Showing papers by "University of Nebraska–Lincoln published in 2013"

Achieving Integration in Mixed Methods Designs—Principles and Practices

Abstract: Mixed methods research offers powerful tools for investigating complex processes and systems in health and health care. This article describes integration principles and practices at three levels in mixed methods research and provides illustrative examples. Integration at the study design level occurs through three basic mixed method designs—exploratory sequential, explanatory sequential, and convergent—and through four advanced frameworks—multistage, intervention, case study, and participatory. Integration at the methods level occurs through four approaches. In connecting, one database links to the other through sampling. With building, one database informs the data collection approach of the other. When merging, the two databases are brought together for analysis. With embedding, data collection and analysis link at multiple points. Integration at the interpretation and reporting level occurs through narrative, data transformation, and joint display. The fit of integration describes the extent the qualitative and quantitative findings cohere. Understanding these principles and practices of integration can help health services researchers leverage the strengths of mixed methods.

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

Abstract: The type II CRISPR/Cas system from Streptococcus pyogenes and its simplified derivative, the Cas9/single guide RNA (sgRNA) system, have emerged as potent new tools for targeted gene knockout in bacteria, yeast, fruit fly, zebrafish and human cells. Here, we describe adaptations of these systems leading to successful expression of the Cas9/sgRNA system in two dicot plant species, Arabidopsis and tobacco, and two monocot crop species, rice and sorghum. Agrobacterium tumefaciens was used for delivery of genes encoding Cas9, sgRNA and a non-fuctional, mutant green fluorescence protein (GFP) to Arabidopsis and tobacco. The mutant GFP gene contained target sites in its 5' coding regions that were successfully cleaved by a CAS9/sgRNA complex that, along with error-prone DNA repair, resulted in creation of functional GFP genes. DNA sequencing confirmed Cas9/sgRNA-mediated mutagenesis at the target site. Rice protoplast cells transformed with Cas9/sgRNA constructs targeting the promoter region of the bacterial blight susceptibility genes, OsSWEET14 and OsSWEET11, were confirmed by DNA sequencing to contain mutated DNA sequences at the target sites. Successful demonstration of the Cas9/sgRNA system in model plant and crop species bodes well for its near-term use as a facile and powerful means of plant genetic engineering for scientific and agricultural applications.

Clinical practice guidelines for antimicrobial prophylaxis in surgery.

Abstract: These guidelines were developed jointly by the American Society of Health-System Pharmacists (ASHP), the Infectious Diseases Society of America (IDSA), the Surgical Infection Society (SIS), and the Society for Healthcare Epidemiology of America (SHEA). This work represents an update to the

A Survey on Smart Grid Communication Infrastructures: Motivations, Requirements and Challenges

Abstract: A communication infrastructure is an essential part to the success of the emerging smart grid. A scalable and pervasive communication infrastructure is crucial in both construction and operation of a smart grid. In this paper, we present the background and motivation of communication infrastructures in smart grid systems. We also summarize major requirements that smart grid communications must meet. From the experience of several industrial trials on smart grid with communication infrastructures, we expect that the traditional carbon fuel based power plants can cooperate with emerging distributed renewable energy such as wind, solar, etc, to reduce the carbon fuel consumption and consequent green house gas such as carbon dioxide emission. The consumers can minimize their expense on energy by adjusting their intelligent home appliance operations to avoid the peak hours and utilize the renewable energy instead. We further explore the challenges for a communication infrastructure as the part of a complex smart grid system. Since a smart grid system might have over millions of consumers and devices, the demand of its reliability and security is extremely critical. Through a communication infrastructure, a smart grid can improve power reliability and quality to eliminate electricity blackout. Security is a challenging issue since the on-going smart grid systems facing increasing vulnerabilities as more and more automation, remote monitoring/controlling and supervision entities are interconnected.

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.

Abstract: Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.

Proline Mechanisms of Stress Survival

Abstract: Significance: The imino acid proline is utilized by different organisms to offset cellular imbalances caused by environmental stress. The wide use in nature of proline as a stress adaptor molecule indicates that proline has a fundamental biological role in stress response. Understanding the mechanisms by which proline enhances abiotic/biotic stress response will facilitate agricultural crop research and improve human health. Recent Advances: It is now recognized that proline metabolism propels cellular signaling processes that promote cellular apoptosis or survival. Studies have shown that proline metabolism influences signaling pathways by increasing reactive oxygen species (ROS) formation in the mitochondria via the electron transport chain. Enhanced ROS production due to proline metabolism has been implicated in the hypersensitive response in plants, lifespan extension in worms, and apoptosis, tumor suppression, and cell survival in animals. Critical Issues: The ability of proline to influence...

The tree of life and a new classification of bony fishes.

Abstract: The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.

