Digital Commons Network^™

Does The Internet Promote Collaboration And Productivity? Evidence From The Scientific Community In South Africa, R. Sooryamoorthy, Wesley Shrum

Faculty Publications

International collaboration among scientists has been passionately advocated by many in the developing world. Among the several conditions that support collaboration among members of a dispersed scientific community, Internet technology is crucial. We examine the relationships among electronic communication, collaboration, and productivity in South Africa, a country that has undergone remarkable change in the sphere of science and technology. We surveyed 275 scientists in selected research institutes and universities in the province of KwaZulu-Natal to address the questions: Is greater use of the Internet associated with international collaboration? Are collaboration and Internet use associated with publication in national and foreign …

Potato Genotypes With Low Reducing Sugar Content, Arione Da S. Pereira, Roberto Fritsche Neto, Roberta Da S. Silva, Carolina I. Bender, Ana Paula Schünemann, Núbia Marilin L. Ferri, João Luiz Vendruscolo

Faculty Publications

The objectives of this work were to evaluate potato genotypes for reducing sugar content and post-harvest conditions that favored the identification of those with low content. Eight potato clones, previously selected for light frying color, and the cultivar Atlantic were evaluated in autumn seasons of 2004 and 2005. The experiments were carried out at Embrapa Clima Temperado, Pelotas-RS, Brazil (31°52'S, 52°21'W), in a randomized complete block design with four replications. In 2004, the reducing sugar content was quantified after three conditions: curing the tubers; four weeks of refrigerated storage at 4°C; and refrigeration followed by reconditioning for two weeks. In …

Using Open Source Software In Developing A Web-Accessible Database Of Sweetpotato Germplasm Collections In Kenya, Arthur Villordon, Wambui Njuguna, Simon Gichuki, Philip Ndolo, Don Labonte

Faculty Publications

Web-accessible germplasm databases allow stakeholders to interactively search and locate information in real time. These databases can also be configured to permit designated users to remotely add, delete, or update information. These resources assist in decision-making activities that are related to germplasm documentation, conservation, and management. We report the development of a web-accessible database of Kenyan sweetpotato (Ipomoea batatas) varieties using open source software. Kenya is located in eastern Africa, a region that is considered one of the centers of diversity for sweetpotato. We describe the software applications used in developing the germplasm database as well as the web interface …

Sorghum Stay-Green Qtl Individually Reduce Post-Flowering Drought-Induced Leaf Senescence, Karen Harris, P. K. Subudhi, Andrew Borrell, David Jordan, Darrell Rosenow, Henry Nguyen, Patricia Klein, Robert Klein, John Mullet

Faculty Publications

Sorghum is an important source of food, feed, and biofuel, especially in the semi-arid tropics because this cereal is well adapted to harsh, drought-prone environments. Post-flowering drought adaptation in sorghum is associated with the stay-green phenotype. Alleles that contribute to this complex trait have been mapped to four major QTL, Stg1-Stg4, using a population derived from BTx642 and RTx7000. Near-isogenic RTx7000 lines containing BTx642 DNA spanning one or more of the four stay-green QTL were constructed. The size and location of BTx642 DNA regions in each RTx7000 NIL were analysed using 62 DNA markers spanning the four stay-green QTL. RTx7000 …

The Road Also Taken: Lessons From Organic Agriculture For Market- And Risk-Based Regulation, Donald Thomas Hornstein

Faculty Publications

No abstract provided.

