bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of a High Temperature Chamber FED by a Plasma Torch for Thermal Removal of Tars
Authors: Fourcault Alice , Marias Fre´de´ric , Michon Ulysse
Published: August 2009

Biomass is one of the most important sources of renewable energy. One aim of Biomass gasification is to convert a solid feedstock into a valuable syngas for electricity or liquid fuel production. Actual industrial auto-thermal gasification processes achieve a production of syngas mainly polluted by products such as dust, nitrogen oxides, sulfur dioxide and tars. Tars remain, one of the main drawbacks in using the gasification process since they are capable of condensing at low temperature. This could lead to fouling, corrosion, attrition and abrasion of downstream devices such as gas turbines or engines. Tars are often removed from the syngas, decreasing the internal energy of the syngas itself. These tars are heavy aromatic hydrocarbons whose treatment remains difficult by thermal, catalytic or even physical methods. They can condense or polymerize into more complex structures, and the mechanisms responsible for their degradation are not completely identified and understood. Turboplasma© is a thermal process, proposed by Europlasma. The main principle of operation relies on the use of thermal plasma for the cracking of tars inside a syngas produced in an auto-thermal gasification step. Basically, it consists of a degradation chamber where the syngas is heated by a plasma torch. The plasma plume provides a high temperature gas (around 5000K) to the system and enables heating of the incoming stream (above 1300K) and also generates high temperature zones (above 1600 K) inside the device. Due to both high temperature and long residence times of the syngas in the vessel, cracking of the tars occurs. Finally, the species released are mainly CO and H2, leading to an increase in the Lower Heating Value of the syngas. The work presented here describes the design of a high temperature gasification system assisted by thermal plasma. It was performed using a CFD computation implemented with a full chemical model for the thermal degradation of tars. The objectives were to understand the aerodynamic behavior of the vessel and to propose enhancement in its design. We present here some results of this study.
A Look at the Southern California Conversion Technology Project
Authors: Skye Coby J.
Published: August 2009

This presentation provides an overview of conversion technologies, their potential benefits and applicability to solid waste management, and the efforts to develop conversion facilities around the country and specifically, California, including Los Angeles County’s model for development. The Southern California Demonstration Project spearheaded by Los Angeles County is a unique project that proposes to develop up to four conversion technology demonstration facilities throughout Southern California, potentially the first of their kind anywhere in the U.S. These facilities will be collocated with material recovery facilities and will be designed specifically to process municipal solid waste residuals.
Handling Oahu’s Waste Disposal
Authors: Gesell Greg , Langham Stephen
Published: August 2009

Oahu has special needs and requirements when it comes to dealing with solid waste on the island. The City and County of Honolulu has successfully addressed this problem in the past and is working on solutions for the future. Five percent of the island’s electrical power has been generated reliably from the 2000 tons per day of waste processed by their H-POWER Waste-to-Energy Facility. The facility has been processing waste for nearly twenty years and the volume of refuse going to the landfill is reduced by 90 percent. Honolulu is considering the best solutions for the island’s waste for the coming years. Waste-to-energy works in partnership with recycling to reduce the island’s increasing waste volumes. Recycling programs are in place and additional recycling measures are being considered. Landfill space is limited and questions exist regarding the ongoing use of the existing landfill and what will happen when it is closed. In an island setting, some alternatives available to other areas such as long haul to distant landfills are not available to bridge solid waste issues. Therefore practical solutions must be found and implemented in a timely manner. A number of initiatives and plans are in development. Measures are underway to prepare the H-POWER facility for future emission requirements and operation for the next twenty years. Steps have been taken toward expansion of the existing facility. Permitting and negotiations with agencies and utilities are under way. This paper will explore and expand upon these issues showing how they are interrelated to one another.
Lessons Learned From the 1970s Experiments in Solid Waste Conversion Technologies
Authors: Stoller Paul J. , Niessen Walter R.
Published: August 2009

Countless proposals for conversion technologies applied to municipal solid waste (MSW), such as gasification, many of which include mechanical processing of the MSW prior to the thermal conversion steps, have generated significant interest and press over the past few years. Many community groups and local officials are being pressured by developers to view these technologies as better and more politically acceptable alternatives to mass burn waste-to-energy facilities. From a historical perspective, most (but not all) of the basic technologies being promoted today are not new, but are variations of technologies that were evaluated and tested during the 1970s for use in processing and converting MSW. This paper presents overviews and several case studies of the MSW conversion technologies that were developed and tested during the 1970s including MSW processing and gasification technologies, and sets forth: • Lessons learned from those experiments. • Based upon the lessons learned, recommended rules of engagement for those contemplating evaluation or use of a processing and/or conversion technology. • A practical application of the above lessons learned and rules of engagement to the plasma arc gasification technology currently being promoted by a number of developers. The contents of this paper should be carefully considered by anyone contemplating the merits and feasibility of any MSW processing and/or conversion technology being promoted today or in the future.
Gasification of MSW in South Korea
Authors: d’Ailly Jan , Kim Sung Chun
Published: August 2009

