Physical Sciences and Mathematics Commons^™

Targeted Methods For Biomarker Discovery, The Search For A Standard, Catherine Tuglus, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

More often than not biomarker studies analyze large quantities of variables with complicated and generally unknown correlation structure. There are numerous statistical methods which attempt to unravel these variables and determine the underlying mechanism through identification of causally related biomarkers. Results from these methods are generally difficult to interpret and nearly impossible to compare across studies. The FDA has currently called for a standardization of methods and protocol for biomarker detection. In response, we propose targeted variable importance (tVIM) as a standardized method for biomarker discovery. Through the use of targeted Maximum Likelihood, tVIM provides double robust estimates of variable …

A Delphi Study Assessing Long-Term Access To Electronic Medical Records (Emr), Byron D. Nicholson

Theses and Dissertations

This research effort addressed the issue of long-term access to electronic medical records as technological generations become obsolete, thereby preventing the access to patient health information. Using the Delphi methodology, experts with experience in electronic medical records and applicable systems provided insight based on their years of hands-on experience managing and/or using records and these systems. The end result of this research was a collection of ideas that medical institutions and medical informaticians must consider to ensure that patients and hospitals do not lose long-term access to electronic medical records as electronic medical records and technology continually evolves. Results of …

Inside Unlv, Shane Bevell, Donna Mcaleer, David Ashley, Grace Russell, Michelle Mouton, Mamie Peers

Inside UNLV

No abstract provided.

Prostate Segmentation On Pelvic Ct Images Using A Genetic Algorithm, Payel Ghosh, Melanie Mitchell

Computer Science Faculty Publications and Presentations

A genetic algorithm (GA) for automating the segmentation of the prostate on pelvic computed tomography (CT) images is presented here. The images consist of slices from three-dimensional CT scans. Segmentation is typically performed manually on these images for treatment planning by an expert physician, who uses the “learned” knowledge of organ shapes, textures and locations to draw a contour around the prostate. Using a GA brings the flexibility to incorporate new “learned” information into the segmentation process without modifying the fitness function that is used to train the GA. Currently the GA uses prior knowledge in the form of texture …

Marginal Structural Models For Partial Exposure Regimes, Stijn Vansteelandt, Karl Mertens, Carl Suetens, Els Goetghebeur

Harvard University Biostatistics Working Paper Series

Intensive care unit (ICU) patients are ell known to be highly susceptible for nosocomial (i.e. hospital-acquired) infections due to their poor health and many invasive therapeutic treatments. The effects of acquiring such infections in ICU on mortality are however ill understood. Our goal is to quantify these effects using data from the National Surveillance Study of Nosocomial Infections in Intensive Care

Units (Belgium). This is a challenging problem because of the presence of time-dependent confounders (such as exposure to mechanical ventilation)which lie on the causal path from infection to mortality. Standard statistical analyses may be severely misleading in such settings …

Microproteomics: Analysis Of Protein Diversity In Small Samples, Howard B. Gutstein, Jeffrey S. Morris, Suresh P. Annangudi, Jonathan V. Sweedler

Jeffrey S. Morris

Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The …

Comment On Global Dynamics Of Biological Systems, Radhakrishnan Nagarajan

Radhakrishnan Nagarajan

No abstract provided.

C–N Bond Rotation And E–Z Isomerism In Some N-Benzyl-N-Methylcarbamoyl Chlorides: A Dft Study, Michael Horwath, Vladimir Benin

Chemistry Faculty Publications

The current report presents the first theoretical study of the restricted CN bond rotation in carbamoyl chlorides. Several N-benzyl-N-methylcarbamoyl chlorides were investigated, with varying pattern of substitution in the aromatic ring. Optimizations and frequency calculations were conducted employing DFT at the B3LYP/6-31+G(d) level of theory. Each of the studied structures exhibits a pair of rotamers (s-Z and s-E), generated upon rotation around the C(O)N bond. The s-E isomer is the global minimum in every case, but the preference for it is usually less than 1 kcal/mol. Two possible transition state structures were identified …

Infant Feeding Decisions Among Pregnant Black Wic Participants And The Role Of Peer Support, Astrid D. Mickens

Loma Linda University Electronic Theses, Dissertations & Projects

The purpose of this study was to identify the important factors that impact infant feeding decisions among Black women, and to determine whether peer support influences the relationship among theoretical constructs of the social learning theory. A convenience sample of 110 Black pregnant women, ages 18-45, attending Women, Infant and Children (WIC) clinics throughout Riverside and San Bernardino Counties were recruited to participate in the study through the Nutrition Services Department. Eligible participants included pregnant Black WIC clients in any stage of pregnancy.

