bluuebunny/crossref_metadata_2025 huggingface dataset:
A Numerical Study of Flutter in a Transonic Fan
Authors: Isomura K. , Giles M. B.
Published: December 2011

The bending mode Flutter of a modern transonic fan has been studied using a quasi-three-dimensional viscous unsteady CFD code. The type of flutter in this research is that of a highly loaded blade with a tip relative Mach number just above unity, commonly referred to as transonic stall flutter. This type of Flutter is often encountered in modern wide chord fans without a part span shroud. The CFD simulation uses an upwinding scheme with Roe’s third-order flux differencing, and Johnson and King’s turbulence model with the later modification due to Johnson and Coakley. A dynamic transition point model is developed using the en method and Schubauer and Klebanoff’s experimental data. The calculations of the flow in this fan reveal that the source of the flutter of IHI transonic fan is an oscillation of the passage shock, rather than a stall. As the blade loading increases, the passage shock moves forward. Just before the passage shock unstarts, the stability of the passage shock decreases, and a small blade vibration causes the shock to oscillate with a large amplitude between unstarted and started positions. The dominant component of the blade excitation force is due to the foot of the oscillating passage shock on the blade pressure surface.
Computation of Unsteady Flows Around Oscillating Blades Using Linear and Nonlinear Harmonic Euler Methods
Authors: Ning W. , He L.
Published: December 2011

A quasi-three-dimensional time-linearized Euler method has been developed to compute unsteady flows around oscillating blades. In the baseline method, unsteady flow is decomposed into a steady flow plus a linear harmonically varying unsteady flow. Both the steady flow equations and the unsteady perturbation equations are solved using a pseudo-time-marching method. Based upon this method, a novel nonlinear harmonic Euler method has been developed. Due to the nonlinearity of the aerodynamic governing equations, time-averaging generates extra “unsteady stress” terms. These nonlinear effects are included by a strongly coupled approach between the perturbation equations and the time-averaged equations. Numerical results demonstrate that nonlinear effects are very effectively modeled by the nonlinear harmonic method.
45 deg Staggered Rib Heat Transfer Coefficient Measurements in a Square Channel
Authors: Taslim M. E. , Lengkong A.
Published: December 2011

For high-blockage ribs with large heat transfer areas, commonly used in small gas turbine blades, the rib heat transfer is a significant portion of the overall heat transfer in the cooling passages. Three staggered 45 deg rib geometries corresponding to blockage ratios of 0.133, 0.167, and 0.25 were tested in a square channel for pitch-to-height ratios of 5, 8.5, and 10, and for two distinct thermal boundary conditions of heated and unheated channel walls. Comparisons were made between the surface-averaged heat transfer coefficients and friction factors for 45 deg ribs, and 90 deg ribs reported previously. Heat transfer coefficients of the furthest upstream rib and that of a typical rib located in the middle of the rib-roughened region were also compared. It was concluded that: (a) For the geometries tested, the rib average heat transfer coefficient was much higher than that for the area between the ribs. (b) Except for two cases corresponding to the highest blockage ribs mounted at pitch-to-height ratios of 8.5 and 10 for which the heat transfer results of 45 deg ribs were very close to those of 90 deg ribs, 45 deg ribs produced higher heat transfer coefficients than 90 deg ribs. (c) At pitch-to-height ratios of 8.5 and 10, all 45 deg ribs produced lower friction factors than 90 deg ribs. However, when they were brought closer to each other (S/e = 5), they produced higher friction factors than 90 deg ribs. (d) Heat transfer coefficients for the two smaller rib geometries (e/Dh = 0.133 and 0.167) did not vary significantly with the pitch-to-height ratio in the range tested. However, the heat transfer coefficient for the high blockage rib geometry increased significantly as the ribs were brought closer to each other. (e) Under otherwise identical conditions, ribs in the furthest upstream position produced lower heat transfer coefficients than those in the midstream position. (f) Rib thermal performance decreased with the rib blockage ratio. For both angles of attack, the smallest rib geometry in the midstream position and at a pitch-to-height ratio of 10 had the highest thermal performance, and the highest blockage rib in the furthest upstream position produced the lowest thermal performance.
Effect of Rib Height and Pitch on the Thermal Performance of a Passage Disturbed by Detached Solid Ribs
Authors: Liou Tong-Miin , Shuy Woei-Jiunn , Tsao Yu-Houe
Published: December 2011

Laser holographic interferometry and pressure measurements are presented for the effects of rib-to-duct height ratio (H/2B), rib pitch-to-height ratio (Pi/H), and Reynolds number (Re) on the spatially periodic-fully developed turbulent heat transfer and friction in a rectangular duct of width-to-height ratio of 4:1 with an array of ribs detached from one wall at a clearance to rib-height ratio of 0.38. The ranges of H/2B, Pi/H, and Re examined were 0.13 to 0.26, 7 to 13, and 5 × 103 to 5 × 104, respectively. The difference in the H/2B dependence of the thermal performance between the detached and attached solid-rib array is documented. H/2B = 0.17 and Pi/H = 10 are found to provide the best thermal performance for the range of parameters tested. Compact heat transfer and friction correlations are developed. Additionally, it is found that heat transfer augmentation with a detached solid-rib array is superior to with a detached perforated-rib array, and the mechanism responsible for the difference is revealed by the complementary flow visualization results.
Heat Transfer in a Two-Pass Internally Ribbed Turbine Blade Coolant Channel With Cylindrical Vortex Generators
Authors: Hibbs R. G. , Acharya S. , Chen Y. , Nikitopoulos D. E. , Myrum T. A.
Published: December 2011

