bluuebunny/crossref_metadata_2025 huggingface dataset:
Acoustic Vibration Behavior of Full Size Steam Generator and Tubular Heat Exchanger In-Line Tube Banks: A Brief Note
Authors: Eisinger Frantisek L. , Sullivan Robert E.
Published: August 2008

Based on recent laboratory experimental data by Feenstra et al. (2004, “The Effects of Duct Width and Baffles on Acoustic Resonance in a Staggered Tube Array,” in Proceedings of the Eighth International Conference on Flow-Induced Vibration FIV 2004, E. de Langre and F. Axisa, eds., Paris France, Jul. 6–9, pp. 459–464; 2006, “A Study of Acoustic Resonance in a Staggered Tube Array,” ASME J. Pressure Vessel Technol., 128, pp. 533–540), it has been determined that for larger test section widths, the maximum acoustic pressures generated during acoustic resonance were greater by more than a factor of 4 than those predicted by Blevins and Bressler (1993, “Experiments on Acoustic Resonance in Heat Exchanger Tube Bundles,” J. Sound Vib., 164, 503–533). We have evaluated a great number of resonant and nonresonant cases from in-service experience of full size steam generator and tubular heat exchanger tube banks in order to see the general vibratory behavior of the full size units. Fifteen vibrating and twenty-seven nonvibrating cases were evaluated and compared to the Feenstra et al. relationship. It is shown that on average the results from the full size units correlate well with the relationship of Feenstra et al. A gap exists between the vibratory and the nonvibratory cases. The nonvibratory cases produce acoustic pressures, which are at or below the Blevins and Bressler relationship. From the results, it can be concluded that the full size units, regardless of their size and also acoustic mode, produce high acoustic pressures at resonance, with the maximum acoustic pressure on average more than 50–75 times higher than the input energy parameter defined by the product of Mach number and pressure drop through the tube bank. The results are tabulated and plotted for comparison.
Pressure Vessels With Reinforcing Space-Filling Skeletons
Authors: Doyoyo Mulalo , Faure Nadia
Published: August 2008

Light-weight high pressure vessels are recently in demand mainly because of the need to replace gasoline engines with hydrogen fuel cells. One of the main problems delaying this transition is our inability to store sufficient hydrogen in automobiles without (1) sacrificing safety and cabin space and (2) achieving the same driving range and performance as gasoline-powered vehicles. While hydrogen is more efficient as a fuel than gasoline and has zero greenhouse gas emissions, it occupies a larger volume and violently explodes in contact with air. Thus, hydrogen tanks are significantly larger and heavier than those of gasoline. Storage of compressed fluids has always relied on round tanks because of their high membrane resistance and low surface-to-volume ratios. Multilayered composite and metal designs are then used to reinforce and reduce their weight. Apparently, the best idea—but still early in its development—is to store hydrogen based on metal hydrides. Nevertheless, we present a new concept of replacing conventional hydrogen tanks with tanks that are internally reinforced by space-filling skeletons or simply with strut/shell networks. This enables designs of lighter, stronger tanks with shapes that can fit into nonfunctional regions of the vehicle to significantly increase storage volume. This approach promises immediate integration with existing storage technologies. Treating the reinforced vessel as joined plates on elastic foundations, we analyze cylindrical and rectangular tanks and show that the idea is more efficient in terms of pressure gain and weight reduction in the latter because large wall deformations favor the skeleton reinforcement. This result validates the skeleton reinforcement idea, and its practicality is discussed.
Cyclic Elastoplastic Analysis of Structures Concerning a Fatigue Assessment According to the Local Strain Approach: An Overview
Authors: De Jesus Abílio M. P. , Pereira Hélder F. S. G. , Ribeiro Alfredo S. , Fernandes António A.
Published: August 2008

This Technical Brief presents an overview about the current methodologies for elastoplastic calculation of structures undergoing cyclic loading, aiming a fatigue assessment according to the local strain approaches. The possibilities and limitations of the plasticity models available in most popular commercial finite element codes are discussed. Also, several methodologies for structural elastoplastic analysis, concerning the derivation of the stabilized material response, are also addressed highlighting their potentialities and drawbacks. The discussion proposed in this Technical Brief is intended as guidance for design engineers needing to ponder all calculation alternatives for assessing fatigue damage parameters before a rational decision is carried out, in the framework of local approaches to fatigue.
Crystallographic texture, morphology, optical, and microwave dielectric properties of dc magnetron sputtered nanostructured zirconia thin films
Authors: Pamu D. , Sudheendran K. , Ghanashyam Krishna M. , James Raju K. C.
Published: August 2008

Nanocrystalline zirconia thin films have been deposited at ambient temperature by dc magnetron sputtering on glass and quartz substrates. The crystallite size as calculated from the x-ray diffraction patterns in the films varies between 10 and 25nm and is dependent on oxygen percentage in the sputtering gas. Interestingly, the presence of monoclinic and cubic phase is observed for the films deposited on glass at 40%, 60%, and 80% of oxygen in the sputtering gas, while those deposited on quartz showed only the monoclinic phase. Refractive index decreased with increase in percentage of oxygen in the sputter gas. Significantly, even at 100% oxygen in the sputtering gas, films of thickness of the order of 500nm have been grown starting from the metallic Zr target. The dielectric constants were measured using the extended cavity perturbation technique at X-band frequency (8–12GHz). The dielectric constant and loss tangent showed a very small decrease with increase in frequency but exhibited a stronger dependence on processing parameters. The dielectric constants of the films at microwave frequencies ranged between 12.16 and 22.3.
Study of a micro chamber quadrupole mass spectrometer
Authors: Wang Jinchan , Zhang Xiaobing , Mao Fuming , Xiao Mei , Cui Yunkang , den Engelsen Daniel , Lei Wei
Published: August 2008

