Digital Commons Network^™

Chemalign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties, Hyrum Carroll, Mark J. Clement, Quinn O. Snell, David Mcclellan

Faculty Publications

We present a new algorithm, ChemAlign, that uses physicochemical properties and secondary structure elements to create biologically relevant multiple sequence alignments (MSAs). Additionally, we introduce the Physicochemical Property Difference (PPD) score for the evaluation of MSAs. This score is the normalized difference of physicochemical property values between a calculated and a reference alignment. It takes a step beyond sequence similarity and measures characteristics of the amino acids to provide a more biologically relevant metric. ChemAlign is able to produce more biologically correct alignments and can help to identify potential drug docking sites.

Consumer Interest In Corporate Law, David Yosifon

Faculty Publications

This Article provides a comprehensive assessment of the consumer interest in dominant theories of the corporation and in the fundamental doctrines of corporate law. In so doing, the Article fills a void in contemporary corporate law scholarship, which has failed to give sustained attention to consumers in favor of exploring the interests of other corporate stakeholders, especially shareholders, creditors, and workers. Utilizing insights derived from the law and behavioralism movement, this Article examines, in particular, the limitations of the shareholder primacy norm at the heart of prevailing "nexus of contracts" and "team production" theories of the firm. The Article concludes …

Historians And The Many Lyndon Johnsons: A Review Essay, Kent B. Germany

Faculty Publications

No abstract provided.

Deporting Grandma: Why Grandparent Deportation May Be The Next Big Immigration Crisis And How To Solve It, Marcia A. Yablon-Zug

Faculty Publications

This Article explores the issue of grandparent caregiver deportation. The phenomenon of grandparents raising grandchildren is not new, but the number of children being raised by grandparents is at an all-time high and growing. Numerous circumstances can lead to a grandparent's assumption of caregiving responsibilities, but in most cases, grandparents assume this role because there is no one else. For thousands of children, grandparents are the only family they have, and without them these children would be placed in foster care and subject to the serious problems that plague children in foster care. The importance of grandparent caregivers cannot be …

A Cost Analysis Of A Physical Activity Intervention For Older Adults, Erik J. Groessl, Robert M. Kaplan, Steven N. Blair, W. Jack Rejeski, Jeffrey A. Katula, Abby C. King, Roger A. Fielding, Nancy W. Glynn, Marco Pahor

Faculty Publications

We examined the costs of a physical activity (PA) and an educational comparison intervention. 424 older adults at risk for mobility disability were randomly assigned to either condition. The PA program consisted of center-based exercise sessions 3x weekly for 8 weeks, 2x weekly for weeks 9 to 24 and weekly behavioral counseling for 10 weeks. Optional sessions were offered during maintenance weeks (25-52). The comparison intervention consisted of weekly education meetings for 24 weeks, and then monthly for 6 months. Cost analyses were conducted from the "payer's" perspective, with a 1-year time horizon. Intervention costs were estimated by tracking personnel …

A Review Of The National Physical Activity Plans Of Six Countries, Daniel B. Bornstein, Russell R. Pate, Michael Pratt

Faculty Publications

Background: Architects of the United States national physical activity plan can benefit from a thorough understanding of national physical activity plans from other nations. The purpose of this paper was to search for and analyze comprehensive national physical activity plan documents that can best inform the development of the U.S. plan. Methods: Electronic databases were searched for national physical activity plan documents, yielding 252 documents from 56 countries. After eliminating documents that were not written in English, did not address physical activity primarily, and did not meet our definition of a national physical activity plan, we were left with physical …

Synthetic Science: A Response To Rainbow, David S. Caudill

Faculty Publications

Rabinow’s description of the unique collaborative goal of synthetic biology at Berkeley, to foster a coproduction among multiple disciplines and perspectives from the outset (as opposed to downstream reflection upon ethical, legal, and social implications), is somewhat misleading. While that particular assemblage is represented as coproductive, the inevitability of science as a coproduction is eclipsed. That shortcoming may well be a strategic compromise to ensure effective collaboration, but it could backfire. Idealized images of science, which might be termed synthetic or artificial, have had adverse consequences in legal and administrative assessments of reliable science.