Over the past 15 years, South Korea has been actively pursuing a sustainable waste management strategy, which includes the thermal treatment of non-recyclable waste. Over 18,000 tons/day of waste are thermally treated in South Korea in over 40 plants. Since municipalities are not allowed to export waste outside of their respective jurisdictions, plants range in size from 25 ton/day to over 500 tons/day. There are currently 7 plants on 6 sites using gasification technology in South Korea, with the first plant in operation since 2001. The purpose of this paper is to describe how the downdraft gasification technology works, integration of the technology into a complete energy from waste facility, operating history, availability, emission levels and lessons learned. Synopsis of the technology: Curbside Municipal Solid Waste (MSW) is rough shredded and fed into the primary chamber through an air lock. The gasification occurs in the low temperature negative pressurized primary chamber where the MSW goes through drying, pyrolysis and gasification stages. The resulting syn-gas is filtered through the char bed into a secondary chamber where combustion takes place, producing a hot inert flue gas. A Heat Recovery Steam Generator (boiler) is used to recover the thermal energy from the flue gas. The char at the bottom of the primary chamber is oxidized, creating the heat for the gasification process. The air pollution control system is located after the Boiler and consists of carbon and lime injection followed by a bag filter. Operating history, availability and emission levels are presented.
SYNCOM-Plus: An Optimized Residue Treatment Process
Authors: Koralewska Ralf
Published: August 2009

In a large-scale pilot plant, studies on wet-mechanical treatment of bottom ash using the SYNCOM-Plus process were carried out by MARTIN GmbH in the SYNCOM waste-to-energy plant in Arnoldstein, Austria (approx. 11000 kg/h waste throughput). Granulate of > 2 mm and fine fraction of < 5 mm were produced by dry screening, washing and wet screening. Additionally, sludge was separated from the wash water. The fine fraction and sludge as well as the boiler ash were recirculated into the furnace. In conclusion, the SYNCOM-Plus process meets all requirements which need to be complied with in an optimized and effluent-free commercial residue treatment process for the recovery of industrial products. This paper documents successful continuous operation of the SYNCOM-Plus process in direct connection with bottom ash discharge as well as the effects on combustion, flue gas composition and residue qualities.
Virtual Prototyping by Using Holographic Displays: But What About Large Data Problems?
Authors: Opiyo Eliab Z. , Horva´th Imre , Kooijman Adrie
Published: August 2009

The work reported in this paper is part of the research that explores the viability of using holographic displays as part of virtual prototyping package of supporting tools. The focus is principally on handling of large data problems, which are among the common problems of most volumetric displays. The paper first reviews related works. After describing the large data related problems that designers might face in using holographic displays and identifying the conceptual design tasks that could be supported by using these displays, a concept for handling the large data problems through elimination of irrelevant image details is introduced. An application example showing how some elements of the proposed concept function in the real world is also presented. The main contributions of this work can be summarized as follows: (i) we have demonstrated that through simplifications, visual abstractions, data clustering or other generalization methods, less complicated holographic images that require less computing resources but yet suitable 3D for some conceptual design tasks or virtual prototyping can be created; and (ii) we have defined the steps of a scalable high-level algorithm, that can be expanded or tuned to suit visualization demands in various conceptual design tasks. In the ongoing work, we aim to develop built in procedures within the proposed algorithm that would reduce the amount of image details without significantly affecting the appropriateness of the overall virtual model. And because of the reduced image details, it would be possible to display less complicated 3D virtual objects and in this way computing resources could be saved.
From Virtual Reality to Tangible Virtuality: An Inventory of the Technological Challenges
Authors: Horva´th Imre , Rusa´k Zolta´n , de Smit Bram , Kooijman Adrie , Opiyo Eliab Z.
Published: August 2009

The paradigm of tangible virtuality (TV) has grown out from the paradigm of virtual reality (VR), leaving some key concepts of projective and immersive VR behind, but introducing many new ones. The ultimate objective of TV is to intuitively generate air-borne synthetic objects (SOs), share them between remote work environments in real time, simulate their physical behavior, and enable a physics-obeying interaction of humans with SOs. The major challenges for the implementation of TV originate in the need for multi-sensory integral rendering of SOs and un-instrumented generation of high fidelity sensations. These scientific and technological challenges have a strong influence on the current advancement of TV. Actually, implementation of fully featured TV environments is still in its infancy. The goal of this paper is to analyze the main implementation concepts and to make an inventory of the technological challenges and opportunities. Six major issues have been identified: (i) use of natural interaction modalities to express SOs, (ii) multi-aspect (e.g., tactile, haptic and auditory) volumetric rendering and sensation of air-borne SOs, (iii) simulation of physical behavior of interacting SOs, and (iv) manipulative human interaction with SOs. The paper investigates the opportunities of a short-term implementation based on the current technologies and of a near-future implementation based on emerging and anticipated technologies. The conclusion is that current technologies allow only a limited implementation of SOs and a low fidelity multi-sensorial experience. For a full scale implementation, radically new technologies and implementation concepts are needed, but it also requires a goal-driven extension of the existing scientific knowledge.
Affordable Interaction Systems for Design Review on a Virtual Room
Authors: Pignatel Alice , Brevi Fausto
Published: August 2009

