Showing papers by "Virginia Tech published in 2006"

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Insights into social insects from the genome of the honeybee Apis mellifera

Abstract: Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes, the A. mellifera genome has high A+T and CpG contents, lacks major transposon families, evolves more slowly, and is more similar to vertebrates for circadian rhythm, RNA interference and DNA methylation genes, among others. Furthermore, A. mellifera has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen utilization, consistent with its ecology and social organization. Compared to Drosophila, genes in early developmental pathways differ in Apis, whereas similarities exist for functions that differ markedly, such as sex determination, brain function and behaviour. Population genetics suggests a novel African origin for the species A. mellifera and insights into whether Africanized bees spread throughout the New World via hybridization or displacement.

Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

Abstract: Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.

CO/FT Regulatory Module Controls Timing of Flowering and Seasonal Growth Cessation in Trees

Abstract: Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day–induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.

Insect vectors of phytoplasmas

Abstract: Plant diseases caused by, or associated with, phytoplasmas occur in hundreds of commercial and native plants, causing minor to extensive damage. Insect vectors, primarily leafhoppers, planthoppers, and psyllids, have been identified for relatively few phytoplasma diseases, limiting the capacity of managers to make informed decisions to protect crops and endangered indigenous plants. In the past two decades our knowledge of insect vector-phytoplasma interactions has increased dramatically, allowing researchers to make more accurate predictions about the nature and epidemiology of phytoplasma diseases. These better-characterized systems also may provide clues to the identity of insect vectors of other phytoplasma-associated diseases. We review the literature addressing the ecology of insect vectors, phytoplasma-insect ecological and molecular interactions, vector movement and dispersal, and possible management strategies with an emphasis on research from the past 20 years.

Variational formulation for the stationary fractional advection dispersion equation

Abstract: In this article a theoretical framework for the Galerkin finite element approximation to the steady state fractional advection dispersion equation is presented. Appropriate fractional derivative spaces are defined and shown to be equivalent to the usual fractional dimension Sobolev spaces Hs. Existence and uniqueness results are proven, and error estimates for the Galerkin approximation derived. Numerical results are included that confirm the theoretical estimates. © 2005 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2005

Efficient step size selection for the tau-leaping simulation method

Abstract: The tau-leaping method of simulating the stochastic time evolution of a well-stirred chemically reacting system uses a Poisson approximation to take time steps that leap over many reaction events. Theory implies that tau leaping should be accurate so long as no propensity function changes its value “significantly” during any time step τ. Presented here is an improved procedure for estimating the largest value for τ that is consistent with this condition. This new τ-selection procedure is more accurate, easier to code, and faster to execute than the currently used procedure. The speedup in execution will be especially pronounced in systems that have many reaction channels.

Gas Turbine Film Cooling

Abstract: The durability of gas turbine engines is strongly dependent on the component temperatures. For the combustor and turbine airfoils and endwalls, film cooling is used extensively to reduce component temperatures. Film cooling is a cooling method used in virtually all of today's aircraft turbine engines and in many power-generation turbine engines and yet has very difficult phenomena to predict. The interaction of jets-in-crossflow, which is representative of film cooling, results in a shear layer that leads to mixing and a decay in the cooling performance along a surface. This interaction is highly dependent on the jet-to-crossflow mass and momentum flux ratios. Film-cooling performance is difficult to predict because of the inherent complex flowfields along the airfoil component surfaces in turbine engines. Film cooling is applied to nearly all of the external surfaces associated with the airfoils that are exposed to the hot combustion gasses such as the leading edges, main bodies, blade tips, and endwalls. In a review of the literature, it was found that there are strong effects of freestream turbulence, surface curvature, and hole shape on the performance of film cooling. Film cooling is reviewed through a discussion of the analyses methodologies, a physical description, and the various influences on film-cooling performance.

Individual equity return data from thomson datastream: handle with care!

Abstract: We compare individual U.S. equity return data from Thomson Datastream (TDS) with similar data from the Center for Research in Security Prices (CRSP) to evaluate TDS for use in studies involving large numbers of individual equities in markets outside the United States. We document important issues of coverage, classification, and data integrity and find that naive use of TDS data can have a large impact on economic inferences. We show that after careful screening of the TDS data, inferences drawn from TDS data are similar to those drawn from CRSP. We illustrate the importance of the screens we develop using U.S. TDS data by applying the screens to TDS data from four European equity markets.

