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 1,387 records · Page 77Linked to original sources

Simultaneous phase correction and SENSE reconstruction for navigated multi-shot DWI with non-cartesian k-space sampling.

Phase-navigated multi-shot acquisition and parallel imaging are two techniques that have been applied to diffusion-weighted imaging (DWI) to diminish distortions and to enhance spatial resolution. Specifically, sensitivity encoding (SENSE) has been combined with single-shot echo planar imaging (EPI). Thus far, it has been difficult to apply parallel imaging methods, like SENSE, to multi-shot DWI because motion-induced phase error varies from shot to shot and interferes with sensitivity encoding. Although direct phase subtraction methods have been introduced to correct this phase error, they generally are not suitable for SENSE reconstruction, and they cannot remove all the motion artifacts even if the phase error is fully known. Here, an effective algorithm is proposed to correct the motion-induced phase error using an iterative reconstruction. In this proposed conjugate-gradient (CG) algorithm, the phase error is treated as an image encoding function. Given the complex perturbation terms, diffusion-weighted images can be reconstructed using an augmented sensitivity map. The mathematical formulation and image reconstruction procedures of this algorithm are similar to the SENSE reconstruction. By defining a dynamic composite sensitivity, the CG phase correction method can be conveniently incorporated with SENSE reconstruction for the application of multi-shot SENSE DWI. Effective phase correction and multi-shot SENSE DWI (R = 1 to 3) are demonstrated on both simulated and in vivo data acquired with PROPELLER and SNAILS.

Algorithms↗

Dynamics of Drop Formation in an Electric Field.

The effect of an electric field on the formation of a drop of an inviscid, perfectly conducting liquid from a capillary which protrudes from the top plate of a parallel-plate capacitor into a surrounding dynamically inactive, insulating gas is studied computationally. This free boundary problem which is comprised of the surface Bernoulli equation for the transient drop shape and the Laplace equation for the velocity potential inside the drop and the electrostatic potential outside the drop is solved by a method of lines incorporating the finite element method for spatial discretization. The finite element algorithm employed relies on judicious use of remeshing and element addition to a two-region adaptive mesh to accommodate large domain deformations, and allows the computations to proceed until the thickness of the neck connecting an about to form drop to the rest of the liquid in the capillary is less than 0.1% of the capillary radius. The accuracy of the computations is demonstrated by showing that in the absence of an electric field predictions made with the new algorithm are in excellent agreement with boundary integral calculations (Schulkes, R. M. S. M. J. Fluid Mech. 278, 83 (1994)) and experimental measurements on water drops (Zhang, X., and Basaran, O. A. Phys. Fluids 7(6), 1184 (1995)). In the presence of an electric field, the algorithm predicts that as the strength of the applied field increases, the mode of drop formation changes from simple dripping to jetting to so-called microdripping, in accordance with experimental observations (Cloupeau, M., and Prunet-Foch, B. J. Aerosol Sci. 25(6), 1021 (1994); Zhang, X., and Basaran, O. A. J. Fluid Mech. 326, 239 (1996)). Computational predictions of the primary drop volume and drop length at breakup are reported over a wide range of values of the ratios of electrical, gravitational, and inertial forces to surface tension force. In contrast to previously mentioned cases where both the flow rate in the tube and the electric field strength are nonzero, situations are also considered in which the flow rate is zero and the dynamics are initiated by impulsively changing the field strength from a certain value to a larger value. When the magnitude of the step change in field strength is small, the results of the new transient calculations accord well with those of an earlier stability analysis (Basaran, O. A., and Scriven, L. E. J. Colloid Interface Sci. 140(1), 10 (1990)) and thereby provide yet another testament to the accuracy of the new algorithm. Copyright 1999 Academic Press.

Journal Article↗

Progression of heterogeneous breast tumors.

