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Ontology For Psychophysiological Dysregulation Of Anger/Aggression, Swathi Vasanthapuram

School of Computing: Dissertations, Theses, and Student Research

The advancement of Information Technology in the last four decades led to the use of computers in medicine. A new area called Medical Informatics has emerged. This area comprises the application of IT to healthcare with the aim of creating tools that help healthcare personnel diagnose and treat patients more accurately and efficiently. IT not only provides tools for storing, integrating, and updating patient information base but also for processing information efficiently. One of such tools is a Clinical Decision Support System. Ontologies are an integral part of clinical decision support systems because they help formalize and integrate domain knowledge. …

Direct, Physically-Motivated Derivation Of The Contagion Condition For Spreading Processes On Generalized Random Networks, Peter Sheridan Dodds, Kameron Decker Harris, Joshua L. Payne

Dartmouth Scholarship

For a broad range of single-seed contagion processes acting on generalized random networks, we derive a unifying analytic expression for the possibility of global spreading events in a straightforward, physically intuitive fashion. Our reasoning lays bare a direct mechanical understanding of an archetypal spreading phenomena that is not evident in circuitous extant mathematical approaches.

An Analysis Of The Mortality Risks Associated With Heat And Heat Waves In Ireland, To Assist In Planning For Climate Change, Mathilde Pascal

Doctoral

Although extreme temperatures have not been identified as a major cause of mortality in Ireland, climate change calls for an evaluation of the past, present and future health risks associated with heat and heat waves. The health impacts of heat were investigated using mortality and temperature data for the period 1981-2003. Data were aggregated in urban areas (Dublin, Cork, Drogheda, Arklow, Dundalk, Galway, Limerick, Waterford and Wexford) and rural areas. Seven heat waves were identified between 1981 and 2003, corresponding to 254 excess deaths (197 in rural areas, and 57 in urban areas). A major episode was observed in rural …

2011 - The Sixteenth Annual Symposium Of Student Scholars

Symposium of Student Scholars Program Books

The full program book from the Sixteenth Annual Symposium of Student Scholars, held on April 26, 2011. Includes abstracts from the presentations and posters.

Epistatic Roles For Pseudomonas Aeruginosa Muts And Dinb (Dna Pol Iv) In Coping With Reactive Oxygen Species-Induced Dna Damage, Laurie H. Sanders, Babho Devadoss, Geraldine V. Raja, Jaime O'Connor, Shengchang Su, Daniel J. Wozniak, Daniel J. Hassett, Anthony J. Berdis, Mark D. Sutton

Chemistry Faculty Publications

Pseudomonas aeruginosa is especially adept at colonizing the airways of individuals afflicted with the autosomal recessive disease cystic fibrosis (CF). CF patients suffer from chronic airway inflammation, which contributes to lung deterioration. Once established in the airways, P. aeruginosa continuously adapts to the changing environment, in part through acquisition of beneficial mutations via a process termed pathoadaptation. MutS and DinB are proposed to play opposing roles in P. aeruginosa pathoadaptation: MutS acts in replication-coupled mismatch repair, which acts to limit spontaneous mutations; in contrast, DinB (DNA polymerase IV) catalyzes error-prone bypass of DNA lesions, contributing to mutations. As part of …

Optimization Of Multiplex Pcr For Multiple Locus Variable Number Tandem Repeat Analysis For Salmonella Typhimurium, George Hafez, Remington Turner, Andrea Haskett, Rajesh Nagarajan

College of Arts and Sciences Poster Presentations

Salmonella typhimurium infects an estimated 1.4 million in the United States and kills over five hundred annually.  The current way of categorization, Pulse Field Gel Electrophoresis (PFGE) and antibiotic sensitivity testing, lack the ability to distinguish between some closely related strains.  We are attempting to optimize a new technique of categorization, Multiple Locus Variable number tandem repeat Analysis (MLVA).  We made changes to temperature and concentration variables within the multiplex PCR procedure to streamline the identification process.  By optimizing the multiplex PCR procedure we intend to create more consistent amplification of the loci used in MLVA analysis, which will improve …

Circulation, Vol. 16, No. 3, Center For Coastal Physical Oceanography, Old Dominion University, Larry P. Atkinson

