Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Parallel Algorithms”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,315 records · Page 73Linked to original sources
PubMed2002

Lack of agreement between direct magnetic resonance imaging and statistical determination of a subthalamic target: the role of electrophysiological guidance.

OBJECT: The goal of this study was to determine the most suitable procedure(s) to localize the optimal site for high-frequency stimulation of the subthalamic nucleus (STN) for the treatment of advanced Parkinson disease. METHODS: Stereotactic coordinates of the STN were determined in 14 patients by using three different methods: direct identification of the STN on coronal and axial T2-weighted magnetic resonance (MR) images and indirect targeting in which the STN coordinates are referred to the anterior commissure-posterior commissure (AC-PC) line, which, itself, is determined either by using stereotactic ventriculography or reconstruction from three-dimensional (3D) MR images. During the surgical procedure, electrode implantation was guided by single-unit microrecordings on multiple parallel trajectories and by clinical assessment of stimulations. The site where the optimal functional response was obtained was considered to be the best target. Computerized tomography scanning was performed 3 days later and the scans were combined with preoperative 3D MR images to transfer the position of the best target to the same system of stereotactic coordinates. An algorithm was designed to convert individual stereotactic coordinates into an all-purpose PC-referenced system for comparing the respective accuracy of each method of targeting, according to the position of the best target. CONCLUSIONS: The target that is directly identified by MR imaging is more remote (mainly in the lateral axis) from the site of the optimal functional response than targets obtained using other procedures, and the variability of this method in the lateral and superoinferior axes is greater. In contrast, the target defined by 3D MR imaging is closest to the target of optimal functional response and the variability of this method is the least great. Thus, 3D reconstruction adjusted to the AC-PC line is the most accurate technique for STN targeting, whereas direct visualization of the STN on MR images is the least effective. Electrophysiological guidance makes it possible to correct the inherent inaccuracy of the imaging and surgical techniques and is not designed to modify the initial targeting.

Adult↗
PubMed1999

Assessment of the uncertainties in dose delivery of a commercial system for linac-based stereotactic radiosurgery.

PURPOSE: Linac-based stereotactic radiosurgery (SRS) was introduced in our department in 1992, and since then, more than 200 patients have been treated with this method. An in-house-developed algorithm for target localization and dose calculation has recently been replaced with a commercially available system. In this study, both systems have been compared, and positional accuracy, as well as dose calculation, have been verified experimentally. METHODS AND MATERIALS: The in-house-developed software for target localization and dose calculation is an extension to George Sherouse's GRATIS(R) software for radiotherapy treatment planning, and has been replaced by a commercial (BrainSCAN version 3.1; BrainLAB, Germany) treatment planning system (TPS) for SRS. The positional accuracy for the entire SRS procedure (from image acquisition to treatment) has been investigated by treatment of simulated targets in the form of 0.2-cm lead beads inserted into an anthropomorphic phantom. Both dose calculation algorithms have been verified against manual calculations (based on basic beam data and CT data from phantom and patients), and measurements with the anthropomorphic phantom applying ionization chamber, thermoluminescent detectors, and radiographic film. This analysis has been performed on a variety of experimental situations, starting with static beams and simple one-arc treatments, to more complex and clinical relevant applications. Finally, 11 patients have been evaluated with both TPS in parallel for comparison and continuity of clinical experience. RESULTS: Phantom studies evaluating the entire SRS procedure have shown that a target, localized by CT, can be irradiated with a positional accuracy of 0.08 cm in any direction with 95% confidence. Neglecting the influence of dose perturbation when the beam passes through bone tissue or air cavities, the calculated dose values obtained from both TPSs agreed within 1% (SD 1%) for phantom and patient studies. The application of a one-dimensional path length correction for tissue heterogeneity influences the treatment prescription 4% on average (SD 1%), which is in compliance with theoretical predictions. The phantom measurements confirmed the predicted dose at isocenter within uncertainty for the different treatment schedules in this study. CONCLUSION: The full SRS procedure applied to an anthropomorphic phantom has been used as a comprehensive method to assess the uncertainties involved in dose delivery and target positioning. The results obtained with both TPSs are in agreement with AAPM Report 54, TG 42 and clinical continuity is assured. However, the use of a one-dimensional path length correction will result in an increase of 4% in dose prescription, which is slightly more than that predicted in the literature.

