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Ames, IA, United States

Iowa State University of Science and Technology, more commonly known as Iowa State University, Iowa State, or ISU, a Land grant of the Iowa university system, is a public land-grant and space-grant research university located in Ames, Iowa, United States. Until 1959 it was known as the Iowa State College of Agriculture and Mechanic Arts.Founded in 1858 and coeducational from its start, Iowa State became the nation’s first designated land-grant institution when the Iowa Legislature accepted the provisions of the 1862 Morrill Act on September 11, 1862, making Iowa the first state in the nation to do so. Iowa State's academic offerings are administered today through eight colleges, including the graduate college, that offer over 100 bachelor's degree programs, 112 master's degree programs, and 83 at the Ph.D. level, plus a professional degree program in Veterinary Medicine.ISU is classified as a Research University with very high research activity by the Carnegie Foundation for the Advancement of Teaching. The university is a group member of the prestigious American Association of Universities and the Universities Research Association, and a charter member of the Big 12 Conference. Wikipedia.


HilleRisLambers J.,University of Washington | Adler P.B.,Utah State University | Harpole W.S.,Iowa State University | Levine J.M.,ETH Zurich | Mayfield M.M.,Utah State University
Annual Review of Ecology, Evolution, and Systematics | Year: 2012

Although research on the role of competitive interactions during community assembly began decades ago, a recent revival of interest has led to new discoveries and research opportunities. Using contemporary coexistence theory that emphasizes stabilizing niche differences and relative fitness differences, we evaluate three empirical approaches for studying community assembly. We show that experimental manipulations of the abiotic or biotic environment, assessments of trait-phylogeny-environment relationships, and investigations of frequency-dependent population growth all suggest strong Influences of stabilizing niche differences and fitness differences on the outcome of plant community assembly. Nonetheless, due to the limitations of these approaches applied in isolation, we still have a poor understanding of which niche axes and which traits determine the outcome of competition and community structure. Combining current approaches represents our best chance of achieving this goal, which is fundamental to conceptual ecology and to the management of plant communities under global change. © 2012 by Annual Reviews. All rights reserved. Source


Adams D.C.,Iowa State University | Nistri A.,University of Florence
BMC Evolutionary Biology | Year: 2010

Background. A major goal in evolutionary biology is to understand the evolution of phenotypic diversity. Both natural and sexual selection play a large role in generating phenotypic adaptations, with biomechanical requirements and developmental mechanisms mediating patterns of phenotypic evolution. For many traits, the relative importance of selective and developmental components remains understudied. Results. We investigated ontogenetic trajectories of foot morphology in the eight species of European plethodontid cave salamander to test the hypothesis that adult foot morphology was adapted for climbing. Using geometric morphometrics and other approaches, we found that developmental patterns in five species displayed little morphological change during growth (isometry), where the extensive interdigital webbing in adults was best explained as the retention of the juvenile morphological state. By contrast, three species exhibited significant allometry, with an increase in interdigital webbing during growth. Phylogenetic analyses revealed that multiple evolutionary transitions between isometry and allometry of foot webbing have occurred in this lineage. Allometric parameters of foot growth were most similar to those of a tropical species previously shown to be adapted for climbing. Finally, interspecific variation in adult foot morphology was significantly reduced as compared to variation among juveniles, indicating that ontogenetic convergence had resulted in a common adult foot morphology across species. Conclusions. The results presented here provide evidence of a complex history of phenotypic evolution in this clade. The common adult phenotype exhibited among species reveals that selection plays an important part in generating patterns of foot diversity in the group. However, developmental trajectories arriving at this common morphology are distinct; with some species displaying developmental stasis (isometry), while others show an increase in foot webbing during growth. Thus, multiple developmental solutions exist to the same evolutionary challenge. Our findings underscore the importance of examining morphological adaptations from multiple perspectives, and emphasize that both selective hypotheses and developmental processes must be considered for a more comprehensive understanding of phenotypic evolution. © 2010 Adams and Nistri; licensee BioMed Central Ltd. Source


Adams D.C.,Iowa State University
BMC Evolutionary Biology | Year: 2010

Background. Parallel evolution can occur when common environmental factors exert similar selective forces on morphological variation in populations in different geographic localities. Competition can also generate morphological shifts, and if competing species co-occur in multiple geographic regions, then repeated instances of competitively-driven morphological divergence (character displacement) can occur. Despite the importance of character displacement for inferring the role of selection in morphological evolution however, replicated instances of sympatric morphological divergence are understudied. Results. I tested the hypothesis that interspecific competition generated patterns of parallel morphological divergence in multiple geographic locations where two competing salamander species, Plethodon jordani and P. teyahalee, come into contact. I used geometric morphometrics to characterize head shape and found ecological character displacement in sympatric localities on each of three distinct mountains (geographic transects), where sympatric specimens displayed greater cranial differences and an increase in cranial robustness as compared to allopatric specimens. Using a recently developed analytical procedure, I also found that the observed morphological evolution within each species was consistent among transects; both in the total amount of morphological change as well as the direction of evolution in the morphological data space. This provided strong statistical evidence of parallel morphological evolution within species across replicate geographic transects. Conclusions. The results presented here reveal that the morphological evolution of each species followed a common evolutionary path in each transect. Because dispersal between sympatric locations among transects is unlikely, these findings suggest that the repeated instances of character displacement have evolved in situ. They also suggest that selection from competitive interactions plays an important role in initiating sympatric morphological divergence in these species, and drives parallel sympatric morphological divergence between species. © 2010 Adams; licensee BioMed Central Ltd. Source


Seo J.,Iowa State University | Linzell D.G.,Pennsylvania State University
Engineering Structures | Year: 2012

Most computational research related to steel bridge seismic vulnerability has focused on statistical extrapolation of analysis results for individual straight bridges. However, there has been a steady growth in the use of horizontally curved steel bridges in highways and interchanges in large urban regions. Given the large number of curved steel bridge structures in use in the US and abroad, with some of those structures being located in seismic zones, the feasibility of examining the effects of curvature on bridge vulnerability should be investigated. In this study, the seismic performance characteristics of an existing inventory of horizontally curved, steel, I-girder bridges located in Pennsylvania, New York, and Maryland were used to generate fragility curves. Representative fragility curves for horizontally curved, steel, I-girder bridges were estimated using Response Surface Metamodels (RSMs) in conjunction with Monte Carlo simulation. The methodology was used to construct fragility curves for select bridge components (bearings, columns and abutments). The curves were generated for four different, preexisting, performance states that represented slight, moderate, extensive, and complete damage under varying levels of earthquake intensity. The generated fragility curves provided information related to seismic response of the bridge inventory that was investigated, such as radial deformations at the bearings being the most susceptible component to seismic loads. © 2011 Elsevier Ltd. Source


Opriessnig T.,Iowa State University | Langohr I.,Michigan State University
Veterinary Pathology | Year: 2013

Porcine circovirus type 2 (PCV2), a small single-stranded DNA virus, was initially discovered in 1998 and is highly prevalent in the domestic pig population. Disease manifestations associated with PCV2 include postweaning multisystemic wasting disease (PMWS), enteric disease, respiratory disease, porcine dermatitis and nephropathy syndrome (PDNS), and reproductive failure. Although these clinical manifestations involve different organ systems, there is considerable overlap in clinical expression of disease and presence of lesions between pigs and within herds. It is now widely accepted that PCV2 can be further subdivided into different types, of which PCV2a and PCV2b are present worldwide and of greatest importance. This review will focus on PCV2-associated lesions in different organ systems. © The Author(s) 2012. Source


Licona A.C.,University of Arizona | Maldonado M.M.,Iowa State University
Antipode | Year: 2014

This paper explores the sociospatial dynamics unfolding in Perry, a rural Iowa town that has been facing rapid change since the 1990s due to growing Latin@ settlement. We focus on what we call the social production of Latin@ visibilities and invisibilities: spatialized practices by individuals, families, communities, and institutions that render different Latin@ groups visible or invisible, with repercussions for survival, community integration, and political praxis. We discuss the border within as an extension of border politics and borderlands rhetorics to the US "heartland", and how the entrenchment of a regime of deportability creates racialized and gendered conditions for the in/visibility of Latin@ immigrants and Latin@s more broadly. We conclude by considering some of the theoretical and political implications of our analysis for such geographies of power and the social relations, locations, and discourses that constitute and are constituted by them. © 2013 Antipode Foundation Ltd. Source


Dai J.,Zhejiang University | Zhang S.,Iowa State University
Optics and Lasers in Engineering | Year: 2013

Our recent study showed that the Bayer-dithering technique could substantially improve 3D measurement quality for the binary defocusing method. Yet, the dithering technique was developed to optimize the appearance or intensity representation, rather than the phase, of an image. This paper presents a framework to optimize the Bayer-dithering technique in phase domain by iteratively mutating the status (0 or 1) of a binary pixel. We will demonstrate that the proposed optimization technique can drastically reduce the phase error when the projector is nearly focused. © 2013 Elsevier Ltd. Source


Lemmens J.S.,University of Amsterdam | Valkenburg P.M.,University of Amsterdam | Gentile D.A.,Iowa State University
Psychological Assessment | Year: 2015

Recently, the American Psychiatric Association included Internet gaming disorder (IGD) in the appendix of the 5th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). The main aim of the current study was to test the reliability and validity of 4 survey instruments to measure IGD on the basis of the 9 criteria from the DSM-5: a long (27-item) and short (9-item) polytomous scale and a long (27-item) and short (9-item) dichotomous scale. The psychometric properties of these scales were tested among a representative sample of 2,444 Dutch adolescents and adults, ages 13-40 years. Confirmatory factor analyses demonstrated that the structural validity (i.e., the dimensional structure) of all scales was satisfactory. Both types of assessment (polytomous and dichotomous) were also reliable (i.e., internally consistent) and showed good criterion-related validity, as indicated by positive correlations with time spent playing games, loneliness, and aggression and negative correlations with self-esteem, prosocial behavior, and life satisfaction. The dichotomous 9-item IGD scale showed solid psychometric properties and was the most practical scale for diagnostic purposes. Latent class analysis of this dichotomous scale indicated that 3 groups could be discerned: normal gamers, risky gamers, and disordered gamers. On the basis of the number of people in this last group, the prevalence of IGD among 13- through 40-year-olds in the Netherlands is approximately 4%. If the DSM-5 threshold for diagnosis (experiencing 5 or more criteria) is applied, the prevalence of disordered gamers is more than 5%. © 2015 American Psychological Association. Source


Thakur V.K.,Iowa State University | Thakur M.K.,Himachal Pradesh University | Gupta R.K.,Indian Institute of Technology Kanpur
Carbohydrate Polymers | Year: 2013

Cellulose is the most abundant natural polysaccharide polymer, which is used as such or its derivatives in a number of advanced applications, such as in paper, packaging, biosorption, and biomedical. In present communication, in an effort to develop a proficient way to rapidly synthesize poly(methyl acrylate)-graftcellulose (PMA-g-cellulose) copolymers, rapid graft copolymerization synthesis was carried out under microwave conditions using ferrous ammonium sulfate-potassium per sulfate (FAS-KPS) as redox initiator. Different reaction parameters such as microwave radiation power, ratio of monomer, solvent and initiator concentrations were optimized to get the highest percentage of grafting. Grafting percentage was found to increase with increase in microwave power up to 70%, and maximum 36.73% grafting was obtained after optimization of all parameters. Fourier transforms infrared spectroscopy (FT-IR), scanning electron microscopy (SEM) and thermogravimetric analysis (TGA/DTA/DTG) analysis were used to confirm the graft copolymerization of poly(methyl acrylate) (PMA) onto the mercerized cellulose. The grafted cellulosic polymers were subsequently subjected to the evaluation of different physico-chemical properties in order to access their application in everyday life, in a direction toward green environment. The grafted copolymers demonstrated increased chemical resistance, and higher thermal stability. Source


Spoth R.,Iowa State University | Greenberg M.,Pennsylvania State University
American Journal of Community Psychology | Year: 2011

At present, evidence-based programs (EBPs) to reduce youth violence are failing to translate into widespread community practice, despite their potential for impact on this pervasive public health problem. In this paper we address two types of challenges in the achievement of such impact, drawing upon lessons from the implementation of a partnership model called PROSPER. First, we address five key challenges in the achievement of community-level impact through effective community planning and action: readiness and mobilization of community teams; maintaining EBP implementation quality; sustaining community teams and EBPs; demonstrating community-level impact; and continuous, proactive technical assistance. Second, we consider grand challenges in the large-scale translation of EBPs: (1) building, linking and expanding existing infrastructures to support effective EBP delivery systems, and (2) organizing networks of practitioner-scientist partnerships-networks designed to integrate diffusion of EBPs with research that examines effective strategies to do so. The PROSPER partnership model is an evidence-based delivery system for community-based prevention and has evolved through two decades of NIH-funded research, assisted by land grant universities' Cooperative Extension Systems. Findings and lessons of relevance to each of the challenges are summarized. In this context, we outline how practitioner-scientist partnerships can serve to transform EBP delivery systems, particularly in conjunction with supportive federal policy. © 2011 Society for Community Research and Action. Source


Takai S.,Osaka University | Kumar R.,Iowa State University
IEEE Transactions on Automatic Control | Year: 2012

The task of failure prognosis requires the prediction of impending failures. This technical note formulates and studies the problem of distributed prognosis of discrete event systems, where the local prognosers exchange their observations for the sake of arriving at a prognostic decision. The observations are exchanged over communication channels that introduce bounded delays. A property of joint-prognosability is introduced to capture the condition under which any failure can be predicted by some local prognoser prior to its occurrence. We provide an algorithm to check the joint-prognosability property. © 2012 IEEE. Source


Levitas V.I.,Iowa State University
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2013

A recently suggested melt-dispersion mechanism (MDM) for fast reaction of aluminium (Al) nano- and a few micrometre-scale particles during fast heating is reviewed. Volume expansion of 6% during Al melting produces pressure of several GPa in a core and tensile hoop stresses of 10GPa in an oxide shell. Such stresses cause dynamic fracture and spallation of the shell. After spallation, an unloading wave propagates to the centre of the particle and creates a tensile pressure of 3-8 GPa. Such a tensile pressure exceeds the cavitation strength of liquid Al and disperses the melt into small, bare clusters (fragments) that fly at a high velocity. Reaction of the clusters is not limited by diffusion through a pre-existing oxide shell. Some theoretical and experimental results related to the MDM are presented. Various theoretical predictions based on the MDM are in good qualitative and quantitative agreement with experiments, which resolves some basic puzzles in combustion of Al particles. Methods to control and improve reactivity of Al particles are formulated, which are exactly opposite to the current trends based on diffusion mechanism. Some of these suggestions have experimental confirmation. © 2013 The Author(s) Published by the Royal Society. All rights reserved. Source


Willson S.J.,Iowa State University
Bulletin of Mathematical Biology | Year: 2010

A phylogenetic network is a rooted acyclic digraph with vertices corresponding to taxa. Let X denote a set of vertices containing the root, the leaves, and all vertices of outdegree 1. Regard X as the set of vertices on which measurements such as DNA can be made. A vertex is called normal if it has one parent, and hybrid if it has more than one parent. The network is called normal if it has no redundant arcs and also from every vertex there is a directed path to a member of X such that all vertices after the first are normal. This paper studies properties of normal networks. Under a simple model of inheritance that allows homoplasies only at hybrid vertices, there is essentially unique determination of the genomes at all vertices by the genomes at members of X if and only if the network is normal. This model is a limiting case of more standard models of inheritance when the substitution rate is sufficiently low. Various mathematical properties of normal networks are described. These properties include that the number of vertices grows at most quadratically with the number of leaves and that the number of hybrid vertices grows at most linearly with the number of leaves. © 2009 Society for Mathematical Biology. Source


Peppas N.A.,University of Texas at Austin | Narasimhan B.,Iowa State University
Journal of Controlled Release | Year: 2014

In this review we present some of the seminal contributions that have established the mathematical foundations of controlled drug delivery and led to the modern models. Mathematical modeling is no longer just a dry exercise in generating more and more complex models or a parametric fitting process, but rather an advanced analysis that can lead to a priori examination of a release/delivery process or a series of design equations that help the practitioner achieve a better formulation. © 2014 Elsevier B.V. Source


Li T.,Iowa State University
Methods in molecular biology (Clifton, N.J.) | Year: 2013

TALENs, fusion proteins of DNA binding domains of TAL (transcription activator-like) effectors and the DNA cleavage domains of endonuclease FokI, have emerged as genetic tools for targeted gene modification, holding great potential for basic and applied research, even for gene therapy. Here we present a simple and efficient approach to custom-engineering TALEN genes with four basic TAL repeats and their DNA recognition cipher. The "modular assembly" method also involves the "Golden Gate" cloning strategy, using 53 ready-to-use plasmids in just two rounds of restriction and ligation to assemble TALENs with up to 24 repeat units that recognize up to 24 bp of target DNA. Source


Bain C.,Iowa State University
Biomass and Bioenergy | Year: 2011

The rapid expansion of ethanol plants across the U.S. state of Iowa has fueled debate about the burdens and benefits of local (in-state investors) versus non-local ownership of biorefineries. Central to these concerns is the extent to which non-local, absentee owners might reap the benefits of the ethanol industry at the expense of local communities. A key argument within the rural development literature is that local ownership of firms has a positive effect on the long-term well-being and sustainability of the communities in which they are situated. This literature asserts that firms operate at different scales, with local firms embedded within local supply chains and institutions, and non-local firms embedded within national and international networks and institutions. Conversely, there is a growing body of work within the alternative agrifood systems literature that cautions against the 'local trap'; the assumption that the local scale is inherently good and therefore advantageous. Despite this broader debate, the literature on local ownership and renewable energy remains limited. This paper addresses this gap by drawing on case study research of the community effects of ethanol plant ownership structure from the perspective of community leaders. My findings suggest that differences between the structure and effects of local versus non-local ownership of firms on communities are rather more ambiguous than the literature asserts. Therefore, assumptions about the benefits of local ownership may be overstated and concepts of 'local' and 'non-local' may be inadequate for considering firm outcomes on the civic welfare and socioeconomic well-being of a community. © 2010 Elsevier Ltd. Source


Semrau J.D.,University of Michigan | Dispirito A.A.,Iowa State University | Yoon S.,University of Michigan
FEMS Microbiology Reviews | Year: 2010

Methanotrophs, cells that consume methane (CH4) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH4, the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH4 to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH4 fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH 4 oxidation by the particulate CH4 monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs. © 2010 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved. Source


O'Connor A.,Iowa State University
Preventive Veterinary Medicine | Year: 2010

Reporting guidelines aim to facilitate publication of a full and accurate description of research conducted. The motivations for a full and accurate description of research is to enable reproduction of the study, assessment of bias, extraction of data from the study, and to fulfill an ethical obligation to maximize the utility of research findings. Many reporting guidelines exist and most are based on a specific study design such as randomized controlled trials (CONSORT statement) and observational studies (STROBE statement). The REFLECT statement focuses on randomized control trials in livestock and food safety studies. The REFLECT statement has increased emphasis on conveying information about animal housing, group level allocation and challenge studies. Guidelines can be used by authors, reviewers and editors to provide readers with a full and accurate description of the work conducted. © 2010 Elsevier B.V. Source


Heindel T.J.,Iowa State University
Journal of Fluids Engineering, Transactions of the ASME | Year: 2012

Fluidized beds are common equipment in many process industries. Knowledge of the hydrodynamics within a fluidized bed on the local scale is important for the improvement of scale-up and process efficiencies. This knowledge is lacking due to limited observational technologies at the local scale. This paper uses X-ray computed tomography (CT) imaging to describe the local time-average gas holdup differences of annular hydrodynamic structures that arise through axisymmetric annular flow in a 10.2 cm and 15.2 cm diameter cold flow fluidized bed. The aeration scheme used is similar to that provided by a porous plate and hydrodynamic results can be directly compared. Geldart type B glass bead, ground walnut shell, and crushed corncob particles were studied at various superficial gas velocities. Assuming axisymmetry, the local 3D time-average gas holdup data acquired through X-ray CT imaging was averaged over concentric annuli, resulting in a 2D annular and time-average gas holdup map. These gas holdup maps show that four different types of annular hydrodynamic structures occur in the fluidized beds of this study: zones of (1) aeration jetting, (2) bubble coalescence, (3) bubble rise, and (4) particle shear. Changes in the superficial gas velocities, bed diameters, and bed material densities display changes in these zones. The 2D gas holdup maps provide a benchmark that can be used by computational fluid dynamic (CFD) users for the direct comparisons of 2D models, assuming axisymmetric annular flow. © 2012 American Society of Mechanical Engineers. Source


Olsen S.C.,Bacterial Diseases of Livestock Research Unit | Carlson S.A.,Iowa State University
International Journal of Antimicrobial Agents | Year: 2015

Plazomicin is a next-generation aminoglycoside with a potentially unique set of clinical characteristics compared with other aminoglycosides. This study assessed the minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of plazomicin against 15 clinical isolates as well as three reference strains representing Brucella abortus, Brucella melitensis and Brucella suis. These data were compared with those obtained for six other aminoglycosides and two aminocyclitols. Plazomicin and gentamicin were the only drugs demonstrating bactericidal activity towards two of the three Brucella spp., whilst plazomicin was the only drug exhibiting bactericidal activity against B. suis. This is the first study to assess the bactericidal nature of plazomicin against Brucella spp. in vitro. © 2014 Elsevier B.V. and the International Society of Chemotherapy. Source


Flora C.B.,Iowa State University
Renewable Agriculture and Food Systems | Year: 2010

Food insecurity remains high in most of sub-Saharan African. That insecurity is made even more acute by the increasing scarcity and degradation of natural resources. Low soil fertility is a consistent problem faced by agriculturalists and herders. The dominant international thrust to increase food production has been to stimulate trade, enhanced by technology and its transfer. While international bodies acknowledge the importance of small farmers, they operate as if improving the technologies, trade regimes and value chains that are characteristic of industrial agriculture will have the same results in local ecosystems in developing countries. Price volatility makes access to purchased inputs more risky for smallholders and the governments that subsidize those inputs. The diverse local contexts that serve as the base of African agriculture are thus assumed to be overridden by technology. In contrast, a systems approach that focuses on sustainability of the local ecosystem, social and cultural relationships and economic security can be as, or more productive than industrial agriculture and have a much better opportunity to increase food security in developing countries. Such a systems-based shift in practices, such as the application of conservation agriculture and integrated systemic approaches in Millennium Villages, have potential of addressing household livelihood strategies and production issues in a sustainable, farmer-based way. Resource-conserving agriculture has been shown to increase yields in developing countries. Priority should be given to developing technologies that follow the systems principles of sustainable agriculture, integrating biological and ecological processes (such as nutrient cycling, nitrogen fixation, soil regeneration and biodiversity) into the production processes; minimizing use of non-renewable inputs that cause harm to the environment or to the health of farmers and consumers; and making productive use of the knowledge and skills of farmers and their collective capacities to work together to solve common problems. A variety of models are on the ground in Africa, and there is political will in the African Union to increase investment in agriculture. What sort of investments, policy interventions and capacity building are more effective in increasing productivity and the well-being of agricultural producers? Are strategies aimed at reducing the number of people involved in farming and herding viable in the context of a stagnant world economy? © 2010 Cambridge University Press. Source


Salmon A.,Iowa State University | Ainouche M.L.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
Molecular Ecology | Year: 2010

Most plant species are recent or ancient polyploids (displaying at least one round of genome duplication in their history). Cultivated species (e.g. wheat, cotton, canola, sugarcane, coffee) and invasive species are often relatively recent polyploids, and frequently of hybrid origin (i.e. allopolyploids). Despite the genetic bottleneck occurring during the allopolyploid speciation process, the formation of such species from two divergent lineages leads to fixed heterozygosity decisive to their success. New phenotypes and new niche occupation are usually associated with this mode of speciation, as a result of both genomic rearrangements and gene expression changes of different magnitudes depending on the different polyploid species investigated. These gene expression changes affecting newly formed polyploid species may result from various, interconnected mechanisms, including (i) functional interactions between the homoeologous copies and between their products, that are reunited in the same nucleus and cell; (ii) the fate of duplicated copies, selective pressure on one of the parental copy being released which could lead to gene loss, pseudogenization, or alternatively, to subfunctionalization or neofunctionalization; and (iii) epigenetic landscape changes that in turn affect gene expression. As one of the interrelated processes leading to epigenetic regulation of gene expression, the DNA methylation status of newly formed species appears to be consistently affected following both hybridization and genome doubling. In this issue, Verhoeven et al. have investigated the fate of DNA methylation patterns that could affect naturally occurring new asexual triploid lineages of dandelions. As a result of such a ploidy level change, the authors demonstrate stably transmitted DNA methylation changes leading to unique DNA methylation patterns in each newly formed lineage. Most studies published to date on plant DNA methylation polymorphism were performed using restriction enzymes sensitive to methylation. Recently, new high-throughput methods were made available, thanks to the development of 'next-generation sequencing' techniques. The combination of these methods offers powerful and promising tools to investigate epigenetic variation in both model and non-model systems. © 2010 Blackwell Publishing Ltd. Source


Janke B.H.,Iowa State University
Current topics in microbiology and immunology | Year: 2013

In this chapter, the clinical presentations, the development of infection and the macroscopic and microscopic lesions of swine influenza virus (SIV) infection are described. Both natural and experimental infections are discussed. Source


Kezunovic M.,Texas A&M University | McCalley J.D.,Iowa State University | Overbye T.J.,University of Illinois at Urbana - Champaign
Proceedings of the IEEE | Year: 2012

This paper explores how electricity systems may evolve in the 21st century. The paper focuses on some fundamental challenges facing the utilization of electricity today and for years to come. Paralleling the challenges, several directions of how new solutions may emerge are suggested. In this context, some new approaches to manage power system development and deployment are outlined. © 2012 IEEE. Source


Accurately determining the attenuation along the propagation path leading to a region of interest could significantly improve diagnostic ultrasound tissue characterization since tissue characterization requires exact compensation for the frequency-dependent attenuation along the propagation path. In a previous study (JASA, 124:1367, 2008), it was shown that the total attenuation can be determined by using the backscattered echoes from multiple sources. The preliminary computer simulation results, had an average error between -0.3 and +0.2 dB/MHz for the cases tested with a trend towards increasing error with increasing correlation length (i.e., characteristic size of the tissue microstructure of the scattering medium) and attenuation along the propagation path. Therefore, the goal of this study was to improve the accuracy of previously derived algorithm and reduce the dependence of the algorithm on correlation length and attenuation. In this study, the previous derivations were redone and the assumptions made by the algorithm regarding the scattering properties of the medium and the shape of the backscattered power spectrum were relaxed. The revised algorithm was then verified using computer simulations of five sources (6, 8, 10, 12, and 14 MHz, 50% bandwidth) exposing a homogeneous tissue region. The simulated tissue had microstructure following a Gaussian spatial correlation function (i.e., exp (-0.827(kaeff)2) where k is the wavenumber) with effective radii, aeff, of 5-55 μm (one size per simulated case) placed at a density of 250/mm3 (∼5 scatterers/resolution cell for 14 MHz transducer). The attenuation of the tissue was also varied from 0.1 to 0.9 dB/cm-MHz. The computer simulations demonstrated that the modifications significantly improved the accuracy of the algorithm resulting in average errors between -0.04 and 0.1 dB/MHz which is three times better than the error performance of the original algorithm. © 2009 Elsevier B.V. All rights reserved. Source


Dwek E.,NASA | Krennrich F.,Iowa State University
Astroparticle Physics | Year: 2013

The extragalactic background light (EBL) is one of the fundamental observational quantities in cosmology. All energy releases from resolved and unresolved extragalactic sources, and the light from any truly diffuse background, excluding the cosmic microwave background (CMB), contribute to its intensity and spectral energy distribution. It therefore plays a crucial role in cosmological tests for the formation and evolution of stellar objects and galaxies, and for setting limits on exotic energy releases in the universe. The EBL also plays an important role in the propagation of very high energy c-rays which are attenuated en route to Earth by pair producing γ- γ interactions with the EBL and CMB. The EBL affects the spectrum of the sources, predominantly blazars, in the ∼10 GeV-10 TeV energy regime. Knowledge of the EBL intensity and spectrum will allow the determination of the intrinsic blazar spectrum in a crucial energy regime that can be used to test particle acceleration mechanisms and very high energy (VHE) γ-ray production models. Conversely, knowledge of the intrinsic c-ray spectrum and the detection of blazars at increasingly higher redshifts will set strong limits on the EBL and its evolution. This paper reviews the latest developments in the determination of the EBL and its impact on the current understanding of the origin and production mechanisms of c-rays in blazars, and on energy releases in the universe. The review concludes with a summary and future directions in Cherenkov Telescope Array techniques and in infrared ground-based and space observatories that will greatly improve our knowledge of the EBL and the origin and production of very high energy c-rays. © 2012 Elsevier B.V. All rights reserved. Source


