Digital Commons Network^™

Seqnls: Nuclear Localization Signal Prediction Based On Frequent Pattern Mining And Linear Motif Scoring, J.-R. Lin, Jianjun Hu

Faculty Publications

Nuclear localization signals (NLSs) are stretches of residues in proteins mediating their importing into the nucleus. NLSs are known to have diverse patterns, of which only a limited number are covered by currently known NLS motifs. Here we propose a sequential pattern mining algorithm SeqNLS to effectively identify potential NLS patterns without being constrained by the limitation of current knowledge of NLSs. The extracted frequent sequential patterns are used to predict NLS candidates which are then filtered by a linear motif-scoring scheme based on predicted sequence disorder and by the relatively local conservation (IRLC) based masking.

The experiment results on …

An Update On Vitamin D: The Role In Chronic Disease, Clinical Practice Implications, And The Current Status Of Nurse Practitioner Knowledge, Sara E. Robertson

DNP Projects

The discovery that a large portion of the United States population is vitamin D deficient, has led to hundreds of studies in the last decade which aim to discover the role of vitamin D in overall health and to determine what clinical consequences occur in a deficient state. The current clinical knowledge regarding vitamin D deficiency is reviewed, including the definition of vitamin D insufficiency and deficiency and its correlation to chronic disease states; the risk factors and epidemiology of vitamin D deficiency; and appropriate clinical screening and treatment of vitamin D deficiency. A research study completed in 2012 to …

Predicting The Risk Of Obstructive Sleep Apnea And Difficult Endotracheal Intubation In A Surgical Population In A Rural Community Hospital Setting, Craig S. Atkins

DNP Projects

Purpose:

The purpose of this paper is to provide a theoretical framework with practical application for facilitating patient flow through the operative process using the Lean philosophy to minimized delays and cancellations.

Theoretical orientation:

Efficient, quality patient care has always been the hallmark of Nurse Anesthetist practice. Lean healthcare introduces continuous quality improvement (CQI) processes used in Lean manufacturing to the healthcare system. The principal aspect of Lean healthcare is the concept of a value stream where work is standardized, work flow is streamlined and waste is eliminated, thus creating value.

Nature of Review:

In the surgical suite waits, delays …

Family-Focused Physical Activity, Diet, And Obesity Interventions In African-American Girls: A Systematic Review, Daheia J. Barr-Anderson, Alexis W. Adams-Wynn, Katherine I. Disantis, Shiriki Kumanyika

Faculty Publications

Obesity interventions that involve family members may be effective with racial/ethnic minority youth. This review assessed the nature and effectiveness of family involvement in obesity interventions among African-American girls aged 5-18 years, a population group with high rates of obesity. Twenty-six databases were searched between January 2011 and March 2012, yielding 27 obesity pilot or full-length prevention or treatment studies with some degree of family involvement and data specific to African-American girls. Interventions varied in type and level of family involvement, cultural adaptation, delivery format, and behavior change intervention strategies; most targeted parent-child dyads. Some similarities in approach based on …

Nitrate Reduction Coupled To Iron(Ii) And Manganese(Ii) Oxidation In An Agricultural Soil, Stephanie Pyzola

Theses and Dissertations--Plant and Soil Sciences

New evidence shows iron(II) oxidation is strongly coupled to nitrate reduction under anaerobic conditions in freshwater sediments and agricultural soils. However, the contribution of iron(II) oxidation to nitrate reduction is unknown. Furthermore, oxidation of manganese(II) by nitrate has been largely overlooked. This study investigated nitrate-dependent iron(II) and manganese(II) oxidation in an agricultural soil (Sadler silt loam) using stirred-batch kinetic techniques with native soil organic carbon (SOC) as the electron donor and included addition of amendments (hydrogen gas and wheat residue). In the presence of native SOC, nitrate-dependent Fe(II) and Mn(II) oxidation occurred at early stages of the reaction while organic …

Calendula Officinalis Growth And Production Of Secondary Compounds In Greenhouse And Soil-Based Herbal Organic Production Systems, Victoria M. Anderson

Theses and Dissertations--Plant and Soil Sciences

Calendula officinalis is a useful model crop because calendula flowers are used both ornamentally and medicinally. Organic production systems have many challenges; among these is the synchrony of nitrogen mineralization with the requirements of the crop. Organic greenhouse substrates have significantly different initial nitrogen levels which influence the performance of calendula, the highest initial N and plant performance was found in the organic compost peat substrate (OCP). The addition of supplemental nitrogen improved performance, but only OCP performed as well as the conventionally fertilized peat-based substrate. The nitrogen mineralization patterns in a soil-based greenhouse pot experiment showed that highly processed …

