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PubMed1991

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations.

Algorithms↗
PubMed1995

A comparison of two photon planning algorithms for 8 MV and 25 MV X-ray beams in lung.

We report results of a comparison of two photon planning algorithms, the Clarkson Scatter Integration algorithm and the Equivalent Tissue-air Ratio algorithm, using a simple lung phantom for 8 MV and 25 MV X-ray beams of field sizes 5 cm x 5cm and 10 cm x 10 cm. Central axis depth-dose distributions were measured with a thimble chamber or a Markus parallel-plate chamber. Dose profile distributions were measured with TLD rods and films. Measured dose distributions were then compared to predicted dose distributions. Both agorithms overestimate the dose at mid-lung as they do not account for the effect of electronic disequilibrium. The Clarkson algorithm consistently shows less accurate results in comparison with the ETAR algorithm. There is additional error in the case of the Clarkson algorithm because of the assumption of a unit density medium in calculating scatter, which gives an overestimate in the effective scatter-air ratios in lung. For a 5 cm x 5 cm field, the error of dose prediction (Dpredicted-Dmeasured) for 25 MV x-ray beam at mid-lung is 15.8% and 12.8% for Clarkson and ETAR algorithm respectively. At 8 MV the error is 9.3% and 5.1% respectively. In addition, both algorithms underestimate the penumbral width at mid-lung as they do not account for the penumbral flaring effect in low density medium. It is very important for medical physicists, radiation therapists and clinicians to be aware of the limitation of their radiotherapy treatment planning systems.

Algorithms↗
PubMedDate not supplied

Real-time pulse oximetry artifact annotation on computerized anaesthetic records.

OBJECTIVES: Adoption of computerised anaesthesia record keeping systems has been limited by the concern that they record artifactual data and accurate data indiscriminately. Data resulting from artifacts does not reflect the patient's true condition and presents a problem in later analysis of the record, with associated medico-legal implications. This study developed an algorithm to automatically annotate pulse oximetry artifacts and sought to evaluate the algorithm's accuracy in routine surgical procedures. METHODS: MacAnaesthetist is a semi-automatic anaesthetic record keeping system developed for the Apple Macintosh computer, which incorporated an algorithm designed to automatically detect pulse oximetry artifacts. The algorithm labeled artifactual oxygen saturation values < 90%. This was done in real-time by analyzing physiological data captured from a Datex AS/3 Anaesthesia Monitor. An observational study was conducted to evaluate the accuracy of the algorithm during routine surgical procedures (n = 20). An anaesthetic record was made by an anaesthetist using the Datex AS/3 record keeper, while a second anaesthetic record was produced in parallel using MacAnaesthetist. A copy of the Datex AS/3 record was kept for later review by a group of anaesthetists (n = 20), who judged oxygen saturation values < 90% to be either genuine or artifact. RESULTS: MacAnaesthetist correctly labeled 12 out of 13 oxygen saturations < 90% (92.3% accuracy). A post-operative review of the Datex AS/3 anaesthetic records (n = 8) by twenty anaesthetists resulted in 127 correct responses out of total of 200 (63.5% accuracy). The remaining Datex AS/3 records (n = 12) were not reviewed, as they did not contain any oxygen saturations <90%. CONCLUSIONS: The real-time artifact detection algorithm developed in this study was more accurate than anaesthetists who post-operatively reviewed records produced by an existing computerised anaesthesia record keeping system. Algorithms have the potential to more accurately identify and annotate artifacts on computerised anaesthetic records, assisting clinicians to more correctly interpret abnormal data.

Algorithms↗
PubMed2004

Modelling an extreme water-lung interface using a single pencil beam algorithm and the Monte Carlo method.

The goal of this study was to quantify, in a heterogeneous phantom, the difference between experimentally measured beam profiles and those calculated using both a commercial convolution algorithm and the Monte Carlo (MC) method. This was done by arranging a phantom geometry that incorporated a vertical solid water-lung material interface parallel to the beam axis. At nominal x-ray energies of 6 and 18 MV, dose distributions were modelled for field sizes of 10 x 10 cm(2) and 4 x 4 cm(2) using the CadPlan 6.0 commercial treatment planning system (TPS) and the BEAMnrc-DOSXYZnrc Monte Carlo package. Beam profiles were found experimentally at various depths using film dosimetry. The results showed that within the lung region the TPS had a substantial problem modelling the dose distribution. The (film-TPS) profile difference was found to increase, in the lung region, as the field size decreased and the beam energy increased; in the worst case the difference was more than 15%. In contrast, (film-MC) profile differences were not found to be affected by the material density difference. BEAMnrc-DOSXYZnrc successfully modelled the material interface and dose profiles to within 2%.

