Digital Commons Network^™

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 …

A Miniature Implanted Inverted-F Antenna For Gps Application, Mohammed Z. Azad, Mohammod Ali

Faculty Publications

A miniature implanted Hilbert inverted-F antenna design at the 1.575 GHz; global positioning system (GPS) frequency is proposed, which can be used to track the location of its user, e.g., the elderly with declining mental capacity (alzheimer's disease). A detailed parametric study of the antenna design is performed by considering it to be implanted within a human muscle model. The effects of the substrate, superstrate, and the nearby muscle tissue on antenna performance are carefully investigated. A laboratory prototype of the antenna was built and tested within a muscle equivalent fluid indicating good VSWR performance. Finally the said antenna when …

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 …

Admixture Mapping Of Quantitative Trait Loci For Bmi In African Americans: Evidence For Loci On Chromosomes 3q, 5q, And 15q, Analabha Basu, Hua Tang, Donna Arnett, C. Charles Gu, Tom Mosley, Sharon Kardia, Amy Luke, Bamidele Tayo, Richard Cooper, Xiaofeng Zhu, Neil Risch

Faculty Publications

Obesity is a heritable trait and a major risk factor for highly prevalent common diseases such as hypertension and type 2 diabetes. Previously we showed that BMI was positively correlated with African ancestry among the African Americans (AAs) in the US National Heart, Lung, and Blood Institute's Family Blood Pressure Program (FBPP). In a set of 1,344 unrelated AAs, using Individual Ancestry (IA) estimates at 284 marker locations across the genome, we now present a quantitative admixture mapping analysis of BMI. We used a set of unrelated individuals from Nigeria to represent the African ancestral population and the European American …

Shilianhua Extract Inhibits Gsk-3Β And Promotes Glucose Metabolism, Jun Yin, Aamir Zuberi, Zhanguo Gao, Dong Liu, Zhijun Liu, Jianping Ye

Faculty Publications

The extract of plant Shilianhua (SLH; Sinocrassula indica Berge) is a component in a commercial product for control of blood glucose. However, it remains to be investigated whether the SLH extract enhances insulin sensitivity in a model of type 2 diabetes. To address this question, the SLH crude extract was fractionated into four parts on the basis of polarity, and bioactivities of each part were tested in cells. One of the fractions, F100, exhibited a strong activity in the stimulation of glucose consumption in vitro. Glucose consumption was induced significantly by F100 in 3T3-L1 adipocytes, L6 myotubes, and H4IIE hepatocytes …

Employed Parents' Satisfaction With Food Choice Coping Strategies: Influence Of Gender And Structure, Christine E. Blake, Carol M. Devine, Elaine Wethington, Margaret M. Jastran, Tracy J. Farrell, Carole A. Bisogni

Faculty Publications

This study aimed to understand parents' evaluations of the way they integrated work-family demands to manage food and eating. Employed, low/moderate-income, urban, U.S., Black, White, and Latino mothers (35) and fathers (34) participated in qualitative interviews exploring work and family conditions and spillover, food roles, and food-choice coping and family-adaptive strategies. Parents expressed a range of evaluations from overall satisfaction to overall dissatisfaction as well as dissatisfaction limited to work, family life, or daily schedule. Evaluation criteria differed by gender. Mothers evaluated satisfaction on their ability to balance work and family demands through flexible home and work conditions, while striving …

Growing As A College, Geoffrey D. Reynolds

Faculty Publications

Growing as a College is the second of a series of short articles concerning the history of Hope College, located in Holland, Michigan.

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 …

The Vacant Parish: Managing A Pastoral Search Process, Skip Bell

Faculty Publications

No abstract provided.