The effect of vortex generators on the mass (heat) transfer from the ribbed passage of a two-pass turbine blade coolant channel is investigated with the intent of optimizing the vortex generator geometry so that significant enhancements in mass/heat transfer can be achieved. In the experimental configuration considered, ribs are mounted on two opposite walls; all four walls along each pass are active and have mass transfer from their surfaces but the ribs are nonparticipating. Mass transfer measurements, in the form of Sherwood number ratios, are made along the centerline and in selected interrib modules. Results are presented for Reynolds number in the range of 5000 to 40,000, pitch to rib height ratios of 10.5 and 21, and vortex generator-rib spacing to rib height ratios of 0.55 and 1.5. Centerline and spanwise-averaged Sherwood number ratios are presented along with contours of the Sherwood number ratios. Results indicate that the vortex generators lead to substantial increases in the local mass transfer rates, particularly along the side walls, and modest increases in the average mass transfer rates. The vortex generators have the effect of making the interrib profiles along the ribbed walls more uniform. Along the side walls, vortices that characterize the vortex generator wake are associated with significant mass transfer enhancements. The wake effects and the levels of enhancement decrease somewhat with increasing Reynolds number and decreasing pitch.
A High-Temperature Assessment of Air-Cooled Unsteady Pressure Transducers
Authors: Ferguson D. G. , Ivey P. C.
Published: December 2011

This paper discusses the problem of measuring unsteady pressure in a high-temperature environment using standard transducers. Commercially available cooling adapters for these transducers use water as the cooling medium to provide thermal protection. This arrangement is suitable only for some test bed applications and not suitable for integration into in-flight active control systems. An assessment of the cooling effectiveness of a commercial water-cooled adapter using air as the cooling medium is presented using an experimentally validated finite element heat transfer model. The assessment indicates survival of an air-cooled transducer, itself rated to 235°C, at source flow temperatures up to 800°C.
Dual Time Stepping Algorithms With the High Order Harmonic Balance Method for Contact Interfaces With Fretting-Wear
Authors: Salles Loïc , Blanc Laurent , Thouverez Fabrice , Gouskov Alexander M. , Jean Pierrick
Published: December 2011

Contact interfaces with dry friction are frequently used in turbomachinery. Dry friction damping produced by the sliding surfaces of these interfaces reduces the amplitude of bladed-disk vibration. The relative displacements at these interfaces lead to fretting-wear which reduces the average life expectancy of the structure. Frequency response functions are calculated numerically by using the multi-harmonic balance method (mHBM). The dynamic Lagrangian frequency-time method is used to calculate contact forces in the frequency domain. A new strategy for solving nonlinear systems based on dual time stepping is applied. This method is faster than using Newton solvers. It was used successfully for solving Nonlinear CFD equations in the frequency domain. This new approach allows identifying the steady state of worn systems by integrating wear rate equations a on dual time scale. The dual time equations are integrated by an implicit scheme. Of the different orders tested, the first order scheme provided the best results.
Application of Dielectric Barrier Discharge to Improve the Flashback Limit of a Lean Premixed Dump Combustor
Authors: Versailles Philippe , Ali Chishty Wajid , Duc Vo Huu
Published: December 2011

In recent years, lean-premixed (LP) combustors have been widely studied due to their potential to reduce NOx emissions in comparison to diffusion type combustors. However, the fact that the fuels and oxidizers are mixed upstream of the combustion zone makes LP type of combustors a candidate for upstream flame propagation (i.e., flashback) in the premixer that is typically not designed to sustain high temperatures. Moreover, there has been a recent demand for fuel-flexible gas turbines that can operate on hydrogen-enriched fuels like Syngas. Combustors originally designed for slower kinetics fuels like natural gas can potentially encounter flashback if operated with faster burning fuels like those containing hydrogen as a constituent. There exists a clear need in fuel-flexible lean-premixed combustors to control flashback that will not only prevent costly component damage but will also enhance the operability margin of engines. A successful attempt has been made to control flashback in an atmospheric LP combustor, burning natural gas-air mixtures, via the application of dielectric barrier discharge (DBD). A low-power DBD actuator was designed, fabricated and integrated into a premixer made out of quartz. The actuator was tuned to produce a low magnitude ionic wind with an intention to modify the velocity profile in the premixer. Flashback conditions were created by decreasing the air flow rate while keeping the fuel flow rate constant. Within this experimental setup, flashback happened in the core flow along the axis of the cylindrical premixer. Results show that the utilization of the DBD delays the occurrence of flashback to higher equivalence ratios. Improvements as high as about 5% of the flashback limit have been obtained without compromising the blowout limit. It is anticipated that this novel application of DBD will lead to future demonstrations of the concept under realistic gas turbine operating conditions.
Control of Uncertain Nonlinear Systems Using an Uncertainty and Disturbance Estimator
Authors: Deshpande V. S. , Phadke S. B.
Published: December 2011

In this paper, we extend a recently developed method (Zhong and Rees, 2004, “Control of Uncertain LTI Systems Based on an Uncertainty and Disturbance Estimator,” ASME J. Dyn. Syst., Meas., Control, 126(4), pp. 905–910), for controlling uncertain linear systems using an uncertainty and disturbance estimator, to uncertain nonlinear systems. Further the control proposed in this paper removes the drawback of large initial control underlying the method. The stability of the overall system of the plant and the estimator is proved. The efficacy of the method is illustrated by simulation.
Flatness-Based High Frequency Control of a Hydraulic Actuator
Authors: Kock Florian , Ferrari Cornelius
Published: December 2011

