Physical Sciences and Mathematics Commons^™

Integrative Bayesian Analysis Of High-Dimensional Multi-Platform Genomics Data, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju C. Manyam, Kim-Anh Do

Jeffrey S. Morris

Motivation: Analyzing data from multi-platform genomics experiments combined with patients’ clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current integration approaches that treat the data are limited in that they do not consider the fundamental biological relationships that exist among the data from platforms.

Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes/biomarkers that are associated with clinical outcome. This framework uses a hierarchical modeling technique to combine the data obtained from multiple platforms …

A Systematic Mapping Approach Of 16q12.2/Fto And Bmi In More Than 20,000 African Americans Narrows In On The Underlying Functional Variation: Results From The Population Architecture Using Genomics And Epidemiology (Page) Study

Shuo Jiao

Genetic variants in intron 1 of the fat mass– and obesity-associated (FTO) gene have been consistently associated with body mass index (BMI) in Europeans. However, follow-up studies in African Americans (AA) have shown no support for some of the most consistently BMI–associated FTO index single nucleotide polymorphisms (SNPs). This is most likely explained by different race-specific linkage disequilibrium (LD) patterns and lower correlation overall in AA, which provides the opportunity to fine-map this region and narrow in on the functional variant. To comprehensively explore the 16q12.2/FTO locus and to search for second independent signals in the broader region, we fine-mapped …

Genome-Wide Search For Gene-Gene Interactions In Colorectal Cancer

Shuo Jiao

Genome-wide association studies (GWAS) have successfully identified a number of single-nucleotide polymorphisms (SNPs) associated with colorectal cancer (CRC) risk. However, these susceptibility loci known today explain only a small fraction of the genetic risk. Gene-gene interaction (GxG) is considered to be one source of the missing heritability. To address this, we performed a genome-wide search for pair-wise GxG associated with CRC risk using 8,380 cases and 10,558 controls in the discovery phase and 2,527 cases and 2,658 controls in the replication phase. We developed a simple, but powerful method for testing interaction, which we term the Average Risk Due to …

James-Stein Estimation And The Benjamini-Hochberg Procedure, Debashis Ghosh

Debashis Ghosh

For the problem of multiple testing, the Benjamini-Hochberg (B-H) procedure has become a very popular method in applications. Based on a spacings theory representation of the B-H procedure, we are able to motivate the use of shrinkage estimators for modifying the B-H procedure. Several generalizations in the paper are discussed, and the methodology is applied to real and simulated datasets.

Shrinkage In Adaptive Procedures For False Discovery Rate Estimation In Multiple Testing: Structure And Synthesis, Debashis Ghosh

Debashis Ghosh

There has been much interest in the study of adaptive estimation procedures for controlling the false discovery rate (FDR). In this article, we take the direct approach to estimation of FDR of Storey (2002) and show how it can reexpressed as a particular type of shrinkage estimator. This representation leads to natural conditions on finite-sample FDR control for a general class of shrinkage estimators. In addition, many previous proposals from the literature can be unified under this framework for which finite-sample FDR results can be developed. Some asymptotic results are also provided.

A Positive Trait Item Response Model, Joseph F. Lucke

Joseph Lucke

All current models from item response theory (IRT) assume the latent trait follows a standard normal distribution. While this assumption is appropriate for traits such as ability or attitude, it creates both conceptual and technical problems traits such as addiction (alcohol, drugs, gambling). The distribution of an addiction trait is better assumed to be anchored at zero (no addiction) and positively skewed. A small change to the usual IRT model yields a class of positive-trait item response models (PTIRMs). I discuss PTIRMs and present one model in detail, including item characteristic curves and item information curves. I present an example …

A Systematic Selection Method For The Development Of Cancer Staging Systems, Yunzhi Lin, Richard Chappell, Mithat Gonen