The survey questions contained information about perceived support, cognitive knowledge, abilities and beliefs regarding breastfeeding. The goal …

The Expression Of Microrna Mir-107 Decreases Early In Alzheimer's Disease And May Accelerate Disease Progression Through Regulation Of Β-Site Amyloid Precursor Protein-Cleaving Enzyme 1, Wang-Xia Wang, Bernard W. Rajeev, Arnold J. Stromberg, Na Ren, Guiliang Tang, Qingwei Huang, Isidore Rigoutsos, Peter T. Nelson

Sanders-Brown Center on Aging Faculty Publications

MicroRNAs (miRNAs) are small regulatory RNAs that participate in posttranscriptional gene regulation in a sequence-specific manner. However, little is understood about the role(s) of miRNAs in Alzheimer's disease (AD). We used miRNA expression microarrays on RNA extracted from human brain tissue from the University of Kentucky Alzheimer's Disease Center Brain Bank with near-optimal clinicopathological correlation. Cases were separated into four groups: elderly nondemented with negligible AD-type pathology, nondemented with incipient AD pathology, mild cognitive impairment (MCI) with moderate AD pathology, and AD. Among the AD-related miRNA expression changes, miR-107 was exceptional because miR-107 levels decreased significantly even in patients with …

The T-Mixture Model Approach For Detecting Differentially Expressed Genes In Microarrays, Shuo Jiao, Shunpu Zhang

Shuo Jiao

The finite mixture model approach has attracted much attention in analyzing microarray data due to its robustness to the excessive variability which is common in the microarray data. Pan (2003) proposed to use the normal mixture model method (MMM) to estimate the distribution of a test statistic and its null distribution. However, considering the fact that the test statistic is often of t-type, our studies find that the rejection region from MMM is often significantly larger than the correct rejection region, resulting an inflated type I error. This motivates us to propose the t-mixture model (TMM) approach. In this paper, …

Mapping As A Knowledge Translation Tool For Ontario Early Years Centres: Views From Data Analysts And Managers, Anita Kothari, S. Michelle Driedger, Julia Bickford, Jason Morrison, Michael Sawada, Ian D. Graham, Eric Crighton

Anita Kothari

Background: Local Ontario Early Years Centres (OEYCs) collect timely and relevant local data, but knowledge translation is needed for the data to be useful. Maps represent an ideal tool to interpret local data. While geographic information system (GIS) technology is available, it is less clear what users require from this technology for evidence-informed program planning. We highlight initial challenges and opportunities encountered in implementing a mapping innovation (software and managerial decision-support) as a knowledge translation strategy.

Methods: Using focus groups, individual interviews and interactive software development events, we taped and transcribed verbatim our interactions with nine OEYCs in Ontario, Canada. …

In Situ Measurement Of Three-Dimensional Ion Densities In Focused Femtosecond Pulses, James Strohaber, Cornelis J. Uiterwaal

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

We image spatial distribution of xenon ions in the focus of a laser beam of ultrashort, intense pulses in all three dimensions, with a resolution of three by twelve microns in the two transverse directions. This allows for studying ionization processes without spatially averaging ion yields. Our in situ ion imaging is also useful to analyze focal intensity profiles and to investigate the transverse modal purity of tightly focused beams of complex light. As an example, the intensity profile of a Hermite-Gaussian beam mode HG recorded with ions is found to be in good agreement with optical images.

Estimation Of Controlled Direct Effects, Sylvie Goetgeluk, Stijn Vansteelandt, Els Goetghebeur

Harvard University Biostatistics Working Paper Series

No abstract provided.

A Spatial Sirs Boolean Network Model For The Spread Of H5n1 Avian Influenza Virus Among Poultry Farms, Alexander Kasyanov, Leona Kirkland, Mihaela Teodora Matache

Mathematics Faculty Proceedings & Presentations

To predict the spread of Avian Influenza we propose a synchronous Susceptible-Infected-Recovered-Susceptible (SIRS) Boolean network of poultry farms, using probabilistic Boolean rules. Gravity models from transportation theory are used for the probability of infection of a node in one time step, taking into account farm sizes, distances be- tween farms, and mean distance travelled by birds. Basic reproduction numbers are computed analytically and numerically. The dynamics of the network are analyzed and various statistics considered such as number of infected nodes or time until eradication of the epidemic. We conclude that mostly when large farms (eventually) become infected the epidemic …