Two decades of self‐leadership theory and research: Past developments, present trends, and future possibilities

Abstract: Purpose – The purpose of this paper is to provide a thorough review of self‐leadership literature past and present, including a historical overview of how the concept was created and expanded as well as a detailed look at more recent self‐leadership research trends and directions. The paper also presents a theoretical and conceptual explanation and differentiation of the self‐leadership concept relative to other related motivational, personality, and self‐influence constructs.Design/methodology/approach – Self‐leadership research and related literatures of motivation, personality and self‐influence are discussed and described in order to present the current state of the self‐leadership body of knowledge and to suggest future directions to explore and study.Findings – It is suggested that self‐leadership is a normative model of self‐influence that operates within the framework of more descriptive and deductive theories such as self‐regulation and social cognitive theory.Research limitations/implications – ...

Effects of Parameter Estimation on Control Chart Properties; A Literature Review

Abstract: Control chart limits are often calculated using parameter estimates from an in-control Phase I reference sample. In Phase II monitoring, statistics based on new samples are compared with the estimated control limits to monitor for departures from the in..

Analytical loss model of power MOSFET

Abstract: An accurate analytical model is proposed in this paper to calculate the power loss of a metal-oxide semiconductor field-effect transistor. The nonlinearity of the capacitors of the devices and the parasitic inductance in the circuit, such as the source inductor shared by the power stage and driver loop, the drain inductor, etc., are considered in the model. In addition, the ringing is always observed in the switching power supply, which is ignored in the traditional loss model. In this paper, the ringing loss is analyzed in a simple way with a clear physical meaning. Based on this model, the circuit power loss could be accurately predicted. Experimental results are provided to verify the model. The simulation results match the experimental results very well, even at 2-MHz switching frequency.

The Use of Control Charts in Health-Care and Public-Health Surveillance

Abstract: There are many applications of control charts in health-care monitoring and in public-health surveillance. We introduce these applications to industrial practitioners and discuss some of the ideas that arise that may be applicable in industrial monitoring. The advantages and disadvantages of the charting methods proposed in the health-care and public-health areas are considered. Some additional contributions in the industrial statistical process control literature relevant to this area are given. There are many application and research opportunities available in the use of control charts for health-related monitoring.

Cognitive networks: adaptation and learning to achieve end-to-end performance objectives

Abstract: In this article we advance the idea of a cognitive network, capable of perceiving current network conditions and then planning, learning, and acting according to end-to-end goals. Cognitive networks are motivated by the complexity, heterogeneity, and reliability requirements of tomorrow's networks, which are increasingly expected to self-organize to meet user and application objectives. We compare and contrast cognitive networks with related research on cognitive radios and cross-layer design. By defining cognitive networks, examining their relationship to other technologies, discussing critical design issues, and providing a framework for implementation, we aim to establish a foundation for further research and discussion

Enhancement of Chilling Resistance of Inoculated Grapevine Plantlets with a Plant Growth-Promoting Rhizobacterium, Burkholderia phytofirmans Strain PsJN

Abstract: In vitro inoculation of Vitis vinifera L. cv. Chardonnay explants with a plant growth-promoting rhizobacterium, Burkholderia phytofirmans strain PsJN, increased grapevine growth and physiological activity at a low temperature. There was a relationship between endophytic bacterial colonization of the grapevine plantlets and their growth at both ambient (26°C) and low (4°C) temperatures and their sensitivities to chilling. The major benefits of bacterization were observed on root growth (11.8- and 10.7-fold increases at 26°C and 4°C, respectively) and plantlet biomass (6- and 2.2-fold increases at 26°C and 4°C, respectively). The inoculation with PsJN also significantly improved plantlet cold tolerance compared to that of the nonbacterized control. In nonchilled plantlets, bacterization enhanced CO2 fixation and O2 evolution 1.3 and 2.2 times, respectively. The nonbacterized controls were more sensitive to exposure to low temperatures than were the bacterized plantlets, as indicated by several measured parameters. Moreover, relative to the noninoculated controls, bacterized plantlets had significantly increased levels of starch, proline, and phenolics. These increases correlated with the enhancement of cold tolerance of the grapevine plantlets. In summary, B. phytofirmans strain PsJN inoculation stimulates grapevine growth and improves its ability to withstand cold stress.

Social-cognitive determinants of physical activity: the influence of social support, self-efficacy, outcome expectations, and self-regulation among participants in a church-based health promotion study.

Abstract: A social-cognitive model of physical activity was tested, using structural equation analysis of data from 999 adults (21% African American; 66% female; 38% inactive) recruited from 14 southwestern Virginia churches participating in the baseline phase of a health promotion study. Within the model, age, race, social support, self-efficacy, and self-regulation contributed to participants' physical activity levels, but outcome expectations did not. Of the social-cognitive variables, self-regulation exerted the strongest effect on physical activity. Independent of self-regulation, self-efficacy had little effect. Social support influenced physical activity as a direct precursor to self-efficacy and self-regulation. The model provided a good fit to the data and explained 46% of the variance in physical activity among the diverse group of adults.

