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PubMed2003

Low cost, highly effective parallel computing achieved through a Beowulf cluster.

A Beowulf cluster is a means of bringing together several computers and using software and network components to make this cluster of computers appear and function as one computer with multiple parallel computing processors. A cluster of computers can provide comparable computing power usually found only in very expensive super computers or servers.

Benchmarking↗
PubMedDate not supplied

[Method of penile scintigraphy].

A method of phalloscintigraphy, based on the gamma camera and computerized data processing, is offered. The results of examination of patients are described.

Computing Methodologies↗
PubMed2001

A connectivity standard for point-of-care testing.

A software standard has been designed that will facilitate the linking of all point-of-care testing (POCT) devices to information systems. This standard will replace the myriad of proprietary and incompatible solutions that currently exist. The standard is expected to be a feature of new POCT instruments by 2002.

Computer Communication Networks↗
PubMed2003

[The NMR implementation of quantum algorithm].

A quantum computer is a device that processes information in a quantum-mechanically coherent fashion. In principle, it can exploit coherent quantum interference and entanglement to perform computations, such as factoring large numbers or searching an unsorted database, more rapidly than classical computers. Noise, decoherence, and manufacturing problems make constructing large scale quantum computers difficult. Ion traps and optical cavities offer promising experimental approaches, but no quantum algorithm has yet been implemented with those systems. On the other hand, because of their natural isolation from the environment, nuclear spins are particularly good 'quantum bits', and their use for quantum computation is possible by applying nuclear magnetic resonance (NMR) techniques in an unconventional manner. Here, we report on the experimental implementation of a quantum algorithm using NMR to solve a purely mathematical problem in fewer steps than is possible classically. Our simple quantum computer can determine the type of an unknown function using fewer function 'calls' than is possible using a classical computer.

Algorithms↗
PubMed2003

Accelerating comparative genomics using parallel computing.

In the past decade there has been an increase in the number of completely sequenced genomes due to the race of multibillion-dollar genome-sequencing projects. The enormous biological sequence data thus flooding into the sequence databases necessitates the development of efficient tools for comparative genome sequence analysis. The information deduced by such analysis has various applications viz. structural and functional annotation of novel genes and proteins, finding gene order in the genome, gene fusion studies, constructing metabolic pathways etc. Such study also proves invaluable for pharmaceutical industries, such as in silico drug target identification and new drug discovery. There are various sequence analysis tools available for mining such useful information of which FASTA and Smith-Waterman algorithms are widely used. However, analyzing large datasets of genome sequences using the above codes seems to be impractical on uniprocessor machines. Hence there is a need for improving the performance of the above popular sequence analysis tools on parallel cluster computers. Performance of the Smith-Waterman (SSEARCH) and FASTA programs were studied on PARAM 10000, a parallel cluster of workstations designed and developed in-house. FASTA and SSEARCH programs, which are available from the University of Virginia, were ported on PARAM and were optimized. In this era of high performance computing, where the paradigm is shifting from conventional supercomputers to the cost-effective general-purpose cluster of workstations and PCs, this study finds extreme relevance. Good performance of sequence analysis tools on a cluster of workstations was demonstrated, which is important for accelerating identification of novel genes and drug targets by screening large databases.

Algorithms↗
PubMed1992

Nerve conduction and electromyography.

The advent of computer-based methodology in routine electromyography has much improved the analysis of motor unit (MU) decomposition, of interference pattern study, and of MU counting. Measuring minimum motor and sensory conduction velocities is becoming more accessible and is considered an essential procedure in assessing the condition of peripheral nerves. A series of studies has shown that nerve resistance and vulnerability can be modified by a steep temperature gradient, by ciguatera toxin, or by hyperventilation-induced changes in the electrical properties of the axonal membrane. The controversy as to the diagnostic procedures to use in cases of radiculopathy and carpal tunnel syndrome (CTS) shows no sign of abating. There is, however, general consensus that electrophysiologic procedures must play a key diagnostic role in these conditions. Lastly, several interesting articles have been published describing the use of electrophysiologic tests in motor neurone diseases. Moreover, some advances have been made in the diagnostic yield of single-fibre electromyography (SFEMG) with axonal microstimulation in myasthenia gravis and Eaton-Lambert myasthenic syndrome.

