Digital Commons Network^™

The Malina Oceanographic Expedition: How Do Changes In Ice Cover, Permafrost And Uv Radiation Impact On Biodiversity And Biogeochemical Fluxes In The Arctic Ocean?, Phillippe Massicotte, Rainer Amon, David Antoine, Philippe Archambault, Sergio Balzano, Simon Bélanger, Ronald Benner, Dominique Boeuf, Annick Bricaud, Flavienne Bruyant, Gwenaëlle Chaillou, Malik Malik, Bruno Charrière, Jing Chen, Hervé Claustre, Pierre Coupel, Nicole Delsaut, David Doxaran, Et. Al.

Faculty Publications

The MALINA oceanographic campaign was conducted during summer 2009 to investigate the carbon stocks and the processes controlling the carbon fluxes in the Mackenzie River estuary and the Beaufort Sea. During the campaign, an extensive suite of physical, chemical and biological variables was measured across seven shelf–basin transects (south-north) to capture the meridional gradient between the estuary and the open ocean. Key variables such as temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll-a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured onboard the Canadian research icebreaker CCGS Amundsen and from a barge …

Minimum Flow Rules For South Carolina Rivers, William L. Graf

Faculty Publications

No abstract provided.

A Single Theory Of Limited Liability Companies: An Evolutionary Analysis, Thomas Geu

Faculty Publications

No abstract provided.

X-Ray Absorption Near Edge Structure Spectra As A Basis For The Speciation Of Lead, G. L. Bovenkamp, A. Prange, A. Roy, W. Schumacher, J. Hormes

Faculty Publications

For this study several inorganic lead (II) compounds were measured at the Pb-L -(13035 eV), L - (15860 eV) and M - (2484 eV) edge using X-Ray Absorption Near Edge Structure Spectroscopy (XANES) to determine experimentally which edge is most sensitive to the coordination environment. Each edge probes a different electronic configuration because of the selection rules and has a different resolution because of life-time broadening. Pb-L -XANES spectra are only sensitive to the first coordination shell. Pb-M -XANES spectra show a better energy resolution which is due to decreased lifetime broadening, but the pure lead spectra are also sensitive …

X-Ray Absorption Near Edge Structure Spectra As A Basis For The Speciation Of Lead, G. L. Bovenkamp, A. Prange, A. Roy, W. Schumacher, J. Hormes

Faculty Publications

For this study several inorganic lead (II) compounds were measured at the Pb-L -(13035 eV), L - (15860 eV) and M - (2484 eV) edge using X-Ray Absorption Near Edge Structure Spectroscopy (XANES) to determine experimentally which edge is most sensitive to the coordination environment. Each edge probes a different electronic configuration because of the selection rules and has a different resolution because of life-time broadening. Pb-L -XANES spectra are only sensitive to the first coordination shell. Pb-M -XANES spectra show a better energy resolution which is due to decreased lifetime broadening, but the pure lead spectra are also sensitive …

Satellite-Detected Fluorescence Reveals Global Physiology Of Ocean Phytoplankton, Michael J. Behrenfeld, T.K. Westberry, Emmanuel Boss, R.T. O'Malley, D.A. Siegel, Jerry D. Wiggert, B.A. Franz, G.C. Feldman, S.C. Doney, J.K. Moore, G. Dall'olmo, A.J. Milligan, I. Lima, N. Mahowald

Faculty Publications

Phytoplankton photosynthesis links global ocean biology and climate-driven fluctuations in the physical environment. These interactions are largely expressed through changes in phytoplankton physiology, but physiological status has proven extremely challenging to characterize globally. Phytoplankton fluorescence does provide a rich source of physiological information long exploited in laboratory and field studies, and is now observed from space. Here we evaluate the physiological underpinnings of global variations in satellite-based phytoplankton chlorophyll fluorescence. The three dominant factors influencing fluorescence distributions are chlorophyll concentration, pigment packaging effects on light absorption, and light-dependent energy-quenching processes. After accounting for these three factors, resultant global distributions of …

