bluuebunny/crossref_metadata_2025 huggingface dataset:
A fractional Fourier transform analysis of a bubble excited by an ultrasonic chirp
Authors: Barlow Euan , Mulholland Anthony J.
Published: November 2011

The fractional Fourier transform is proposed here as a model based, signal processing technique for determining the size of a bubble in a fluid. The bubble is insonified with an ultrasonic chirp and the radiated pressure field is recorded. This experimental bubble response is then compared with a series of theoretical model responses to identify the most accurate match between experiment and theory which allows the correct bubble size to be identified. The fractional Fourier transform is used to produce a more detailed description of each response, and two-dimensional cross correlation is then employed to identify the similarities between the experimental response and each theoretical response. In this paper the experimental bubble response is simulated by adding various levels of noise to the theoretical model output. The method is compared to the standard technique of using time-domain cross correlation. The proposed method is shown to be far more robust at correctly sizing the bubble and can cope with much lower signal to noise ratios.
Effect of temperature on rectified diffusion during ultrasound-induced heating
Authors: Webb Ian R. , Payne Stephen J. , Coussios Constantin-C.
Published: November 2011

Experimental observations of delayed-onset cavitation during ultrasound insonation have been suggested as being caused by a change in the size distribution of the bubble population due to rectified diffusion. To investigate this hypothesis, a single bubble model is used here to explore the effect of heating and the subsequent elevated temperatures on the rectified diffusion process. Numerical solution of the model, which includes the temperature dependences of seven relevant physical parameters, allows quantification of the change in the pressure threshold for rectified diffusion, as well as the importance of the bulk liquid saturation concentration in determining bubble evolution. Although elevated temperatures and liquid supersaturation reduce the rectified diffusion threshold, it remains coincident with the inertial cavitation thresholds at submicron bubble sizes at all temperatures. This observation suggests that changes in the nucleation environment, rather than bubble growth due to rectified diffusion, is a more likely cause of delayed-onset cavitation events.
Quantitative observations of cavitation activity in a viscoelastic medium
Authors: Collin Jamie R. T. , Coussios Constantin C.
Published: November 2011

Quantitative experimental observations of single-bubble cavitation in viscoelastic media that would enable validation of existing models are presently lacking. In the present work, single bubble cavitation is induced in an agar gel using a 1.15 MHz high intensity focused ultrasound transducer, and observed using a focused single-element passive cavitation detection (PCD) transducer. To enable quantitative observations, a full receive calibration is carried out of a spherically focused PCD system by a bistatic scattering substitution technique that uses an embedded spherical scatterer and a hydrophone. Adjusting the simulated pressure received by the PCD by the transfer function on receive and the frequency-dependent attenuation of agar gel enables direct comparison of the measured acoustic emissions with those predicted by numerical modeling of single-bubble cavitation using a modified Keller–Miksis approach that accounts for viscoelasticity of the surrounding medium. At an incident peak rarefactional pressure near the cavitation threshold, period multiplying is observed in both experiment and numerical model. By comparing the two sets of results, an estimate of the equilibrium bubble radius in the experimental observations can be made, with potential for extension to material parameter estimation. Use of these estimates yields good agreement between model and experiment.
Optical nucleation of bubble clouds in a high pressure spherical resonator
Authors: Anderson Phillip , Sampathkumar A. , Murray Todd W. , Gaitan D. Felipe , Glynn Holt R.
Published: November 2011

An experimental setup for nucleating clouds of bubbles in a high-pressure spherical resonator is described. Using nanosecond laser pulses and multiple phase gratings, bubble clouds are optically nucleated in an acoustic field. Dynamics of the clouds are captured using a high-speed CCD camera. The images reveal cloud nucleation, growth, and collapse and the resulting emission of radially expanding shockwaves. These shockwaves are reflected at the interior surface of the resonator and then reconverge to the center of the resonator. As the shocks reconverge upon the center of the resonator, they renucleate and grow the bubble cloud. This process is repeated over many acoustic cycles and with each successive shock reconvergence, the bubble cloud becomes more organized and centralized so that subsequent collapses give rise to stronger, better defined shockwaves. After many acoustic cycles individual bubbles cannot be distinguished and the cloud is then referred to as a cluster. Sustainability of the process is ultimately limited by the detuning of the acoustic field inside the resonator. The nucleation parameter space is studied in terms of laser firing phase, laser energy, and acoustic power used.
Cross-language specialization in phonetic processing: English and Hindi perception of /w/-/v/ speech and nonspeech
Authors: Iverson Paul , Wagner Anita , Pinet Melanie , Rosen Stuart
Published: November 2011

This study examined the perceptual specialization for native-language speech sounds, by comparing native Hindi and English speakers in their perception of a graded set of English /w/-/v/ stimuli that varied in similarity to natural speech. The results demonstrated that language experience does not affect general auditory processes for these types of sounds; there were strong cross-language differences for speech stimuli, and none for stimuli that were nonspeech. However, the cross-language differences extended into a gray area of speech-like stimuli that were difficult to classify, suggesting that the specialization occurred in phonetic processing prior to categorization.
Focusing of longitudinal ultrasonic waves in air with an aperiodic flat lens
Authors: Welter John T. , Sathish Shamachary , Christensen Daniel E. , Brodrick Philip G. , Heebl Jason D. , Cherry Matthew R.
Published: November 2011

