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Evolution Of Small Putative Group I Introns In The Ssu Rrna Gene Locus Of Phialophora Species, Scott O. Rogers

Biological Sciences Faculty Publications

Background: Group I introns (specifically subgroup IC1) are common in the nuclear ribosomal RNA genes of fungi. While most range in length from more than 200 to nearly 1800 nucleotides (nt) in length, several small putative (or degenerate) group I introns have been described that are between 56 and 81 nt. Although small, previously we demonstrated that the PaSSU intron in the rRNA small subunit gene of Phialophora americana isolate Wang 1046 is capable of in vitro splicing using a standard group I intron pathway, thus qualifying it as a functional ribozyme. Findings. Here, we describe eight short putative group …

The Sky In The Classroom, Susan Burggraf, Kidder Smith

Journal of Pedagogy, Pluralism, and Practice

We have all experienced the sky – its vast expanse, endless possibilities, the feeling of playful freedom one might have during vacation. It’s less obvious, though, how it fits into the classroom, neither slimming down its vastness nor overwhelming precise academic discourse. This article describes a multi-disciplinary course we taught at Bowdoin College, where we sought to expand students’ views of themselves, their minds, and the nature of academic inquiry by accomplishing the marriage of this vastness with precision. Our purpose here is to evoke that learning experience for other educators who might have similar goals.

Holistically Informed: A Scientist-Practitioner Offers The Perspective Of Inclusion Over Exclusion In Two Undergraduate Psychology Courses, Katherine A. Barone

Journal of Pedagogy, Pluralism, and Practice

An overview of some scientist-practitioner dilemmas that still exist in psychology sets the stage for an examination of how both models might be incorporated in the undergraduate psychology curriculum. The difficulty of guiding the applied psychology student towards respect for inclusion is explored and suggestions are offered for the curriculum in two courses, Theories of Personality and Cognitive Psychology. Specifically, multicultural emphases and work on case material seem to be the most helpful adjunctive curriculum and these are demonstrated through some aspects of a holistically informed practitioner focus. Using case material from diverse cultures, represented in a snowflake image, helps …

Creating A Learning Environment To Increase Early Adolescent Motivation: A Dissertation, Mark Logan

Educational Studies Dissertations

This study focuses on early adolescent motivation in school. It is an inquiry that seeks to understand the factors that contribute to students’ engagement in their learning through student and teacher perceptions. I examined significant research often cited as impacting motivation, including early adolescent development, middle school structures, transitions, student/teacher relationships, and parental involvement. I surveyed 345 sixth grade students on their perceptions of their own learning, thoughts, and behaviors. Participating students attended schools with various middle school age configurations, including K-8, K-12, 5-8, and 6-8. Schools represented public and charter public schools and were located in urban, suburban, and …

Factors That Contribute To Turbidity On The West Fork Of The White River In Arkansas, Chris Cotton, Brian Haggard

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

The West Fork of the White River (WFWR) exceeds the water quality standard for turbidity (10 NTU) set by the Arkansas Department of Environmental Quality and, since 1998, the river has been on Arkansas’s 303 (d) list of impaired water bodies unsuitable for aquatic life because of turbidity exceedances. To understand the factors that could be related to turbidity, total suspended solids (TSS), total inorganic suspended solids (TISS), total volatile suspended solids (TVSS), sestonic chlorophyll-a (Chl-a) concentrations, and turbidity were measured on three sample dates from nine sites on the WFWR. As the site location changed in the downstream direction, …

A Novel Gene Silencing Vector For Plant Genomics And Biotechnology, Dustin Hoover, Scott Nicholson, Vibha Srivastava

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Gene silencing is a process of suppressing activity of specific genes by producing “interfering” RNA encoded by foreign genes. This process serves as the principle of genetic modification in plants and animals, which is an important tool in genomics and biotechnology, allowing scientists to manipulate organisms to better meet human demands. New approaches of gene silencing may enable improvements on current practices of genetic modification, and broaden the application and impact of gene silencing in biotechnology. Recently, a novel vector design consisting of the transcription of short gene fragments lacking transcription termination signals was demonstrated to be effective in partial …

Whatever Works: Teaching Adults With Learning Difficulties In Adult Basic Education Programs: A Dissertation, Susan Noyes Spear