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, …

Transdisciplinary Green Engineering Education At San José State University, Belle Wei, Patricia Backer

Faculty Publications

Climate change is a pressing issue for the world today. There are an increasing number of technological by-products posing a threat to the stability and quality of the world environment. According to the United Nations’ Intergovernmental Panel on Climate Change (IPCC), global warming appears to be accelerating, resulting in higher increases in global temperature and higher rises in the sea level. To effectively address this problem, there is a need for transdisciplinary, transnational approaches, reflecting the complexity of the problem and the interdependence of people’s lives around the world. Consequently, the Davidson College of Engineering at San José State University …

Patterns Of User Activity In The Different Features Of The Blackboard Cms Across All Courses For An Academic Year At Brigham Young University, Michael E. Griffiths, Charles R. Graham

Faculty Publications

In the past decade, course management systems (CMS) have become an integral part of most institutions of higher education. While there has been a significant amount of research looking at CMS usage at the course level, there has been less research looking at the institution-wide CMS usage from a CMS activity database perspective. This article shares findings from a study which analyzes over 36 million student and instructor clicks within the Blackboard CMS across the entire campus of Brigham Young University (BYU) during one full academic year. This research reports overall levels of user activity across campus, patterns of user …

A Survey Of Perspectives On Intergovernmental Relations: A Comparative Analysis Of The Czech And Slovak Republics, Phillip J. Bryson, Gary C. Cornia, Scott M. Smith

Faculty Publications

The results of a survey of local government officials from the Slovak and Czech Republics taken in December of 2005 are presented and analyzed. Attitudes about and perspectives of intergovernmental fiscal relations in the two republics are probed. Differences and similarities in Czech and Slovak views are established regarding some of the perceptions of: local autonomy and the sufficiency of available funds; whether or not public services are supplied by the appropriate levels of government; the potential benefits of adopting a serious rather than a nominal property tax; and the flexibility of local budget planning in Czech and Slovak cities …

Developing Systems For Cyber Situational Awareness, James. S. Okolica, J. Todd Mcdonald, Gilbert L. Peterson, Robert F. Mills, Michael W. Haas

Faculty Publications

In both military and commercial settings, the awareness of Cyber attacks and the effect of those attacks on the mission space of an organization has become a targeted information goal for leaders and commanders at all levels. We present in this paper a defining framework to understand situational awareness (SA)—especially as it pertains to the Cyber domain—and propose a methodology for populating the cognitive domain model for this realm based on adversarial knowledge involved with Cyber attacks. We conclude with considerations for developing Cyber SA systems of the future.

Developing And Implementing A Simulation Program: Baccalaureate Nursing Education, Patricia K. Ravert

Faculty Publications

Brigham Young University (BYU) is a private university (owned by the Church of Jesus Christ of Latter-day Saints), established in 1875. The main campus is located in Provo, Utah, 45 miles south of Salt Lake City at the base of the Wasatch Mountains and serves approximately 33,000 students. The College of Nursing (CON) was founded in 1952. The CON offers two programs, the undergraduate Bachelor of Science and the Master of Science; the latter program prepares family nurse practitioners. The CON programs are approved by the Utah State Board of Nursing and are accredited by the National League for Nursing …

Associations Between Cardiorespiratory Fitness And Health-Related Quality Of Life, Robert A. Sloan, Susumu S. Sawada, Corby K. Martin, Timothy S. Church, Steven N. Blair

Faculty Publications

Background: There is limited data examining the association between cardiorespiratory fitness (CRF) and health related quality of life (HRQOL) in healthy young adults. We examined the association between CRF and HRQOL Physical Component Summary (PCS) and Mental Component Summary (MCS) scores in apparently health males in the United States Navy.

Methods: A total of 709 males (18-49 yr) performed a submaximal exercise test and HRQOL assessment (SF-12v2^TM) between 2004-2006. CRF level was classified into fourths depending on age distribution with the lowest fitness quartile serving as the referent group. PCS and MCS scores ≥ 50 were defined as …

Genome Degradation In Brucella Ovis Corresponds With Narrowing Of Its Host Range And Tissue Tropism, Renee M. Tsolis, Rekha Seshadri, Renato L. Santos, Felix J. Sangari, Juan M. García Lobo, Maarten F. De Jong, Qinghu Ren, Garry Myers, Lauren M. Brinkac, William C. Nelson, Robert T. Deboy, Samuel Angiuoli, Hoda Khouri, George Dimitrov, Jeffrey R. Robinson, Stephanie Mulligan, Richard L. Walker, Philip E. Elzer, Karl A. Hassan, Ian T. Paulsen

