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Innovative Applications Of Genetic Algorithms To Problems In Accelerator Physics, Alicia Hofler, Balša Terzić, Matthew Kramer, Anton Zvezdin, Vasiliy Morozov, Yves Roblin, Fanglei Lin, Colin Jarvis

Physics Faculty Publications

The genetic algorithm (GA) is a powerful technique that implements the principles nature uses in biological evolution to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

Intensity-Based Skeletonization Of Cryoem Gray-Scale Images Using A True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the …

College Of Health Sciences Newsletter, December 2012, Tammie Smith (Ed.)

Ellmer College of Health Sciences Newsletters

December 2012 issue of Old Dominion University's College of Health Sciences Newsletter.

Glacial Shortcut Of Arctic Sea-Ice Transport, Michael Stärz, Xun Gong, Rüdiger Stein, Dennis A. Darby, Frank Kauker, Gerrit Lohmann

OES Faculty Publications

Due to the lack of data, the extent, thickness and drift patterns of sea ice and icebergs in the glacial Arctic remains poorly constrained. Earlier studies are contradictory proposing either a cessation of the marine cryosphere or an ice drift system operating like present-day. Here we examine the marine Arctic cryosphere during the Last Glacial Maximum (LGM) using a high-resolution, regional ocean-sea ice model. Whereas modern sea ice in the western Arctic Basin can circulate in the Beaufort Gyre for decades, our model studies present an extreme shortcut of glacial ice drift. In more detail, our results show a clockwise …

Communications And Energy-Harvesting In Nanosensor Networks, Michele C. Weigle

Computer Science Presentations

PDF of a powerpoint presentation from the National Science Foundation (NSF) Workshop on Biological Computations and Communications in Boston, Massachusetts, November 9, 2012. Also available on Slideshare.

Graduate News, Office Of Graduate Studies, Old Dominion University

Graduate News

November 2012 issue of Graduate News from the Office of Graduate Studies (now, ODU Graduate School).

Inactivation Of Bacterial Opportunistic Skin Pathogens By Nonthermal Dc-Operated Afterglow Atmospheric Plasma, L. C. Heller, C. M. Edelblute, A. M. Mattson, X. Hao, J. F. Kolb

Bioelectrics Publications

AIMS: Multidrug-resistant opportunistic pathogens are clinically significant and require the development of new antimicrobial methods. In this study, Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus cells were exposed to atmospheric plasma on agar plates and in vitro on porcine skin for the purpose of testing bacterial inactivation.

METHODS AND RESULTS: Microbial inactivation at varying exposure durations was tested using a nonthermal plasma jet generated with a DC voltage from ambient air. The observed reduction in colony forming units was quantified as log₁₀ reductions.

CONCLUSIONS: Direct plasma exposure significantly inactivated seeded bacterial cells by approx. 6 log_{10 …}

Graduate News, Office Of Graduate Studies, Old Dominion University

Graduate News

October 2012 issue of Graduate News from the Office of Graduate Studies (now, ODU Graduate School).

Circulation, Vol. 18, No. 1, Center For Coastal Physical Oceanography, Old Dominion University, John M. Klinck

CCPO Circulation

Fall 2012 issue of CCPO Circulation featuring article "Ross Sea Cruise: PRISM Project - Processes Regulating Iron Supply at the Mesoscale" by Dr. John Klinck

A Centennial Record Of Paleosalinity Change In The Tidal Reaches Of The Potomac And Rappahannock Rivers, Tributaries To Chesapeake Bay, Neil E. Tibert, Lindsay J. Walker, William P. Patterson, J. Bradford Hubeny, Emma Jones, Olivia R. Cooper

Virginia Journal of Science

Gravity and push cores from the Potomac and Rappahannock Rivers (Virginia Tidewater) were collected from central and proximal estuarine zones with known seasonal salinity stratification. The lowermost microfossil associations in the cores comprise alternating ostracode populations of Cyprideis salebrosa and Cytheromorpha. This microfossil association gives way to an oligohaline association dominated by the freshwater ostracode Darwinula stevensoni. Stable oxygen isotope values (δ¹⁸O) of Rapphannock Cyprideis salebrosa are highly variable ranging between -6.6 to -3.2‰ VPDB. δ¹⁸O values for Potomac Cytheromorpha fuscata range from -8.2 to -3.2‰ VPDB. Positive excursions in δ¹⁸O values …

2012 Undergraduate Research Awards

Virginia Journal of Science

List, with photos, of the Virginia Academy of Science Fall 2012 Undergraduate Research Awards.