Two possible pathways of breast tumor progression were investigated by searching for values of transition rates that could reproduce the clinically observed co-occurrence frequencies of grades of ductal carcinoma in situ and grades of invasive ductal carcinoma in heterogeneous tumors. Two different pathways were analysed, a linear pathway with seven parameters, and a nonlinear pathway with three parameters. In each pathway ductal carcinoma in situ (DCIS) is a progenitor of invasive carcinoma (IDC). In the linear pathway breast tumor progression is along increasing grades: DCIS 1-DCIS 2-DCIS 3-IDC 1-IDC 2-IDC 3. In the nonlinear pathway progression of DCIS and progression of IDC can proceed in parallel steps, and in addition, with transitions from each grade of DCIS to a corresponding grade of IDC. The biological pathways were interpreted mathematically as compartment models with transition rates between stages in an explicit series of coupled differential equations. Two methods were used to search for transition rates that could reproduce the observed co-occurrence frequencies, a limited empirical search and an extensive genetic algorithmic search. Neither search method, with either pathway, could find a combination of transition rates that would reproduce the set of observed co-occurrence frequencies. We conclude that neither the linear pathway, nor the nonlinear pathway considered here, is an adequate description of progression in heterogeneous breast tumors. This quantitative investigation lends support to previous evidence from histopathology and molecular biology that the grades of DCIS and IDC seen together in heterogeneous breast tumors may not be obligate steps in tumor progression.

Breast Neoplasms↗

A distributed simulation technique for multiple input multiple output systems.

Distributed computing concepts have been attempted in the realm of real-time process control for a long time. This started with the systolic arrays of processors and an enormous amount of research has been done in this field. This paper proposes a methodology by which a multiple input multiple output system representing a plant and defined in terms of connected blocks of transfer functions can be decomposed into a set of parallel simulation processes in a message passing environment viz. a network of work stations. The paper also analyzes the scope of optimization of the processing time associated with each task. The methodology includes online reconfiguration of the system.

Algorithms↗

The immune system as a neural network: a multi-epitope approach.

The term "neural network" has been applied to arrays of simple activation units linked by weighted connections. If the connections are modified according to a defined learning algorithm, such networks can be trained to store and retrieve patterned information. Memories are distributed throughout the network, allowing the network to recall complete patterns from incomplete input (pattern completion). The major biological application of neural network theory to date has been in the neurosciences, but the immune system may represent an alternative organ system in which to search for neural network architecture. Previous applications of parallel distributed processing to idiotype network theory have focused upon the recognition of individual epitopes. We argue here that this approach may be too restrictive, underestimating the power of neural network architecture. We propose that the network stores and retrieves large, complex patterns consisting of multiple epitopes separated in time and space. Such a network would be capable of perceiving an entire bacterium, and of storing the time course of a viral infection. While recognition of solitary epitopes occurs at the cellular level in this model, recognition of structures larger than the width of an antibody binding site takes place at the organ level, via network architecture integration of, i.e. individual epitope responses. The Oudin-Cazenave enigma, the sharing of idiotypic determinants by antibodies directed against distinct regions of the same antigen, suggests that some network level of integration of the individual clonal responses to large antigens does occur. The role of cytokines in prior neural network models of the immune system is unclear. We speculate that cytokines may influence the temperature of the network, such that changes in the cytokine milieu serve to "anneal" the network, allowing it to achieve the optimum steady-state in the shortest period of time.

Artificial Intelligence↗

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

We develop a new free-energy method, based on the combination of parallel tempering and metadynamics, and apply this method to the calculation of the free-energy landscape of the folding beta hairpin in explicit water. We show that the combined method greatly improves the performance of both parallel tempering and metadynamics. In particular, we are able to sample the high free-energy regions, which are not accessible with conventional parallel tempering. We use our results to calculate the difference in entropy and enthalpy between the folded and the unfolded state and to characterize the most populated configurations in the relevant free-energy basins.

Algorithms↗

Motion of a branched polymer chain in confinement: a Monte Carlo study.

The aim of the study was a theoretical investigation of the polymer molecules located between two parallel and impenetrable surfaces which were also attractive for polymer segments. The chains were constructed of identical segments and were restricted to knots of a simple cubic lattice. Since the chains were at good solvent conditions the only interactions between the segments of the chain were the excluded volume. The properties of the model chains were determined by means of Monte Carlo simulations with a sampling algorithm based on the chain's local changes of conformation. The differences and similarities in the structure for different adsorption regimes and the size of the slit were shown and discussed. It was observed that at certain conditions the polymer chain was adsorbed at one of the confining surfaces, and then after a certain period of time it detached from this surface and approached the opposite wall; this switch was repeated many times. The influence of the strength of the adsorption, the size of the slit, and the chain's length on the frequency of these jumps were determined. The mechanism of the chain's motion during the switch was also shown.

