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PubMed1996

Reduction of computational complexity in the butterfly search technique.

In the butterfly search technique, echoes from repeated firings of a transducer are resampled along a set of predetermined trajectories of constant velocities, called "butterfly lines," because of their intersection and crossing at a reference range. The slope of the trajectory on which the sampled signals satisfy a predetermined criterion appropriate for the type of signal in question, provides an estimate of the velocity of the target. The search for this trajectory is called "butterfly search," which can be carried out efficiently in a parallel processing scheme. The estimator can be based on the radio frequency (RF) A-lines, the envelopes, or the quadrature components. The butterfly search on quadrature components has shown outstanding noise immunity, even with relatively few successive scan lines, and was found to outperform all the common time domain and Doppler techniques in simulations and experiments with strong noise. It can be simply implemented using elementary digital signal processing hardware. However, it is possible to further improve upon its computational complexity to make the technique even simpler to implement, without any complex multipliers in the parallel channels. In this paper, we present some modifications that significantly reduce the computational complexity of butterfly search on quadrature components.

Algorithms↗
PubMed2003

The transtheoretical model applied to an oral self-care behavioral change: development and testing of instruments for stages of change and decisional balance.

PURPOSE: The Transtheoretical Model is a theory-based approach for conceptualizing behavioral change. Inherent in this model is the determination and use of appropriate interventions to assist clients in improving their health behaviors. In the Transtheoretical Model, behavioral change progresses through a series of stages (precontemplation, contemplation, preparation, action, and maintenance) where movement from stage to stage is dependent upon decisional balance (the pros and cons that influence the decision). The purpose of this study was to develop instruments to test the validity and reliability of two components of the Transtheoretical Model--stages of change and decisional balance--as they relate to a new application in oral self-care behavior. An additional purpose was to determine if there was an association between these two components that would be applicable to a specific oral self-care behavior. METHODS: A three-part questionnaire was developed consisting of 1) stages of change instrument (4 items), 2) decisional balance instrument (40 items), and 3) demographic and dental experience information (9 items). Regular interdental cleaning was chosen as a behavior representing a commitment to oral self-care. The study population consisted of 709 subjects aged 35 to 55 who were recruited from 17 dental practices. RESULTS: A 70% (n = 521) response rate was obtained. Based upon the stages of change portion of the questionnaire, nearly 60% (n = 309) of the subjects were in the maintenance stage, while 21% (n = 109) were in precontemplation, with the rest distributed among the other stages. Reliability of the instrument was established with Kappa scoring. The decisional balance instrument was subjected to factor analysis resulting in a final decisional balance instrument of 28 items. There was a statistically significant relationship between the two components of stages of change and decisional balance. CONCLUSIONS: Stages of change and decisional balance instruments were developed and shown to be valid and reliable. Based upon the oral self-care behavior defined in this study, these instruments can identify an individual's current behavior and assess readiness to change by analyzing the distribution of the pros and cons a person considers when making a behavioral change. Understanding a client's behavioral stage would enable the practitioner to select and provide appropriate interventions. Further research should focus upon development of stage-appropriate intervention strategies and techniques, in order to move individuals along the continuum of stages toward behavioral change. Additionally, research with parallel and diverse populations is indicated.

Adult↗
PubMedDate not supplied

Similarity searching in databases of three-dimensional molecules and macromolecules.

This paper discusses algorithmic techniques for measuring the degree of similarity between pairs of three-dimensional (3-D) chemical molecules represented by interatomic distance matrices. A comparison of four methods for the calculation of 3-D structural similarity suggests that the most effective one is a procedure that identifies pairs of atoms, one from each of the molecules that are being compared, that lie at the center of geometrically-related volumes of 3-D space. This atom mapping method enables the calculation of a wide range of types of intermolecular similarity coefficient, including measures that are based on physicochemical data. Massively-parallel implementations of the method are discussed, using the AMT Distributed Array Processor, that achieve a substantial increase in performance when compared with a sequential implementation on a UNIX workstation. Current work involves the use of angular information and the extension of the method to field-based similarity searching. Similarity searching in 3-D macromolecules is effected by the use of a maximal common subgraph (MCS) isomorphism algorithm with a novel, graph-based representation of the tertiary structures of proteins. This algorithm is being used to identify similarities between the 3-D structures of proteins in the Brookhaven Protein Data Bank; its use is exemplified by searches involving the NAD-binding fold motif.