CCPO Circulation

Spring 2011 issue of CCPO Circulation featuring article "Offshore Wind Power and Oceanography" by Larry Atkinson

Collaborative Strategic Board Games As A Site For Distributed Computational Thinking, Matthew Berland, Victor R. Lee

Instructional Technology and Learning Sciences Faculty Publications

This paper examines the idea that contemporary strategic board games represent an informal, interactional context in which complex computational thinking takes place. When games are collaborative – that is, a game requires that players work in joint pursuit of a shared goal – the computational thinking is easily observed as distributed across several participants. This raises the possibility that a focus on such board games are profitable for those who wish to understand computational thinking and learning in situ. This paper introduces a coding scheme, applies it to the recorded discourse of three groups of game players, and provides qualitative …

Preliminary Analysis Of An Agent-Based Model For A Tick-Borne Disease, Holly Gaff

Biological Sciences Faculty Publications

Ticks have a unique life history including a distinct set of life stages and a single blood meal per life stage. This makes tick-host interactions more complex from a mathematical perspective. In addition, any model of these interactions must involve a significant degree of stochasticity on the individual tick level. In an attempt to quantify these relationships, I have developed an individual-based model of the interactions between ticks and their hosts as well as the transmission of tick-borne disease between the two populations. The results from this model are compared with those from previously published differential equation based population models. …

Biogas Technology On Uzi Island, Zanzibar: A Feasibility Study, Peter J. Mcinerney

Independent Study Project (ISP) Collection

With realization of the finite quantity of fossil fuels and improved study on the effects of global climate change there has been an increasing demand for energy production from renewable, sustainable sources in developed and developing nations alike. The population of Tanzania relies overwhelmingly on biomass as a source of primary energy, with such impacts as deforestation and negative health effects. Biogas generation is a renewable energy technology that utilizes organic waste sources to produce a methane-rich gas suitable for cooking and lighting with the potential to replace current unsustainable energy sources and provide several environmental and socioeconomic benefits. A …

Age-Gaps In Sexual Partnerships: Seeing Beyond ‘Sugar Daddies’, Miles Q. Ott, Till Bärnighausen, Frank Tanser, Mark N. Lurie, Marie-Louise Newell

Statistical and Data Sciences: Faculty Publications

We examine for the first time age-mixing in sexual relationships in a population with very high HIV incidence and prevalence in rural South Africa. The highest levels of age assortativity (the pairing of like with like) were casual partnerships reported by men, the lowest levels were spousal relationships reported by women. Given the age–sex distribution of HIV prevalence in this population, interventions to decrease age-gaps in spousal relationships may be effective in reducing HIV incidence.

Combating Biological Terrorism From Imported Food, Jeffrey S. Nelson

Theses and Dissertations

There is a threat that a terrorist or terrorist organization will use access to the US food supply to kill or sicken Americans by contaminating imported food products from Mexico. The food that Americans eat is coming more and more often from foreign countries such as Mexico. Foodborne diseases infect nearly fifty million people in the US each year, resulting in over three thousand deaths. There are many terrorist organizations that would like to deliberately contaminate American food. Drug cartels and terrorist organizations currently operate in Mexico, one of the leading food importers into the US. The purpose of this …

Isolation By Distance Explains Genetic Structure Of Buggy Creek Virus, A Bird-Associated Arbovirus, Abinash Padhi, Amy T. Moore, Mary Bomberger Brown, Jerome E. Foster, Martin Pfeffer, Charles R. Brown

School of Natural Resources: Faculty Publications

Many of the arthropod-borne viruses (arboviruses) show extensive genetic variability and are widely distributed over large geographic areas. Understanding how virus genetic structure varies in space may yield insight into how these pathogens are adapted to and dispersed by different hosts or vectors, the relative importance of mutation, drift, or selection in generating genetic variability, and where and when epidemics or epizootics are most likely to occur. However, because most arboviruses tend to be sampled opportunistically and often cannot be isolated in large numbers at a given locale, surprisingly little is known about their spatial genetic structure on the local …

Maximal Sensitive Dependence And The Optimal Path To Epidemic Extinction, Eric Forgoston, Simone Bianco, Leah B. Shaw, Ira B. Schwartz