Genetic Variation For Carcass Quality Traits In Cultured Sea Bass (Dicentrarchus Labrax), Eric A. Saillant, Mathilde Dupont-Nivet, Marie Sabourault, Pierrick Haffray, Stanislas Laureau, Marie-Odile Vidal, Béatrice Chatain

Faculty Publications

Genetic parameters for carcass quality traits were estimated in 27 families of sea bass (3 dams x 9 sires factorial mating design), raised mixed in the same tanks starting before hatching. O. spring parentage was determined a posteriori using 6 microsatellite loci. Carcass quality traits were recorded at 818 days post fertilization (mean standard length: 32.6 +/- 3.1 cm). Genetic parameters were estimated from the sire half sib variance and covariance components. Heritability of body weight (BW) and carcass processing traits (standardized to body weight) percent head weight (Head%), percent viscera weight (Viscera%) and percent visceral fat weight (VisceFat%) were …

Comparing 2-Nt 3' Overhangs Against Blunt-Ended Sirnas: A Systems Biology Based Study, Preetam Ghosh, Robert Dullea, James E. Fischer, Tom G. Turi, Ronald W. Sarver, Chaoyang Zhang, Kalyan Basu, Sajal K. Das

Faculty Publications

In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us to study the potency difference between 2-nt 3' overhangs against blunt-ended siRNA molecules in an RNA interference (RNAi) system. The rate constant predicted by this model was fed into a stochastic simulation of the RNAi system (using the Gillespie stochastic simulator) to study the overall potency effect. We observed that the stochasticity in the transcription/translation machinery has no observable effects in the RNAi pathway. Sustained gene silencing using siRNAs …

Variation Of Morphology And Elemental Concentrations In The California Nickel Hyperaccumulator Streptanthus Polygaloides (Brassicaceae), Robert S. Boyd, Michael A. Wall, Scott R. Santos, Michael A. Davis

Faculty Publications

The Ni hyperaccumulator Strepthanthus polygaloides (Brassicaceae) is one of a handful of Ni hyperaccumulators known from continental North America. Surveys have revealed four distinctive morphs of this species, relying primarily on floral traits (sepal color and shape): a purple sepal morph (P), a yellow sepal morph (Y), a morph in which sepals start yellow and mature to purple (Y/P), and a morph with light yellow undulate sepals (U). In this study, we raised plants from ten populations (five Y, three P, one Y/P, and one U) under uniform greenhouse conditions to determine if morphs varied in morphology and elemental concentrations …

A Distribution-Free Convolution Model For Background Correction Of Oligonucleotide Microarray Data, Zhongxue Chen, Monnie Mcgee, Qingzhong Liu, Megan Kong, Youping Deng, Richard H. Scheuermann

Faculty Publications

Introduction

Affymetrix GeneChip^® high-density oligonucleotide arrays are widely used in biological and medical research because of production reproducibility, which facilitates the comparison of results between experiment runs. In order to obtain high-level classification and cluster analysis that can be trusted, it is important to perform various pre-processing steps on the probe-level data to control for variability in sample processing and array hybridization. Many proposed preprocessing methods are parametric, in that they assume that the background noise generated by microarray data is a random sample from a statistical distribution, typically a normal distribution. The quality of the final results depends …

High-Throughput Next-Generation Sequencing Technologies Foster New Cutting-Edge Computing Techniques In Bioinformatics, Mary Qu Yang, Brian D. Athey, Hamid R. Arabnia, Andrew H. Sung, Qingzhong Liu, Jack Y. Yang, Jinghe Mao, Youping Deng