Algorithms↗
PubMed2003

Cool walking: a new Markov chain Monte Carlo sampling method.

Effective relaxation processes for difficult systems like proteins or spin glasses require special simulation techniques that permit barrier crossing to ensure ergodic sampling. Numerous adaptations of the venerable Metropolis Monte Carlo (MMC) algorithm have been proposed to improve its sampling efficiency, including various hybrid Monte Carlo (HMC) schemes, and methods designed specifically for overcoming quasi-ergodicity problems such as Jump Walking (J-Walking), Smart Walking (S-Walking), Smart Darting, and Parallel Tempering. We present an alternative to these approaches that we call Cool Walking, or C-Walking. In C-Walking two Markov chains are propagated in tandem, one at a high (ergodic) temperature and the other at a low temperature. Nonlocal trial moves for the low temperature walker are generated by first sampling from the high-temperature distribution, then performing a statistical quenching process on the sampled configuration to generate a C-Walking jump move. C-Walking needs only one high-temperature walker, satisfies detailed balance, and offers the important practical advantage that the high and low-temperature walkers can be run in tandem with minimal degradation of sampling due to the presence of correlations. To make the C-Walking approach more suitable to real problems we decrease the required number of cooling steps by attempting to jump at intermediate temperatures during cooling. We further reduce the number of cooling steps by utilizing "windows" of states when jumping, which improves acceptance ratios and lowers the average number of cooling steps. We present C-Walking results with comparisons to J-Walking, S-Walking, Smart Darting, and Parallel Tempering on a one-dimensional rugged potential energy surface in which the exact normalized probability distribution is known. C-Walking shows superior sampling as judged by two ergodic measures.

Journal Article↗
PubMed1985

Cortical ultrastructure of Coleps bicuspis Noland, 1925 and the phylogeny of the class Prostomatea (Ciliophora).

The ultrastructure of Coleps bicuspis Noland, 1925 is described. The ciliate is a typical prostomate: the somatic kinetid is a monokinetid with a postciliary ribbon at triple 9, a kinetodesmal fibril originating near triplets 5, 6, 7 and an apparently radial transverse ribbon at triplet 4. The oral area is circular and has three brosse kineties associated with it. The brosse kineties are composed of dikinetids whose anterior kinetosome bears a tangential transverse ribbon and whose posterior kinetosome bears the fibrillar associates typical of a somatic monokinetid. The oral dikinetids are oriented parallel to the circumference of the oral cavity, which is surrounded by oral papillae and oral ridges. Pairs of nematodesmata, originating from oral dikinetid kinetosomes, are typically triangular in transection. A phylogeny of rhabdophoran ciliates is presented using the mixed parsimony algorithm and is discussed with reference to the systematic revisions of the phylum Ciliophora.

Animals↗
PubMed2000

SPLASH: structural pattern localization analysis by sequential histograms.

MOTIVATION: The discovery of sparse amino acid patterns that match repeatedly in a set of protein sequences is an important problem in computational biology. Statistically significant patterns, that is patterns that occur more frequently than expected, may identify regions that have been preserved by evolution and which may therefore play a key functional or structural role. Sparseness can be important because a handful of non-contiguous residues may play a key role, while others, in between, may be changed without significant loss of function or structure. Similar arguments may be applied to conserved DNA patterns. Available sparse pattern discovery algorithms are either inefficient or impose limitations on the type of patterns that can be discovered. RESULTS: This paper introduces a deterministic pattern discovery algorithm, called Splash, which can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences. Sparse patterns of any length, up to the size of the input sequence, can be discovered without significant loss in performances. Splash is extremely efficient and embarrassingly parallel by nature. Large databases, such as a complete genome or the non-redundant SWISS-PROT database can be processed in a few hours on a typical workstation. Alternatively, a protein family or superfamily, with low overall homology, can be analyzed to discover common functional or structural signatures. Some examples of biologically interesting motifs discovered by Splash are reported for the histone I and for the G-Protein Coupled Receptor families. Due to its efficiency, Splash can be used to systematically and exhaustively identify conserved regions in protein family sets. These can then be used to build accurate and sensitive PSSM or HMM models for sequence analysis. AVAILABILITY: Splash is available to non-commercial research centers upon request, conditional on the signing of a test field agreement. CONTACT: acal@us.ibm.com, Splash main page http://www.research.ibm.com/splash

Algorithms↗
PubMed2000

Algorithms for estimating blood velocities using ultrasound.