Modeling and experimental results of an ultrasonic aperiodic flat lens for use in air are presented. Predictive modeling of the lens is performed using a hybrid genetic-greedy algorithm constrained to a linear structure. The optimized design parameters are used to fabricate a lens. A method combining a fiber-disk arrangement and scanning laser vibrometer measurements is developed to characterize the acoustic field distribution generated by the lens. The focal spot size is determined to be 0.88 of the incident wavelength of 80−90 kHz at a distance of 2.5 mm from the lens. Theoretically computed field distributions, optimized frequency of operation, and spatial resolution focal length are compared with experimental measurements. The differences between experimental measurements and the theoretical computations are analyzed. The theoretical calculation of the focal spot diameter is 1.7 mm which is 48% of the experimental measurement at a frequency of 80–90 kHz. This work illustrates the capabilities of a hybrid algorithm approach to design of flat acoustic lenses to operate in air with a resolution of greater than the incident wavelength and the challenges of characterizing acoustic field distribution in air.
A nonlocal effective operator for coupling forward and backward propagating modes in inhomogeneous media
Authors: Knobles D. P. , Sagers J. D.
Published: November 2011

In an acoustic waveguide spatial inhomogeneities couple the forward and backward propagating modal amplitudes. To address the nature of such coupling the integral equation for the range-dependent modal amplitudes is decomposed into components that satisfy the asymptotic boundary conditions of the free Green’s function operator. An equivalent set of equations is obtained by eliminating the components that become the asymptotically backward propagating channels to leave a set of integral equations that describe only the components that become asymptotically the forward propagating channels. The elimination of the components that become asymptotically the backward propagating channels is done at the expense of introducing a nonlocal effective coupling operator. The nonlocal operator contains all the effects of the asymptotically backward propagating field on the asymptotically forward propagating field. An expansion of the effective coupling operator allows an investigation of the importance of the coupling and provides a systematic approach to add correction terms to the forward only equation. Idealistic underwater waveguides with various degrees of inhomogeneities are used to illustrate the main features of the convergence characteristics for the expansion.
Implementing an exact finite boundary integral equation method for finite rough surfaces (L)
Authors: Fawcett John A.
Published: November 2011

An exact integral equation approach to solving scattering from a finite section of roughness in an otherwise infinitely flat surface was described in DeSanto and Martin [J. Acoust. Soc. Am. 102, 67–77]. In this letter, the details of a numerical implementation of this approach are presented for a rough pressure release surface. An example comparing the results from this method to those from a standard, truncated integral approach is given.
The importance for speech intelligibility of random fluctuations in “steady” background noise
Authors: Stone Michael A. , Füllgrabe Christian , Mackinnon Robert C. , Moore Brian C. J.
Published: November 2011

Spectrally shaped steady noise is commonly used as a masker of speech. The effects of inherent random fluctuations in amplitude of such a noise are typically ignored. Here, the importance of these random fluctuations was assessed by comparing two cases. For one, speech was mixed with steady speech-shaped noise and N-channel tone vocoded, a process referred to as signal-domain mixing (SDM); this preserved the random fluctuations of the noise. For the second, the envelope of speech alone was extracted for each vocoder channel and a constant was added corresponding to the root-mean-square value of the noise envelope for that channel. This is referred to as envelope-domain mixing (EDM); it removed the random fluctuations of the noise. Sinusoidally modulated noise and a single talker were also used as backgrounds, with both SDM and EDM. Speech intelligibility was measured for N = 12, 19, and 30, with the target-to-background ratio fixed at −7 dB. For SDM, performance was best for the speech background and worst for the steady noise. For EDM, this pattern was reversed. Intelligibility with steady noise was consistently very poor for SDM, but near-ceiling for EDM, demonstrating that the random fluctuations in steady noise have a large effect.
An evaluation of objective measures for intelligibility prediction of time-frequency weighted noisy speech
Authors: Taal Cees H. , Hendriks Richard C. , Heusdens Richard , Jensen Jesper
Published: November 2011

Existing objective speech-intelligibility measures are suitable for several types of degradation, however, it turns out that they are less appropriate in cases where noisy speech is processed by a time-frequency weighting. To this end, an extensive evaluation is presented of objective measure for intelligibility prediction of noisy speech processed with a technique called ideal time frequency (TF) segregation. In total 17 measures are evaluated, including four advanced speech-intelligibility measures (CSII, CSTI, NSEC, DAU), the advanced speech-quality measure (PESQ), and several frame-based measures (e.g., SSNR). Furthermore, several additional measures are proposed. The study comprised a total number of 168 different TF-weightings, including unprocessed noisy speech. Out of all measures, the proposed frame-based measure MCC gave the best results (ρ = 0.93). An additional experiment shows that the good performing measures in this study also show high correlation with the intelligibility of single-channel noise reduced speech.
Experimental source characterization techniques for studying the acoustic properties of perforates under high level acoustic excitation
Authors: Bodén Hans
Published: November 2011