In the design field, digital models are used for evaluation purposes during design reviews that take place into special rooms equipped with dedicated software and large display. The chief designer leads the review, interacting with his audience and staying near the screen. Therefore, the workstation used in the virtual room is, generally, very distant to the display, so that an additional operator is needed to manage the model. Moreover, the input system generally used is still based on “traditional” devices such as mouse and keyboard. Thus, the review process becomes slow and inefficient. This research aims to investigate different interaction techniques, based on existing devices and supported by position sensors, to make the design review more effective. The first case study is based on graphic interface that was implemented on a device with independent storage and processing resources (PDA). The second interaction methodology, in contrast, is built for maximising ease of use by reducing features and device complexity and it is based on a game console controller. Finally, the last case study applies direct human interaction and it is based on a glove-like device.
Isis: Patient Data Visualization and Surgical Planning in an Interactive Virtual Environment
Authors: Foo Jung Leng , Lobe Thom , Winer Eliot
Published: August 2009

As medical scanning technology continues to accommodate the need for higher quality medical imaging, there is a continuing need for additional research in efficient ways of extracting crucial information from these vast amounts of data. The visualization software, Isis, has been developed to view and manipulate digital medical images in an immersive environment for surgical planning. Isis is designed to display any DICOM/PACS compatible three-dimensional image data for visualization and interaction in an immersive environment. Pseudo-coloring can be applied in real time, with multiple interactive clipping planes to slice into the volume for an interior view, and the windowing feature controls the tissue density ranges to display. Features such as virtual trocars placement, tumor inspection, and an endoscopic view provides surgeons with essential tools for surgical planning. A wireless gamepad controller and an intuitive menu interface allow the user to interact with the software. By wearing a pair of stereo glasses, the surgeon is immersed within the model, providing a sense of realism as if the surgeon is “inside” the patient.
Virtual Reality Interface Design for Multi-Modal Teleoperation
Authors: Kadavasal Muthukkumar S. , Oliver James H.
Published: August 2009

A multi modal teleoperation interface is introduced featuring an integrated virtual reality (VR) based simulation augmented by sensors and image processing capabilities on-board the remotely operated vehicle. The proposed virtual reality interface fuses an existing VR model with live video feed and prediction states, thereby creating a multi modal control interface. Virtual reality addresses the typical limitations of video-based teleoperation caused by signal lag and limited field of view. The 3D environment in VR along with visual cues generated from real time sensor data allows the operator to navigate in a continuous fashion. The vehicle incorporates an on-board computer and a stereo vision system to facilitate obstacle detection. A vehicle adaptation system with a priori risk maps and real state tracking system enables temporary autonomous operation of the vehicle for local navigation around obstacles and automatic re-establishment of the vehicle’s teleoperated state. Finally, the system provides real time update of the virtual environment based on anomalies encountered by the vehicle. The VR interface architecture is discussed and implementation results are presented. The VR based multi modal teleoperation interface is expected to be more adaptable and intuitive when compared to other interfaces.
Development Methods and a Scenegraph Animation API for Cluster Driven Immersive Applications
Authors: Newendorp Brandon , Noon Christian , Chan Chiu-Shui , Winer Eliot , Oliver Jim
Published: August 2009

This paper presents a scenegraph animation application programming interface (API), known as the Animation Engine, which was constructed for software developers to easily perform smooth transitions and manipulations to scenegraph nodes. A developer can use one line of code to enter the property, end state and number of frames to describe the animation, then the Animation Engine handles the rest in the background. The goal of the Animation Engine is to provide a simple API that integrates into existing applications with minimal effort. Additionally, techniques to improve virtual reality (VR) application performance on a large computer cluster are presented. These techniques include maintaining high frame rates with 4096 × 4096 pixel textures, eliminating extraneous network traffic and reducing long model loading time. To demonstrate the Animation Engine and the development techniques, an application known as the Virtual Universe was created. The Virtual Universe, designed to run in a six walled CAVE, allows users to freely explore a set of space themed environments. The architecture and development techniques for writing a stable immersive VR application on a large computer cluster, in addition to the creation of the Animation Engine, is presented in this paper.
An Augmented Reality Tool for Conceptual Design
Authors: Koehring Andrew , Winer Eliot
Published: August 2009

Currently, there are many engineering software packages targeted toward high fidelity modeling. Computer aided design (CAD) tools are one example of this. The need for increasingly accurate models has caused this class of software to become even more detailed and comprehensive. Modeling a single design can be a time intensive process; so much so, that most modeling is done by specifically trained CAD professionals, not designers. These advancements in CAD software are at odds with the goal of conceptual design, which is to generate and evaluate as many concepts as possible in a limited amount of time. Within the engineering design process, changes made in preliminary stages have much greater impact for significantly less cost. Unfortunately, few software packages exist that are tailored for use so early in a product’s design cycle. This paper presents an application developed specifically for conceptual design. Through the use of an augmented reality environment, designers are able to quickly and intuitively assemble concepts. Potential designs can be easily manipulated in three dimensions, enhancing the ability to communicate the idea to others.
Virtual Assembly Environment Modelling
Authors: Zaldivar-Colado Ulises , Garbaya Samir
Published: August 2009

In this paper, we present the virtual environment of assembly sequence generation of a product at the design stage. The interaction technique developed for the manipulation of virtual parts includes visual and haptic feedback limited to force sensation in the fingertips and weight and inertia parts sensation. At this stage of development, the parts and subassemblies have kinematics behaviour in the virtual scene. We present some guidelines for modeling a generic virtual environment for performing assembly tasks. Virtual parts modeling and connections modeling is based on characteristics of real parts and connections. The mating phase of assembly is based on the Snap-Fitting technique, which is improved by the addition of vectors in the symmetry axis of virtual parts. An XML modeling allows the environment to be generic and supporting different products.
An Approach for Studying the Effect of High-Level Spatial Properties of 3D Audio in Interactive Systems
Authors: Ortega-Gonza´lez Vladimir , Garbaya Samir , Merienne Fre´de´ric
Published: August 2009

