Simulation of diagnostic ultrasound image pulse sequences in cavitation bioeffects research

Research on cavitational bioeffects of diagnostic ultrasound (DUS) typically involves a diagnostic scanner as the exposure source. However, this can limit the ranges of exposure parameters for experimentation. Anesthetized hairless rats were mounted in a water bath and their right kidneys were exposed to ultrasound. Amplitude modulation with Gaussian envelopes simulated the image pulse sequences (IPSs) produced by diagnostic scanning. A 10 mulkgmin IV dose of Definity((R)) contrast agent was given during 1-5 min exposures. Glomerular capillary hemorrhage was assessed by histology. A stationary exposure approximated the bioeffects induced by DUS within the beam area. However, the use of five closely spaced exposures more faithfully reproduced the total effect produced within a DUS scan plane. Single pulses delivered at 1 s intervals induced the same effect as the simulated DUS. Use of 100 ms triangle-wave modulations for ramp-up or ramp-down of the IPS gave no effect or a large effect, respectively. Finally, an air-backed transducer simulating DUS without contrast agent showed a zero effect even operating at twice the present DUS guideline upper limit. Relatively simple single-element laboratory exposure systems can simulate diagnostic ultrasound exposure and allow exploration of parameter ranges beyond those available on present clinical systems.     

Blue and fin whale call source levels and propagation range in the Southern Ocean

Blue (Balaenoptera musculus) and fin whales (B. physalus) produce high-intensity, low-frequency calls, which probably function for communication during mating and feeding. The source levels of blue and fin whale calls off the Western Antarctic Peninsula were calculated using recordings made with calibrated, bottom-moored hydrophones. Blue whales were located up to a range of 200 km using hyperbolic localization and time difference of arrival. The distance to fin whales, estimated using multipath arrivals of their calls, was up to 56 km. The error in range measurements was 3.8 km using hyperbolic localization, and 3.4 km using multipath arrivals. Both species produced high-intensity calls; the average blue whale call source level was 189+/-3 dB re:1 microPa-1 m over 25-29 Hz, and the average fin whale call source level was 189+/-4 dB re:1 microPa-1 m over 15-28 Hz. Blue and fin whale populations in the Southern Ocean have remained at low numbers for decades since they became protected; using source level and detection range from passive acoustic recordings can help in calculating the relative density of calling whales.     

Ergodicity,mixing and the Bernoulli property in a DNA hybridization microarray

Pulsed source–sink devices are an effective way of achieving dynamic hybridization in DNA microarrays. These can be modelled as linked twist maps, and in particular, basing the design on the dynamics of a hyperbolic toral automorphism allows the application of a set of techniques from ergodic theory. This gives a rigorous framework in which to discuss mixing. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Increases in deep ocean ambient noise in the Northeast Pacific west of San Nicolas Island, California

Recent measurement at a previously studied location illustrates the magnitude of increases in ocean ambient noise in the Northeast Pacific over the past four decades. Continuous measurements west of San Nicolas Island, California, over 138 days, spanning 2003-2004 are compared to measurements made during the 1960s at the same site. Ambient noise levels at 30-50 Hz were 10-12 dB higher (95% CI = 2.6 dB) in 2003-2004 than in 1964-1966, suggesting an average noise increase rate of 2.5-3 dB per decade. Above 50 Hz the noise level differences between recording periods gradually diminished to only 1-3 dB at 100-300 Hz. Above 300 Hz the 1964-1966 ambient noise levels were higher than in 2003-2004, owing to a diel component which was absent in the more recent data. Low frequency (10-50 Hz) ocean ambient noise levels are closely related to shipping vessel traffic. The number of commercial vessels plying the world's oceans approximately doubled between 1965 and 2003 and the gross tonnage quadrupled, with a corresponding increase in horsepower. Increases in commercial shipping are believed to account for the observed low-frequency ambient noise increase.     

Fluid particle dynamics and stokes drift in gravity and capillary waves generated by the faraday instability

In this paper we study particle motions in nearly square containers due to gravity and capillary waves generated by vertical, periodic oscillation of the container. The method of second order partial averaging is used to decompose the particle motions into periodic oscillations and a slow Stokes drift. In the case of gravity waves, it is shown that long distance (several wavelengths) particle transport is possible. In the case of capillary waves, it is shown that, in agreement with experimental observations of Ramshankaret al., particle trajectories can be chaotic even when the wave pattern is regular so long as the pattern is spatially modulated.Dedicated to Professor P. R. Sethna on the Occasion of His 70th BirthdayThis research was partially supported by an NSF Presidential Young Investigator Award and an ONR Grant No. N00014-89-J-3023.     

A method for assessing and maintaining the reproducibility of mass spectrometric analyses of complex samples

Direct injection mass spectrometric analysis of biological samples is potentially an attractive approach to the discovery of diagnostic patterns for specific pathophysiological conditions because of its speed and simplicity. Despite the possible benefits offered by such a method, its extensive application has been limited so far by several factors, including the inadequate reproducibility of the analytical results. We describe a method for monitoring and optimizing the performance of mass spectrometers used for biomarker discovery studies, based on the analysis of patterns of standardized spectral features. The method was successfully applied to maintaining spectral reproducibility during a multi‐day analysis of hundreds of serum samples despite an ion source failure, which necessitated minor maintenance. The monitoring method allowed the early detection of that failure and the restoration of the spectral profiles after the system was restarted. Copyright © 2009 John Wiley & Sons, Ltd.     

Process pathway inference via time series analysis

Motivated by recent experimental developments in functional genomics, we construct and test a numerical technique for inferring process pathways, in which one process calls another process, from time series data. We validate using a case in which data are readily available and we formulate an extension, appropriate for genetic regulatory networks, which exploits Bayesian inference and in which the present-day undersampling is compensated for by prior understanding of genetic regulation.