Journal Article↗

Directional bonding in compacted microcrystalline cellulose.

The mechanical properties of compacts of microcrystalline cellulose (MCC) and silicified microcrystalline cellulose (SMCC) were evaluated by tensile testing, diametric compression testing, and compression testing. For tensile and compression testing, cubic specimens were carefully machined from MCC and SMCC compacts, and the tensile and compression strengths were evaluated both normal and parallel to the compaction direction. The cubic tensile strengths were compared to values obtained from the diametric compression test. The results obtained using the diametric compression test suggested compacts of SMCC exhibit greater strength than those of MCC. In addition, the cubes machined from compacts of MCC and SMCC exhibited directional strength; the direction normal to the compaction direction display ed the greater tensile strength, and the parallel direction had greater compression strength. The diametric compression test afforded strength values with reduced spread compared to the values collected from the cubic tensile test, suggesting that the errors involved in collecting diametric compression test data of compacts are less than those for the cubic tensile test. Analysis of the cubes using X-ray diffraction (XRD) suggested that they display directional structural anisotropy, with the direction normal to the compaction direction being more crystalline than the parallel direction. However, it is not clear whether the difference in the directional strength is solely a consequence of the increased crystallinity or a culmination of crystallographic and mechanical keying effects.

Algorithms↗

Pharmacokinetic-pharmacogenetic modelling in the detection of polymorphisms in xenobiotic metabolism.

Study of the genetic control of xenobiotic metabolism is hindered in the areas of detecting new polymorphisms and estimating the frequency and enzyme activity of each phenotype. Using computer simulation we have looked at pharmacogenetic-pharmacokinetic models based on two alleles under Hardy-Weinberg equilibrium. The distributions of the area under the concentration-time curve (AUC) or urinary ratios were modelled and the effects of incomplete urine collections, sequential, parallel and non-linear pathways investigated. The statistical methods for the detection of bimodality in these distributions were explored. The drug/metabolite ratio, which has a good theoretical basis, was confirmed to be most sensitive and robust to changes in bioavailability, urinary excretion, hepatic blood flow and variation in non-polymorphic enzyme activity but not parallel, sequential or non-linear routes of metabolism. Graphical methods, while able to illustrate deviations from normality, were not specific in detecting bimodality and the hypothesis testing methods were found to be heavily dependent upon their assumptions.

Algorithms↗

The determination of the three-dimensional structure of barley serine proteinase inhibitor 2 by nuclear magnetic resonance, distance geometry and restrained molecular dynamics.

The solution structure of the 64 residue structured domain (residues 20-83) of barley serine proteinase inhibitor 2 (BSPI-2) is determined on the basis of 403 interproton distance, 34 phi backbone torsion angle and 26 hydrogen bonding restraints derived from n.m.r. measurements. A total of 11 converged structures were computed using a metric matrix distance geometry algorithm and refined by restrained molecular dynamics. The average rms difference between the final 11 structures and the mean structure obtained by averaging their coordinates is 1.4 +/- 0.2 A for the backbone atoms and 2.1 +/- 0.1 A for all atoms. The overall structure, which is almost identical to that found by X-ray crystallography, is disc shaped and consists of a central four component mixed parallel and antiparallel beta-sheet flanked by a 13 residue alpha-helix on one side and the reactive site loop on the other.

Edible Grain↗

Scanning scene tunnel for city traversing.

This paper proposes a visual representation named scene tunnel for capturing urban scenes along routes and visualizing them on the Internet. We scan scenes with multiple cameras or a fish-eye camera on a moving vehicle, which generates a real scene archive along streets that is more complete than previously proposed route panoramas. Using a translating spherical eye, properly set planes of scanning, and unique parallel-central projection, we explore the image acquisition of the scene tunnel from camera selection and alignment, slit calculation, scene scanning, to image integration. The scene tunnels cover high buildings, ground, and various viewing directions and have uniformed resolutions along the street. The sequentially organized scene tunnel benefits texture mapping onto the urban models. We analyze the shape characteristics in the scene tunnels for designing visualization algorithms. After combining this with a global panorama and forward image caps, the capped scene tunnels can provide continuous views directly for virtual or real navigation in a city. We render scene tunnel dynamically by view warping, fast transmission, and flexible interaction. The compact and continuous scene tunnel facilitates model construction, data streaming, and seamless route traversing on the Internet and mobile devices.

