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The University of Nebraska–Lincoln is a public research university located in Lincoln, Nebraska, United States. It is the state's oldest and largest university and the flagship university of the University of Nebraska system.The university was chartered by the legislature in 1869 as a land-grant university under the 1862 Morrill Act, two years after Nebraska's statehood into the United States. Around the turn of the 20th century, the university began to expand significantly, hiring professors from eastern schools to teach in the newly organized professional colleges while also producing groundbreaking research in agricultural science. The "Nebraska method" of ecological study developed here during this time, which pioneered grassland ecology and laid the foundation for research in theoretical ecology for the rest of the 20th century. The university is organized into eight colleges, located on two campuses in Lincoln with over 100 classroom buildings and research facilities.Its athletic program, called the Cornhuskers, is a member of the Big Ten Conference. The Nebraska football team has won a total of 46 conference championships, and since 1970, five national championships. The women's volleyball team has won three national championships along with eight other appearances in the Final Four. The Husker football team plays its home games at Memorial Stadium, selling out every game since 1962. The stadium's current capacity is about 92,000 people, larger than the population of Nebraska's third-largest city. Wikipedia.

Bahar E.,University of Nebraska - Lincoln
Journal of the Optical Society of America A: Optics and Image Science, and Vision | Year: 2011

Optical polarimetric techniques to identify and characterize biological and chemical materials have received much attention recently for their broad applications in biophotonics, biochemistry, biomedicine, and pharmacology. We present here several options for the measurement of optical rotation, diattenuation, and the index of depolarization. These include polar decomposition, identification of specific pairs of Mueller matrix elements that are proportional to optical activity, and the cross-polarized components of lateral waves and surface waves at the interface between free space and the optically active material. © 2011 Optical Society of America.

Meister R.,Monsanto Corporation | Rajani M.S.,Monsanto Corporation | Ruzicka D.,Monsanto Corporation | Schachtman D.P.,University of Nebraska - Lincoln
Trends in Plant Science | Year: 2014

Roots play an ssential role in the acquisition of water and minerals from soils. Measuring crop root architecture and assaying for changes in function can be challenging, but examples have emerged showing that modifications to roots result in higher yield and increased stress tolerance. In this review, we focus mainly on the molecular genetic advances that have been made in altering root system architecture and function in crop plants, as well as phenotyping methods. The future for the modification of crop plant roots looks promising based on recent advances, but there are also important challenges ahead. © 2014 Elsevier Ltd.

Steiner B.,University of Nebraska - Lincoln | Wooldredge J.,University of Cincinnati
Criminal Justice and Behavior | Year: 2014

This study involved a comparison of the influences on inmate misconduct among female and male inmates. Data were collected from over 5,500 inmates housed in 46 facilities in Ohio and Kentucky (570 women and 5,059 men), and the relative effects of these inmates' background characteristics and confinement experiences were examined for sex-specific samples. The magnitudes of effects were then compared across the two groups. Findings revealed that background characteristics (e.g., age) and confinement experiences (e.g., involvement in education/vocational program) influence women's and men's odds of misconduct. Equality of coefficient tests revealed only three differences in the magnitude of these effects across the analyses of the sex-specific samples, suggesting there are far more similarities than differences in the predictors of misconduct among men versus women. © 2013 International Association for Correctional and Forensic Psychology.

Kannan M.,National Jewish Health | Riekhof W.R.,University of Nebraska - Lincoln | Voelker D.R.,National Jewish Health
Traffic | Year: 2015

Over the past two decades, most of the genes specifying lipid synthesis and metabolism in yeast have been identified and characterized. Several of these biosynthetic genes and their encoded enzymes have provided valuable tools for the genetic and biochemical dissection of interorganelle lipid transport processes in yeast. One such pathway involves the synthesis of phosphatidylserine (PtdSer) in the endoplasmic reticulum (ER), and its non-vesicular transport to the site of phosphatidylserine decarboxylase2 (Psd2p) in membranes of the Golgi and endosomal sorting system. In this review, we summarize the identification and characterization of the yeast phosphatidylserine decarboxylases, and examine their role in studies of the transport-dependent pathways of de novo synthesis of phosphatidylethanolamine (PtdEtn). The emerging picture of the Psd2p-specific transport pathway is one in which the enzyme and its non-catalytic N-terminal domains act as a hub to nucleate the assembly of a multiprotein complex, which facilitates PtdSer transport at membrane contact sites between the ER and Golgi/endosome membranes. After transport to the catalytic site of Psd2p, PtdSer is decarboxylated to form PtdEtn, which is disseminated throughout the cell to support the structural and functional needs of multiple membranes. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Soulakova J.N.,University of Nebraska - Lincoln
Statistical Methods in Medical Research | Year: 2011

The problem of detecting all effective and superior combinations in a factorial drug efficacy trial is stated in terms of two hypothesis families, full and reduced. The reduced problem formulation allows identification of all simultaneously effective and superior combinations. The full formulation allows individual detection of the efficacy and superiority of combinations resulting in more detailed conclusions. While the full hypothesis family deals with simpler parameters, the true mean effect differences, it has three times as many hypotheses as the reduced family. The reduced family is comprised of hypotheses concerning a gain-parameter, which is defined as the minimum of the true mean differences and leading to a fairly complicated structure. For each problem formulation, Holm's, Hochberg's and two resampling approaches are studied with respect to strong control of overall error rate and several power measures. Holm's and Hochberg's approaches are recommended for the reduced family, while the step-down resampling approach is recommended for the full hypothesis family. Moreover, the correct problem formulation is of great importance, because if the sample size is not sufficient there is a high potential for lack of power associated with the full problem due to a large number of hypotheses. © The Author(s), 2011.

Awada L.,University of Saskatchewan | Yiannaka A.,University of Nebraska - Lincoln
Food Policy | Year: 2012

The study develops a general analytical framework of heterogeneous consumer preferences to examine the effects of country of origin labeling (COOL) regulation on consumer purchasing decisions and welfare. We show that while differences in consumer perceptions about COOL information, namely, whether it is viewed as an attribute that differentiates products vertically or horizontally, do not alter the nature of the market and consumer welfare effects of mandatory COOL, the relative strength of consumer preferences for COOL are shown to be important in determining the magnitude of these effects. In addition, our results show that the benchmark used (a no COOL versus a voluntary COOL regime) is critical in evaluating the effects of the policy. We show that, under both horizontal and vertical product differentiation, a change from a no COOL to a mandatory COOL regime decreases (increases) the welfare of consumers with weak (strong) preference for COOL while a change from a voluntary to a mandatory COOL regime leads to an unambiguous loss in consumer welfare. © 2011 Elsevier Ltd.

Head J.J.,University of Nebraska - Lincoln | Polly P.D.,Indiana University Bloomington
Nature | Year: 2015

Hox genes regulate regionalization of the axial skeleton in vertebrates, and changes in their expression have been proposed to be a fundamental mechanism driving the evolution of new body forms. The origin of the snake-like body form, with its deregionalized pre-cloacal axial skeleton, has been explained as either homogenization of Hox gene expression domains, or retention of standard vertebrate Hox domains with alteration of downstream expression that suppresses development of distinct regions. Both models assume a highly regionalized ancestor, but the extent of deregionalization of the primaxial domain (vertebrae, dorsal ribs) of the skeleton in snake-like body forms has never been analysed. Here we combine geometric morphometrics and maximum-likelihood analysis to show that the pre-cloacal primaxial domain of elongate, limb-reduced lizards and snakes is not deregionalized compared with limbed taxa, and that the phylogenetic structure of primaxial morphology in reptiles does not support a loss of regionalization in the evolution of snakes. We demonstrate that morphometric regional boundaries correspond to mapped gene expression domains in snakes, suggesting that their primaxial domain is patterned by a normally functional Hox code. Comparison of primaxial osteology in fossil and modern amniotes with Hox gene distributions within Amniota indicates that a functional, sequentially expressed Hox code patterned a subtle morphological gradient along the anterior-posterior axis in stem members of amniote clades and extant lizards, including snakes. The highly regionalized skeletons of extant archosaurs and mammals result from independent evolution in the Hox code and do not represent ancestral conditions for clades with snake-like body forms. The developmental origin of snakes is best explained by decoupling of the primaxial and abaxial domains and by increases in somite number, not by changes in the function of primaxial Hox genes. ©2015 Macmillan Publishers Limited. All rights reserved.

Schmidt E.G.,University of Nebraska - Lincoln
Astrophysical Journal | Year: 2015

Spectral energy distributions for 132 classical and type II Cepheids were searched for evidence of excess flux above the photospheric level in the mid-infrared. Eight of them were found to have unambiguously strong excess emission while a further 13 showed evidence of weak emission. The presence of emission appears to be unrelated to either the pulsational amplitude or the effective temperature while strong emission is limited to stars with periods longer than 11 days, with a single exception. For the stars with strong emission we attempted to fit the energy distribution with a stellar wind model. No acceptable fit could be found for silicate grains. With graphite or iron grains we could only obtain an acceptable fit if the maximum dust temperature was significantly lower than the condensation temperature. We conclude that the excess emission is not evidence of mass loss. © 2015. The American Astronomical Society. All rights reserved.

Stupar R.M.,University of Minnesota | Specht J.E.,University of Nebraska - Lincoln
Advances in Agronomy | Year: 2013

The complete assembly of the soybean genome sequence was a paradigm-shifting event for legume genomicists and offered a promising new resource for breeders and geneticists. Subsequent and ongoing resequencing of additional soybean accessions and wild relatives is building a comprehensive infrastructure for understanding soybean gene content and germplasm diversity. In this chapter, we first revisit the major events in soybean genomics that preceded and led to the soybean-sequencing project. Next, we delve into the important and unique features of the soybean genome that have been revealed through recent sequencing and resequencing efforts. We highlight the immediate impacts of the genome sequence, including the integration of the soybean genetic and physical maps and how the. genome sequence has accelerated gene cloning. Last, we address ongoing and new projects that are leveraging the genome sequence to address previously inaccessible questions, and providing new genetic resources. The purpose of this chapter is to give an insight into the ways that the soybean genome has enabled the research community to address standing issues in both fundamental and applied areas. © 2013 Elsevier Inc.

Holland K.H.,Holland Scientific | Schepers J.S.,University of Nebraska - Lincoln
Precision Agriculture | Year: 2013

Active crop canopy sensors make possible in-season fertilizer nitrogen (N) applications by using the crop as a bio-indicator of vigor and N status. However, sensor calibration is difficult early in the growing season when crops are rapidly growing. Studies were conducted in the United States and Mexico to evaluate procedures to determine the vegetation index of adequately fertilized plants in producer fields without establishing a nitrogen-rich reference area. The virtual-reference concept uses a histogram to characterize and display the sensor data from which the vegetation index of adequately fertilized plants can be identified. Corn in Mexico at the five-leaf growth stage was used to evaluate opportunities for variable rate N fertilizer application using conventional tractor-based equipment. A field in Nebraska, USA at the twelve-leaf growth stage was used to compare data interpretation strategies using: (1) the conventional virtual reference concept where the vegetation index of adequately fertilized plants was determined before N application was initiated; and (2) a drive-and-apply approach (no prior canopy sensor information for the field before initiating fertilizer application) where the fertilizer flow-rate control system continuously updates a histogram and automatically calculates the vegetation index of adequately fertilized plants. The 95-percentile value from a vegetation-index histogram was used to determine the vegetation index of adequately fertilized plants. This value was used to calculate a sufficiency index value for other plants in the fields. The vegetation index of reference plants analyzed using an N-rich approach was 3-5 % lower than derived using the virtual-reference concept. © 2012 Springer Science+Business Media New York.

The monotyopic genera Astroscara Schürhoff, 1937, Chiriquibia Bates, 1889, Hadrosticta Kraatz, 1892, Jansonia Schürhoff, 1937 (revised status), Macrocranius Schürhoff, 1935, and Tiarocera Burmeister, 1842 (Coleoptera: Scarabaeidae: Cetoniinae: Gymnetini) are reviewed. Redescriptions, diagnoses, distributions, and illustrations of the species are provided. A type species for Tiarocera is designated.

Laurance W.F.,James Cook University | Sayer J.,James Cook University | Cassman K.G.,University of Nebraska - Lincoln
Trends in Ecology and Evolution | Year: 2014

The human population is projected to reach 11 billion this century, with the greatest increases in tropical developing nations. This growth, in concert with rising per-capita consumption, will require large increases in food and biofuel production. How will these megatrends affect tropical terrestrial and aquatic ecosystems and biodiversityα We foresee (i) major expansion and intensification of tropical agriculture, especially in Sub-Saharan Africa and South America; (ii) continuing rapid loss and alteration of tropical old-growth forests, woodlands, and semi-arid environments; (iii) a pivotal role for new roadways in determining the spatial extent of agriculture; and (iv) intensified conflicts between food production and nature conservation. Key priorities are to improve technologies and policies that promote more ecologically efficient food production while optimizing the allocation of lands to conservation and agriculture. © 2013 Elsevier Ltd.

Siegfried B.D.,University of Nebraska - Lincoln
GM crops & food | Year: 2012

The European corn borer, Ostrinia nubilalis Hübner (Lepidoptera: Crambidae) has been a major pest of corn and other crops in North America since its accidental introduction nearly a hundred years ago. Wide adoption of transgenic corn hybrids that express toxins from Bacillus thuringiensis, referred to as Bt corn, has suppressed corn borer populations and reduced the pest status of this insect in parts of the Corn Belt. Continued suppression of this pest, however, will depend on managing potential resistance to Bt corn, currently through the high-dose refuge (HDR) strategy. In this review, we describe what has been learned with regard to O. nubilalis resistance to Bt toxins either through laboratory selection experiments or isolation of resistance from field populations. We also describe the essential components of the HDR strategy as they relate to O. nubilalis biology and ecology. Additionally, recent developments in insect resistance management (IRM) specific to O. nubilalis that may affect the continued sustainability of this technology are considered.

Li X.,CAS Hefei Key Laboratory of Materials for Energy Conversion | Wu X.,CAS Hefei Key Laboratory of Materials for Energy Conversion | Wu X.,Anhui University of Science and Technology | Zeng X.C.,University of Nebraska - Lincoln | Yang J.,Anhui University of Science and Technology
ACS Nano | Year: 2012

We perform a comprehensive study of the effects of line defects on electronic and magnetic properties of monolayer boron-nitride (BN) sheets, nanoribbons, and single-walled BN nanotubes using first-principles calculations and Born-Oppenheimer quantum molecular dynamic simulation. Although line defects divide the BN sheet (or nanotube) into domains, we show that certain line defects can lead to tailor-made edges on BN sheets (or imperfect nanotube) that can significantly reduce the band gap of the BN sheet or nanotube. In particular, we find that the line-defect-embedded zigzag BN nanoribbons (LD-zBNNRs) with chemically homogeneous edges such as B- or N-terminated edges can be realized by introducing a B 2, N 2, or C 2 pentagon-octagon-pentagon (5-8-5) line defect or through the creation of the antisite line defect. The LD-zBNNRs with only B-terminated edges are predicted to be antiferromagnetic semiconductors at the ground state, whereas the LD-zBNNRs with only N-terminated edges are metallic with degenerated antiferromagnetic and ferromagnetic states. In addition, we find that the hydrogen-passivated LD-zBNNRs as well as line-defect-embedded BN sheets (and nanotubes) are nonmagnetic semiconductors with markedly reduced band gap. The band gap reduction is attributed to the line-defect-induced impurity states. Potential applications of line-defectembedded BN nanomaterials include nanoelectronic and spintronic devices. © 2012 American Chemical Society.

Facies analysis of the Upper Cretaceous (Turonian) Ferron Sandstone in the western Henry Mountains of southcentral Utah, U.S.A., indicates sediment accumulation in a series of flood-dominated, marine current- and wave-influenced, deltas. Twelve lithofacies are recognized: 1. erosionally based, thick cross-bedded sandstone bodies (Distributary Channels), 2. similar though thinner bodies containing common bioturbation (Marine-Influenced Distributary Channels), 3. root-penetrated, plant fossil bearing siltstone with minor sandstone (Coastal Floodplain and Floodbasin), 4. coal and carbonaceous shale (Coastal Mire), 5. thin-bedded, carbonaceous and bioturbated sandstone-siltstone (Coastal Lagoon), 6. erosionally based sandstone with large- and small-scale cross-bedding and bioturbation (Mouth-Bar Complex), 7. sharply based sandstone bodies internally dominated by hummocky cross-stratification, soft-sediment deformation, or lacking structure (Proximal Delta Front), 8. sharply bounded, calcareous, fossiliferous and bioturbated sandstone sheets (Abandoned Delta Lobe), 9. thickly interbedded sandstone, coarse- and fine-grained siltstone (Medial Delta Front), 10. thinly interbedded sandstone, coarse- and fine-grained siltstone (Distal Delta Front), 11. mainly siltstone with minor thin-bedded sandstone (Prodelta) and 12. finegrained siltstone with bentonite beds (Offshore). Deltas prograded into shallow water, forming sharp-based mouth-bar sand bodies. The upper delta front was evidently fluidal and prone to failure, leading to the development of rotational slope failures, debris-flow filled gullies, and, in places, growth faults. Paleocurrent data indicate that the regional sediment dispersal direction was eastward. Data from delta-front facies, however, suggest that outflow plumes and associated bottom currents were deflected towards the southeast, giving rise to an asymmetric delta planform. The Holocene and modern Burdekin River Delta of NE Australia is considered a close planform, process, and facies analog for the Ferron Notom deltas. The Burdekin Delta facies assemblage is vertically and laterally heterogeneous, despite being the product of a consistent array of environmental controls. Adopting a model that incorporates such a degree of heterogeneity negates the need for multiple depositional models for complex stratigraphie intervals such as the Ferron Sandstone. The facies model also suggests that asymmetric deltas may be produced by directional growth of delta lobes, rather than by deflection of beach ridges. Stratigraphie stacking patterns strongly suggest that sediment accumulation in the Ferron Sandstone of the western Henry Mountains was forced by a regime of progressively more limited accommodation through time. Copyright © 2010, SEPM (Sodety for Sedimentary Geology).

Wardlow B.D.,University of Nebraska - Lincoln | Egbert S.L.,University of Kansas
International Journal of Remote Sensing | Year: 2010

Multi-temporal vegetation index (VI) data from the Moderate Resolution Imaging Spectroradiometer (MODIS) are becoming widely used for large-area crop classification. Most crop-mapping studies have applied enhanced vegetation index (EVI) data from MODIS instead of the more traditional normalized difference vegetation index (NDVI) data because of atmospheric and background corrections incorporated into EVI's calculation and the index's sensitivity over high biomass areas. However, the actual differences in the classification results using EVI versus NDVI have not been thoroughly explored. This study evaluated time-series MODIS 250-m EVI and NDVI for crop-related land use/land cover (LULC) classification in the US Central Great Plains. EVI-and NDVI-derived maps classifying general crop types, summer crop types and irrigated/non-irrigated crops were produced for southwest Kansas. Qualitative and quantitative assessments were conducted to determine the thematic accuracy of the maps and summarize their classification differences. For the three crop maps, MODIS EVI and NDVI data produced equivalent classification results. High thematic accuracies were achieved with both indices (generally ranging from 85% to 90%) and classified cropping patterns were consistent with those reported for the study area (> 0.95 correlation between the classified and USDA-reported crop areas). Differences in thematic accuracy (< 3% difference), spatially depicted patterns (> 90% pixel-level thematic agreement) and classified crop areas between the series of EVI-and NDVI-derived maps were negligible. Most thematic disagreements were restricted to single pixels or small clumps of pixels in transitional areas between cover types. Analysis of MODIS composite period usage in the classification models also revealed that both VIs performed equally well when periods from a specific growing season phase (green, peak or senescence) were heavily utilized to generate a specific crop map. © 2010 Taylor & Francis.

Church S.H.,University of Nebraska - Lincoln
Information Society | Year: 2013

I conduct a textual analysis of a digital memorial to understand the ways in which the digital sphere has disrupted or altered material and aesthetic displays of death and the associated genre of discourses surrounding death. I first use Morris's history of traditional gravescapes to situate digital memorials within their broader historical context. I then draw on the functional genre of eulogies, in particular Jamieson and Campbell's systematic description of eulogies, as a textual analytic to understand Facebook's unique memorializing discourse. My analysis suggests that the affordances of the Internet allow for a peculiar dynamic wherein the bereaved engage in communication with the deceased instead of with each other and yet strengthen the communal experience, as their personal communications are visible to the entire community. While the digital memorials lack the permanence of traditional gravescapes, the ongoing conversation they foster sublimates death into the process of communication. © 2013 Copyright Taylor and Francis Group, LLC.

Goosby B.J.,University of Nebraska - Lincoln
Journal of Health and Social Behavior | Year: 2013

Applying cumulative inequality theory, this study examines the extent to which childhood socioeconomic disadvantage and maternal depression increase the risk of major depression and chronic pain in U.S. working-aged adults. Further, I assess whether low socioeconomic status amplifies the risk of adult depression and/or pain. Using data from the 2003 National Comorbidity Survey Replication (N=4339), I find that socioeconomic disadvantage and maternal depression during youth increases the risk of adult depression and/or chronic pain. The probability of having chronic pain increases in magnitude over the life course for adults whose parents have lower educational attainment relative to those with more highly educated parents. Childhood socioeconomic circumstances are not completely explained by adulthood socioeconomic status indicators. These findings help illustrate the far-reaching influence of childhood context on adult physical and mental health. © American Sociological Association 2013.

Goodrich C.S.,University of Nebraska - Lincoln
Computers and Mathematics with Applications | Year: 2010

In this paper, we consider a fractional initial value problem (IVP) in the case where the order ν of the fractional difference satisfies 0 < ν ≤ 1. We show that solutions of this IVP satisfy a continuity condition both with respect to the order of the difference, ν, and with respect to the initial conditions, and we deduce several important corollaries from this theorem. Thus, we address a complication that arises in the fractional case but not in the classical (integer-order) case. © 2010 Elsevier Ltd. All rights reserved.

Keshwani D.R.,University of Nebraska - Lincoln | Cheng J.J.,North Carolina State University
Biotechnology and Bioengineering | Year: 2010

This study used two different approaches to model changes in biomass composition during microwave-based pretreatment of switchgrass: kinetic modeling using a time-dependent rate coefficient, and a Mamdani-type fuzzy inference system. In both modeling approaches, the dielectric loss tangent of the alkali reagent and pretreatment time were used as predictors for changes in amounts of lignin, cellulose, and xylan during the pretreatment. Training and testing data sets for development and validation of the models were obtained from pretreatment experiments conducted using 1-3% w/v NaOH (sodium hydroxide) and pretreatment times ranging from 5 to 20 min. The kinetic modeling approach for lignin and xylan gave comparable results for training and testing data sets, and the differences between the predictions and experimental values were within 2%. The kinetic modeling approach for cellulose was not as effective, and the differences were within 5-7%. The time-dependent rate coefficients of the kinetic models estimated from experimental data were consistent with the heterogeneity of individual biomass components. The Mamdani-type fuzzy inference was shown to be an effective approach to model the pretreatment process and yielded predictions with less than 2% deviation from the experimental values for lignin and with less than 3% deviation from the experimental values for cellulose and xylan. The entropies of the fuzzy outputs from the Mamdani-type fuzzy inference system were calculated to quantify the uncertainty associated with the predictions. Results indicate that there is no significant difference between the entropies associated with the predictions for lignin, cellulose, and xylan. It is anticipated that these models could be used in process simulations of bioethanol production from ligno-cellulosic materials. © 2009 Wiley Periodicals, Inc.

Wang H.,University of Massachusetts Dartmouth | Qian Y.,University of Nebraska - Lincoln | Sharif H.,University of Massachusetts Dartmouth
IEEE Wireless Communications | Year: 2013

Wireless networks play a major role in smart grid applications such as automatic meter reading, remote system monitoring, remote home/customer site monitoring, and equipment fault diagnosing. Many smart grid applications face harsh environmental conditions but have high reliability and low latency requirements. Many communication challenges posed by the smart grid applications require careful research and customized communication and networking solutions. For example, huge amount of data related to monitoring and control will be transmitted across smart grid wireless communication infrastructures, with intensive interference and increasing competition over the limited and crowded radio spectrum for the existing wireless networking standards. The opportunistic spectrum access with cognitive radios is a promising wireless technology to improve the frequency/spectrum utilization by detecting unoccupied spectrum holes of primary users and assigning them to secondary users. The versatile features of cognitive radio technology satisfy the requirements of smart grid communications. On the other hand, there are growing needs of multimedia applications via smart grid communication infrastructures that require large bandwidth and network resources. To meet the requirements of this important paradigm in smart grid communications, in this paper, we investigate the technical challenges and the solutions of cognitive radio networking with multimedia applications for smart grid communication infrastructures, and present a guideline for future smart grid multimedia communication infrastructure design. ©2013 IEEE.

Soulakova J.N.,University of Nebraska - Lincoln
Journal of Biopharmaceutical Statistics | Year: 2011

In this paper several multiple testing procedures are discussed with respect to the problem of detecting combination drug superiority for a bifactorial design with monotone gains. The testing methods include the generalized maximum test procedure (GMAXP) proposed by Soulakova (2009), and gatekeeping strategies: the general multistage gatekeeping method (GMGP) proposed by Dmitrienko et al. (2008a), and the serial Bonferroni gatekeeping method (TREE), proposed by Dmitrienko et al. (2007). The GMGP with the truncated Holm and Hochberg components is discussed. In addition, the truncated Sidak-Holm component is proposed, and shortcut alternatives to the GMGP are addressed. It is shown by simulations that the GMAXP achieves higher power if there are relatively many superior combinations, i.e., if the lower combinations are superior, while the gatekeeping methods perform better if there is a single or just a few superior combinations. While in some cases the GMGP with the truncated Sidak-Holm component outperforms the GMGP with the truncated Hochberg component, the observed power advantages are not substantial. Thus, the GMGP with the truncated Hochberg component is recommended as it can dominate the other methods when the Min test statistics are independent. Copyright © Taylor & Francis Group, LLC.

Jang W.M.,University of Nebraska - Lincoln
IEEE Transactions on Vehicular Technology | Year: 2014

Recently, multiple-input-multiple-output (MIMO) relay networks have been an active area of research, particularly with combining single transmit antenna selection (TAS) and receiver maximal ratio combining (MRC). Moreover, general-order rectangular quadrature amplitude modulation (QAM) has received much attention for its high spectral efficiency and flexible modulation scheme. However, the analytical performance of general-order rectangular QAM has not been found in the literature for MIMO relay with TAS/MRC in Nakagami-m fading channels in spite of its practical usefulness. In addition, the analytical performance of general-order rectangular QAM often comes with enormous computational complexity. Therefore, it is hardly possible to understand the analytical solution unless the symbol error probability (SEP) is plotted graphically. In this paper, we present the SEP of general-order rectangular QAM in a MIMO relay with TAS/MRC using the sampling property of the delta impulse function. The SEP of MIMO relay networks is shown in terms of diversity order and coding gain. The proposed sampling method can also significantly reduce the computational complexity of the SEP of general-order rectangular QAM. © 2014 IEEE.

Goodrich C.S.,University of Nebraska - Lincoln
Computers and Mathematics with Applications | Year: 2011

In this paper, we consider a discrete fractional boundary value problem of the form -Δνy(t)=f(t+ν-1,y(t+ν-1)), y(ν-2)=g(y), y(ν+b)=0, where f:[ν-1,⋯,ν+b-1]Nν-2×R→R is continuous, g:C([ν-2,ν+b]Nν-2,R) is a given functional, and 1<ν≤2. We give a representation for the solution to this problem. Finally, we prove the existence and uniqueness of solution to this problem by using a variety of tools from nonlinear functional analysis including the contraction mapping theorem, the Brouwer theorem, and the Krasnosel'skii theorem. © 2010 Elsevier Ltd. All rights reserved.

Li Q.C.,Utah State University | Hu R.Q.,Utah State University | Xu Y.,Utah State University | Qian Y.,University of Nebraska - Lincoln
IEEE Transactions on Wireless Communications | Year: 2013

Heterogeneous wireless networks have emerged as a new paradigm to meet the fast growing wireless network capacity and coverage demands. Due to the co-deployment of high power and low power nodes in the same network using the same spectrum, more advanced interference coordination and radio resource management schemes are required than in the traditional cellular network in order to achieve a high network capacity and good user experience. In this paper, we propose an optimal fractional frequency reuse and power control scheme that can effectively coordinate the interference among high power and low power nodes. The scheme can be optimized to maximize the sum of the long term log-scale throughput among all the user equipments (UEs). Towards that end, the Lagrange dual function is first derived for the proposed optimization problem. Gradient descent method is then used to search the optimal solution for the convex dual problem. Due to the strong duality condition, the optimal solution for the dual problem is also the optimal solution for the primal problem. Simulation results show that the proposed scheme can greatly improve the wireless heterogeneous network performance on system capacity and user experience. © 2002-2012 IEEE.

Goodrich C.S.,University of Nebraska - Lincoln
Computers and Mathematics with Applications | Year: 2011

In this paper, we consider a system of (continuous) fractional boundary value problems given by -D0+ν1y1(t)= λ1a1(t)f(y1(t),y2(t)),- D0+ν2y2(t)=λ2 a2(t)g(y1(t),y2(t)), where ν1, ν2∈(n-1,n] for n>3 and n∈N, subject either to the boundary conditions y1(i)(0)=0=y2(i)(0), for 0≤i≤n-2, and [D0 +αy1(t)]t=1=0=[D0+αy2(t) ]t=1, for 1≤α≤n-2, or y1(i)(0)=0=y2(i)(0), for 0≤i≤n-2, and [D0+αy1(t)]t=1=φ1(y), for 1≤α≤n-2, and [D0+αy2(t)]t=1= φ2(y), for 1≤α≤n-2. In the latter case, the continuous functionals φ1, φ2:C([0,1])→R represent nonlocal boundary conditions. We provide conditions on the nonlinearities f and g, the nonlocal functionals φ1 and φ2, and the eigenvalues λ1 and λ2 such that the system exhibits at least one positive solution. Our results here generalize some recent results on both scalar fractional boundary value problems and systems of fractional boundary value problems, and we provide two explicit numerical examples to illustrate the generalizations that our results afford. © 2011 Elsevier Ltd. All rights reserved.

Li X.-Z.,University of Nebraska - Lincoln
Journal of Applied Crystallography | Year: 2012

The processing and quantification of electron diffraction patterns have become vital in advanced electron crystallographic analysis work. A computer program, QPCED2.0, has been developed for the handling of selected-area electron diffraction patterns for polycrystalline materials. QPCED2.0 can be used to enhance the visibility of electron diffraction patterns, to convert electron diffraction patterns into intensity profiles, and to retrieve precisely the lattice d spacings and the integral intensities of the diffraction rings. The design and implementation of QPCED2.0 are elucidated and application examples are given. © 2012 International Union of Crystallography. Printed in Singapore-all rights reserved.

Beatty M.F.,University of Nebraska - Lincoln
Mathematics and Mechanics of Solids | Year: 2011

The small amplitude radial oscillation and infinitesimal stability about an equilibrium configuration of an arbitrary incompressible, isotropic and homogeneous elastic spherical shell under constant inflation pressure loading is studied for both thick- and thin-walled shells and for a spherical cavity within an unbounded continuum. The classical criterion of infinitesimal stability yields a general stability theorem relating the frequency and the pressure response. It follows that points at which the pressure is stationary are unstable or neutrally stable. All results are expressed in terms of the shear response function for a general incompressible, isotropic elastic material, and specific results are illustrated for the Mooney-Rivlin and Gent material models, the latter having limited extensibility. The classical neo-Hookean material exhibits results that are lower bounds for both models. A criterion obtained by others to characterize the possible bifurcation from a spherical to an aspherical shape is cast in terms of the general shear response function, and the physical nature of all elastic materials for which a shape bifurcation may occur is characterized. The result is illustrated in several examples. © 2011 The Author(s) .

