Physical Sciences and Mathematics Commons^™

Direct Detection Of Double-Stranded Dna: Molecular Methods And Applications For Dna Diagnostics, Indraneel Ghosh, Cliff I. Stains, Aik T. Ooi, David J. Segal

Cliff Stains Publications

Methodologies to detect DNA sequences with high sensitivity and specificity have tremendous potential as molecular diagnostic agents. Most current methods exploit the ability of single-stranded DNA (ssDNA) to base pair with high specificity to a complementary molecule. However, recent advances in robust techniques for recognition of DNA in the major and minor groove have made possible the direct detection of double-stranded DNA (dsDNA), without the need for denaturation, renaturation, or hybridization. This review will describe the progress in adapting polyamides, triplex DNA, and engineered zinc finger DNA-binding proteins as dsDNA diagnostic systems. In particular, the sequence-enabled reassembly (SEER) method, involving …

Scaling A Dataflow Testing Methodology To The Multiparadigmworld Of Commercial Spreadsheets, Marc Fisher Ii, Gregg Rothermel, Tyler Creelan, Margaret Burnett

CSE Conference and Workshop Papers

Spreadsheets are widely used but often contain faults. Thus, in prior work we presented a data-flow testing methodology for use with spreadsheets, which studies have shown can be used cost-effectively by end-user programmers. To date, however, the methodology has been investigated across a limited set of spreadsheet language features. Commercial spreadsheet environments are multiparadigm languages, utilizing features not accommodated by our prior approaches. In addition, most spreadsheets contain large numbers of replicated formulas that severely limit the efficiency of data-flow testing approaches. We show how to handle these two issues with a new data-flow adequacy criterion and automated detection of …

Helping End-User Programmers “Engineer” Dependable Software, Gregg Rothermel

CSE Conference and Workshop Papers

Not long ago, most software was written by professional programmers, who could be presumed to have an interest in software engineering methodologies and in tools and techniques for improving software dependability. Today, however, a great deal of software is written not by professionals but by end-users, who create applications such as multimedia simulations, dynamic web pages, and spreadsheets. Applications such as these are often used to guide important decisions or aid in important tasks, and it is important that they be sufficiently dependable, but evidence shows that they frequently are not. For example, studies have shown that a large percentage …

Eraid: Conserving Energy In High Performance Raid Systems With Conventional Disks, Dong Li, Jun Wang

CSE Technical Reports

Recently energy consumption becomes an ever critical concern for both low-end and high-end storage server and data centers. A majority of existing energy conservation solutions resort to multi-speed disks. However, current server systems are still built with conventional disks.
In this paper, we propose an energy saving policy, eRAID, for conventional disk based RAID-1 systems. eRAID saves energy by spinning down partial or entire mirror disk group with predictable performance degradation. The heart work of eRAID is to develop an accurate dynamic performance control (including disk power management) scheme. To guarantee service quality, the dynamic performance control works for two …

The Performance Of Elliptic Curve Based Group Diffie-Hellman Protocols For Secure Group Communication Over Ad Hoc Networks, Yong Wang, Byrav Ramamurthy, Xukai Zou

CSE Conference and Workshop Papers

The security of the two party Diffie-Hellman key exchange protocol is currently based on the discrete logarithm problem (DLP). However, it can also be built upon the elliptic curve discrete logarithm problem (ECDLP). Most proposed secure group communication schemes employ the DLP-based Diffie-Hellman protocol. This paper proposes the ECDLP-based Diffie-Hellman protocols for secure group communication and evaluates their performance on wireless ad hoc networks. The proposed schemes are compared at the same security level with DLP-based group protocols under different channel conditions. Our experiments and analysis show that the Tree-based Group Elliptic Curve Diffie-Hellman (TGECDH) protocol is the best in …

Integrated Intermediate Waveband And Wavelength Switching For Optical Wdm Mesh Networks, Mengke Li, Byrav Ramamurthy

CSE Conference and Workshop Papers

As wavelength-division multiplexing (WDM) evolves towards practical applications in optical transport networks, waveband switching (WBS) has been introduced to cut down the operational costs and to reduce the complexities and sizes of network components, e.g., optical cross-connects (OXCs). This paper considers the routing, wavelength assignment and waveband assignment (RWWBA) problem in a WDM network supporting mixed waveband and wavelength switching. First, the techniques supporting waveband switching are studied, where a node architecture enabling mixed waveband and wavelength switching is proposed. Second, to solve the RWWBA problem with reduced switching costs and improved network throughput, the cost savings and call blocking …

A Maximum-Likelihood Approach To Symbolic Indirect Correlation, Ashutosh Joshi, George Nagy, Daniel Lopresti, Sharad C. Seth

CSE Conference and Workshop Papers

Symbolic Indirect Correlation (SIC) is a nonparametric method that offers significant advantages for recognition of ordered unsegmented signals. A previously introduced formulation of SIC based on subgraph-isomorphism requires very large reference sets in the presence of noise. In this paper, we seek to address this issue by formulating SIC classification as a maximum likelihood problem. We present experimental evidence that demonstrates that this new approach is more robust for the problem of online handwriting recognition using noisy input.