Gallus Jr. W.A.,Iowa State University
Weather and Forecasting | Year: 2010

Both the Method for Object-basedDiagnostic Evaluation (MODE) and contiguous rain area (CRA) object-based verification techniques have been used to analyze precipitation forecasts from two sets of ensembles to determine if spread-skill behavior observed using traditional measures can be seen in the object parameters. One set consisted of two eight-member Weather Research and Forecasting (WRF) model ensembles: one having mixed physics and dynamics with unperturbed initial and lateral boundary conditions (Phys) and another using common physics and a dynamic core but with perturbed initial and lateral boundary conditions (IC/LBC). Traditional measures found that spread grows much faster in IC/LBC than in Phys so that after roughly 24 h, better skill and spread are found in IC/LBC. These measures also reflected a strong diurnal signal of precipitation. The other set of ensembles included five members of a 4-km grid-spacing WRF ensemble (ENS4) and five members of a 20-km WRF ensemble (ENS20). Traditional measures suggested that the diurnal signal was better in ENS4 and spread increased more rapidly than in ENS20. Standard deviations (SDs) of four object parameters computed for the first set of ensembles using MODE and CRA showed the trend of enhanced spread growth in IC/LBC compared to Phys that had been observed in traditional measures, with the areal coverage of precipitation exhibiting the greatest growth in spread with time. The two techniques did not produce identical results; although, they did show the same general trends.A diurnal signal could be seen in the SDs of all parameters, especially rain rate, volume, and areal coverage. MODE results also found evidence of a diurnal signal and faster growth of spread in object parameters in ENS4 than in ENS20. Some forecasting approaches based onMODEand CRAoutput are also demonstrated. Forecasts based on averages of object parameters from each ensemble member were more skillful than forecasts based on MODE or CRA applied to an ensemble mean computed using the probability matching technique for areal coverage and volume, but differences in the two techniques were less pronounced for rain rate and displacement. The use of a probability threshold to define objects was also shown to be a valid forecasting approach with MODE. © 2010 American Meteorological Society. Source


Ni N.,Princeton University | Bud'Ko S.L.,Iowa State University
MRS Bulletin | Year: 2011

We present a brief review of the phase diagrams of the transition metal, electron-doped BaFe2As2 systems and a comparison between them. This article also reviews the phase diagrams of hole-and isoelectronic-doped BaFe2As2, as well as BaFe 2As2 under pressure. Empirical rules on the conditions necessary to induce superconductivity in this material are outlined. Evidence for multiple Lifshitz transitions in Co-doped BaFe2As2 and possible connections to superconductivity are also discussed. © 2011 Materials Research Society. Source


Lamsal B.P.,Iowa State University
Journal of the Science of Food and Agriculture | Year: 2012

Galactooligosaccharides are sugars composed of 3-10 molecules of galactose and glucose via a transgalactosylation reaction mediated by the enzyme β-galactosidase. Prebiotics are non-digestible food ingredients that pass through the upper digestive system relatively intact and ferment in the lower colon, producing short-chain fatty acids that support the growth of supplemented or indigenous colonic microbiota. Galactooligosaccharides and other prebiotic ingredients are increasingly being recognized as useful dietary tools for the modulation of the colonic microflora toward a healthy balance. Galactooligosaccharides compare well to other oligosaccharides in terms of their prebiotic, immunomodulation, and functional properties in foods. This review elucidates the galactooligosaccharide production process from refined lactose and/or cheese whey permeates, galactooligosaccharide market share and economic value, their health properties, and potential food applications. © 2012 Society of Chemical Industry. Source


Walters G.D.,Kutztown University of Pennsylvania | DeLisi M.,Iowa State University
Law and Human Behavior | Year: 2015

The purpose of this study was to determine whether proactive and reactive antisocial cognition mediate the effect of Factors 1 (core personality features) and 2 (behavioral deviance) of the Psychopathy Checklist: Youth Version (PCL: YV; Forth, Kosson, and Hare, 2003) on violent offending. In this study Bandura et al.'s (1996) Moral Disengagement (MD) scale and the Impulse Control (IC) scale of the Weinberger Adjustment Inventory (WAI; Weinberger and Schwartz, 1990) served as proxies for proactive and reactive antisocial cognition, respectively. It was hypothesized that proactive antisocial cognition (MD) would mediate the Factor 1'violence relationship and that both proactive antisocial cognition and reactive antisocial cognition (IC) would mediate the Factor 2'violence relationship. A 3-wave path analysis of data from 1,354 adjudicated delinquents produced results consistent with the first part of the hypothesis (i.e., proactive antisocial mediation of the Factor 1'violence relationship) but inconsistent with the second part of the hypothesis (i.e., only proactive antisocial cognition mediated the Factor 2'violence relationship). Whereas the direct path from Factor 1 to violent offending was no longer significant when MD and IC were taken into account, the direct path from Factor 2 to violent offender remained significant even after MD and IC were included as mediators. This suggests that whereas proactive antisocial cognition plays a major role in mediating the Factor 1'violence relationship, the Factor 2'violence relationship is mediated by proactive antisocial cognition and variables not included or not adequately covered in the current study. © 2015 American Psychological Association. Source


Kato-Noguchi H.,Kagawa University | Peters R.J.,Iowa State University
Journal of Chemical Ecology | Year: 2013

Large field screening programs and laboratory experiments in many countries have indicated that rice is allelopathic and releases allelochemical(s) into its environment. A number of compounds, such as phenolic acids, fatty acids, phenylalkanoic acids, hydroxamic acids, terpenes, and indoles, have been identified as potential rice allelochemicals. However, the studies reviewed here demonstrate that the labdane-related diterpenoid momilactones are the most important, with momilactone B playing a particularly critical role. Rice plants secrete momilactone B from their roots into the neighboring environments over their entire life cycle at phytotoxic levels, and momilactone B seems to account for the majority of the observed rice allelopathy. In addition, genetic studies have shown that selective removal of the momilactones only from the complex mixture found in rice root exudates significantly reduces allelopathy, demonstrating that these serve as allelochemicals, the importance of which is reflected in the presence of a dedicated momilactone biosynthetic gene cluster in the rice genome. © 2013 Springer Science+Business Media New York. Source


Zhu D.,Iowa State University
Decision Support Systems | Year: 2010

An ensemble of classifiers, or a systematic combination of individual classifiers, often results in better classifications in comparison to a single classifier. However, the question regarding what classifiers should be chosen for a given situation to construct an optimal ensemble has often been debated. In addition, ensembles are often computationally expensive since they require the execution of multiple classifiers for a single classification task. To address these problems, we propose a hybrid approach for selecting and combining data mining models to construct ensembles by integrating Data Envelopment Analysis and stacking. Experimental results show the efficiency and effectiveness of the proposed approach. © 2009 Elsevier B.V. All rights reserved. Source


Yang X.,Broad Institute | Chockalingam S.P.,Indian Institute of Technology Bombay | Aluru S.,Iowa State University
Briefings in Bioinformatics | Year: 2013

Error Correction is important for most next-generation sequencing applications because highly accurate sequenced reads will likely lead to higher quality results. Many techniques for error correction of sequencing data from next-gen platforms have been developed in the recent years. However, compared with the fast development of sequencing technologies, there is a lack of standardized evaluation procedure for different error-correction methods, making it difficult to assess their relative merits and demerits. In this article, we provide a comprehensive review of many error-correction methods, and establish a common set of benchmark data and evaluation criteria to provide a comparative assessment. We present experimental results on quality, run-time, memory usage and scalability of several error-correction methods. Apart from providing explicit recommendations useful to practitioners, the review serves to identify the current state of the art and promising directions for future research. Availability: All error-correction programs used in this article are downloaded from hosting websites. The evaluation tool kit is publicly available at: http://aluru-sun.ece.iastate.edu/doku.php?id=ecr. © The Author 2012. Published by Oxford University Press. Source


West R.,Iowa State University | Bailey K.,University of Missouri
Psychophysiology | Year: 2012

Event-related brain potentials (ERPs) were used to examine the neural correlates of proactive and reactive cognitive control within the context of the Dual Mechanisms of Control theory. Individuals performed the counting Stroop task and the proportion of congruent and incongruent trials was varied across blocks. The Stroop effect was smaller in the mostly incongruent block than in the mostly congruent block. The ERP data revealed a double dissociation between the medial frontal negativity (MFN) and the medial posterior negativity (MPN), where the amplitude of the MFN was greater in the mostly incongruent block and the amplitude of the MPN was greater in the mostly congruent block. The ERP data also revealed slow wave activity that distinguished the mostly incongruent and mostly congruent blocks. These findings support the idea that different regions of the cingulate and anterior frontal cortex underpin proactive and reactive control. © 2012 Society for Psychophysiological Research. Source


Jiang Z.,Iowa State University
Decision Support Systems | Year: 2010

Free software offer as a promotional tool has been employed by software firms of all sizes. In this research, we propose an extended multi-generation diffusion model that separates substitution from switching, and develop methodologies to help a firm determine the optimal number of free adoptions for each version. Our analyses show that due to the word-of-mouth effect, free offer can help increase a firm's total profit for all versions of a product. Furthermore, we find that in the presence of low-valuation free adopters, the optimal number of high-valuation free adopters decreases, the total number of free adopters increases, and the total profit improves substantially as a result. © 2010 Elsevier B.V. All rights reserved. Source


Laurson K.R.,Illinois State University | Welk G.J.,Iowa State University | Eisenmann J.C.,Michigan State University
Pediatrics | Year: 2014

OBJECTIVES: To compare the diagnostic performance of the Centers for Disease Control and Prevention (CDC) and FITNESSGRAM (FGram) BMI standards for quantifying metabolic risk in youth. METHODS: Adolescents in the NHANES (n = 3385) were measured for anthropometric variables and metabolic risk factors. BMI percentiles were calculated, and youth were categorized by weight status (using CDC and FGram thresholds). Participants were also categorized by presence or absence of metabolic syndrome. The CDC and FGram standards were compared by prevalence of metabolic abnormalities, various diagnostic criteria, and odds of metabolic syndrome. Receiver operating characteristic curves were also created to identify optimal BMI percentiles to detect metabolic syndrome. RESULTS: The prevalence of metabolic syndrome in obese youth was 19% to 35%, compared with <2% in the normal-weight groups. The odds of metabolic syndrome for obese boys and girls were 46 to 67 and 19 to 22 times greater, respectively, than for normal-weight youth. The receiver operating characteristic analyses identified optimal thresholds similar to the CDC standards for boys and the FGram standards for girls. Overall, BMI thresholds were more strongly associated with metabolic syndrome in boys than in girls. CONCLUSIONS: Both the CDC and FGram standards are predictive of metabolic syndrome. The diagnostic utility of the CDC thresholds outperformed the FGram values for boys, whereas FGram standards were slightly better thresholds for girls. The use of a common set of thresholds for school and clinical applications would provide advantages for public health and clinical research and practice. Copyright © 2014 by the American Academy of Pediatrics. Source


Momeni K.,Iowa State University
Nano Energy | Year: 2014

A multiscale approach is pursued to develop a modified shear-lag model for capturing size-scale effects on electrostatic potential generated by a zinc oxide (ZnO) nanowire (NW) in a nanocomposite electrical generator (NCEG). The size-scale effect on elastic modulus of ZnO NWs is captured using a core-surface model. Closed form of governing equations is derived considering linear elasticity for axisymmetric problem and cylindrical coordinate system. Two different configurations based on parallel and series connecting of NCEGs for application in NEMS/MEMS devices are also studied. Parametric studies are performed for sample cases to demonstrate application of the developed model. It is shown that aspect ratio and diameter of NWs are crucial controlling parameters for determining the performance of nanocomposite electrical generators. Numerical results disclose that there is an optimum aspect ratio for each NW of specific diameter. It was also shown that despite the symmetry of loading with respect to mid-plane normal to the NW's axis, the electric potential is not symmetric. © 2013 Elsevier Ltd. Source


Ramamoorthy A.,Iowa State University | Langberg M.,Open University of Israel
IEEE Journal on Selected Areas in Communications | Year: 2013

We consider the network communication scenario, over directed acyclic networks with unit capacity edges in which a number of sources si each holding independent unit-entropy information Xi wish to communicate the sum sum Xi to a set of terminals tj. We show that in the case in which there are only two sources or only two terminals, communication is possible if and only if each source terminal pair s i/tj is connected by at least a single path. For the more general communication problem in which there are three sources and three terminals, we prove that a single path connecting the source terminal pairs does not suffice to communicate sum Xi. We then present an efficient encoding scheme which enables the communication of \sum Xi for the three sources, three terminals case, given that each source terminal pair is connected by em two edge disjoint paths. © 1983-2012 IEEE. Source


Hong W.,Iowa State University | Zhao X.,Harvard University | Suo Z.,Harvard University
Journal of the Mechanics and Physics of Solids | Year: 2010

Immersed in an ionic solution, a network of polyelectrolytes imbibes the solution and swells, resulting in a polyelectrolyte gel. The swelling is reversible, and the amount of swelling is regulated by ionic concentrations, mechanical forces, and electric potentials. This paper develops a field theory to couple large deformation and electrochemistry. A specific material model is described, including the effects of stretching the network, mixing the polymers with the solvent and ions, and polarizing the gel. We show that the notion of osmotic pressure in a gel has no experimental significance in general, but acquires a physical interpretation within the specific material model. The theory is used to analyze several phenomena: a gel swells freely in an ionic solution, a gel swells under a constraint of a substrate, electric double layer at the interface between the gel and the external solution, and swelling of a gel of a small size. © 2010 Elsevier Ltd. All rights reserved. Source


D'Alessandro D.,Iowa State University
Systems and Control Letters | Year: 2013

We consider a control scheme where a quantum system S is put in contact with an auxiliary quantum system A and the control can affect A only, while S is the system of interest. The system S is then controlled indirectly through the interaction with A. Complete controllability of S+A means that every unitary state transformation for the system S+A can be achieved with this scheme. Indirect controllability means that every unitary transformation on the system S can be achieved. We prove in this paper, under appropriate conditions and definitions, that these two notions are equivalent in finite dimension. We use Lie algebraic methods to prove this result. © 2012 Elsevier B.V. All rights reserved. Source


Cutler T.D.,Iowa State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2011

We review the principles of ultraviolet (UV) irradiation, the inactivation of infectious agents by UV, and current applications for the control of microorganisms. In particular, wavelengths between 200 and 280 nm (germicidal UV) affect the double-bond stability of adjacent carbon atoms in molecules including pyrimidines, purines and flavin. Thus, UV inactivation of microorganisms results from the formation of dimers in RNA (uracil and cytosine) and DNA (thymine and cytosine). The classic application of UV irradiation is the inactivation of microorganisms in biological safety cabinets. In the food-processing industry, germicidal UV irradiation has shown potential for the surface disinfection of fresh-cut fruit and vegetables. UV treatment of water (potable and wastewater) is increasingly common because the process is effective against a wide range of microorganisms, overdose is not possible, chemical residues or by-products are avoided, and water quality is unaffected. UV has been used to reduce the concentration of airborne microorganisms in limited studies, but the technology will require further development if it is to gain wider application. For bioaerosols, the primary technical challenge is delivery of sufficient UV irradiation to large volumes of air, but the absence of UV inactivation constants for airborne pathogens under a range of environmental conditions (temperature, relative humidity) further compounds the problem. Source


Schwartz T.J.,University of Wisconsin - Madison | O'Neill B.J.,University of Wisconsin - Madison | Shanks B.H.,Iowa State University | Dumesic J.A.,University of Wisconsin - Madison
ACS Catalysis | Year: 2014

Recent advances in metabolic engineering have allowed for the production of a wide array of molecules via biocatalytic routes. The high selectivity of biocatalysis to remove functionality from biomass can be used to produce platform molecules that are suitable for subsequent upgrading over heterogeneous catalysts. Accordingly, the more robust continuous processing allowed by chemical catalysis could be leveraged to upgrade biologically derived platform molecules to produce direct or functional replacements for petroleum products. Herein, we highlight recent results that utilize a combination of chemical and biological catalysis, and using the perspective of heterogeneous chemical catalysis, we identify challenges that need to be addressed to bridge the gap between the two catalytic approaches. Specifically, studies are required to address the effects on catalyst performance of impurities that originate during bioprocessing. In addition, new generations of heterogeneous catalysts are required for stable operation under liquid phase reaction conditions in the presence of biogenic impurities. Finally, the design and syntheses of new catalysts are required to tailor the active sites and the environment around these sites to achieve selective conversion of the functional groups present in biologically derived platform molecules. © 2014 American Chemical Society. Source


Yu H.,CAS South China Botanical Garden | Nason J.D.,Iowa State University
New Phytologist | Year: 2013

This study uses a phylogeographic approach to investigate how interspecific interactions in an obligate pollination mutualism enhance or constrain dispersal and the range distributions of species through time. Fifteen populations of Ficus hirta, a bird-dispersed fig pollinated by a species-specific fig wasp, were sampled from Thailand to the northern limits of the tropical forest in China. These populations were assayed for six nuclear microsatellite loci and two intergenic chloroplast DNA sequences. Analyses of range expansion and genetic clustering indicated a relatively slow rate of range expansion from two or more southern glacial refugia. Low nuclear differentiation, combined with high interpopulation differentiation, and phylogeographic structuring of chloroplast variation indicated that seed dispersal has had a greater constraint than obligate interactions with fig wasps on the rate of post-glacial range expansion. This study is the first to investigate the phylogeographic history of a widely distributed southeast Asian tropical plant whose distribution extends to the northern limits of tropical forest habitat in China. It is also the first study of Ficus utilizing molecular data to evaluate whether species-specific pollination is a limitation or an aid to range expansion in response to climate change. © 2012 New Phytologist Trust. Source


Travesset A.,Iowa State University
Science | Year: 2011

A set of simple rules is used to design and control the self-assembly of nanoparticles into complex structures. Source


Mittal S.,Iowa State University
International Journal of Computer Aided Engineering and Technology | Year: 2014

Recent technological advances have greatly improved the performance and features of embedded systems. With the number of just mobile devices now reaching nearly equal to the population of Earth, embedded systems have truly become ubiquitous. These trends, however, have also made the task of managing their power consumption extremely challenging. In recent years, several techniques have been proposed to address this issue. In this paper, we survey the techniques for managing power consumption of embedded systems. We discuss the need of power management and provide a classification of the techniques on several important parameters to highlight their similarities and differences. This paper is intended to help the researchers and application-developers in gaining insights into the working of power management techniques and designing even more efficient high-performance embedded systems of tomorrow. Copyright © 2014 Inderscience Enterprises Ltd. Source


Goldman A.I.,Iowa State University
Science and Technology of Advanced Materials | Year: 2014

Progress in our understanding of the magnetic properties of R-containing icosahedral quasicrystals (R = rare earth element) from over 20 years of experimental effort is reviewed. This includes the much studied R-Mg-Zn and R-Mg-Cd ternary systems, as well as several magnetic quasicrystals that have been discovered and investigated more recently including Sc-Fe-Zn, R-Ag-In, Yb-Au-Al, the recently synthesized R-Cd binary quasicrystals, and their periodic approximants. In many ways, the magnetic properties among these quasicrystals are very similar. However, differences are observed that suggest new experiments and promising directions for future research. © 2014 National Institute for Materials Science. Source


Bakac A.,Iowa State University
Inorganic Chemistry | Year: 2010

Coordination to transition-metal complexes changes both the thermodynamics and kinetics of oxygen reduction. Some of the intermediates (superoxo, hydroperoxo, and oxo species) are close analogues of organic oxygen-centered radicals and peroxides (ROO•, ROOH, and RO•). Metal-based intermediates are typically less reactive, but more persistent, than organic radicals, which makes the two types of intermediates similarly effective in their reactions with various substrates. The self-exchange rate constant for hydrogen-atom transfer for the couples CraqOO 2+/CraqOOH2+ and L1(H 2O)RhOO2+/L1(H2O)RhOOH2+ was estimated to be 101±1 M-1 s-1. The use of this value in the simplified Marcus equation for the Cr aqO2+/CraqOOH2+ cross reaction provided an upper limit kCrO,CrOH ≤10(-2±1) M-1 s-1 for CraqO2+/Cr aqOH2+ self-exchange. Even though superoxo complexes react very slowly in bimolecular self-reactions, extremely fast cross reactions with organic counterparts, i.e., acylperoxyl radicals, have been observed. Many of the intermediates generated by the interaction of O2 with reduced metal complexes can also be accessed by alternative routes, both thermal and photochemical. © 2010 American Chemical Society. Source


Corbett J.D.,Iowa State University
Inorganic Chemistry | Year: 2010

Exploratory synthetic adventures regarding the inorganic chemistry of polar intermetalllc phases have proven to be especially productive of novel compositions, new and unprecedented structures, and unusual bonding regimes. Reactions of diverse elements with widely different electronegativities allow the definition of two opposed classes of products: polycationic or polyanionic clusters or networks of metals paired with the corresponding monatomic anions or cations. These can be usefully viewed as Intermetallic "salts", redox products of simpler neutral intermetallic systems but with widely different factors governing their stabilities. Thus, combinations of rare-earth metals alone or with late transition metals form a novel variety of polymetal network structures with relatively isolated telluride (or halide) spacer anions. Similarly, extensions of traditional Zintl phases of the alkali or alkaline-earth metals from the later p elements to the earlier triels, Ga-TI especially, yield many new and elegant polyanionic structures. The substitution or addition of still earlier p or late d metal components produces still electron-poorer and more condensed polar intermetallic phases with increasingly delocalized bonding, higher coordination numbers, and more unusual structures and bonding. These discoveries have also led to new approaches: electronic tuning via band calculations to generate new families of quasicrystals and their crystalline approximatifs with their characteristic structural regimes and regularities. Gold as a substituent generates particularly novel bonding In arrays of mixed metals or polygold anionic networks. © 2009 American Chemical Society. Source


Luo S.,Iowa State University
Journal of Computational Physics | Year: 2013

A uniformly second order method with a local solver based on the piecewise linear discontinuous Galerkin formulation is introduced to solve the eikonal equation with Dirichlet boundary conditions. The method utilizes an interesting phenomenon, referred as the superconvergence phenomenon, that the numerical solution of monotone upwind schemes for the eikonal equation is first order accurate on both its value and gradient when the solution is smooth. This phenomenon greatly simplifies the local solver based on the discontinuous Galerkin formulation by reducing its local degrees of freedom from two (1-D) (or three (2-D), or four (3-D)) to one with the information of the gradient frozen. When considering the eikonal equation with point-source conditions, we further utilize a factorization approach to resolve the source singularities of the eikonal by decomposing it into two parts, either multiplicatively or additively. One part is known and captures the source singularities; the other part serves as a correction term that is differentiable at the sources and satisfies the factored eikonal equations. We extend the second order method to solve the factored eikonal equations to compute the correction term with second order accuracy, then recover the eikonal with second order accuracy. Numerical examples are presented to demonstrate the performance of the method. © 2013 Elsevier Inc. Source


Liu J.,Iowa State University
Computer Physics Communications | Year: 2013

A least square based fitting scheme is proposed to extract an optimal one-particle spectral function from any one-particle temperature Green function. It uses the existing non-negative least square (NNLS) fit algorithm to do the fit, and Tikhonov regularization to help with possible numerical singular behaviors. By flexibly adding delta peaks to represent very sharp features of the target spectrum, this scheme guarantees a global minimization of the fitted residue. The performance of this scheme is manifested with diverse physical examples. The proposed scheme is shown to be comparable in performance to the standard Padé analytic continuation scheme. © 2012 Elsevier B.V. All rights reserved. Source


Martin R.J.,Iowa State University
Advances in Experimental Medicine and Biology | Year: 2010

There are a number of reasons why the development of novel anthelmintics is very necessary.1 In domestic animals, parasites cause serious loss of production and are a welfare concern. The control of these parasites requires changes in management practices to reduce the spread of infection and the use of therapeutic agents to treat affected animals. The development of vaccines against parasites is desirable but their development so far has been very limited. One notable exception is the vaccination of calves against infection by Dictyocaulus viviparous (lungworm) which has proved to be very effective.2 In domestic animals, the total market for anti-parasitic agents (both ecto- and endo-parasites) is in excess of a billion US dollars. In humans there are serious problems of morbidity and mortality associated with parasite infections. 1.6 billion People throughout the world are infected with ascariasis (Fig. 1A) and/or hookworm. Approximately one-third of the world's population is suffering from the effects of intestinal nematode parasites, causing low growth-rates in infants, ill-thrift, diarrhea and in 2% of cases, loss of life. Despite the huge number of affected individuals, the market for anti-parasitic drugs for humans is not big enough to foster the development of anthelmintics because most infestations that occur are in undeveloped countries that lack the ability to pay for the development of these drugs. The major economic motivator then, is for the development of animal anthelmintics. In both domestic animals and now in humans, there is now a level of resistance to the available anthelmintic compounds.2 The resistance is either: constitutive, where a given species of parasite has never been sensitive to the compound; or acquired, where the resistance has developed through Darwinian selection fostered by the continued exposure to the anti-parasitic drugs. The continued use of all anthelmintics has and will, continue to increase the level of resistance. Cure rates are now often less than 100% and resistance of parasites to agents acting on the neuromuscular systems is present in a wide range of parasites of animals and humans hosts.3,4 In the face of this resistance the development of novel and effective agents is an urgent and imperative need. New drugs which act on the neuromuscular system have an advantage for medication for animals and humans because they have a rapid therapeutic effect within 3 hours of administration. The effects on the neuromuscular system include: spastic paralysis with drugs like levamisole and pyrantel; flaccid paralysis as with piperazine; or disruption of other vital muscular © 2010 Landes Bioscience and Springer Science+Business Media. Source


Han J.,Iowa State University
Frontiers in cellular and infection microbiology | Year: 2012

The prevalence of fluoroquinolone (FQ)-resistant Campylobacter has become a concern for public health. To facilitate the control of FQ-resistant (FQ(R)) Campylobacter, it is necessary to understand the impact of FQ(R) on the fitness of Campylobacter in its natural hosts as understanding fitness will help to determine and predict the persistence of FQ(R)Campylobacter. Previously it was shown that acquisition of resistance to FQ antimicrobials enhanced the in vivo fitness of FQ(R)Campylobacter. In this study, we confirmed the role of the Thr-86-Ile mutation in GyrA in modulating Campylobacter fitness by reverting the mutation to the wild-type (WT) allele, which resulted in the loss of the fitness advantage. Additionally, we determined if the resistance-conferring GyrA mutations alter the enzymatic function of the DNA gyrase. Recombinant WT gyrase and mutant gyrases with three different types of mutations (Thr-86-Ile, Thr-86-Lys, and Asp-90-Asn), which are associated with FQ(R) in Campylobacter, were generated in E. coli and compared for their supercoiling activities using an in vitro assay. The mutant gyrase with the Thr-86-Ile change showed a greatly reduced supercoiling activity compared with the WT gyrase, while other mutant gyrases did not show an altered supercoiling. Furthermore, we measured DNA supercoiling within Campylobacter cells using a reporter plasmid. Consistent with the results from the in vitro supercoiling assay, the FQ(R) mutant carrying the Thr-86-Ile change in GyrA showed much less DNA supercoiling than the WT strain and the mutant strains carrying other mutations. Together, these results indicate that the Thr-86-Ile mutation, which is predominant in clinical FQ(R)Campylobacter, modulates DNA supercoiling homeostasis in FQ(R)Campylobacter. Source


Johnston D.C.,Iowa State University
Physical Review Letters | Year: 2012

Predictions of the anisotropic magnetic susceptibility χ below the antiferromagnetic (AFM) ordering temperatures T N of local moment Heisenberg AFMs have been made previously using molecular field theory (MFT) but are very limited in their applicability. Here a MFT calculation of χ(T≤T N) is presented for a wide variety of collinear and noncollinear Heisenberg AFMs containing identical crystallographically equivalent spins without recourse to magnetic sublattices. The results are expressed in terms of directly measurable experimental parameters and are fitted with no adjustable parameters to experimental χ(T≤T N) data from the literature for several collinear and noncollinear AFMs. The influence of spin correlations and fluctuations beyond MFT is quantified by the deviation of the theory from the data. The origin of the universal χ(T≤T N) observed for triangular lattice AFMs exhibiting coplanar noncollinear 120° AFM ordering is clarified. © 2012 American Physical Society. Source


Garrod R.T.,Cornell University | Pauly T.,Iowa State University
Astrophysical Journal | Year: 2011

We investigate the formation and evolution of interstellar dust-grain ices under dark-cloud conditions, with a particular emphasis on CO2. We use a three-phase model (gas/surface/mantle) to simulate the coupled gas-grain chemistry, allowing the distinction of the chemically active surface from the ice layers preserved in the mantle beneath. The model includes a treatment of the competition between barrier-mediated surface reactions and thermal-hopping processes. The results show excellent agreement with the observed behavior of CO2, CO, and water ice in the interstellar medium. The reaction of the OH radical with CO is found to be efficient enough to account for CO 2 ice production in dark clouds. At low visual extinctions, with dust temperatures ≳12K, CO2 is formed by direct diffusion and reaction of CO with OH; we associate the resultant CO2-rich ice with the observational polar CO2 signature. CH4 ice is well correlated with this component. At higher extinctions, with lower dust temperatures, CO is relatively immobile and thus abundant; however, the reaction of H and O atop a CO molecule allows OH and CO to meet rapidly enough to produce a CO:CO2 ratio in the range 2-4, which we associate with apolar signatures. We suggest that the observational apolar CO2/CO ice signatures in dark clouds result from a strongly segregated CO:H 2O ice, in which CO2 resides almost exclusively within the CO component. Observed visual-extinction thresholds for CO2, CO, and H2O are well reproduced by depth-dependent models. Methanol formation is found to be strongly sensitive to dynamical timescales and dust temperatures. © 2011. The American Astronomical Society. All rights reserved.. Source


Hong M.,Iowa State University | DeGrado W.F.,University of California at San Francisco
Protein Science | Year: 2012

The influenza M2 protein forms an acid-activated and drug-sensitive proton channel in the virus envelope that is important for the virus lifecycle. The functional properties and high-resolution structures of this proton channel have been extensively studied to understand the mechanisms of proton conduction and drug inhibition. We review biochemical and electrophysiological studies of M2 and discuss how high-resolution structures have transformed our understanding of this proton channel. Comparison of structures obtained in different membrane-mimetic solvents and under different pH using X-ray crystallography, solution NMR, and solid-state NMR spectroscopy revealed how the M2 structure depends on the environment and showed that the pharmacologically relevant drug-binding site lies in the transmembrane (TM) pore. Competing models of proton conduction have been evaluated using biochemical experiments, high-resolution structural methods, and computational modeling. These results are converging to a model in which a histidine residue in the TM domain mediates proton relay with water, aided by microsecond conformational dynamics of the imidazole ring. These mechanistic insights are guiding the design of new inhibitors that target drug-resistant M2 variants and may be relevant for other proton channels. © 2012 The Protein Society. Source


