Physical Sciences and Mathematics Commons^™

Superior 5' Homogeneity Of Rna From Atp-Initiated Transcription Under The T7 Φ2.5 Promoter, Tricia M. Coleman, Guocan Wang, Faqing Huang

Faculty Publications

Transcription from the commonly used GTP- initiating T7 class III promoter phi6.5 frequently produces heterogeneous RNA at both 3' and 5' ends. We demonstrate here that RNA transcripts from the T7 class II promoter phi2.5 have superior 5' homogeneity over those from the phi6.5 promoter, with comparable total RNA yields. The overall homogeneity of RNA transcripts is improved to different degrees depending on RNA sequences, although transcription under phi2.5 does not affect the 3' heterogeneity of RNA. In combination with 3' RNA trimming by DNAzymes or ribozymes, this ATP- initiated transcription system based on the T7 phi2.5 promoter can provide …

Surveying Cost Growth, Michael A. Greiner, Vince Sipple, Edward D. White

Faculty Publications

Cost growth that weapon systems incur throughout their acquisition life cycle concerns those who work in the acquisition environment. One way to reduce the amount of unexpected cost growth is to develop better cost estimates. In attaining better cost estimates though, it is often helpful to understand and account for potential cost drivers. Several cost studies, some of which specifically focus on the aircraft industry, have been performed documenting and investigating these growth factors. Overviews of these various cost growth studies are presented as other tools for the cost estimators and program managers.

Diel Activity Patterns Of The Louisiana Pine Snakes (Pituophis Ruthveni) In Eastern Texas, Marc J. Ealy, Robert R. Fleet, D. Craig Rudolph

Faculty Publications

This study examined the diel activity patterns of six Louisiana pine snakes in eastern Texas using radio-telemetry. snakes were monitored for 44 days on two study areas from May to October 1996. Louisana pine snakes were primarily diurnal with moderate crepuscular activity, spending the night within pocket gopher burrows or inactive on the surface. During daylight hours, snakes spent approximately 59% of their time underground within gopher burrows, burned out/rotten stumps, or nine-branded armadillo (Dasypus novemcinctus) burrows. Remaining time was spent on the surface either close to subteranean refuge, or in long distance movements that generally terminet at …

Effects Of Low Tide Rainfall On Intertidal Zone Material Cycling, Raymond Torres, Miguel A. Goni, George Voulgaris, Charles R. Lovell, James T. Morris

Faculty Publications

Sediment transport by rainfall-runoff processes is well documented for terrestrial landscapes but few studies have focused on rainfall-runoff effects in intertidal areas. Here we present geochemical analyses performed on sediment samples collected during low tide irrigation experiments, and tidal channel turbidity measurements taken during natural rainfall over North Inlet Marsh, South Carolina. Order of magnitude approximations indicate that a single 10 minute storm may entrain 8-15% of the local annual average sediment accumulation. This rainfall-entrained material is enriched in organic nitrogen and marine algal matter, and therefore of high nutritional quality.

Rectification Of Thermal Fluctuations In Ideal Gases, Alejandro Garcia, P. Meurs, C. Van De Broeck

Faculty Publications

We calculate the systematic average speed of the adiabatic piston and a thermal Brownian motor, introduced by C. Van den Broeck, R. Kawai and P. Meurs [Phys. Rev. Lett. 93, 090601 (2004)], by an expansion of the Boltzmann equation and compare with the exact numerical solution.

Integrating Perception, Language And Problem Solving In A Cognitive Agent For A Mobile Robot., Deryle W. Lonsdale, D. Paul Benjamin, Damian M. Lyons

Faculty Publications

We are implementing a unified cognitive architecture for a mobile robot. Our goal is to endow a robot agent with the full range of cognitive abilities, including perception, use of natural language, learning and the ability to solve complex problems. The perspective of this work is that an architecture based on a unified theory of robot cognition has the best chance of attaining human-level performance.

