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Results for “Parallel Algorithms”

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PubMed2001

RNA folding pathway functional intermediates: their prediction and analysis.

The massively parallel genetic algorithm (GA) for RNA structure prediction uses the concepts of mutation, recombination, and survival of the fittest to evolve a population of thousands of possible RNA structures toward a solution structure. As described below, the properties of the algorithm are ideally suited to use in the prediction of possible folding pathways and functional intermediates of RNA molecules given their sequences. Utilizing Stem Trace, an interactive visualization tool for RNA structure comparison, analysis of not only the solution ensembles developed by the algorithm, but also the stages of development of each of these solutions, can give strong insight into these folding pathways. The GA allows the incorporation of information from biological experiments, making it possible to test the influence of particular interactions between structural elements on the dynamics of the folding pathway. These methods are used to reveal the folding pathways of the potato spindle tuber viroid (PSTVd) and the host killing mechanism of Escherichia coli plasmid R1, both of which are successfully explored through the combination of the GA and Stem Trace. We also present novel intermediate folds of each molecule, which appear to be phylogenetically supported, as determined by use of the methods described below.

Algorithms↗

PubMed2001

A novel microphysiometer based on MLAPS for drugs screening.

This paper presents a novel microphysiometer for simultaneous measurements of several extracellular ions concentrations in living cells based on MLAPS (multi-light addressable potentiometric sensor). In the microphysiometer, different sensitive membranes are illuminated in parallel with n light sources at different frequencies, the response amplitudes of each frequency component can be measured on-line by parallel processing algorithm. By the experiments, we can analyze the relations of the extracellular environmental H(+), Na(+), K(+), Ca(2+) under the effects of western medicines (dilantin, phenobarbital sodium, penicillin sodium) and Chinese drugs (scutellaria, medlar, hemlock parsley), and estimate the effects of several drugs. As the novel microphysiometer works under regular cell culture conditions, cells can be repeatedly simulated with drugs to complete dose-response curve within a few hours. With the detection of a general parameter (extruded protons and ions), the system can be used to monitor the real-time process of the cells' metabolism, observe the functional responses of different kinds of membrane-bound receptors, evaluate the drugs.

Anticonvulsants↗

PubMed2005

Entropic stabilization of isolated beta-sheets.

Temperature-dependent electric deflection measurements have been performed for a series of unsolvated alanine-based peptides (Ac-WA(n)-NH(2), where Ac = acetyl, W = tryptophan, A = alanine, and n = 3, 5, 10, 13, and 15). The measurements are interpreted using Monte Carlo simulations performed with a parallel tempering algorithm. Despite alanine's high helix propensity in solution, the results suggest that unsolvated Ac-WA(n)-NH(2) peptides with n > 10 adopt beta-sheet conformations at room temperature. Previous studies have shown that protonated alanine-based peptides adopt helical or globular conformations in the gas phase, depending on the location of the charge. Thus, the charge more than anything else controls the structure.

Alanine↗

PubMed2005

On the convergence of parallel tempering Monte Carlo simulations of LJ38.

The convergence of parallel tempering Monte Carlo simulations of the 38-atom Lennard-Jones cluster starting from the Oh global minimum and from the C(5v) second-lowest-energy minimum is investigated. It is found that achieving convergence is appreciably more difficult, particularly at temperatures in the vicinity of the Oh --> C(5v) transformation when starting from the C(5v) structure. A strategy combining the Tsallis generalized ensemble and the parallel tempering algorithm is implemented and used to improve the convergence of the simulations in the vicinity of the Oh --> C(5v) transformation.

Journal Article↗

PubMedDate not supplied

Computational vision and regularization theory.

Descriptions of physical properties of visible surfaces, such as their distance and the presence of edges, must be recovered from the primary image data. Computational vision aims to understand how such descriptions can be obtained from inherently ambiguous and noisy data. A recent development in this field sees early vision as a set of ill-posed problems, which can be solved by the use of regularization methods. These lead to algorithms and parallel analog circuits that can solve 'ill-posed problems' and which are suggestive of neural equivalents in the brain.