Soukoulis C.M.,Iowa State University | Soukoulis C.M.,Foundation for Research and Technology Hellas | Wegener M.,Karlsruhe Institute of Technology
Nature Photonics | Year: 2011

Photonic metamaterials are man-made structures composed of tailored micro- or nanostructured metallodielectric subwavelength building blocks. This deceptively simple yet powerful concept allows the realization of many new and unusual optical properties, such as magnetism at optical frequencies, negative refractive index, large positive refractive index, zero reflection through impedance matching, perfect absorption, giant circular dichroism and enhanced nonlinear optical properties. Possible applications of metamaterials include ultrahigh-resolution imaging systems, compact polarization optics and cloaking devices. This Review describes recent progress in the fabrication of three-dimensional metamaterial structures and discusses some of the remaining challenges. © 2011 Macmillan Publishers Limited. All rights reserved. Source


Kraus B.L.H.,Iowa State University
Journal of the American Veterinary Medical Association | Year: 2014

Objective-To evaluate the effectiveness of orally administered maropitant citrate in preventing vomiting after hydromorphone hydrochloride administration in dogs. Design-Randomized, blinded, prospective clinical study. Animals-40 dogs with American Society of Anesthesiologists status of I or II, > 6 months of age, and weighing between 24 and 58.2 kg (52.8 and 128.04 lb). Procedures-Dogs were randomly selected to receive maropitant (2.0 to 4.0 mg/kg [0.9 to 1.8 mg/lb]) or placebo (lactose monohydrate) orally 2 hours prior to receiving hydromorphone (0.1 mg/kg [0.045 mg/lb], IM). A blinded observer recorded the occurrence of vomiting or signs of nausea (eg, salivation or lip-licking) during a 30-minute period after hydromorphone administration. Two-tailed Fisher exact tests were used to compare the incidences of vomiting and signs of nausea with or without vomiting between treatment groups. Results-Of the 20 dogs receiving maropitant, none vomited but 12 (60%) developed signs of nausea. Of the 20 dogs receiving placebo, 5 (25%) vomited and 11 (55%) developed signs of nausea; overall, 16 of 20 (80%) dogs in the placebo treatment group vomited or developed signs of nausea. Compared with the effects of placebo, maropitant significantly decreased the incidence of vomiting but not signs of nausea in dogs administered hydromorphone. Conclusions and Clinical Relevance-Among the 40 study dogs, the incidence of vomiting associated with hydromorphone administration was 25%. Oral administration of maropitant prevented vomiting but not signs of nausea associated with hydromorphone administration in dogs. Source


Becraft P.W.,Iowa State University | Gutierrez-Marcos J.,University of Warwick
Wiley Interdisciplinary Reviews: Developmental Biology | Year: 2012

The endosperm is a product of fertilization that evolved to support and nourish its genetic twin sibling embryo. Cereal endosperm accumulates starch and protein stores, which later support the germinating seedling. These nutritional stores prompted the domestication of cereals and are the focus of ongoing efforts for crop improvement and biotechnological innovations. Endosperm development entails several novel modifications to basic cellular and developmental processes. Cereals display nuclear endosperm development, which begins with a period of free nuclear division to generate a coenocyte. Cytoskeletal arrays distribute nuclei around the periphery of the cytoplasm and direct the subsequent deposition of cell wall material during cellularization. Positional cues and signaling systems function dynamically in the specification of the four major cell types: transfer cells, embryo-surrounding cells, starchy endosperm (SE), and aleurone. Genome balance, epigenetic gene regulation, and parent-of-origin effects are essential for directing these processes. Transfer cells transport solutes, including sugars and amino acids, from the maternal plant tissues into the developing grain where they are partitioned between embryo and SE cells. Cells of the embryo-surrounding region appear to coordinate development of the embryo and endosperm. As the seed matures, SE cells assimilate starch and protein stores, undergo DNA endoreduplication, and finally undergo programmed cell death. In contrast, aleurone cells follow a maturation program similar to the embryo, allowing them to survive desiccation. At germination, the aleurone cells secrete amylases and proteases that hydrolyze the storage products of the SE to nourish the germinating seedling. © 2012 Wiley Periodicals, Inc. Source


Bowler N.,Iowa State University
Measurement Science and Technology | Year: 2011

The technique of measuring the voltage difference (potential drop) between two of the four electrodes of a four-point probe, in order to determine conductivity or surface resistivity of a test piece, is well established in the direct-current (dc) or quasi-dc regime. The technique finds wide usage in the semiconductor industry for the purpose of measuring surface resistivity of semiconductors, and also in the measurement of conductivity of metals, particularly of ferromagnetic metals for which conductivity cannot be easily measured using eddy-current nondestructive evaluation (NDE). In these applications, the conductivity of the test piece is deduced from an analytic formula that depends on the geometry of the probe and test piece. Such a formula requires, as an input, the measured value of the potential drop. Several analytical expressions exist for a variety of test-piece geometries and probe arrangements. Recently, it has been shown that broadband measurements of the potential drop, known as 'alternating current potential drop' (ac PD) measurements, can be used not only to obtain the conductivity of a test piece, but also its linear permeability μ. The beauty of this measurement is that the two parameters are completely decoupled in the quasi-static regime. In fact, μ does not appear in the quasi-static expression for σ. Hence, σ may be obtained from low-frequency ac PD measurements and then μ may be deduced as the frequency increases beyond the quasi-static regime, once σ is known. In this review, both dc and ac solutions that are useful in determining the conductivity of metals and semiconductors, and the permeability of ferromagnetic conductors, are summarized. In particular, flat test pieces with arbitrary thickness are considered. At the next level of complexity, a solution for a half-space coated with a surface layer is given, along with a discussion of the use of the four-point potential drop method for determining thickness of a surface layer, such as exists as the result of a surface-hardening process. Recent literature on the topic of surface crack sizing using dc and ac PD is briefly summarized and simple formulas for determining the depth of a long surface crack from ac PD measurements are given. The review also includes four-point potential drop data measured on surface-hardened steel rods and points toward how those data may be used to determine the depth of surface hardening. © 2011 IOP Publishing Ltd. Source


Hay Kraus B.L.,Iowa State University
Journal of the American Veterinary Medical Association | Year: 2014

Objective—To evaluate the effect of dosing interval on the efficacy of maropitant for prevention of opioid-induced vomiting and signs of nausea in dogs.Design—Randomized prospective clinical study.Animals—50 client-owned dogs that underwent an elective surgical procedure.Procedures—Dogs were randomly assigned to receive maropitant (1 mg/kg [0.45 mg/lb], SC), then hydromorphone (0.1 mg/kg [0.045 mg/lb], IM) at 0 (simultaneously; group 0; n = 10), 15 (group 15; 10), 30 (group 30; 10), 45 (group 45; 10), or 60 (group 60; 10) minutes later. Dogs were monitored for vomiting and signs of nausea for 30 minutes after hydromorphone administration. A historical control group of similar dogs (n = 9) that were administered hydromorphone (0.1 mg/kg, IM) but not maropitant served as the referent for comparison purposes.Results—Vomiting was recorded for 6 dogs in group 0 and 2 dogs in group 15. Signs of nausea were recorded for 10 dogs in group 0, 9 dogs in group 15, 8 dogs in group 30, 6 dogs in group 45, and 1 dog in group 60. Compared with dogs in the historical control group, vomiting was significantly decreased and prevented when maropitant was administered 15 and 30 minutes, respectively, before hydromorphone; signs of nausea were significantly decreased only when maropitant was administered 60 minutes before hydromorphone.Conclusions and Clinical Relevance—Results indicated that vomiting was significantly decreased and then prevented when maropitant was administered to dogs 15 and 30 minutes before hydromorphone. However, signs of nausea were significantly decreased only when the dosing interval was 60 minutes. © 2014 American Veterinary Medical Association. Source


Zhu Y.,University of Iowa | Hollis J.H.,Iowa State University
Journal of the Academy of Nutrition and Dietetics | Year: 2014

Eating slowly contributes to a lower risk of obesity, probably because it could aid appetite control. Chewing thoroughly is an effective strategy to reduce eating rate; however, insufficient data are available to demonstrate the relationship between such an eating behavior and energy intake. To investigate the effect of increasing the number of chews before swallowing on meal size, a randomized cross-over trial was conducted in 18- to 45-year-old normal-weight, overweight, and obese participants (n=45) who were recruited from the local community (Ames, IA). After assessment of baseline number of chews, participants were asked to attend three test sessions to eat pizza for lunch until comfortably full by chewing each portion of food either 100%, 150%, or 200% of their baseline number of chews before swallowing. Two-way analysis of variance was used to test the effect of treatment and body-weight status, as well as their interactions on food intake, meal duration, eating rate, and appetite at meal termination. Appetite data during 60 minutes were analyzed by repeated measures analysis of variance. Food intake in the sessions with 150% and 200% of their baseline number of chews was reduced significantly, by 9.5% and 14.8%, respectively, compared with the 100% session. Increasing the number of chews also prolonged meal duration and reduced eating rate. However, subjective appetite at meal termination or during the immediate postprandial period did not differ. These data indicate that increasing the number of chews before swallowing might be a behavioral strategy to reduce food intake and potentially aid body-weight management. © 2014 Academy of Nutrition and Dietetics. Source


Zhang S.,Iowa State University
Optics Letters | Year: 2010

A recently proposed flexible 3D shape measurement technique using a defocused projector [Opt. Lett. 34, 3080 (2009)] shows great potential because of its elimination of projector's gamma calibration. However, it cannot handle step-height surfaces. I present here a technique to extend its measurement range to an arbitrary shape by integrating a binary coding method. A computational framework is also proposed to tackle the problems related to the defocusing. © 2010 Optical Society of America. Source


Zhang S.,Iowa State University
Optics and Lasers in Engineering | Year: 2012

This paper presents a method to recover absolute phase by using only four images: three phase-shifted patterns and one stair pattern. The stair pattern is designed in such a way that the stair changes are perfectly aligned with the phase jumps, and thus absolute phase can be recovered by referring to the stair pattern. Due to system noises and camera and/or projector blurring, a computational framework is also proposed. Because this technique only requires four fringe images for absolute phase recovery, it has the merit of measurement speed. And since the absolute phase is obtained, this technique is suitable for measuring step-height objects. We have developed a digital fringe projection system to verify the performance of the proposed technique. © 2012 Elsevier Ltd. Source


It is widely recognized that nonradiative quenching of excitons by other excitons and polarons become the dominant decay mechanism of these excitons at high excitation densities. These quenching processes cause the roll-off in the efficiency of organic light-emitting devices (OLEDs) and prevent lasing at high injection current densities. This review presents the optically-detected magnetic resonance (ODMR) evidence for these photoluminescence- and electroluminescence-quenching processes. And while it provides such evidence for quenching of singlet excitons by polarons and triplet excitons, it reveals the central role of the strongly spin-dependent annihilation of triplet excitons by polarons, since under normal excitation conditions the steady-state polaron and triplet exciton populations are 100-10 4 times the singlet exciton population. In addition, it also suggests that quenching of singlet excitons by bipolarons, likely stabilized by a counterpolaron or countercharge at specific sites, may also be a significant quenching mechanism that also affects the charge transport properties. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this article, I describe a generalization of the K statistic of Blomberg et al. that is useful for quantifying and evaluating phylogenetic signal in highly dimensional multivariate data. The method (Kmult) is found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices. Using computer simulations based on Brownian motion, I demonstrate that the expected value of Kmult remains at 1.0 as trait variation among species is increased or decreased, and as the number of trait dimensions is increased. By contrast, estimates of phylogenetic signal found with a squared-change parsimony procedure for multivariate data change with increasing trait variation among species and with increasing numbers of trait dimensions, confounding biological interpretations. I also evaluate the statistical performance of hypothesis testing procedures based on K mult and find that the method displays appropriate Type I error and high statistical power for detecting phylogenetic signal in highdimensional data. Statistical properties of Kmult were consistent for simulations using bifurcating and random phylogenies, for simulations using different numbers of species, for simulations that varied the number of trait dimensions, and for different underlying models of trait covariance structure. Overall these findings demonstrate that Kmult provides a useful means of evaluating phylogenetic signal in high-dimensional multivariate traits. Finally, I illustrate the utility of the new approach by evaluating the strength of phylogenetic signal for head shape in a lineage of Plethodon salamanders. © The Author(s) 2014. Source


Chen Q.,Iowa State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2012

Influenza virus infects a wide variety of species including humans, pigs, horses, sea mammals and birds. Weight loss caused by influenza infection and/or co-infection with other infectious agents results in significant financial loss in swine herds. The emergence of pandemic H1N1 (A/CA/04/2009/H1N1) and H3N2 variant (H3N2v) viruses, which cause disease in both humans and livestock constitutes a concerning public health threat. Influenza virus contains eight single-stranded, negative-sense RNA genome segments. This genetic structure allows the virus to evolve rapidly by antigenic drift and shift. Antigen-specific antibodies induced by current vaccines provide limited cross protection to heterologous challenge. In pigs, this presents a major obstacle for vaccine development. Different strategies are under development to produce vaccines that provide better cross-protection for swine. Moreover, overriding interfering maternal antibodies is another goal for influenza vaccines in order to permit effective immunization of piglets at an early age. Herein, we present a review of influenza virus infection in swine, including a discussion of current vaccine approaches and techniques used for novel vaccine development. Source


Xiao L.,Hunan Normal University | Yeung E.S.,Iowa State University
Annual Review of Analytical Chemistry | Year: 2014

Imaging of plasmonic nanoparticles (PNP) with optical microscopy has aroused considerable attention in recent years. The unique localized surface plasmon resonance (LSPR) from metal nanoparticles facilitates the transduction of a chemical or physical stimulus into optical signals in a highly efficient way. It is therefore possible to perform chemical or biological assays at the single object level with the help of standard optical microscopes. Because the source of background noise from different samples is different, distinct imaging modalities have been developed to discern the signals of interest in complex surroundings. With these convenient yet powerful techniques, great improvements in chemical and biological assays have been demonstrated, and many interesting phenomena and dynamic processes have also been elucidated. Further development and application of optical imaging methods for plasmonic probes should lead to many exciting results in chemistry and biology in the future. © Copyright ©2014 by Annual Reviews. All rights reserved. Source


Dornbush M.E.,University of Wisconsin - Green Bay | Wilsey B.J.,Iowa State University
Journal of Ecology | Year: 2010

1. In relatively fertile ecosystems, such as the tallgrass prairie, local species diversity is largely controlled by the competitive effects of community dominants. Despite the relative importance of soil resources in shaping competitive outcomes, we have a limited understanding of the ways by which plants partition below-ground space and resources while competing, and thus, how these interactions feedback to affect local diversity. 2. We experimentally tested whether potential rooting depth affected plant species diversity and composition by seeding 36 tallgrass prairie species into replicated, bare-ground plots in which soil depth was manipulated to produce shallow- (20 cm), medium- (42 cm) and deep-soil treatments all within one soil type. Because root architecture and foraging strategies differ among species, we hypothesized that soil depth alone could affect plant richness, diversity and community composition. 3. After 3 years, richness (S) significantly increased with soil depth (P < 0.0001), but there was no significant change in species diversity (P > 0.1) or composition (multi-response permutation procedure, P > 0.2). The lack of a depth effect upon diversity resulted from the opposing effect of increasing soil depth enhancing S, but decreasing evenness. 4. Species presence among depth treatments was strongly nested, with species found in shallow soils reflecting a subset of the species found in the medium-depth treatment, and the species found within the medium-depth treatment reflecting a subset of those found in the deepest soils. 5. All depth treatments contained the same dominant grasses, thus differences in S resulted from the nested loss of forbs. Conversely, increasing soil depth added sets of new species, but the specific identity of the species present appeared interchangeable among replicates of a given depth. 6. Synthesis. Our results provide the first field-based experimental evidence that altering soil depth alters species occurrence and diversity in predictable ways in seeded tallgrass prairie. Our results have important theoretical implications for understanding the processes promoting plant co-occurrence in grasslands, and generate testable hypotheses concerning the conditions under which root-niche partitioning is probably important for maintaining local richness in grasslands. Future work is needed to elucidate the generality and mechanistic basis of our results. © 2009 British Ecological Society. Source


Dyer R.J.,Virginia Commonwealth University | Nason J.D.,Iowa State University | Garrick R.C.,Yale University
Molecular Ecology | Year: 2010

Landscape genetics is a burgeoning field of interest that focuses on how site-specific factors influence the distribution of genetic variation and the genetic connectivity of individuals and populations. In this manuscript, we focus on two methodological extensions for landscape genetic analyses: the use of conditional genetic distance (cGD) derived from population networks and the utility of extracting potentially confounding effects caused by correlations between phylogeographic history and contemporary ecological factors. Individual-based simulations show that when describing the spatial distribution of genetic variation, cGD consistently outperforms the traditional genetic distance measure of linearized FST under both 1- and 2-dimensional stepping stone models and Cavalli-Sforza and Edward's chord distance D c in 1-dimensional landscapes. To show how to identify and extract the effects of phylogeographic history prior to embarking on landscape genetic analyses, we use nuclear genotypic data from the Sonoran desert succulent Euphorbia lomelii (Euphrobiaceae), for which a detailed phylogeographic history has previously been determined. For E. lomelii, removing the effect of phylogeographic history significantly influences our ability to infer both the identity and the relative importance of spatial and bio-climatic variables in subsequent landscape genetic analyses. We close by discussing the utility of cGD in landscape genetic analyses. © 2010 Blackwell Publishing Ltd. Source


The anticancer drug amsacrine is loaded inside the mesopores of mercaptopropyl-functionalized mesoporous silica nanoparticles and entrapped by capping the mesopore-entrances with Ru(bpy)2(PPh3)- moieties (bpy = bipyridine, PPh3 = triphenylphosphine) through mercaptopropyl-Ru coordination. Exposure to visible light irradiation leads to cleavage of the Ru-S coordination bond, which releases the anticancer drug and capping moieties from the material, as determined by absorption and fluorescence measurements. Viability tests on HeLa cells confirmed the capability of the constructed drug delivery system to induce cell death upon exposure to visible light irradiation. These results prove the applicability of a harmless, visible light as the stimulus for cancer targeting, which may lead to better clinical outcomes in anticancer therapy. © 2013 The Royal Society of Chemistry. Source


Wie B.,Iowa State University
Acta Astronautica | Year: 2013

A direct intercept mission with nuclear explosives is the only practical mitigation option against the most probable impact threat of near-Earth objects (NEOs) with warning times much shorter than 10 years. However, state-of-the-art penetrating subsurface nuclear explosion technology limits the penetrator's impact velocity to less than approximately 300 m/s because higher impact velocities prematurely destroy the nuclear fusing mechanisms. Therefore, significant advances in hypervelocity nuclear interceptor/penetrator technology are required to enable a last-minute nuclear disruption mission with intercept velocities as high as 30 km/s. This paper briefly describes both the current and planned research activities at the Iowa State Asteroid Deflection Research Center for developing such a game-changing space technology to mitigate the most probable impact threat of NEOs with a short warning time. © 2012 IAA. Published by Elsevier Ltd. All rights reserved. Source


Ramamoorthy A.,Iowa State University
IEEE Transactions on Information Theory | Year: 2011

This paper considers the problem of transmitting multiple compressible sources over a network at minimum cost. The aim is to find the optimal rates at which the sources should be compressed and the network flows using which they should be transmitted so that the cost of the transmission is minimal. We consider networks with capacity constraints and linear cost functions. The problem is complicated by the fact that the description of the feasible rate region of distributed source coding problems typically has a number of constraints that is exponential in the number of sources. This renders general purpose solvers inefficient. We present a framework in which these problems can be solved efficiently by exploiting the structure of the feasible rate regions coupled with dual decomposition and optimization techniques such as the subgradient method and the proximal bundle method. © 2006 IEEE. Source


Yayla A.A.,Binghamton University State University of New York | Hu Q.,Iowa State University
European Journal of Information Systems | Year: 2012

Aligning information technology (IT) strategy with business strategy has been one of the top concerns of practitioners and scholars for decades. Although numerous studies have documented positive effects of IT-business alignment on organizational performance, our knowledge about this relationship is still limited due to the complexity of contingent factors. The extant literature is largely based on research in the context of developed countries and few studies have explicitly considered the effects of contextual factors such as market environment and competitive strategy on this relationship. In this study, we attempt to fill these gaps by testing the alignment-performance relationship in a developing country setting and investigating the moderating roles of environmental uncertainty and strategic orientation on the performance effects of strategic alignment using survey data collected in Turkey. Our analyses show that this positive effect is statistically significant in highly uncertain environments and varies across performance measures. Our results also show that the strategic alignment between IT and business has a significant impact on performance across all choices of strategic orientation- defender, prospector, or analyzer. Theoretical and practical implications are discussed and future research directions are explored. © 2012 Operational Research Society Ltd. All rights reserved. Source


Ke L.,Qualcomm | Wang Z.,Iowa State University
IEEE Transactions on Information Theory | Year: 2012

We study the degrees of freedom (DoF) regions of two-user multiple-input multiple-output Z and full interference channels in this paper. We assume that the receivers always have perfect channel state information. We first derive the DoF region of Z interference channel with channel state information at transmitter (CSIT). For full interference channel without CSIT, the DoF region has been fully characterized recently and it is shown that the previously known outer bound is not achievable. In this paper, we investigate the no-CSIT case further by assuming that one transmitter has the ability of antenna mode switching. We obtain the DoF region as a function of the number of available antenna modes and reveal the incremental gain in DoF that each additional antenna mode can bring. It is shown that, in certain cases, the reconfigurable antennas can increase the DoF. In these cases, the DoF region is maximized when the number of modes is at least equal to the number of receive antennas at the corresponding receiver, in which case the previous outer bound is achieved. In all cases, we propose systematic constructions of the beamforming and nulling matrices for achieving the DoF region. The constructions bear an interesting space-frequency coding interpretation. © 1963-2012 IEEE. Source


Ekkekakis P.,Iowa State University | Parfitt G.,University of South Australia | Petruzzello S.J.,University of Illinois at Urbana - Champaign
Sports Medicine | Year: 2011

The public health problem of physical inactivity has proven resistant to research efforts aimed at elucidating its causes and interventions designed to alter its course. Thus, in most industrialized countries, the majority of the population is physically inactive or inadequately active. Most theoretical models of exercise behaviour assume that the decision to engage in exercise is based on cognitive factors (e.g. weighing pros and cons, appraising personal capabilities, evaluating sources of support). Another, still-under-appreciated, possibility is that these decisions are influenced by affective variables, such as whether previous exercise experiences were associated with pleasure or displeasure. This review examines 33 articles published from 1999 to 2009 on the relationship between exercise intensity and affective responses. Unlike 31 studies that were published until 1998 and were examined in a 1999 review, these more recent studies have provided evidence of a relation between the intensity of exercise and affective responses. Pleasure is reduced mainly above the ventilatory or lactate threshold or the onset of blood lactate accumulation. There are pleasant changes at sub-threshold intensities for most individuals, large inter-individual variability close to the ventilatory or lactate threshold and homogeneously negative changes at supra-threshold intensities. When the intensity is self-selected, rather than imposed, it appears to foster greater tolerance to higher intensity levels. The evidence of a dose-response relation between exercise intensity and affect sets the stage for a reconsideration of the rationale behind current guidelines for exercise intensity prescription. Besides effectiveness and safety, it is becoming increasingly clear that the guidelines should take into account whether a certain level of exercise intensity would be likely to cause increases or decreases in pleasure. © 2011 Adis Data Information BV. All rights reserved. Source


Adams D.C.,Iowa State University
Systematic Biology | Year: 2013

In recent years, likelihood-based approaches have been used with increasing frequency to evaluate macroevolutionary hypotheses of phenotypic evolution under distinct evolutionary processes in a phylogenetic context (e.g., Brownian motion, Ornstein-Uhlenbeck, etc.), and to compare one or more evolutionary rates for the same phenotypic trait along a phylogeny. It is also of interest to determine whether one trait evolves at a faster rate than another trait. However, to date no study has compared phylogenetic evolutionary rates between traits using likelihood, because a formal approach has not yet been proposed. In this article, I describe a new likelihood procedure for comparing evolutionary rates for two or more phenotypic traits on a phylogeny. This approach compares the likelihood of a model where each trait evolves at a distinct evolutionary rate to the likelihood of a model where all traits are constrained to evolve at a common evolutionary rate. The method can also account for within-species measurement error and within-species trait covariation if available. Simulations revealed that the method has appropriate Type I error rates and statistical power. Importantly, when compared with existing approaches based on phylogenetically independent contrasts and methods that compare confidence intervals for model parameters, the likelihood method displays preferable statistical properties for a wide range of simulated conditions. Thus, this likelihood-based method extends the phylogenetic comparative biology toolkit and provides evolutionary biologists with a more powerful means of determining when evolutionary rates differ between phenotypic traits. Finally, I provide an empirical example illustrating the approach by comparing rates of evolution for several phenotypic traits in Plethodon salamanders. Evolutionary rates; macroevolution; morphological evolution; phenotype; phylogenetic comparative method; phylogeny. © 2012 The Author(s). Source


Patterson A.R.,Iowa State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2010

Porcine circovirus type 2 (PCV2) is a small, non-enveloped, circular, single-stranded DNA virus of economic importance in the swine industry worldwide. Based on the sequence analyses of PCV2 strains, isolates can be divided into five subtypes (PCV2a-e). PCV2 is an ubiquitous virus based on serological and viremia data from countries worldwide. In addition, PCV2 DNA was discovered in archived samples prior to the first recognition of clinical disease. Recently, a worldwide shift in PCV2 subtype from PCV2a to PCV2b occurred. PCV2 DNA can be detected in fecal, nasal, oral and tonsillar swabs as well as in urine and feces from both naturally and experimentally infected pigs. PCV2 DNA can be detected early in the infectious process and persists for extended periods of time. The effectiveness of disinfectants for reducing PCV2 in vitro is variable and PCV2 is very stable in the pig environment. Limited data exist on the horizontal transmission of PCV2. Direct transmission of PCV2 between experimentally or naturally infected animals and naïve animals has been documented and the incorporation of clinical or subclinically infected animals into a population represents a risk to the herd. Indirect transmission through the oral, aerosol or vaccine routes is likely a lesser risk for the transmission of PCV2 in most swine populations but may be worth evaluating in high heath herds. The objective of this review was to discuss data on the epidemiology and horizontal transmission of PCV2. Source


Roth J.A.,Iowa State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2010

Concerns about possible adverse effects from annual vaccination have prompted the reanalysis of vaccine protocols for cats and dogs. In the last decade, several veterinary advisory groups have published protocols that recommend extended revaccination intervals for certain 'core' vaccines. In addition, practicing veterinarians have been asked to consider vaccination as an individualized medical procedure, based on an analysis of risks and benefits for each vaccine in an individual animal. The calls for extended revaccination intervals prompted considerable debate in USA and internationally. Areas of concern include the amount of evidence to support prolonged immunity from various vaccines, the risk of poor responses in individual animals and the possible effects on population immunity. This review examines how the duration of immunity (DOI) to a vaccine is established in animals and humans. It reviews factors that can affect the DOI in an individual animal, including the types of immune defenses stimulated by the pathogen, and the vaccine, host factors such as age and the level of exposure to the pathogen. In addition, it examines DOI studies that were published for canine and feline core vaccines. Source


Sivasankar S.,Iowa State University | Sivasankar S.,Ames Laboratory
Journal of Investigative Dermatology | Year: 2013

Cadherins are Ca2+-dependent cell-cell adhesion proteins that maintain the structural integrity of the epidermis; their principle function is to resist mechanical force. This review summarizes the biophysical mechanisms by which classical cadherins tune adhesion and withstand mechanical stress. We first relate the structure of classical cadherins to their equilibrium binding properties. We then review the role of mechanical perturbations in tuning the kinetics of cadherin adhesion. In particular, we highlight recent studies that show that cadherins form three types of adhesive bonds: catch bonds, which become longer lived and lock in the presence of tensile force; slip bonds, which become shorter lived when pulled; and ideal bonds, which are insensitive to tugging. © 2013 The Society for Investigative Dermatology. Source


Chou H.-H.,Iowa State University
BMC Bioinformatics | Year: 2010

Background: Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations.Results: PICKY 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. PICKY 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, PICKY does not sacrifice the quality of shared probes when choosing them. The latest PICKY 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making PICKY 2.1 more versatile to microarray users.Conclusions: Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations. © 2010 Chou; licensee BioMed Central Ltd. Source


Chen C.,Iowa State University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

In this paper we study the identification of the b quark inside a boosted hadronically decaying top quark in the center-of-mass frame of the jet. We demonstrate that the method can be used to greatly reduce the QCD jet background even in a very high pileup condition. The method has a much smaller fake rate for QCD jets compared to typical b quark identification algorithms in jets at the same signal efficiency. When combining the b quark identification in the center-of-mass frame of the jet with jet substructure information, we can improve the rejection rate of QCD jet background by almost an order of magnitude while maintaining the same identification efficiency for the boosted top quark. © 2013 American Physical Society. Source


Green J.M.,DuPont Pioneer | Owen M.D.K.,Iowa State University
Journal of Agricultural and Food Chemistry | Year: 2011

