Digital Commons Network^™

Discovery Of Novel Viruses From Animals, Plants, And Insect Vectors Using Viral Metagenomics, Terry Fei Fan Ng

USF Tampa Graduate Theses and Dissertations

Understanding emerging viruses is critical for disease monitoring and prediction; however, surveys of novel viruses are hindered by the lack of a universal assay for viruses. Viral metagenomics, consisting of viral particle purification and shotgun sequencing, is a powerful technique for discovering viruses in a wide variety of sample types. However, current protocols are not effective on tissue samples (e.g., lungs, livers and tumors), where they are hindered by the high amount of host nucleic acids which limits the percentage of sequences that originate from viruses. In this dissertation, a modified viral metagenomics protocol was developed and utilized to effectively …

Urban And Rural-Residential Land Uses: Their Role In Watershed Health And The Rehabilitation Of Oregon’S Wild Salmonids, Michael Harte, Victor W. Kaczynski, Clinton C. Shock, J. Alan Yeakley, Robert M. Hughes, Nancy Molina, Carl B. Schreck

Environmental Science and Management Faculty Publications and Presentations

This technical report by the Independent Multidisciplinary Science Team (IMST) is a comprehensive review of how human activities in urban and rural-residential areas can alter aquatic ecosystems and resulting implications for salmonid recovery, with a geographic focus on the state of Oregon. The following topics are considered in the form of science questions, and comprise the major components of this report:

1. The effects of urban and rural-residential development on Oregon’s watersheds and native wild salmonids.
2. Actions that can be used to avoid or mitigate undesirable changes to aquatic ecosystems near developing urban and rural-residential areas.
3. The benefits and pitfalls of …

The Major Cause Of Observed Erosion Surge On The Beaches North Of Dar Es Salaam City, N. Nyandwi

Tanzania Journal of Science

Surges in coastal erosion north of Dar es Salaam city have been documented from 1977 to the early 1980s and around 1997/98. Analysis of the wind data shows that the documented increase in coastal erosion coincided with increased wind speeds. Extreme winds in excess of 10-11 m s-1 were experienced during 1976-78, 1984 and after 1996. Their coincidence with extreme high tides produced the high erosion rates. Using beach profile data for the years 1998-2000 the evolution of the beach profile with the changing monsoon winds and sediment input by rivers could be demonstrated. The beach erosion took place during …

ϒ(1s)→Γf'2(1525); F'2(1525)->K0sk0s Decays, Raymond Mountain, Marina Artuso, T. Skwarnicki, S. Stone

Physics - All Scholarship

We report on a study of exclusive radiative decays of the Upsilon(1S) resonance into a final state consisting of a photon and two K0s candidates. We find evidence for a signal for Upsilon(1S)->gamma f_2'(1525); f_2'(1525)->K0sK0s, at a rate (4.0+/-1.3+/-0.6)x10^{-5}, consistent with previous observations of Upsilon(1S)->gamma f_2'(1525); f_2'(1525)->K+K-, and isospin. Combining this branching fraction with existing branching fraction measurements of Upsilon(1S)->gamma f_2'(1525) and J/psi->gamma f_2'(1525), we obtain the ratio of branching fractions: B(Upsilon(1S)->gamma f_2'(1525))/B(J/psi->gamma f_2'(1525))=0.09+/-0.02, approximately consistent with expectations based on soft collinear effective theory.

