Physical Sciences and Mathematics Commons^™

Evaluating The Concordance Between Sequencing, Imputation And Microarray Genotype Calls In The Gaw18 Data, Ally Rogers, Andrew Beck, Nathan L. Tintle

Faculty Work Comprehensive List

Genotype errors are well known to increase type I errors and/or decrease power in related tests of genotypephenotype association, depending on whether the genotype error mechanism is associated with the phenotype. These relationships hold for both single and multimarker tests of genotype-phenotype association. To assess the potential for genotype errors in Genetic Analysis Workshop 18 (GAW18) data, where no gold standard genotype calls are available, we explored concordance rates between sequencing, imputation, and microarray genotype calls. Our analysis shows that missing data rates for sequenced individuals are high and that there is a modest amount of called genotype discordance between …

Genetic Analysis Workshop 18: Methods And Strategies For Analyzing Human Sequence And Phenotype Data In Members Of Extended Pedigrees, Heike Bickeboller, Julia N. Bailey, Joseph Beyene, Rita M. Cantor, Heather J. Cordell, Robert C. Culverhouse, Corinne D. Engelman, David W. Fardo, Saurabh Ghosh, Inke R. Konig, Justo Lorenzo Bermejo, Phillip E. Melton, Stephanie A. Santorico, Glen A. Satten, Lei Sun, Nathan L. Tintle, Andreas Ziegler, Jean W. Maccluer, Laura Almasy

Faculty Work Comprehensive List

Genetic Analysis Workshop 18 provided a platform for developing and evaluating statistical methods to analyze whole-genome sequence data from a pedigree-based sample. In this article we present an overview of the data sets and the contributions that analyzed these data. The family data, donated by the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples Consortium, included sequence-level genotypes based on sequencing and imputation, genome-wide association genotypes from prior genotyping arrays, and phenotypes from longitudinal assessments. The contributions from individual research groups were extensively discussed before, during, and after the workshop in theme-based discussion groups before being submitted …

Application Of Family-Based Tests Of Association For Rare Variants To Pathways, Brian Greco, Alexander Luedtke, Allison Hainline, Carolina Alvarez, Andrew Beck, Nathan L. Tintle

Faculty Work Comprehensive List

Pathway analysis approaches for sequence data typically either operate in a single stage (all variants within all genes in the pathway are combined into a single, very large set of variants that can then be analyzed using standard “gene-based” test statistics) or in 2-stages (gene-based p values are computed for all genes in the pathway, and then the gene-based p values are combined into a single pathway p value). To date, little consideration has been given to the performance of gene-based tests (typically designed for a smaller number of single-nucleotide variants [SNVs]) when the number of SNVs in the gene …

Inactivation Of Ascaris In Double-Vault Urine-Diverting Composting Latrines In Panama: Methods And Environmental Health Engineering Field Applications, Daragh A. Gibson

USF Tampa Graduate Theses and Dissertations

The United Nations Millennium Development Goals have prioritized improving access to sanitation, but unfortunately about a third of the global population is still without an improved sanitation source and one billion still practice open defecation. Lack of access to adequate and safe sanitation means the proliferation of dangerous pathogens in the environment, especially soil-transmitted helminths (STHs). In the Bocas del Toro Province of Panama (and similar locations in the world), composting latrines have been built in many of the indigenous communities in the area. They are a form of dry or ecological sanitation and are designed to produce an end …

A Non-Contrast Magnetic Resonance Imaging Technique To Assess Blood-Brain Barrier Permeability, Harini Pandithasekera

Electronic Thesis and Dissertation Repository

The Blood-brain barrier (BBB) regulates the entry of compounds between the blood and the brain, thus plays an important role in brain homeostasis. Studies indicate in disease states such as Alzheimer’s the BBB integrity is compromised. The motive of this project is to investigate the sensitivity of the diffusion-weighted arterial spin labeling (DW-ASL) technique to detect water exchange. Testing the sensitivity requires a reliable method of opening the barrier at specific locations of the brain. Here, a unique technology named focused ultrasound (FUS) has been used to mimic a compromised BBB environment.