Colloidal gold nanoparticles: a novel nanoparticle platform for developing multifunctional tumor‐targeted drug delivery vectors

Abstract: Nanotechnology applied to biological problems represents an emerging field with the potential to offer extremely sensitive diagnostics and targeted cancer therapies. However, to achieve these goals, nanoparticle delivery systems must outwit the many barriers that are intrinsic to the body's defenses, as well as those that develop during the growth and progression of tumors. The science is advancing and, for example, true nanoscale tumor-targeted drug delivery vectors are now able to reduce the likelihood of opsonization in the bloodstream and uptake by the reticuloendothelial system. Other advances hold promise for delivering multiple therapeutic agents to non-homogeneous populations of cancer cells in solid tumors. We briefly summarize herein our attempts to build such multifunctional nanotherapeutics using colloidal gold nanoparticles. Specifically we discuss the development of colloidal gold-based drugs that are designed to target the delivery of TNF and paclitaxel to solid tumors. Drug Dev. Res. 67:47–54, 2006. © 2006 Wiley-Liss, Inc.

Game theory for wireless engineers

Abstract: The application of mathematical analysis to wireless networks has met with limited success, due to the complexity of mobility and traffic models, coupled with the dynamic topology and the unpredictability of link quality that characterize such networks. The ability to model individual, independent decision makers whose actions potentially affect all other decision makers makes game theory particularly attractive to analyze the performance of ad hoc networks. Game theory is a field of applied mathematics that describes and analyzes interactive decision situations. It consists of a set of analytical tools that predict the outcome of complex interactions among rational entities, where rationality demands a strict adherence to a strategy based on perceived or measured results. In the early to mid-1990's, game theory was applied to networking problems including flow control, congestion control, routing and pricing of Internet services. More recently, there has been growing interest in adopting game-theoretic methods to model today's leading communications and networking issues, including power control and resource sharing in wireless and peer-to-peer networks. This work presents fundamental results in game theory and their application to wireless communications and networking. We discuss normal-form, repeated, and Markov games with examples selected from the literature. We also describe ways in which learning can be modeled in game theory, with direct applications to the emerging field of cognitive radio. Finally, we discuss challenges and limitations in the application of game theory to the analysis of wireless systems. We do not assume familiarity with game theory. We introduce major game theoretic models and discuss applications of game theory including medium access, routing, energy-efficient protocols, and others. We seek to provide the reader with a foundational understanding of the current research on game theory applied to wireless communications and networking.

Channel flow, ductile extrusion and exhumation in continental collision zones: an introduction