The design of a micro chamber quadrupole mass spectrometer (MCQMS) having a small total volume of only 20 cm3, including Faraday cup ion detector and ion source, is described. This MCQMS can resist a vacuum baking temperature of 400–500 °C. The quadrupole elements with a hyperbolic surface are made of a ceramic material and coated with a thin metal layer. The quadrupole mass filter has a field radius of 3 mm and a length of 100 mm. Prototypes of this new MCQMS can detect a minimum partial pressure of 10−8 Pa, have a peak width of ΔM=1 at 10% peak height from mass number 1 to 60, and show an excellent long-term stability. The new MCQMS is intended to be used in residual gas analyses of electron devices during a mutual pumping and baking process.
First principles calculation of Stillinger-Weber potential parameters for InN
Authors: Fulk C. , Walkosz W. , Chatterjee A. , Ogut S. , Grein C. H. , Chung P. W.
Published: August 2008

The compliance coefficients and Stillinger-Weber interatomic potential parameters of wurtzite InN were determined by first principles methods. The structural parameters of InN were calculated within the local density approximation of Ceperley-Alder and the generalized gradient approximation of Perdew-Wang exchange-correlation functionals. It was found that the shallow 4d electrons were required as part of the valence shell to obtain accurate results due to the large difference in electronegativity between In and N. The calculated compliance parameters were in good agreement with previously reported theoretical values and in fair agreement with the scattered experimental values. The ab initio results were then fitted to Stillinger-Weber potential forms.
High sensitivity attenuated total reflection Fourier transform infrared spectroscopy study of ultrathin ZrO2 films: A study of phase change
Authors: Sayan S. , Chandler-Horowitz D. , Nguyen N. V. , Ehrstein J. R.
Published: August 2008

Attenuated total reflection fourier transform infrared spectroscopy (FTIR ATR) was performed on ultrathin ZrO2 films as thin as ≈3.0nm deposited on silicon. An observed vibrational mode near 710cm−1 undergoes a very pronounced absorption line shape change, corresponding to a structural phase change, as a function of film thickness and thermal processing. This absorption, attributed to the Eu(LO2) and A2u(LO) modes of tetragonal ZrO2, marks the first experimental measurement and verification of vibrational modes for tetragonal ZrO2 in this spectral range. The FTIR-ATR method shows promise as an extremely sensitive and nondestructive tool for high-κ dielectric film characterization.
Etching characteristics and mechanism of Ge2Sb2Te5 thin films in inductively coupled Cl2∕Ar plasma
Authors: Min Nam-Ki , Efremov Alexander , Kim Yun-Ho , Kim Mansu , Park Hyung-Ho , Lee Hyun Woo , Kwon Kwang-Ho
Published: August 2008

This work reports the investigations of both etch characteristics and mechanisms for the Ge2Sb2Te5 (GST) thin films in the Cl2∕Ar inductively coupled plasma. The GST etch rates and etch selectivities over SiO2 were measured as functions of the Cl2∕Ar mixing ratio (43%–86% Ar), gas pressure (4–10mTorr), and source power (400–700W). Langmuir probe diagnostics and zero-dimensional (global) plasma modeling provided the information on plasma parameters and behaviors of plasma active species. From the model-based analysis of surface kinetics, it was found that with variations of the Cl2∕Ar mixing ratio and gas pressure, the GST etch rate follows the changes of Cl atom density and flux but contradicts with those for positive ions. The GST etch mechanism in the Cl2-containing plasmas represents a combination of spontaneous and ion-assisted chemical reactions with no limitation by ion-surface interaction kinetics such as physical sputtering of the main material or the ion-stimulated desorption of low volatile reaction products.
Molecular dynamics simulations of GaAs sputtering under low-energy argon ion bombardment
Authors: Despiau-Pujo Emilie , Chabert Pascal , Graves David B.
Published: August 2008

Results from molecular dynamics (MD) simulations of low-energy (50–200eV) Ar+ ion bombardment on (110) GaAs surfaces are reported. A new analytical bond-order potential, originally developed for molecular beam epitaxy studies, is used and tested in the context of etching to investigate the nature and effects of physical sputtering on GaAs compounds. It is found that a thermal desorption model, which accounts for long time scale phenomena between MD simulated impacts, is necessary to achieve steady state sputtering. An initial rapid etch of both atomic species is observed up to 4×1016ions∕cm2 fluence with preferential sputtering of Ga atoms. At high fluences, simulations show the formation of an As-rich layer on the top surface, a subsurface enrichment of Ga, and a return to stoichiometry deeper in the solid. More than 97% of sputtered or desorbed species appear to be Ga or As atoms; sputtering of GaAs molecules is negligible. All these observations are in agreement with published experimental results. Finally, a significant fraction of the atoms leave the surface with more than 10% of the incident ion energy, which could alter passivation layers on sidewalls during etching.
Graded refractive-index SiOx infrared filters prepared by reactive magnetron sputtering
Authors: Song Qiuming , Huang Feng , Li Ming , Xie Bin , Wang Haiqian , Jiang Yousong , Song Yizhou
Published: August 2008