Since 1996, genetically modified herbicide-resistant (HR) crops, particularly glyphosate-resistant (GR) crops, have transformed the tactics that corn, soybean, and cotton growers use to manage weeds. The use of GR crops continues to grow, but weeds are adapting to the common practice of using only glyphosate to control weeds. Growers using only a single mode of action to manage weeds need to change to a more diverse array of herbicidal, mechanical, and cultural practices to maintain the effectiveness of glyphosate. Unfortunately, the introduction of GR crops and the high initial efficacy of glyphosate often lead to a decline in the use of other herbicide options and less investment by industry to discover new herbicide active ingredients. With some exceptions, most growers can still manage their weed problems with currently available selective and HR crop-enabled herbicides. However, current crop management systems are in jeopardy given the pace at which weed populations are evolving glyphosate resistance. New HR crop technologies will expand the utility of currently available herbicides and enable new interim solutions for growers to manage HR weeds, but will not replace the long-term need to diversify weed management tactics and discover herbicides with new modes of action. This paper reviews the strengths and weaknesses of anticipated weed management options and the best management practices that growers need to implement in HR crops to maximize the long-term benefits of current technologies and reduce weed shifts to difficult-to-control and HR weeds. © 2010 American Chemical Society. Source


Chen C.,Iowa State University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

In this paper we study the identification of the boosted hadronically decaying top quarks using jet substructure in the center-of-mass frame of the jet. We demonstrate that the method can greatly reduce the QCD jet background while maintaining high identification efficiency of the boosted top quark even in a very high pileup condition. Applications to searches for heavy resonances that decay to a tt̄ final state are also discussed. © 2013 American Physical Society. Source


Levitas V.I.,Iowa State University
Journal of the Mechanics and Physics of Solids | Year: 2014

Thermodynamically consistent phase field theory for multivariant martensitic transformations, which includes large strains and interface stresses, is developed. Theory is formulated in a way that some geometrically nonlinear terms do not disappear in the geometrically linear limit, which in particular allowed us to introduce the expression for the interface stresses consistent with the sharp interface approach. Namely, for the propagating nonequilibrium interface, a structural part of the interface Cauchy stresses reduces to a biaxial tension with the magnitude equal to the temperature-dependent interface energy. Additional elastic and viscous contributions to the interface stresses do not require separate constitutive equations and are determined by solution of the coupled system of phase field and mechanics equations. Ginzburg-Landau equations are derived for the evolution of the order parameters and temperature evolution equation. Boundary conditions for the order parameters include variation of the surface energy during phase transformation. Because elastic energy is defined per unit volume of unloaded (intermediate) configuration, additional contributions to the Ginzburg-Landau equations and the expression for entropy appear, which are important even for small strains. A complete system of equations for fifth- and sixth-degree polynomials in terms of the order parameters is presented in the reference and actual configurations. An analytical solution for the propagating interface and critical martensitic nucleus which includes distribution of components of interface stresses has been found for the sixth-degree polynomial. This required resolving a fundamental problem in the interface and surface science: how to define the Gibbsian dividing surface, i.e., the sharp interface equivalent to the finite-width interface. An unexpected, simple solution was found utilizing the principle of static equivalence. In fact, even two equations for determination of the dividing surface follow from the equivalence of the resultant force and zero-moment condition. For the obtained analytical solution for the propagating interface, both conditions determine the same dividing surface, i.e., the theory is noncontradictory. A similar formalism can be developed for the phase field approach to diffusive phase transformations described by the Cahn-Hilliard equation, twinning, dislocations, fracture, and their interaction. © 2014 Elsevier Ltd. Source


Johnston D.C.,Iowa State University
Physical Review B - Condensed Matter and Materials Physics | Year: 2015

A unified molecular field theory (MFT) is presented that applies to both collinear and planar noncollinear Heisenberg antiferromagnets (AFs) on the same footing. The spins in the system are assumed to be identical and crystallographically equivalent. This formulation allows calculations of the anisotropic magnetic susceptibility χ versus temperature T below the AF ordering temperature TN to be carried out for arbitrary Heisenberg exchange interactions Jij between arbitrary neighbors j of a given spin i without recourse to magnetic sublattices. The Weiss temperature θp in the Curie-Weiss law is written in terms of the Jij values and TN in terms of the Jij values and an assumed AF structure. Other magnetic and thermal properties are then expressed in terms of quantities easily accessible from experiment as laws of corresponding states for a given spin S. For collinear ordering these properties are the reduced temperature t=T/TN, the ratio f=θp/TN, and S. For planar noncollinear helical or cycloidal ordering, an additional parameter is the wave vector of the helix or cycloid. The MFT is also applicable to AFs with other AF structures. The MFT predicts that χ(T≤TN) of noncollinear 120° spin structures on triangular lattices is isotropic and independent of S and T and thus clarifies the origin of this universally observed behavior. The high-field magnetization and heat capacity for fields applied perpendicular to the ordering axis (collinear AFs) and ordering plane (planar noncollinear AFs) are also calculated and expressed for both types of AF structures as laws of corresponding states for a given S, and the reduced perpendicular field versus reduced temperature phase diagram is constructed. © 2015 American Physical Society. Source


Downing J.A.,Iowa State University
Limnetica | Year: 2010

Until recently, small continental waters have been completely ignored in virtually all global processes and cycles. This has resulted from the neglect of these systems and processes by ecologists and the assumption that ecosystems with a small areal extent cannot play a major role in global processes. Recent inventories based on modern geographical and mathematical approaches have shown that continental waters occupy nearly twice as much area as was previously believed. Further, these inventories have shown that small lakes and ponds dominate the areal extent of continental waters, correcting a centurylong misconception that large lakes are most important. The global importance of any ecosystem type in a process or cycle is the product of the areal extent and the intensity of the process in those ecosystems. Several analyses have shown the disproportionately great intensity of many processes in small aquatic ecosystems, indicating that they play an unexpectedly major role in global cycles. Assessments of the global carbon cycle underscore the need for aquatic scientists to view their work on a global scale in order to respond to the Earth's most pressing environmental problems. © Asociación Ibérica de Limnología, Madrid. Spain. Source


Jia M.,Iowa State University
BMC bioinformatics | Year: 2010

Linking high-throughput experimental data with biological networks is a key step for understanding complex biological systems. Currently, visualization tools for large metabolic networks often result in a dense web of connections that is difficult to interpret biologically. The MetNetGE application organizes and visualizes biological networks in a meaningful way to improve performance and biological interpretability. MetNetGE is an interactive visualization tool based on the Google Earth platform. MetNetGE features novel visualization techniques for pathway and ontology information display. Instead of simply showing hundreds of pathways in a complex graph, MetNetGE gives an overview of the network using the hierarchical pathway ontology using a novel layout, called the Enhanced Radial Space-Filling (ERSF) approach that allows the network to be summarized compactly. The non-tree edges in the pathway or gene ontology, which represent pathways or genes that belong to multiple categories, are linked using orbital connections in a third dimension. Biologists can easily identify highly activated pathways or gene ontology categories by mapping of summary experiment statistics such as coefficient of variation and overrepresentation values onto the visualization. After identifying such pathways, biologists can focus on the corresponding region to explore detailed pathway structure and experimental data in an aligned 3D tiered layout. In this paper, the use of MetNetGE is illustrated with pathway diagrams and data from E. coli and Arabidopsis. MetNetGE is a visualization tool that organizes biological networks according to a hierarchical ontology structure. The ERSF technique assigns attributes in 3D space, such as color, height, and transparency, to any ontological structure. For hierarchical data, the novel ERSF layout enables the user to identify pathways or categories that are differentially regulated in particular experiments. MetNetGE also displays complex biological pathway in an aligned 3D tiered layout for exploration. Source


Maris P.,Iowa State University
Journal of Physics: Conference Series | Year: 2012

We perform no-core configuration interaction calculations for nuclei in the p-shell. We show that for typical light nuclei, a truncation on the total number of quanta in the many-body system converges much more rapidly than a full configuration interaction (FCI) truncation, which is a truncation on the single-particle basis space. We present new results for the ground state energies of the Be isotopes with the nonlocal two-body potential JISP16, and discuss emerging phenomena such as clustering and rotational band structures in 9Be. We also show that the anomalously suppressed beta decay of 14C to the ground state of 14N can be reproduced using two- and three-nucleon forces from chiral effective field theory. In particular the structure of the ground state of 14N is sensitive to the three-nucleon force. © Published under licence by IOP Publishing Ltd. Source


Momeni K.,Iowa State University | Odegard G.M.,Michigan Technological University | Yassar R.S.,Michigan Technological University
Acta Materialia | Year: 2012

The size scale effect on the piezoelectric response of bulk ZnO and ZnO nanobelts has been studied using molecular dynamics simulation. Six molecular dynamics models of ZnO nanobelts are constructed and simulated with lengths of 150.97 Å and lateral dimensions ranging between 8.13 and 37.37 Å. A molecular dynamics model of bulk ZnO has also been constructed and simulated using periodic boundary conditions. The piezoelectric constants of the bulk ZnO and each of the ZnO nanobelts are predicted. The predicted piezoelectric coefficient of bulk ZnO is 1.4 C m -2, while the piezoelectric coefficient of ZnO nanobelts increases from 1.639 to 2.322 C m -2 when the lateral dimension of the ZnO NBs is reduced from 37.37 to 8.13 Å. The changes in the piezoelectric constants are explained in the context of surface charge redistribution. The results give a key insight into the field of nanopiezotronics and energy scavenging because the piezoelectric response and voltage output scale with the piezoelectric coefficient. © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. Source


Tuchin K.,Iowa State University
Physical Review C - Nuclear Physics | Year: 2013

We calculate a novel "magnetic contribution" to the dilepton spectrum in heavy-ion collisions arising from interaction of relativistic quarks with intense magnetic field. Synchrotron radiation by quarks, which can be approximated by the equivalent photon flux, is followed by dilepton decay of photons in an intense magnetic field. We argue that the "magnetic contribution" dominates the dilepton spectrum at low lepton energies, whereas a conventional photon dilepton decay dominates at higher lepton energies. © 2013 American Physical Society. Source


Elmegreen B.G.,IBM | Struck C.,Iowa State University
Astrophysical Journal Letters | Year: 2013

Stellar scattering off of orbiting or transient clumps is shown to lead to the formation of exponential profiles in both surface density and velocity dispersion in a two-dimensional non-self gravitating stellar disk with a fixed halo potential. The exponential forms for both nearly flat rotation curves and near-solid-body rotation curves. The exponential does not depend on initial conditions, spiral arms, bars, viscosity, star formation, or strong shear. After a rapid initial development, the exponential saturates to an approximately fixed scale length. The inner exponential in a two-component profile has a break radius comparable to the initial disk radius; the outer exponential is primarily scattered stars. © 2013. The American Astronomical Society. All rights reserved. Source


Hewezi T.,Iowa State University
Plant signaling & behavior | Year: 2012

The beet cyst nematode, Heterodera schachtii, is a sedentary root parasite that induces the formation of a specialized root feeding structure, the syncytium. We previously have shown that coordinated regulation of miR396 and its target genes GRF1 and GRF3 in the syncytium is required for proper formation. To gain a better understanding of this coordinated regulation, we used quantitative real-time PCR to assess the abundance of primary (pri)-miRNA396a, pri-miRNA396b and mature miRNA396 in transgenic Arabidopsis plants overexpressing either wild-type variants of the GRF1 or GRF3 coding sequences or miR396-resistant variants. We also included a grf1/grf2/grf3 triple mutant in these analyses. We observed significant decreases in the abundance of pri-miRNA396a, pri-miRNA396b and mature miR396 in the transgenic plants overexpressing GRF1 or GRF3, particularly with the miRNA396-resistant variants. In contrast, the primary transcripts and mature miRNA396 abundance were significantly increased in the grf1/grf2/grf3 triple knockout mutant. These results demonstrate that homeostasis between miR396 and the target genes GRF1 and GRF3 is established through reciprocal feedback regulation, in which GRF1/GRF3 and miR396 negatively regulate each other's expression. In addition, we found that constitutive expression of GRF1 or GRF3 decreases the mRNA abundance of other GRFs, even those that are not targeted by miR396, as well as their own endogenous transcripts, which documents further regulatory facets of this equilibrium. Source


Luecke G.R.,Iowa State University
IEEE Transactions on Robotics | Year: 2011

Haptic interactions have become increasingly important as an interface to computer-generated simulations in virtual-reality (VR) applications. Many haptic devices are designed to be used as a force feedback mouse, where the users hand is in contact with the haptic device while the object contact and force generation occur on a computer screen. In this paper, we present an approach using a virtual probe to interact with the environment and introduce a new method to generate impedance-based haptic forces based on the use of a virtual manipulator. The virtual probe is connected directly to the haptic device and is projected from the hand to the environment, much like a scalpel or sword. As the probe comes in contact with the environment, the haptic device generates appropriate forces on the hand. We extend this approach to include underactuated haptic devices, which do not have fully powered joints. We show that the approach compensates for missing joint actuation in the underactuated haptic devices. We show experimental results for a simple case of haptic interaction; we also present an experimental implementation in six degrees of freedom (DOF) using one of the most popular devices: the PHANTOM. © 2011 IEEE. Source


Hartzler R.G.,Iowa State University
Crop Protection | Year: 2010

The role of common milkweed in the lifecycle of the monarch butterfly has increased interest in the presence of this weed in the north central United States. An initial survey conducted in 1999 found that low densities of common milkweed occurred in approximately 50% of Iowa corn and soybean fields. In 2009, common milkweed was present in only 8% of surveyed fields, and the area within infested fields occupied by common milkweed was reduced by approximately 90% compared to 1999. The widespread adoption of glyphosate resistant corn and soybean cultivars and the reliance on post-emergence applications of glyphosate for weed control in crop fields likely has contributed to the decline in common milkweed in agricultural fields. © 2010 Elsevier Ltd. Source


Gassman P.W.,Iowa State University | Sadeghi A.M.,U.S. Department of Agriculture | Srinivasan R.,Texas A&M University
Journal of Environmental Quality | Year: 2014

The Soil and Water Assessment Tool (SWAT) model has emerged as one of the most widely used water quality watershed- and river basin-scale models worldwide, applied extensively for a broad range of hydrologic and/or environmental problems. The international use of SWAT can be attributed to its flexibility in addressing water resource problems, extensive networking via dozens of training workshops and the several international conferences that have been held during the past decade, comprehensive online documentation and supporting software, and an open source code that can be adapted by model users for specific application needs. The catalyst for this special collection of papers was the 2011 International SWAT Conference & Workshops held in Toledo, Spain, which featured over 160 scientific presentations representing SWAT applications in 37 countries. This special collection presents 22 specific SWAT-related studies, most of which were presented at the 2011 SWAT Conference; it represents SWAT applications on five different continents, with the majority of studies being conducted in Europe and North America. The papers cover a variety of topics, including hydrologic testing at a wide range of watershed scales, transport of pollutants in northern European lowland watersheds, data input and routing method effects on sediment transport, development and testing of potential new model algorithms, and description and testing of supporting software. In this introduction to the special section, we provide a synthesis of these studies within four main categories: (i) hydrologic foundations, (ii) sediment transport and routing analyses, (iii) nutrient and pesticide transport, and (iv) scenario analyses. We conclude with a brief summary of key SWAT research and development needs. © American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. Source


Beattie G.A.,Iowa State University
Annual Review of Phytopathology | Year: 2011

This review examines the many ways in which water influences the relations between foliar bacterial pathogens and plants. As a limited resource in aerial plant tissues, water is subject to manipulation by both plants and pathogens. A model is emerging that suggests that plants actively promote localized desiccation at the infection site and thus restrict pathogen growth as one component of defense. Similarly, many foliar pathogens manipulate water relations as one component of pathogenesis. Nonvascular pathogens do this using effectors and other molecules to alter hormonal responses and enhance intercellular watersoaking, whereas vascular pathogens use many mechanisms to cause wilt. Because of water limitations on phyllosphere surfaces, bacterial colonists, including pathogens, benefit from the protective effects of cellular aggregation, synthesis of hygroscopic polymers, and uptake and production of osmoprotective compounds. Moreover, these bacteria employ tactics for scavenging and distributing water to overcome water-driven barriers to nutrient acquisition, movement, and signal exchange on plant surfaces. © 2011 by Annual Reviews. All rights reserved. Source


Tuchin K.,Iowa State University
Physical Review C - Nuclear Physics | Year: 2013

The electromagnetic radiation by quark-gluon plasma in a strong magnetic field is calculated. The contributing processes are synchrotron radiation and one-photon annihilation. It is shown that in relativistic heavy-ion collisions at the BNL Relativistic Heavy Ion Collider (RHIC) and CERN Large Hadron Collider (LHC) synchrotron radiation dominates over the annihilation. Moreover, it constitutes a significant part of all photons produced by the plasma at low transverse momenta; its magnitude depends on the plasma temperature and the magnetic field strength. Electromagnetic radiation in a magnetic field is probably the missing piece that resolves a discrepancy between the theoretical models and the experimental data. It is argued that electromagnetic radiation increases with the magnetic field strength and plasma temperature. © 2013 American Physical Society. Source


Weerasinghe A.,Iowa State University
Mathematics of Operations Research | Year: 2014

We consider a sequence of many-server queueing systems with impatient customers of the type G/M/n+CGI in heavy traffic. This sequence is indexed by n, where the parameter n represents the number of servers in the nth system. The state process is considered to be the diffusion-scaled total customer count in the system and the service rate is a state-dependent perturbation of a given basic service rate μ0 > 0. When the system is critically loaded in the Halfin-Whitt heavy traffic regime, we obtain the limiting diffusion for the state processes. We also establish the asymptotic relationships among the diffusion-scaled processes representing the total customer count, virtual waiting time, and the number of customer abandonments. Motivated by the cost structures of telephone call centers, we formulate a cost functional and show that the expected value of this cost functional in the nth system converges to that of the limiting diffusion under mild assumptions. © 2014 INFORMS. Source


Opriessnig T.,Iowa State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2011

Respiratory disease in pigs is common in modern pork production worldwide and is often referred to as porcine respiratory disease complex (PRDC). PRDC is polymicrobial in nature, and results from infection with various combinations of primary and secondary respiratory pathogens. As a true multifactorial disease, environmental conditions, population size, management strategies and pig-specific factors such as age and genetics also play critical roles in the outcome of PRDC. While non-infectious factors are important in the initiation and outcome of cases of PRDC, the focus of this review is on infectious factors only. There are a variety of viral and bacterial pathogens commonly associated with PRDC including porcine reproductive and respiratory syndrome virus (PRRSV), swine influenza virus (SIV), porcine circovirus type 2 (PCV2), Mycoplasma hyopneumoniae (MHYO) and Pasteurella multocida (PMULT). The pathogenesis of viral respiratory disease is typically associated with destruction of the mucocilliary apparatus and with interference and decrease of the function of pulmonary alveolar and intravascular macrophages. Bacterial pathogens often contribute to PRDC by activation of inflammation via enhanced cytokine responses. With recent advancements in pathogen detection methods, the importance of polymicrobial disease has become more evident, and identification of interactions of pathogens and their mechanisms of disease potentiation has become a topic of great interest. For example, combined infection of pigs with typically low pathogenic organisms like PCV2 and MHYO results in severe respiratory disease. Although the body of knowledge has advanced substantially in the last 15 years, much more needs to be learned about the pathogenesis and best practices for control of swine respiratory disease outbreaks caused by concurrent infection of two or more pathogens. This review discusses the latest findings on polymicrobial respiratory disease in pigs. Source


Tuchin K.,Iowa State University
Physical Review C - Nuclear Physics | Year: 2013

Exact analytical solution for the space-time evolution of electromagnetic field in electrically conducting nuclear matter produced in heavy-ion collisions is discussed. It is argued that the parameter that controls the strength of the matter effect on the field evolution is σγb, where σ is electrical conductivity, γ is the Lorentz boost-factor, and b is the characteristic transverse size of the matter. When this parameter is of the order 1 or larger, which is the case at the Relativistic Heavy Ion Collider and the Large Hadron Collider, the space-time dependence of the electromagnetic field completely differs from that in vacuum. © 2013 American Physical Society. Source


Madson D.M.,Iowa State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2011

Porcine circovirus type 2 (PCV2) causes great economic losses in growing pigs and there are several reviews on disease manifestations and lesions associated with PCV2 in growing pigs. Reproductive failure in breeding herds, predominately associated with increased numbers of mummies and non-viable piglets at parturition, is one of the disease manifestations of PCV2 infection. Boars shed low amounts of infectious PCV2 in semen for extended time periods, and vertical transmission of PCV2 to fetuses during PCV2 viremia of the dam has been experimentally confirmed. However, intrauterine-infected piglets often are clinically normal. Nevertheless, pigs infected with PCV2 by the intrauterine route can be born viremic, possibly contributing to horizontal spread of PCV2 within the breeding herd and into the nursery. Shedding of PCV2 in semen and prevalence of intrauterine-infected piglets can both be greatly reduced by PCV2 vaccination well ahead of expected PCV2 exposure. This review is a discussion on current knowledge on the effects of PCV2 infection in the dam and in in utero fetuses, including clinical signs, lesions, diagnosis and prevention through vaccination. Infection of boars with PCV2, the potential for PCV2 transmission via semen and prevention of PCV2 shedding are also discussed. Source


Kittawornrat A.,Iowa State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2011

Pork production began to flourish in the USA after the practice of finishing pigs on corn was popularized in the late 1600s. By the 1840s, there were 35 million pigs and 20 million people in the USA and Cincinnati was the world's largest pork market. Between 1890 and the present, the total number of pigs in the USA has remained at 50-60 million, but dramatic changes in swine husbandry over the course of the 20th century have metamorphosed pig production from small, extensive (outdoor), labor-dependent enterprises into large, intensive (indoor), capital-dependent, production systems. This development has led to debate concerning the impact of swine production on animal/human health, the environment, and the welfare of the animals under our care. In a very tangible way, the future of pork production depends on effectively addressing the public's concerns regarding animal welfare and health. Here, we review basic sensory and behavioral aspects of swine with the objective of reaching a better understanding of pig behavior and pig welfare. The premise of this discussion is that safeguarding animal welfare and health is good for pigs, pork producers and the animal-conscious public. Source


Romano R.,Iowa State University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

We consider the problem of controlling in minimum time a two-level quantum system which can be subject to a drift. The control is assumed to be bounded in magnitude and to affect two or three independent generators of the dynamics. We describe the time optimal trajectories in SU(2), the Lie group of possible evolutions for the system, by means of a particularly simple parametrization of the group. A key ingredient of our analysis is the introduction of the optimal front line. This tool allows us to fully characterize the time evolution of the reachable sets and to derive the worst-case operators and the corresponding times. The analysis is performed in any regime - controlled dynamics stronger than, of the same magnitude as, or weaker than the drift term - and gives a method to synthesize quantum logic operations on a two-level system in minimum time. © 2014 American Physical Society. Source


Cotos E.,Iowa State University
ReCALL | Year: 2014

Learner corpora have become prominent in language teaching and learning, enhancing data-driven learning (DDL) pedagogy by promoting 'learning driven data' in the classroom. This study explores the potential of a local learner corpus by investigating the effects of two types of DDL activities, one relying on a native-speaker corpus (NSC) and the second combining native-speaker and learner corpora. Both types of activities aimed at improving second language writers' knowledge of linking adverbials and were based on a preliminary analysis of adverbial use in the local learner corpus produced by 31 study participants. Quantitative and qualitative data, obtained from writing samples, pre/post-tests, and questionnaires, were converged through concurrent triangulation. The results showed an increase in frequency, diversity and accuracy in all participants' use of adverbials, but more significant improvement was made by the students who were exposed to the corpus containing their own writing. The findings of this study are thus interpreted as suggestive that combining learner and native-speaker data is a feasible and effective practice, which can be readily integrated in DDL-based instruction with positive impact. Copyright © 2014 European Association for Computer Assisted Language Learning 2014Â. Source


Vela J.,Iowa State University
Journal of Physical Chemistry Letters | Year: 2013

Colloidal semiconductor nanocrystals possess unique properties that are unmatched by other chromophores such as organic dyes or transition-metal complexes. These versatile building blocks have generated much scientific interest and found applications in bioimaging, tracking, lighting, lasing, photovoltaics, photocatalysis, thermoelectrics, and spintronics. Despite these advances, important challenges remain, notably how to produce semiconductor nanostructures with predetermined architecture, how to produce metastable semiconductor nanostructures that are hard to isolate by conventional syntheses, and how to control the degree of surface loading or valence per nanocrystal. Molecular chemists are very familiar with these issues and can use their expertise to help solve these challenges. In this Perspective, we present our group's recent work on bottom-up molecular control of nanoscale composition and morphology, low-temperature photochemical routes to semiconductor heterostructures and metastable phases, solar-to-chemical energy conversion with semiconductor-based photocatalysts, and controlled surface modification of colloidal semiconductors that bypasses ligand exchange. © 2013 American Chemical Society. Source


Sanchez-Ken J.G.,National Autonomous University of Mexico | Clark L.G.,Iowa State University
American Journal of Botany | Year: 2010

Premise of the study: The subfamily Panicoideae (Poaceae) encompasses nearly one-third of the diversity of grass species, including important crops such as maize and sugarcane. Previous analyses recovered strong support for a Panicoideae+Centothecoideae lineage within the diverse Panicoideae+Arundinoideae+Chloridoideae+Micrairoideae+Aristidoideae+Danthonioideae (PAC-MAD) clade, although support for internal relationships was inconsistent. The objectives of this research were to (1) further test the monophyly of each subfamily and previously recovered clades within the Panicoideae+Centothecoideae lineage, (2) establish phylogenetic relationships among these groups, and (3) propose a new tribal classification for this lineage based explicitly on the phylogeny. Methods: Maximum parsimony and Bayesian inference analyses of 37 taxa were based on previously published sequences (ndhF and rpl16 intron) and on new plastid and nuclear (rbcL and granule-bound starch synthase I) sequence data as well as structural data. Key results. The Panicoideae+Centothecoideae lineage and a majority of the clades identified in previous analyses continue to be robustly supported, but resolution along the backbone of the topology remains elusive. Support for the monophyly of both subfamilies was lacking although support values for some clades increased. The tribes Centotheceae and Arundinelleae were confirmed as polyphyletic. Conclusions: Subfamily Centothecoideae is formally submerged into the Panicoideae, and a new tribal classification for the expanded Panicoideae is proposed based explicitly on the phylogeny. This classification includes 12 tribes of which Chasmanthieae and Zeugiteae are segretated from the Centotheceae; Tristachyideae is segregated from Arundinelleae, and a new tribe, Cyperochloeae, is validated to accommodate two isolated genera. A key to the tribes is provided. © 2010 Botanical Society of America. Source


Zhao X.,Iowa State University | Rapp R.,Texas A&M University
Nuclear Physics A | Year: 2011

A previously constructed transport approach to calculate the evolution of quarkonium yields and spectra in heavy-ion collisions is applied to Pb. Pb (s=2.76 A TeV) collisions at the Large Hadron Collider (LHC). In this approach spectral properties of charmonia are constrained by Euclidean correlators from thermal lattice QCD and subsequently implemented into a Boltzmann equation accounting for both suppression and regeneration reactions. Based on a fair description of SPS and RHIC data, we provide predictions for the centrality dependence of J/ψ yields at LHC. The main uncertainty is associated with the input charm cross section, in particular its hitherto unknown reduction due to shadowing in nuclear collisions. Incomplete charm-quark thermalization and non-equilibrium in charmonium chemistry entail a marked reduction of the regeneration yield compared to the statistical equilibrium limit. © 2011 Elsevier B.V. Source


Basmajian C.,Iowa State University
Transportation | Year: 2010

Though driving to and from work has become a prevalent experience in the lives of individuals in every metropolitan region in the US, much remains to be learned about the activity from the perspective of the drivers. To increase our understanding of the motivation for certain travel behaviors, we must first know something about what those drivers experience. The existing literature explains much, but the application of new methodologies could improve our ability to explain the willingness of individuals to choose to drive through increasingly congested road networks. The results of this study of oral histories of 12 women commuters underscore the idea that commute should be seen as a set of subjective behaviors that contradict some existing assumptions about why individuals commute. © 2009 Springer Science+Business Media, LLC. Source


Leckband D.,University of Illinois at Urbana - Champaign | Sivasankar S.,Iowa State University
Current Opinion in Cell Biology | Year: 2012

Classical cadherins are the principle adhesive proteins at cohesive intercellular junctions, and are essential proteins for morphogenesis and tissue homeostasis. Because subtype-dependent differences in cadherin adhesion are at the heart of cadherin functions, several structural and biophysical approaches have been used to elucidate relationships between cadherin structures, biophysical properties of cadherin bonds, and cadherin-dependent cell functions. Some experimental approaches appeared to provide conflicting views of the cadherin binding mechanism. However, recent structural and biophysical data, as well as computer simulations generated new insights into classical cadherin binding that increasingly reconcile diverse experimental findings. This review summarizes these recent findings, and highlights both the consistencies and remaining challenges needed to generate a comprehensive model of cadherin interactions that is consistent with all available experimental data. © 2012 Elsevier Ltd. Source


Cheville N.F.,Iowa State University
Toxicologic Pathology | Year: 2013

Mitochondria, endoplasmic reticulum (ER), cytoplasmic lipid droplets (CLD), and Golgi vesicles use cross talk to control hepatocyte metabolism, growth, and stress. Interpretation of ultrastructural change requires knowledge of how cross talk pathways function, how differential activation of hepatocellular signals influences organelle structure, and how organelles position themselves to become central hubs for stress responses. Mitochondria, by coupling energy production to pathways for protection, form critical platforms for innate signaling. Mitochondrial outer and inner membranes activate channels and signals to translocate peptides that drive oxidative phosphorylation, β-oxidation of fatty acids, and calcium ion (Ca2+) flux. In cell stress, mitochondrial signals initiate fusion and fission, reactive oxygen species (ROS) control, autophagy, apoptosis, and senescence. Specialized tethering proteins tie mitochondria to ER to support translocation of metabolites. For Ca2+ translocation, ER pores are connected to mitochondrial voltage-dependent anion channels, and for mitochondrial fission, unique membrane proteins pull ER to mitochondria. In toxic injury, cytosolic cytokines translocate to alter metabolism. Toxic effects on ER lipid synthesis lead to Golgi vesicle reduplication and transport of perilipin and other protein cargos into CLDs. How cellular proteostasis, oxidative homeostasis, and ion balance are maintained depend upon the effectiveness of mitochondrial ROS defense responses, unfolded protein responses in mitochondria and ER, and other organelle defenses. © 2013 by The Author(s). Source