Davidson M.M.,University of Nebraska - Lincoln
Journal of counseling psychology | Year: 2012

The purpose of this research was to conduct a replication-based and extension study examining the effectiveness of a 5-week career group counseling intervention, Advancing Career Counseling and Employment Support for Survivors (ACCESS; Chronister, 2008). The present study was conducted in a markedly different geographic region within a larger community as compared with the original investigation conducted by Chronister and McWhirter (2006). Women survivors of intimate partner violence (N = 73) participated in ACCESS, with career-search self-efficacy, perceived career barriers, perceived career supports, anxiety, and depression assessed at preintervention, postintervention, and 8-week follow-up. Women survivors demonstrated significant improvements in career-search self-efficacy and perceived career barriers at postintervention. Moreover, these same improvements were maintained at the 8-week follow-up assessment with the addition of significant improvements in perceived future financial supports, anxiety, and depression compared with preintervention scores. This work replicates the initial findings regarding the effectiveness of ACCESS with respect to career-search self-efficacy (Chronister & McWhirter, 2006) as well as extends the initial research to include improvements in perceived career barriers and perceived career supports. Moreover, the present study extends the work to include the mental health outcomes of anxiety and depression; results demonstrated improvements in these areas at 8-week follow-up. This investigation begins to fill a critical need for evaluated career-focused interventions for the underserved population of women survivors of intimate partner violence.

Feng S.,Lanzhou University | Feng S.,University of Nebraska - Lincoln | Feng S.,University of Arkansas | Fu Q.,Lanzhou University | Fu Q.,University of Washington
Atmospheric Chemistry and Physics | Year: 2013

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 × 106 km2 (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. © Author(s) 2013.

Fu J.,WJB Group | To C.W.S.,University of Nebraska - Lincoln
Engineering Structures | Year: 2012

An approach based on the transverse or out-of-plane nonlinear dynamic responses at the centers of edges of cracks is being proposed as a viable alternative to bulging factors for damage tolerance design and characterization of cracked cylindrical shell structures under applied internal pressure. This approach circumvents the problems of mesh selection at the crack tip in the finite element analysis for bulging factors and provides information about the influence of crack lengths as well as crack widths on responses. The influence of crack widths on responses has been found to be significant but it is not available in bulging factors. Furthermore, existing individual bulging factor only applies to a different range of ratios of crack length to radius of shell. It is concluded that (i) the proposed approach has no limit on the range of ratios of crack length to radius of shell; (ii) conceptually, the proposed approach is simple, and (iii) computationally, the nonlinear responses at the centers of edges of cracks are relatively easy to obtain accurately and efficiently by using the mixed formulation-based shell finite elements since the present dynamic approach converges quickly at very coarse meshes. © 2012 Elsevier Ltd.

Louis J.,University of Nebraska - Lincoln | Shah J.,University of North Texas
Journal of Experimental Botany | Year: 2015

In Arabidopsis thaliana, PHYTOALEXIN DEFICIENT 4 (PAD4) functions as a key player in modulating defence against the phloem sap-feeding aphid Myzus persicae (Sülzer), more commonly known as the green peach aphid (GPA), an important pest of a wide variety of plants. PAD4 controls antibiosis and antixenosis against the GPA. In addition, PAD4 deters aphid feeding from sieve elements on Arabidopsis. In the past few years, substantial progress has been made in dissecting the role of PAD4 and its interaction with other signalling components in limiting aphid infestation. Several key genes/mechanisms involved in providing aphid resistance/susceptibility in Arabidopsis regulate the aphid infestation-stimulated expression of PAD4. Together, PAD4 and its interacting signalling partners provide a critical barrier to curtail GPA colonization of Arabidopsis. © 2014 The Author. All rights reserved.

Wang T.,NIWA - National Institute of Water and Atmospheric Research | Zlotnik V.A.,University of Nebraska - Lincoln
Journal of Hydrology | Year: 2012

A complementary relationship (CR) between potential (ET p) and actual (ET a) evapotranspiration is obtained using two independent approaches, and the role of soils in formulating the CR is also investigated. The first approach employs a process-based vadose zone model that links ET p and ET a by explicitly considering the role of soils. To drive the model, hydrometeorological, soil, and remotely sensed physiological data are utilized. The second approach utilizes the products of the MODIS_. ET (MOD16) data set that is derived from remotely sensed data by mainly considering above-ground land surface processes. Both methods are applied for 42 sites across Nebraska, USA. The results from both approaches demonstrate the CR; however, according to previously reported ET a and ET p values, MODIS_. ET tends to underestimate ET a in wet years and systematically overestimate ET p across Nebraska, which leads the wet surface evapotranspiration (ET w) to decrease with increasing annual humidity index Φ (i.e., the ratio of annual precipitation over annual ET p). In comparison, ET w estimated from the vadose zone model is similar to ET w calculated from the Priestley-Taylor equation, and remains relatively constant over a wide range of annual Φ with a mean of 105.1. cm/year. Both approaches show that ET w is not sensitive to soil properties, which provides a rationale for combining historical data from different locations to study the impact of climate variability on evapotranspiration processes at annual time scales. © 2012 Elsevier B.V.

Antipsychotic sensitization and tolerance refer to the increased and decreased drug effects due to past drug use, respectively. Both effects reflect the long-term impacts of antipsychotic treatment on the brain and result from the brain's adaptive response to the foreign property of the drug. In this review, clinical evidence of the behavioral aspect of antipsychotic sensitization and tolerance is selectively reviewed, followed by an overview of preclinical literature that examines these behavioral characteristics and the related pharmacological and nonpharmacological factors. Next, recent work on the developmental impacts of adolescent antipsychotic sensitization and tolerance is presented and recent research that delineates the neurobiological mechanisms of antipsychotic sensitization and tolerance is summarized. A theoretical framework based on "drug learning and memory" principles is proposed to account for the phenomena of antipsychotic sensitization and tolerance. It is maintained that antipsychotic sensitization and tolerance follow basic principles of learning or acquisition ("induction") and memory ("expression"). The induction and expression of both effects reflect the consequences of associative and nonassociative processing and are strongly influenced by various pharmacological, environmental, and behavioral factors. Drug-induced neuroplasticity, such as functional changes of striatal dopamine D2 and prefrontal serotonin (5-HT)2A receptors and their mediated signaling pathways, in principle, is responsible for antipsychotic sensitization and tolerance. Understanding the behavioral characteristics and neurobiological underpinnings of antipsychotic sensitization and tolerance has greatly enhanced our understanding of mechanisms of antipsychotic action, and may have important implications for future drug discovery and clinical practice. © British Association for Psychopharmacology.

Hudson E.J.,University of Nebraska - Lincoln | Price T.D.,University of Chicago
Journal of Heredity | Year: 2014

Sexual selection has been widely implicated as a driver of speciation. However, allopatric forms are often defined as species based on divergence in sexually selected traits and it is unclear how much such trait differences affect reproductive isolation upon secondary contact, the defining feature of biological species. We show that in birds, divergence in song and plumage in allopatry corresponds poorly with whether species mate assortatively in hybrid zones and argue that this is because many other factors besides trait divergence affect propensity to hybridize, including rarity of conspecific mates and choice based on territory rather than male traits. We then present a general model for the establishment of sympatry that assumes a period of differentiation in allopatry followed by secondary contact and often hybridization, with hybridization subsequently reduced by reinforcement of mate preferences. We suggest that reinforcement commonly operates by a narrowing of a "window of recognition" for traits that are different between the species, rather than evolution of the traits themselves. Our arguments imply that it is important to study postmating as well as premating reproductive isolation in limiting sympatry and suggest that studies of reinforcement should focus on evolution of female preferences for diagnostic traits, rather than evolution of traits per se. © 2014 © The American Genetic Association. 2014. All rights reserved.

Wilson P.B.,University of Nebraska - Lincoln
Journal of Strength and Conditioning Research | Year: 2015

Ginger is a popular spice used to treat a variety of maladies, including pain. Nonsteroidal anti-inflammatory drugs (NSAIDs) are frequently used by athletes to manage and prevent pain; unfortunately, NSAIDs contribute to substantial adverse effects, including gastrointestinal (GI) dysfunction, exercise-induced bronchoconstriction, hyponatremia, impairment of connective tissue remodeling, endurance competition withdrawal, and cardiovascular disease. Ginger, however, may act as a promoter of GI integrity and as a bronchodilator. Given these potentially positive effects of ginger, a systematic review of randomized trials was performed to assess the evidence for ginger as an analgesic and ergogenic aid for exercise training and sport. Among 7 studies examining ginger as an analgesic, the evidence indicates that roughly 2 g·d -1 of ginger may modestly reduce muscle pain stemming from eccentric resistance exercise and prolonged running, particularly if taken for a minimum of 5 days. Among 9 studies examining ginger as an ergogenic aid, no discernable effects on body composition, metabolic rate, oxygen consumption, isometric force generation, or perceived exertion were observed. Limited data suggest that ginger may accelerate recovery of maximal strength after eccentric resistance exercise and reduce the inflammatory response to cardiorespiratory exercise. Major limitations to the research include the use of untrained individuals, insufficient reporting on adverse events, and no direct comparisons with NSAID ingestion. While ginger taken over 1-2 weeks may reduce pain from eccentric resistance exercise and prolonged running, more research is needed to evaluate its safety and efficacy as an analgesic for a wide range of athletic endeavors. © 2015 National Strength and Conditioning Association.

Zhang W.,University of Nebraska Medical Center | Creswell J.,University of Nebraska - Lincoln
Medical Care | Year: 2013

BACKGROUND:: Mixed methods research has emerged alongside qualitative and quantitative approaches as an important tool for health services researchers. Despite growing interest, among health services researchers, in using mixed methods designs, little has been done to identify the procedural aspects of doing so. PURPOSE:: To describe how mixed methods researchers mix the qualitative and quantitative aspects of their studies in health services research. DATA SOURCE:: We searched the PubMed for articles, using mixed methods in health services research, published between January 1, 2006 and December 30, 2010. STUDY SELECTION:: We identified and reviewed 30 published health services research articles on studies in which mixed methods had been used. We selected 3 articles as illustrations to help health services researcher conceptualize the type of mixing procedures that they were using. RESULTS:: Three main mixing procedures have been applied within these studies: (1) the researchers analyzed the 2 types of data at the same time but separately and integrated the results during interpretation; (2) the researchers connected the qualitative and quantitative portions in phases in such a way that 1 approach was built upon the findings of the other approach; and (3) the researchers mixed the 2 data types by embedding the analysis of 1 data type within the other. CONCLUSIONS:: Mixing in mixed methods is more than just the combination of 2 independent components of the quantitative and qualitative data. The use of mixing procedure in health services research involves the integration, connection, and embedding of these 2 data components. Copyright © 2013 by Lippincott Williams & Wilkins.

Pei Y.,Xiangtan University | Zeng X.C.,University of Nebraska - Lincoln
Nanoscale | Year: 2012

Unlike bulk materials, the physicochemical properties of nano-sized metal clusters can be strongly dependent on their atomic structure and size. Over the past two decades, major progress has been made in both the synthesis and characterization of a special class of ligated metal nanoclusters, namely, the thiolate-protected gold clusters with size less than 2 nm. Nevertheless, the determination of the precise atomic structure of thiolate-protected gold clusters is still a grand challenge to both experimentalists and theorists. The lack of atomic structures for many thiolate-protected gold clusters has hampered our in-depth understanding of their physicochemical properties and size-dependent structural evolution. Recent breakthroughs in the determination of the atomic structure of two clusters, [Au 25(SCH 2CH 2Ph) 18] q (q = -1, 0) and Au 102(p- MBA) 44, from X-ray crystallography have uncovered many new characteristics regarding the gold-sulfur bonding as well as the atomic packing structure in gold thiolate nanoclusters. Knowledge obtained from the atomic structures of both thiolate-protected gold clusters allows researchers to examine a more general "inherent structure rule" underlying this special class of ligated gold nanoclusters. That is, a highly stable thiolate-protected gold cluster can be viewed as a combination of a highly symmetric Au core and several protecting gold-thiolate "staple motifs", as illustrated by a general structural formula [Au] a+a′[Au(SR) 2] b[Au 2(SR) 3] c[Au 3(SR) 4] d[Au 4(SR) 5] e where a, a′, b, c, d and e are integers that satisfy certain constraints. In this review article, we highlight recent progress in the theoretical exploration and prediction of the atomic structures of various thiolate-protected gold clusters based on the "divide-and-protect" concept in general and the "inherent structure rule" in particular. As two demonstration examples, we show that the theoretically predicted lowest-energy structures of Au 25(SR) 8 - and Au 38(SR) 24 (-R is the alkylthiolate group) have been fully confirmed by later experiments, lending credence to the "inherent structure rule". This journal is © 2012 The Royal Society of Chemistry.

Nguy-Robertson A.L.,University of Nebraska - Lincoln
International Journal of Remote Sensing | Year: 2013

Vegetation indices (VIs), which are combinations of various remote-sensing spectral bands, are widely used to study various biophysical properties. There are many articles introducing new VIs with the intention of minimizing factors such as soil background, canopy architecture, and row structure, while maximizing sensitivity to a specific biophysical characteristic such as the green leaf area index. Two VIs introduced in a previous study for the estimation of the biophysical characteristic green leaf area index are the modified chlorophyll absorption ratio index 2 (MCARI2) and modified triangular vegetation index 2 (MTVI2). This study and another study indicated that MTVI2 and MCARI2 gave identical results, but the mathematical similarity was not described in detail. Thus, future studies investigating the accuracy of VIs for estimating the biophysical characteristics need to examine either MCARI2 or MTVI2. © 2013 Copyright Taylor & Francis.

Frolov M.V.,Voronezh State University | Manakov N.L.,Voronezh State University | Starace A.F.,University of Nebraska - Lincoln
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2010

The experimental finding of significant enhancement or suppression of particular harmonics generated by the ionic component of laser-produced plasmas of transition-metal atoms is explained theoretically in terms of the standard three-step scenario for strong-field harmonic generation, taking into account the potential barrier effects that lead to a strong 3p→3d electric dipole transition that dominates the photoionization cross sections of the outer subshells of those ions. © 2010 The American Physical Society.

Harris S.D.,University of Nebraska - Lincoln
Annals of the New York Academy of Sciences | Year: 2012

Conidiophores are reproductive structures that enable filamentous fungi to produce and disseminate large numbers of asexual spores. The diversity in conidiophore morphology is sufficiently large to serve as a basis for fungal systematics. Aspergillus and Penicillium species are members of the family Trichocomaceae that form conidiophores with characteristic architecture. Whereas the Penicillium conidiophore appears to be a modified branched hyphal structure, the Aspergillus conidiophore is seemingly more complex and includes additional cell types. Here, it is proposed that the "aspergillioid" conidiophore may have evolved from a "penicillioid" ancestor via changes in expression of key regulators of the cell cycle and the GTPase Cdc42. Because the transcriptional regulatory network that controls conidiophore development in Aspergillus is well characterized, further study of how this network links to regulators of the cell cycle and Cdc42 should provide fundamental insight into the evolution of developmental morphogenesis in fungi (i.e., fungal evo-devo). © 2012 New York Academy of Sciences.

Benson A.K.,University of Nebraska - Lincoln
Genome Biology | Year: 2015

Comparative analyses of the control of mammalian microbiomes by host genetic architecture reveal striking conserved features that have implications for the evolution of host-microbiome interactions. See related Research article: http://www.genomebiology.com/2015/16/1/191 © 2015 Benson.

Fabrikant I.I.,University of Nebraska - Lincoln
Journal of Physics: Conference Series | Year: 2010

We present a summary of recent progress in theoretical studies of low-energy dissociative electron attachment (DEA) to halogen molecules and polyatomic molecules based on the resonance R-matrix theory. It explains many observed features in DEA cross sections including low-energy behavior, threshold resonances and cusps. It also gives correct description of the temperature dependence of the attachment rate coefficients. More recently the theory was applied to two molecules of biological interest, formic acid and glycine. DEA mechanisms in these systems are very similar to those in hydrogen halides. © 2010 IOP Publishing Ltd.

Irmak S.,University of Nebraska - Lincoln
Transactions of the ASABE | Year: 2010

Surface energy and water vapor fluxes play a critical role in understanding the response of agro-ecosystems to changes in environmental and atmospheric parameters. These fluxes play a crucial role in exploring the dynamics of water and energy use efficiencies of these systems. Quantification of the fluxes is also necessary for assessing the impact of land use and management changes on water balances. Accomplishing these goals requires measurement of water vapor and energy exchanges between various vegetation surfaces and microclimates for long-enough periods to understand the behavior and dynamics involved with the flux transfer so that robust models can be developed to predict these processes under different scenarios. Networks of flux towers such as AMERIFLUX, FLUXNET, FLUXNET-CANADA, EUROFLUX, ASIAFLUX, and CAR-BOEUROPE have been collecting data on exchange processes between biosphere and atmosphere for multiple years across the globe to better understand the functioning of terrestrial ecosystems and their role in regional and/or continental and global carbon, water, and energy cycles, providing a unique service to the scientific community. Nonetheless, there is an imperative need for these kinds of networks to increase in number and intensity due to the great diversity among ecosystems and agro-ecosystems in species composition, physiological properties, physical structure, microclimatic and climatic conditions, and management practices. The Nebraska Water and Energy Flux Measurement, Modeling, and Research Network (NEBFLUX) is a comprehensive network that is designed to measure surface energy and water vapor fluxes, microclimatic variables, plant physiological parameters, soil water content, surface characteristics, and their interactions for various vegetation surfaces. The NEBFLUX is a network of micrometeorological tower sites that uses mainly Bowen ratio energy balance systems (BREBS) to measure surface water vapor and energy fluxes between terrestrial agro-ecosystems and microclimate. At present, ten BREBSs and one eddy covariance system are operating on a long-term and continuous basis for vegetation surfaces ranging from tilled and untilled irrigated and rainfed croplands, irrigated and rainfed grasslands, alfalfa, to Phragmites (Phragmites australis)-dominated cottonwood (Populus deltoides var. occidentalis) and willow stand (Willow salix) plant communities. The NEBFLUX project will provide good-quality flux and other extensive supportive data on plant physiology [leaf area index, stomatal resistance, within-canopy radiation parameters, productivity (yield and/or biomass), and plant height], soil characteristics, soil water content, and surface characteristics to the micrometeorology, water resources and agricultural engineering, and science community on broad spectrum of agro-ecosystems. The fundamental premise of the NEBFLUX project is to measure continuous and long-term (at least ten complete annual cycles for each surface) exchange of water vapor and energy fluxes. In addition to the scientific and research objectives, information dissemination to educate the general public and youth is another important objective and output of the network. This article describes the specific goals and objectives, basic principles, and operational characteristics of the NEBFLUX. © 2010 American Society of Agricultural and Biological Engineers ISSN 2151-0032.

Graybosch R.A.,University of Nebraska - Lincoln | Peterson C.J.,Oregon State University
Crop Science | Year: 2010

Data from USDA-coordinated winter wheat (Triticum aestivum L.) regional performance nurseries collected over the time period 1959 to 2008 were used to estimate genetic gain (loss) in grain yield, grain volume weight, days to heading, and plant height in winter wheats adapted to the Great Plains of North America. In both the Southern Regional (SRPN) and Northern Regional Performance Nurseries (NRPN), linear regression revealed significant positive relationships between relative grain yields of advanced breeding lines and calendar year of the nursery trial. The estimated genetic gain in grain yield potential since 1959 was approximately 1.1% (of the control cultivar Kharkof) yr-1 for all entries in the SRPN, and 1.3% yr-1 if only the most productive entry was considered. For the NRPN, the estimates of genetic gain in grain yield were 0.79% yr-1 for all entries, and also 0.79% yr-1 for the most productive entry. Linear regressions of relative grain yields vs. year over the time period 1984 to 2008, however, showed no statistically significant trend in the SRPN. For the same time period in the NRPN, a statistically significant positive slope of 0.83 was observed, though the coefficient of determination (R2) was only 0.28. Relative grain yields of Great Plains hard winter wheats may have peaked in the early to mid- 1990s, and further improvement in the genetic potential for grain yield awaits some new technological or biological advance. © Crop Science Society of America.

Weber M.G.,Cornell University | Keeler K.H.,University of Nebraska - Lincoln
Annals of Botany | Year: 2013

Background and Aims Understanding the evolutionary patterns of ecologically relevant traits is a central goal in plant biology. However, for most important traits, we lack the comprehensive understanding of their taxonomic distribution needed to evaluate their evolutionary mode and tempo across the tree of life. Here we evaluate the broad phylogenetic patterns of a common plant-defence trait found across vascular plants: extrafloral nectaries (EFNs), plant glands that secrete nectar and are located outside the flower. EFNs typically defend plants indirectly by attracting invertebrate predators who reduce herbivory. Methods Records of EFNs published over the last 135 years were compiled. After accounting for changes in taxonomy, phylogenetic comparative methods were used to evaluate patterns of EFN evolution, using a phylogeny of over 55 000 species of vascular plants. Using comparisons of parametric and non-parametric models, the true number of species with EFNs likely to exist beyond the current list was estimated. Key Results To date, EFNs have been reported in 3941 species representing 745 genera in 108 families, about 1-2% of vascular plant species and approx. 21% of families. They are found in 33 of 65 angiosperm orders. Foliar nectaries are known in four of 36 fern families. Extrafloral nectaries are unknown in early angiosperms, magnoliids and gymnosperms. They occur throughout monocotyledons, yet most EFNs are found within eudicots, with the bulk of species with EFNs being rosids. Phylogenetic analyses strongly support the repeated gain and loss of EFNs across plant clades, especially in more derived dicot families, and suggest that EFNs are found in a minimum of 457 independent lineages. However, model selection methods estimate that the number of unreported cases of EFNs may be as high as the number of species already reported. Conclusions EFNs are widespread and evolutionarily labile traits that have repeatedly evolved a remarkable number of times in vascular plants. Our current understanding of the phylogenetic patterns of EFNs makes them powerful candidates for future work exploring the drivers of their evolutionary origins, shifts, and losses. © 2012 The Author. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.

Fomenko D.E.,University of Nebraska - Lincoln | Gladyshev V.N.,Harvard University
Antioxidants and Redox Signaling | Year: 2012

Aims: Redox regulation of cellular processes is an important mechanism that operates in organisms from bacteria to mammals. Much of the redox control is provided by thiol oxidoreductases: proteins that employ cysteine residues for redox catalysis. We wanted to identify thiol oxidoreductases on a genome-wide scale and use this information to obtain insights into the general principles of thiol-based redox control. Results: Thiol oxidoreductases were identified by three independent methods that took advantage of the occurrence of selenocysteine homologs of these proteins and functional linkages among thiol oxidoreductases revealed by comparative genomics. Based on these searches, we describe thioredoxomes, which are sets of thiol oxidoreductases in organisms. Their analyses revealed that these proteins are present in all living organisms, generally account for 0.5%-1% of the proteome and that their use correlates with proteome size, distinguishing these proteins from those involved in core metabolic functions. We further describe thioredoxomes of Saccharomyces cerevisiae and humans, including proteins which have not been characterized previously. Thiol oxidoreductases occur in various cellular compartments and are enriched in the endoplasmic reticulum and cytosol. Innovation: We developed bioinformatics methods and used them to characterize thioredoxomes on a genome-wide scale, which in turn revealed properties of thioredoxomes. Conclusion: These data provide information about organization and properties of thiol-based redox control, whose use is increased with the increase in complexity of organisms. Our data also show an essential combined function of a set of thiol oxidoreductases, and of thiol-based redox regulation in general, in all living organisms. © 2012 Mary Ann Liebert, Inc.

van Etten J.L.,University of Nebraska - Lincoln
Viruses | Year: 2011

Viruses with genomes larger than 300 kb and up to 1.2 Mb, which encode hundreds of proteins, are being discovered and characterized with increasing frequency. Most, but not all, of these large viruses (often referred to as giruses) infect protists that live in aqueous environments. Bioinformatic analyses of metagenomes of aqueous samples indicate that large DNA viruses are quite common in nature and await discovery. One issue that is perhaps not appreciated by the virology community is that large viruses, even those classified in the same family, can differ significantly in morphology, lifestyle, and gene complement. This brief commentary, which will mention some of these unique properties, was stimulated by the characterization of the newest member of this club, virus CroV (Fischer, M.G.; Allen, M.J.; Wilson, W.H.; Suttle, C.A. Giant virus with a remarkable complement of genes infects marine zooplankton. Proc. Natl. Acad. Sci. USA 2010, 107, 19508-19513 [1]). CroV has a 730 kb genome (with ~544 protein-encoding genes) and infects the marine microzooplankton Cafeteria roenbergensis producing a lytic infection. © 2011 by the authors; licensee MDPI, Basel, Switzerland.

Lu T.,University of Nebraska - Lincoln
Database : the journal of biological databases and curation | Year: 2012

Fungal pathogens cause various diseases for plant and animal hosts. Despite the extensive impact of fungi on human health and life, the threats posed by emerging fungal pathogens are poorly understood. Specifically, there exist few fungal virulence gene databases, which prevent effective bioinformatics studies on fungal pathogens. Therefore, we constructed a comprehensive online database of known fungal virulence factors, which collected 2058 pathogenic genes produced by 228 fungal strains from 85 genera. This database creates a pivotal platform capable of stimulating and facilitating further bench studies on fungal pathogens.

Gardner S.A.,University of Nebraska - Lincoln
Library Resources and Technical Services | Year: 2012

This review covers cataloging and classification literature published in 2009 and 2010, including relevant explorations of knowledge organization systems and theory. Only English-language literature is reviewed, though not all of the literature covered is U.S.-based. Overarching themes presented in the literature include the merging of library metadata into the Web environment, the continuation of cooperative cataloging in libraries, the role of both controlled and uncontrolled headings in catalog records, and reconsiderations of workflow in light of impending changes to cataloging rules. Notably, several relevant foundational documents were either completed or revised during the review period.

Chini M.,University of Central Florida | Zhao B.,University of Nebraska - Lincoln | Wang H.,Lawrence Berkeley National Laboratory | Cheng Y.,University of Central Florida | And 2 more authors.
Physical Review Letters | Year: 2012

Recent advances in attosecond science have relied upon the nearly instantaneous response of free electrons to an external field. However, it is still not clear whether bound electrons are able to rearrange on sublaser cycle time scales. Here, we probe the optical Stark shifts induced by a few-cycle near infrared laser field in helium bound states using isolated attosecond pulses in a transient absorption scheme and uncover a subcycle laser-induced energy level shift of the laser-dressed 1s3p state. © 2012 American Physical Society.

Cragg L.,University of Nottingham | Chevalier N.,University of Nebraska - Lincoln
Quarterly Journal of Experimental Psychology | Year: 2012

It is now well established in the adult literature that the ability to engage in flexible thought and action is a complex skill that relies on a number of underlying processes. The development of this skill has received growing interest in recent years. However, theories explaining children's ability to switch between different tasks typically focus on a single underlying process and are rarely extended to explain development beyond the preschool years. This article reviews the current literature on set shifting in children in comparison with task switching in adults, in order to highlight the range of factors that impact on children's ability to flexibly shift between tasks. In doing this we hope to set the scene for future research that can begin to establish the relationships between these processes and how they change with age. © 2012 Copyright The Experimental Psychology Society.

Goosby B.J.,University of Nebraska - Lincoln | Walsemann K.M.,University of South Carolina
Health and Place | Year: 2012

We investigate whether school racial composition is associated with racial and ethnic differences in early adult health. We then examine whether perceived discrimination, social connectedness, and parent support attenuates this relationship. Using U.S. data from Waves I and IV of the National Longitudinal Survey of Adolescent Health, we found that black adolescents attending predominantly white schools reported poorer adult health while Asians reported better health. Further research is warranted to understand whether there are qualitative differences in the treatment of racial and ethnic minorities within certain school contexts and how that differential treatment is related to adult health outcomes. © 2011 Elsevier Ltd.

Gallup G.A.,University of Nebraska - Lincoln
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

A enhanced procedure implementing the finite-element-discrete-model method for determining atomic or molecular shape resonances and widths is described. The present procedure includes an approximation for the static exchange plus polarization model involving Möller-Plesset perturbation theory. Applications to Mg, N2, CH2O, and uracil are described. Compared with experiment, the results for Mg are within 5 meV for the resonance position and 75 meV for the width. The vertical geometry results for N 2 and CH2O compare well with experiment insofar as can be determined in the presence of nuclear motion complications. Uracil is calculated as an example where the large dipole moment (4.8 D) has an impact on threshold properties and possible dipole bound states. © 2011 American Physical Society.

Fabrikant I.I.,University of Nebraska - Lincoln | Gribakin G.F.,Queens University of Belfast
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

A pseudopotential for positronium-atom interaction, based on electron-atom and positron-atom phase shifts, is constructed, and the phase shifts for Ps-Kr and Ps-Ar scattering are calculated. This approach allows us to extend the Ps-atom cross sections, obtained previously in the impulse approximation [I. I. Fabrikant and G. F. Gribakin, Phys. Rev. Lett. 112, 243201 (2014)PRLTAO0031-900710.1103/PhysRevLett.112.243201], to energies below the Ps ionization threshold. Although experimental data are not available in this low-energy region, our results describe well the tendency of the measured cross sections to drop with decreasing velocity at v<1 a.u. Our results show that the effect of the Ps-atom van der Waals interaction is weak compared to the polarization interaction in electron-atom and positron-atom scattering. As a result, the Ps scattering length for both Ar and Kr is positive, and the Ramsauer-Townsend minimum is not observed for Ps scattering from these targets. This makes Ps scattering quite different from electron scattering in the low-energy region, in contrast to the intermediate energy range from the Ps ionization threshold up to v∼2 a.u., where the two are similar. © 2014 American Physical Society.

Waters B.M.,University of Nebraska - Lincoln | Sankaran R.P.,Lehman College, CUNY
Plant Science | Year: 2011

The micronutrients iron (Fe), zinc (Zn), and copper (Cu) are essential for plants and the humans and animals that consume plants. Increasing the micronutrient density of staple crops, or biofortification, will greatly improve human nutrition on a global scale. This review discusses the processes and genes needed to translocate micronutrients through the plant to the developing seeds, and potential strategies for developing biofortified crops. © 2010 Elsevier Ireland Ltd.

Patel K.P.,University of Nebraska Medical Center | Schultz H.D.,University of Nebraska Medical Center | Schultz H.D.,University of Nebraska - Lincoln
Antioxidants and Redox Signaling | Year: 2013

Significance: The renin-angiotensin system (RAS) plays an important role in the normal control of cardiovascular and renal function in the healthy state and is a contributing factor in the development and progression of various types of cardiovascular diseases (CVD), including hypertension, diabetes, and heart failure. Recent Advances: Evidence suggests that a balance between activation of the ACE/Ang II/AT1 receptor axis and the ACE2/Ang-(1-7)/Mas receptor axis is important for the function of the heart, kidney, and autonomic nervous system control of the circulation in the normal healthy state. An imbalance in these opposing pathways toward the ACE/Ang II/AT1 receptor axis is associated with CVD. The key component of this imbalance with respect to neural control of the circulation is the negative interaction between oxidative and NO • mechanisms, which leads to enhanced sympathetic tone and activation in disease conditions such as hypertension and heart failure. Critical Issues: The key mechanisms that disrupt normal regulation of Ang II and Ang-(1-7) signaling and promote pathogenesis of CVD at all organ levels remain poorly understood. The reciprocal relation between ACE and ACE2 expression and function suggests they are controlled interdependently at pre- and post-translational levels. Insights from neural studies suggest that an interaction between oxidative and nitrosative pathways may be key. Future Directions: The role of redox mechanisms in the control of expression and activity of RAS enzymes and Ang receptors may provide important insight into the function of local tissue RAS in health and disease. Antioxid. Redox Signal. 19, 1121-1132. © Copyright 2013, Mary Ann Liebert, Inc. 2013.