Dense, uniform SiOx (0⩽x⩽2) films were deposited by reactive magnetron sputtering. By controlling the oxygen flow rate and/or sputtering power during deposition, the refractive index of SiOx films can be continuously tuned from 1.44 to 3.69 at λ=1550nm. The authors fabricated an 11-layer bandpass filter of SiOx∕SiO2 with high refractive-index contrast (nH∕nL=1.91 at λ=1550nm) and a 35-layer SiOx optical filter with a graded refractive-index profile. The measured reflectance and transmittance spectra correlate well with the designed spectra. This work demonstrates that SiOx material can be used to make infrared optical filters with graded refractive index and high refractive-index contrast.
Deposition of nanoscale multilayer CrN/NbN physical vapor deposition coatings by high power impulse magnetron sputtering
Authors: Purandare Y. P. , Ehiasarian A. P. , Hovsepian P. Eh.
Published: August 2008

Nanoscale multilayer CrN/NbN physical vapor deposition (PVD) coatings are gaining reputation for their high corrosion and wear resistance. However, the CrN/NbN films deposited by ABS™ (arc bond sputtering) technology have some limitations such as macrodroplets, porosity, and less dense structures. The novel HIPIMS (high power impulse magnetron sputtering) technique produces macroparticle-free, highly ionized metal plasma, which brings advantages in both surface pretreatment and coating deposition stages of the PVD process. In this study, nanoscale multilayer CrN/NbN PVD coatings were pretreated and deposited with HIPIMS technology and compared with those deposited by HIPIMS-UBM (unbalanced magnetron) and by the ABS™ technique. In all cases Cr+ etching was utilized to enhance adhesion by low energy ion implantation. The coatings were deposited at 400 °C with substrate biased (Ub) at −75 V. During coating deposition, HIPIMS produced significantly high activation of nitrogen compared to the UBM as observed with mass spectroscopy. HIPIMS-deposited coatings revealed a bilayer period of 4.1 nm (total thickness: 2.9 μm) and hardness of 3025 HK0.025. TEM results revealed droplet free, denser microstructure with (200) preferred orientation for the HIPIMS coating owing to the increased ionization as compared to the more porous structure with random orientation observed in UBM coating. The dry sliding wear coefficient (Kc) of the coating was 1.8×10−15 m3 N−1 m−1, whereas the steady state coefficient of friction was 0.32. Potentiodynamic polarization tests revealed higher Ecorr values, higher pitting resistance (around potentials +400 to +600 mV), and lower corrosion current densities for HIPIMS deposited coatings as compared to the coatings deposited by ABS or HIPIMS-UBM. The corrosion behavior of the coatings qualitatively improved with the progressive use of HIPIMS from pretreatment stage to the coating deposition step.
Characterization of zirconium nitride films sputter deposited with an extensive range of nitrogen flow rates
Authors: Farkas N. , Zhang G. , Ramsier R. D. , Evans E. A. , Dagata J. A.
Published: August 2008

Zr N x films are deposited by rf magnetron sputtering using a wide range of nitrogen flow rates to control film properties. Scanned probe microscope (SPM) oxidation is presented as a complimentary characterization tool to x-ray diffraction, colorimetric, and four point probe analyses. The SPM oxidation behavior of the ZrNx films is related to their structural, optical, and electrical properties. Whereas stoichiometric ZrN films have applications as protective and/or decorative coatings, ZrNx films sputtered with higher nitrogen flow rates have potential applications in devices where arrays of high aspect ratio nanostructures would be useful.
Coating techniques of metal chambers for remote catalytic chemical vapor deposition applications
Authors: Umemoto Hironobu , Setoguchi Shota , Uemura Hitoshi , Matsumura Hideki
Published: August 2008

To obtain information for remote catalytic chemical vapor deposition, the authors constructed a two-chamber system in which the decomposition and deposition areas were separated. H2 molecules were decomposed on a heated tungsten filament in the first area and the H atoms produced were carried to the second area, where the absolute H-atom densities were measured by a vacuum-ultraviolet laser absorption technique. The gas pressure in the decomposition area was maintained ten times higher than that in the deposition area by mounting a diffusion barrier to prevent the possible back-diffusion of the material gases. The inner walls of the decomposition area as well as the diffusion barrier were coated with SiO2 or polytetrafluoroethene to minimize the recombination of H atoms. The H-atom density could be increased by one order of magnitude by such coatings, and it is shown that H-atom densities in the order of 1012 cm−3 can be achieved in the deposition area in the present system.
Brown Carbon Spheres in East Asian Outflow and Their Optical Properties
Authors: Alexander Duncan T. L. , Crozier Peter A. , Anderson James R.
Published: August 2008

Atmospheric aerosols play a substantial role in climate change through radiative forcing. Combustion-produced carbonaceous particles are the main light-absorbing aerosols; thus, quantifying their optical properties is essential for determining the magnitude of direct forcing. By using the electron energy-loss spectrum in the transmission electron microscope, we quantified the optical properties of individual, submicrometer amorphous carbon spheres that are ubiquitous in East Asian–Pacific outflow. The data indicate that these common spheres are brown, not black, with a mean refractive index of 1.67 – 0.27
i
(where
i
=

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) at a wavelength of 550 nanometers. The results suggest that brown carbon aerosols should be explicitly included in radiative forcing models.
The Rupture and Repair of Cooperation in Borderline Personality Disorder
Authors: King-Casas Brooks , Sharp Carla , Lomax-Bream Laura , Lohrenz Terry , Fonagy Peter , Montague P. Read
Published: August 2008