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

Extinction of an epidemic or a species is a rare event that occurs due to a large, rare stochastic fluctuation. Although the extinction process is dynamically unstable, it follows an optimal path that maximizes the probability of extinction. We show that the optimal path is also directly related to the finite-time Lyapunov exponents of the underlying dynamical system in that the optimal path displays maximum sensitivity to initial conditions. We consider several stochastic epidemic models, and examine the extinction process in a dynamical systems framework. Using the dynamics of the finite-time Lyapunov exponents as a constructive tool, we demonstrate that …

Factors Affecting Space Use Overlap By White-Tailed Deer In An Urban Landscape, W. David Walter, Jeff Beringer, Lonnie P. Hansen, Justin W. Fischer, Joshua J. Millspaugh, Kurt C. Vercauteren

United States Department of Agriculture Wildlife Services: Staff Publications

Variation in the size and overlap of space use by white-tailed deer (Odocoileus virginianus) has broad implications for managing deer–human conflicts and disease spread and transmission in urban landscapes. Understanding which factors affect overlap of home range by various segments (i.e., age, sex) of an urban deer population has implications to direct contact between deer on disease epidemiology. We assessed size of home range and overlap of space use using the volume of intersection index (VI) for deer in an urban landscape by sex, age, season, and time of day. We found mean space use was larger for …

Studies Of A Cyanine-Based Biosensor And Light-Induced Antibacterial Activities Of Oligo(Phenylene Ethynylene)S, Zhijun Zhou

Chemistry and Chemical Biology ETDs

This dissertation has been focusing on two subjects: biosensor development and light-activated antimicrobials. A cyanine-based fluorescent biosensor is developed with high sensitivity to detect the presence and activity of caspase-3/7. We demonstrated that supramolecular self-assembly can be useful for designing biosensors. A series of p-Phenylene Ethynylenes (OPEs) have been synthesized. Further photophysical studies show that these molecules have good singlet oxygen yields. The antimicrobial capability increases dramatically when exposed to UV-365 radiation, though dark biocidal activity can be obtained as well. This phenomenon is probably due to the high yields of singlet oxygen of these OPEs, which oxidizes unsaturated membrane …

110 Years Of Avipoxvirus In The Galapagos Islands, Patricia Parker, Elizabeth Buckles, Heather Farrington, Kenneth Petren, Noah Whiteman, Robert Ricklefs, Jennifer Bollmer, Gustavo Jiménez-Uzcátegui

Biology Department Faculty Works

The role of disease in regulating populations is controversial, partly owing to the absence of good disease records in historic wildlife populations. We examined birds collected in the Galapagos Islands between 1891 and 1906 that are currently held at the California Academy of Sciences and the Zoologisches Staatssammlung Muenchen, including 3973 specimens representing species from two well-studied families of endemic passerine birds: finches and mockingbirds. Beginning with samples collected in 1899, we observed cutaneous lesions consistent with Avipoxvirus on 226 (6.3%) specimens. Histopathology and viral genotyping of 59 candidate tissue samples from six islands showed that 21 (35.6%) were positive …

The Application Of Gis And Spatiotemporal Analyses To Investigations Of Unusual Marine Mammal Strandings And Mortality Events, Stephanie A. Norman, Jessie Huggins, Tim E. Carpenter, James T. Case, Dyanna M. Lambourn, Jim Rice, John Calambokidis, Joseph K. Gaydos, M. Bradley Hanson, Deborah A. Duffield, Sandra Dubpernell, Susan Berta, Matt Klope

United States Department of Commerce: Staff Publications

In 2006–2007, an unusually high number of harbor porpoises (Phocoena phocoena) stranded along the Washington and Oregon coastlines. Spatiotemporal analyses were used to examine their ability to detect clusters of porpoise strandings during an unusualmortality event (UME) in the Pacific Northwest using stranding location data. Strandings were evaluated as two separate populations, outer coast and inland waters. The presence of global clustering was evaluated using the Knox spatiotemporal test, and the presence of local clusters was investigated using a spatiotemporal scan statistic (space–time permutation). There was evidence of global clustering, but no local clustering, supporting the hypothesis that …

Sci-Tech Book News Reviews, Susan Fingerman

Sci-Tech News

The following section consists of 100 book reviews selected from Sci-Tech Book News, reprinted with the permission of Book News Inc. This review journal is published four times a year, each issue reviewing over 2,000 new titles in the physical and biological sciences, mathematics, engineering, computer science, technology, and agriculture. For a sample issue and subscription information, contact Book News Inc. at 5739 NE Sumner Street, Portland, OR 97218. Phone: (503)281-9230; Fax: (503)287-4485; E-mail: [email protected].