Educational Studies Dissertations

Research indicates that significant numbers of adult learners who attend adult basic education (ABE) programs have learning difficulties and/or learning disabilities. However, most ABE teachers have not been trained to teach students with these complex learning needs. This qualitative study, conducted through an interpretivist/constructivist lens, used in-depth individual interviews to garner the voices and experiences of ten ABE teachers as they described how they identify and manage the learning needs of their students. Results showed that ABE teachers described their practice in terms of how they identified their students' learning difficulties; their perceptions of their identity and role as an …

A Multi-Agent Prediction Market Based On Boolean Network Evolution, Janyl Jumadinova, Mihaela Teodora Matache, Prithviraj Dasgupta

Mathematics Faculty Proceedings & Presentations

—Prediction markets have been shown to be a useful tool in forecasting the outcome of future events by aggregating public opinion about the events’ outcome. Previous research on prediction markets has mostly analyzed the prediction markets by building complex analytical models. In this paper, we posit that simpler yet powerful Boolean rules can be used to adequately describe the operations of a prediction market. We have used a multi-agent based prediction market where Boolean network based rules are used to capture the evolution of the beliefs of the market’s participants, as well as to aggregate the prices in the market. …

Boolean Modeling Of Biochemical Networks, Tomáš Helikar, Naomi Kochi, John Konvalina, Jim A. Rogers

Mathematics Faculty Publications

The use of modeling to observe and analyze the mechanisms of complex biochemical network function is becoming an important methodological tool in the systems biology era. Number of different approaches to model these networks have been utilized-- they range from analysis of static connection graphs to dynamical models based on kinetic interaction data. Dynamical models have a distinct appeal in that they make it possible to observe these networks in action, but they also pose a distinct challenge in that they require detailed information describing how the individual components of these networks interact in living cells. Because this level of …

Bereaved Parents' Experiences Of Supportive And Unsupportive Communication, Paige W. Toller

Communication Faculty Publications

This study examines bereaved parents' experiences of supportive and unsupportive communication using the optimal matching model of stress and social support (Cutrona & Russell, 1990). Analysis of the interviews revealed that parents described action-facilitating support as supportive, although information-giving was experienced as unsupportive. Regarding nurturant support, bereaved parents felt emotionally supported when family and friends were willing to talk about their deceased child. Parents also described network support as helping them cope with their grief. The results of this study indicate that listening, being present, and honoring the ongoing connection parents have with their deceased child are key ways …

Sla P-16 Initiative, Volume 2, Issue 1, Fall 2011, University Of Nebraska Omaha, Service Learning Academy

SLA Newsletters

No abstract provided.

Family Structure As A Social Context For Family Conflict: Unjust Strain And Serious Delinquency, Ryan E. Spohn, Don L. Kurtz

Criminology and Criminal Justice Faculty Publications

Two major themes in the delinquency literature are the roles of family structure and childhood victimization. Combining these two lines of research, the current project examines the unique contribution of family structure and victimization on the serious delinquency of a nationally representative sample of adolescents. In addition, we examine whether the form of families serves to condition the relationship between victimization and delinquency. Past research indicates that abuse is more likely to occur in two-parent families of a ‘‘mixed’’ form, specifically in the presence of a live-in boyfriend or stepfather. However, little is known regarding the impact of victimization on …

2010 Nebraska Population Reports, David Drozd

Past Publications

This report compiles a selection of data analysis tables that were created throughout 2011 and 2012 by staff at the UNO Center for Public Affairs Research using data from the 2000 Census.

Identifying Modular Function Via Edge Annotation In Gene Correlation Networks Using Gene Ontology Search, Kathryn Dempsey Cooper, Ishwor Thapa, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks provide a powerful tool for analyzing large sets of biological information. This method of high-throughput data modeling has important implications in uncovering novel knowledge of cellular function. Previous studies on other types of network modeling (protein-protein interaction networks, metabolomes, etc.) have demonstrated the presence of relationships between network structures and organization of cellular function. Studies with correlation network further confirm the existence of such network structure and biological function relationship. However, correlation networks are typically noisy and the identified network structures, such as clusters, must be further investigated to verify actual cellular function. This is traditionally done using …

Evaluation Of Essential Genes In Correlation Networks Using Measures Of Centrality, Kathryn Dempsey Cooper, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks are emerging as powerful tools for modeling relationships in high-throughput data such as gene expression. Other types of biological networks, such as protein-protein interaction networks, are popular targets of study in network theory, and previous analysis has revealed that network structures identified using graph theoretic techniques often relate to certain biological functions. Structures such as highly connected nodes and groups of nodes have been found to correspond to essential genes and protein complexes, respectively. The correlation network, which measures the level of co-variation of gene expression levels, shares some structural properties with other types of biological networks. We …