Sos (Safeguard Our Survival): Understanding And Alleviating The Lethal Legacy Of Survival Threatening Child Abuse, Nancy A. Wright, Eric Wright

Faculty Publications

To try to achieve the goal of fully protecting a child the first time the child is subjected to potentially survival-threatening abuse, this Article suggests the creation of a model program, called the SOS ("Save Our Survival") Program, with the hope that this model program might ultimately be adopted by child protective agencies throughout the United States. Specially trained teams, known as SOS ("Safeguard Our Survival") Teams, comprised of child protection workers, police officers, medical personnel, attorneys and social workers would staff the program. SOS Team members, who would be on call 24/7, would be notified as soon as a …

Teaching Race/Teaching Whiteness: Transforming Colorblindness To Color Insight, Margalynne J. Armstrong, Stephanie Wildman

Faculty Publications

This Article argues that whiteness operates as the normative foundation of most discussions of race. Legal educators often overlook the role of whiteness in the law school setting and in law more generally. Identifying and understanding whiteness should be an essential component of legal education. This Article considers reasons why legal education rarely addresses this normative role played by whiteness. An incomplete understanding of the nature of white privilege and the modern move toward "colorblindness" conceal the raced nature of much law. To draw the harmful operation of colorblindness into relief, this Article proposes adopting "color insight, " which would …

Characteristics Of Reduced Fat Milks As Influenced By The Incorporation Of Folic Acid, K. Achanta, C. A. Boeneke, K. J. Aryana

Faculty Publications

Folic acid plays an important role in the prevention of neural tube defects (e.g., spina bifida and anencephaly), heart defects, facial clefts, urinary abnormalities, and limb deficiencies. Milk and milk products serve as a potential source for folic acid fortification because of the presence of folate-binding proteins that seem to be involved in folate bioavailability. Although milk is not a good source of folic acid, fortification could help in the prevention of the above-mentioned defects. The objective of this study was to examine the physicochemical characteristics of reduced fat milks fortified with folic acid. Reduced fat milks were prepared using …

Genomics, Molecular Imaging, Bioinformatics, And Bio-Nano-Info Integration Are Synergistic Components Of Translational Medicine And Personalized Healthcare Research, Jack Y. Yang, Mary Qu Yang, Hamid R. Arabnia, Youping Deng

Faculty Publications

Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International Journal of Functional Informatics and Personalized Medicine, IEEE 7th Bioinformatics and Bioengineering attracted more than 600 papers and 500 researchers and medical doctors. It was the only synergistic inter/multidisciplinary IEEE conference with 24 Keynote Lectures, 7 Tutorials, 5 Cutting-Edge Research Workshops and 32 Scientific Sessions including 11 Special Research Interest Sessions that were designed dynamically at Harvard in response to the current research trends and advances. The committee was very grateful for the IEEE Plenary Keynote Lectures …

Analyzing Adjuvant Radiotherapy Suggests A Non Monotonic Radio-Sensitivity Over Tumor Volumes, Jack Y. Yang, Andrzej Niemierko, Mary Qu Yang, Youping Deng

Faculty Publications

Background: Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics have been used extensively to validate clinical data. Results: We found that Poisson statistics on RT is actually derived from bacterial cells despite of many validations from clinical data. However cancerous cells do have abnormal cellular communications and use chemical messengers to signal both surrounding normal and cancerous cells to develop new blood vessels …

A Hybrid Machine Learning-Based Method For Classifying The Cushing's Syndrome With Comorbid Adrenocortical Lesions, Jack Y. Yang, Mary Qu Yang, Zuojie Lao, Yan Ma, Jianling Li, Youping Deng, Xudong Huang

Faculty Publications

Background

The prognosis for many cancers could be improved dramatically if they could be detected while still at the microscopic disease stage. It follows from a comprehensive statistical analysis that a number of antigens such as hTERT, PCNA and Ki-67 can be considered as cancer markers, while another set of antigens such as P27KIP1 and FHIT are possible markers for normal tissue. Because more than one marker must be considered to obtain a classification of cancer or no cancer, and if cancer, to classify it as malignant, borderline, or benign, we must develop an intelligent decision system that can fullfill …

Improving Prediction Accuracy Of Tumor Classification By Reusing Genes Discarded During Gene Selection, Jack Y. Yang, Guo-Zheng Li, Hao-Hua Meng, Mary Qu Yang, Youping Deng

Faculty Publications

Background

Since the high dimensionality of gene expression microarray data sets degrades the generalization performance of classifiers, feature selection, which selects relevant features and discards irrelevant and redundant features, has been widely used in the bioinformatics field. Multi-task learning is a novel technique to improve prediction accuracy of tumor classification by using information contained in such discarded redundant features, but which features should be discarded or used as input or output remains an open issue.

