Medicine and Health Sciences Commons^™

Manifest Greatness Version5 By Marc Guerrero With Tato Malay, Emmanuel Mario B. Santos Aka Marc Guerrero

Emmanuel Mario B Santos aka Marc Guerrero

MANIFEST GREATNESS version5 by Marc Guerrero with Tato Malay

Manifest Greatness Version3 By Marc Guerrero With Jay Fajardo, Emmanuel Mario B. Santos Aka Marc Guerrero

Emmanuel Mario B Santos aka Marc Guerrero

MANIFEST GREATNESS version3 by Marc Guerrero with Jay Fajardo

Manifest Greatness Version2 With Danielle Van Asch-Prevot, Emmanuel Mario B. Santos Aka Marc Guerrero

Emmanuel Mario B Santos aka Marc Guerrero

MANIFEST GREATNESS version2 by Marc Guerrero with Danielle van Asch-Prevot

Manifest Greatness... Panahon Ng Mga Filipino Ang 21st Century: Ang Asian Century (Ang Pagpapanumbalik Sa Likas Na Karangalan Ng Lahat Ng Filipino Sa Buong Mundo), Emmanuel Mario B. Santos Aka Marc Guerrero

Emmanuel Mario B Santos aka Marc Guerrero

MANIFEST GREATNESS Panahon ng mga Filipino ang 21st century: Ang Asian Century (Ang pagpapanumbalik sa likas na Karangalan ng lahat ng Filipino sa buong mundo) Manifest Greatness is a work-in-progress Manifesto of, for and by Filipino citizens of the world in synergy with foreign national friends of the Filipino people worldwide in pursuit of genuine entrepreneurial wisdom

Multiple Loci Within The Major Histocompatibility Complex Confer Risk Of Psoriasis, Bing-Jian Feng, Liang-Dan Sun, Razieh Soltani-Arabshahi, Anne M. Bowcock, Rajan P. Nair, Philip Stuart, James T. Elder, Steven J. Schrodi, Ann B. Begovich, Goncalo R. Abecasis, Xue-Jun Zhang, Kristina P. Callis Duffin, Gerald G. Krueger, David E. Goldgar

Steven J Schrodi

Psoriasis is a common inflammatory skin disease characterized by thickened scaly red plaques. Previously we have performed a genome-wide association study (GWAS) on psoriasis with 1,359 cases and 1,400 controls, which were genotyped for 447,249 SNPs. The most significant finding was for SNP rs12191877, which is in tight linkage disequilibrium with HLA-Cw*0602, the consensus risk allele for psoriasis. However, it is not known whether there are other psoriasis loci within the MHC in addition to HLA-C. In the present study, we searched for additional susceptibility loci within the human leukocyte antigen (HLA) region through in-depth analyses of the GWAS data; …

E-Science @ Umass: Anticipating And Supporting E-Science Activities At The University Of Massachusetts, Maxine G. Schmidt, Rebecca Reznik-Zellen

Maxine G Schmidt

In March of 2008 an Ad Hoccommittee of Science Librarians from the University of Massachusetts Five Campus System convened to discuss the challenges of e-science and prepare the Libraries for their role in e-science initiatives. Three primary outcomes intended to support e-science activities emerged from the work of the Ad Hoc committee.

Regression When The Predictors Are Images, Philip T. Reiss

Philip T. Reiss

No abstract provided.

Smoothing Parameter Selection For A Class Of Semiparametric Linear Models, Philip T. Reiss, R. Todd Ogden

Philip T. Reiss

Spline-based approaches to nonparametric and semiparametric regression, as well as to regression of scalar outcomes on functional predictors, entail choosing a parameter controlling the extent to which roughness of the fitted function is penalized. In this paper we demonstrate that the equations determining two popular methods for smoothing parameter selection, generalized cross-validation and restricted maximum likelihood, share a similar form that allows us to prove several results common to both, and to derive a condition under which they yield identical values. These ideas are illustrated by application of functional principal component regression, a method for regressing scalars on functions, to …

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 …

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.

Alamethicin In Lipid Bilayers: Combined Use Of X-Ray Scattering And Md Simulations, Jianjun Pan, D. Peter Tieleman, John F. Nagle, Norbert Kučerka, Prof. Stephanie Tristram-Nagle Ph.D.

Prof. Stephanie Tristram-Nagle Ph.D.