Raman Spectroscopy For The Microbiological Characterization And Identification Of Medically Relevant Bacteria, Khozima Mahmoud Hamasha

Wayne State University Dissertations

The detection and identification of pathogenic bacteria has become more important than ever due to the increase of potential bioterrorism threats and the high mortality rate of bacterial infections worldwide. Raman spectroscopy has recently gained popularity as an attractive robust approach for the molecular characterization, rapid identification, and accurate classification of a wide range of bacteria.

In this dissertation, Raman spectroscopy utilizing advanced statistical techniques was used to identify and discriminate between different pathogenic and non-pathogenic bacterial strains of E. coli and Staphylococcus aureus bacterial species by probing the molecular compositions of the cells.

The five-carbon sugar xylitol, which cannot …

Evidence Of Susceptibility To Morbillivirus Infection In Cetaceans From The United States, T. K. Rowles, L. S. Schwacke, R. S. Wells, J. T. Saliki, L. Hansen, A. Hohn, F. Townsend, R. A. Sayre, A. J. Hall

United States Department of Commerce: Staff Publications

Cetacean morbilliviruses (CeMV) are viruses that can cause mass mortalities among various odontocete species. In this study levels of “herd” immunity in cetaceans from the U.S. coast are described from the distribution and prevalence of antibodies against morbilliviruses. Neutralizing antibody titers against dolphin morbillivirus (DMV), porpoise morbillivirus (PMV), phocine distemper (PDV), and canine distemper viruses (CDV) were measured. Positive samples had higher titers against the CeMV than against the other morbilliviruses tested, indicating that although PDV or CDV can be used to investigate exposure their use may result in a higher false negative rate. The results suggest that morbillivirus did …

Proceedings Of The 123rd Annual Meeting Of The Iowa Academy Of Science [Program, 2011], Iowa Academy Of Science

Iowa Academy of Science Documents

Contents:

Program Summary --- 2-3
Acknowledgements --- 4
Contents --- 5
Welcome --- 5
Iowa Junior Academy of Science Competition --- 6
Geology Special Event Using Geographic Information Systems in Iowa's K-16 Classrooms --- 7
General Session I-Roaming Mars, a Personal Perspective --- 8
Iowa Junior Academy of Science Award Luncheon --- 9
Iowa Academy of Science Business Meeting --- 9
Iowa Academy of Science Volunteers for 2010-2011 --- 10
Symposium A-Unintended Health & Environmental Consequences of Confinement Agriculture --- 11
Symposium B-Investigating Forensic Science --- 12
Symposium C-150th Anniversary-Science and the Civil War --- 13
Symposia Speakers --- 14-15 …

Searching The Protein Structure Database For Ligand-Binding Site Similarities Using Cpass V.2, Robert Powers, Jennifer C. Copeland, Jaime L. Stark, Adam Caprez, Ashu Guru, David R. Swanson

Robert Powers Publications

Background: A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as “hypothetical” or “uncharacterized” protein. Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number …

The Water Project: A Short-Term Study Abroad Program Design For Alfred University, Caitlin Paul

Capstone Collection

The Water Project is a short term, faculty-led program, which will address the global water crisis by using the strengths of Alfred University (AU). The Water Project will include students from five different disciplines -Engineering, Art, Business, Language, and Anthropology- and have them work in collaboration with each other and the faculty of AU to create low-cost, ceramic water filters for a community in need of a clean water source in a rural area of Burkina Faso. The Water Project is not intended to be an imposing force on the community, but a welcomed collaborator that works to create a …

Calculus, Biology And Medicine: A Case Study In Quantitative Literacy For Science Students, Kim Rheinlander, Dorothy Wallace

Numeracy

This paper describes a course designed to enhance the numeracy of biology and pre-medical students. The course introduces students with the background of one semester of calculus to systems of nonlinear ordinary differential equations as they appear in the mathematical biology literature. Evaluation of the course showed increased enjoyment and confidence in doing mathematics, and an increased appreciation of the utility of mathematics to science. Students who complete this course are better able to read the research literature in mathematical biology and carry out research problems of their own.