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

The tumor-node-metastasis (TNM) staging system has been the anchor of cancer diagnosis, treatment, and prognosis for many years. For meaningful clinical use, an orderly, progressive condensation of the T and N categories into an overall staging system needs to be defined, usually with respect to a time-to-event outcome. This can be considered as a cutpoint selection problem for a censored response partitioned with respect to two ordered categorical covariates and their interaction. The aim is to select the best grouping of the TN categories. A novel bootstrap cutpoint/model selection method is proposed for this task by maximizing bootstrap estimates of …

The Use Of A Ditopic Gd(Iii) Paramagnetic Probe For Investigating Α-Bungarotoxin Surface Accessibility, Andrea Bernini, Ottavia Spiga, Vincenzo Venditti, Filippo Prischi, Mauro Botta, Gianluca Croce, Angela Pui-Ling Tong, Wing-Talk Wong, Neri Niccolai

Vincenzo Venditti

Protein surface accessibility is a critical parameter which drives all intermolecular interaction processes. In this respect a big deal of information has been derived by analyzing paramagnetic perturbation profiles obtained from NMR protein spectra, particularly in the case that the effects due to different soluble paramagnets can be compared. Here Gd2L7, a neutral ditopic paramagnetic NMR probe, has been characterized in terms of structure and relaxivity and its paramagnetic perturbations on α-bungarotoxin CαH signals in 1H–13C HSQC (heteronuclear single quantum coherence) spectra have been analyzed. Then, these signal attenuations have been compared with the ones previously obtained in the presence …

An Efficient Protocol For Incorporation Of An Unnatural Amino Acid In Perdeuterated Recombinant Proteins Using Glucose-Based Media, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore

Vincenzo Venditti

The in vivo incorporation of unnatural amino acids into proteins is a well-established technique requiring an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is incorporated at a position encoded by a TAG amber codon. Although this technology provides unique opportunities to engineer protein structures, poor protein yields are usually obtained in deuterated media, hampering its application in the protein NMR field. Here, we describe a novel protocol for incorporating unnatural amino acids into fully deuterated proteins using glucose-based media (which are relevant to the production, for example, of amino acid-specific methyl-labeled proteins used in the study …

Conformational Selection And Substrate Binding Regulate The Monomer/Dimer Equilibrium Of The C-Terminal Domain Of Escherichia Coli Enzyme I, Vincenzo Venditti, G. Marius Clore

Vincenzo Venditti

The bacterial phosphotransferase system (PTS) is a signal transduction pathway that couples phosphoryl transfer to active sugar transport across the cell membrane. The PTS is initiated by the binding of phosphoenolpyruvate (PEP) to the C-terminal domain (EIC) of enzyme I (EI), a highly conserved protein that is common to all sugar branches of the PTS. EIC exists in a dynamic monomer/dimer equilibrium that is modulated by ligand binding and is thought to regulate the overall PTS. Isolation of EIC has proven challenging, and conformational dynamics within the EIC domain during the catalytic cycle are still largely unknown. Here, we present …

Health Effects Associated With Foreclosure: A Secondary Analysis Of Hospital Discharge Data, Nancy Menzel, Sheniz Moonie, Melva V. Thompson-Robinson

Nursing Faculty Publications

Objectives. The purpose of this study was to assess the health effects of high home foreclosure rates in an area of the United States of America and the utility of hospital discharge data for this purpose. Methods. We analyzed hospital discharge data from three postal zip codes using the principal diagnosis for 25 Diagnostic Related Groups associated with stress. Descriptive statistics were used to characterize hospital discharge rates for each condition by year and zip code. To test for differences across time, the Cochran-Armitage trend test was performed. Results. Most conditions did not demonstrate a statistical change between …

Santa Clara Magazine, Volume 54 Number 1, Summer 2012, Santa Clara University

Santa Clara Magazine

14 - BELLA VITA By Ron Hansen M.a. '95. After 66 years, Professor Victor Vari is retiring. He's imparted to generations of Santa Clara students an understanding of Italian language and culture-and how to live a beautiful life.

