Digital Commons Network^™

Comparing Performance Of Non-Tree-Based And Tree-Based Association Mapping Methods, Katherine L. Thompson, David W. Fardo

Statistics Faculty Publications

A central goal in the biomedical and biological sciences is to link variation in quantitative traits to locations along the genome (single nucleotide polymorphisms). Sequencing technology has rapidly advanced in recent decades, along with the statistical methodology to analyze genetic data. Two classes of association mapping methods exist: those that account for the evolutionary relatedness among individuals, and those that ignore the evolutionary relationships among individuals. While the former methods more fully use implicit information in the data, the latter methods are more flexible in the types of data they can handle. This study presents a comparison of the 2 …

On Combining Family- And Population- Based Sequencing Data, Yuriko Katsumata, David W. Fardo

Biostatistics Faculty Publications

Several statistical group-based approaches have been proposed to detect effects of variation within a gene for each of the population- and family-based designs. However, unified tests to combine gene-phenotype associations obtained from these 2 study designs are not yet well established. In this study, we investigated the efficient combination of population-based and family-based sequencing data to evaluate best practices using the Genetic Analysis Workshop 19 (GAW19) data set. Because one design employed whole genome sequencing and the other whole exome sequencing, we examined variants overlapping both data sets. We used the family-based sequence kernel association test (famSKAT) to analyze the …

Causal Effect Estimation In Sequencing Studies: A Bayesian Method To Account For Confounder Adjustment Uncertainty, Chi Wang, Jinpeng Liu, David W. Fardo

Biostatistics Faculty Publications

Estimating the causal effect of a single nucleotide variant (SNV) on clinical phenotypes is of interest in many genetic studies. The effect estimation may be confounded by other SNVs as a result of linkage disequilibrium as well as demographic and clinical characteristics. Because a large number of these other variables, which we call potential confounders, are collected, it is challenging to select and adjust for the variables that truly confound the causal effect. The Bayesian adjustment for confounding (BAC) method has been proposed as a general method to estimate the average causal effect in the presence of a large number …

A Thermodynamic Description Of The Adsorption Of Simple Water-Soluble Peptoids To Silica, Anna L. Calkins, Jennifer Yin, Jacenda L. Rangel, Madeleine R. Landry, Amelia A. Fuller, Grace Y. Stokes

Chemistry and Biochemistry

The first report of a water-soluble peptoid adsorbed to silica monitored by second harmonic generation (SHG) at the liquid/solid interface is presented here. The molecular insights gained from these studies will inform the design and preparation of novel peptoid coatings. Simple 6- and 15-residue peptoids were dissolved in phosphate buffered saline and adsorbed to bare silica surfaces. Equilibrium binding constants and relative surface concentrations of adsorbed peptoids were determined from fits to the Langmuir model. Complementary fluorescence spectroscopy studies were used to quantify the maximum surface excess. Binding constants, determined here by SHG, were comparable to those previously reported for …

A Framework For Hybrid Intrusion Detection Systems, Robert N. Bronte

Master of Science in Information Technology Theses

Web application security is a definite threat to the world’s information technology infrastructure. The Open Web Application Security Project (OWASP), generally defines web application security violations as unauthorized or unintentional exposure, disclosure, or loss of personal information. These breaches occur without the company’s knowledge and it often takes a while before the web application attack is revealed to the public, specifically because the security violations are fixed. Due to the need to protect their reputation, organizations have begun researching solutions to these problems. The most widely accepted solution is the use of an Intrusion Detection System (IDS). Such systems currently …

Sources, Distributions, And Dynamics Of Dissolved Organic Matter In The Canada And Makarov Basins, Yuan Shen, Ronald Benner, Lisa Robbins, Jonathan Wynn

Faculty Publications

A comprehensive survey of dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) was conducted in the Canada and Makarov Basins and adjacent seas during 2010–2012 to investigate the dynamics of dissolved organic matter (DOM) in the Arctic Ocean. Sources and distributions of DOM in polar surface waters were very heterogeneous and closely linked to hydrological conditions. Canada Basin surface waters had relatively low DOC concentrations (69 ± 6 μmol L−1), CDOM absorption (a325: 0.32 ± 0.07 m−1) and CDOM-derived lignin phenols (3 ± 0.4 nmol L−1), and high spectral slope values (S275–295: 31.7 ± …

Detecting Conceptual Change With Latent Transition Analysis, Glen Davenport

Doctoral Dissertations

To uphold the core premise of cognitive diagnostic assessment, it is necessary to align different aspects of assessment design. The structure of the test, the measurement model, and the score reporting must align with each other and with the construct being targeted. Conceptual knowledge, as targeted by the Force and Motion Conceptual Evaluation (FMCE), can be modeled as a set of overlapping categorical states. As such, latent class analysis (LCA) is the most appropriate measurement model—where students have a probabilistic membership within classes that tend to match with observed mental models.

