bluuebunny/crossref_metadata_2025 huggingface dataset:
High stimulus variability in nonnative speech learning supports formation of abstract categories: Evidence from Japanese geminates
Authors: Sadakata Makiko , McQueen James M.
Published: August 2013

This study reports effects of a high-variability training procedure on nonnative learning of a Japanese geminate-singleton fricative contrast. Thirty native speakers of Dutch took part in a 5-day training procedure in which they identified geminate and singleton variants of the Japanese fricative /s/. Participants were trained with either many repetitions of a limited set of words recorded by a single speaker (low-variability training) or with fewer repetitions of a more variable set of words recorded by multiple speakers (high-variability training). Both types of training enhanced identification of speech but not of nonspeech materials, indicating that learning was domain specific. High-variability training led to superior performance in identification but not in discrimination tests, and supported better generalization of learning as shown by transfer from the trained fricatives to the identification of untrained stops and affricates. Variability thus helps nonnative listeners to form abstract categories rather than to enhance early acoustic analysis.
Mode-converted diffuse ultrasonic backscatter
Authors: Hu Ping , Kube Christopher M. , Koester Lucas W. , Turner Joseph A.
Published: August 2013

Diffuse ultrasonic backscatter describes the scattering of elastic waves from interfaces within heterogeneous materials. Previously, theoretical models have been developed for the diffuse backscatter of longitudinal-to-longitudinal (L-L) wave scattering within polycrystalline materials. Following a similar formalism, a mode-conversion scattering model is presented here to quantify the component of an incident longitudinal wave that scatters and is converted to a transverse (shear) wave within a polycrystalline sample. The model is then used to fit experimental measurements associated with a pitch-catch transducer configuration performed using a sample of 1040 steel. From these measurements, an average material correlation length is determined. This value is found to be in agreement with results from L-L scattering measurements and is on the order of the grain size as determined from optical micrographs. Mode-converted ultrasonic backscatter is influenced much less by the front-wall reflection than an L-L measurement and it provides additional microstructural information that is not accessible in any other manner.
Optimal apparent damping as a function of the bandwidth of an array of vibration absorbers
Authors: Vignola Joseph , Glean Aldo , Judge John , Ryan Teresa
Published: August 2013

The transient response of a resonant structure can be altered by the attachment of one or more substantially smaller resonators. Considered here is a coupled array of damped harmonic oscillators whose resonant frequencies are distributed across a frequency band that encompasses the natural frequency of the primary structure. Vibration energy introduced to the primary structure, which has little to no intrinsic damping, is transferred into and trapped by the attached array. It is shown that, when the properties of the array are optimized to reduce the settling time of the primary structure's transient response, the apparent damping is approximately proportional to the bandwidth of the array (the span of resonant frequencies of the attached oscillators). Numerical simulations were conducted using an unconstrained nonlinear minimization algorithm to find system parameters that result in the fastest settling time. This minimization was conducted for a range of system characteristics including the overall bandwidth of the array, the ratio of the total array mass to that of the primary structure, and the distributions of mass, stiffness, and damping among the array elements. This paper reports optimal values of these parameters and demonstrates that the resulting minimum settling time decreases with increasing bandwidth.
Bayesian adaptive estimation of the auditory filter
Authors: Shen Yi , Richards Virginia M.
Published: August 2013

A Bayesian adaptive procedure for estimating the auditory-filter shape was proposed and evaluated using young, normal-hearing listeners at moderate stimulus levels. The resulting quick-auditory-filter (qAF) procedure assumed the power spectrum model of masking with the auditory-filter shape being modeled using a spectrally symmetric, two-parameter rounded-exponential (roex) function. During data collection using the qAF procedure, listeners detected the presence of a pure-tone signal presented in the spectral notch of a noise masker. Dependent on the listener's response on each trial, the posterior probability distributions of the model parameters were updated, and the resulting parameter estimates were then used to optimize the choice of stimulus parameters for the subsequent trials. Results showed that the qAF procedure gave similar parameter estimates to the traditional threshold-based procedure in many cases and was able to reasonably predict the masked signal thresholds. Additional measurements suggested that occasional failures of the qAF procedure to reliably converge could be a consequence of incorrect responses early in a qAF track. The addition of a parameter describing lapses of attention reduced the likelihood of such failures.
Temporal weighting functions for interaural time and level differences. III. Temporal weighting for lateral position judgments
Authors: Stecker G. Christopher , Ostreicher Jennifer D. , Brown Andrew D.
Published: August 2013

Temporal variation in listeners' sensitivity to interaural time and level differences (ITD and ILD) was assessed using the temporal weighting function (TWF) paradigm [Stecker and Hafter (2002). J. Acoust. Soc. Am. 112, 1046–1057] in the context of sound-source lateralization. Brief Gabor click trains were presented over headphones with overall ITD and/or ILD ranging ±500 μs ITD and/or ±5 dB ILD across trials; values for individual clicks within each train varied by an additional ±100 μs or ±2 dB to allow TWF calculation by multiple regression. In separate conditions, TWFs were measured for (i) ITD alone, (ii) ILD alone, (iii) ITD and ILD covarying (“in agreement”), and (iv) ITD and ILD varying independently across clicks. Consistent with past studies that measured TWF for binaural discrimination, TWFs demonstrated high weight on the first click for stimuli with short interclick interval (ICI = 2 ms), but flatter weighting for longer ICI (5–10 ms). Some conditions additionally demonstrated greater weight for clicks near the offset than near the middle of the train [Stecker and Hafter (2009). J. Acoust. Soc. Am. 125, 3914–3924]. The latter result was observed only when stimuli carried ILD, and appeared more reliably for 5 ms than for 2 or 10 ms ICI.
Viscous effects in a static physical model of the uniform glottis
Authors: Fulcher Lewis P. , Scherer Ronald C. , Powell Travis
Published: August 2013