Algorithms↗
PubMed2003

Ultimate intrinsic signal-to-noise ratio for parallel MRI: electromagnetic field considerations.

A method is described for establishing an upper bound on the spatial encoding capabilities of coil arrays in parallel MRI. Ultimate intrinsic signal-to-noise ratio (SNR), independent of any particular conductor arrangement, is calculated by expressing arbitrary coil sensitivities in terms of a complete set of basis functions that satisfy Maxwell's equations within the sample and performing parallel imaging reconstructions using these basis functions. The dependence of the ultimate intrinsic SNR on a variety of experimental conditions is explored and a physically intuitive explanation for the observed behavior is provided based on a comparison between the electromagnetic wavelength and the distance between aliasing points. Imaging at high field strength, with correspondingly short wavelength, is shown to offer advantages for parallel imaging beyond those already expected due to the larger available spin polarization. One-dimensional undersampling of k-space yields a steep drop in attainable SNR for more than a 5-fold reduction of scan time, while 2D undersampling permits access to much higher degrees of acceleration. Increased tissue conductivity decreases baseline SNR, but improves parallel imaging performance. A procedure is also provided for generating the optimal coil sensitivity pattern for a given acceleration, which will serve as a useful guide for future coil designs.

Algorithms↗
PubMed1993

Magnetic field distribution in models of trabecular bone.

A magnetostatic model consisting of a tetragonal lattice of struts of diamagnetic material, mimicking vertebral trabecular bone, was developed. The model allows estimation of the magnetic field histogram within the lattice's unit cell as a function of geometric parameters. The field was computed analytically from the induced magnetic surface charge density on the faces of the struts. The contribution from the induced magnetic field to the effective transverse relaxation rate, R2', was obtained as the mean decay rate of the Fourier transformed histograms, for both fixed and randomly oriented lattices. The model predicts the field distribution to increase with both strut thickness and density, paralleling material density. Finally, significant changes in R2' are predicted at constant material density, in that the field distribution widens with simultaneously increasing strut number density and decreasing strut thickness.

Algorithms↗
PubMed2005

A parallel approach to post source decay MALDI-TOF analysis.

We present a novel enhancement to matrix-assisted laser desorption ionization (MALDI) post-source decay (PSD) analysis whereby fragment ions from multiple precursor ions are acquired into the same spectrum without employing a timed ion gate to preselect each parent ion. Fragment ions are matched to their corresponding precursor ions by comparing spectra acquired at slightly different reflectron electric fields. By measuring the difference in time-of-flight (TOF) between the two spectra for each fragment, it is possible to calculate the mass of the fragment ion and its parent. This new "parallel PSD" technique reduces analysis time and consumes less sample than conventional PSD, which requires an ion gate for serial preselection of precursor ions.

Algorithms↗
PubMed2004

Parallel magnetic resonance imaging using coils with localized sensitivities.

The purpose of this study was to present clinical examples and illustrate the inefficiencies of a conventional reconstruction using a commercially available phased array coil with localized sensitivities. Five patients were imaged at 1.5 T using a cardiac-synchronized gadolinium-enhanced acquisition and a commercially available four-element phased array coil. Four unique sets of images were reconstructed from the acquired k-space data: (a) sum-of-squares image using four elements of the coil; localized sum-of-squares images from the (b) anterior coils and (c) posterior coils and a (c) local reconstruction. Images were analyzed for artifacts and usable field-of-view. Conventional image reconstruction produced images with fold-over artifacts in all cases spanning a portion of the image (mean 90 mm; range 36-126 mm). The local reconstruction removed fold-over artifacts and resulted in an effective increase in the field-of-view (mean 50%; range 20-70%). Commercially available phased array coils do not always have overlapping sensitivities. Fold-over artifacts can be removed using an alternate reconstruction method. When assessing the advantages of parallel imaging techniques, gains achieved using techniques such as SENSE and SMASH should be gauged against the acquisition time of the localized method rather than the conventional sum-of-squares method.

Adult↗
PubMed2005

Quantitative analysis of errors in alveolar crest level caused by discrepant projection geometry in digital subtraction radiography: an in vivo study.

