Physical Sciences and Mathematics Commons^™

E-Science @ The University Of Massachusetts, Maxine G. Schmidt, Rebecca Reznik-Zellen, Raquel Rivera, Cecilia P. Mullen

Maxine G Schmidt

e-Science @ the University of Massachusetts Abstract: What is e-Science and how can libraries and librarians support it? The University of Massachusetts takes a proactive approach to support network-enabled research on its campuses and provides examples where e-Science is already at work. Statement: “e-Science” is a term commonly used to describe research in a networked environment, a growing trend not only in the sciences, but the arts and humanities as well. e-Science creates both opportunities and challenges for academic libraries. The opportunities lie in leveraging the basic skill set that libraries and librarians already possess: the knowledge of and practical …

Analysis Of Randomized Comparative Clinical Trial Data For Personalized Treatment Selections, Tianxi Cai, Lu Tian, Peggy H. Wong, L. J. Wei

Harvard University Biostatistics Working Paper Series

No abstract provided.

Modeling Thermal Inactivation Of Bacillus Spores, Emily A. Knight

Theses and Dissertations

This research models and analyzes methods to damage Bacillus anthracis spores through heat treatment. AFIT researchers have developed methods to characterize the effects of heating spores to high temperatures and for short durations similar to the thermal pulse of conventional weapon detonation. This research models the current experiment and evaluates the rate of thermal diffusion throughout the spores. A micro-model of the effects of dry and wet heating on a spore is presented. Heating a spore energizes adsorbed, absorbed, and chemically bound water molecules. These energized molecules have greater mobility within the spore, as well as between the spore and …

Group Comparison Of Eigenvalues And Eigenvectors Of Diffusion Tensors, Armin Schwartzman, Robert F. Dougherty, Jonathan E. Taylor

Harvard University Biostatistics Working Paper Series

No abstract provided.

Retention Of Polarization Signatures In Shg Microscopy Of Scattering Tissues Through Optical Clearing, Oleg Nadiarnykh, Paul J. Campagnola

UCHC Articles - Research

Polarization responses in Second Harmonic Generation (SHG) imaging microscopy are a valuable method to quantify aspects of tissue structure, and may be a means to differentiate normal and diseased tissues. Due to multiple scattering, the polarization data is lost in turbid tissues. Here we investigate if this information can be retained through the use of optical clearing which greatly reduces the scattering coefficient and increases the corresponding mean free path. To this end, we have measured the SHG intensity as a function of laser polarization and the SHG signal anisotropy in murine tendon and striated muscle over a depth range …

Multimeric Hemicellulases Facilitate Biomass Conversion, Zhanmin Fan, Kurt Wagschal, Wei Chen, Michael D. Montross, Charles C. Lee, Ling Yuan

Plant and Soil Sciences Faculty Publications

Two highly active trifunctional hemicellulases were constructed by linking the catalytic portion of a xylanase with an arabinofuranosidase and a xylosidase, using either flexible peptide linkers or linkers containing a cellulose-binding domain. The multifunctional enzymes retain the parental enzyme properties and exhibit synergistic effects in hydrolysis of natural xylans and corn stover.

The Prevalence And Determinants Of Health Risk Behaviors Among High School Students In Mexico, Nellie León

Loma Linda University Electronic Theses, Dissertations & Projects

The Centers for Disease Control and Prevention report that despite health promotion efforts, adolescents continue to engage in behaviors that put them at risk for morbidity and mortality. Alcohol consumption, illicit drug use, smoking, and risky sexual behaviors are among the behaviors that contribute to leading causes of morbidity and mortality in youth; these four behaviors were explored in this study. An observational cross-sectional design was utilized. The Youth Risk Behavior Survey from the Centers for Disease Control and Prevention was utilized to assess the prevalence of the four risk behaviors among high school students in Jalisco, Mexico. Items constructed …

Immediate Loading Of Unsplinted Implants In The Anterior Mandible For Overdentures, Phillip Roe

Loma Linda University Electronic Theses, Dissertations & Projects

In this one-year prospective study, eight completely edentulous patients were selected from the Loma Linda University School of Dentistry (LLUSD) patient population to participate. There were five male and three female patients, between the ages of 58 and 82 (mean age of 69.1 years). All participants received new maxillary and mandibular complete dentures prior to implant placement. Two 4.0 mm x 13 mm threaded implants with a fluoride-modified, micro-roughened, titanium surface were placed mesial to each mandibular canine position. Locator abutments were connected and torqued to 25 Ncm and primary closure was achieved with a nonresorbable suture material. The Locator …