This paper discusses experimental techniques for obtaining the acoustic properties of in-duct samples with non-linear acoustic characteristic. The methods developed are intended both for studies of non-linear energy transfer to higher harmonics for samples only accessible from one side such as wall treatment in aircraft engine ducts or automotive exhaust systems and for samples accessible from both sides such as perforates or other top sheets. When harmonic sound waves are incident on the sample nonlinear energy transfer results in sound generation at higher harmonics at the sample (perforate) surface. The idea is that these sources can be characterized using linear system identification techniques similar to one-port or two-port techniques which are traditionally used for obtaining source data for in-duct sources such as IC-engines or fans. The starting point will be so called polyharmonic distortion modeling which is used for characterization of nonlinear properties of microwave systems. It will be shown how acoustic source data models can be expressed using this theory. Source models of different complexity are developed and experimentally tested. The results of the experimental tests show that these techniques can give results which are useful for understanding non-linear energy transfer to higher harmonics.
Temporal-envelope constancy of speech in rooms and the perceptual weighting of frequency bands
Authors: Watkins Anthony J. , Raimond Andrew P. , Makin Simon J.
Published: November 2011

Three experiments measured constancy in speech perception, using natural-speech messages or noise-band vocoder versions of them. The eight vocoder-bands had equally log-spaced center-frequencies and the shapes of corresponding “auditory” filters. Consequently, the bands had the temporal envelopes that arise in these auditory filters when the speech is played. The “sir” or “stir” test-words were distinguished by degrees of amplitude modulation, and played in the context; “next you’ll get _ to click on.” Listeners identified test-words appropriately, even in the vocoder conditions where the speech had a “noise-like” quality. Constancy was assessed by comparing the identification of test-words with low or high levels of room reflections across conditions where the context had either a low or a high level of reflections. Constancy was obtained with both the natural and the vocoded speech, indicating that the effect arises through temporal-envelope processing. Two further experiments assessed perceptual weighting of the different bands, both in the test word and in the context. The resulting weighting functions both increase monotonically with frequency, following the spectral characteristics of the test-word’s [s]. It is suggested that these two weighting functions are similar because they both come about through the perceptual grouping of the test-word’s bands.
Whistling of an orifice in a reverberating duct at low Mach number
Authors: Lacombe Romain , Moussou Pierre , Aurégan Yves
Published: November 2011

An experimental investigation of the parameters controlling the whistling frequency and amplitude of an orifice in a confined turbulent flow is undertaken. A circular single hole orifice with sharp edges, a hole diameter equal to 0.015 m and a thickness equal to 0.005 m, is arranged in an air test rig with an inner diameter equal to 0.03 m. The Mach number ranges around 0.02 and the Reynolds number around 104. Variable reflecting boundary conditions are arranged upstream and downstream, and several flow velocities are tested. It is found that the Bode–Nyquist criterion accurately predicts the conditions of self-sustained oscillation and the value of the whistling frequency. Furthermore, it is found that the acoustic velocity in whistling regime varies from 1% to 15% of the steady flow velocity, and that it depends on the overall acoustic reflection of the surrounding pipe and on the Strouhal number.
Characteristics of biosonar signals from the northern bottlenose whale, Hyperoodon ampullatus
Authors: Wahlberg Magnus , Beedholm Kristian , Heerfordt Anders , Møhl Bertel
Published: November 2011

The biosonar pulses from free-ranging northern bottlenose whales (Hyperoodon ampullatus) were recorded with a linear hydrophone array. Signals fulfilling criteria for being recorded close to the acoustic axis of the animal (a total of 10 clicks) had a frequency upsweep from 20 to 55 kHz and durations of 207 to377 μs (measured as the time interval containing 95% of the signal energy). The source level of these signals, denoted pulses, was 175−202 dB re 1 μPa rms at 1 m. The pulses had a directionality index of at least 18 dB. Interpulse intervals ranged from 73 to 949 ms (N = 856). Signals of higher repetition rates had interclick intervals of 5.8−13.1 ms (two sequences, made up of 59 and 410 clicks, respectively). These signals, denoted clicks, had a shorter duration (43−200 μs) and did not have the frequency upsweep characterizing the pulses of low repetition rates. The data show that the northern bottlenose whale emits signals similar to three other species of beaked whale. These signals are distinct from the three other types of biosonar signals of toothed whales. It remains unclear why the signals show this grouping, and what consequences it has on echolocation performance.
Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid
Authors: Higginbotham A. P. , Guillen A. , Jones N. , Donnelly T. D. , Bernoff A. J.
Published: November 2011

A popular method for generating micron-sized aerosols is to submerge ultrasonic (ω~MHz) piezoelectric oscillators in a water bath. The submerged oscillator atomizes the fluid, creating droplets with radii proportional to the wavelength of the standing wave at the fluid surface. Classical theory for the Faraday instability predicts a parametric instability driving a capillary wave at the subharmonic (ω/2) frequency. For many applications it is desirable to reduce the size of the droplets; however, using higher frequency oscillators becomes impractical beyond a few MHz. Observations are presented that demonstrate that smaller droplets may also be created by increasing the driving amplitude of the oscillator, and that this effect becomes more pronounced for large driving frequencies. It is shown that these observations are consistent with a transition from droplets associated with subharmonic (ω/2) capillary waves to harmonic (ω) capillary waves induced by larger driving frequencies and amplitudes, as predicted by a stability analysis of the capillary waves.
Acoustical properties of double porosity granular materials
Authors: Venegas Rodolfo , Umnova Olga
Published: November 2011