Clevers J.G.P.W.,Wageningen University | Gitelson A.A.,University of Nebraska - Lincoln
International Journal of Applied Earth Observation and Geoinformation | Year: 2013

Sentinel-2 is planned for launch in 2014 by the European Space Agency and it is equipped with the Multi Spectral Instrument (MSI), which will provide images with high spatial, spectral and temporal resolution. It covers the VNIR/SWIR spectral region in 13 bands and incorporates two new spectral bands in the rededge region, which can be used to derive vegetation indices using red-edge bands in their formulation. These are particularly suitable for estimating canopy chlorophyll and nitrogen (N) content. This band setting is important for vegetation studies and is very similar to the ones of the Ocean and Land Colour Instrument (OLCI) on the planned Sentinel-3 satellite and the Medium Resolution Imaging Spectrometer (MERIS) on Envisat, which operated from 2002 to early 2012. This paper focuses on the potential of Sentinel-2 and Sentinel-3 in estimating total crop and grass chlorophyll and N content by studying in situ crop variables and spectroradiometer measurements obtained for four different test sites. In particular, the red-edge chlorophyll index (CIred-edge), the green chlorophyll index (CIgreen) and the MERIS terrestrial chlorophyll index (MTCI) were found to be accurate and linear estimators of canopy chlorophyll and N content and the Sentinel-2 and-3 bands are well positioned for deriving these indices. Results confirm the importance of the red-edge bands on particularly Sentinel-2 for agricultural applications, because of the combination with its high spatial resolution of 20 m. © 2012 Elsevier B.V.

Marcus N.J.,University of Nebraska Medical Center | Del Rio R.,University of Nebraska Medical Center | Schultz E.P.,University of Nebraska - Lincoln | Xia X.-H.,Hebei Academy of Medical science | Schultz H.D.,University of Nebraska Medical Center
Journal of Physiology | Year: 2014

In congestive heart failure (CHF), carotid body (CB) chemoreceptor activity is enhanced and is associated with oscillatory (Cheyne-Stokes) breathing patterns, increased sympathetic nerve activity (SNA) and increased arrhythmia incidence. We hypothesized that denervation of the CB (CBD) chemoreceptors would reduce SNA, reduce apnoea and arrhythmia incidence and improve ventricular function in pacing-induced CHF rabbits. Resting breathing, renal SNA (RSNA) and arrhythmia incidence were measured in three groups of animals: (1) sham CHF/sham-CBD (sham-sham); (2) CHF/sham-CBD (CHF-sham); and (3) CHF/CBD (CHF-CBD). Chemoreflex sensitivity was measured as the RSNA and minute ventilatory (V̇E) responses to hypoxia and hypercapnia. Respiratory pattern was measured by plethysmography and quantified by an apnoea-hypopnoea index, respiratory rate variability index and the coefficient of variation of tidal volume. Sympatho-respiratory coupling (SRC) was assessed using power spectral analysis and the magnitude of the peak coherence function between tidal volume and RSNA frequency spectra. Arrhythmia incidence and low frequency/high frequency ratio of heart rate variability were assessed using ECG and blood pressure waveforms, respectively. RSNA and V̇E responses to hypoxia were augmented in CHF-sham and abolished in CHF-CBD animals. Resting RSNA was greater in CHF-sham compared to sham-sham animals (43 ± 5% max vs. 23 ± 2% max, P < 0.05), and this increase was not found in CHF-CBD animals (25 ± 1% max, P < 0.05 vs. CHF-sham). Low frequency/high frequency heart rate variability ratio was similarly increased in CHF and reduced by CBD (P < 0.05). Respiratory rate variability index, coefficient of variation of tidal volume and apnoea-hypopnoea index were increased in CHF-sham animals and reduced in CHF-CBD animals (P < 0.05). SRC (peak coherence) was increased in CHF-sham animals (sham-sham 0.49 ± 0.05; CHF-sham 0.79 ± 0.06), and was attenuated in CHF-CBD animals (0.59 ± 0.05) (P < 0.05 for all comparisons). Arrhythmia incidence was increased in CHF-sham and reduced in CHF-CBD animals (213 ± 58 events h-1 CHF, 108 ± 48 events h-1 CHF-CBD, P < 0.05). Furthermore, ventricular systolic (3.8 ± 0.7 vs. 6.3 ± 0.5 ml, P < 0.05) and diastolic (6.3 ± 1.0 vs. 9.1 ± 0.5 ml, P < 0.05) volumes were reduced, and ejection fraction preserved (41 ± 5% vs. 54 ± 2% reduction from pre-pace, P < 0.05) in CHF-CBD compared to CHF-sham rabbits. Similar patterns of changes were observed longitudinally within the CHF-CBD group before and after CBD. In conclusion, CBD is effective in reducing RSNA, SRC and arrhythmia incidence, while improving breathing stability and cardiac function in pacing-induced CHF rabbits. © 2013 The Physiological Society.

Walker E.L.,University of Massachusetts Amherst | Waters B.M.,University of Nebraska - Lincoln
Current Opinion in Plant Biology | Year: 2011

For human health, transition metal accumulation in edible seeds like cereal grains is of worldwide importance, since Fe and Zn deficiencies are among the most prevalent human nutritional disorders in the world. There have been many recent developments in our understanding of the patterns in which transition metals accumulate in the seeds, the identity of some specific transporters that are required for efficient seed metal accumulation, and the central role played by the ubiquitous plant metal chelator nicotianamine (NA). These and other recent discoveries will be reviewed here. © 2011 Elsevier Ltd.

α-Herpesvirinae subfamily members, including herpes simplex virus type 1 (HSV-1) and bovine herpes virus 1 (BHV-1), initiate infection in mucosal surfaces. BHV-1 and HSV-1 enter sensory neurons by cell-cell spread where a burst of viral gene expression occurs. When compared to non-neuronal cells, viral gene expression is quickly extinguished in sensory neurons resulting in neuronal survival and latency. The HSV-1 latency associated transcript (LAT), which is abundantly expressed in latently infected neurons, inhibits apoptosis, viral transcription, and productive infection, and directly or indirectly enhances reactivation from latency in small animal models. Three anti-apoptosis genes can be substituted for LAT, which will restore wild type levels of reactivation from latency to a LAT null mutant virus. Two small non-coding RNAs encoded by LAT possess anti-apoptosis functions in transfected cells. The BHV-1 latency related RNA (LR-RNA), like LAT, is abundantly expressed during latency. The LR-RNA encodes a protein (ORF2) and two microRNAs that are expressed in certain latently infected neurons. Wild-type expression of LR gene products is required for stress-induced reactivation from latency in cattle. ORF2 has anti-apoptosis functions and interacts with certain cellular transcription factors that stimulate viral transcription and productive infection. ORF2 is predicted to promote survival of infected neurons by inhibiting apoptosis and sequestering cellular transcription factors which stimulate productive infection. In addition, the LR encoded microRNAs inhibit viral transcription and apoptosis. In summary, the ability of BHV-1 and HSV-1 to interfere with apoptosis and productive infection in sensory neurons is crucial for the life-long latency-reactivation cycle in their respective hosts. © the author(s), publisher and licensee Libertas Academica Ltd.

Tectonic forcing of stratigraphic architecture is likely in foreland basins. Tectonic driving forces are increasingly being invoked to explain stratigraphic patterns in the Cretaceous Western Interior Seaway Basin of North America, yet the evidence is largely circumstantial, and the details of driving forces remain elusive. In this paper I show direct stratigraphic evidence for syndepositional growth of a structural arch with at least 50 m of relief during accumulation of the upper Turonian Ferron Sandstone in south-central Utah, United States. Progressive growth of the arch was superimposed on several high-frequency stratal cycles that were driven by a more regionally extensive process (geodynamic or eustatic) and that produced laterally amalgamated sandstone bodies in a depositional strike-parallel orientation (north-south). All of this stratigraphy was then truncated by a more or less planar erosion surface (sequence boundary) that can be traced physically over at least 67 km north-south. This surface was later tilted northward, such that the upper member of the Ferron Sandstone thins progressively southward from 50 to 10 m over 67 km. The facies juxtapositions revealed by the Ferron Sandstone could, if seen in exposure of limited lateral extent, be wrongly interpreted as recording regionally extensive relative sea-level drops and potentially used in error as evidence for substantial eustatic sea-level falls during the Turonian. The folding and tilting documented in this study can be clearly attributed to geodynamic and/or tectonic driving forces, likely related to migration of a forebulge. © 2011 Geological Society of America.

Savory P.,University of Nebraska - Lincoln
Journal of Industrial Engineering and Management | Year: 2010

It can be difficult estimating all of the cost components that are attributed to a machined part. This problem is more pronounced when a factory uses group technology manufacturing cells as opposed to a functional or process layout of a job shop. This paper describes how activity-based costing (ABC) concepts can be integrated into a discrete-event simulation model of a U-shaped manufacturing cell producing a part family with four members. The simulation model generates detailed Bills of Activity for each part type and includes specific information about the cost drivers and cost pools. The enhanced model output can be used for cost estimation and analysis, manufacturing cell design, part scheduling and other manufacturing decision processes that involve economic considerations. Although the scope of this effort is restricted to a small scale manufacturing cell, the costing concepts have general applicability to manufacturing operations at all levels. © Journal of Industrial Engineering and Management, 2010.

Pavlista A.D.,University of Nebraska - Lincoln
American Journal of Potato Research | Year: 2015

Droughts are common in the US High Plains, causing declining water availability and lowering water allocations. The objective of this 4-year field study was to identify a period of water deficit least detrimental to potato production. Fully irrigated ‘Atlantic’ potato received 62–63 cm of applied water. Total applied water was reduced by 25 % in three seasonal periods, 50 % water from emergence to 8 weeks after emergence (WAE) (early stress), 50 % water from 8 to 13 WAE (late stress), and 50 % from 0 to 5 WAE and again from 10 to 13 WAE (outer stress). Main plots were irrigation regime and split with three N levels, 101, 168, and 235 kg/ha. Soil and petiole N were higher when applied water was reduced. Lower irrigation inhibited growth, i.e., canopy height (10–20 %), weight (20–30 %) and leaf area index (50–70 %). Yield decreased 25 % and 13 % with early and outer stress, respectively. Chip color was darkest with early stress compared to fully irrigated plots. Common scab occurrence was greater in early stress than with other regimes. N rate had no effect on canopy growth, yield, chip color, or common scab. If applied water is reduced 15 cm, it is best late in the season and worst between 5 and 8 WAE compared to fully irrigated plants © 2015, The Potato Association of America.

Smith S.D.,Duke University | Smith S.D.,University of Nebraska - Lincoln | Wang S.,Duke University | Wang S.,Nanchang University | Rausher M.D.,Duke University
Molecular Biology and Evolution | Year: 2013

Dissecting the genetic basis for the evolution of species differences requires a combination of phylogenetic and molecular genetic perspectives. By mapping the genetic changes and their phenotypic effects onto the phylogeny, it is possible to distinguish changes that may have been directly responsible for a new character state from those that fine tune the transition. Here, we use phylogenetic and functional methods to trace the evolution of substrate specificity in dihydroflavonol-4-reductase (Dfr), an anthocyanin pathway gene known to be involved in the transition from blue to red flowers in Iochroma. Ancestral state reconstruction indicates that three substitutions occurred during the flower color transition, whereas several additional substitutions followed the transition. Comparisons of enzymatic function between ancestral proteins in blue-and red-flowered lineages and proteins from present-day taxa demonstrate that evolution of specificity for red pigment precursors was caused by the first three substitutions, which were fixed by positive selection and which differ from previously documented mutations affecting specificity. Two inferred substitutions subsequent to the initial flower color transition were also adaptive and resulted in an additional increase in specificity for red precursors. Epistatic interactions among both sets of substitutions may have limited the order of substitutions along branches of the phylogeny leading from blue-pigmented ancestors to the present-day red-flowered taxa. These results suggest that the species differences in DFR specificity may arise by a combination of selection on flower color and selection for improved pathway efficiency but that the exact series of genetic changes resulting in the evolution of specificity is likely to be highly contingent on the starting state. © 2012 The Author.

Ratcliffe B.C.,University of Nebraska - Lincoln
Coleopterists Bulletin | Year: 2015

The South American genus Allorrhina Burmeister (Coleoptera: Scarabaeidae: Cetoniinae: Gymnetini) is comprehensively revised. Redescriptions, diagnoses, distributions, and illustrations of nine species are provided. Allorrhina denotata Abadie and Ratcliffe from Brazil is described as a new species. The following new synonyms are established: Cotinis amazonica Thomson is Allorrhina carmelita (Burmeister); Gymnetis rhinoceros Gory and Percheron, Gymnetis cornifrons Gory and Percheron, Allorrhina baeri Bourgoin, Allorrhina viridicans Bourgoin, and Allorrhina gounellei Bourgoin are all Allorrhina menetriesii (Swederus); Gymnetis lugubris Thomson is Allorrhina nigerrima Burmeister.

Wei H.,University of Nebraska - Lincoln
Nature Photonics | Year: 2016

The large mobilities and carrier lifetimes of hybrid perovskite single crystals and the high atomic numbers of Pb, I and Br make them ideal for X-ray and gamma-ray detection. Here, we report a sensitive X-ray detector made of methylammonium lead bromide perovskite single crystals. A record-high mobility–lifetime product of 1.2 × 10-2 cm2 V-1 and an extremely small surface charge recombination velocity of 64 cm s-1 are realized by reducing the bulk defects and passivating surface traps. Single-crystal devices with a thickness of 2–3 mm show 16.4% detection efficiency at near zero bias under irradiation with continuum X-ray energy up to 50 keV. The lowest detectable X-ray dose rate is 0.5 μGyair s-1 with a sensitivity of 80 μC Gy-1 air cm-2, which is four times higher than the sensitivity achieved with α-Se X-ray detectors. This allows the radiation dose applied to a human body to be reduced for many medical and security check applications. © 2016 Nature Publishing Group

Rack F.R.,University of Nebraska - Lincoln
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2016

Clean hot water drill systems (CHWDSs) are used with clean access protocols for the exploration of subglacial lakes and other subglacial aquatic environments (e.g. ice-shelf cavities) in Antarctica. A CHWDS developed for the Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project by the Science Management Office at the University of Nebraska-Lincoln (UNL-SMO), USA, was specifically designed for use in West Antarctica, where the US Antarctic Program's South Pole Traverse could assist with logistical support. The initial goal was to provide clean access holes through ice up to 1000m thick following environmental stewardship guidelines; however, the existing design allows this CHWDS to be used for ice thicknesses up to 2000m following modifications to accommodate longer hose lengths. In January 2013, the WISSARD CHWDS successfully provided for the first time a clean access borehole through 800m of ice into Subglacial Lake Whillans beneath the West Antarctic Ice Sheet for the deployment of scientific instruments and sampling tools. The development and initial use of the WISSARD CHWDS required the project team to address a number of constraints while providing contingencies to meet the defined project scope, schedule and budget. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Wykes T.,Kings College London | Spaulding W.D.,University of Nebraska - Lincoln
Schizophrenia Bulletin | Year: 2011

This article reviews progress in the development of effective cognitive remediation therapy (CRT) and its translational process. There is now enough evidence that cognitive difficulties experienced by people with schizophrenia can change and that the agenda for the next generation of studies is to increase these effects systematically through cognitive remediation. We examine the necessary steps and challenges of moving CRT to treatment dissemination. Theories which have been designed to explain the effects of cognitive remediation, are important but we conclude that they are not essential for dissemination which could progress in an empirical fashion. One apparent barrier is that cognitive remediation therapies look different on the surface. However, they still tend to use many of the same training procedures. The only important marker for outcome identified in the current studies seems to be the training emphasis. Some therapies concentrate on massed practice of cognitive functions, whereas others also use direct training of strategies. These may produce differing effects as noted in the most recent meta-analyses. We recommend attention to several critical issues in the next generation of empirical studies. These include developing more complex models of the therapy effects that take into account participant characteristics, specific and broad cognitive outcomes, the study design, as well as the specific and nonspecific effects of treatment, which have rarely been investigated in this empirical programme. © 2011 The Author.

Royer J.,University of Nebraska - Lincoln
Agricultural Finance Review | Year: 2015

Purpose – The purpose of this paper is to describe an equity management and planning tool used by rural electric cooperatives (RECs) and based on the times-interest-earned ratio (TIER). The objectives of the paper are to construct a mathematical model that provides a rigorous foundation for the TIER approach, modify the approach so the rate of return on equity is a function of the cooperative’s equity position, demonstrate how elements of the model can be used by RECs in setting electric rates that will enable them to accelerate the retirement of member equity, and derive a generalized form of the “modified Goodwin formula” that can be used by both RECs and agricultural cooperatives. Design/methodology/approach – Mathematical and graphical expressions of the TIER approach are developed. Simulations are used to demonstrate how RECs can set electric rates according to a target revolving period. The modified Goodwin formula is generalized to include the payment of cash patronage refunds through use of a growth model of an agricultural cooperative developed in Royer (1993). Findings – This paper demonstrates how TIER analysis and the modified Goodwin formula can be used by cooperatives to aid their decisions regarding debt and equity financing and their choices regarding cash patronage refunds, equity retirement, and growth. The paper demonstrates that cooperatives that fail to recognize the functional relationship between the rate of return on equity and the equity position may substantially underestimate the equity position necessary to meet interest coverage requirements and overestimate their ability to grow and retire equity. It also shows that RECs may be able to make substantial improvements in equity revolvement with only modest increases in electric rates. Research limitations/implications – The model developed in this paper has been simplified to focus on fundamental financial relationships. To apply this model, cooperatives may need to modify it to accommodate the complexities of their business operations. Practical implications – TIER analysis can provide a useful equity management and planning tool for both RECs and agricultural cooperatives. It also can be used by lending institutions to assess the financial health of individual cooperative organizations. Originality/value – Constructing a mathematical model that provides a foundation for TIER analysis, modifying the approach so that the rate of return on equity is a function of the equity position, demonstrating how RECs can use the model to set electric rates according to a target revolving period, and generalizing the modified Goodwin formula so it can be used by agricultural cooperatives are all original contributions. © Emerald Group Publishing Limited.

Rose D.J.,University of Nebraska - Lincoln | Inglett G.E.,U.S. Department of Agriculture
Journal of Agricultural and Food Chemistry | Year: 2010

Two-stage hydrothermal processing was employed to obtain feruloylated arabinoxylooligosaccharides (AXOS) from wheat bran. First, wheat bran in water (10% w/w solids) was heated to 130 °C, releasing 36.3% of total solids, 70.3% of starch, and 6.06% of pentose sugars. Wheat bran was then heated to 170-220 °C. Heating to 200 and 210 °C released the most AXOS (70% of the insoluble arabinoxylan) and esterified ferulate (30% of the initial ferulic acid). Treatment of 200 °C retained a higher proportion of high molecular weight (>1,338) compounds than 210 °C and was the preferred treatment temperature because autohydrolysate liquors contained lower concentrations of many contaminants. Purification of this autohydrolysate liquor with ethyl acetate extraction, vacuum concentration, and ion exchange resulted in a product containing 32.0% AXOS and 4.77% esterified ferulate, accompanied by 36.0% other oligosaccharides and free sugars, with an antioxidant activity of 29.7 μmol Trolox equivalents/g dry matter. © This article not subject to U.S. Copyright. Published 2010 by the American Chemical Society.

Yu B.,University of Nebraska - Lincoln
Progress in molecular and subcellular biology | Year: 2010

MicroRNAs (miRNAs) are 21-24 nucleotide riboregulators, which selectively repress gene expression through transcript cleavage and/or translational inhibition. It was thought that most plant miRNAs act through target transcript cleavage due to the high degree of complementarity between miRNAs and their targets. However, recent studies have suggested widespread translational inhibition by miRNAs in plants. The mechanisms underlining translational inhibition by plant miRNAs are largely unknown, but existing evidence has indicated that plants and animals share some mechanistic similarity of translational inhibition. Translational inhibition by miRNAs has been shown to regulate floral patterning, floral timing, and stress responses. This chapter covers recent progress on plant miRNA-mediated translational control.

Espy K.A.,University of Nebraska - Lincoln
Journal of Child Psychology and Psychiatry and Allied Disciplines | Year: 2011

Background: Despite the widespread recognition of the importance of executive control (EC) in externalizing psychopathology, the relation between EC and problem behavior has not been well characterized, particularly in typically developing preschoolers. Method: Using the sample, battery of laboratory tasks, and latent variable modeling methods described in Wiebe, Espy, and Charak (2008), systematic latent dimensions of parent-rated problem behavior, measured by integrating scales from developmental and clinical traditions, were determined empirically, and then were related to EC. Results: Substantial relations between EC and problem behaviors were revealed by extracting the common variance of interest and eliminating extraneous variance, which were robust to estimated child intelligence and differed somewhat in preschool boys and girls. Conclusion: Preschool EC measured by laboratory tasks appears to tap abilities that strongly and robustly support broad control processes enabling behavioral regulation across cognitive and emotional domains. © 2010 The Authors. Journal of Child Psychology and Psychiatry. © 2010 Association for Child and Adolescent Mental Health.

Erickson G.,University of Nebraska - Lincoln
Journal of animal science | Year: 2010

Nitrogen losses from open beef feedlots are a concern. Methods that decrease volatilization losses will lead to greater manure N, which is likely to be beneficial in open lot beef operations. Twelve or more pens were dedicated to N research whereby N intake, retention, and excretion were quantified and a mass balance conducted using manure, runoff, soil balance, and loss quantities. The objective was to decrease N volatilization losses or increase manure N or both. Dietary CP affects N excretion and N volatilization losses. Four experiments across 2 yr compared industry average CP (13%) to diets that were phase-fed to not exceed protein requirements (12.1 to 10.9%). Phase-fed cattle excreted 12 to 21% less N (P < 0.01), and N volatilization losses were reduced 15 to 33% (P < 0.01). In 2 other experiments, phase-fed diets were formulated to recycle undegradable intake protein. Steer G:F was similar (P = 0.18) or improved (P = 0.09), whereas N excretion and N volatilization losses tended to be reduced (P < 0.11) and N in manure was not affected (P > 0.35) compared with cattle fed 13% CP. Feeding less protein did not affect manure N, indicating manure N from open lots is related to other factors. A series of experiments evaluated increasing OM on the pen surface to increase N in manure. Feeding less digestible diets using fiber increased manure N (P < 0.01) and decreased (P < 0.10) N volatilization losses in 2 experiments conducted from November to May, but did not affect (P > 0.30) manure N or volatilization losses during 2 summer experiments. Adding bedding (i.e., OM) increased manure N in the winter as well. Another method evaluated was increasing pen cleaning frequency, which decreased N volatilization losses by 19 to 44% and increased manure N by 26 to 41% across 3 experiments. Other methods, such as acidifying manure by manipulating dietary cation anion difference, clinoptilite zeolite clay addition, and feeding different amounts of by-products had variable impacts on N volatilization losses. No treatments markedly affected runoff N, which is <5% of excreted N. Dietary protein affects N volatilization losses but not manure N. Other factors, such as OM on the pen surface, affect manure N. Cleaning manure frequently, which decreases exposure of manure N to air, decreases volatilization losses. Treatments should be evaluated across seasons due to seasonal effects.

Burger O.,University of Kent | Burger O.,Max Planck Institute for Demographic Research | DeLong J.P.,University of Nebraska - Lincoln
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

‘Demographic transition theory’ assumes that fertility decline is irreversible. This commonly held assumption is based on observations of recent and historical reductions in fertility that accompany modernization and declining mortality. The irreversibility assumption, however, is highly suspect from an evolutionary point of view, because demographic traits are at least partially influenced by genetics and are responsive to social and ecological conditions. Nonetheless, an inevitable shift from high mortality and fertility to low mortality and fertility is used as a guiding framework for projecting human population sizes into the future. This paper reviews some theoretical and empirical evidence suggesting that the assumption of irreversibility is ill-founded, at least without considerable development in theory that incorporates evolutionary and ecological processes. We offer general propositions for how fertility could increase in the future, including natural selection on high fertility variants, the difficulty of maintaining universal norms and preferences in a large, diverse and economically differentiated population, and the escalating resource demands of modernization. © 2016 The Author(s) Published by the Royal Society. All rights reserved.

Argyropoulos C.,University of Nebraska - Lincoln
Optics Express | Year: 2015

We present a hybrid graphene/dielectric metasurface design to achieve strong tunable and modulated transmission at near-infrared (near- IR) frequencies. The proposed device is constituted by periodic pairs of asymmetric silicon nanobars placed over a silica substrate. An one-atomthick graphene sheet is positioned over the all-dielectric metasurface. The in-plane electromagnetic fields are highly localized and enhanced with this metasurface due to its very low Ohmic losses at near-IR wavelengths. They strongly interact with graphene. Sharp Fano-type transmission spectrum is obtained at the resonant frequency of this hybrid configuration due to the cancelation of the electric and magnetic dipole responses at this frequency point. The properties of the graphene monolayer flake can be adjusted by tuning its Fermi energy or chemical potential, leading to different doping levels and, equivalently, material parameters. As a result, the Q-factor and the Fano-type resonant transmission spectrum of the proposed hybrid system can be efficiently tuned and controlled due to the strong light- graphene interaction. Higher than 60% modulation in the transmission coefficient is reported at near-IR frequencies. The proposed hybrid graphene/dielectric nanodevice has compact footprint, fast speed, and can be easily integrated to the current CMOS technology. These features would have promising applications to near-IR tunable filters, faster optical interconnects, efficient sensors, switches, and amplitude modulators. © 2015 Optical Society of America.

Cutler J.,Montclair State University | Radcliffe A.J.,University of Nebraska - Lincoln
Journal of Combinatorial Theory. Series B | Year: 2014

Extremal problems involving the enumeration of graph substructures have a long history in graph theory. For example, the number of independent sets in a d-regular graph on n vertices is at most (2d+1-1)n/2d by the Kahn-Zhao theorem [7,13]. Relaxing the regularity constraint to a minimum degree condition, Galvin [5] conjectured that, for n≥2d, the number of independent sets in a graph with δ(G)≥d is at most that in Kd,n-d.In this paper, we give a lower bound on the number of independent sets in a d-regular graph mirroring the upper bound in the Kahn-Zhao theorem. The main result of this paper is a proof of a strengthened form of Galvin's conjecture, covering the case n≤2d as well. We find it convenient to address this problem from the perspective of G-. From this perspective, we show that the number of complete subgraphs of a graph G on n vertices with δ(G)≤r, where n=a(r+1)+b with 0≤b≤r, is bounded above by the number of complete subgraphs in aKr+1∪Kb. © 2013 Elsevier Inc.

Powlson D.S.,Rothamsted Research | Stirling C.M.,International Maize and Wheat Improvement Center | Jat M.L.,International Maize and Wheat Improvement Center | Gerard B.G.,International Maize and Wheat Improvement Center | And 3 more authors.
Nature Climate Change | Year: 2014

The Emissions Gap Report 2013 from the United Nations Environment Programme restates the claim that changing to no-till practices in agriculture, as an alternative to conventional tillage, causes an accumulation of organic carbon in soil, thus mitigating climate change through carbon sequestration. But these claims ignore a large body of experimental evidence showing that the quantity of additional organic carbon in soil under no-till is relatively small: in large part apparent increases result from an altered depth distribution. The larger concentration near the surface in no-till is generally beneficial for soil properties that often, though not always, translate into improved crop growth. In many regions where no-till is practised it is common for soil to be cultivated conventionally every few years for a range of agronomic reasons, so any soil carbon benefit is then lost. We argue that no-till is beneficial for soil quality and adaptation of agriculture to climate change, but its role in mitigation is widely overstated. © 2014 Macmillan Publishers Limited. All rights reserved.

Napier J.A.,Rothamsted Research | Haslam R.P.,Rothamsted Research | Beaudoin F.,Rothamsted Research | Cahoon E.B.,University of Nebraska - Lincoln
Current Opinion in Plant Biology | Year: 2014

The manipulation of plant seed oil composition so as to deliver enhanced fatty acid compositions suitable for feed or fuel has long been a goal of metabolic engineers. Recent advances in our understanding of the flux of acyl-changes through different key metabolic pools such as phosphatidylcholine and diacylglycerol have allowed for more targeted interventions. When combined in iterative fashion with further lipidomic analyses, significant breakthroughs in our capacity to generate plants with novel oils have been achieved. Collectively these studies, working at the interface between metabolic engineering and synthetic biology, demonstrate the positive fundamental and applied outcomes derived from such research. © 2014 The Authors.

Quantification of various water use efficiency (crop water productivity) indices for different irrigation regimes can aid in making effective in-season water management decisions and developing crop water productivity models. However, these critical variables can be affected by interannual variation in climatic conditions, and long-term research that provides such data and information is extremely rare. Maize (Zea mays L.) irrigation water use efficiency (IWUE), crop water use efficiency (CWUE), evapotranspiration water use efficiency (ETWUE), annual precipitation use efficiency (ANNPUE), growing season precipitation use efficiency (GRSPUE), and the newly developed growing season precipitation use efficiency with respect to rainfed yield (GRSPUErainfed) were measured under full and limited irrigation and rainfed conditions from 2005 to 2010 in south-central Nebraska. An additional new irrigation efficiency term [irrigation-evapotranspiration use efficiency (IRRETUE)] was developed and tested to evaluate the efficiency of irrigation management with respect to actual crop evapotranspiration (ETa). Four irrigation treatments were imposed [fully irrigated treatment (FIT), 75% FIT, 60% FIT, and 50% FIT] and a control rainfed treatment. CWUE varied from 1.21 kg/m3 for rainfed treatment in the dry year of 2005 to 2.51 kg/m3 for 60% FIT in the below average year of 2009. CWUE exhibited substantial interannual variation. The lowest CWUE was always obtained under rainfed production, whereas the highest value was usually observed under FIT, except in 2009. The FIT and 75% FIT CWUE values were very similar. Six-year average CWUE values were 2.34, 2.32, 2.29, 2.24, and 1.73 kg/m3 for FIT, 75% FIT, 60% FIT, 50% FIT, and rainfed, respectively, with SDs of 0.06, 0.09, 0.14, 0.12, and 0.38 kg/m3, respectively. IWUE varied from 1.75 kg/m3 for 50% FIT in the wettest year (2008) to 5.9 kg/m3 for the same treatment in 2009. The six-year average IWUE values were 4.01, 4.45, 4.48, and 4.13 kg/m3 for FIT, 75% FIT, 60% FIT, and 50% FIT, respectively, with SD values of 0.82, 0.84, 0.83, and 1.88 kg/m3 for the same treatments. There was considerable interannual variation in IWUE for the same treatment; this variation between treatments in a given year was greater than the interannual variation for the same treatment. The IWUE was maximized with limited irrigation treatments (mostly 50% FIT, followed by 75% FIT and 60% FIT). ETWUE values varied from 1.18 for 50% FIT in 2008 to 7.16 kg/m3 for 60% FIT in 2010; ETWUE decreased linearly with seasonal ETa (R2 > 0.80) in 2006, 2007, and 2009 and decreased with seasonal ETa, displaying a low R2 of 0.26 in 2010. In the wettest year (2008), ETWUE increased with ETa (R2 = 0.31). The new efficiency index, IRRETUE, ranged from 37.8% (62.2% underirrigation) for 50% FIT in 2010 to as high as 149.6% (49.6% overirrigation) for 50% FIT in 2008. On a long-term average, IRRETUE values were 87, 93.2, 88, and 89.2% for FIT, 75% FIT, 60% FIT, and 50% FIT, respectively. The new IRRETUE can be a very effective tool to evaluate the effectiveness of irrigation management practices with respect to meeting crop ETa for maximum yield. When the annual precipitation is considered, FIT resulted in greater ANNPUE, followed closely by 75% FIT and other limited irrigation treatments. The GRSPUErainfed values on all-treatment average basis were 32, 46, 66, 90, 61, and 82% (for FIT, 75% FIT, 60% FIT, and 50% FIT) lower than the GRSPUE values from 2005 through 2010. May precipitation consistently had the greatest influence on GRSPUE in all years, with high R2 of 0.73, 0.72, 0.71, and 0.76 for FIT, 75% FIT, 60% FIT, and 50% FIT, respectively. The rainfed treatment, however, was most influenced by April precipitation (R2 = 0.62). May precipitation was also the most influential on the GRSPUErainfed, with high R2 values of 0.67, 0.77, 0.87, and 0.82 for FIT, 75% FIT, 60% FIT, and 50% FIT, respectively. These research results are some of the first long-term research results reported in the literature for full and limited irrigated and rainfed maize productivity indices and can provide invaluable data and information for developing effective in-season water management decisions and determining crop productivity responses to different irrigation/water management conditions. © 2014 American Society of Civil Engineers.