To sustain or repair cooperation during a social exchange, adaptive creatures must understand social gestures and the consequences when shared expectations about fair exchange are violated by accident or intent. We recruited 55 individuals afflicted with borderline personality disorder (BPD) to play a multiround economic exchange game with healthy partners. Behaviorally, individuals with BPD showed a profound incapacity to maintain cooperation, and were impaired in their ability to repair broken cooperation on the basis of a quantitative measure of coaxing. Neurally, activity in the anterior insula, a region known to respond to norm violations across affective, interoceptive, economic, and social dimensions, strongly differentiated healthy participants from individuals with BPD. Healthy subjects showed a strong linear relation between anterior insula response and both magnitude of monetary offer received from their partner (input) and the amount of money repaid to their partner (output). In stark contrast, activity in the anterior insula of BPD participants was related only to the magnitude of repayment sent back to their partner (output), not to the magnitude of offers received (input). These neural and behavioral data suggest that norms used in perception of social gestures are pathologically perturbed or missing altogether among individuals with BPD. This game-theoretic approach to psychopathology may open doors to new ways of characterizing and studying a range of mental illnesses.
Programming DNA Tube Circumferences
Authors: Yin Peng , Hariadi Rizal F. , Sahu Sudheer , Choi Harry M. T. , Park Sung Ha , LaBean Thomas H. , Reif John H.
Published: August 2008

Synthesizing molecular tubes with monodisperse, programmable circumferences is an important goal shared by nanotechnology, materials science, and supermolecular chemistry. We program molecular tube circumferences by specifying the complementarity relationships between modular domains in a 42-base single-stranded DNA motif. Single-step annealing results in the self-assembly of long tubes displaying monodisperse circumferences of 4, 5, 6, 7, 8, 10, or 20 DNA helices.
Frontiers in Surface Scattering Simulations
Authors: Kroes Geert-Jan
Published: August 2008

Theorists have recently made substantial progress in simulating reactive molecule-metal surface scattering but still face major challenges. The grand challenge is to develop an approach that enables accurate predictive calculations of reactions involving electronically excited states with potential curve crossings. This challenge is all the more daunting because collisions involving molecules heavier than H
2
may be accompanied by substantial energy exchange with the surface vibrations (phonons), and because an electronic structure approach that allows molecule-surface interaction energies to be computed with chemical accuracy (1 kilocalorie per mole) is not yet available even for the electronic ground state of molecule-metal surface systems.
Challenges in Modeling Materials Properties Without Experimental Input
Authors: Carter Emily A.
Published: August 2008

Simulations of materials behavior are an important component of materials science research, partly because measurements are indirect, requiring theoretical interpretation, and partly because often the ideal experiment simply cannot be performed (due to technological limitations). Empirical physical models used in this context often rely on parameters drawn from experiments on simpler systems, and so introduce various inaccuracies. In contrast, a quantum mechanical model can potentially offer an independent source of data more closely attuned to the complexities of the system at hand. This Perspective reviews current quantum mechanics–based materials modeling approaches and their successes and limitations, and offers a view to the future.
Dynamic Shifts of Limited Working Memory Resources in Human Vision
Authors: Bays Paul M. , Husain Masud
Published: August 2008

Our ability to remember what we have seen is very limited. Most current views characterize this limit as a fixed number of items—only four objects—that can be held in visual working memory. We show that visual memory capacity is not fixed by the number of objects, but rather is a limited resource that is shared out dynamically between all items in the visual scene. This resource can be shifted flexibly between objects, with allocation biased by selective attention and toward targets of upcoming eye movements. The proportion of resources allocated to each item determines the precision with which it is remembered, a relation that we show is governed by a simple power law, allowing quantitative estimates of resource distribution in a scene.
Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells
Authors: Gardner James M. , DeVoss Jason J. , Friedman Rachel S. , Wong David J. , Tan Ying X. , Zhou Xuyu , Johannes Kellsey P. , Su Maureen A. , Chang Howard Y. , Krummel Matthew F. , Anderson Mark S.
Published: August 2008

The prevention of autoimmunity requires the elimination of self-reactive T cells during their development and maturation. The expression of diverse self-antigens by stromal cells in the thymus is essential to this process and depends, in part, on the activity of the autoimmune regulator (
Aire
) gene. Here we report the identification of extrathymic
Aire
-expressing cells (eTACs) resident within the secondary lymphoid organs. These stromally derived eTACs express a diverse array of distinct self-antigens and are capable of interacting with and deleting naïve autoreactive T cells. Using two-photon microscopy, we observed stable antigen-specific interactions between eTACs and autoreactive T cells. We propose that such a secondary network of self-antigen–expressing stromal cells may help reinforce immune tolerance by preventing the maturation of autoreactive T cells that escape thymic negative selection.
Large Electrocaloric Effect in Ferroelectric Polymers Near Room Temperature
Authors: Neese Bret , Chu Baojin , Lu Sheng-Guo , Wang Yong , Furman E. , Zhang Q. M.
Published: August 2008

Applying an electrical field to a polar polymer may induce a large change in the dipolar ordering, and if the associated entropy changes are large, they can be explored in cooling applications. With the use of the Maxwell relation between the pyroelectric coefficient and the electrocaloric effect (ECE), it was determined that a large ECE can be realized in the ferroelectric poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] copolymer at temperatures above the ferroelectric-paraelectric transition (above 70°C), where an isothermal entropy change of more than 55 joules per kilogram per kelvin degree and adiabatic temperature change of more than 12°C were observed. We further showed that a similar level of ECE near room temperature can be achieved by working with the relaxor ferroelectric polymer of P(VDF-TrFE-chlorofluoroethylene).
Phyllosilicate Diversity and Past Aqueous Activity Revealed at Mawrth Vallis, Mars
Authors: Bishop Janice L. , Dobrea Eldar Z. Noe , McKeown Nancy K. , Parente Mario , Ehlmann Bethany L. , Michalski Joseph R. , Milliken Ralph E. , Poulet Francois , Swayze Gregg A. , Mustard John F. , Murchie Scott L. , Bibring Jean-Pierre
Published: August 2008