A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks are emerging as a powerful tool for modeling temporal mechanisms within the cell. Particularly useful in examining coexpression within microarray data, studies have determined that correlation networks follow a power law degree distribution and thus manifest properties such as the existence of “hub” nodes and semicliques that potentially correspond to critical cellular structures. Difficulty lies in filtering coincidental relationships from causative structures in these large, noise-heavy networks. As such, computational expenses and algorithm availability limit accurate comparison, making it difficult to identify changes between networks. In this vein, we present our work identifying temporal relationships from microarray data …

A Noise Reducing Sampling Approach For Uncovering Critical Properties In Large Scale Biological Networks, Karthik Duraisamy, Kathryn Dempsey Cooper, Hesham Ali, Sanjukta Bhowmick

Interdisciplinary Informatics Faculty Proceedings & Presentations

A correlation network is a graph-based representation of relationships among genes or gene products, such as proteins. The advent of high-throughput bioinformatics has resulted in the generation of volumes of data that require sophisticated in silico models, such as the correlation network, for in-depth analysis. Each element in our network represents expression levels of multiple samples of one gene and an edge connecting two nodes reflects the correlation level between the two corresponding genes in the network according to the Pearson correlation coefficient. Biological networks made in this manner are generally found to adhere to a scale-free structural nature, that …

Graduate Academic Catalog (2011-2012), University Of Nebraska At Omaha

Graduate Catalogs

For many, earning a graduate degree is a way to advance in a career, for others it's the next step toward a doctorate degree and for others it's the right thing to do. At the University of Nebraska at Omaha (UNO) you'll experience a university dedicated to being a leading resource for graduate study, one that offers the right learning environment focused on your success.

As a graduate student at UNO, you will have the opportunity to develop independent scholarship and gain greater competence in research and other applied activities. Rigor, combined with real-world experience and innovation help create a …

Virtual Cgh: An Integrative Approach To Predict Genetic Abnormalities From Gene Expression Microarray Data Applied In Lymphoma, Huimin Geng, Javeed Iqbal, Hesham Ali

Information Systems and Quantitative Analysis Faculty Publications

Background: Comparative Genomic Hybridization (CGH) is a molecular approach for detecting DNA Copy Number Alterations (CNAs) in tumor, which are among the key causes of tumorigenesis. However in the post-genomic era, most studies in cancer biology have been focusing on Gene Expression Profiling (GEP) but not CGH, and as a result, an enormous amount of GEP data had been accumulated in public databases for a wide variety of tumor types. We exploited this resource of GEP data to define possible recurrent CNAs in tumor. In addition, the CNAs identified by GEP would be more functionally relevant CNAs in the disease …

Rigorous Assessment And Integration Of The Sequence And Structure Based Features To Predict Hot Spots, Ruoying Chen, Wenjing Chen, Sixiao Yang, Di Wu, Yong Wang, Yingjie Tian, Yong Shi

Information Systems and Quantitative Analysis Faculty Publications

Background

Systematic mutagenesis studies have shown that only a few interface residues termed hot spots contribute significantly to the binding free energy of protein-protein interactions. Therefore, hot spots prediction becomes increasingly important for well understanding the essence of proteins interactions and helping narrow down the search space for drug design. Currently many computational methods have been developed by proposing different features. However comparative assessment of these features and furthermore effective and accurate methods are still in pressing need.

Results

In this study, we first comprehensively collect the features to discriminate hot spots and non-hot spots and analyze their distributions. We …

Biomimetic Precipitation Of Uniaxially Grown Calcium Phosphate Crystals From Full-Length Human Amelogenin Sols, Vuk Uskoković, Wu Li, Stefan Habelitz

Pharmacy Faculty Articles and Research

Human dental enamel forms over a period of 2 – 4 years by substituting the enamel matrix, a protein gel mostly composed of a single protein, amelogenin with fibrous apatite nanocrystals. Self-assembly of a dense amelogenin matrix is presumed to direct the growth of apatite fibers and their organization into bundles that eventually comprise the mature enamel, the hardest tissue in the mammalian body. This work aims to establish the physicochemical and biochemical conditions for the synthesis of fibrous apatite crystals under the control of a recombinant fulllength human amelogenin matrix in combination with a programmable titration system. The growth …