In this paper we briefly describe an approach for understanding the psychoacoustic and perceptual effects of what we have identified as the high-level spatial properties of 3D audio. The necessity of this study is firstly presented within the context of interactive applications such as Virtual Reality and Human Computer Interfaces. As a result of the bibliographic research in the field we identified the main potential functions of 3D audio spatial stimulation in interactive applications beyond traditional sound spatialization. In the same sense, a classification of the high-level aspects involved in spatial audio stimulation is proposed and explained. Immediately, the case of study, the experimental methodology and the framework are described. Finally, we present the expected results as well as their usefulness within the context of a larger project.
Pd/Ru/Au Ohmic contacts to InAlSb/InAs heterostructures for high electron mobility transistors
Authors: Dormaier R. , Zhang Q. , Chou Y.-C. , Lange M. D. , Yang J. M. , Oki A. , Mohney S. E.
Published: August 2009

The authors describe a Pd/Ru/Au Ohmic contact with enhanced thermal stability over the more commonly used Pd/Pt/Au Ohmic contact for InAlSb/InAs high electron mobility transistors. Transmission electron microscopy shows that reaction between Pd and the semiconductor begins in samples even before they are annealed. Decreases in contact resistance are correlated with increasing reaction between Pd and the semiconductor for annealing and aging at 175–225 °C for 3 h or 1 week. Small voids form in severely aged samples but do not increase the contact resistance. The Ru diffusion barrier is never observed to react with any other materials in either the contact or the semiconductor, and Au remains isolated from the Pd-bearing reaction products and semiconductor.
Introducing Modern Science into Schools
Authors: Willingale-Theune Julia , Manaia Alexandra , Gebhardt Philipp , De Lorenzi Rossana , Haury Matthias
Published: August 2009

A multinational research institution provides advanced training to help high-school teachers bring inquiry into the classroom.
Comment on “Floral Iridescence, Produced by Diffractive Optics, Acts As a Cue for Animal Pollinators”
Authors: Morehouse Nathan I. , Rutowski Ronald L.
Published: August 2009

Whitney
et al
. (Reports, 2 January 2009, p. 130) investigated the mechanism of iridescence in hibiscus and tulip flowers and suggested that bumblebees are able to use this iridescence as a pollination cue. However, their study failed to isolate iridescence from other coincident visual cues, leaving open questions regarding the importance of iridescent stimuli in foraging-based associative learning in bumblebees.
Gene-for-Gene Resistance in
Striga
-Cowpea Associations
Authors: Li Jianxiong , Timko Michael P.
Published: August 2009

A gene thought to defend plants against infectious bacterial pathogens also supplies defense against a parasitic plant.
The E3 Ligase TRAF6 Regulates Akt Ubiquitination and Activation
Authors: Yang Wei-Lei , Wang Jing , Chan Chia-Hsin , Lee Szu-Wei , Campos Alejandro D. , Lamothe Betty , Hur Lana , Grabiner Brian C. , Lin Xin , Darnay Bryant G. , Lin Hui-Kuan
Published: August 2009

Regulating Akt

The protein kinase Akt is activated in response to receptor-activated generation of the signaling second messenger phosphatidylinositol 3,4,5-trisphosphate and has roles in regulation of diverse processes from metabolism and cell survival to transcription and tumorigenesis.

Yang
et al.

(p.
1134
; see the Perspective by

Restuccia and Hemmings

) report a previously unrecognized mode of regulation of Akt: covalent modification of Akt by linkage to lysine 63 of ubiquitin molecules. Such ubiquitination of Akt promotes localization to the cell membrane and consequent activation in cells stimulated with growth factors. TRAF6 (TNF receptor–associated factor 6) was implicated as the E3 ubiquitin ligase that mediates ubiquitination of Akt. Ubiquitination of Akt may influence its role in cancer cells: A mutant form of Akt associated with human cancer showed increased ubiquitination, and depletion of TRAF6 decreased tumorigenicity of a prostate cancer cell line in a mouse cancer model.
Five “Easy” Questions
Science and Decisions
Advancing Risk Assessment

by the National Research Council. Committee on Improving Risk Analysis Approaches Used by the U.S. EPA

National Academies Press, Washington, DC, 2009. 421 pp. Paper, $54.95. ISBN 9780309120463. www.nap.edu/catalog.php?record_id=12209
Authors: Brewer Garry D.
Published: August 2009

This NRC report suggests approaches to overcoming obstacles to effective risk assessment such as lengthy delays in evaluating complex problems, substantial uncertainties that arise from the lack of data, the backlog of chemicals that have not been evaluated, and the continuing development of new materials requiring study.
On the Origin and Spread of an Adaptive Allele in Deer Mice
Authors: Linnen Catherine R. , Kingsley Evan P. , Jensen Jeffrey D. , Hoekstra Hopi E.
Published: August 2009

Adapting Coat Color

Simple phenotypic changes can often be the target of selection—for example, variations in coat color that provide protection against detection by predators.

