the effect of school food and physical activity environments on energy balance-related behaviors and Body Mass Index (BMI) and to simulate the effect of school-based nutrition and physical activity policies on childhood obesity prevention. Four models based on the Social Ecological Framework of childhood obesity were developed. Parameters of these models were calibrated and validated with empirical data derived from the Early Childhood Longitudinal Study – Kindergarten Class of 1998-99 and the 2003-2004 National Health and Nutrition Examination Study. The correlation between observed and simulated BMI was 0.85 for 5th grade children …

Monarch, Philip Walzer (Editor)

Monarch Magazine

Fall 2016 issue of Monarch, the Old Dominion University Magazine.

Subtitled: A New Era in Dining

Association Between Combat, Morally Injurious Experiences, Spiritual Injury, And Alcohol Use Among Active Duty Military Personnel And Veterans, Allison T. Robbins

Psychology Theses & Dissertations

Literature has supported that, along with physical and psychological injuries, combat profoundly impacts veterans’ moral and spiritual belief systems and may contribute to negative health behaviors. Moral injury is a developing construct related to negative consequences associated with war-zone stressors that transgress military veterans’ deeply held values and belief systems. Additionally, spiritual injury addresses negative responses to an event that damages their relationship with God, self, and others, and alienates an individual from that which gives meaning to their lives. The purpose of the present study was to examine the relationship between combat exposure, morally injurious experiences (MIEs), spiritual injury, …

Reconceptualizing Women's Stem Experiences: Building A Theory Of Positive Marginality, Valerie N. Streets

Psychology Theses & Dissertations

Since the 1980s, disciplines such as psychology and sociology have discussed the construct of positive marginality. Positive marginality describes the perception that belonging to a non-dominant cultural or demographic group can be advantageous rather than oppressing. To date, research on positive marginality has explored the construct in a qualitative manner across a number of demographic groups (e.g., Jewish women in social sciences, African American women in predominantly Caucasian workplaces). Because women are largely underrepresented in science, technology, engineering, and mathematics (STEM) fields, the current research examined positive marginality in a STEM context. This research advances the existing understanding of positive …

Abiotic Factors Contributing To The Survival Of Three Tick Species In Southeastern Virginia, Amblyomma Americanum (Lone Star Tick), Dermacentor Variabilis (American Dog Tick), And Amblyomma Maculatum (Gulf Coast Tick), Lindsey A. Bidder

Biological Sciences Theses & Dissertations

Amblyomma americanum, Amblyomma maculatum, and Dermacentor variabilis are hard-bodied ticks in the Hampton Roads area of southeastern Virginia. This study consisted of two field projects focused on these tick species. To estimate the off-host survival of local tick species, a capture-mark-recapture (CMR) study was performed. An environmental survival study was performed to quantify the ability of these three tick species to survive in situ. Four field sites were used in the Hampton Roads region covering a variety of habitat types and vegetation; specifically two drier, upland field sites and two flood-prone sites. CMR was conducted from May through …

Prejudice Toward Atheists In The United States As Related To Perceived Prevalence, Wanda D. Brooks

Psychology Theses & Dissertations

By manipulating mortality salience (MS) in place of life-threatening events to stimulate death-related thoughts, the current research contributes to the body of research supporting Terror Management Theory. It was hypothesized that religious participants should exhibit cultural worldview defense by scoring higher in anti-atheist prejudice following the MS manipulation than would those in the control condition. Further, this research extends the current research into Terror Management Theory as a cause for conflict among out-groups and explores its effects on cultural worldviews in the area of prejudice toward atheists. This includes examining how the perception of an increasing prevalence of atheists contributes …

A General Theory Of Emergence In Engineered Systems, John J. Johnson Iv

Engineering Management & Systems Engineering Theses & Dissertations

Engineered systems are designed to satisfy specific needs and produce explainable/predictable results. But despite this intent, engineered systems don’t always do what they are designed to do once they are implemented. Some engineered systems produce properties and behaviors that are not clearly explainable or predictable by the properties of their components. This is a problem recognized in government and private sectors as having broad ranging financial and security consequences. It is also the essence of the emergence phenomena. A review of the literature reveals two significant gaps in the current body of knowledge on emergence as it pertains to engineered …

Potential Impacts Of Climate Change On Photochemistry Of Zostera Marina L., Billur Celebi

OES Theses and Dissertations

Seagrasses account for approximately 10% of the ocean’s total carbon storage, although photosynthesis of seagrasses is carbon limited at today’s oceanic pH. Therefore, increasing atmospheric CO₂ concentration, which results in ocean acidification/carbonation, is predicted to have a positive impact on seagrass productivity. Previous studies have confirmed the positive influence of increasing CO₂ on photosynthesis and survival of the temperate eelgrass Zostera marina L., but the acclimation of photoprotective mechanisms in this context has not been characterized. This study aimed to quantify the long-term impacts of ocean acidification on photochemical control mechanisms that promote photosynthesis while simultaneously protecting …

An Evaluation Of Pathways To Community College Student Success In Anatomy And Physiology I, Staci Brooke Forgey

Educational Leadership & Workforce Development Theses & Dissertations

The demand for healthcare workers is increasing nationwide. Higher education is responding by examining various interventions designed to increase completion (Abele, Penprase, & Ternes, 2011). Anatomy and Physiology is often identified as a gatekeeper course for students, since many withdraw or fail this course (Hopper, 2011). Within the VCCS, two colleges have implemented a prerequisite course, NAS 2, for Anatomy and Physiology. This study analyzed student data from before and after NAS 2 implementation, and examined General Biology to determine if it was a predictor of success in Anatomy and Physiology.

When NAS 2 was a significant predictor of grade …