Granular materials have been conventionally used for acoustic treatment due to their sound absorptive and sound insulating properties. An emerging field is the study of the acoustical properties of multiscale porous materials. An example of these is a granular material in which the particles are porous. In this paper, analytical and hybrid analytical-numerical models describing the acoustical properties of these materials are introduced. Image processing techniques have been employed to estimate characteristic dimensions of the materials. The model predictions are compared with measurements on expanded perlite and activated carbon showing satisfactory agreement. It is concluded that a double porosity granular material exhibits greater low-frequency sound absorption at reduced weight compared to a solid-grain granular material with similar mesoscopic characteristics.
Three-dimensional impedance map analysis of rabbit liver
Authors: Pawlicki Alexander D. , Dapore Alexander J. , Sarwate Sandhya , O’Brien William D.
Published: November 2011

Three-dimensional impedance maps (3DZMs) are computational models of acoustic impedance of tissue constructed from histology images. 3DZMs can be analyzed to estimate model-based quantitative ultrasound parameters such as effective scatterer diameter (ESD). In this study, 3DZMs were constructed from normal and fatty rabbit livers. Estimates of ESD were made using the fluid-filled sphere scattering model. Weighting toward smaller scatterer sizes produced ESD estimates of 7.5 ± 1.3 and 7.0 ± 0.3 μm for normal and fatty liver, respectively, approximately the size of a liver cell nucleus. This suggests the nucleus could be a primary source of scattering in liver.
Waveguide invariant analysis for modeling time-frequency striations in a range-dependent environment
Authors: Sell Alexander W. , Lee Culver R.
Published: November 2011

The waveguide invariant is a useful parameter for understanding the behavior of interference patterns (e.g., striations in time–frequency plots) resulting from broadband acoustic sources in shallow water waveguides. It is possible to model these striations for range-dependent environments using conventional parabolic equation methods; although this approach can be computationally intensive as a full field must be created for each frequency and azimuthally dependent geometry. This letter discusses the formulation and use of a range-dependent waveguide invariant distribution that can be used to describe spectral striation patterns using a fraction of the computing power required by parabolic equation methods.
Characterization of the perceived sound of trauma-induced tinnitus in gerbils
Authors: Nowotny Manuela , Remus Martina , Kössl Manfred , Gaese Bernhard H.
Published: November 2011

Tinnitus often develops following inner ear pathologies, like acoustic trauma. Therefore, an acoustic trauma model of tinnitus in gerbils was established using a modulated acoustic startle response. Cochlear trauma evoked by exposure to narrow-band noise at 10 kHz was assessed by auditory brainstem responses (ABR) and distortion product otoacoustic emissions (DPOAE). Threshold shift amounted to about 25 dB at frequencies > 10 kHz. Induction of a phantom-noise perception was documented by an acoustic startle response paradigm. A reduction of the gap-prepulse inhibition of acoustic startle (GPIAS) was taken as evidence for tinnitus at the behavioral level. Three to five weeks after trauma the ABR and DPOAE thresholds were back to normal. At that time, a reduction of GPIAS in the frequency range 16–20 kHz indicated a phantom noise perception. Seven weeks post trauma the tinnitus-affected frequency range became narrow and shifted to the center-trauma frequency at 10 kHz. Taken together, by investigating frequency-dependent effects in detail, this study in gerbils found trauma-evoked tinnitus developing in the frequency range bordering the low frequency slope of the induced noise trauma. This supports the theory of lateral inhibition as the physiological basis of tinnitus.
Lateral reflections are favorable in concert halls due to binaural loudness
Authors: Lokki Tapio , Pätynen Jukka
Published: November 2011

A recent study on perceptual difference in simulated concert halls showed that a concert hall renders stronger sound with more bass when the temporal envelope of a signal is preserved in the reflections [Lokki et al., J. Acoust. Soc. Am. 129, EL223–EL228 (2011)]. In the same study the lateral reflections were shown to contribute to the perceived envelopment and openness. Moreover, the listening test results suggest that lateral reflections contribute to perception of sound source distance. Here, it is shown that lateral reflections are beneficial due to their increasing effect on binaural loudness—the phenomenon known well in psychoacoustics, but not in architectural acoustics. The reflections from the side are amplified more than median plane reflections, in particular at high frequencies, due to the shape of the human head.
Standards Meetings Calendar–National
Authors: Blaeser Susan B. , Schomer Paul D.
Published: November 2011

American National Standards (ANSI Standards) developed by Accredited Standards Committees S1, S2, S3, and S12 in the areas of acoustics, mechanical vibration and shock, bioacoustics, and noise, respectively, are published by the Acoustical Society of America (ASA). In addition to these standards, ASA publishes catalogs of Acoustical Standards, both National and International. To receive copies of the latest Standards Catalogs, please contact Susan B. Blaeser.

Comments are welcomed on all material in Acoustical Standards News.