Linnen
et al.

(p.
1095
) explore the underlying molecular mechanisms behind the production of pale deer mice living on the light-colored Nebraska Sand Hills. The mice that live on the sand are significantly lighter in color than conspecifics living nearby on darker soils. This lighter color was found to be due to de novo changes at the Agouti coat color locus. Thus, rapid adaptive change does not always rely on preexisting genetic variation.
Antarctica's Orbital Beat
Authors: Huybers Peter
Published: August 2009

What do Antarctic ice core records really record?
The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy
Authors: Gross Leo , Mohn Fabian , Moll Nikolaj , Liljeroth Peter , Meyer Gerhard
Published: August 2009

Atomic Imaging Within Adsorbed Molecules

Scanning tunneling microscopy provides atomic resolution images of surfaces and adsorbed atoms, but imaging atoms within an organic molecule adsorbed on a surface is difficult because contrast is lacking in the states that determine the tunneling current. Atomic force microscopy should be able to resolve atoms through changes in short-range chemical forces, but resolution is lost if the scanning tip undergoes modifications or if it moves the molecule.

Gross
et al.

(p.
1110
) show that in situ functionalization of the tip—for example, with CO—can dramatically improve the resolution of images of pentacene molecules adsorbed on conducting surfaces, like copper, and nonconductors, like NaCl.
Spectroscopic Fingerprint of Phase-Incoherent Superconductivity in the Underdoped Bi
2
Sr
2
CaCu
2
O
8+δ
Authors: Lee Jhinhwan , Fujita K. , Schmidt A. R. , Kim Chung Koo , Eisaki H. , Uchida S. , Davis J. C.
Published: August 2009

Mind the Pseudogap

Below the transition temperature, an energy gap opens in superconductors, which effectively protects the superconducting phase. Above the transition temperature, the gap closes, creating excitations and a loss of superconductivity. In the high-temperature superconducting cuprates, however, the gap persists above the transition temperature. Understanding the electronic structure of this pseudogap region is important in understanding the mechanism of superconductivity in the cuprates.

Lee
et al.

(p.
1099
; see the Perspective by

Norman

) use high-resolution, temperature-dependent scanning tunneling microscopy to reveal that the pseudogap regime is an incoherent (or phase-disordered) d-wave superconductor.
Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora
Authors: Sommer Morten O. A. , Dantas Gautam , Church George M.
Published: August 2009

Hidden Pockets of Resistance

Groups of bacteria indulge in gene swapping at frequencies correlated with prevailing selection pressures and phylogenetic relatedness. When assaulted by antibiotics, antibiotic resistance genes become favored currency for exchange among bacteria. During sequencing of human gut microflora,

Sommer
et al.

(p.
1128
) found a very large reservoir of distinct genes that, when put into
Escherichia coli
, conferred resistance to a wide range of drugs. By contrast, analysis of the culturable aerobic gut microbiome, which constitutes a tiny fraction of the entire gut flora, revealed resistance genes highly similar to those harbored by human pathogens. Although there is a risk of novel modes of antibiotic resistance emerging from this reservoir, because they are evolutionarily distant, gene transfer between pathogens and the poorly known majority of the microbiome might actually be quite restricted.
Chasing Arcs in Cuprate Superconductors
Authors: Norman Michael R.
Published: August 2009

Scanning tunneling microscopy studies of cuprate superconductors clarify the origin of their unusual electronic structure.
Using Taste to Clear the Air(ways)
Authors: Kinnamon Sue C. , Reynolds Susan D.
Published: August 2009

Cilia of epithelial cells in the human airway increase their beating frequency in response to compounds that are sensed through receptors for bitter compounds.
Blocking Akt-ivity
Authors: Restuccia David F. , Hemmings Brian A.
Published: August 2009

Inhibiting the addition of ubiquitin molecules to the enzyme AKT could improve the effects of anticancer drugs.
The Large Hadron Collider Redux: Hoping for a Long, Hard Slog
Authors: Cho Adrian
Published: August 2009

As they prepare to restart the Large Hadron Collider, accelerator physicists are confident that, instead of suffering a second catastrophic breakdown, the world's largest atom smasher will perform to the standards set by its predecessors—and give them lots of smaller headaches to struggle with.
emm1/Sequence Type 28 Strains of Group A Streptococci That ExpresscovRat Early Stationary Phase Are Associated with Increased Growth and Earlier SpeB Secretion
Authors: Chiang-Ni Chuan , Zheng Po-Xing , Ho Yueh-Ren , Wu Hsiu-Mei , Chuang Woei-Jer , Lin Yee-Shin , Lin Ming-T. , Liu Ching-Chuan , Wu Jiunn-Jong
Published: August 2009

