Digital Commons Network^™

Natural Document Clustering By Clique Percolation In Random Graphs, Wei Gao, Kam-Fai Wong

Research Collection School Of Computing and Information Systems

Document clustering techniques mostly depend on models that impose explicit and/or implicit priori assumptions as to the number, size, disjunction characteristics of clusters, and/or the probability distribution of clustered data. As a result, the clustering effects tend to be unnatural and stray away more or less from the intrinsic grouping nature among the documents in a corpus. We propose a novel graph-theoretic technique called Clique Percolation Clustering (CPC). It models clustering as a process of enumerating adjacent maximal cliques in a random graph that unveils inherent structure of the underlying data, in which we unleash the commonly practiced constraints in …

Theory And Anti-Theory In The Work Of Allan Farnsworth, Wayne R. Barnes

Faculty Scholarship

When Allan Farnsworth passed away on January 31, 2005, the world lost a titan in the field of contracts. Farnsowrth has been described as “the great contemporary American scholar, and one of a handful of great world scholars, on the law of agreement...[He] was...perhaps The Authority on the law of contracts and much more.” Similarly, others have called him “the premiere figure in American Contracts law scholarship since the passing of Corbin and Dawson. The treatise and his half of the Second Restatement would be quite a contribution if there was nothing else.” Farnsworth’s casebook is perennially the most widely-adopted …

Endocarditis And Biofilm-Associated Pili Of Enterococcus Faecalis, Sreedhar R Nallapareddy, Kavindra V Singh, Jouko Sillanpää, Danielle A Garsin, Magnus Höök, Stanley L Erlandsen, Barbara E Murray

Faculty, Staff and Student Publications

Increasing multidrug resistance in Enterococcus faecalis, a nosocomial opportunist and common cause of bacterial endocarditis, emphasizes the need for alternative therapeutic approaches such as immunotherapy or immunoprophylaxis. In an earlier study, we demonstrated the presence of antibodies in E. faecalis endocarditis patient sera to recombinant forms of 9 E. faecalis cell wall-anchored proteins; of these, we have now characterized an in vivo-expressed locus of 3 genes and an associated sortase gene (encoding sortase C; SrtC). Here, using mutation analyses and complementation, we demonstrated that both the ebp (encoding endocarditis and biofilm-associated pili) operon and srtC are important for biofilm production …

Time To Renal Disease And End-Stage Renal Disease In Profile: A Multiethnic Lupus Cohort, Graciela S. Alarcón, Gerald Mcgwin, Michelle Petri, Rosalind Ramsey-Goldman, Barri J. Fessler, Luis M. Vilá, Jeffrey C. Edberg, John D. Reveille, Robert P. Kimberly

Faculty, Staff and Student Publications

BACKGROUND: Renal involvement is a serious manifestation of systemic lupus erythematosus (SLE); it may portend a poor prognosis as it may lead to end-stage renal disease (ESRD). The purpose of this study was to determine the factors predicting the development of renal involvement and its progression to ESRD in a multi-ethnic SLE cohort (PROFILE).

METHODS AND FINDINGS: PROFILE includes SLE patients from five different United States institutions. We examined at baseline the socioeconomic-demographic, clinical, and genetic variables associated with the development of renal involvement and its progression to ESRD by univariable and multivariable Cox proportional hazards regression analyses. Analyses of …

A New Colorimetric Assay For Methionyl Aminopeptidases: Examination Of The Binding Of A New Class Of Pseudopeptide Analog Inhibitors, Sanghamitra Mitra, Anna M. Dygas-Holz, Jiri Jiracek, Miroslava Zertova, Lenka Zakova, Richard C. Holz

Chemistry Faculty Research and Publications

A direct and convenient spectrophotometric assay has been developed for methionine aminopeptidases (MetAPs). The method employs the hydrolysis of a substrate that is a methionyl analogue of p-nitroaniline (l-Met-p-NA), which releases the chromogenic product p-nitroaniline. This chromogenic product can be monitored continuously using a UV–Vis spectrophotometer set at 405 nm. The assay was tested with the type I MetAP from Escherichia coli (EcMetAP-I) and the type II MetAP from Pyrococcus furiosus (PfMetAP-II). Using l-Met-p-NA, the kinetic constants k_cat and K_m were determined for EcMetAP-I and PfMetAP-II …

