Showing papers by "Virginia Tech published in 2010"

Review: current international research into cellulose nanofibres and nanocomposites

Abstract: This paper provides an overview of recent progress made in the area of cellulose nanofibre-based nanocomposites. An introduction into the methods used to isolate cellulose nanofibres (nanowhiskers, nanofibrils) is given, with details of their structure. Following this, the article is split into sections dealing with processing and characterisation of cellulose nanocomposites and new developments in the area, with particular emphasis on applications. The types of cellulose nanofibres covered are those extracted from plants by acid hydrolysis (nanowhiskers), mechanical treatment and those that occur naturally (tunicate nanowhiskers) or under culturing conditions (bacterial cellulose nanofibrils). Research highlighted in the article are the use of cellulose nanowhiskers for shape memory nanocomposites, analysis of the interfacial properties of cellulose nanowhisker and nanofibril-based composites using Raman spectroscopy, switchable interfaces that mimic sea cucumbers, polymerisation from the surface of cellulose nanowhiskers by atom transfer radical polymerisation and ring opening polymerisation, and methods to analyse the dispersion of nanowhiskers. The applications and new advances covered in this review are the use of cellulose nanofibres to reinforce adhesives, to make optically transparent paper for electronic displays, to create DNA-hybrid materials, to generate hierarchical composites and for use in foams, aerogels and starch nanocomposites and the use of all-cellulose nanocomposites for enhanced coupling between matrix and fibre. A comprehensive coverage of the literature is given and some suggestions on where the field is likely to advance in the future are discussed.

Impacts of biodiversity on the emergence and transmission of infectious diseases

Abstract: Current unprecedented declines in biodiversity reduce the ability of ecological communities to provide many fundamental ecosystem services. Here we evaluate evidence that reduced biodiversity affects the transmission of infectious diseases of humans, other animals and plants. In principle, loss of biodiversity could either increase or decrease disease transmission. However, mounting evidence indicates that biodiversity loss frequently increases disease transmission. In contrast, areas of naturally high biodiversity may serve as a source pool for new pathogens. Overall, despite many remaining questions, current evidence indicates that preserving intact ecosystems and their endemic biodiversity should generally reduce the prevalence of infectious diseases.

Synchronized Phasor Measurement Applications in Power Systems

Abstract: Synchronized phasor measurements have become a mature technology with several international manufacturers offering commercial phasor measurement units (PMUs) which meet the prevailing industry standard for synchrophasors. With the occurrence of major blackouts in many power systems around the world, the value of data provided by PMUs has been recognized, and installation of PMUs on power transmission networks of most major power systems has become an important current activity. This paper provides a brief introduction to the PMU and wide-area measurement system (WAMS) technology and discusses the uses of these measurements for improved monitoring, protection, and control of power networks.

Verification and Validation in Scientific Computing

Abstract: Advances in scientific computing have made modelling and simulation an important part of the decision-making process in engineering, science, and public policy. This book provides a comprehensive and systematic development of the basic concepts, principles, and procedures for verification and validation of models and simulations. The emphasis is placed on models that are described by partial differential and integral equations and the simulations that result from their numerical solution. The methods described can be applied to a wide range of technical fields, from the physical sciences, engineering and technology and industry, through to environmental regulations and safety, product and plant safety, financial investing, and governmental regulations. This book will be genuinely welcomed by researchers, practitioners, and decision makers in a broad range of fields, who seek to improve the credibility and reliability of simulation results. It will also be appropriate either for university courses or for independent study.

Whole-genome resequencing reveals loci under selection during chicken domestication

Abstract: Domestic animals are excellent models for genetic studies of phenotypic evolution They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens We have generated 445-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research

Water Purification by Membranes: The Role of Polymer Science

Abstract: Two of the greatest challenges facing the 21st century involve providing sustainable supplies of clean water and energy, two highly interrelated resources, at affordable costs. Membrane technology is expected to continue to dominate the water purifica- tion technologies owing to its energy efficiency. However, there is a need for improved membranes that have higher flux, are more selective, are less prone to various types of fouling, and are more resistant to the chemical environment, especially chlorine, of these processes. This article summarizes the nature of the global water problem and reviews the state of the art of membrane technology. Existing deficiencies of current membranes and the opportunities to resolve them with innovative polymer chemistry and physics are identified. Extensive background is provided to help the reader understand the fundamental issues involved. V C 2010 Wiley Periodi- cals, Inc. J Polym Sci Part B: Polym Phys 48: 1685-1718, 2010