OBJECTIVE: This study compared the difference between 3 intraoral radiographic techniques on digital subtraction radiography (DSR) in vivo that are commonly used in a clinical setting. STUDY DESIGN: We evaluated and statistically analyzed the errors in the DSR image in 6 regions with 3 radiographic techniques: paralleling technique with a bite block attached to XCP, paralleling technique using XCP, and bisecting-angle technique. RESULTS: The amount of error using the bisecting-angle technique was too large for DSR, compared to that of the paralleling technique with a bite block attached to XCP. In the mandibular anterior region, the paralleling technique using XCP was not different from paralleling technique with a bite block attached to XCP. The lowest degree of error was present in the anterior region whereas the highest was present in the molar region. CONCLUSION: Bisecting-angle technique should be avoided, and paralleling technique using XCP can be used in the mandibular anterior region for DSR.

Adult↗
PubMed2002

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

SUMMARY: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers. AVAILABILITY: http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).

Algorithms↗
PubMed2004

In-flight measured and predicted ambient dose equivalent and latitude differences on effective dose estimates.

The results from 2 years (2001-2002) of experimental measurements of in-board radiation doses received at IBERIA commercial flights are presented. The routes studied cover the most significant destinations and provide a good estimate of the route doses as required by the new Spanish regulations on air crew radiation protection. Details on the experimental procedures and calibration methods are given. The experimental measurements from the different instruments (Tissue Equivalent Proportional Counter and the combination of a high pressure ion chamber and a high-energy neutron compensated rem-counter) and their comparison with the predictions from some route-dose codes (CARI-6, EPCARD 3.2) are discussed. In contrast with the already published data, which are mainly focused on North latitudes over parallel 50, many of the data presented in this work have been obtained for routes from Spain to Central and South America.

Aircraft↗
PubMed1997

New finite difference formulations for general inhomogeneous anisotropic bioelectric problems.

Due to its low computational complexity, finite difference modeling offers a viable tool for studying bioelectric problems, allowing the field behavior to be observed easily as different system parameters are varied. Previous finite difference formulations, however, have been limited mainly to systems in which the conductivity is orthotropic, i.e., a strictly diagonal conductivity tensor. This in turn has limited the effectiveness of the finite difference, technique in modeling complex anatomies with arbitrarily anisotropic conductivities, e.g., detailed fiber structures of muscles where the fiber can lie in any arbitrary direction. In this paper, we present both two-dimensional and three-dimensional finite difference formulations that are valid for structures with an inhomogeneous and nondiagonal conductivity tensor. A data parallel computer, the connection machine CM-5, is used in the finite difference implementation to provide the computational power and memory for solving large problems. The finite difference grid is mapped effectively to the CM-5 by associating a group of nodes with one processor. Details on the new approach and its data parallel implementation are presented together with validation and computational performance results. In addition, an application of the new formulation in providing the potential distribution inside a canine torso during electrical defibrillation is demonstrated.

Algorithms↗
PubMed1992

Fast computation of genetic likelihoods on human pedigree data.

Gene mapping and genetic epidemiology require large-scale computation of likelihoods based on human pedigree data. Although computation of such likelihoods has become increasingly sophisticated, fast calculations are still impeded by complex pedigree structures, by models with many underlying loci and by missing observations on key family members. The current paper 'introduces' a new method of array factorization that substantially accelerates linkage calculations with large numbers of markers. This method is not limited to nuclear families or to families with complete phenotyping. Vectorization and parallelization are two general-purpose hardware techniques for accelerating computations. These techniques can assist in the rapid calculation of genetic likelihoods. We describe our experience using both of these methods with the existing program MENDEL. A vectorized version of MENDEL was run on an IBM 3090 supercomputer. A parallelized version of MENDEL was run on parallel machines of different architectures and on a network of workstations. Applying these revised versions of MENDEL to two challenging linkage problems yields substantial improvements in computational speed.

Algorithms↗
PubMed2005

Wildfire: distributed, Grid-enabled workflow construction and execution.

