Digital Commons Network^™

Predictive Power Estimation Algorithm (Ppea) - A New Algorithm To Reduce Overfitting For Genomic Biomarker Discovery, Jiangang Liu, Robert A. Jolly, Aaron T. Smith, George H. Searfoss, Keith M. Goldstein, Vladimir N. Uversky, Keith Dunker, Shuyu Li, Craig E. Thomas, Tao Wei

Molecular Medicine Faculty Publications

Toxicogenomics promises to aid in predicting adverse effects, understanding the mechanisms of drug action or toxicity, and uncovering unexpected or secondary pharmacology. However, modeling adverse effects using high dimensional and high noise genomic data is prone to over-fitting. Models constructed from such data sets often consist of a large number of genes with no obvious functional relevance to the biological effect the model intends to predict that can make it challenging to interpret the modeling results. To address these issues, we developed a novel algorithm, Predictive Power Estimation Algorithm (PPEA), which estimates the predictive power of each individual transcript through …

Effects Of Hmgn Variants On The Cellular Transcription Profile, Mark Rochman, Leila Taher, Toshihiro Kurahashi, Srujana Cherukuri, Vladimir N. Uversky, David Landsman, Ivan Ovcharenko, Michael Bustin

Molecular Medicine Faculty Publications

High mobility group N (HMGN) is a family of intrinsically disordered nuclear proteins that bind to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between the various members of the HMGN protein family. Here, we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. We find that both up- and downregulation of HMGN expression altered the cellular transcription profile. Most, but not all of the changes were variant specific, suggesting limited redundancy in transcriptional regulation. Analysis …

An Empirical Approach To Derive Modis Ocean Color Patterns Under Severe Sun Glint, Chuanmin Hu

Marine Science Faculty Publications

Oil tracking in the Gulf of Mexico in response to the Deepwater Horizon accident requires timely and accurate observations of major circulation patterns such as the Loop Current and LC eddies. When the eastern GOM becomes nearly isothermal at the surface and the use of sea surface temperature imagery is limited, MODIS ocean color data can be used instead. However, frequent and extensive sun glint prevents such an application when glint reflectance, Lg, is >0.01 sr⁻¹. Here, an empirical approach is developed to remove sun glint and clouds based on band ratios between the Rayleigh-corrected reflectance ( …

Cover, Ornitología Neotropical

Ornitología Neotropical

No abstract provided.

Proceedings Of The 2011 International Conference On Karst Hydrogeology And Ecosystems, Jason Samuel Polk, Leslie A. North

Environmental Sustainability Books

Jointly sponsored by the Hoffman Environmental Research Institute, the National Cave & Karst Research Institute, and the International Association of Hydrogeologists, the 2011 International Conference on Karst Hydrogeology and Ecosystems was held at Western Kentucky University in Bowling Green, Kentucy on 8-10 June 2011. Topics include karst geomorphology, engineering and modeling, isotope geochemistry, and cultural and educational aspects of karst environments.

Concerning Statutory Changes Involving K-12 Education, And Making An Appropriation In Connection Therewith., Colorado General Assembly

Session Laws 2001-Present

No abstract provided.

Concerning The Creation Of A Cash Fund For Fees Collected In Connection With The Department Of Public Health And Environment's Laboratories., Colorado General Assembly

Session Laws 2001-Present

No abstract provided.

Concerning The Protection Of Livestock Producer Information Collected By The Department Of Agriculture., Colorado General Assembly

Session Laws 2001-Present

No abstract provided.

