Digital Commons Network^™

Correlated Response In A Driven Flow Of Self-Organizing Particles Around A Slit In Porous Media By Interacting Lattice Gas, Ras B. Pandey, J.F. Gettrust

Faculty Publications

The flow of immiscible particles (A, B) through a porous medium with a vertical slit is studied by an interacting lattice-gas computer simulation on a discrete lattice. The source of the particles is connected to the bottom and particles are driven upward by concentration gradient and a pressure bias against gravity. Distribution of flowing particles around the slit is examined as a function of the slit width and bias at high and low porosity at a steady state. At the low bias, a sharp change in the densities (high in slit to low in adjacent porous media) of both constituents …

Carbohydrate Intake And Overweight And Obesity Among Healthy Adults, Anwar T. Merchant, Hassanali Vatanparast, Shahzaib Barlas, Mahshid Dehghan, Syed Mahboob Ali Shah, Lawrence De Koning, Susan E. Steck

Faculty Publications

Background - Little is known about the dietary habits of people with optimal body weight in communities with high overweight and obesity prevalence.

Objective - To evaluate carbohydrate intake in relation to overweight and obesity in healthy, free-living adults

Design - We used a cross-sectional analysis

Subjects/setting - The Canadian Community Health Survey Cycle 2.2 is a cross-sectional survey of Canadians conducted in 2004-2005. There were 4,451 participants aged 18 years and older with anthropometric and dietary data and no comorbid conditions in this analysis.

Main outcome measures - Outcome variables were body mass index (BMI; calculated as kg/m^{2 …}

Disability-Selective Abortion And The Americans With Disabilities Act, Dov Fox, Christopher L. Griffin Jr.

Faculty Publications

This Article examines the influence of the Americans with Disabilities Act (ADA) on affective attitudes toward children with disabilities and on the incidence of disability-selective abortion. Applying regression analysis to U.S. natality data, we find that the birthrate of children with Down syndrome declined significantly in the years following the ADA’s passage. Controlling for technological, demographic, and cultural variables suggests that the ADA may have encouraged prospective parents to prevent the existence of the very class of people it was designed to protect. We explain this paradox by showing the way in which specific ADA provisions could have given rise …

A Narrative Account Of The Wider Impact Of The 7 July 2005 London Bomb Attacks, Shahid Bux, Sarah M. Coyne

Faculty Publications

The London bombings on 7 July 2005 highlighted the prevailing terrorist threat to the UK. The present study addressed the psychological response of community (n=294) indirectly exposed to the attacks to discern he broader impact and effects of terrorism. Qualitative content analysis was used to develop a profile of emotions and responses to the attacks. This was supplemented by the use of linguistic analysis demonstrating the enormous heterogeneity and complexity of responses to terrorism. In light of previous work on the wider impact of terrorism, the present study highlighted a relatively restrained impact of terrorism. Notwithstanding this observation, responses were …

A Sophisticated Library Search Strategy Using Folksonomies And Similarity Matching, William Lund, Yiu-Kai D. Ng, Maria Soledad Pera

Faculty Publications

Libraries, private and public, offer valuable resources to library patrons. As of today the only way to locate information archived exclusively in libraries is through their catalogs. Library patrons, however, often find it difficult to formulate a proper query, which requires using specific keywords assigned to different fields of desired library catalog records, to obtain relevant results. These improperly formulated queries often yield irrelevant results or no results at all. This negative experience in dealing with existing library systems turn library patrons away from library catalogs; instead, they rely on Web search engines to perform their searches first and upon …

Nutrient Allocations And Metabolism In Two Collembolans With Contrasting Reproduction And Growth Strategies, Thomas Larsen, Marc Ventura, Christian Damgaard, Erik A. Hobbie, Paul Henning Krogh

Faculty Publications

Physiological mechanisms such as allocation and release of nutrients are keys to understanding an animal's adaptation to a particular habitat. This study investigated how two detrivores with contrasting life‐history traits allocated carbon (C) and nitrogen (N) to growth, reproduction and metabolism. As model organisms we used the collembolans, Proisotoma minuta (Tullberg 1871) and Protaphorura fimata (Gisin 1952).