Magnetic And Nonmagnetic Nanoparticles From A Group Of Uniform Materials Based On Organic Salts, Aaron Tesfai, Bilal El-Zahab, Algernon T. Kelley, Min Li, Jayne C. Garno, Gary A. Baker, Isiah M. Warner

Faculty Publications

The size and uniformity of magnetic nanoparticles developed from a group of uniform materials based on organic salts (GUMBOS) were controlled using an in situ ion exchange, water-in-oil (w/o) microemulsion preparation. Most of these nanoGUMBOS are in fact ionic liquids (i.e., melting points less than 100 °C), while others have melting points above the conventional 100 °C demarcation. Simple variations in the reagent concentrations following a w/o approach allowed us to smoothly and predictably vary nanoparticle dimensions across a significant size regime with excellent uniformity. Average sizesofGUMBOS particles ranging from 14 to 198 nm were achieved by manipulation of the …

Role Of Lifestyle And Aging On The Longitudinal Change In Cardiorespiratory Fitness, Andrew S. Jackson, Xuemei Sui, James R. Hébert, Timothy S. Church, Steven N. Blair

Faculty Publications

Background - Cardiorespiratory fitness (CRF) in adults decreases with age and is influenced by lifestyle. Low CRF is associated with risk of diseases and the ability of older persons to function independently. We defined the longitudinal rate of CRF decline with aging and the association of aging and lifestyle with CRF.

Methods - We studied a cohort of 3429 women and 16,889 men, aged 20 to 96 years, from the Aerobics Center Longitudinal Study who completed 2 to 33 health examinations from 1974 to 2006. The lifestyle variables were body mass index, self-reported aerobic exercise, and smoking behavior. Cardiorespiratory fitness …

Failure To Ferment Dietary Resistant Starch In Specific Mouse Models Of Obesity Results In No Body Fat Loss, June Zhou, Roy J. Martin, Richard T. Tulley, Anne M. Raggio, Li Shen, Elizabeth Lissy, Kathleen Mccutcheon, Michael J. Keenan

Faculty Publications

Resistant starch (RS) is a fermentable fiber that decreases dietary energy density and results in fermentation in the lower gut. The current studies examined the effect of RS on body fat loss in mice. In a 12 week study (study 1), the effect of two different types of RS on body fat was compared with two control diets (0% RS) in C57Bl/6J mice: regular control diet or the control diet that had energy density equal to that of the RS diet (EC). All testing diets had 7% (w/w) dietary fat. In a 16 week study (study 2), the effect of …

Progressive Fatigue Effects On Manual Lifting Factors, Anthony D. Banks, Fereydoun Aghazadeh

Faculty Publications

The purpose of this study was to evaluate the effect of progressive fatigue on factors that previously have been associated with increased risk of low back pain in various occupational settings, during a repetitive lifting task where a freestyle lifting technique was used. A laboratory experiment was conducted to evaluate electromyography amplitude, kinematic, and kinetic parameters of repetitive freestyle lifting during a 2-hour lifting period. Subjective fatigue rating increased over time, indicating that the participant "felt" increasingly fatigued as the experiment progressed. Static composite strength decreased an average of 20% from the beginning to the end of the experiment. Effect …

Your Personal Renaissance: 12 Steps To Finding Your Life’S True Calling By D. Dreher, E Michael Brady Phd

Faculty Publications

The article reviews the book Your Personal Renaissance: 12 Steps to Finding Your Life's True Calling, by Diane Dreher.