Zhao X.,Iowa State University
Few-Body Systems | Year: 2015

Basis light-front quantization has been developed as a first-principles nonperturbative approach to quantum field theory. In this article we report our recent progress on the applications to the single electron and the positronium system in QED. We focus on the renormalization procedure in this method. © 2015, Springer-Verlag Wien. Source


Shanks B.H.,Iowa State University
Industrial and Engineering Chemistry Research | Year: 2010

For biorenewable feedstocks to serve as a significant source of chemicals and/or fuels, the development of new chemical processes as well as biological processes will be required. However, the conversion of biorenewable feedstocks with heterogeneous catalyst-based processes provides new challenges in inorganic catalyst research and development relative to historical work with petrochemical feedstocks. These catalyst and process challenges include the need to convert highly functionalized molecules with high selectivity, to develop stable catalytic liquid-solid interfaces in which the liquid phase is commonly aqueous, to control solvent phase effects and to develop novel reaction systems. While some of these challenges will be addressed using novel catalytic materials, others will need to be overcome through design of new catalytic reaction systems. Examples of emerging research results demonstrating unique approaches that have been taken to begin to address the efficient conversion of biorenewable feedstocks to chemicals and fuels are discussed. © 2010 American Chemical Society. Source


Huang L.,Iowa State University
Nature Materials | Year: 2016

In a type I Dirac or Weyl semimetal, the low-energy states are squeezed to a single point in momentum space when the chemical potential μ is tuned precisely to the Dirac/Weyl point. Recently, a type II Weyl semimetal was predicted to exist, where the Weyl states connect hole and electron bands, separated by an indirect gap. This leads to unusual energy states, where hole and electron pockets touch at the Weyl point. Here we present the discovery of a type II topological Weyl semimetal state in pure MoTe2, where two sets of Weyl points (, ) exist at the touching points of electron and hole pockets and are located at different binding energies above EF. Using angle-resolved photoemission spectroscopy, modelling, density functional theory and calculations of Berry curvature, we identify the Weyl points and demonstrate that they are connected by different sets of Fermi arcs for each of the two surface terminations. We also find new surface ‘track states’ that form closed loops and are unique to type II Weyl semimetals. This material provides an exciting, new platform to study the properties of Weyl fermions. © 2016 Nature Publishing Group Source


Marcelin G.,St Jude Childrens Research Hospital | Sandbulte M.R.,Iowa State University | Webby R.J.,St Jude Childrens Research Hospital
Reviews in Medical Virology | Year: 2012

Vaccines are instrumental in controlling the burden of influenza virus infection in humans and animals. Antibodies raised against both major viral surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), can contribute to protective immunity. Vaccine-induced HA antibodies have been characterized extensively, and they generally confer protection by blocking the attachment and fusion of a homologous virus onto host cells. Although not as well characterized, some functions of NA antibodies in influenza vaccine-mediated immunity have been recognized for many years. In this review, we summarize the case for NA antibodies in influenza vaccine-mediated immunity. In the absence of well-matched HA antibodies, NA antibodies can provide varying degrees of protection against disease. NA proteins of seasonal influenza vaccines have been shown in some instances to elicit serum antibodies with cross-reactivity to avian-origin and swine-origin influenza strains, in addition to HA drift variants. NA-mediated immunity has been linked to (i) conserved NA epitopes amongst otherwise antigenically distinct strains, partly attributable to the segmented influenza viral genome; (ii) inhibition of NA enzymatic activity; and (iii) the NA content in vaccine formulations. There is a potential to enhance the effectiveness of existing and future influenza vaccines by focusing greater attention on the antigenic characteristics and potency of the NA protein. © 2012 John Wiley & Sons, Ltd. Source


Gene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree. Gene tree parsimony approaches seek the evolutionary scenario that implies the fewest gene duplications, duplications and losses, or deep coalescence (incomplete lineage sorting) events needed to reconcile a gene tree and a species tree. While a gene tree parsimony approach can be informative about genome evolution and phylogenetics, error in gene trees can profoundly bias the results. We introduce efficient algorithms that rapidly search local Subtree Prune and Regraft (SPR) or Tree Bisection and Reconnection (TBR) neighborhoods of a given gene tree to identify a topology that implies the fewest duplications, duplication and losses, or deep coalescence events. These algorithms improve on the current solutions by a factor of n for searching SPR neighborhoods and n2 for searching TBR neighborhoods, where n is the number of taxa in the given gene tree. They provide a fast error correction protocol for ameliorating the effects of gene tree error by allowing small rearrangements in the topology to improve the reconciliation cost. We also demonstrate a simple protocol to use the gene rearrangement algorithm to improve gene tree parsimony phylogenetic analyses. The new gene tree rearrangement algorithms provide a fast method to address gene tree error. They do not make assumptions about the underlying processes of genome evolution, and they are amenable to analyses of large-scale genomic data sets. These algorithms are also easily incorporated into gene tree parsimony phylogenetic analyses, potentially producing more credible estimates of reconciliation cost. Source


Willson S.J.,Iowa State University
Algorithms for Molecular Biology | Year: 2012

A phylogenetic network N has vertices corresponding to species and arcs corresponding to direct genetic inheritance from the species at the tail to the species at the head. Measurements of DNA are often made on species in the leaf set, and one seeks to infer properties of the network, possibly including the graph itself. In the case of phylogenetic trees, distances between extant species are frequently used to infer the phylogenetic trees by methods such as neighbor-joining.This paper proposes a tree-average distance for networks more general than trees. The notion requires a weight on each arc measuring the genetic change along the arc. For each displayed tree the distance between two leaves is the sum of the weights along the path joining them. At a hybrid vertex, each character is inherited from one of its parents. We will assume that for each hybrid there is a probability that the inheritance of a character is from a specified parent. Assume that the inheritance events at different hybrids are independent. Then for each displayed tree there will be a probability that the inheritance of a given character follows the tree; this probability may be interpreted as the probability of the tree. The tree-average distance between the leaves is defined to be the expected value of their distance in the displayed trees.For a class of rooted networks that includes rooted trees, it is shown that the weights and the probabilities at each hybrid vertex can be calculated given the network and the tree-average distances between the leaves. Hence these weights and probabilities are uniquely determined. The hypotheses on the networks include that hybrid vertices have indegree exactly 2 and that vertices that are not leaves have a tree-child. © 2012 Willson; licensee BioMed Central Ltd. Source


Rivera R.M.,University of Missouri | Ross J.W.,Iowa State University
Progress in Biophysics and Molecular Biology | Year: 2013

Epigenetic reprogramming of the parental genomes upon fertilization is required for proper embryonic development. It has long been appreciated that asymmetric distribution of histone modifications as well as differences in the level of DNA methylation exist between the parental pronuclei in mammalian zygotes and during preimplantation development. The speed at which the paternal genome is demethylated after entering the oocyte and the fact that rapid demethylation occurs in the absence of DNA replication have led many to hypothesize that a DNA demethylase must exist. However, such an enzyme has not been found. That the genome of mammalian preimplantation embryos undergo a wave of global demethylation was first reported 25 years ago but only in the past three years has data surfaced that can partially explain the elusive nature of this phenomenon. In addition to the global reorganization of the methylation and histone modification patterns, oocyte development prior to germinal vesicle breakdown involves the production of numerous small RNA, including miRNA. Despite their presence, miRNA functional activity is thought to be limited in the mature mouse oocyte. Additionally, molecular signatures in the 3' untranslated region of maternally expressed transcripts may impact mRNA stability during the transcriptionally quiescent period following germinal vesicle breakdown and prior to the maternal to zygote transition. In this review, we reference some of the recent works which attempt to shed light into the importance of the dynamic epigenetic landscape observed during oocyte maturation and preimplantation embryo development in mammals. © 2013 Elsevier Ltd. Source


Coetzee J.F.,Iowa State University
Veterinary Clinics of North America - Food Animal Practice | Year: 2013

Extralabel drug use for pain relief in the United States is regulated under the Animal Medicinal Drug Use Clarification Act. Agents that may provide analgesia in livestock include local anesthetics, nonsteroidal antiinflammatory drugs, opioids, α2-agonists, and N-methyl-d-aspartate receptor antagonists. The challenges associated with providing pain relief in food animals and the salient pharmacokinetic and pharmacodynamic features of the analgesic compounds that could potentially be used in livestock are reviewed. The potential use of novel agents such as bicarbonate, magnesium, ethanol, and gabapentin to augment analgesia is also discussed. © 2013 Elsevier Inc. Source


To infer a species phylogeny from unlinked genes, phylogenetic inference methods must confront the biological processes that create incongruence between gene trees and the species phylogeny. Intra-specific gene variation in ancestral species can result in deep coalescence, also known as incomplete lineage sorting, which creates incongruence between gene trees and the species tree. One approach to account for deep coalescence in phylogenetic analyses is the deep coalescence problem, which takes a collection of gene trees and seeks the species tree that implies the fewest deep coalescence events. Although this approach is promising for phylogenetics, the consensus properties of this problem are mostly unknown and analyses of large data sets may be computationally prohibitive. We prove that the deep coalescence consensus tree problem satisfies the highly desirable Pareto property for clusters (clades). That is, in all instances, each cluster that is present in all of the input gene trees, called a consensus cluster, will also be found in every optimal solution. Moreover, we introduce a new divide and conquer method for the deep coalescence problem based on the Pareto property. This method refines the strict consensus of the input gene trees, thereby, in practice, often greatly reducing the complexity of the tree search and guaranteeing that the estimated species tree will satisfy the Pareto property. Analyses of both simulated and empirical data sets demonstrate that the divide and conquer method can greatly improve upon the speed of heuristics that do not consider the Pareto consensus property, while also guaranteeing that the proposed solution fulfills the Pareto property. The divide and conquer method extends the utility of the deep coalescence problem to data sets with enormous numbers of taxa. Source


Cornick N.A.,Iowa State University
Veterinary Microbiology | Year: 2010

Previously we have shown that experimentally infected swine, fed an antibiotic-free diet, can become colonized and shed Escherichia coli O157:H7 for at least 2 months. However, in epidemiological studies this organism is only rarely recovered from domestic swine and the basis for this discrepancy is not clear. In this report we demonstrate that significantly fewer pigs fed diets containing subtherapeutic levels of either tylosin or chlorotetracycline shed E. coli O157:H7 for longer than 2 weeks compared to those fed an antibiotic-free diet. In contrast to tylosin and chlorotetracycline, the addition of bacitracin methylene disalicylate to the diet did not influence the recovery of E. coli O157:H7. These results suggest that some antibiotics may alter the gastrointestinal tract flora in ways that create a less favorable environment for E. coli O157:H7 in swine. © 2009 Elsevier B.V. Source


Shanks B.H.,Iowa State University
ACS Catalysis | Year: 2013

The ketonization of small organic acids is a valuable reaction for biorenewable applications. Ceria has long been used as a catalyst for this reaction; however, under both liquid and vapor phase conditions, it was found that given the right temperature regime of about 150-300 °C, cerium oxide, which was previously believed to be a stable catalyst for ketonization, can undergo bulk transformations. This result, along with other literature reports, suggest that the long held belief of two separate reaction pathways for either bulk or surface ketonization reactions are not required to explain the interaction of cerium oxide with organic acids. X-ray photon spectroscopy, scanning electron microscopy, and temperature programmed decomposition results supported the formation of metal acetates and explained the occurrence of cerium reduction as well as the formation of cerium oxide/acetate whiskers. After thermogravimetry/mass spectrometry and FT-IR experiments, a single reaction sequence is proposed that can be applied to either surface or bulk reactions with ceria. © 2013 American Chemical Society. Source


Hannapel D.J.,Iowa State University
Journal of Integrative Plant Biology | Year: 2010

BEL1-like transcription factors are ubiquitous in plants and interact with KNOTTED1-types to regulate numerous developmental processes. In potato, the RNA of several BEL1-like transcription factors has been identified in phloem cells. One of these, StBEL5, and its Knox protein partner regulate tuber formation by targeting genes that control growth. RNA detection methods and grafting experiments demonstrated that StBEL5 transcripts move across a graft union to localize in stolon tips, the site of tuber induction. This movement of RNA originates in source leaf veins and petioles and is induced by a short-day photoperiod, regulated by the untranslated regions, and correlated with enhanced tuber production. Addition of the StBEL5 untranslated regions to another BEL1-like mRNA resulted in its preferential transport to stolon tips leading to increased tuber production. Upon fusion of the untranslated regions of StBEL5 to a β-glucuronidase marker, translation in tobacco protoplasts was repressed by those constructs containing the 3′ untranslated sequence. The untranslated regions of the StBEL5 mRNA are involved in mediating its long-distance transport and in controlling translation. The 3′ untranslated sequence contains an abundance of conserved motifs that may serve as binding motifs for RNA-binding proteins. Because of their presence in the phloem sieve tube system, their unique untranslated region sequences and their diverse RNA accumulation patterns, the family of BEL1-like RNAs from potato represents a valuable model for studying the long-distance transport of full-length mRNAs and their role in development. © 2010 Institute of Botany, Chinese Academy of Sciences. Source


Vignaroli N.,Iowa State University
Journal of High Energy Physics | Year: 2012

A possible composite nature of the Higgs could be revealed at the early stage of the LHC, by analyzing the channels where the Higgs is produced from the decay of a heavy fermion. The Higgs production from a singly-produced heavy bottom, in particular, proves to be a promising channel. For a value λ = 3 of the Higgs coupling to a heavy bottom, for example, we find that, considering a 125 GeV Higgs which decays into a pair of b-quarks, a discovery is possible at the 8TeV LHC with 30 fb -1 if the heavy bottom is lighter than roughly 530 GeV (while an observation is possible for heavy bottom masses up to ≃ 650 GeV). Such a relatively light heavy bottom is realistic in composite Higgs models of the type considered and, up to now, experimentally allowed. At √s = 14 TeV the LHC sensitivity on the channel increases significantly. With λ = 3 a discovery can occur, with 100 fb -1, for heavy bottom masses up to ≃ 1040 GeV. In the case the heavy bottom was as light as ≃ 500 GeV, the 14 TeV LHC would be sensitive to the measure of the λ coupling in basically the full range λ > 1 predicted by the theory. © SISSA 2012. Source


Kim J.K.,Iowa State University
Biometrika | Year: 2011

Parametric fractional imputation is proposed as a general tool for missing data analysis. Using fractional weights, the observed likelihood can be approximated by the weighted mean of the imputed data likelihood. Computational efficiency can be achieved using the idea of importance sampling and calibration weighting. The proposed imputation method provides efficient parameter estimates for the model parameters specified in the imputation model and also provides reasonable estimates for parameters that are not part of the imputation model. Variance estimation is discussed and results from a limited simulation study are presented. 2011 Biometrika Trust2011 © 2011 Biometrika Trust. Source


Kling C.L.,Iowa State University
American Journal of Agricultural Economics | Year: 2011

The Wadeable Streams Assessment was completed in 2004 with the aim of evaluating the biological condition of streams while also collecting data on physical and chemical stressors of the system. The characteristics of the process by which agricultural sources contribute to poor water quality creates difficult challenges for the design and use of policy instruments generally, and economic incentives in particular. The degree of this attenuation will depend on many physical features, including slope, soils, vegetation, and weather. Further complicating this problem in the case of agricultural emission is the fact that the degree of this attenuation can depend on land use choices made by others in watershed. There are many ways such a system could work, but one way these requirements could be operationalized is via a point-based system where conservation practices are assigned a point value based on their effectiveness at reducing emissions from a field. Source


Mason W.A.,Boys Town National Research Institute for Child and Family Studies | Spoth R.L.,Iowa State University
Addiction | Year: 2012

Aims: This study tests risk factors for four dimensions of alcohol use in the sequence from (i) early onset prior to age 13 to (ii) adolescent alcohol use and (iii) alcohol problems to (iv) young adult alcohol abuse. It also examines whether family-focused preventive interventions buffer predictive relationships. Design: Data were from a randomized prevention trial extending from ages 11 to 21 years. Setting: Families of sixth graders enrolled in 33 rural schools in the Midwestern United States were invited to participate. Participants: Families (n=667) were pretested and assigned randomly to a control group (n=208) or to family interventions (n=459). The average age of participating youth was 11.3 years when the study began (52% female). Measurements: Questionnaire data were collected on alcohol dimensions during adolescence (early onset, alcohol use, alcohol problems) and young adulthood (alcohol abuse), and on risk factors in early adolescence (male gender, impulsive behaviors, aggression-hostility, peer deviance and parent problem drinking). Findings: Impulsive behaviors predicted early onset, peer deviance predicted alcohol use and parent problem drinking predicted alcohol problems (P<0.05). Aggression-hostility and alcohol problems predicted alcohol abuse in the control group (P<0.05), but not in the family interventions group (P>0.05). Conclusions: Different dimensions of alcohol use and problems from before age 13 to young adulthood are predicted by different risk factors. Family-focused preventive interventions can reduce the influence of some of these risk factors, including early adolescent aggression-hostility and late adolescent alcohol problems. © 2012 The Authors, Addiction © 2012 Society for the Study of Addiction. Source


Raju M.,Convergent Science Inc. | Khaitan S.K.,Iowa State University
Journal of Power Sources | Year: 2012

This paper deals with the storage of excess wind energy, in a hybrid wind power system, in the form of compressed hydrogen. A system simulation model is developed in Matlab/Simulink platform for the charging and discharging dynamics of compressed hydrogen storage system integrated with the wind turbine and the fuel cell. Wind model is used to estimate the power generation in the wind turbine. When the wind power generation exceeds the load, the excess power is diverted to the electrolyzer to produce hydrogen. As and when the pressure inside the electrolyzer builds, a compressor is operated intermittently (for higher efficiency) to divert the hydrogen into high pressure cylinders. When demand exceeds the power generation, fuel cell supplies the power to the load. A number of fuel cell stacks are provided to meet the required load. The overall efficiency of the storage system, defined as the ratio of the useful energy derived from the storage system to the energy diverted to the storage system is found to be 24.5% for the compressed hydrogen storage based system. © 2012 Elsevier B.V. All rights reserved. Source


Yoo M.-J.,University of Florida | Wendel J.F.,Iowa State University
PLoS Genetics | Year: 2014

The single-celled cotton (Gossypium hirsutum) fiber provides an excellent model to investigate how human selection affects phenotypic evolution. To gain insight into the evolutionary genomics of cotton domestication, we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Seq. Analysis of single-celled fiber transcriptomes from four wild and five domesticated accessions from two developmental time points revealed that at least one-third and likely one-half of the genes in the genome are expressed at any one stage during cotton fiber development. Among these, ~5,000 genes are differentially expressed during primary and secondary cell wall synthesis between wild and domesticated cottons, with a biased distribution among chromosomes. Transcriptome data implicate a number of biological processes affected by human selection, and suggest that the domestication process has prolonged the duration of fiber elongation in modern cultivated forms. Functional analysis suggested that wild cottons allocate greater resources to stress response pathways, while domestication led to reprogrammed resource allocation toward increased fiber growth, possibly through modulating stress-response networks. This first global transcriptomic analysis using multiple accessions of wild and domesticated cottons is an important step toward a more comprehensive systems perspective on cotton fiber evolution. The understanding that human selection over the past 5,000+ years has dramatically re-wired the cotton fiber transcriptome sets the stage for a deeper understanding of the genetic architecture underlying cotton fiber synthesis and phenotypic evolution. © 2014 Wendel, Yoo. Source


Dobson I.,Iowa State University
IEEE Transactions on Power Systems | Year: 2012

Large blackouts typically involve the cascading outage of transmission lines. We estimate from observed utility data how much transmission line outages propagate, and obtain parameters of a probabilistic branching process model of the cascading. The branching process model is then used to predict the distribution of total number of outages for a given number of initial outages. We study how the total number of lines outaged depends on the propagation as the cascade proceeds. The analysis gives a new way to quantify the effect of cascading failure from standard utility line outage data. © 1969-2012 IEEE. Source


Dobson I.,Iowa State University
IEEE Transactions on Power Systems | Year: 2012

We define the voltage across an area of a resistive network by suitably combining voltages at buses (nodes) on the border of the area. The new voltage across the area satisfies circuit laws. The same concept works to define the voltage angle difference across an area of a DC load flow network and the complex voltage difference across an area of an AC load flow network. We first define the voltage across a cutset of lines, and then derive and explain the voltages across areas, including generalizations to several voltages across an area and multiple areas. The new voltages across areas seem promising for both power system monitoring and network reduction, and we describe their application to monitoring area stress. © 2012 IEEE. Source


Lee J.-S.,Sungkyunkwan University | Olafsson S.,Iowa State University
Information Sciences | Year: 2013

An important and challenging problem in data clustering is the determination of the best number of clusters. A variety of estimation methods has been proposed over the years to address this problem. Most of these methods depend on several nontrivial assumptions about the data structure; and such methods may thus fail to discover the true clusters in a dataset that does not satisfy those assumptions. We develop a new approach that takes as a starting point the simple and intuitive observation that close objects should fall within the same cluster, whereas distant ones should not. Based on this simple notion we utilize a new measurement of good clustering called disconnectivity as well as existing goodness measurements; and we embed these measures into a meta-learning approach for estimating the number of clusters. A simulation experiment based on 13 representative models and an application to real world datasets are conducted to show the effectiveness of the proposed method. © 2013 Elsevier Inc. All rights reserved. Source


Angelici R.J.,Iowa State University
Catalysis Science and Technology | Year: 2013

Oxidative reactions that are catalysed by bulk gold consisting of ∼50000 nm gold powder particles or gold (∼50 nm) supported on Al 2O3 are reviewed. Using O2 as the oxidizing agent, bulk gold catalyzes the following types of reactions in organic solvents at 45-90 °C: (1) the conversion of amines to imines [(RCH2) 2NH → RCH2NCHR], (2) the oxidation of benzyl alcohol to benzaldehyde, (3) the reaction of isocyanides with primary amines to give carbodiimides [CN-R + H2N-R′ → R′-NCN-R] and with secondary amines to give ureas, (4) the reactions of CO with primary amines to give ureas [CO + H2N-R → OC(NHR)2], and (5) the reactions of diazoalkanes with amines to give enamines. In some of these reactions, amine oxides (e.g., Me3N-O) may be used in place of O 2. Mechanisms of these and related reactions are examined. These studies show that bulk, non-nanogold is capable of catalysing a variety of different reactions. This journal is © The Royal Society of Chemistry 2013. Source


Chandler C.H.,Iowa State University | Chandler C.H.,Michigan State University
Heredity | Year: 2010

Sex determination mechanisms (SDMs) show striking diversity and appear to evolve rapidly. Although interspecific comparisons and studies of ongoing major transitions in sex determination (such as the establishment of new sex chromosomes) have shed light on how SDMs evolve, comparatively little attention has been paid to intraspecific variation with less drastic effects. In this study, I used mutant strains carrying a temperature-sensitive sex determination mutation, along with a second null mutation, in different wild genetic backgrounds to uncover hidden variation in the SDM of the model nematode Caenorhabditis elegans. I then used quantitative trait locus (QTL) mapping to begin to investigate its genetic basis. I identified several QTLs, and although this variation apparently involved genotype-by-temperature interactions, QTL effects were generally consistent across temperatures. These QTLs collectively and individually explained a relatively large fraction of the variance in tail morphology (a sexually dimorphic trait), and two QTLs contained no genes known to be involved in somatic sex determination. These results show the existence of within-species variation in sex determination in this species, and underscore the potential for microevolutionary change in this important developmental pathway. © 2010 Macmillan Publishers Limited All rights reserved. Source


Tuchin K.,Iowa State University
Nuclear Physics A | Year: 2013

We consider heavy quark production in high energy pA collisions and investigate the contribution of interactions of valence quarks of proton with the nucleus. The often made assumption that valence quarks of proton can be factored out is justified only if the nucleus saturation momentum is much smaller than the heavy quark mass. This is not the case in phenomenologically relevant situations. Breakdown of factorization manifests itself in substantial decrease of the cross section at large total and small relative transverse momenta of the heavy quark-antiquark pair. © 2013 Elsevier B.V. Source


Fietz C.,Iowa State University
Journal of the Optical Society of America B: Optical Physics | Year: 2013

We present an absorbing boundary condition for electromagnetic frequency domain simulations of photonic crystals and metamaterials. This boundary condition can simultaneously absorb multiple Bloch-Floquet eigenmodes of a periodic crystal, including both propagating and evanescent modes. The photonic crystal or metamaterial in question can include lossy, active, anisotropic, and even bi-anisotropic inclusions. The absorbing boundary condition is dependent on an orthogonality condition for Bloch-Floquet eigenmodes, a generalized version of which is presented here. We test this absorbing boundary condition numerically and present the results. © 2013 Optical Society of America. Source


Miliordos E.,Pacific Northwest National Laboratory | Ruedenberg K.,Iowa State University | Xantheas S.S.,Pacific Northwest National Laboratory
Angewandte Chemie - International Edition | Year: 2013

The biradical character β (1 for an ideal biradical) is determined from multi-reference configuration interaction (MRCI) wavefunctions. Triatomics in the series FX2+ (X=O, S, Se, Te, Po) exhibit unusually high biradical characters for X=Te, Po (0.76<β<0.92), the largest among the homologous 18 valence electron molecules CX22-, NX2-, X3, and OX2. On the same scale, the biradical character of O3 is just 0.19, whereas that of C(CH2)3 is 0.97. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Johnston D.C.,Iowa State University
Advances in Physics | Year: 2010

The response of the worldwide scientific community to the discovery in 2008 of superconductivity at Tc = 26 K in the Fe-based compound LaFeAsO1-xFx has been very enthusiastic. In short order, other Fe-based superconductors with the same or related crystal structures were discovered with Tc up to 56 K. Many experiments were carried out and theories formulated to try to understand the basic properties of these new materials and the mechanism for Tc. In this selective critical review of the experimental literature, we distill some of this extensive body of work, and discuss relationships between different types of experiments on these materials with reference to theoretical concepts and models. The experimental normal-state properties are emphasized, and within these the electronic and magnetic properties because of the likelihood of an electronic/magnetic mechanism for superconductivity in these materials. © 2010 Taylor & Francis. Source


Kogan V.G.,Iowa State University
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

It is argued that the stress caused by vortex cores in the mixed state of superconductors may result in a measurable field-dependent contribution to the free energy and magnetization. For sufficiently strong stress dependence of the critical temperature, ∂Tc/∂p, this contribution may result in the "second peak" in the field dependence of the reversible magnetization, the effect often masked by vortex pinning and creep. © 2013 American Physical Society. Source


Levitas V.I.,Iowa State University
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

An exact expression for the temperature-dependent interface stress tensor (tension) and energy is derived within a phase field approach. The key problem, of which part of the thermal energy should contribute to the surface tension, is resolved with the help of an analytical solution for a nonequilibrium interface. Thus, for a propagating interface at any temperature, the interface stress tensor represents biaxial tension with magnitude equal to the temperature-dependent interface energy. Explicit expressions for the distributions of interface stresses are obtained for a nonequilibrium interface and a critical nucleus. The results obtained are applicable for various phase transformations (solid-solid, melting-solidification, sublimation, etc.) and structural changes (twinning, grain evolution), and can be generalized for anisotropic interface energy, for dislocations, fracture, and diffusive phase transformations described by Cahn-Hilliard theory. © 2013 American Physical Society. Source


Kelly C.D.,Iowa State University | Kelly C.D.,Australian National University | Jennions M.D.,Australian National University
Biological Reviews | Year: 2011

Multiple mating or group spawning leads to post-copulatory sexual selection, which generally favours ejaculates that are more competitive under sperm competition. In four meta-analyses we quantify the evidence that sperm competition (SC) favours greater sperm number using data from studies of strategic ejaculation. Differential investment into each ejaculate emerges at the individual level if males exhibit phenotypic plasticity in ejaculate properties in response to the likely risk and/or intensity of sperm competition after a given mating. Over the last twenty years, a series of theoretical models have been developed that predict how ejaculate size will be strategically adjusted in relation to: (a) the number of immediate rival males, with a distinction made between 0 versus 1 rival ('risk' of SC) and 1 versus several rivals ('intensity' of SC); (b) female mating status (virgin or previously mated); and © female phenotypic quality (e.g. female size or condition). Some well-known studies have reported large adjustments in ejaculate size depending on the relevant social context and this has led to widespread acceptance of the claim that strategic sperm allocation occurs in response to each of these factors. It is necessary, however, to test each claim separately because it is easy to overlook studies with weak or negative findings. Compiling information on the variation in outcomes among species is potentially informative about the relevance of these assumptions in different taxa or mating systems. We found strong evidence that, on average, males transfer larger ejaculates to higher quality females. The effect of female mating status was less straightforward and depended on how ejaculate size was measured (i.e. use of proxy or direct measure). There is strong evidence that ejaculate size increased when males were exposed to a single rival, which is often described as a response to the risk of SC. There is, however, no evidence for the general prediction that ejaculate size decreases as the number of rivals increases from one to several males (i.e. in response to a higher intensity of SC which lowers the rate of return per sperm released). Our results highlight how meta-analysis can reveal unintentional biases in narrative literature reviews. We note that several assumptions of theoretical models can alter an outcome's predicted direction in a given species (e.g. the effect of female mating status depends on whether there is first- or last-male sperm priority). Many studies do not provide this background information and fail to make strong a priori predictions about the expected response of ejaculate size to manipulation of the mating context. Researchers should be explicit about which model they are testing to ensure that future meta-analyses can better partition studies into different categories, or control for continuous moderator variables. © 2011 The Authors. Biological Reviews © 2011 Cambridge Philosophical Society. Source