This paper presents the design and implementation of a nonlinear feedforward control algorithm for a hydraulic actuator driven by a multistage servo valve. Combined with a conventional feedback control algorithm, high frequencies can be achieved even for large-scale strokes. In addition to the desired trajectory, the feedforward controller accepts the predicted dynamic load on the hydraulic actuator as an input. The performance of the control concept as well as the advantages of the load input are verified in simulations and experiments. Being exemplarily used for realizing a crankshaft-less test stand for free piston engines, the control algorithm is potentially suitable for further applications using hydraulic actuators in high frequency domain.
A Uniform Control Method for Imbalance Compensation and Automation Balancing in Active Magnetic Bearing-Rotor Systems
Authors: Kejian Jiang , Changsheng Zhu , Ming Tang
Published: December 2011

The undesired synchronous vibration due to rotor mass imbalance is a main disturbance source in all rotating machinery including active magnetic bearing (AMB)-rotor systems. In the AMB-rotor system, imbalance compensation, which causes the AMB actuators to spin a rotor about its geometric axis, and automation balancing, which spins a rotor about its inertial axis, are two kinds of common control aim for the rotor imbalance control. In this study, the internal relation between the imbalance compensation and the automation balancing is analyzed and a uniform control method is proposed. With the identical control algorithm, the proposed control method can realize the automation balancing or the imbalance compensation, respectively, by switching the controller’s junction position in the original control loop. The proposed control method does not depend on the dynamic plant model, because its algorithm is based on the real-time identification for the Fourier coefficient of the rotor imbalance disturbance. In this paper, the process of identification algorithm is given in detail and all the possible junction forms of the controller are illustrated. By the simulations, the identification performances of the control algorithm are compared in the conditions with three variable factors, including the signal noise ratio (SNR), the imbalance phase and the identification delay time. The noise level has considerable influence on the identification precision, but the imbalance phase has little. To prolong the identification delay time will be of benefit to improve the identification precision but slow down the identification process. Experiments, which are carried out on an AMB-rigid rotor test rig, indicate that by switching the junction position of the controller in control loop, both kinds of rotor imbalance control can achieve the good effectiveness.
Immunological Response to Parenteral Vaccination with Recombinant Hepatitis B Virus Surface Antigen Virus-Like Particles Expressing Helicobacter pylori KatA Epitopes in a Murine H. pylori Challenge Model
Authors: Kotiw Michael , Johnson Megan , Pandey Manisha , Fry Scott , Hazell Stuart L. , Netter Hans J. , Good Michael F. , Olive Colleen
Published: December 2011

Virus-like particles (VLPs) based on the small envelope protein of hepatitis B virus (HBsAg-S) are immunogenic at the B- and T-cell level. In this study, we inserted overlapping sequences encoding the carboxy terminus of theHelicobacter pylori katAgene product into HBsAg-S. The HBsAg-S–KatA fusion proteins were able to assemble into secretion-competent VLPs (VLP-KatA). The VLP-KatA proteins were able to induce KatA-specific antibodies in immunized mice. The mean total IgG antibody titers 41 days post-primary immunization with VLP-KatA (2.3 × 103) were significantly greater (P< 0.05) than those observed for vaccination with VLP alone (5.2 × 102). Measurement of IgG isotypes revealed responses to both IgG1 and IgG2a (mean titers, 9.0 × 104and 2.6 × 104, respectively), with the IgG2a response to vaccination with VLP-KatA being significantly higher than that for mice immunized with KatA alone (P< 0.05). Following challenge of mice withH. pylori, a significantly reduced bacterial load in the gastric mucosa was observed (P< 0.05). This is the first report describing the use of VLPs as a delivery vehicle forH. pyloriantigens.
Anti-Toxoplasma Antibody Prevalence, Primary Infection Rate, and Risk Factors in a Study of Toxoplasmosis in 4,466 Pregnant Women in Japan
Authors: Sakikawa Makiko , Noda Shunichi , Hanaoka Masachi , Nakayama Hirotoshi , Hojo Satoshi , Kakinoki Shigeko , Nakata Maki , Yasuda Takashi , Ikenoue Tsuyomu , Kojima Toshiyuki
Published: December 2011

Toxoplasmosis is a zoonosis caused by infection withToxoplasma gondiiand is prevalent worldwide under various climatic conditions. It is usually asymptomatic, but infection in pregnant women can pose serious health problems for the fetus. However, epidemiological information regarding toxoplasmosis in Japanese pregnant women is limited. This study aimed to determine the prevalence of anti-Toxoplasmaantibodies, the primary infection rate, and the risk factors for toxoplasmosis in Japanese pregnant women. We measured anti-Toxoplasmaantibody titers in 4,466 pregnant women over a period of 7.5 years and simultaneously conducted interviews to identify the risk factors for toxoplasmosis. The overall prevalence of anti-Toxoplasmaantibodies was 10.3%, and it was significantly higher in women aged above 35 years. The rate of primaryToxoplasmainfection during pregnancy was estimated to be 0.25%. A possibility of infection in the later stages of pregnancy was identified for those women who were not infected in the early stages. A history of raw meat intake was identified to be a risk factor related to toxoplasmosis. Therefore, to lower the risk of toxoplasmosis, pregnant women should refrain from eating raw and undercooked meat and maintain personal hygiene.
Human Endogenous Retrovirus K(HML-2) Gag- and Env-Specific T-Cell Responses Are Infrequently Detected in HIV-1-Infected Subjects Using Standard Peptide Matrix-Based Screening
Authors: Jones R. Brad , John Vivek M. , Hunter Diana V. , Martin Eric , Mujib Shariq , Mihajlovic Vesna , Burgers Peter C. , Luider Theo M. , Gyenes Gabor , Sheppard Neil C. , SenGupta Devi , Tandon Ravi , Yue Feng-Yun , Benko Erika , Kovacs Colin , Nixon Douglas F. , Ostrowski Mario A.
Published: December 2011