Oracle And Multiple Robustness Properties Of Survey Calibration Estimator In Missing Response Problem, Kwun Chuen Gary Chan

UW Biostatistics Working Paper Series

In the presence of missing response, reweighting the complete case subsample by the inverse of nonmissing probability is both intuitive and easy to implement. However, inverse probability weighting is not efficient in general and is not robust against misspecification of the missing probability model. Calibration was developed by survey statisticians for improving efficiency of inverse probability weighting estimators when population totals of auxiliary variables are known and when inclusion probability is known by design. In missing data problem we can calibrate auxiliary variables in the complete case subsample to the full sample. However, the inclusion probability is unknown in general …

Modification And Improvement Of Empirical Likelihood For Missing Response Problem, Kwun Chuen Gary Chan

UW Biostatistics Working Paper Series

An empirical likelihood (EL) estimator was proposed by Qin and Zhang (2007) for a missing response problem under a missing at random assumption. They showed by simulation studies that the finite sample performance of EL estimator is better than some existing estimators. However, the empirical likelihood estimator does not have a uniformly smaller asymptotic variance than other estimators in general. We consider several modifications to the empirical likelihood estimator and show that the proposed estimator dominates the empirical likelihood estimator and several other existing estimators in terms of asymptotic efficiencies. The proposed estimator also attains the minimum asymptotic variance among …

Modification And Improvement Of Empirical Liklihood For Missing Response Problem, Gary Chan

UW Biostatistics Working Paper Series

An empirical likelihood (EL) estimator was proposed by Qin and Zhang (2007) for a missing response problem under a missing at random assumption. They showed by simulation studies that the finite sample performance of EL estimator is better than some existing estimators. However, the empirical likelihood estimator does not have a uniformly smaller asymptotic variance than other estimators in general. We consider several modifications to the empirical likelihood estimator and show that the proposed estimator dominates the empirical likelihood estimator and several other existing estimators in terms of asymptotic efficiencies. The proposed estimator also attains the minimum asymptotic variance among …

Spatial Distribution Of Calcium-Gated Chloride Channels In Olfactory Cilia, Donald A. French, Dorjsuren Badamdorj, Steven J. Kleene

Mathematical Sciences Faculty Research

Background

In vertebrate olfactory receptor neurons, sensory cilia transduce odor stimuli into changes in neuronal membrane potential. The voltage changes are primarily caused by the sequential openings of two types of channel: a cyclic-nucleotide-gated (CNG) cationic channel and a calcium-gated chloride channel. In frog, the cilia are 25 to 200 µm in length, so the spatial distributions of the channels may be an important determinant of odor sensitivity.

Principal Findings

To determine the spatial distribution of the chloride channels, we recorded from single cilia as calcium was allowed to diffuse down the length of the cilium and activate the channels. …

Measurements Of The Electric Form Factor Of The Neutron Up To Q(2)=3.4 Gev2 Using The Reaction (3)(He)Over-Right-Arrowe((E)Over-Right-Arrow, E ' N)Pp, S. Riordan, Timothy Holmstrom

Chemistry & Physics Faculty Publications

The electric form factor of the neutron was determined from studies of the reaction ³He⃗(e⃗,e^′n)pp in quasielastic kinematics in Hall A at Jefferson Lab. Longitudinally polarized electrons were scattered off a polarized target in which the nuclear polarization was oriented perpendicular to the momentum transfer. The scattered electrons were detected in a magnetic spectrometer in coincidence with neutrons that were registered in a large-solid-angle detector. More than doubling the Q² range over which it is known, we find G_Eⁿ=0.0236±0.0017(stat)±0.0026(syst), 0.0208±0.0024±0.0019, and 0.0147±0.0020±0.0014 for Q²=1.72, 2.48, and 3.41  GeV², respectively.

A Tactical Information Management Middleware For Resource-Constrained Mobile P2p Networks, Bo Xu, Mark Linderman, Sanjay Madria, Ouri Wolfson

Computer Science Faculty Research & Creative Works

In this paper we provide an architecture for Tactical Information Middleware for bandwidth constrained information management. We propose the ideas of rank-Based data dissemination, and the use of a tactical information management query language. These ideas will deal with dynamic changes in bandwidth and explore opportunistic data dissemination. Thus, will lead to a cross-layer design of a system capable of handling the dynamic data management issues relevant in many missions' critical applications. © 2010 IEEE.

