Estimation of speed of sound in dual-layered media using medical ultrasound image deconvolution

The speed of sound in soft tissues is usually assumed to be 1540 m/s in medical pulse-echo ultrasound imaging systems. When the true speed is different, the mismatch can lead to distortions in the acquired images, and so reduce their clinical value. Previously we reported a new method of sound-speed estimation in the context of image deconvolution. Unlike most other sound-speed estimation methods, this enables the use of unmodified ultrasound machines and a normal scanning pattern. Our approach was validated for largely homogeneous media with single sound speeds. In this article, we demonstrate that sound speeds of dual-layered media can also be estimated through image deconvolution. An ultrasound simulator has been developed for layered media assuming that, for moderate speed differences, the reflection at the interface may be neglected. We have applied our dual-layer algorithm to simulations and in vitro phantoms. The speed of the top layer is estimated by our aforesaid method for homogeneous media. Then, when the layer boundary position is known, a series of deconvolutions are carried out with dual-layered point-spread functions having different lower-layer speeds. The best restoration is selected using a correlation metric. The error level (e.g., a mean error of −9 m/s with a standard deviation of 16 m/s) for in vitro phantoms is found to be not as good as that of our single-speed algorithm, but is comparable to other local speed estimation methods where the data acquisition may not be as simple as in our proposed method.     

Sound field prediction in long enclosures with branches: A combined method

The propagation of sound in long enclosures with branches has been studied theoretically and experimentally, and an efficient combined method is proposed to predict the sound field in long enclosures with branches. Based on the wave-acoustics theory, the theoretical analysis of the sound field of the long enclosures with branches is performed. This paper also investigated the sound field prediction of long enclosures with branches, by using the acoustic modeling program, ODEON. The results obtained by the theoretical analysis and the numerical simulation ODEON are compared with the experimental measurements, and the characteristics of the two methods for predicting the sound field of long enclosures with branches are analyzed. Compared with the experimental results, it is found that: (1) the results predicted by the theoretical analysis fluctuate relatively large with respect to the source-receiver distance, and the sound pressure level (SPL) attenuation obtained is smaller than that measured; and (2) the results predicted by the numerical simulation is smoother, and the calculated SPL attenuation is larger than that measured. To effectively predict the sound field of long enclosures with branches, a combined numerical method is thus proposed. The effectiveness of the proposed combined method is demonstrated by the scale-model experiments.     

Acoustic signature of a submarine hull under harmonic excitation

The structural and acoustic responses of a submarine under harmonic force excitation are presented. The submarine hull is modelled as a cylindrical shell with internal bulkheads and ring stiffeners. The cylindrical shell is closed by truncated conical shells, which in turn are closed at each end using circular plates. The entire structure is submerged in a heavy fluid medium. The structural responses of the submerged vessel are calculated by solving the cylindrical shell equations of motion using a wave approach and the conical shell equations with a power series solution. The far-field radiated sound pressure is then calculated by means of the Helmholtz integral. The contribution of the conical end closures on the radiated sound pressure for the lowest circumferential mode numbers is clearly observed. Results from the analytical model are compared with computational results from a fully coupled finite element/boundary element model.     

Enhancing micro-perforated panel attenuation by partitioning the adjoining cavity

The sound attenuation performance of micro-perforated panels (MPP) with adjoining air cavity is investigated for a plenum. The sound field inside of a plenum is compared for two cases. In the first case, the plenum is treated with an MPP and adjoining air cavity without any partitioning. For the second case, the adjoining air cavity is partitioned into a number of sub-cavities. The resulting sound pressure fields indicate that partitioning the adjoining air cavity increases the overall sound attenuation due to the MPP by approximately 4 dB. The explanation for this phenomenon was investigated by measuring the sound pressure level on planes in front of the MPP. Additionally, boundary element analyses were conducted to simulate the effect of the MPP and adjoining cavity with and without partitioning on the sound field in the plenum. It was demonstrated that a MPP can be modeled as a transfer impedance and that partitioning the adjoining cavity enhances attenuation to acoustic modes that propagate transverse to the MPP.     

