Physical Sciences and Mathematics Commons^™

Rnaml: A Standard Syntax For Exchanging Rna Information, Neocles B. Leontis, Allison Waugh, Patrick Gendron, Russ Altman, James W. Brown, David Case, Daniel Gautheret, Stephen C. Harvey, John Westbrook, Eric Westhof, Michael Zuker, François Major

Chemistry Faculty Publications

Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, …

Residential Radon Exposure And Lung Cancer: Variation In Risk Estimates Using Alternative Exposure Scenarios, R. William Field, Brian J. Smith, Daniel J. Steck, Charles F. Lynch

Physics Faculty Publications

The most direct way to derive risk estimates for residential radon progeny exposure is through epidemiologic studies that examine the association between residential radon exposure and lung cancer. However, the National Research Council concluded that the inconsistency among prior residential radon case-control studies was largely a consequence of errors in radon dosimetry. This paper examines the impact of applying various epidemiologic dosimetry models for radon exposure assessment using a common data set from the Iowa Radon Lung Cancer Study (IRLCS). The IRLCS uniquely combined enhanced dosimetric techniques, individual mobility assessment, and expert histologic review to examine the relationship between cumulative …

A Unique Examination Of The Buffer Overflow Condition, Terry Bruce Gillette

Theses and Dissertations

Buffer overflows have been the most common form of security vulnerability for the last ten years. More over, buffer overflow vulnerabilities enable the type of exploits that dominate remote network penetration. As our reliance on commercial third party software is critical in the current computing environment one must consider the question of how these vulnerabilities are discovered in released proprietary software. This thesis presents research focused on the fundamental issues surrounding the buffer overflow vulnerability. The objective is to analyze and understand the technical nature of this type of vulnerability and, on the basis of this, develop an efficient generic …

Oceanic Transport And Life History Of The Tropical Western Atlantic Opossum Pipefish, Microphis Brachyurus Lineatus, Sarah Frias-Torres

Theses and Dissertations

The opossum pipefish, Microphis brachyurus lineatus, is a tropical migratory syngnathid. Adults live and breed in freshwater tributaries in specific emergent vegetative habitats. Juveniles associate with pelagic Sargassum in the tropical western Atlantic. Reproduction occurs during the wet season (May-November). Juvenile recruitment occurs during the dry season (December-April). The objective of this dissertation is to study the east Florida breeding population in the freshwater tributaries of the Indian River Lagoon and focus on: 1) Larval drift to the Gulf Stream and, 2) recruitment of pelagic juveniles from the Gulf Stream onto the freshwater breeding habitat. Pouch released larvae face sharp …

Design And Implementation Of The L-Bone And Logistical Tools, Edward Scott Atchley

Masters Theses

The purpose of this paper is to outline the design criteria and implementation of the Logistical Backbone (L-Bone) and the Logistical Tools. These tools, along with IBP and the exNode Library, allow storage to be used as a network resource. These are components of the Network Storage Stack, a design by the Logistical Computing and Internetworking Lab at the University of Tennessee. Having storage as a network resource enables users to do many things that are either difficult or not possible today, such as moving and sharing very large files across administrative domains, improving performance through caching and improving fault-tolerance …

N-Person Cooperative Game Theory Solutions, Coalitions, And Applications, Ragan Nicole Brackin

Masters Theses

This study explores the topic of N-person cooperative game theory. The following paper begins with an introduction to the basic definitions and the- orems of game theory. These definitions and theorems are then used to in- troduce various solution methods and methods of coalition formation. These results are then applied to the airport game, to the supplier-firm-buyer game, and to evolutionary games.

Marine Protected Areas In The Gulf Of Maine: Policy For A Common Resource, Carolyn F. Skinder

Electronic Theses and Dissertations

In the wake of 25 years of unsuccessful single-fisheries management in the Gulf of Maine, there has been growing support for reform. Ecosystem management has been proposed as one alternative, but the information needed to manage whole ecosystems is greatly lacking. Implementing fully-protected marine protected areas (MPAs) is one way to preserve habitat while at the same time acquiring data for future ecosystem management. Under the current institutional arrangement in the Gulf, engineering agreement for MPAs is difficult due to the differing goals of varied user groups. The situation is reflective of a common property resource problem in that there …

Determining Atmospheric Deposition Inputs To Two Small Watersheds At Acadia National Park, Sarah J. Nelson