T-cell responses to human endogenous retrovirus (HERV) K(HML-2) Gag and Env were mapped in HIV-1-infected subjects using 15mer peptides. Small peptide pools and high concentrations were used to maximize sensitivity. In the 23 subjects studied, only three bona fide HERV-K(HML-2)-specific responses were detected. At these high peptide concentrations, we detected false-positive responses, three of which were mapped to an HIV-1 Gag peptide contaminant. Thus, HERV-K(HML-2) Gag- and Env-specific T-cell responses are infrequently detected by 15mer peptide mapping.
Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls
Authors: Masai Eiji , Kamimura Naofumi , Kasai Daisuke , Oguchi Akio , Ankai Akiho , Fukui Shigehiro , Takahashi Mikio , Yashiro Isao , Sasaki Hiroki , Harada Takeshi , Nakamura Sanae , Katano Yoko , Narita-Yamada Sachiko , Nakazawa Hidekazu , Hara Hirofumi , Katayama Yoshihiro , Fukuda Masao , Yamazaki Shuji , Fujita Nobuyuki
Published: December 2011

Sphingobium
sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls and monoaryls, and the catabolic genes for these compounds are useful for the production of industrially valuable metabolites from lignin. Here we report the complete nucleotide sequence of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and the 148,801-bp-long plasmid.
Whole-Genome Sequences of Borrelia bissettii, Borrelia valaisiana, and Borrelia spielmanii
Authors: Schutzer Steven E. , Fraser-Liggett Claire M. , Qiu Wei-Gang , Kraiczy Peter , Mongodin Emmanuel F. , Dunn John J. , Luft Benjamin J. , Casjens Sherwood R.
Published: December 2011

It has been known for decades that human Lyme disease is caused by the three spirochete species
Borrelia burgdorferi
,
Borrelia afzelii
, and
Borrelia garinii
. Recently,
Borrelia valaisiana
,
Borrelia spielmanii
, and
Borrelia bissettii
have been associated with Lyme disease. We report the complete genome sequences of
B. valaisiana
VS116,
B. spielmanii
A14S, and
B. bissettii
DN127.
Complete Sequences of Plasmids from the Hemolytic-Uremic Syndrome-Associated Escherichia coli Strain HUSEC41
Authors: Künne Carsten , Billion Andre , Mshana Stephen E. , Schmiedel Judith , Domann Eugen , Hossain Hamid , Hain Torsten , Imirzalioglu Can , Chakraborty Trinad
Published: December 2011

The complete and annotated sequences of four plasmids from a historical enteroaggregative Shiga toxin-producing
Escherichia coli
(HUSEC) serotype O104:H4 strain, HUSEC41/01-09591, isolated in 2001 in Germany are reported.
Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z
Authors: Vuilleumier Stéphane , Khmelenina Valentina N. , Bringel Françoise , Reshetnikov Alexandr S. , Lajus Aurélie , Mangenot Sophie , Rouy Zoé , Op den Camp Huub J. M. , Jetten Mike S. M. , Dispirito Alan A. , Dunfield Peter , Klotz Martin G. , Semrau Jeremy D. , Stein Lisa Y. , Barbe Valérie , Médigue Claudine , Trotsenko Yuri A. , Kalyuzhnaya Marina G.
Published: December 2011

Methylomicrobium
strains are widespread in saline environments. Here, we report the complete genome sequence of
Methylomicrobium alcaliphilum
20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making
M. alcaliphilum
20Z the first methanotrophic bacterium of known genome sequence for which a plasmid has been reported.
Draft Genome Sequence of Enterococcus mundtii CRL1656
Authors: Magni Christian , Espeche Carolina , Repizo Guillermo D. , Saavedra Lucila , Suárez Cristian A. , Blancato Víctor S. , Espariz Martín , Esteban Luis , Raya Raúl R. , Font de Valdez Graciela , Vignolo Graciela , Mozzi Fernanda , Taranto María Pía , Hebert Elvira M. , Nader-Macías María Elena , Sesma Fernando
Published: December 2011

We report the draft genome sequence of
Enterococcus mundtii
CRL1656, which was isolated from the stripping milk of a clinically healthy adult Holstein dairy cow from a dairy farm of the northwestern region of Tucumán (Argentina). The 3.10-Mb genome sequence consists of 450 large contigs and contains 2,741 predicted protein-coding genes.
Genome Sequence of the Bacteriocin-Producing Lactobacillus curvatus Strain CRL705
Authors: Hebert Elvira María , Saavedra Lucila , Taranto María Pía , Mozzi Fernanda , Magni Christian , Nader María Elena F. , Font de Valdez Graciela , Sesma Fernando , Vignolo Graciela , Raya Raúl R.
Published: December 2011

Lactobacillus curvatus
is one of the most prevalent lactic acid bacteria found in fermented meat products. Here, we present the draft genome sequence of
Lactobacillus curvatus
CRL705, a bacteriocin producer strain isolated from an Argentinean artisanal fermented sausage, which consists of 1,833,251 bp (GC content, 41.9%) and two circular plasmids of 12,342 bp (pRC12; GC, 43.9%) and 18,664 bp (pRC18; GC, 34.4%).
Complete Genome Sequence of the Rice Pathogen Pantoea ananatis Strain PA13
Authors: Choi Okhee , Lim Jae Yun , Seo Young-Su , Hwang Ingyu , Kim Jinwoo
Published: December 2011