This agent architecture is an integration of three theories: a theory of cognition embodied in the Soar system, the RS formal model of sensorimotor activity and an algebraic theory of decomposition and reformulation.

These three …

Fast Registration Of Tabular Document Images Using The Fourier-Mellin Transform, William A. Barrett, Luke A. D. Hutchison

Faculty Publications

A new technique is presented for quickly identifying global affine transformations applied to tabular document images, and to correct for those transformations. This technique, based on the Fourier-Mellin transform, is used to register (align) a set of tabular documents to each other. Each component of the affine transform is handled separately, which dramatically reduces the total parameter space of the problem. This method is robust, and deals with all components of the affine transform in a uniform way. The Fourier-Mellin transform is also extended to handle shear, which can approximate a small amount of perspective distortion, and to not need …

Self-Aligned Mechanical Attachment Of Carbon Nanotubes To Silicon Dioxide Structures By Selective Silicon Dioxide Chemical-Vapor Deposition, Jed D. Whittaker, Ghaleb A. Husseini, Matthew A. Linford, Robert C. Davis, Markus Brink

Faculty Publications

A self-aligned thin-film deposition technique was developed to mechanically attach carbon nanotubes to surfaces for the fabrication of structurally robust nanotube-based nanomechanical devices. Single-walled carbon nanotubes were grown by thermal chemical-vapor deposition (CVD) across 150-nm-wide SiO2 trenches. The nanotubes were mechanically attached to the trench tops by selective silicon tetraacetate-based SiO2 CVD. No film was deposited on the nanotubes where they were suspended across the trenches.

A Study Of The Suitability Of Irobex For High-Speed Exchange Of Large Data Objects, Casey T. Deccio, Joseph Ekstrom, Charles D. Knutson, D. Ryan Partridge, Kevin B. Tew

Faculty Publications

This paper demonstrates that careful tuning of the OBEX and IrLAP negotiated parameters allows OBEX to scale well for use with large data objects and high transmission rates. Due to the substantial time overhead inherent in link turnarounds, minimizing turnarounds during the transmission of a large object helps to maximimize link efficiency. The IrLAP window size and OBEX packet size significantly impact the number of required turnarounds during the transmission of a large object. When these parameters are properly tuned, maximum throughput can be achieved, and OBEX performs efficiently at high data rates.

Synthesis Of Adenosine Derivatives As Transcription Initiators And Preparation Of 5 ' Fluorescein- And Biotin-Labeled Rna Through One-Step In Vitro Transcription, Faqing Huang, Guocan Wang, Tricia Coleman, Na Li

Faculty Publications

Expanding our previous finding of an adenosine-initiated transcription system, we now demonstrate that either the 5' site or the N6 site of adenosine nucleotides can be modified extensively without abolishing their ability to initiate transcription under the T7 phi2.5 promoter. Two series of amino derivatives of adenosine nucleotides were synthesized. Fluorescein and biotin groups were coupled to AMP derivatives through linkers of different sizes and hydrophobicities. Both fluorescein- and biotin-conjugated (at either the 5' or N6 site) adenosine nucleotides can act as efficient transcription initiators, producing fluorescein- and biotin-labeled RNA at the specific 5' end by a one-step transcription procedure, …

Measurement Of High-Q2 Charged Current Cross Sections In E +P Deep Inelastic Scattering At Hera, S. Chekanov, M. Derrick, D. Krakauer, J. H. Loizides, S. Magill, B. Musgrave, J. Repond, R. Yoshida, Margarita C. K. Mattingly, P. Antonioli, G. Bari, M. Basile, L. Bellagamba, D. Boscherini, A. Bruni, G. Bruni, G. Cara Romeo, L. Cifarelli, F. Cindolo, A. Contin, M. Corradi, S. De Pasquale, P. Giusti, G. Iacobucci, A. Margotti, R. Nania, F. Palmonari, A. Pesci, G. Sartorelli, A. Zichichi, G. Aghuzumtsyan