Varvel G.E.,University of Nebraska - Lincoln | Wilhelm W.W.,U.S. Department of Agriculture
Soil Science Society of America Journal | Year: 2010

The use of conservation tillage systems for corn (Zea mays L.) and soybean [Glycine max (L) Merr. production has increased in recent years because of several factors including their potential to reduce losses or sequester soil organic C (SOC). This study evaluated the effects on SOC of three cropping systems (continuous corn [CC], continuous soybean [CSB], and soybean-corn [SB-C]) in six primary Tillage systems (chisel, disk, plow, no-rill, ridge-till, and subtill) under rainfed conditions in southeastern Nebraska. Soil samples were collected in depth increments of 0 to 7.5,7.5 to 15, and 15 to 30cm in the fall of 1989 and 2004 after harvest and analyzed for SOC. No significant differences in SOC concentrations were obtained among tillage treatments in any depth in a partial sampling of a study that was done in 1989. Tillage treatment and cropping system both significantly affected SOC concentrations and reserves at all depths in 2004 but only bulk density at a few depths. No-till SOC reserves ranged from 4.8 ro 11.6 Mg ha-1 greater than SOC reserves in the other tillage treatments in the 0- to 30-cm depth. Similarly, SOC concentrations and reserves were greatest in CC and least in CSB, with intermediate values for SB-C in all tillage systems. Soil organic C levels were maintained or even increased in all tillage systems; however, the greatest increases were obtained in systems wirh the least amount of soil disturbance, which strongly supports the adoption and use of conservation tillage systems for soil sustainability. © Soil Science Society of America, 5585 Guiltord Rd., Madison WI 53711 USA All rights reserved.

Coates B.S.,Iowa State University | Siegfried B.D.,University of Nebraska - Lincoln
Insect Biochemistry and Molecular Biology | Year: 2015

Field evolved resistance of insect populations to Bacillus thuringiensis (Bt) crystalline (Cry) toxins expressed by crop plants has resulted in reduced control of insect feeding damage to field crops, and threatens the sustainability of Bt transgenic technologies. A single quantitative trait locus (QTL) that determines resistance in Ostrinia nubilalis larvae capable of surviving on reproductive stage transgenic corn that express the Bt Cry1Fa toxin was previously mapped to linkage group 12 (LG12) in a backcross pedigree. Fine mapping with high-throughput single nucleotide polymorphism (SNP) anchor markers, a candidate ABC transporter (. abcc2) marker, and de novo mutations predicted from a genotyping-by-sequencing (GBS) data redefined a 268.8 cM LG12. The single QTL on LG12 spanned an approximate 46.1 cM region, in which marker 02302.286 and abcc2 were ≤2.81 cM, and the GBS marker 697 was an estimated 1.89 cM distant from the causal genetic factor. This positional mapping data showed that an O. nubilalis genome region encoding an abcc2 transporter is in proximity to a single QTL involved in the inheritance of Cry1F resistance, and will assist in the future identification the mutation(s) involved with this phenotype. © 2015.

Storz J.F.,University of Nebraska - Lincoln | Opazo J.C.,Austral University of Chile | Hoffmann F.G.,Mississippi State University
Molecular Phylogenetics and Evolution | Year: 2013

The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α2β2). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages. © 2012 Elsevier Inc.

Opazo J.C.,Austral University of Chile | Butts G.T.,Mississippi State University | Nery M.F.,Austral University of Chile | Storz J.F.,University of Nebraska - Lincoln | Hoffmann F.G.,Mississippi State University
Molecular Biology and Evolution | Year: 2013

Subsequent to the two rounds of whole-genome duplication that occurred in the common ancestor of vertebrates, a third genome duplication occurred in the stem lineage of teleost fishes. This teleost-specific genome duplication (TGD) is thought to have provided genetic raw materials for the physiological, morphological, and behavioral diversification of this highly speciose group. The extreme physiological versatility of teleost fish is manifest in their diversity of blood-gas transport traits, which reflects the myriad solutions that have evolved to maintain tissue O2 delivery in the face of changing metabolic demands and environmental O2 availability during different ontogenetic stages. During the course of development, regulatory changes in blood-O2 transport are mediated by the expression of multiple, functionally distinct hemoglobin (Hb) isoforms that meet the particular O2-transport challenges encountered by the developing embryo or fetus (in viviparous or oviparous species) and in free-swimming larvae and adults. The main objective of the present study was to assess the relative contributions of whole-genome duplication, large-scale segmental duplication, and small-scale gene duplication in producing the extraordinary functional diversity of teleost Hbs. To accomplish this, we integrated phylogenetic reconstructions with analyses of conserved synteny to characterize the genomic organization and evolutionary history of the globin gene clusters of teleosts. These results were then integrated with available experimental data on functional properties and developmental patterns of stage-specific gene expression. Our results indicate that multiple α-and β-globin genes were present in the common ancestor of gars (order Lepisoteiformes) and teleosts. The comparative genomic analysis revealed that teleosts possess a dual set of TGD-derived globin gene clusters, each of which has undergone lineage-specific changes in gene content via repeated duplication and deletion events. Phylogenetic reconstructions revealed that paralogous genes convergently evolved similar functional properties in different teleost lineages. Consistent with other recent studies of globin gene family evolution in vertebrates, our results revealed evidence for repeated evolutionary transitions in the developmental regulation of Hb synthesis. © 2012 The Author.

Jones C.,University of Nebraska - Lincoln
Journal of neurovirology | Year: 2011

Like other α-herpesvirinae subfamily members, the primary site for bovine herpesvirus 1 (BHV-1) latency is ganglionic sensory neurons. Periodically BHV-1 reactivates from latency, virus is shed, and consequently virus transmission occurs. Transcription from the latency-related (LR) gene is readily detected in neurons of trigeminal ganglia (TG) of calves or rabbits latently infected with BHV-1. Two micro-RNAs and a transcript encompassing a small open reading frame (ORF-E) located within the LR promoter can also be detected in TG of latently infected calves. A BHV-1 mutant that contains stop codons near the beginning of the first open reading frame (ORF2) within the major LR transcript (LR mutant virus) has been characterized. The LR mutant virus does not express ORF2, a reading frame that lacks an initiating ATG (reading frame B), and has reduced expression of ORF1 during productive infection. The LR mutant virus does not reactivate from latency following dexamethasone treatment suggesting that LR protein expression regulates the latency-reactivation cycle. Higher levels of apoptosis occur in TG neurons of calves infected with the LR mutant viruses when compared to wild-type BHV-1 indicating that the anti-apoptotic properties of the LR gene is necessary for the latency-reactivation cycle. ORF2 inhibits apoptosis and regulates certain viral promoters, in part, because it interacts with three cellular transcription factors (C/EBP-alpha, Notch1, and Notch3). Although ORF2 is important for the latency-reactivation cycle, we predict that other LR gene products play a supportive role during life-long latency in cattle.

Liu C.,Xiangtan University | Lin S.,Xiangtan University | Pei Y.,Xiangtan University | Zeng X.C.,University of Nebraska - Lincoln
Journal of the American Chemical Society | Year: 2013

The semiring chemistry of the Au25(SR)18, particularly its fragmentation mechanism and catalytic active site, is explored using density functional theory (DFT) calculations. Our calculations show that the magically stable fragmental cluster, Au21(SR)14 -, as detected in several mass spectrometry (MS) measurements of fragmentation of the Au25(SR)18-, contains a quasi-icosahedral Au13-core fully protected by four -SR-Au-SR- and two -SR-Au-SR-Au-SR- staple motifs. A stepwise fragmentation mechanism of the semiring staple motifs on the surface of Au25(SR)18 - is proposed for the first time. Initially, the Au 25(SR)18- transforms into a metastable structure with all staple motifs binding with two neighboring vertex Au-atoms of the Au-core upon energy uptake. Subsequently, a 'step-by-step' detachment and transfer of [Au(SR)]x (x = 1-4) units occurs, which leads to the formation of highly stable products including Au21(SR) 14- and a cyclic [Au(SR)]4 unit. The continued fragmentation of Au21(SR)14- to Au 17(SR)10- is observed as well, which shows same stepwise fragmentation mechanism. The proposed mechanism well explains the favorable formation of Au21(SR)14- and Au 17(SR)10- from Au25(SR) 18- as observed from experimental abundance. Taking the Au21(SR)14 and its parent cluster Au25(SR) 18 as the benchmark model systems, the catalytic active site of the thiolate protected gold clusters toward the styrene oxidation and the associated reaction mechanism are further investigated. We show that the Au atom in the staple motifs is the major active site for the styrene oxidation in presence of TBHP as oxidant or initiator. The Au atom in the staple motifs can change from Au(I) (bicoordinated) to Au(III) (tetracoordinated). The O2 activation is achieved during this process. © 2013 American Chemical Society.

Veliz-Cuba A.,University of Nebraska - Lincoln
Journal of Theoretical Biology | Year: 2011

Boolean networks have been successfully used in modelling gene regulatory networks. However, for large networks, analysis by simulation becomes unfeasible. In this paper we propose a reduction method for Boolean networks that decreases the size of the network, while preserving important dynamical properties and topological features. As a result, the reduced network can be used to infer properties about the original network and to gain a better understanding of the role of network topology on the dynamics. In particular, we use the reduction method to study steady states of Boolean networks and apply our results to models of Th-lymphocyte differentiation and the lac operon. © 2011 Elsevier Ltd.

Bobaru F.,University of Nebraska - Lincoln | Duangpanya M.,Chulachomklao Royal Military Academy
Journal of Computational Physics | Year: 2012

We introduce a multidimensional peridynamic formulation for transient heat-transfer. The model does not contain spatial derivatives and uses instead an integral over a region around a material point. By construction, the formulation converges to the classical heat transfer equations in the limit of the horizon (the nonlocal region around a point) going to zero. The new model, however, is suitable for modeling, for example, heat flow in bodies with evolving discontinuities such as growing insulated cracks. We introduce the peridynamic heat flux which exists even at sharp corners or when the isotherms are not smooth surfaces. The peridynamic heat flux coincides with the classical one in simple cases and, in general, it converges to it in the limit of the peridynamic horizon going to zero. We solve test problems and compare results with analytical solutions of the classical model or with other numerical solutions. Convergence to the classical solutions is seen in the limit of the horizon going to zero. We then solve the problem of transient heat flow in a plate in which insulated cracks grow and intersect thus changing the heat flow patterns. We also model heat transfer in a fiber-reinforced composite and observe transient but steep thermal gradients at the interfaces between the highly conductive fibers and the low conductivity matrix. Such thermal gradients can lead to delamination cracks in composites from thermal fatigue. The formulation may be used to, for example, evaluate effective thermal conductivities in bodies with an evolving distribution of insulating or permeable, possibly intersecting, cracks of arbitrary shapes. © 2011 Elsevier Inc.

Quinn J.E.,University of Nebraska - Lincoln
Renewable Agriculture and Food Systems | Year: 2013

Conservation biology and agriculture share a common landscape and a future that demands novel research and practice. Inevitably, limited resources create conflict in the absence of a shared vision forward. Therefore, given the similarities in proximate and even ultimate goals, we must envision a joint path toward renewable and resilient agroecosystems. In this commentary, I highlight the root of past conflicts and share a vision of progress forward that encompasses mutually beneficial outcomes. I include six areas of anticipatory research and inquiry at the intersection of conservation biology and agriculture to better identify shared goals and facilitate more frequent communication among disciplines. © 2012 Cambridge University Press.

Brown C.R.,University of Tulsa | Brown M.B.,University of Nebraska - Lincoln | Roche E.A.,University of Tulsa
Ecological Monographs | Year: 2013

Most colonially breeding animals occupy colonies that range in size from a few pairs to thousands of individuals, but the causes of colony size variation are largely unknown. Three general hypotheses are: (1) that variation in colony size is maintained by fluctuating selection via spatial and temporal changes in fitness associated with different colony sizes; (2) that colony formation reflects heterogeneity in habitat, with some sites having resources to support more individuals than others; and (3) that individuals assess the presence or annual reproductive success of current colony residents at each site and aggregate preferentially at high-quality sites. These hypotheses make predictions about how consistent colony size should be across sites and among years. We examined temporal and spatial variability of colony size for >200 Cliff Swallow (Petrochelidon pyrrhonota) colony sites in western Nebraska across a 30-year period. A colony's substrate type, annual population size in the study area, and whether the nesting season was relatively warm or cool, influenced average annual colony size. While some Cliff Swallow colony sites hosted perennially large colonies and others perennially small ones, between-year variability in colony size at most sites was high. Annual colony size distributions were relatively stable over 30 years and provided no evidence for long-term directional changes in colony size. The only ecological characteristic that was strongly associated with Cliff Swallow colony size at a site was the type of nesting substrate, with bridges tending to have larger colonies and being more frequently occupied than other substrates. Some sites showed annual changes in colony size consistent with the birds' basing their choice of colony on the presence or success of conspecifics, but many sites did not conform to a pattern expected if coloniality is a by-product of traditional aggregation. Colony size in Cliff Swallows was temporally and spatially unpredictable when viewed across the 30 years of this study. Each of the three hypotheses to explain size variation may have applied at certain sites, but the pattern of colony size variability leant the most support to the hypothesis that fluctuating selection on group size maintains colonies of widely different sizes. © 2013 by the Ecological Society of America.

Qiao D.,University of Nebraska - Lincoln | Gursoy M.C.,Syracuse University | Velipasalar S.,Syracuse University
IEEE Transactions on Information Theory | Year: 2012

Effective capacity, which provides the maximum constant arrival rate that a given service process can support while satisfying statistical queueing constraints, is analyzed in a multiuser scenario. In particular, the effective capacity region of fading multiple-access channels in the presence of quality of service (QoS) constraints is studied. Perfect channel side information is assumed to be available at both the transmitters and the receiver. It is initially assumed that the transmitters send the information at a fixed power level and, hence, do not employ power control policies. Under this assumption, the performance achieved by superposition coding with successive decoding techniques is investigated. It is shown that varying the decoding order with respect to the channel states can significantly increase the achievable throughput region. In the two-user case, the optimal decoding strategy is determined for the scenario in which the users have the same QoS constraints. The performance of orthogonal transmission strategies is also analyzed. It is shown that for certain QoS constraints, time-division multiple access can achieve better performance than superposition coding if fixed successive decoding order is used at the receiver side. In the subsequent analysis, power control policies are incorporated into the transmission strategies. The optimal power allocation policies for any fixed decoding order over all channel states are identified. For a given variable decoding-order strategy, the conditions that the optimal power control policies must satisfy are determined, and an algorithm that can be used to compute these optimal policies is provided. © 2011 IEEE.

Blanco-Canqui H.,University of Nebraska - Lincoln | Schlegel A.J.,Kansas State University
Journal of Environmental Quality | Year: 2013

Inorganic fertilizers are widely used for crop production, but their long-term impacts on soil organic carbon (SOC) pools and soil physical attributes are not fully understood. We studied how half a century of N application at 0, 45, 90, 134, 179, and 224 kg ha-1 and P application at 0, 20, and 40 kg ha-1 (since 1992) affected SOC pools and soil structural and hydraulic parameters in irrigated continuous corn (Zea mays L.) under conventional till on an Aridic Haplustoll in the central Great Plains. Application of 45, 90, 134, 179, and 224 kg N ha-1 increased the SOC pool by 4.6, 6.8, 7.6, 7.9, and 9.7 Mg ha-1, respectively, relative to nonfertilized plots in the 0-to 45-cm depth. Application of 20 kg P ha-1 increased the SOC pool by 2.9 Mg ha-1 in the 0-to 30-cm depth. Th e highest N rate increased the SOC pool by 195 kg ha-1 yr-1. Th e C gains may be, however, offset by the C hidden costs of N fertilization. Application of >45 kg N ha-1 reduced the proportion of soil macroaggregates (>0.25 mm) in the 7.5-to 30-cm depth. Fertilization did not affect hydraulic properties, but application of ≥90 kg N ha-1 slightly increased aggregate water repellency. An increase in SOC concentration did not increase the mean weight diameter of wet aggregates (r = 0.1; P > 0.10), but it slightly increased aggregate water repellency (r = 0.5; P < 0.005). Overall, long-term inorganic fertilization to irrigated corn can increase SOC pool, but it may reduce soil structural stability. © American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

Paparozzi E.T.,University of Nebraska - Lincoln
HortTechnology | Year: 2013

As a floriculturist, when I first decided to grow strawberries (Fragaria · ananassa) in the greenhouse, I thought it would be a snap. After all, I could practice what I preach to my classes in that I would use all the sustainable growing tricks from floriculture, create a production time line and it would be ready, set grow. However, moving a field-grown summer crop into a greenhouse as a winter crop was not the same as moving a winter greenhouse-grown crop outside for the summer. Not only were the plants typically grown in lush field soil, but also the fertilizer recommendations were not directly translatable (i.e., parts per million nitrogen). The pesticides used were not licensed for greenhouses and of course, there were no clues as to schedules of what to do when. Finally, there were the mystery problems that occurred.With high gas prices and the interest in local food production, it seems probable that over the next 5 to 10 years, more and more fruit, vegetables and even nut plants will be moved into greenhouse and high tunnel production. The purpose of this article is to identify the kinds of information needed to make a "smooth" transition from field to greenhouse for alternative crops, like strawberries, grown during nontraditional seasons.

Bahar E.,University of Nebraska - Lincoln
Journal of the Optical Society of America B: Optical Physics | Year: 2011

Biological and chemical materials can be detected, identified, and characterized through their optical activity: Optical rotation and circular dichroism. The optical activity of chiral materials leaves their footprints on the elements of the two off-diagonal quadrants of the Mueller matrices, which are proportional to the cross-linearly polarized reflection and transmission coefficients. At the free-space-chiral interface, lateral waves that propagate just below the interface are excited by waves that enter and emerge from the chiral material at the critical angle for total internal reflection. As the waves enter and emerge from the chiral material, the transmitted waves also undergo cross polarization. In the neighborhood of the critical angle, the cross-polarized transmission coefficients are relatively large, and they also exhibit the impact of the optical activity of the material. Therefore, the lateral waves can also be used to identify optically active materials. © 2011 Optical Society of America.

Bahar E.,University of Nebraska - Lincoln
Journal of the Optical Society of America B: Optical Physics | Year: 2011

At a free-space-chiral interface, the complete modal expansion of the electromagnetic fields consists of the radiation fields and lateral waves, associated with branch cut integrals as well as guided surface waves associated with the poles of the like- and cross-polarized elements of the reflection matrix. The cross-polarized surface waves, considered here in detail, are proportional to the chiral measure and contain the footprints of the optical activity of the material. Explicit expressions are desired for the residue contributions at the poles of the cross-polarized reflection coefficients in terms of the optical activity. Thus, measurements of the ratio of the cross- to likepolarized surface waves, which can be excited by electric or magnetic dipoles near the interface, can be used to identify the optically active materials. © 2011 Optical Society of America.

Stevens J.R.,University of Nebraska - Lincoln
Proceedings of the Royal Society B: Biological Sciences | Year: 2014

From finding food to choosing mates, animals must make intertemporal choices that involve fitness benefits available at different times. Species vary dramatically in their willingness to wait for delayed rewards. Why does this variation across species exist? An adaptive approach to intertemporal choice suggests that time preferences should reflect the temporal problems faced in a species's environment. Here, I use phylogenetic regression to test whether allometric factors relating to body size, relative brain size and social group size predict how long 13 primate species will wait in laboratory intertemporal choice tasks. Controlling for phylogeny, a composite allometric factor that includes body mass, absolute brain size, lifespan and home range size predicted waiting times, but relative brain size and social group size did not. These findings support the notion that selective pressures have sculpted inter-temporal choicesto solve adaptive problems faced byanimals. Collecting these types of data across a large number of species can provide key insights into the evolution of decision making and cognition. © 2014 The Author(s).

Cheviron Z.A.,University of Nebraska - Lincoln | Brumfield R.T.,Louisiana State University
Heredity | Year: 2012

Elucidating the molecular genetic basis of adaptive traits is a central goal of evolutionary genetics. The cold, hypoxic conditions of high-altitude habitats impose severe metabolic demands on endothermic vertebrates, and understanding how high-altitude endotherms cope with the combined effects of hypoxia and cold can provide important insights into the process of adaptive evolution. The physiological responses to high-altitude stress have been the subject of over a century of research, and recent advances in genomic technologies have opened up exciting opportunities to explore the molecular genetic basis of adaptive physiological traits. Here, we review recent literature on the use of genomic approaches to study adaptation to high-altitude hypoxia in terrestrial vertebrates, and explore opportunities provided by newly developed technologies to address unanswered questions in high-altitude adaptation at a genomic scale. © 2012 Macmillan Publishers Limited All rights reserved.

Adams S.A.,University of Nebraska - Lincoln
Journal of Sex and Marital Therapy | Year: 2014

It is not uncommon for older adults to feel uncomfortable engaging in sexual health communication with a doctor. Nevertheless, there is reason to expect that marital quality is associated with older adults comfort discussing sexual issues with a doctor. This study examined the relation between marital quality and comfort discussing sexual issues with a doctor among older married men and women using a nationally representative sample of older adults. Data were analyzed using partial proportional odds models. Positive marital quality predicted higher levels of comfort discussing sexual issues with a doctor, but only for men. In contrast, negative marital quality had no significant effect on comfort discussing sex with a doctor for men or women. These results suggest that for older married men, a positive marriage is an important factor in promoting comfort in regard to sexual health communication with a doctor. © 2014 Copyright Taylor and Francis Group, LLC.

Nip I.S.B.,San Diego State University | Green J.R.,University of Nebraska - Lincoln
Child Development | Year: 2013

Age-related increases of speaking rate are not fully understood, but have been attributed to gains in biologic factors and learned skills that support speech production. This study investigated developmental changes in speaking rate and articulatory kinematics of participants aged 4 (N = 7), 7 (N = 10), 10 (N = 9), 13 (N = 7), 16 (N = 9) years, and young adults (N = 11) in speaking tasks varying in task demands. Speaking rate increased with age, with decreases in pauses and articulator displacements but not increases in articulator movement speed. Movement speed did not appear to constrain the speaking. Rather, age-related increases in speaking rate are due to gains in cognitive and linguistic processing and speech motor control. © 2013 Society for Research in Child Development, Inc.

Hemsath T.L.,University of Nebraska - Lincoln
Energy and Buildings | Year: 2016

Housing orientation has an effect on the total heating and cooling loads that consumers pay for as part of their monthly utility bills. Often suburban developments lack consideration of the precise optimal solar orientation of each home, therefore, costing homeowners money over the life span of their tenure. This study aims to evaluate the effect of a home's orientation at the community level evaluating energy use and annual energy costs. The scope of the paper simulates the effect of orientation for 7000 existing homes for four typical Midwestern suburban developments and the resulting annual energy costs. Appling the same housing sample to four different U.S. locations the study compares climatic differences. This analysis evaluates the cost and energy performance of existing suburban communities using optimal solar orientation. Results show that individual home orientation has minimal cost implications, whereas the aggregated suburban community house orientation has more significant total annual energy costs. In addition, results reinforce optimizing solar orientation for planning and design of suburban housing. © 2016 Elsevier B.V. All rights reserved.

Olson D.L.,University of Nebraska - Lincoln | Chae B.,Kansas State University
Decision Support Systems | Year: 2012

Decision support techniques and models for marketing decisions are critical to retail success. Among different marketing domains, customer segmentation or profiling is recognized as an important area in research and industry practice. Various data mining techniques can be useful for efficient customer segmentation and targeted marketing. One such technique is the RFM method. Recency, frequency, and monetary methods provide a simple means to categorize retail customers. We identify two sets of data involving catalog sales and donor contributions. Variants of RFM-based predictive models are constructed and compared to classical data mining techniques of logistic regression, decision trees, and neural networks. The spectrum of tradeoffs is analyzed. RFM methods are simpler, but less accurate. The effect of balancing cells, of the value function, and classical data mining algorithms (decision tree, logistic regression, neural networks) are also applied to the data. Both balancing expected cell densities and compressing RFM variables into a value function were found to provide models similar in accuracy to the basic RFM model, with slight improvement obtained by increasing the cutoff rate for classification. Classical data mining algorithms were found to yield better prediction, as expected, in terms of both prediction accuracy and cumulative gains. Relative tradeoffs among these data mining algorithms in the context of customer segmentation are presented. Finally we discuss practical implications based on the empirical results. © 2012 Elsevier B.V. All rights reserved.

Brown C.R.,University of Tulsa | Brown M.B.,University of Nebraska - Lincoln
Ecology | Year: 2014

Global climate change is altering the breeding phenology of many organisms, and one reported consequence of warmer average temperatures is earlier breeding times in migratory songbirds of north temperate latitudes. Less studied are the potential interactions between earlier breeding and social behavior in colonial species. We investigated how breeding time, as measured by colony initiation dates across the entire summer, in Cliff Swallows (Petrochelidon pyrrhonota) of southwestern Nebraska, USA, changed over a 30-year period and could be predicted by climatic variables, year, and colony size. Mean colony initiation date became earlier over the study, with variation best predicted by the extent of drought severity on the breeding grounds: colonies initiated earlier in warmer and drier years. Colony initiation dates were more asynchronous across the population in cooler and wetter years. There was no effect of climatic conditions during the nonbreeding season. Larger colonies started earlier in the year than smaller ones, probably because of the cost of ectoparasitism and the benefit of social foraging, both of which varied with colony size, date, and climatic conditions. The inverse relationship between breeding time and colony size was more pronounced in years with more severe drought. This study is one of the few to show that breeding phenology of a long-distance migrant bird is sensitive primarily to drought severity on the breeding grounds and that climate change can influence social behavior. If climate change exacerbates drought in the future, Cliff Swallow breeding time will likely become more strongly linked to group size. © 2014 by the Ecological Society of America.

Schnable J.C.,University of Nebraska - Lincoln
Annual Review of Plant Biology | Year: 2015

Maize occupies dual roles as both (a) one of the big-three grain species (along with rice and wheat) responsible for providing more than half of the calories consumed around the world, and (b) a model system for plant genetics and cytogenetics dating back to the origin of the field of genetics in the early twentieth century. The long history of genetic investigation in this species combined with modern genomic and quantitative genetic data has provided particular insight into the characteristics of genes linked to phenotypes and how these genes differ from many other sequences in plant genomes that are not easily distinguishable based on molecular data alone. These recent results suggest that the number of genes in plants that make significant contributions to phenotype may be lower than the number of genes defined by current molecular criteria, and also indicate that syntenic conservation has been underemphasized as a marker for gene function. ©2015 by Annual Reviews. All rights reserved.

Vogel K.P.,University of Nebraska - Lincoln
Crop Science | Year: 2013

Two breeding systems, between- and withinfamily selection (BWFS) and multistep family selection (MFS), were compared using three switchgrass (Panicum virgatum L.) populations to determine which system was the most effective in improving biomass yield and in vitro dry matter digestibility (IVDMD). With BWFS, half-sib families are produced and evaluated on a family basis and then the best plants within the best families are selected for crossing to produce a new strain. With MFS, parent genotypes of the half-sib families being evaluated in the BWFS selection nursery are maintained and the genotypes whose progeny were the best in the BWFS evaluation trial are selected and polycrossed to produce a new strain. Methods were compared using two populations in which improved biomass yield and IVDMD were the selected traits and with a population for which improved IVDMD and winter survival were the selected traits. For the populations for which yield was a selection criteria, the BWFS breeding system produced strains with significantly greater biomass yields than the MFS system. For one of these populations, the BWFS and MFS systems did not differ for IVDMD but the MFS system produced a strain with higher IVDMD for the other population. For the population in which IVDMD and winter survival were the selection criteria, the BWFS strain had greater IVDMD than the MFS strain. Overall, the BWFS system was superior and required less work. © Crop Science Society of America.

Brisson J.A.,University of Southern California | Brisson J.A.,University of Nebraska - Lincoln
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2010

Both genetic and environmental factors underlie phenotypic variation. While research at the interface of evolutionary and developmental biology has made excellent advances in understanding the contribution of genes to morphology, less well understood is the manner in which environmental cues are incorporated during development to influence the phenotype. Also virtually unexplored is how evolutionary transitions between environmental and genetic control of trait variation are achieved. Here, I review investigations into molecular mechanisms underlying phenotypic plasticity in the aphid wing dimorphism system. Among aphids, some species alternate between environmentally sensitive (polyphenic) and genetic (polymorphic) control of wing morph determination in their life cycle. Therefore, a traditional molecular genetic approach into understanding the genetically controlled polymorphism may provide a unique avenue into not only understanding the molecular basis of polyphenic variation in this group, but also the opportunity to compare and contrast the mechanistic basis of environmental and genetic control of similar dimorphisms. © 2010 The Royal Society.

Hoberg E.P.,U.S. Department of Agriculture | Brooks D.R.,University of Nebraska - Lincoln
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2015

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host–parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)—phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference—provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Drought, salinity, extreme temperature variations, pathogen and herbivory attacks are recurring environmental stresses experienced by plants throughout their life. To survive repeated stresses, plants provide responses that may be different from their response during the first encounter with the stress. A different response to a similar stress represents the concept of 'stress memory'. A coordinated reaction at the organismal, cellular and gene/genome levels is thought to increase survival chances by improving the plant's tolerance/avoidance abilities. Ultimately, stress memory may provide a mechanism for acclimation and adaptation. At the molecular level, the concept of stress memory indicates that the mechanisms responsible for memory-type transcription during repeated stresses are not based on repetitive activation of the same response pathways activated by the first stress. Some recent advances in the search for transcription 'memory factors' are discussed with an emphasis on super-induced dehydration stress memory response genes in Arabidopsis. Significance Statement Chromatin as a potential epigenetic factor in the memory responses to recurrent environmental stresses is discussed. © 2015 The Authors.

Hardy S.A.,Brigham Young University | Carlo G.,University of Nebraska - Lincoln
Child Development Perspectives | Year: 2011

The study of moral identity may be one of the more promising new trends in moral psychology. Moral identity is the degree to which being a moral person is important to a person's identity. This article reviews the various ways in which moral identity is understood, discusses predictors and processes of moral identity, and presents evidence regarding links between moral identity and various moral actions. The article closes with a critical evaluation of the moral identity concept and a discussion of future research directions. © 2011 The Authors. Child Development Perspectives © 2011 The Society for Research in Child Development.