Dna-Binding Site Recognition By Bhlh And Mads-Domain Transcription Factors, Joshua R. Werkman

Theses and Dissertations--Plant and Soil Sciences

Herewithin, two transcription factor (TF) regulatory complexes were investigated. A bHLH–MYB–WDR (BMW) DNA-binding complex from maize was the first complex to be studied. R, a maize bHLH involved in the activation of genes in the anthocyanin pathway, had been characterized to indirectly bind DNA despite the presence of a functional DNA-binding domain. Findings presented here reveal that this is only partially correct. Direct DNA-binding by R was found to be dependent upon two distinct dimerization domains that function as a switch. This switch-like mechanism allows R to be repurposed for the activation of promoters of differing cis-element structure.

The …

Ecophysiological Responses Of Tall Fescue Genotypes To Endophyte Infection And Climate Change, Marie Bourguignon

Theses and Dissertations--Plant and Soil Sciences

Tall fescue is a widely used forage grass in the eastern USA and can form a symbiosis with a fungal endophyte, which can be beneficial for the plant but can cause livestock health issues. Little is known regarding the symbiotic response to predicted climate change. To address this knowledge gap, I analyzed tall fescue variety trial data collected throughout the U.S., exploring relationships between climate variables and yield for two different fescue cultivars that were either endophyte-free or infected. This study showed no endophyte or cultivar effect on fescue yield, but identified temperature, precipitation and location as significant predictors of …

Abiotic Nitrate And Nitrite Reactivity With Iron Oxide Minerals, Prakash Dhakal

Theses and Dissertations--Plant and Soil Sciences

Under iron (Fe³⁺)-reducing conditions where aqueous Fe²⁺ and unreduced solid Fe³⁺-oxides commonly coexist, soil Fe²⁺ oxidation has been shown to be coupled with nitrate (NO₃^-) reduction. One possible secondary reaction is the involvement of NO₃^- and nitrite (NO₂^-) with Fe-oxide minerals found in many natural environments. Yet, spectroscopic measurements and kinetic data on reactivity of NO₃^- and NO₂^- with Fe-containing oxide minerals such as goethite (a-FeOOH), and magnetite (Fe₃O­₄) are not found in the literature. The reactivity of …

Reduced Tillage And Living Mulches For Organic Vegetable Production, Alex G. Hessler

Theses and Dissertations--Plant and Soil Sciences

Reduced tillage and living mulches are alternative management strategies that can improve soil quality by minimizing disturbance and building soil organic matter. Weed suppression by these two practices alone is often insufficient to avoid crop yield losses, but their performance in an integrated system is not well understood. This project investigated the production of bell pepper (Capsicum annuum L.) and dry bean (Phaseolus vulgaris L.) in conventional tillage and strip tillage with a living mulch of teff (Eragrostis tef Zucc.) and Korean lespedeza (Kummerowia stipulacea Maxim.). Yields of pepper and bean were …

Control Of Erwinia Tracheiphila In Cucumis Melo, John R. Caudle

Theses and Dissertations--Plant and Soil Sciences

Currently there is no control of bacterial wilt disease, Erwinia tracheiphila, in susceptible cucurbit crops, once infection of the plant occurs. Conventional and organic production systems rely on insecticide applications to kill the vectors, striped and spotted cucumber beetles, Acalymma vittatum and Diabrotica undecimpunctata, respectively, prior to transmission of the pathogen which indirectly controls the disease to some extent. Physical barriers such as row covers are used to exclude the vectors from plants prior to flowering; however, pollination requirements expose plants to potential infection. Experimental field plots were developed to test various enhanced organic production systems in an …

Molten Carbonates As An Effective Oxygen Reduction Catalyst For 550–650°C Solid Oxide Fuel Cells, Yunhui Gong, Xue Li, Lingling Zhang, Whitney Tharp, Changyong Qin, Kevin Huang

Faculty Publications

We report the first study that investigates the use of molten carbonates as an effective catalyst to promote electrochemical oxygen reduction reaction (ORR) at the cathode of intermediate temperature solid oxide fuel cells (IT-SOFCs). A series of binary Li-K carbonate compositions were incorporated into the porous backbones of a commercial cathode assembled in symmetrical impedance cells for electrochemical characterization. Within the temperature range of 550–650◦C, we observed that the polarization and ohmic area-specific resistances of the original sample can be significantly reduced by the introduction of molten carbonates. A new ORR charge-transfer model involving two intermediate species CO5 2− and …