Switchgrass, Kenneth P. Vogel, Gautam Sarath, Aaron J. Saathoff, Robert B. Mitchell

Department of Agronomy and Horticulture: Faculty Publications

17.1 Introduction

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that is native to North America that is being developed into a biomass energy crop. It has been used in pastures and for conservation purposes in the Great Plains and the Midwest, USA, for over 70 years.1 The research supporting its use as a pasture and conservation species was largely conducted by US Department of Agriculture (USDA) research programs, most notably the Agricultural Research Service (ARS) project located at the University of Nebraska-Lincoln and USDA Plant Materials Centers that are located throughout the United States. In this report, …

Identification Of A Second Asian Soybean Rust Resistance Gene In Hyuuga Soybean, Mandy D. Kendrick, Donna K. Harris, Bo-Keun Ha, D. L. Hyten, P. B. Cregan, Reid D. Frederick, H. Roger Boerma, Kerry F. Pedley

Department of Agronomy and Horticulture: Faculty Publications

Asian soybean rust (ASR) is an economically significant disease caused by the fungus Phakopsora pachyrhizi. The soybean genes Rpp3 and Rpp?(Hyuuga) confer resistance to specific isolates of the pathogen. Both genes map to chromosome 6 (Gm06) (linkage group [LG] C2). We recently identified 12 additional soybean accessions that harbor ASR resistance mapping to Gm06, within 5 centimorgans of Rpp3 and Rpp?(Hyuuga). To further characterize genotypes with resistance on Gm06, we used a set of eight P. pachyrhizi isolates collected from geographically diverse areas to inoculate plants and evaluate them for differential phenotypic responses. …

Mutational Analysis Of The Major Soybean Uref Paralogue Involved In Urease Activation, Joe C. Polacco, D. L. Hyten, Mônica Medeiros-Silva, David A. Sleper, Kristin D. Bilyeu

Department of Agronomy and Horticulture: Faculty Publications

The soybean genome duplicated ~14 and 45 million years ago and has many paralogous genes, including those in urease activation (emplacement of Ni and CO₂ in the active site). Activation requires the UreD and UreF proteins, each encoded by two paralogues. UreG, a third essential activation protein, is encoded by the single-copy Eu3, and eu3 mutants lack activity of both urease isozymes. eu2 has the same urease-negative phenotype, consistent with Eu2 being a single-copy gene, possibly encoding a Ni carrier. Unexpectedly, two eu2 alleles co-segregated with missense mutations in the chromosome 2 UreF paralogue (Ch02UreF), suggesting …

Cytokinin-Mediated Source ⁄Sink Modifications Improve Drought Tolerance And Increase Grain Yield In Rice Under Water-Stress, Zvi Peleg, Maria Reguera, Ellen Tumimbang, Harkamal Walia, Eduardo Blumwald

Department of Agronomy and Horticulture: Faculty Publications

Drought is the major environmental factor limiting crop productivity worldwide. We hypothesized that it is possible to enhance drought tolerance by delaying stress-induced senescence through the stress-induced synthesis of cytokinins in crop-plants. We generated transgenic rice (Oryza sativa) plants expressing an isopentenyltransferase (IPT) gene driven by PSARK, a stress- and maturation-induced promoter. Plants were tested for drought tolerance at two yield-sensitive developmental stages: pre- and post-anthesis. Under both treatments, the transgenic rice plants exhibited delayed response to stress with significantly higher grain yield (GY) when compared to wild-type plants. Gene expression analysis revealed a significant shift in expression of hormone-associated …

Evolutionary Variation Of Papillomavirus E2 Protein And E2 Binding Sites, Adam Rogers, Mackenzie Waltke, Peter C. Angeletti

Nebraska Center for Virology: Faculty Publications

Background: In an effort to identify the evolutionary changes relevant to E2 function, within and between papillomavirus genera, we evaluated the E2 binding sites (E2BS)s inside the long-control-region (LCR), and throughout the genomes. We identified E2BSs in the six largest genera of papillomaviruses: Alpha, Beta, Gamma, Delta, Lambda, and Xi-papillomaviruses (128 genomes), by comparing the sequences with a model consensus we created from known functional E2BSs (HPV16, HPV18, BPV1). We analyzed the sequence conservation and nucleotide content of the 4-nucleotide spacer within E2BSs. We determined that there is a statistically significant difference in GC content of the four-nucleotide E2BS …

Critical Role Of Leucine-Valine Change In Distinct Low Ph Requirements For Membrane Fusion Between Two Related Retrovirus Envelopes, Marceline Côté, Yi-Min Zheng, Kun Li, Shi-Hua Xiang, Lorraine M. Albritton, Shan-Lu Liu