Results

We demonstrate a framework for automatically selecting features to be input, output, and discarded by using a genetic algorithm, and propose two algorithms: GA-MTL …

Promoting Synergistic Research And Education In Genomics And Bioinformatics, Jack Y. Yang, Mary Qu Yang, Hamid R. Arabnia, Youping Deng

Faculty Publications

Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.

High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to …

Investigation Of Transmembrane Proteins Using A Computational Approach, Jack Y. Yang, Mary Qu Yang, Keith A. Dunker, Youping Deng, Xudong Huang

Faculty Publications

Background

An important subfamily of membrane proteins are the transmembrane α-helical proteins, in which the membrane-spanning regions are made up of α-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmembrane segments. The difficulty of inferring the secondary or tertiary structure of transmembrane proteins using experimental techniques has led to a surge of interest in applying techniques from machine learning and bioinformatics to infer secondary structure from primary structure in these proteins. We are therefore interested in determining which physicochemical properties are most useful for discriminating transmembrane …

Structure And Function Predictions Of The Msa Protein In Staphylococcus Aureus, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Background

Staphylococcus aureus is a human pathogen that causes a wide variety of life-threatening infections using a large number of virulence factors. One of the major global regulators used by S. aureus is the staphylococcal accessory regulator (sarA). We have identified and characterized a new gene (modulator of sarA: msa) that modulates the expression of sarA. Genetic and functional analysis shows that msa has a global effect on gene expression in S. aureus. However, the mechanism of Msa function is still unknown. Function predictions of Msa are complicated by the fact that it does …

Iloop - A Web Application For Two-Channel Microarray Interwoven Loop Design, Mehdi Pirooznia, Ping Gong, Jack Y. Yang, Mary Qu Yang, Edward J. Perkins, Youping Deng

Faculty Publications

Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistical analysis. Interwoven loop design has several advantages over other designs. However it suffers in the complexity of design. We have implemented an online web application which allows users to find optimal loop designs for two-color microarray experiments. Given a number of conditions (such as treatments or time points) and replicates, the application will find the best possible design of the experiment and output experimental parameters. It is freely available from http://mcbc.usm.edu/iloop …

Batch Blast Extractor: An Automated Blastx Parser Application, Mehdi Pirooznia, Edward J. Perkins, Youping Deng

Faculty Publications

Motivation

BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time consuming, insufficient, and inaccurate. Therefore implementation of a parser application would be extremely useful in extracting information from BLAST outputs.

Results

We have developed a java application, Batch Blast Extractor, with a user friendly graphical interface to extract information from BLAST output. The application generates a tab delimited text file that can be easily imported into any statistical package such as Excel or SPSS for further …

A Comparative Study Of Different Machine Learning Methods On Microarray Gene Expression Data, Mehdi Pirooznia, Jack Y. Yang, Mary Qu Yang, Youping Deng

Faculty Publications

Background

Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as SVM, RBF Neural Nets, MLP Neural Nets, Bayesian, Decision Tree and Random Forrest methods have been used in recent studies. The accuracy of these methods has been calculated with validation methods such as v-fold validation. However there is lack of comparison between these methods to find a better framework for classification, clustering and analysis of microarray gene expression results.

