Digital Commons Network^™

A Snp Discovery Method To Assess Variant Allele Probability From Next-Generation Resequencing Data, Yufeng Shen, Zhengzheng Wan, Cristian Coarfa, Rafal Drabek, Lei Chen, Elizabeth A. Ostrowski, Yue Liu, George M. Weinstock, David A. Wheeler, Richard A. Gibbs, Fuli Yu

Open Access Publications

No abstract provided.

More Than Tuskegee: Understanding Mistrust About Research Participation, Darcell P. Scharff, Katherine J. Mathews, Pamela Jackson, Jonathan Hoffsuemmer, Emeobong Martin, Dorothy Edwards

Open Access Publications

No abstract provided.

Loss Of Par-1a/Mark3/C-Tak1 Kinase Leads To Reduced Adiposity, Resistance To Hepatic Steatosis, And Defective Gluconeogenesis, Jochen K. Lennerz, Jonathan B. Hurov, Lynn S. White, Katherine T. Lewandowski, Julie L. Prior, G. James Planer, Robert W. Gereau Iv, David Piwnica-Worms, Robert E. Schmidt, Helen Piwnica-Worms

Open Access Publications

No abstract provided.

Cd46 Engagement On Human Cd4+ T Cells Produces T Regulatory Type 1-Like Regulation Of Antimycobacterial T Cell Responses, Steven M. Truscott, Getahun Abate, Jeffrey D. Price, Claudia Kemper, John P. Atkinson, Daniel F. Hoft

Open Access Publications

No abstract provided.

Characterization Of A Novel Murine Model Of Staphylococcus Saprophyticus Urinary Tract Infection Reveals Roles For Ssp And Sdri In Virulence, Kimberly A. Kline, Molly A. Ingersoll, Hailyn V. Nielsen, Turkan Sakinc, Michael G. Caparon, Scott J. Hultgren

Open Access Publications

No abstract provided.

Ccpa And Lacd.1 Affect Temporal Regulation Of Streptococcus Pyogenes Virulence Genes, Colin C. Kietzman, Michael G. Caparon

Open Access Publications

No abstract provided.

Macroecology Of Caribbean Bats: Effects Of Area, Elevation, Latitude, And Hurricane-Induced Disturbance, Michael R. Willig, Steven J. Presley, Christopher P. Bloch, Hugh H. Genoways

University of Nebraska State Museum: Mammalogy Papers

Understanding the geographic and environmental characteristics of islands that affect aspects of biodiversity is a major theme in ecology (Begon et al. 2006; Krebs 2001) and biogeography (Cox and Moore 2000; Drakare et al. 2006; Lomolino et al. 2006). Such understanding has become particularly relevant over the past century because human activities on continents have fragmented natural landscapes, often creating islands of isolated habitat dispersed within a sea of land uses that include agriculture, forestry, and various degrees of urban and suburban development. The increasingly fragmented or islandlike structure of mainland habitats has critical ramifications to conservation biology, as it …

Observations Of Reproduction In Mountain Lions From Nebraska, Sam Wilson, Justin D. Hoffman, Hugh H. Genoways

University of Nebraska State Museum: Mammalogy Papers

Occurrences of mountain lions (Puma concolor) in Nebraska have been steadily increasing; however, reproductive activity in mountain lions has not been documented in the state. We present the first evidence of mountain lion reproduction in Nebraska since mountain lions recolonized the state in the early 1990s. On 28 February 2007, a spotted kitten was hit by a vehicle in northwestern Nebraska; and based on body length and weight, we estimate its age at 3.9 months. On 20 December 2008, a female mountain lion and spotted kitten were photographed in the northwestern part of the state. On 9 May …

The Seed, Bob Henrickson, Justin R. Evertson

Nebraska Statewide Arboretum: Publications

Too often, groundcovers are not considered when new landscape plantings are installed. Traditionally, the soil surface of new planting beds that incorporate trees, shrubs and herbaceous perennials is covered with a 2-3” layer of organic mulch. The organic mulch helps to conserve moisture, control weeds and give the landscape a uniform, finished look. However, it usually takes a number of years before the plants mature, prompting a yearly top-dressing of mulch to keep the open areas covered. This yearly addition of mulch can be relatively expensive and excessive mulch can build up on the soil. It can also be a …

Droughtscape, Winter 2010, Kelly Smith

DroughtScape: Quarterly Newsletter of the National Drought Mitigation Center (2007–2023)

USDM Forum Highlights

Drought Likely to Ease

Research Shows Birds Vulnerable to Drought

Drought Recedes in 2009

CA, TX Suffer Impacts from Ongoing Drought

NDMC Wishes Ryu Well

Conferees Pick SPI for Global Drought Index

Will California Law Apply To Hubbs-Seaworld Research Institute’S Offshore Aquaculture Demonstration Project? An Analysis Of Theextraterritorial Application Of State Aquaculture Laws, Stephanie Showalter

UC Law Environmental Journal

No abstract provided.