Exploratory Modeling Indicates Red-Backed Salamander Detections Are Sensitive To Soil Ph At C. F. Phelps Wildlife Management Area, Virginia, Jay D. Mcghee, Michael D. Killian

Virginia Journal of Science

Red-backed salamanders represent an important component of Virginia ecosystems, but there are few habitat models that can reliably predict the presence/absence of this species. We surveyed the habitats of red-backed salamanders at one site in the Piedmont region of Virginia and collected data on an array of habitat variables with which this species is normally associated. We used logistic regression to develop a model predicting the presence or absence of the species at a given 50m-transect. Our final model incorporated soil organic layer pH variability and mineral layer average pH, and accounted for 30% of the variation in our data. …

Camera Trap Success Among Carnivores And Prey Animals In Tazewell County, Virginia, David L. Chambers, James A. Vance

Virginia Journal of Science

Obtaining basic ecological information on occurrence and activity levels in cryptic and elusive species is often difficult. Camera trapping provides a relatively inexpensive opportunity to acquire such data. We used infrared-triggered cameras to assess trap success and activity levels of several species across four consecutive seasons, including: Ursus americanus (black bear), Lynx rufus (bobcat), Canis latrans (coyote), Vulpes vulpes (red fox), Urocyon cinereoargenteus (gray fox), Procyon lotor (raccoon), Odocoileus virginianus (white-tailed deer), Didelphis virginiana (opossum), Sciurus carolinensis (gray squirrel), and Meleagris gallopavo (wild turkey). With a total of 396 trap nights (TN) at one station over the span of four …

Monarch, Jim Raper (Editor)

Monarch Magazine

Fall 2012 issue of Monarch, the Old Dominion University Magazine.

Subtitled: Epicure at Large: Tips for Tailgaters

Current Status And Long-Term Trends In Water Quality And Living Resources In The Virginia Tributaries And Chesapeake Bay Mainstem From 1985 Through 2011, Daniel M. Dauer, Harold G. Marshall, John R. Donat, Michael F. Lane, Suzanne C. Doughten, Cindy Johnson

Status and Trends for Virginia Chesapeake Bay

The period prior to the implementation of the Chesapeake Bay Monitoring Program was characterized by a marked decline in the water quality of the Chesapeake Bay. The disappearance of submerged aquatic vegetation in certain regions of the Bay, declines in the abundance of some commercially and recreationally important species, increases in the incidence of low dissolved oxygen events, changes in the Bay's food web, and other ecological problems have been related to the deteriorating water quality (e.g. USEPA, 1982,1983;Officer et al.,1984; Orth and Moore, 1984). The results of concentrated research efforts in the late 1970s and early 1980s stimulated the …

Unmanned Signatures, Brian Macaskill

Reconstruction: Studies in Contemporary Culture

UNMANNED SIGNATURES? In addition to its more common significations, “unmanned” is used also in the ‘sport’ of falconry, where it means “not broken in”; the term will in falconry be applied to a hawk or kestrel not (yet?) broken into obedience. “Unwomanned” is similarly linked to deviation from control and controlled norms, but is more likely to appear as a reflexive verb (“to unwoman [herself]”) than as an adjective, and is more likely to be tightly tied in gendered fashion to ‘degeneracy.’ As phrase, title and incipit, “Unmanned Signatures” is in all sorts of ways an oddly descended, perhaps even …

Toward A Concept Of Post-Postmodernism Or Lady Gaga’S Reconfigurations Of Madonna, Danuta Fjellestad, Maria Engberg

Reconstruction: Studies in Contemporary Culture

How can we describe the landscape of what is increasingly referred to as post-postmodernism? Is post-postmodernism but a revision (however significant) of postmodernism or is it a new, perhaps even original, episteme? As must be clear from the title, the article takes Ihab Hassan’s much discussed essay “Toward a Concept of Postmodernism” as its point of departure, but proposes a double revision of his chart. First, it supplements the chart with a set of concepts used to designate post-postmodernism. Second, it provides a re-vision of the very layout of the chart, arguing with Johanna Drucker that form is constitutive …

