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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↗
PubMed2006

Generalized encoding through the use of selective excitation in accelerated parallel MRI.

Selective RF excitation is employed in magnetic resonance imaging (MRI) to achieve a variety of effects, such as slice selection. More elaborate transverse magnetization patterns can be realized via tailored RF excitation pulses, useful for example to image any specific region geometry within the field of view, or, to acquire non-Fourier encoded samples of the underlying magnetization distribution. In this manuscript, we review prior work on the combination of selective RF excitation with parallel MRI acquisition techniques. This combination can be used both to advantageously manipulate the numerical conditioning of the reconstruction problem, as well as to compact the information content of the acquired data so as to improve the achievable acceleration rate. With the latter application it is possible to also consider the acceleration provided by parallel imaging alone as a compaction of information content, which in certain cases can be used to reduce the length of the selective excitations. The main contribution of this review is to show how the combination of selective excitation with parallel imaging provides the latter an added flexibility that can be used to either enhance image quality, increase imaging speed, or both.

Algorithms↗
PubMed2004

Automatic domain decomposition of proteins by a Gaussian Network Model.

Proteins are often comprised of domains of apparently independent folding units. These domains can be defined in various ways, but one useful definition divides the protein into substructures that seem to move more or less independently. The same methods that allow fairly accurate calculation of motion can be used to help classify these substructures. We show how the Gaussian Network Model (GNM), commonly used for determining motion, can also be adapted to automatically classify domains in proteins. Parallels between this physical network model and graph theory implementation are apparent. The method is applied to a nonredundant set of 55 proteins, and the results are compared to the visual assignments by crystallographers. Apart from decomposing proteins into structural domains, the algorithm can generally be applied to any large macromolecular system to decompose it into motionally decoupled sub-systems.

Algorithms↗
PubMed2006

Motion compensation in digital subtraction angiography using graphics hardware.

An inherent disadvantage of digital subtraction angiography (DSA) is its sensitivity to patient motion which causes artifacts in the subtraction images. These artifacts could often reduce the diagnostic value of this technique. Automated, fast and accurate motion compensation is therefore required. To cope with this requirement, we first examine a method explicitly designed to detect local motions in DSA. Then, we implement a motion compensation algorithm by means of block matching on modern graphics hardware. Both methods search for maximal local similarity by evaluating a histogram-based measure. In this context, we are the first who have mapped an optimizing search strategy on graphics hardware while paralleling block matching. Moreover, we provide an innovative method for creating histograms on graphics hardware with vertex texturing and frame buffer blending. It turns out that both methods can effectively correct the artifacts in most case, as the hardware implementation of block matching performs much faster: the displacements of two 1024 x 1024 images can be calculated at 3 frames/s with integer precision or 2 frames/s with sub-pixel precision. Preliminary clinical evaluation indicates that the computation with integer precision could already be sufficient.

Angiography↗
PubMed2004

Three-dimensional reconstruction of biological objects' internal structure heterogeneity from the set of ultrasonic tomograms.

The paper presents the method of the three-dimensional reconstruction of biological objects' internal structure heterogeneity based on the ultrasonic examination of a woman's breast biopsy phantom. The phantom is made of quasi-homogeneous dense gel in which drops of lesions, characterized by fixed sizes and two different acoustic impedances, were dipped at random. For the purpose of this research a special measurement setup was elaborated, enabling a non-invasive in vitro imaging of biological objects' internal structure in cross-sections for fixed levels, by means of ultrasound transmission tomography (UTT) using the parallel-ray projection geometry of scanning. The two-dimensional images of the local values of ultrasonic wave's propagation velocity in the phantom's internal structure (ultrasonic tomograms) were reconstructed for fixed levels (by using the convolution and back-projection algorithm) from the measurements of average values of ultrasonic signals' runtime propagated from many directions around the object dipped in water. Analyzing the values of particular pixels and using an appropriate image processing technique, in effect the three-dimensional image of heterogeneity boundaries in the examined phantom's internal structure was computer-reconstructed. The obtained results are compatible with the specification provided by the phantom's producer in terms of sizes and acoustic parameters of lesions, which can simulate pathological changes and of the gel imitating the healthy tissue. It means that the method presented, after an appropriate modification and development of the measurement setup with an aim to accelerate the object scanning process and thus provide an opportunity for non-invasive in vivo examinations, could be applied for detecting and diagnosing tumors in women's breasts.

Breast Neoplasms↗
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↗
PubMed2006

Mass spectrometric identification of proteins in complex post-genomic projects. Soluble proteins of the metabolically versatile, denitrifying 'Aromatoleum' sp. strain EbN1.

The rapidly developing proteomics technologies help to advance the global understanding of physiological and cellular processes. The lifestyle of a study organism determines the type and complexity of a given proteomic project. The complexity of this study is characterized by a broad collection of pathway-specific subproteomes, reflecting the metabolic versatility as well as the regulatory potential of the aromatic-degrading, denitrifying bacterium 'Aromatoleum' sp. strain EbN1. Differences in protein profiles were determined using a gel-based approach. Protein identification was based on a progressive application of MALDI-TOF-MS, MALDI-TOF-MS/MS and LC-ESI-MS/MS. This progression was result-driven and automated by software control. The identification rate was increased by the assembly of a project-specific list of background signals that was used for internal calibration of the MS spectra, and by the combination of two search engines using a dedicated MetaScoring algorithm. In total, intelligent bioinformatics could increase the identification yield from 53 to 70% of the analyzed 5,050 gel spots; a total of 556 different proteins were identified. MS identification was highly reproducible: most proteins were identified more than twice from parallel 2DE gels with an average sequence coverage of >50% and rather restrictive score thresholds (Mascot >or=95, ProFound >or=2.2, MetaScore >or=97). The MS technologies and bioinformatics tools that were implemented and integrated to handle this complex proteomic project are presented. In addition, we describe the basic principles and current developments of the applied technologies and provide an overview over the current state of microbial proteome research.

Amino Acid Sequence↗
PubMed2003

Scattering matrices for large ice crystal particles.

The problem of light scattering by ice crystal particles whose sizes are essentially larger than the incident wavelength is divided into two parts. First, the scattered field is represented as a set of plane-parallel outgoing beams in the near zone of the particle. Then, in the far zone the scattered field is represented as a result of both diffraction and interference of these beams within the framework of physical optics. A proper ray-tracing algorithm for calculation of the amplitude (Jones) scattering matrix is developed and applied. For large particles, a number of reduced Mueller matrices are introduced and discussed, since the pure Mueller matrix obtained from the Jones matrix becomes a rather cumbersome and quickly oscillating value. Backscattering by hexagonal ice crystals, including polarization properties, is considered in detail.

Journal Article↗
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↗
PubMed2005

Using parallel evolutionary development for a biologically-inspired computer vision system for mobile robots.

We describe a new approach to attacking the problem of robust computer vision for mobile robots. The overall strategy is to mimic the biological evolution of animal vision systems. Our basic imaging sensor is based upon the eye of the common house fly, Musca domestica. The computational algorithms are a mix of traditional image processing, subspace techniques, and multilayer neural networks.

Algorithms↗
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↗