Humans↗

PubMed2005

Thermodynamics of folding and association of lattice-model proteins.

Closely related to the "protein folding problem" is the issue of protein misfolding and aggregation. Protein aggregation has been associated with the pathologies of nearly 20 human diseases and presents serious difficulties during the manufacture of pharmaceutical proteins. Computational studies of multiprotein systems have recently emerged as a powerful complement to experimental efforts aimed at understanding the mechanisms of protein aggregation. We describe the thermodynamics of systems containing two lattice-model 64-mers. A parallel tempering algorithm abates problems associated with glassy systems and the weighted histogram analysis method improves statistical quality. The presence of a second chain has a substantial effect on single-chain conformational preferences. The melting temperature is substantially reduced, and the increase in the population of unfolded states is correlated with an increase in interactions between chains. The transition from two native chains to a non-native aggregate is entropically favorable. Non-native aggregates receive approximately 25% of their stabilizing energy from intraprotein contacts not found in the lowest-energy structure. Contact maps show that for non-native dimers, nearly 50% of the most probable interprotein contacts involve pairs of residues that form native contacts, suggesting that a domain-swapping mechanism is involved in self-association.

Binding Sites↗

PubMed2006

Structural differentiation of the HIV-1 polyA signals.

The Human Immunodeficiency Virus Type 1 (HIV-1) encodes the polyadenylation (polyA) signal (AAUAAA) within the highly conserved untranslated region (UTR) at both 5' and 3' terminals of the viral transcript. In polyadenylation, an RNA transcript is cleaved and then elongated with adenine nucleotides while repression of the 5' signal and utilization of the 3' signal occurs. Because experimental studies have yet to analyze the structures of both 5' and 3' signals from a global perspective, other structural conformations involving these signals may exist and could be pivotal to understanding key functional processes. To distinguish the differential regulation of the 5' and 3' polyA signals, we studied the structural tendencies of both the 5' and 3' UTR in HIV-1. Through computational folding predictions of multiple HIV-1 strains using the Massively Parallel Genetic Algorithm (MPGAfold) capable of dynamically elucidating key alternative conformations, the 5' polyA signal was found to be dominantly occluded in a hairpin loop while the 3' polyA signal showed variability between hairpin and linear conformations with a propensity for the linear structure with an asymmetric internal loop. Furthermore, the energies and predictions of these structures indicate that the polyA signals have some metastable characteristics indicating an ability to switch into different conformations that can regulate viral function.

3' Untranslated Regions↗

PubMed1997

Reduced space sequence alignment.

MOTIVATION: Sequence alignment is the problem of finding the optimal character-by-character correspondence between two sequences. It can be readily solved in O(n2) time and O(n2) space on a serial machine, or in O(n) time with O(n) space per O(n) processing elements on a parallel machine. Hirschberg's divide-and-conquer approach for finding the single best path reduces space use by a factor of n while inducing only a small constant slowdown to the serial version. RESULTS: This paper presents a family of methods for computing sequence alignments with reduced memory that are well suited to serial or parallel implementation. Unlike the divide-and-conquer approach, they can be used in the forward-backward (Baum-Welch) training of linear hidden Markov models, and they avoid data-dependent repartitioning, making them easier to parallelize. The algorithms feature, for an arbitrary integer L, a factor proportional to L slowdown in exchange for reducing space requirement from O(n2) to O(n1 square root of n). A single best path member of this algorithm family matches the quadratic time and linear space of the divide-and-conquer algorithm. Experimentally, the O(n1.5)-space member of the family is 15-40% faster than the O(n)-space divide-and-conquer algorithm.

Algorithms↗

PubMed2004

GLAD: a system for developing and deploying large-scale bioinformatics grid.