BACKGROUND: We observe two trends in bioinformatics: (i) analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii) multiple CPU clusters and Grids are available to more scientists. The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers. RESULTS: We present Wildfire, a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other) programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids. CONCLUSION: Wildfire simplifies the tasks of constructing and executing bioinformatics workflows.

Algorithms↗
PubMed2005

Dynamic time-resolved diffuse spectroscopy based on supercontinuum light pulses.

We present a detailed characterization of a system for fast time-resolved spectroscopy of turbid media based on supercontinuum generation in a photonic crystal fiber. The light source provides subpicosecond pulses in the 550-1000-nm spectral range, at 85 MHz, at an average power of up to 50 mW. Wavelength-resolved detection is accomplished by means of a spectrometer coupled to a 16-channel, multianode photomultiplier tube, giving a resolution of 4.5-35 nm/channel, depending on the grating. Time-dispersion curves are acquired with time-correlated single-photon counting, and absorption and reduced scattering coefficients are determined by fitting the data to the diffusion equation. We characterized the system by measuring the time-resolved diffuse reflectance of epoxy phantoms and by assessing the performance in terms of accuracy, linearity, noise sensitivity, stability, and reproducibility. The results were similar to those from previous systems, whereas the full-spectrum (610-810 nm) acquisition time was as short as 1 s owing to the parallel acquisition. We also present the first in vivo real-time dynamic spectral measurements showing tissue oxygenation changes in the arm of a human subject.

Algorithms↗
PubMed1998

Algorithmic approach to high-throughput molecular screening for alpha interferon-resistant genotypes in hepatitis C patients.

This study was designed to analyze the feasibility and validity of using Cleavase Fragment Length Polymorphism (CFLP) analysis as an alternative to DNA sequencing for high-throughput screening of hepatitis C virus (HCV) genotypes in a high-volume molecular pathology laboratory setting. By using a 244-bp amplicon from the 5' untranslated region of the HCV genome, 61 clinical samples received for HCV reverse transcription-PCR (RT-PCR) were genotyped by this method. The genotype frequencies assigned by the CFLP method were 44.3% for type 1a, 26.2% for 1b, 13.1% for type 2b, and 5% type 3a. The results obtained by nucleotide sequence analysis provided 100% concordance with those obtained by CFLP analysis at the major genotype level, with resolvable differences as to subtype designations for five samples. CFLP analysis-derived HCV genotype frequencies also concurred with the national estimates (N. N. Zein et al., Ann. Intern. Med. 125:634-639, 1996). Reanalysis of 42 of these samples in parallel in a different research laboratory reproduced the CFLP fingerprints for 100% of the samples. Similarly, the major subtype designations for 19 samples subjected to different incubation temperature-time conditions were also 100% reproducible. Comparative cost analysis for genotyping of HCV by line probe assay, CFLP analysis, and automated DNA sequencing indicated that the average cost per amplicon was lowest for CFLP analysis, at $20 (direct costs). On the basis of these findings we propose that CFLP analysis is a robust, sensitive, specific, and an economical method for large-scale screening of HCV-infected patients for alpha interferon-resistant HCV genotypes. The paper describes an algorithm that uses as a reflex test the RT-PCR-based qualitative screening of samples for HCV detection and also addresses genotypes that are ambiguous.

Algorithms↗
PubMed2006

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

BACKGROUND: Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations produce a more accurate picture of single cell dynamics, including interesting phenomena missed by deterministic methods, such as noise-induced oscillations and transitions between stable states. However, the computational cost of the original stochastic simulation algorithm can be high, motivating the use of hybrid stochastic methods. Hybrid stochastic methods partition the system into multiple subsets and describe each subset as a different representation, such as a jump Markov, Poisson, continuous Markov, or deterministic process. By applying valid approximations and self-consistently merging disparate descriptions, a method can be considerably faster, while retaining accuracy. In this paper, we describe Hy3S, a collection of multiscale simulation programs. RESULTS: Building on our previous work on developing novel hybrid stochastic algorithms, we have created the Hy3S software package to enable scientists and engineers to both study and design extremely large well-mixed biological systems with many thousands of reactions and chemical species. We have added adaptive stochastic numerical integrators to permit the robust simulation of dynamically stiff biological systems. In addition, Hy3S has many useful features, including embarrassingly parallelized simulations with MPI; special discrete events, such as transcriptional and translation elongation and cell division; mid-simulation perturbations in both the number of molecules of species and reaction kinetic parameters; combinatorial variation of both initial conditions and kinetic parameters to enable sensitivity analysis; use of NetCDF optimized binary format to quickly read and write large datasets; and a simple graphical user interface, written in Matlab, to help users create biological systems and analyze data. We demonstrate the accuracy and efficiency of Hy3S with examples, including a large-scale system benchmark and a complex bistable biochemical network with positive feedback. The software itself is open-sourced under the GPL license and is modular, allowing users to modify it for their own purposes. CONCLUSION: Hy3S is a powerful suite of simulation programs for simulating the stochastic dynamics of networks of biochemical reactions. Its first public version enables computational biologists to more efficiently investigate the dynamics of realistic biological systems.