A Comparison Of Different Methods For Predicting Cancer Mortality Counts At The State Level, Corinne Wilson

Virginia Journal of Science

Cancer is a major health issue in the United States. Reliable estimates of yearly cancer mortality counts are essential for resourcing and planning. The American Cancer Society has used several methods of forecasting to estimate the future cancer burden and researchers are continually working to develop new methods with improved performance. There have been studies comparing different models for predicting the US cancer mortality counts. This study explores and compares several different models for cancer mortality count predictions at the state level, principally for the state of Virginia. Results of the comparisons appear to show the final improved model to …

A Watershed Analysis Of Pattee Pond: Implications For Water Quality And Land Use Management, Problems In Environmental Science Course (Biology 493), Colby College, Colby Environmental Assessment Team, Colby College

Colby College Watershed Study: Pattee Pond (2008, 1992)

The Colby Environmental Assessment Team (CEAT) investigated the impact of land use patterns on the water quality of Pattee Pond in Winslow, Maine, during the summer and fall of 2008. Physical, chemical, and biological characteristics of water quality were analyzed to evaluate the current health of the lake. Data collected were compared with previous studies conducted by the Maine Department of Environmental Protection (DEP) and CEAT to examine changes in water quality and land use over time. Trends in Pattee Pond water quality suggest an improvement since the 1970s. However, the lake is still experiencing algal blooms resulting from phosphorus …

Effects, Uptake, And Fate Of 2,4,6-Trinitrotoluene Aged In Soil In Plants And Worms, Elly Ph Best, Henry E. Tatem, Kaaren N. Geter, Melissa L. Wells, Brian K. Lane

US Army Corps of Engineers

The present study was aimed at providing data to be used at predicting exposure-based effects of 2,4,6-trinitrotoluene (TNT) aged in soil on endpoint organisms representing two trophic levels. These data can be used to define criteria or reference values for environmental management and conducting specific risk assessment. Long-term exposure tests were conducted to evaluate sublethal toxicity and uptake of aged soil-based explosives, with TNT as the main contaminant. In these tests, plants were exposed for 55 d, and biomass and explosives residues were determined. Worms were exposed for 28 and 42 d, and biomass, number, and tissue residues were determined. …

Droid: The Drosophila Interactions Database, A Comprehensive Resource For Annotated Gene And Protein Interactions, Jingkai Yu, Svetlana Pacifico, Guozhen Liu, Russell L. Finley Jr

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computational approaches, and literature mining methods. Quick and efficient access to this data has become a critical issue for biologists. Several excellent multi-organism databases for gene and protein interactions are available, yet most of these have understandable difficulty maintaining comprehensive information for any one organism. No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster. …

Software For Fitting Hierarchical Spatial Functional Models, Veera Baladandayuthapani

Veera Baladandayuthapani

No abstract provided.

Direct Effect Models, Mark J. Van Der Laan, Maya L. Petersen

Maya Petersen

The causal effect of a treatment on an outcome is generally mediated by several intermediate variables. Estimation of the component of the causal effect of a treatment that is not mediated by an intermediate variable (the direct effect of the treatment) is often relevant to mechanistic understanding and to the design of clinical and public health interventions. Robins, Greenland and Pearl develop counterfactual definitions for two types of direct effects, natural and controlled, and discuss assumptions, beyond those of sequential randomization, required for the identifiability of natural direct effects. Building on their earlier work and that of others, this article …

Characterizing Pharmacy And Medical Claims For A Private Insurance Polypharmacy Population, Brian W. Bresnahan, Kent M. Koprowicz, Sanchita Roy Choudhury, Louis P. Garrison, Ed Wong

Kent M Koprowicz

Objectives: To describe and characterize a group of private insurance members taking multiple medications over a one-year period. Methods: Persons were selected for this polypharmacy analysis if they had at least five unique maintenance prescriptions in their pharmacy claims records for the period of January-March 2005, based on a customized list of chronic medications. The full set of pharmacy and medical claims for these members were evaluated for a twelve month period, October 2004 to September 2005. Standard descriptive statistics were calculated to characterize the population. Logistic regression models were used to assess the association of pharmacy claims and “safety …

Multiple Testing Procedures Under Confounding, Debashis Ghosh

Debashis Ghosh

While multiple testing procedures have been the focus of much statistical research, an important facet of the problem is how to deal with possible confounding. Procedures have been developed by authors in genetics and statistics. In this chapter, we relate these proposals. We propose two new multiple testing approaches within this framework. The first combines sensitivity analysis methods with false discovery rate estimation procedures. The second involves construction of shrinkage estimators that utilize the mixture model for multiple testing. The procedures are illustrated with applications to a gene expression profiling experiment in prostate cancer.