What's Law Got To Do With It?: Why We Should Mediate, Rather Than Litigate, Cases Of Wrongful Life, Shawna Benston

Cardozo Journal of Conflict Resolution

In light of the legal and societal disfavor toward wrongful life suits, this Note examines the cultural, (bio)ethical, legal, and philosophical background of the wrongful life tort. While the disability rights movement and the pro-life strains of the abortion debate hope to silence proponents of wrongful life suits, the evolution of a legal right to die underscores the importance of autonomy and privacy for the individual. Philosophical exploration of prospective children-including the nonidentity problem, claim-rights and corresponding duties, and the subjunctive-threshold notion of harmhelps explain the confusion and moral conundrum that pervade the very notion of "wrongful life" and that …

Horizontal Buccal Cortical Bone Thickness For Miniscrew Placement Strategies, Patrick B. Holmes

MUSC Theses and Dissertations

Introduction: Miniscrew implants or MSI's are reported to be used by upwards of 80% of orthodontists today, and failure rates can reach as high as 30%. The aim of this study was to identify horizontal buccal cortical bone thickness patterns in the maxilla and mandible and to create MSI placement strategies based upon the identified pattern. Methods: Fifty randomly selected cone beam computed tomography scans or CBCT's from healthy subjects with intact dentitions were studied using one quadrant from a maxillary arch and one from the mandibular arch. 900 maxillary and 900 mandibular cortical bone thickness measurements were made. Measurements …

Reduced Translocation Is Associated With Tolerance Of Common Lambsquarters (Chenopodium Album) To Glyphosate, M. K. Yerka, Andrew T. Wiersma, R. Bradley Lindenmayer, Philip Westra, William G. Johnson, Natalia De Leon, David E. Stoltenberg

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Common lambsquarters tolerance to glyphosate is problematic because of the species’ widespread distribution, competitive ability with many crop species, the widespread use of glyphosate in agriculture, and the weed’s potential to develop decreased sensitivity to multiple herbicide sites of action. The mechanism that confers common lambsquarters tolerance to glyphosate is not known. Therefore, we conducted experiments to determine the mechanism of tolerance to glyphosate in an accession of common lambsquarters from Indiana relative to a sensitive accession from Wisconsin. The ED₅₀ (the effective dose that reduced shoot mass 50% relative to nontreated plants) value for the tolerant accession (1.6 …

Stand Establishment And Persistence Of Perennial Cool-Season Grasses In The Intermountain West And The Central And Northern Great Plains, Joseph G. Robins, Kevin B. Jensen, Thomas A. Jones, Blair L. Waldron, Michael D. Peel, Craig W. Rigby, Kenneth P. Vogel, Robert B. Mitchell, Antonio J. Palazzo, Timothy J. Cary

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The choice of plant materials is an important component of revegetation following disturbance. To determine the utility and effectiveness of various perennial grass species for revegetation on varied landscapes, a meta analysis was used to evaluate the stand establishment and persistence of 18 perennial cool-season grass species in 34 field studies in the Intermountain and Great Plains regions of the United States under monoculture conditions. Combined across the 34 studies, stand establishment values ranged from 79% to 43% and stand persistence values ranged from 70% to 0%. Intermediate wheatgrass (Thinopyrum intermedium [Host] Barkworth & D. R. Dewey), tall wheatgrass …

Nitrogen–Climate Interactions In Us Agriculture, G. Philip Robertson, Tom W. Bruulsema, Ron J. Gehl, David Kanter, Denise L. Mauzerall, C. Alan Rotz, Candiss O. Williams

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Agriculture in the United States (US) cycles large quantities of nitrogen (N) to produce food, fuel, and fiber and is a major source of excess reactive nitrogen (Nr) in the environment. Nitrogen lost from cropping systems and animal operations moves to waterways, groundwater, and the atmosphere. Changes in climate and climate variability may further affect the ability of agricultural systems to conserve N. The N that escapes affects climate directly through the emissions of nitrous oxide (N₂O), and indirectly through the loss of nitrate (NO₃^-), nitrogen oxides (NO_x) and ammonia to downstream and …

Reimagining Merit As Achievement, Aaron N. Taylor

All Faculty Scholarship

Higher education plays a central role in the apportionment of opportunities within the American meritocracy. Unfortunately, narrow conceptions of merit limit the extent to which higher education broadens racial and socioeconomic opportunity. This article proposes an admissions framework that transcends these limited notions of merit. This “Achievement Framework” would reward applicants from disadvantaged backgrounds who have achieved beyond what could have reasonably been expected. Neither race nor ethnicity is considered as part of the framework; however, its nuanced and contextual structure would ensure that racial and ethnic diversity is encouraged in ways that traditional class-conscious preferences do not. The overarching …