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell

Faculty Publications

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …

Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell

Faculty Publications

DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach, has been shown to be effective in combining alignment and phylogenetic search in order to avoid the problems associated with poor guide trees. The optimization alignment algorithm operates at a small grain size, aligning each tree found, wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain size algorithm for optimization alignment that …

Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor

Faculty Publications

Each year people suffer from complications of adverse drug reactions, but with pharmacogenomics there is hope to prevent thousands of these people from suffering or dying needlessly. The CYP2D6 gene is responsible for metabolizing a large portion of these drugs. Because of the gene’s importance, various approaches have been taken to analyze CYP2D6 and single nucleotide polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyze the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each nonsynonymous substitution using the program TreeSAAP. We apply this technique to SNPs found in the …

Unf Journal Fall 2006, University Of North Florida

UNF Journal

A university periodical for alumni and friends of the University of North Florida.

My Two Dads: Disaggregating Biological And Social Paternity, Melanie B. Jacobs

Faculty and Staff Scholarship

Examines the question of what the basis for establishing fatherhood should be. Explores how legal parentage is determined, examines the two-parent paradigm, and compares biological and social paternity in order to recognize two legal fathers.

What’S An Embryo?: The Debate About Human Embryonic Stem Cells, Janet L. Dolgin

Hofstra Law Faculty Scholarship

In July 2006 the Senate passed the Stem Cell Research Enhancement Act.1 The House of Representatives had passed the bill, referred to as H.R. 810, in May 2005. The day after the Senate vote, President Bush vetoed the legislation. It was the first time he exercised the veto power in almost six years in office. That day, the House voted to override the veto. The vote was 235 to 193, less than the two-thirds majority needed to set aside a presidential veto.

H.R. 810 did not aim to legalize human embryonic stem cell research. It already was legal. It would, …

Integrated Farming Systems And Pollution Prevention Initiatives Stimulate Co-Learning Extension Strategies, Christy Getz, Keith Douglass Warner

Journal of Extension

Increasing environmental regulatory pressure on agriculture is stimulating increased attention to integrated farming systems and more participatory forms of Extension. Agro-environmental partnerships, which have become the primary strategy for agricultural pollution prevention strategies in California, demonstrate the potential of alternative pest management strategies. We argue that the organizational structure of these partnerships, which facilitates co-learning strategies and greater participation, has been key to their success. The shift from a "transfer of technology" model to participatory co-learning and decision-making making support could improve Extension's service delivery and serve as an important strategy for Extension to engage a broader client constituency.

Whole Systems Inquiry: Designing Large Educational Events, Ray D. William, Molly Engle, Peter B. Goodell, Carrie Koplinka-Loehr

Journal of Extension

Whole systems inquiry (WSI) helps people see complex topics as functional activities with inputs, outputs, interactions, and performance of the system over time. The authors used WSI to design a national symposium with 800 attendees who responded to two questions at the end of 70 topical sessions. Responses were aggregated onto a mega-map, synthesized into themes, and drawn as an emerging system. Work groups compared emerging themes with national priorities while individual participants evaluated utility in their disciplinary programs. We conclude that large meetings can be designed as functional systems with participation, synthesis, and evaluation of intentional learning.

Goats: A Tool For Controlling Spotted Knapweed, Shannon Williams, Tim Prather

Journal of Extension

Spotted knapweed has invaded a number of habitats, and some of those habitats have restrictions on the tools used for control. An experiment was designed to examine the effects of grazing spotted knapweed with goats. The study explored the utilization of spotted knapweed by goats, the effects on plant cover, plant counts, and seed head production. Three years of study determined that goats would consume spotted knapweed, reducing plant cover, plant density, and seed head production. An extensive education outreach program has assisted with adaptation and recognition of goat grazing as a viable tool for noxious weed control.