A Study To Minimize Or Eliminate Hardbottom And Reef Impacts From Anchoring Activities In Designated Anchorages At The Ports Of Miami And Palm Beach, Brian K. Walker

Marine & Environmental Sciences Faculty Reports

No abstract provided.

Global Patterns And Predictions Of Seafloor Biomass Using Random Forests, Chih-Lin Wei, Gilbert T. Rowe, Elva Escobar-Briones, Antje Boetius, Thomas Soltwedel, M. Julian Caley, Yousria Soliman, Falk Huettmann, Fangyuan Qu, Zishan Yu, C. Roland Pitcher, Richard L. Haedrich, Mary K. Wicksten, Michael A. Rex, Jeffrey G. Baguley, Jyotsna Sharma, Roberto Danovaro, Ian R. Macdonald, Clifton C. Nunnally, Jody W. Deming, Paul Montagna, Mélanie Lévesque, Jan Marcin Weslawski, Maria Wlodarska-Kowalczuk, Baban S. Ingole, Brian J. Bett, David S. M. Billett, Andrew Yool, Bodil A. Bluhm, Katrin Iken, Bhavani E. Narayanaswamy

Biology Faculty Publication Series

A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive …

Upsilon(1s)->Gamma+F2'(1525); F2'(1525)->K0sk0s Decays, Raymond Mountain, Marina Artuso, S. Blusk, T. Skwarnicki

Physics - All Scholarship

We report on a study of exclusive radiative decays of the Upsilon(1S) resonance into a final state consisting of a photon and two K0s candidates. We find evidence for a signal for Upsilon(1S)->gamma f_2'(1525); f_2'(1525)->K0sK0s, at a rate (4.0+/-1.3+/-0.6)x10^{-5}, consistent with previous observations of Upsilon(1S)->gamma f_2'(1525); f_2'(1525)->K+K-, and isospin. Combining this branching fraction with existing branching fraction measurements of Upsilon(1S)->gamma f_2'(1525) and J/psi->gamma f_2'(1525), we obtain the ratio of branching fractions: B(Upsilon(1S)->gamma f_2'(1525))/B(J/psi->gamma f_2'(1525))=0.09+/-0.02, approximately consistent with expectations based on soft collinear effective theory.

The Development Of A Training Curriculum For The Development Of Physical And Athletic Abilities, And The Development Of The Performance Of The Footballs Of The College Of Mathematical Education, Mowaffaq Abis Khudair

Modern Sport

The thesis consists of five parts. The first part presents the thesis topic, its significance, the research problem, objectives, hypotheses, and the three dimensions of the study: location, time, and human factors. The second part focuses on the methodology, including definitions and classifications of muscular strength, how to train and develop it, and how to improve the speed of executing penalties. The third part explains the research program and procedures carried out in the field, identifying and analyzing the study sample from the College of Physical Education, second stage, Health Department, where the researcher works as a faculty member at …

Next-To-Next-To-Leading Soft-Gluon Corrections For The Top Quark Cross Section And Transverse Momentum Distribution, Nikolaos Kidonakis

Faculty Articles

I present results for top quark production in hadronic collisions at LHC and Tevatron energies. The soft-gluon corrections to the differential cross section are resummed at next-to-next-to-leading-logarithm accuracy via the two-loop soft anomalous dimension matrices. Approximate next-to-next-to-leading-order differential and total cross sections are calculated. Detailed theoretical predictions are shown for the t (t) over bar cross section and the top quark p(T) distribution at the Tevatron and the LHC.