Faculty Publications

Cross sections for e+p charged current deep inelastic scattering at a centre-of-mass energy of 318 GeV have been determined with an integrated luminosity of 60.9 pb-1 collected with the ZEUS detector at HERA. The differential cross sections dσ/dQ2, dσ/dx and dσ/dy for Q2 > 200 GeV2 are presented. In addition, d2σ/dxdQ2 has been measured in the kinematic range 280 GeV2 < Q2 < 17 000 GeV2 and 0.008 < x < 0.42. The predictions of the Standard Model agree well with the measured cross sections. The mass of the W boson propagator is determined to be MW = 78.9 ± 2.0 (stat.) ± 1.8 (syst.) -1.8+2.0 (PDF) GeV from a fit to dσ/dQ2. The chiral structure of the Standard Model is also investigated in terms of the (1-y)2 dependence of the double-differential cross section. The structure-function F2CC has been extracted by combining the measurements presented here with previous ZEUS results from e-p scattering, extending the measurement obtained in a neutrino-nucleus scattering experiment to a significantly higher Q2 region.

Long Coherence Times At 300 K For Nitrogen-Vacancy Center Spins In Diamond Grown By Chemical Vapor Deposition, John S. Colton, T. A. Kennedy, J. E. Butler, R. C. Linares, P.J. Doering

Faculty Publications

Electron-spin-echo experiments reveal phase-memory times as long as 58 μs at 300 K for nitrogen-vacancy centers in chemical vapor deposition (CVD) single crystals. The spins were optically polarized and optically detected. Two high-quality CVD samples were studied. From the current results, it is not clear whether these phase-memory times represent a fundamental limit or are limited by an external source of decoherence.

Measurement Of The Open-Charm Contribution To The Diffractive Proton Structure Function, S. Chekanov, M. Derrick, D. Krakauer, J. H. Loizides, S. Magill, B. Musgrave, J. Repond, R. Yoshida, Margarita C. K. Mattingly, P. Antonioli, G. Bari, M. Basile, L. Bellagamba, D. Boscherini, A. Bruni, G. Bruni, G. Cara Romeo, L. Cifarelli, F. Cindolo, A. Contin, M. Corradi, S. De Pasquale, P. Giusti, G. Iacobucci, A. Margotti, R. Nania, F. Palmonari, A. Pesci, G. Sartorelli, A. Zichichi, G. Aghuzumtsyan

Faculty Publications

Production of D*±(2010) mesons in diffractive deep inelastic scattering has been measured with the ZEUS detector at HERA using an integrated luminosity of 82 pb-1. Diffractive events were identified by the presence of a large rapidity gap in the final state. Differential cross sections have been measured in the kinematic region 1.5

Jet Production In Charged Current Deep Inelastic E+P Scattering At Hera, S. Chekanov, M. Derrick, D. Krakauer, J. H. Loizides, S. Magill, B. Musgrave, J. Repond, R. Yoshida, Margarita C. K. Mattingly, P. Antonioli, G. Bari, M. Basile, L. Bellagamba, D. Boscherini, A. Bruni, G. Bruni, G. Cara Romeo, L. Cifarelli, F. Cindolo, A. Contin, M. Corradi, S. De Pasquale, P. Giusti, G. Iacobucci, A. Margotti, R. Nania, F. Palmonari, A. Pesci, G. Sartorelli, A. Zichichi, G. Aghuzumtsyan

Faculty Publications

The production rates and substructure of jets have been studied in charged current deep inelastic e+p scattering for Q2 > 200 GeV2 with the ZEUS detector at HERA using an integrated luminosity of 110.5 pb-1. Inclusive jet cross sections are presented for jets with transverse energies ETjet > 14 GeV and pseudorapidities in the range -1 < ηjet < 2. Dijet cross sections are presented for events with a jet having ETjet > 14 GeV and a second jet having ETjet > 5 GeV. Measurements of the mean subjet multiplicity, 〈ηsbj〉, of the inclusive jet sample are presented. Predictions based on parton-shower Monte Carlo models and next-to-leading-order QCD calculations are compared to the measurements. The value of αs (MZ), determined …

