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Results for “Parallel Algorithms”

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At least 433 records · Page 24Linked to original sources

PubMed1994

A comparison of three electron planning algorithms for a 16 MeV electron beam.

PURPOSE: We report results of a comparison of three electron planning algorithms, an Age-Diffusion Pencil beam algorithm and two (2-D) and three dimensional (3-D) Hogstrom pencil beam algorithms, using simple 2 x 2 cm air and hard bone inhomogeneities and a complex anthropomorphic head and neck phantom. METHODS AND MATERIALS: The simple inhomogeneities have variable dimensions outside the plane of calculation to test the effects of out of plane scattering on 2-D algorithms, compared with dose measured by film below the inhomogeneity in the dose fall-off range. Comparisons are also made of a parotid treatment field for 16 MeV electrons, and the dose measured by high sensitivity thermoluminescent dosimeters in the head and neck phantom. RESULTS: Behind the simple inhomogeneities, the electron algorithms are found to underestimate the dose behind the air cavity by up to 40% and overestimated the dose behind bone by up to 30%. In the head phantom, the presence of inhomogeneities also presents problems for the algorithms, with overestimations of dose of up to 20% found behind bone-tissue interfaces, apparently due to shielding by high density bone. Overestimations of up to 17% are also found beside interfaces parallel to the beam. Underestimations of dose of up to 10% are found on the beam-side of interfaces, due to under-prediction of backscattered electrons. All three investigated algorithms underestimate the dose by up to 20% behind extreme surface curvature. One algorithm is found to underestimate the dose in the falloff region while another overestimates the dose around the 90% isodose. CONCLUSION: Clinicians should be aware of the limitations of their planning systems.

Algorithms↗

PubMed1999

Inexpensive, semi-automated system for measuring mechanical properties of soft tissues.

Stiffness and strength are important properties of many tissues, but standard material-testing equipment is expensive, often ill-suited for testing soft tissues, and rarely accessible to biologists. We describe a system built around a microcomputer and an electronic balance which is particularly well-suited for measuring stress and strain in small samples of soft tissue. We use a discarded floppy disk drive as a linear actuator to strain the sample, while an electronic balance measures the tension (used to calculate stress). We give an algorithm for a program to drive a microcomputer which controls the floppy disk drive via its parallel port and records the balance measurements via its serial port. We used this system to obtain stress-strain curves from a sample of latex rubber and a sample of soft insect cuticle. Three tests of the rubber sample gave nearly identical results, with smooth, J-shaped stress-strain curves. The stress-strain curves gave a modulus elasticity value of 1.72 Mpa over the steep, straight region, well within the range for natural latex rubber. We also tested a sample of abdominal cuticle from a caterpillar (Manduca sexta). The caterpillar cuticle had a J-shaped stress-strain curve with a modulus of elasticity of 2.11 Mpa over the steep part of the curve. J. Exp. Zool. 284:374-378, 1999.

Animals↗

PubMed1985

Design and fitting of neural network transfer functions.

An algorithm is presented which (a) allows construction of mathematical models involving arbitrary combinations of linear cascades, parallel pathways, and feedback loops, (b) computes a total transfer function of the system, (c) performs a least-squares optimization of model parameters to best fit the model to experimental data, and (d) provides a measure of goodness-of-fit to the data. The technique has been employed to construct and test models of neural networks which mimic a class of responses observed in the cat vestibular nuclei in response to tilt, namely responses which show both a gain increase and progressive phase lag as the stimulation frequency goes from 0.01 to 2 Hz. A network consisting of a simple gain element in parallel with an inhibitory high-pass filtered version of the input provided a satisfactory fit to these data.

Animals↗

PubMed1984

Evoked potential techniques in the evaluation of visual function.

Visual evoked potentials (VEPs) can be used in a multitude of ways to assess the various levels of visual processing. The human visual system consists of multiple, parallel channels which process different information, and each channel constitutes a set of sequential processes. An algorithm of sequential steps that can be used to assess visual function is reviewed. The pathophysiology of retinal, anterior visual pathways and retrochiasmal pathways can be objectively evaluated by VEPs.

Adolescent↗

PubMed1999

A unified reconstruction framework for both parallel-beam and variable focal-length fan-beam collimators by a Cormack-type inversion of exponential radon transform.