Livestock-Influenced Water Quality Risk Assessment Tool, Tipton D. Hudson, Joe H. Harrison, Rick Koelsch

Journal of Extension

This article describes a livestock-influenced water quality risk assessment tool that was developed to assist livestock producers with conducting a self-assessment of their operation and management relative to a facility's risk of negatively affecting water quality. The tool focuses on factors likely to influence designation of the operation as a Concentrated Animal Feeding Operation by a permitting authority and was also designed to be used in cooperation with a technical service provider to make a site-specific assessment. The tool is available in paper format and an interactive Microsoft ExcelTM spreadsheet version.

Parker Mountain Greater Sage-Grouse Local Conservation Plan, Utah State University Extension

All Current Publications

No abstract provided.

The Problems Of The Utility Analysis In Fisher And Its Associated Policy Implications And Flaws, Samantha A. Jameson

Duke Law Journal

No abstract provided.

Lower Incisors Of Prairie Dogs (Cynomys) As Biorecorders Of Hibernation And Season Of Death, H. Thomas Goodwin, Eva M. Ryckman

Faculty Publications

Incremental dentin and associated enamel, features visible at the surface of lower incisors of rodents, may chronicle important life-history information. This study investigated surface features of lower incisors representing 4 taxa of prairie dogs (Cynomys) in relation to hibernation and season of year. A set of abnormalities in dentin and enamel, observed on 20 of 138 incisors, always chronicled an event ending in late winter or early spring and was interpreted as a hibernation mark. Hibernation was recorded in the incisors of obligate hibernators, C. leucurus and C. gunnisoni, as well as in 20% of specimens of the facultative heterotherm, …

Plan B Contraceptive And The Role Of Politics In Medicine: A Comparative Analysis Of The "Switch" Of Emergency Contraception From Prescription To Non-Prescription In The United States, France, The United Kingdom, And Canada, Mary E. Armstrong

ExpressO

Of the approximately 6 million pregnancies in the United States each year, almost half are unintended. Of these unintended pregnancies, approximately four in ten will end in abortion. Plan B emergency contraception is a drug that has the potential to reduce the number of abortions performed each year in half. Despite contentions from various religious and political sects, Plan B is not an abortifacient. It acts by preventing a pregnancy from starting rather than terminating a pregnancy that is already established. On December 16, 2003, a panel of medical and scientific experts gathered by the Food and Drug Administration (FDA), …

Annual Report Of Lands Under Control Of The U.S. Fish And Wildlife Service As Of September 30, 2006, United States Fish And Wildlife Service

United States Fish and Wildlife Service: Publications

Annual Report of Lands Under Control Of the U.S. Fish and Wildlife Service As of September 30, 2006

Message from the Director

Key to Real Property Numbers

Map of National Fish and Wildlife Management Areas

Map of Waterfowl Productions Areas

Significant Land Acquisition Accomplishments in Fiscal Year 2006

Tables
1 Summary by Categories
2 Summary by States, Associated Governments and Possessions
2A FY 2006 Summary by States, Associated Governments and Possessions
3 National Wildlife Refuges
4 Waterfowl Production Areas
5 Coordination Areas
6 Administrative Sites
7 National Fish Hatcheries
8 Wilderness Areas in National Wildlife Refuges and National Fish Hatcheries …

Murray Ledger And Times, September 30, 2006, Murray Ledger And Times

The Murray Ledger & Times

No abstract provided.