On Thin Ice: How A Binding Treaty Regime Can Save The Arctic, Bonnie A. Malloy

UC Law Environmental Journal

No abstract provided.

A Dreadful Prognosis: Patentability Of Diagnostic And Personalized Medical Procedures In The Wake Of In Re Bilski, Matthew D. Show

UC Law Science and Technology Journal

Over the past few decades, patent applicants in certain technological fields are discovering a conflict inherent between the nature of their claimed inventions and judicial interpretation of Jefferson's Patent Act language throughout the 19th and 20th Centuries. This conflict is particularly apparent in the fields of diagnostic and personalized medicine. This note discusses both modern Supreme Court precedent regarding the requirements for a patentable method claim as how Bilski v. Doll, a business method case, threatens to make such methods unpatentable. Additionally, this note offers the results of an analysis demonstrating how patent agents and attorneys currently draft these types …

Weed Control In Organic Cropping Systems, Stephen L. Young

West Central Research and Extension Center, North Platte

Organic producers and many conventional producers rank weed control as their number one production cost. For organic producers particularly, weed control has become increasingly important as organic production has increased its market share. According to the USDA Census of Agriculture, in 2005, for the first time, all 50 states had certified organic farmland, with over 1.6 million total ha (4 million acres) dedicated to organic production systems. In 2006, four major universities in the United States offered new degree programs in organic agriculture with the anticipation that, in five to six years, organic crops will comprise 5 to 10 percent …

The Development Of An Efficient Multipurpose Bean Pod Mottle Virus Viral Vector Set For Foreign Gene Expression And Rna Silencing, Chunquan Zhang, Jeffrey Bradshaw, Steven A. Whitham, John H. Hill

Panhandle Research and Extension Center

Plant viral vectors are valuable tools for heterologous gene expression, and because of virus-induced gene silencing (VIGS), they also have important applications as reverse genetics tools for gene function studies. Viral vectors are especially useful for plants such as soybean (Glycine max) that are recalcitrant to transformation. Previously, two generations of bean pod mottle virus (BPMV; genus Comovirus) vectors have been developed for overexpressing and silencing genes in soybean. However, the design of the previous vectors imposes constraints that limit their utility. For example, VIGS target sequences must be expressed as fusion proteins in the same reading …

Effect Of Crop Residue On Soil Water Content And Yield Of Deficit-Irrigated Corn And Soybean, Simon Van Donk, Steven R. Melvin, Jim Peterson, Don Davison

West Central Research and Extension Center, North Platte

It is believed that reduced tillage, with more crop residue on the soil surface, conserves water, especially in arid and semi-arid climates. However, the magnitude of water conservation is not clear. In 2007, a study was initiated on the effect of residue on soil water content and crop yield at North Platte, Nebraska. The experiment was conducted on plots planted to field corn (Zea mays L.) in 2007 and 2008, and soybean (Glycine max) in 2009. There were two treatments: residue-covered soil and bare soil. Bare-soil plots were created in April 2007 by using a dethatcher …

Effect Of Crop Residue On Soil Water Content And Yield Of Deficit-Irrigated Corn And Soybean, Simon Van Donk, Steven R. Melvin, James L. Petersen, Don Davison

West Central Research and Extension Center, North Platte

It is believed that reduced tillage, with more crop residue on the soil surface, conserves water, especially in arid and semi-arid climates. However, the magnitude of water conservation is not clear. In 2007, a study was initiated on the effect of residue on soil water content and crop yield at North Platte, Nebraska. The experiment was conducted on plots planted to field corn (Zea mays L.) in 2007 and 2008, and soybean (Glycine max) in 2009. There were two treatments: residue-covered soil and bare soil. Bare-soil plots were created in April 2007 by using a dethatcher and …

Ascochyta Blight Of Chickpeas, Robert M. Harveson, Samuel G. Markell, Rubella Goswami, Carlos A. Urrea, Mary E. Burrows, Frank Dugan, Weidong Chen, Linnea G. Skoglund

Panhandle Research and Extension Center

The chickpea (Cicer arietinum L.), also known as the garbanzo bean, is an annual grain legume crop that ranks among the world’s three most important pulses (seed legumes used as food). It is an important source of protein in many parts of central Asia and Africa. It was one of the first grain legumes domesticated in the Old World and is thought to have originated in present-day southeastern Turkey and northern Syria due to the endemic presence of its progenitor (Cicer reticulatum Ladiz.) in this area (1,36).