We study fully hydrated bilayers of two di-monounsaturated phospholipids diC18:1PC (DOPC) and diC22:1PC with varying amounts of alamethicin (Alm). We combine the use of X-ray diffuse scattering and molecular dynamics simulations to determine the orientation of alamethicin in model lipids. Comparison of the experimental and simulated form factors shows that Alm helices are inserted transmembrane at high humidity and high concentrations, in agreement with earlier results. The X-ray scattering data and the MD simulations agree that membrane thickness changes very little up to 1/10 Alm/ DOPC. In contrast, the X-ray data indicate that the thicker diC22:1PC membrane thins with added …

Evaluation Of Heterogeneity In Pharmacotherapy Trials For Drug Dependence: A Bayesian Approach, Charles E. Green, F. G. Moeller, J. M. Schmitz, Joseph F. Lucke, S. D. Lane, A. C. Swann, Robert E. Lasky, Joseph P. Carbonari

Joseph Lucke

Difficulty identifying effective pharmacotherapies for cocaine dependence has led to suggestions that subgroup differences may account for some of the heterogeneity in treatment response. Well-attested methodologicalifficulties associated with these analyses recommend the use of Bayesian statistical reasoning for evaluation of salient interaction effects.

Methods: A secondary data analysis of a previously published, double-blind, randomized controlled trial examines the interaction of decision-making, as measured by the Iowa Gambling Task, and citalopram in increasing longest sustained abstinence from cocaine use.

Results: Bayesian analysis indicated that there was a 99% chance that improved decision-making enhances response to citalopram. Given the strong positive nature …

When To Spray: A Time-Scale Calculus Approach To Controlling The Impact Of West Nile Virus, Diana Thomas, Marion Weedermann, Lora Billings, Joan Hoffacker, Robert A. Washington-Allen

Lora Billings

Should Biomarker Estimates Of Hiv Incidence Be Adjusted?, Ron Brookmeyer

Ron Brookmeyer

Objective: To evaluate adjustment procedures that have been proposed to correct HIV incidence rates derived from cross-sectional surveys of biomarkers (BED). These procedures were motivated by some reports that the biomarker BED approach overestimates incidence when compared to cohort studies.

Design: Considered the Hargrove and McDougal adjustment procedures that adjust biomarker estimates of HIV incidence rates for misclassification with respect to the timing of infections.

Methods: Performed mathematical and statistical analysis of the adjustment formulas. Evaluated sources of error in cohort studies of incidence that could also explain discrepancies between cohort and biomarker estimates.

Results: The McDougal adjustment has no …

The Effects Of Herd Immunity On The Power Of Vaccine Trials, Blake Charvat, Ron Brookmeyer, Jay Herson

Ron Brookmeyer

We evaluate the effects of herd immunity on the power of vaccine trials. We consider large-scale trials in which persons are individually randomized to either placebo or vaccine. We evaluate the adequacy of naive power calculations that ignore the effects of herd immunity such as those based on the comparison of two independent binomials. We developed a simulation design to evaluate the quantitative effects of herd immunity on power. The simulation design accounted for nonhomogeneous mixing. We found that naive power calculations that ignore the effects of herd immunity can seriously overestimate power. In fact, we found that as sample …

Genome-Wide Scan Reveals Association Of Psoriasis With Il-23 And Nf-B Pathways, Rajan P. Nair, Kristina C. Duffin, Cynthia Helms, Jun Ding, Philip E. Stuart, David Goldgar, Johann E. Gudjonsson, Yun Li, Trilokraj Tejasvi, Bing-Jiag Feng, Andreas Ruether, Stefan Schreiber, Michael Weichenthal, Dafna Gladman, Proton Rahman, Steven J. Schrodi, Sampath Prahalad, Stephen L. Guthery, Judith Fischer, Wilson Liao, Pui-Yan Kwok, Alan Menter, G Mark Lathrop, Carol A. Wise, Ann B. Begovich, John J. Voorhees, James T. Elder, Gerald G. Krueger, Anne M. Bowcock, Goncalo R. Abecasis

Steven J Schrodi

Psoriasis is a common immune-mediated disorder that affects the skin, nails and joints. To identify psoriasis susceptibility loci, we genotyped 438,670 SNPs in 1,409 psoriasis cases and 1,436 controls of European ancestry. We followed up 21 promising SNPs in 5,048 psoriasis cases and 5,041 controls. Our results provide strong support for the association of at least seven genetic loci and psoriasis (each with combined P < 5 10-8). Loci with confirmed association include HLA-C, three genes involved in IL-23 signaling (IL23A, IL23R, IL12B), two genes that act downstream of TNF- and regulate NF-B signaling (TNIP1, TNFAIP3) and two genes involved in the modulation of Th2 immune responses (IL4, IL13). Although the proteins encoded in these loci are known to interact biologically, we found no evidence for epistasis between associated SNPs. Our results expand the catalog of genetic loci implicated in psoriasis susceptibility and suggest priority targets for study in other auto-immune disorders.

A Fine Mapping Theorem To Refine Results From Association Genetics Studies, Steven J. Schrodi

Steven J Schrodi

No abstract provided.

Bayesian Statistics, Joseph F. Lucke

Joseph Lucke

No abstract provided.

Characterization Of Unknown Genetic Modifications Using High Throughput Sequencing And Computational Subtraction, Torstein Tengs

Dr. Torstein Tengs

Background

When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown.

Results

We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of …