Streptococcus pyogenes(group A streptococcus [GAS]) is a versatile human pathogen, andemm1/sequence type 28 (ST28) is the most frequently isolated type from GAS infections. Theemm1/ST28 strain is associated with necrotizing fasciitis and streptococcal toxic shock syndrome. Growth-phase regulation is one of the important regulatory mechanisms in GAS, which controls gene expression at restricted phases of growth. CovRS, a two-component regulatory system, is considered the regulator of streptococcal pyrogenic exotoxin B (SpeB) and is thought to be activated in the exponential phase of growth. In the present study, Northern hybridization analysis showed that 52% of the analyzed GAS strains expressedcovRat the exponential phase, but 48% of the strains expressedcovRat the early stationary phase of growth. Strains transcribingcovRat the early stationary phase showed better growth and earlier SpeB expression than the other group of strains. Multilocus sequence typing and pulsed-field gel electrophoresis analysis showed onlyemm1/ST28 strains (which comprise a clonal cluster) were expressingcovRat the early stationary phase of growth, indicating thatemm1/ST28 strains have special characteristics which may be related to their worldwide distribution.
International Clones ofKlebsiella pneumoniaeandEscherichia coliwith Extended-Spectrum β-Lactamases in a Czech Hospital
Authors: Hrabák Jaroslav , Empel Joanna , Bergerová Tamara , Fajfrlík Karel , Urbášková Pavla , Kern-Zdanowicz Izabela , Hryniewicz Waleria , Gniadkowski Marek
Published: August 2009

A 2-month survey of extended-spectrum β-lactamase (ESBL) producers was performed in a Czech hospital.Klebsiella pneumoniaeproduced SHV-2, -5, or -12,Escherichia coliproduced CTX-M-9 or -15, and other species produced TEM-92 or -132. AllK. pneumoniaeandE. coliisolates belonged to sequence types (STs) or clonal complexes (CCs) spread across the world (K. pneumoniaeclonal complex 11 [CC11], CC14, and sequence type 101 [ST101] andE. coliCC31, CC73, CC131, and CC405) and carried various plasmids (mainly with A/C- and FII-type replicons).
In Vitro Activity of Seven Systemically Active Antifungal Agents against a Large Global Collection of RareCandidaSpecies as Determined by CLSI Broth Microdilution Methods
Authors: Diekema D. J. , Messer S. A. , Boyken L. B. , Hollis R. J. , Kroeger J. , Tendolkar S. , Pfaller M. A.
Published: August 2009

FiveCandidaspecies (C. albicans,C. glabrata,C. tropicalis,C. parapsilosis, andC. krusei) account for over 95% of invasive candidiasis cases. Some less commonCandidaspecies have emerged as causes of nosocomial candidiasis, but there is little information about their in vitro susceptibilities to antifungals. We determined the in vitro activities of fluconazole, voriconazole, posaconazole, amphotericin B, anidulafungin, caspofungin, and micafungin against invasive, unique patient isolates ofCandidacollected from 100 centers worldwide between January 2001 and December 2007. Antifungal susceptibility testing was performed by the CLSI M27-A3 method. CLSI breakpoints for susceptibility were used for fluconazole, voriconazole, anidulafungin, caspofungin, and micafungin, while a provisional susceptibility breakpoint of ≤1 μg/ml was used for amphotericin and posaconazole. Of 14,007Candidaisolates tested, 658 (4.7%) were among the less common species. Against all 658 isolates combined, the activity of each agent, expressed as the MIC50/MIC90ratio (and the percentage of susceptible isolates) was as follows: fluconazole, 1/4 (94.8%); voriconazole, 0.03/0.12 (98.6%); posaconazole, 0.12/0.5 (95.9%); amphotericin, 0.5/2 (88.3%); anidulafungin, 0.5/2 (97.4%); caspofungin, 0.12/0.5 (98.0%); and micafungin, 0.25/1 (99.2%). Among the isolates not susceptible to one or more of the echinocandins, most (68%) wereC. guilliermondii. All isolates of the less common species within theC. parapsilosiscomplex (C. orthopsilosisandC. metapsilosis) were susceptible to voriconazole, posaconazole, anidulafungin, caspofungin, and micafungin. Over 95% of clinical isolates of the rareCandidaspecies were susceptible to the available antifungals. However, activity did vary by drug-species combination, with some species (e.g.,C. rugosaandC. guilliermondii) demonstrating reduced susceptibilities to commonly used agents such as fluconazole and echinocandins.
Identification of Amino Acid Residues Critical for the Anti-Interferon Activity of the Nucleoprotein of the Prototypic Arenavirus Lymphocytic Choriomeningitis Virus
Authors: Martínez-Sobrido Luis , Emonet Sébastien , Giannakas Panagiotis , Cubitt Beatrice , García-Sastre Adolfo , de la Torre Juan C.
Published: August 2009

Lymphocytic choriomeningitis virus (LCVM) nucleoprotein (NP) counteracts the host type I interferon (IFN) response by inhibiting activation of the IFN regulatory factor 3 (IRF3). In this study, we have mapped the regions and specific amino acid residues within NP involved in its anti-IFN activity. We identified a region spanning residues 382 to 386 as playing a critical role in the IFN-counteracting activity of NP. Alanine substitutions at several positions within this region resulted in NP mutants that lacked the IFN-counteracting activity but retained their functions in virus RNA synthesis and assembly of infectious particles. We used reverse genetics to rescue a recombinant LCMV strain carrying mutation D382A in its NP [rLCMV/NP*(D382A)]. Compared to wild-type (WT) LCMV, rLCMV/NP*(D382A) exhibited a higher level of attenuation in IFN-competent than IFN-deficient cells. In addition, A549 cells infected with rLCMV/NP*(D382A), but not with WT LCMV, produced IFN and failed to rescue replication of the IFN-sensitive Newcastle disease virus.
Random Mutagenesis Defines a Domain of Theiler's Virus Leader Protein That Is Essential for Antagonism of Nucleocytoplasmic Trafficking and Cytokine Gene Expression
Authors: Ricour Céline , Borghese Fabian , Sorgeloos Frédéric , Hato Stanleyson V. , van Kuppeveld Frank J. M. , Michiels Thomas
Published: August 2009