The classic work on laryngeal flow resistance by van den Berg et al. [J. Acoust. Soc. Am. 29, 626–631 (1957)] is revisited. These authors used a formula to summarize their measurements, and thus they separated the effects of entrance loss and pressure recovery from those of viscosity within the glottis. Analysis of intraglottal pressure distributions obtained from the physical model M5 [R. Scherer et al., J. Acoust. Soc. Am. 109, 1616–1630 (2001)] reveals substantial regions within the glottis where the pressure gradient is almost constant for glottal diameters from 0.005 to 0.16 cm, as expected when viscous effects dominate the flow resistance of a narrow channel. For this set of glottal diameters, the part of the pressure gradient that has a linear dependence on the glottal volume velocity is isolated. The inverse cube diameter of the Poiseuille expression for glottal flows is examined with the data set provided by the M5 intraglottal pressure distributions. The Poiseuille effect is found to give a reasonable account of viscous effects in the diameter interval from 0.0075 to 0.02 cm, but an inverse 2.59 power law gives a closer fit across all diameters.
Computation of nonlinear ultrasound fields using a linearized contrast source method
Authors: Verweij Martin D. , Demi Libertario , van Dongen Koen W. A.
Published: August 2013

Nonlinear ultrasound is important in medical diagnostics because imaging of the higher harmonics improves resolution and reduces scattering artifacts. Second harmonic imaging is currently standard, and higher harmonic imaging is under investigation. The efficient development of novel imaging modalities and equipment requires accurate simulations of nonlinear wave fields in large volumes of realistic (lossy, inhomogeneous) media. The Iterative Nonlinear Contrast Source (INCS) method has been developed to deal with spatiotemporal domains measuring hundreds of wavelengths and periods. This full wave method considers the nonlinear term of the Westervelt equation as a nonlinear contrast source, and solves the equivalent integral equation via the Neumann iterative solution. Recently, the method has been extended with a contrast source that accounts for spatially varying attenuation. The current paper addresses the problem that the Neumann iterative solution converges badly for strong contrast sources. The remedy is linearization of the nonlinear contrast source, combined with application of more advanced methods for solving the resulting integral equation. Numerical results show that linearization in combination with a Bi-Conjugate Gradient Stabilized method allows the INCS method to deal with fairly strong, inhomogeneous attenuation, while the error due to the linearization can be eliminated by restarting the iterative scheme.
Phase-shift perfluorocarbon agents enhance high intensity focused ultrasound thermal delivery with reduced near-field heating
Authors: Phillips Linsey C. , Puett Connor , Sheeran Paul S. , Dayton Paul A. , Wilson Miller G. , Matsunaga Terry O.
Published: August 2013

Ultrasound contrast agents are known to enhance high intensity focused ultrasound (HIFU) ablation, but these perfluorocarbon microbubbles are limited to the vasculature, have a short half-life in vivo, and may result in unintended heating away from the target site. Herein, a nano-sized (100–300 nm), dual perfluorocarbon (decafluorobutane/dodecafluoropentane) droplet that is stable, is sufficiently small to extravasate, and is convertible to micron-sized bubbles upon acoustic activation was investigated. Microbubbles and nanodroplets were incorporated into tissue-mimicking acrylamide-albumin phantoms. Microbubbles or nanodroplets at 0.1 × 106 per cm3 resulted in mean lesion volumes of 80.4 ± 33.1 mm3 and 52.8 ± 14.2 mm3 (mean ± s.e.), respectively, after 20 s of continuous 1 MHz HIFU at a peak negative pressure of 4 MPa, compared to a lesion volume of 1.0 ± 0.8 mm3 in agent-free control phantoms. Magnetic resonance thermometry mapping during HIFU confirmed undesired surface heating in phantoms containing microbubbles, whereas heating occurred at the acoustic focus of phantoms containing the nanodroplets. Maximal change in temperature at the target site was enhanced by 16.9% and 37.0% by microbubbles and nanodroplets, respectively. This perfluorocarbon nanodroplet has the potential to reduce the time to ablate tumors by one-third during focused ultrasound surgery while also safely enhancing thermal deposition at the target site.
Spatial patterning of endothelial cells and vascular network formation using ultrasound standing wave fields
Authors: Garvin Kelley A. , Dalecki Diane , Yousefhussien Mohammed , Helguera Maria , Hocking Denise C.
Published: August 2013