Faculty Publications

The advent of high-throughput next generation sequencing technologies have fostered enormous potential applications of supercomputing techniques in genome sequencing, epi-genetics, metagenomics, personalized medicine, discovery of non-coding RNAs and protein-binding sites. To this end, the 2008 International Conference on Bioinformatics and Computational Biology (Biocomp) - 2008 World Congress on Computer Science, Computer Engineering and Applied Computing (Worldcomp) was designed to promote synergistic inter/multidisciplinary research and education in response to the current research trends and advances. The conference attracted more than two thousand scientists, medical doctors, engineers, professors and students gathered at Las Vegas, Nevada, USA during July 14-17 and received great …

An Ensemble Learning Approach To Reverse-Engineering Transcriptional Regulatory Networks From Time-Series Gene Expression Data, Jianhua Ruan, Youping Deng, Edward J. Perkins, Weixiong Zhang

Faculty Publications

Background

One of the most challenging tasks in the post-genomic era is to reconstruct the transcriptional regulatory networks. The goal is to reveal, for each gene that responds to a certain biological event, which transcription factors affect its expression, and how a set of transcription factors coordinate to accomplish temporal and spatial specific regulations.

Results

Here we propose a supervised machine learning approach to address these questions. We focus our study on the gene transcriptional regulation of the cell cycle in the budding yeast, thanks to the large amount of data available and relatively well-understood biology, although the main ideas …

Nonpoint Source Pollution, Lu Lin, Zhi Qiang Deng, Daniel Dianchen Gang

Faculty Publications

A critical review of the peer-reviewed literature published in 2008 on topics related to nonpoint source pollution (NPS) is presented. This review is divided into three sections: sources of NPS pollution, modeling of NPS pollution, and NPS control strategies. Copyright © 2009 Water Environment Federation.

The Metal Chelators, Trientine And Citrate, Inhibit The Development Of Cardiac Pathology In The Zucker Diabetic Rat, John W. Baynes, David B. Murray

Faculty Publications

Purpose. The objective of this study was to determine the efficacy of dietary supplementation with the metal chelators, trientine or citric acid, in preventing the development of cardiomyopathy in the Zucker diabetic rat.

Hypothesis. We hypothesized that dietary chelators would attenuate metal-catalyzed oxidative stress and damage in tissues and protect against pathological changes in ventricular structure and function in type II diabetes.

Methods. Animals (10 weeks old) included lean control (LC, fa/+), untreated Zucker diabetic fatty (ZDF, fa/fa), and ZDF rats treated with either trientine (triethylenetetramine) or citrate at 20 mg/d in drinking water, starting …

Subcellular Localization Of Marine Bacterial Alkaline Phosphatases, H. Luo, Ronald Benner, R. A. Long, Jianjun Hu

Faculty Publications

Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane (12%), …

Integrative Disease Classification Based On Cross-Platform Microarray Data, C.-C. Liu, Jianjun Hu, M. Kalakrishnan, H. Huang, X. J. Zhou

Faculty Publications

Background

Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generated by different laboratories or with different platforms can not be compared directly due to systematic variations. This issue has severely limited the practical use of microarray-based disease classification.

Results

In this study, we tested the feasibility of disease classification by integrating the large amount of heterogeneous microarray datasets from the public microarray repositories. Cross-platform data compatibility is created by deriving expression log-rank ratios within datasets. One may then compare vectors of log-rank …

Agents And Service-Oriented Computing For Autonomic Computing: A Research Agenda, Frances M.T. Brazier, Jeffrey O. Kephart, H. Van Dyke Parunak, Michael N. Huhns

Faculty Publications

Autonomic computing is the solution proposed to cope with the complexity of today's computing environments. Self-management, an important element of autonomic computing, is also characteristic of single and multiagent systems, as well as systems based on service-oriented architectures. Combining these technologies can be profitable for all - in particular, for the development of autonomic computing systems.