Abstract: The channel flow model aims to explain features common to metamorphic hinterlands of some collisional orogens, notably along the Himalaya–Tibet system. Channel flow describes a protracted flow of a weak, viscous crustal layer between relatively rigid yet deformable bounding crustal slabs. Once a critical low viscosity is attained (due to partial melting), the weak layer flows laterally due to a horizontal gradient in lithostatic pressure. In the Himalaya–Tibet system, this lithostatic pressure gradient is created by the high crustal thicknesses beneath the Tibetan Plateau and ‘normal’ crustal thickness in the foreland. Focused denudation can result in exhumation of the channel material within a narrow, nearly symmetric zone. If channel flow is operating at the same time as focused denudation, this can result in extrusion of the mid-crust between an upper normal-sense boundary and a lower thrust-sense boundary. The bounding shear zones of the extruding channel may have opposite shear sense; the sole shear zone is always a thrust, while the roof shear zone may display normal or thrust sense, depending on the relative velocity between the upper crust and the underlying extruding material. This introductory chapter addresses the historical, theoretical, geological and modelling aspects of channel flow, emphasizing its applicability to the Himalaya–Tibet orogen. Critical tests for channel flow in the Himalaya, and possible applications to other orogenic belts, are also presented. The hinterlands of collisional orogens are often characterized by highly strained, high-grade metamorphic rocks that commonly display features consistent with lateral crustal flow and extrusion of material from mid-crustal depths towards the orogenic foreland. A recent model for lateral flow of such weak mid-crustal layers has become widely known as the ‘channel flow’ model. The channel flow model has matured through efforts by several research groups and has also been applied to a variety of geodynamic settings. Thermal-mechanical modelling of collision zones, including the Himalayan–Tibetan system, has brought the concept of channel flow to the forefront of orogenic studies. Original contributors to the concept of channel flow initiated an important paradigm shift (Kuhn 1979), from geodynamic models of continental crust with finite rheological layering to the more encompassing channel flow model. This time-dependent midto lower crustal flow process, which will be reviewed in this chapter, may progress into foreland fold-and-thrust tectonics in the upper crust, thereby providing a spatial and temporal link between the early development of a metamorphic core in the hinterland and the foreland fold-and-thrust belt at shallower structural levels. Outcomes and implications of such a viscous flowing middle to lower crust include a dynamic coupling between mid-crustal and surface processes, and limitations to accurate retro-deformation of orogens (non-restorable orogens, e.g. Jamieson et al. 2006). This Special Publication contains a selection of papers that were presented at the conference ‘Channel flow, extrusion, and exhumation of lower to mid-crust in continental collision zones’ hosted by the Geological Society of London at Burlington House, in December 2004. Because most of the ongoing debate on crustal flow focuses on the Cenozoic age Himalaya–Tibet collisional system, some of the key questions that are addressed in this volume include the following. . Does the model for channel flow in the Himalaya–Tibet system concur with all available geological and geochronological data? From: LAW, R. D., SEARLE, M. P. & GODIN, L. (eds) Channel Flow, Ductile Extrusion and Exhumation in Continental Collision Zones. Geological Society, London, Special Publications, 268, 1–23. 0305-8719/06/$15.00 # The Geological Society of London 2006. . How do the pressure–temperature-time (P-T-t) data across the crystalline core of the Himalaya fit with the proposed channel flow? . Are the microstructural fabric data (pure shear and simple shear components) compatible with crustal extrusion (thickening or thinning of the slab)? . If the channel flow model is viable for the Himalaya–Tibet system, what may have initiated channel flow and ductile extrusion? . Why did the extrusion phase of the Himalayan metamorphic core apparently cease during the late Miocene–Pliocene? . Are some of the bounding faults of the potential channel still active, or were they recently active? . Is the Himalayan channel flow model exportable to other mountain ranges? This introductory paper addresses the historical, theoretical, geological and modelling aspects of crustal flow in the Himalaya–Tibet orogen. Critical tests for crustal flow in the Himalaya, and possible applications to other orogenic belts, are presented and difficulties associated with applying these tests are discussed. Personal communication citations (pers. comm. 2004) identify comments expressed during the conference. The Himalaya–Tibetan plateau system The Himalaya–Tibet system initiated in Early Eocene times, following collision of the Indian and Eurasian plates (see Hodges (2000) and Yin & Harrison (2000) for reviews). The collision resulted in closure of the Tethyan Ocean, southward imbrication of the Indian crust, and northward continental subduction of Indian lower crust and mantle beneath Asia. The collision thickened the southern edge of the Asian crust to 70 km, and created the Tibetan Plateau, the largest uplifted part of the Earth’s surface with an average elevation of 5000 m (Fielding et al. 1994). The Himalayan orogen coincides with the 2500km-long topographic front at the southern limit of the Tibetan Plateau. It consists of five broadly parallel lithotectonic belts, separated by mostly north-dipping faults (Fig. 1). The Himalayan metamorphic core, termed the Greater Himalayan sequence (GHS), is bounded by two parallel and opposite-sense shear zones that were both broadly active during the Miocene (Hubbard & Harrison 1989; Searle & Rex 1989; Hodges et al. 1992, 1996). The Main Central thrust (MCT) zone marks the lower boundary of the GHS, juxtaposing the metamorphic core above the underlying Lesser Himalayan sequence. The South Tibetan detachment (STD) system defines the upper boundary roof fault of the GHS, marking the contact with the overlying unmetamorphosed Tethyan sedimentary sequence. The apparent coeval movement of the MCT and STD, combined with the presence of highly sheared rocks and high grade to migmatitic rocks within the GHS, has led many workers to view the GHS as a north-dipping, southward-extruding slab of mid-crustal material flowing away from the thick southern edge of the Tibetan Plateau, towards the thinner foreland fold-thrust belt. Dynamics of channel flow The concepts of crustal extrusion and channel flow originated in the continental tectonics literature in the early 1990s. Unfortunately, these two processes are often referred to interchangeably without justification. One of the main points that emerged from the Burlington House conference was that a distinction between channel flow and crustal extrusion must be made. Parallel versus tapering bounding walls on channel flow and/or extrusion processes, and how these processes may replenish over time, are two resolvable parameters that are critical for distinguishing channel flow from extrusion. Brief definitions and overviews of the two processes are presented below. A more detailed overview of the mechanics of the related processes is provided by Grujic (2006).