A series of experiments were conducted in a …

Water And Health In The Nandamojo Watershed Of Costa Rica: Community Perceptions Towards Water, Sanitation, And The Environment, James Mcknight

USF Tampa Graduate Theses and Dissertations

Understanding the relationships between human health, water, sanitation, and environmental health is a requirement to understanding the challenges that face researchers when it comes to addressing global health relating to water and sanitation. Access to improved water and sanitation is not only a precondition to health, but to all aspects of daily living. Target 7.C of the Millennium Development Goals (MDGs) addresses worldwide disparities in access to improved water and sanitation by calling for the reduction in "half of the proportion of people without sustainable access to safe drinking water and sanitation by 2015". Over 90% of the population of …

Community Level Impacts Associated With The Invasion Of English Ivy (Hedera Spp.) In Forest Park: A Look At The Impacts Of Ivy On Community Composition And Soil Moisture, Sara Rose Copp

Dissertations and Theses

Invasive species degrade ecosystems by altering natural processes and decreasing the abundance and diversity of native flora. Communities with major fluctuations in resource supply allow invasive species to exploit limiting resources making the community prone to invasion. In the Pacific Northwest, urban forests characterized with limited light and seasonally limited soil moisture are being dominated by nonnative English ivy (Hedera spp). Three observational studies were conducted in the Southern end of Forest Park within the Balch Creek Subwatershed in Portland, Oregon in order to understand 1) how English ivy changes over three growing seasons, 2) how the native …

How Do Management Treatments Affect Invasive Cattail (Typha X Glauca) And Pore Water Nutrient Concentrations?, Yarency Rodriguez

DePaul Discoveries

Invasive species are problematic for wetland managers, but little is known about how common management treatments influence nutrient cycling or plant responses. This study tested three experimental treatments (mowing, herbiciding, and harvesting (i.e., removal of aboveground biomass)) on several response variables: wetland soil porewater nutrient content (NO₃^-, NH₄⁺, PO₄^-), native plant and invasive-Typha density, and light attenuation through the plant canopy. Seventeen days post-treatment, herbiciding resulted in higher porewater phosphate concentrations (55.63 µg-P/L) than harvesting (8.95 µg-P/L). After 24 days, herbicide had higher porewater phosphate concentration (72.03 µg-P/L) than all …

Vitamin D Status And Demographic And Lifestyle Determinants Among Adults In The United States (Nhanes 2001-2006), Yan Cao, Katie L. Callahan, Sreenivas P. Veeranki, Yang Chen, Ying Liu, Shimin Zheng

ETSU Faculty Works

This study looked at risk factors associated with vitamin D levels in the body among a representative sample of adults in the U.S., NHANES III (2001-2006) data were used to assess the relationship between several demographic and health risk factors and vitamin D levels in the body. The Baseline-Category Logit Model was used to test the association between vitamin D level and the potential risk factors age, education, ethnicity, poverty status, physical activity, smoking, alcohol, obesity, diabetes and total cholesterol with both genders. Vitamin D insufficiency and deficiency were significantly associated with age, race, education, physical activity, obesity, diabetes and …

Slides: Understanding The Impacts: Issues Of Research, Cindy Beeler

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Cindy Beeler, U.S. Environmental Protection Agency, Denver, CO

10 slides

Slides: Public Health Research On Near O&G Development: Challenges And Needs, John L. Adgate

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: John L. Adgate, PhD, MSPH, Professor and Chair, Department of Environmental and Occupational Health, University of Colorado

19 slides

Slides: Details Of The Regulatory Framework: Air Quality Regulation Of Oil And Gas Development, Olivia D. Lucas

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Olivia D. Lucas, Esq., Counsel, Faegre Baker Daniels

22 slides

Slides: Regulating Oil And Gas Emissions In The Denver Julesberg Basin, Garry Kaufman

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Garry Kaufman, Deputy Director, Colorado Air Pollution Control Division

25 slides

Slides: The Stronger State Review Process: Draft Air Quality Guideline, Bruce Baizel

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Bruce Baizel, Chair, STRONGER Board

17 slides

Slides: Colorado Home Rule And Fracking, Richard Collins

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Richard Collins, University of Colorado Law School

33 slides

Slides: Exploring New Frameworks Of Regulation: Negotiating Model Regulations, Mark K. Boling

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Mark K. Boling, President, Southwestern Energy

13 slides

Slides: Solutions For Responsible Shale Development, Steve D'Esposito, Richard Whitley

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenters: Steve D'Esposito, RESOLVE; Richard Whitley, RESOLVE

8 slides

Slides: What We Know (And Don't Know) About Air Quality Impacts Of Oil And Gas Development, Anna Karion

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Anna Karion, NOAA/ESRL, University of Colorado/CIRES

35 slides

Slides: The Efd Program: Addressing Environmental Issues And Increasing Environmental Awareness, Richard Haut

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Rich Haut, Houston Advanced Research Center

8 slides

Slides: What We Know (And Don’T Know) About The Effects Of Oil And Gas Development On Water Quality, Joseph N. Ryan

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Prof. Joe Ryan, University of Colorado Boulder, Environmental Engineering, AirWaterGas Sustainability Research Network, www.airwatergas.org

28 slides

Draft Genome Sequence Of Acetobacter Aceti Strain 1023, A Vinegar Factory Isolate, John Hung, Christopher Mill, Sandra Clifton, Vincent Magrini, Ketaki Bhide, Julie Francois, Aaron Ransome, Lucinda Fulton, Jyothi Thimmapuram, Richard Wilson, T. Joseph Kappock

Cyber Center Publications

The genome sequence of Acetobacter aceti 1023, an acetic acid bacterium adapted to traditional vinegar fermentation, comprises 3.0 Mb (chromosome plus plasmids). A. aceti 1023 is closely related to the cocoa fermenter Acetobacter pasteurianus 386B but possesses many additional insertion sequence elements.

