Digital Commons Network^™

Computational Methods For The Analysis Of Primate Mobile Elements, Richard Cordaux, Shurjo K. Sen, Miriam K. Konkel, Mark A. Batzer

Faculty Publications

Transposable elements (TE), defined as discrete pieces of DNA that can move from one site to another site in genomes, represent significant components of eukaryotic genomes, including primates. Comparative genome-wide analyses have revealed the considerable structural and functional impact of TE families on primate genomes. Insights into these questions have come in part from the development of computational methods that allow detailed and reliable identification, annotation, and evolutionary analyses of the many TE families that populate primate genomes. Here, we present an overview of these computational methods and describe efficient data mining strategies for providing a comprehensive picture of TE …

Laboratory Methods For The Analysis Of Primate Mobile Elements, David A. Ray, Kyudong Han, Jerilyn A. Walker, Mark A. Batzer

Faculty Publications

Mobile elements represent a unique and powerful set of tools for understanding the variation in a genome. Methods exist not only to utilize the polymorphisms among and within taxa to various ends but also to investigate the mechanism through which mobilization occurs. The number of methods to accomplish these ends is ever growing. Here, we present several protocols designed to assay mobile element-based variation within and among individual genomes. © 2010 Springer Science + Business Media, LLC.

Phenological Partitioning Among Drifting Insect Genera Within Families In A Subtropical, Coastal Plain Stream (Louisiana, Usa), Michael D. Kaller, James D. Hudson

Faculty Publications

We investigated invertebrate drift in a subtropical, coastal plain stream in Louisiana, USA. Once monthly, at a single site on Big Brushy Creek, eight three-hour drift samples (24 hours total) were collected using two 250-micron, 0.13-m2 drift nets. We examined the data for seasonal trends in overall drift density by analysis of covariance and taxonomic composition by principal component analysis and multivariate analysis of covariance. We found no statistically significant seasonal differences in overall drift density, although community composition did statistically differ among months. More interestingly, we found that 26 genera (38%) exhibited asynchrony in peak drift timing within families. …

Reputation In A Networked World: Revisiting The Social Foundations Of Defamation Law, David S. Ardia

Faculty Publications

No abstract provided.

Enabling Responsible Public Genomics, John M. Conley, Adam K. Doerr, Daniel B. Vorhaus

Faculty Publications

No abstract provided.

Resting Energy Expenditure Changes With Weight Loss: Racial Differences, Xuewen Wang, Tongjian You, Leon Lenchik, Barbara J. Nicklas

Faculty Publications

It is controversial whether weight loss reduces resting energy expenditure (REE) to a different magnitude in black and white women. This study was to determine whether changes in REE with weight loss were different between black and white postmenopausal women, and whether changes in body composition (including regional lean and fat mass) were associated with REE changes within each race. Black (n= 26) and white (n= 65) women (age= 58.2±5.4 years, 25< BMI< 40 kg·m⁻²) completed a 20-week weight loss intervention. Body weight, lean and fat mass (total body, limb and trunk) via dual energy X-ray absorptiometry, and REE via indirect …

Evolution Of An Mhc Class La Gene Fragment In Four North American Morone Species, J. X. Liu, Bert Ely

Faculty Publications

A nucleotide sequence analysis of a fragment of a Morone MHC class Ia gene detected high levels of polymorphism in striped bass Morone saxatilis, white perch Morone americana and yellow bass Morone mississippiensis. Extremely low levels of MHC diversity, however, were detected in white bass Morone chrysops, suggesting the possibility of a severe population bottleneck for this species.