Electronic Theses and Dissertations

Two small upland watersheds have been gauged and monitored at Acadia National Park since 1998. Cadillac Brook watershed burned in a wildfire in 1947. Hadlock Brook watershed has been undisturbed for several centuries, and serves as the reference site. Precipitation and throughfall volume and chemistry data have been collected using wetonly and continuously open collectors. Hydrologic and chemical inputs to the sites have been determined for each site. Differences in watershed and vegetation characteristics control the input of water and major ions to these watersheds. Vegetation type was the dominant control on enhancement of precipitation across the heterogeneous watersheds. Relative …

Impact Of Preservative Treatments And Fungal Exposure On Phenolic Fiber Reinforced Polymer (Frp) Composite Material Utilized In Wood Reinforcement, Cihat Tascioglu

Electronic Theses and Dissertations

When wood products are exposed to environmental conditions conducive to biodeterioration, wood preservation becomes a necessity, especially when long-term utilization is desired. Although considerable literature exists on the treatment of laminated timbers and wood composites with wood preservatives, almost no information is available on the exposure of Fiber Reinforced Polymer (FRP) composites to wood preservative chemicals. In this work, FRP material was treated with common preservative chemicals and the effect of wood preservative treatments on mechanical properties of FRP material were investigated. Although the longitudinal elastic modulus was unaffected, some longitudinal strength losses were recorded for CCA and CDDC (water …

Guidelines For Management Of Farmland Adjacent To The Busselton Wetlands, William Oldfield, Department Of Conservation And Land Management, Department Of Planning And Infrastructure

Bulletins 4000 -

The Busselton Wetlands are a chain of wetlands that lie parallel with the coastline of Geographe Bay, Western Australia and in close proximity to the town of Busselton. The main issues for the maintenance of quality of the wetlands are nutrient levels and habitat value. This guide outlines many of the current best practices related to farming around wetlands.

Design And Simulation Of Self-Organizing Microbial Cellular Automata, Michael Patrick Campfield

Masters Theses

This paper discusses the design and implementation of cellular automata based on the alteration of genetic sequences in bacteria. The work is composed of five chapters covering the problem, the system’s design, the software simulation of the system and future issues on the problem. The section covering the problem explores the reasons for this work as well as issues that this work solves. The section covering system design details the modified genetic sequences and the algorithm that these sequences implement. The simulation section describes the layout of an experiment along with the test cases experimented on. Finally, the future work …

Using The Maple Computer Algebra System As A Tool For Studying Group Theory, Thomas Edmond Cooper, Iii

Masters Theses

The purpose of this study was to show that computers can be powerful tools for studying group theory. Specifically the author examined ways that the computer algebra system Maple can be used to assist in the study of group theory. The study consists of four main parts.

After a brief introduction in chapter one, chapter two discusses simple procedures written by the author to study small finite groups. These procedures rely on the fact that for small finite groups, the elements can all be stored on a computer and tested for various properties. All of the procedures are contained in …

The Chemistry Of Trifluoromethyl Indenes And Trifluoromethyl Indenyl Complexes, Maud J. Urbanski

Seton Hall University Dissertations and Theses (ETDs)

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A Study Of Obstacles To Use Of Methane Gas Produced In Landfills For Energy, Sharee Lynn Bowdidge

UNLV Theses, Dissertations, Professional Papers, and Capstones

The purpose of this study is to examine why landfill generated methane gas is not being treated as a resource, and used more widely as an energy source in the Southwestern United States. In this thesis, I have identified four possible barriers that may describe why this resource is not being used more often at landfill operations: 1) technological difficulties, 2) economic limitations, 3) regulatory constraints, and 4) insufficient desire to use. I have explored each of the possibilities in depth through case study interviews with individuals employed at six landfill operations, and individuals associated with landfill policy making. Although …

Seagrass And Caulerpa Monitoring In Hillsborough Bay Thirteenth Annual Report, City Of Tampa Department Of Sanitary Sewers

Reports

This is the thirteenth annual report to FDER to satisfy the requirements set forth in Reclaimed Water and Effluent Limitations and Monitoring Requirements condition #10 of the Howard F. Curren WWTP operation permit FL0020940-001-DW1P.

The City of Tampa, Bay Study Group (BSG), has monitored the effects of sewage pollution abatement in Hillsborough Bay since 1976. During the mid 1980's, water quality improvements and evidence of minor seagrass revegetation in Hillsborough Bay prompted the BSG to initiate a seagrass study to compliment other programs assessing the environmental status of Hillsborough Bay.

Direct And Sensitive Measurement Of Two-Photon Absorption Cross Sections, Peifang Tian, D. Keusters, Warren Warren

Peifang Tian

Summary form only given. We present a direct method to detect weak two-photon absorption (TPA) signals. As a proof of principle, we have measured the TPA cross section δ for rhodamine 6G (R6G) in methanol and obtained a value which agrees with other results. The technique may be very useful in biomedical imaging.