Adaptive Routing Scheme For Emerging Wireless Ad Hoc Networks, Behdis Eslamnour, Sarangapani Jagannathan

Electrical and Computer Engineering Faculty Research & Creative Works

Node mobility causes fading wireless channels, which in turn renders topology changes in emerging wireless ad hoc networks. in this paper, on-line estimators and Markov models are utilized to estimate fading channel conditions. using the estimated channel conditions as well as queue occupancy, available energy and link delay, approximate dynamic programming (ADP) techniques are utilized to find dynamic routes, while solving discrete-time Hamilton-Jacobi-Bellman (HJB) equation forward-in-time for route cost in multichannel multi-interface networks. the performance of the proposed load balancing method in the presence of fading channels and the performance of the optimal route selection approach for multichannel multi-interface wireless …

A Resource-Efficient Adaptive Caching Scheme For Mobile Ad-Hoc Networks, Dan Hirsch, Sanjay Madria

Computer Science Faculty Research & Creative Works

In a Mobile Ad-Hoc Network environment, wireless devices have finite resources such as memory, energy and they work within the wireless constraints such as limited bandwidth and unreliable communication. Therefore, storage space, bandwidth, and battery life must be managed effectively in order to extend the usefulness and lifespan of wireless devices and the network. Caching is one of those techniques which reduce the latency and tuning time for mobile devices in the wireless network. We propose a novel scheme that seeks to distribute the storage, bandwidth and energy burden through a resource-efficient adaptive caching scheme for mobile ad-hoc networks. Our …

Preservd - Privacy Ensured Service Discovery In Mobile Peer-To-Peer Networks, Santhosh Muthyapu, Sanjay Kumar Madria, Mark Linderman

Computer Science Faculty Research & Creative Works

In mobile peer-to-peer networks, proposed service discovery protocols disregard the exposure of the participating peers' privacy details (privileged information). in these methods, the participating peers must provide their identities during the service discovery process to be authorized to utilize services. However, a peer may not be willing to reveal its privileged information until it identifies the service providing peer. So, these peers face a problem; should the service requesting or the service providing peer reveal the identity first. the protocol presented in [12] solves this problem to some extent and discover the services available in the service requester's vicinity in …

Comparative Study Of Field Enhancement Between Isolated And Coupled Metal Nanoparticles: An Analytical Approach, Greg Sun, Jacob B. Khurgin

Physics Faculty Publications

We present an analytical model that takes into account the coupling between the surface plasmon modes in complex metal nanostructures. We apply this model to evaluate the field enhancement in the gap of two coupled Au metal spheres embedded in GaN dielectric and compare the result with that obtained by the single sphere. The results show additional improvement can be obtained in the gap depending on the width of the gap. This approach offers a clear physical insight for the enhancement and a straightforward method for optimization.

Vygotsky And The Virtual Classroom: Sociocultural Theory Comes To The Communications Classroom, Michael Freeman

Christian Perspectives in Education

No abstract provided.

Coherent Heteroepitaxy Of Bi2se3 On Gaas (111)B, Anthony Richardella, Duming M. Zhang, Joon S. Lee, Alison E. Patteson (Koser), David W. Rench, Andrew L. Yeats, Bob B. Buckley, David D. Awschalom, Nitin Samarth

Physics - All Scholarship

We report the heteroepitaxy of single crystal thin films of Bi2Se3 on the (111)B surface of GaAs by molecular beam epitaxy. We find that Bi2Se3 grows highly c-axis oriented, with an atomically sharp interface with the GaAs substrate. By optimizing the growth of a very thin GaAs buffer layer before growing the ⁠Bi2Se3, we demonstrate the growth of thin films with atomically flat terraces over hundreds of nanometers. Initial time-resolved Kerr rotation measurements herald opportunities for probing coherent spin dynamics at the interface between a candidate topological insulator and a large class of GaAs-based heterostructures.

Effect Of A Strategically Positioned Methoxy Substituent On The Photochemistry Of 3-Aryl-3h-1-Oxacyclopenta[L]Phenanthren-2-Ones, Roshini Thumpakara, Binoy Jose, Perupparampil Unnikrishnan, Sreedharan Prathapan, Nigam Rath

Chemistry & Biochemistry Faculty Works

Irradiation of 3-methoxy-3-aryl-3H-1-oxacyclopenta[l]phenanthren-2-one derivatives 5a–d resulted in singlet-mediated decarbonylation reaction leading to the formation of phenanthrene derivatives 9a–d. The structure of the photoproduct was unequivocally established on the basis of X-ray crystallographic analysis.