Historically chickpea has been a minor crop in the United States, …

Crop Residue Cover Effects On Evaporation, Soil Water Content, And Yield Of Deficit‐Irrigated Corn In West‐Central Nebraska, Simon Van Donk, Derrel L. Martin, Suat Irmak, Steven R. Melvin, Jim Peterson, Don Davison

West Central Research and Extension Center, North Platte

Competition for water is becoming more intense in many parts of the U.S., including west‐central Nebraska. It is believed that reduced tillage, with more crop residue on the soil surface, conserves water, but the magnitude of water conservation is not clear. A study was initiated on the effect of residue on soil water content and corn yield at North Platte, Nebraska. The experiment was conducted in 2007 and 2008 on plots planted to field corn (Zea mays L.). In 2005 and 2006, soybean was grown on these plots. There were two treatments: residue‐covered soil and bare soil. Bare‐soil plots …

Nebline, January 2010

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Feature: Tips for Positive Interactions with Tweens

Farm Views

Horticulture

Food & Fitness

Home & Family Living

Environmental Focus

Urban Agriculture

4-H & Youth

Community Focus

Extension Calendar

Nutrition Education Program

Family and Community Education (FCE) Clubs

and other extension news and events

Annual Report Special Pullout Section

The Trypanosoma Brucei Mitocarta And Its Regulation And Splicing Pattern During Development, Xiaobai Zhang, Juan Cui, Daniel Nilsson, Kapila Gunasekera, Astrid Chanfon, Xiaofeng Song, Huinan Wang, Ying Xu, Torsten Ochsenreiter

School of Computing: Faculty Publications

It has long been known that trypanosomes regulate mitochondrial biogenesis during the life cycle of the parasite; however, the mitochondrial protein inventory (MitoCarta) and its regulation remain unknown. We present a novel computational method for genome-wide prediction of mitochondrial proteins using a support vector machine-based classifier with ~90% prediction accuracy. Using this method, we predicted the mitochondrial localization of 468 proteins with high confidence and have experimentally verified the localization of a subset of these proteins. We then applied a recently developed parallel sequencing technology to determine the expression profiles and the splicing patterns of a total of 1065 predicted …

A Study Of Health Effects Of Long-Distance Ocean Voyages On Seamen Using A Data Classification Approach, Yunmei Lu, Yanhong Gao, Zhongbo Cao, Juan Cui, Zhennan Dong, Yaping Tian, Ying Xu

School of Computing: Faculty Publications

Background: Long-distance ocean voyages may have substantial impacts on seamen’s health, possibly causing malnutrition and other illness. Measures can possibly be taken to prevent such problems from happening through preparing special diet and making special precautions prior or during the sailing if a detailed understanding can be gained about what specific health effects such voyages may have on the seamen.

Methods: We present a computational study on 200 seamen using 41 chemistry indicators measured on their blood samples collected before and after the sailing. Our computational study is done using a data classification approach with a support vector machine-based classifier …

In-Silico Prediction Of Blood-Secretory Human Proteins Using A Ranking Algorithm, Qi Liu, Juan Cui, Qiang Yang, Ying Xu

School of Computing: Faculty Publications

Background: Computational identification of blood-secretory proteins, especially proteins with differentially expressed genes in diseased tissues, can provide highly useful information in linking transcriptomic data to proteomic studies for targeted disease biomarker discovery in serum.