This dissertation focuses on one particular application of conceptual …

Comparing Machine Learning And Logistic Regression Methods For Predicting Hypertension Using A Combination Of Gene Expression And Next-Generation Sequencing Data, Elizabeth Held, Joshua Cape, Nathan L. Tintle

Faculty Work Comprehensive List

Machine learning methods continue to show promise in the analysis of data from genetic association studies because of the high number of variables relative to the number of observations. However, few best practices exist for the application of these methods. We extend a recently proposed supervised machine learning approach for predicting disease risk by genotypes to be able to incorporate gene expression data and rare variants. We then apply 2 different versions of the approach (radial and linear support vector machines) to simulated data from Genetic Analysis Workshop 19 and compare performance to logistic regression. Method performance was not radically …

Green Chemistry: Progress And Barriers, Sarah A. Green

Michigan Tech Publications, Part 1

Green chemistry can advance both the health of the environment and the primary objectives of the chemical enterprise: to understand the behavior of chemical substances and to use that knowledge to make useful substances. We expect chemical research and manufacturing to be done in a manner that preserves the health and safety of workers; green chemistry extends that expectation to encompass the health and safety of the planet. While green chemistry may currently be treated as an independent branch of research, it should, like safety, eventually become integral to all chemistry activities. While enormous progress has been made in shifting …

A Multistep Approach To Single Nucleotide Polymorphism–Set Analysis: An Evaluation Of Power And Type I Error Of Gene-Based Tests Of Association After Pathway-Based Association Tests, Alessandra Valcarcel, Kelsey Griinde, Kaitlyn Cook, Alden Green, Nathan L. Tintle

Faculty Work Comprehensive List

The aggregation of functionally associated variants given a priori biological information can aid in the discovery of rare variants associated with complex diseases. Many methods exist that aggregate rare variants into a set and compute a single p value summarizing association between the set of rare variants and a phenotype of interest. These methods are often called gene-based, rare variant tests of association because the variants in the set are often all contained within the same gene. A reasonable extension of these approaches involves aggregating variants across an even larger set of variants (eg, all variants contained in genes within …

Exoplanet Research: Differential Photometry For Kepler 6b, Garrett T. Benson, Charlotte Alexandra Olsen

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

No abstract provided.

Sedimentation Risk Assessment Using Satellite And Geospatial Data In Lagoa Feia, Brazil, Ualas B. Rohrer, Buddhika D. Madurapperuma

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

No abstract provided.

Teaching The Library To Students Of Higher Education, Steven Weiland

Charleston Library Conference

The academic library and its digital transformation are ignored in graduate programs of higher education administration, which train a significant number of postsecondary professionals. A course in scholarly communications in the digital age recently introduced at one such program includes an invitation to aspiring administrators to study the contributions of the library to the ways that faculty members are coming to understand and capitalize on new technologies in teaching, research, and career development. The library is represented in the course in its traditional and new roles. It is an essential campus location for attention to what technological change means for …

“Help, We Started A Journal!”: Adventures In Supporting Open Access Publishing Using Open Journal Systems, Anna R. Craft

Charleston Library Conference

The University Libraries at The University of North Carolina at Greensboro (UNCG) have an active and growing implementation of Open Journal Systems (OJS), a free, open source scholarly publishing platform. But even a free software system is not without its costs, both to the hosting institution and to the creators and staff of individual journals. Institutions that wish to host OJS must be able to install, maintain, and support the product. And while faculty members and other academics are often experts in their content areas, not all of them are prepared to handle other needs associated with creating and publishing …

Learning Mendeley Through Its Certification Program For Librarians, Rajiv Nariani, Yath Ithayakumar