Pantoea ananatis
is the causative agent of sheath and grain rot in rice. Here, we present the complete genome sequence of
P. ananatis
strain PA13, originally isolated from a diseased rice grain.
Shotgun Genome Sequence of a Yersinia enterocolitica Isolate from the Philippines
Authors: Klinzing David C. , Matias Ronald R. , Skowronski Evan , Alvarez May , Liles Veni , Dimamay Mark Pierre , Natividad Filipinas F.
Published: December 2011

The first shotgun genome sequence of a microbial pathogen from the Philippines is reported.
Yersinia enterocolitica
subsp.
palearctica
strain PhRBD_Ye1 is the first
Y. enterocolitica
strain sequenced from an animal source, swine, which is a natural source of yersiniosis. The closest phylogenetic match is a human clinical isolate from Germany.
New Species of Madurella, Causative Agents of Black-Grain Mycetoma
Authors: de Hoog G. Sybren , van Diepeningen Anne D. , Mahgoub El-Sheikh , van de Sande Wendy W. J.
Published: December 2011

A new species of nonsporulating fungus, isolated in a case of black-grain mycetoma in Sudan, is described as
Madurella fahalii
. The species is characterized by phenotypic and molecular criteria. Multigene phylogenies based on the ribosomal DNA (rDNA) internal transcribed spacer (ITS), the partial β-tubulin gene (
BT2
), and the RNA polymerase II subunit 2 gene (
RPB2
) indicate that
M. fahalii
is closely related to
Madurella mycetomatis
and
M. pseudomycetomatis
; the latter name is validated according to the rules of botanical nomenclature.
Madurella ikedae
was found to be synonymous with
M. mycetomatis
. An isolate from Indonesia was found to be different from all known species based on multilocus analysis and is described as
Madurella tropicana. Madurella
is nested within the order Sordariales, with
Chaetomium
as its nearest neighbor.
Madurella fahalii
has a relatively low optimum growth temperature (30°C) and is less susceptible to the azoles than other
Madurella
species, with voriconazole and posaconazole MICs of 1 μg/ml, a ketoconazole MIC of 2 μg/ml, and an itraconazole MIC of >16 μg/ml. Since eumycetoma is still treated only with azoles, correct species identification is important for the optimal choice of antifungal therapy.
Molecular and Microbiological Characterization of Clostridium difficile Isolates from Single, Relapse, and Reinfection Cases
Authors: Oka Kentaro , Osaki Takako , Hanawa Tomoko , Kurata Satoshi , Okazaki Mitsuhiro , Manzoku Taki , Takahashi Motomichi , Tanaka Mamoru , Taguchi Haruhiko , Watanabe Takashi , Inamatsu Takashi , Kamiya Shigeru
Published: December 2011

In this study, we investigated the correlation between the microbiological characteristics of
Clostridium difficile
clinical isolates and the recurrence of
C. difficile
-associated disease (CDAD). Twenty
C. difficile
isolates recovered from 20 single infection cases and 53 isolates from 20 recurrent cases were analyzed by pulsed-field gel electrophoresis (PFGE) and PCR ribotyping, and the cytotoxicity, antimicrobial susceptibility, and sporulation/germination rates of the isolates were examined. Recurrent cases were divided into relapse or reinfection cases by the results of
C. difficile
DNA typing. Among the 20 recurrent cases, 16 cases (80%) were identified to be relapse cases caused by the initial strain and the remaining 4 cases (20%) were identified to be reinfection cases caused by different strains. All 73 isolates were susceptible to both vancomycin and metronidazole, but resistance against clindamycin, ceftriaxone, erythromycin, and ciprofloxacin was found in 87.7%, 93.2%, 87.7%, and 100% of the isolates, respectively. No correlations between DNA typing group, cytotoxicity, and sporulation rate of isolates and infection status, i.e., single, relapse, or reinfection, were observed. However, the isolates recovered from relapse cases showed a significantly higher germination rate when incubated in medium lacking the germination stimulant sodium taurocholate. These results indicate that the germination ability of
C. difficile
may be a potential risk factor for the recurrence of CDAD.
Comprehensive Multicenter Evaluation of a New Line Probe Assay Kit for Identification of Mycobacterium Species and Detection of Drug-Resistant Mycobacterium tuberculosis
Authors: Mitarai Satoshi , Kato Seiya , Ogata Hideo , Aono Akio , Chikamatsu Kinuyo , Mizuno Kazue , Toyota Emiko , Sejimo Akiko , Suzuki Katsuhiro , Yoshida Shiomi , Saito Takefumi , Moriya Ataru , Fujita Akira , Sato Shuko , Matsumoto Tomoshige , Ano Hiromi , Suetake Toshinori , Kondo Yuji , Kirikae Teruo , Mori Toru
Published: December 2011

We evaluated a new line probe assay (LiPA) kit to identify
Mycobacterium
species and to detect mutations related to drug resistance in
Mycobacterium tuberculosis
. A total of 554 clinical isolates of
Mycobacterium tuberculosis
(
n
= 316),
Mycobacterium avium
(
n
= 71),
Mycobacterium intracellulare
(
n
= 51),
Mycobacterium kansasii
(
n
= 54), and other
Mycobacterium
species (
n
= 62) were tested with the LiPA kit in six hospitals. The LiPA kit was also used to directly test 163 sputum specimens. The results of LiPA identification of
Mycobacterium
species in clinical isolates were almost identical to those of conventional methods. Compared with standard drug susceptibility testing results for the clinical isolates, LiPA showed a sensitivity and specificity of 98.9% and 97.3%, respectively, for detecting rifampin (RIF)-resistant clinical isolates; 90.6% and 100%, respectively, for isoniazid (INH) resistance; 89.7% and 96.0%, respectively, for pyrazinamide (PZA) resistance; and 93.0% and 100%, respectively, for levofloxacin (LVX) resistance. The LiPA kit could detect target species directly in sputum specimens, with a sensitivity of 85.6%. Its sensitivity and specificity for detecting RIF-, PZA-, and LVX-resistant isolates in the sputum specimens were both 100%, and those for detecting INH-resistant isolates were 75.0% and 92.9%, respectively. The kit was able to identify mycobacterial bacilli at the species level, as well as drug-resistant phenotypes, with a high sensitivity and specificity.
Pediococcus acidilactici Endocarditis Successfully Treated with Daptomycin
Authors: Iwen Peter C. , Mindru Cezarina , Kalil Andre C. , Florescu Diana F.
Published: December 2011