Crop Updates 2009 - Genetically Modified Crops, Nutrition, Soils, & Others, Wallace Cowling, Art Diggle, Caroline Peek, Frank D'Emden, Fiona Evans, Bob French, Rob Grima, Sam Harburg, Abul Hashem, John Holmes, Jeromy Lemon, Peter Newman, Janet Paterson, Steve Penny, Peter Portman, Mark Slatter, Angus Maclennan, Andrew Wells, Bill Bowden, Wayne Pluske, Wen Chen, Geoff Anderson, Ross Brennan, Richard Bell, Hannah Rigby, Deborah Pritchard, David Collins, Katrina Walton, David Allen, Nancy Penney, Michael Robertson, Roger Lawes, Stephen Davies, Chris Gazey, Breanne Best, David Gartner, Quenten Knight, Joel Andrew, Ryan Pearce, F. C. Hoyle, A. Bennett, Rick Llewellyn, Ken Flower, Julian Krieg, Owen Catto, Cindy Parsons

Crop Updates

This session covers fifteen papers from different authors:

1. Performance of Canola Breeders Roundup Ready^® canola hybrid CHYB-166 in 2008, Wallace Cowling, Canola Breeders Western Australia Pty Ltd

2. The implications of GM glyphosate resistant lupin, Art Diggle, Caroline Peek, Frank D’Emden, Fiona Evans, Bob French, Rob Grima, Sam Harburg, Abul Hashem,, John Holmes, Jeremy Lemon, Peter Newman, Janet Paterson, Steve Penny,Department of Agriculture and Food, Peter Portmann, Agriconnect

3. Nufarm Roundup Ready® Canola Systems Trials— 2008 Mark Slatter, Research and Development …

39th Annual Wku Student Research Conference, Student Research Council, Western Kentucky University

Student Research Conference Select Presentations

No abstract provided.

Archetype Alignment: A Two-Level Driven Semantic Matching Approach To Interoperability In The Clinical Domain, Damon Berry, Jesus Bisbal

Conference Papers

Semantic interoperability between electronic health record systems and other information systems in the health domain implies agreement about the structure and the meaning of the information that is communicated. There are still a number of similar but different EHR system approaches. Some of the newer approaches adopt the two-layer model approach where a generic reference model is constrained by archetypes into valid clinical concepts which can be exchanged. The meaning of the concepts that are represented by an archetype can be conveyed by embedding codes from a commonly recognised terminology at appropriate points in the archetype. However, as the number …

Hydroxyl Radical Is Produced Via The Fenton Reaction In Submitochondrial Particles Under Oxidative Stress: Implications For Diseases Associated With Iron Accumulation, Carin Thomas, Melissa M. Mackey, Amy A. Diaz, David P. Cox

All Faculty Scholarship for the College of the Sciences

Mitochondrial dysfunction and reactive oxygen species (ROS) are often implicated in diseases involving oxidative stress and elevated iron. As mitochondria produce ATP by oxidative phosphorylation, ROS by-products are generated from the electron transport chain. Although superoxide and hydrogen peroxide have been thoroughly investigated, little evidence documents hydroxyl radical (HO•) production in mitochondria. In order to determine whether HO• is generated under oxidative stress conditions by a Fenton-type mechanism, bovine heart submitochondrial particles were examined for HO• in the presence and absence of iron ligands, antioxidant enzymes and HO• scavengers. HO• was measured as 2,3- and 2,5-dihydroxybenzoic acid (DHBA), using HPLC …

Singlet Oxygen Delivery Through The Porous Cap Of A Hollow-Core Fiber Optic Device, Matibur Zamadar, David Aebisher, Alexander Greer

Faculty Publications

The development of the first photosensitizer/fiber optic device is reported. An oxygen-flowing, fiber-capped configuration is used for the application of heterogeneous, spatially confined singlet oxygen delivery in aqueous media. This is a unique device, unlike other heterogeneous photosensitizers, in which local concentrations of singlet oxygen can be delivered via introduction and withdrawal of the fiber tip.

Barriers Encountered During Enrollment In An Internet-Mediated Randomized Controlled Trial, Lorraine R. Buis, Adrienne W. Janney, Michael L. Hess, Silas A. Culver, Caroline R. Richardson

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Online technology is a promising resource for conducting clinical research. While the internet may improve a study's reach, as well as the efficiency of data collection, it may also introduce a number of challenges for participants and investigators. The objective of this research was to determine the challenges that potential participants faced during the enrollment phase of a randomized controlled intervention trial of Stepping Up to Health, an internet-mediated walking program that utilized a multi-step online enrollment process.

Methods

We conducted a quantitative content analysis of 623 help tickets logged in a participant management database during the enrollment …

Uniqueprimer - A Web Utility For Design Of Specific Pcr Primers And Probes, Torstein Tengs

Dr. Torstein Tengs

We have developed a web-based tool for design of specific PCR primers and probes. The program allows you to enter primer sequence information as well as an optional probe, and sequence similarity searches (MegaBLAST) will be performed to see if the sequences match the same sequence entry in the specified database. If primers (and probe) match, this will be reported. The program can handle overlapping amplicons, amplification from a single primer, ambiguous bases and other problematic cases.