Measurement Of Deeply Virtual Compton Scattering At Hera, S. Chekanov, M. Derrick, D. Krakauer, J. H. Loizides, S. Magill, B. Musgrave, J. Repond, R. Yoshida, Margarita C. K. Mattingly, P. Antonioli, G. Bari, M. Basile, L. Bellagamba, D. Boscherini, A. Bruni, G. Bruni, G. Cara Romeo, L. Cifarelli, F. Cindolo, A. Contin, M. Corradi, S. De Pasquale, P. Giusti, G. Iacobucci, A. Margotti, R. Nania, F. Palmonari, A. Pesci, G. Sartorelli, A. Zichichi, G. Aghuzumtsyan

Faculty Publications

The cross-section for deeply virtual Compton scattering in the reaction ep → eγp has been measured with the ZEUS detector at HERA using integrated luminosities of 95.0 pb-1 of e+p and 16.7 pb-1 of e-p collisions. Differential cross-sections are presented as a function of the exchanged-photon virtuality, Q2, and the centre-of-mass energy, W, of the γ*p system in the region 5 < Q2 < 100 GeV2 and 40 < W < 140 GeV. The measured cross-sections rise steeply with increasing W. The measurements are compared to QCD-based calculations. © 2003 Elsevier B.V. All rights reserved.

Ordering Tendencies In Octahedral Mgo-Zno Alloys, Gus L. W. Hart, Mahdi Sanati, Alex Zunger

Faculty Publications

Isostrutural II-VI alloys whose components are either rocksalt stable (e.g., CaO-MgO) or zincblende stable (e.g., ZnS-ZnSe) are known to be thermodynamically unstable at low temperatures, showing a miscibility gap and no bulk ordering. In contrast, we show that heterostructural MgO-ZnO is stable, under certain conditions, in the sixfold-coordinated structure for Zn concentrations below 67%, giving rise to spontaneously ordered alloys. Using first-principles calculations, we explain the origin of this stability, the structures of their low-temperature ordered phases, short-range-order patterns, and their optical band-gap properties.

Pyridoxamine Traps Intermediates In Lipid Peroxidation Reactions In Vivo: Evidence On The Role Of Lipids In Chemical Modification Of Protein And Development Of Diabetic Complications, Thomas O. Metz, Nathan L. Alderson, Mark E. Chachich, Suzanne R. Thorpe, John W. Baynes

Faculty Publications

Maillard or browning reactions between reducing sugars and protein lead to formation of advanced glycation end products (AGEs) and are thought to contribute to the pathogenesis of diabetic complications. AGE inhibitors such as aminoguanidine and pyridoxamine (PM) inhibit both the formation of AGEs and development of complications in animal models of diabetes. PM also inhibits the chemical modification of protein by advanced lipoxidation end products (ALEs) during lipid peroxidation reactions in vitro. We show here that several PM adducts, formed in incubations of PM with linoleate and arachidonate in vitro, are also excreted in the urine of PM-treated animals. The …

Allowed Mesoscopic Point Group Symmetries In Domain Average Engineering Of Perovskite Ferroelectric Crystals, Dorian M. Hatch, H. T. Stokes, W. Cao

Faculty Publications

In multivariant systems, several energetically degenerate low temperature domain states can be produced at the structural phase transition. Coexistence of these domain states can produce mesoscopic structures that possess symmetries distinct from the microscopic single domain crystal symmetry. Such engineered domain structures in certain ferroelectric materials have been proven to give superior piezoelectric properties and extremely soft shear moduli. The objective of this article is to consider the variety of symmetries that can be produced through domain average engineering in proper ferroelectric systems arising from the cubic Pm[overline 3]m symmetry perovskite structure.