Algorithms↗

FACT--a framework for the functional interpretation of high-throughput experiments.

BACKGROUND: Interpreting the results of high-throughput experiments, such as those obtained from DNA-microarrays, is an often time-consuming task due to the high number of data-points that need to be analyzed in parallel. It is usually a matter of extensive testing and unknown beforehand, which of the possible approaches for the functional analysis will be the most informative. RESULTS: To address this problem, we have developed the Flexible Annotation and Correlation Tool (FACT). FACT allows for detection of important patterns in large data sets by simplifying the integration of heterogeneous data sources and the subsequent application of different algorithms for statistical evaluation or visualization of the annotated data. The system is constantly extended to include additional annotation data and comparison methods. CONCLUSION: FACT serves as a highly flexible framework for the explorative analysis of large genomic and proteomic result sets. The program can be used online; open source code and supplementary information are available at http://www.factweb.de.

Algorithms↗

Single-photon imaging at 20,000 frames/s.

A complete two-dimensional imaging system based on a silicon monolithic array of 60 single-photon counters is presented. The fabricated solid-state array is rugged and operates at low voltages. Detection efficiency is higher than 40% in the visible range, and cross talk among 50 microm pixels is lower than 10(-4). The complete system provides a maximum throughput of 20 kframes/s with truly parallel readout and nanosecond gating, thanks to the use of an integrated active quenching circuit for each pixel of the array. We report optical and electrical characterizations of the whole imaging system.

Algorithms↗

Empirical bayes microarray ANOVA and grouping cell lines by equal expression levels.

In the exploding field of gene expression techniques such as DNA microarrays, there are still few general probabilistic methods for analysis of variance. Linear models and ANOVA are heavily used tools in many other disciplines of scientific research. The usual F-statistic is unsatisfactory for microarray data, which explore many thousand genes in parallel, with few replicates. We present three potential one-way ANOVA statistics in a parametric statistical framework. The aim is to separate genes that are differently regulated across several treatment conditions from those with equal regulation. The statistics have different features and are evaluated using both real and simulated data. Our statistic B1 generally shows the best performance, and is extended for use in an algorithm that groups cell lines by equal expression levels for each gene. An extension is also outlined for more general ANOVA tests including several factors. The methods presented are implemented in the freely available statistical language R. They are available at http://www.math.uu.se/staff/pages/?uname=ingrid.

Journal Article↗

Advances in radiation therapy: conventional to 3D, to IMRT, to 4D, and beyond.

Modern advances in computers have fueled parallel advances in imaging technologies. The improvements in imaging have in turn allowed a higher level of complexity to be incorporated into radiotherapy treatment planning systems. As a result of these changes, the delivery of radiotherapy evolved from therapy designed based primarily on plain (two dimensional) x-ray images and hand calculations to three-dimensional x-ray based images incorporating increasingly complex computer algorithms. More recently, biologic variables based on differences between tumor metabolism, tumor antigens, and normal tissues have been incorporated into the treatment process. In addition, greater awareness of the challenges to the accuracy of the treatment planning process, such as problems with set-error and organ movement, have begun to be systematically addressed, ushering in an era of so-called Four-Dimensional Radiotherapy. This review article discusses how these advances have changed the way the most common neoplasms are treated now and will be treated in the near future.

Algorithms↗

Computerized body plethysmography: an algorithm for minimizing drift and hysteresis.

The use of linear regression for on-line data processing of airway resistance measurements in the body plethysmograph may be difficult. When airflow (V) is plotted against plethysmographic pressure (Pbox), the resulting loop exhibits hysteresis and may drift along the PBox axis. Although the slope of the V-PBox loop can be estimated visually, computer calculations of the slope are difficult if baseline drift is present. Taking the derivatives of V and PBox eliminates the effect of drift and reduces the loops to a series of essentially parallel lines from which the slope can be readily calculated using linear regression. The identical technique can be employed when mouth pressure is plotted against plethysmographic pressure, enabling on-line calculation of thoracic gas volume.