Nebraska Center for Virology: Faculty Publications

Many viruses use a pH-dependent pathway for fusion with host cell membrane, the mechanism of which is still poorly understood. Here we report that a subtle leucine (Leu)-valine (Val) change at position 501 in the envelope glycoproteins (Envs) of two related retroviruses, jaagsiekte sheep retro-virus (JSRV) and enzootic nasal tumor virus (ENTV), is responsible for their distinct low pH requirements for membrane fusion and infection. The Leu and Val residues are predicted to reside within the C-terminal heptad repeat (HR2) region of JSRV and ENTV Envs, particularly proximal to the hairpin turn of the putative six-helix bundle (6HB). Substitution of …

Hiv-1 Effects On Neuropsychological Performance In A Resource-Limited Country, Zambia, Gabriel Holguin, Mwanza Banda, Elizabeth J. Willen, Costantine Malama, Kaseya O. Chiyenu, Victor C. Mudenda, Charles Wood

Nebraska Center for Virology: Faculty Publications

Zambia has substantially been affected by the HIV/AIDS epidemic with prevalence rates at 14% in a population estimated at 12 million. Yet, the extent of HIV-associated neurocognitive disorders (HAND) in this population remains to be clearly understood. A series of culturally appropriate neuropsychological (NP) assessments [International HIV Dementia Scale (IHDS), Color Trails Test 1 and 2, Grooved pegboard Test, and Time Gait Test] were used to test the effects of HIV on NP performance of HIV seropositive and seronegative individuals. Twenty-two percent HIV positive individuals ARV naïve met the criteria for IHDS-defined NP impairment. Gender significantly influenced the performance on …

Characterization Of Species C Human Adenovirus Serotype 6 (Ad6), Eric A. Weaver, Reeti Khare, Mathew L. Hillestad, Donna Palmer, Philip Ng, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Adenovirus serotype (Ad5) is the most studied Ad. Ad1, 2, and 6 are also members of species C Ad and are presumed to have biologies similar to Ad5. In this work, we have compared the ability of Ad1, 2, 5, and 6 to infect liver and muscle after intravenous and intramuscular injection. We found that Ad6 was surprisingly the most potent at liver gene delivery and that Ad1 and Ad2 were markedly weaker than Ad5 and 6. To understand these differences, we sequenced the Ad6 genome. This revealed that the Ad6 fiber protein is surprisingly three shaft repeats shorter than …

Generation Of A Kupffer Cell-Evading Adenovirus For Systemic And Liver-Directed Gene Transfer, Reeti Khare, Shannon M. May, Francesco Vetrini, Eric A. Weaver, Donna Palmer, Amanda Rosewell, Nathan Grove, Philip Ng, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

As much as 90% of an intravenously (i.v.) injected dose of adenovirus serotype 5 (Ad5) is absorbed and destroyed by liver Kupffer cells. Viruses that escape these cells can then transduce hepatocytes after binding factor X (FX). Given that interactions with FX and Kupffer cells are thought to occur on the Ad5 hexon protein, we replaced its exposed hypervariable regions (HVR) with those from Ad6. When tested in vivo in BALB/c mice and in hamsters, the Ad5/6 chimera mediated >10 times higher transduction in the liver. This effect was not due to changes in FX binding. Rather, Ad5/6 appeared to …

Great Lakes, Great Potential: Examining The Regulatory Framework For Wind Farms In The Great Lakes, Katherine Saks

Canada-United States Law Journal

No abstract provided.

Fact Book 2010-2011, Various

General Fiscal Chronicle

Annual Report to the Board Of Trustees of George Fox College

Receptivity To Library Involvement In Scientific Data Curation: A Case Study At The University Of Colorado Boulder, Kathryn Lage, Barbara Losoff, Jack M. Maness

University Libraries: Faculty Scholarship

Increasingly libraries are expected to play a role in scientific data curation initiatives, i.e., "the management and preservation of digital data over the long-term." This case study offers a novel approach for identifying researchers who are receptive toward library involvement in data curation. The authors interviewed researchers at the University of Colorado Boulder and, after analysis, created eight design "personas." Each persona represents an aggregation of researcher attributes and can be used to target strategic relationships for nascent or emerging data management initiatives. These personas are applicable to any academic library seeking to provide data curation support.