Observations by the Mars Reconnaissance Orbiter/Compact Reconnaissance Imaging Spectrometer for Mars in the Mawrth Vallis region show several phyllosilicate species, indicating a wide range of past aqueous activity. Iron/magnesium (Fe/Mg)–smectite is observed in light-toned outcrops that probably formed via aqueous alteration of basalt of the ancient cratered terrain. This unit is overlain by rocks rich in hydrated silica, montmorillonite, and kaolinite that may have formed via subsequent leaching of Fe and Mg through extended aqueous events or a change in aqueous chemistry. A spectral feature attributed to an Fe
2+
phase is present in many locations in the Mawrth Vallis region at the transition from Fe/Mg-smectite to aluminum/silicon (Al/Si)–rich units. Fe
2+
-bearing materials in terrestrial sediments are typically associated with microorganisms or changes in pH or cations and could be explained here by hydrothermal activity. The stratigraphy of Fe/Mg-smectite overlain by a ferrous phase, hydrated silica, and then Al-phyllosilicates implies a complex aqueous history.
A Sharp Look at Stories of Smell
Authors: Firestein Stuart
Published: August 2008

What the Nose Knows
. The Science of Scent in Everyday Life.
By Avery Gilbert
. Crown, New York, 2008. 304 pp. $23.95, C$27.95. ISBN 9781400082346.

The author provides a wide-ranging and well-grounded account of the science and culture of smell.
Seroreactivity against Streptococcal DRS (Distantly Related to SIC) Protein Is a Predictor for End-Stage Renal Failure
Authors: Boon Virginia A. F. , Munro James L. , Kan George W. , Burnell James , Speare Richard
Published: August 2008

We hypothesized that immunoreactivity against antigens from nephritic strains of
Streptococcus pyogenes
may be elevated in patients with end-stage renal failure (ESRF). Additionally, we investigated whether a difference in seroreactivity exists between nonindigenous and indigenous (Aboriginal/Torres Strait Islander) patients. To examine these possibilities, antibodies against potentially nephritogenic proteins, streptokinase (Ska1) (from M1), streptococcal pyrogenic exotoxin type B (SpeB) (from M1), the streptococcal inhibitor of complement-mediated cell lysis (SIC) (from M1) and its two variants, closely related to SIC (CRS) (from M57) and distantly related to SIC (DRS) (from M12) were determined in 66 patients and 31 healthy controls by enzyme-linked immunosorbent assays. A significantly higher proportion of patients compared to controls were seropositive to Ska1 (
P
= 0.004), DRS (
P
= 0.0003), CRS (
P
= 0.001), and SIC (
P
= 0.018). Regression analysis showed that seroreactivity to DRS (
r
2
= 0.85,
P
= 0.001) predicted the development of ESRF and that being diabetic was positively associated with being an ESRF patient (
r
2
= 0.37,
P
< 0.0001) and being indigenous (
r
2
= 0.47,
P
< 0.0001). These results suggest that these ESRF patients were exposed to strains of
S. pyogenes
that secrete Ska1, DRS, CRS, and SIC and may have pathological significance. No significant difference was observed between the indigenous patients and nonindigenous patients.
Development and Validation of a Quantitative PCR Assay for Diagnosis of Scedosporiosis
Authors: Castelli Maria V. , Buitrago Maria J. , Bernal-Martinez Leticia , Gomez-Lopez Alicia , Rodriguez-Tudela Juan L. , Cuenca-Estrella Manuel
Published: August 2008

Scedosporium apiospermum
and
Scedosporium prolificans
are fungal pathogens that can cause severe human infections, including disseminated mycosis in immunocompromised patients. Two real-time PCR (RT-PCR) assays for the diagnosis of these species were developed and validated for the classification of clinical strains and for the detection of DNA in clinical samples by use of a murine model of invasive infection. A total of 14 clinical strains and 141 samples, including blood, serum, and lung samples from infected CD1 mice, were analyzed. Each RT-PCR methodology used a species-specific molecular beacon probe targeting a highly conserved region of the fungal ribosomal DNA gene. Results showed 100% specificity and a detection limit of 10 fg of DNA for both assays. The sensitivities for the
S. prolificans
-specific PCR assay were 100% for cultured clinical strains, 95.5% for lung tissues, 85% for serum, and 83.3% for blood. For
S. apiospermum
, the sensitivities were 100% for clinical strains and 97.2%, 81.8%, and 54.5% for lung tissues, serum, and blood, respectively. Both techniques can be useful for clinical diagnosis, and further studies are warranted.
Detection and Serotyping of Dengue Virus in Serum Samples by Multiplex Reverse Transcriptase PCR-Ligase Detection Reaction Assay
Authors: Das S. , Pingle M. R. , Muñoz-Jordán J. , Rundell M. S. , Rondini S. , Granger K. , Chang G.-J. J. , Kelly E. , Spier E. G. , Larone D. , Spitzer E. , Barany F. , Golightly L. M.
Published: August 2008