Statistical Models For Empirical Component Properties And Assembly-Level Property Predictions: Toward Standard Labeling, Gabriel A. Moreno, Scott A. Hissam, Kurt C. Wallnau

Gabriel A. Moreno

One risk inherent in the use of software components has been that the behavior of assemblies of components is discovered only after their integration. The objective of our work is to enable designers to use known (and certified) component properties as parameters to models that can be used to predict assembly-level properties. Our concern in this paper is with empirical component properties and compositional reasoning, rather than formal properties and reasoning. Empirical component properties must be measured; assessing the effectiveness of predictions based on these properties also involves measurement. This, in turn, introduces systematic and random measurement error. As a …

Photovoltaics — A Path To Sustainable Futures, Joshua M. Pearce

Joshua M. Pearce

Comparision Of Measured Convection Velocities With Calcuulations Based On Electric Potential Model, Daniel E. Britton

Honors Capstone Projects and Theses

No abstract provided.

Uncertainty Of Exploitation Estimates Made From Tag Returns, L.E. Miranda, R.E. Brock, B.S. Dorr

United States Department of Agriculture Wildlife Services: Staff Publications

Over 6,000 crappies Pomoxis spp. were tagged in five water bodies to estimate exploitation rates by anglers. Exploitation rates were computed as the percentage of tags returned after adjustment for three sources of uncertainty: post-release mortality due to the tagging process, tag loss, and the reporting rate of tagged fish. Confidence intervals around exploitation rates were estimated by re-sampling from the probability distributions of tagging mortality, tag loss, and reporting rate. Estimates of exploitation rates ranged from 17% to 54% among the five study systems. Uncertainty around estimates of tagging mortality, tag loss, and reporting resulted in 90% confidence intervals …

Search For The Scalar Top Quark In Pp̅ Collisions At √S = 1.8 Tev, V. M. Abazov, Gregory R. Snow, Do Collaboration

Gregory Snow Publications

We have performed a search for scalar top quark (stop) pair production in the inclusive electronmuon- missing transverse energy final state, using a sample of pp̅ events corresponding to 108.3 pb^-1 of data collected with the D0 detector at Fermilab. The search is done in the framework of the minimal supersymmetric standard model assuming that the sneutrino is the lightest supersymmetric particle. For the dominant decays of the lightest stop, t̅→ b χ₁⁺ and t̅→bℓν, no evidence for signal is found. We derive cross-section limits as a function of stop (t̅), …

The Drought Monitor, Mark D. Svoboda, Doug Lecomte, Mike Hayes, Richard Heim, Karin Gleason, Jim Angel, Brad Rippey, Rich Tinker, Mike Palecki, David Stooksbury, David Miskus, Scott Stephens

Drought Mitigation Center: Faculty Publications

There is a need for improved drought monitoring and assessment methods in the United States. Drought is the most costly natural disaster [Federal Emergency Management Agancy (FEMA 1995; Wilhite 2000)], but it is often neglected by developers of assessment and forecast products. Drought is more nebulous than other disasters and does not lend itself to traditional assessments or forecast methods. Its relatively slow onset and the complexity of its impacts are reasons for the new assessment methodology. Improvements in drought monitoring and forecasting techniques will allow for better preparation, lead to better management practices, and reduce the vulnerability of society …

Spatial Modeling Of Biomass In Nebraska Windbreaks, Qingjiang Hou, Linda J. Young, James R. Brandle, Michele M. Schoeneberger

Conference on Applied Statistics in Agriculture

Field windbreaks have the potential of sequestering large amounts of carbon. Predicting how much carbon would be sequestered in a newly planted windbreak after ten or more years is of interest. The amount of carbon in a tree depends on its biomass. In a pilot study of Nebraska windbreaks, a Markov random field was used to predict the biomass of green ash in windbreaks as a function of soil and climate conditions. The spatial dependence parameter was significantly different from zero, indicating the presence of small scale variation. In addition to age, the 30 year average summer precipitation and the …

Effect On Boll Weight Of Cotton Plants Planted At Various Densities, B. G. Mullinix, C. W. Bednarz

Conference on Applied Statistics in Agriculture

Previous research has shown that yield of cotton increases with plant density until density reaches 16 to 20 plants m^-2. In 1997 and 1998 cotton was planted at various densities ranging from 2.5 to 22.5 plants m^-2 in a RCB design. Ten row feet (3.048 m) of cotton were cut at ground level in each plot and placed into separate bags. Plant density for each plot was found by counting the number of plants in the bag representing that plot. For each plant, a boll found was placed in a small bag representing the fruiting branch and …