Teacher Bullies: A Factorial Analysis Of Perceptions Of Teachers' Bullying Behaviors, Sally Walter Davies

All-Inclusive List of Electronic Theses and Dissertations

Bullying in schools is a global phenomenon that can infringe upon the rights of students to learn and grow in a secure and fostering environment. Most of the past and current research on school bullying focuses on peer bullying, but there is a gap in the understanding of types and characteristics of bullying behaviors. This study centered on a type of abusive behavior that has received very limited attention: teachers bullying students. For the purpose of this study, the definition of teacher bullying behavior is a repeated pattern of conduct used to punish, manipulate, or disparage a student, rooted in …

The Affective Blindness Of Evidence Law, Teneille R. Brown

Utah Law Faculty Scholarship

Evidentiary rules and practices reveal a folk psychological view of emotion, placing it at odds with reason. Specifically, many substantive and procedural rules of evidence explicitly require jurors to turn off their emotions in favor of rational, so-called “top-down,” executive thinking. In order to make the point that this dichotomy between emotion and reason is simultaneously reflected in our evidence law and also empirically wrong, I will address how emotion is treated in (a) the use of limiting instructions, (b) the exclusion of prejudicial evidence, (c) credibility assessments, (d) sentencing and damages instructions, (e) instructions related to the “heat of …

Perry V. Schwarzenegger And The Future Of Same-Sex Marriage Law, Clifford Rosky

Utah Law Faculty Scholarship

In Perry v. Schwarzenegger, Chief Judge Vaughn Walker held that Proposition 8 — an amendment to the California Constitution that prohibits same-sex couples from marrying — violates the Due Process and Equal Protection Clauses of the Fourteenth Amendment. To date, legal experts have claimed that although Judge Walker’s factual findings may be novel and significant, his legal analysis is familiar and not likely to have a significant impact, in this case or others. This Article argues that the common wisdom about Judge Walker’s ruling is misguided, because it overlooks novel aspects of Judge Walker’s legal analysis that have the potential …

Immediate Implant Placement And Provisionalization With Simultaneous Guided Bone Regeneration In The Esthetic Zone, Chih-Long Chen, Chih-Ling Chang, Shih-Jung Lin

Journal of Dental Sciences

Abstract The procedure for immediate implant placement and provisionalization is time-saving, possibly with only one surgical intervention required, although allowing maximal preservation of peri-implant tissues. In this case, we extracted a fractured maxillary right central incisor of a 46-year-old woman with high esthetic expectations, and a transmucosal implant was immediately installed. Simultaneous guided bone regeneration was performed to correct the defects at the facial side of the socket and augment the alveolar ridge horizontally. Primary stability of the implant body and wound closure without tension were confirmed. Connection of a 15° angled abutment and fabrication of a provisional acrylic resin …

Molecular Bases Of Cutaneous And Uveal Melanomas, Sudeep Gaudi, Jane L. Messina

Pathology and Cell Biology Faculty Publications

Intensive research in recent years has begun to unlock the mysteries surrounding the molecular pathogenesis of melanoma, the deadliest of skin cancers. The high-penetrance, low-frequency susceptibility gene CDKN2A produces tumor suppressor proteins that function in concert with p53 and retinoblastoma protein to thwart melanomagenesis. Aberrant CDKN2A gene products have been implicated in a great many cases of familial cutaneous melanoma. Sporadic cases, on the other hand, often involve constitutive signal transduction along the mitogen-activated protein kinase (MAPK) pathway, with particular focus falling upon mutated RAS and RAF protooncogenes. The proliferative effects of the MAPK pathway may be complemented by the …

Primary Colorectal Adenocarcinoma Metastatic To The Breast: Case Report And Review Of Nineteen Cases, Rodney E. Shackelford, Pushpa Allam-Nandyala, Marilyn M. Bui, John V. Kiluk, Nicole Nicosia Esposito