A Program Evaluation Of A Polypharmacy Sub-Population: Medications, Emergency Room Visits, And Hospitalizations, Brian W. Bresnahan, Kent M. Koprowicz, Sanchita Roy Choudhury, Ed Wong

Kent M Koprowicz

No abstract provided.

Hierarchical Hidden Markov Model With Application To Joint Analysis Of Chip-Chip And Chip-Seq Data, Hyungwon Choi, Debashis Ghosh, Zhaohui S. Qin

Debashis Ghosh

Motivation: Identication of transcription factor binding sites (TFBS) is a fundamental problem in understanding the mechanism of gene regulation. The ChIP-chip technology has accelerated this eort by providing a simultaneous genome-wide map of TFBS in a high-throughput fashion. Recently, a sequencing-based ChIP-seq has appeared as a promising alternative that can identify targets with an improved sensitivity/specicity in high resolution. However, studies have suggested that distinct experimental platforms can be complementary in TFBS identication. The availability of data obtained from multiple platforms motivates a meta-analysis for improved identication of candidate motifs.

Results: In this work, we propose a hierarchical hidden Markov …

A Double-Layered Mixture Model For The Joint Analysis Of Dna Copy Number And Gene Expression Data, Debashis Ghosh

Debashis Ghosh

Copy number aberration is a common form of genomic instability in cancer. Gene expression is closely tied to cytogenetic events by the central dogma of molecular biology, and serves as a mediator of copy number changes in disease phenotypes. Accordingly, it is of interest to develop proper statistical methods for jointly analyzing copy number and gene expression data. This work describes a novel Bayesian inferential approach for a double-layered mixture model (DLMM) which directly models the stochastic nature of copy number data and identifies abnormally expressed genes due to aberrant copy number. Simulation studies were conducted to illustrate the robustness …

Discrete Nonparametric Algorithms For Outlier Detection With Genomic Data, Debashis Ghosh

Debashis Ghosh

In high-throughput studies involving genetic data such as from gene expression microarrays, differential expression analysis between two or more experimental conditions has been a very common analytical task. Much of the resulting literature on multiple comparisons has paid relatively little attention to the choice of test statistic. In this article, we focus on the issue of choice of test statistic based on a special pattern of differential expression. The approach here is based on recasting multiple comparisons procedures for assessing outlying expression values. A major complication is that the resulting p-values are discrete; some theoretical properties of sequential testing procedures …

A Double-Layered Mixture Model For The Joint Analysis Of Dna Copy Number And Gene Expression Data, Debashis Ghosh

Debashis Ghosh

Copy number aberration is a common form of genomic instability in cancer. Gene expression is closely tied to cytogenetic events by the central dogma of molecular biology, and serves as a mediator of copy number changes in disease phenotypes. Accordingly, it is of interest to develop proper statistical methods for jointly analyzing copy number and gene expression data. This work describes a novel Bayesian inferential approach for a double-layered mixture model (DLMM) which directly models the stochastic nature of copy number data and identifies abnormally expressed genes due to aberrant copy number. Simulation studies were conducted to illustrate the robustness …

Discrete Nonparametric Algorithms For Outlier Detection With Genomic Data, Debashis Ghosh

Debashis Ghosh

In high-throughput studies involving genetic data such as from gene expression microarrays, differential expression analysis between two or more experimental conditions has been a very common analytical task. Much of the resulting literature on multiple comparisons has paid relatively little attention to the choice of test statistic. In this article, we focus on the issue of choice of test statistic based on a special pattern of differential expression. The approach here is based on recasting multiple comparisons procedures for assessing outlying expression values. A major complication is that the resulting p-values are discrete; some theoretical properties of sequential testing procedures …

An Examination Of The Persistence Of The Residual Child Welfare System In The United States: Addressing Charges Of Radical Theoretical Myopia With Implications For Social Work Practice, Peter Cabrera

Elián P. Cabrera-Nguyen

The United States follows what has been termed a residual approach to its public child welfare system. This article describes the residual model and contrasts it with the policies of other industrialized nations. It also explores the causes and persistence of the residual model in the United States through the lens of structural-functionalist theory. By doing so, this article attempts to respond to critics of structural social work who maintain that it is overly reliant on conflict theory and has nothing to offer in terms of distinct practice methods. Suggestions for a structurally informed social work practice are made.