Ying L.,Iowa State University | Shakkottai S.,University of Texas at Austin
IEEE Transactions on Information Theory | Year: 2011

The problem of routing/scheduling in a wireless network with partial/delayed network (channel and queue) state information (NSI) is studied in this paper. Two cases are considered: (i) centralized routing/scheduling, where a central controller obtains heterogeneously delayed information from each of the nodes (thus, the controller has NSI with different delays from different nodes), and makes routing/scheduling decisions; (ii) decentralized routing/scheduling, where each node makes a decision based on its current channel and queue states along with homogeneous delayed NSI from other nodes. For each of the cases (with additional flow restrictions for the decentralized routing/scheduling case), the optimal network throughput regions are characterized under the above described NSI models and it is shown that the throughput regions shrinks with the increase of delay. Further, channel and queue length based routing/scheduling algorithms that achieve the above throughput regions are proposed in this paper. © 2011 IEEE. Source


Srirangam P.,McMaster University | Kramer M.J.,Iowa State University | Shankar S.,McMaster University
Acta Materialia | Year: 2011

High-energy X-ray diffraction experiments were performed using a synchrotron beam source to investigate the effect of strontium on the liquid atomic structure of Al-Si hypoeutectic alloys. The high-temperature liquid diffraction experiments were carried out on Al alloys with 3, 7, 10 and 12.5 (eutectic) wt.% Si, respectively, with 0 and 0.04 wt.% addition of Sr to each of the alloys. Further, the diffraction data for all the alloys were obtained at various melt temperatures (5-220 K) above the respective liquidus temperature. It was observed that the addition of 0.04 wt.% Sr results in significant change in the liquid structure parameters, such as structure factor, pair distribution function, radial distribution function, coordination number and packing density, at any given melt temperature of the alloy. Salient observations were that, for any specific alloy and temperature, addition of Sr significantly decreases coordination number and packing density. Further, with the addition of Sr in the liquid alloy, the atomic coordination number and packing density increases with decreasing temperature and decreasing Si content of the alloy. The results coupled with prior knowledge have enabled an in-depth understanding of the nucleation environment of the solidifying phases, specifically the role of Sr in delaying the clustering tendencies (nucleation) of the eutectic Si phase. © 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. Source


Kelly J.W.,Iowa State University | McNamara T.P.,Vanderbilt University
Cognition | Year: 2010

Four experiments investigated the role of reference frames during the acquisition and development of spatial knowledge, when learning occurs incrementally across views. In two experiments, participants learned overlapping spatial layouts. Layout 1 was first studied in isolation, and Layout 2 was later studied in the presence of Layout 1. The Layout 1 learning view was manipulated, whereas the Layout 2 view was held constant. Manipulation of the Layout 1 view influenced the reference frame used to organize Layout 2, indicating that reference frames established during early environmental exposure provided a framework for organizing locations learned later. Further experiments demonstrated that reference frames established after learning served to reorganize an existing spatial memory. These results indicate that existing reference frames can structure the acquisition of new spatial memories and that new reference frames can reorganize existing spatial memories. © 2010 Elsevier B.V. Source


Vardeman S.B.,Iowa State University
Quality Engineering | Year: 2016

In broad terms, effective probability modeling of modern measurement requires the development of (usually parametric) distributions for increasingly complex multivariate outcomes driven by the physical realities of particular measurement technologies. "Differences" between measures of distribution center and truth function as "bias." Model features that allow hierarchical compounding of variation function to describe "variance components" like "repeatability," "reproducibility," "batch-to-batch variation," etc. Mixture features in models allow for description (and subsequent downweighting) of outliers. For a variety of reasons (including high-dimensionality of parameter spaces relative to typical sample sizes, the ability to directly include "Type B" considerations in assessing uncertainty, and the relatively direct path to uncertainty quantification for the real objectives of measurement), Bayesian methods of inference in these models are increasingly natural and arguably almost essential.We illustrate the above points first in an overly simple but instructive example. We then provide a set of formalisms for expressing these notions. Then we illustrate them with real modern measurement applications including (1) determination of cubic crystal orientation via electron backscatter diffraction, (2) determination of particle size distribution through sieving, and (3) analysis of theoretically monotone functional responses from thermogravimetric analysis in a materials study. © 2016 Taylor & Francis. Source


Jia Y.-B.,Iowa State University
International Journal of Robotics Research | Year: 2013

Impact is indispensable in robotic manipulation tasks in which objects and/or manipulators move at high speeds. Applied research using impact has been hindered by underdeveloped computational foundations for rigid-body collision. This paper studies the computation of tangential impulse as two rigid bodies in the space collide at a point with both tangential compliance and friction. It extends Stronge's spring-based planar contact structure to three dimensions by modeling the contact point as a massless particle able to move tangentially on one body while connected to an infinitesimal region on the other body via three orthogonal springs. Slip or stick is indicated by whether the particle is still or moving. Impact analysis is carried out using normal impulse rather than time as the only independent variable, unlike in previous work on tangential compliance. This is due to the ability to update the energies stored in the three springs. Collision is governed by a system of differential equations that are solvable numerically. Modularity of the impact model makes it easy to be integrated into a multibody system, with one copy at each contact, in combination with a model for multiple impacts that governs normal impulses at different contacts. © The Author(s) 2013. Source


Zhang S.,Iowa State University
Applied Optics | Year: 2011

This paper presents a novel pixel-level resolution 3D profilometry technique that only needs binary phase-shifted structured patterns. This technique uses four sets of three phase-shifted binary patterns to achieve the phase error of less than 0.2%, and only requires two sets to reach similar quality if the projector is slightly defocused. Theoretical analysis, simulations, and experiments will be presented to verify the performance of the proposed technique. © 2011 Optical Society of America. Source


Salmon A.,Iowa State University
G3 (Bethesda, Md.) | Year: 2012

Targeted sequence capture is a promising technology in many areas in biology. These methods enable efficient and relatively inexpensive sequencing of hundreds to thousands of genes or genomic regions from many more individuals than is practical using whole-genome sequencing approaches. Here, we demonstrate the feasibility of target enrichment using sequence capture in polyploid cotton. To capture and sequence both members of each gene pair (homeologs) of wild and domesticated Gossypium hirsutum, we created custom hybridization probes to target 1000 genes (500 pairs of homeologs) using information from the cotton transcriptome. Two widely divergent samples of G. hirsutum were hybridized to four custom NimbleGen capture arrays containing probes for targeted genes. We show that the two coresident homeologs in the allopolyploid nucleus were efficiently captured with high coverage. The capture efficiency was similar between the two accessions and independent of whether the samples were multiplexed. A significant amount of flanking, nontargeted sequence (untranslated regions and introns) was also captured and sequenced along with the targeted exons. Intraindividual heterozygosity is low in both wild and cultivated Upland cotton, as expected from the high level of inbreeding in natural G. hirsutum and bottlenecks accompanying domestication. In addition, levels of heterozygosity appeared asymmetrical with respect to genome (A(T) or D(T)) in cultivated cotton. The approach used here is general, scalable, and may be adapted for many different research inquiries involving polyploid plant genomes. Source


Fietz C.,Iowa State University
Journal of the Optical Society of America B: Optical Physics | Year: 2013

We apply the method of asymptotic homogenization to metamaterials with microscopically bianisotropic inclusions to calculate a full set of constitutive parameters in the long-wavelength limit. Two different implementations of electromagnetic asymptotic homogenization are presented. We test the homogenization procedure on two different metamaterial examples. Finally, the analytical solution for long-wavelength homogenization of a one-dimensional metamaterial with microscopically bi-isotropic inclusions is derived. © 2013 Optical Society of America. Source


Thakur V.K.,Iowa State University | Thakur M.K.,Himachal Pradesh University | Gupta R.K.,Indian Institute of Technology Kanpur
Carbohydrate Polymers | Year: 2013

Cellulose, a linear polysaccharide polymer with numerous glucose monosaccharide units is of enormous interest because of its applications in biosorption, biomedical, packaging, biofiltration and biocomposites. In this study, cellulose-graft-poly(butyl acrylate) copolymers were synthesized under microwave conditions. Effects of microwave radiation doses and different reaction parameters were optimized to get the optimum percentage of grafting. The dependence of optimum conditions for better physico-chemical properties of the cellulosic polymers was also determined. Fourier transform infrared spectroscopy (FTIR) analysis was used to authenticate the chemical reaction taking place between cellulosic polymers and monomer. The thermogravimetric behavior of the raw and grafted cellulosic polymers was characterized by thermogravimetric analysis (TGA). The surface structure of the raw and grafted cellulosic polymers was analyzed through scanning electron microscopy (SEM). The graft copolymers have been found to be more moisture resistant and also showed better chemical and thermal resistance. © Published by Elsevier Ltd. Source


Lu P.,Iowa State University
Journal of Guidance, Control, and Dynamics | Year: 2014

During the past five decades, entry guidance methods have gone through major evolutions, largely driven by the needs of different types of entry vehicles and greatly increased onboard computation capabilities. Numerical predictor-corrector algorithms have emerged in recent years to hold the potential to become the next prevalent entry guidance method. This paper aims at developing a method that is centered on a single baseline predictor-corrector algorithm and will be applicable to a wide range of vehicles with varying lifting capabilities for orbital as well as suborbital entry missions. Different needs for additional (vehicle- and mission-dependent) trajectory shaping and inequality constraint enforcement are met by appropriate augmentations of altitude-rate feedback to the baseline algorithm. In particular, the long-standing challenge of enforcing common inequality trajectory constraints (such as the heating rate and load factor) with a predictor-corrector algorithm is now satisfactorily overcome, for either lowlifting or high-lifting vehicles. The method is successfully applied to three very different vehicles, a capsule, a shuttleclass vehicle, and a high-lifting hypersonic gliding vehicle. Copyright © 2013 by the American Institute of Aeronautics and Astronautics, Inc. Source


Rajan K.,Iowa State University
Structure and Bonding | Year: 2010

Inorganic crystallography is a data intensive field of science. Much of the work in this vast field is focused on ways to acquire, model, organize and manage that data. To a lesser extent, there are efforts to survey that information from which one hopes to glean patterns of behavior that would offer insight into the complex chemical and geometrical relationships governing the existence or stability of a given compound. In this article we provide an overview of the types of information that can be gleaned by applying data mining and statistical learning techniques to inorganic crystallography. The focus of the paper is in two broad areas, classification and prediction of data, and the two primary roles of data mining as a field. © Springer-Verlag Berlin Heidelberg 2009. Source


Zhao Y.,Iowa State University
ChemPhysChem | Year: 2013

The concept of preorganization suggests that organizing a receptor around its guest during binding is detrimental, because the cost of conformational change is assumed to be paid out of the binding energy. Although this concept has historically guided the synthesis of a great many synthetic hosts, in recent years, chemists have begun to synthesize receptors that resemble proteins in their cooperative conformational changes. Such changes could enhance the host-guest interactions, in particular if the binding of the guest triggers previously unengaged noncovalent interactions within the host. These hosts, referred to as cooperatively enhanced receptors, corroborate with their biological counterparts to support the approach of creating high-affinity receptors through the combined strategies of cooperativity and preorganization. Solvents, often the invisible participants of any solution-based supramolecular process, should be properly considered in the design of synthetic receptors, whether preorganized or cooperatively enhanced. Stick, twist, or fold? A characteristic of protein receptors is the delocalization of binding interactions. Unlike preorganized hosts, these cooperatively enhanced receptors rely on positive cooperativity between intrahost interactions, altered solvent shells, and released solvent molecules to achieve high binding affinity. Such receptors abound in nature and have inspired chemists to create synthetic hosts that mimic proteins in their binding cooperativity. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Raju M.,Optimal CAE Inc. | Kumar Khaitan S.,Iowa State University
Applied Energy | Year: 2012

An accurate dynamic simulation model for compressed air energy storage (CAES) inside caverns has been developed. Huntorf gas turbine plant is taken as the case study to validate the model. Accurate dynamic modeling of CAES involves formulating both the mass and energy balance inside the storage. In the ground reservoir based storage bed, the heat transfer from the ground reservoir plays an important role in predicting the cavern storage behavior and is therefore taken into account. The heat transfer coefficient between the cavern walls and the air inside the cavern is accurately modeled based on the real tests data obtained from the Huntorf plant trial tests. Finally the model is validated based on a typical daily schedule operation of the Huntorf plant. A comparison is also made with the results obtained from adiabatic and isothermal assumptions inside the cavern to gain further insights. Such accurate modeling of cavern dynamics will affect the design of the cavern storage beds for future explorations. © 2011 Elsevier Ltd. Source


Arghode V.K.,University of Maryland University College | Gupta A.K.,University of Maryland University College | Bryden K.M.,Iowa State University
Applied Energy | Year: 2012

Combustion characteristics of colorless distributed combustion have been investigated for application to gas turbine combustors. Very high intensity distributed combustion has been shown for application to stationary gas turbine engines. Various configurations examined have revealed reverse cross-flow mode to be more favorable for desirable combustion characteristics. The reverse-cross flow geometry is further investigated experimentally at range thermal intensities from 53 to 85MW/m3atm with specific focus on exhaust emissions, radical emission, global flame photographs and flowfield using novel but simplified geometry for easy transition to applications in gas turbine engine applications. The high combustion intensity demonstrated here is higher than that used in present stationary gas turbine engines. Numerical simulations are also performed and compared with the experiments for the new design configuration under non-reacting conditions. Ultra low NOx emissions are achieved for both the novel premixed (1ppm) and non-premixed (4ppm) combustion modes reported here. Carbon monoxide levels of about 30ppm are achieved in both novel premixed and non-premixed modes of combustion with a pressure drop of less than 5% across the combustor at the favorable condition. Almost no visible flame color in the reaction zones are observed for both novel premixed and non-premixed modes with volume distributed combustion so that this mode is termed as colorless distributed combustion. This mode of volume distributed colorless combustion is dramatically different than that used in contemporary gas turbine combustion operating under lean premixed, lean direct injection or rich burn, quick quench lean burn gas turbine combustion. © 2011 Elsevier Ltd. Source


Vignaroli N.,Iowa State University | Vignaroli N.,Michigan State University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

We analyze the bounds on the spectrum of composite Higgs models that come from flavor observables, by means of simple two-site effective Lagrangians, which incorporate a custodial symmetry and a left-right parity, and which could also be adopted in further phenomenological studies on composite Higgs models. We derive, in particular, an important constraint on the masses of the (t L,bL) partners, which does not depend on the flavor structure of the sector beyond the Standard Model. This bound is obtained from the "infrared" contribution to b→sγ induced by the flavor-conserving effective vertex WtRbR. We find that the presence of a custodial symmetry can play a role in protecting this effective coupling and, as a consequence, in attenuating the constraint, which, however, remains of the order of 1 TeV. In addition to this bound, we calculate the constraints from the "ultraviolet" contribution to b→sγ, induced by loops of heavy fermions, and to μ′/μ K. © 2012 American Physical Society. Source


Vignaroli N.,Iowa State University | Vignaroli N.,Michigan State University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

Top partners from a new strong sector can be discovered soon, at the 8 TeV LHC, by analyzing their single production, which exhibits a large enhancement in the cross section compared to the analogous productions of bottom partners and exotic quarks. We analyze the subsequent decay of the top partners into a 125 GeV Higgs. This channel proves to be very promising for both the discovery of top partners and a test of the Higgs sector. For a reference value λ T∼=3 of the Higgs coupling to the top partner, we could have a discovery (observation) at the 8 TeV LHC, with 30fb -1, for top partner masses up to 760 (890) GeV. If the LHC and Tevatron excesses near 125 GeV are really due to a composite Higgs, naturalness arguments demand top partners below ∼1TeV. Our results highlight thus that the 8 TeV LHC already has a large sensitivity on probing the composite Higgs hypothesis. The LHC reach is even wider at √s=14TeV. With λ T∼=3 the LHC with 100fb -1 can observe (at 5σ) a Higgs from a top partner decay for masses of this latter up to ≃1450GeV. In the case that the top partner is as light as ≃500GeV, the 14 TeV LHC would be sensitive to the measure of the λ T∼ coupling in basically the full range λ T∼>1 predicted by the theory. © 2012 American Physical Society. Source


Pouliot S.,Iowa State University
American Journal of Agricultural Economics | Year: 2011

This article measures the willingness to pay for the traceability of steers. I use data on the price of steers in Quebec and Ontario to identify a demand shifter in a hedonic framework. I estimate error correction models to provide the first market-based econometric estimates of the willingness to pay for traceability. My best assessment is that a premium between C$0.02 and C$0.05 per pound of carcass (between 1.2 and 3.1) is paid for traceable steers. © The Author (2011). Source


Chimenti D.E.,Iowa State University
Ultrasonics | Year: 2014

This article presents a review of air-coupled ultrasonics employed in the characterization or nondestructive inspection of industrial materials. Developments in air-coupled transduction and electronics are briefly treated, although the emphasis here is on methods of characterization and inspection, and in overcoming limitations inherent in the use of such a tenuous sound coupling medium as air. The role of Lamb waves in plate characterization is covered, including the use of air-coupled acoustic beams to measure the elastic and/or viscoelastic properties of a material. Air-coupled acoustic detection, when other methods are employed to generate high-amplitude sound beams is also reviewed. Applications to civil engineering, acoustic tomography, and the characterization of both paper and wood are dealt with here. A brief summary of developments in air-coupled acoustic arrays and the application of air-coupled methods in nonlinear ultrasonics complete the review. In particular, the work of Professor Bernard Hosten and his collaborators at Bordeaux is carefully examined. © 2014 Elsevier B.V. All rights reserved. Source


Prickett J.R.,Iowa State University
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2010

The purpose of this review was to discuss the history of the development and implementation of oral fluid diagnostics for infectious diseases of humans and domestic animals. The use of oral fluid for the assessment of health and diagnosis of disease in humans and animals has a surprisingly long history. As early as 1909, Pollaci and Ceraulo reported sensitive and specific agglutination of 'Micrococcus melitensis' (Brucella melitensis) by oral fluid from patients diagnosed with Malta Fever. A 1986 report of the detection of antibodies against human immunodeficiency virus (HIV) in oral fluid from patients with acquired immunodeficiency syndrome (AIDS) marked the start of a remarkably rapid series of developments in oral fluid-based assays. Cumulatively, the literature strongly supports implementation of oral fluid-based diagnostics in veterinary diagnostic medicine. Pathogen-specific IgA, IgM and IgG antibodies have all been demonstrated in oral fluid collected from diverse domestic animal species in response to infection. A variety of infectious agents, both local and systemic, are shed in oral fluid, including some of the most economically significant pathogens of production animals (e.g. foot-and-mouth disease virus, classical swine fever virus and porcine reproductive and respiratory syndrome virus) Ultimately, point-of-care rapid assays (i.e. cow-side, sow-side or pen-side tests) and access to real-time infectious disease data will revolutionize our delivery of health management services. Source


Sexual development has long been the target of study and despite great advances in our understanding of the composition and regulation of the gene network underlying gonadogenesis, our knowledge remains incomplete. Of particular interest is the relative role that the environment and the genome play in directing gonadal formation, especially the effect of environmental temperature in directing this process in vertebrates. Comparative analyses in closely related taxa with contrasting sex-determining mechanisms should help fill this gap. Here I present a multivariate study of the regulation of the gene network underlying sexual development in turtles with temperature-dependent (TSD; Chrysemys picta) and genotypic sex determination (GSD; Apalone mutica). I combine novel data on SOX9 and DMRT1 from these species with contrasting sex-determining mechanisms for the first time with previously reported data on DAX1, SF-1 (NR5A1), WT1, and aromatase (CYP19A1) from these same taxa. Comparative expression analyses of SOX9 and DMRT1 from these and other species indicate additional elements whose expression has diverged among TSD taxa, further supporting the notion that significant evolutionary changes have accrued in the regulation of the TSD gene network in reptiles. A non-parametric MANOVA revealed that temperature had a significant effect in multivariate gene expression in C. picta that varied during embryonic development, whereas the covariation of gene expression in A. mutica was insensitive to temperature. A phenotypic trajectory analysis (PTA) of gene expression comparing both species directly indicated that the relative covariation in gene expression varied between temperatures in C. picta. Furthermore, the 25°C trajectory of C. picta differed from that of A. mutica in the magnitude of gene expression change. Additional analyses revealed a stronger covariation in gene expression and a more interconnected regulatory network in A. mutica, consistent with the hypothesis that sexual development is a more canalized process in A. mutica, as would be expected if GSD evolved in this lineage through directional selection from its TSD ancestor. Copyright © 2010 S. Karger AG, Basel. Source


Zhang S.,Iowa State University
Applied Optics | Year: 2012

This paper presents the idea of naturally encoding three-dimensional (3D) range data into regular twodimensional (2D) images utilizing computer graphics rendering pipeline. The computer graphics pipeline provides a means to sample 3D geometry data into regular 2D images, and also to retrieve the depth information for each sampled pixel. The depth information for each pixel is further encoded into red, green, and blue color channels of regular 2D images. The 2D images can further be compressed with existing 2D image compression techniques. By this novel means, 3D geometry data obtained by 3D range scanners can be instantaneously compressed into 2D images, providing a novel way of storing 3D range data into its 2D counterparts. We will present experimental results to verify the performance of this proposed technique. © 2012 Optical Society of America. Source


Adams D.C.,Evolution and Organismal Biology | Adams D.C.,Iowa State University
Systematic Biology | Year: 2014

Many questions in evolutionary biology require the quantification and comparison of rates of phenotypic evolution. Recently, phylogenetic comparative methods have been developed for comparing evolutionary rates on a phylogeny for single, univariate traits (σ2), and evolutionary rate matrices (R) for sets of traits treated simultaneously. However, high-dimensional traits like shape remain under-examined with this framework, because methods suited for such data have not been fully developed. In this article, I describe a method to quantify phylogenetic evolutionary rates for high-dimensional multivariate data, found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices (R-mode and Q-mode methods). I then use simulations to evaluate the statistical performance of hypothesis-testing procedures that compare for two or more groups of species on a phylogeny. Under both isotropic and non-isotropic conditions, and for differing numbers of trait dimensions, the proposed method displays appropriate Type I error and high statistical power for detecting known differences in among groups. In contrast, the Type I error rate of likelihood tests based on the evolutionary rate matrix (R) increases as the number of trait dimensions (p) increases, and becomes unacceptably large when only a few trait dimensions are considered. Further, likelihood tests based on R cannot be computed when the number of trait dimensions equals or exceeds the number of taxa in the phylogeny (i.e., when p ≥ N). These results demonstrate that tests based on provide a useful means of comparing evolutionary rates for high-dimensional data that are otherwise not analytically accessible to methods based on the evolutionary rate matrix. This advance thus expands the phylogenetic comparative toolkit for high-dimensional phenotypic traits like shape. Finally, I illustrate the utility of the new approach by evaluating rates of head shape evolution in a lineage of Plethodon salamanders. © 2013 The Author(s). Source


Shi F.,Iowa State University
Topics in current chemistry | Year: 2010

The catalytic activation of a C-H bond is a fundamentally important organic transformation. There are now numerous reports of palladium-mediated C-H activation by the through-space interaction of a palladium center with a neighboring C-H bond. This type of C-H activation can lead to a net "palladium migration" from the carbon atom where the palladium is first introduced to a remote carbon atom where C-H activation occurs. This process provides a novel method to introduce a palladium moiety into a position where direct palladium introduction may not be straightforward. This process is accompanied by concurrent migration of a hydrogen atom in the direction opposite to that of the palladium migration. Analogous rhodium migrations have also been reported. In this account, different types of palladium and rhodium migrations are reviewed and the reaction mechanism is discussed. Source


Gentile D.A.,Iowa State University
Child Development Perspectives | Year: 2011

Video games are at the center of a debate over what is helpful or harmful to children and adolescents, and there is research to substantiate both sides. The existing research suggests that there are at least 5 dimensions on which video games can affect players: the amount of play, the content of play, the game context, the structure of the game, and the mechanics of game play. This article describes each of these 5 dimensions with support from the scientific literature, arguing that this approach can allow people to get beyond the typical "good-bad" dichotomous thinking to have a more nuanced understanding of video game effects and to provide testable hypotheses for future research. © 2011 The Author. Child Development Perspectives © 2011 The Society for Research in Child Development. Source


Wolt J.D.,Iowa State University
Environmental Toxicology and Chemistry | Year: 2011

Multiple substance considerations applied to chemical mixtures in ecological risk assessments can be logically extended to nontarget organism (NTO) risk assessment for pyramided trait crops expressing multiple insect resistance genes. A case instance is developed that considers a two-protein pyramid of Cry1F and Cry1Ac synthetic proteins expressed in cotton (Gossypium hirsutum L.). A mixture toxicity approach was used to arrive at the aggregated multisubstance potentially affected fraction (msPAF) of NTOs that may be at risk from exposure to Cry1F+Cry1Ac cotton in representative-use environments. Development of the msPAF for putative susceptible NTOs considered laboratory toxicity data for Lepidoptera expressed in terms of additive mixture toxicity as well as data on in planta expression of the Cry1F and Cry1Ac proteins and their translation into environmental loads and exposure concentrations. The msPAF based on tier 1 estimated environmental concentrations (EECs) and toxicity to Lepidoptera species-used as surrogate data for adverse effects to a putative susceptible species-provided a highly conservative estimate of effects on beneficial species and therefore is a ready means to conduct screening-level NTO risk assessments for pyramided crops. Environ. Toxicol. Chem. 2011; 30:763-772. © 2011 SETAC Copyright © 2010 SETAC. Source


Arendt S.,Iowa State University
International journal of environmental research and public health | Year: 2013

During 2009-2010, a total of 1,527 foodborne disease outbreaks were reported by the Centers for Disease Control and Prevention (CDC) (2013). However, in a 2011 CDC report, Scallan et al. estimated about 48 million people contract a foodborne illness annually in the United States. Public health officials are concerned with this under-reporting; thus, the purpose of this study was to identify why consumers and healthcare professionals don't report foodborne illness. Focus groups were conducted with 35 consumers who reported a previous experience with foodborne illness and with 16 healthcare professionals. Also, interviews with other healthcare professionals with responsibility of diagnosing foodborne illness were conducted. Not knowing who to contact, being too ill, being unsure of the cause, and believing reporting would not be beneficial were all identified by consumers as reasons for not reporting foodborne illness. Healthcare professionals that participated in the focus groups indicated the amount of time between patients' consumption of food and seeking treatment and lack of knowledge were barriers to diagnosing foodborne illness. Issues related to stool samples such as knowledge, access and cost were noted by both groups. Results suggest that barriers identified could be overcome with targeted education and improved access and information about the reporting process. Source


Hebert K.R.,Iowa State University | Albu S.P.,Friedrich - Alexander - University, Erlangen - Nuremberg | Paramasivam I.,Friedrich - Alexander - University, Erlangen - Nuremberg | Schmuki P.,Friedrich - Alexander - University, Erlangen - Nuremberg
Nature Materials | Year: 2012

Electrochemical oxidation of metals, in solutions where the oxide is somewhat soluble, produces anodic oxides with highly regular arrangements of pores. Although porous aluminium and titanium oxides have found extensive use in functional nanostructures, pore initiation and self-ordering are not yet understood. Here we present an analysis that examines the roles of oxide dissolution and ionic conduction in the morphological stability of anodic films. We show that patterns of pores with a minimum spacing are possible only within a narrow range of the oxide formation efficiency (the fraction of oxidized metal atoms retained in the film), which should exist when the metal ion charge exceeds two. Experimentally measured efficiencies, over diverse anodizing conditions on both aluminium and titanium, lie within the different ranges predicted for each metal. On the basis of these results, the relationship between dissolution chemistry and the conditions for pore initiation can now be understood in quantitative terms. © 2012 Macmillan Publishers Limited. All rights reserved. Source


Dong J.,Iowa State University | Liu C.,Oak Ridge National Laboratory | Lin Z.,Oak Ridge National Laboratory
Transportation Research Part C: Emerging Technologies | Year: 2014

This paper studies electric vehicle charger location problems and analyzes the impact of public charging infrastructure deployment on increasing electric miles traveled, thus promoting battery electric vehicle (BEV) market penetration. An activity-based assessment method is proposed to evaluate BEV feasibility for the heterogeneous traveling population in the real world driving context. Genetic algorithm is applied to find (sub)optimal locations for siting public charging stations. A case study using the GPS-based travel survey data collected in the greater Seattle metropolitan area shows that electric miles and trips could be significantly increased by installing public chargers at popular destinations, with a reasonable infrastructure investment. © 2013 Elsevier Ltd. Source


Three samples of modern-day vegetation collected in 2009-2010 and a sample of bioethanol produced in 2010 were analyzed for radiocarbon by 5 different accelerator mass spectrometry (AMS) laboratories in a blind analysis study. The magnitude of any variability in the reported results for percent modern carbon (pMC) was observed. Results indicated that the interlaboratory repeatability on the samples of vegetation was generally very good, varying by no more than ~1 pMC for 2 of the 3 samples. Results for the bioethanol were less consistent, and varied by 5.5 pMC (ranging from 101.9 to 107.4 pMC). Variations in the δ 13C values used to correct for isotopic fractionation did not account for the variability observed in the pMC values for this sample. In view of the homogeneity of the bioethanol and its inherent simplicity in composition, this suggests that volatile liquid fuels may be more difficult to prepare for analysis without incurring significant sample processing errors. When viewing all of the results as a whole, the analytical errors (incorporating both instrumental and sample processing errors) appeared to be more random than systematic in nature. Because of analytical uncertainties in pMC measurements, as well as inherent local and regional variations in 14C activity levels known to occur in modern-day biomass, there is not a precise (accurate to 2 decimal places) correction factor for negating the bomb carbon effect that is applicable to all biofuels or other biobased products being analyzed in accordance with ASTM Method D6866. Therefore, a reasonable correction factor (currently set at 0.95) needs to be consistently applied in order to make comparisons of biobased content data from different laboratories more valid. Results from this study indicate that, for samples containing predominantly modern carbon, reporting results to the nearest 0.1 pMC is not warranted. © 2011 by the Arizona Board of Regents on behalf of the University o Arizona. Source