Solar Neutrinos, Sno And Neutrino-Deuteron Reactions, Vladimir Gudkov, Kuniharu Kubodera

Faculty Publications

The standard nuclear physics approach and effective field theory approach for calculations of neutrino–deuteron cross sections for the solar neutrino energies are considered. Their main features, the level of accuracy and problems to be addressed for further developments are discussed.

Runoff And Sediment Losses From Annual And Unusual Storm Events From The Alto Experimental Watersheds, Texas: 23 Years After Silvicultural Treatments, Matthew W. Mcbroom, R Scott Beasley, Mingteh Chang, Brian Gowin, George G. Ice

Faculty Publications

Evaluating the potential impacts of intensive silvicultural practices on water quality is critical for establishing the long-term sustainability of contemporary forest management practices. From 1979 to 1985, a study involving nine small (~2.5 ha) forested watersheds was conducted near Alto, Texas in the upper western Gulf-Coastal Plain to evaluate the impacts then-current silvicultural practices on water quality. In the years following the study, silvicultural Best Management Practices (BMPs) including Streamside Management Zones (SMZs) and other erosion control practices evolved and questions arose about the applicability of earlier results to current practices. In 1999, these same watersheds were reinstrumented to evaluate …

Search For ΝΜ→ΝE Oscillations In The Nomad Experiment, Nomad Collaboration, P. Astier, D. Autiero, A. Baldisseri, M. Baldo-Ceolin, M. Banner, G. Bassompierre, K. Benslama, N. Besson, I. Bird, B. Blumenfeld, F. Bobisut, J. Bouchez, S. Boyd, A. Bueno, S. Buyatov, L. Camilleri, A. Cardini, P. W. Cattaneo, V. Cavasinni, Roberto Petti, Et. Al.

Faculty Publications

We present the results of a search for ν_µ → ν_e oscillations in the NOMAD experiment at CERN. The experiment looked for the appearance of ν_e in a predominantly ν_µ wide-band neutrino beam at the CERN SPS. No evidence for oscillations was found. The 90% confidence limits obtained are ∆m² < 0.4 eV² for maximal mixing and sin²(2θ)−3 for large ∆m². This result excludes the LSND allowed region of oscillation parameters with ∆m² ≳∆10 eV².

Trust Negotiation For Authentication And Authorization In Healthcare Information Systems, Charles D. Knutson, Kent E. Seamons, Tore L. Sundelin, David K. Vawdrey

Faculty Publications

The expanding availability of health information in an electronic format is strategic for industry-wide efforts to improve the quality and reduce the cnst of health care. The implementation of electronic medical record systems has been hindered by inadequate security provisions. This paper describes the use of frust negotiation as a framework for providing authentication and access control services in healthcare information systems. nust negotiation enables two parties with no pre-existing relationship to establish the trust necessary to perform sensitive transactions via the mutual disclosure of attributes contained within digital credentials. An extension of this system, surrogate irusf negoikiion is introduced …

A Stochastic Sediment Delivery Model For A Steep Mediterranean Landscape, Emmanuel Gabet, Thomas Dunne

Faculty Publications

It is a truism in geomorphology that climatic events operate on a landscape to drive sediment transport processes, yet few investigations have formally linked climate and terrain characteristics with geomorphological processes. In this study, we incorporate sediment transport equations derived from fieldwork into a computer model that predicts the delivery of sediment from hillslopes in a steep Mediterranean landscape near Santa Barbara, California. The sediment transport equations are driven by rainstorms and fires that are stochastically generated from probability distributions. The model is used to compare the rates and processes of sediment delivery under two vegetation types: coastal sage scrub …

Dynamic Sociometry In Particle Swarm Optimization, Mark Richards, Dan A. Ventura

Faculty Publications

The performance of Particle Swarm Optimization is greatly affected by the size and sociometry of the swarm. This research proposes a dynamic sociometry, which is shown to be more effective on some problems than the standard star and ring sociometries. The performance of various combinations of swarm size and sociometry on six different test functions is qualitatively analyzed.