The spatial organization of cells is essential for proper tissue assembly and organ function. Thus, successful engineering of complex tissues and organs requires methods to control cell organization in three dimensions. In particular, technologies that facilitate endothelial cell alignment and vascular network formation in three-dimensional tissue constructs would provide a means to supply essential oxygen and nutrients to newly forming tissue. Acoustic radiation forces associated with ultrasound standing wave fields can rapidly and non-invasively organize cells into distinct multicellular planar bands within three-dimensional collagen gels. Results presented herein demonstrate that the spatial pattern of endothelial cells within three-dimensional collagen gels can be controlled by design of acoustic parameters of the sound field. Different ultrasound standing wave field exposure parameters were used to organize endothelial cells into either loosely aggregated or densely packed planar bands. The rate of vessel formation and the morphology of the resulting endothelial cell networks were affected by the initial density of the ultrasound-induced planar bands of cells. Ultrasound standing wave fields provide a rapid, non-invasive approach to pattern cells in three-dimensions and direct vascular network formation and morphology within engineered tissue constructs.
High-speed observation of bubble cloud generation near a rigid wall by second-harmonic superimposed ultrasound
Authors: Yoshizawa Shin , Yasuda Jun , Umemura Shin-ichiro
Published: August 2013

Cavitation bubbles are known to accelerate therapeutic effects of ultrasound. Although negative acoustic pressure is the principle factor of cavitation, positive acoustic pressure has a role for bubble cloud formation at a high intensity of focused ultrasound when cavitation bubbles provide pressure release surfaces converting the pressure from highly positive to negative. In this study, the second-harmonic was superimposed onto the fundamental acoustic pressure to emphasize either peak positive or negative pressure. The peak negative and positive pressure emphasized waves were focused on a surface of an aluminum block. Cavitation bubbles induced near the block were observed with a high-speed camera by backlight and the size of the cavitation generation region was measured from the high-speed images. The negative pressure emphasized waves showed an advantage in cavitation inception over the positive pressure emphasized waves. In the sequence of the negative pressure emphasized waves immediately followed by the positive pressure emphasized waves, cavitation bubbles were generated on the block by the former waves and the cavitation region were expanded toward the transducer in the latter waves with high reproducibility. The sequence demonstrated its potential usefulness in enhancing the effects of therapeutic ultrasound at a high acoustic intensity.
Rapid ultrasonic stimulation of inflamed tissue with diagnostic intent
Authors: McClintic Abbi M. , Dickey Trevor C. , Gofeld Michael , Ray Illian P. , Kliot Michel , Kucewicz John C. , Loeser John D. , Richebe Philippe G. , Mourad Pierre D.
Published: August 2013

Previous studies have observed that individual pulses of intense focused ultrasound (iFU) applied to inflamed and normal tissue can generate sensations, where inflamed tissue responds at a lower intensity than normal tissue. It was hypothesized that successively applied iFU pulses will generate sensation in inflamed tissue at a lower intensity and dose than application of a single iFU pulse. This hypothesis was tested using an animal model of chronic inflammatory pain, created by injecting an irritant into the rat hind paw. Ultrasound pulses were applied in rapid succession or individually to rats' rear paws beginning at low peak intensities and progressing to higher peak intensities, until the rats withdrew their paws immediately after iFU application. Focused ultrasound protocols consisting of successively and rapidly applied pulses elicited inflamed paw withdrawal at lower intensity and estimated tissue displacement values than single pulse protocols. However, both successively applied pulses and single pulses produced comparable threshold acoustic dose values and estimates of temperature increases. This raises the possibility that temperature increase contributed to paw withdrawal after rapid iFU stimulation. While iFU-induction of temporal summation may also play a role, electrophysiological studies are necessary to tease out these potential contributors to iFU stimulation.
A heuristic model of stone comminution in shock wave lithotripsy
Authors: Smith Nathan B. , Zhong Pei
Published: August 2013

A heuristic model is presented to describe the overall progression of stone comminution in shock wave lithotripsy (SWL), accounting for the effects of shock wave dose and the average peak pressure, P+(avg), incident on the stone during the treatment. The model is developed through adaptation of the Weibull theory for brittle fracture, incorporating threshold values in dose and P+(avg) that are required to initiate fragmentation. The model is validated against experimental data of stone comminution from two stone types (hard and soft BegoStone) obtained at various positions in lithotripter fields produced by two shock wave sources of different beam width and pulse profile both in water and in 1,3-butanediol (which suppresses cavitation). Subsequently, the model is used to assess the performance of a newly developed acoustic lens for electromagnetic lithotripters in comparison with its original counterpart both under static and simulated respiratory motion. The results have demonstrated the predictive value of this heuristic model in elucidating the physical basis for improved performance of the new lens. The model also provides a rationale for the selection of SWL treatment protocols to achieve effective stone comminution without elevating the risk of tissue injury.
Assessment of high-intensity focused ultrasound treatment of rodent mammary tumors using ultrasound backscatter coefficients
Authors: Kemmerer Jeremy P. , Ghoshal Goutam , Karunakaran Chandra , Oelze Michael L.
Published: August 2013