Far-Field Optical Nanoscopy Based On Continuous Wave Laser Stimulated Emission Depletion, C. Kuang, Wei Zhao, Guiren Wang

Faculty Publications

Stimulated emission depletion (STED) microscopy is one of the breakthrough technologies that belong to far-field optical microscopy and can achieve nanoscale spatial resolution. We demonstrate a far-field optical nanoscopy based on continuous wave lasers with different wavelengths, i.e., violet and green lasers for excitation and STED, respectively. Fluorescent dyes Coumarin 102 and Atto 390 are used for validating the depletion efficiency. Fluorescent nanoparticles are selected for characterizing the spatial resolution of the STED system. Linear scanning of the laser beams of the STED system along one line of a microscope slide, which is coated with the nanoparticles, indicates that a …

Metabolic Actions Of Insulin In Men And Women, Faidon Magkos, Xuewen Wang, Bettina Mittendorfer

Faculty Publications

Insulin is an important regulator of glucose, lipid and protein metabolism. It suppresses hepatic glucose and triglyceride production, inhibits adipose tissue lipolysis and whole-body and muscle proteolysis and stimulates glucose uptake in muscle. In this review we discuss what is currently known about the control of substrate metabolism by insulin in men and women. The data available so far indicate that women are more sensitive to insulin with regards to glucose metabolism (both in the liver and in muscle) whereas there are no differences between men and women in insulin action on lipolysis. Potential differences exist in the regulation of …

Taxation Of Domestic Partner Benefits: The Hidden Costs, Patricia A. Cain

Faculty Publications

Many employers provide domestic partner benefits to their employees, especially in the form of health care plans. Domestic partners are not considered spouses under the Internal Revenue Code. Nor, of course, are same-sex spouses so long as DOMA is in effect. Many employers assume that this means all domestic partner (or same-sex spouse) benefits are taxable under the federal tax law. But this is not true. A partner (or same-sex spouse) can qualify as a dependent and benefits paid to dependents are also tax-exempt. A person can qualify as a dependent for purposes of excluding the value of health care …

An Equal Protection View Of The First Amendment, Patrick Garry

Faculty Publications

No abstract provided.

Greenhouse Gas Regulation Under The Clean Air Act: Does Chevron Set The Epa Free, Nathan D. Richardson

Faculty Publications

No abstract provided.

Comprehensive Planning, Dominant-Use-Zones, And User Rights: A New Era In Ocean Governance, James N. Sanchirico, Josh Eagle, Steve Palumbi, Barton H. Thompson Jr.

Faculty Publications

Ocean-zoning arguments often center on the biology of ocean species, the geography of fishing-use patterns, and the need for preventing use conflicts. Here we expand this discussion to the social and legal aspects of ocean zoning, focusing on comprehensive planning, segregation of activities into use-priority areas, and the allocation of user rights within each zone. The inclusion of all of these features within an ocean-zoning regime can be a catalyst for a variety of ancillary benefits, including opportunities for user groups to form informal or formal long-lived institutions and a reassessment of the focus and scope of the regulatory institutions …

Introduction: Why A Political Ecology Of The U.S. South?, P. T. Hurley, Edward R. Carr

Faculty Publications

No abstract provided.

Dynamic Path Bifurcation For The Beckmann Reaction: Observation And Implication, H. Yamataka, M. Sato, H. Hasegawa, Salai Cheettu Ammal

Faculty Publications

The reaction of oximes to amides, known as the Beckmann rearrangement, may undergo fragmentation to form carbocations + nitriles instead of amides when the cations have reasonable stability. The reactions of oxime derivatives of 1-substituted-phenyl-2-propanones and 3-substituted-phenyl-2-butanones in aqueous solvents gave both rearrangement and fragmentation products, the ratio of which was dependent on substituents. Transition state (TS) optimizations and intrinsic reaction coordinate (IRC) calculations for the reaction of 1-phenyl-2-propanone oximes showed that there is a single TS for each substituted compound. The IRC path from the TS either led to a rearrangement product or a fragmentation product depending on the …

First Report Of Viral Pathogens Wssv And Ihhnv In Argentine Crustaceans, Sergio R. Martorelli, Robin M. Overstreet, Jean A. Jovonovich

