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Modulation of muscle and pulmonary O2 uptakes by circulatory dynamics during exercise.

The effect of cardiovascular adjustments on the coupling of cellular to pulmonary gas exchange during unsteady states of exercise remains controversial. Computer simulations were performed to assess these influences on O2 delivery and pulmonary O2 uptake (pVO2). Algorithms were developed representing muscle and "rest-of-body" compartments, connected in parallel by arterial and venous circulations to a pump-and-lungs compartment. Exercise-induced increases in VO2 and cardiac output went to the muscle compartment. Model parameters [e.g., time constants for blood flow and muscle O2 uptake (mVO2)] could be varied independently. Simulation results demonstrated that 1) the rise in pVO2 during exercise contains three phases; 2) the contribution of changes in venous O2 stores to pVO2 kinetics and the O2 deficit occur almost entirely in phase 1; 3) under a wide variety of manipulations, the kinetics of pVO2 in phase 2 were within a couple of seconds of that assigned to mVO2 (i.e., there is not an obligatory slowing of VO2 kinetics at the lungs relative to those at the muscles; 4) by use of available estimates of blood flow adjustment, O2 delivery would not limit mVO2 after exercise onset; and 5) blood flow could limit O2 delivery in recovery, if blood flow returned to base-line levels at rates similar to those during the on-transient phase.

Cardiac Output↗

PepTool and GeneTool: platform-independent tools for biological sequence analysis.

Although we are unable to discuss all of the functionality available in PepTool and GeneTool, it should be evident from this brief review that both packages offer a great deal in terms of functionality and ease-of-use. Furthermore, a number of useful innovations including platform-independent GUI design, networked parallelism, direct internet connectivity, database compression, and a variety of enhanced or improved algorithms should make these two programs particularly useful in the rapidly changing world of biological sequence analysis. More complete descriptions of the programs, algorithms and operation of PepTool and GeneTool are available on the BioTools web site (www.biotools.com), in the associated program user manuals and in the on-line Help pages.

Amino Acid Sequence↗

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors.

MOTIVATION: Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith-Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced sensitivity or very expensive hardware. RESULTS: A fast implementation of the Smith-Waterman sequence-alignment algorithm using Single-Instruction, Multiple-Data (SIMD) technology is presented. This implementation is based on the MultiMedia eXtensions (MMX) and Streaming SIMD Extensions (SSE) technology that is embedded in Intel's latest microprocessors. Similar technology exists also in other modern microprocessors. Six-fold speed-up relative to the fastest previously known Smith-Waterman implementation on the same hardware was achieved by an optimized 8-way parallel processing approach. A speed of more than 150 million cell updates per second was obtained on a single Intel Pentium III 500 MHz microprocessor. This is probably the fastest implementation of this algorithm on a single general-purpose microprocessor described to date.

Algorithms↗

Apparent cerebral cytochrome aa3 reduction during cardiopulmonary bypass in hypoxaemic children with congenital heart disease. A critical analysis of in vivo near-infrared spectrophotometric data.

The purpose of this analysis was critically to examine the changes of cerebral cytochrome oxidase as detected by near-infrared spectrophotometry (NIRS) during induction of cardiopulmonary bypass (CPB) in fourteen children undergoing open heart surgery. Five children were hypoxaemic (arterial oxygen saturation 49%-84%) before the switch to CPB and nine children were not. In the hypoxaemic children, the total cerebral hemoglobin concentration [tHb] decreased rapidly and markedly, reaching a plateau after 2 min. Surprisingly, cytochrome aa3 concentration in its oxygenated form [CytO2] decreased in parallel while the cerebral haemoglobin oxygenation index [HbO2]-[Hb] increased gradually. In the eight normoxaemic children, changes in the NIRS signals were insignificant. When a standard NIRS algorithm was used, the magnitude of the change in [CytO2] was closely associated with the magnitude of the change in [tHb] (p < 0.0001), the time courses of the [CytO2] and [tHb] signals were parallel in 11 of the 14 children and the error of fit in the NIRS multicomponent analysis increased 10- to 100-fold over system noise. A new NIRS algorithm, using wavelength specific optical pathlengths, did not improve the error of fit but produced smaller estimates of [CytO2] changes, which were unrelated to the [tHb] changes. In our opinion the interesting possibility of monitoring cytochrome oxidation by NIRS requires further validation.

Algorithms↗

Edge encoding mechanisms in the parallel L4 neuron array of the fly (Musca domestica).