The detection and successful typing of dengue virus (DENV) from patients with suspected dengue fever is important both for the diagnosis of the disease and for the implementation of epidemiologic control measures. A technique for the multiplex detection and typing of DENV serotypes 1 to 4 (DENV-1 to DENV-4) from clinical samples by PCR-ligase detection reaction (LDR) has been developed. A serotype-specific PCR amplifies the regions of genes C and E simultaneously. The two amplicons are targeted in a multiplex LDR, and the resultant fluorescently labeled ligation products are detected on a universal array. The assay was optimized using 38 DENV strains and was evaluated with 350 archived acute-phase serum samples. The sensitivity of the assay was 98.7%, and its specificity was 98.4%, relative to the results of real-time PCR. The detection threshold was 0.017 PFU for DENV-1, 0.004 PFU for DENV-2, 0.8 PFU for DENV-3, and 0.7 PFU for DENV-4. The assay is specific; it does not cross-react with the other flaviviruses tested (West Nile virus, St. Louis encephalitis virus, Japanese encephalitis virus, Kunjin virus, Murray Valley virus, Powassan virus, and yellow fever virus). All but 1 of 26 genotypic variants of DENV serotypes in a global DENV panel from different geographic regions were successfully identified. The PCR-LDR assay is a rapid, sensitive, specific, and high-throughput technique for the simultaneous detection of all four serotypes of DENV.
Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Nonfermenting Gram-Negative Bacilli Isolated from Cystic Fibrosis Patients
Authors: Degand Nicolas , Carbonnelle Etienne , Dauphin Brunhilde , Beretti Jean-Luc , Le Bourgeois Muriel , Sermet-Gaudelus Isabelle , Segonds Christine , Berche Patrick , Nassif Xavier , Ferroni Agnès
Published: August 2008

The identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis (CF) patients is usually achieved by using phenotype-based techniques and eventually molecular tools. These techniques remain time-consuming, expensive, and technically demanding. We used a method based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) for the identification of these bacteria. A set of reference strains belonging to 58 species of clinically relevant nonfermenting gram-negative bacilli was used. To identify peaks discriminating between these various species, the profile of 10 isolated colonies obtained from 10 different passages was analyzed for each referenced strain. Conserved peaks with a relative intensity greater than 0.1 were retained. The spectra of 559 clinical isolates were then compared to that of each of the 58 reference strains as follows: 400
Pseudomonas aeruginosa
, 54
Achromobacter xylosoxidans
, 32
Stenotrophomonas maltophilia
, 52
Burkholderia cepacia
complex (BCC), 1
Burkholderia gladioli
, 14
Ralstonia mannitolilytica
, 2
Ralstonia pickettii
, 1
Bordetella hinzii
, 1
Inquilinus limosus
, 1
Cupriavidus respiraculi
, and 1
Burkholderia thailandensis
. Using this database, 549 strains were correctly identified. Nine BCC strains and one
R. mannnitolilytica
strain were identified as belonging to the appropriate genus but not the correct species. We subsequently engineered BCC- and
Ralstonia
-specific databases using additional reference strains. Using these databases, correct identification for these species increased from 83 to 98% and from 94 to 100% of cases, respectively. Altogether, these data demonstrate that, in CF patients, MALDI-TOF-MS is a powerful tool for rapid identification of nonfermenting gram-negative bacilli.
Comparison of Two Rapid Human Immunodeficiency Virus (HIV) Assays, Determine HIV-1/2 and OraQuick Advance Rapid HIV-1/2, for Detection of Recent HIV Seroconversion
Authors: Kshatriya Rachana , Cachafeiro Ada A. , Kerr Ryan J. S. , Nelson Julie A. E. , Fiscus Susan A.
Published: August 2008

Modified protocols of two rapid tests were compared with a less sensitive (LS) (detuned) enzyme immunoassay (EIA) for their abilities to distinguish recent human immunodeficiency virus (HIV) seroconversion from long-term infections. The results for samples from 100 HIV-positive patient that had previously been tested by the Vironostika LS EIA had a 97% concordance with the results of the Determine HIV 1/2 assay and 93% concordance with those of the OraQuick HIV 1/2 assay.
Evaluation of the OSOM
Trichomonas
Rapid Test versus Wet Preparation Examination for Detection of
Trichomonas vaginalis
Vaginitis in Specimens from Women with a Low Prevalence of Infection
Authors: Campbell L. , Woods V. , Lloyd T. , Elsayed S. , Church D. L.
Published: August 2008

The OSOM
Trichomonas
rapid test (OSOM Trich) was compared to the wet preparation examination (WP) for the detection of
Trichomonas vaginalis
vaginitis in women with a low prevalence of infection. A total of 19/1,009 (2%) women had
T. vaginalis
infection. OSOM Trich had very good performance, with sensitivity, specificity, efficiency, positive predictive value, and negative predictive value of 94.7, 100, 99.9, 100, and 99.9%, respectively. The implementation of OSOM Trich would decrease labor costs.
Production of White Colonies on CHROMagar
Candida
Medium by Members of the
Candida glabrata
Clade and Other Species with Overlapping Phenotypic Traits
Authors: Bishop Justin A. , Chase Nancy , Lee Richard , Kurtzman Cletus P. , Merz William G.
Published: August 2008

We hypothesized that species of the
Candida glabrata
clade and species with phenotypic traits that overlap those of
C. glabrata
would produce white colonies on CHROMagar
Candida
medium. Of 154 isolates (seven species) tested,
C. bracarensis, C. nivariensis, C. norvegensis, C. glabrata
, and
C. inconspicua
produced white colonies; the
Pichia fermentans
group and
C. krusei
did not. Many of these species are difficult to identify phenotypically; white colonies may signal the need for the use of molecular approaches.
Predominance of Methicillin-Resistant
Staphylococcus aureus
among Pathogens Causing Skin and Soft Tissue Infections in a Large Urban Jail: Risk Factors and Recurrence Rates
Authors: David Michael Z. , Mennella Connie , Mansour Mohamed , Boyle-Vavra Susan , Daum Robert S.
Published: August 2008