Fischer 344 rats with subcutaneous mammary adenocarcinoma tumors were exposed to therapeutic ultrasound at one of three exposure levels (335, 360, and 502 W/cm2 spatial-peak temporal-average intensity). Quantitative ultrasound estimates were generated from ultrasound radio frequency (RF) data from tumors before and after high-intensity focused ultrasound treatment. Treatment outcome was independently assessed by triphenyl tetrazolium chloride (TTC) staining, histological analysis by a pathologist, and thermocouple data. The average backscatter coefficient (BSC) and integrated backscatter coefficient (IBSC) were estimated before and after therapeutic ultrasound exposure for each tumor from RF data collected using clinical (Ultrasonix Sonix RP) and small-animal (Visualsonics Vevo 2100) array systems. Changes in the BSC with treatment were comparable to inter-sample variation of untreated tumors, but statistically significant differences in the change in the IBSCs were observed when comparing the exposures collectively (p < 0.10 for Sonix RP, p < 0.05 for Vevo 2100). Several exposure levels produced statistically significant differences in the change in IBSC when examined pair-wise, including two exposures having similar intensities (p < 0.05, Vevo 2100). A comparison of the IBSC results with temperature data, histology, and TTC staining revealed that the BSC was not always sensitive to thermal insult and that peak exposure pressure appeared to correlate with observed BSC increases.
Time-reversal acoustics and ultrasound-assisted convection-enhanced drug delivery to the brain
Authors: Olbricht William , Sistla Manjari , Ghandi Gaurav , Lewis George , Sarvazyan Armen
Published: August 2013

Time-reversal acoustics is an effective way of focusing ultrasound deep inside heterogeneous media such as biological tissues. Convection-enhanced delivery is a method of delivering drugs into the brain by infusing them directly into the brain interstitium. These two technologies are combined in a focusing system that uses a “smart needle” to simultaneously infuse fluid into the brain and provide the necessary feedback for focusing ultrasound using time-reversal acoustics. The effects of time-reversal acoustics-focused ultrasound on the spatial distribution of infused low- and high-molecular weight tracer molecules are examined in live, anesthetized rats. Results show that exposing the rat brain to focused ultrasound significantly increases the penetration of infused compounds into the brain. The addition of stabilized microbubbles enhances the effect of ultrasound exposure.
Ultrafast dynamics of the acoustic vaporization of phase-change microdroplets
Authors: Shpak Oleksandr , Kokhuis Tom J. A. , Luan Ying , Lohse Detlef , de Jong Nico , Fowlkes Brian , Fabiilli Mario , Versluis Michel
Published: August 2013

Acoustically sensitive emulsions are a promising tool for medical applications such as localized drug delivery. The physical mechanisms underlying the ultrasound-triggered nucleation and subsequent vaporization of these phase-change emulsions are largely unexplored. Here, the acoustic vaporization of individual micron-sized perfluoropentane (PFP) droplets is studied at a nanoseconds timescale. Highly diluted emulsions of PFP-in-water and oil-in-PFP-in-water droplets, ranging from 3.5 to 11 μm in radius, were prepared and the nucleation and growth of the vapor bubbles was imaged at frame rates of up to 20 Mfps. The droplet vaporization dynamics was observed to have three distinct regimes: (1) prior to nucleation, a regime of droplet deformation and oscillatory translations within the surrounding fluid along the propagation direction of the applied ultrasound; (2) a regime characterized by the rapid growth of a vapor bubble enhanced by ultrasound-driven rectified heat transfer; and (3) a final phase characterized by a relatively slow expansion, after ultrasound stops, that is fully dominated by heat transfer. A method to measure the moment of inception of the nucleation event with respect to the phase of the ultrasound wave is proposed. A simple physical model captures quantitatively all of the features of the subsequent vapor bubble growth.
A multi-element interstitial ultrasound applicator for the thermal therapy of brain tumors
Authors: Canney Michael S. , Chavrier Françoise , Tsysar Sergey , Chapelon Jean-Yves , Lafon Cyril , Carpentier Alexandre
Published: August 2013

Interstitial thermal therapy is a minimally invasive treatment modality that has been used clinically for ablating both primary and secondary brain tumors. Here a multi-element interstitial ultrasound applicator is described that allows for increased spatial control during thermal ablation of tumors as compared to existing clinical devices. The device consists of an array of 56 ultrasound elements operating at 6 MHz, oriented on the seven faces of a 3.2 mm flexible catheter. The device was first characterized using the acoustic holography method to examine the functioning of the array. Then experiments were performed to measure heating in tissue-mimicking gel phantoms and ex vivo tissue samples using magnetic resonance imaging-based thermometry. Experimental measurements were compared with results obtained using numerical simulations. Last, simulations were performed to study the feasibility of using the device for thermal ablation in the brain. Experimental results show that the device can be used to induce a temperature rise of greater than 20 °C in ex vivo tissue samples and numerical simulations further demonstrate that tumors with diameters of greater than 30-mm could potentially be treated.
Acoustic field characterization of the Duolith: Measurements and modeling of a clinical shock wave therapy device
Authors: Perez Camilo , Chen Hong , Matula Thomas J. , Karzova Maria , Khokhlova Vera A.
Published: August 2013