Cell Physiological Phenomena↗
PubMed2001

A new approach to optimization-based defibrillation.

The purpose of this paper is to develop a new model for optimal cardiac defibrillation, based on simultaneous minimization of energy consumption and defibrillation time requirements. In order to generate optimal defibrillation waveforms that will accomplish the objective stated above, one parameter rho has been introduced as a part of the performance measure to weigh the relative importance of time and energy. All the results of this theoretical study have been obtained for the proposed model, under the assumption that cardiac tissue can be represented by a simple parallel resistor-capacitor circuit. It is well known from modern control theory that the selection of a numerical value of the weight factor is the matter of subjective judgment of a designer. However, it has been shown that defining a cost function can help in selecting a value for rho. Some results of the mathematical development of the algorithm and computer simulations will be included in the paper.

Computer Simulation↗
PubMed1997

Quantitation of T2' anisotropic effects on magnetic resonance bone mineral density measurement.

In this paper, the authors quantitate the anisotropy of susceptibility effects in an uniaxial trabecular bone model and show its relevance to clinical MR bone mineral density measurements. A physical model is described that quantitates the anisotropic MR behavior of uniaxial trabecular bone. To test the model; a phantom of parallel polyethylene filaments was scanned every 15 degrees between 0 degrees and 90 degrees with respect to the system's main magnetic field (B0). The distal radial metaphysis of a healthy female volunteer was scanned in orthogonal projections. The signal from each phantom image and each radial image was separated in a pixel-wise fashion into R2 and R2' maps. As predicted, R2' relaxation showed anisotropic behavior and changed according to sin2 (theta), confirming that columnar structures parallel with B0 will cause no MR susceptibility effects. Scans of the distal radius showed that R2' relaxation was twice as great with the forearm perpendicular to B0 as when it was parallel to it, demonstrating different contributions from struts and columns. For both phantom and radial bone scans, R2 relaxation was isotropic and did not change with object orientation.

Adult↗
PubMed2006

Direct parallel image reconstructions for spiral trajectories using GRAPPA.

The use of spiral trajectories is an efficient way to cover a desired k-space partition in magnetic resonance imaging (MRI). Compared to conventional Cartesian k-space sampling, it allows faster acquisitions and results in a slight reduction of the high gradient demand in fast dynamic scans, such as in functional MRI (fMRI). However, spiral images are more susceptible to off-resonance effects that cause blurring artifacts and distortions of the point-spread function (PSF), and thereby degrade the image quality. Since off-resonance effects scale with the readout duration, the respective artifacts can be reduced by shortening the readout trajectory. Multishot experiments represent one approach to reduce these artifacts in spiral imaging, but result in longer scan times and potentially increased flow and motion artifacts. Parallel imaging methods are another promising approach to improve image quality through an increase in the acquisition speed. However, non-Cartesian parallel image reconstructions are known to be computationally time-consuming, which is prohibitive for clinical applications. In this study a new and fast approach for parallel image reconstructions for spiral imaging based on the generalized autocalibrating partially parallel acquisitions (GRAPPA) methodology is presented. With this approach the computational burden is reduced such that it becomes comparable to that needed in accelerated Cartesian procedures. The respective spiral images with two- to eightfold acceleration clearly benefit from the advantages of parallel imaging, such as enabling parallel MRI single-shot spiral imaging with the off-resonance behavior of multishot acquisitions.

Algorithms↗