On Reoptimizing Multi-Class Classifiers, Kun Deng, Chris Bourke, Stephen Scott, Robert E. Schapire, N. V. Vinodchandran

CSE Technical Reports

Significant changes in the instance distribution or associated cost function of a learning problem require one to reoptimize a previously learned classifier to work under new conditions. We study the problem of reoptimizing a multi-class classifier based on its ROC hypersurface and a matrix describing the costs of each type of prediction error. For a binary classifier, it is straightforward to find an optimal operating point based on its ROC curve and the relative cost of true positive to false positive error. However, the corresponding multi-class problem (finding an optimal operating point based on a ROC hypersurface and cost matrix) …

A Cross-Layer Protocol For Wireless Sensor Networks, Ian F. Akyildiz, Mehmet C. Vuran, Ӧzgür B. Akan

CSE Conference and Workshop Papers

Severe energy constraints of battery-powered sensor nodes necessitate energy-efficient communication protocols in order to fulfill application objectives of wireless sensor networks (WSN). However, the vast majority of the existing solutions are based on classical layered protocols approach. It is much more resource-efficient to have a unified scheme which melts common protocol layer functionalities into a cross-layer module for resource-constrained sensor nodes. To the best of our knowledge, to date, there is no unified cross-layer communication protocol for efficient and reliable event communication which considers transport, routing, medium access functionalities with physical layer (wireless channel) effects for WSNs.
In this paper, …

An Interactive Constraint-Based Approach To Minesweeper, Ken Bayer, Josh Snyder, Berthe Y. Choueiry

CSE Conference and Workshop Papers

We present a Java applet that uses Constraint Processing (CP) to assist a human in playing the popular game Minesweeper. Our goal is to illustrate the power of CP techniques to model and solve combinatorial problems in a context accessible to the general public.

Minesweeper is a video game that has been included with Microsoft Windows since 1989. In this game, the player is presented with a grid of squares. Each of these squares may conceal a mine. When the player clicks on a square, it is revealed. If the square is a mine, the game is over. If the …

Reversible Paramagnetism To Ferromagnetism In Transition Metal-Doped Tio2 Nanocrystals Prepared By Microwave Irradiation, Garry Glaspell, Asit B. Panda, M. S. El-Shall

Chemistry Publications

TiO2nanoparticlesdoped with 1%, 5%, and 10% M (M=Co, Fe, and Ni) were prepared by microwave irradiation and characterized using x-ray diffraction, transmission electron microscopy, and magnetometry. The as-prepared samples are found to be paramagnetic at room temperature, with the magnetic susceptibility following the Curie-Weiss law in the investigated range of 2–300K. However, transformation from paramagnetism to room-temperature ferromagnetism (RTFM) was observed by hydrogenating the samples at 400°C. Reheating in air converted the samples back to paramagnetic while rehydrogenating the samples again induced ferromagnetism. It is argued that the reversible RTFM observed is due to interaction between the dopant metal ions …

Cation Occupancy Determination In Manganese Zinc Ferrites Using Fourier Transform Infrared Spectroscopy, M. D. Shultz, E. E. Carpenter, S. A. Morrison, S. Calvin

Chemistry Publications

The magnetic and electric properties of ferrites are influenced by the cation distribution within the crystalline spinel lattice. Methods such as extended x-ray-absorption fine structure(EXAFS) have been used to determine cation occupancies within the crystalline structure of materials such as manganesezincferrite (MZFO); however, it is not practical to be used for daily analysis. Fourier transform infrared (FTIR)spectroscopy is another technique which has the potential to determine cation occupancy while offering speed and convenience. In the literature it has been demonstrated that in ferrite systems FTIR data can be correlated to cation percentages when comparing tetrahedral (Td) and octahedral (Oh) sites. …

Orientational Correlations In Liquid Acetone And Dimethyl Sulfoxide: A Comparative Study, Sylvia E. Mclain, Alan K. Soper, Alenka Luzar

Chemistry Publications

The structure of acetone and dimethyl sulfoxide in the liquid state is investigated using a combination of neutron diffractionmeasurements and empirical potential structure refinement (EPSR) modeling. By extracting the orientational correlations from the EPSR model, the alignment of dipoles in both fluids is identified. At short distances the dipoles or neighboring molecules are found to be in antiparallel configurations, but further out the molecules tend to be aligned predominately as head to tail in the manner of dipolar ordering. The distribution of these orientations in space around a central molecule is strongly influenced by the underlying symmetry of the central …