Gaupp R.,University of Nebraska - Lincoln
Frontiers in cellular and infection microbiology | Year: 2012

Staphylococci are a versatile genus of bacteria that are capable of causing acute and chronic infections in diverse host species. The success of staphylococci as pathogens is due in part to their ability to mitigate endogenous and exogenous oxidative and nitrosative stress. Endogenous oxidative stress is a consequence of life in an aerobic environment; whereas, exogenous oxidative and nitrosative stress are often due to the bacteria's interaction with host immune systems. To overcome the deleterious effects of oxidative and nitrosative stress, staphylococci have evolved protection, detoxification, and repair mechanisms that are controlled by a network of regulators. In this review, we summarize the cellular targets of oxidative stress, the mechanisms by which staphylococci sense oxidative stress and damage, oxidative stress protection and repair mechanisms, and regulation of the oxidative stress response. When possible, special attention is given to how the oxidative stress defense mechanisms help staphylococci control oxidative stress in the host.

Delong J.P.,Yale University | Delong J.P.,University of Nebraska - Lincoln | Vasseur D.A.,Yale University
Oikos | Year: 2013

The potential connection between exploitation and interference competition was recognized long ago but has not been evaluated. We measured the levels of both forms of competition for the protist Didinium preying upon Paramecium. Across populations, exploitation intensity was tightly linked to interference intensity, and the form of this relationship follows from a simple model of interaction speeds. The variation in interference competition was as large across populations of Didinium as has been observed previously across species from a variety of taxa including birds, mammals, insects, crustaceans, flatworms and protists. The link between exploitation and interference competition alters our understanding of how interference competition influences population dynamics. Instead of simply stabilizing systems, variation in interference levels can shift population dynamics through qualitatively different regimes because of its association with exploitation competition. Strong interference competition pushes a system to a regime of deterministic extinction, but intermediate interference generates a system that is stable with a high competitive ability. This may help to explain why the distribution of interference values is unimodal and mostly intermediate in intensity. Synthesis Exploitation and interference competition are typically viewed as separate processes. Exploitation is described with a functional response in which the inclusion of interference competition - the effect of predator density on foraging rates - is optional. Although recent work indicates that interference competition is widespread, there is little work linking the two forms of competition. In this article we present evidence that exploitation and interference competition are linked mechanistically through movement patterns that simultaneously generate beneficial interactions of consumers with resources and detrimental interactions with other consumers. This connection alters our view of the role that interference plays in ecological dynamics. © 2013 The Authors.

Gebbers R.,Leibniz Institute for Agricultural Engineering | Adamchuk V.I.,University of Nebraska - Lincoln
Science | Year: 2010

Precision agriculture comprises a set of technologies that combines sensors, information systems, enhanced machinery, and informed management to optimize production by accounting for variability and uncertainties within agricultural systems. Adapting production inputs site-specifically within a field and individually for each animal allows better use of resources to maintain the quality of the environment while improving the sustainability of the food supply. Precision agriculture provides a means to monitor the food production chain and manage both the quantity and quality of agricultural produce. © 2010 American Association for the Advancement for Science. All Rights Reserved.

Hoffman L.,University of Nebraska - Lincoln | McDowd J.M.,University of Kansas Medical Center
Psychology and Aging | Year: 2010

L. Hoffman, J. M. McDowd, P. Atchley, and R. A. Dubinsky (2005) reported that visual and attentional impairment (measured by the Useful Field of View test and DriverScan) and performance in a low-fidelity driving simulator did not predict self-reported accidents in the previous 3 years. The present study applied these data to predict accidents occurring within a subsequent 5-year period (N = 114 older adults, 75% retention rate). Multivariate path models revealed that accidents in which the driver was at least partially at fault were significantly more likely in persons who had shown impaired simulator performance. These results suggest that even low-fidelity driving simulators may be useful in predicting real-world outcomes. © 2010 American Psychological Association.

Morehouse M.,University of Nebraska - Lincoln
Studies in Conflict and Terrorism | Year: 2014

While the use of targeted killings by the United States and Israel has received the most press coverage, Colombia has also utilized targeted killings in its conflict with the Revolutionary Armed Forces of Colombia (FARC). Utilizing an original dataset, this study quantitatively gauges the effectiveness of Colombia's targeted killing program, by examining the influence of FARC leadership deaths upon the number and severity of FARC attacks during the years 2004 to 2011. The results suggest that the Colombian government's killing of FARC leaders has been effective in decreasing the number of attacks, but not the severity of attacks. © 2014 Copyright Taylor & Francis Group, LLC.

Allocating resources between population size and replication affects both genetic gain through phenotypic selection and quantitative trait loci detection power and effect estimation accuracy for marker-assisted selection (MAS). It is well known that because alleles are replicated across individuals in quantitative trait loci mapping and MAS, more resources should be allocated to increasing population size compared with phenotypic selection. Genomic selection is a form of MAS using all marker information simultaneously to predict individual genetic values for complex traits and has widely been found superior to MAS. No studies have explicitly investigated how resource allocation decisions affect success of genomic selection. My objective was to study the effect of resource allocation on response to MAS and genomic selection in a single biparental population of doubled haploid lines by using computer simulation. Simulation results were compared with previously derived formulas for the calculation of prediction accuracy under different levels of heritability and population size. Response of prediction accuracy to resource allocation strategies differed between genomic selection models (ridge regression best linear unbiased prediction [RR-BLUP], BayesCπ) and multiple linear regression using ordinary least-squares estimation (OLS), leading to different optimal resource allocation choices between OLS and RR-BLUP. For OLS, it was always advantageous to maximize population size at the expense of replication, but a high degree of flexibility was observed for RR-BLUP. Prediction accuracy of doubled haploid lines included in the training set was much greater than of those excluded from the training set, so there was little benefit to phenotyping only a subset of the lines genotyped. Finally, observed prediction accuracies in the simulation compared well to calculated prediction accuracies, indicating these theoretical formulas are useful for making resource allocation decisions © 2013 Lorenz.

Chen X.,University of Nebraska - Lincoln
Hydrological Processes | Year: 2011

Characterization of streambed hydraulic conductivity from the channel surface to a great depth below the channel surface can provide needed information for the determination of stream-aquifer hydrologic connectedness, and it is also important to river restoration. However, knowledge on the streambed hydraulic conductivity for sediments 1 m below the channel surface is scarce. This study describes a method that was used to determine the distribution patterns of streambed hydraulic conductivity for sediments from channel surface to a depth of 15 m below. The method includes Geoprobe's direct-push techniques and Permeameter tests. Direct-push techniques were used to generate the electrical conductivity (EC) logs and to collect sequences of continuous sediment cores from river channels, as well as from the alluvial aquifer connected to the river. Permeameter tests on these sediment cores give the profiles of vertical hydraulic conductivity (Kv) of the channel sediments and the aquifer materials. This method was applied to produce Kv profiles for a streambed and an alluvial aquifer in the Platte River Valley of Nebraska, USA. Comparison and statistical analysis of the Kv profiles from the river channel and from the proximate alluvial aquifer indicates a special pattern of Kv in the channel sediments. This depth-dependent pattern of Kv distribution for the channel sediments is considered to be produced by hyporheic processes. This Kv-distribution pattern implied that the effect of hyporheic processes on streambed hydraulic conductivity can reach the sediments about 9 m below the channel surface. © 2010 John Wiley & Sons, Ltd.

Arai N.,University of Electro - Communications | Yasuoka K.,Keio University | Zeng X.C.,University of Nebraska - Lincoln
Nanoscale | Year: 2013

We investigate translocation dynamics of a vesicle cell under collision with a Janus or a homogeneous hydrophobic/hydrophilic nanoparticle. To this end, we perform dissipative particle dynamics simulation by setting the nanoparticle with different initial velocities, different chemical patterns of the surface for the nanoparticle, and different orientations (for the Janus nanoparticle). Particular attention is given to translocation dynamics, in-cell water discharge, and the late-stage morphologies of the vesicle/nanoparticle system after the collision. We observe three late-stage states for the Janus nanoparticle, and four late-stage states for the homogeneous nanoparticles. We find that the late-stage state and the associated dynamical pathway not only depend on the relative velocity but also on the chemical pattern of the nanoparticle surface, as well as on the orientation of the incident Janus nanoparticle. We have examined the time-dependent mean radius of the vesicle, the number of in-cell water beads lost from the vesicle, as well as the collision-induced pore size on the lipid membrane during the course of collision. Our simulation provides microscopic insights into the resilience of the vesicle-cell membrane and dynamical behavior of the vesicle under the attack of a foreign nanoparticle. Knowledge and insights gained through the simulation will have implication to the drug delivery with different chemical coatings. © The Royal Society of Chemistry 2013.

Hamza A.S.,University of Nebraska - Lincoln | Khalifa S.S.,Cairo University | Hamza H.S.,Cairo University | Elsayed K.,Cairo University
IEEE Communications Surveys and Tutorials | Year: 2013

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. © 1998-2012 IEEE.

Xue D.,Ohio State University | Ekici E.,Ohio State University | Vuran M.C.,University of Nebraska - Lincoln
IEEE Transactions on Wireless Communications | Year: 2014

In this paper, a multidimensional-correlation-based sensing scheduling algorithm, (CORN)2, is developed for cognitive radio networks to minimize energy consumption. A sensing quality metric is defined as a measure of the correctness of spectral availability information based on the fact that spectrum sensing information at a given space and time can represent spectrum information at a different point in space and time. The scheduling algorithm is shown to achieve a cost of sensing (e.g., energy consumption, sensing duration) arbitrarily close to the possible minimum, while meeting the sensing quality requirements. To this end, (CORN)2 utilizes a novel sensing deficiency virtual queue concept and exploits the correlation between spectrum measurements of a particular secondary user and its collaborating neighbors. The proposed algorithm is proved to achieve a distributed and arbitrarily close to optimal solution under certain, easily satisfied assumptions. Furthermore, a distributed Selective-(CORN)2 (S-(CORN)2) is introduced by extending the distributed algorithm to allow secondary users to select collaboration neighbors in densely populated cognitive radio networks. In addition to the theoretically proved performance guarantees, the algorithms are evaluated through simulations. © 2002-2012 IEEE.

Tyler K.A.,University of Nebraska - Lincoln
Archives of Sexual Behavior | Year: 2013

The purpose of this study was to examine the relationship between homeless youths' HIV risk behaviors with strangers and risk and protective characteristics of their social networks. Data were from the Social Network and Homeless Youth Project. A total of 249 youth aged 14-21 years were interviewed over 15 months in three Midwestern cities in the United States using a systematic sampling strategy. Multivariate results revealed that homeless youth with a greater average number of network members who engaged in more drug risk behaviors and who pressured them into precarious behaviors at least once were more likely to have participated in a greater number of HIV risk behaviors with strangers compared to homeless youth without such network characteristics. Additionally, 19-21 year olds, gay, lesbian, bisexual, and transgendered youth, and those who have run away from home more frequently, participated in more HIV risk behaviors with strangers than 14-18 year olds, heterosexual youth, and those who have run away less often. The final model explained 43 % of the variance in homeless youths' HIV risk behaviors with strangers. It is important to identify network characteristics that are harmful to homeless youth because continued exposure to such networks and participation in dangerous behaviors may result in detrimental outcomes, including contraction of sexually transmitted infections and potentially HIV. © 2013 Springer Science+Business Media New York.

Wilson P.B.,University of Nebraska - Lincoln
Journal of Strength and Conditioning Research | Year: 2015

The concept of multiple transportable carbohydrates (MTC) refers to a combination of saccharides that rely on distinct transporters for intestinal absorption. Ingestion of MTC during prolonged exercise has been purported to increase carbohydrate absorption efficiency, increase exogenous carbohydrate oxidation, reduce gastrointestinal (GI) distress, and improve athletic performance when carbohydrate intake is high (>50-60 g·h -1). Although reviews of MTC research have been published previously, a comprehensive literature evaluation underscoring methodological limitations has not been conducted to guide future work. Accordingly, this review outlined the plausible mechanisms of MTC and subsequently evaluated MTC research based on several factors, including participant characteristics, exercise modality, exercise task, treatment formulation, treatment blinding, and pre-exercise nutrition status. A total of 27 articles examining MTC during exercise were identified and reviewed. Overall, ingestion of MTC led to increased exogenous carbohydrate oxidation, reduced GI distress, and improved performance during cycling lasting ≥2.5 hours, particularly when carbohydrate was ingested at ≥1.2 g·min -1. Despite the apparent benefits, several limitations in the literature were apparent, including that only 3 studies used running, only 2 studies were conducted in the field, most participants were fasted, and women and adolescents were underrepresented. In addition, the majority of the studies fed carbohydrate at ≥1.2 g·min -1, which may have inflated levels of GI distress and exaggerated performance decrements with single-saccharide feedings. Based on these limitations, future MTC investigations should consider focusing on running, examining team-based sports, including women and adolescents, conducting experiments under field conditions, examining the modifying effects of pre-exercise nutrition, and using modest feeding protocols (1.0-1.2 g·min -1). © 2015 National Strength and Conditioning Association.

Sheeder R.J.,Permitting Section | Lynne G.D.,University of Nebraska - Lincoln
Land Economics | Year: 2011

Conservation tillage on farms can improve downstream water quality. Using a dual-interests theoretical framework guided by the metaeconomics approach, this paper examines the role of self-interest and shared other-interest in the conservation tillage adoption decision. The data is from a 2007 survey of farmers in the Blue River/Tuttle Creek watershed of Nebraska and Kansas. Logit models show that farmers who temper their pursuit of selfinterest with shared other-interest reflecting empathy-sympathy are more likely to adopt conservation tillage. Habit and control also play a role. Farmers pursue a joint and interdependent own-interest and not only self-interest as presumed in microeconomics. © 2011 by the Board of Regents of the University of Wisconsin System.

Yuan X.,University of Maryland University College | Cohen M.B.,University of Nebraska - Lincoln | Memon A.M.,University of Maryland University College
IEEE Transactions on Software Engineering | Year: 2011

Graphical user interfaces (GUIs), due to their event-driven nature, present an enormous and potentially unbounded way for users to interact with software. During testing, it is important to "adequately cover" this interaction space. In this paper, we develop a new family of coverage criteria for GUI testing grounded in combinatorial interaction testing. The key motivation of using combinatorial techniques is that they enable us to incorporate context into the criteria in terms of event combinations, sequence length, and by including all possible positions for each event. Our new criteria range in both efficiency (measured by the size of the test suite) and effectiveness (the ability of the test suites to detect faults). In a case study on eight applications, we automatically generate test cases and systematically explore the impact of context, as captured by our new criteria. Our study shows that by increasing the event combinations tested and by controlling the relative positions of events defined by the new criteria, we can detect a large number of faults that were undetectable by earlier techniques. © 2006 IEEE.

Smith S.D.,Duke University | Smith S.D.,University of Nebraska - Lincoln | Rausher M.D.,Duke University
Molecular Biology and Evolution | Year: 2011

Although the importance of regulatory and functional sequence evolution in generating species differences has been studied to some extent, much less is known about the role of other types of genomic changes, such as fluctuation in gene copy number. Here, we apply analyses of gene function and expression of anthocyanin pigment pathway genes, as well as cosegregation analyses in backcross populations, to examine the genetic changes involved in the shift from blue to red flowers in Andean Iochroma (Solanaceae). We demonstrate that deletion of a gene coding for an anthocyanin pathway enzyme was necessary for the transition to red floral pigmentation. The downregulation of a second pathway gene was also necessary for the novel flower color, and this regulatory pattern parallels the genetic change in the two other red-flowered species in the sister family Convolvulaceae in which flower color change has been examined genetically. Finally, we document a shift in enzymatic function at a third locus, but the importance of this change in the transition to red flowers depends on the exact order with which the three changes occurred. This study shows that gene inactivation or loss can be involved in the origin of phenotypic differences between species, thereby restricting the possibility of reversion to the ancestral state. It also demonstrates that parallel evolution of red flowers in three different species occurs via a common developmental/regulatory change but by mutations in different genes. © The Author 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All reserved.

Bickel R.D.,University of Nebraska - Lincoln | Bickel R.D.,University of Southern California | Kopp A.,University of California at Davis | Nuzhdin S.V.,University of Southern California
PLoS Genetics | Year: 2011

Many agriculturally, evolutionarily, and medically important characters vary in a quantitative fashion. Unfortunately, the genes and sequence variants accounting for this variation remain largely unknown due to a variety of biological and technical challenges. Drosophila melanogaster contains high levels of sequence variation and low linkage disequilibrium, allowing us to dissect the effects of many causative variants within a single locus. Here, we take advantage of these features to identify and characterize the sequence polymorphisms that comprise major effect QTL alleles segregating at the bric-a-brac locus. We show that natural bric-a-brac alleles with large effects on cuticular pigmentation reflect a cumulative impact of polymorphisms that affect three functional regions: a promoter, a tissue-specific enhancer, and a Polycomb response element. Analysis of allele-specific expression at the bric-a-brac locus confirms that these polymorphisms modulate transcription at the cis-regulatory level. Our results establish that a single QTL can act through a confluence of multiple molecular mechanisms and that sequence variation in regions flanking experimentally validated functional elements can have significant quantitative effects on transcriptional activity and phenotype. These findings have important design and conceptual implications for basic and medical genomics. © 2011 Bickel et al.

Zhou H.,Iowa State University | Liu B.,Iowa State University | Weeks D.P.,University of Nebraska - Lincoln | Spalding M.H.,Iowa State University | Yang B.,Iowa State University
Nucleic acids research | Year: 2014

The Cas9/sgRNA of the CRISPR/Cas system has emerged as a robust technology for targeted gene editing in various organisms, including plants, where Cas9/sgRNA-mediated small deletions/insertions at single cleavage sites have been reported in transient and stable transformations, although genetic transmission of edits has been reported only in Arabidopsis and rice. Large chromosomal excision between two remote nuclease-targeted loci has been reported only in a few non-plant species. Here we report in rice Cas9/sgRNA-induced large chromosomal segment deletions, the inheritance of genome edits in multiple generations and construction of a set of facile vectors for high-efficiency, multiplex gene targeting. Four sugar efflux transporter genes were modified in rice at high efficiency; the most efficient system yielding 87-100% editing in T0 transgenic plants, all with di-allelic edits. Furthermore, genetic crosses segregating Cas9/sgRNA transgenes away from edited genes yielded several genome-edited but transgene-free rice plants. We also demonstrated proof-of-efficiency of Cas9/sgRNAs in producing large chromosomal deletions (115-245 kb) involving three different clusters of genes in rice protoplasts and verification of deletions of two clusters in regenerated T0 generation plants. Together, these data demonstrate the power of our Cas9/sgRNA platform for targeted gene/genome editing in rice and other crops, enabling both basic research and agricultural applications. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Schmidt D.,University of Nebraska - Lincoln
Thin Solid Films | Year: 2014

Generalized ellipsometry, a non-destructive optical characterization technique, is employed to determine geometrical structure parameters and anisotropic dielectric properties of highly spatially coherent three-dimensionally nanostructured thin films grown by glancing angle deposition. The (piecewise) homogeneous biaxial layer model approach is discussed, which can be universally applied to model the optical response of sculptured thin films with different geometries and from diverse materials, and structural parameters as well as effective optical properties of the nanostructured thin films are obtained. Alternative model approaches for slanted columnar thin films, anisotropic effective medium approximations based on the Bruggeman formalism, are presented, which deliver results comparable to the homogeneous biaxial layer approach and in addition provide film constituent volume fraction parameters as well as depolarization or shape factors. Advantages of these ellipsometry models are discussed on the example of metal slanted columnar thin films, which have been conformally coated with a thin passivating oxide layer by atomic layer deposition. Furthermore, the application of an effective medium approximation approach to in-situ growth monitoring of this anisotropic thin film functionalization process is presented. It was found that structural parameters determined with the presented optical model equivalents for slanted columnar thin films agree very well with scanning electron microscope image estimates. © 2013 Elsevier B.V. All rights reserved.

Markham J.E.,University of Nebraska - Lincoln
Methods in Molecular Biology | Year: 2013

Sphingolipids generate signals in plants in response to a variety of biotic and abiotic stresses. Measuring these signaling compounds is complicated by the heterogeneity of structures within the sphingolipid family and the comparatively low concentration of their metabolites in plant tissues. To date, the only method with the sensitivity, dynamic range, and specificity to measure all sphingolipids in a plant extract is liquid chromatography coupled to mass spectrometry. The drawback of this method is the cost of the hardware, the expertise in mass spectrometry required to critically assess the outcome and the lack of suitable standards for accurate quantitative analysis. The goal of this chapter is to assist researchers in setting up experiments to measure sphingolipids and explain some of the pitfalls and solutions along the way. © 2013 Springer Science+Business Media, LLC.

Huynh T.N.,Dublin City University | Nguyen L.,University of Nebraska - Lincoln | Barry L.P.,Dublin City University
Journal of Lightwave Technology | Year: 2013

This study employed the coherent phase modulation (PM) detection method to characterize the phase noise of a Sampled-Grating Distributed Bragg Reflector (SGDBR) laser via delayed self-heterodyne (DSH) measurements. We derived the formula for phase-error variance from the FM noise spectrum of the laser and performed measurements on the Distributed Feedback (DFB) and SGDBR lasers. The results confirmed that the DFB laser phase noise is well described by white FM noise while the SGDBR laser has additional frequency fluctuations below 400 MHz. The measurement and simulation results also demonstrated that the low frequency excess noise significantly broadens the linewidth of SGDBR lasers and can degrade the performance of coherent optical communication systems. © 1983-2012 IEEE.

Casler M.D.,U.S. Department of Agriculture | Vogel K.P.,University of Nebraska - Lincoln
Crop Science | Year: 2014

Switchgrass (Panicum virgatum L.) is a candidate for cellulosic bioenergy feedstock development in many parts of North America, Europe, and Asia. Breeding for increased biomass yield is a viable and desirable research objective to improve both economic and energy yields per hectare. The objectives of this study were to estimate progress from (i) selection for biomass yield in upland switchgrass, (ii) selection for winter survival, biomass yield, and biomass quality in lowland switchgrass, and (iii) advanced-generation heterosis effects in four upland × lowland hybrid switchgrass populations. Selection for increased biomass yield in upland switchgrass resulted in mean genetic gains for of 0.71 Mg ha-1 per cycle (8% per cycle = 4% yr-1) for biomass yield. Selection for increased biomass yield in lowland switchgrass resulted in mean genetic gains of 0.89 Mg ha-1 (18% = 1% yr-1) for biomass yield. Mean high-parent heterosis between upland and lowland ecotypes was 3.57 Mg ha-1 (43%). These gains in biomass yield resulted in significant increases in ethanol production for a fermentation platform or high heating value for a combustion platform. Biomass yield is a moderately heritable trait in switchgrass and it can be readily improved in both upland and lowland populations using conventional breeding methods. © Crop Science Society of America.

Kravchenko I.,University of Nebraska - Lincoln
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2012

The RICE experiment on detection of UHE neutrinos has been running over a decade. The experiment comprises an array of radio antennas buried in ice to the depth of up to 300 m near the geographic South Pole, and is designed to observe neutrino interactions in ice employing the radio Cherenkov technique. We discuss new limits on the diffuse UHE neutrino flux that now include the full dataset accumulated over 10 years and benefit from new analysis techniques. We also present our recent measurements of birefringent properties of ice at the experiment location. © 2010 ElsevierB.V.Allrightsreserved.

Head J.J.,University of Nebraska - Lincoln
Palaeontologia Electronica | Year: 2015

Snakes possess a dense fossil record through the Late Cretaceous and Cenozoic and are an important clade for studies of molecular phylogenetics. The use of the snake fossil record has historically been a limited and inaccurate source of temporal data in molecular studies due to taxonomic and phylogenetic ambiguities. Here I provide 10 fossil calibration dates for phylogenetic analysis of higher-order interrelationships of snakes. Calibration points include apomorphy-based systematic justifications and precise dates for hard minimum divergence timings. Calibrated nodes are for the snake total clade, Alethinophidia, and boid and pythonid taxa. Hard minimum divergence timings range from earliest late Cretaceous to middle Miocene. These dates provide precise minima for constraining the early evolutionary history of Serpentes. Comparisons of phylogenetically justified calibrations with published studies that employed form-taxon assignments suggests greatly younger divergences for justified nodes and indicates that deep-time divergence estimates that have been correlated with tectonic histories may be considerably too old and reliant on presumptions of Early Cretaceous Gondwanan vicariance as a mechanism of speciation. © Society for Vertebrate Paleontology April 2015.

Gong X.,General Motors | Qiao W.,University of Nebraska - Lincoln
IEEE Transactions on Industrial Electronics | Year: 2015

Online fault detection is an effective means to improve wind turbine reliability and performance and reduce wind turbine downtime and operating and maintenance costs. Current-based wind turbine fault detection techniques have received more and more attention in academia and industry due to their nonintrusive character and economic advantages. This paper presents a novel computationally efficient high-resolution wideband synchronous sampling algorithm for the mechanical fault detection of variable-speed direct-drive wind turbines (i.e., no gearbox) only using nonstationary generator stator current measurements. The proposed algorithm synchronously resamples the current signals such that the varying characteristic frequencies of the excitations generated by wind turbine faults in the current signals become constant values. An impulse detection algorithm is then proposed to detect the faults by identifying the excitations from the frequency spectra of the synchronously sampled stator current signals. Experimental studies are carried out to demonstrate the effectiveness of the proposed algorithms for the detection of rotor eccentricity and bearing faults of a direct-drive wind turbine operating in variable-speed conditions. © 2014 IEEE.

Kelly A.M.,University of Nebraska - Lincoln
Molecular Therapy | Year: 2015

Human mesenchymal stem cells (hMSCs) are one of the most widely researched stem cell types with broad applications from basic research to therapeutics, the majority of which require introduction of exogenous DNA. However, safety and scalability issues hinder viral delivery, while poor efficiency hinders nonviral gene delivery, particularly to hMSCs. Here, we present the use of a pharmacologic agent (glucocorticoid) to overcome barriers to hMSC DNA transfer to enhance transfection using three common nonviral vectors. Glucocorticoid priming significantly enhances transfection in hMSCs, demonstrated by a 3-fold increase in efficiency, 4–15-fold increase in transgene expression, and prolonged transgene expression when compared to transfection without glucocorticoids. These effects are dependent on glucocorticoid receptor binding and caused in part by maintenance of normal metabolic function and increased cellular (5-fold) and nuclear (6–10-fold) DNA uptake over hMSCs transfected without glucocorticoids. Results were consistent across five human donors and in cells up to passage five. Glucocorticoid cell priming is a simple and effective technique to significantly enhance nonviral transfection of hMSCs that should enhance their clinical use, accelerate new research, and decrease reliance on early passage cells.Molecular Therapy (2015); doi:10.1038/mt.2015.195. © 2015 American Society of Gene & Cell Therapy

Shank N.,University of Nebraska - Lincoln
Journal of the American Medical Informatics Association | Year: 2012

Objective To assess behavioral health providers' beliefs about the benefits and barriers of health information exchange (HIE). Methods Survey of a total of 2010 behavioral health providers in a Midwestern state (33% response rate), with questions based on previously reported open-ended beliefs elicitation interviews. Results Factor analysis resulted in four groupings: beliefs that HIE would improve care and communication, add cost and time burdens, present access and vulnerability concerns, and impact workflow and control (positively and negatively). A regression model including all four factors parsimoniously predicted attitudes toward HIE. Providers clustered into two groups based on their beliefs: a majority (67%) were positive about the impact of HIE, and the remainder (33%) were negative. There were some professional/demographic differences between the two clusters of providers. Discussion Most behavioral health providers are supportive of HIE; however, their adoption and use of it may continue to lag behind that of medical providers due to perceived cost and time burdens and concerns about access to and vulnerability of information.

Schmidt E.G.,University of Nebraska - Lincoln
Astronomical Journal | Year: 2013

We have obtained VR photometry of 447 Cepheid variable star candidates with declinations north of -14°30′, most of which were identified using the Northern Sky Variability Survey (NSVS) data archive. Periods and other photometric properties were derived from the combination of our data with the NSVS data. Atmospheric parameters were determined for 81 of these stars from low-resolution spectra. The identification of type II Cepheids based on the data presented in all four papers in this series is discussed. On the basis of spectra, 30 type II Cepheids were identified while 53 variables were identified as cool, main sequence stars and 283 as red giants following the definitions in Paper III. An additional 30 type II Cepheids were identified on the basis of light curves. The present classifications are compared with those from the Machine-learned All Sky Automated Survey Classification Catalog for 174 stars in common. © 2013. The American Astronomical Society. All rights reserved.

Francis C.A.,University of Nebraska - Lincoln | Porter P.,University of Minnesota
Critical Reviews in Plant Sciences | Year: 2011

Sustainable and productive agroecosystems must be developed that will meet today's needs for food and other products, as well as preserving the vital natural resource base that will allow future generations to meet their needs. To increase production efficiency, to improve farming strategies based on local resources, and to design systems that are resilient in the face of changing climate require thorough understanding of the ecology of agricultural systems. Organic and sustainable farmers have developed many production practices and integrated crop/animal systems that are finding application in more conventional farming enterprises. While they do seek greater resource use efficiency and substitution of more environmentally benign inputs to replace chemicals used in conventional farming, sustainable farmers increasingly depend on thoughtful redesign of production systems to provide internal management of soil fertility and pests, careful use of contemporary energy and rainfall, and reliance on internal resources rather than imported inputs. Evaluation of systems based on productivity, sustained economic return, viable environmental indicators, and equitable social consequences of agricultural production are central to future sustainable farming and food systems. © Taylor & Francis Group, LLC.

Bloom K.,University of Nebraska - Lincoln
Journal of Physics: Conference Series | Year: 2014

CMS is in the process of deploying an Xrootd based infrastructure to facilitate a global data federation. The services of the federation are available to export data from half the physical capacity and the majority of sites are configured to read data over the federation as a back-up. CMS began with a relatively modest set of use-cases for recovery of failed local file opens, debugging and visualization. CMS is finding that the data federation can be used to support small scale analysis and load balancing. Looking forward we see potential in using the federation to provide more flexibility in the location workflows are executed as the difference between local access and wide area access are diminished by optimization and improved networking. In this presentation we discuss the application development work and the facility deployment work, the use-cases currently in production, and the potential for the technology moving forward. © Published under licence by IOP Publishing Ltd.

Ge H.,ISO New England | Asgarpoor S.,University of Nebraska - Lincoln
IEEE Transactions on Power Delivery | Year: 2012

The increasing size, aging equipment, and complexity of power systems, coupled with present day financial constraints, have made the use of probabilistic methods and reliability indices a necessity for maintaining continuity and quality of service to customers. Proper maintenance-related decisions should address all of these issues to improve system reliability while meeting limited budget constraints. This paper proposes algorithms that enable system-level reliability assessment with detailed modeling of maintenance for aging equipment. Stochastic-based reliability modeling of substations with aging equipment is presented, which enables the study of equipment aging, failures, and maintenance and their effect on substation-level availability and frequency of failure. Several case studies are provided which describe optimization of maintenance activities and the impact on maximum substation reliability. The algorithms provide a valuable tool for processing detailed models of aging equipment and maintenance of individual pieces in system reliability assessment applications. These algorithms are consistent with existing reliability models and are capable of being integrated into utility asset-management programs. © 2012 IEEE.