Cytokine Production But Lack Of Proliferation In Peripheral Blood Mononuclear Cells From Chronic Chagas' Disease Cardiomyopathy Patients In Response To T. Cruzi Ribosomal P Proteins, Silvia A. Longhi, Augusto Atienza, Graciela Perez Prados, Alcinette Buying, Virginia Balouz, Carlos A. Buscaglia, Radleigh Santos, Laura M. Tasso, Ricardo Bonato, Pablo Chiale, Clemencia Pinilla, Valeria A. Judkowski, Karina A. Gomez

Mathematics Faculty Articles

Background

Trypanosoma cruzi ribosomal P proteins, P2β and P0, induce high levels of antibodies in patients with chronic Chagas' disease Cardiomyopathy (CCC). It is well known that these antibodies alter the beating rate of cardiomyocytes and provoke apoptosis by their interaction with β1-adrenergic and M2-muscarinic cardiac receptors. Based on these findings, we decided to study the cellular immune response to these proteins in CCC patients compared to non-infected individuals.

Methodology/Principal findings

We evaluated proliferation, presence of surface activation markers and cytokine production in peripheral blood mononuclear cells (PBMC) stimulated with P2β, the C-terminal portion of P0 (CP0) proteins and T. …

Characterization Of Methylene Diphenyl Diisocyanate Protein Conjugates, Morgen Mhike

Dissertations and Theses

Diisocyanates (dNCO) such as methylene diphenyl diisocyanate (MDI) are used primarily as cross-linking agents in the production of polyurethane products such as paints, elastomers, coatings and adhesives, and are the most frequently reported cause of chemically induced immunologic sensitization and occupational asthma (OA). Immune mediated hypersensitivity reactions to dNCOs include allergic rhinitis, asthma, hypersensitivity pneumonitis and allergic contact dermatitis.

There is currently no simple diagnosis for the identification of dNCO asthma due to the variability of symptoms and uncertainty regarding the underlying mechanisms. Immunological sensitization due to dNCO exposure is traditionally thought to require initial conjugation of the dNCO to …

Agenda: Water And Air Quality Issues In Oil And Gas Development: The Evolving Framework Of Regulation And Management, University Of Colorado Boulder. Getches-Wilkinson Center For Natural Resources, Energy, And The Environment, University Of Colorado Boulder. Airwatergas Sustainability Research Network

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

This Conference is presented by the Getches-Wilkinson Center for Natural Resources, Energy, and the Environment, in conjunction with the Air-Water-Gas Sustainability Research Network. Technological advances for extracting oil and gas from shale deposits have ushered in a new era of energy development in key resource-rich pockets throughout the US. In this event, we review the ongoing efforts of governments and industry to develop the regulatory and management practices necessary to protect water and air resources, drawing on the latest scientific research to tackle areas of uncertainty and to inform future action.

Slides: Framing The Discussion: Issues Of Uncertainty, Terminology, And Sensitivity, Patty Limerick

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Patty Limerick, University of Colorado

22 slides

Slides: Propublica Coverage Pavillion, Wy, Abrahm Lustgarten

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Abrahm Lustgarten, ProPublica

19 slides

Slides: Experience On The Ground, Part Two: Water Use In The Marcellus, Susan Packard Legros

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Susan Packard LeGros, President & Executive Director, Center for Sustainable Shale Development (CSSD)

16 slides

Slides: Groundwater Protection Council, Steven P. Musick

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Steven P. Musick, P.G., Groundwater Protection Council

11 slides

Slides: Session 2, Water Supply And Quality: The Regulatory Framework, Richard E. Schwartz

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Richard E. Schwartz, Crowell & Moring LLP

38 slides

Slides: Industry Growth And Change, Stuart Ellsworth

Water and Air Quality Issues in Oil and Gas Development: The Evolving Framework of Regulation and Management (Martz Summer Conference, June 5-6)

Presenter: Stuart Ellsworth, P.E., Engineering Manager, Colorado Oil & Gas Conservation Commission

33 slides