Nil: The Value Of Patents In A Major Crisis Such As An Influenza Pandemic, Dennis D. Crouch

Faculty Publications

This essay focuses on the role of patents in relation to a potential global crisis such as an influenza pandemic or other public health crisis. I argue that patent rights will be largely ignored during an epidemic and that any post-crisis compensation would likely be low when compared to traditional patent rewards or settlements entered under threat of injunctive relief. In some situations, such as use of a patented invention by a state or local government, a patentee may have no recourse. Part III of the essay raises a separate issue that stems from the relatively long time frame for …

We Have A "Purpose" Requirement If We Can Keep It, James F. Flanagan

Faculty Publications

The Supreme Court in Giles v. California held that a defendant forfeits the right to confront a witness only when he purposefully keeps the witness away. Many see the "purpose" requirement as an unjustified bar to the use of victim hearsay, particularly in domestic violence prosecutions where victims often refuse to appear. The author defends Giles as a correct reading of history, and independently justified by longstanding precedent that constitutional trial rights can only be lost by intentional manipulation of the judicial process. Moreover, the purpose requirement does not prevent prosecutions or convictions because the definition of testimonial hearsay is …

From Privacy To Liberty: The Fourth Amendment After Lawrence, Thomas P. Crocker

Faculty Publications

This Article explores a conflict between the protections afforded interpersonal relations in Lawrence v. Texas and the vulnerability experienced under the Fourth Amendment by individuals who share their lives with others. Under the Supreme Court's third-party doctrine, we have no constitutionally protected expectation of privacy in what we reveal to other persons. The effect of this doctrine is to leave many aspects of ordinary life shared in the company of others constitutionally unprotected. In an increasingly socially networked world, the Fourth Amendment may fail to protect precisely those liberties-to live in the company of others free from state surveillance and …

The Impact Of Retrotransposons On Human Genome Evolution, Richard Cordaux, Mark A. Batzer

Faculty Publications

Their ability to move within genomes gives transposable elements an intrinsic propensity to affect genome evolution. Non-long terminal repeat (LTR) retrotransposons including LINE-1, Alu and SVA elements have proliferated over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human genome: from generating insertion mutations and genomic instability to altering gene expression and contributing to genetic innovation. Increasingly detailed analyses of human and other primate genomes are revealing the scale and …

The Impact Of News Coverage On Conflict: Toward Greater Understanding, Richard C. Reuben

Faculty Publications

This article develops an approach for the empirical study of the news media’s impact on the conflict that it covers. While mass communications research has studied how the news media covers conflict, it has not taken the next step of assessing the impact of that coverage. This article contends that such an inquiry is necessarily an inter-disciplinary task, and joins conflict theory with mass communications research to identify the kinds of questions that may be empirically tested to determine whether the news media is having a constructive or destructive effect on the conflict that it covers.

Copper Oxide Nanoparticles Induce Oxidative Stress And Cytotoxicity In Airway Epithelial Cells, Baher Fahmy, Stephania A. Cormier

Faculty Publications

Metal oxide nanoparticles are often used as industrial catalysts and elevated levels of these particles have been clearly demonstrated at sites surrounding factories. To date, limited toxicity data on metal oxide nanoparticles are available. To understand the impact of these airborne pollutants on the respiratory system, airway epithelial (HEp-2) cells were exposed to increasing doses of silicon oxide (SiO2), ferric oxide (Fe2O3) and copper oxide (CuO) nanoparticles, the leading metal oxides found in ambient air surrounding factories. CuO induced the greatest amount of cytotoxicity in a dose-dependent manner; while even high doses (400 μg/cm2) of SiO2 and Fe2O3 were non-toxic …

Theoretical And Numerical Study Of Mlem And Osem Reconstruction Algorithms For Motion Correction In Emission Tomography, Joyoni Dey, Michael A. King

Faculty Publications

Patient body-motion and respiratory-motion impacts the image quality of cardiac SPECT and PET perfusion images. Several algorithms exist in the literature to correct for motion within the iterative maximum-likelihood reconstruction framework. In this work, three algorithms are derived starting with Poisson statistics to correct for patient motion. The first one is a motion compensated MLEM algorithm (MC-MLEM). The next two algorithms called MGEM-1 and MGEM-2 (short for Motion Gated OSEM, 1 and 2) use the motion states as subsets, in two different ways. Experiments were performed with NCAT phantoms (with exactly known motion) as the source and attenuation distributions. Experiments …

Nutrition Literacy Status And Preferred Nutrition Communication Channels Among Adults In The Lower Mississippi Delta, Jamie Zoellner, Carol L. Connell, Wendy Bounds, Lashaundrea Crook, M. Kathleen Yadrick

Faculty Publications

Introduction

The objective of this cross-sectional study was to examine the nutrition literacy status of adults in the Lower Mississippi Delta.