In the 1990s, community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) strains emerged as pathogens outside of the health care environment. Epidemic foci of CA-MRSA infections were reported in jails and prisons, but risk factors for MRSA infection there are not known. All skin and soft tissue infections (SSTIs) cultured in the Cook County Jail in March 2004 to August 2005 were reviewed. Demographic and clinical risk factors were compared among patients with methicillin-susceptible
S. aureus
(MSSA) SSTIs and those with MRSA SSTIs. Antibiotic susceptibilities were recorded, and we performed multilocus sequence typing on a sample of MRSA isolates. There were 378 SSTIs from different patients requiring culture, of which 240 (63.5%) were of MRSA and 43 (11.4%) were of MSSA; 84.8% of
S. aureus
isolates were MRSA. MRSA- and MSSA-infected patients were similar with regard to age, gender, ethnicity, previous exposure to the jail, and comorbidities. In the 12 months prior to the index culture, MRSA patients were more likely to have received a β-lactam antibiotic (25% versus 9%;
P
= 0.02). Among 26 MRSA strains, 24 (92%) had the sequence type 8 (ST8) genotype. Within 6 months, 14% (95% confidence interval, 8.7% to 22.3%) of MRSA SSTI patients in the jail had a recurrent SSTI compared with 8.8% (95% confidence interval, 2.1% to 32.6%) of MSSA SSTI patients (
P
= 0.004). MRSA is the predominant cause of SSTIs requiring culture in the jail. Few risk factors differentiated MRSA from MSSA SSTIs, and detainee patients with MRSA SSTIs are at high risk for recurrent SSTIs.
Differentiation of Highly Virulent Strains of
Streptococcus suis
Serotype 2 According to Glutamate Dehydrogenase Electrophoretic and Sequence Type
Authors: Kutz Russell , Okwumabua Ogi
Published: August 2008

The glutamate dehydrogenase (GDH) enzymes of 19
Streptococcus suis
serotype 2 strains, consisting of 18 swine isolates and 1 human clinical isolate from a geographically varied collection, were analyzed by activity staining on a nondenaturing gel. All seven (100%) of the highly virulent strains tested produced an electrophoretic type (ET) distinct from those of moderately virulent and nonvirulent strains. By PCR and nucleotide sequence determination, the
gdh
genes of the 19 strains and of 2 highly virulent strains involved in recent Chinese outbreaks yielded a 1,820-bp fragment containing an open reading frame of 1,344 nucleotides, which encodes a protein of 448 amino acid residues with a calculated molecular mass of approximately 49 kDa. The nucleotide sequences contained base pair differences, but most were silent. Cluster analysis of the deduced amino acid sequences separated the isolates into three groups. Group I (ETI) consisted of the seven highly virulent isolates and the two Chinese outbreak strains, containing Ala
299
-to-Ser, Glu
305
-to-Lys, and Glu
330
-to-Lys amino acid substitutions compared with groups II and III (ETII). Groups II and III consisted of moderately virulent and nonvirulent strains, which are separated from each other by Tyr
72
-to-Asp and Thr
296
-to-Ala substitutions. Gene exchange studies resulted in the change of ETI to ETII and vice versa. A spectrophotometric activity assay for GDH did not show significant differences between the groups. These results suggest that the GDH ETs and sequence types may serve as useful markers in predicting the pathogenic behavior of strains of this serotype and that the molecular basis for the observed differences in the ETs was amino acid substitutions and not deletion, insertion, or processing uniqueness.
Evaluation of the Xpert Methicillin-Resistant
Staphylococcus aureus
(MRSA) Assay Using the GeneXpert Real-Time PCR Platform for Rapid Detection of MRSA from Screening Specimens
Authors: Rossney Angela S. , Herra Celine M. , Brennan Gráinne I. , Morgan Pamela M. , O'Connell Brian
Published: August 2008

The need for rapid methods to accurately detect methicillin-resistant
Staphylococcus aureus
(MRSA) is widely acknowledged, and a number of molecular assays are commercially available. This study evaluated the Xpert MRSA assay, which is run on the GeneXpert real-time PCR platform (Cepheid) for use in a clinical laboratory. The following parameters were investigated: (i) the limits of detection (LoDs) for four MRSA strains; (ii) the ability to detect isolates of MRSA from a collection representative of MRSA in Ireland since 1974 (
n
= 114) and the ability to detect control strains with staphylococcal cassette chromosome
mec
types IVa (IV.1.1.1), IVb (IV.2.1.1), IVc (IV.3.1.1), IVd (IV.4.1.1), V (V.1.1.1), V
T
, and VI; and (iii) performance in a clinical trial with swabs from nose, throat, and groin/perineum sites from 204 patients, where results were compared with those obtained by direct and enrichment cultures. The average LoD of the four test strains was 610 CFU/ml (equivalent to 58 CFU/swab). All 114 MRSA isolates and 7 control strains tested were detected. Sensitivity, specificity, and positive and negative predictive values for clinical specimens from all sites investigated were 90%, 97%, 86%, and 98%, respectively, but throat specimens yielded poor sensitivity (75%). Sensitivity, specificity, and positive and negative predictive values for nasal specimens were 95%, 98%, 90%, and 99%, respectively. Overall, the assay was rapid and easy to perform, but performance might be enhanced by the inclusion of an equivocal interpretive category based on analysis of all available amplification data.
Latent Membrane Protein 1 of Epstein-Barr Virus Activates the hTERT Promoter and Enhances Telomerase Activity in B Lymphocytes
Authors: Terrin Liliana , Dal Col Jessica , Rampazzo Enrica , Zancai Paola , Pedrotti Moreno , Ammirabile Grazia , Bergamin Stefano , Rizzo Silvana , Dolcetti Riccardo , De Rossi Anita
Published: August 2008