Results

In this study, we compared the efficiency of the classification methods including; SVM, RBF Neural Nets, …

Transcriptome Profiling Of Saccharomyces Cerevisiae Mutants Lacking C2h2 Zinc Finger Proteins, Jinghe Mao, Tanwir Habib, Ming Shenwu, Baobin Kang, Wilbur Allen, Lashonda Robertson, Jack Y. Yang, Youping Deng

Faculty Publications

Background

The budding yeast Saccharomyces cerevisiae is a eukaryotic organism with extensive genetic redundancy. Large-scale gene deletion analysis has shown that over 80% of the ~6200 predicted genes are nonessential and that the functions of 30% of all ORFs remain unclassified, implying that yeast cells can tolerate deletion of a substantial number of individual genes. For example, a class of zinc finger proteins containing C2H2 zinc fingers in tandem arrays of two or three is predicted to be transcription factors; however, seven of the thirty-one predicted genes of this class are nonessential, and their functions are poorly understood. In this …

Antibacterial Fluoromicas: A Novel Delivery Medium, Bekir Dizman, Jonathan C. Badger, Mohamed O. Elasri, Lon J. Mathias

Faculty Publications

Antibacterial fluoromicas were prepared by ion-exchanging fluoromicas with different antibacterial agents including various quaternary ammonium compounds, AgNO₃, and norfloxacin. Antibacterial activities of the ion-exchanged fluoromicas were determined against Staphylococcus aureus and Escherichia coli. Minimum inhibitory concentration (MIC) and zone of inhibition (ZOI) tests were performed to determine both antibacterial effectiveness and mode of action associated with the fluoromicas. All treated fluoromicas showed excellent antibacterial activities against both types of bacteria. The antibacterial activities of treated fluoromicas were found to be either better than or the same as those of neat antibacterial agents. The repeated antibacterial activity tests demonstrated …

Whole Genome Duplications And Contracted Breakpoint Graphs, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

The genome halving problem, motivated by the whole genome duplication events in molecular evolution, was solved by El-Mabrouk and Sankoff in the pioneering paper [SIAM J. Comput., 32 (2003), pp. 754–792]. The El-Mabrouk–Sankoff algorithm is rather complex, inspiring a quest for a simpler solution. An alternative approach to the genome halving problem based on the notion of the contracted breakpoint graph was recently proposed in [M. A. Alekseyev and P. A. Pevzner, IEEE/ACM Trans. Comput. Biol. Bioinformatics, 4 (2007), pp. 98–107]. This new technique reveals that while the El-Mabrouk–Sankoff result is correct in most cases, it does not hold in …

Colored De Bruijn Graphs And The Genome Halving Problem, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, thus limiting their applications in rearrangement analysis. We discuss a connection between the breakpoint graphs and de Bruijn graphs that leads to a generalization of the notion of breakpoint graph for genomes with duplicated genes. We further use the generalized breakpoint graphs to study the Genome Halving Problem (first introduced and solved by Nadia El-Mabrouk and David Sankoff). The El-Mabrouk-Sankoff algorithm is rather complex, and, in this paper, we present an alternative approach that is based …

Transcriptomic Analysis Of Rdx And Tnt Interactive Sublethal Effects In The Earthworm Eisenia Fetida, Ping Gong, Xin Guan, Laura S. Anouye, Youping Deng, Mehdi Pirooznia, Edward J. Perkins

Faculty Publications

Background

Explosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on earthworms, an important ecological and bioindicator species at the molecular level, we sampled worms (Eisenia fetida) exposed singly or jointly to TNT (50 mg/kg soil) and RDX (30 mg/kg soil) for 28 days and profiled gene expression in an interwoven loop designed microarray experiment using a 4k-cDNA array. Lethality, growth and reproductive endpoints were measured.

Results

Sublethal doses of TNT and RDX had no significant effects on the survival …

Exploring Special Places: Connecting Secondary Art Students To Their Island Community, Mark Graham

Faculty Publications

No abstract provided.