A variety of inversions of exponential Radon transform has been derived based on the circular harmonic transform in Fourier space by several research groups. However, these inversions cannot be directly applied to deal with the reconstruction for fan-beam or variable-focal-length fan-beam collimator geometries in single photon emission computed tomography (SPECT). In this paper, we derived a Cormack-type inversion of the exponential Radon transform by employing the circular harmonic transform directly in the projection space and the image space instead of the Fourier space. Thus, a unified reconstruction framework is established for parallel-, fan-, and variable-focal-length fan-beam collimator geometries. Compared to many existing algorithms, the presented one greatly mitigates the difficulty of image reconstruction due to the complicated collimator geometry and significantly reduces the computational burden of the special functions, such as Chebyshev or Bessel functions. By the well-established fast-Fourier transform (FFT), our algorithm is very efficient, as demonstrated by several numerical simulations.

Algorithms↗

PubMedDate not supplied

A field demonstration of the simulation optimization approach for remediation system design.

While significant progress has been made in the theoretical development of the simulation/optimization (S/O) approach for ground water remediation design, its application to large, field-scale problems has remained limited. To demonstrate the applicability and usefulness of the S/O approach under real field conditions, an optimization demonstration project was conducted at the Massachusetts Military Reservation in Cape Cod, Massachusetts, involving the design of a pump-and-treat system for the containment and cleanup of a large trichloroethylene (TCE) plume. The optimization techniques used in this study are based on evolutionary algorithms coupled with a response function approach for greater computational efficiency. The S/O analysis was performed parallel to a conventional trial-and-error analysis based on simulation alone. The results of this study demonstrate that not only would it be possible to remove more TCE mass under the same amount of pumping assumed in the trial-and-error design, but also substantial cost savings could be achieved by reducing the number of wells needed and adapting dynamic pumping. In spite of the large model size of more than 500,000 nodes and a long planning horizon of 30 years, the optimization modeling was carried out successfully on desktop PCs. This field demonstration project clearly illustrates the potential benefits of applying optimization techniques in remediation system design.

Facility Design and Construction↗

PubMed2002

Multigroup discrete ordinates modeling of 125I 6702 seed dose distributions using a broad energy-group cross section representation.

Our purpose in this work is to demonstrate that the efficiency of dose-rate computations in 125I brachytherapy, using multigroup discrete ordinates radiation transport simulations, can be significantly enhanced using broad energy group cross sections without a loss of accuracy. To this end, the DANTSYS multigroup discrete ordinates neutral particle transport code was used to estimate the absorbed dose-rate distributions around an 125I-model 6702 seed in two-dimensional (2-D) cylindrical R-Z geometry for four different problems spanning the geometries found in clinical practice. First, simulations with a high resolution 210 energy groups library were used to analyze the photon flux spectral distribution throughout this set of problems. These distributions were used to design an energy group structure consisting of three broad groups along with suitable weighting functions from which the three-group cross sections were derived. The accuracy of 2-D DANTSYS dose-rate calculations was benchmarked against parallel Monte Carlo simulations. Ray effects were remedied by using the DANTSYS internal first collision source algorithm. It is demonstrated that the 125I primary photon spectrum leads to inappropriate weighting functions. An accuracy of +/-5% is achieved in the four problem geometries considered using geometry-independent three-group libraries derived from either material-specific weighting functions or a single material-independent weighting function. Agreement between Monte Carlo and the three-group DANTSYS calculations, within three standard Monte Carlo deviations, is observed everywhere except for a limited region along the Z axis of rotational symmetry, where ray effects are difficult to mitigate. The three-group DANTSYS calculations are 10-13 times faster than ones with a 210-group cross section library for 125I dosimetry problems. Compared to 2-D EGS4 Monte Carlo calculations, the 3-group DANTSYS simulations are a 100-fold more efficient. Provided that these efficiency gains can be sustained in three-dimensional geometries, the results suggest that discrete ordinates simulations may have the potential to serve as an efficient and accurate dose-calculation algorithm for low-energy brachytherapy treatment planning.

Brachytherapy↗

PubMedDate not supplied

The relationship between traumatic tympanic membrane perforations and pneumatization of the mastoid.

We evaluated the possible relationship between tympanic membrane perforations resulting from blast trauma or slap and pneumatization of the mastoid cells. A total of 25 male patients with tympanic membrane perforations resulting from blast injury (n = 7), slap (n = 17), and football hit (n = 1) and 20 healthy male volunteers without any ear problem had temporal bone computed tomographic scans in the axial plane, parallel to the infraorbitomeatal line, with 2 mm slice thickness and 2-mm intervals using bone algorithm with a ProSpeed Spiral tomography machine. The area of air cells in each slice was measured using trace and area measurement functions of the tomography machine, and by multiplying the resulting area by slice thickness, the volume of each slice was calculated. For each ear, the total of volumes of air cells was calculated by adding the volumes of each slice containing air cells. The calculated volumes of mastoid cells were evaluated by comparing microscopic findings. Both patient and control groups consisted of males, and their ages ranged from 17 to 32 (mean 24.5) years. Microscopic examinations revealed that perforations were frequently located in the lower quadrants and that most of them were less than 3 mm. There were no pars flaccida and marginal perforations. Ossicular chain destruction was noted neither in temporal bone tomographic nor during intraoperative examinations. The mean (+/- SD) volumes of right and left ear mastoid air cells in patient and control groups were 6.92 +/- 2.45 vs. 7.00 +/- 2.59 cm(3) and 9.04 +/- 4.55 vs. 8.95 +/- 4.53 cm(3), respectively, and the differences were not statistically significant. It was found that the level of mastoid pneumatization has no statistically significant effect on tympanic membrane pathologies due to blast or other injuries.