To estimate allocations of C and N in tissue, we changed the isotopic composition of the animal's yeast diets when they became sexually mature and followed isotope turnover in tissue, growth and reproduction for 28 days. In addition, we measured the composition of …

Open Access: What Is It And What Does It Mean For Academic Authors?, C. Jeffrey Belliston

Faculty Publications

What is Open Access? The modern Open Access (or OA) movement has historical roots — some fairly recent and some much older. If one has a correct understanding of these historical roots, the OA movement will properly be seen as evolutionary rather than as revolutionary. In addition to this theoretical treatment of the "what is OA" question, a treatment of what John Willinsky has called the "flavors" of OA will elucidate the very practical side of the same question." What does OA mean for academic authors? Just as with the "what is OA" question, there are multiple sides to the …

The Effect Of Ambiguous Data On Phylogenetic Estimates Obtained By Maximum Likelihood And Bayesian Inference, Alan R. Lemmon, Jeremy M. Brown, Kathrin Stanger-Hall, Emily Moriarty Lemmon

Faculty Publications

Although an increasing number of phyiogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum, likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes confounding factors, we provide the first clear understanding of 1 mechanism, by which ambiguous data can mislead phylogenetic analyses. We find that in both ML and Bayesian frameworks, among-site rate variation can interact with, ambiguous data to produce misleading estimates of topology and branch, lengths. Furthermore, …

Findsite: A Combined Evolution/Structure-Based Approach To Protein Function Prediction, Jeffrey Skolnick, Michal Brylinski

Faculty Publications

A key challenge of the post-genomic era is the identification of the function(s) of all the molecules in a given organism. Here, we review the status of sequence and structure-based approaches to protein function inference and ligand screening that can provide functional insights for a significant fraction of the ∼50% of ORFs of unassigned function in an average proteome. We then describe FINDSITE, a recently developed algorithm for ligand binding site prediction, ligand screening and molecular function prediction, which is based on binding site conservation across evolutionary distant proteins identified by threading. Importantly, FINDSITE gives comparable results when high-resolution experimental …

Local Conformations And Competitive Binding Affinities Of Single-And Double-Stranded Primer-Template Dna At The Polymerization And Editing Active Sites Of Dna Polymerases, Kausiki Datta, Neil P. Johnson, Vince J. Licata, Peter H. Von Hippel

Faculty Publications

In addition to their capacity for template-directed 5′ → 3′ DNA synthesis at the polymerase (pol) site, DNA polymerases have a separate 3′ → 5′ exonuclease (exo) editing activity that is involved in assuring the fidelity of DNA replication. Upon misincorporation of an incorrect nucleotide residue, the 3′ terminus of the primer strand at the primer-template (P/T) junction is preferentially transferred to the exo site, where the faulty residue is excised, allowing the shortened primer to rebind to the template strand at the pol site and incorporate the correct dNTP. Here we describe the conformational changes that occur in the …

Aintegumenta And Aintegumenta-Like6 Act Redundantly To Regulate Arabidopsis Floral Growth And Patterning, Beth A. Krizek

Faculty Publications

An Arabidopsis (Arabidopsis thaliana) flower consists of four types of organs arranged in a stereotypical pattern. This complex floral structure is elaborated from a small number of floral meristem cells partitioned from the shoot apical meristem during reproductive development. The positioning of floral primordia within the periphery of the shoot apical meristem depends on transport of the phytohormone auxin with floral anlagen arising at sites of auxin maxima. An early marker of lateral organ fate is the AP2/ERF-type transcription factor AINTEGUMENTA (ANT), which has been proposed to act downstream of auxin in organogenic growth. Here, I show that …