Expansion of global drylands under a warming climate

Abstract: . Global drylands encompassing hyper-arid, arid, semiarid, and dry subhumid areas cover about 41 percent of the earth's terrestrial surface and are home to more than a third of the world's population. By analyzing observations for 1948–2008 and climate model simulations for 1948–2100, we show that global drylands have expanded in the last sixty years and will continue to expand in the 21st~century. By the end of this century, the world's drylands (under a high greenhouse gas emission scenario) are projected to be 5.8 × 10 6 km 2 (or 10%) larger than in the 1961–1990 climatology. The major expansion of arid regions will occur over southwest North America, the northern fringe of Africa, southern Africa, and Australia, while major expansions of semiarid regions will occur over the north side of the Mediterranean, southern Africa, and North and South America. The global dryland expansions will increase the population affected by water scarcity and land degradations.

Observation of a new boson with mass near 125 GeV in pp collisions at $ \sqrt{s}=7 $ and 8 TeV

Abstract: A detailed description is reported of the analysis used by the CMS Collaboration in the search for the standard model Higgs boson in pp collisions at the LHC, which led to the observation of a new boson. The data sample corresponds to integrated luminosities up to 5.1 inverse femtobarns at sqrt(s) = 7 TeV, and up to 5.3 inverse femtobarns at sqrt(s) = 8 TeV. The results for five Higgs boson decay modes gamma gamma, ZZ, WW, tau tau, and bb, which show a combined local significance of 5 standard deviations near 125 GeV, are reviewed. A fit to the invariant mass of the two high resolution channels, gamma gamma and ZZ to 4 ell, gives a mass estimate of 125.3 +/- 0.4 (stat) +/- 0.5 (syst) GeV. The measurements are interpreted in the context of the standard model Lagrangian for the scalar Higgs field interacting with fermions and vector bosons. The measured values of the corresponding couplings are compared to the standard model predictions. The hypothesis of custodial symmetry is tested through the measurement of the ratio of the couplings to the W and Z bosons. All the results are consistent, within their uncertainties, with the expectations for a standard model Higgs boson.

Distinguishing between yield advances and yield plateaus in historical crop production trends

Abstract: Food security and the conservation of natural ecosystems largely rely on the increase in crop yields. Here, the authors examine global crop yield trends since 1960, and establish a robust statistical framework for estimating historical trajectories and identifying yield plateaus.

New technologies reduce greenhouse gas emissions from nitrogenous fertilizer in China

Abstract: Synthetic nitrogen (N) fertilizer has played a key role in enhancing food production and keeping half of the world's population adequately fed. However, decades of N fertilizer overuse in many parts of the world have contributed to soil, water, and air pollution; reducing excessive N losses and emissions is a central environmental challenge in the 21st century. China's participation is essential to global efforts in reducing N-related greenhouse gas (GHG) emissions because China is the largest producer and consumer of fertilizer N. To evaluate the impact of China's use of N fertilizer, we quantify the carbon footprint of China's N fertilizer production and consumption chain using life cycle analysis. For every ton of N fertilizer manufactured and used, 13.5 tons of CO2-equivalent (eq) (t CO2-eq) is emitted, compared with 9.7 t CO2-eq in Europe. Emissions in China tripled from 1980 [131 terrogram (Tg) of CO2-eq (Tg CO2-eq)] to 2010 (452 Tg CO2-eq). N fertilizer-related emissions constitute about 7% of GHG emissions from the entire Chinese economy and exceed soil carbon gain resulting from N fertilizer use by several-fold. We identified potential emission reductions by comparing prevailing technologies and management practices in China with more advanced options worldwide. Mitigation opportunities include improving methane recovery during coal mining, enhancing energy efficiency in fertilizer manufacture, and minimizing N overuse in field-level crop production. We find that use of advanced technologies could cut N fertilizer-related emissions by 20-63%, amounting to 102-357 Tg CO2-eq annually. Such reduction would decrease China's total GHG emissions by 2-6%, which is significant on a global scale.

Gut microbiome composition is linked to whole grain-induced immunological improvements

Abstract: The involvement of the gut microbiota in metabolic disorders, and the ability of whole grains to affect both host metabolism and gut microbial ecology, suggest that some benefits of whole grains are mediated through their effects on the gut microbiome. Nutritional studies that assess the effect of whole grains on both the gut microbiome and human physiology are needed. We conducted a randomized cross-over trial with four-week treatments in which 28 healthy humans consumed a daily dose of 60 g of whole-grain barley (WGB), brown rice (BR), or an equal mixture of the two (BR+WGB), and characterized their impact on fecal microbial ecology and blood markers of inflammation, glucose and lipid metabolism. All treatments increased microbial diversity, the Firmicutes/Bacteroidetes ratio, and the abundance of the genus Blautia in fecal samples. The inclusion of WGB enriched the genera Roseburia, Bifidobacterium and Dialister, and the species Eubacterium rectale, Roseburia faecis and Roseburia intestinalis. Whole grains, and especially the BR+WGB treatment, reduced plasma interleukin-6 (IL-6) and peak postprandial glucose. Shifts in the abundance of Eubacterium rectale were associated with changes in the glucose and insulin postprandial response. Interestingly, subjects with greater improvements in IL-6 levels harbored significantly higher proportions of Dialister and lower abundance of Coriobacteriaceae. In conclusion, this study revealed that a short-term intake of whole grains induced compositional alterations of the gut microbiota that coincided with improvements in host physiological measures related to metabolic dysfunctions in humans.