Faculty Publications

The pathogenic penaeid shrimp viruses white spot syndrome virus (WSSV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) are reported for the first time from Argentina. They both occurred in wild crustaceans in Bahia Blanca Estuary, with WSSV detected by polymerase chain reaction (PCR) or real time quantitative PCR (qPCR) methods as infecting samples as high as 56% of the penaeid Artemesia longinaris Bate, 1888, 67% of the grapsoid Cyrtograpsus angulatus Dana, 1851, and 40% of the introduced palaemonid Palaemon macrodactylus Rathbun, 1902. The highest detected copy number was 39,600 copies/mu g DNA. IHHNV was tested for using PCR in …

Environmental Correlates Of Abundances Of Mosquito Species And Stages In Discarded Vehicle Tires, Donald A. Yee, Jamie M. Kneitel, Steven A. Juliano

Faculty Publications

Discarded vehicle tires are a common habitat for container mosquito larvae, although the environmental factors that may control their presence or abundance within a tire are largely unknown. We sampled discarded vehicle tires in six sites located within four counties of central Illinois during the spring and summer of 2006 to determine associations between a suite of environmental factors and community composition of container mosquitoes. Our goal was to find patterns of association between environmental factors and abundances of early and late instars. We hypothesized that environmental factors correlated with early instars would be indicative of oviposition cues, whereas environmental …

Improving Teacher's Self Confidence In Learning Technology Skills And Math Education Through Professional Development, Taralynn Hartsell, Sherry S. Herron, Houbin Lewis Fang, Avinash Rathod

Faculty Publications

Using technology tools in math instruction can help stimulate problem-solving skills and understanding of math concepts. However, teachers need to be confident in their abilities to use technology tools. This study investigated whether or not a four-week in-service professional development institute that addressed the use of technology in math education helped improved the teachers’ attitude and confidence in applying technology. Findings indicated that as the teachers explored and used the available technology tools relevant to math instruction during the institute, the more proactive and motivated they became to continue their professional development in using technology for classroom instruction. They realized …

Nonpoint Source Pollution, Shaowei Sun, Zhiqiang Deng, Daniel Dianchen Gang

Faculty Publications

This article presents a comprehensive review of research advances in 2009 on nonpoint source water pollution caused by urban stormwater, highway stormwater, agricultural runoff, and atmospheric deposition. Modeling progresses in total maximum daily load calculations for nonpoint source pollution are also reviewed. Various low impact development technologies and best management practices for mitigating nonpoint source pollution and their socioeconomic impacts are assessed. Copyright © 2010 Water Environment Federation.

Air Quality During Demolition And Recovery Activities In Post-Katrina New Orleans, Raghunathan Ravikrishna, Han Woong Lee., Stephen Mbuligwe, K. T. Valsaraj, John H. Pardue

Faculty Publications

Air samples were collected during demolition and cleanup operations in the Lakeview district of New Orleans, Louisiana,USA, in late 2005 during the period immediately after Hurricane Katrina. Three different high-volume air samples were collected around waste collection areas that were created to temporarily hold the debris from the cleanup of residential properties in the area. Particular teconcentrations were elevated and included crystalline fibers associated with asbestos. Metal concentrations on particulate matter aesembled those measured in sediments deposited by floodwaters with the exception of B a, which was elevated at all three locations. The highest organic contaminant concentration measured on particulates …

On The Thermodynamics Of Friction And Wear-A Review, M. Amiri, Michael M. Khonsari

Faculty Publications

An extensive survey of the papers pertaining to the thermodynamic approach to tribosystems, particularly using the concept of entropy as a natural time base, is presented with a summary of the important contributions of leading researchers. © 2010 by the authors; licensee MDPI, Basel, Switzerland.

The Railroads Must Have Ties: A Legal History Of Forest Conservation And The Oregon & California Railroad Land Grant, 1887-1916, Sean Kammer

Faculty Publications

No abstract provided.