18 - THE SPORTING LIFE By Ann Killion. From when women first arrived on the Mission Campus 50 years ago and athletics was a dirty word-to internationally known programs and penalty shots heard 'round the world.

20 - RESPECT THE GAME By Britt Yap. They've been national champs and the subject of dreams-may-cometrue movies. But in the beginning, they were women who …

Santa Clara Magazine, Volume 54 Number 2, Fall 2012, Santa Clara University

Santa Clara Magazine

18 - WE, ROBOTS By John Deever. Adventures with the Robotics Systems Laboratory by land, sea, and sky. And in orbit.

20 - SARAH KATE WILSON VS. GODZILLA By Jeff Gire. Tackling big problems- like attracting more women to engineering and transferring mountains of data through the air.

22 - DELUGE AND DROUGHT By Erica Klarreich. Lessons in how to wedge more data into less space-and build a smarter energy grid.

24 - BUILDING BIOMEDICAL TESTS By Melissae Fellet. Where engineering meets biology, the work ranges from diagnosing voice disorders to tracking toxicity in the brain.

26 - THE LONG …

Santa Clara Magazine, Volume 53 Number 4, Spring 2012, Santa Clara University

Santa Clara Magazine

20 - WHAT WILL YOU BE? By David Mckay Wilson. San Francisco's Immaculate Conception Academy has found a work-study program that gives low-income students what they need. Starting with a bigger view of the world.

22 - BUCKY BRONCO CONFIDENTIAL By Jeff Gire And Sam Scott '96. Who wears the costume today may be classified information. But here are a few secrets revealed-including how Bucky came to be.

26 - TALKIN' DUST BOWL BLUES By David Mckay Wilson. The ghost of Woody Guthrie stalks the stage-with Rob Tepper '00 playing the role. This year marks the centennial of the iconic …

Measuring And Applying Data About Users In The Seton Hall Library, Rachel Volentine, Lisa M. Rose-Wiles, Carol Tenopir

Lisa M Rose-Wiles

We present data on how faculty and students at Seton Hall University use scholarly articles and books, how the library can present its findings to stakeholders, and how librarians can learn from these findings to better meet user needs. The data were gathered using questionnaire surveys of university faculty, graduate students, and undergraduate students as part of the IMLS Lib-Value project and based on Tenopir and King Studies conducted since 1977. Many questions used the critical incident of the last article and book reading to enable analysis of the characteristics of readings, in addition to characteristics of readers. Seton Hall’s …

Scholars Day Program Of Events 2012, Carl Goodson Honors Program

Scholars Day

The 2012 Scholars Day Program of Events lists the presenters and their papers, posters, recitals, theatre scenes, art shows, or theses.

Artl@ S And Basart: A Loose Coupling Strategy For Digital Humanities, Sorin Matei

Cyber Center Publications

The core ARTL@S digital humanities
strategy is that of loosely coupling
resources, platforms, and use scenarios.
A number of sites will feed from
the same geodatabase (BasArt),
which will be enriched by users with
new content. Inspired by the Web 2.0
design principles, ARTL@S relies on
the BasArt API, which will enable an
ecosystem of sites to use primary
data to generate their own maps,
charts, and tables. A variety of economic
models will also be used to
support the site, from free to paybased.
User-generated content will be
monitored by data management and
curation techniques that will ensure
the …

Efficient Error Correction For Next-Generation Sequencing Of Viral Amplicons, Pavel Skums, Zoya Dimitrova, David S. Campo, Gilberto Vaughan, Livia Rossi, Joseph C. Forbi, Jonny Yokosawa, Alexander Zelikovskiy, Yury Khudyakov

Computer Science Faculty Publications

Background: Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All …

Linus Pauling: Scientist Of The 20th Century, Laura Ward

Natural Sciences Student Research Presentations

This poster describes the contributions scientist Linus Pauling made to the fields of chemistry and molecular biology, including his hybridization theory.