Ultrasound has been used intensively for the last 15 years for studying the hemodynamics of the human body. Systems for determining both the velocity distribution at one point of interest (spectral systems) and for displaying a map of velocity in real time have been constructed. A number of schemes have been developed for performing the estimation, and the various approaches are described. The current systems only display the velocity along the ultrasound beam direction and a velocity transverse to the beam is not detected. This is a major problem in these systems, since most blood vessels are parallel to the skin surface. Angling the transducer will often disturb the flow, and new techniques for finding transverse velocities are needed. The various approaches for determining transverse velocities will be explained. This includes techniques using two-dimensional correlation (speckle tracking), multiple beams, and the new transverse modulation technique. The different advantages and disadvantages of the approaches are explained.

Algorithms↗
PubMed1993

Automated tuning of a closed-loop hand grasp neuroprosthesis.

An automated tuning algorithm was developed to reduce the time and skill required to tune a closed-loop hand grasp neuroprosthesis. The time reduction results from simultaneous tuning of four gain parameters controlling the dynamic response of the system, and from automation of the calculation and decision processes. The new tuning method is therefore an automated parallel tuning method, replacing a manual sequential method in which only one parameter at a time was tuned. RMS error between the step input and the grasp output is minimized, with absence of oscillation as a constraint. The difference between the system's RMS ramp tracking errors for the two tuning methods was less than 1% of the ramp size regardless of the initial values of the parameters, implying that the tuning methods were equivalent. However, the parallel tuning method was faster and required fewer trials than the sequential method. The capability of the closed-loop system to regulate grasp output in the presence of disturbances was compared with the capability without feedback. Patients were instructed to either grasp an object at a certain force level or to match a certain grasp opening. They would then lock their command at a fixed value, and either remain immobile to test time dependence or pronate and supinate their forearm to test postural disturbances. With closed-loop control, the grasp output was better regulated in the presence of disturbances, with an average output variance 60% lower than without feedback control.

Algorithms↗
PubMed1998

Reduced test time by early identification of patients requiring atropine during dobutamine stress echocardiography.

In a randomized, controlled clinical trial, we evaluated the ability of an algorithm to identify, before peak stress, patients who will ultimately require atropine during dobutamine stress echocardiography. The effects of early atropine administration on test duration, atropine dose, dobutamine dose, and heart rate response also were studied. Compared with conventional atropine administration at peak dobutamine infusion, early atropine administration reduced test duration 8% (1.1 minutes, p = 0.02) and total dobutamine use 11% (0.41 mg/kg, p = 0.02) but required 90% more atropine (0.36 mg, p < 0.001). Conventional atropine administration resulted in a late, rapid rise in both heart rate and rate-pressure product. However, the heart rate and rate-pressure product curves for patients receiving early atropine paralleled those seen in patients not requiring atropine during dobutamine stress echocardiography. In conclusion, early atropine administration provides a more balanced stress and reduces test duration, thus decreasing total exposure to dobutamine and potentially increasing test efficiency.

Algorithms↗
PubMed2000

Activation linearity and parallelism of the superficial quadriceps across the isometric intensity spectrum.

The purpose of this study was to assess neuromuscular activation of the three superficial portions of the quadriceps femoris muscles during linearly increasing isometric contraction intensities. Thirty healthy volunteers were assessed for isometric electromyographic (EMG) activity of the vastus medialis (VM), vastus lateralis (VL), and rectus femoris (RF) muscles with the knee at 60 degrees of flexion. For 5 s, subjects performed isometric contractions equivalent to 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, and 90% of the average of three maximal voluntary contractions (MVC), in random order. Full-wave rectified and integrated EMG signals over the middle 3 s of each contraction were expressed as a percentage of the activity recorded during the three averaged MVCs. One sample t-tests and 95% confidence intervals were calculated at each relative torque level. A two-factor analysis of variance (muscle by intensity) with repeated measures was performed to evaluate parallel activation across the intensity levels. Activation linearity was assessed via regression analysis for each muscle. VM activation was shown to be significantly lower than expected at 20-70% MVC. VL and RF activations were significantly higher than expected at 10% MVC, and RF EMG was less than expected at 40-70% MVC. EMG of VM was shown to increase significantly more than VL and RF from 80% to 90% MVC. Significant linear and quadratic relations were also demonstrated for all three muscles. Parallel activation of the superficial quadriceps muscles occurred from low to moderate intensities, whereas convergence was noted at near maximal intensities.