Faculty Publications

Brucella ovis is a veterinary pathogen associated with epididymitis in sheep. Despite its genetic similarity to the zoonotic pathogens B. abortus, B. melitensis and B. suis, B. ovis does not cause zoonotic disease. Genomic analysis of the type strain ATCC25840 revealed a high percentage of pseudogenes and increased numbers of transposable elements compared to the zoonotic Brucella species, suggesting that genome degradation has occurred concomitant with narrowing of the host range of B. ovis. The absence of genomic island 2, encoding functions required for lipopolysaccharide biosynthesis, as well as inactivation of genes encoding urease, nutrient uptake and utilization, and outer …

Contemporary Proton Therapy Systems Adequately Protect Patients From Exposure To Stray Radiation, Wayne D. Newhauser, Jonas D. Fontenot, Phillip J. Taddei, Dragan Mirkovic, Annelise Giebeler, Rui Zhang, Anita Mahajan, David Kornguth, Marilyn Stovall, Pablo Yepes, Shiao Woo, Radhe Mohan

Faculty Publications

Proton beam therapy has provided safe and effective treatments for a variety of adult cancers. In recent years, there has been increasing interest in utilizing proton therapy for pediatric cancers because it allows better sparing of healthy tissues. Minimizing exposures of normal tissues is especially important in children because they are highly susceptible to consequential late effects, including the development of a radiogenic second cancer, which may occur years or even decades after treatment of the first cancer. While the dosimetric advantage of therapeutic proton beams is well understood, relatively little attention has been paid to the whole-body exposure to …

Effective Dose From Stray Radiation For A Patient Receiving Proton Therapy For Liver Cancer, Phillip J. Taddei, Sunil Krishnan, Dragan Mirkovic, Pablo Yepes, Wayne D. Newhauser

Faculty Publications

Because of its advantageous depth-dose relationship, proton radiotherapy is an emerging treatment modality for patients with liver cancer. Although the proton dose distribution conforms to the target, healthy tissues throughout the body receive low doses of stray radiation, particularly neutrons that originate in the treatment unit or in the patient. The aim of this study was to calculate the effective dose from stray radiation and estimate the corresponding risk of second cancer fatality for a patient receiving proton beam therapy for liver cancer. Effective dose from stray radiation was calculated using detailed Monte Carlo simulations of a double-scattering proton therapy …

Childhood Sexual Abuse, Other Childhood Factors, And Pathways To Survivors’ Adult Relationship Quality, Eric C. Walker, Thomas B. Holman, Dean M. Busby

Faculty Publications

We were interested in understanding how the effects of childhood sexual abuse, in concert with other negative childhood experiences, were carried forward into adult romantic relationships. Data from 15,831 married or cohabitating individuals were gathered via the RELATE Questionnaire. Empirical research, attachment theory, and a general model of adult relationship quality suggested that the path from negative childhood events to adult relationship quality was mediated by a number of individual and relational affect-laden variables. Results showed that childhood abuse and other family-of-origin variables work primarily through the adult survivor’s perceptions of the events of his or her childhood. This “current …

Can We Apply The Mendelian Randomization Methodology Without Considering Epigenetic Effects?, Ikechkwu U. Ogbuanu, Hongmei Zhang, Wilfried J. Karmaus

Faculty Publications

Introduction: Instrumental variable (IV) methods have been used in econometrics for several decades now, but have only recently been introduced into the epidemiologic research frameworks. Similarly, Mendelian randomization studies, which use the IV methodology for analysis and inference in epidemiology, were introduced into the epidemiologist's toolbox only in the last decade.

Analysis: Mendelian randomization studies using instrumental variables (IVs) have the potential to avoid some of the limitations of observational epidemiology (confounding, reverse causality, regression dilution bias) for making causal inferences. Certain limitations of randomized controlled trials, such as problems with generalizability, feasibility and ethics for some exposures, and high …

Modelling Optimal Location For Pre-Hospital Helicopter Emergency Medical Services, Nadine Schuurman, Nathaniel Bell, Randy L'Heureux, Syed M. Hameed

Faculty Publications

BACKGROUND: Increasing the range and scope of early activation/auto launch helicopter emergency medical services (HEMS) may alleviate unnecessary injury mortality that disproportionately affects rural populations. To date, attempts to develop a quantitative framework for the optimal location of HEMS facilities have been absent. METHODS: Our analysis used five years of critical care data from tertiary health care facilities, spatial data on origin of transport and accurate road travel time catchments for tertiary centres. A location optimization model was developed to identify where the expansion of HEMS would cover the greatest population among those currently underserved. The protocol was developed using …

