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PubMed1998

Astigmatic single photon emission computed tomography imaging with a displaced center of rotation.

A filtered backprojection algorithm is developed for single photon emission computed tomography (SPECT) imaging with an astigmatic collimator having a displaced center of rotation. The astigmatic collimator has two perpendicular focal lines, one that is parallel to the axis of rotation of the gamma camera and one that is perpendicular to this axis. Using SPECT simulations of projection data from a hot rod phantom and point source arrays, it is found that a lack of incorporation of the mechanical shift in the reconstruction algorithm causes errors and artifacts in reconstructed SPECT images. The collimator and acquisition parameters in the astigmatic reconstruction formula, which include focal lengths, radius of rotation, and mechanical shifts, are often partly unknown and can be determined using the projections of a point source at various projection angles. The accurate determination of these parameters by a least squares fitting technique using projection data from numerically simulated SPECT acquisitions is studied. These studies show that the accuracy of parameter determination is improved as the distance between the point source and the axis of rotation of the gamma camera is increased. The focal length of the focal line perpendicular to the axis of rotation is determined more accurately than the focal length to the focal line parallel to this axis.

Algorithms↗

PubMed2001

Rebinning-based algorithms for helical cone-beam CT.

Several image reconstruction algorithms based on rebinning have been proposed recently for helical cone-beam CT. These algorithms separate the 3D reconstruction into a set of independent 2D reconstructions for a set of surfaces: planar or non-planar surfaces are defined and then reconstructed using 2D filtered backprojection from a 2D fan-beam or parallel-beam set of data estimated from the cone-beam (CB) measurements. The first part of this paper presents a unified derivation of rebinning algorithms for planar and non-planar surfaces. An integral equation is derived for the surface allowing the best rebinning and an iterative algorithm converging to the solution of that equation is given. The second part presents an efficient method to correct the residual reconstruction artefacts observed with rebinning algorithms when the cone-angle is too large for the required accuracy. This correction algorithm involves a CB backprojection and the reconstruction time is slightly longer than for the zero-boundary (ZB) method.

Algorithms↗

PubMed2006

Independence estimating equations for controlled clinical trials with small sample sizes--interval estimation.

OBJECTIVES: The application of independence estimating equations (IEE) for controlled clinical trials (CCTs) has recently been discussed, and recommendations for its use have been derived for testing hypotheses. The robust estimator of variance has been shown to be liberal for small sample sizes. Therefore a series of modifications has been proposed. In this paper we systematically compare confidence intervals (CIs) proposed in the literature for situations that are common in CCTs. METHODS: Using Monte-Carlo simulation studies, we compared the coverage probabilities of CIs and non-convergence probabilities for the parameters of the mean structure for small samples using modifications of the variance estimator proposed by Mancl and de Rouen [7], Morel et al. [8] and Pan [3]. RESULTS: None of the proposed modifications behave well in each investigated situation. For parallel group designs with repeated measurements and binary response the method proposed by Pan maintains the nominal level. We observed non-convergence of the IEE algorithm in up to 10% of the replicates depending on response probabilities in the treatment groups. For comparing slopes with continuous responses, the approach of Morel et al. can be recommended. CONCLUSIONS: Results of non-convergence probabilities show that IEE should not be used in parallel group designs with binary endpoints and response probabilities close to 0 or 1. Modifications of the robust variance estimator should be used for sample sizes up to 100 clusters for CI estimation.

Algorithms↗

PubMed1999

Parallel image segmentation using the L4 network.