Mitchell N.J.,University of Western Australia | Janzen F.J.,Iowa State University
Sexual Development | Year: 2010

Whether species that have persisted throughout historic climatic upheavals will survive contemporary climate change will depend on their ecological and physiological traits, their evolutionary potential, and potentially upon the resources that humans commit to prevent their extinction. For those species where temperatures influence sex determination, rapid global warming poses a unique risk of skewed sex ratios and demographic collapse. Here we review the specific mechanisms by which reptiles with temperature-dependent sex determination (TSD) may be imperilled at current rates of warming, and discuss the evidence for and against adaptation via behavioural or physiological means. We propose a scheme for ranking reptiles with TSD according to their vulnerability to rapid global warming, but note that critical data on the lability of the sex determining mechanism and on the heritability of behavioural and threshold traits are unavailable for most species. Nevertheless, we recommend a precautionary approach to management of reptiles identified as being at relatively high risk. In such cases, management should aim to neutralise directional sex ratio biases (e.g. by manipulating incubation temperatures or assisted migration) and promote adaptive processes, possibly by genetic supplementation of populations. These practices should aid species' persistence and buy time for research directed at more accurate prediction of species' vulnerability. Copyright © 2010 S. Karger AG, Basel. Source


D'alessandro D.,Iowa State University
IEEE Transactions on Automatic Control | Year: 2010

In this technical note, we show how to use the analysis of the controllability Lie algebra of a quantum mechanical system to study its dynamics and facilitate the design of controls. We give algorithms to decompose the dynamics and describe an example of application to two coupled spin 1/2's. © 2006 IEEE. Source


Copes H.,University of Alabama at Birmingham | Hochstetler A.,Iowa State University | Forsyth C.J.,University of Louisiana at Lafayette
Criminology | Year: 2013

Considerable theoretical and empirical inquiry has focused on the role codes for violence play in generating crime. A large part of this work has examined the attitudes and codes condoning retaliation and violence as well as the prevalence of these among minorities residing in impoverished neighborhoods. Much about the nature of codes remains unknown, however, and this may in part reflect a narrow interest in beliefs about provocation and uses of violence among the inner-city poor. In this study, we elaborate on a code of violence as part of a system of order and honor as articulated by a network of White, working-class males in a southern U.S. city who participate in bar fights. The findings suggest that the code these men use prohibits predatory violence, puts exclusive limitations on situations that warrant violence, and constrains the level of violence in a fight. We detail the contours of this code (e.g., purpose of fighting, the rules of honorable fighting, and justifications for violating these rules) and discuss the code as both a cause and a consequence of behavior. © 2013 American Society of Criminology. Source


Heindel T.J.,Iowa State University
Journal of Fluids Engineering, Transactions of the ASME | Year: 2011

Flow visualization and characterization of multiphase flows have been the quest of many fluid mechanicians. The process is fairly straight forward only when there is good optical access (i.e., the vessel is not opaque or there are appropriate viewing ports) and the flow is transparent, implying a very low volume fraction of the dispersed phase; however, when optical access is not good or the fluid is opaque, alternative methods must be developed. Several different noninvasive visualization tools have been developed to provide high-quality qualitative and quantitative data of various multiphase flow characteristics, and overviews of these methods have appeared in the literature. X-ray imaging is one family of noninvasive measurement techniques used extensively for product testing and evaluation of static objects with complex structures. X-rays can also be used to visualize and characterize multiphase flows. This paper provides a review of the current status of X-ray flow visualization and details various X-ray flow visualization methods that can provide qualitative and quantitative information about the characteristics of complex multiphase flows. © 2011 American Society of Mechanical Engineers. Source


Suzuki Y.,Iowa State University
Computers and Industrial Engineering | Year: 2014

The fixed-route vehicle-refueling problem (FRVRP) is a difficult combinatorial problem that is used extensively in the US truckload industry to manage fuel costs. This paper proposes a preprocessing technique for the FRVRP that cuts the problem size noticeably without eliminating the optimal solution(s), which allows users to enlarge the size of solvable instances or save the CPU time of solving the problem dramatically. Empirical testing with real-world instances shows that our method: (i) reduces the problem size by 54.8% and (ii) solves the FRVRPs to optimality in roughly 1/4 of the time it is currently taking. © 2013 Elsevier Ltd. All rights reserved. Source


Delisi M.,Iowa State University
Journal of Forensic Sciences | Year: 2014

In recent years, multiple homicide offending has received increased research attention from criminologists; however, there is mixed evidence about the role of rape toward the perpetration of multiple murder. Drawing on criminal career data from a nonprobability sample of 618 confined male homicide offenders selected from eight U.S. states, the current study examines the role of rape as a predictor of multiple homicide offending. Bivariate analyses indicated a significant association between rape and murder charges. Multivariate path regression models indicated that rape had a significant and robust association with multiple murder. This relationship withstood the confounding effects of kidnapping, prior prison confinement, and prior murder, rape, and kidnapping. These results provide evidence that rape potentially serves as a gateway to multiple murder for some serious offenders. Suggestions for future research are proffered. © 2013 American Academy of Forensic Sciences. Source


General thermodynamic and kinetic approaches for sublimation inside an elastoplastic material are developed for large strains. Various conceptual problems related to the effect of irreversible plastic deformation and dissipation, path-dependence of the appearance of a critical nucleus, and the presence of large strains are considered. Two transformation paths are studied: nucleation via homogeneous transformation in the nucleus of fixed mass and nucleation via continuous interface propagation. For both paths, the expressions for the thermodynamic driving forces and activation energies are derived. The activation energy is equal to the negative driving force for the appearance of a nucleus maximized with respect to nucleus mass and minimized over the nucleus shape, transformation path, and position. This definition corresponds to the principle of the minimum of transformation time and reduces to the traditional one in the limit of elastic materials. An Arrhenius-type kinetic equation for nucleation time and kinetic nucleation criterion are formulated. Algorithms for the determination of the critical nucleus are suggested. After appearance of the nucleus via homogeneous transformation, the possibility of its growth should be checked. Growth may occur by further sublimation or by mechanical expansion without phase transformation due to mechanical instability. Because the driving force for forward and reverse transformations maybe different, several scenarios are possible. The nucleus can grow, disappear, or be arrested; in the last case, it represents a stable rather than a critical nucleus. It is demonstrated that with small modifications, our approach to sublimation can be applied to chemical decomposition and melting inside an elastoplastic material. In the accompanying paper (Levitas and Altukhova, 2012) we will apply the developed theory to nucleation of a spherical gas bubble inside an elastoplastic material. © 2012 Elsevier Ltd. All rights reserved. Source


Iverson N.R.,Iowa State University
Journal of Glaciology | Year: 2011

The field observations of G.S. Boulton stimulated widespread interest in deformable beds. Shear resistance of till in its critical state is insensitive to strain rate and increases linearly with effective pressure. During unsteady deformation, pseudo-viscous shear resistance can be caused by dilation of consolidated tills and resultant pore-pressure decline. This effect is probably uncommon, however, because susceptible tills of low hydraulic diffusivity are also those least likely to consolidate significantly during effective-pressure transients. Stick-slip motion at Whillans Ice Stream, Antarctica, indicates that its basal till must weaken during rapid slip and strengthen during longer periods of slower slip. Recurrence intervals for rapid-slip episodes there (6-18 hours) indicate that till-strength variations, if driven by changes in pore pressure either related or unrelated to basal freezing, are focused in the uppermost several centimeters of the bed. Ploughing of grains at the bed surface and associated excess pore pressures in adjacent till can account for rate-weakening during rapid slip, with pore-pressure decay causing strengthening between slip episodes. By promoting shallow, sluggish subglacial water flow and low effective pressure, soft beds may help sustain themselves by slowing their own transport. Soft-bed shear resistance, kinematics and continuity are problems rooted in subglacial hydrology. Source


He X.-G.,Shanghai JiaoTong University | He X.-G.,National Taiwan University | Valencia G.,Iowa State University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

It is expected that the LHC will soon discover the Higgs boson, or that failure to find it will severely constrain its production cross-section over a large mass range. Either one of these results spells trouble for a fourth generation that significantly enhances the Higgs production cross-section at LHC. In fact the LHC has already ruled out a SM Higgs mass in the range of 120-600 GeV with a fourth generation at the 95% C.L. In this Letter we explore options within extended scalar sectors to maintain the viability of a heavy fourth generation if an enhanced (relative to the standard model) Higgs production cross-section is not observed. © 2011 Elsevier B.V. Source


Feuillet C.,French National Institute for Agricultural Research | Leach J.E.,Colorado State University | Rogers J.,The Genome Analysis Center | Schnable P.S.,Iowa State University | Eversole K.,Eversole Associates
Trends in Plant Science | Year: 2011

2010 marks the 10th anniversary of the completion of the first plant genome sequence (Arabidopsis thaliana). Triggered by advancements in sequencing technologies, many crop genome sequences have been produced, with eight published since 2008. To date, however, only the rice (Oryza sativa) genome sequence has been finished to a quality level similar to that of the Arabidopsis sequence. This trend to produce draft genomes could affect the ability of researchers to address biological questions of speciation and recent evolution or to link sequence variation accurately to phenotypes. Here, we review the current crop genome sequencing activities, discuss how variability in sequence quality impacts utility for different studies and provide a perspective for a paradigm shift in selecting crops for sequencing in the future. © 2010 Elsevier Ltd. Source


Arbuckle Jr. J.G.,Iowa State University
Society and Natural Resources | Year: 2013

Calls for improved targeting of conservation resources are increasingly common. However, arguments for improving the effectiveness and efficiency of agricultural conservation programs through proactive targeting are often tempered by questions regarding political feasibility. Such questions rest on an assumption that there will be resistance to these approaches, whether from farmers, farm groups, or elected officials, yet there is little research-based evidence supporting that assumption. Analysis of data on Iowa farmers' attitudes toward targeted conservation indicates that most farmers support targeted approaches. Specific factors associated with endorsement of targeted approaches include awareness of agriculture's environmental impacts, belief that farmers should address water quality problems, having experienced significant soil erosion, belief that extreme weather will become more common, participation in the Conservation Reserve Program, and belief that farmers who have natural resource issues are less likely to seek conservation assistance. Concerns about government intrusion were negative predictors of support for targeted approaches. © 2013 Copyright Taylor and Francis Group, LLC. Source


Powell-Coffman J.A.,Iowa State University
Trends in Endocrinology and Metabolism | Year: 2010

In normal development and homeostasis and in many disease states, cells and tissues must overcome the challenge of oxygen deprivation (hypoxia). The nematode C. elegans is emerging as an increasingly powerful system in which to understand how animals adapt to moderate hypoxia and survive extreme hypoxic insults. This review provides an overview of C. elegans responses to hypoxia, ranging from adaptation and arrest to death, and highlights some of the recent studies that have provided important insights into hypoxia signaling and resistance. Many of the key genes and pathways are evolutionarily conserved, and C. elegans hypoxia research promises to inform our understanding of oxygen-sensitive signaling and survival in mammalian development and disease. © 2010 Elsevier Ltd. Source


Bradbury S.L.,Iowa State University
Journal of Transport Geography | Year: 2013

Since September 11, 2001 numerous security measures have been implemented along the Canada-US border, including the Western Hemisphere Travel Initiative (WHTI). Concerns have been raised about the impact of these security measures on the movement of people across the border. This paper examines the impact of security on the number of travelers crossing the border by employing a multivariate regression analysis utilizing monthly data from January 1991 to December 2007. In addition, the impact of the WHTI is specifically examined by employing a similar multivariate regression analysis with monthly data from October 2001 to December 2011. Controlling for the effects of a number of factors, such as exchange rates and gas prices, results showed that security measures, including the WHTI, have negatively impacted the number of Canadian visitors to the US and American visitors to Canada traveling by automobile. The findings of this study will be of interest to researchers, policy makers, and a variety of stakeholders in the tourism industry in both countries. © 2012. Source


Takai S.,Osaka University | Kumar R.,Iowa State University
IEEE Transactions on Automatic Control | Year: 2011

For discrete event systems, we study the problem of predicting failures prior to their occurrence, also referred to as prognosis, in the inference-based decentralized framework where multiple decision-makers interact to make the global prognostic decisions. We characterize the class of systems for which there are no missed detections (all failures can be prognosed prior to their occurrence) and no false alarms (all prognostic decisions are correct) by introducing the notion of N -inference-prognosability, where the parameter N represents the maximum ambiguity level of any winning prognostic decision. An algorithm for verifying N-inference-prognosability is presented. We also show that the notion of coprognosability introduced in our prior work is the same as 0-inference-prognosability, and as the parameter N is increased, a larger class of prognosable systems is obtained. © 2010 IEEE. Source


Janke B.H.,Iowa State University
Veterinary Pathology | Year: 2014

Influenza has been recognized as a respiratory disease in swine since its first appearance concurrent with the 1918 "Spanish flu" human pandemic. All influenza viruses of significance in swine are type A, subtype H1N1, H1N2, or H3N2 viruses. Influenza viruses infect epithelial cells lining the surface of the respiratory tract, inducing prominent necrotizing bronchitis and bronchiolitis and variable interstitial pneumonia. Cell death is due to direct virus infection and to insult directed by leukocytes and cytokines of the innate immune system. The most virulent viruses consistently express the following characteristics of infection: (1) higher or more prolonged virus replication, (2) excessive cytokine induction, and (3) replication in the lower respiratory tract. Nearly all the viral proteins contribute to virulence. Pigs are susceptible to infection with both human and avian viruses, which often results in gene reassortment between these viruses and endemic swine viruses. The receptors on the epithelial cells lining the respiratory tract are major determinants of infection by influenza viruses from other hosts. The polymerases, especially PB2, also influence cross-species infection. Methods of diagnosis and characterization of influenza viruses that infect swine have improved over the years, driven both by the availability of new technologies and by the necessity of keeping up with changes in the virus. Testing of oral fluids from pigs for virus and antibody is a recent development that allows efficient sampling of large numbers of animals. © The Author(s) 2013. Source


Zhang J.,Iowa State University | Baden-Fuller C.,City University London
Journal of Management Studies | Year: 2010

This study investigates how an incumbent company's internal characteristics influence its propensity to form learning alliances. A firm may be reluctant to enter a research alliance when it has deep knowledge in a certain technological field due to concerns about knowledge leakage and the low possibility of being able to learn much from collaboration. On the contrary, when the firm has a broad knowledge base, it may have high propensity to enter alliances due to more self-confidence in its ability to learn fast from partners. In addition, we argue that when a firm concentrates its R&D at a central location, this neutralizes the positive and negative influences of the two knowledge base features on alliance formation. We tested and found support for the hypotheses using a database of 1550 alliances undertaken by 78 large incumbent pharmaceutical, chemical, and agro-food companies active in the biotechnology sector during 1993-2002. © 2010 Blackwell Publishing Ltd and Society for the Advancement of Management Studies. Source


Zhou C.,Magnatech LLC. | Kumar R.,Iowa State University
IEEE Transactions on Automatic Control | Year: 2011

For discrete event systems, the control to enforce bisimilarity with respect to a given specification has been studied in , ,. In this note we consider the case when the control is required to be deterministic. While a deterministic control is restrictive compared to a nondeterministic one, the case of deterministic control has its own practical significance as it is easier to implement and computationally less expensive to verify. We provide a necessary and sufficient condition for the existence of a bisimilarity enforcing deterministic control, and discuss its computational complexity. We also study properties related to the synthesis of subspecification and superspecification. © 2006 IEEE. Source


Gallagher P.W.,Iowa State University
Biofuels, Bioproducts and Biorefining | Year: 2010

This study addresses the question: 'How does a 15 billion gallon per year renewable fuel standard (RFS) compare to the capacity of the US corn market to generate necessary input supplies for the ethanol industry?' The analysis accounts for adjustments in world corn and soybean markets, including corn technology improvements (yield increases) that allow substantial production growth on the existing corn area, and byproduct (DDG) replacement of displaced corn-feed demand. Our midpoint estimate suggests that increased production on foreign lands only accounts for a small fraction (6%) of the RFS demand expansion. Further, corn yield response to moderate price increases would likely offset much of the foreign production increase. US policies that could sever any remaining link between US ethanol expansion and environmentally sensitive regions of the world feed economy are discussed. © 2010 Society of Chemical Industry and John Wiley & Sons, Ltd. Source


Durbin P.,Iowa State University
Journal of Fluids Engineering, Transactions of the ASME | Year: 2011

Scalar, eddy viscosity models are widely used for predicting engineering turbulent flows. System rotation, or streamline curvature, can enhance or reduce the intensity of turbulence. Methods to incorporate the effects of rotation and streamline curvature consist of introducing parametric variation of model coefficients, such that either the growth rate of turbulent energy is altered; or such that the equilibrium solution bifurcates from healthy to decaying solution branches. For general use, parameters must be developed in coordinate invariant forms. Effects of rotation and of curvature can be unified by introducing the convective derivative of the rate of strain eigenvectors as their measure. © 2011 American Society of Mechanical Engineers. Source


Martin R.,Iowa State University
Electronic Journal of Combinatorics | Year: 2013

The edit distance between two graphs on the same labeled vertex set is the size of the symmetric difference of the edge sets. The distance between a graph, G, and a hereditary property, ℋ, is the minimum of the distance between G and each G'∈ℋ. The edit distance function of ℋ is a function of p∈[0,1] and is the limit of the maximum normalized distance between a graph of density p and ℋ. This paper utilizes a method due to Sidorenko [Combinatorica 13(1), pp. 109-120], called "symmetrization", for computing the edit distance function of various hereditary properties. For any graph H, Forb(H) denotes the property of not having an induced copy of H. This paper gives some results regarding estimation of the function for an arbitrary hereditary property. This paper also gives the edit distance function for Forb(H), where H is a cycle on 9 or fewer vertices. Source


Selsby J.T.,Iowa State University
Experimental Physiology | Year: 2011

It has been well established that oxidative stress contributes to pathology associated with Duchenne muscular dystrophy (DMD). I hypothesized that overexpression of the antioxidant enzyme catalase would improve muscle function in the mdx mouse, the mouse model of DMD. To test this hypothesis, neonatal mdx mice were injected with a recombinant adeno-associated virus driving the catalase transgene. Animals were killed 4 or 6 weeks or 6 months following injection. Muscle function was generally improved by catalase overexpression. Four weeks following injection, extensor digitorum longus specific tension was improved twofold, while soleus was similar between groups. Resistance to contraction-induced injury was similar between groups; however, resistance to fatigue was increased 25% in catalase-treated soleus compared with control muscle. Six weeks following injection, extensor digitorum longus specific tension was increased 15%, while soleus specific tension was similar between treated and untreated limbs. Catalase overexpression reduced contraction-induced injury by 30-45% and fatigue by 20% compared with control limbs. Six months following injection, diaphragm specific tension was similar between groups, but resistance to contraction-induced injury was improved by 35% and fatigue by 25%. Taken together, these data indicate that catalase can improve a subset of parameters of muscle function in dystrophin-deficient skeletal muscle. © 2010 The Author. Journal compilation © 2011 The Physiological Society. Source


Suzuki Y.,Iowa State University
Transportation Research Part D: Transport and Environment | Year: 2011

The paper develops an approach to the time-constrained, multiple-stop, truck-routing problem that minimizes the fuel consumption and pollutants emission. Features of framework are; it minimizes the distance a delivery vehicle must travel with a heavy payload in a given tour by sequencing the customer visits such that heavier items are unloaded first while lighter items are unloaded later, and it considers the amount of fuel burned during the time a truck is detained at customer sites. Our simulations, based on the routing of an actual motor carrier, suggest the approach may produce up to 6.9% in fuel savings over existing methods. © 2010 Elsevier Ltd. Source


Xie Y.,Iowa State University
Journal of Statistical Software | Year: 2013

Animated graphs that demonstrate statistical ideas and methods can both attract interest and assist understanding. In this paper we first discuss how animations can be related to some statistical topics such as iterative algorithms, random simulations, (re)sampling methods and dynamic trends, then we describe the approaches that may be used to create animations, and give an overview to the R package animation, including its design, usage and the statistical topics in the package. With the animation package, we can export the animations produced by R into a variety of formats, such as a web page, a GIF animation, a Flash movie, a PDF document, or an MP4/AVI video, so that users can publish the animations fairly easily. The design of this package is flexible enough to be readily incorporated into web applications, e.g., we can generate animations online with Rweb, which means we do not even need R to be installed locally to create animations. We will show examples of the use of animations in teaching statistics and in the presentation of statistical reports using Sweave or knitr. In fact, this paper itself was written with the knitr and animation package, and the animations are embedded in the PDF document, so that readers can watch the animations in real time when they read the paper (the Adobe Reader is required). Animations can add insight and interest to traditional static approaches to teaching statistics and reporting, making statistics a more interesting and appealing subject. Source


Suzuki Y.,Iowa State University
Decision Support Systems | Year: 2012

Given the recent trend of raising fuel cost and the increased time-sensitiveness of shippers, an extensive pressure is placed on the motor-carrier industry to meet the time-constrained customer demands at minimum fuel cost. We propose a decision support system that allows motor carriers to route each vehicle such that the vehicle not only visits all the customers in time (without violating time windows), but also utilizes the cheapest gas stations (cheapest truck stops in the region) as refueling points during the tour. While this approach does not necessarily minimize a vehicle's fuel consumption, as it often suggests using non-shortest routes with cheap gas stations (truck stops), it allows the vehicle to reduce the unit cost of buying fuel. Computational testing shows that the proposed approach may attain up to 4.29% savings in fuel cost for motor carriers. © 2012 Elsevier B.V. All rights reserved. Source


Levitas V.I.,Iowa State University
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

The definition of all properties of the nonequilibrium interface depends on the choice of the position of the dividing surface. However, the definition of its position has been an unsolved problem for more than a century. A missing principle to unambiguously determine the position of the Gibbs' dividing surface is found: the principle of static equivalence. A sharp interface (dividing surface) is statically equivalent to a nonequilibrium finite-width interface with distributed tensile stresses if it possesses (a) the same resultant force, equal to the interface energy, and (b) the same moment, which is zero about the interface position. Each of these conditions determines the position of a sharp interface, which may be contradictory. This principle is applied to resolve another basic problem: the development of a phase field approach to an interface motion that includes an expression for interface stresses, which are thermodynamically consistent, and consistent with a sharp-interface limit. Using an analytical solution for a curved propagating interface, it is shown that both conditions determine the same dividing surface, i.e., the theory is self-consistent. The expression for the interface energy is also consistent with the expression for the velocity of the curved sharp interface. Applications to more complex interfaces that support elastic stresses are discussed. © 2014 American Physical Society. Source


Trivedi R.,Iowa State University | Wang N.,Northwestern Polytechnical University
Acta Materialia | Year: 2012

The growth of eutectic under large undercooling conditions is important in obtaining nanoscale composite microstructures. Many glass-forming eutectic systems also exhibit a fine rod eutectic microstructure and often show a direct transition from eutectic to glass with increasing undercooling at the interface. A theoretical model of rod eutectic growth is developed in this paper, which quantitatively evaluates the system and growth parameters that will give rise to large undercooling at the interface. In addition to the diffusion and capillary undercooling, the model incorporates the effects of a sharp decrease in the diffusion coefficient that is exhibited by fragile glass-forming systems, the presence of highly nonlinear liquidus lines at large undercooling, and the effects of non-equilibrium at the interface. The results of the model are then discussed to obtain an insight into the system and growth parameters that are critical for obtaining a large undercooling at the eutectic interface, which is important in the design of nanoscale composite materials and in the selection of potential glass-forming systems. © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. Source


Levitas V.I.,Iowa State University
International Journal of Plasticity | Year: 2013

General phase-field theory for multivariant martensitic phase transformations and explicit models are formulated at large strains. Each order parameter is unambiguously related to the transformation strain of the corresponding variant. Thermodynamic potential includes energy related to the gradient of the order parameters that mimics the interface energy. Application of the global form of the second law of thermodynamics resulted in the determination of the driving force for change of the order parameters and the boundary conditions for the order parameters. Kinetic relationships between the rate of change of the order parameters and the conjugate driving force lead to the Ginzburg-Landau equations. For homogeneous fields, conditions for instabilities of the equilibrium states (which represent criteria for the phase transformation between austenite and martensitic variants and between martensitic variants) are found for the prescribed Piola-Kirchoff stress tensor. It was proved that these criteria are invariant with respect to change in the prescribed stresses. The expression for the rigid-body rotation tensor is derived for the prescribed Piola-Kirchoff stress. The explicit expressions for the Helmholtz free energy and for transformation strain in terms of order parameters are derived for the most general case of large elastic and transformational strains, rotations, as well as nonlinear, anisotropic, and different elastic properties of phases. For negligible elastic strains, explicit expression for the Gibbs potential is formulated. Results are obtained for fifth- and sixth-degree potentials in Cartesian order parameters and for similar potentials in hyperspherical order parameters. Geometric interpretation of transformation conditions in the stress space and similarity with plasticity theory are discussed. All material parameters are obtained for cubic to tetragonal transformation in NiAl. Phase transformations in NiAl, boron nitride, and graphite to diamond under uniaxial loading are described explicitly, and the importance of geometrically nonlinear terms is demonstrated. A similar approach can be applied for twinning, dislocations, reconstructive transformations, and fracture. © 2013 Elsevier Ltd. All rights reserved. Source


Decades of studies on the role of decomposition in carbon (C) and nitrogen (N) cycling have focused on organic matter (OM) of plant origin. Despite potentially large inputs of belowground OM from fungal cell walls and invertebrate exoskeletons, studies of the decomposability of their major constituent, chitin, are scarce. To explore effects on soil C dynamics of chitin, in comparison with two plant-derived chemicals, cellulose and lignin, I conducted a field-based chemical-addition experiment. The design contained three chemical treatments plus a control, with four replicates in each of two species of tropical trees grown in plantations. The chemicals were added in reagent-grade form at a rate that doubled the natural detrital C inputs of 1000 g C m-2 y-1. Despite its purported recalcitrance, chitin was metabolized quickly, with soil respiration (R soil) increasing by 64% above the control within days, coupled with a 32% increase in soil extractable ammonium. Cellulose, which was expected to be labile, was not readily decomposed, whereas lignin was rapidly metabolized at least partially in one of the forest types. I examined effects of stoichiometry by adding to all treatments ammonium nitrate in a quantity that adjusted the C:N of cellulose (166) to that of chitin (10), using both field and in vitro experiments. For cellulose, CO2 release increased more than five- to eightfold after N addition in root-free soil incubated in vitro, but only 0-20% in situ where roots were intact. By the end of the 2-year-long field experiment, fine-root biomass tended to be higher in the chitin treatment, where R soil was significantly higher. Together these findings suggest that soil N availability limited cellulose decomposition, even in this Neotropical forest with high soil N stocks, and also that trees successfully competed for N that became available as chitin decomposed. These results indicate that the major constituent of cell walls of soil fungi, chitin, can decompose rapidly and release substantial N that is available for plant and microbial growth. As a consequence, soil fungi can stimulate soil OM decomposition and N cycling, and thereby play a disproportionate role in ecosystem C and N dynamics. © 2014 Springer Science+Business Media New York. Source


Banerjee J.,Indian Institute of Science | Nilsen-Hamilton M.,Iowa State University
Journal of Molecular Medicine | Year: 2013

Aptamers are single-stranded oligonucleotides that fold into well-defined three-dimensional shapes, allowing them to bind their targets with high affinity and specificity. They can be generated through an in vitro process called "Systemic Evolution of Ligands by Exponential Enrichment" and applied for specific detection, inhibition, and characterization of various targets like small organic and inorganic molecules, proteins, and whole cells. Aptamers have also been called chemical antibodies because of their synthetic origin and their similar modes of action to antibodies. They exhibit significant advantages over antibodies in terms of their small size, synthetic accessibility, and ability to be chemically modified and thus endowed with new properties. The first generation of aptamer drug "Macugen" was available for public use within 25 years of the discovery of aptamers. With others in the pipeline for clinical trials, this emerging field of medical biotechnology is raising significant interest. However, aptamers pose different problems for their development than for antibodies that need to be addressed to achieve practical applications. It is likely that current developments in aptamer engineering will be the basis for the evolution of improved future bioanalytical and biomedical applications. The present review discusses the development of aptamers for therapeutics, drug delivery, target validation and imaging, and reviews some of the challenges to fully realizing the promise of aptamers in biomedical applications. © 2013 Springer-Verlag Berlin Heidelberg. Source


Tuchin K.,Iowa State University
Physical Review C - Nuclear Physics | Year: 2016

When the quark-gluon plasma emerges in the wake of a heavy-ion collision, a magnetic field created by the valence charges has already permeated the entire interaction region. Evolution of this "initial" field in the plasma is governed by the Maxwell equations in an electrically conducting medium. As the plasma expands, external valence charges induce a magnetic field that also contributes to the total magnetic field in the plasma. I solve the initial value problem describing these processes and argue that the initial magnetic field often dominates over the one induced by the valence charges. In particular, it grows approximately proportional to the collision energy, unlike the induced component, which is energy independent. As a result, the magnetic field has a significant phenomenological influence on the quark-gluon plasma at CERN Large Hadron Collider energies over its entire lifetime. © 2016 American Physical Society. Source


Gottschall P.E.,University of Arkansas for Medical Sciences | Howell M.D.,Iowa State University
Matrix Biology | Year: 2015