Algorithms↗
PubMed2001

Alopex-B: a new, simpler, but yet faster version of the alopex training algorithm.

Experimenting with some changes and simplifications to the Alopex algorithm, we obtained a new faster version (Alopex-B), that also shows lower failure rates on training attempts. Like Alopex, our version is network-architecture independent, does not require error or transfer functions to be differentiable, has a high potential for parallelism, and is stochastic (which helps avoid local minima), but unlike Alopex it follows no annealing scheme, and uses less parameters which makes it simpler to implement and to use.

Algorithms↗
PubMed1992

An algorithm for protein engineering: simulations of recursive ensemble mutagenesis.

An algorithm for protein engineering, termed recursive ensemble mutagenesis, has been developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Starting from partially randomized "wild-type" DNA sequences, a highly parallel search of sequence space for peptides fitting an experimenter's criteria is performed. Each iteration uses information gained from the previous rounds to search the space more efficiently. Simulations of the technique indicate that, under a variety of conditions, the algorithm can rapidly produce a diverse population of proteins fitting specific criteria. In the experimental analog, genetic selection or screening applied during recursive ensemble mutagenesis should force the evolution of an ensemble of mutants to a targeted cluster of related phenotypes.

Algorithms↗
PubMed1999

Dose calculation models for proton treatment planning using a dynamic beam delivery system: an attempt to include density heterogeneity effects in the analytical dose calculation.

The gantry for proton radiotherapy at the Paul Scherrer Institute (PSI) is designed specifically for the spot-scanning technique. Use of this technique to its full potential requires dose calculation algorithms which are capable of precisely simulating each scanned beam individually. Different specialized analytical dose calculations have been developed, which attempt to model the effects of density heterogeneities in the patient's body on the dose. Their accuracy has been evaluated by a comparison with Monte Carlo calculated dose distributions in the case of a simple geometrical density interface parallel to the beam and typical anatomical situations. A specialized ray casting model which takes range dilution effects (broadening of the spectrum of proton ranges) into account has been found to produce results of good accuracy. This algorithm can easily be implemented in the iterative optimization procedure used for the calculation of the optimal contribution of each individual scanned pencil beam. In most cases an elemental pencil beam dose calculation has been found to be most accurate. Due to the long computing time, this model is currently used only after the optimization procedure as an alternative method of calculating the dose.

Algorithms↗
PubMed2006

P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R.

UNLABELLED: The software tool P2BAT provides a massive parallel and user friendly implementation of the PBAT-analysis tools for family-based association tests (FBATs) in large-scale studies, including genome-wide association studies with several thousand subjects. Built on the original PBAT-implementation of the Lange-Van Steen algorithm to bypass the multiple testing problem in family-based association studies, P2BAT integrates all PBAT-analysis tools for binary and complex traits into R and makes them accessible through a user-friendly GUI. The genome-wide analysis tools are fully automated and can be ran massively parallel directly through the GUI. P2BAT is fully documented and contains graphical output tools for time-to-onset analysis. P2BAT also features the ability to test for gene and environment/drug interaction. AVAILABILITY: The P2BAT package is available as the R package 'pbatR' which can be downloaded from http://cran.r-project.org/. The PBAT-software is available at http://www.biostat.harvard.edu/~clange/.

Algorithms↗
PubMed2004

3D RBI-EM reconstruction with spherically-symmetric basis function for SPECT rotating slat collimator.