Adult↗
PubMed2002

A blood vessel exposed to ultrasound: a mathematical simulation of the temperature field.

In this article we present a mathematical simulation of the temperature field in and around a blood vessel when it is sonicated by a focused ultrasound beam. A simplified geometry is considered: a cylindrical blood vessel is embedded in tissue parallel to a flat skin surface. The ultrasound transducer is placed on the skin above the blood vessel, perpendicular to the skin surface. The 3D geometry of the problem is simplified by transformation, which maps the domain into a parallelepiped. A computational algorithm and computer program were developed. The simulation provides the conditions for successful occlusion of a blood vessel and demonstrates the significant role of the blood flow rate on the temperature difference between the vessel wall and the surrounding tissue. Comparing the predictions with published experimental data tested the validity of the method.

Blood Flow Velocity↗
PubMed2001

A surface-matching technique for robot-assisted registration.

Successful implementation of robot-assisted surgery (RAS) requires coherent integration of spatial image data with sensing and actuating devices, each having its own coordinate system. Hence, accurate estimation of the geometric relationships between relevant reference frames, known as registration, is a crucial procedure in all RAS applications. The purpose of this paper is to present a new registration scheme, along with the results of an experimental evaluation of a robot-assisted registration method for RAS applications in orthopedics. The accuracy of the proposed registration is appropriate for specified orthopedic surgical applications such as Total Knee Replacement. The registration method is based on a surface-matching algorithm that does not require marker implants, thereby reducing surgical invasiveness. Points on the bone surface are sampled by the robot, which in turn directs the surgical tool. This technique eliminates additional coordinate transformations to an external device (such as a digitizer), resulting in increased surgical accuracy. The registration technique was tested on an RSPR six-degrees-of-freedom parallel robot specifically designed for medical applications. A six-axis force sensor attached to the robot's moving platform enables fast and accurate acquisition of positions and surface normal directions at sampled points. Sampling with a robot probe was shown to be accurate, fast, and easy to perform. The whole procedure takes about 2 min, with the robot performing most of the registration procedures, leaving the surgeon's hands free. Robotic registration was shown to provide a flawless link between preoperative planning and robotic assistance during surgery.

Algorithms↗
PubMed2002

An iterative method for viscoelastic modeling of prosthetic feet.

Prosthetic foot designs are growing in complexity, but a few material and structural properties, including stiffness and viscoelasticity, remain critical to foot function. Consistent identification of these critical properties would aid prosthesis prescription. This investigation evaluates a new technique to model prosthetic feet as a combination of springs and dampers, and therefore characterize a foot's stiffness and viscoelasticity by means of spring and damper coefficients. A quasi-Newton iterative algorithm was developed to determine model coefficients for 9 prosthetic feet based on compressive creep, stress-relaxation, and constant strain rate tests. A broad range of current energy-storing feet including designs from Otto Bock, Seattle, Kingsley, and Ohio Willow Wood were very accurately modeled with the iterative technique. Feet without a solid ankle from Flex and College Park were the least accurately modeled. The Flex foot, tested without a cover, had a considerably lower damping coefficient. Damper coefficients were similar for most all other feet, suggesting similar material properties of the foam cover. Stiffness varied and generally agreed with published data. The ability of the model to produce two separate parallel spring stiffness constants might provide insight into foot structure. The model represents a means to objectively quantify material properties for a range of solid ankle dynamic elastic response prosthetic feet, but may be limited in its characterization of other foot varieties.

Algorithms↗
PubMed1997

Implicit representation in genetic algorithms using redundancy.

A new representation combining redundancy and implicit fitness constraints is introduced that performs better than a simple genetic algorithm (GA) and a structured GA in experiments. The implicit redundant representation (IRR) consists of a string that is over-specified, allowing for sections of the string to remain inactive during function evaluation. The representation does not require the user to prespecify the number of parameters to evaluate or the location of these parameters within the string. This information is obtained implicitly by the fitness function during the GA operations. The good performance of the IRR can be attributed to several factors: less disruption of existing fit members due to the increased probability of crossovers and mutation affecting only redundant material; discovery of fit members through the conversion of redundant material into essential information; and the ability to enlarge or reduce the search space dynamically by varying the number of variables evaluated by the fitness function. The IRR GA provides a more biologically parallel representation that maintains a diverse population throughout the evolution process. In addition, the IRR provides the necessary flexibility to represent unstructured problem domains that do not have the explicit constraints required by fixed representations.