Pavlista A.D.,University of Nebraska - Lincoln
American Journal of Potato Research | Year: 2011

Hormones play key roles in potato tuber formation and growth. Early Harvest, a commercial product, is a mixture of gibberellic acid, indole-butyric acid and kinetin, all involved in tuber formation in vitro. Auxigro contains 4-aminobutyric acid and L-glutamate. Can these growth regulators affect field yields? These mixtures were tested on 'Atlantic' potato in western Nebraska from 1998 to 2004. Early Harvest was applied to seed pieces at 178 mg/kg and to foliage once or twice at 234 ml/ha between 7 and 28 days after emergence (DAE). Auxigro was applied to seed pieces at 20 and 40 mg/kg, to foliage at 21 to 70 DAE at 350 g/ha, and to foliage at rates from 140 to 700 g/ha when tubers began bulking. Seed treatments were ineffective. Early Harvest increased yields 15%, when applied twice, 11 to 14 days apart, prior to tuber formation at 28 DAE, but not when applied once. Auxigro was not affective when applied at 21 or 28 DAE. Yield was increased 13% when Auxigro was applied during early tuber bulking between 42 and 56 DAE but not at 70 DAE. Auxigro rates of 280 to 560 g/ha applied at early tuber bulking increased yield of 5. 7 to 8. 2 cm diameter tubers over 20% compared to the check. Early Harvest increased Atlantic yield when applied early after emergence to affect tuber formation. Auxigro stimulated tuber bulking in Atlantic when applied during the early log phase of tuber growth. © 2011 Potato Association of America.

Houston A.L.,University of Nebraska - Lincoln | Wilhelmson R.B.,University of Illinois at Urbana - Champaign
Monthly Weather Review | Year: 2012

A suite of experiments conducted using a cloud-resolving model is examined to assess the role that preexisting airmass boundaries can play in regulating storm propagation. The 27 May 1997 central Texas tornadic event is used to guide these experiments. The environment of this event was characterized by multiple preexisting airmass boundaries, large CAPE, and weak vertical shear. Only the experiments with preexisting airmass boundaries produce back-building storm propagation (storm motion in opposition to the mean wind). When both the cold front and dryline are present, storm maintenance occurs through the quasi-continuous maintenance of a set of long-lived updrafts and not through discrete updraft redevelopment. Since the cold front is not required for back building, it is clear that back building in this environment does not require quasi-continuous updraft maintenance. The back-building storm simulated with both the cold front and dryline is found to be anchored to the boundary zipper (the intersection of the cold front and dryline). However, multiple preexisting airmass boundaries are not required for back building since experiments with only a dryline also support back building. A conceptual model of back building and boundary zippering is developed that highlights the important role that preexisting boundaries can play in back-building propagation. © 2012 American Meteorological Society.

Whitman M.,University of Nebraska - Lincoln | Ackerman J.D.,University of Puerto Rico at San Juan
Ecology | Year: 2015

Suitable habitat for a species is often modeled by linking its distribution patterns with landscape characteristics. However, modeling the relationship between fitness and landscape characteristics is less common. In this study we take a novel approach towards species distribution modeling (SDM) by investigating factors important not only for species occurrence, but also abundance and physical size, as well as fitness measures. We used the Neotropical terrestrial orchid Prescottia stachyodes as our focal species, and compiled geospatial information on habitat and neighboring plants for use in a two-part conditional SDM that accounted for zero inflation and reduced spatial autocorrelation bias. First, we modeled orchid occurrence, and then within suitable sites we contrasted habitat characteristics important for orchid abundance as compared to plant size. We then tested possible fitness implications, informed by analyses of allometric scaling of reproductive effort and lamina area, as well as size-density relationships in areas of P. stachyodes co-occurrence. We determined that orchid presence was based on a combination of biotic and abiotic factors (indicator species, diffuse solar radiation). Within these sites, P. stachyodes abundance was higher on flat terrain, with fine, moderately well-drained soil, and areas without other native orchids, whereas plant size was greater in less rocky areas. In turn, plant size determined reproductive effort, with floral display height proportionate to lamina area (more photosynthates); however, allometric scaling of flower quantity suggests a higher energy cost for production, or maintenance, of flowers. Overall, habitat factors most important for abundance differed from those for size (and thus reproductive effort), suggesting that sites optimal for either recruitment or survival may not be the primary source of seeds. For plots with multiple P. stachyodes plants, size-density relationships differed depending on the size class examined, which may reflect context-dependent population dynamics. Thus, ecological resolution provided by SDM can be enhanced by incorporating abundance and fitness measures. © 2015 by the Ecological Society of America.

Houston A.L.,University of Nebraska - Lincoln | Wilhelmson R.B.,University of Illinois at Urbana - Champaign
Monthly Weather Review | Year: 2011

The sensitivity of storm longevity to the pattern of deep convection initiation (e.g., multiple, quasi-linearly arranged initial deep convective cells versus an isolated deep convective cell) is examined using idealized cloud-resolving simulations conducted with a low-shear initial environment. When multiple deep convective cells are initialized in close proximity to one another using either a line of thermals or a shallow airmass boundary, long-lived storms are produced. However, when isolated deep convection is initiated, the resultant storm steadily decays following initiation. These results illustrate that a quasi-linear mechanism, such as a preexisting airmass boundary, that initiates multiple deep convective cells in close proximity can lead to longer-lived storms than a mechanism that initiates isolated deep convection. The essential difference between the experiments conducted is that an isolated initial storm produces a shallower cold pool than when a quasi-linear initiation is used. It is argued that the deep cold pools promote deep forced ascent, systematic convective cell redevelopment, and thus long-lived storms, even in environments with small values of vertical shear. The difference in cold pool depth between the simulations is attributed to differences in the horizontal flux of cold air to the gust front. With a single initial storm, the few convective cells that subsequently form provide only a limited source of cold air, leading to a cold pool that is shallow and incapable of fostering continued updraft redevelopment. © 2011 American Meteorological Society.

Hergert G.W.,University of Nebraska - Lincoln
Sugar Tech | Year: 2010

Global sugar beet production spans diverse regions and a wide range of climatic and agroecological regions from rainfed to irrigated production which presents unique management challenges. Sound nutrient management now and into the future must be balanced between production efficiency and managing to have less impact on the environment. N management continues to improve with more precise N rates. Soil testing for N supplying capability plus residual N will need to be increased to enhance productivity and N use efficiency. Newer cultivation techniques, N placement and timing can also fine tune N rates. In irrigated areas, improvements in N management will be coupled with better water management and conversion of furrow irrigation to sprinklers will accelerate improvements. Enhanced efficiency fertilizer products hold promise but require additional research under a range of conditions to determine cost and production effectiveness. Management for secondary and micronutrients seems adequate at this time. Precision agricultural applications for expanded site specific management in sugar beet are just beginning. Work with maize and wheat point to the potential of creating different management zones in fields and by using remote or close sensing to determine N status for N applications. Similar research will be needed to continue efficient sugar beet production. © 2011 Society for Sugar Research & Promotion.

Wilson M.A.,University of Nebraska - Lincoln
Antioxidants and Redox Signaling | Year: 2011

DJ-1 is a member of the large and functionally diverse DJ-1/PfpI superfamily and has homologs in nearly all organisms. Because of its connection to parkinsonism and cancer, human DJ-1 has been intensely studied for over a decade. The current view is that DJ-1 is a multifunctional oxidative stress response protein that defends cells against reactive oxygen species and mitochondrial damage, although the details of its biochemical function remain unclear. A conserved cysteine residue in DJ-1 (Cys106) is both functionally essential and subject to oxidation to the cysteine-sulfinate and cysteine-sulfonate. Consequently, the oxidative modification of Cys106 has been proposed to allow DJ-1 to act as a sensor of cellular redox homeostasis and to participate in cytoprotective signaling pathways in the cell. This review explores the current evidence for the role of cysteine oxidation in DJ-1 function, with emphasis on emerging models for how oxidative modification may regulate DJ-1's protective function and also contribute to dysfunction and disease. © 2011 Mary Ann Liebert, Inc.

Odermatt D.,University of Zurich | Gitelson A.,University of Nebraska - Lincoln | Brando V.E.,CSIRO | Schaepman M.,University of Zurich
Remote Sensing of Environment | Year: 2012

We provide a comprehensive overview of water constituent retrieval algorithms and underlying definitions and models for optically deep and complex (i.e. case 2) waters using earth observation data. The performance of constituent retrieval algorithms is assessed based on matchup validation experiments published between January 2006 and May 2011. Validation practices range from singular vicarious calibration experiments to comparisons using extensive in situ time series. Band arithmetic and spectral inversion algorithms for all water types are classified using a method based scheme that supports the interpretation of algorithm validity ranges. Based on these ranges we discuss groups of similar algorithms in view of their strengths and weaknesses. Such quantitative literature analysis reveals clear application boundaries. With regard to chlorophyll retrieval, validation of blue-green band ratios in coastal waters is limited to oligotrophic, predominantly ocean waters, while red-NIR ratios apply only at more than 10mg/m 3. Spectral inversion techniques - although not validated to the same extent - are necessary to cover all other conditions. Suspended matter retrieval is the least critical, as long as the wavelengths used in empirical models are increased with concentrations. The retrieval of dissolved organic matter however remains relatively inaccurate and inconsistent, with large differences in the accuracy of comparable methods in similar validation experiments. We conclude that substantial progress has been made in understanding and improving retrieval of constituents in optically deep and complex waters, enabling specific solutions to almost any type of optically complex water. Further validation and intercomparison of spectral inversion procedures are however needed to learn if solutions with a larger validity range are feasible. © 2011 Elsevier Inc.

Rose D.J.,University of Nebraska - Lincoln
British Journal of Nutrition | Year: 2014

The gut microbiota plays important roles in proper gut function and can contribute to or help prevent disease. Whole grains, including oats, constitute important sources of nutrients for the gut microbiota and contribute to a healthy gut microbiome. In particular, whole grains provide NSP and resistant starch, unsaturated TAG and complex lipids, and phenolics. The composition of these constituents is unique in oats compared with other whole grains. Therefore, oats may contribute distinctive effects on gut health relative to other grains. Studies designed to determine these effects may uncover new human-health benefits of oat consumption. Copyright © 2014 The Authors.

McMahan C.S.,Clemson University | Tebbs J.M.,University of South Carolina | Bilder C.R.,University of Nebraska - Lincoln
Biostatistics | Year: 2013

Group testing is widely used to reduce the cost of screening individuals for infectious diseases. There is an extensive literature on group testing, most of which traditionally has focused on estimating the probability of infection in a homogeneous population. More recently, this research area has shifted towards estimating individual-specific probabilities in a regression context. However, existing regression approaches have assumed that the sensitivity and specificity of pooled biospecimens are constant and do not depend on the pool sizes. For those applications, where this assumption may not be realistic, these existing approaches can lead to inaccurate inference, especially when pool sizes are large. Our new approach, which exploits the information readily available from underlying continuous biomarker distributions, provides reliable inference in settings where pooling would be most beneficial and does so even for larger pool sizes. We illustrate our methodology using hepatitis B data from a study involving Irish prisoners. © The Author 2012. Published by Oxford University Press. All rights reserved.

Powers R.,University of Nebraska - Lincoln
Journal of Medicinal Chemistry | Year: 2014

The pharmaceutical industry has significantly contributed to improving human health. Drugs have been attributed to both increasing life expectancy and decreasing health care costs. Unfortunately, there has been a recent decline in the creativity and productivity of the pharmaceutical industry. This is a complex issue with many contributing factors resulting from the numerous mergers, increase in out-sourcing, and the heavy dependency on high-throughput screening (HTS). While a simple solution to such a complex problem is unrealistic and highly unlikely, the inclusion of metabolomics as a routine component of the drug discovery process may provide some solutions to these problems. Specifically, as the binding affinity of a chemical lead is evolved during the iterative structure-based drug design process, metabolomics can provide feedback on the selectivity and the in vivo mechanism of action. Similarly, metabolomics can be used to evaluate and validate HTS leads. In effect, metabolomics can be used to eliminate compounds with potential efficacy and side effect problems while prioritizing well-behaved leads with druglike characteristics. © 2014 American Chemical Society.

Riethoven J.J.,University of Nebraska - Lincoln
Methods in molecular biology (Clifton, N.J.) | Year: 2010

One of the mechanisms through which protein levels in the cell are controlled is through transcriptional regulation. Certain regions, called cis-regulatory elements, on the DNA are footprints for the trans-acting proteins involved in transcription, either for the positioning of the basic transcriptional machinery or for the regulation - in simple terms turn on or turn off - thereof. The basic transcriptional machinery is DNA-dependent RNA polymerase (RNAP) which synthesizes various types of RNA and core promoters on the DNA are used to position the RNAP. Other nearby regions will regulate the transcription: in prokaryotic organisms operators are involved; in eukaryotic organisms, proximal promoter regions, enhancers, silencers, and insulators are present. This chapter will describe the various DNA regions involved in transcription and transcriptional regulation.

Messman-Moore T.L.,Miami University Ohio | Walsh K.L.,Miami University Ohio | DiLillo D.,University of Nebraska - Lincoln
Child Abuse and Neglect | Year: 2010

Objective: The current study examined emotion dysregulation as a mechanism underlying risky sexual behavior and sexual revictimization among adult victims of child sexual abuse (CSA) and child physical abuse (CPA). Methods: Participants were 752 college women. Victimization history, emotion dysregulation, and risky sexual behavior were assessed with anonymous, self-report surveys utilizing a cross-sectional design. Results: Approximately 6.3% of participants reported CSA, 25.5% reported CPA, and 17.8% reported rape during adolescence or adulthood. CSA and CPA were associated with increased risk for adolescent/adult rape; 29.8% of CSA victims and 24.3% of CPA victims were revictimized. Path analytic models tested hypothesized relationships among child abuse, emotion dysregulation, adolescent/adult rape and three forms of risky sexual behavior (e.g., failure to use condoms, contraception, or having sex with someone under the influence of alcohol/drugs), including frequency of risky sexual behavior with a regular dating partner, with a stranger, and lifetime number of intercourse partners. Emotion dysregulation mediated revictimization for both CSA and CPA. Emotion dysregulation also predicted lifetime number of sexual partners and frequency of risky sex with a stranger, but not frequency of risky sex with a regular dating partner. Conclusions: Findings suggest that emotion dysregulation is a distal predictor, and risky sex, particularly with lesser known partners, is a proximal predictor of sexual revictimization. Because emotion dysregulation also maintained a significant direct path to revictimization, risky sexual behavior appears to be one of several proximal risk factors for revictimization. Practice implications: Findings confirm that emotion dysregulation is a critical pathway to more proximal risk factors such as risky sexual behavior, and suggest that clinical interventions aimed at improving emotion dysregulation may help reduce risky sexual behavior and risk for revictimization. © 2010 Elsevier Ltd.

Neal T.M.S.,University of Nebraska - Lincoln
Behavioral Sciences and the Law | Year: 2014

This review of women's participation in the legal system as expert witnesses examines the empirical literature on the perceived credibility and persuasiveness of women compared with men experts. The effects of expert gender are complex and sometimes depend on the circumstances of the case. Some studies find no differences, some find favorable effects for women and others for men, and still others find that expert gender interacts with other circumstances of the case. The findings are interpreted through social role theory and the role incongruity theory of prejudice. Future directions for research are identified and implications are considered for attorneys who select and prepare expert witnesses. Suggestions for men's and women's behavior as expert witnesses are provided. © 2014 John Wiley & Sons, Ltd.

Rathnaiah G.,Hebrew University of Jerusalem | Rathnaiah G.,University of Nebraska - Lincoln
Frontiers in cellular and infection microbiology | Year: 2014

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne's Disease in ruminants. This enteritis has significant economic impact and worldwide distribution. Vaccination is one of the most cost effective infectious disease control measures. Unfortunately, current vaccines reduce clinical disease and shedding, but are of limited efficacy and do not provide long-term protective immunity. Several strategies have been followed to mine the MAP genome for virulence determinants that could be applied to vaccine and diagnostic assay development. In this study, a comprehensive mutant bank of 13,536 MAP K-10 Tn5367 mutants (P > 95%) was constructed and screened in vitro for phenotypes related to virulence. This strategy was designated to maximize identification of genes important to MAP pathogenesis without relying on studies of other mycobacterial species that may not translate into similar effects in MAP. This bank was screened for mutants with colony morphology alterations, susceptibility to D-cycloserine, impairment in siderophore production or secretion, reduced cell association, and decreased biofilm and clump formation. Mutants with interesting phenotypes were analyzed by PCR, Southern blotting and DNA sequencing to determine transposon insertion sites. These insertion sites mapped upstream from the MAP1152-MAP1156 cluster, internal to either the Mod operon gene MAP1566 or within the coding sequence of lsr2, and several intergenic regions. Growth curves in broth cultures, invasion assays and kinetics of survival and replication in primary bovine macrophages were also determined. The ability of vectors carrying Tn5370 to generate stable MAP mutants was also investigated.

Keshwani D.R.,University of Nebraska - Lincoln | Cheng J.J.,North Carolina State University
Biotechnology Progress | Year: 2010

Switchgrass and coastal bermudagrass are promising lignocellulosic feedstocks for bioethanol production. However, pretreatment of lignocelluloses is required to improve production of fermentable sugars from enzymatic hydrolysis. Microwave-based alkali pretreatment of switchgrass and coastal bermudagrass was investigated in this study. Pretreatments were carried out by immersing the biomass in dilute alkali reagents and exposing the slurry to microwave radiation at 250 W for residence times ranging from 5 to 20 min. Simons' stain method was used to quantify changes in biomass porosity as a result of the pretreatment. Pretreatments were evaluated based on yields of total reducing sugars, glucose, and xylose. An evaluation of different alkalis identified sodium hydroxide as the most effective alkali reagent for microwave-based pretreatment of switchgrass and coastal bermudagrass. 82% glucose and 63% xylose yields were achieved for switchgrass and 87% glucose and 59% xylose yields were achieved for coastal bermudagrass following enzymatic hydrolysis of biomass pretreated under optimal conditions. Dielectric properties for dilute sodium hydroxide solutions were measured and compared with solid losses, lignin reduction, and reducing sugar levels in hydrolyzates. Results indicate that dielectric loss tangent of alkali solutions is a potential indicator of the severity of microwave-based pretreatments. © 2009 American Institute of Chemical Engineers.

Yancey C.T.,Georgia Southern University | Hansen D.J.,University of Nebraska - Lincoln
Aggression and Violent Behavior | Year: 2010

An examination of the literature on factors related to outcome following child sexual abuse (CSA) revealed many factors that may contribute to symptoms displayed by victims. Factors are divided into three categories: Personal Factors, Familial Factors, and Abuse-Specific Factors. Personal factors are those inherent to the victim, including age, gender, developmental disability, attributions regarding the abuse, and treatment following abuse. Familial factors are defined as those factors associated with other family members. These include parental history of abuse, parental reaction to the disclosure, parental support of the victim, parental mental health, family stress, and treatment following abuse for the parent and other family members. Finally, factors related to the abuse are delineated, including severity of abuse, duration of the abuse, and victim-perpetrator relationship. Directions for future research are discussed. © 2010 Elsevier Ltd.

Pierobon M.,University of Nebraska - Lincoln
Nano Communication Networks | Year: 2014

Recent advances in synthetic biology, in particular towards the engineering of DNA-based circuits, are providing tools to program man-designed functions within biological cells, thus paving the way for the realization of biological nanoscale devices, known as nanomachines. By stemming from the way biological cells communicate in the nature, Molecular Communication (MC), i.e., the exchange of information through the emission, propagation, and reception of molecules, has been identified as the key paradigm to interconnect these biological nanomachines into nanoscale networks, or nanonetwork. The design of MC nanonetworks built upon biological circuits is particularly interesting since cells possess many of the elements required to realize this type of communication, thus enabling the design of cooperative functions in the biological environment. In this paper, a systems-theoretic modeling is realized by analyzing a minimal subset of biological circuit elements necessary to be included in an MC nanonetwork design where the message-bearing molecules are propagated via free diffusion between two cells. The obtained system-theoretic models stem from the biochemical processes underlying cell-to-cell MC, and are analytically characterized by their transfer functions, attenuation and delay experienced by an information signal exchanged by the communicating cells. Numerical results are presented to evaluate the obtained analytical expressions as functions of realistic biological parameters. © 2014 Elsevier Ltd.

Christensen A.C.,University of Nebraska - Lincoln
Genome Biology and Evolution | Year: 2013

Plant mitochondrial genomes are notorious for their large and variable size, nonconserved open reading frames of unknown function, and high rates of rearrangement. Paradoxically, the mutation rates are very low. However, mutation rates can only be measured in sequences that can be aligned-a very small part of plant mitochondrial genomes. Comparison of the complete mitochondrial genome sequences of two ecotypes of Arabidopsis thaliana allows the alignment of noncoding as well as coding DNA and estimation of the mutation rates in both. A recent chimeric duplication is also analyzed. A hypothesis is proposed that the mechanisms of plant mitochondrial DNA repair account for these features and includes different mechanisms in transcribed and nontranscribed regions. Within genes, a bias toward gene conversion would keep measured mutation rates low, whereas in noncoding regions, break-induced replication (BIR) explains the expansion and rearrangements. Both processes are types of double-strand break repair, but enhanced second-strand capture in transcribed regions versus BIR in nontranscribed regions can explain the two seemingly contradictory features of plant mitochondrial genome evolution-the low mutation rates in genes and the striking expansions of noncoding sequences. © The Author(s) 2013.

Fritz S.C.,University of Nebraska - Lincoln | Anderson N.J.,Loughborough University
Journal of Paleolimnology | Year: 2013

Following deglaciation, the long-term pattern of change in diatom communities and the inferred history of the aquatic environment are affected by a hierarchy of environmental controls. These include direct climate impacts on a lake's thermal and hydrologic budgets, as well as the indirect affects of climate on catchment processes, such as weathering, soil development, microbial activity, fire, and vegetation composition and productivity, which affect the transfer of solutes and particulates from the terrestrial ecosystem into the lake. Some of these catchment influences on lacustrine systems operate as time-dependent patterns of primary succession that are set in motion by glacier retreat. This paper provides a conceptual model of some dominant pathways of catchment influence on long-term lake development in glaciated regions and uses a series of paleolimnological examples from arctic, boreal, and temperate regions to evaluate the relative role of direct climate influences and of catchment processes in affecting the trajectory of aquatic ecosystems during the Holocene in different environmental contexts. © 2013 Springer Science+Business Media Dordrecht.

Wegulo S.N.,University of Nebraska - Lincoln
Toxins | Year: 2012

Deoxynivalenol (DON) is a mycotoxin produced by the plant pathogenic fungi Fusarium graminearum and F. culmorum. These and other closely related fungi cause a disease known as Fusarium head blight (FHB) in small grain cereals. Other mycotoxins produced by FHB-causing fungi include nivalenol, T-2 toxin, and zearalenone. Ingestion of mycotoxin-contaminated food and feed can lead to toxicosis in humans and animals, respectively. DON is the predominant and most economically important of these mycotoxins in the majority of small grain-producing regions of the world. This review examines the factors that influence DON accumulation in small grain cereals from an agricultural perspective. The occurrence and economic importance of FHB and DON in small grain cereals, epidemiological factors and cereal production practices that favor FHB development and DON accumulation in grain under field conditions, and regulatory/advisory standards for DON in food and feed are discussed. This information can be used to develop strategies that reduce DON accumulation in grain before harvest and to mitigate the human and animal health risks associated with DON contamination of food and feed. © 2012 by the authors; licensee MDPI, Basel, Switzerland.

Gitelson A.A.,University of Nebraska - Lincoln
International Journal of Remote Sensing | Year: 2013

Many algorithms have been developed for the remote estimation of vegetation fraction in terms of combinations of spectral bands, derivatives of reflectance spectra, neural networks, inversion of radiative transfer models, and several multispectral statistical approaches. The most widespread type of algorithm used is the mathematical combination of visible and near-infrared reflectance, in the form of spectral vegetation indices. The general objective of this study is to evaluate different vegetation indices for the remote estimation of the fractional vegetation cover in two crop types, maize and soybean, with contrasting canopy architectures and leaf structures. The noise equivalent of vegetation indices was used as an indicator of sensitivity and accuracy of vegetation fraction estimation. Among the indices tested, the enhanced vegetation index (EVI2), wide dynamic range vegetation index (WDRVI), green- and red-edge normalized difference vegetation index (NDVI) were found to be accurate in estimating vegetation fraction. These results were obtained using reflectance data acquired with close-range sensors (i.e. spectroradiometers mounted 6 m above the top of canopy). WDRVI was able to estimate vegetation fraction in both crops with no re-parameterization with RMSE below 6% and mean normalized bias below 2%. © 2013 Copyright Taylor and Francis Group, LLC.

Kovalev A.A.,University of Nebraska - Lincoln
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

We derive thermomagnonic torque and its a-typea dissipative correction from the stochastic Landau-Lifshitz-Gilbert equation. The I-type dissipative correction describes viscous coupling between magnetic dynamics and magnonic current and it stems from spin mistracking of the magnetic order. We show that thermomagnonic torque is important for describing temperature gradient induced motion of skyrmions in helical magnets while dissipative correction plays an essential role in generating transverse Magnus force. We propose to detect such skyrmionic motion by employing the transverse spin Seebeck effect geometry. © 2014 American Physical Society.

Cole K.D.,University of Nebraska - Lincoln
International Journal of Heat and Mass Transfer | Year: 2010

Simulations are presented for thermal sensing of steady laminar flow in a parallel-plate microchannel. Steady-periodic heating is introduced at the channel wall and temperatures are reported at upstream and downstream locations to represent temperature sensors. Exact analytical expressions for the temperature are given in the form of integrals, and numerical values are found by quadrature. Because axial conduction is prominent, there is a well-defined measurable flow range associated with each thermal-sensor geometry. Various fluid-flow rates, heating frequencies, sensor locations, and wall properties are explored. The results are given as a design correlation which shows the extent to which a given sensor can be tuned, by adjusting the heating frequency, to the flow-measurement range of interest. © 2009 Elsevier Ltd. All rights reserved.

Pearse I.S.,Cornell University | Koenig W.D.,Cornell University | Knops J.M.H.,University of Nebraska - Lincoln
Oikos | Year: 2014

Masting, the intermittent and synchronized production of seeds, is a common and important phenomenon throughout the plant kingdom. Surprisingly, the proximate mechanisms by which populations of masting plants synchronize their seed sets have been relatively unexplored. We examined how temperature influences the acorn crop of the valley oak Quercus lobata, a masting species common in California, USA, over 33 years in order to assess whether temperature acts directly on acorn crop as a cue or whether it acts instead through intermediate steps indicative of a direct mechanistic connection to acorn production. Compared to several alternatives, the difference in temperature during the spring flowering period over the prior two years (Δt) was a good predictor of annual acorn crop in valley oak, as proposed recently by Kelly et al. Significantly, Δt correlates positively with temperatures the previous April, a likely driver of pollination success in valley oak, and negatively with the previous year's acorn crop, which is in turn negatively correlated with the current year's acorn crop, presumably due to resource limitation. Thus, the success of Δt is not as a cue but rather explained by its close relationship to the proximate drivers that have a direct, mechanistic relationship with acorn crop size. © 2013 The Authors.

Ratcliffe B.C.,University of Nebraska - Lincoln
Coleopterists Bulletin | Year: 2013

The genus Amithao Thomson, 1878 is comprehensively revised. Redescriptions of previously known species, a key for identification, and illustrations of the 13 species are provided. Guatemalica marginicollis (Burmeister) is transferred to Amithao. The following new synonyms are established: Desicasta nonfriedi Schoch and Amithao erici Mitter are Amithao erythropus (Burmeister); Amithao thomsoni (Janson) is Amithao haematopus (Schaum); Amithao niveosparsus Moser and Amithao sparsus Casey are Amithao lafertei (Thomson); and Amithao spence (Gory and Percheron) is Amithao tristis (F.). Amithao obscurus Schoch is a female of Tiaocera rhinoceros (Gory and Percheron). Amithao staudingeri Schürhoff is rediscovered. Amithao tristis (F.) is transferred from junior to senior synonymy. Amithao anthracinus Ratcliffe from Panama is described as a new species.

Forbes V.E.,University of Nebraska - Lincoln
Integrated environmental assessment and management | Year: 2013

Ecological risk assessments (ERAs) are not used as well as they could be in risk management. Part of the problem is that they often lack ecological relevance; that is, they fail to grasp necessary ecological complexities. Adding realism and complexity can be difficult and costly. We argue that predictive systems models (PSMs) can provide a way of capturing complexity and ecological relevance cost-effectively. However, addressing complexity and ecological relevance is only part of the problem. Ecological risk assessments often fail to meet the needs of risk managers by not providing assessments that relate to protection goals and by expressing risk in ratios that cannot be weighed against the costs of interventions. Once more, PSMs can be designed to provide outputs in terms of value-relevant effects that are modulated against exposure and that can provide a better basis for decision making than arbitrary ratios or threshold values. Recent developments in the modeling and its potential for implementation by risk assessors and risk managers are beginning to demonstrate how PSMs can be practically applied in risk assessment and the advantages that doing so could have. Copyright © 2013 SETAC.

Demirel Y.,University of Nebraska - Lincoln
Journal of Non-Newtonian Fluid Mechanics | Year: 2010

Living cells represent open, nonequilibrium, self-organizing, and dissipative systems maintained with the continuous supply of outside and inside material, energy, and information flows. The energy in the form of adenosine triphosphate is utilized in biochemical cycles, transport processes, protein synthesis, reproduction, and performing other biological work. The processes in molecular and cellular biological systems are stochastic in nature with varying spatial and time scales, and bounded with conservation laws, kinetic laws, and thermodynamic constraints, which should be taken into account by any approach for modeling biological systems. In component biology, this review focuses on the modeling of enzyme kinetics and fluctuation of single biomolecules acting as molecular motors, while in systems biology it focuses on modeling biochemical cycles and networks in which all the components of a biological system interact functionally over time and space. Biochemical cycles emerge from collective and functional efforts to devise a cyclic flow of optimal energy degradation rate, which can only be described by nonequilibrium thermodynamics. Therefore, this review emphasizes the role of nonequilibrium thermodynamics through the formulations of thermodynamically coupled biochemical cycles, entropy production, fluctuation theorems, bioenergetics, and reaction-diffusion systems. Fluctuation theorems relate the forward and backward dynamical randomness of the trajectories or paths, bridge the microscopic and macroscopic domains, and link the time-reversible and irreversible descriptions of biological systems. However, many of these approaches are in their early stages of their development and no single computational or experimental technique is able to span all the relevant and necessary spatial and temporal scales. Wide range of experimental and novel computational techniques with high accuracy, precision, coverage, and efficiency are necessary for understanding biochemical cycles. © 2010 Elsevier B.V.

Koenig W.D.,Cornell University | Knops J.M.H.,University of Nebraska - Lincoln
Ecology | Year: 2013

Seed production that varies greatly from year to year, known as 'masting' or 'mast-fruiting' behavior, is a population-level phenomenon known to exhibit geographic synchrony extending, at least in some cases, hundreds of kilometers. The two main nonexclusive hypotheses for the driver of such geographically extensive synchrony are (1) environmental factors (the Moran effect), and (2) the mutual dependence of trees on outcrossed pollen (pollen coupling). We tested 10 predictions relevant to these two hypotheses using 18 years of acorn production data on two species of California oaks. Data were obtained across the entire ranges of the two species at 12 sites (10 for each species) separated by up to 745 km. In general, our results provided strong support for the importance of the Moran effect as a driver of spatial synchrony in and between these two species. Particularly compelling was evidence of close concordance between spatial synchrony in acorn production and key environmental factors extending over the range of both species and significant spatial cross-synchrony between the two species, despite considerable differences in their geographical ecology. Because oaks are monoecious, female flowers are not necessarily related to pollen production, and thus, our tests do not address the role of pollen coupling in bisexual species where pollen and flower production are necessarily correlated. For the oak species considered here, however, the Moran effect is a key driver of large-scale spatial synchrony in acorn production. © 2013 by the Ecological Society of America.