This Acoustical Standards News section in JASA, as well as the National and International Catalogs of Acoustical Standards, and other information on the Standards Program of the Acoustical Society of America, are available via the ASA home page: http://acousticalsociety.org.
Structural Basis of Silencing: Sir3 BAH Domain in Complex with a Nucleosome at 3.0 Å Resolution
Authors: Armache Karim-Jean , Garlick Joseph D. , Canzio Daniele , Narlikar Geeta J. , Kingston Robert E.
Published: November 2011

A regulatory protein forms extensive interactions with the nucleosome core particle to create the basis for gene silencing.
Preparing to Manage Climate Change Financing
Authors: Donner Simon D. , Kandlikar Milind , Zerriffi Hisham
Published: November 2011

Lessons from the failures and successes of international development should guide investment in developing-world responses to climate change.
Analyzing Solar Cycles
Authors: Solanki Sami K. , Krivova Natalie A.
Published: November 2011

Does the recent longer-than-usual minimum in sunspot activity indicate that we are heading for an extended period of solar inactivity?
Human Locomotor Circuits Conform
Authors: Grillner Sten
Published: November 2011

Similar patterns of neural activity that drive locomotion in humans, mammals, and birds suggest a conserved mechanism over vertebrate evolution.
Low Costs and Considerable Gains

Design with the Other 90%: Cities
Cynthia E. Smith, curator

Cooper-Hewitt National Design Museum, Smithsonian Institution. At the United Nations Headquarters, New York. Through 9 January 2012. http://designother90.org/cities/home

Design with the Other 90%: Cities
by Cynthia E. Smith
et al.

Cooper-Hewitt National Design Museum, New York, 2011. 234 pp. Paper, $29.95. ISBN 9780910503839.
Authors: Sternberg Esther M.
Published: November 2011

The exhibition features 60 design projects that address the complex issues arising from the explosive growth of informal urban settlements in emerging and developing economies.
Revolution Brings New Hopes for Libyan Archaeology
Authors: Enserink Martin
Published: November 2011

Now that Libya's civil war is over, scientists are hoping that from the turmoil will arise a new, democratic nation that invests more of its oil wealth in research and takes a keener interest in its archaeological treasures.
Will Busting Dams Boost Salmon?
Authors: Service Robert F.
Published: November 2011

As dams fall on the Elwha River in Washington state and other rivers around the country, scientists are relishing rare opportunities to watch natural ecosystems restore themselves.
Out of the Frying Pan?
Authors: Service Robert F.
Published: November 2011

A new climate-modeling effort called the Riverscape Analysis Project finds that climate change will affect rivers throughout the Pacific Rim.
Saving for a Rainy Day
Authors: Cartlidge Edwin
Published: November 2011

Materials for thermal storage may make cheap solar energy available around the clock—even when the sun doesn't shine.
Treatment and Prevention of Urinary Tract Infection with Orally Active FimH Inhibitors
Authors: Cusumano Corinne K. , Pinkner Jerome S. , Han Zhenfu , Greene Sarah E. , Ford Bradley A. , Crowley Jan R. , Henderson Jeffrey P. , Janetka James W. , Hultgren Scott J.
Published: November 2011

Optimized mannoside compounds that block uropathogenic
E. coli
entry into bladder epithelium were effective in the treatment and prevention of urinary tract infections in mice.
Biomarker-Based Early Cancer Detection: Is It Achievable?
Authors: Hazelton William D. , Luebeck E. Georg
Published: November 2011

A new mathematical model evaluates the power of blood-based biomarkers for early cancer detection.
Poly-γ-Glutamic Acid Nanoparticles and Aluminum Adjuvant Used as an Adjuvant with a Single Dose of Japanese Encephalitis Virus-Like Particles Provide Effective Protection from Japanese Encephalitis Virus
Authors: Okamoto Shigefumi , Yoshii Hironori , Matsuura Masaaki , Kojima Asato , Ishikawa Toyokazu , Akagi Takami , Akashi Mitsuru , Takahashi Michiaki , Yamanishi Koichi , Mori Yasuko
Published: November 2011

To maintain immunity against Japanese encephalitis virus (JEV), a formalin-inactivated Japanese encephalitis (JE) vaccine should be administered several times. The repeated vaccination is not helpful in the case of a sudden outbreak of JEV or when urgent travel to a high-JEV-risk region is required; however, there are few single-injection JE vaccine options. In the present study, we investigated the efficacy of a single dose of a new effective JE virus-like particle preparation containing the JE envelope protein (JE-VLP). Although single administration with JE-VLP protected less than 50% of mice against lethal JEV infection, adding poly(γ-glutamic acid) nanoparticles (γ-PGA-NPs) or aluminum adjuvant (alum) to JE-VLP significantly protected more than 90% of the mice. A single injection of JE-VLP with either γ-PGA-NPs or alum induced a significantly greater anti-JEV neutralizing antibody titer than JE-VLP alone. The enhanced titers were maintained for more than 6 months, resulting in long-lasting protection of 90% of the immunized mice. Although the vaccine design needs further modification to reach 100% protection, a single dose of JE-VLP with γ-PGA-NPs may be a useful step in developing a next-generation vaccine to stop a JE outbreak or to immunize travelers or military personnel.
Performance Assessment of the CapitalBio Mycobacterium Identification Array System for Identification of Mycobacteria
Authors: Liu Jingbo , Yue Jun , Yan Zihe , Han Min , Han Zhijun , Jin Lingjie , Zhao Yanlin
Published: November 2011