The current model of fly's cartridge termed Olson's Algorithm employs seven photoreceptors (R1-R6, Rref) to encode edge orientation. The models provide a sinusoidal output for an edge rotated about the reference photoreceptor. Although the model is powerful in providing insight into a fly's visual apparatus, it has several shortcomings. The model: does not respond to horizontal edges, does not provide Gaussian overlapped weighting of the photoreceptors which provides hyperacuity capability, and does not provide for a unique encoding of edge information. We are currently working on modifications to the model to remedy these issues. These issues must be resolved prior to pursuing object segmentation, tracking, and identification. In this paper we will investigate enhancements to the model and what they provide in solving some of the issues.

Algorithms↗

Glycaemic control in type 1 diabetic patients using optimised insulin aspart or human insulin in a randomised multinational study.

Insulin aspart (IAsp), is a rapid-acting analogue of human insulin (HI), for use in the meal related treatment of diabetes mellitus. The degree of glycaemic control achieved by IAsp in comparison with HI after algorithm-driven dose optimisation was tested over 3 months. The prospective, multicentre, randomised, open-label study with parallel groups was performed in 48 centres in 11 countries and included 423 basal-bolus treated patients with Type 1 diabetes. Main outcome measures were blood glucose control assessed by HbA1c, nine-point self-monitored blood glucose profiles, insulin dose, quality of life, hypoglycaemia and adverse events. An algorithm-driven increase occurred in the dose and number of daily injections of basal insulin, particularly in the IAsp group. After 12 weeks of treatment, HbA1c was significantly lower in IAsp compared to HI treated subjects by 0.17 (95% CI 0.30-0.04) (P<0.05). Comparison of the blood glucose profiles showed lower blood glucose levels with IAsp after breakfast (mean 8.4 vs 10.1 mmol/l; P<0.0001) and dinner (8.2 vs 9.3 mmol/l; P<0.01). There were no differences between treatments in the incidence of hypoglycaemic episodes or in the adverse event profiles. The WHO Diabetes Treatment Satisfaction Questionnaire score for perceived hyperglycaemia was lower with Iasp (P=0.005), and patients found the insulin aspart treatment more flexible (P=0.022). The current study underlines the need for optimising the basal insulin regimen in order to take full advantage of the pharmacodynamics of IAsp.

Adult↗

Use of transputers for real time dose calculation and presentation for three-dimensional radiation treatment planning.

PURPOSE: Real-time 3-dimensional dose calculation will allow display of isodose contours and other metrics for a planner to assess plan effectiveness during plan development, facilitating optimization. METHODS AND MATERIALS: Parallel processing provides an effective means to calculate 3-dimensional dose distribution in real-time while plan parameters are being chosen and adjusted. An array of 20 transputers and a high performance graphics workstation have demonstrated the feasibility of real-time 3-dimensional beam parameter specification, dose calculation, and dose-distribution presentation for evaluation. A mesh connected set of processors using surface processors to generate and terminate rays, and ray processors to calculate ray attenuation and dose distribution has been developed to efficiently utilize large numbers of processors and provide good load sharing, even for small beams that intersect only a small part of the volume. RESULTS: Our feasibility study has calculated dose distribution by the Effective Path Length method in about one second per beam for a treatment volume of 56,400 voxels. We expect to reduce the total time for computation, communication, and display, with even larger volumes, to less than one second. The number of processors can easily be increased for larger treatment volumes or more accurate and computation-intensive dose-calculation algorithms. Transputers provide an elegant and economical method for harnessing up to hundreds of powerful general-purpose processors for computational tasks including dose calculation and isodose contour generation. The same distributed-memory parallel-processing configuration is also suitable for calculation of isodose contours and dose-volume histograms for plan evaluation, automatic calculation of apertures and filters as beam parameters are manipulated, and more accurate dose calculation algorithms that incorporate the effects of scatter. CONCLUSION: Parallel processors can efficiently provide real-time calculation of the information necessary to evaluate treatment plans as they are developed allowing the planner to optimize the plan based on dose distribution and its effects on tumor control and complications.

Humans↗

ECG recording by a microdot thermal printer.

Recently high quality ECG records have been obtained by means of microdot thermal printers, because of their numerous advantages. Usually they contain a shift register in the thermal head and the fast control of the dot locations to be heated is an important software problem. We implemented the TLP 480Z-N Gotemba thermal printer (made in Japan) in our ECG instruments, and elaborated two algorithms for lengthwise and crosswise printing on the paper. They use 'black and white' strips loaded into the shift register by 1-byte parallel data organization. The lengthwise mode can operate in real time, while the crosswise one is intended for memorized signals.

Algorithms↗

Speckle tracking for multi-dimensional flow estimation.