Animals↗
PubMed1992

Gene expression, signal transduction and tissue-specific biomineralization during mammalian tooth development.

Tooth development provides a paradigm for intrinsic molecular controls for cell- and extracellular matrix (ECM)-mediated biomineralization. The intent of this review is to evaluate the sequential timing and positional information prerequisite for tissue-specific biomineralization. Recent investigations suggest that 1,25-dihydroxyvitamin D3 functions to up-regulate VDR (vitamin D receptor) that in turn could induce structural gene products, including calcium-binding proteins and several ECM proteins (e.g., enamelins, amelogenins, dentine sialoglycoproteins (DSP) and dentine phosphoproteins (DPP)), resulting in dentine and enamel formation. Inhibition of regulatory gene products and/or their receptors likely results in hypoplastic and/or hypomineralized ECM as a direct consequence of down-regulated (1) transcription and/or translation of structural and regulatory genes, (2) posttranslational modifications, (3) and/or decreased calcium transport to the forming dentine and enamel matrices. Advances in serumless in vitro culture methodology; computer-assisted access to nucleic acid sequences for probes to define when, where, and how many specific regulatory and structural gene products are expressed; antisense oligodeoxynucleotides to inhibit specific translation; and microtechniques to analyze biomineralization all provide additional avenues to investigate tissue-specific biomineralization.

Animals↗
PubMed2003

Digital image processing: a primer for JVIR authors and readers: part 1: the fundamentals.

Online submission of manuscripts will be mandatory for most journals in the near future. To prepare authors for this requirement and to acquaint readers with this new development, herein the basics of digital image processing are described. From the fundamentals of digital image architecture, through acquisition, editing, and storage of digital images, the steps necessary to prepare an image for online submission are reviewed. In this article, the first of a three-part series, the structure of the digital image is described. In subsequent articles, the acquisition and editing of digital images will be reviewed.

Computer Graphics↗
PubMed2002

Distributed computing in bioinformatics.

This paper provides an overview of methods and current applications of distributed computing in bioinformatics. Distributed computing is a strategy of dividing a large workload among multiple computers to reduce processing time, or to make use of resources such as programs and databases that are not available on all computers. Participating computers may be connected either through a local high-speed network or through the Internet.

Computational Biology↗
PubMed2002

Parallel Monte Carlo methods for physical mapping of chromosomes.

Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity. Parallel Monte Carlo methods for a maximum likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a simulated Monte Carlo algorithm. A two-tier parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the simulated Monte Carlo algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a network of shared-memory symmetric multiprocessors (SMPs) are presented.

Algorithms↗
PubMed2002

Parallelizing a DNA simulation code for the Cray MTA-2.

The Cray MTA-2 (Multithreaded Architecture) is an unusual parallel supercomputer that promises ease of use and high performance. We describe our experience on the MTA-2 with a molecular dynamics code, SIMU-MD, that we are using to simulate the translocation of DNA through a nanopore in a silicon based ultrafast sequencer. Our sequencer is constructed using standard VLSI technology and consists of a nanopore surrounded by Field Effect Transistors (FETs). We propose to use the FETs to sense variations in charge as a DNA molecule translocates through the pore and thus differentiate between the four building block nucleotides of DNA. We were able to port SIMU-MD, a serial C code, to the MTA with only a modest effort and with good performance. Our porting process needed neither a parallelism support platform nor attention to the intimate details of parallel programming and interprocessor communication, as would have been the case with more conventional supercomputers.

Algorithms↗