Building Spaces To Grow New Ideas: Research 2011, University Office Of Research, South Dakota State University

State of Discovery South Dakota State University's Research Magazine

CONTENTS:

Feeding the World [Page] 2
A Light on New Possibilities [Page] 4
Designing New Tools [Page] 6
Wellness Science [Page] 8
Renovating a Science Resource [Page] 10
Connect World Possibilities [Page] 12
Transfer Research [Page] 14

Patent Protection Of Medical Records—Focusing On Ethical Issues, Yūsuke Satō, Jiameng Kathy Liu

Washington International Law Journal

The following is a translation of “Patent Protection of Medical Methods—Focusing on Ethical Issues,” an article written by Professor Yūsuke Satō in the June 2007 issue of the Japanese periodical Annual of Industrial Property Law. In Japan, despite the lack of an explicit statutory prohibition, methods of medical treatment have never been patentable. The Japan Patent Office (“JPO”) has rejected patenting medical processes on ethical grounds, interpreting that they do not fulfill the statutory requirement of “industrial applicability” in the main sentence of Article 29, Section 1 of the Patent Act, and courts have been confirming this practice. In light …

Establishing Appropriate Water Quality Numeric Standards Under The Clean Water Act: Lessons From A Case Study Of Coalbed Methane Produced Water Discharge To The Powder River, Wyoming And Montana, Carol D. Frost, Jason M. Mailloux

Wyoming Law Review

No abstract provided.

Family Law - Blood As Best Interests: The Wyoming Supreme Court Expands Associational Rights And The Preference For Kinship Placement; In Re Jw, 226 P.3d 873 (Wyo, 2010), Leah C. Schwartz

Wyoming Law Review

No abstract provided.

Analysis Of Electrodeposited Nickel-Iron Alloy Film Composition Using Particle-Induced X-Ray Emission, Alyssa Frey, Nicholas Wozniak, Timothy Nagi, Matthew Keller, J. Mark Lunderberg, Graham F. Peaslee, Paul Deyoung, Jennifer R. Hampton

Faculty Publications

The elemental composition of electrodeposited NiFe thin films was analyzed with particle-induced X-ray emission (PIXE). The thin films were electrodeposited on polycrystalline Au substrates from a 100mM NiSO₄, 10 mM FeSO₄, 0.5M H₃BO₃, and 1M Na₂SO₄ solution. PIXE spectra of these films were analyzed to obtain relative amounts of Ni and Fe as a function of deposition potential and deposition time. The results show that PIXE can measure the total deposited metal in a sample over at least four orders of magnitude with similar fractional uncertainties. The technique is …

H.B. 190: Policing School Districts, But At What Expense?, Andrew Schoenling

University of Dayton Law Review

No abstract provided.

Summary Of Findings From The 2011 Child Death Review Annual Report, Nevada Institute For Children's Research And Policy Reports

Nevada Institute for Children's Research and Policy Reports

The 2011 Annual Report of Child Deaths in Clark County, Nevada provides data regarding all infant, child, and fetal (over 20 weeks gestation) deaths occurring in Clark County in 2011. This represents the second year that the Child Death Review Team in Clark County reviewed 100% of the child deaths referred to the team by the Clark County Office of the Coroner/Medical Examiner; this includes all natural deaths, as well as all accidents, homicides, suicides, and undetermined cases. The team also reviewed all fetal deaths over 20 weeks gestation.

Parental Influence On Adolescent’S Academic Performance, Jessica Schmuck

The Journal of Undergraduate Research

The purpose of this survey research was to uncover how the relationship of parental involvement and parenting styles influence their adolescent’s academic performance and success. Parents need to be actively involved in their adolescent’s life, support and provide assistance with school and help instill motivation and confidence. This research was conducted by personally distributing surveys to a class of students at the Brookings High School in October 2010. The survey found that half of the participating adolescent’s stated that their parents had a strong influence on their academic performance. This was critical information because it supported previous research conducted regarding …

Vibrational Analysis Of Soloflex Whole Body Vibration Platform, Zachary Croatt, Josh Robers

The Journal of Undergraduate Research

A Soloflex Whole Body Vibration (WBV) Platform was tested for its frequency and magnitude of vibration at multiple settings on the supplied dial. An accelerometer was used to measure the vibrations on different points mapped across the platform. The motor attached to the board was also tested for its frequency using a high-speed camera. The amplitude measurements found from the accelerometer data was compared to the readings on the supplied control module to “calibrate” the platform for medical testing.