The Psbp Protein, But Not The Psbq Protein, Is Required For Normal Thylakoid Architecture In Arabidopsis Thaliana, Xiaoping Yi, Stefan R. Hargett, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

Interfering RNA was used to suppress the expression of the genes At1g06680 and At2g30790 in Arabidopsis thaliana, which encode the PsbP-1 and PsbP-2 proteins, respectively, of Photosystem II. A phenotypic series of transgenic plants was recovered that expressed intermediate and low amounts of PsbP. Earlier we had documented significant alterations in a variety of Photosystem II parameters in these plant lines [Yi, X., Liu, H., Hargett, S. R., Frankel, L. K., Bricker, T. M. (2007). The PsbP protein is required for photosystem II complex assembly/stability and photoautotrophy in Arabidopsis thaliana. J. Biol. Chem. 34, 24833-24841]. In this communication, we document …

Complex Segregation Analysis Of Pedigrees From The Gilda Radner Familial Ovarian Cancer Registry Reveals Evidence For Mendelian Dominant Inheritance, Bamidele O. Tayo, Richard A. Dicioccio, Yulan Liang, Maurizio Trevisan, Richard S. Cooper, Shashikant Lele, Lara Sucheston, Steven M. Piver, Kunle Odunsi

Faculty Publications

Background: Familial component is estimated to account for about 10% of ovarian cancer. However, the mode of inheritance of ovarian cancer remains poorly understood. The goal of this study was to investigate the inheritance model that best fits the observed transmission pattern of ovarian cancer among 7669 members of 1919 pedigrees ascertained through probands from the Gilda Radner Familial Ovarian Cancer Registry at Roswell Park Cancer Institute, Buffalo, New York. Methodology/Principal Findings: Using the Statistical Analysis for Genetic Epidemiology program, we carried out complex segregation analyses of ovarian cancer affection status by fitting different genetic hypothesis-based regressive multivariate logistic models. …

Nutrient Limitation On Phytoplankton Growth In The Upper Barataria Basin, Louisiana: Microcosm Bioassays, Ling Ren, Nancy N. Rabalais, R. Eugene Turner, Wendy Morrison, Warren Mendenhall

Faculty Publications

The Davis Pond Diversion (DPD) was constructed to divert Mississippi River (MR) water into the Barataria Basin to reduce the salinity in support of wetland restoration on the Louisiana coast. To assess the phytoplankton nutrient limitation in adjacent water systems and potential impacts of DPD, 12 seasonal nutrient-phytoplankton bioassay experiments were conducted from October 2003 to July 2004 using the natural phytoplankton assemblages from freshwater and brackish-water lakes, Cataouatche and Salvador, LA (USA), which receive Mississippi River water from the DPD, and from a nearby freshwater lake, Lac des Allemands, that does not. Dissolved inorganic nitrogen (N), phosphorus (P), and …

Isca/Sufa Paralogues Are Required For The [4fe-4s] Cluster Assembly In Enzymes Of Multiple Physiological Pathways In Escherichia Coli Under Aerobic Growth Conditions, Guoqiang Tan, Jianxin Lu, Jacob P. Bitoun, Hao Huang, Huangen Ding

Faculty Publications

IscA/SufA paralogues are the members of the iron-sulfur cluster assembly machinery in Escherichia coli. Whereas deletion of either IscA or SufA has only a mild effect on cell growth, deletion of both IscA and SufA results in a null-growth phenotype in minimal medium under aerobic growth conditions. Here we report that cell growth of the iscA/sufA double mutant (E. coli strain in which both iscA and sufA had been in-frame-deleted) can be partially restored by supplementing with BCAAs (branched-chain amino acids) and thiamin. We further demonstrate that deletion of IscA/SufA paralogues blocks the [4Fe-4S] cluster assembly in IlvD (dihydroxyacid dehydratase) …

Purification Of A Water Extract Of Chinese Sweet Tea Plant (Rubus Suavissimus S. Lee) By Alcohol Precipitation, Gar Yee Koh, Guixin Chou, Zhijun Liu