Extracorporeal shock wave therapy (ESWT) uses acoustic pulses to treat certain musculoskeletal disorders. In this paper the acoustic field of a clinical portable ESWT device (Duolith SD1) was characterized. Field mapping was performed in water for two different standoffs of the electromagnetic head (15 or 30 mm) using a fiber optic probe hydrophone. Peak positive pressures at the focus ranged from 2 to 45 MPa, while peak negative pressures ranged from −2 to −11 MPa. Pulse rise times ranged from 8 to 500 ns; shock formation did not occur for any machine settings. The maximum standard deviation in peak pressure at the focus was 1.2%, indicating that the Duolith SD1 generates stable pulses. The results compare qualitatively, but not quantitatively with manufacturer specifications. Simulations were carried out for the short standoff by matching a Khokhlov-Zabolotskaya-Kuznetzov equation to the measured field at a plane near the source, and then propagating the wave outward. The results of modeling agree well with experimental data. The model was used to analyze the spatial structure of the peak pressures. Predictions from the model suggest that a true shock wave could be obtained in water if the initial pressure output of the device were doubled.
Non-invasive ultrasonic surgery of the brain in non-human primates
Authors: Marquet Fabrice , Boch Anne-Laure , Pernot Mathieu , Montaldo Gabriel , Seilhean Danielle , Fink Mathias , Tanter Mickael , Aubry Jean-Francois
Published: August 2013

High-intensity focused ultrasound causes selective tissue necrosis efficiently and safely, namely, in the prostate, liver, and uterine fibroid. Nevertheless, ablation of brain tissue using focused ultrasound remains limited due to strong aberrations induced by the skull. To achieve ultrasonic transcranial brain ablation, such aberrations have to be compensated. In this study, non-invasive therapy was performed on monkeys using adaptive correction of the therapeutic beam and 3D simulations of transcranial wave propagation based on 3D computed tomographic (CT) scan information. The aim of the study was two-fold: induce lesions in a non-human primate brain non-invasively and investigate the potential side effects. Stereotactic targeting was performed on five Macaca fascicularis individuals. Each hemisphere was treated separately with a 15-day interval and animals were sacrificed two days after the last treatment. The ultrasonic dose delivered at the focus was increased from one treatment location to the other to estimate the thermal dose for tissue alteration. Thermal doses in the brain were determined by numerical computations. Treatment efficiency and safety were evaluated histologically. The threshold for tissue damage in the brain was measured to be between 90 and 280 cumulative equivalent minutes at 43 °C. Intravenous injection of corticoids before the treatment limited the side effects.
High intensity focused ultrasound ablation and antitumor immune response
Authors: Wu Feng
Published: August 2013

The ideal cancer therapy not only induces the death of all localized tumor cells without damage to surrounding normal tissue, but also activates a systemic antitumor immunity. High intensity focused ultrasound (HIFU) has the potential to be such a treatment, as it can non-invasively ablate a targeted tumor below the skin surface, and may subsequently augment host antitumor immunity. This paper is to review increasing pre-clinical and clinical evidence linking antitumor immune response to HIFU ablation, and to discuss the potential mechanisms involved in HIFU-enhanced host antitumor immunity. The seminal studies performed so far indicate that although it is not possible to conclude definitively on the connection between HIFU treatment and antitumor immune response, it is nonetheless important to conduct extensive studies on the subject in order to elucidate the processes involved.
Variations of bubble cavitation and temperature elevation during lesion formation by high-intensity focused ultrasound
Authors: Zhou Yufeng , Wilson Gao Xiaobin
Published: August 2013

High-intensity focused ultrasound (HIFU) is emerging as an effective therapeutic modality in both thermal ablations for solid tumor/cancer and soft-tissue fragmentation. Mechanical and thermal effects, which play an important role in the HIFU treatment simultaneously, are dependent on the operating parameters and may vary with the progress of therapy. Mechanical erosion in the shape of a “squid,” a “dumbbell” lesion with both mechanical and thermal lesions, or a “tadpole” lesion with mechanical erosion at the center and thermal necrosis on the boundary in the transparent gel phantom could be produced correspondingly with the pulse duration of 5–30 ms, which is much longer than histotripsy burst but shorter than the time for tissue boiling, and pulse repetition frequency (PRF) of 0.2–5 Hz. Meanwhile, variations of bubble cavitation (both inertial and stable cavitation) and temperature elevation in the focal region (i.e., z = −2.5, 0, and 2.5 mm) were measured by passive cavitation detection (PCD) and thermocouples during the therapeutic procedure, respectively. Stable cavitation increased with the pulse duration, PRF, and the number of pulses delivered. However, inertial cavitation was found to increase initially and then decrease with long pulse duration and high PRF. Temperature in the pre-focal region is always higher than those at the focal and post-focal position in all tests. Great variations of PCD signals and temperature elevation are due to the generation and persistence of large bubble, which is resistant to collapse and occurs with the increase of pulse duration and PRF. Similar lesion pattern and variations were also observed in ex vivo porcine kidneys. Hyperechoes in the B-mode ultrasound image were comparable to the shape and size of lesions in the dissected tissue. Thermal lesion volume increased with the increase of pulse duration and PRF, but mechanical erosion reached its maximum volume with the pulse duration of 20 ms and PRF of 1 Hz. Altogether, bubble cavitation and thermal field vary with the progress of HIFU treatment with different sonication parameters, which provide insights into the interaction of ultrasound burst with the induced bubbles for both soft tissue fractionation and enhancement in thermal accumulation. Appropriate synergy and monitoring of mechanical and thermal effects would broaden the HIFU application and enhance its efficiency as well as safety.
Control of inertial acoustic cavitation in pulsed sonication using a real-time feedback loop system
Authors: Desjouy Cyril , Poizat Adrien , Gilles Bruno , Inserra Claude , Bera Jean-Christophe
Published: August 2013