Automated Generation Of Context-Aware Tests, Zhimin Wang, Sebastian Elbaum, David Rosenblum

CSE Technical Reports

The incorporation of context-awareness capabilities into pervasive applications allows them to leverage contextual information to provide additional services while maintaining an acceptable quality of service. These added capabilities, however, introduce a distinct input space that can affect the behavior of these applications at any point during their execution, making their validation quite challenging. In this paper, we introduce an approach to improve the test suite of a context-aware application by identifying context-aware program points where context changes may affect the application’s behavior, and by systematically manipulating the context data fed into the application to increase its exposure to potentially valuable …

Web Application Characterization Through Directed Requests, Sebastian Elbaum, Kalyanram Chilakamarri, Marc Randall Fisher Ii, Gregg Rothermel

CSE Technical Reports

Web applications are increasingly prominent in society, serving a wide variety of user needs. Engineers seeking to enhance, test, and maintain these applications must be able to understand and characterize their interfaces. Third-party programmers (professional or end user) wishing to incorporate the data provided by such services into their own applications would also benefit from such characterization when the target site does not provide adequate programmatic interfaces. In this paper, therefore, we present methodologies for characterizing the interfaces to web applications through a form of dynamic analysis, in which directed requests are sent to the application, and responses are analyzed …

An Ontology-Based Metamodel For Software Patterns, Scott Henninger, Padmapriya Ashokkumar

CSE Technical Reports

Patterns have been successfully used in software design to reuse proven solutions. But the complex interconnections and the number of pattern collections is becoming a barrier for identifying relevant patterns and pattern combinations for a given design context. More formal representations of patterns are needed that allow machine processing and the creation of systematic pattern languages that guide composition of patterns into coherent design solutions. In this paper, we present a technique based on Description Logic and Semantic Web technologies to address these problems. A metamodel is presented for developing pattern languages using this technology. Usability patterns are used to …

Stability Of Warfarin Solutions For Drug–Protein Binding Measurements: Spectroscopic And Chromatographic Studies, Annette C. Moser, Charles A. Kingsbury, David S. Hage

Chemistry Department: Faculty Publications

Warfarin is commonly used in drug–protein binding studies as a displacement marker for Sudlow site I on the protein human serum albumin (HSA). This study examined the stability of aqueous warfarin solutions prepared for such experiments. This was investigated using NMR spectroscopy and affinity chromatography. It was found by 1H NMR that warfarin underwent a slow first-order conversion in aqueous solution. The rate of this reaction increased with temperature, giving rate constants at pH 7.4 of 0.0086 h⁻¹ at 25 °C and 0.041 h⁻¹ at 37 °C. It was concluded from further 1H and 13C NMR studies, along …

Trends In Satellite-Observed Circumpolar Photosynthetic Activity From 1982 To 2003: The Influence Of Seasonality, Cover Type, And Vegetation Density, Andrew Godard Bunn, Scott J. Goetz

Environmental Sciences Faculty and Staff Publications

Time series analyses of a 22-yr record of satellite observations across the northern circumpolar high latitudes were conducted, and trends in vegetation photosynthetic activity were assessed using a series of statistical tests. The results indicate that most of the northern circumpolar high latitudes (>85%) showed no significant trend in vegetation activity despite systematic climate warming during the period of analysis. Of the areas that did change, many showed the expected trends in “greening” of vegetation activity. There were, however, significant differences in the magnitude and even in the direction of trends when stratified by vegetation type and density. Tundra …

Geochronology And Tectonic Significance Of Middle Proterozoic Granitic Orthogneiss, North Qaidam Hp/Uhp Terrane, Western China, Chris G. Mattinson, Joseph L. Wooden, Juhn G. Liou, D. K. Bird, C. L. Wu

All Faculty Scholarship for the College of the Sciences

Amphibolite-facies para- and orthogneisses near Dulan, in the southeast part of the North Qaidam terrane, enclose minor ultra-high pressure (UHP) eclogite and peridotite. Field relations and coesite inclusions in zircons from paragneiss suggest that felsic, mafic, and ultramafic rocks all experienced UHP metamorphism and a common amphibolite-facies retrogression. Ion microprobe U–Pb and REE analyses of zircons from two granitic orthogneisses indicate magmatic crystallization at 927 ± Ma and 921 ± 7 Ma. Zircon rims in one of these samples yield younger ages (397–618 Ma) compatible with partial zircon recrystallization during in-situ Ordovician-Silurian eclogite-facies metamorphism previously determined from eclogite and paragneiss …