An Empirical And Consumer Psychology Analysis Of Trademark Distinctiveness, Thomas R. Lee, Eric D. Derosia, Glenn L. Christensen

Faculty Publications

This article analyzes the taxonomy of trademark distinctiveness that has long been endorsed in the courts and scholarly commentary. This distinctiveness scale is routinely justified on the basis of an assumption about consumer psychology: that consumers perceive suggestive, arbitrary, or fanciful marks as source-indicating, but see descriptive marks as "merely descriptive." Although this core premise of trademark law is a fundamental matter of consumer psychology, it has never been subjected to scrutiny under the light of consumer psychology theory and empirical analysis. We offer a consumer psychology model for questioning the law of distinctiveness (or "source indication") and then test …

Demonstration Of Microcantilever Array With Simultaneous Readout Using An In-Plane Photonic Transduction Method, Seunghyun Kim, Gregory P. Nordin, Ryan Anderson, Weisheng Hu, Yusheng Qian, Jiguo Song, Jong Wook Noh

Faculty Publications

We demonstrate a microcantilever array with an in-plane photonic transduction method for simultaneous readout of each microcantilever. The array is fabricated on a silicon-on-insulator substrate. Rib waveguides in conjunction with a compact waveguide splitter network comprised of trench-based splitters and trench-based bends route light from a single optical input to each microcantilever on the chip. Light propagates down a rib waveguide integrated into the microcantilever and, at the free end of the microcantilever, crosses a small gap. Light is captured in static asymmetric multimode waveguides that terminate in Y-branches, the outputs of which are imaged onto an InGaAs line scan …

Nps' Perceptions Of Disaster Preparedness Education: Quantitative Survey Research, Milada Tichy, A. Elaine Bond, Renea L. Beckstrand, Barbara Heise

Faculty Publications

Nurse practitioners need to be effective in responding to large-scale natural and man-made disasters. However, disaster core competencies for NPs are largely nonexistent. The purpose of this study was to assess NPs' level of disaster preparedness and determine how NPs acquired knowledge about disaster preparation. Findings suggest that a consistent national NP curriculum for disaster preparedness, including communication with other disaster agencies, is needed. With proper education, NPs can play a major role in disaster management.

Changing Patterns Of Family Care In Uganda: Father Absence And Patrilineal Neglect In The Face Of Hiv/Aids, Jini Roby, Stacey Shaw, Elinor Wanyama Chemonges, Cole D. Hooley

Faculty Publications

In this study, 162 HIV-positive mothers in Uganda were interviewed about the involvement of fathers and paternal kin, regarding current support they provide to children and as child placement options in the event of the mother’s death. More than half of the children had fathers who were already deceased. Another one third had fathers who were alive but did not live with the children. Only 16% of the children were living with and being supported by their fathers. Mothers indicated a strong preference for placement with maternal kin, in contrast to traditional expectations of paternal kin care. Patterns of change …

Will Directed Evolution Destroy Humanity, And If So, What Can We Do About It?, Maxwell J. Mehlman

Faculty Publications

In contemplating the technologies emerging from the Human Genome Project, nothing scares people more than the prospect that we will attempt to use genetic engineering to control the human evolutionary process.

Habitat Selection By Anolis Carolinensis (Green Anole) In Open Pine Forests In Eastern Texas, Richard R. Schaefer, Robert R. Fleet, D. Craig Rudolph, Nancy E. Koerth

Faculty Publications

We initiated a mark-recapture study to determine the effects of shrub density on Anolis carolinensis (Green Anole) populations. Green Anole perch site, shrub species, and shrub volume preferences were also examined. We established two study plots of different shrub densities in open pine forests on the Angelina National Forest in eastern Texas. In late spring, the Green Anole population at the higher shrub-density plot was estimated to be 16 times greater than the population at the lower shrub-density plot. Green Anoles most commonly perched on live shrubs, but exhibited very little preference or avoidance of any particular species of live …

Using The Fourteenth Amendment To Protect The Integrity Of Kinship Foster Families, Jennifer Baum, Teresa J. Grogan

Faculty Publications

(Excerpt)