Density Based Pruning For Identification Of Differentially Expressed Genes From Microarray Data, Jianjun Hu, J. Xu

Faculty Publications

Motivation

Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a single statistics. The false positive rate of these methods can be improved by considering other features of differentially expressed genes.

Results

We proposed a pattern recognition strategy for identifying differentially expressed genes. Genes are mapped to a two dimension feature space composed of average difference of gene expression and average expression levels. A density based pruning algorithm (DB Pruning) is developed to screen out potential differentially expressed genes usually …

Bayesmotif: De Novo Protein Sorting Motif Discovery From Impure Datasets, Jianjun Hu, F. Zhang

Faculty Publications

Background

Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms.

Methods

We formulated the protein sorting motif discovery problem as a classification problem …

Using Jackknife To Assess The Quality Of Gene Order Phylogenies, Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang

Faculty Publications

Background
In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.

Results
In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to …

Constructing A Fish Metabolic Network Model, Shuzhao Li, Alexander Pozhitkov, Rachel A. Ryan, Charles Steve Manning, Nancy J. Brown-Peterson, Marius Brouwer

Faculty Publications

We report the construction of a genome-wide fish metabolic network model, MetaFishNet, and its application to analyzing high throughput gene expression data. This model is a stepping stone to broader applications of fish systems biology, for example by guiding study design through comparison with human metabolism and the integration of multiple data types. MetaFishNet resources, including a pathway enrichment analysis tool, are accessible at http://metafishnet.appspot.com.

Understanding Positive Father-Child Interaction: Children's, Fathers', And Mothers' Contributions, Erin K. Holmes, Aletha C. Huston

Faculty Publications

Guided by a systemic ecological framework for father involvement, we investigate children's, mothers', and fathers' contributions to observed father-child interaction. Analyses of 586 married resident fathers, their wives, and a target first-grade child (participants in the NICHD Study of Early Child Care) demonstrate that an additive model of father involvement accounts for the quality of father-child interaction better than a model which focuses on only one component of the system. Father parenting beliefs, child language skills, child social skills, maternal employment, and dyadic mother-child interaction quality each additively and significantly contribute to positive father-child interaction. Father average income and education …

Multiscale Modeling Of Cellular Systems In Biology, J. C. Dallon

Faculty Publications

Here we review eight different multiscale modeling efforts dealing with cellular systems in biology. The first two models focus on collagen based tissue, one dealing with the biomechanical properties of the tissue and the other focusing on how the dermis is remodeled in scar tissue formation. The next two models deal with first avascular tumor growth and then the role of the vasculature in tumor growth. We then consider two models which use the Immersed Boundary method to model tissue properties and cell-cell adhesion. Finally we conclude with two models with treatments of the Cellular Potts Model. The first models …

Are Older Adults Less Or More Physiologically Reactive? A Meta-Analysis Of Age-Related Differences In Cardiovascular Reactivity To Laboratory Tasks, Wendy C. Birmingham, Bert N. Uchino, Cynthia A. Berg

Faculty Publications

In this meta-analytic review of 31 laboratory studies, we examined if relatively older adults showed lower or higher cardiovascular reactivity compared with relatively younger adults. Results revealed that age was associated with lower heart rate reactivity but higher systolic blood pressure (SBP) reactivity during emotionally evocative tasks. Consistent with the predictions of dynamic integration theory, the result for SBP was moderated by the degree of task activation. These data are discussed in light of existing self-regulatory models and important future research directions.

Norms, Conformity, And Controls, William B. Tayler, Robert J. Bloomfield

Faculty Publications

Research in behavioral economics suggests that in addition to their traditional incentive effects, formal control systems can influence psychological motivations. We extend this literature by demonstrating experimentally that formal controls directly influence people’s sense of what behaviors are appropriate in the setting (personal norms), and indirectly alter people’s tendency to conform to the behavior of those around them (descriptive norms). These effects persist even after the controls are changed, so that the effects of current controls can be strongly influenced by past control strength. Our results support those who are incorporating psychological factors into principal-agent models (such as Fischer and …