Speckle tracking methods overcome the major limitations of current Doppler methods for flow imaging and quantification: angle dependence and aliasing. In this paper, we review the development of speckle tracking, with particular attention to the advantages and limitations of two-dimensional algorithms that use a single transducer aperture. Ensemble tracking, a recent speckle tracking method based upon parallel receive processing, is described. Experimental results with ensemble tracking indicate the ability to measure laminar flow in a phantom at a beam-vessel angle of 60 degrees, which had not been possible with previous 2D speckle tracking methods. Finally, important areas for future research in speckle tracking are briefly summarized.

Algorithms↗

Detection of jumps in single-channel data containing subconductance levels.

Detection algorithms are widely used for the analysis of single-channel data because they remove the background noise from the measured current signal and reconstruct the noise-free time series. Standard detection algorithms assume channels switching only between zero and full conductance. Many types of channels, however, show subconductance levels. A new detection algorithm for data containing sublevels, the so-called sublevel Hinkley-detector (SHD), calculates several test values in parallel, one for each possible jump. The velocity of increase has a maximum for the correct jump. This feature is used to detect the jump and to diagnose the new level of current. Because patch-clamp data are always filtered by an antialiasing low-pass filter before sampling, the algorithm is supplemented by a special diagnosis phase accounting for the distortion of the originally rectangular jumps. Along with the reconstructed (noise-free) time series the SHD also gives a matrix of the transition counts between the levels. This matrix is a useful statistical tool for the decision whether the observed channel(s) have in fact a subconductance conformation or if there are simply several channels of different conductivity contained within the patch.

Algorithms↗

Isotropic connections generate functional asymmetrical behavior in visual cortical cells.

1. We study the relationship between structure and function in inhibitory long-range interactions in visual cortex. The sharpening of orientation tuning with "cross-orientation inhibition" is used as an example to discuss anisotropies that are generated by long-range connections. 2. In this study, as opposed to the detailed cortex model described in a previous report, a model of the cortical orientation column structure is proposed in which cortical cells are described only by their orientation preference. 3. We present results using different geometric arrangements of orientation columns. In the simplest case, straight parallel orientation columns were used. We also utilized more realistic, curved columns generated by a simple algorithm. The results were confirmed by the study of a patch of real column structure, determined experimentally by Swindale et al. 4. A given cell receives functionally defined cross-orientation inhibition if the cell receives inhibitory input that is strongest along its nonpreferred orientation. On the other hand, a cell is said to receive structurally defined cross-orientation inhibition if the inhibition arises from source cells with an orientation preference orthogonal to that of the target cell. Even though those definitions seem to describe similar situations, we show that, in the general case, structurally defined cross-orientation inhibition does not efficiently sharpen orientation selectivity. In particular, for straight and parallel columns, structurally defined cross-orientation inhibition results in unequal amounts of inhibition for whole cell populations with different preferred orientations. 5. In more realistic column structures, we studied the question of whether structural cross-orientation inhibition could be implemented in a more efficient way. However, for the majority of cells, it is demonstrated that their nonpreferred stimulus will not preferably excite "cross-oriented" cells. Thus structural cross-orientation inhibition is not efficient in real cortical columns. 6. We propose a new mechanism called circular inhibition. In this connection scheme, a target cell receives inhibitory input from source cells that are located at a given distance (the same for all cells) from the target cell. Circular inhibition can be regarded as two-dimensional long-range lateral inhibition. As opposed to structural cross-orientation inhibition, this mechanism does not introduce unwanted anisotropies in the orientation tuning of the target cells. It is also conceptually much simpler and developmentally advantageous. It is shown that this connection scheme results in a net functional cross-orientation inhibition in all realistic column geometries. The inhibitory tuning strength obtained with circular inhibition is weak and similar to that measured in reality.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗

Protein tertiary structure prediction using a branch and bound algorithm.

We report a new method for predicting protein tertiary structure from sequence and secondary structure information. The predictions result from global optimization of a potential energy function, including van der Waals, hydrophobic, and excluded volume terms. The optimization algorithm, which is based on the alphaBB method developed by Floudas and coworkers (Costas and Floudas, J Chem Phys 1994;100:1247-1261), uses a reduced model of the protein and is implemented in both distance and dihedral angle space, enabling a side-by-side comparison of methodologies. For a set of eight small proteins, representing the three basic types--all alpha, all beta, and mixed alpha/beta--the algorithm locates low-energy native-like structures (less than 6A root mean square deviation from the native coordinates) starting from an unfolded state. Serial and parallel implementations of this methodology are discussed.

Algorithms↗

The two polypeptide chains in fibronectin are joined in antiparallel fashion: NMR structural characterization.