Each processing element in the outer plexiform layer of the fly's (Musca domestica) compound eye has a single copy of a monopolar cell called L4 whose function is still unknown. This paper proposes that L4 acts as an image segmentor receiving data from the L1 and L2 cell layer above it. The photoreceptor terminals R1 through R6 and L1 and L2 form a cartridge with shunting current inhibition that enhances contrast at the first synaptic contact. The photoreceptors feeding their respective terminals share a common optical axis. What was realized for this entire structure that led up to and included L1 and L2, was that it forms a single processing element which outputs a weighted function based on current shunting between the photoreceptor axon terminals around L1 and L2. Thus the basic biological 'algorithm' that this paper proposes for L1 and L2 involves a summation of the differences between a central reference cell (referred to as Rref) and the six neighboring photoreceptor terminals R1-R6 within the cartridge of L1 and L2. Simulation implementing this simple algorithm on a hexagonal packed matrix in Matlab, suggest that objects with even small differences in intensity with the background, can readily be distinguished from the background. This high pass filter biological model allows edge detection and segmentation, independent of scale in a parallel, modular fashion. Implementation of such a biological algorithm using analog circuitry forms a preprocessing unit that introduces virtually no delay in the processing of image information, in comparison to present DSP techniques, that require iterative approaches and costly computing time.

Algorithms↗

PubMed2004

Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running.

BACKGROUND: Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. METHODS: We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. RESULTS: We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. CONCLUSIONS: Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described.

Anisotropy↗

PubMed2002

Proteins wriggle.

We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model, when proteins fold under physiological conditions, their backbone dihedral angles change synchronously in groups of four or more to avoid steric clashes and respect the kinematic conservation laws. They wriggle; they do not thrash. We describe a simple algorithm that can be used to incorporate wriggling in Monte Carlo simulations of protein folding. We have tested this wriggling algorithm against a code in which the dihedral angles are varied independently (thrashing). Our standard of success is the average root-mean-square distance (rmsd) between the alpha-carbons of the folding protein and those of its native structure. After 100,000 Monte Carlo sweeps, the relative decrease in the mean rmsd, as one switches from thrashing to wriggling, rises from 11% for the protein 3LZM with 164 amino acids (aa) to 40% for the protein 1A1S with 313 aa and 47% for the protein 16PK with 415 aa. These results suggest that wriggling is useful and that its utility increases with the size of the protein. One may implement wriggling on a parallel computer or a computer farm.

Algorithms↗

PubMed2005

Using the GRID to improve the computation speed of electrical impedance tomography (EIT) reconstruction algorithms.

In our group at University College London, we have been developing electrical impedance tomography (EIT) of brain function. We have attempted to improve image quality by the use of realistic anatomical meshes and, more recently, non-linear reconstruction methods. Reconstruction with linear methods, with pre-processing, may take up to a few minutes per image for even detailed meshes. However, iterative non-linear reconstruction methods require much more computational resources, and reconstruction with detailed meshes was taking far too long for clinical use. We present a solution to this timing bottleneck, using the resources of the GRID, the development of coordinated computing resources over the internet that are not subject to centralized control using standard, open, general-purpose protocols and are transparent to the user. Optimization was performed by splitting reconstruction of image series into individual jobs of one image each; no parallelization was attempted. Using the GRID middleware 'Condor' and a cluster of 920 nodes, reconstruction of EIT images of the human head with a non-linear algorithm was speeded up by 25-40 times compared to serial processing of each image. This distributed method is of direct practical value in applications such as EIT of epileptic seizures where hundreds of images are collected over the few minutes of a seizure and will be of value to clinical data collection with similar requirements. In the future, the same resources could be employed for the more ambitious task of parallelized code.

Algorithms↗

PubMed1998

Molecular evidence for parallel evolution of adaptive syndromes in fig-breeding Lissocephala (Drosophilidae).

Afrotropical Lissocephala (Drosophilidae) breed strictly in syconia (figs) of Ficus (Moraceae) and have accordingly evolved specific features including modified female and eggshell morphologies, ovipositing, larval foraging, and mating behaviors. These various traits may exist as two or three alternative states. Each species displays a specific suite of traits so closely coordinated with one another that alternative states of the overall suites of traits can be seen as "adaptive syndromes." Three clear-cut adaptive syndromes can be recognized while two taxonomic lineages (juncta and sanu species groups) are traditionally accepted on the basis of male terminalia. A crucial evolutionary question results from the consideration that ecological clusters and taxonomic groups have conflicting compositions: the three syndromes are found in the juncta group while two of them occur in the sanu group. To resolve this conflict, we present molecular data which provide a robust phylogeny: mitochondrial DNA (12S + 16S ribosomal DNA and cytochrome b) sequence data are in agreement with one another regardless of the algorithm used. All molecular data consistently support male terminalia dichotomy. Such a level of consistency unambiguously indicates that parallel evolution of adaptive syndromes occurred. Thus, homoplasy may affect morphological and behavioral traits concomitantly when these are involved in a network of functional relationships.