The components of the adult extracellular matrix in the central nervous system form a lattice-like structure that is deposited as perineuronal nets, around axon initial segments and as synapse-associated matrix. An abundant component of this matrix is the lecticans, chondroitin sulfate-bearing proteoglycans that are the major substrate for several members of the ADAMTSs (a disintegrin and metalloproteinase with thrombospondin motifs) family. Since lecticans are key regulators of neural plasticity, ADAMTS cleavage of lecticans would likely also contribute to neuroplasticity. Indeed, many studies have examined the neuroplastic contribution of the ADAMTSs to damage and recovery after injury and in central nervous system disease. Much of this data supports a role for the ADAMTSs in recovery and repair following spinal cord injury by stimulating axonal outgrowth after degradation of a glial scar and improving synaptic plasticity following seizure-induced neural damage in the brain. The action of the ADAMTSs in chronic diseases of the central nervous system appears to be more complex and less well-defined. Increasing evidence indicates that lecticans participate in synaptic plasticity in neurodegenerative disease states. It will be interesting to examine how ADAMTS expression and action would affect the progression of these diseases. © 2015 Published by Elsevier B.V. Source


Peters R.J.,Iowa State University
Natural Product Reports | Year: 2010

Unlike the majority of terpenoids, a significant fraction of the polycyclic diterpenoids (∼7000 already known) are now understood to originate from dual, rather than single, biosynthetic cyclization and/or rearrangement reactions, which proceed via a bicyclic diphosphate intermediate. The trivial name for the hydrocarbon skeleton of the most commonly found version of this biosynthetic intermediate forms the basis for a unifying "labdane- related" designation for this large super-family of natural products. Notably, many of these are found in plants, where the requisite biosynthetic machinery for gibberellin phytohormones, particularly the relevant diterpene cyclases, provides a biosynthetic reservoir that appears to have been repeatedly drawn upon to evolve new labdane-related diterpenoids. The potent biological activity of the "ancestral" gibberellins, which has led to the independent evolution of distinct gibberellin biosynthetic pathways in plants, fungi, and bacteria, is further discussed as an archetypical example of the selective pressure driving evolution of the large super-family of labdane-related diterpenoid natural products, with the observed diversification suggesting that their underlying hydrocarbon skeletal structures might serve as privileged scaffolds from which biological activity is readily derived. © 2010 The Royal Society of Chemistry. Source


D'Alessandro D.,Iowa State University | Romano R.,University of Trieste
IEEE Transactions on Automatic Control | Year: 2012

A quantum mechanical system S is indirectly controlled when the control affects an ancillary system A and the evolution of S is modified through the interaction with A only. A study of indirect controllability gives a description of the set of states that can be obtained for S with this scheme. In this paper, we study the indirect controllability of quantum systems in the finite dimensional case. After discussing the relevant definitions, we give a general necessary condition for controllability in Lie algebraic terms. We present a detailed treatment of the case where both systems, S and A, are two-dimensional (qubits). In particular, we characterize the dynamical Lie algebra associated with S + A, extending previous results, and prove that complete controllability of S + A and an appropriate notion of indirect controllability are equivalent properties for this system. We also prove several further indirect controllability properties for the system of two qubits, and illustrate the role of the Lie algebraic analysis in the study of reachable states. © 2012 IEEE. Source


McPhail L.L.,Market and Trade Economics Division at the Economic Research | Babcock B.A.,Iowa State University
Energy | Year: 2012

Despite a large number of studies that examine the influence of biofuels and biofuel policy on commodity prices, the impact of biofuel policy on commodity price variability is poorly understood. A good understanding of biofuel policy's impact on price variability is important for mitigating food insecurity and assisting policy formation. We examine how U.S. ethanol policies such as the Renewable Fuel Standard (RFS) mandates and the blend wall affect the price variability of corn and gasoline. We first present an analytical and graphical framework to identify the effect and then use stochastic partial equilibrium simulation to measure the magnitude of the impacts. We show that RFS mandates and the blend wall both reduce the price elasticity of demand for corn and gasoline and therefore increase the price variability when supply shocks occur to the markets. This has important implications for policy actions with respect to maintaining or changing the current RFS mandates and/or blend wall in the US. © 2011. Source


Yu E.W.,Iowa State University
Annual Review of Biophysics | Year: 2014

Infections caused by bacteria are a leading cause of death worldwide. Although antibiotics remain a key clinical therapy, their effectiveness has been severely compromised by the development of drug resistance in bacterial pathogens. Multidrug efflux transporters- A common and powerful resistance mechanism-are capable of extruding a number of structurally unrelated antimicrobials from the bacterial cell, including antibiotics and toxic heavy metal ions, facilitating their survival in noxious environments. Transporters of the resistance-nodulation-cell division (RND) superfamily typically assemble as tripartite efflux complexes spanning the inner and outer membranes of the cell envelope. In Escherichia coli, the CusCFBA complex, which mediates resistance to copper(I) and silver(I) ions, is the only known RND transporter specific to heavy metals. Here, we describe the current knowledge of individual pump components of the Cus system, a paradigm for efflux machinery, and speculate on how RND pumps assemble to fight diverse antimicrobials. Copyright © 2014 by Annual Reviews. All rights reserved. Source


Grewell D.,Iowa State University
Ultrasonics Sonochemistry | Year: 2015

The utilization of ultrasonics to rapidly dissolve switchgrass in ionic liquid, 1-butyl-3-methylimidazolium chloride ([Bmim][Cl]) was evaluated in this work. The objective of the study focused on determining the effects of various ultrasonic conditions on the recovery of carbohydrate from biomass, lignin removal, and enzymatic hydrolysis. Dried ground switchgrass was added to ionic liquid, then sonicated at a frequency of 20 kHz. The experiments were conducted using a catenoidal horn at varying amplitudes of 96 μm, 128 μm, and 160 μm and sonication times of 2, 3, and 4 min. Similarly, ground switchgrass was dissolved in ionic liquid assisted by conventional heat treatment at 130 °C for 12 and 24 h. The results showed good delignification results of 53% for the 24 h heat pretreated samples and of 50.8% for ultrasonic assisted samples at 160 μm amplitude and 4 min. Even in the presence of lignin in the recovered biopolymer, both of heat treated and ultrasonicated samples obtained 100% glucan digestibility after only 3 h of enzymatic hydrolysis. Heat pretreated samples exhibited 44-59% lower xylan digestibility compared to ultrasonic pretreated samples (160 μm amplitude and 4 min sonication time). Scanning electron microscope images displayed significant changes in biomass structure from intact and crystalline of the untreated biomass to disintegrated and amorphous of the treated biomass (heat treated and ultrasonicated). With increasing ultrasonic amplitude the carbohydrate recovery decreased. Also, more than 50% of the hemicellulose fraction was lost during biomass recovery. Overall, it was concluded that ultrasonication was a promising technology to enhance dissolution of lignocellulose in ionic liquid. © 2014 Elsevier B.V. All rights reserved. Source


Tucker J.M.,North Dakota State University | Welk G.J.,Iowa State University | Beyler N.K.,Mathematica Policy Research Inc.
American Journal of Preventive Medicine | Year: 2011

Background: To date, no study has objectively measured physical activity levels among U.S. adults according to the 2008 Physical Activity Guidelines for Americans (PAGA). Purpose: The purpose of this study was to assess self-reported and objectively measured physical activity among U.S. adults according to the PAGA. Methods: Using data from the NHANES 2005-2006, the PAGA were assessed using three physical activity calculations: moderate plus vigorous physical activity ≥150 minutes/week (MVPA); moderate plus two instances of vigorous physical activity ≥150 minutes/week (M2VPA); and time spent above 3 METs ≥500 MET-minutes/week (METPA). Self-reported physical activity included leisure, transportation, and household activities. Objective activity was measured using Actigraph accelerometers that were worn for 7 consecutive days. Analyses were conducted in 2009-2010. Results: U.S. adults reported 324.5±18.6 minutes/week (M±SE) of moderate physical activity and 73.6±3.9 minutes/week of vigorous physical activity, although accelerometry estimates were 45.1±4.6 minutes/week of moderate physical activity and 18.6±6.6 minutes/week of vigorous physical activity. The proportion of adults meeting the PAGA according to M2VPA was 62.0% for self-report and 9.6% for accelerometry. Conclusions: According to the NHANES 2005-2006, fewer than 10% of U.S. adults met the PAGA according to accelerometry. However, physical activity estimates vary substantially depending on whether self-reported or measured via accelerometer. © 2011 American Journal of Preventive Medicine. Source


Hendrich S.,Iowa State University
Advances in Nutrition | Year: 2010

Recent human clinical trials of the effects of (n-3) fatty acids on participants with type 2 diabetes (T2D) were reviewed, focusing on 11 clinical trials conducted within the past 4 y, and subsequent to a Cochrane Database meta-analysis of this topic. Doses of eicosapentaenoic acid (EPA) anddocosahexaenoic acid (DHA) in these studies were mostly in the range ofw2 g/d provided for 6 wk to 6 mo. Summarizing across these studies, there were no changes in fasting glucose or insulin compared with baseline or placebo. (n-3) Fatty acids generally decreased serum triglyceridesbut had varying effects on serum cholesterol, LDL cholesterol, and HDL cholesterol. A few studies indicated beneficial effects of (n-3) fatty acids on arterial blood flow. The effects of EPA and/or DHA have not yet been studied in clinical trials in participants at risk for T2D; the prevention or exacerbation of T2D by fish oil or EPA and DHA supplements of amounts >0.5 g/d deserves study. The prevention of adverse vascular effects of T2D by (n-3) fatty acids may be a promising direction for further study. © 2010 American Society for Nutrition. Source


There has been a dramatic increase in the number of insect-specific flaviviruses (ISFs) discovered in the last decade. Historically, these viruses have generated limited interest due to their inability to infect vertebrate cells. This viewpoint has changed in recent years because some ISFs have been shown to enhance or suppress the replication of medically important flaviviruses in co-infected mosquito cells. Additionally, comparative studies between ISFs and medically important flaviviruses can provide a unique perspective as to why some flaviviruses possess the ability to infect and cause devastating disease in humans while others do not. ISFs have been isolated exclusively from mosquitoes in nature but the detection of ISF-like sequences in sandflies and chironomids indicates that they may also infect other dipterans. ISFs can be divided into two distinct phylogenetic groups. The first group currently consists of approximately 12 viruses and includes cell fusing agent virus, Kamiti River virus and Culex flavivirus. These viruses are phylogenetically distinct from all other known flaviviruses. The second group, which is apparently not monophyletic, currently consists of nine viruses and includes Chaoyang virus, Nounané virus and Lammi virus. These viruses phylogenetically affiliate with mosquito/vertebrate flaviviruses despite their apparent insect-restricted phenotype. This article provides a review of the discovery, host range, mode of transmission, superinfection exclusion ability and genomic organization of ISFs. This article also attempts to clarify the ISF nomenclature because some of these viruses have been assigned more than one name due to their simultaneous discoveries by independent research groups. © 2015 by the authors; licensee MDPI, Basel, Switzerland. Source


Zhang S.,Iowa State University
Optics and Lasers in Engineering | Year: 2010

Over the past few years, we have been developing techniques for high-speed 3D shape measurement using digital fringe projection and phase-shifting techniques: various algorithms have been developed to improve the phase computation speed, parallel programming has been employed to further increase the processing speed, and advanced hardware technologies have been adopted to boost the speed of coordinate calculations and 3D geometry rendering. We have successfully achieved simultaneous 3D absolute shape acquisition, reconstruction, and display at a speed of 30 frames/s with 300 K points per frame. This paper presents the principles of the real-time 3D shape measurement techniques that we developed, summarizes the most recent progresses that have been made in this field, and discusses the challenges for advancing this technology further. © 2009 Elsevier Ltd. All rights reserved. Source


Tuchin K.,Iowa State University
International Journal of Modern Physics E | Year: 2014

I review properties of electromagnetic fields generated by colliding relativistic heavy ions and argue that they have a profound impact on the heavy-ion phenomenology. I discuss magnetic field effects on the quark gluon plasma flow, J/ψ dissociation, photon and dilepton production and quark energy loss. © 2014 World Scientific Publishing Company. Source


Gardel M.L.,University of Chicago | Gardel M.L.,James Franck Institute | Schneider I.C.,Iowa State University | Aratyn-Schaus Y.,University of Chicago | Waterman C.M.,U.S. National Institutes of Health
Annual Review of Cell and Developmental Biology | Year: 2010

Directed cell migration is a physical process that requires dramatic changes in cell shape and adhesion to the extracellular matrix. For efficientmovement, these processesmust be spatiotemporally coordinated. To a large degree, the morphological changes and physical forces that occur during migration are generated by a dynamic filamentous actin (F-actin) cytoskeleton. Adhesion is regulated by dynamic assemblies of structural and signaling proteins that couple the F-actin cytoskeleton to the extracellular matrix. Here, we review current knowledge of the dynamic organization of the F-actin cytoskeleton in cell migration and the regulation of focal adhesion assembly and disassembly with an emphasis on how mechanical and biochemical signaling between these two systems regulate the coordination of physical processes in cell migration. Copyright © 2010 by Annual Reviews. All rights reserved. Source


Raman V.,University of Michigan | Fox R.O.,Iowa State University
Annual Review of Fluid Mechanics | Year: 2016

The generation of nanostructured particles in high-temperature flames is important both for the control of emissions from combustion devices and for the synthesis of high-value chemicals for a variety of applications. The physiochemical processes that lead to the production of fine particles in turbulent flames are highly sensitive to the flow physics and, in particular, the history of thermochemical compositions and turbulent features they encounter. Consequently, it is possible to change the characteristic size, structure, composition, and yield of the fine particles by altering the flow configuration. This review describes the complex multiscale interactions among turbulent fluid flow, gas-phase chemical reactions, and solid-phase particle evolution. The focus is on modeling the generation of soot particles, an unwanted pollutant from automobile and aircraft engines, as well as metal oxides, a class of high-value chemicals sought for specialized applications, including emissions control. Issues arising due to the numerical methods used to approximate the particle number density function, the modeling of turbulence-chemistry interactions, and model validation are also discussed. © Copyright 2016 by Annual Reviews. All rights reserved. Source


Problem In several countries, physical activity is now recommended in clinical practice guidelines as an option for the treatment of subthreshold, mild, and moderate adult depression. However, most physicians do not present this option to their patients, attributing their decision to the perception that the supporting research evidence is inadequate. To assist readers in developing a strategy for evaluating pertinent research evidence, the present analysis offers a critical appraisal of the Cochrane systematic review and meta-analysis examining the effects of exercise on depression. Remarkably, successive updates of this review have reported a gradual "shrinkage" of the pooled standardized mean difference associated with exercise by 44%, from -1.10 in 2001 to -0.62 in 2013. Method The analysis evaluated the inclusion and exclusion criteria, the uniformity of rules, the rationale behind protocol changes, the procedures followed in assessing methodological quality, and reporting errors. Results Inspection of the details of the review demystifies the "shrinkage" phenomenon, revealing that it is attributable to specific, questionable methodological choices and the fluidity of the review protocol. Reanalysis of the same database following rational modifications shows that the effect of exercise is large. Restricting the analysis to high-quality trials yields an effect size significantly different from zero. Conclusions Although the clinical value of the Cochrane review is questionable, its educational potential is undeniable. Clinicians, students, referees, editors, systematic reviewers, guideline developers, and policymakers can use the present analysis as a template for evaluating the influence of methodological choices on the conclusions of systematic reviews and meta-analyses. © 2015 Elsevier Ltd. Source


Iverson N.R,Iowa State University
Geology | Year: 2012

Numerical models are used commonly to study the topographic evolution of glacially eroded landscapes. These models are grounded on a power-law rule that relates bedrock erosion rate to either the sliding speed or discharge of glaciers. This rule, however, is poorly linked to the principal process of glacial erosion, quarrying, in which bedrock blocks are dislodged from the bed by sliding ice. A new model of quarrying allows this erosion rule to be evaluated. As in past quarrying models, ice-bed separation during sliding controls deviatoric stresses in the rock that cause crack growth. Unlike past models, bedrock strength heterogeneity resulting from preglacial fractures is included using a Weibull statistical distribution of rock strength. This strength distribution is predicated on the observation that larger rock bodies have lower strengths because they have a greater probability of containing a large fracture. Results can, indeed, be closely fitted with a power-law erosion rule, but its nonlinearity, the range of sliding speed over which it applies, and erosion rates depend sensitively on bedrock strength heterogeneity and effective pressure. This theory anchors large-scale models of glacial erosion to the primary small-scale process that these models hope to simulate and reinforces recent emphasis on the role of bedrock fractures in accelerating geomorphic processes. Moreover, by linking basal water pressure to erosion rate, the theory can improve efforts with numerical models to study feedbacks between subglacial hydrology and landscape evolution. © 2012 Geological Society of America. Source


Kang Z.-B.,Brookhaven National Laboratory | Qiu J.-W.,Iowa State University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2010

Using the latest quark Sivers functions extracted from the global analysis of available data on single transverse spin asymmetry (SSA), we calculate the SSA of Drell-Yan inclusive production of lepton pairs of invariant mass Q at both 4 Source


Tuchin K.,Iowa State University | Tuchin K.,RIKEN
Physical Review C - Nuclear Physics | Year: 2011

We calculate the photon pair production rate in a strong magnetic field created in off-central heavy-ion collisions. Photon decay leads to depletion of the photon yield by a few percent at RHIC and by as much as 20% at the LHC. It also generates a substantial azimuthal asymmetry ("elliptic flow") of the final photon distribution. We estimate v2≈2% at RHIC and v2≈ 14% at LHC. Photon decay measurements is an important tool for studying the magnetic fields in early stages of heavy-ion collisions. © 2011 American Physical Society. Source


Lee D.-C.,Iowa State University | Pate R.R.,University of South Carolina | Lavie C.J.,University of New Orleans | Lavie C.J.,Louisiana State University | And 3 more authors.
Journal of the American College of Cardiology | Year: 2014

Background Although running is a popular leisure-time physical activity, little is known about the long-term effects of running on mortality. The dose-response relations between running, as well as the change in running behaviors over time, and mortality remain uncertain. Objectives We examined the associations of running with all-cause and cardiovascular mortality risks in 55,137 adults, 18 to 100 years of age (mean age 44 years). Methods Running was assessed on a medical history questionnaire by leisure-time activity. Results During a mean follow-up of 15 years, 3,413 all-cause and 1,217 cardiovascular deaths occurred. Approximately 24% of adults participated in running in this population. Compared with nonrunners, runners had 30% and 45% lower adjusted risks of all-cause and cardiovascular mortality, respectively, with a 3-year life expectancy benefit. In dose-response analyses, the mortality benefits in runners were similar across quintiles of running time, distance, frequency, amount, and speed, compared with nonrunners. Weekly running even <51 min, <6 miles, 1 to 2 times, <506 metabolic equivalent-minutes, or <6 miles/h was sufficient to reduce risk of mortality, compared with not running. In the analyses of change in running behaviors and mortality, persistent runners had the most significant benefits, with 29% and 50% lower risks of all-cause and cardiovascular mortality, respectively, compared with never-runners. Conclusions Running, even 5 to 10 min/day and at slow speeds <6 miles/h, is associated with markedly reduced risks of death from all causes and cardiovascular disease. This study may motivate healthy but sedentary individuals to begin and continue running for substantial and attainable mortality benefits. © 2014 by the American College of Cardiology Foundation. Source


Moore P.L.,Iowa State University
Reviews of Geophysics | Year: 2014

Mixtures of rock debris and ice are common in high-latitude and high-altitude environments and are thought to be widespread elsewhere in our solar system. In the form of permafrost soils, glaciers, and rock glaciers, these debris-ice mixtures are often not static but slide and creep, generating many of the landforms and landscapes associated with the cryosphere. In this review, a broad range of field observations, theory, and experimental work relevant to the mechanical interactions between ice and rock debris are evaluated, with emphasis on the temperature and stress regimes common in terrestrial surface and near-surface environments. The first-order variables governing the deformation of debris-ice mixtures in these environments are debris concentration, particle size, temperature, solute concentration (salinity), and stress. A key observation from prior studies, consistent with expectations, is that debris-ice mixtures are usually more resistant to deformation at low temperatures than their pure end-member components. However, at temperatures closer to melting, the growth of unfrozen water films at ice-particle interfaces begins to reduce the strengthening effect and can even lead to profound weakening. Using existing quantitative relationships from theoretical and experimental work in permafrost engineering, ice mechanics, and glaciology combined with theory adapted from metallurgy and materials science, a simple constitutive framework is assembled that is capable of capturing most of the observed dynamics. This framework highlights the competition between the role of debris in impeding ice creep and the mitigating effects of unfrozen water at debris-ice interfaces. ©2014. American Geophysical Union. Source


Abbott K.C.,Iowa State University
Ecology Letters | Year: 2011

Understanding how dispersal influences the dynamics of spatially distributed populations is a major priority of both basic and applied ecologists. Two well-known effects of dispersal are spatial synchrony (positively correlated population dynamics at different points in space) and dispersal-induced stability (the phenomenon whereby populations have simpler or less extinction-prone dynamics when they are linked by dispersal than when they are isolated). Although both these effects of dispersal should occur simultaneously, they have primarily been studied separately. Herein, I summarise evidence from the literature that these effects are expected to interact, and I use a series of models to characterise that interaction. In particular, I explore the observation that although dispersal can promote both synchrony and stability singly, it is widely held that synchrony paradoxically prevents dispersal-induced stability. I show here that in many realistic scenarios, dispersal is expected to promote both synchrony and stability at once despite this apparent destabilising influence of synchrony. This work demonstrates that studying the spatial and temporal impacts of dispersal together will be vital for the conservation and management of the many communities for which human activities are altering natural dispersal rates. © 2011 Blackwell Publishing Ltd/CNRS. Source


Holland S.D.,Iowa State University
Infrared Physics and Technology | Year: 2011

Vibrothermography, also known as thermosonics or sonic infrared, is a method of nondestructive evaluation that finds cracks or delaminations from the heat given off in response to vibration. In vibrothermography, finding cracks requires identifying and localizing pulsed surface and subsurface heat sources from a time sequence of infrared images. Traditionally this identification involves manually stepping through and studying the images. Careful observation of the heating and subsequent cooling is needed to distinguish cracks from false indications. In this paper, we present an algorithm that reduces the entire time sequence to a single static plot. The plot uses only a few coefficients per pixel to reconstruct the original sequence; this is possible because the reduction is based on a physical model. As an added bonus, the algorithm reduces noise and improves sensitivity. A single false-color image summarizes all the information from the entire sequence, simplifying the task of identifying cracks. © 2011 Elsevier B.V. All rights reserved. Source


Dai R.,Iowa State University | Mesbahi M.,University of Washington
Energy Conversion and Management | Year: 2013

This paper addresses the optimal power generation and load management problems in off-grid hybrid electric systems with renewable sources based on appropriately constructed optimization problems. In this venue, the capacity and operating constraints for generating, storage and load units are first formulated as mixed-integer linear programming (MILP) models. In addition, we integrate the power curtailment strategies, such as temporary pause and multiple power supplies, for the load units in the MILP models to alleviate the peak power demands and power shortage without an adverse effect on the overall operation of the system. We subsequently consider the application of this framework for representative scenarios in the context of a residential power system with solar sources. Simulation results for the case of predetermined schedules with preset power requests, as well as for the case of varying schedules with updated power requests, are presented using the proposed optimization-based approach. © 2013 Elsevier Ltd. All rights reserved. Source


Leonardi B.,General Electric | Ajjarapu V.,Iowa State University
IEEE Transactions on Power Systems | Year: 2013

This study proposes a man-in-loop control method to boost reactive power reserves (RPRs) while maintaining a minimum amount of voltage stabilitymargin (VSM) bus voltage limits. The objective is to determine the most effective control actions in order to reestablish critical RPRs across the system. Initially, the concept of reactive power reserve sensitivity with respect to control actions is introduced. In the sequel, a control approach based on convex quadratic optimization is used to find the minimal amount of control necessary to increase RPRs above their pre-specified (offline) levels. Voltage stability margin constraints are incorporated using a linear approximation of critical RPRs. Simulation results show that system operators can optimally determine the right amount and location of control actions in order to restore criticalRPRs and enhanceVSMby using reactive power reserve sensitivities. Moreover, the optimization problem size can be made small if only the most effective control actions are selected, a desirable advantage for real time implementations of man-in-loop control. © 2012 IEEE. Source


Howell S.H.,Iowa State University
Annual Review of Plant Biology | Year: 2013

Endoplasmic reticulum (ER) stress is of considerable interest to plant biologists because it occurs in plants subjected to adverse environmental conditions. ER stress responses mitigate the damage caused by stress and confer levels of stress tolerance to plants. ER stress is activated by misfolded proteins that accumulate in the ER under adverse environmental conditions. Under these conditions, the demand for protein folding exceeds the capacity of the system, which sets off the unfolded protein response (UPR). Two arms of the UPR signaling pathway have been described in plants: one that involves two ER membrane-associated transcription factors (bZIP17 and bZIP28) and another that involves a dual protein kinase (RNA-splicing factor IRE1) and its target RNA (bZIP60). Under mild or short-term stress conditions, signaling from IRE1 activates autophagy, a cell survival response. But under severe or chronic stress conditions, ER stress can lead to cell death. © Copyright ©2013 by Annual Reviews. All rights reserved. Source


Olsen K.M.,Washington University in St. Louis | Wendel J.F.,Iowa State University
Annual Review of Plant Biology | Year: 2013

Human selection during crop domestication has resulted in remarkable transformations of plant phenotypes, providing a window into the genetic basis of morphological evolution. Recent progress in our understanding of the genetic architecture of novel plant traits has emerged from combining advanced molecular technologies with improved experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies reveal a diversity of underlying causative mutations affecting phenotypes important in plant domestication and crop improvement, including coding sequence substitutions, presence/absence and copy number variation, transposon activation leading to novel gene structures and expression patterns, diversification following gene duplication, and polyploidy leading to altered combinatorial capabilities. The genomic regions unknowingly targeted by human selection include both structural and regulatory genes, often with results that propagate through the transcriptome as well as to other levels in the biosynthetic and morphogenetic networks. © Copyright ©2013 by Annual Reviews. All rights reserved. Source


Ke P.C.,Clemson University | Lamm M.H.,Iowa State University
Physical Chemistry Chemical Physics | Year: 2011

In this article we present a biophysical perspective that describes the fate of nanoparticles in both the aqueous phase and in living systems. Specifically, we show the correlations between the physicochemistry of fullerenes and their uptake, translocation, transformation, transport, and biodistribution in mammalian and plant systems, at the molecular, cellular, and whole organism level. In addition to fullerenes and their structural derivatives, we describe the biological and environmental implications and applications of the condensed matter of carbon nanotubes and quantum dots, and the soft condensed matter of plastic and dendrimers. The main purpose of this article is to demonstrate the vast opportunities and unique advantages of applying experimental and simulation biophysics to the nascent research field of understanding nanoparticles at large. © the Owner Societies. Source


Garrick D.J.,Iowa State University | Garrick D.J.,Massey University
Genetics Selection Evolution | Year: 2011

Artificial selection has proven to be effective at altering the performance of animal production systems. Nevertheless, selection based on assessment of the genetic superiority of candidates is suboptimal as a result of errors in the prediction of genetic merit. Conventional breeding programs may extend phenotypic measurements on selection candidates to include correlated indicator traits, or delay selection decisions well beyond puberty so that phenotypic performance can be observed on progeny or other relatives. Extending the generation interval to increase the accuracy of selection reduces annual rates of gain compared to accurate selection and use of parents of the next generation at the immediate time they reach breeding age. Genomic prediction aims at reducing prediction errors at breeding age by exploiting information on the transmission of chromosome fragments from parents to selection candidates, in conjunction with knowledge on the value of every chromosome fragment. For genomic prediction to influence beef cattle breeding programs and the rate or cost of genetic gains, training analyses must be undertaken, and genomic prediction tools made available for breeders and other industry stakeholders. This paper reviews the nature or kind of studies currently underway, the scope or extent of some of those studies, and comments on the likely predictive value of genomic information for beef cattle improvement. © 2011 Garrick; licensee BioMed Central Ltd. Source


Kim T.-W.,Korea Research Institute of Chemical Technology | Chung P.-W.,Iowa State University
Chemistry of Materials | Year: 2010

A rapid and facile synthesis route to the monodisperse spherical MCM-48 mesoporous silica nanoparticles (MSN) with cubic Ia3d mesostructure is developed based on the modified Stöber method. The phase domain of MCM-48-type MSNs can be extended by controlling the stirring rate and molar ratios of silica source and surfactant. The formation of monodispersed spherical MCM-48-type MSNs is obtained using triblock copolymer Pluronic F127 as a particle size designer. The average size of monodisperse spherical MSN can be controlled within the range of 70-500 nm depending on the amount of F127. Moreover, the pore diameter of MSNs can be precisely controllable in pore diameters from 2.3 to 3.3 nm using different alkyl chain surfactants and simple posthydrothermal treatment. An investigation of MCM-48-type MSN materials using powder X-ray diffraction, transmission electron microscopy, scanning electron microscopy, and nitrogen physisorption clearly reveals that MSNs show high specific surface area, high pore volumes, controllable morphological aspects, and tunable pore diameters. The MCM-48-type MSNs thus obtained are demonstrated as a good hard template for the preparation of other mesoporous nanoparticles, such as mesoporous metal oxides. The present discovery of the extended synthesis conditions and the binary surfactant system in MCM-48 synthesis offers reproducible and facile synthesis of the monodisperse spherical MCM-48 mesoporous silica nanoparticles with precise structural control, and thus has vast prospects for future applications of ultrafine mesostructured nanoparticle materials. © 2010 American Chemical Society. Source


Phanse Y.,Iowa State University
Journal of visualized experiments : JoVE | Year: 2012