Niu W.-N.,Northwestern Polytechnical University | Yadav P.K.,University of Michigan | Adamec J.,University of Nebraska - Lincoln | Banerjee R.,University of Michigan
Antioxidants and Redox Signaling | Year: 2015

Aims: Cystathionine β-synthase (CBS) catalyzes the first and rate-limiting step in the two-step trans-sulfuration pathway that converts homocysteine to cysteine. It is also one of three major enzymes responsible for the biogenesis of H2S, a signaling molecule. We have previously demonstrated that CBS is activated in cells challenged by oxidative stress, but the underlying molecular mechanism of this regulation has remained unclear. Results: Here, we demonstrate that S-glutathionylation of CBS enhances its activity ∼2-fold in vitro. Loss of this post-translational modification in the presence of dithiothreitol results in reversal to basal activity. Cys346 was identified as the site for S-glutathionylation by a combination of mass spectrometric, mutagenesis, and activity analyses. To test the physiological relevance of S-glutathionylation-dependent regulation of CBS, HEK293 cells were oxidatively challenged with peroxide, which is known to enhance the trans-sulfuration flux. Under these conditions, CBS glutathionylation levels increased and were correlated with a ∼3-fold increase in CBS activity. Innovation: Collectively, our results reveal a novel post-translational modification of CBS, that is, glutathionylation, which functions as an allosteric activator under oxidative stress conditions permitting enhanced synthesis of both cysteine and H2S. Conclusions: Our study elucidates a molecular mechanism for increased cysteine and therefore glutathione, synthesis via glutathionylation of CBS. They also demonstrate the potential for increased H2S production under oxidative stress conditions, particularly in tissues where CBS is a major source of H2S. Antioxid. Redox Signal. 22, 350-361. © Copyright 2015, Mary Ann Liebert, Inc. 2015.

Goodrich C.S.,University of Nebraska - Lincoln
International Journal of Dynamical Systems and Differential Equations | Year: 2011

In this paper, we introduce several existence theorems for a discrete fractional boundary value problem with Dirichlet boundary conditions in the case where the order ? of the fractional difference satisfies 1 < v ≤ 2. We use cone theoretic techniques to deduce the existence of one or more positive solutions. We then deduce uniqueness theorems for the same problem by assuming a Lipschitz condition. We show that many of the classical existence and uniqueness theorems for second-order discrete boundary value problems extend to the fractional-order case. Copyright © 2011 Inderscience Enterprises Ltd.

Holm M.,University of Nebraska - Lincoln
International Journal of Dynamical Systems and Differential Equations | Year: 2011

We consider a discrete, nonlinear, (N - 1, 1) fractional-order boundary value problem in one variable with a fractional-order derivative specified as the right boundary condition. We first derive and establish properties of the corresponding Green's function and then apply these properties - together with Krasnosel'skii's Theorem and Banach's Contraction Mapping Theorem - to show the existence of a positive solution to the given problem. Copyright © 2011 Inderscience Enterprises Ltd.

Demirel Y.,University of Nebraska - Lincoln
Entropy | Year: 2014

Some critical trends in information theory, its role in living systems and utilization in fluctuation theory are discussed. The mutual information of thermodynamic coupling is incorporated into the generalized fluctuation theorem by using information theory and nonequilibrium thermodynamics. Thermodynamically coupled dissipative structures in living systems are capable of degrading more energy, and processing complex information through developmental and environmental constraints. The generalized fluctuation theorem can quantify the hysteresis observed in the amount of the irreversible work in nonequilibrium regimes in the presence of information and thermodynamic coupling. © 2014 by the authors.

Wei T.,University of Nebraska - Lincoln | Mark R.,United States Swimming | Hutchison S.,IKKOS
Annual Review of Fluid Mechanics | Year: 2014

Nowhere in sport is performance so dependent on the interaction of the athlete with the surrounding medium than in competitive swimming. As a result, understanding (at least implicitly) and controlling (explicitly) the fluid dynamics of swimming are essential to earning a spot on the medal stand. This is an extremely complex, highly multidisciplinary problem with a broad spectrum of research approaches. This review attempts to provide a historical framework for the fluid dynamics-related aspects of human swimming research, principally conducted roughly over the past five decades, with an emphasis on the past 25 years. The literature is organized below to show a continuous integration of computational and experimental technologies into the sport. Illustrations from the authors' collaborations over a 10-year period, coupling the knowledge and experience of an elite-level coach, a lead biomechanician at USA Swimming, and an experimental fluid dynamicist, are intended to bring relevance and immediacy to the review. Copyright © 2014 by Annual Reviews. All rights reserved.

Bovine viral diarrhea virus (BVDV) continues to be of economic significance to the livestock industry in terms of acute disease and fetal loss. Many of the lesions relating to BVDV infection have been well described previously. The virus is perpetuated in herds through the presence of calves that are persistently infected. Relationships between various species and biotypes of BVDV and host defenses are increasingly understood. Understanding of the host defense mechanisms of innate immunity and adaptive immunity continues to improve, and the effects of the virus on these immune mechanisms are being used to explain how persistent infection develops. The noncytopathic biotype of BVDV plays the major role in its effects on the host defenses by inhibiting various aspects of the innate immune system and creation of immunotolerance in the fetus during early gestation. Recent advances have allowed for development of affordable test strategies to identify and remove persistently infected animals. With these improved tests and removal strategies, the livestock industry can begin more widespread effective control programs. © The Author(s) 2014.

Christensen A.C.,University of Nebraska - Lincoln
Genome biology and evolution | Year: 2014

Plant mitochondrial genomes have very low mutation rates. In contrast, they also rearrange and expand frequently. This is easily understood if DNA repair in genes is accomplished by accurate mechanisms, whereas less accurate mechanisms including nonhomologous end joining or break-induced replication are used in nongenes. An important question is how different mechanisms of repair predominate in coding and noncoding DNA, although one possible mechanism is transcription-coupled repair (TCR). This work tests the predictions of TCR and finds no support for it. Examination of the mutation spectra and rates in genes and junk reveals what DNA repair mechanisms are available to plant mitochondria, and what selective forces act on the repair products. A model is proposed that mismatches and other DNA damages are repaired by converting them into double-strand breaks (DSBs). These can then be repaired by any of the DSB repair mechanisms, both accurate and inaccurate. Natural selection will eliminate coding regions repaired by inaccurate mechanisms, accounting for the low mutation rates in genes, whereas mutations, rearrangements, and expansions generated by inaccurate repair in noncoding regions will persist. Support for this model includes the structure of the mitochondrial mutS homolog in plants, which is fused to a double-strand endonuclease. The model proposes that plant mitochondria do not distinguish a damaged or mismatched DNA strand from the undamaged strand, they simply cut both strands and perform homology-based DSB repair. This plant-specific strategy for protecting future generations from mitochondrial DNA damage has the side effect of genome expansions and rearrangements. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Hu R.Q.,Utah State University | Qian Y.,University of Nebraska - Lincoln
IEEE Communications Magazine | Year: 2014

In this article we explore a system framework of cooperative green heterogeneous networks for 5G wireless communication systems. We first survey the state-of-the-art on spectrum efficiency (SE), energy efficiency (EE), and quality of service (QoS) based mobile association, multi-layer interference management and power control, network wide cooperation and dynamic resource allocation for heterogeneous wireless networks. We also present the system framework of cooperative green heterogeneous networks, which aims at balancing and optimizing SE, EE, and QoS in heterogeneous wireless networks. We discuss the design principles and show some preliminary performance results on the tradeoffs among SE, EE, and QoS. Finally, we identify the technical challenges that remain in the cooperative green heterogeneous network design. The presented wireless system framework is expected to advance the understandings of the critical technical issues toward energy and spectrum efficient 5G wireless communication systems. © 2014 IEEE.

Wei L.,Utah State University | Hu R.Q.,Utah State University | Qian Y.,University of Nebraska - Lincoln | Wu G.,Intel Corporation
IEEE Communications Magazine | Year: 2014

Device-to-device communication underlaying a cellular network is a promising technology in future wireless networks to improve network capacity and user experience. While D2D communication has great potential to improve wireless system spectral and energy efficiency due to the proximity of communication parties and higher spectrum reuse gain, tremendous work is still ongoing to turn the promising technology into a reality. This article discusses D2D technical challenges as well as standards progress and important research aspects that enable D2D communications underlaying cellular networks. The key research areas addressed include interference management, multihop D2D communications, and D2D communications in heterogeneous networks. When enabling D2D communications underlaying cellular networks, D2D communications can use either cellular downlink or cellular uplink resources. The two resource sharing modes will create different interference scenarios. The performance evaluation on D2D communications underlaying cellular networks under these two different scenarios is provided. © 1979-2012 IEEE.

Mills M.,University of Nebraska - Lincoln
Journal of vision | Year: 2011

The purpose of the present study was to examine the influence of task set on the spatial and temporal characteristics of eye movements during scene perception. In previous work, when strong control was exerted over the viewing task via specification of a target object (as in visual search), task set biased spatial, rather than temporal, parameters of eye movements. Here, we find that more participant-directed tasks (in which the task establishes general goals of viewing rather than specific objects to fixate) affect not only spatial (e.g., saccade amplitude) but also temporal parameters (e.g., fixation duration). Further, task set influenced the rate of change in fixation duration over the course of viewing but not saccade amplitude, suggesting independent mechanisms for control of these parameters. © ARVO

Wu M.,Huazhong University of Science and Technology | Fu H.,Huazhong University of Science and Technology | Zhou L.,Miami University Ohio | Yao K.,Huazhong University of Science and Technology | Zeng X.C.,University of Nebraska - Lincoln
Nano Letters | Year: 2015

We predict a new class of monolayer phosphorus allotropes, namely, ε-P, ζ-P, η-P, and η-P. Distinctly different from the monolayer α-P (black) and previously predicted β-P (Phys. Rev. Lett. 2014, 112, 176802), γ-P, and δ-P (Phys. Rev. Lett. 2014, 113, 046804) with buckled honeycomb lattice, the new allotropes are composed of P4 square or P5 pentagon units that favor tricoordination for P atoms. The new four polymorphs, together with five additional hybrid polymorphs, greatly enrich the phosphorene structures, and their stabilities are confirmed by first-principles calculations. In particular, the η-P is shown to be equally stable as the α-P (black) and more stable than all previously reported phosphorene polymorphs. Prediction of nonvolatile ferroelastic switching and structural transformation among different polymorphs under strains points out their potential applications via strain engineering. © 2015 American Chemical Society.

King C.,University of Nebraska - Lincoln
Review of Economics of the Household | Year: 2016

Reducing the prevalence of household food insecurity has been a long-standing objective of the federal government. Previous research has found many negative consequences of food insecurity for families and households but has not examined its relationship with housing instability. Using longitudinal data from the Fragile Families and Child Wellbeing Study, difference-in-difference models show that food insecurity is associated with housing instability. The association remains statistically significant after accounting for potential selection and unobserved heterogeneity using propensity score matching and excluding households that experienced prior housing instability from the sample. Examining potential mediating factors, I find that material hardship explains about half of this association. These findings suggest that maintaining a strong social safety net would reduce the risk that families experience material hardship and housing instability, which may also reduce the risk of homelessness. © 2016 Springer Science+Business Media New York

Gonzalez-Munoz E.,Centro Andaluz Of Nanomedicina Y Biotecnologia Andalucia | Arboleda-Estudillo Y.,Centro Andaluz Of Nanomedicina Y Biotecnologia Andalucia | Otu H.H.,Istanbul Bilgi University | Otu H.H.,University of Nebraska - Lincoln | And 2 more authors.
Science | Year: 2014

Unfertilized oocytes have the intrinsic capacity to remodel sperm and the nuclei of somatic cells. The discoveries that cells can change their phenotype from differentiated to embryonic state using oocytes or specific transcription factors have been recognized as two major breakthroughs in the biomedical field. Here, we show that ASF1A, a histone-remodeling chaperone specifically enriched in the metaphase II human oocyte, is necessary for reprogramming of human adult dermal fibroblasts (hADFs) into undifferentiated induced pluripotent stem cell. We also show that overexpression of just ASF1A and OCT4 in hADFs exposed to the oocyte-specific paracrine growth factor GDF9 can reprogram hADFs into pluripotent cells. Our Report underscores the importance of studying the unfertilized MII oocyte as a means to understand the molecular pathways governing somatic cell reprogramming.

Kim Y.-R.,University of Nebraska - Lincoln
International Journal of Pavement Engineering | Year: 2011

Cohesive zone (CZ) modelling has been receiving increasing attention from the asphaltic materials and pavement mechanics community as a mechanistic approach to model crack initiation and propagation in materials and structures. The CZ model provides a powerful and efficient tool that can be easily implemented in existing computational methods for brittle, quasi-brittle and ductile failure as well as interfacial fracture, all of which are frequently observed in asphaltic materials. Accordingly, this paper introduces the CZ modelling approach in the form of a state-of-the-art review addressing the concept of CZ modelling, CZ constitutive relations, their implementation into computational methods and up-to-date applications of CZ modelling to bituminous mixtures and pavement structures. This paper also includes a brief discussion on the current challenges that researchers face and the future directions to the modelling of fracture in bituminous materials and pavements. CZ modelling is not a topic that can be possibly discussed in a single article; therefore, it should be clearly noted that this review primarily attempts to deliver some of the core aspects of CZ modelling in the area of bituminous composites. © 2011 Taylor & Francis.

Von der Dunk F.G.,University of Nebraska - Lincoln
Space Policy | Year: 2011

The arrival of 'space tourism', or more appropriately 'private spaceflight', requires the law of outer space to change and adapt to this revolutionary development, as deriving precisely from the principled private participation in these activities. After defining the proper concepts, this paper discusses key legal aspects of authorisation and supervision, liability and registration, and how they reflect and impact on space tourism. Key legal aspects related to certification of craft, crew and passengers, while not yet much articulated at the international level will also be touched upon precisely in order to demonstrate that the law could well be driven first and foremost by national legislative interests on a domestic level, before (possibly) reaching the level of international law. The possible use of air law or even adventure tourism law to regulate relevant activities is also touched on. © 2011.

O'Connell S.,Wesleyan University | Holmes M.A.,University of Nebraska - Lincoln
GSA Today | Year: 2011

The lack of geoscience undergraduates has been attributed to many factors, especially precollege exposure. Undergraduate experiences attract most geoscientists to the major. An informal survey of members of the National Association for Black Geologists and Geophysicists found that its members were attracted by a positive undergraduate experience. Geoscientists celebrate their connection with the outdoors, but a survey of 620 high school and college students taking a geoscience course in California revealed little outdoor appeal to underrepresented minority students. The lack of participation by Hispanics in outdoor activities like fishing, canoeing, backpacking, or birdwatching has been noted by marketing agencies. Geoscientists need to increase exposure to the geosciences and geoscience careers at all educational levels. Precollege, successful afterschool, outdoor, and parent programs can increase awareness and relevance of the geosciences. It is likely, therefore, that underrepresented minorities may find geoscience's emphasis on fieldwork and the outdoors a deterrent to majoring in the discipline.

McQuaid R.G.P.,Queens University of Belfast | Gruverman A.,University of Nebraska - Lincoln | Scott J.F.,University of Cambridge | Gregg J.M.,Queens University of Belfast
Nano Letters | Year: 2014

Using piezoresponse force microscopy, we have observed the progressive development of ferroelectric flux-closure domain structures and Landau-Kittel-type domain patterns, in 300 nm thick single-crystal BaTiO 3 platelets. As the microstructural development proceeds, the rate of change of the domain configuration is seen to decrease exponentially. Nevertheless, domain wall velocities throughout are commensurate with creep processes in oxide ferroelectrics. Progressive screening of macroscopic destabilizing fields, primarily the surface-related depolarizing field, successfully describes the main features of the observed kinetics. Changes in the separation of domain-wall vertex junctions prompt a consideration that vertex-vertex interactions could be influencing the measured kinetics. However, the expected dynamic signatures associated with direct vertex-vertex interactions are not resolved. If present, our measurements confine the length scale for interaction between vertices to the order of a few hundred nanometers. © 2014 American Chemical Society.

Bahar E.,University of Nebraska - Lincoln
Journal of the Optical Society of America A: Optics and Image Science, and Vision | Year: 2010

The common definition of the Brewster angles for dielectric and magnetic achiral materials are the angles at which the vertically and horizontally polarized reflection coefficients vanish. We examine broader definitions of the Brewster conditions for waves that are incident on a free-space-chiral interface. Besides the common definition, the Brewster angles have been defined as the angles at which the polarizations of the reflected waves are independent of the polarizations of the incident waves. We consider total transmission of incident plane waves that satisfy the Brewster conditions at a free-space-chiral medium planar interface. In this case we determine the polarization of the incident wave for which the reflected vertically and horizontally polarized waves vanish simultaneously. Thus with this definition of the Brewster conditions the polarization of the reflected wave is undefined. The conditions for the excitation of surface waves are considered. The characteristic polarizations that are the same for the reflected and incident waves are also examined subject to the Brewster conditions. Potential applications of this analysis are to experimentally determine the chiral or geotropic measure of the medium and to identify and characterize biological and chemical materials through their optical activity in real time. Several independent measurements can be taken with the same polarimetric instrument to avoid false identifications. Since measurements can be conducted in the reflection mode they can be nonintrusive. © 2010 Optical Society of America.

Berry V.,Kansas State University | Saraf R.F.,University of Nebraska - Lincoln
Small | Year: 2011

Using an electrostatic self-assembly process, metal nanoparticles are deposited on polyelectrolyte fibers such that the interparticle distance between the nanoparticles is comparable to the polyelectrolyte's molecular width. By modulating the dielectric properties of the interparticle polymer layer, a highly sensitive, reversible humidity sensor with an ultrafast response time of ≈3 ms is demonstrated. The higher sensitivity at low humidity shows a conductivity increase by over two orders of magnitude in response to a change in relative humidity from 21 to 1%. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Brooks D.W.,University of Nebraska - Lincoln
Chemistry Education Research and Practice | Year: 2012

While lecture demonstrations have been conducted in chemistry classrooms for hundreds of years, little research exists to document the frequency with which such demonstrations are employed or their effect on learners' motivation and performance. A mixed-methods research study was performed, using quantitative and qualitative survey data, along with qualitative data from follow-up interviews and structured email correspondence. Fifty-two randomly selected chemistry teachers completed a survey regarding their present and projected use of classroom demonstrations. Twelve of the survey participants provided elaboration in the form of an extended questionnaire. Data indicate that all except one of the survey participants currently employ lecture demonstrations, and all anticipate performing the same number of, or more, demonstrations in their future instruction. Extended questionnaire and survey data reveal that the participating chemistry teachers perceive substantial positive effects on students' performance on classroom assignments and a lesser, though still positive, effect, on learners' motivation. No correlations were observed between the number of lecture demonstrations performed and educators' years of experience teaching chemistry, previous exposure to demonstrations, or undergraduate degrees earned. This journal is © The Royal Society of Chemistry.

Somerville G.A.,University of Nebraska - Lincoln | Proctor R.A.,University of Wisconsin - Madison
BMC Microbiology | Year: 2013

Bacterial cultivation requires consideration of three things: The bacterial strain, cultivation medium, and cultivation conditions. Most microbiologists dutifully report their choice of strains and cultivation media in manuscripts; however, these same microbiologists often overlook reporting cultivation conditions. Without this information, it is difficult to determine if cultures were grown aerobically, microaerobically, or anaerobically. To cultivate bacteria aerobically, it is necessary to understand that oxygen does not readily diffuse into culture media; it needs help to get in. Microbiologists can do this by altering the flask-to-medium ratio, rpm of agitation, and/or the concentration of atmospheric oxygen, or by using baffled flasks. © 2013 Somerville and Proctor.

Harris S.D.,University of Nebraska - Lincoln
Fungal Biology | Year: 2011

Two modes of cellular morphogenesis predominate within the fungal kingdom; yeast growth and hyphal growth. The availability of complete genome sequences that span the kingdom has made possible the use of comparative approaches that address important questions regarding the evolution of these growth modes. These comparisons have also emphasized the point that not all hyphae are the same despite outward appearances. Topics considered here include the origins of hyphal growth, as well as the potential causes of and the consequences resulting from the loss of hyphal growth in yeast lineages. The mechanisms that enable distinct morphological outputs (i.e., yeast vs. hyphae) using an essentially identical inventory of gene products are also considered. Finally, processes implicated in the regulation of hyphal tip complexes are addressed from an evolutionary perspective. © 2011 The British Mycological Society.

Berlin K.S.,University of Memphis | Parra G.R.,University of Southern Mississippi | Williams N.A.,University of Nebraska - Lincoln
Journal of Pediatric Psychology | Year: 2014

Objective Pediatric psychologists are often interested in finding patterns in heterogeneous longitudinal data. Latent variable mixture modeling is an emerging statistical approach that models such heterogeneity by classifying individuals into unobserved groupings (latent classes) with similar (more homogenous) patterns. The purpose of the second of a 2-article set is to offer a nontechnical introduction to longitudinal latent variable mixture modeling. Methods 3 latent variable approaches to modeling longitudinal data are reviewed and distinguished. Results Step-by-step pediatric psychology examples of latent growth curve modeling, latent class growth analysis, and growth mixture modeling are provided using the Early Childhood Longitudinal Study-Kindergarten Class of 1998-1999 data file. Conclusions Latent variable mixture modeling is a technique that is useful to pediatric psychologists who wish to find groupings of individuals who share similar longitudinal data patterns to determine the extent to which these patterns may relate to variables of interest. © The Author 2013. Published by Oxford University Press on behalf of the Society of Pediatric Psychology. All rights reserved.

Veliz-Cuba A.,University of Nebraska - Lincoln | Stigler B.,Southern Methodist University
Journal of Computational Biology | Year: 2011

The lac operon in Escherichia coli has been studied extensively and is one of the earliest gene systems found to undergo both positive and negative control. The lac operon is known to exhibit bistability, in the sense that the operon is either induced or uninduced. Many dynamical models have been proposed to capture this phenomenon. While most are based on complex mathematical formulations, it has been suggested that for other gene systems network topology is sufficient to produce the desired dynamical behavior. We present a Boolean network as a discrete model for the lac operon. Our model includes the two main glucose control mechanisms of catabolite repression and inducer exclusion. We show that this Boolean model is capable of predicting the ON and OFF steady states and bistability. Further, we present a reduced model which shows that lac mRNA and lactose form the core of the lac operon, and that this reduced model exhibits the same dynamics. This work suggests that the key to model qualitative dynamics of gene systems is the topology of the network and Boolean models are well suited for this purpose. Supplementary Material is available online at www.libertonline.com/cmb. © Copyright 2011, Mary Ann Liebert, Inc.

Roche M.,University of Waikato | Haar J.M.,Massey University | Luthans F.,University of Nebraska - Lincoln
Journal of Occupational Health Psychology | Year: 2014

In today's highly competitive and extremely complex global economy, organizational leaders at all levels are facing unprecedented challenges. Yet, some seem to be handling the pressure better than others. Utilizing 4 samples of CEOs/presidents/top (n = 205), middle (n = 183), and junior (n = 202) managers, as well as 107 entrepreneurs, using Structural Equation Modeling we tested the direct effect that their level of mindfulness (heightened awareness) and the mediating effect of their psychological capital (i.e., hope, efficacy, resilience, and optimism) may have on their mental well-being. In all 4 samples, mindfulness was found to be negatively related to various dysfunctional outcomes such as anxiety, depression, and negative affect of the managerial leaders and burnout (i.e., emotional exhaustion and cynicism) of the entrepreneurs. For all 4 samples, the model with psychological capital mediating the effects of mindfulness on dysfunctional outcomes fit the data best. The study limitations, future research and practical implications of these findings conclude the article. © 2014 American Psychological Association.

Wu M.,Huazhong University of Science and Technology | Zeng X.C.,University of Nebraska - Lincoln
Nano Letters | Year: 2016

Phosphorene and phosphorene analogues such as SnS and SnSe monolayers are promising nanoelectronic materials with desired bandgap, high carrier mobility, and anisotropic structures. Here, we show first-principles calculation evidence that these monolayers are potentially the long-sought two-dimensional (2D) materials that can combine electronic transistor characteristic with nonvolatile memory readable/writeable capability at ambient condition. Specifically, phosphorene is predicted to be a 2D intrinsic ferroelastic material with ultrahigh reversible strain, whereas SnS, SnSe, GeS, and GeSe monolayers are multiferroic with coupled ferroelectricity and ferroelasticity. Moreover, their low-switching barriers render room-temperature nonvolatile memory accessible, and their notable structural anisotropy enables ferroelastic or ferroelectric switching readily readable via electrical, thermal, optical, mechanical, or even spintronic detection upon the swapping of the zigzag and armchair direction. In addition, it is predicted that the GeS and GeSe monolayers as well as bulk SnS and SnSe can maintain their ferroelasticity and ferroelectricity (anti-ferroelectricity) beyond the room temperature, suggesting high potential for practical device application. © 2016 American Chemical Society.

Walker M.E.,University of Nebraska - Lincoln
Selecta Mathematica, New Series | Year: 2016

We develop a theory of “ad hoc” Chern characters for twisted matrix factorizations associated to a scheme X, a line bundle L, and a regular global section W∈ Γ(X, L). As an application, we establish the vanishing, in certain cases, of hcR(M,N), the higher Herbrand difference, and, ηcR(M,N), the higher codimensional analogue of Hochster’s theta pairing, where R is a complete intersection of codimension c with isolated singularities and M and N are finitely generated R-modules. Specifically, we prove such vanishing if R= Q/(f1, ⋯ , fc) has only isolated singularities, Q is a smooth k-algebra, k is a field of characteristic 0, the fi’s form a regular sequence, and c≥ 2. Such vanishing was previously established in the general characteristic, but graded, setting in Moore et al. (Math Z 273(3–4):907–920, 2013). © 2016, Springer International Publishing.

Onstad D.W.,Urbana University | Meinke L.J.,University of Nebraska - Lincoln
Journal of Economic Entomology | Year: 2010

A simulation model of the population dynamics and genetics of western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), was created to evaluate the use of refuges in the management of resistance to transgenic insecticidal corn, Zea mays L., expressing one or two toxin traits. Hypothetical scenarios and a case study of a corn hybrid pyramided with existing toxins are simulated. In the hypothetical situations, results demonstrated that evolution is generally delayed by pyramids compared with deployment of a single-toxin corn hybrid. However, soil insecticide use in the refuge reduced this delay and quickened the evolution of resistance. Results were sensitive to the degree of male beetle dispersal before mating and to the effectiveness of both toxins in the pyramid. Resistance evolved faster as fecundity increased for survivors of insecticidal corn. Thus, effects on fecundity must be measured to predict which resistance management plans will work well. Evolution of resistance also occurred faster if the survival rate due to exposure to the two toxins was not calculated by multiplication of two independent survival rates (one for each insect gene) but was equivalent to the minimum of the two. Furthermore, when single-trait and pyramided corn hybrids were planted within rootworm-dispersal distance of each other, the toxin traits lost efficacy more quickly than they did in scenarios without single-trait corn. For the case study involving transgenic corn expressing Cry34/35Ab1 and Cry3Bb1, the pyramid delayed evolution longer than a single trait corn hybrid and longer than a sequence of toxins based on at least one resistance-allele frequency remaining below 50%. Results are discussed within the context of a changing transgenic corn marketplace and the landscape dynamics of resistance management. © 2010 Entomological Society of America.

Grass G.,University of Nebraska - Lincoln | Rensing C.,University of Arizona | Solioz M.,University of Bern
Applied and Environmental Microbiology | Year: 2011

Bacteria, yeasts, and viruses are rapidly killed on metallic copper surfaces, and the term "contact killing" has been coined for this process. While the phenomenon was already known in ancient times, it is currently receiving renewed attention. This is due to the potential use of copper as an antibacterial material in health care settings. Contact killing was observed to take place at a rate of at least 7 to 8 logs per hour, and no live microorganisms were generally recovered from copper surfaces after prolonged incubation. The antimicrobial activity of copper and copper alloys is now well established, and copper has recently been registered at the U.S. Environmental Protection Agency as the first solid antimicrobial material. In several clinical studies, copper has been evaluated for use on touch surfaces, such as door handles, bathroom fixtures, or bed rails, in attempts to curb nosocomial infections. In connection to these new applications of copper, it is important to understand the mechanism of contact killing since it may bear on central issues, such as the possibility of the emergence and spread of resistant organisms, cleaning procedures, and questions of material and object engineering. Recent work has shed light on mechanistic aspects of contact killing. These findings will be reviewed here and juxtaposed with the toxicity mechanisms of ionic copper. The merit of copper as a hygienic material in hospitals and related settings will also be discussed. © 2011, American Society for Microbiology.

Gota M.,University of Nebraska - Lincoln | Gianola D.,University of Wisconsin - Madison
Frontiers in Genetics | Year: 2014

Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright's models to confront new challenges. In particular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways), thus generating interactions. Motivated by this view, a growing number of statistical approaches based on kernels attempt to capture non-additive effects, either parametrically or non-parametrically. This review centers on whole-genome regression using kernel methods applied to a wide range of quantitative traits of agricultural importance in animals and plants. We discuss various kernel-based approaches tailored to capturing total genetic variation, with the aim of arriving at an enhanced predictive performance in the light of available genome annotation information. Connections between prediction machines born in animal breeding, statistics, and machine learning are revisited, and their empirical prediction performance is discussed. Overall, while some encouraging results have been obtained with non-parametric kernels, recovering non-additive genetic variation in a validation dataset remains a challenge in quantitative genetics. © 2014 Morota and Gianola.

Muchhala N.,University of Nebraska - Lincoln | Thomson J.D.,University of Toronto
Functional Ecology | Year: 2012

Although competition for pollination is often invoked as a driver of broad-scale evolutionary and ecological patterns, we still lack a clear understanding of the mechanics of such competition. When flower visitors alternate between two species of flower, heterospecific pollen transfer takes place. The impact of these mixed loads on the female reproductive success of a recipient has received considerable attention, but the concomitant loss of male reproductive success - because of pollens grains being lost to foreign stigmas - has received less. Furthermore, pollen losses are not limited to grains that land on stigmas, but can also include deposition on non-stigmatic surfaces of the intervening flowers, or loss from the animal's body through passive detachment or active grooming. We collectively term these losses because of competition 'pollen misplacement'. Here, we quantify pollen transferred by nectar bats between focal flowers (Aphelandra acanthus) with and without intervening visits to one of two competitor species. One competitor (Centropogon nigricans) places its pollen in the same region of bats' heads as the focal species, while the other (Burmeistera sodiroana) places its pollen farther forward. We found that (i) any intervening visit caused some reduction in the number of pollen grains transferred, (ii) competitor flowers with similar pollen-placement locations caused greater reductions in pollen transfer and (iii) of these competitors, those in male phase (dispensing pollen) caused greater pollen loss than those in female phase (without pollen). This study provides rare empirical support for the detrimental effects of competition for pollination on male fitness via pollen misplacement and is the first to show an added cost imposed by male-phase competitors. Although this competition is especially strong when competitors overlap in pollen placement, diverging in pollen placement will not completely eliminate pollen loss during visits to foreign flowers, simply because pollen sheds or is groomed from pollinator's bodies at some background rate over time. This suggests that any angiosperms that share pollinators face pervasive selection through male fitness to diverge in floral traits, alleviating competition by attracting different pollinators, altering floral phenology or encouraging floral constancy. © 2012 The Authors. Functional Ecology © 2012 British Ecological Society.