Simulation And Response Surface Methodology To Optimize Winter Wheat Response To Global Climate Change, P. Dhungana, K. M. Eskridge, A. Weiss, P. S. Baenziger

Conference on Applied Statistics in Agriculture

Future climate changes can have a major impact on crop production. But, whatever the climatic changes, crop production can be adapted to climate change by implementing alternative management practices and developing new genotypes that will take full advantage of the future climatic conditions. Since the classical agronomic research approach is not possible in identifying these new agronomic technologies for the future climatic conditions, we used response surface methodology (RSM) in connection with the CERES-Wheat crop model and the HADCM2 climate simulation model to identify optimal configuration of plant traits and management practices that maximize yield of winter wheat under high …

Using Nonlinear Fixed And Mixed Models To Study Acclimation To Heat Stress In Cattle, L. Lan, A. M. Parkhurst, D. A. Spiers, K. M. Eskridge, G. L. Hahn

Conference on Applied Statistics in Agriculture

Researchers studying acclimation of cattle to heat stress want to know if exposure to heat stress in controlled chambers will help cattle adjust to climatic conditions in the field. The four parameter nonlinear PET model is used to study the relationship between core body temperature and ambient temperature. This model works well when cattle are challenged by heat stress but the model is less useful for thermoneutral conditions. Both proc Nlin and Nlmixed are used to compare and contrast the field parameters between the controlled and the potentially acclimated group. Simulation studies were used to compare the effectiveness of proc …

Spline Models For Estimating Heat Stress Thresholds In Cattle, A. M. Parkhurst, D. A. Spiers, G. L. Hahn

Conference on Applied Statistics in Agriculture

Studies of the relationship between animal body temperature and air temperature suggest body temperature is essentially unresponsive until a threshold is reached, then it responds dramatically to increasing air temperature. The goal is to estimate the threshold between the thermoneutral plateau and the beginning of the heat stress challenge. One approach is to fit a polynomial to estimate the knot position and use spline functions to perform linear least squares piecewise polynomial fitting. Another alternative is to use nonlinear regression to estimate the knot or an inflection point of a nonlinear function. In both approaches the cyclic nature of body …

Using Landscape Characteristics As Prior Information For Bayesian Classification Of Remotely Sensed Imagery, William J. Price, Bahman Shafii

Conference on Applied Statistics in Agriculture

Yellow starthistle is a dominant weed of north-central Idaho canyon grasslands. The distribution of yellow starthistle can be affected by general landscape characteristics, such as land use, as well as specific terrain related features such as elevation, slope, and aspect. Slope and aspect can be considered as indicators of plant community composition and distribution. Hence, these variables may be incorporated into prediction models to estimate the likelihood of yellow starthistle occurrence. An empirically derived nonlinear model based on landscape characteristics was developed to predict the likelihood of yellow starthistle occurrence in north central Idaho (Shafii, et al. 1999). While the …

Estimating The Contribution Of Specific Wheat Varieties To State-Level Production, Bingxin Yu, Richard K. Perrin, David B. Marx

Conference on Applied Statistics in Agriculture

This paper addresses measurement issues involved in estimating the benefits from a university wheat breeding program. The conceptual foundation is to estimate the spatial distribution of farm-level yields for varieties in each year, based on Nebraska winter wheat variety test data from 1972 to 2001, with 9-20 locations per year. We can then estimate the state average yield difference that would occur between the portfolios of varieties that farmers actually grew, and the portfolio of varieties excluding those varieties from the university breeding program. This paper reports estimates of the statewide annual yields of individual varieties using a standard fixed …

Impact Of Data Transformation On The Performance Of Different Clustering Methods And Cluster Number Determination Statistics For Analyzing Gene Expression Profile Data, Guoping Shu, Beiyan Zeng, Deanne Wright, Oscar Smith

Conference on Applied Statistics in Agriculture

We have assessed the impact of 13 different data transformation methods on the performance of four types of clustering methods (partitioning (K-mean), hierarchical distance (Average Linkage), multivariate normal mixture, and non-parametric kernel density) and four cluster number determination statistics (CNDS) (Pseudo F, Pseudo t², Cubic Clustering Criterion (CCC), and Bayesian Information Criterion (BIC), using both simulated and real gene expression profile data. We found that Square Root, Cubic Root, and Spacing transformations have mostly positive impacts on the performance of the four types of clustering methods whereas Tukey's Bisquare and Interquantile Range have mostly negative impacts. The impacts …