A Survey Of The Chemical Content And Medicinal Activity Of Shrub-Steppe Plants Of The Pacific Northwest, Aaron M. John

Undergraduate Honors Theses

A need for new modes of antibiotic therapy has resulted from the increasing incidence of bacterial resistance to drugs. One approach to this problem involves the search for plant compounds that may help to overcome multi-drug resistance. Many plant genera have been utilized in Native American traditional medicine for their beneficial properties. Such plants include the shrub-steppe genera, Eriogonun and Collomia, which have been used as cold remedies, pain relievers, and for antibiotic-related uses. Limited chemical studies of these genera have revealed medicinally useful compounds such as flavonoids and terpenoids, and further research may result in the identification of …

Rock Pigeon Use Of Livestock Facilities In Northern Colorado: Implications For Improving Farm Bio-Security., James C. Carlson, Larry Clark, Michael F. Antolin, M. D. Salman

United States Department of Agriculture Wildlife Services: Staff Publications

Rock pigeons (Columba livia) have been implicated in the spread of pathogens within commercial livestock facilities. Currently, there is no data characterizing pigeon habitat use and movement patterns within and among commercial livestock facilities. To better understand the capacity for pigeons to spread pathogens, we used radio-telemetry techniques to estimate the home-range, travel distance, activity, and habitat use of pigeons roosting on and off dairies and feedlots in western Weld County, Colorado. Our observations suggest that pigeons roosting on (resident) and off (nonresident) livestock facilities use habitat differently. Nonresident pigeons used larger home-range areas than did resident pigeons. Nonresident pigeons …

Pituophis Catenifer Deserticola (Great Basin Gophersnake) Predation, Steven J. Wamback, Richard M. Engeman

United States Department of Agriculture Wildlife Services: Staff Publications

A variety of taxa have been observed to· prey upon Pituophis catenifer, including mammals, birds-of prey, and other snakes. Here, we describe an unusual two-day observation of predation on a mature Great Basin gophersnake by a brown trout (Salmo trutta).

The observation took place in Jones Canyon, Utah, USA, on the grounds of the Jones Hole National Fish Hatchery (JHNFH). Jones Creek' emanates from springs at the head of Jones Canyon on hatchery grounds, and flows north to south 6.4 km to the Green River, approximately paralleling the Utah-Colorado border. The stream runs for about 0.3 km …

Epidemic Spread Of Influenza Viruses: The Impact Of Transient Populations On Disease Dynamics, Karen R. Ríos-Soto, Baojun Song, Carlos Castillo-Chavez

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

The recent H1N1 ("swine u") pandemic and recent H5N1 ("avian u") outbreaks have brought increased attention to the study of the role of animal populations as reservoirs for pathogens that could invade human populations. It is believed that pigs acquired u strains from birds and humans, acting as a mixing vessel in generating new influenza viruses. Assessing the role of animal reservoirs, particularly reservoirs involving highly mobile populations (like migratory birds), on disease dispersal and persistence is of interests to a wide range of researchers including public health experts and evolutionary biologists. This paper studies the interactions between transient and …

Characterizing The Oligomeric Structure And Catalytic Activity Of The Dihydroorotase And Aspartate Transcarbamoylase From The Bacterium, Bacillus Anthracis, Reshma Kankanala

Master's Theses and Doctoral Dissertations

Bacteremia refers to bacterial presence in the blood. Bacterial proliferation in the blood requires that the organism adapt its metabolism to available nutrients. Nucleotide precursors that could be used are present at low levels in the blood, and thus the invading bacteria must rely on de novo nucleotide biosynthesis for survival. The dihydroorotase domain is a key enzyme in pyrimidine biosynthesis and a promising drug target. The genes encoding the dihydroorotase (DHOase) and aspartate transcarbamoylase (ATCase) of Bacillus anthracis (B. anthracis) were cloned for expression in Escherichia coli (E. coli). The proteins were purified by affinity …