Annual Report: 2005, N/A N/A

Annual Reports

I submit herewith the annual report from the Agricultural and Forestry Experiment Station, School of Natural Resources and Agricultural Sciences, University of Alaska Fairbanks, for the period ending December 31, 2005. Carol E. Lewis, Dean and Director

Properties Of Intracellular Magnetite Crystals Produced By Desulfovibrio Magneticus Strain Rs-1, Mihály Pósfai, B. M. Moskowitz, Balázs Arató, Dirk Schüler, Christine Flies, Dennis A. Bazylinski, Richard B. Frankel

Physics

Desulfovibrio magneticus strain RS-1 is an anaerobic sulfate-reducing bacterium. Cells form intracellular nanocrystals of magnetite but are only weakly magnetotactic. In order to understand the unusual magnetic response of this strain, we studied magnetite crystals within cells grown with fumarate and sulfate. Many cells grown under either condition did not form magnetic crystals while others contained only 1 to 18 small (~40 nm) magnetite-containing magnetosomes. Bulk magnetic measurements of whole cells showed a superparamagnetic-like behavior, indicating that many of the magnetite crystals are too small to have a permanent magnetic moment at ambient temperature. The temperature of the Verwey transition …

Little River Park, Phase Two Report, Laurel Cox

PREP Reports & Publications

No abstract provided.

Lake Mead National Recreation Area Vegetation Monitoring And Management: Final Close-Out Report, Time Period: October 1, 2005 To September 30, 2006, Margaret N. Rees

Vegetation Monitoring

The National Park Service (NPS) at Lake Mead National Recreation Area (LAME) entered into a cooperative agreement with the University of Nevada, Las Vegas (UNLV) to accomplish vegetation monitoring and management activities. This report summarizes activities that took place by UNLV under this task agreement between October 1, 2005, and September 30, 2006. The activities included:

• Weed Sentry mapping and treating incipient populations of exotic invasive plants throughout Clark County, including along shorelines of Lakes Mead and Mohave;
• Monitoring of targeted rare native plant species;
• Sahara mustard research; and
• Providing technical assistance upon request to the NPS vegetation manager.

In …

Lake Mead National Recreation Area National Park Service: Final Progress Report, Period Ending September 30, 2006, Margaret N. Rees

Wildlife Monitoring

This task agreement was awarded by the National Park Service (NPS), Lake Mead National Recreation Area (LAME), to the Public Lands Institute (PLI) at the University of Nevada, Las Vegas (UNLV) on October 1, 2005. This monitoring, research, and management project consisted of several project elements focused on: bald eagles, peregrine falcons, rare songbird species (including southwest willow flycatcher); aquatic birds, relict leopard frog, desert tortoise, and bighorn sheep. In general, actions associated with this project focused on the development and implementation of inventory and monitoring programs to determine the distribution, status, abundance, trends, and potential threats to these animals, …

The Daily Egyptian, September 29, 2006, The Daily Egyptian

September 2006

No abstract provided.

Volume 42 - Issue 04 - Friday, September 29, 2006, Rose Thorn Staff

The Rose Thorn Archive

The Rose Thorn, Rose-Hulman's independent student newspaper.

Intsormil Crsp: Sorghum, Millet And Other Grains Collaborative Research Support Program: Leader With Associates Cooperative Agreement No. Eep-A-00-06-0016-00; Award From The U.S. Agency For International Development To The University Of Nebraska-Lincoln, Joseph Schmidt

INTSORMIL Scientific Publications

Pursuant to the authority contained in the Foreign Assistance Act of 1961, as amended, the U.S. Agency for International Development (USAID) hereby awards to University of Nebraska - Lincoln (hereinafter referred to as the "Recipient"), the sum of $9,000,000.00 to provide support for a program in Sorghum, Millet, and Other Grains Collaborative Research Support Program as described in the Schedule of this award and in Attachment B, entitled "Program Description."

This Leader with Associates Cooperative Agreement is effective and obligation is made as of 09-30-2006 and shall apply to expenditures made by the Recipient in furtherance of program objectives during …

09-29-2006 Swosu Group Attends Oklahoma Bioblitz, Southwestern Oklahoma State University

THE BARK ARCHIVE 2006

The Southwestern Oklahoma State University Department of Biological Sciences in Weatherford recently participated in the 6th annual Oklahoma BioBlitz, a rapid inventory of biological diversity hosted by the Oklahoma Biological Survey.