Faculty Publications

The aqueous extraction process of the leaves of Rubus suavissimus often brings in a large amount of nonactive Polysaccharides as part of the constituents. To purify this water extract for potential elevated bioactivity, an alcohol precipitation (AP) consisting of gradient regimens was applied, and its resultants were examined through colorimetric and HPLC analyses. AP was effective in partitioning the aqueous crude extract into a soluble supernatant and an insoluble precipitant, and its effect varied significantly with alcohol regimens. Generally, the higher the alcohol concentration, the purer was the resultant extract. At its maximum, approximately 36% (w/w) of the crude extract, …

Aebp2 As A Potential Targeting Protein For Polycomb Repression Complex Prc2, Hana Kim, Keunsoo Kang, Joomyeong Kim

Faculty Publications

AEBP2 is a zinc finger protein that has been shown to interact with the mammalian Polycomb Repression Complex 2 (PRC2). In the current study, we characterized this unknown protein and tested its potential targeting roles for the PRC2. AEBP2 is an evolutionarily well-conserved gene that is found in the animals ranging from flying insects to mammals. The transcription of mammalian AEBP2 is driven by two alternative promoters and produces at least two isoforms of the protein. These isoforms show developmental stage-specific expression patterns: the adult-specific larger form (51 kDa) and the embryo-specific smaller form (32 kDa). The AEBP2 protein binds …

Enzymatic Digestion Of Single Dna Molecules Anchored On Nanogold-Modified Surfaces, Junhong Lü, Ming Ye, Na Duan, Bin Li

Faculty Publications

To study enzyme-DNA interactions at single molecular level, both the attachment points and the immediate surroundings of surfaces must be carefully considered such that they do not compromise the structural information and biological properties of the sample under investigation. The present work demonstrates the feasibility of enzymatic digestion of single DNA molecules attached to nanoparticle-modified surfaces. With Nanogold linking DNA to the mica surface by electrostatic interactions, advantageous conditions with fewer effects on the length and topography of DNA are obtained, and an appropriate environment for the activities of DNA is created. We demonstrate that by using Dip-Pen Nanolithography, individual …

Why Some Species Of Birds Do Not Avoid Inbreeding: Insights From New Zealand Robins And Saddlebacks, Ian G. Jamieson, Sabrina S. Taylor, Lisa N. Tracy, Hanna Kokko, Doug P. Armstrong

Faculty Publications

When dispersal options are limited and encounters with relatives are likely, individuals need to recognize and avoid mating with kin to avoid the fitness costs of close inbreeding. New Zealand robins and saddlebacks are genetically monogamous and possess life-history traits that predict they should show zero tolerance of close inbreeding. However, of 11 population-years of pedigree data, there was evidence of inbreeding avoidance in only 1 year. We also found no indication that incestuous pairings were avoided or that individuals were choosing genetically dissimilar mates based on microsatellite DNA analysis. Furthermore, a review of the literature revealed that inbreeding avoidance …

Hostility And Anger In: Cardiovascular Reactivity And Recovery To Mental Arithmetic Stress., Elizabeth J. Vella, Bruce H. Friedman

Faculty Publications

Hostility and anger have been attributed as psychosocial risk factors for coronary heart disease. Heightened cardiovascular reactivity (CVR), and poor recovery, to provocative stressors are thought to hasten this risk. Purpose: To examine the relationship between hostility and anger inhibition (AI), and the moderating situational influences of harassment and evaluation, in predicting CVR and recovery to mental arithmetic (MA) stress using a multiple regression approach.