Transformation of primary B lymphocytes by Epstein-Barr virus requires the establishment of a strictly latent infection, the expression of several latent viral proteins, and sustained telomerase activity. Our previous findings indicated that induction of hTERT, the rate-limiting catalytic unit of the telomerase complex, was associated with the expression of the viral latent membrane protein 1 (LMP1). In the present study, we demonstrate that ectopic expression of LMP1 in BJAB and Ramos B cells resulted in an increase of hTERT transcripts, thus suggesting that LMP1 acts at the transcriptional level. This was confirmed by transient expression of a luciferase reporter plasmid containing the hTERT promoter cotransfected with an LMP1-expressing vector or transfected into B cells in which LMP1 expression was inducible. Consistently, silencing of LMP1 by small interfering RNA resulted in a reduction ofhTERTtranscripts. We also provide evidence indicating that LMP1-inducedhTERTactivation is independently mediated by NF-κB and by mitogen-activated protein kinase and extracellular signal-regulated kinase 1/2 pathways, whereas CD40, Akt, and mTOR signaling has no involvement. Moreover, our results do not support a role for c-Myc in mediating these effects onhTERT, since ectopic expression of LMP1 did not upregulate c-Myc and silencing of this oncogene or E box mutagenesis failed to inhibit LMP1-inducedhTERTactivation. These findings indicate that LMP1 simultaneously modulates multiple signal transduction pathways in B cells to transactivate thehTERTpromoter and enhance telomerase activity, thus confirming the pleiotropic nature of this viral oncoprotein.
Identification of a Conserved RNA Replication Element (
cre
) within the 3D
pol
-Coding Sequence of Hepatoviruses
Authors: Yang Yan , Yi MinKyung , Evans David J. , Simmonds Peter , Lemon Stanley M.
Published: August 2008

Internally located,
cis
-acting RNA replication elements (
cre
) have been identified within the genomes of viruses representing each of the major picornavirus genera (
Enterovirus, Rhinovirus, Aphthovirus
, and
Cardiovirus
) except
Hepatovirus
. Previous efforts to identify a stem-loop structure with
cre
function in hepatitis A virus (HAV), the type species of this genus, by phylogenetic analyses or thermodynamic predictions have not succeeded. However, a region of markedly suppressed synonymous codon variability was identified in alignments of HAV sequences near the 5′ end of the 3D
pol
-coding sequence of HAV, consistent with noncoding constraints imposed by an underlying RNA secondary structure. Subsequent MFOLD predictions identified a 110-nucleotide (nt) complex stem-loop in this region with a typical AAACA/G
cre
motif in its top loop. A potentially homologous RNA structure was identified in this region of the avian encephalitis virus genome, despite little nucleotide sequence relatedness between it and HAV. Mutations that disrupted secondary RNA structure or the AAACA/G motif, without altering the amino acid sequence of 3D
pol
, ablated replication of a subgenomic HAV replicon in transfected human hepatoma cells. Replication competence could be rescued by reinsertion of the native 110-nt stem-loop structure (but not an abbreviated 45-nt stem-loop) upstream of the HAV coding sequence in the replicon. These results suggest that this stem-loop is functionally similar to
cre
elements of other picornaviruses and likely involved in templating VPg uridylylation as in other picornaviruses, despite its significantly larger size and lower free folding energy.
Subviral Particle Release Determinants of Prototype Foamy Virus
Authors: Stange Annett , Lüftenegger Daniel , Reh Juliane , Weissenhorn Winfried , Lindemann Dirk
Published: August 2008

Glycoproteins of several viruses have the capacity to induce release of noninfectious, capsidless particulate structures containing only the viral glycoprotein. Such structures are often called subviral particles (SVP). Foamy viruses (FVs), a special type of retroviruses with a replication strategy combining features of both orthoretroviruses and hepadnaviruses, express a glycoprotein (Env) which has the ability to induce SVP release. However, unlike human hepatitis B virus, prototype FV (PFV) naturally secretes only small amounts of SVPs, because ubiquitination of the Env protein seems to suppress the intrinsic capacity for induction of SVP release. In this study, we characterized the structural determinants influencing PFV SVP release, examined the role of specific Env ubiquitination sites in the regulation of this process, and analyzed the requirement of the cellular vacuolar protein sorting (VPS) machinery for SVP egress. We observed that the cytoplasmic and membrane-spanning domains of both the leader peptide (LP) and the transmembrane (TM) subunit harbor essential as well as inhibitory domains. Furthermore, only ubiquitination at the most N-terminal lysine residues (K
14
and K
15
) in LP reduced cell surface expression and suppressed SVP release to wild-type levels. This suggests that interaction of Env with cellular components required for SVP release suppression is effective only when Env is ubiquitinated at these lysine residues but not at others. Finally, SVP release was sensitive to dominant-negative mutants of late components, but not early components, of the cellular VPS machinery. PFV therefore differs from hepatitis B virus in using the same cellular pathway for egress of both virions and SVPs.