Genetic Diversity And Low Reproductive Success In Isolated Populations Of Utah Juniper (Juniperus Osteosperma, Cupressaceae), Loreen Allphin, Val J. Anderson, Amy F. Hunt

Faculty Publications

Utah juniper (Juniperus osteosperma) has greatly expanded its historical range in the western United States. Management plans for the species have focused on curtailing its encroachment into sagebrush and grassland communities. These plans often include burning or other methods of elimination. These methods may result in subdivision or fragmentation of existing juniper stands. We initiated a study at Dugway Proving Ground, a U.S. Army facility, to examine the effects of fragmentation on the reproductive success of Utah juniper in isolated populations. We used enzyme electrophoresis to quantify genetic variability in isolated populations. We also determined population reproductive success by examining …

Cultural Competence And Instructional Design: Exploration Research Into The Delivery Of Online Instruction Cross, P. Clint Rogers, Charles R. Graham, Clifford T. Mayes

Faculty Publications

The amount of resources being poured by Western universities, companies, and governments into creating educational content to be exported (via the Internet) to other cultures is astounding. Those assigned to accomplish this task are left with the great challenge of meeting the needs of learners who come from cultures that are foreign to them, and who often have very different abilities and expectations than originally assumed. This study explores the cultural competence in the lived experience of 12 professionals who have been involved with such efforts. Often they have had to question their assumptions, recognizing flaws in their own thinking …

Empowering Or Compelling Reluctant Participators Using Audience Response Systems, Charles R. Graham, Tonya R. Tripp, Larry Seawright, George L. Joeckel Iii

Faculty Publications

This article investigates the impact of an audience response system (ARS) on student engagement in undergraduate university courses. A survey was administered to students in a dozen courses piloting the ARS system. On 13 out of 14 measures the majority of students thought the system was helpful. Overall, students were more positive about the use of the ARS in courses that used the tool for formative feedback (empowering) rather than for grading or attendance purposes (compelling). The authors discuss the positive impact of the ARS on the engagement of ‘reluctant participators’ or students who reported that they are least likely …

Bite Mark Analysis, Paul C. Giannelli

Faculty Publications

Courts have admitted bite mark comparison evidence in homicide, rape, and child abuse cases. By the 1980s, the technique had gained widespread judicial acceptance. Hundreds of cases have admitted this type of evidence, and no reported case has rejected it. Moreover, some courts speak of bite mark comparison as a "science." Indeed, its acceptance is so well-established that several courts have taken judicial notice of its reliability, implying that the validity of the technique is not subject to reasonable dispute.

Yet, the scientific foundations for bite mark comparisons has never been demonstrated. Such basic issues as the uniqueness of the …

Spatial Ecology Of The Coachwhip, Masticophis Flagellum (Squamata: Colubridae), In Eastern Texas, Richard W. Johnson, Robert R. Fleet, Michael B. Keck, D. Craig Rudolph

Faculty Publications

We radio-tracked nine Masticophis flagellum (Coachwhips) to determine home range, habitat use, and movements in eastern Texas from April to October 2000. Home ranges of Coachwhips contained more oak savanna macrohabitat than early-successional pine plantation or forested seep, based on the availability of these three macrohabitats in the study area. Likewise, within their individual home ranges, Coachwhips used oak savanna more than the other two macrohabitats, based on availability. An analysis of microhabitat use revealed that, relative to random sites within their home range, Coachwhips were found at sites with fewer pine trees and more herbaceous vegetation taller than 30 …

A Concise History Of International Criminal Law, Beth Van Schaack, Ron Slye

Faculty Publications

This work is an introductory chapter for a forthcoming book on Understanding International Criminal Law to be published by Aspen Publishers as part of Aspen's Essentials series. This chapter presents a succinct history of international criminal law (ICL), drawing upon major developments in the law of armed conflict, international human rights law, and the criminal prohibitions against piracy and the slave trade. The chapter interweaves the history of substantive norms with that of evolving principles of domestic and international jurisdiction, as these narratives are virtually inseparable in ICL. Additional chapters in the text will address the sources of ICL, the …