Owing to the complex behavior of ultrasound-induced bubble clouds (nucleation, linear and nonlinear oscillations, collapse), acoustic cavitation remains a hardly controllable phenomenon, leading to poorly reproducible ultrasound-based therapies. A better control of the various aspects of cavitation phenomena for in vivo applications is a key requirement to improve emerging ultrasound therapies. Previous publications have reported on systems performing regulation of acoustic cavitation in continuous sonication when applied in vitro, but the main challenge today is to achieve real-time control of cavitation activity in pulsed sonication when used in vivo. The present work aims at developing a system to control acoustic cavitation in a pulsed wave condition using a real-time feedback loop. The experimental setup consists of a water bath in which is submerged a focused transducer (pulsed waves, frequency 550 kHz) used for sonication and a hydrophone used to listen to inertial cavitation. The designed regulation process allows the cavitation activity to be controlled through a 300 μs feedback loop. Without regulation, cavitation exhibits numerous bursts of intense activity and large variations of inertial cavitation level over time. In a regulated regime, the control of inertial cavitation activity within a pulse leads to consistent cavitation levels over time with an enhancement of the reproducibility.
Changes in backscatter of liver tissue due to thermal coagulation induced by focused ultrasound
Authors: Shishitani Takashi , Matsuzawa Ryo , Yoshizawa Shin , Umemura Shin-ichiro
Published: August 2013

Ultrasonic imaging has advantages in its self-consistency in guiding and monitoring ultrasonic treatment such as high-intensity focused ultrasound (HIFU) treatment. Changes in ultrasonic backscatter of tissues due to HIFU treatment have been observed, but their mechanism is still under discussion. In this paper, ultrasonic backscatter of excised and degassed porcine liver tissue was observed before and after HIFU exposure using a diagnostic scanner, and its acoustic impedance was mapped using an ultrasonic microscope. The histology of its pathological specimen was also observed using an optical microscope. The observed decrease in backscatter intensity due to HIFU exposure was consistent with a spatial Fourier analysis of the histology, which also showed changes due to the exposure. The observed increase in acoustic impedance due to the exposure was also consistent with the histological change assuming that the increase was primarily caused by the increase in the concentration of hepatic cells.
From Cosmology to Cold Atoms: Observation of Sakharov Oscillations in a Quenched Atomic Superfluid
Authors: Hung Chen-Lung , Gurarie Victor , Chin Cheng
Published: August 2013

Tinyverse

Quantum many-systems, such superfluids, are difficult to study in equilibrium, and thus understanding their dynamics poses a particular challenge. When the strength of interactions was suddenly changed in a two-dimensional gas of cesium atoms,

Hung
et al.

(p.
1213
, published online 1 August; see the Perspective by

Schmiedmayer and Berges

) observed oscillations in the time and space domains analogous to the peaks in the spectrum of the cosmic microwave background.
Titration of Four Replication Factors Is Essential for the
Xenopus laevis
Midblastula Transition
Authors: Collart Clara , Allen George E. , Bradshaw Charles R. , Smith James C. , Zegerman Philip
Published: August 2013

Regulating the MBT

It has been known for more than 30 years that a defined number of cell divisions in the frog embryo precede a crucial developmental event called the midblastula transition (MBT).

Collart
et al.

(p.
893
, published online 1 August) now elucidate a mechanism involved in the control of the MBT. DNA replication initiation factors are titrated out during early cell divisions, which controls the elongation of the cell cycle and the onset of zygotic transcription during the MBT.
Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1
Authors: Everroad R. Craig , Woebken Dagmar , Singer Steven W. , Burow Luke C. , Kyrpides Nikos , Woyke Tanja , Goodwin Lynne , Detweiler Angela , Prufert-Bebout Leslie , Pett-Ridge Jennifer
Published: August 2013

The nonheterocystous filamentous cyanobacterium strain ESFC-1 has recently been isolated from a marine microbial mat system, where it was identified as belonging to a recently discovered lineage of active nitrogen-fixing microorganisms. Here, we report the draft genome sequence of this isolate. The assembly consists of 3 scaffolds and contains 5,632,035 bp with a GC content of 46.5%.
Complete Genome Sequence of a Papillomavirus Isolated from the European Mole
Authors: Maes Piet , Sijmons Steven , Stevens Hans , Van Ranst Marc
Published: August 2013

A papillomavirus was isolated from healthy epithelial tissue of two European moles (
Talpa europaea
) and the complete genomic sequence was determined. To our knowledge, this is the first papillomavirus to be isolated from a mole. Phylogenetic analysis shows it to be most closely related to viruses of the genus
Kappapapillomavirus
.
Complete Genome Sequence of Lactobacillus plantarum Strain 16, a Broad-Spectrum Antifungal-Producing Lactic Acid Bacterium
Authors: Crowley Sarah , Bottacini Francesca , Mahony Jennifer , van Sinderen Douwe
Published: August 2013

Lactobacillus plantarum
strain 16 restricts the growth of various food spoilage fungi and has the potential to be used as a biopreservative to improve the shelf life of foods. The complete genome sequence contains 3,044,678 bp with a G+C content of 44.74% and harbors the largest plasmid complement reported for this species to date.
De Novo
Assembly of the
Streptomyces
sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing
Authors: Hoefler B. Christopher , Konganti Kranti , Straight Paul D.
Published: August 2013