How Does A Mycobacterium Change Its Spots? Applying Molecular Tools To Track Diverse Strains Of Mycobacterium Avium Subspecies Paratuberculosis, John Bannantine, L.-L. Li, Srinand Sreevatsan, Vivek Kapur

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Defining genetic diversity in the wake of the release of several Mycobacterium avium subsp. paratuberculosis (MAP) genome sequences has become a major emphasis in the molecular biology and epidemiology of Johne’s disease research. These data can now be used to define the extent of strain diversity on the farm. However, to perform these important tasks, researchers must have a way to distinguish the many MAP isolates/strains that are present in the environment or host to enable tracking over time. Recent studies have described genetic diversity of the Mycobacterium avium complex (MAC), of which MAP is a member, through pulsed-field gel …

Ursinus Magazine, Winter 2013, Wendy Greenberg, Kathryn Campbell, Ellen Labrecque, Bobby Fong, Jessica Driscoll, Joseph F. Pirro

Ursinus Magazine, 1995–Present

A unique partnership between Ursinus and Columbia University • New Director for the Philip and Muriel Berman Museum of Art • Exploring consumer health literacy • City Year • Ursinus "Pause for Paws" a big, barking success • Heinzl first speaker for Center for Science and the Common Good • Pulitzer Prize-winning journalist Michael Vitez • Alumni Gary R. McClellan lectures on career as Defense Intelligence Agency analyst • Book on educator Marcus Foster sets context of school reform debates • Senior athlete Tony Rosa in the spotlight for mentoring • Upcoming lectures • The Philip and Muriel Berman Museum …

The Safety Of Onrab®In Select Non-Target Wildlife, Tricia L. Fry, Kaci K. Vandalen, Colleen Duncan, Kurt Vercauteren

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

ONRAB^® is a recombinant human adenovirus type 5 (HAd5) with the rabies glycoprotein gene incorporated into its genome. ONRAB^® has been used in Canada as an oral rabies vaccine in target wildlife species such as: red fox (Vulpes vulpes), raccoon (Procyon lotor), and striped skunk (Mepthis mephitis). We evaluated the safety of ONRAB^® in non-target wildlife species likely to contact the vaccine baits during oral rabies vaccine campaigns in the United States. We investigated the effects of oral inoculation of high titer ONRAB^®, approximately ten times the dose given …

Land Cover Controls On Summer Discharge And Runoff Solution Chemistry Of Semi-Arid Urban Catchments, Erika L. Gallo, Paul D. Brooks, Kathleen A. Lohse, Jean E.T. Mclain

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Recharge of urban runoff to groundwater as a stormwater management practice has gained importance in semi-arid regions where water resources are scarce and urban centers are growing. Despite this trend, the importance of land cover in controlling semi-arid catchment runoff quantity and quality remains unclear. Here we address the question: How do land cover characteristics control the amount and quality of storm runoff in semi-arid urban catchments? We monitored summertime runoff quantity and quality from five catchments dominated by distinct urban land uses: low, medium, and high density residential, mixed use, and commercial. Increasing urban land cover increased runoff duration …

Soil Type And Moisture Regime Control Microbial C And N Mineralization In Grassland Soils More Than Atmospheric Co2-Induced Changes In Litter Quality, Virginia L. Jin, Richard L. Haney, Philip A. Fay, H. Wayne Polley

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Global change-induced alterations in litter quality and soil moisture regime will likely impact grassland C and N dynamics, but how these changes interact with edaphic properties across the landscape is unclear. We measured the effects of litter quality, soil type, soil moisture level, and soil drying-rewetting frequency (D-RW) on microbial C and N mineralization of litter and soil organic matter (SOM) in a full-factorial, controlled incubation experiment. Four levels of litter quality (no litter; or litter from Bouteloua curtipendula grown under 280, 380, 500 μL L^‒1 CO₂) were surface-applied to three contrasting soils common to Blackland Prairie …

Economic Analysis Of Small-Scale Agricultural Digesters In The United States, Katherine H. Klavon, Stephanie A. Lansing, Walter Mulbry, Andrew R. Moss, Gary Felton

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Anaerobic digestion (AD) is an economically viable manure treatment option for large dairies (>500 cows) in the U.S. However, roughly 90% of U.S. dairies have less than 200 cows, making this technology economically inaccessible to the vast majority of U.S. dairies. While there have been case studies of individual small dairies with anaerobic digesters, there are no comparative studies using cost data from these systems. The objectives of this study were to (1) determine the economic viability of small-scale U.S. digesters using cost data from nine existing 100 to 250-cow dairies and seven theoretical systems and (2) reevaluate the …