MOTIVATION: Grid computing is used to solve large-scale bioinformatics problems with gigabytes database by distributing the computation across multiple platforms. Until now in developing bioinformatics grid applications, it is extremely tedious to design and implement the component algorithms and parallelization techniques for different classes of problems, and to access remotely located sequence database files of varying formats across the grid. In this study, we propose a grid programming toolkit, GLAD (Grid Life sciences Applications Developer), which facilitates the development and deployment of bioinformatics applications on a grid. RESULTS: GLAD has been developed using ALiCE (Adaptive scaLable Internet-based Computing Engine), a Java-based grid middleware, which exploits the task-based parallelism. Two bioinformatics benchmark applications, such as distributed sequence comparison and distributed progressive multiple sequence alignment, have been developed using GLAD.

Computational Biology↗

PubMed2005

Structural polymorphism of the HIV-1 leader region explored by computational methods.

Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5'-untranslated leader region (5'-UTR) can fold in vitro into two alternative conformations, branched (BMH) and 'linearized' (LDI) and switch between them to achieve different functionality. In this study we computationally explored in detail, with our massively parallel genetic algorithm (MPGAfold), the propensity of 13 HIV-1 5'-UTRs to fold into the BMH and the LDI conformation types. Besides the BMH conformations these results predict the existence of two functionally equivalent types of LDI conformations. One is similar to what has been shown in vitro to exist in HIV-1 LAI, the other is a novel conformation exemplified by HIV-1 MAL long-distance interactions. These novel MPGAfold results are further corroborated by a consensus probability matrix algorithm applied to a set of 155 HIV-1 sequences. We also have determined in detail the impact of various strain mutations, domain sizes and folds of elongating sequences simulating folding during transcription on HIV-1 RNA secondary structure folding dynamics.

5' Untranslated Regions↗

PubMedDate not supplied

Peripheral enhancement and spatial contrast uptake heterogeneity of primary breast tumours: quantitative assessment with dynamic MRI.

PURPOSE: The purpose of our study was to determine if quantitative analysis of peripheral enhancement and spatial contrast uptake heterogeneity is useful in the characterisation of abnormalities seen at breast MRI. METHOD: Ninety-one women underwent dynamic gadolinium-enhanced breast MRI. Regions of interest were processed by a parallel thinning algorithm to define central and peripheral subregions of lesions. Peripheral enhancement was quantified at every time point of the dynamic sequence as a signal difference-to-noise ratio. Moreover, a radiologist assessed the images for the presence of peripheral enhancement and classified the regional and subregional time-intensity profiles of each lesion. RESULTS: Sixty-four invasive carcinomas and 30 benign lesions were analysed. Significant differences were found between benign and malignant lesions in peripheral enhancement as determined from the dynamic images (p = 0.0002; sensitivity, 0.34; specificity, 1.00) in time-intensity profiles (p < 0.000005; sensitivity, 0.67; specificity, 0.93) and in peripheral percentage signal changes at 1 min postcontrast (p = 0.001). There was a much higher relative signal increase centrally than peripherally (p < 0.0005), but peripheral signal changes had greater diagnostic value than central ones (Az = 0.72 vs. 0.63; p = 0.02). Carcinomas showed higher peripheral enhancement than benign lesions (p = 0.001). Peripheral enhancement reached maximum diagnostic value at 4 min postcontrast (Az = 0.80) and performed best as a highly sensitive but moderately specific diagnostic index. CONCLUSION: Quantification of peripheral enhancement is diagnostically useful and offers insight into the enhancement mechanisms encountered in breast MRI. Primary breast tumours show substantial spatial contrast uptake heterogeneity. Lesion differentiation based on percentage signal changes is improved by restricting sampling to the periphery of tumours.

Adult↗

PubMed2006

Effective dose equivalent for point gamma sources located 10 cm near the body.