DNA recombination through assembly graphs

Motivated by DNA rearrangements and DNA homologous recombination modeled in [A. Angeleska, N. Jonoska, M. Saito, L.F. Landweber, RNA-guided DNA assembly, Journal of Theoretical Biology, 248(4) (2007), 706–720], we investigate smoothings on graphs that consist of only 4-valent and 1-valent rigid vertices, called assembly graphs. An assembly graph can be seen as a representation of the DNA during certain recombination processes in which 4-valent vertices correspond to the alignment of the recombination sites. A single gene is modeled by a polygonal path in an assembly graph. A polygonal path makes a “right-angle” turn at every vertex, defining smoothings at the 4-valent vertices and therefore modeling the recombination process. We investigate the minimal number of polygonal paths visiting all vertices of a given graph exactly once, and show that for every positive integer n there are graphs that require at least n such polygonal paths. We show that there is an embedding in three-dimensional space of each assembly graph such that smoothing of vertices according to a given set of polygonal paths results in an unlinked graph. As some recombination processes may happen simultaneously, we characterize the subsets of vertices whose simultaneous smoothings keep a given gene in tact and give a characterization of all sequences of sets of vertices defining successive simultaneous smoothings that can realize complete gene rearrangement.     

A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches

Pharmacophore multiplets are useful tools for 3D database searching, with the queries used ordinarily being derived from ensembles of random conformations of active ligands. It seems reasonable to expect that their usefulness can be augmented by instead using queries derived from single ligand conformations obtained from aligned ligands. Comparisons of pharmacophore multiplet searching using random conformations with multiplet searching using single conformations derived from GALAHAD (a genetic algorithm with linear assignment for hypermolecular alignment of datasets) models do indeed show that, while query hypotheses based on random conformations are quite effective, hypotheses based on aligned conformations do a better job of discriminating between active and inactive compounds. In particular, the hypothesis created from a neuraminidase inhibitor model was more similar to half of 18 known actives than all but 0.2% of the compounds in a structurally diverse subset of the World Drug Index. Similarly, a model developed from five angiotensin II antagonists yielded hypotheses that placed 65 known antagonists within the top 0.1–1% of decoy databases. The differences in discriminating power ranged from 2 to 20-fold, depending on the protein target and the type of pharmacophore multiplet used.     

Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors

G-protein coupled receptors (GPCRs) comprise a large superfamily of proteins that are targets for nearly 50% of drugs in clinical use today. In the past, the use of structure-based drug design strategies to develop better drug candidates has been severely hampered due to the absence of the receptor’s three-dimensional structure. However, with recent advances in molecular modeling techniques and better computing power, atomic level details of these receptors can be derived from computationally derived molecular models. Using information from these models coupled with experimental evidence, it has become feasible to build receptor pharmacophores. In this study, we demonstrate the use of the Hybrid Structure Based (HSB) method that can be used effectively to screen and identify prospective ligands that bind to GPCRs. Essentially; this multi-step method combines ligand-based methods for building enriched libraries of small molecules and structure-based methods for screening molecules against the GPCR target. The HSB method was validated to identify retinal and its analogues from a random dataset of ∼300,000 molecules. The results from this study showed that the 9 top-ranking molecules are indeed analogues of retinal. The method was also tested to identify analogues of dopamine binding to the dopamine D2 receptor. Six of the ten top-ranking molecules are known analogues of dopamine including a prodrug, while the other thirty-four molecules are currently being tested for their activity against all dopamine receptors. The results from both these test cases have proved that the HSB method provides a realistic solution to bridge the gap between the ever-increasing demand for new drugs to treat psychiatric disorders and the lack of efficient screening methods for GPCRs. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Ultrasonic characterization of proteins and blood cells

Ultrasound changes its intensity and speed when propagating through a liquid or a suspension containing particles. In addition it generates a weak electric signal by altering the motion of ions and charged particles. Hence acoustic and electroacoustic measurements provide information about the properties of suspended particles and molecules. Here we present both acoustic and electroacoustic results on blood suspensions and protein solutions, relevant to life sciences. For blood cells a strong increase in acoustic attenuation with volume fraction is found, from which the speed of sound in an erythrocyte is found to be about 1900 m/s, assuming the attenuation is due to scattering only. A similar value of 1700 m/s is found from the increase in sound speed of the dispersion with concentration. Electroacoustic measurements on bovine serum albumin (BSA) yield a charge of about seven elementary charges per BSA molecule. These results show the power and usefulness of acoustic and electroacoustic measurement techniques for biological systems.     

The polynomial invariants of twisted links

A twisted link is a generalization of a virtual link, which is related to a link diagram on a closed, possibly non-orientable surface. In this paper we generalize the Miyazawa polynomial invariant of a virtual link to an invariant of a twisted link in two formulae one of which is introduced by A. Ishii and the other by the author.