Genetic Diversity Of Resident Soil Rhizobia Isolated From Nodules Of Distinct Hairy Vetch (Vicia Villosa Roth) Genotypes, N.V. Mothapo, J.M. Grossman, J. E. Maul, W. Shi, T. Isleib

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Hairy vetch (Vicia villosa Roth, HV) is widely grown as a legume cover crop throughout the U.S.A., with biological nitrogen fixation (BNF) through symbiosis with Rhizobium leguminosarum biovar viciae (Rlv) being one of the most sought after benefits of its cultivation. This study determined if HV cultivation history and plant genotype affect genetic diversity of resident Rlv. Soil samples were collected from within farmers’ fields at Graham, Cedar Grove and Ivanhoe sites in North Carolina and pairs of genetically similar hairy vetch genotypes used as trap hosts. A total of 519 Rlv strains were isolated from six paired field …

Hybridization In Natural Sympatric Populations Of Dermacentor Ticks In Northwestern North America, A. Araya-Anchetta, G. A. Scoles, J. Giles, J. D. Busch, D. M. Wagner

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Hybridization in ticks has been described in a handful of species and mostly as a result of laboratory experiments. We used 148 AFLP loci to describe putative hybridization events between D. andersoni and D. variabilis in sympatric populations from northwestern North America. Recently, D. variabilis has expanded its range westward into the natural range of D. andersoni. Using a sample of 235 D. andersoni and 62 D. variabilis, we identified 31 individuals as putative hybrids: four F₂ individuals and 27 backcrosses to D. andersoni (as defined by NEWHYBRIDS). We found no evidence of hybrids backcrossing into D. …

Adoption Of Site-Specific Variable Rate Sprinkler Irrigation Systems, Robert G. Evans, Jake Larue, Kenneth C. Stone, Bradley A. King

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

More than 20 years of private and public research on site-specific variable rate sprinkler irrigation (SS-VRI) technology on self-propelled center pivot and linear move irrigation systems has resulted in limited commercial adoption of the technology. Competing patents, liability, and proprietary software have affected industry’s willingness to move into a new technology area. Documented and proven water conservation strategies using site specific irrigation are quite limited. Marginal costs associated with site-specific technologies are high. Although sales of SS-VRI are increasing, they are primarily being used for eliminating irrigation and chemigation on non-cropped areas of a field or for land application of …

Impacts Of Drought On Plant Water Relations And Nitrogen Nutrition In Dryland Perennial Grasses, Albina Khasanova, Jeremy J. James, Rebecca E. Drenovsky

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Background and aims Extensive worldwide dryland degradation calls for identification of functional traits critical to dryland plant performance and restoration outcomes. Most trait examination has focused on drought tolerance, although most dryland systems are water and nutrient co-limited. We studied how drought impacts both plant water relations and nitrogen (N) nutrition.

Methods We grew a suite of grasses common to the Intermountain West under both well-watered and drought conditions in the greenhouse. These grasses represented three congener pairs (Agropyron, Elymus, Festuca) differing in their habitat of origin (“wetter” or “drier”). We measured growth, water relations, N resorption efficiency …

Seasonal Changes In Shoot And Root Nitrogen Distribution In Switchgrass (Panicum Virgatum), Sandra Wayman, Richard D. Bowden, Robert B. Mitchell

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Switchgrass is a promising bioenergy source that is perennial, productive, native to a broad geographic region, and can grow on marginal, nitrogen (N)-poor soils. Understanding N dynamics in switchgrass is critical to predicting productivity, conserving N, and optimizing the timing of harvest. We examined seasonal changes in N distribution in above- and belowground tissues in switchgrass to quantify N retranslocation rates. Above- and belowground biomass from three sites (two in PA and one in NE) were collected and analyzed for biomass growth and N concentrations at 30-day intervals from June through October. Total living plant mass ranged from 10.3± 2.4 …

Comprehensive Genotyping Of The Usa National Maize Inbred Seed Bank, Maria C. Romay, Mark J. Millard, Jeffrey C. Glaubitz, Jason A. Peiffer, Kelly L. Swarts, Terry M. Casstevens, Robert J. Elshire, Charlotte B. Acharya, Sharon E. Mitchell, Sherry A. Flint-Garcia, Michael D. Mcmullen, James B. Holland, Edward S. Buckler, Candice A. Gardner

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Background: Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.

Results: The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is …