Migration-Selection Balance And Local Adaptation Of Mitochondrial Haplotypes In Rufous-Collared Sparrows (Zonotrichia Capensis) Along An Elevational Gradient, Zachary A. Cheviron, Robb T. Brumfield

Faculty Publications

Variable selection pressures across heterogeneous landscapes can lead to local adaptation of populations. The extent of local adaptation depends on the interplay between natural selection and gene flow, but the nature of this relationship is complex. Gene flow can constrain local adaptation by eroding differentiation driven by natural selection, or local adaptation can itself constrain gene flow through selection against maladapted immigrants. Here we test for evidence that natural selection constrains gene flow among populations of a widespread passerine bird (Zonotrichia capensis) that are distributed along an elevational gradient in the Peruvian Andes. Using multilocus sequences and microsatellites screened in …

FindsiteLhm: A Threading-Based Approach To Ligand Homology Modeling, Michal Brylinski, Jeffrey Skolnick

Faculty Publications

Ligand virtual screening is a widely used tool to assist in new pharmaceutical discovery. In practice, virtual screening approaches have a number of limitations, and the development of new methodologies is required. Previously, we showed that remotely related proteins identified by threading often share a common binding site occupied by chemically similar ligands. Here, we demonstrate that across an evolutionarily related, but distant family of proteins, the ligands that bind to the common binding site contain a set of strongly conserved anchor functional groups as well as a variable region that accounts for their binding specificity. Furthermore, the sequence and …

Risk Of Secondary Malignant Neoplasms From Proton Therapy And Intensity-Modulated X-Ray Therapy For Early-Stage Prostate Cancer, Jonas D. Fontenot, Andrew K. Lee, Wayne D. Newhauser

Faculty Publications

Purpose: To assess the risk of a secondary malignant neoplasm (SMN) from proton therapy relative to intensity-modulated radiation therapy (IMRT) using X-rays, taking into account contributions from both primary and secondary sources of radiation, for prostate cancer. Methods and Materials: A proton therapy plan and a 6-MV IMRT plan were constructed for 3 patients with early-stage adenocarcinoma of the prostate. Doses from the primary fields delivered to organs at risk of developing an SMN were determined from treatment plans. Secondary doses from the proton therapy and IMRT were determined from Monte Carlo simulations and available measured data, respectively. The risk …

High-Throughput Single Cell Arrays As A Novel Tool In Biopreservation, Kenneth L. Roach, Kevin R. King, Korkut Uygun, Steven C. Hand, Isaac S. Kohane, Martin L. Yarmush, Mehmet Toner

Faculty Publications

Microwell array cytometry is a novel high-throughput experimental technique that makes it possible to correlate pre-stress cell phenotypes and post-stress outcomes with single cell resolution. Because the cells are seeded in a high density grid of cell-sized microwells, thousands of individual cells can be tracked and imaged through manipulations as extreme as freezing or drying. Unlike flow cytometry, measurements can be made at multiple time points for the same set of cells. Unlike conventional image cytometry, image analysis is greatly simplified by arranging the cells in a spatially defined pattern and physically separating them from one another. To demonstrate the …

Sampling And Dynamics Of Pseudacteon Tricuspis (Diptera: Phoridae) In Louisiana, Donald C. Henne, Seth J. Johnson

Faculty Publications

The population dynamics ofa fire ant (Solenopsis invicta Buren) parasitoid (Pseudacteon tricuspis Borgmeier) was studied in Louisiana. The objectives of this study were to understand the daily and seasonal population dynamics of P. tricuspis in the context of environmental variables, determine whether P. tricuspis populations were synchronized over local and regional scales, determine the sex ratios and frequency distributions of P. tricuspis at disturbed S. invicta mounds, and determine the minimum sample size and sampling methodology that would provide an estimate of the true relative abundance of P. tricuspis at any location. Daily patterns of relative abundance of P. tricuspis …

Gene Order Phylogeny And The Evolution Of Methanogens, Haiwei Luo, Zhiyi Sun, William Arndt, Jian Shi, Robert Friedman, Jijun Tang