We report a draft genome assembly of
Streptomyces
sp. strain Mg1, a competitive soil isolate with multiple secondary metabolite gene clusters.
Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium tuberculosis East African Indian Strain OSDD271
Authors: Karuthedath Vellarikkal Shamsudheen , Patowary Ashok , Singh Meghna , Periwal Vinita , Singh Ajay Vir , Singh Pravin Kumar , Garg Parul , Mohan Katoch Viswa , Katoch Kiran , Jangir Pramod Kumar , Sharma Rakesh ,   Open Source Drug Discovery Consortium, Chauhan D. S. , Scaria Vinod , Sivasubbu Sridhar
Published: August 2013

We describe the genome sequencing and analysis of a clinical isolate of
Mycobacterium tuberculosis
East African Indian (EAI) strain OSDD271 from India.
Genome Sequence of Clostridium diolis Strain DSM 15410, a Promising Natural Producer of 1,3-Propanediol
Authors: Wang Yu , Tao Fei , Tang Hongzhi , Xu Ping
Published: August 2013

Clostridium diolis
strain DSM 15410 is considered one of the best natural producers of 1,3-propanediol because of its appreciable substrate-tolerant ability, yield, and productivity. Here, we present a 5.85-Mb assembly of its genome sequence. We have annotated the coding sequences responsible for glycerol utilization and 1,3-propanediol fermentation.
Complete Genome Sequence of a Reassortant H14N2 Avian Influenza Virus from California
Authors: Boyce Walter M. , Schobel Seth , Dugan Vivien G. , Halpin Rebecca , Lin Xudong , Wentworth David E. , Lindsay LeAnn L. , Mertens Eva , Plancarte Magdalena
Published: August 2013

We report the complete genome sequence of a reassortant H14N2 avian influenza virus isolated in 2011 from a northern shoveler in California. This introduced Eurasian subtype acquired seven segments from North American viruses and circulated in the Pacific Flyway 1 year after its detection in the Mississippi Flyway.
Complete Genome Sequence of
Enterobacter
sp. Strain R4-368, an Endophytic N-Fixing Gammaproteobacterium Isolated from Surface-Sterilized Roots of
Jatropha curcas
L
Authors: Madhaiyan Munusamy , Peng Ni , Ji Lianghui
Published: August 2013

Enterobacter
sp. strain R4-368 is one of the few characterized
Jatropha
endophytic diazotrophic bacteria and was isolated from surface-sterilized roots. This bacterium shows strong growth-promoting effects, being able to increase plant biomass and seed yields.
Enterobacter
sp. R4-368 is the second fully sequenced diazotrophic
Enterobacter
species. The sequence information shall facilitate the elucidation of the molecular mechanisms of plant growth promotion, nitrogen fixation in nonlegume plant species, and evolution of biological nitrogen fixation systems.
Draft Genome Sequence of the Bisphenol A-Degrading Bacterium
Sphingobium
sp. Strain YL23
Authors: Hu Anyi , Lv Min , Yu Chang-Ping
Published: August 2013

Sphingobium
sp. strain YL23, a novel bacterium isolated from sewage sludge of a domestic wastewater treatment plant, has been shown to completely degrade bisphenol A under aerobic conditions. Here, we describe a 3.8-Mb assembly of its genome sequence and major findings from its annotation.
Draft Genome Sequence of Pseudomonas putida Strain MTCC5279
Authors: Chaudhry Vasvi , Asif Mehar H. , Bag Sumit , Goel Ridhi , Mantri Shrikant S. , Singh Sunil K. , Chauhan Puneet S. , Sawant Samir V. , Nautiyal Chandra Shekhar
Published: August 2013

Here we report the genome sequence of a plant-growth-promoting rhizobacterium,
Pseudomonas putida
strain MTCC5279. The length of the draft genome sequence is approximately 5.2 Mb, with a GC content of 62.5%. The draft genome sequence reveals a number of genes whose products are possibly involved in plant growth promotion and abiotic stress tolerance.
Draft Genome Sequence of Bacillus cereus Strain F, Isolated from Ancient Permafrost
Authors: Brenner Evgeniy V. , Brouchkov Anatoli V. , Kurilshikov Alexander M. , Griva Gennady I. , Kashuba Elena , Kashuba Vladimir I. , Melefors O. , Repin Vladimir E. , Melnikov Vladimir P. , Vlassov Valentin V.
Published: August 2013

Bacillus cereus
strain F was isolated and cultured from a sample of permafrost, aged presumably about 3 million years, on the Mammoth Mountain (62°56′N, 133°59′E). These genome data provide the basis to investigate
Bacillus cereus
F, identified as a long-term survivor of the extremely cold and close environment.
Complete Genome Sequence of Persistent Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain RP73
Authors: Jeukens Julie , Boyle Brian , Bianconi Irene , Kukavica-Ibrulj Irena , Tümmler Burkhard , Bragonzi Alessandra , Levesque Roger C.
Published: August 2013

Pseudomonas aeruginosacan establish lifelong chronic airway infections in cystic fibrosis (CF) patients. However, the genetic features associated with long-term persistence in the lung are not understood. We sequenced the genome ofP. aeruginosastrain RP73, which was isolated after 16.9 years of chronic lung infection in a CF patient.
Genome Sequence of Paenibacillus polymyxa ATCC 12321, a Promising Strain for Optically Active (
R
,
R
)-2,3-Butanediol Production
Authors: Tong Ying-Jia , Ji Xiao-Jun , Liu Lu-Gang , Shen Meng-Qiu , Huang He
Published: August 2013