Pathology and Cell Biology Faculty Publications

Metastases to the breast from extramammary primaries are uncommon and account for 0.5–6% of all breast malignancies (Georgiannos et al., 2001, and Vizcaíno et al., 2001). Malignant melanoma, lymphoma, and lung and gastric carcinomas are the most frequently encountered nonmammary metastases to the breast in adults (Georgiannos et al., 2001, and Chaignaud et al., 1994). Primary colorectal adenocarcinoma (CRC) metastatic to the breast is extremely rare, with the medical literature having only 19 recorded cases. Typically CRC metastatic to the breast is indicative of widely disseminated disease and a poor prognosis. Here we present a case of poorly differentiated colon …

Pathology Of Breast Carcinoma: Diagnostic, Prognostic, And Therapeutic Issues And Challenges, Rohit Bhargava, Sunati Sahoo, Nicole Nicosia Esposito, Beiyun Chen

Pathology and Cell Biology Faculty Publications

No abstract provided.

Novel Molecular Markers Of Malignancy In Histologically Normal And Benign Breast, Aejaz Nasir, Dung-Tsa Chen, Mike Gruidl, Evita B. Henderson-Jackson, Chinnambally Venkataramu, Susan M. Mccarthy, Heyoung L. Mcbrid, Eleanor Harris, Nazanin Khakpour, Timothy J. Yeatman

Pathology and Cell Biology Faculty Publications

To detect the molecular changes of malignancy in histologically normal breast (HNB) tissues, we recently developed a novel 117-gene-malignancy-signature. Here we report validation of our leading malignancy-risk-genes, topoisomerase-2-alpha (TOP2A), minichromosome-maintenance-protein-2 (MCM2) and “budding-uninhibited-by-benzimidazoles-1-homolog-beta” (BUB1B) at the protein level. Using our 117-gene malignancy-signature, we classified 18 fresh-frozen HNB tissues from 18 adult female breast cancer patients into HNB-tissues with low-grade (HNB-LGMA; ) and high-grade molecular abnormality (HNB-HGMA; ). Archival sections of additional HNB tissues from these patients, and invasive ductal carcinoma (IDC) tissues from six other patients were immunostained for these biomarkers. TOP2A/MCM2 expression was assessed as staining index (%) and …

Ovarian Epithelial-Stromal Interactions: Role Of Interleukins 1 And 6, Kamisha T. Woolery, Patricia A. Kruk

Pathology and Cell Biology Faculty Publications

Ovarian epithelial cancer is the most lethal gynecologic malignancy. The high mortality is attributed to the fact that most cases typically present in late stage when ovarian cancer (OC) has already spread beyond the ovary. Ovarian epithelial cancer cells are shed into intraperitoneal ascites and easily disseminate throughout the peritoneal cavity with preferential metastasis to the omentum, peritoneum, and local organs. Understanding how ovarian epithelial cells interact with and modulate their microenvironment can provide insight into the molecular mechanism(s) involved with malignant transformation and progression which may eventually identify novel diagnostic, prognostic, and therapeutic targets. The objective of this paper …

Toward Personalized Cell Therapies: Autologous Menstrual Blood Cells For Stroke, Maria Carolina O. Rodrigues, Loren E. Glover, Nathan Weinbren, Jessica A. Rizzi, Kazutaka Shinozuka, Naoki Tajiri, Yuji Kaneko, Paul R. Sanberg, Julie G. Allickson, Nicole Kuzmin-Nichols, Svitlana Garbuzova-Davis, Julio Cesar Voltarelli, Eduardo Cruz, Cesar V. Borlongan

Neurosurgery and Brain Repair Faculty Publications

Cell therapy has been established as an important field of research with considerable progress in the last years. At the same time, the progressive aging of the population has highlighted the importance of discovering therapeutic alternatives for diseases of high incidence and disability, such as stroke. Menstrual blood is a recently discovered source of stem cells with potential relevance for the treatment of stroke. Migration to the infarct site, modulation of the inflammatory reaction, secretion of neurotrophic factors, and possible differentiation warrant these cells as therapeutic tools. We here propose the use of autologous menstrual blood cells in the restorative …