Results: A new algorithm for prediction of blood-secretory proteins is presented using an information-retrieval technique, called manifold ranking. On a dataset containing 305 known blood-secretory human proteins and a large number of other proteins that are either not blood-secretory or unknown, the new method performs better than the previous published method, measured in terms of the area under the recall-precision curve (AUC). A key advantage …

Clustering Of Protein Families Into Functional Subtypes Using Relative Complexity Measure With Reduced Amino Acid Alphabets, Aydin Albayrak, Hasan H. Otu, Ugur O. Sezerman

Department of Electrical and Computer Engineering: Faculty Publications

Background: Phylogenetic analysis can be used to divide a protein family into subfamilies in the absence of experimental information. Most phylogenetic analysis methods utilize multiple alignment of sequences and are based on an evolutionary model. However, multiple alignment is not an automated procedure and requires human intervention to maintain alignment integrity and to produce phylogenies consistent with the functional splits in underlying sequences. To address this problem, we propose to use the alignment-free Relative Complexity Measure (RCM) combined with reduced amino acid alphabets to cluster protein families into functional subtypes purely on sequence criteria. Comparison with an alignment-based approach was …

Bioinformatic Identification And Characterization Of Human Endothelial Cell-Restricted Genes, Manoj Bhasin, Lei Yuan, Derin B. Keskin, Hasan H. Otu, Towia A. Libermann, Peter Oettgen

Department of Electrical and Computer Engineering: Faculty Publications

Background: In this study, we used a systematic bioinformatics analysis approach to elucidate genes that exhibit an endothelial cell (EC) restricted expression pattern, and began to define their regulation, tissue distribution, and potential biological role.

Results:Using a high throughput microarray platform, a primary set of 1,191 transcripts that are enriched in different primary ECs compared to non-ECs was identified (LCB >3, FDR

Conclusion: The study provides an initial catalogue of EC-restricted genes most of which are ubiquitously expressed in different endothelial cells.

Numerical And Analytical Verification Of A Multiscale Computational Model For Impact Problems In Heterogeneous Viscoelastic Materials With Evolving Damage, Bruno Bachiega Araujo

Department of Engineering Mechanics: Dissertations, Theses, and Student Research

Composites are engineered materials that take advantage of the particular properties of each of its two or more constituents. They are designed to be stronger, lighter and to last longer which can lead to the creation of safer protection gear, more fuel efficient transportation methods and more affordable materials, among other examples.

This thesis proposes a numerical and analytical verification of an in-house developed multiscale model for predicting the mechanical behavior of composite materials with various configurations subjected to impact loading. This verification is done by comparing the results obtained with analytical and numerical solutions with the results found when …

The Tiger Career Fair Spring 2010, Clemson University

Tiger Newspapers

No abstract provided.

Not Everything In Its Path Confusion And Coping On The Bolivar Penninsula After Hurricane Ike, Mary Barnes

Theses & ETDs

This is an ethnographic study of the social effects of Hurricane Ike (2008) on Gilchrist and Crystal Beach, two communities on the Bolivar Peninsula, a strip of land near Galveston, TX. Using community member�s experiences, I examine the ways in which their recovery efforts were complicated by disputes with insurance agencies and engagement with the media. I then discuss some of the coping mechanisms that residents employed, including reestablishing community groups, using online communication tools, comparing Hurricane Ike to the Hurricane Katrina, verbally affirming their resilience, and reflecting on the importance of place and material belongings. I found that, nine …

Waterfowl Of North America: Stiff-Tailed Ducks, Tribe Oxyurini, Paul A. Johnsgard

Waterfowl of North America, Revised Edition (2010) by Paul A. Johnsgard

This bizarre group of diving ducks differs from the rest of the Anatidae in so many respects that by any standard it demands special attention. Of the eight species that are presently recognized, most are placed in the genus Oxyura, which name refers to the stiffened, elongated tail feathers typical of the group. In these species the tail feathers extend well beyond the rather short tail coverts and are usually narrow-vaned, so that the individual rectrices tend to separate when spread. The feet are unusually large, and the legs are placed farther to the rear of the body than …

Ducks, Geese, And Swans Of The World: Tribe Dendrocygnini (Whistling Or Tree Ducks), Paul A. Johnsgard

Ducks, Geese, and Swans of the World by Paul A. Johnsgard

Spotted Whistling Duck
Plumed Whistling Duck
Fulvous Whistling Duck
Wandering Whistling Duck
Lesser Whistling Duck
White-faced Whistling Duck
Cuban Whistling Duck
Magellan Goose
Black-bellied Whistling Duck
White-backed Duck

The whistling ducks are a group of nine species, eight of which are readily placed in the single genus Dendrocygna, or "tree ducks." However, they are not primarily perching birds, and thus "whistling ducks" is a better vernacular designation than the frequently used "tree ducks." In nearly all species both sexes utter a clear, often multisyllabic whistle that readily identifies the bird as to its species and apparently provides important communication signals …