Methods

Survey instruments included the Newest Vital Sign and an adapted version of the Health Information National Trends Survey. A proportional quota sampling plan was used to represent educational achievement of residents in the Delta region. Participants included 177 adults, primarily African Americans (81%). Descriptive statistics, X(2) analysis, analysis of variance, and multivariate analysis of covariance tests were used to examine survey data.

Results

Results indicated that 24% of participants had a high likelihood of limited nutrition literacy, 28% …

Quality Health Information On The Internet: Developing A Diabetes Pathfinder For The Chinese Population, Ana D. Cleveland, Jodi Philbrick, Xuequn Pan, Xinyu Yu, Jiangping Chen, Marty O'Neill, Lisa Smith

Faculty Publications

A Web-based bilingual diabetes information pathfinder was created to help the Chinese population access quality health information on the Internet as part of a collaborative outreach project in the Dallas-Fort Worth area. A survey was conducted to identify the demographics, Internet usage, health information needs, and preferences for training sessions of the Chinese population. Breast cancer, diabetes, and hepatitis B were the top three diseases of interest. The process of developing the pathfinder is described from start to finish, and it can serve as a model for the development of others. Pathfinder training sessions also were held. Taylor & Francis …

In With The New, Out With The Old: Expanding The Scope Of Retroactive Amelioration, S. David Mitchell

Faculty Publications

The legislative decision to amend a statute and reduce a sentence but not to apply it retroactively to pending prosecutions or to finalized convictions is in accord with the principles of retroactivity, but contrary to legitimate goals of punishment, i.e. deterrence and retributivism. Genarlow Wilson, convicted at seventeen of aggravated child molestation, a felony, for consensual oral sex with a fifteen-year old classmate, was sentenced to a mandatory minimum of ten years. While his appeal was pending, the Georgia Legislature reclassified the conduct as a misdemeanor and reduced the sentence to a maximum of one year but decided not to …

“A Space For Myself To Go:” Early Patterns In Small Ya Spaces, Anthony Bernier

Faculty Publications

While young adults (teenagers) are routinely recognized as constituting nearly 25 percent of the nation's public library users, the vast majority of libraries devote more space and design attention to restrooms than to young people. Worse, there are currently no consistent or established metrics, no evaluation criteria, few conceptual standards of best practices, and little consistency in the methods by which we collect empirical evidence about young adult (YA) spaces. This study is the first systematic attempt to both collect and analyze empirical data on libraries' recent trend toward providing greater spatial equity for YA library service.

A Framework For Detecting Glaucomatous Progression In The Optic Nerve Head Of An Eye Using Proper Orthogonal Decomposition, Madhusudhanan Balasubramanian, Stanislav Žabić, Christopher Bowd, Hilary W. Thompson, Peter Wolenski, S. Sitharama Iyengar, Bijaya B. Karki, Linda M. Zangwill

Faculty Publications

Glaucoma is the second leading cause of blindness worldwide. Often, the optic nerve head (ONH) glaucomatous damage and ONH changes occur prior to visual field loss and are observable in vivo. Thus, digital image analysis is a promising choice for detecting the onset and/or progression of glaucoma. In this paper, we present a new framework for detecting glaucomatous changes in the ONH of an eye using the method of proper orthogonal decomposition (POD). A baseline topograph subspace was constructed for each eye to describe the structure of the ONH of the eye at a reference/baseline condition using POD. Any glaucomatous …

Ethylene Dichloride Disruption Of Fertility In Male Mice, Harold J. Daigle, Derek N. Cole, J. Andrew Carlson, William R. Lee, Vincent L. Wilson

Faculty Publications

Ethylene dichloride (EDC) is a high use compound in chemical industry today. Although a potent alkylating agent and carcinogen, EDC has not been associated previously with adverse fertility consequences. Intraperitoneal 5 to 40 mg/kg once a day for five days in C57BL/6 mice rendered males infertile for 6 months and longer. Two of three mice treated with EDC at 5 mg/kg recovered to fertility after a 3 and 5-week sterile period, respectively. Significant testicular pathology was evident within 8 days post treatment with EDC, which progressed to resemble Sertoli Cell-Only syndrome. Although the observed effects on Leydig cell populations were …