This report describes the first case of persistent bacteremia with endocarditis caused by
Pediococcus acidilactici
in a 32-year-old male with a history of short gut syndrome following a small bowel transplant. The results showed the utility of sequencing the intergenic spacer region for species identification and successful treatment using daptomycin.
Novel Real-Time Simultaneous Amplification and Testing Method To Accurately and Rapidly Detect Mycobacterium tuberculosis Complex
Authors: Cui Zhenling , Wang Yongzhong , Fang Liang , Zheng Ruijuan , Huang Xiaochen , Liu Xiaoqin , Zhang Gang , Rui Dongmei , Ju Jinliang , Hu Zhongyi
Published: December 2011

The aim of this study was to establish and evaluate a simultaneous amplification and testing method for detection of the
Mycobacterium tuberculosis
complex (SAT-TB assay) in clinical specimens by using isothermal RNA amplification and real-time fluorescence detection. In the SAT-TB assay, a 170-bp
M. tuberculosis
16S rRNA fragment is reverse transcribed to DNA by use of Moloney murine leukemia virus (M-MLV) reverse transcriptase, using specific primers incorporating the T7 promoter sequence, and undergoes successive cycles of amplification using T7 RNA polymerase. Using a real-time PCR instrument, hybridization of an internal 6-carboxyfluorescein–4-[4-(dimethylamino)phenylazo] benzoic acid
N
-succinimidyl ester (FAM-DABCYL)-labeled fluorescent probe can be used to detect RNA amplification. The SAT-TB assay takes less than 1.5 h to perform, and the sensitivity of the assay for detection of
M. tuberculosis
H37Rv is 100 CFU/ml. The TB probe has no cross-reactivity with nontuberculous mycobacteria or other common respiratory tract pathogens. For 253 pulmonary tuberculosis (PTB) specimens and 134 non-TB specimens, the SAT-TB results correlated with 95.6% (370/387 specimens) of the Bactec MGIT 960 culture assay results. The sensitivity, specificity, and positive and negative predictive values of the SAT-TB test for the diagnosis of PTB were 67.6%, 100%, 100%, and 62.0%, respectively, compared to 61.7%, 100%, 100%, and 58.0% for Bactec MGIT 960 culture. For PTB diagnosis, the sensitivities of the SAT-TB and Bactec MGIT 960 culture methods were 97.6% and 95.9%, respectively, for smear-positive specimens and 39.2% and 30.2%, respectively, for smear-negative specimens. In conclusion, the SAT-TB assay is a novel, simple test with a high specificity which may enhance the detection rate of TB. It is therefore a promising tool for rapid diagnosis of
M. tuberculosis
infection in clinical microbiology laboratories.
Leptotrichia Bacteremia in Patients Receiving High-Dose Chemotherapy
Authors: Couturier Marc Roger , Slechta E. Susan , Goulston Claudia , Fisher Mark A. , Hanson Kimberly E.
Published: December 2011

Leptotrichia
spp. are anaerobic, pencil-shaped, Gram-negative rods that are part of the normal oral and intestinal human flora. Although not typically considered pathogenic, invasive
Leptotrichia
infections have been reported in immunosuppressed patients. A perceived rise in the identification of
Leptotrichia
spp. at our institution prompted a retrospective evaluation of these infections. Laboratory and clinical records were reviewed to identify
Leptotrichia
culture-positive patients. Over a 5-year period, 68
Leptotrichia
-positive specimens were identified. Of these, 21% (14/68) were identified in original samples submitted from 13 different patients at our institution, and the remainder (79% [54/68]) were unknown isolates referred from outside hospitals for molecular identification. All in-house
Leptotrichia
were identified from blood cultures. Only 64% (9/14) of these grew on solid media, and 5 were a part of polymicrobial bacteremias containing other enteric pathogens. All local patients were receiving chemotherapy and a majority received hematopoietic stem cell transplant (HSCT) (11/13). All had neutropenic fever with symptoms of mucositis and/or enteritis. Most of the HSCT patients (73% [8/11]) were autologous recipients hospitalized after recent high-dose chemotherapy for multiple myeloma.
L. hongkongensis
, a novel species, was found in the majority of myeloma cases (63% [5/8]). In conclusion, we suggest that
Leptotrichia
spp. may be an underappreciated cause of bacteremia, particularly in multiple myeloma patients receiving cytotoxic chemotherapy for autologous HSCT. In our cohort, these infections were associated with neutropenic fever from an enteric source, and most isolates remained sensitive to standard antibiotics.
Molecular Diagnosis of Subcutaneous Pythium insidiosum Infection by Use of PCR Screening and DNA Sequencing
Authors: Salipante Stephen J. , Hoogestraat Daniel R. , SenGupta Dhruba J. , Murphey Donald , Panayides Kyriacos , Hamilton Emma , Castañeda-Sánchez Irene , Kennedy Jason , Monsaas Peter W. , Mendoza Leonel , Stephens Karen , Dunn James J. , Cookson Brad T.
Published: December 2011

