Erik A. Cheever

Using signal processing techniques for DNA sequence comparison

The most widely used algorithm for the comparison of two sequences of DNA are O(m*n) on the lengths, m and n, of the sequences been compared. The authors present a comparison algorithm that is O(nlog n) on the length, n, of the longer sequence. This algorithm uses techniques developed for rapid comparison of two discrete signals, in particular, cross-correlation using the fast Fourier transform (FFT). The authors treat the DNA as a discrete signal with each nucleotide base represented by a single point in the signal. There are only four possible values that the signal can assume which they represent by one of four complex numbers. The comparison is made by performing a cross correlation between one signal and the complex conjugate of the other. Any significant peak in the resulting signal indicates a strong similarity between the two sequences. The authors present the results of comparison of two strains of the human immunodeficiency virus and of human and simian immunodeficiency viruses. Their results suggest that this technique is a powerful method for comparing very long sequences of DNA.<<ETX>>

Self-diffusion of water in ionic and nonionic microemulsions

Abstract The self-diffusion coefficient of water in four microemulsion systems was measured using an NMR-pulsed field gradient technique. The systems studied were two containing ionic surfactants and two with nonionic surfactants. The dielectric relaxation properties of two of these systems had been previously shown to exhibit large hydration effects. Comparable self-diffusion properties were observed for the water in all of these systems that were interpreted as reflecting a combination of obstruction and hydration effects. An analysis using the Maxwell and Hanai mixture theories shows that the amount of motionally altered water corresponds to approximately two water molecules of hydration per ethylene oxide and hydroxyl group in the nonionic systems, which is in the range expected from chemical considerations. The present results show the large contribution of hydration effects to the bulk transport properties of these microemulsions.

Microwave radiometry in living tissue: what does it measure?

The sensitivity of microwave radiometry for detecting subcutaneous targets was studied both experimentally and theoretically. The radiometer used a dielectric loaded rectangular waveguide antenna in contact with a lossy dielectric medium. A cylindrical target with dielectric properties and/or temperature different from that of the surrounding medium was located beneath this surface. The results indicate that microwave radiometry responds to the temperature averaged over the field pattern of the antenna with very strong weighting of regions near the surface. A simple quasi-static analysis provides a good indication of the sensitivity of the technique for detecting cylindrical targets whose dielectric properties are different from those of the surrounding medium.<<ETX>>

Fast Fourier transform-based correlation of DNA sequences using complex plane encoding

The detection of similarities between DNA sequences can be accomplished using the signal-processing technique of cross-correlation. An early method used the fast Fourier transform (FFT) to perform correlations on DNA sequences in O(n log n) time for any length sequence. However, this method requires many FFTs (nine), runs no faster if one sequence is much shorter than the other, and measures only global similarity, so that significant short local matches may be missed. We report that, through the use of alternative encodings of the DNA sequence in the complex plane, the number of FFTs performed can be traded off against (i) signal-to-noise ratio, and (ii) a certain degree of filtering for local similarity via k-tuple correlation. Also, when comparing probe sequences against much longer targets, the algorithm can be sped up by decomposing the target and performing multiple small FFTs in an overlap-save arrangement. Finally, by decomposing the probe sequence as well, the detection of local similarities can be further enhanced. With current advances in extremely fast hardware implementations of signal-processing operations, this approach may prove more practical than heretofore.

A versatile microprocessor-based multichannel stimulator for skeletal muscle cardiac assist

A versatile, microprocessor-based stimulator for skeletal muscle cardiac assist (SMCA) has been designed, constructed, and used in several studies. The stimulator uses multiple bipolar electrodes to deliver arbitrarily specified electrical stimulus sequences to three nerve branches of the latissimus dorsi muscle. The electrodes are electrically isolated to effect regional stimulation of the muscle. The width, amplitude, and interpulse interval of each pulse in the stimulus sequence are independently variable, and the three channels are independently programmable, allowing a wide variety of stimulus patterns. Battery powered units have been used in studies for up to one year. In this paper, the stimulator and sample applications in SMCA are described.

Transport properties of polymer solutions. A comparative approach.