The leader protein of cardioviruses, Theiler's murine encephalomyelitis virus (TMEV) and encephalomyocarditis virus (EMCV), is a multifunctional protein known to antagonize type I interferon expression and to interfere with nucleocytoplasmic trafficking of host proteins and mRNA. This protein plays an important role in the capacity of TMEV to establish persistent infection of the central nervous system. Mutant forms of the TMEV leader protein were generated by random mutagenesis and selected after retroviral transduction on the basis of the loss of the highly toxic nature of this protein. Selected mutations define a short C-terminal domain of the leader conserved in TMEV and Saffold virus but lacking in the EMCV leader and thus called the Theilo domain. Mutations in this domain had a dramatic impact on TMEV L protein activity. Like the zinc finger mutation, Theilo domain mutations affected all of the activities of the L protein tested: interferon gene transcription and IRF-3 dimerization antagonism, alteration of nucleocytoplasmic trafficking, nucleoporin 98 hyperphosphorylation, and viral persistence in vivo. This suggests that the Zn finger and the Theilo domain of the protein cooperate for function. Moreover, the fact that all of the activities tested were affected by these mutations suggests that the various leader protein functions are somehow coupled.
Functional Surfaces of the Hepatitis B Virus Capsid
Authors: Pairan Alexander , Bruss Volker
Published: August 2009

The hepatitis B virus (HBV) core protein (CP) forms the shell of an icosahedral nucleocapsid. In a former work, we identified 11 amino acid residues of CP exposed on the capsid surface by an alanine mutation scan as being important for capsid envelopment. We now introduced several other amino acids at six of these positions and found that almost all 27 tested point mutations at S17, K96, and I126 reproduced the phenotype of the alanine mutation (with only two exceptions): the formation of nucleocapsids and of the viral DNA genome was wild type, but capsid envelopment and virion release were strongly inhibited. This indicates that these side chains have a very specific function during nucleocapsid envelopment. We also identified several CP point mutations (e.g., F122V/S/Y and R127D/G) allowing the formation of capsids but preventing the packaging of pregenomic RNA. The envelopment of such mutant capsids was blocked. Apparently, these CP mutations hampered the recognition/packaging of the pregenome-P-protein complex by CP, a process which is still barely understood, and the mutant capsids devoid of HBV-specific nucleic acid did not express the capsid maturation signal required for envelopment.
High Levels of Chronic Immune Activation in the T-Cell Compartments of Patients Coinfected with Hepatitis C Virus and Human Immunodeficiency Virus Type 1 and on Highly Active Antiretroviral Therapy Are Reverted by Alpha Interferon and Ribavirin Treatment
Authors: Gonzalez Veronica D. , Falconer Karolin , Blom Kim G. , Reichard Olle , Mørn Birgitte , Laursen Alex Lund , Weis Nina , Alaeus Annette , Sandberg Johan K.
Published: August 2009

Chronic immune activation is a driver of human immunodeficiency virus type 1 (HIV-1) disease progression. Here, we describe that subjects with chronic hepatitis C virus (HCV)/HIV-1 coinfection display sharply elevated immune activation as determined by CD38 expression in T cells. This occurs, despite effective antiretroviral therapy, in both CD8 and CD4 T cells and is more pronounced than in the appropriate monoinfected control groups. Interestingly, the suppression of HCV by pegylated alpha interferon and ribavirin treatment reduces activation. High HCV loads and elevated levels of chronic immune activation may contribute to the high rates of viral disease progression observed in HCV/HIV-1-coinfected patients.
Mammalian Orthoreovirus Particles Induce and Are Recruited into Stress Granules at Early Times Postinfection
Authors: Qin Qingsong , Hastings Craig , Miller Cathy L.
Published: August 2009

Infection with many mammalian orthoreovirus (MRV) strains results in shutoff of host, but not viral, protein synthesis via protein kinase R (PKR) activation and phosphorylation of translation initiation factor eIF2α. Following inhibition of protein synthesis, cellular mRNAs localize to discrete structures in the cytoplasm called stress granules (SGs), where they are held in a translationally inactive state. We examined MRV-infected cells to characterize SG formation in response to MRV infection. We found that SGs formed at early times following infection (2 to 6 h postinfection) in a manner dependent on phosphorylation of eIF2α. MRV induced SG formation in all four eIF2α kinase knockout cell lines, suggesting that at least two kinases are involved in induction of SGs. Inhibitors of MRV disassembly prevented MRV-induced SG formation, indicating that viral uncoating is a required step for SG formation. Neither inactivation of MRV virions by UV light nor treatment of MRV-infected cells with the translational inhibitor puromycin prevented SG formation, suggesting that viral transcription and translation are not required for SG formation. Viral cores were found to colocalize with SGs; however, cores from UV-inactivated virions did not associate with SGs, suggesting that viral core particles are recruited into SGs in a process that requires the synthesis of viral mRNA. These results demonstrate that MRV particles induce SGs in a step following viral disassembly but preceding viral mRNA transcription and that core particles are themselves recruited to SGs, suggesting that the cellular stress response may play a role in the MRV replication cycle.
Ribose 2′-O Methylation of the Vesicular Stomatitis Virus mRNA Cap Precedes and Facilitates Subsequent Guanine-N-7 Methylation by the Large Polymerase Protein
Authors: Rahmeh Amal A. , Li Jianrong , Kranzusch Philip J. , Whelan Sean P. J.
Published: August 2009