As children’s advocates, we know well the value of an extended family to a dependency case. Living with a family member is often considered by children removed from their parents to be the “second best.” Such arrangements are often more comforting, less socially stigmatizing, and more capable at facilitating children’s normal daily routines, including school, medical care, and religious training, than stranger foster care. The social and psychological benefits of kinship care are well documented. One recent retrospective study concluded that children in kinship foster care have fewer behavioral problems three years after placement than do children who were …

Who Says "I Do"? Reviewing Judith Butler & Gayatri Chakravorty Spivak, Who Sings The Nation-State? Language, Politics, Belonging (2007), Noa Ben-Asher

Faculty Publications

This Book Review offers an analogy between two forms of resistance to legal discrimination by marginalized minorities: singing the national anthem in Spanish on the streets of Los Angeles in the spring of 2006 by undocumented immigrants, and possible future public marriage ceremonies by LGBT people and other marriage outlaws. Based on the conceptual grounds laid by Judith Butler and Gayatri Spivak, and earlier by Hannah Arendt, the Review uses an analogy to the public singing of the anthem in Spanish in order to argue that the performance of public marriage ceremonies by LGBT people and other marriage outlaws may …

In Re Tenancy By The Entirety-Married Couples, Common Law Marriages, And Same-Sex Partners: Orth V. Orth, John V. Orth

Faculty Publications

No abstract provided.

A Remote Sensing And Gis-Assisted Spatial Decision Support System For Hazardous Waste Site Monitoring, John R. Jensen, Michael E. Hodgson, Maria Garcia-Quijano, Jungho Im, Jason A. Tullis

Faculty Publications

Humans produce large amounts of waste that must be processed or stored so that it does not contaminate the environment. When hazardous wastes are stored, waste site monitoring is typically conducted in situ which can lead to a serious time lag between the onset of a problem and detection. A Remote Sensing and GIS-assisted Spatial Decision Support System for Hazardous Waste Site Monitoring was developed to improve hazardous waste site management. The system was designed to be recursive, flexible, and integrative. It is recursive because the system is implemented iteratively until the risk assessment subsystem determines that an event is …

Dying To Know: A Demand For Genuine Public Access To Clinical Trial Results Data, Christine Galbraith Davik

Faculty Publications

Four years ago at the age of 34, I heard the awful words "I'm sorry, but you have breast cancer" coming from my doctor. After the initial shock of the diagnosis wore off, I like many others who have faced life-threatening diseases began to work with a team of physicians to develop an appropriate treatment plan, which included contemplating enrollment in a clinical trial. Quite unexpectedly, my position as an intellectual property professor whose scholarship focuses primarily on information control, my role as a member of my university's Institutional Review Board that oversees studies involving human subjects, and my newly …

Understanding Generalist Function, F. Matthew Mihelic

Faculty Publications

A major concern in dealing with multi-agent complex adaptive systems is the understanding of how such systems build order in the midst of an otherwise chaotic universe. The ordering principles of such systems that are found at the biological level can be applied to better understanding human organizations, and can also be used to develop or modify highly complex intelligent agent software systems for greater efficacy. This paper describes the theoretical mechanism of how huge multi-agent complex adaptive systems overcome the exponential increases in entropy that would otherwise cause system collapse, through the use of agents that function to maintain …

Survey Of Blueberry (Vaccinium Spp.) Problems In The Gulf South, Melinda A. Miller-Butler, Kenneth J. Curry, Barbara J. Smith, Jeffrey S. Braswell

Faculty Publications

The blueberry (Vaccinium) industry in Mississippi has been steadily increasing since the early 1980s, but some plants in older fields are now in decline. The root rot pathogen, Phytophthora cinnamomi, is endemic in the southeastern United States and has caused severe losses to blueberries in North Carolina and Arkansas. Because the warm, humid climate of Mississippi, with periods of high precipitation, provides a favorable environment for Phytophthora root rot disease, it was suspected to be the cause of plant decline in older blueberry fields. Members of the Gulf South Blueberry Growers Association were mailed surveys to determine …