Target Sets: A Tool For Understanding And Predicting The Behavior Of Interacting Q-Learners, Nancy Fulda, Dan A. Ventura

Faculty Publications

Reinforcement learning agents that interact in a common environment frequently affect each others’ perceived transition and reward distributions. This can result in convergence of the agents to a sub-optimal equilibrium or even to a solution that is not an equilibrium at all. Several modifications to the Q-learning algorithm have been proposed which enable agents to converge to optimal equilibria under specified conditions. This paper presents the concept of target sets as an aid to understanding why these modifications have been successful and as a tool to assist in the development of new modifications which are applicable in a wider range …

Interactive Level-Set Smoothing For Photo Editing, Thomas C. Howard, Bryan S. Morse

Faculty Publications

This paper presents an interactive image-smoothing tool based on properties and manipulation of image level sets. This tool uses PDE-based level-set smoothing to preserve edge sharpness while smoothing noise and jagged contours. Unlike existing approaches using PDEs, the duration and areas of application are controlled interactively with immediate feedback to the user. Interaction issues are addressed, and parameters for adjusting the PDE are automatically estimated based on image characteristics.

Modular Verification Of Timed Circuits Using Automatic Abstraction, Eric G. Mercer, Chris Myers, Hao Zheng

Faculty Publications

The major barrier that prevents the application of formal verification to large designs is state explosion. This paper presents a new approach for verification of timed circuits using automatic abstraction. This approach partitions the design into modules, each with constrained complexity. Before verification is applied to each individual module, irrelevant information to the behavior of the selected module is abstracted away. This approach converts a verification problem with big exponential complexity to a set of subproblems, each with small exponential complexity. Experimental results are promising in that they indicate that our approach has the potential of completing much faster while …

First-Principles Calculations For Nitrogen-Containing Single-Walled Carbon Nanotubes, James P. Lewis, Mingwen Zhao, Yueyugan Xia, Ruiqin Zhang

Faculty Publications

We present calculations for possible configurations of nitrogen-containing single-walled carbon nanotubes and their electronic properties obtained with the ab initio tight-binding FIREBALL method. It is found that nitrogen atoms can be energetically incorporated into the carbon network in three forms: Substitution, substitution with formation of a vacancy structure, and chemical adsorption. The different forms exhibit different local densities of states near the Fermi levels, which might suggest a potential method to control the electronic properties of nitrogen-doped carbon nanotubes

Explaining And Predicting Patterns In Stochastic Population Systems, Shandelle M. Henson, Aaron A. King, R. F. Costantino, J. M. Cushing, Brian Dennis, Robert A. Desharnais

Faculty Publications

Lattice effects in ecological time-series are patterns that arise because of the inherent discreteness of animal numbers. In this paper, we suggest a systematic approach for predicting lattice effects. We also show that an explanation of all the patterns in a population time-series may require more than one deterministic model, especially when the dynamics are complex.

High-Field Measurements Of Electron Decoherence Time In Metallic Nanowires: Switching Off Magnetic Impurity Spins, P. Mohanty, Richard A. Webb

Faculty Publications

We report low-temperature measurements of electron decoherence time in a series of pure gold wires, 18 nm thick and 30 nm wide. At fields up to 15 T, large enough to polarize any concentration of magnetic impurity spins, conductance fluctuation measurements show almost no temperature dependence of the decoherence time below 300 mK, both in the correlation field for interference and the root-mean-square value of the fluctuations. Combined with previous low-field weak localization measurements on samples from similar material, our experiment suggests that the ubiquitous saturation of decoherence time in these samples is not due to any mechanism based on …