Succination Of Thiol Groups In Adipose Tissue Proteins In Diabetes: Succination Inhibits Polymerization And Secretion Of Adiponectin, Norma Frizzell, Mathur Rajesh, Matthew J. Jepson, Ryoji Nagai, James A. Carson, Suzanne R. Thorpe, John W. Baynes

Faculty Publications

S-(2-Succinyl)cysteine (2SC) is formed by reaction of the Krebs cycle intermediate fumarate with cysteine residues in protein, a process termed succination of protein. Both fumarate and succination of proteins are increased in adipocytes cultured in high glucose medium (Nagai, R., Brock, J. W., Blatnik, M., Baatz, J. E., Bethard, J., Walla, M. D., Thorpe, S. R., Baynes, J. W., and Frizzell, N. (2007) J. Biol. Chem. 282, 34219-34228). We show here that succination of protein is also increased in epididymal, mesenteric, and subcutaneous adipose tissue of diabetic (db/db) mice and that adiponectin is a major target for succination in both …

Phage-Induced Alignment Of Membrane Proteins Enables The Measurement And Structural Analysis Of Residual Dipolar Couplings With Dipolar Waves And Lambda-Maps, Sang Ho Park, Woo Sung Son, Rishi Mukhopadhyay, Homayoun Valafar, Stanley J. Opella

Faculty Publications

At pH > 6 added filamentous bacteriophage fd is compatible with many of the detergents used to solubilize membrane proteins for solution NMR studies of membrane proteins and, therefore, serves as an alignment media. In combination with strained polyacrylamide gel alignment, Dipolar Waves can be used to directly assess the secondary structure and a λ-map extracts the order tensors for de novo structure calculation of membrane proteins without distance restraints.

Teaching Torture, Beth Van Schaack, Ron Slye

Faculty Publications

This chapter, to appear in the 2nd edition of Beth Van Schaack & Ron Slye's International Criminal Law & Its Enforcement (Foundation Press 2010), covers the crime of torture under international criminal law. It begins with a doctrinal discussion of the elements of torture as elucidated in the international criminal law jurisprudence with a focus on cases concerning gender-based violence and sex crimes. It then enables a comparison of this established doctrine with the "torture memos" produced during the administration of President Bush. Using a rich set of Notes, Questions and Problems, the chapter offers a compelling tool for teaching …

The Continuity Of Protein Structure Space Is An Intrinsic Property Of Proteins, Jeffrey Skolnick, Adrian K. Arakaki, Yup Lee Seung, Michal Brylinski

Faculty Publications

The classical view of the space of protein structures is that it is populated by a discrete set of protein folds. For proteins up to 200 residues long, by using structural alignments and building upon ideas of the completeness and continuity of structure space, we show that nearly any structure is significantly related to any other using a transitive set of no more than 7 intermediate structurally related proteins. This result holds for all structures in the Protein Data Bank, even when structural relationships between evolutionary related proteins (as detected by threading or functional analyses) are excluded. A similar picture …

High Efficiency Lipid-Based Sirna Transfection Of Adipocytes In Suspension, Gail Kilroy, David H. Burk, Z. Elizabeth Floyd

Faculty Publications

Background: Fully differentiated adipocytes are considered to be refractory to introduction of siRNA via lipid-based transfection. However, large scale siRNA-based loss-of-function screening of adipocytes using either electroporation or virally-mediated transfection approaches can be prohibitively complex and expensive. Methodology/Principal Findings: We present a method for introducing small interfering RNA (siRNA) into differentiated 3T3-L1 adipocytes and primary human adipocytes using an approach based on forming the siRNA/ cell complex with the adipocytes in suspension rather than as an adherent monolayer, a variation of "reverse transfection". Conclusions/Significance: Transfection of adipocytes with siRNA by this method is economical, highly efficient, has a simple workflow, …