During conventional mRNA cap formation, two separate methyltransferases sequentially modify the cap structure, first at the guanine-N-7 (G-N-7) position and subsequently at the ribose 2′-O position. For vesicular stomatitis virus (VSV), a prototype of the nonsegmented negative-strand RNA viruses, the two methylase activities share a binding site for the methyl donor
S
-adenosyl-
l
-methionine and are inhibited by individual amino acid substitutions within the C-terminal domain of the large (L) polymerase protein. This led to the suggestion that a single methylase domain functions for both 2′-O and G-N-7 methylations. Here we report a
trans
-methylation assay that recapitulates both ribose 2′-O and G-N-7 modifications by using purified recombinant L and in vitro-synthesized RNA. Using this assay, we demonstrate that VSV L typically modifies the 2′-O position of the cap prior to the G-N-7 position and that G-N-7 methylation is diminished by pre-2′-O methylation of the substrate RNA. Amino acid substitutions in the C terminus of L that prevent all cap methylation in recombinant VSV (rVSV) partially retain the ability to G-N-7 methylate a pre-2′-O-methylated RNA, therefore uncoupling the effect of substitutions in the C terminus of the L protein on the two methylations. In addition, we show that the 2′-O and G-N-7 methylase activities act specifically on RNA substrates that contain the conserved elements of a VSV mRNA start at the 5′ terminus. This study provides new mechanistic insights into the mRNA cap methylase activities of VSV L, demonstrates that 2′-O methylation precedes and facilitates subsequent G-N-7 methylation, and reveals an RNA sequence and length requirement for the two methylase activities. We propose a model of regulation of the activity of the C terminus of L protein in 2′-O and G-N-7 methylation of the cap structure.
2008 Macromolecular Science and Engineering Division Award Lecture — Conjugated polymers: From micro-electronics to genomics
Authors: Leclerc Mario , Najari Ahmed , Beaupré Serge
Published: August 2009

Conjugated polymers have received a lot of attention, since they combine the best features of metals or semiconductors with those of synthetic polymers. For instance, solar cells based on poly(2,7-carbazole) derivatives have revealed power-conversion efficiencies up to 6%. This class of materials could lead to printable and flexible photovoltaic devices. Moreover, water-soluble luminescent polythiophenes have allowed the specific, rapid, and ultra-sensitive detection of unlabelled DNA, RNA, or proteins. This new optical detection mechanism is based on electrostatic interactions between a cationic polythiophene derivative and negatively charged oligonucleotides. This method makes now possible the rapid assessment of the identity of single nucleotide polymorphisms (SNPs), genes, and pathogens without the need for nucleic acid amplification.
Morphology-dependent luminescence from ZnO nanostructures — An X-ray excited optical luminescence study at the Zn K-edge
Authors: Lobacheva Olga , Murphy Michael W. , Ko Jun Young Peter , Sham Tsun-Kong
Published: August 2009

ZnO nanostructures have been synthesized by thermal evaporation on Si substrates. It is found that the morphologies of the nanostructures are governed by growth conditions such as temperature, carrier-gas flow rate, and the nature of the substrate (with and without a catalyst). We report X-ray excited optical luminescence from ZnO nanostructures of distinctly different morphologies in the energy and time domain using excitation photon energies across the Zn K-edge. X-ray excited optical luminescence (XEOL) and X-ray absorption near edge structure (XANES) study has clearly shown the morphology dependence of the ZnO optical properties. A correlation of luminescence with morphology, size, and crystallinity emerges.
LATTICE GLUON PROPAGATOR IN THE LANDAU GAUGE: A STUDY USING ANISOTROPIC LATTICES
Authors: GONG M. , CHEN Y. , MENG G. , LIU C.
Published: August 2009

Lattice gluon propagators are studied using tadpole and Symanzik improved gauge action in Landau gauge. The study is performed using anisotropic lattices with asymmetric volumes. The Landau gauge dressing function for the gluon propagator measured on the lattice is fitted according to a leading power behavior: Z(q2) ≃ (q2)2κ with an exponent κ at small momenta. The gluon propagators are also fitted using other models and the results are compared. Our result is compatible with a finite gluon propagator at zero momentum in Landau gauge.
COSMOLOGICAL SOLUTION IN THE BRANE WITH GAUSS–BONNET GRAVITY IN THE BULK
Authors: CHAKRABORTY SUBENOY , BANDYOPADHYAY TANWI
Published: August 2009

The paper deals with Gauss–Bonnet gravity in five dimension without a Cosmological Constant and the coupling parameter is taken to be negative. Cosmological solutions are obtained for both bulk and the brane. The matter in the brane is chosen in the form of perfect fluid with barotropic equation of state (except the one with Modified Chaplygin Gas, which is not solvable) and the solutions are consistent with the recent observations.