The CapitalBio
Mycobacterium
identification microarray system is a rapid system for the detection of
Mycobacterium tuberculosis
. The performance of this system was assessed with 24 reference strains, 486
Mycobacterium tuberculosis
clinical isolates, and 40 clinical samples and then compared to the “gold standard” of DNA sequencing. The CapitalBio
Mycobacterium
identification microarray system showed highly concordant identification results of 100% and 98.4% for
Mycobacterium tuberculosis
complex (MTC) and nontuberculous mycobacteria (NTM), respectively. The sensitivity and specificity of the CapitalBio
Mycobacterium
identification array for identification of
Mycobacterium tuberculosis
isolates were 99.6% and 100%, respectively, for direct detection and identification of clinical samples, and the overall sensitivity was 52.5%. It was 100% for sputum, 16.7% for pleural fluid, and 10% for bronchoalveolar lavage fluid, respectively. The total assay was completed in 6 h, including DNA extraction, PCR, and hybridization. The results of this study confirm the utility of this system for the rapid identification of mycobacteria and suggest that the CapitalBio
Mycobacterium
identification array is a molecular diagnostic technique with high sensitivity and specificity that has the capacity to quickly identify most mycobacteria.
Characterization and Comparison of Invasive Corynebacterium diphtheriae Isolates from France and Poland
Authors: Farfour E. , Badell E. , Zasada A. , Hotzel H. , Tomaso H. , Guillot S. , Guiso N.
Published: November 2011

Corynebacterium diphtheriae
, the agent of diphtheria, is rarely responsible for bacteremia. However, high numbers of bacteremia have been reported in countries with extensive immunization coverage. Here, we used molecular and phenotypic tools to characterize and compare 42 invasive isolates collected in France (including New Caledonia) and Poland over a 23-year period.
Yield of Sputum for Viral Detection by Reverse Transcriptase PCR in Adults Hospitalized with Respiratory Illness
Authors: Falsey Ann R. , Formica Maria A. , Walsh Edward E.
Published: November 2011

Diagnostic tests for respiratory viral infections have traditionally been performed on nasopharyngeal swabs or washings. Reverse transcriptase PCR (RT-PCR) is rapid, sensitive, and specific for viral infection diagnosis but is rarely applied to sputum samples. Thus, we evaluated the diagnostic yield of RT-PCR for detection of nine virus types by the use of nose and throat swabs (NTS) and sputum samples from patients admitted to the hospital with acute respiratory tract illnesses. Adults hospitalized with acute respiratory tract illnesses were recruited during the winters of 2008 and 2009. At enrollment, combined nose and throat swabs and sputum samples were collected for RT-PCR for detection of nine common respiratory virus types. A total of 532 subjects admitted for 556 respiratory illnesses were enrolled. A total of 189 virus strains were identified. The diagnostic yields for detection of any virus were 23% (126/556) for NTS RT-PCR and 36% (146/404) for sputum RT-PCR. A total of 83 (44%) of 189 viral detections were positive by both methods, 43 (23%) were positive by NTS alone, and 63 (33%) were positive only with sputum samples. The inclusion of RT-PCR performed with sputum samples significantly increased the diagnostic yield for respiratory viral infections in adults. Further studies designed to adapt the use of sputum samples for commercial RT-PCR respiratory virus assays are needed.
The Cellular Chaperone Hsc70 Is Specifically Recruited to Reovirus Viral Factories Independently of Its Chaperone Function
Authors: Kaufer Susanne , Coffey Caroline M. , Parker John S. L.
Published: November 2011

Mammalian orthoreoviruses replicate and assemble in the cytosol of infected cells. A viral nonstructural protein, μNS, forms large inclusion-like structures called viral factories (VFs) in which assembling viral particles can be identified. Here we examined the localization of the cellular chaperone Hsc70 and found that it colocalizes with VFs in infected cells and also with viral factory-like structures (VFLs) formed by ectopically expressed μNS. Small interfering RNA (siRNA)-mediated knockdown of Hsc70 did not affect the formation or maintenance of VFLs. We further showed that dominant negative mutants of Hsc70 were also recruited to VFLs, indicating that Hsc70 recruitment to VFLs is independent of the chaperone function. In support of this finding, μNS was immunoprecipitated with wild-type Hsc70, with a dominant negative mutant of Hsc70, and with the minimal substrate-binding site of Hsc70 (amino acids 395 to 540). We identified a minimal region of μNS between amino acids 222 and 271 that was sufficient for the interaction with Hsc70. This region of μNS has not been assigned any function previously. However, neither point mutants with alterations in this region nor the complete deletion of this domain abrogated the μNS-Hsc70 interaction, indicating that a second portion of μNS also interacts with Hsc70. Taken together, these findings suggest a specific chaperone function for Hsc70 within viral factories, the sites of reovirus replication and assembly in cells.
Kaposi's Sarcoma-Associated Herpesvirus Latency-Associated Nuclear Antigen Induction by Hypoxia and Hypoxia-Inducible Factors
Authors: Veeranna Ravindra P. , Haque Muzammel , Davis David A. , Yang Min , Yarchoan Robert
Published: November 2011