A single photon emission computed tomography (SPECT) rotating slat collimator with strip detector acquires distance-weighted plane integral data, along with the attenuation factor and distance-dependent detector response. In order to image a 3D object, the slat collimator device has first to spin around its axis and then rotate around the object to produce 3D projection measurements. Compared to the slice-by-slice 2D reconstruction for the parallel-hole collimator and line integral data, a more complex 3D reconstruction is needed for the slat collimator and plane integral data. In this paper, we propose a 3D RBI-EM reconstruction algorithm with spherically-symmetric basis function, also called 'blobs', for the slat collimator. It has a closed and spherically symmetric analytical expression for the 3D Radon transform, which makes it easier to compute the plane integral than the voxel. It is completely localized in the spatial domain and nearly band-limited in the frequency domain. Its size and shape can be controlled by several parameters to have desired reconstructed image quality. A mathematical lesion phantom study has demonstrated that the blob reconstruction can achieve better contrast-noise trade-offs than the voxel reconstruction without greatly degrading the image resolution. A real lesion phantom study further confirmed this and showed that a slat collimator with CZT detector has better image quality than the conventional parallel-hole collimator with NaI detector. The improvement might be due to both the slat collimation and the better energy resolution of the CZT detector.

Algorithms↗
PubMed1987

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.

The crystal structure of M4 apo-lactate dehydrogenase from the spiny dogfish (Squalus acanthius) was initially refined by a constrained-restrained, and subsequently restrained, least-squares technique. The final structure contained 286 water molecules and two sulfate ions per subunit and gave an R-factor of 0.202 for difraction data between 8.0 and 2.0 A resolution. The upper limit for the co-ordinate accuracy of the atoms was estimated to be 0.25 A. The elements of secondary structure of the refined protein have not changed from those described previously, except for the appearance of a one-and-a-half turn 3(10) helix immediately after beta J. There is also a short segment of 3(10) helix between beta C and beta D in the part of the chain that connects the two beta alpha beta alpha beta units of the six-stranded parallel sheet (residues Tyr83 to Ala87). Examination of the interactions among the different elements of secondary structure by means of a surface accessibility algorithm supports the four structural clusters in the subunit. The first of the two sulfate ions is in the active site and occupies a cavity near the essential His195. Its nearest protein ligands are Arg171, Asp168 and Asn140. The second sulfate ion is located near the P-axis subunit interface. It is liganded by His188 and Arg173. These two residues are conserved in bacterial lactate dehydrogenase and form part of the fructose 1,6-bisphosphate effector binding site. Two other data sets in which one (collected at pH 7.8) or both (collected at pH 6.0) sulfate ions were replaced by citrate ions were also analyzed. Five cycles of refinement with respect to the pH 6.0 data (25 to 2.8 A resolution) resulted in an R value of 0.191. Only water molecules occupy the subunit boundary anion binding site at pH 7.8. The amino acid sequence was found to be in poor agreement with (2Fobs-Fcalc) electron density maps for the peptide between residues 207 and 211. The original sequence WNALKE was replaced by NVASIK. The essential His195 is hydrogen bonded to Asp168 on one side and Asn140 on the other. The latter residue is part of a turn that contains the only cis peptide bond of the structure at Pro141. The "flexible loop" (residues 97 to 123), which folds down over the active center in ternary complexes of the enzyme with substrate and coenzyme, has a well-defined structure. Analysis of the environment of Tyr237 suggests how its chemical modification inhibits the enzyme.

Amino Acid Sequence↗
PubMed2004

MRI diffusion tensor reconstruction with PROPELLER data acquisition.

MRI diffusion imaging is effective in measuring the diffusion tensor in brain, cardiac, liver, and spinal tissue. Diffusion tensor tomography MRI (DTT MRI) method is based on reconstructing the diffusion tensor field from measurements of projections of the tensor field. Projections are obtained by appropriate application of rotated diffusion gradients. In the present paper, the potential of a novel data acquisition scheme, PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction), is examined in combination with DTT MRI for its capability and sufficiency for diffusion imaging. An iterative reconstruction algorithm is used to reconstruct the diffusion tensor field from rotated diffusion weighted blades by appropriate rotated diffusion gradients. DTT MRI with PROPELLER data acquisition shows significant potential to reduce the number of weighted measurements, avoid ambiguity in reconstructing diffusion tensor parameters, increase signal-to-noise ratio, and decrease the influence of signal distortion.

Algorithms↗
PubMed2002

Simulation of packed-bed chromatography utilizing high-resolution flow fields: comparison with models.