A variety of transport properties have been measured for solutions of the water soluble polymer poly(ethylene oxide)(PEO) with molecular weights ranging from 200 to 14,000, and volume fractions ranging from 0-80%. The transport properties are thermal conductivity, electrical conductivity at audio frequencies (in solutions containing dilute electrolyte), and water self-diffusion. These data, together with dielectric relaxation data previously reported, are amenable to analysis by the same mixture theory. The ionic conductivity and water self-diffusion coefficient, but not the thermal conductivity, are substantially smaller than predicted by the Maxwell and Hanai mixture relations, calculated using the known transport properties of pure liquid water. A 25% (by volume) solution of PEO exhibits an average dielectric relaxation frequency of the suspending water of one half that of pure water, with clear evidence of a distribution of relaxation times present. The limits of the cumulative distribution of dielectric relaxation times that are consistent with the data are obtained using a linear programming technique. The application of simple mixture theory, under appropriate limiting conditions, yields hydration values for the more dilute polymer solutions that are somewhat larger than values obtained from thermodynamic measurements.

High-resolution measurements of the specific absorption rate produced by small antennas in lossy media

We describe a thermistor-based technique for measurement of the specific absorption rate (SAR) of radio frequency energy from a small antenna in lossy matter with high spatial resolution. The apparatus employs a small thermistor probe, that is moved about the antenna using a computer-controlled positioning system. The antenna is excited by pulses of radio frequency energy, and the SAR is obtained from the measured rate of temperature increase. We present a simplified thermal model to account for heating of the thermistor by the applied electromagnetic energy, which is a major potential artifact in the method. The apparatus is useful for studies of radio frequency ablation of tissue or near-field exposure in models of the body by transmitters.

A multi-sensor array to measure anisotropic thermal conductivity of tissue

Recent advances in the theory of bioheat transfer suggest that perfused tissue might be modeled best by a thermally conductive solid with a perfusion-dependent conductivity. The blood perfusion is believed to enhance the conductivity anisotropically in the direction of thermally significant counter current blood vessels. Traditionally, heat transfer in tissue has been modeled as an isotropic heat sink. Due to the directional nature of recent theory, single point probes cannot adequately quantify the thermal characteristics of tissue. The theoretical analysis and hardware design of a multiple sensor probe that can be used to determine the coefficients of the thermal conductivity tensor are presented. The probe consists of an array of thermistors with the central thermistor acting as a heat source and the surrounding thermistors as temperature sensors. The system is computer-controlled and heating is done either in a pulse-decay mode or as a step input of power. Results of model calculations and of tests on a prototype are presented.<<ETX>>

Selective stimulation of latissimus dorsi muscle for cardiac assist

AbstractThe contractile power of the latissimus dorsi muscle (LDM) is used in skeletal muscle cardiac assist (SMCA) to augment the blood pumping ability of a failing heart. The LDM has three anatomically distinct, independently innervate segments—the transverse, oblique, and lateral. There are potential advantages to selectively stimulating these LDM regions. We hypothesized that (1) the three nerve branches could be stimulated selectively to activate individual muscle regions with little or no functional overlap, (2) the three muscle regions would generate similar force, and (3) nerves stimulated in combinations would generate forces corresponding to the sum of forces generated by the individual regions. In acute studies of canine LDM (n=5), regional electromyogram (EMG) and isometric force were recorded while branches of the thoracodorsal nerve were stimulated (via nerve-cuff electrodes) individually and in combinations. Analysis of regional EMG and force confirmed selective activation. Stimulation of lateral, oblique, and transverse branches of thoracodorsal nerve activated 53 ±5%, 20 ± 9%, and 36 ± 9% of the muscle, respectively; with corresponding developed forces of 48 ± 6%, 21 ± 8%, and 31 ± 8% of total muscle force (R=0.98, p < 0.05). Selective activation of LDM is possible with little or no functional overlap; however, the muscle regions were nonuniform. Selective stimulation may ultimately facilitate the use of performance enhancing stimulus protocols for SMCA.

An anisotropic thermal phantom of perfused tissue

Initial development and test of instruments for measuring anisotropic conductivity in vivo is difficult to carry out in animal models and would benefit from trials in a nonbiological physical model, a phantom. Here, a phantom that conducts heat anisotropically is described. The phantom also mimics the small-scale temperature nonuniformities that may be found near individual blood vessels. Design criteria, along with modeled and experimental results, are presented. Based on the analysis and experimental results, the time-dependence of the conductivity observed in living tissue is explained.<<ETX>>