Joint Variable Selection And Classification With Immunohistochemical Data, Debashis Ghosh, Ratna Chakrabarti

Debashis Ghosh

To determine if candidate cancer biomarkers have utility in a clinical setting, validation using immunohistochemical methods is typically done. Most analyses of such data have not incorporated the multivariate nature of the staining profiles. In this article, we consider modelling such data using recently developed ideas from the machine learning community. In particular, we consider the joint goals of feature selection and classification. We develop esti- mation procedures for the analysis of immunohistochemical profiles using the least absolute selection and shrinkage operator. These lead to novel and flexible models and algorithms for the analysis of compositional data. The techniques are …

An Improved Model Averaging Scheme For Logistic Regression, Debashis Ghosh, Zheng Yuan

Debashis Ghosh

Recently, penalized regression methods have attracted much attention in the statistical literature. In this article, we argue that such methods can be improved for the purposes of prediction by utilizing model averaging ideas. We propose a new algorithm that combines penalized regression with model averaging for improved prediction. We also discuss the issue of model selection versus model averaging and propose a diagnostic based on the notion of generalized degrees of freedom. The proposed methods are studied using both simulated and real data.

Measuring The Dynamic Surface Accessibility Of Rna With The Small Paramagnetic Molecule Tempol, Vincenzo Venditti, Neri Niccolai, Samuel E. Butcher

Vincenzo Venditti

The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible surface of RNA using NMR and the small paramagnetic molecule TEMPOL. We investigated two RNAs with known structures, one that is extremely stable and one that is dynamic. For helical regions, the TEMPOL probing data correlate well with the predicted RNA surface, and the method is able to distinguish subtle variations in atom …

Important, But Odd And Obscure, Reasons To Use The Library, Maxine G. Schmidt

Maxine G Schmidt

No abstract provided.

Santa Clara Magazine, Volume 50 Number 3, Winter 2008, Santa Clara University

Santa Clara Magazine

12 - ONE GOLD...AND A HOST OF MEMORIES By Ann Killion. A Beijing Olympic scrapbook.

16 - GOD AND WOMAN AT YALE By Steven Boyd Saum. For more than 300 years, the role of Yale University’s chaplain has never been filled by a woman, a layperson, or a Catholic—until now. Meet Sharon M. K. Kugler ’81.

20 - WITH RENEWED VIGOR AND ZEAL By Michael G. Boughton, S.J. How six decrees define the mission of the Society of Jesus in the years to come.

22 - LIBERTY AND THE PURSUIT By Michael S. Malone ’75, MBA ’77. Without meaning to, …

Photochemical Studies Of Nutraceuticals In The Presence Of Cyclodextrins, Zlata Tofzikovskaya, Christine O'Connor, Mary Mcnamara

Conference Papers

The photostability studies of Folic acid and Menadione Sodium Bisulfite, also known as vitamin K3, were carried out in their aqueous solutions at room temperature. Solutions of Folic acid ( 4.8 x 10-5 M) and Menadione Sodium Bisulfite (4.0 x 10-4 M) were exposed to ultraviolet radiation at a wavelength of 365 nm. During exposure absorbance of both solutions was measured using a Perkin Elmer Lamda 900 UV/VIS/NIR Spectrometer. During the stability tests it was noted that addition of β Cyclodextrin (1:1 ratio) to aqueous solutions containing the vitamin slowed down the photodegradation process. The unique shape of Cyclodextrins allows …

In-Vivo Delivery Of Dna Vaccines Using Metallo-Lipid Nanoparticles, Clarissa Sara Gomez

Open Access Theses & Dissertations

There has been a rapidly growing area of research in the design and synthesis of molecules that self-organize in water to form functional nanosystems and due to the high interest in the area metal ligand complexes were tested as drug delivery systems with a Leishmania vaccine. Herein, we present the design, synthesis and functional activity of Cu(II) and Zn(II) complexes that self-assemble in water to form spherical nanoscale structures that exhibit an affinity to bind DNA and deliver it into eukaryotic cells with a high percent efficiency in-vitro. In order to assess the effectiveness of these nanoparticles to deliver DNA …