The total antioxidant content of more than 3100 foods, beverages, spices, herbs and supplements used worldwide

Abstract: Background: A plant-based diet protects against chronic oxidative stress-related diseases. Dietary plants contain variable chemical families and amounts of antioxidants. It has been hypothesized that plant antioxidants may contribute to the beneficial health effects of dietary plants. Our objective was to develop a comprehensive food database consisting of the total antioxidant content of typical foods as well as other dietary items such as traditional medicine plants, herbs and spices and dietary supplements. This database is intended for use in a wide range of nutritional research, from in vitro and cell and animal studies, to clinical trials and nutritional epidemiological studies. Methods: We procured samples from countries worldwide and assayed the samples for their total antioxidant content using a modified version of the FRAP assay. Results and sample information (such as country of origin, product and/or brand name) were registered for each individual food sample and constitute the Antioxidant Food Table. Results: The results demonstrate that there are several thousand-fold differences in antioxidant content of foods. Spices, herbs and supplements include the most antioxidant rich products in our study, some exceptionally high. Berries, fruits, nuts, chocolate, vegetables and products thereof constitute common foods and beverages with high antioxidant values. Conclusions: This database is to our best knowledge the most comprehensive Antioxidant Food Database published and it shows that plant-based foods introduce significantly more antioxidants into human diet than nonplant foods. Because of the large variations observed between otherwise comparable food samples the study emphasizes the importance of using a comprehensive database combined with a detailed system for food registration in clinical and epidemiological studies. The present antioxidant database is therefore an essential research tool to further elucidate the potential health effects of phytochemical antioxidants in diet.

The Microarray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Abstract: Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.

The BioPAX community standard for pathway data sharing

Abstract: Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth.

Abstract: Plant drought stress response and resistance are complex biological processes that need to be analyzed at a systems level using genomics and physiological approaches to dissect experimental models that address drought stresses encountered by crops in the field. Toward this goal, a controlled, sublethal, moderate drought (mDr) treatment system was developed in Arabidopsis (Arabidopsis thaliana) as a reproducible assay for the dissection of plant responses to drought. The drought assay was validated using Arabidopsis mutants in abscisic acid (ABA) biosynthesis and signaling displaying drought sensitivity and in jasmonate response mutants showing drought resistance, indicating the crucial role of ABA and jasmonate signaling in drought response and acclimation. A comparative transcriptome analysis of soil water deficit drought stress treatments revealed the similarity of early-stage mDr to progressive drought, identifying common and specific stress-responsive genes and their promoter cis-regulatory elements. The dissection of mDr stress responses using a time-course analysis of biochemical, physiological, and molecular processes revealed early accumulation of ABA and induction of associated signaling genes, coinciding with a decrease in stomatal conductance as an early avoidance response to drought stress. This is accompanied by a peak in the expression of expansin genes involved in cell wall expansion, as a preparatory step toward drought acclimation by the adjustment of the cell wall. The time-course analysis of mDr provides a model with three stages of plant responses: an early priming and preconditioning stage, followed by an intermediate stage preparatory for acclimation, and a late stage of new homeostasis with reduced growth.

Discovery and Characterization of Silver Sulfide Nanoparticles in Final Sewage Sludge Products

Abstract: Nanosized silver sulfide (α-Ag2S) particles were identified in the final stage sewage sludge materials of a full-scale municipal wastewater treatment plant using analytical high-resolution transmission electron microscopy. The Ag2S nanocrystals are in the size range of 5−20 nm with ellipsoidal shape, and they form very small, loosely packed aggregates. Some of the Ag2S nanoparticles (NPs) have excess S on the surface of the sulfide minerals under S-rich environments, resulting in a ratio of Ag to S close to 1. Considering the current extensive production of Ag NPs and their widespread use in consumer products, it is likely that they are entering wastewater streams and the treatment facilities that process this water. This study suggests that in a reduced, S-rich environment, such as the sedimentation processes during wastewater treatment, nanosized silver sulfides are being formed. This field-scale study provides for the first time nanoparticle-level information of the Ag2S present in sewage sludge produc...