The fibronectin C-terminal interchain disulfide-linked heptapeptide dimer (Val-Asn-Cys-Pro-Ile-Glu-Cys)2 has been investigated via 1H NMR spectroscopy in both water and dimethyl sulfoxide (DMSO) solutions. Proton Overhauser experiments in DMSO indicate unambiguously that the two fibronectin polypeptide chains are linked head-to-tail (N-terminus to C-terminus), in an antiparallel fashion. It is found that the structure of the peptide is extended. From the 1H NMR interproton distance and angle constraints, the preferred mean (time-averaged) conformations in both H2O and DMSO were derived using distance geometry and molecular mechanics algorithms. The two conformations, although significantly dissimilar, exhibit the common feature of a structurally parallel (as opposed to chemically antiparallel) fibronectin alpha/beta chain array.

Amino Acid Sequence↗

Patenting computer-designed peptides.

The problem of designing new peptides that possess specific properties, such as bactericidal activity, is of wide interest. Recently, attention has focused on the use of Computer-Aided Molecular Design techniques in parallel with more traditional 'synthesise and test' methods. These techniques may typically use Genetic Algorithms to optimise molecules based on Neural Network models that predict activity. In this paper we describe a successful application of this Molecular Design methodology that has resulted in novel bactericidal peptides of real value. A key issue for commercial utilisation of such results is the ability to protect the intellectual property rights associated with the discovery of new molecules. Typically peptide patents use structural templates of amino acid hydrophobicity-hydrophilicity that define highly regular peptide patent spaces. In an extension of established patenting practice we describe a patent application that uses a Neural Net predictive model to define the regions of peptide space that we claim within the patent. This formalism makes no a priori assumptions about the regularity of the patent space. A preliminary comparative investigation of the shape and size of this and other bactericidal peptide patent spaces is conducted.

Algorithms↗

Further development and validation of empirical scoring functions for structure-based binding affinity prediction.

New empirical scoring functions have been developed to estimate the binding affinity of a given protein-ligand complex with known three-dimensional structure. These scoring functions include terms accounting for van der Waals interaction, hydrogen bonding, deformation penalty, and hydrophobic effect. A special feature is that three different algorithms have been implemented to calculate the hydrophobic effect term, which results in three parallel scoring functions. All three scoring functions are calibrated through multivariate regression analysis of a set of 200 protein-ligand complexes and they reproduce the binding free energies of the entire training set with standard deviations of 2.2 kcal/mol, 2.1 kcal/mol, and 2.0 kcal/mol, respectively. These three scoring functions are further combined into a consensus scoring function, X-CSCORE. When tested on an independent set of 30 protein-ligand complexes. X-CSCORE is able to predict their binding free energies with a standard deviation of 2.2 kcal/mol. The potential application of X-CSCORE to molecular docking is also investigated. Our results show that this consensus scoring function improves the docking accuracy considerably when compared to the conventional force field computation used for molecular docking.

Binding Sites↗

Coupled map lattices as computational systems.

The coupled map lattice (CML) as a mathematical model for a computer is considered. Using the theory of synchronous concurrent algorithms, it is shown that the CML is a valid new model for a parallel deterministic analog machine, but that, in principle, such a CML computer does not generate computations that cannot be reproduced by the standard mathematical models for computing on real numbers. The analysis is based on new general mathematical definitions of CMLs, and an axiomatic approach to determining which models of computation can be used to simulate CMLs.

Journal Article↗

Filtered backprojection reconstruction of combined parallel beam and cone beam SPECT data.

The reconstruction problem for a combined parallel beam (PB) and cone beam (CB) imaging geometry has been addressed. The general algorithm (CB-FBP) of Defrise and Clack has been applied to this geometry and shown to provide accurate images as expected. A second algorithm specifically tailored to the PB-CB geometry was developed. It uses the general principles of the CB-FBP method to combine a shift-variant filtering of the PB data with a standard reconstruction of the CB data using the algorithm of Feldkamp, Davis and Kress (FDK). This 'mixed' algorithm has the advantage of fewer interpolation steps, thereby reducing reconstruction time and providing more accurate reconstructions. The algorithms were applied to noiseless data from a computer-generated 3D Shepp phantom. Both the CB-FBP algorithm and the mixed algorithm successfully combine the CB and the PB data to correct the well known artefacts observed when reconstructing CB data acquired with a circular orbit. The mixed algorithm is about twice as fast as CB-FBP and results in better image quality, due to decreased discretization errors. However, the two algorithms yield comparable image quality when applied to a disc phantom measured with a two-headed SPECT system.

Algorithms↗