Algorithms↗
PubMed2002

Patchy distribution fields: sampling distance unit of a zigzag survey and reconstruction adequacy.

A mathematical model was used to examine the effects of choosing various units of sampling distance of a zigzag survey on the adequacy of reconstructing patchy distribution fields. The model simulates fish or plankton patches (or gaps) of different shapes and spatial orientations, and an acoustic survey by zigzag or parallel transects along which a unit of sampling distance is set. Adequacy of the reconstructed fields to those originally generated is evaluated by calculating their correlations (r). A priori information on the autocorrelation radii for the field in the directions of the survey (Rs) and perpendicular direction (Rp) allows optimisation of the survey design and the algorithm of data analysis. A field can be reconstructed properly (r2 > 0.70) if the distance between transects D < (1.0-1.5)Rs and the unit of sampling distance d < (1.0-1.5)Rp. A posteriori determination of patch orientation allows reconstruction of the best field attainable on the basis of the survey data. In cases of field movement, if the dimension of patches in the direction of movement exceeds that of a surveyed area, a survey in the opposite direction gives best results; in contrast, if the dimension of moving patches is smaller than that of a surveyed area, it is reasonable to carry out a survey in the same direction. The criterion remains valid when a survey is carried out by zigzag transects and a unit of sampling distance is set along them. The results obtained indicate that, for a fixed transect spacing and a given number of sampling points on each full transect, zigzag pattern allows less adequate reconstruction of an original distribution field (in cases of both immovable and movable fields) than corresponding parallel pattern.

Animals↗
PubMed1995

Application of high-performance computing to numerical simulation of human movement.

We have examined the feasibility of using massively-parallel and vector-processing supercomputers to solve large-scale optimization problems for human movement. Specifically, we compared the computational expense of determining the optimal controls for the single support phase of gait using a conventional serial machine (SGI Iris 4D25), a MIMD parallel machine (Intel iPSC/860), and a parallel-vector-processing machine (Cray Y-MP 8/864). With the human body modeled as a 14 degree-of-freedom linkage actuated by 46 musculotendinous units, computation of the optimal controls for gait could take up to 3 months of CPU time on the Iris. Both the Cray and the Intel are able to reduce this time to practical levels. The optimal solution for gait can be found with about 77 hours of CPU on the Cray and with about 88 hours of CPU on the Intel. Although the overall speeds of the Cray and the Intel were found to be similar, the unique capabilities of each machine are better suited to different portions of the computational algorithm used. The Intel was best suited to computing the derivatives of the performance criterion and the constraints whereas the Cray was best suited to parameter optimization of the controls. These results suggest that the ideal computer architecture for solving very large-scale optimal control problems is a hybrid system in which a vector-processing machine is integrated into the communication network of a MIMD parallel machine.

Computer Systems↗
PubMed2002

A large scale molecular dynamics simulation code using the fast multipole algorithm (FMD): performance and application.

We present the performance of the fast classical molecular dynamics (MD) code, fast molecular dynamics (FMD), designed for efficient, object-oriented, and scalable large scale simulations, and summarize its application to a liquid crystalline cluster. FMD uses an implementation of the three-dimensional fast multipole method, developed in our group. The fast multipole method offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus, enabling more realistic simulations of large molecular systems. Performance testing was carried out on IBM SP2, SGI Origin 2000, and CRAY T3E massively parallel systems using the MPI massage passing library. The electrostatic forces were tested on models of up to 100,000 randomly placed charges, and on protein and liquid crystalline molecular systems of over 99,000 atoms. Tests on the stability of the method are presented, along with comparisons with direct calculations, the NAMD2 code, and the physical multipole-based cell-multipole method.

Algorithms↗
PubMed1987

Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase.

The tertiary structure of the alpha-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the alpha/beta-class of supersecondary structures. The two-domain structure of the alpha-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a beta-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the alpha-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the beta-sheet eliminated all but one structure. The native structure is predicted to have a parallel beta-sheet flanked on both sides by alpha-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for beta 2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.

Amino Acid Sequence↗