Edward C. Bronson

Short-Term Longitudinal Effects of the Transcendental Meditation Technique on EEG Power and Coherence

EEG alpha coherence and slow alpha power were recorded from frontal and occipital derivations during relaxation or the Transcendental Meditation (TM) technique in fifteen subjects. Subjects were tested before and after a two-week baseline period in which half practiced twice daily relaxation and half did not change their schedule. All subjects were then instructed in the TM technique and retested after a two-week period of twice daily practice of the technique. During the first two-week period there were no group differences or group by session interactions, but there was a significant effect of repeated measurement, indicating a decrease in occipital power independent of group. After the two-week TM technique period, subjects showed a significant increase in frontal alpha coherence above a 0.95 threshold. Frontal alpha coherence was found to be a more sensitive discriminator of the TM technique than alpha power, which may clarify previously reported nonsignificant EEG differences between the TM technique and general relaxation.

Nucleotide composition as a driving force in the evolution of retroviruses.

All complete retrovirus sequences in the GenEMBL database were examined with the goal of assessing possible relationships between the nucleotide composition of retroviral genomes, the amino acid composition of retroviral proteins, and evolutionary strategies used by retroviruses. The results demonstrated that the genome of each viral lineage has a characteristic base composition and that the variations between groups are related to retroviral phylogeny. By analogy to microbial species, we suggest that the variations arise from group-specific patterns of directional mutations where the bias can be exerted on any of the four nucleotides. It is most likely that the mutational patterns are introduced during reverse transcription, and a direct participation of reverse transcriptase in the process is suspected.A straightforward strategy was used to analyze the compositional relationship between nucleotides and encoded amino acids. The procedure entailed calculations of amino acid frequencies from nucleotide content and the comparison of the calculated values to the observed amino acid frequencies in retroviruses. The results revealed an excellent correspondence between variation in genomic base composition and variation in amino acid composition of proteins with the compositional differences extending into all major coding regions of the viruses. Because of the magnitude and dispersion of these effects, and because of the nonconservative nature of many of the substitutions between groups with different genomic biases, we suggest that the variations in protein composition driven by biased nucleotide frequencies are an important factor in shaping the characteristic phenotypes of the different viral lineages.A clue to the nature of the evolutionary forces that are responsible for the generation of nucleotide biases was provided by the observation that viruses with radically different base frequencies most often inhabit the same cell type. This observation, along with analysis of amino acid and nucleotide replacement patterns between and within reverse transcriptase sequences from the various groups, permitted us to advance a model for the evolution of retroviruses. According to the model, speciation could initiate when daughter virions from a single progenitor vary in the direction of their mutational bias. These variations would exert a pleiotropic effect on the frequencies of nucleotides in all viral genes and consequently on the frequencies of amino acids in the encoded proteins. The variants with the most extreme compositional differences would have a selective advantage because their different precursor requirements would enable them to occupy different ecological niches within a single cell. Once the viruses have adapted to different amino acid compositions, continued presence of the diverging viruses in the same cell would no longer be needed to maintain different phenotypes. Each virus would then possess a distinct mutational bias which would fix the patterns of amino acid substitution. These patterns would favor a degree of conservation of the phenotype in the viral progeny, thus promoting the concerted evolution of the species.

Experimental application-driven architecture analysis of an SIMD/MIMD parallel processing system

An experimental analysis of the architecture of an SIMD/MIMD parallel processing system is presented. Detailed implementations of parallel fast Fourier transform (FFT) programs were used to examine the performance of the prototype of the PASM (Partitionable SIMD/MIMD) parallel processing system. Detailed execution-time measurements using specialized timing hardware were made for the complete FFT and for components of SIMD, MIMD, and barrier-synchronized MIMD implementations. The component measurements isolated the effects of floating-point arithmetic operations, interconnection network transfer operations, and program control overhead. The measurements allow an accurate extrapolation of the execution time, speedup, and efficiency of the MIMD, SIMD, and barrier-synchronized MIMD programs to a full 1024-processor PASM system. This constitutes one of the first results of this kind, in which controlled experiments on fixed hardware were used to make comparisons of these fundamental modes of computing. Overall, the experimental results demonstrate the value of mixed-mode SIMD/MIMD computing and its suitability for computational intensive algorithms such as the FET. >

A parallel architecture for speech understanding

The complexity of the speech understanding task requires extensive computation. To improve the processing speed, methods are explored by which the various tasks involved in speech understanding can be structured for execution on a parallel processing system. An architecture is described in which a speech understanding system is decomposed into a series of distributed processing computation stations.