Faculty Publications

Methanogens are a phylogenetically diverse group belonging to Euryarchaeota. Previously, phylogenetic approaches using large datasets revealed that methanogens can be grouped into two classes, “Class I” and “Class II”. However, some deep relationships were not resolved. For instance, the monophyly of “Class I” methanogens, which consist of Methanopyrales, Methanobacteriales and Methanococcales, is disputable due to weak statistical support. In this study, we use MSOAR to identify common orthologous genes from eight methanogen species and a Thermococcale species (outgroup), and apply GRAPPA and FastME to compute distance-based gene order phylogeny. The gene order phylogeny supports two classes of methanogens, but it …

Nondestructive Electromagnetic Material Characterization Using A Dual Waveguide Probe: A Full Wave Solution, Milo W. Hyde Iv, James W. Stewart, Michael J. Havrilla, William P. Baker, Edward Rothwell, Dennis P. Nyquist

Faculty Publications

A nondestructive technique for determining the complex permittivity and permeability of a perfect electric conductor backed magnetic shielding material using a dual waveguide probe is presented. The dual waveguide probe allows for the simultaneous collection of reflection and transmission coefficients which distinguishes it from single probe methods common in the literature. Theoretical development of these coefficients, which is accomplished through a coupled magnetic field integral equations formulation using Love's equivalence principle and solved via the method of moments (MOM), is discussed. Evaluation of the resulting MOM impedance matrix elements is performed using complex plane integration leading to enhanced computational efficiency …

On The Mechanisms Of Episodic Salinity Outflow Events In The Strait Of Hormuz, Prasad G. Thoppil, Patrick J. Hogan

Faculty Publications

Observations in the Strait of Hormuz (26.26 degrees N, 56.08 degrees E) during 1997-98 showed substantial velocity fluctuations, accompanied by episodic changes in the salinity outflow events with amplitude varying between 1 and 2 psu on time scales of several days to a few weeks. These events are characterized by a rapid increase in salinity followed by an abrupt decline. The mechanisms behind these strong pulses of salinity events are investigated with a whigh-resolution (similar to 1 km) Hybrid Coordinate Ocean Model (HYCOM) with particular reference to the year 2005. In accordance with the observations, the simulated salinity events are …

Association Between Plasma 25-Hydroxyvitamin D And Breast Cancer Risk, Katherine D. Crew, Marilie D. Gammon, Susan E. Steck, Dawn L. Hershman, Serge Cremers, Elzbieta Dworakowski, Elizabeth Shane, Mary Beth Terry, Manisha Desai, Susan L. Teitelbaum, Alfred I. Neugut, Regina M. Santella

Faculty Publications

Vitamin D has been associated with decreased risk of several cancers. In experimental studies, vitamin D has been shown to inhibit cell proliferation and induce differentiation and apoptosis in normal and malignant breast cells. Using a population-based case-control study on Long Island, New York, we examined the association of breast cancer with plasma 25-hydroxyvitamin D (25-OHD) levels, a measure of vitamin D body stores. In-person interviews and blood specimens were obtained from 1,026 incident breast cancer cases diagnosed in 1996 to 1997 and 1,075 population-based controls. Plasma 25-OHD was measured in batched, archived specimens by Diasorin RIA. The mean (SD) …

Mapping Cancer Mortality-To-Incidence Ratios To Illustrate Racial And Sex Disparities In A High-Risk Population, James R. Hébert, Virginie Daguise, Deborah M. Hurley, Rebecca C. Wilkerson, Catishia M. Mosley, Swann Arp Adams, Robin C. Puett, James B. Burch, Susan E. Steck, Susan Bolick-Aldrich

Faculty Publications

Background - Comparisons of incidence and mortality rates are the metrics used most commonly to define cancer-related racial disparities. In the US, and particularly in South Carolina, these largely disfavor African Americans (AAs). Computed from readily available data sources, the mortality-to-incidence rate ratio (MIR) provides a population-based indicator of survival.

Methods - South Carolina Central Cancer Registry incidence data and Vital Registry death data were used to construct MIRs. ArcGIS 9.2 mapping software was used to map cancer MIRs by sex and race for 8 Health Regions within South Carolina for all cancers combined and for breast, cervical, colorectal, lung, …