Adolescent↗

PubMed1996

Parallel hardware for sequence comparison and alignment.

Sequence comparison, a vital research tool in computational biology, is based on a simple O(n2) algorithm that easily maps to a linear array of processors. This paper reviews and compares high-performance sequence analysis on general-purpose supercomputers and single-purpose reconfigurable, and programmable co-processors. The difficulty of comparing hardware from published performance figures is also noted.

Algorithms↗

PubMed2003

[Algorithm for diagnosis and therapy of pain].

Certain basic principles are applicable to all forms of pain treatment when the aims are pain relief and the avoidance of chronicety. Such algorithms, as guidelines are even more important when pain is becoming chronic. The use of the described algorithms is necessary in the diagnosis and therapy of acute pain and also to avoid the establishment of chronic pain due to the changes of neuroplasticity in the central nervous system. The most important basic principles in the form of algorithms are first of all that therapies should be simultaneously applied and not sequentially. Secondly, the challenge should be met to create a concept where by various therapies can be preformed in a parallel fashion, without compete one another and being effective on different aspects and causes of the pain.

Administration, Oral↗

PubMed1997

Comparison of non parallel immunoassay curves resulting from mixtures of competing antigens.

Relative potency is a measure that has been used for many years to summarize the comparison of dose-response curves in parallel line bioassays. When response curves for two preparations are not parallel the traditional definition of relative potency no longer applies. We review the concept of relative potency and show that, in some situations, it can be given meaning for non-parallel curves as the ratio of biological activity in full strength assay preparations. Under an assumption that non-parallel curves result from the competition of mixtures of antigens for receptor binding sites, estimation of relative potency for non-parallel curves can be accomplished. We show that estimation of models for both parallel curve and response attenuation situations may be accomplished within the framework of generalized linear models. This estimation depends on the ability to deal with non-linear parameters appearing in the link function, and an iterative algorithm depending on direct parameter updates is outlined. The topics discussed are illustrated with the analysis of data from two immunoassays conducted with veterinary vaccines. The models developed here depend in an essential way on the assumption of response attenuation by competing antigens. Our methods may not be appropriate for non-parallel curves caused by other phenomena.

Algorithms↗

PubMedDate not supplied

Efficient split synthesis for targeted libraries.

We propose a new approach for fabricating more sophisticated combinatorial chemistry libraries via split synthesis and evaluate its potential through extensive simulation. Our algorithmically intensive method promises to reduce the time and materials costs of synthesizing libraries which are (1) too large to synthesize economically by sequential or parallel synthesis, (2) too long or irregular for conventional split synthesis generation techniques, and (3) not used in sufficient quantity to justify the setup costs of array makers. It also encourages the design of more focused and interesting libraries than are typically constructed using split synthesis. Our algorithms automate the design of efficient synthesis procedures for motif-based libraries which are too complex to design by hand. Our software allows the user to select the most desirable tradeoff between minimizing the number of steps in the synthesis process and containing the combinatorial explosion of the number of compounds synthesized.

Algorithms↗

PubMed1991

Sample size estimation for comparing two or more treatment groups in clinical trials.

Methods for estimating required sample size for comparing two population means have been published. Most involve the use of complicated formulae and tables. These methods are limited to comparing two groups. Although techniques exist to determine sample sizes for comparing more than two groups, they are intrinsically far more complicated. A simple linear nomogram is proposed as a solution to these problems, and its use is illustrated with examples of parallel group, ordered parallel group and factorial designs.

Algorithms↗

PubMed2003

Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6.