Cosmic Voices: Searching For Signs Of Life Elsewhere In The Universe, Shane L. Larson

Public Talks

No abstract provided.

Levone Butts V. Lloyd Weisz

2010 Decisions

USDC for the Western District of Pennsylvania

Unavoidable Topological Minors Of Infinite Graphs, Carolyn Chun, Guoli Ding

Faculty Publications

A graph G is loosely-c-connected, or ℓ-c-connected, if there exists a number d depending on G such that the deletion of fewer than c vertices from G leaves precisely one infinite component and a graph containing at most d vertices. In this paper, we give the structure of a set of ℓ-c-connected infinite graphs that form an unavoidable set among the topological minors of ℓ-c-connected infinite graphs. Corresponding results for minors and parallel minors are also obtained. © 2010 Elsevier B.V. All rights reserved.

Strategies To Resolve The Three-Dimensional Structure Of The Genome Of Small Single-Stranded Icosahedral Viruses, Eduardo Sanz Garcia

Theses and Dissertations

The aim of this study is the three-dimensional structural characterization of the genome packaging inside viral capsids via cryo-electron microscopy and three-dimensional reconstruction. The genome of some single-stranded viruses can be densely packaged within their capsid shells. Several stretches of the genome are known to adopt stable secondary structures, however, to date, little is known about the three-dimensional organization of the genome inside their capsid shells. Two techniques have been developed to facilitate the structural elucidation of genome packaging: the asymmetric random-model method, and the symmetry-mismatch, random model method. Both techniques were successfully tested with model and experimental data. The …

An Fpga-Based System For Tracking Digital Information Transmitted Via Peer-To-Peer Protocols, Karl R. Schrader, Barry E. Mullins, Gilbert L. Peterson, Robert F. Mills

Faculty Publications

This paper presents a Field Programmable Gate Array (FPGA)-based tool designed to process file transfers using the BitTorrent Peer-to-Peer (P2P) protocol and VoIP phone calls made using the Session Initiation Protocol (SIP). The tool searches selected control messages in real time and compares the unique identifier of the shared file or phone number against a list of known contraband files or phone numbers. Results show the FPGA tool processes P2P packets of interest 92% faster than a software-only configuration and is 97.6% accurate at capturing and processing messages at a traffic load of 89.6 Mbps.

Recent Graduate From Chester, S.C., Killed In Automobile Accident In Mecklenburg County, Winthrop University

Winthrop News 2010

• The funeral will be 2 p.m. Wednesday at First Baptist Church of Chester with Revs. Clay Waldrip and Steve Bishop officiating. The interment will be in Old Purity Cemetery. The family will receive friends Tuesday from 6-8 p.m. at Barron Funeral Home.
• She was a graduate of the S.C. Governor’s School for Science and Mathematics and an honor graduate from Winthrop University, having received a B.A. in psychology and B.S. in biology where she worked as a research assistant.

Deafdigest: Gold Edition, December 26, 2010, Barry Strassler

DeafDigest Gold 2010

No abstract provided.

Trial Of The Engagement Matrix: Component 1: The Effectiveness Of Labels. Report, Petra Lietz, Mollie Tobin, Sarah Buckley

Student learning processes

The Engagement Matrix (EM) was designed by the Department of Education and Children’s Services in South Australia to measure engagement levels of students enrolled in the Innovative Community Action Networks (ICAN)/ Flexible Learning Options (FLO) program once a term. Innovative ICANs work with young people (year 6-age 19), families, schools, community groups, businesses and different levels of government to encourage young people to finish their secondary education. Flexible Learning Options (FLO) was first introduced in 2006 as an enrolment option in ICAN schools which is funded by DECS. FLO is an approach that is more flexible than the traditional full-time …