Irmak S.,University of Nebraska - Lincoln
Journal of Irrigation and Drainage Engineering | Year: 2011

The magnitude and driving forces of nocturnal evaporative losses, ET cnight , and the interactions of other surface energy fluxes and microclimatic variables under various climatic, soil, and management conditions are not well understood. Such relationships are important for ecophysiological studies. This research attempts to investigate such relationships. Furthermore, ET cnight can be a sizable portion of the daily total evaporative losses. Most empirical equations, especially ones that use solar or net radiation to estimate daily evapotranspiration (ET), either ignore or poorly treat the contribution of ET cnight to the daily total ET. Neglecting ET cnight can lead to errors in determining the daily or the sum-of-hourly ET c (i.e., ET cSOH) and can also cause cumulative errors when making long-term water balance analyses. In this paper, the magnitudes, trends, and contribution to the nocturnal surface energy balance of various microclimatic variables (air temperature, T a; vapor pressure deficit, VPD; relative humidity, RH; and wind speed at 3 m, u 3) and surface energy fluxes (ET cnight; soil heat flux, G; sensible heat flux, H; and net radiation, R n); were quantified and interpreted for a nonstressed and subsurface-drip-irrigated maize canopy. The effect of microclimatic variables and surface energy flux components on the Bowen ratio energy balance system (BREBS)-measured ET cnight and daytime evaporative loss, ETcday , were investigated in the growing season of 2005 (i.e., April 22-September 30) and 2006 (May 12-September 27). The nighttime evaporative losses were high early in the season during partial canopy closure because of increased surface soil evaporation and were also high later in the season during and after leaf aging, physiological maturity, and leaf senescence. The seasonal average nighttime evaporative losses for 2005 and 2006 were 0.19 and 0:11 mm=night, respectively. Losses of 0.50 mm or more occurred in 2005 and 2006 on eight and seven nights, respectively. The seasonal total ETcnight , ET cday , and ET cSOH in 2005 were 31, 612, and 642 mm, respectively. The ET c values in 2006 were 16, 533, and 547 mm, respectively. In both years, the percent ratio of ET cday to ET cSOH usually was more than 80-85%. ET cnight was affected primarily by u 3, VPD, and T a. A strong relationship between ET cnight and nighttime sensible heat was observed. Some of the largest ratios of ET cnight to ET cSOH occurred on rainy nights with strong winds. Because of strong winds, the ET cnight was high owing to the clear coupling among all energy exchanges within and above the canopy as a result of the mixing of the lower boundary layer of the microclimate. The results of this study showed that the ET cnight can be up to 5% of the ET cSOH , even for a subsurface-drip-irrigated maize canopy in which the soil surface is usually dry, thus, less evaporative losses potential compared with the surface or sprinkler-irrigated surfaces in which ET cnight would be expected to be considerably higher because of wetter surface conditions. ET cnight needs to be quantified for different vegetation surfaces and management practices, surface wetting, and climatic conditions to better account for nighttime water losses and better understand nighttime energy balance mechanisms. © 2011 American Society of Civil Engineers.

Alvarez-Venegas R.,CINVESTAV | Avramova Z.,University of Nebraska - Lincoln
BMC Evolutionary Biology | Year: 2012

Background: Conserved domains are recognized as the building blocks of eukaryotic proteins. Domains showing a tendency to occur in diverse combinations ('promiscuous' domains) are involved in versatile architectures in proteins with different functions. Current models, based on global-level analyses of domain combinations in multiple genomes, have suggested that the propensity of some domains to associate with other domains in high-level architectures increases with organismal complexity. Alternative models using domain-based phylogenetic trees propose that domains have become promiscuous independently in different lineages through convergent evolution and are, thus, random with no functional or structural preferences. Here we test whether complex protein architectures have occurred by accretion from simpler systems and whether the appearance of multidomain combinations parallels organismal complexity. As a model, we analyze the modular evolution of the PWWP domain and ask whether its appearance in combinations with other domains into multidomain architectures is linked with the occurrence of more complex life-forms. Whether high-level combinations of domains are conserved and transmitted as stable units (cassettes) through evolution is examined in the genomes of plant or metazoan species selected for their established position in the evolution of the respective lineages. Results: Using the domain-tree approach, we analyze the evolutionary origins and distribution patterns of the promiscuous PWWP domain to understand the principles of its modular evolution and its existence in combination with other domains in higher-level protein architectures. We found that as a single module the PWWP domain occurs only in proteins with a limited, mainly, species-specific distribution. Earlier, it was suggested that domain promiscuity is a fast-changing (volatile) feature shaped by natural selection and that only a few domains retain their promiscuity status throughout evolution. In contrast, our data show that most of the multidomain PWWP combinations in extant multicellular organisms (humans or land plants) are present in their unicellular ancestral relatives suggesting they have been transmitted through evolution as conserved linear arrangements ('cassettes'). Among the most interesting biologically relevant results is the finding that the genes of the two plant Trithorax family subgroups (ATX1/2 and ATX3/4/5) have different phylogenetic origins. The two subgroups occur together in the earliest land plants Physcomitrella patens and Selaginella moellendorffii. Conclusion: Gain/loss of a single PWWP domain is observed throughout evolution reflecting dynamic lineage- or species-specific events. In contrast, higher-level protein architectures involving the PWWP domain have survived as stable arrangements driven by evolutionary descent. The association of PWWP domains with the DNA methyltransferases in O. tauri and in the metazoan lineage seems to have occurred independently consistent with convergent evolution. Our results do not support models wherein more complex protein architectures involving the PWWP domain occur with the appearance of more evolutionarily advanced life forms. © 2012 Alvarez-Venegas and Avramova; licensee BioMed Central Ltd.

Cole K.D.,University of Nebraska - Lincoln | Cetin B.,Middle East Technical University
International Journal of Heat and Mass Transfer | Year: 2011

Analysis is presented for conjugate heat transfer in a parallel-plate microchannel. Axial conduction in the fluid and in the adjacent wall are included. The fluid is a constant property liquid with a fully-developed velocity distribution. The microchannel is heated by a uniform heat flux applied to the outside of the channel wall. The analytic solution is given in the form of integrals by the method of Green's functions. Quadrature is used to obtain numerical results for the local and average Nusselt number for various flow velocities, heating lengths, wall thicknesses, and wall conductivities. These results have application in the optimal design of small-scale heat transfer devices in areas such as biomedical devices, electronic cooling, and advanced fuel cells. © 2011 Elsevier Ltd. All rights reserved.

Kim G.-H.,Electronics and Telecommunications Research Institute | Trimi S.,University of Nebraska - Lincoln | Chung J.-H.,Electronics and Telecommunications Research Institute
Communications of the ACM | Year: 2014

Businesses, governments, and the research community can all derive value from the massive amounts of digital data they collect. Analyzing big-data application projects by governments offers guidance for follower countries for their own future big-data initiatives. Decision making in government usually takes much longer and is conducted through consultation and mutual consent of a large number of diverse actors, including officials, interest groups, and ordinary citizens. Governments deal not only with general issues of big-data integration from multiple sources and in different formats and cost but also with some special challenges. The biggest is collecting data; governments have difficulty, as the data not only comes from multiple channels but from different sources. Most governments operating or planning big-data projects need to take a step-by-step approach for setting the right goals and realistic expectations. Success depends on their ability to integrate and analyze information, develop supporting systems, and support decision making through analytics.

Koenig W.D.,Cornell University | Knops J.M.H.,University of Nebraska - Lincoln | Pearse I.S.,Cornell University
Ecology | Year: 2015

Annually variable and synchronous seed production, or masting behavior, is a widespread phenomenon with dramatic effects on wildlife populations and their associated communities. Proximally, masting is often correlated with environmental factors and most likely involves differential pollination success and resource allocation, but little is known about how these factors interact or how they influence seed production. We studied masting in the valley oak (Quercus lobata Née), a California endemic tree, and report evidence that phenological synchrony in flowering driven by microclimatic variability determines the size of the acorn crop through its effects on pollen availability and fertilization success. These findings integrate two of the major factors believed to influence seed production in wind-pollinated species-environmental conditions and pollen limitation-by means of a coherent mechanistic hypothesis for how highly variable and synchronized annual seed production is accomplished. We illustrate how, by means of a simulation based on the mechanism proposed here, climate change may influence masting patterns through its effects on environmental variability. © 2015 by the Ecological Society of America.

Le Conte Y.,French National Institute for Agricultural Research | Ellis M.,University of Nebraska - Lincoln | Ritter W.,CVUA
Apidologie | Year: 2010

Since 2006, disastrous colony losses have been reported in Europe and North America. The causes of the losses were not readily apparent and have been attributed to overwintering mortalities and to a new phenomenon called Colony Collapse Disorder. Most scientists agree that there is no single explanation for the extensive colony losses but that interactions between different stresses are involved. As the presence of Varroa in each colony places an important pressure on bee health, we here address the question of how Varroa contributes to the recent surge in honey bee colony losses. © 2010 INRA/DIB-AGIB/EDP Sciences.

Turner J.A.,University of Nebraska - Lincoln | Ghoshal G.,University of Illinois at Urbana - Champaign
Applied Physics Letters | Year: 2010

The authors report results for the second-order statistics of the effective elastic moduli of polycrystals as a function of applied stress. These results are indicative of scattering behavior that occurs in such materials at ultrasonic frequencies. Numerical examples are given for materials of general interest with cubic symmetry subject to an applied uniaxial stress. The results suggest that the second-order statistics (scattering) may be more significantly affected than the first-order statistics (wave speed) with application of load for some materials. This work may be useful for development of techniques for monitoring changes in stress of loaded structures. © 2010 American Institute of Physics.

Anderson J.E.,University of Nebraska - Lincoln
G3 (Bethesda, Md.) | Year: 2014

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits. Copyright © 2014 Anderson et al.

Zhou L.,Nanjing University of Posts and Telecommunications | Hu R.Q.,Utah State University | Qian Y.,University of Nebraska - Lincoln | Chen H.-H.,National Cheng Kung University
IEEE Journal on Selected Areas in Communications | Year: 2013

In this work, we investigate the properties of energy-efficiency (EE) and spectrum-efficiency (SE) for video streaming over mobile ad hoc networks by developing an energy-spectrum-aware scheduling (ESAS) scheme. To describe a practical mobile scenario, we use a random walk mobility model, in which each node can choose its mobility direction and velocity randomly and independently. Through rigorous analysis and extensive simulations, we demonstrate that the node mobility is beneficial to EE but not to SE. The contributions of this work are twofold: 1) We propose an ESAS scheme with a dynamic transmission range, which significantly outperforms the previous minimum-distortion video scheduling in terms of joint EE and SE performance; 2) We derive an achievable EE-SE tradeoff range and a tight upper/lower bound with respect to energy-spectrum efficiency index for various node velocities. We believe that this work helps to shed insights on the fundamental design guidelines on building an energy and spectrum efficient mobile video transmission system. © 1983-2012 IEEE.

Hunt Jr. R.M.,University of Nebraska - Lincoln
Bulletin of the American Museum of Natural History | Year: 2011

This study describes and summarizes the Temnocyoninae (Mammalia, Carnivora), a subfamily of amphicyonid carnivores of considerable diversity and singular ecomorphology within Cenozoic faunas of North America. In temnocyonines, we see the first carnivorans to occupy an ecological niche as large cursorial predators. The subfamily is confined to the Arikareean NALMA, ranging in age from the latest early Oligocene to the early Miocene. Distributed from the Pacific Northwest to the Great Plains and Florida, there are four genera (Temnocyon, Mammacyon, Delotrochanter n. gen., Rudiocyon n. gen.) and 12 species, of which eight are newly described (Temnocyon subferox, T. fingeruti, T. macrogenys; Rudiocyon amplidens; Mammacyon ferocior; Delotrochanter petersoni, D. oryktes, D. major). Among the specimens examined are eight skulls, three with intact basicranial morphology that establish the presence of a plesiomorphic arctoid auditory region in the subfamily. Temnocyonine dentitions and postcranial skeletons reveal a blend of morphological characteristics not previously nor subsequently seen among the Carnivora. From a stem species, Temnocyon altigenis, there evolve both large hypercarnivorous (Temnocyon) and durophagous forms (Mammacyon, Delotrochanter); these genera share a derived dentition that defines the Temnocyoninae. Delotrochanter oryktes n. sp., an early Miocene species, was found in a den, suggesting a possible burrowing capability and sheltering of offspring. The John Day basin of Oregon and the central Great Plains (western Nebraska, southeast Wyoming) are the source of most temnocyonine fossils; a few have been found in southern California and Florida, indicative of a continent-wide distribution. Temnocyonines have often been confused with canids, however their basicranial anatomy places them securely within the Amphicyonidae. First discovered in the 1870s, only ∼30 individuals comprise the entire record of the subfamily. Many were found in proximity to radioisotopically calibrated tuffs and ignimbrites and/or were closely associated with mammals of established biochronologic age. Thus, most species can be placed in a temporal context. With rare exception, the fossils represent isolated occurrences, hence estimates of variation within a population are lacking. Cursorial postcranial features characterize several lineages (Mammacyon, Delotrochanter) and probably were present in other temnocyonines known only from dental remains. Late Oligocene Mammacyon ferocior and early Miocene Delotrochanter oryktes evolved uniquely configured crushing cheek teeth and cursorial limbs, combining distinctive dental and skeletal traits in a manner not seen in any living carnivore. These species are interpreted as large durophagous predators with craniodental characteristics that parallel living hyaenids (Crocuta crocuta) and postcranial adaptations approaching those of cursorial canids such as the wolf (Canis lupus). Expansion of semiarid grasslands and savanna during the late Oligocene and early Miocene in the central Great Plains seems to have favored the evolution of these wide-ranging durophagous amphicyonid carnivores. Analysis of the jaws of temnocyonines employing Therrien's method of beam analysis demonstrates pronounced bending strength focused beneath the crushing dental battery in the molar region. Similarly, the canines and mandibular symphysis manifest an ability to resist strong parasagittal, transverse, and torsional forces occurring during prey capture and feeding. Temnocyonines share a pronounced similarity in dentition with European haplocyonine beardogs, which doubtless are their sister group among the Amphicyonidae. Some haplocyonines also show cursorial tendencies. Examination of European material, however, reveals subtle dental distinctions indicating that the evolution of the two subfamilies proceeded separately yet in parallel in Europe and North America. Copyright © American Museum of Natural History 2011.

Church S.H.,University of Nebraska - Lincoln
Journal of Information Technology and Politics | Year: 2010

The present study employs both qualitative and quantitative research methods to examine the discourse of leadership in the YouTube video clips of 16 candidates who competed in the 2008 U.S. presidential race. The introduction and farewell videos of the candidates included on the YouChoose portion of YouTube are inductively analyzed for leadership utterances. Common categories are constructed through a grounded theory approach, while frequencies of the appearance of leadership traits are discovered through a content analysis of the data. The findings are then compared with relevant literature to determine the nature of presidential campaigns within the participatory culture of YouTube. The study suggests that the YouChoose videos favor the candidate's character over political experience and explores the possibility that the medium promotes passive (rather than active) political engagement on the part of the user. The idea of the construction of the YouTube audience as a "postmodern constituency" is also proposed. Finally, the implications of the study are discussed. © Taylor & Francis Group, LLC.

Hoover J.R.,Indiana University | Storkel H.L.,University of Kansas | Hogan T.P.,University of Nebraska - Lincoln
Journal of Memory and Language | Year: 2010

Two experiments examined the effects of phonotactic probability and neighborhood density on word learning by 3-, 4-, and 5-year-old children. Nonwords orthogonally varying in probability and density were taught with learning and retention measured via picture naming. Experiment 1 used a within story probability/across story density exposure context. Experiment 2 used an across story probability/within story density exposure context. Results showed that probability and density interacted to create optimal learning conditions. Specifically, rare/sparse sound sequences appeared to facilitate triggering of word learning. In contrast, the optimal convergence for lexical configuration and engagement was dependent on exposure context. In particular, common sound sequences and dense neighborhoods were optimal when density was manipulated across stories, whereas rare sound sequences and sparse neighborhoods were optimal when density was manipulated within a story. Taken together, children's phonological and lexical representations were hypothesized to be interdependent on one another resulting in a convergence of form characteristics for optimal word learning. © 2010 Elsevier Inc.

Hunt B.G.,Georgia Institute of Technology | Brisson J.A.,University of Nebraska - Lincoln | Yi S.V.,Georgia Institute of Technology | Goodisman M.A.D.,Georgia Institute of Technology
Genome Biology and Evolution | Year: 2010

DNA methylation is a fundamental epigenetic mark known to have wide-ranging effects on gene regulation in a variety of animal taxa. Comparative genomic analyses can help elucidate the function of DNA methylation by identifying conserved features of methylated genes and other genomic regions. In this study, we used computational approaches to distinguish genes marked by heavy methylation from those marked by little or no methylation in the pea aphid, Acyrthosiphon pisum. We investigated if these two classes had distinct evolutionary histories and functional roles by conducting comparative analysis with the honeybee, Apis (Ap.) mellifera. We found that highly methylated orthologs in A. pisum and Ap. mellifera exhibited greater conservation of methylation status, suggesting that highly methylated genes in ancestral species may remain highly methylated over time. We also found that methylated genes tended to show different rates of evolution than unmethylated genes. In addition, genes targeted by methylation were enriched for particular biological processes that differed from those in relatively unmethylated genes. Finally, methylated genes were preferentially ubiquitously expressed among alternate phenotypes in both species, whereas genes lacking signatures of methylation were preferentially associated with condition-specific gene expression. Overall, our analyses support a conserved role for DNA methylation in insects with comparable methylation systems. © The Author(s) 2010.

Guan Q.,University of Nebraska - Lincoln | Clarke K.C.,University of California at Santa Barbara
International Journal of Geographical Information Science | Year: 2010

A general-purpose parallel raster processing programming library (pRPL) was developed and applied to speed up a commonly used cellular automaton model with known tractability limitations. The library is suitable for use by geographic information scientists with basic programming skills, but who lack knowledge and experience of parallel computing and programming. pRPL is a general-purpose programming library that provides generic support for raster processing, including local-scope, neighborhood-scope, regional-scope, and global-scope algorithms as long as they are parallelizable. The library also supports multilayer algorithms. Besides the standard data domain decomposition methods, pRPL provides a spatially adaptive quad-tree-based decomposition to produce more evenly distributed workloads among processors. Data parallelism and task parallelism are supported, with both static and dynamic load-balancing. By grouping processors, pRPL also supports data-task hybrid parallelism, i.e., data parallelism within a processor group and task parallelism among processor groups. pSLEUTH, a parallel version of a well-known cellular automata model for simulating urban land-use change (SLEUTH), was developed to demonstrate full utilization of the advanced features of pRPL. Experiments with realworld data sets were conducted and the performance of pSLEUTH measured.We conclude not only that pRPL greatly reduces the development complexity of implementing a parallel raster-processing algorithm, it also greatly reduces the computing time of computationally intensive raster-processing algorithms, as demonstrated with pSLEUTH. © 2010 Taylor & Francis.

Zhang S.,University of Nebraska - Lincoln
Environmental and Ecological Statistics | Year: 2011

Despite recent advances in nonparametric methods for estimating animal abundance, parametric methods are still used widely among biometricians due to their simplicity. In this paper, we propose an optimal shrinkage-type estimator and an empirical Bayes estimator for estimating animal density from line transect sampling data. The performances of the proposed estimators are compared with those of the maximum likelihood estimator and a bias-corrected maximum likelihood estimator both theoretically and numerically. Simulation results show that the optimal shrinkage-type estimator works the best if the detection function has a very thin tail (for example, the half normal detection function), while the maximum likelihood estimator is the best estimator if the detection function has relatively thick tail (for example, the polynomial detection function). © 2009 Springer Science+Business Media, LLC.

Melander L.A.,Kansas State University | Tyler K.A.,University of Nebraska - Lincoln
Journal of Adolescent Health | Year: 2010

Purpose: The purpose of our study was to examine the relationship between child maltreatment, physical and sexual victimization, and partner violence victimization with human immunodeficiency virus (HIV) risk behaviors among a sample of homeless young adults from the midwestern United States. Methods: Data are from the Homeless Young Adult Project. A total of 199 young adults aged 19-26 years were interviewed over 14 months using a systematic sampling strategy. The final sample included 172 young adults who were homeless or had a history of running away and being homeless. Results: Results from the path analysis revealed that sexual abuse is directly linked with street sexual victimization which was positively associated with a greater number of HIV risk behaviors. Experiencing more types of physical abuse and neglect were positively correlated with partner violence victimization, which was, in turn, associated with more HIV risk behaviors. Those who suffered from more types of neglect also experienced more forms of sexual and physical victimization. Conclusions: These findings have implications for service providers. Clinicians who serve homeless youth should recognize the potential effect that experiencing a variety of forms of victimization may have on health risk behaviors. © 2010 Society for Adolescent Health and Medicine. All rights reserved.

Lenton R.,University of Nebraska - Lincoln
Irrigation and Drainage | Year: 2014

Irrigated agriculture will come under increased global pressures in the twenty-first century to be more efficient, productive, profitable and sustainable. This paper considers the implications of these pressures. It concludes that we will need the best of science to develop the scientific underpinnings for innovative approaches in irrigated agriculture; effective policies and institutions to control use, manage storage, balance water needs, and create incentives for adoption of innovations; and a broader set of actors working together as part of the solution set. Copyright © 2014 John Wiley & Sons, Ltd.

Zhang Z.,Nanjing University of Aeronautics and Astronautics | Zeng X.C.,University of Nebraska - Lincoln | Guo W.,Nanjing University of Aeronautics and Astronautics
Journal of the American Chemical Society | Year: 2011

Cubic boron nitride (c-BN) possesses a number of extreme properties rivaling or surpassing those of diamond. Especially, owing to the high chemical stability, c-BN is desired for fabricating electronic devices that can stand up to harsh environments. However, realization of c-BN-based functional devices is still a challenging task due largely to the subtlety in the preparation of high-quality c-BN films with uniform thickness and controllable properties. Here, we present a simple synthetic strategy by surface fluorination of few-layered hexagonal boron nitride (h-BN) sheets to produce thermodynamically favorable F-terminated c-BN nanofilms with an embedded N-N bond layer and strong inbuilt electric polarization. Due to these specific features, the fluorinated c-BN nanofilms have controllable band gap by thickness or inbuilt and applied electric fields. Especially, the produced nanofilms can be tuned into substantial ferromagnetism through electron doping within a reasonable level. The electron-doping-induced deformation ratio of the c-BN nanofilms is found to be 1 order of magnitude higher than those of carbon nanotubes and graphene. At sufficient high doping levels, the nanofilm can be cleaved peculiarly along the N-N bond layer into diamond-like BN films. As the proposed synthesis strategy of the fluorinated c-BN nanofilms is well within the reach of current technologies, our results represent an extremely cost-effective approach for producing high-quality c-BN nanofilms with tunable electronic, magnetic, and electromechanical properties for versatile applications. © 2011 American Chemical Society.

Yang W.H.,University of California at Berkeley | Weber K.A.,University of Nebraska - Lincoln | Silver W.L.,University of California at Berkeley
Nature Geoscience | Year: 2012

The oxidation of ammonium is a key step in the nitrogen cycle, regulating the production of nitrate, nitrous oxide and dinitrogen. In marine and freshwater ecosystems, anaerobic ammonium oxidation coupled to nitrite reduction, termed anammox, accounts for up to 67% of dinitrogen production 1-3. Dinitrogen production through anaerobic ammonium oxidation has not been observed in terrestrial ecosystems, but the anaerobic oxidation of ammonium to nitrite has been observed in wetland soils under iron-reducing conditions 4,5. Here, we incubate tropical upland soil slurries with isotopically labelled ammonium and iron(iii) to assess the potential for anaerobic ammonium oxidation coupled to iron(iii) reduction, otherwise known as Feammox 6, in these soils. We show that Feammox can produce dinitrogen, nitrite or nitrate in tropical upland soils. Direct dinitrogen production was the dominant Feammox pathway, short-circuiting the nitrogen cycle and resulting in ecosystem nitrogen losses. Rates were comparable to aerobic nitrification 7,8 and to denitrification 9, the latter being the only other process known to produce dinitrogen in terrestrial ecosystems. We suggest that Feammox could fuel nitrogen losses in ecosystems rich in poorly crystalline iron minerals, with low or fluctuating redox conditions. © 2012 Macmillan Publishers Limited. All rights reserved.

Peterson D.,National Research Council Italy | Hyer E.,U.S. Navy | Wang J.,University of Nebraska - Lincoln
Journal of Geophysical Research: Atmospheres | Year: 2014

All chemical transport models require an estimation of the vertical distribution of smoke particles near the source. This study quantitatively examines the strengths and weaknesses of several fire products for characterizing plume buoyancy and injection heights in the North American boreal forest during 2004-2005. Observations from the Multiangle Imaging Spectroradiometer show that 21% of smoke plumes are injected more than 500 m above the boundary layer (BL500) and 8% exceed 2.5 km above ground level. Corresponding observations from the Moderate Resolution Imaging Spectroradiometer (MODIS) show that probability of injection above the BL 500 exceeds 60% for pixel-based fire radiative power (FRP p) values above ∼2500 MW. Increasing values of subpixel-retrieved fire area and temperature also correspond to higher injections but only after removing fire pixels with a weak 11 μm fire signal and clustering. The probability of injection above the BL500 reaches 50% when the subpixel radiant flux (FRPf flux) exceeds 20 kW/m2, highlighting its potential for estimating plume buoyancy. However, these data have limitations similar to FRPp, where the highest probability of injection corresponds to a small percentage of the data set (5-18%), and many high-altitude injections occur with lower values. Examinations of individual smoke plumes highlight the importance of combining pixel-level and subpixel outputs and show that plume injection is also sensitive to the fire pixel spatial distribution and meteorology. Therefore, an optimal method for predicting high-altitude injections will require some combination of injection climatology, FRPp, FRPf flux, and meteorology, but each variable's importance will depend on fire event characteristics. © 2014 American Geophysical Union. All Rights Reserved.

Case A.J.,University of Nebraska Medical Center | Zimmerman M.C.,University of Nebraska Medical Center | Zimmerman M.C.,University of Nebraska - Lincoln
Hypertension | Year: 2015

Sympathoexcitation, increased circulating norepinephrine, and elevated levels of reactive oxygen species are driving forces underlying numerous cardiovascular diseases, including hypertension. However, the effects of elevated norepinephrine and subsequent reactive oxygen species production in splenic T-lymphocytes during hypertension are not currently understood. We hypothesized that increased systemic levels of norepinephrine inhibits the activation of splenic T-lymphocytes via redox signaling. To address this hypothesis, we examined the status of T-lymphocyte activation in spleens of a mouse model of sympathoexcitation-driven hypertension (ie, norepinephrine infusion). Splenic T-lymphocytes from norepinephrine-infused mice demonstrated decreased proliferation accompanied by a reduction in interferon gamma and tumor necrosis factor-α production as compared with T-lymphocytes from saline-infused mice. Additionally, norepinephrine directly inhibited splenic T-lymphocyte proliferation and cytokine production ex vivo in a dose-dependent manner. Furthermore, norepinephrine caused an increase in G1 arrest in norepinephrine-treated T-lymphocytes, and this was accompanied by a decrease in pro-growth cyclin D3, E1, and E2 mRNA expression. Interestingly, norepinephrine caused an increase in cellular superoxide, which was shown to be partially causal to the inhibitory effects of norepinephrine, as antioxidant supplementation (ie, Tempol) to norepinephrine-infused mice moderately restored T-lymphocyte growth and proinflammatory cytokine production. Our findings indicate that suppression of splenic T-lymphocyte activation occurs in a norepinephrine-driven model of hypertension due to, at least in part, an increase in superoxide. We speculate that further understanding of how norepinephrine mediates its inhibitory effects on splenic T-lymphocytes may elucidate novel pathways for therapeutic mimicry to suppress T-lymphocyte-mediated inflammation in an array of diseases. © 2015 American Heart Association, Inc.

Li X.Z.,University of Nebraska - Lincoln
Ultramicroscopy | Year: 2010

A computer program for the simulation of polycrystalline electron diffraction patterns is described. PCED2.0, an upgraded version of the previous JECP/PCED, can be used as a teaching aid and research tool for phase identification, microstructure texture analysis, and phase fraction determination. In addition to kinematical theory for diffraction intensity calculation of polycrystalline samples, Blackman two-beam dynamical correction is included. March model is used for out-of-plane and in-plane texture simulation. A pseudo-Voigt function is used for the peak profile fitting of diffraction rings. User-friendly interface is improved in the handling of experimental diffraction data and the flexibility of indexing. Application of the program for the analysis of FePt thin films is given as an example. © 2009 Elsevier B.V. All rights reserved.

Burgin A.J.,University of Nebraska - Lincoln | Burgin A.J.,Cary Institute of Ecosystem Studies | Groffman P.M.,Cary Institute of Ecosystem Studies
Journal of Geophysical Research: Biogeosciences | Year: 2012

Wetland soil oxygen (O2) is rarely measured, which limits our understanding of a key regulator of nitrogen loss through denitrification. We asked: (1) How does soil [O2] vary in riparian wetlands? (2) How does this [O2] variation affect denitrification rates and end products? and (3) How does [O2] variation and previous exposure to O 2 affect trace gas fluxes? We collected a continuous seven-month record of [O2] dynamics in a "wet" and "dry" riparian zone. In April 2009, soil [O2] ranged from 0 to 13% and consistently increased with increasing distance from the stream. [O2] gradually declined in all sensors until all sensors went anoxic in early September 2009. In mid-fall, a dropping water table increased soil [O 2] to 15-20% within a 2-3 day period. We measured denitrification using the Nitrogen-Free Air Recirculation Method (N-FARM), a direct measurement of N2 production against a helium background. Denitrification rates were significantly higher in the wetter areas, which correlated to lower O 2 conditions. Denitrification rates in the drier areas correlated with [O2] in the early spring and summer, but significantly decreased in late summer despite decreasing O2 concentrations. Increasing [O2] significantly increased core N2O production, and therefore may be an important control on nitrous oxide yield. Field N 2O fluxes, however, were highly variable, ranging from 0 to 800 ug N m-2 hr-1 with no differences between the wet and dry sites. Future research should focus on understanding the biotic and abiotic controls on O2 dynamics, and O2 dynamics should be included in models of soil N cycling and trace gas fluxes. Copyright 2012 by the American Geophysical Union.

Qiao D.,University of Nebraska - Lincoln | Qiao D.,Huawei | Gursoy M.C.,Syracuse University | Velipasalar S.,Syracuse University
IEEE Transactions on Information Theory | Year: 2013

A two-hop wireless communication link in which a source sends data to a destination with the aid of an intermediate relay node is studied. It is assumed that there is no direct link between the source and the destination, and the relay forwards the information to the destination by employing the decode-and-forward scheme. Both the source and intermediate relay nodes are assumed to operate under statistical quality of service (QoS) constraints imposed as limitations on the buffer overflow probabilities. The maximum constant arrival rates that can be supported by this two-hop link in the presence of QoS constraints are characterized by determining the effective capacity of such links as a function of the QoS parameters and signal-to-noise ratios at the source and relay, and the fading distributions of the links. The analysis is performed for both full-duplex and half-duplex relaying. Through this study, the impact upon the throughput of having buffer constraints at the source and intermediate relay nodes is identified. The interactions between the buffer constraints in different nodes and how they affect the performance are studied. The optimal time-sharing parameter in half-duplex relaying is determined, and performance with half-duplex relaying is investigated. © 1963-2012 IEEE.