Hypoxia and hypoxia-inducible factors (HIFs) play an important role in the Kaposi's sarcoma-associated herpesvirus (KSHV) life cycle. In particular, hypoxia can activate lytic replication of KSHV and specific lytic genes, including the replication and transcription activator (RTA), while KSHV infection in turn can increase the levels and activity of HIFs. In the present study, we show that hypoxia increases the levels of mRNAs encoding KSHV latency-associated nuclear antigen (LANA) in primary effusion lymphoma (PEL) cell lines and also increases the levels of LANA protein. Luciferase reporter assays in Hep3B cells revealed a moderate activation of the LANA promoter region by hypoxia as well as by cotransfection with degradation-resistant HIF-1α or HIF-2α expression plasmids. Computer analysis of a 1.2-kb sequence upstream of the LANA translational start site identified six potential hypoxia-responsive elements (HRE). Sequential deletion studies revealed that much of this activity was mediated by one of these HREs (HRE 4R) oriented in the 3′ to 5′ direction and located between the constitutive (LTc) and RTA-inducible (LTi) mRNA start sites. Site-directed mutation of this HRE substantially reduced the response to both HIF-1α and HIF-2α in a luciferase reporter assay. Electrophoretic mobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) assays demonstrated binding of both HIF-1α and HIF-2α to this region. Also, HIF-1α was found to associate with RTA, and HIFs enhanced the activation of LTi by RTA. These results provide evidence that hypoxia and HIFs upregulate both latent and lytic KSHV replication and play a central role in the life cycle of this virus.
The Virion-Associated Open Reading Frame 49 of Murine Gammaherpesvirus 68 Promotes Viral Replication both
In Vitro
and
In Vivo
as a Derepressor of RTA
Authors: Noh Cheol-Woo , Cho Hye-Jeong , Kang Hye-Ri , Jin Hyun Yong , Lee Shaoying , Deng Hongyu , Wu Ting-Ting , Arumugaswami Vaithilingaraja , Sun Ren , Song Moon Jung
Published: November 2011

Replication and transcription activator (RTA), an immediate-early gene, is a key molecular switch to evoke lytic replication of gammaherpesviruses. Open reading frame 49 (ORF49) is conserved among gammaherpesviruses and shown to cooperate with RTA in regulating virus lytic replication. Here we show a molecular mechanism and
in vivo
functions of murine gammaherpesvirus 68 (MHV-68 or γHV-68) ORF49. MHV-68 ORF49 was transcribed and translated as a late gene. The ORF49 protein was associated with a virion, interacting with the ORF64 large tegument protein and the ORF25 capsid protein. Moreover, ORF49 directly bound to RTA and its negative cellular regulator, poly(ADP-ribose) polymerase-1 (PARP-1), and disrupted the interactions of RTA and PARP-1. Productive replication of an ORF49-deficient mutant virus (49S) was attenuated
in vivo
as well as
in vitro
. Likewise, latent infection was also impaired in the spleen of 49S-infected mice. Taken together, our results suggest that the virion-associated ORF49 protein may promote virus replication both
in vitro
and
in vivo
by providing an optimal environment in the early phase of virus infection as a derepressor of RTA.
Apoptosis Induced by Mammalian Reovirus Is Beta Interferon (IFN) Independent and Enhanced by IFN Regulatory Factor 3- and NF-κB-Dependent Expression of Noxa
Authors: Knowlton Jonathan J. , Dermody Terence S. , Holm Geoffrey H.
Published: November 2011

A variety of signal transduction pathways are activated in response to viral infection, which dampen viral replication and transmission. These mechanisms involve both the induction of type I interferons (IFNs), which evoke an antiviral state, and the triggering of apoptosis. Mammalian orthoreoviruses are double-stranded RNA viruses that elicit apoptosis
in vitro
and
in vivo
. The transcription factors interferon regulatory factor 3 (IRF-3) and nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) are required for the expression of IFN-β and the efficient induction of apoptosis in reovirus-infected cells. However, it is not known whether IFN-β induction is required for apoptosis, nor have the genes induced by IRF-3 and NF-κB that are responsible for apoptosis been identified. To determine whether IFN-β is required for reovirus-induced apoptosis, we used type I IFN receptor-deficient cells, IFN-specific antibodies, and recombinant IFN-β. We found that IFN synthesis and signaling are dispensable for the apoptosis of reovirus-infected cells. These results indicate that the apoptotic response following reovirus infection is mediated directly by genes responsive to IRF-3 and NF-κB. Noxa is a proapoptotic BH3-domain-only protein of the Bcl-2 family that requires IRF-3 and NF-κB for efficient expression. We found that Noxa is strongly induced at late times (36 to 48 h) following reovirus infection in a manner dependent on IRF-3 and NF-κB. The level of apoptosis induced by reovirus is significantly diminished in cells lacking Noxa, indicating a key prodeath function for this molecule during reovirus infection. These results suggest that prolonged innate immune response signaling induces apoptosis by eliciting Noxa expression in reovirus-infected cells.
Dynamics of Simian Immunodeficiency Virus SIVmac239 Infection in Pigtail Macaques
Authors: Klatt Nichole R. , Canary Lauren A. , Vanderford Thomas H. , Vinton Carol L. , Engram Jessica C. , Dunham Richard M. , Cronise Heather E. , Swerczek Joanna M. , Lafont Bernard A. P. , Picker Louis J. , Silvestri Guido , Brenchley Jason M.
Published: November 2011