Pyritized Tube Feet In A Protasterid Ophiuroid From The Upper Ordovician Of Kentucky, U.S.A., Alexander Glass

All Faculty Scholarship for the College of the Sciences

A single specimen of the protasterid ophiuroid Protasterina flexuosa from the Kope Formation (Cincinnatian, Upper Ordovician) of Kentucky exhibits three−dimensionally pyritized tube feet. This represents the first report of soft−tissue preservation in an echinoderm from the type−Cincinnatian series. The tube feet are solid and lack all internal structure. They consist of aggregated masses of small euhedral to subhedral pyrite crystals suggesting that pyritization, although decay−induced and mediated, did not necessarily replicate soft−tissues but might instead have formed inside the void−spaces left behind during the decay process. The discovery of pyritized soft−tissue as delicate as ophiuroid tube feet suggests that similar …

Writing Projective Representations Over Subfields, Stephen P. Glasby, C. R. Leedham-Green, E. A. O'Brien

All Faculty Scholarship for the College of the Sciences

Let G=〈X〉be an absolutely irreducible subgroup of GL(d, K), and let F be a proper subfield of the finite field K. We present a practical algorithm to decide constructively whether or not G is conjugate to a subgroup of GL(d, F).K×, where K× denotes the centre of GL(d, K). If the derived group of G also acts absolutely irreducibly, then the algorithm is Las Vegas and costs O(|X|d³+d²log|F|) arithmetic operations in K. This work forms part of a recognition project based on Aschbacher’s classification of maximal subgroups of GL(d, K).

Tr-2006003: Explicit Proofs In Formal Provability Logic, Evan Goris

Computer Science Technical Reports

No abstract provided.

Tr-2006007: Root-Finding With Eigen-Solving, Victor Y. Pan, Brian Murphy, Rhys Eric Rosholt

Computer Science Technical Reports

No abstract provided.

Tr-2006008: Every P-Recursion Category Has An Index Composer, Florian Lengyel

Computer Science Technical Reports

No abstract provided.

Tr-2006005: Logical Omniscience Via Proof Complexity, Sergei Artemov, Roman Kuznets

Computer Science Technical Reports

No abstract provided.

Tr-2006006: Additive Preconditioning And Aggregation In Matrix Computations, Victor Y. Pan, Dmitriy Ivolgin, Brian Murphy, Rhys Eric Rosholt, Islam Taj-Eddin, Yuqing Tang, Xiaodong Yan

Computer Science Technical Reports

No abstract provided.

Tr-2006012: Every P-Recursion Category Has An Index Composer, Florian Lengyel

Computer Science Technical Reports

No abstract provided.

2005 Diamond Lake Submersed Aquatic Vegetation Survey, Mark D. Sytsma, Mary Pfauth

Center for Lakes and Reservoirs Publications and Presentations

Diamond Lake is a large natural lake having a surface area of some 3214 acres (1300.7 hectares) and a maximum depth of 52 feet (15.8 meters). It is located within the Umpqua National Forest in the Southern Cascade Mountains of Oregon, at an elevation of over 5000 feet (>1524 meters). Diamond Lake is a high-use waterbody that supports angling, public campgrounds, recreational boating, swimming, and water skiing. The human activity associated with the lake has been a significant contributor to the economy of southern Oregon since the early part of the twentieth century.

Historically Diamond Lake was fishless but …

Interview With Myo Demayo, Urbanstead Farm (Audio), Myo Demayo

All Sustainability History Project Oral Histories

Interview of Myo DeMayo by Tyler Anderson.

The interview index is available for download.

The year is estimated.

1,1´-Diethyl-2,2´,3,3´,4,4´,5,5´-Octamethylferrocenium Tetracyanoethylenide, [Fe(C5etme4)2]+[Tcne]–, A Charge-Transfer Salt Magnetic Solid With A Novel Structural Motif, T. David Harris, Michael Castellani, Arnold L. Rheingold, William M. Reiff, Gordon T. Yee

Chemistry Faculty Research

1,1′-Diethyl-2,2′,3,3′,4,4′,5,5′-octamethylferrocene has been utilized as a one-electron donor in the synthesis of a tetracyanoethylene charge-transfer salt, [Fe(C₅EtMe₄)₂]⁺[TCNE]⁻. Structural characterization shows that it adopts an arrangement of anions and cations completely different from the usual π stacking seen in analogous decamethylferrocenium compounds. The TCNE radical sits along side of the ferrocene, nearly perpendicular to the planes of the C₅ rings. The nearly square geometry of the TCNE anion creates disorder over two orientations. [Fe(C₅EtMe₄)₂]⁺[TCNE]⁻ is a simple paramagnet exhibiting neither long-range …