Adaptation, Physiological↗

PubMed2001

Advanced single-slice rebinning for tilted spiral cone-beam CT.

Future medical CT scanners and today's micro CT scanners demand cone-beam reconstruction algorithms that are capable of reconstructing data acquired from a tilted spiral trajectory where the vector of rotation is not necessarily parallel to the vector of table increment. For the medical CT scanner this case of nonparallel object motion is met for nonzero gantry tilt: the table moves into a direction that is not perpendicular to the plane of rotation. Since this is not a special application of medical CT but rather a daily routine in head exams, there is a strong need for corresponding reconstruction algorithms. In contrast to medical CT, where the special case of nonperpendicular motion is used on purpose, micro CT scanners cannot avoid aberrations of the rotational axis and the table increment vector due to alignment problems. Especially for those micro CT scanners that have the lifting stage mounted on the rotation table (in contrast to setups where the lifting stage holds the rotation table), this kind of misalignment is equivalent to a gantry tilt. We therefore generalize the advanced single-slice rebinning algorithm (ASSR), which is considered a very promising approach for medical cone-beam reconstruction due to its high image quality and its high reconstruction speed [Med. Phys. 27, 754-772 (2000)], to the case of tilted gantries. We evaluate this extended ASSR approach (which we will denote as ASSR+, for convenience) in comparison to the original ASSR algorithm using simulated phantom data for reconstruction. For the case of nonparallel object motion ASSR+ shows significant improvements over ASSR, however, its computational complexity is slightly increased due to the broken symmetry of the spiral trajectory.

Algorithms↗

PubMedDate not supplied

Monte Carlo methods for small molecule high-throughput experimentation.

By analogy with Monte Carlo algorithms, we propose new strategies for design and redesign of small molecule libraries in high-throughput experimentation, or combinatorial chemistry. Several Monte Carlo methods are examined, including Metropolis, three types of biased schemes, and composite moves that include swapping or parallel tempering. Among them, the biased Monte Carlo schemes exhibit particularly high efficiency in locating optimal compounds. The Monte Carlo strategies are compared to a genetic algorithm approach. Although the best compounds identified by the genetic algorithm are comparable to those from the better Monte Carlo schemes, the diversity of favorable compounds identified is reduced by roughly 60%.

Journal Article↗

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↗

PubMedDate not supplied

Contact angle analysis on polymethylmethacrylate and commercial wax by using an environmental scanning electron microscope.

The environmental scanning electron microscope (ESEM) represents one of the most exciting breakthroughs in electron microscopy since the invention of the electron microscope. Its ability to observe uncoated and hydrated samples enhances the possibility for investigating the wettability of surfaces at a microscopic level; by varying the relative vapour pressure or the temperature inside the chamber, it is possible to condense water drops on a micron scale. A large problem in measuring contact angles by ESEM is that the observation angle is not parallel or perpendicular to the surface; thus, the study of the droplets profile using the common algorithms such as spherical approximation or axisymmetric drop shape analysis (ADSA) is not possible, because only a spherical cap shape is commonly observed. In this paper we provide a useful mathematical model to calculate the real contact angle from the initial images. Initially, some simulated spherical caps with different contact and observation angles were created by an appropriate graphic package in order to test the mathematical model. Some real drops obtained by ESEM on wax and polymethylmethacrylate (PMMA) were then studied and the results compared with contact angles measured by common methods on the same materials.

Journal Article↗

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↗