Of Zombies, Aids, And 'Africa': Non‐Western Disease And The 'Raciocultural' Imagination, Richard Brock

Reconstruction: Studies in Contemporary Culture

This essay investigates the “raciocultural”—a term designating the slippage between, and mutual construction of, “race” and “culture” within discourses of quasi‐biological determinism—as a means of exploring Western representations of non‐Western disease as “foreign” threats to Europe and North America. It suggests that the raciocultural is at once a colonial‐era construction and a reflection of contemporary trends that have seen racist discourse become increasingly displaced onto the notion of the “cultural.” Investigating a range of texts including news media, literary texts, and interactive entertainment, the essay focuses on representations of “African” space as biologically and culturally “infected” in order to examine …

Modeling Martian Planetary Entry Descent And Landing Using Monte Carlo Driven Response Surface Methodology, Narcrisha S. Norman

Mechanical & Aerospace Engineering Theses & Dissertations

Response surface methodology (RSM) is a statistical method that explores the relationships between several descriptive variables and one or more response variables. For over sixty years, among other areas, it has been utilized in quality engineering, process engineering, aircraft engineering, economics, chemical engineering, automotive engineering and design/technique optimization. In this dissertation, RSM is utilized to produce regression models that represent the planetary entry, descent and landing (EDL) process. A complete understanding of EDL process is an essential component of any planetary exploration. Research in this area is ongoing and confidence in the ability to explore known celestial bodies is growing. …

Thresholds Of Change In Decomposition Rate Along A Dune/Swale Transect On A Virginia Barrier Island, Dominic J. Graziani

Biological Sciences Theses & Dissertations

Aboveground and belowground decomposition rates were determined along a barrier island dune/swale transect located on the Virginia Coast Reserve-Long Term Ecological Research Site using litterbags and wooden dowels. The objective was to determine the influence of fine scale changes in the environment on decomposition to identify any potential thresholds affecting decomposition rate. Wax myrtle (Morella cerifera L. Small) leaves and dowels of southern yellow pine wood were used as standard substrates to evaluate environmental influences on decay. Aboveground (F=6.494, p < 0.0001) and belowground (F=5.705, p < 0.0001) decay rates (yr^-1) showed significant variation among litterbag/dowel locations. Aboveground decay rates (yr^-1) ranged from 0.339 (Upper Dune station) …

Configuration Studies Of Electrostatic And Magnetostatic Active Space Radiation Shielding, Trac K. Nguyen

Electrical & Computer Engineering Theses & Dissertations

Developing successful and optimal solutions for mitigating the hazards of radiation in deep space is critical for the success of deep-space long duration explorations, including mission to the Moon, Mars and beyond. A recent report (Tripathi et al., 2008) had explored the feasibility of using electrostatic shielding in conjunction with state-of-the-art materials shielding technologies.

In this thesis research, we study the active electrostatic shielding strategy and examine a hybrid configuration that utilizes both electrostatic and magnetostatic fields. The main advantages of this system are shown to be: (i) much lower magnetic fields that could be below the thresholds set for …

Subnanosecond Exposure Systems For Biological Studies, Jongbong Nah

Electrical & Computer Engineering Theses & Dissertations

The research of bioelectrics has expanded to subnanosecond pulse region and entered a new domain of biophysics of cell interaction with ultra-short and intense electric fields. As subnanosecond pulses may be delivered by antennas to the human body and is very attractive to the medical community, the study of subnanosecond pulse effects calls for exposure systems for both cells and tissues. Two systems were designed in the scope of this thesis, used for cells and tissues respectively. The exposure system designed for cell exposure is a cuvette consisting of two parallel aluminum gaps. This cuvette is placed in a coaxial …

Nonthermal Plasma Jet Efficacy On Candida Kefyr, Amber Marie Mattson Jackson

Electrical & Computer Engineering Theses & Dissertations

The inactivation abilities of a nonthermal plasma jet were investigated with the yeast C. kefyr, a pathogen with increasing importance in healthcare. The plasma is generated using a microhollow cathode discharge (MHCD) geometry operated with a DC voltage of 2 kV and a current of 30 mA using air as the operating gas at an airflow rate of 8 SLM. The plasma discharge approaches room temperature at a few mm away from the plasma jet allowing for the use on heat sensitive surfaces. Dry air and humid air were used as the operating gas to see if humidity plays …