Pythium insidiosum
is an emerging human pathogen classified among brown algae and diatoms that can cause significant morbidity and mortality in otherwise healthy individuals. Here we describe a pediatric patient with pythiosis acquired in the southern United States, diagnosed by molecular screening and DNA sequencing of internal transcribed spacer region 1.
Legionella pneumophila Sequence Type 1/Paris Pulsotype Subtyping by Spoligotyping
Authors: Ginevra Christophe , Jacotin Nathalie , Diancourt Laure , Guigon Ghislaine , Arquilliere Romain , Meugnier Hélène , Descours Ghislaine , Vandenesch Francois , Etienne Jerome , Lina Gérard , Caro Valérie , Jarraud Sophie
Published: December 2011

Endemic strains of
Legionella pneumophila
sequence type 1 (ST1), in particular the ST1/Paris pulsotype, are dispersed worldwide and represent about 10% of culture-proven clinical cases of Legionnaires' disease in France. The high rate of isolation of this strain from both clinical and environmental samples makes identification of the source of infection difficult during epidemiological investigations. The full-length genome sequence of this strain was recently determined, and it revealed the presence of a CRISPR/
cas
complex. The aim of this study was to develop and evaluate a spoligotyping tool based on the diversity of this CRISPR locus that would allow the accurate subtyping of the
L. pneumophila
serogroup 1 ST1/Paris pulsotype. The CRISPR loci of 28
L. pneumophila
ST1/Paris pulsotype isolates were sequenced, and 42 different spacers regions were characterized. A membrane-based spoligotyping method was developed and used to determine the subtypes of 406
L. pneumophila
isolates, including 233 with the ST1/Paris pulsotype profile that were collected in France from 2000 to 2011. A total of 46 different spoligotypes were detected, and 41 of these were specifically identified in the ST1/Paris pulsotype isolates. In 27 of 33 epidemiological investigations, the environmental source of contamination was confirmed by comparing spoligotypes of clinical isolates with those of environmental isolates. With an index of discrimination of 79.72% (95% confidence interval, 75.82 to 83.63), spoligotyping of the
L. pneumophila
ST1/Paris pulsotype has the potential to be a useful complementary genotyping tool for discriminating isolates with undistinguishable pulsed-field gel electrophoresis (PFGE) and ST genotypes, which could help to identify environmental sources of infection.
Presence of Genes Encoding Panton-Valentine Leukocidin Is Not the Primary Determinant of Outcome in Patients with Hospital-Acquired Pneumonia Due to Staphylococcus aureus
Authors: Sharma-Kuinkel Batu K. , Ahn Sun H. , Rude Thomas H. , Zhang Yurong , Tong Steven Y. C. , Ruffin Felicia , Genter Fredric C. , Braughton Kevin R. , DeLeo Frank R. , Barriere Steven L. , Fowler Vance G.
Published: December 2011

The impact of Panton-Valentine leukocidin (PVL) on the outcome in
Staphylococcus aureus
pneumonia is controversial. We genotyped
S. aureus
isolates from patients with hospital-acquired pneumonia (HAP) enrolled in two registrational multinational clinical trials for the genetic elements carrying
pvl
and 30 other virulence genes. A total of 287 isolates (173 methicillin-resistant
S. aureus
[MRSA] and 114 methicillin-susceptible
S. aureus
[MSSA] isolates) from patients from 127 centers in 34 countries for whom clinical outcomes of cure or failure were available underwent genotyping. Of these,
pvl
was detected by PCR and its product confirmed in 23 isolates (8.0%) (MRSA, 18/173 isolates [10.4%]; MSSA, 5/114 isolates [4.4%]). The presence of
pvl
was not associated with a higher risk for clinical failure (4/23 [17.4%] versus 48/264 [18.2%];
P
= 1.00) or mortality. These findings persisted after adjustment for multiple potential confounding variables. No significant associations between clinical outcome and (i) presence of any of the 30 other virulence genes tested, (ii) presence of specific bacterial clone, (iii) levels of alpha-hemolysin, or (iv) delta-hemolysin production were identified. This study suggests that neither
pvl
presence nor
in vitro
level of alpha-hemolysin production is the primary determinant of outcome among patients with HAP caused by
S. aureus
.
The Geographic Origin of Helicobacter pylori Influences the Association of the
homB
Gene with Gastric Cancer
Authors: Kang Jieun , Jones Kathleen R. , Jang Sungil , Olsen Cara H. , Yoo Yun-Jung , Merrell D. Scott , Cha Jeong-Heon
Published: December 2011

We found that South Korean
Helicobacter pylori
isolates predominantly carry
homB
at locus B and that there is no association between the
homB
allele and the
cagA
allele or the development of gastric cancer within this population. Uniquely, several East Asian strains carried multiple copies of the
hom
genes.
Evaluation of Swabs, Transport Media, and Specimen Transport Conditions for Optimal Detection of Viruses by PCR
Authors: Druce Julian , Garcia Katherine , Tran Thomas , Papadakis Georgina , Birch Chris
Published: December 2011

Depletion of swabs and viral transport medium during epidemics may prompt the use of unvalidated alternatives. Swabs collected and transported dry or in saline were compared to commercially available swab/medium combinations for PCR detection of influenza, enterovirus, herpes simplex virus, and adenovirus. Each was detected at an ambient temperature (22°C) and 4°C for 7 days. Detection of influenza on dry or saline swabs is important because of its capacity to cause outbreaks involving large numbers of cases.
Severity of Human Rhinovirus Infection in Immunocompromised Adults Is Similar to That of 2009 H1N1 Influenza
Authors: Kraft Colleen S. , Jacob Jesse T. , Sears Marti H. , Burd Eileen M. , Caliendo Angela M. , Lyon G. Marshall
Published: December 2011