Charleston Library Conference

York University Libraries (YUL) ended its subscription to their default citation management program in the summer of 2015. The Mendeley Certification Program for Librarians was launched during that time and the science librarian at YUL completed this program. The steps undertaken during the completion of the program led to successful migration to the freely available, and libraries supported, citation management programs. This paper details the various initiatives that were done prior to and during the certification program and how completing the program has benefited our academic community. The certification program has helped solidify relations with faculty and students during the …

Multiplying By Division: Mapping The Collection At University Of North Texas Libraries, Karen Harker, Janette Klein, Laurel Crawford

Charleston Library Conference

The University of North Texas (UNT) Libraries has developed a unique collection assessment tool, the Collection Map, to provide support for a new access‐based collection development philosophy. UNT Librarians realized the limitations of traditional assessment methods to gauge the impact of emerging acquisitions models such as demand‐driven acquisitions (DDA) and large interdisciplinary e‐book collections. What was needed was a flexible, nimble assessment system to track access, holdings, and interlibrary loan (ILL) activity for each academic discipline. The Collection Map is a database that links items, and their associated data, to any one of several dozen overlapping subcollections via Library of …

Leveraging Use‐By‐Publication‐Age Data In Serials Collection Decisions, Matthew J. Jabaily, James R. Rodgers, Steven A. Knowlton

Charleston Library Conference

Traditionally, usage figures for electronic serials have lumped all years of publication together. New tools give librarians information about usage according to the year of publication. They allow us to analyze the usage of current material separately from usage of content published in prior years. The relative value of current subscriptions and backfiles has important collection development implications. For example, many libraries subscribe directly to titles that are offered in aggregated databases, but with embargoes. The relative value of current content distinguished from prior years may be useful in reevaluating such subscription decisions.

This paper discusses tools and techniques for …

Evaluated, Removed, And Recycled—The Tale Of Two Deaccession Projects Across The Disciplines, Martha E. Higgins, Lauren Goode, Mary Jordan, John Abbott

Charleston Library Conference

How have two midsized public university libraries approached large‐scale weeding projects in their monograph and bound periodical collections? Space is at a premium in academic libraries as new roles combine and compete with traditional ones. How can the collection be refreshed to promote more use? Where will more collaboration and creative spaces be housed? How does a midsized library refine the collection to bring better campus alignment? How should the project begin? Who should be involved in planning? How can campus faculty be included in the deaccessioning process? How is the campus perception of the project handled? What should be …

Does Format Matter? Reader Preferences In An Academic Library Context, Jennifer L. Robertson, Weijing Yuan, Marlene Van Ballegooie

Charleston Library Conference

Although many academic libraries have dramatically increased their e‐book acquisitions in recent years, questions linger about format preference. When a scholarly monograph is made available in both print and electronic formats, which format will users prefer? Does format even matter? At the University of Toronto Libraries, we analyzed usage data for scholarly monographs from three key university presses, covering thousands of titles over several years of publication. By comparing print and e‐book usage patterns of identical titles, our goal was to examine format preferences and determine if there are differences in usage across subject disciplines or publishers. Through this analysis, …

Paper Session Ii: Computer Forensics Field Triage Process Model, Marcus K. Rogers, James Goldman, Rick Mislan, Timothy Wedge, Steve Debrota

Annual ADFSL Conference on Digital Forensics, Security and Law

With the proliferation of digital based evidence, the need for the timely identification, analysis and interpretation of digital evidence is becoming more crucial. In many investigations critical information is required while at the scene or within a short period of time - measured in hours as opposed to days. The traditional cyber forensics approach of seizing a system(s)/media, transporting it to the lab, making a forensic image(s), and then searching the entire system for potential evidence, is no longer appropriate in some circumstances. In cases such as child abductions, pedophiles, missing or exploited persons, time is of the essence. In …

Can Flight Data Recorder Memory Be Stored On The Cloud?, Yair Wiseman

Journal of Aviation Technology and Engineering

Flight data recorders (FDRs, or black boxes) generate data that is collected on an embedded memory device. A well-known difficulty with these devices is that the embedded memory device runs out of space. To avoid getting into this problematic situation, the software of the FDR is designed to operate in a watchful mode, constantly working to minimize the use of memory space; otherwise a larger FDR would be needed. However, larger FDRs can be a problem because they have very rigorous requirements; thus, enlargement is costly. Outcomes of this research include the recommendation to send FDR data to a remote …

10-17-2016 Ronald Koehn Named Swosu Academic Bridge Program Director, Southwestern Oklahoma State University

THE BARK ARCHIVE 2016

Dr. Ronald Koehn has been named director of the Southwestern Oklahoma State University Academic Bridge Program on the Weatherford campus.