Paenibacillus polymyxa
is a potential strain for (
R
,
R
)-2,3-butanediol production. Here, we report an annotated draft genome sequence of
P. polymyxa
strain ATCC 12321, which contains 4,429 protein-coding genes and 49 structural RNAs. This genome sequence provides a genetic basis for a better understanding of the mechanism for the accumulation of highly optically active (
R
,
R
)-2,3-butanediol.
Genome Sequence of Porcine Escherichia coli Strain IMT8073, an Atypical Enteropathogenic E. coli Strain Isolated from a Piglet with Diarrhea
Authors: Semmler Torsten , Eichhorn Inga , Bethe Astrid , Bauerfeind Rolf , Pickard Derek , Kingsley Robert A. , Dougan Gordon , Wieler Lothar H.
Published: August 2013

Escherichia coli
is a highly diverse bacterial species, with atypical enteropathogenic
E. coli
(aEPEC) causing intestinal disease in both human and animal hosts. Here, we report the first complete genome sequence of an aEPEC strain of sequence type ST794 and serotype Ont:H7, isolated from a diseased piglet.
Trapping and Identification of Cellular Substrates of the Staphylococcus aureus ClpC Chaperone
Authors: Graham Justin W. , Lei Mei G. , Lee Chia Y.
Published: August 2013

ClpC is an ATP-dependent Hsp100/Clp chaperone involved in protein quality control in low-GC Gram-positive bacteria. Previously, we found that ClpC affected the expression of a large number of genes, including capsule genes in
Staphylococcus aureus
. Here we constructed a His-tagged ClpC variant (ClpC
trap
) with mutations within the Walker B motifs to identify the direct substrates of ClpC by copurification with ClpC
trap
followed by gel electrophoresis combined with liquid chromatography-tandem mass spectrometry proteomics. We identified a total of 103 proteins that are potential substrates of ClpC in strain Newman. The direct protein-protein interaction of ClpC with a subset of the captured proteins was verified in a bacterial two-hybrid system. The captured proteins could be grouped into various functional categories, but most were related to proteins involved in the stress response. Several known ClpC substrates were captured, including ClpP, TrfA/MecA, ClpB, DnaK, DnaJ, GroL, RecA, and CodY, supporting the validity of our approach. Our results also revealed many new ClpC substrates, including AgrA, CcpA, RsbW, MurG, FtsA, SrtA, Rex, Atl, ClfA, and SbcC. Analysis of capsule production showed that three of the captured proteins, which were not previously known to be transcriptional regulators, did affect capsule production.
Acute confusional migraine: a variant not to be missed
Authors: Verma Rajesh , Sahu Ritesh , Jaiswal Anupam , Kumar Neeraj
Published: August 2013

A middle age woman who had frequent migraines was admitted with memory loss following severe unilateral headache, restlessness and confusion. Investigations including haematology, biochemistry, cerebrospinal fluid analysis serology and imaging were normal. As she had frequent migraines with a history of ophthalmoplegic migraine, acute confusional migraine was thought of as a possibility. The patient responded dramatically to intravenous sodium valproate. We report this case to emphasise that acute confusional migraine, a rare variant of migraine, is occasionally encountered in adults and prompt recognition will lead to appropriate management.
The impact of targeting all elderly persons in England and Wales for yearly influenza vaccination: excess mortality due to pneumonia or influenza and time trend study
Authors: Mann Andrea G , Mangtani Punam , Russell Colin A , Whittaker John C
Published: August 2013

Objective

To investigate the impact on mortality due to pneumonia or influenza of the change from risk-based to age group-based targeting of the elderly for yearly influenza vaccination in England and Wales.

Design

Excess mortality estimated using time series of deaths registered to pneumonia or influenza, accounting for seasonality, trend and artefacts. Non-excess mortality plotted as proxy for long-term trend in mortality.

Setting

England and Wales.

Participants

Persons aged 65–74 and 75+ years whose deaths were registered to underlying pneumonia or influenza between 1975/1976 and 2004/2005.

Outcome measures

Multiplicative effect on average excess pneumonia and influenza deaths each winter in the 4–6 winters since age group-based targeting of vaccination was introduced (in persons aged 75+ years from 1998/1999; in persons aged 65+ years from 2000/2001), estimated using multivariable regression adjusted for temperature, antigenic drift and vaccine mismatch, and stratified by dominant circulating influenza subtype. Trend in baseline weekly pneumonia and influenza death rates.

Results

There is a suggestion of lower average excess mortality in the six winters after age group-based targeting began compared to before, but the CI for the 65–74 years age group includes no difference. Trend in baseline pneumonia and influenza mortality shows an apparent downward turning point around 2000 for the 65–74 years age group and from the mid-1990s in the 75+ years age group.

Conclusions

There is weakly supportive evidence that the marked increases in vaccine coverage accompanying the switch from risk-based to age group-based targeting of the elderly for yearly influenza vaccination in England and Wales were associated with lower levels of pneumonia and influenza mortality in older people in the first 6 years after age group-based targeting began. The possible impact of these policy changes is observed as weak evidence for lower average excess mortality as well as a turning point in baseline mortality coincident with the changes.