Fecal Indicator Bacteria In Knitting Mill Creek With A Comparison Of Methods Used To Enumerate E. Coli, Manju Nagarajan

OES Theses and Dissertations

This research seeks to evaluate the impact of an urban, multi-use neighborhood on the bacteriological quality of water in Knitting Mill Creek, a blind arm of the Lafayette River, a sub-estuary of the lower Chesapeake Bay. A principal objective was to determine the effects of rainfall, a surrogate for run-off, on water-column concentrations of fecal-indicator bacteria (FIB). I collected water samples weekly (September 2009-December 2010) and biweekly (January 2010-December 2011) at a storm-sewer outfall and a nearby marina and quantified their E. coli and enterococci concentrations using Colilert-18 and Enterolert, most-probable-number assays. In addition, I took monthly samples for these …

Life History Of Stranded Bottlenose Dolphins (Tursiops Truncatus) In Virginia, Margaret Cook Lynott

Biological Sciences Theses & Dissertations

Little is known about the life history and overall ecology of bottlenose dolphins that strand in Virginia. In this study, I examined archived life history samples and stranding data from bottlenose dolphins found in Virginia waters to (1) develop growth curves based on ages from sectioned teeth, (2) document characteristics of male and female reproductive organs, and (3) define the relationship between age/length and presence of neonatal characteristics during the first year of life. The Gompertz growth model provided the best fit of growth data for stranded T. truncatus in Virginia. Length at birth and asymptotic length for males were …

Evolution On The Hawaiian Hotspot: Biogeography And Divergence Time Estimation Of Kadua (Rubiaceae), Kenneth L. Parker

Biological Sciences Theses & Dissertations

Recent studies on the colonization time of Hawaiian plant and animal lineages have suggested certain lineages arrived to the archipelago before the formation of the extant islands. Kadua, a recently resurrected genus, is mostly endemic to the Hawaiian Archipelago, with many member taxa autochthonous to individual islands. This work investigates the colonization time of Kadua to the Hawaiian Islands. Sequence analyses of the quickly evolving nuclear regions ITS, ETS and 5s-NTS regions for 20 Hawaiian and 7 French Polynesian species of Kadua were used to create dated phylogeny calibrated with island ages. The phylogeny suggests a single colonization of Hawaii …

College Of Health Sciences Newsletter, September 2012, College Of Health Sciences

Ellmer College of Health Sciences Newsletters

September 2012 issue of Old Dominion University's College of Health Sciences Newsletter.

The Ross Sea: In A Sea Of Change, Walker O. Smith, Peter N. Sedwick, Kevin R. Arrigo, David G. Ainley, Alejandro H. Orsi

OES Faculty Publications

The Ross Sea, the most productive region in the Antarctic, reaches farther south than any body of water in the world. While its food web is relatively intact, its oceanography, biogeochemistry, and sea ice coverage have been changing dramatically, and likely will continue to do so in the future. Sea ice cover and persistence have been increasing, in contrast to the Amundsen-Bellingshausen sector, which has resulted in reduced open water duration for its biota. Models predict that as the ozone hole recovers, ice cover will begin to diminish. Currents on the continental shelf will likely change in the coming century, …

Understanding The Success And Failure Of Oyster Populations: Periodicities Of Perkinsus Marinus, And Oyster Recruitment, Mortality, And Size, Thomas M. Soniat, John M. Klinck, Eric N. Powell, Eileen E. Hofmann

CCPO Publications

Ten-year time series (1992 to 2002) of salinity, Dermo disease, and size-class structure and mortality measured for an eastern oyster (Crassostrea virginica) population at a reef in Bay Tambour, Terrebonne Parish, LA, were analyzed using wavelet techniques to determine dominant frequencies and correlations. Along the Gulf Coast of the United States, Dermo disease (caused by Perkinsus marinus) responds to the El Nino-Southern Oscillation (ENSO) climate signal through its response to salinity. During the La Nina portion of ENSO, decreased rainfall leads to an increase in salinity, which triggers a rise in Dermo disease prevalence and intensity, producing increased oyster mortality. …