Recognizing And Combating Cybercrime, Marcia L. Dority Baker

Information Technology Services: Publications

Can You Spot the Scam?

Scams make great stories. Tales of Internet crime or other fraud make up some of Hollywood's most exciting thrillers. While cybercrime blockbusters are fun to watch on the big screen, cybercrime is a serious problem on campuses globally.

How many people do you know who are the victim of a scam (Internet or phone)? According to the FBI, cybercrime is a growing threat that affects individuals and businesses around the world. A recent Washington Post article reported that cybercrime cost the global economy $445 billion in 2014.

The Statesman, V. 60, I. 08, Stony Brook University

Stony Brook Statesman-Sucolian

v. 60;i. 08

Columbia Chronicle (10/17/2016), Columbia College Chicago

Columbia Chronicle

Student newspaper from October 17, 2016 entitled The Columbia Chronicle. This issue is 40 pages and is listed as Volume 52, Issue 7. Cover story: "SUE reveals answers millions of years after death'" Editor-in-Chief: Megan Bennett

Abundance And Diversity Of Deep-Sea Crustaceans Of Bear Seamount, New England Seamount Chain, Valerie Renee Miranda

HCNSO Student Theses and Dissertations

Bear Seamount (39° 55’ N; 67° 30’ W) is the westernmost peak of extinct undersea volcanoes in the New England Seamount Chain (Moore et al., 2003). It is located on the continental slope off Georges Bank, and is governed by unique environmental factors and currents that may be unlike those of the other seamounts (Moore et al., 2003). Previous cruises to this seamount have been successful in capturing abundant fishes, cephalopods and invertebrates (Moore et al., 2003; Moore et al., 2004; Moore et al., 2008), but only the distribution patterns of the fishes and cephalopods have been examined, leaving a …

It’S An Aggie Thing | College Of Engineering, Usu College Of Engineering

College of Engineering News

Published in Creating Tomorrow – Oct. 15, 2016 – A group of USU alumni who work at Sandia National Laboratories in Albuquerque, N.M., are doing something to pass along the same benefits they received as students. The team created a scholarship fund that has awarded up to $1,000 per year to multiple recipients. Henry Coakley (BS ’06, MS ’08) initiated the fund.

Emu Today, October 17, 2016, Eastern Michigan University

EMU Today

No abstract provided.

Enhanced Metallic Properties Of Srruo3 Thin Films Via Kinetically Controlled Pulsed Laser Epitaxy, Justin K. Thompson, J. Nichols, S. Lee, S. Ryee, John H. Gruenewald, John G. Connell, Maryam Souri, J. M. Johnson, J. Hwang, M. J. Han, H. N. Lee, D. -W. Kim, Sung S. Ambrose Seo

Physics and Astronomy Faculty Publications

Metal electrodes are a universal element of all electronic devices. Conducting SrRuO₃ (SRO) epitaxial thin films have been extensively used as electrodes in complex-oxide heterostructures due to good lattice mismatches with perovskite substrates. However, when compared to SRO single crystals, SRO thin films have shown reduced conductivity and Curie temperatures (T_C), which can lead to higher Joule heating and energy loss in the devices. Here, we report that high-quality SRO thin films can be synthesized by controlling the plume dynamics and growth rate of pulsed laser epitaxy (PLE) with real-time optical spectroscopic monitoring. The SRO thin …

What Democrats Have Planned For Higher Education., Aldemaro Romero Jr.

Publications and Research

The Democrats have made a number of concrete

promises regarding higher education if they win

the presidential elections. They promise concerted

actions against sexual assaults on campuses that

include comprehensive support for survivors, fair

judicial processes that prevent the use of cultural

biases against females as “inciters,” and increased

prevention efforts through education programs.

The Clinton campaign also promises support for

net neutrality, the idea that Internet service providers

should enable access to all content and applications

regardless of the source without favoring or blocking

particular products or websites. The Democratic plan

also proposes expanding availability of fiber-optic

broadband Internet …