Structure And Functions Of Keratin Proteins In Simple, Stratified, Keratinized And Cornified Epithelia, Hermann H. Bragulla, Dominique G. Homberger

Faculty Publications

Historically, the term 'keratin' stood for all of the proteins extracted from skin modifications, such as horns, claws and hooves. Subsequently, it was realized that this keratin is actually a mixture of keratins, keratin filament-associated proteins and other proteins, such as enzymes. Keratins were then defined as certain filament-forming proteins with specific physicochemical properties and extracted from the cornified layer of the epidermis, whereas those filament-forming proteins that were extracted from the living layers of the epidermis were grouped as 'prekeratins' or 'cytokeratins'. Currently, the term 'keratin' covers all intermediate filament-forming proteins with specific physicochemical properties and produced in any …

Repair-Mediated Duplication By Capture Of Proximal Chromosomal Dna Has Shaped Vertebrate Genome Evolution, John K. Pace, Shurjo K. Sen, Mark A. Batzer, Cédric Feschotte

Faculty Publications

DNA double-strand breaks (DSBs) are a common form of cellular damage that can lead to cell death if not repaired promptly. Experimental systems have shown that DSB repair in eukaryotic cells is often imperfect and may result in the insertion of extra chromosomal DNA or the duplication of existing DNA at the breakpoint. These events are thought to be a source of genomic instability and human diseases, but it is unclear whether they have contributed significantly to genome evolution. Here we developed an innovative computational pipeline that takes advantage of the repetitive structure of genomes to detect repair-mediated duplication events …

Identification Of Single Nucleotide Polymorphisms In The P21 (Cdkn1a) Gene And Correlations With Longevity In The Italian Population, Silvia Gravina, Francesco Lescai, Gregory Hurteau, Graham J. Brock, Anna Saramaki, Stefano Salvioli, Claudio Franceschi, Igor Roninson

Faculty Publications

Longevity in humans is determined by multiple environmental and genetic factors. We have investigated possible associations between longevity and Single Nucleotide Polymorphisms (SNPs) in the p21 (CDKN1A) gene, a stress-inducible senescence-associated cell cycle inhibitor, expression of which upregulates genes implicated in several age-related diseases. By sequencing the promoter and exons of p21 in genomic DNA of ten individuals over 90 years old, we have identified 30 SNPs, many of which had not been previously characterized. A cluster of minor alleles within the -4547/-3489 bp region did not alter the basal activity or p53 responsiveness of the p21 promoter. We then …

Cobaltacarborane-Phthalocyanine Conjugates: Syntheses And Photophysical Properties, Hairong Li, Frank R. Fronczek, M. Graça H. Vicente

Faculty Publications

Syntheses of two new cobaltacarborane-phthalocyanine conjugates, one anionic (Pc 6) and one zwitterionic (Pc 7), were accomplished via cyclotetramerization of the corresponding cobaltacarborane-substituted phthalonitriles (4 or 5) with excess phthalonitrile in quinoline. X-ray structures of two phthalonitrile precursors (2 and 3) were obtained and are discussed, and the absorption and emission properties of the two cobaltacarborane-phthalocyanine conjugates in several solvents were investigated. The anionic conjugate 6 exists mainly as a monomer in polar organic solvents and has fluorescence quantum yields in the region 0.2-0.3. The zwitterionic conjugate 7 aggregates in solution and displays lower quantum yields ∼0.1 in organic solvents. …

Interpreting Facial Expressions: The Influence Of Social Anxiety, Emotional Valence, And Race, Lora Rose Hunter, Julia D. Buckner, Norman B. Schmidt

Faculty Publications

Social anxiety is posited to be linked to interpersonal skills deficits, including accurate interpretation of emotional social cues, such as facial expressions. However, empirical support for an interpersonal skills deficit model of social anxiety is lacking. Studies of information processes indicate that socially anxious individuals may be more accurate at identifying threatening facial expressions in particular. In the present study, undergraduates who self-identified as Caucasian (N = 158) completed a task assessing facial expression accuracy. Relevant parameters such as emotional valence as well as race of the target were assessed. As predicted, socially anxious individuals were overall more accurate at …

How Will You Thrive In An Uncertain Economy?, Sandee Magliozzi, Susan P. Beneville

Faculty Publications

No abstract provided.