Spotlight On Usc: A.C. Moore Herbarium, Allison Marsh

Section 2: Imaging the Microscopic

No abstract provided.

Observing The Minuscule, Allison Marsh

Section 2: Imaging the Microscopic

No abstract provided.

Bridging The Research Gap: Making Hri Useful To Individuals With Autism, Elizabeth Kim, Rhea Paul, Frederick Shic, Brian Scassellati

Communication Disorders Faculty Publications

While there is a rich history of studies involving robots and individuals with autism spectrum disorders (ASD), few of these studies have made substantial impact in the clinical research community. In this paper we first examine how differences in approach, study design, evaluation, and publication practices have hindered uptake of these research results. Based on ten years of collaboration, we suggest a set of design principles that satisfy the needs (both academic and cultural) of both the robotics and clinical autism research communities. Using these principles, we present a study that demonstrates a quantitatively measured improvement in human-human social interaction …

Evaluating Retention In Medical Care And Its Impact On The Health Outcomes Of Individuals Living With Human Inmmunodeficiency Virus, Timothy N. Crawford

Theses and Dissertations--Epidemiology and Biostatistics

In the last few years, engagement in medical care among individuals living with HIV has become a major priority among HIV medical providers and public health researchers. Engagement in medical care is an important concept as it involves the process of linking newly diagnosed individuals into medical care and retaining those individuals in care throughout the course of their infection. Although there have been major advances in the management of HIV, like the advent of Highly Active Antiretroviral Therapy, morbidity and mortality due to HIV cannot be fully reduced if the individual does not optimally retain in care. Retention in …

Cycles Of Electronic Health Records Adaptation By Physicians: How Do The Positive And Negative Experience With The Ehr System Affect Physicians' Ehr Adaptation Process?, Cherie Noteboom, Dhundy Bastola, Sajda Qureshi

Research & Publications

The integration of EHR in IT infrastructures supporting organizations enable improved access and recording of patient data, enhanced ability to make improved decisions, improved quality and reduced errors in patient care. Despite these benefits, there are mixed results as to the use of EHR. The literature suggests that the reasons for the limited use relate to policy, financial and usability considerations, but it does not provide an understanding of reasons for physicians’ limited interaction and adaptation of EHR.

Following an analysis of qualitative data, collected in a case study at a hospital using interviews, this research explains how physicians interact …

Authenticated Top-K Aggregation In Distributed And Authenticated Top-K Aggregation In Distributed And, Sunoh Choi, Hyo-Sang Lim, Elisa Bertino

Cyber Center Publications

Top-k queries have attracted interest in many different areas like network and system monitoring, information retrieval, sensor networks, and so on. Since today many applications issue top-k queries on distributed and outsourced databases,
authentication of top-k query results becomes more important. This paper addresses the problem of authenticated top-k aggregation queries (e.g. “find the k objects with the highest aggregate values”) in a distributed system. We propose a new algorithm, called Authenticated Three Phase Uniform Threshold (A-TPUT), which provides not only efficient top-k aggregation over distributed databases but also authentication on the top-k results. We also introduce several enhancements for …

Momentum 2012, Bryce Linden

Momentum

A journal of undergraduate research

Retrospective Evaluation Of Admissions For Chemotherapy-Inducednausea, Vomiting, And Dehydration, Katelin Van Leer Pharmad, Janine Barnaby Rph, Bcop

Department of Pharmacy

No abstract provided.

Eastern Ichigan University Graduate Catalog, 2012-2013, Office Of The Registrar

Graduate Catalogs

No abstract provided.

Eastern Michigan University Undergraduate Catalog, 2012-2013, Office Of The Registrar

Undergraduate Catalogs

No abstract provided.

Eastern Michigan University Undergraduate Catalog, 2012-2013, Office Of The Registrar

Undergraduate Catalogs

No abstract provided.