A computer simulation of a section of the interior region of a liquid chromatographic column is performed. The detailed fluid flow profile is provided from a microscopic calculation of low Reynolds number flow through a random packed bed of nonporous spherical particles. The fluid mechanical calculations are performed on a parallel processor computer utilizing the lattice Boltzmann technique. Convection, diffusion, and retention in this flow field are calculated using a stochastic-based algorithm. This computational scheme provides for the ability to reproduce the essential dynamics of the chromatographic process from the fundamental considerations of particle geometry, particle size, flow velocity, solute diffusion coefficient, and solute retention parameters when retention is utilized. The simulation data are fit to semiempirical models. The best agreement is found for the "coupling" model of Giddings and the four-parameter Knox model. These models are verified over a wide range of particle sizes and flow velocities at both low and high velocity. The simulations appear to capture the essential dynamics of the chromatographic flow process for non-dimensional flow velocities (Péclet number) less than 500. Since the same packing geometry is utilized for different particle size studies, the interpretation of the parameter estimates from these models can be extended to the physical column model. The simulations reported here agree very well with a number of experiments reported previously.

Journal Article↗
PubMed2006

Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design.

Activator protein-1 (AP-1) is a crucial transcription factor implicated in numerous cancers. For this reason, nine homologues of the AP-1 leucine zipper region have been characterized: Fos (c-Fos, FosB, Fra1, and Fra2), Jun (c-Jun, JunB, and JunD), and semirational library-designed winning peptides FosW and JunW. The latter two were designed to specifically target c-Fos or c-Jun. They have been identified by using protein-fragment complementation assays combined with growth competition. This assay removes nonspecific, unstable, and protease susceptible library members from the pool, leaving winners with excellent drug potential. Thermal melts of all 45 possible dimeric interactions have been surveyed, with the FosW-c-Jun complex displaying a melting temperature (T(m)) of 63 degrees C, compared to only 16 degrees C for wild-type c-Fos-c-Jun interaction. This impressive 70,000-fold K(D) decrease is largely due to optimized core packing, alpha-helical propensity, and electrostatics. Contrastingly, due to a poor c-Fos core, c-Fos-JunW dimerizes with lower affinity. However the T(m) far exceeds wild-type c-Fos-c-Jun and averaged JunW and c-Fos, indicating a preference over either homodimer. Finally, and with wider implications, we have compiled a method for predicting interaction of parallel, dimeric coiled coils, using our T(m) data as a training set, and applying it to 59 bZIP proteins previously reported. Our algorithm, unlike others to date, accounts for helix propensity, which is found to be integral in coiled coil stability. Indeed, in applying the algorithm to these 59(2) bZIP interactions, we were able to correctly identify 92% of all strong interactions and 92% of all noninteracting pairs.

Amino Acid Sequence↗
PubMed2003

Trp-cage: folding free energy landscape in explicit water.

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 A Calpha-RMSD (Calpha-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

Algorithms↗
PubMed2001

Soft-decision array decoding for volume holographic memory systems.

We study the use of soft-decision array decoding in a volume holographic memory (VHM) system that is corrupted by interpixel interference (IPI) and detector noise. Soft-decision methods can unify equalization and error decoding. A highly parallel array decoder is presented in the context of two-dimensional low-pass channel mitigation and error correction. The new decoding algorithm is motivated by iterative turbo-decoding methods and is capable of incorporating a priori knowledge of the corrupting IPI channel during decoding. The resulting joint detection decoding algorithm is shown to offer VHM capacity and density performance superior to that of hard-decision n = 255 Reed-Solomon codes in concatenation with a Wiener filter.

Journal Article↗
PubMed2003

A dynamic nonlinear time domain model for reconstruction and compression of cardiovascular signals with application to telemedicine.

A new nonlinear time domain model is proposed in this paper for signals of cardiovascular origin. An equation of the dynamic nonlinear model has been obtained by considering a masking function, which is modulated by a harmonic series with the baseline drift incorporated into the model. Signal reconstruction using model parameters has established the effectiveness of the model for signal compression. Improvement has been effected by using neural networks for reducing the time for optimizing the initial parameters. An improved adaptive optimization step size algorithm has also been implemented. Results show that the technique is able to provide reasonable compression with low error between the original and reconstructed signals. One of the main advantages of the model is its potential of being used for compression of many different types of biosignals transmitted in parallel. Incorporation of the compression model into a telemedicine system has led to considerable saving in transmission time for patient data.

Algorithms↗