Pigtail macaques (PTM) are an excellent model for HIV research; however, the dynamics of simian immunodeficiency virus (SIV) SIVmac239 infection in PTM have not been fully evaluated. We studied nine PTM prior to infection, during acute and chronic SIVmac239 infections, until progression to AIDS. We found PTM manifest clinical AIDS more rapidly than rhesus macaques (RM), as AIDS-defining events occurred at an average of 42.17 weeks after infection in PTM compared to 69.56 weeks in RM (
P
= 0.0018). However, increased SIV progression was not associated with increased viremia, as both peak and set-point plasma viremias were similar between PTM and RM (
P
= 0.7953 and
P
= 0.1006, respectively). Moreover, this increased disease progression was not associated with rapid CD4
+
T cell depletion, as CD4
+
T cell decline resembled other SIV/human immunodeficiency virus (HIV) models. Since immune activation is the best predictor of disease progression during HIV infection, we analyzed immune activation by turnover of T cells by BrdU decay and Ki67 expression. We found increased levels of turnover prior to SIV infection of PTM compared to that observed with RM, which may contribute to their increased disease progression rate. These data evaluate the kinetics of SIVmac239-induced disease progression and highlight PTM as a model for HIV infection and the importance of immune activation in SIV disease progression.
An Overview of the Vaccinia Virus Infectome: a Survey of the Proteins of the Poxvirus-Infected Cell
Authors: Chou Wayne , Ngo Tuan , Gershon Paul D.
Published: November 2011

We have quantitatively profiled the proteins of vaccinia virus-infected HEK293T cells early and late during vaccinia virus infection. Proteins corresponding to 4,326 accessions were identified, the products of 3,798 genes. One hundred thirty-six of the proteins were vaccinia virus-encoded (∼64% of the known vaccinia virus proteome). The remaining accessions were from the host cell. A total of 3,403 of the 4,326 accessions could be confidently quantitated at the precursor peptide level. Although vaccinia virus gene products spanned the entire abundance dynamic range of the cellular proteome, nearly all of the proteome dynamics observed as a result of infection were manifest in the virus gene products with very little plasticity in the host cell proteome. The vaccinia virus gene products could be grouped into four kinetic classes (i.e., four combinations of pre- and postreplicative expression). These protein kinetic classes reflected, almost entirely, the corresponding gene classes within the recently characterized vaccinia virus transcriptome map. The few cellular gene products that showed notable changes in abundance upon vaccinia virus infection were concentrated largely in just a few functional groups. After all of the quantitated cellular gene products were assigned to Gene Ontology (GO)-specific groups, quantitation values for a number of these GO-specific groups were significantly skewed toward over- or underabundance with respect to the global distribution of quantitation values. Quantitative analysis of host cell functions reflected several known facets of virus infection, along with some novel observations.
Daily consultant gastroenterologist ward rounds: reduced length of stay and improved inpatient mortality
Authors: Singh Salil , Lipscomb George , Padmakumar Kadukkavil , Ramamoorthy Radha , Ryan Shirley , Bates Vivien , Crompton Sandra , Dermody Emma , Moriarty Kieran
Published: November 2011

Background

For gastroenterology, The Royal College of Physicians reiterates the common practice of two to three consultant ward rounds per week. The Royal Bolton Hospital NHS Foundation Trust operated a 26-bed gastroenterology ward, covered by two consultants at any one time. A traditional system of two ward rounds per consultant per week operated, but as is commonplace, discharges peaked on ward round days.

Objective

To determine whether daily consultant ward rounds would improve patient care, shorten length of stay and reduce inpatient mortality.

Methods

A new way of working was implemented in December 2009 with a single consultant taking responsibility for all ward inpatients. Freed from all other direct clinical care commitments for their 2 weeks of ward cover, they conducted ward rounds each morning. A multidisciplinary team (MDT) meeting followed immediately. The afternoon was allocated to gastroenterology referrals and reviewing patients on the medical admissions unit.

Results

The changes had an immediate and dramatic effect on average length of stay, which was reduced from 11.5 to 8.9 days. The number of patients treated over 12 months increased by 37% from 739 to 1010. Moreover, the number of deaths decreased from 88 to 62, a reduction in percentage mortality from 11.2% to 6%. However, these major quality outcomes involved a reduction in consultant-delivered outpatient and endoscopy activity.

Conclusion

This new method of working has both advantages and disadvantages. However, it has had a major impact on inpatient care and provides a compelling case for consultant gastroenterology expansion in the UK.
Intraoperative analysis of sentinel lymph nodes in breast cancer by one-step nucleic acid amplification
Authors: Cserni Gábor
Published: November 2011

One-step nucleic acid amplification (OSNA) is a novel method introduced for the lymph node staging of breast cancer and has been tested in multiple series. The present review summarises current literature and concerns related to the new method. The results of this automated molecular assay based on the quantification of cytokeratin 19 mRNA show a 96% concordance rate with detailed histopathology complemented with immunohistochemistry when alternative slices of the same lymph node are used for the two tests. The low false-negative rate makes OSNA suitable for the intraoperative evaluation of sentinel lymph nodes. The false-positive rate also seems very low. Most discordant cases are explainable by low volume metastases (micrometastases), which may be missing from the material submitted for one test, but not from the different part used for the other test. It is tempting to change the gold standard for comparisons between the methods, and if this is done, histology seems to come out as a weaker test for the identification of metastases. OSNA detects more low volume nodal involvement, but it is uncertain whether these require further axillary treatment, and this will be a subject for future investigations. Therefore, it is also uncertain whether the advantage of OSNA of detecting practically all metastases due to complete sampling of lymph node tissue is clinically more important than the exclusion of metastases greater than micrometastasis that can be reliably done by intraoperative microscopy followed by permanent section histology.