Study of the Mass and Spin-Parity of the Higgs Boson Candidate via Its Decays to Z Boson Pairs

Abstract: A study is presented of the mass and spin-parity of the new boson recently observed at the LHC at a mass near 125 GeV. An integrated luminosity of 17.3 fb^(-1), collected by the CMS experiment in proton-proton collisions at center-of-mass energies of 7 and 8 TeV, is used. The measured mass in the ZZ channel, where both Z bosons decay to e or μ pairs, is 126.2±0.6(stat)±0.2(syst) GeV. The angular distributions of the lepton pairs in this channel are sensitive to the spin-parity of the boson. Under the assumption of spin 0, the present data are consistent with the pure scalar hypothesis, while disfavoring the pure pseudoscalar hypothesis.

A Survey on Inter-Cell Interference Coordination Techniques in OFDMA-Based Cellular Networks

Abstract: Orthogonal Frequency Division Multiplexing Access (OFDMA) has been increasingly deployed in various emerging and evolving cellular systems to reduce interference and improve overall system performance. However, in these systems Inter-Cell Interference (ICI) still poses a real challenge that limits the system performance, especially for users located at the cell edge. Inter-cell interference coordination (ICIC) has been investigated as an approach to alleviate the impact of interference and improve performance in OFDMA-based systems. A common ICIC technique is interference avoidance in which the allocation of the various system resources (e.g., time, frequency, and power) to users is controlled to ensure that the ICI remains within acceptable limits. This paper surveys the various ICIC avoidance schemes in the downlink of OFDMA-based cellular networks. In particular, the paper introduces new parameterized classifications and makes use of these classifications to categorize and review various static (frequency reuse-based) and dynamic (cell coordination-based) ICIC schemes.

Acaricide, fungicide and drug interactions in honey bees (Apis mellifera).

Abstract: Background Chemical analysis shows that honey bees (Apis mellifera) and hive products contain many pesticides derived from various sources. The most abundant pesticides are acaricides applied by beekeepers to control Varroa destructor. Beekeepers also apply antimicrobial drugs to control bacterial and microsporidial diseases. Fungicides may enter the hive when applied to nearby flowering crops. Acaricides, antimicrobial drugs and fungicides are not highly toxic to bees alone, but in combination there is potential for heightened toxicity due to interactive effects.

The effectiveness of intervention programs for perpetrators and victims of intimate partner violence.

Abstract: ion of Data Four of the authors (CE, CM, RS, & KW) abstracted all study data. All study information and results were checked and confirmed by a senior author (CE or CM).

Measurement of the Bs0→μ+μ- branching fraction and search for B0→μ+μ- with the CMS experiment

Abstract: Results are presented from a search for the rare decays B0s→μ+μ− and B0→μ+μ− in pp collisions at s√=7 and 8 TeV, with data samples corresponding to integrated luminosities of 5 and 20 fb−1, respectively, collected by the CMS experiment at the LHC. An unbinned maximum-likelihood fit to the dimuon invariant mass distribution gives a branching fraction B(B0s→μ+μ−)=(3.0+1.0−0.9)×10−9, where the uncertainty includes both statistical and systematic contributions. An excess of B0s→μ+μ− events with respect to background is observed with a significance of 4.3 standard deviations. For the decay B0→μ+μ− an upper limit of B(B0→μ+μ−)<1.1×10−9 at the 95% confidence level is determined. Both results are in agreement with the expectations from the standard model.

Search for top-squark pair production in the single-lepton final state in pp collisions at √s=8 TeV

Abstract: This paper presents a search for the pair production of top squarks in events with a single isolated electron or muon, jets, large missing transverse momentum, and large transverse mass. The data sample corresponds to an integrated luminosity of 19.5 inverse femtobarns of pp collisions collected in 2012 by the CMS experiment at the LHC at a center-of-mass energy of sqrt(s) = 8 TeV. No significant excess in data is observed above the expectation from standard model processes. The results are interpreted in the context of supersymmetric models with pair production of top squarks that decay either to a top quark and a neutralino or to a bottom quark and a chargino. For small mass values of the lightest supersymmetric particle, top-squark mass values up to around 650 GeV are excluded.

Enhanced tunnelling electroresistance effect due to a ferroelectrically induced phase transition at a magnetic complex oxide interface

Abstract: The tunnelling electroresistance effect that occurs at ferroelectric tunnel junctions could form the basis for a class of potential memory applications Now, an enhanced effect is observed in a complex oxide interface as a result of a ferroelectrically induced phase transition