The key component in the so-called EPRI effective dose equivalent (EDE) methodology is an algorithm that utilizes two dosimeters (instead of multiple dosimeters) to predict the EDE for external photon exposures. The exposure scenarios that were previously studied in deriving the algorithm include parallel photon beams and point sources 33 cm from the body surface. The motivation for this study was the need to investigate source locations within 33 cm from the body so the method is more widely applicable. The ORNL stylized mathematical human phantoms and the MCNP code were used to calculate organ doses in this study. This paper presents the EDE data for point gamma sources at 0.3, 1.0, and 1.5 MeV, respectively, which are located at 10 cm from the surface of the body. The results and analyses show that the locations ranging from the overhead to the foot have resulted in conservative ratios except for two general regions near the front upper thigh and directly overhead. If all locations considered in this study were averaged for each photon energy, the overall ratio is on the conservative side. These data suggest that the EPRI EDE methodology is still valid for sources located 10 cm from the body, although the chance for resulting in a non-conservative estimate of the EDE has increased in comparison with the sources located at 30 cm from the body. Finally, this paper provides recommendations on how to apply the EPRI EDE methodology.

Body Burden↗

PubMed2006

Quantitative metrics for evaluating parallel acquisition techniques in diffusion tensor imaging at 3 Tesla.

OBJECTIVES: Single-shot echo-planar based diffusion tensor imaging is prone to geometric and intensity distortions. Parallel imaging is a means of reducing these distortions while preserving spatial resolution. A quantitative comparison at 3 T of parallel imaging for diffusion tensor images (DTI) using k-space (generalized auto-calibrating partially parallel acquisitions; GRAPPA) and image domain (sensitivity encoding; SENSE) reconstructions at different acceleration factors, R, is reported here. MATERIALS AND METHODS: Images were evaluated using 8 human subjects with repeated scans for 2 subjects to estimate reproducibility. Mutual information (MI) was used to assess the global changes in geometric distortions. The effects of parallel imaging techniques on random noise and reconstruction artifacts were evaluated by placing 26 regions of interest and computing the standard deviation of apparent diffusion coefficient and fractional anisotropy along with the error of fitting the data to the diffusion model (residual error). RESULTS: The larger positive values in mutual information index with increasing R values confirmed the anticipated decrease in distortions. Further, the MI index of GRAPPA sequences for a given R factor was larger than the corresponding mSENSE images. The residual error was lowest in the images acquired without parallel imaging and among the parallel reconstruction methods, the R = 2 acquisitions had the least error. The standard deviation, accuracy, and reproducibility of the apparent diffusion coefficient and fractional anisotropy in homogenous tissue regions showed that GRAPPA acquired with R = 2 had the least amount of systematic and random noise and of these, significant differences with mSENSE, R = 2 were found only for the fractional anisotropy index. CONCLUSION: Evaluation of the current implementation of parallel reconstruction algorithms identified GRAPPA acquired with R = 2 as optimal for diffusion tensor imaging.

Adult↗

PubMed2003

Magnetic field chaos in the Sherrington-Kirkpatrick model.

We study the Sherrington-Kirkpatrick model, both above and below the de Almeida-Thouless line, by using a modified version of the Parallel Tempering algorithm in which the system is allowed to move between different values of the magnetic field h. The behavior of the probability distribution of the overlap between two replicas at different values of the magnetic field h(0) and h(1) gives clear evidence for the presence of magnetic field chaos already for moderate system sizes, in contrast to the case of temperature chaos, which is not visible on system sizes that can currently be thermalized.

Journal Article↗

PubMed2004

Structures of Fe(II) spin-crossover complexes from synchrotron powder-diffraction data.

Crystal structure determination and analysis have been carried out for the two spin-crossover compounds [Fe(teeX)(6)](BF(4))(2) (teeX is haloethyltetrazole; X = I: teei; X = Br: teeb), in both their high-spin (near 300 K) and their low-spin states (T = 90 K), using high-resolution powder-diffraction data collected at the ESRF (Grenoble, France) and SPring8 (Japan) synchrotron radiation facilities. The structures of teei have been solved using various direct-space structure determination techniques (grid search, genetic algorithm and parallel tempering) and refined with the Rietveld method using geometrical restraints. In the case of teeb, a structural model was found but a full refinement was not successful because of the presence of a significant amount of an amorphous component. Analysis of the structures (space group P2(1)/c, Z = 2) and diffraction data, and the absence of phase transitions, show the overall structural similarity of these compounds and lead to the conclusion that the gradual spin-crossovers are likely to be accompanied by small structural changes only.