Airway Resistance↗

Determination of a high precision structure of a novel protein, Linum usitatissimum trypsin inhibitor (LUTI), using computer-aided assignment of NOESY cross-peaks.

The solution structure of a novel 69 residue proteinase inhibitor, Linum usitatissimum trypsin inhibitor (LUTI), was determined using a method based on computer aided assignment of nuclear Overhauser enhancement spectroscopy (NOESY) data. The approach applied uses the program NOAH/DYANA for automatic assignment of NOESY cross-peaks. Calculations were carried out using two unassigned NOESY peak lists and a set of determined dihedral angle restraints. In addition, hydrogen bonds involving amide protons were identified during calculations using geometrical criteria and values of HN temperature coefficients. Stereospecific assignment of beta-methylene protons was carried out using a standard procedure based on nuclear Overhauser enhancement intensities and 3J(alpha)(beta) coupling constants. Further stereospecific assignment of methylene protons and diastereotopic methyl groups were established upon structure-based method available in the program GLOMSA and chemical shift calculations. The applied algorithm allowed us to assign 1968 out of 2164 peaks (91%) derived from NOESY spectra recorded in H2O and 2H2O. The final experimental data input consisted of 1609 interproton distance restraints, 88 restraints for 44 hydrogen bonds, 63 torsion angle restraints and 32 stereospecifically assigned methylene proton pairs and methyl groups. The algorithm allowed the calculation of a high precision protein structure without the laborious manual assignment of NOESY cross-peaks. For the 20 best conformers selected out of 40 refined ones in the program CNS, the calculated average pairwise rmsd values for residues 3 to 69 were 0.38 A (backbone atoms) and 1.02 A (all heavy atoms). The three-dimensional LUTI structure consists of a mixed parallel and antiparallel beta-sheet, a single alpha-helix and shows the fold of the potato 1 family of proteinase inhibitors. Compared to known structures of the family, LUTI contains Arg and Trp residues at positions P6' and P8', respectively, instead of two Arg residues, involved in the proteinase binding loop stabilization. A consequence of the ArgTrp substitution at P8' is a slightly more compact conformation of the loop relative to the protein core.

Amino Acid Sequence↗

Advances in 3-dimensional radiation treatment planning systems: room-view display with real time interactivity.

PURPOSE: We describe our 3-dimensional (3-D) radiation treatment planning system for external photon and electron beam 3-D treatment planning which provides high performance computational speed and a real-time display which we have named "room-view" in which the simulated target volumes, critical structures, skin surfaces, radiation beams and/or dose surfaces can be viewed on the display monitor from any arbitrary viewing position. METHODS AND MATERIALS: We have implemented the 3-D planning system on a graphics superworkstation with parallel processing. Patient's anatomical features are extracted from contiguous computed tomography scan images and are displayed as wireloops or solid surfaces. Radiation beams are displayed as a set of diverging rays plus the polygons formed by the intersection of these rays with planes perpendicular to the beam axis. Controls are provided for each treatment machine motion function. Photon dose calculations are performed using an effective pathlength algorithm modified to accommodate 3-D off-center ratios. Electron dose calculations are performed using a 3-D pencil beam model. RESULTS: Dose distribution information can be displayed as 3-D dose surfaces, dose-volume histograms, or as isodoses superimposed on 2-D gray scale images of the patient's anatomy. Tumor-control-probabilities, normal-tissue-complication probabilities and a figure-of-merit score function are generated to aid in plan evaluation. A split-screen display provides a beam's-eye-view for beam positioning and design of patient shielding block apertures and a concurrent "room-view" display of the patient and beam icon for viewing multiple beam set-ups, beam positioning, and plan evaluation. Both views are simultaneously interactive. CONCLUSION: The development of an interactive 3-D radiation treatment planning system with a real-time room-view display has been accomplished. The concurrent real-time beam's-eye-view and room-view display significantly improves the efficacy of the 3-D planning process.

Computer Systems↗