Future electronic power distribution systems a contemplative view

Abstract: Although it has long been argued that electronic power converters can help improve system controllability, reliability, size, and efficiency, their penetration in power systems is still quite low. The often-cited barriers of higher cost and lower reliability of the power converters are quite high if power electronics is used as direct, one-to-one, replacement for the existing electromechanical equipment. However, if the whole power distribution system were designed as a system of controllable converters, the overall system cost and reliability could actually improve, as is currently the case at low power levels within computer and telecom equipment. Starting from the example of a computer power system, the paper contemplates possible future ac and dc electronic power distribution system architectures, especially in the presence of renewable energy sources. The proposed nanogrid-microgrid-…-grid structure achieves hierarchical dynamic decoupling of generation, distribution, and consumption by using bidirectional converters as energy control centers. This is illustrated by the description and simulation of static and dynamic operation of a dc nanogrid in a hypothetical future sustainable home. Several ideas for modeling, analysis, and system-level design of such systems, including power flow control, protection, stability, and subsystem interactions, are presented.

On the rocks: the microbiology of Antarctic Dry Valley soils.

Abstract: For many years, the extreme environment of the Antarctic Dry Valleys was thought to play host to just a few viable microorganisms. However, as Cary and colleagues explain, recent work has led to the identification of a complex community structure that is able to survive in one of the coldest and driest places on Earth. The arid soils of the Antarctic Dry Valleys constitute some of the oldest, coldest, driest and most oligotrophic soils on Earth. Early studies suggested that the Dry Valley soils contained, at best, very low levels of viable microbiota. However, recent applications of molecular methods have revealed a dramatically contrasting picture — a very wide diversity of microbial taxa, many of which are uncultured and taxonomically unique, and a community that seems to be structured solely by abiotic processes. Here we review our understanding of these extreme Antarctic terrestrial microbial communities, with particular emphasis on the factors that are involved in their development, distribution and maintenance in these cold desert environments.

Designed biomaterials to mimic the mechanical properties of muscles

Abstract: The passive elasticity of muscle is largely governed by the I-band part of the giant muscle protein titin, a complex molecular spring composed of a series of individually folded immunoglobulin-like domains as well as largely unstructured unique sequences. These mechanical elements have distinct mechanical properties, and when combined, they provide the desired passive elastic properties of muscle, which are a unique combination of strength, extensibility and resilience. Single-molecule atomic force microscopy (AFM) studies demonstrated that the macroscopic behaviour of titin in intact myofibrils can be reconstituted by combining the mechanical properties of these mechanical elements measured at the single-molecule level. Here we report artificial elastomeric proteins that mimic the molecular architecture of titin through the combination of well-characterized protein domains GB1 and resilin. We show that these artificial elastomeric proteins can be photochemically crosslinked and cast into solid biomaterials. These biomaterials behave as rubber-like materials showing high resilience at low strain and as shock-absorber-like materials at high strain by effectively dissipating energy. These properties are comparable to the passive elastic properties of muscles within the physiological range of sarcomere length and so these materials represent a new muscle-mimetic biomaterial. The mechanical properties of these biomaterials can be fine-tuned by adjusting the composition of the elastomeric proteins, providing the opportunity to develop biomaterials that are mimetic of different types of muscles. We anticipate that these biomaterials will find applications in tissue engineering as scaffold and matrix for artificial muscles.

Ecological and socio-economic impacts of invasive water hyacinth (Eichhornia crassipes): a review.