This retrospective chart review of patients at a tertiary referral center compares characteristics and clinical features of patients diagnosed with human rhinovirus (HRV) infection to those of patients with 2009 H1N1 influenza A (pH1N1) during the pandemic respiratory season of 2009 to 2010. Hospital admission rates, intensive care unit (ICU) admissions, and mortality were not statistically different between the HRV and pH1N1 groups; however, more patients in the HRV group were considered immunocompromised.
Detection of Negative-Sense RNA in Packaged Hepatitis E Virions by Use of an Improved Strand-Specific Reverse Transcription-PCR Method
Authors: Chatterjee Subhashis N. , Devhare Pradip B. , Lole Kavita S.
Published: December 2011

Current hepatitis E virus (HEV) negative-sense RNA detection assays have the drawback of false positivity. cDNA synthesis using tag-based primer and Superscript RT-III followed by exonuclease I treatment increased the specificity. Assays could detect as few as 10 copies of negative-sense RNA and could be used in detecting low levels of HEV replication in cells. Virus particles in stool samples of hepatitis E patients showed encapsidation of negative-sense RNA along with HEV genomic RNA.
Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus ϕ6 from
De Novo
Initiation to Elongation
Authors: Wright Sam , Poranen Minna M. , Bamford Dennis H. , Stuart David I. , Grimes Jonathan M.
Published: December 2011

RNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. A common divalent cation binding site, distinct from the positions of catalytic ions, has been identified in many viral RdRps. We have applied biochemical, biophysical, and structural approaches to show how the RdRp from bacteriophage ϕ6 uses the bound noncatalytic Mn
2+
to facilitate the displacement of the C-terminal domain during the transition from initiation to elongation. We find that this displacement releases the noncatalytic Mn
2+
, which must be replaced for elongation to occur. By inserting a dysfunctional Mg
2+
at this site, we captured two nucleoside triphosphates within the active site in the absence of Watson-Crick base pairing with template and mapped movements of divalent cations during preinitiation. These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in ϕ6 RdRp, and pinpoint the previously unresolved Mn
2+
-dependent step in replication.
The Multibasic Cleavage Site of the Hemagglutinin of Highly Pathogenic A/Vietnam/1203/2004 (H5N1) Avian Influenza Virus Acts as a Virulence Factor in a Host-Specific Manner in Mammals
Authors: Suguitan Amorsolo L. , Matsuoka Yumiko , Lau Yuk-Fai , Santos Celia P. , Vogel Leatrice , Cheng Lily I. , Orandle Marlene , Subbarao Kanta
Published: December 2011

Highly pathogenic avian influenza (HPAI) viruses of the H5 and H7 subtypes typically possess multiple basic amino acids around the cleavage site (MBS) of their hemagglutinin (HA) protein, a recognized virulence motif in poultry. To determine the importance of the H5 HA MBS as a virulence factor in mammals, recombinant wild-type HPAI A/Vietnam/1203/2004 (H5N1) viruses that possessed (H5N1) or lacked (ΔH5N1) the H5 HA MBS were generated and evaluated for their virulence in BALB/c mice, ferrets, and African green monkeys (AGMs) (
Chlorocebus aethiops
). The presence of the H5 HA MBS was associated with lethality, significantly higher virus titers in the respiratory tract, virus dissemination to extrapulmonary organs, lymphopenia, significantly elevated levels of proinflammatory cytokines and chemokines, and inflammation in the lungs of mice and ferrets. In AGMs, neither H5N1 nor ΔH5N1 virus was lethal and neither caused clinical symptoms. The H5 HA MBS was associated with mild enhancement of replication and delayed virus clearance. Thus, the contribution of H5 HA MBS to the virulence of the HPAI H5N1 virus varies among mammalian hosts and is most significant in mice and ferrets and less remarkable in nonhuman primates.
Influenza A Virus Infection Results in a Robust, Antigen-Responsive, and Widely Disseminated Foxp3
+
Regulatory T Cell Response
Authors: Betts Richard J. , Prabhu Nayana , Ho Adrian W. S. , Lew Fei Chuin , Hutchinson Paul E. , Rotzschke Olaf , Macary Paul A. , Kemeny D. Michael
Published: December 2011

Foxp3
+
CD4
+
regulatory T cells (Tregs) represent a highly suppressive T cell subset with well-characterized immunosuppressive effects during immune homeostasis and chronic infections, although the role of these cells in acute viral infections is poorly understood. The present study sought to examine the induction of Foxp3
+
CD4
+
Tregs in a nonlethal murine model of pulmonary viral infection by the use of the prototypical respiratory virus influenza A. We establish that influenza A virus infection results in a robust Foxp3
+
CD4
+
T cell response and that regulatory T cell induction at the site of inflammation precedes the effector T cell response. Induced Foxp3
+
CD4
+
T cells are highly suppressive
ex vivo
, demonstrating that influenza virus-induced Foxp3
+
CD4
+
T cells are phenotypically regulatory. Influenza A virus-induced regulatory T cells proliferate vigorously in response to influenza virus antigen, are disseminated throughout the site of infection and primary and secondary lymphoid organs, and retain Foxp3 expression
in vitro
, suggesting that acute viral infection is capable of inducing a foreign-antigen-specific Treg response. The ability of influenza virus-induced regulatory T cells to suppress antigen-specific CD4
+
and CD8
+
T cell proliferation and cytokine production correlates closely to their ability to respond to influenza virus antigens, suggesting that virus-induced Tregs are capable of attenuating effector responses in an antigen-dependent manner. Collectively, these data demonstrate that primary acute viral infection is capable of inducing a robust, antigen-responsive, and suppressive regulatory T cell response.