Journal Article↗

PubMed1999

Fourier rebinning applied to multiplanar circular-orbit cone-beam SPECT.

We study the application of Fourier rebinning methods to dual-planar cone-beam SPECT. Dual-planar cone-beam SPECT involves the use of a pair of dissimilar cone-beam collimators on a dual-camera SPECT system. Each collimator has its focus in a different axial plane. While dual-planar data is best reconstructed with fully three-dimensional (3-D) iterative methods, these methods are slow and have prompted a search for faster reconstruction techniques. Fourier rebinning was developed to estimate equivalent parallel projections from 3-D PET data, but it simply expresses a relationship between oblique projections taken in planes not perpendicular to the axis of rotation and direct projections taken in those that are. We find that it is possible to put cone-beam data in this context as well. The rebinned data can then be reconstructed using either filtered backprojection (FBP) or parallel iterative algorithms such as OS-EM. We compare the Feldkamp algorithm and fully 3-D OSEM reconstruction with Fourier-rebinned reconstructions on realistically-simulated Tc-99m HMPAO brain SPECT data. We find that the Fourier-rebinned reconstructions exhibit much less image noise and lower variance in region-of-interest (ROI) estimates than Feldkamp. Also, Fourier-rebinning followed by OSEM with nonuniform attenuation correction exhibits less bias in ROI estimates than Feldkamp with Chang attenuation correction. The Fourier-rebinned ROI estimates exhibit bias and variance comparable to those from fully 3-D OSEM and require considerably less processing time. However, in areas off the axis of rotation, the axial-direction resolution of FORE-reconstructed images is poorer than that of images reconstructed with 3-D OSEM. We conclude that Fourier rebinning is a practical and potentially useful approach to reconstructing data from dual-planar circular-orbit cone-beam systems.

Brain↗

PubMed2006

On adaptive learning rate that guarantees convergence in feedforward networks.

This paper investigates new learning algorithms (LF I and LF II) based on Lyapunov function for the training of feedforward neural networks. It is observed that such algorithms have interesting parallel with the popular backpropagation (BP) algorithm where the fixed learning rate is replaced by an adaptive learning rate computed using convergence theorem based on Lyapunov stability theory. LF II, a modified version of LF I, has been introduced with an aim to avoid local minima. This modification also helps in improving the convergence speed in some cases. Conditions for achieving global minimum for these kind of algorithms have been studied in detail. The performances of the proposed algorithms are compared with BP algorithm and extended Kalman filtering (EKF) on three bench-mark function approximation problems: XOR, 3-bit parity, and 8-3 encoder. The comparisons are made in terms of number of learning iterations and computational time required for convergence. It is found that the proposed algorithms (LF I and II) are much faster in convergence than other two algorithms to attain same accuracy. Finally, the comparison is made on a complex two-dimensional (2-D) Gabor function and effect of adaptive learning rate for faster convergence is verified. In a nutshell, the investigations made in this paper help us better understand the learning procedure of feedforward neural networks in terms of adaptive learning rate, convergence speed, and local minima.

Algorithms↗

PubMed1989

Peak-picking fundamental period estimation for hearing prostheses.

A real-time peak-picking fundamental period estimation device is described which is used in advanced hearing prostheses for the totally and profoundly deafened. The operation of the peak picker is compared with three well-established fundamental frequency estimation techniques: the electrolaryngograph, which is used as a "standard" hardware implementations of the cepstral technique, and the Gold/Rabiner parallel processing algorithm. These comparisons illustrate and highlight some of the important advantages and disadvantages that characterize the operation of these techniques. The special requirements of the hearing prostheses are discussed with respect to the operation of each device, and the choice of the peak picker is found to be felicitous in this application.

Cochlear Implants↗