Abstract: Summary 1. Water hyacinth (Eichhornia crassipes) is one of the world’s most invasive aquatic plants and is known to cause significant ecological and socio-economic effects. 2. Water hyacinth can alter water clarity and decrease phytoplankton production, dissolved oxygen, nitrogen, phosphorous, heavy metals and concentrations of other contaminants. 3. The effects of water hyacinth on ecological communities appear to be largely nonlinear. Abundance and diversity of aquatic invertebrates generally increase in response to increased habitat heterogeneity and structural complexity provided by water hyacinth but decrease due to decreased phytoplankton (food) availability. 4. Effects of water hyacinth on fish are largely dependent on original community composition and food-web structure. A more diverse and abundant epiphytic invertebrate community may increase fish abundance and diversity, but a decrease in phytoplankton may decrease dissolved oxygen concentrations and planktivorous fish abundance, subsequently affecting higher trophic levels. 5. Little is known about the effects of water hyacinth on waterbird communities; however, increases in macroinvertebrate and fish abundance and diversity suggest a potentially positive interaction with waterbirds when water hyacinth is at moderate density. 6. The socio-economic effects of water hyacinth are dependent on the extent of the invasion, the uses of the impacted waterbody, control methods and the response to control efforts. Ecosystem-level research programmes that simultaneously monitor the effects of water hyacinth on multiple trophic-levels are needed to further our understanding of invasive species.

Hot Spots and Hot Moments in Riparian Zones: Potential for Improved Water Quality Management

Abstract: Biogeochemical and hydrological processes in riparian zones regulate contaminant movement to receiving waters and often mitigate the impact of upland sources of contaminants on water quality. These heterogeneous processes have recently been conceptualized as ''hot spots and moments'' of retention, degrada- tion, or production. Nevertheless, studies investigating the importance of hot phenomena (spots and moments) in riparian zones have thus far largely focused on nitrogen (N) despite compelling evidence that a variety of elements, chemicals, and particulate contaminant cycles are subject to the influence of both biogeochemical and transport hot spots and moments. In addition to N, this review summarizes current knowledge for phosphorus, organic matter, pesticides, and mercury across riparian zones, identifies variables controlling the occurrence and magnitude of hot phenomena in riparian zones for these contaminants, and discusses the implications for riparian zone management of recognizing the importance of hot phenomena in annual solute budgets at the watershed scale. Examples are presented to show that biogeochemical process-driven hot spots and moments occur along the stream ⁄ riparian zone ⁄ upland interface for a wide variety of constituents. A basic understanding of the possible co-occurrence of hot spots and moments for a variety of contaminants in riparian systems will increase our understanding of the influence of riparian zones on water quality and guide management strategies to enhance nutrient or pollutant removal at the landscape scale. (KEY TERMS: riparian zones; hot spots; hot moments; nitrate; phosphorus; carbon; pesticides; mercury; transport and fate; watershed management; contaminant removal.)

Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics

Abstract: Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.

Frequency and Location of Head Impact Exposures in Individual Collegiate Football Players

Abstract: Context: Measuring head impact exposure is a critical step toward understanding the mechanism and prevention of sport-related mild traumatic brain (concussion) injury, as well as the possi...

Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome

Abstract: Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

Abstract: A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Surface-enhanced Raman spectroscopy (SERS) for environmental analyses

Abstract: The advent of lasers created a revolution in spectroscopic techniques starting in the 1970s. Raman analysis is a fine example, as intense laser light is required to generate detectable signals. Ram...

PowerPack: Energy Profiling and Analysis of High-Performance Systems and Applications

Abstract: Energy efficiency is a major concern in modern high-performance computing system design. In the past few years, there has been mounting evidence that power usage limits system scale and computing density, and thus, ultimately system performance. However, despite the impact of power and energy on the computer systems community, few studies provide insight to where and how power is consumed on high-performance systems and applications. In previous work, we designed a framework called PowerPack that was the first tool to isolate the power consumption of devices including disks, memory, NICs, and processors in a high-performance cluster and correlate these measurements to application functions. In this work, we extend our framework to support systems with multicore, multiprocessor-based nodes, and then provide in-depth analyses of the energy consumption of parallel applications on clusters of these systems. These analyses include the impacts of chip multiprocessing on power and energy efficiency, and its interaction with application executions. In addition, we use PowerPack to study the power dynamics and energy efficiencies of dynamic voltage and frequency scaling (DVFS) techniques on clusters. Our experiments reveal conclusively how intelligent DVFS scheduling can enhance system energy efficiency while maintaining performance.