A Critique Of The False-Positive Report Probability, Joseph Lucke

Joseph Lucke

The false positive report probability (FPRP) was proposed as a Bayesian prophylactic against false reports of significant associations. Unfortunately, the derivation of the FPRP is unsound. A heuristic derivation fails to make its point, and a formal derivation reveals a probabilistic misrepresentation of an observation. As a result, the FPRP can yield serious inferential errors. In particular, the FPRP can use an observation that is many times more likely under the null hypothesis than under the alternative to infer that the null hypothesis is far less probable than the alternative. Contrary to its intended purpose, the FPRP can promote false …

A Quantitative Taqman Mgb Real-Time Polymerase Chain Reaction Based Assay For Detection Of The Causative Agent Of Crayfish Plague Aphanomyces Astaci, Torstein Tengs

Dr. Torstein Tengs

Here we present the development and first validation of a TaqMan minor groove binder (MGB) real-time polymerase chain reaction (RT-PCR) method for quantitative and highly specific detection of Aphanomyces astaci, the causative agent of crayfish plague. The assay specificity was experimentally assessed by testing against DNA representative of closely related oomycetes, and theoretically assessed by additional sequence similarity analyses comparing the primers and probe sequences to available sequences in EMBL/GenBank. The target of the assay is a 59 bp unique sequence motif of A. astaci found in the internal transcribed spacer 1 of the nuclear ribosomal gene cluster. A standard …

Umass Libraries 2009, Maxine G. Schmidt

Maxine G Schmidt

No abstract provided.

Preparation And Characterization Of Some Substituted Benzyl N-Nitrosocarbamates Containing An N-2-(Methylthio)Ethyl Or A Bis(2-Aminoethyl)Sulfide Functionality, Satya Venkata, Eric Shamo, Vladimir Benin

Chemistry Faculty Publications

The synthesis and characterization of some substituted benzyl N-nitrosocarbamates with an N-2-(methylthio)ethyl or a bis(2-aminoethyl)sulfide functionality is reported, as a part of a long-term goal to design and prepare novel photolabile structures that could be used as substances for controlled release of alkylating and/or crosslinking agents. The synthesis was accomplished by reaction of benzyl chloroformates with the corresponding amines, resulting in the preparation of carbamates. The latter were subsequently nitrosated, utilizing two different N-nitrosation methods, to yield the target structures.

Santa Clara Magazine, Volume 51 Number 3, Winter 2009, Santa Clara University

Santa Clara Magazine

18 - EVERYTHING IS ILLUMINATED By Christine Cole. For the first time since the invention of the printing press, artists have put quill pen to paper to hand-write-in calligraphy-the Bible in its entirety. The result is a wonder to behold. And available to readers and gazers at Santa Clara.

24 - HOLD THE LINE By David McKay Wilson. At Harlem's Frederick Douglass Academy, basketball coach Pat Mangan '84 has built a legendary program by making sure his players have their priorities straight. Family first. School second. Then hoops.

28 - LESSONS IN DIPLOMACY. By Sam Scott '96. How Bob LaMonte …

Generalization Of Acid Properties, Brahim Medjahed, Mourad Ouzzani, Ahmed Elmagarmid

Cyber Center Publications

ACID (Atomicity, Consistency, Isolation, and Durability) is a set of properties that guarantee the reliability of database transactions [2]. ACID properties were initially developed with traditional, business-oriented applications (e.g., banking) in mind. Hence, they do not fully support the functional and performance requirements of advanced database applications such as computer-aided design, computer-aided manufacturing, office automation, network management, multidatabases, and mobile databases. For instance, transactions in computer-aided design applications are generally of long duration and preserving the traditional ACID properties in such transactions would require locking resources for long periods of time. This has lead to the generalization of ACID properties …

Beyond K-Anonymity: A Decision Theoretic Framework For Assessing Privacy Risk, Guy Lebanon, Monica Scannapieco, Mohamed Fouad, Elisa Bertino

Cyber Center Publications

An important issue any organization or individual has to face when managing data containing sensitive information, is the risk that can be incurred when releasing such data. Even though data may be sanitized before being released, it is still possible for an adversary to reconstruct the original data using additional information thus resulting in privacy violations. To date, however, a systematic approach to quantify such risks is not available. In this paper we develop a framework, based on statistical decision theory, that assesses the relationship between the disclosed data and the resulting privacy risk. We model the problem of deciding …

Query Mesh: Multiroute, Rimma Nehme, Karen Works, Elke Rundensteiner, Elisa Bertino

Cyber Center Publications

We propose to demonstrate a practical alternative approach to the current state-of-the-art query processing techniques, called the “Query Mesh” (or QM, for short). The main idea of QM is to compute multiple routes (i.e., query plans)1, each designed for a particular subset of data with distinct statistical properties. Based on the execution routes and the data characteristics, a classifier model is induced and is used to partition new data tuples to assign the best routes for their processing. We propose to demonstrate the QM framework in the streaming context using our demo application, called the “Ubi-City”. We will illustrate the …