The interaction of Chlamydomonas cytochrome f (cyt f) with either Chlamydomonas plastocyanin (PC) or Chlamydomonas cytochrome c(6) (cyt c(6)) was studied using Brownian dynamics simulations. The two electron acceptors (PC and cyt c(6)) were found to be essentially interchangeable despite a lack of sequence homology and different secondary structures (beta-sheet for PC and alpha-helix for cyt c(6)). Simulations using PC and cyt c(6) interacting with cyt f showed approximately equal numbers of successful complexes and calculated rates of electron transfer. Cyt f-PC and cyt f-cyt c(6) showed the same types of interactions. Hydrophobic residues surrounding the Y1 ligand to the heme on cyt f interacted with hydrophobic residues on PC (surrounding the H87 ligand to the Cu) or cyt c(6) (surrounding the heme). Both types of complexes were stabilized by electrostatic interactions between K65, K188, and K189 on cyt f and conserved anionic residues on PC (E43, D44, D53, and E85) or cyt c(6) (E2, E70, and E71). Mutations on cyt f had identical effects on its interaction with either PC or cyt c(6). K65A, K188A, and K189A showed the largest effects whereas residues such as K217A, R88A, and K110A, which are located far from the positive patch on cyt f, showed very little inhibition. The effect of mutations observed in Brownian dynamics simulations paralleled those observed in experiments.

Algorithms↗

PubMedDate not supplied

Pharmacokinetics of D,L-3-hydroxy-3-ethyl-3-phenylpropionamide (HEPP) in pregnant rats at different stages of gestation and maternal-fetal disposition during late pregnancy.

The pharmacokinetics of D,L-3-hydroxy-3-ethyl-3-phenylpropionamide (HEPP), an investigational anticonvulsant drug, was evaluated in nonpregnant and in pregnant rats on gestation day (GD) 7, 12, and 21 after an intraperitoneal (i.p.) dose of 50mg/kg. Maternal-fetal disposition in the GD21 group was also evaluated. In all groups, HEPP was rapidly absorbed and the disposition was well described by an open two-compartment kinetic model. The most pronounced effects of pregnancy on the kinetics of HEPP were observed at GD21 in which significant increases in the first-order hybrid disposition rate constants alpha and beta, with corresponding decreases in half-lives were observed. Gestation also affected the intercompartmental transfer rate constants k(12) and k(21), specially at GD12 and at GD21. These changes could be associated with the physiologic increases in blood flow and cardiac output of pregnancy. There was also a slight decrease in the apparent volume of distribution at GD21, and a progressive decrease in the clearance values normalized by the body weight. No other significant differences in kinetic parameters were observed. On GD21, HEPP rapidly transfers from maternal blood to fetuses, to reach concentrations in the placenta and fetuses slightly higher than those of the maternal plasma (fetal:maternal ratio ranging from 1.07 to 1.45). After equilibrium, the concentrations in maternal, placental, and fetal tissues decreased in parallel.

Algorithms↗

PubMedDate not supplied

Toward an optimal procedure for variable selection and QSAR model building.

In this work, we report the development of a novel QSAR technique combining genetic algorithms and neural networks for selecting a subset of relevant descriptors and building the optimal neural network architecture for QSAR studies. This technique uses a neural network to map the dependent property of interest with the descriptors preselected by the genetic algorithm. This technique differs from other variable selection techniques combining genetic algorithms to neural networks by two main features: (1) The variable selection search performed by the genetic algorithm is not constrained to a defined number of descriptors. (2) The optimal neural network architecture is explored in parallel with the variable selection by dynamically modifying the size of the hidden layer. By using both artificial data and real biological data, we show that this technique can be used to build both classification and regression models and outperforms simpler variable selection techniques mainly for nonlinear data sets. The results obtained on real data are compared to previous work using other modeling techniques. We also discuss some important issues in building QSAR models and good practices for QSAR studies.

Algorithms↗

PubMed1991

Asymmetric Boltzmann machines.

We study asymmetric stochastic networks from two points of view: combinatorial optimization and learning algorithms based on relative entropy minimization. We show that there are non trivial classes of asymmetric networks which admit a Lyapunov function L under deterministic parallel evolution and prove that the stochastic augmentation of such networks amounts to a stochastic search for global minima of L. The problem of minimizing L for a totally antisymmetric parallel network is shown to be associated to an NP-complete decision problem. The study of entropic learning for general asymmetric networks, performed in the non equilibrium, time dependent formalism, leads to a Hebbian rule based on time averages over the past history of the system. The general algorithm for asymmetric networks is tested on a feed-forward architecture.

Algorithms↗

PubMed2001

On the parallelisation of bioinformatics applications.

This paper surveys the computational strategies followed to parallelise the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database-searching applications, to very irregularly structured patterns (phylogenetic trees). Fine- and coarse-grained parallel strategies are discussed for these very diverse sets of applications. This overview outlines computational issues related to parallelism, physical machine models, parallel programming approaches and scheduling strategies for a broad range of computer architectures. In particular, it deals with shared, distributed and shared/distributed memory architectures.

Algorithms↗