Circular structures in retroviral and cellular genomes.

A computer program for predicting DNA bending from nucleotide sequence was used to identify circular structures in retroviral and cellular genomes. An 830-base pair circular structure was located in a control region near the center of the genome of the human immunodeficiency virus type I (HIV-I). This unusual structure displayed relatively smooth planar bending throughout its length. The structure is conserved in diverse isolates of HIV-I, HIV-II, and simian immunodeficiency viruses, which implies that it is under selective constraints. A search of all sequences in the GenBank data base was carried out in order to identify similar circular structures in cellular DNA. The results revealed that the structures are associated with a wide range of sequences that undergo recombination, including most known examples of DNA inversion and subtelomeric translocation systems. Circular structures were also associated with replication and transposition systems where DNA looping has been implicated in the generation of large protein-DNA complexes. Experimental evidence for the structures was provided by studies which demonstrated that two sequences detected as circular by computer preferentially formed covalently closed circles during ligation reactions in vitro when compared to nonbent fragments, bent fragments with noncircular shapes, and total genomic DNA. In addition, a single T C substitution in one of these sequences rendered it less planar as seen by computer analysis and significantly reduced its rate of ligase-catalyzed cyclization. These results permit us to speculate that intrinsically circular structures facilitate DNA looping during formation of the large protein-DNA complexes that are involved in site- and region-specific recombination and in other genomic processes.

Experiments with Parallel Fast Fourier Transforms

VLSI technology has made feasible large-scale parallel processing systems. Challenges presented by such systems include how to design algorithms to take advantage of the substantial parallelism and how to obtain the maximum performance from potentially complex parallel machines. In this paper we examine parallel algorithms for the fast Fourier transform. We give an overview of the algorithm structure for highly parallel FFTs then present the results of detailed experimental studies of implementing FFTs on two parallel systems: the PASM partitionable SIMD/MIMD prototype and the Thinking Machine’s CM-2 massively parallel SIMD machine.

Experimental analysis of multi-mode fast Fourier transforms on the PASM parallel processing system

A detailed study is presented of parallel fast Fourier transform programs executing on the prototype of the PASM parallel processing system. Detailed execution time measurements using specialized timing hardware were made for complete fast Fourier transforms (FFTs) and for SIMD, MIMD, and hybrid SIMD/MIMD implementations. The component measurements isolated the effects of floating-point operations, interconnection network transfer operations, and program control overhead. Using these detailed measurements, an expression for projecting the execution time for an M-point FFT executing on M/2 PASM processing elements is derived. This expression is then used to obtain an accurate extrapolation of the execution time and speedup of the MIMD, SIMD, and hybrid programs to a full 1024-processor PASM system. Overall, the experimental results demonstrate the value of the multimode capability of PASM and the stability of PASM for computationally intensive algorithms such as the FFT.<<ETX>>

A phoneme model of English speech for the design of a parallel speech understanding system

A stochastic model of English speech is described that can be used to generate a stream of phonemically labeled frames with the same characteristics as real speech to be used during the design of new computer architectures. Specialized computer architectures to perform speech understanding in real time should incorporate information about the characteristics of English speech. The English speech model described can be used to simulate efficiently the performance of new architectures and eliminates the need for massive amounts of input speech data to determine architecture design parameters. A stochastic model is used to reproduce accurately the phoneme content of English speech, including the transition probabilities, the duration mean, and the duration variance of each phoneme and silence region.<<ETX>>

Modeling of english speech for the design of a distributed speech understanding system

This paper describes the derivation and verification of a phoneme model of English speech. The model is used to generate a stream of phonemically labeled speech frames to model speech input for the design of a distributed speech understanding system. New computer architectures to perform speech understanding in real time should incorporate information about the characteristics of English speech. In order to predict the performance of a new architecture, it is necessary to simulate the design using either massive amounts of speech data or, as an alternative, a statistical model of speech. A statistically generated phoneme stream is used to avoid the difficulty of performing computationally intensive acoustic parameterization on the enormous amount of speech input data which would be required to obtain representative phoneme distributions and patterns of speech.

Syntactic pattern recognition of discrete utterances

This paper describes a discrete utterance recognition technique which applies formal language theory to a symbol string derived from the speech input. Analysis is performed to obtain a representation of the input utterance in terms of acoustically consistent labeled regions. Syntactic pattern recognition is then used to parse this representation of the input word using stored context-free grammars for the allowed vocabulary. Preliminary results are reported.