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PubMed1994

Deriving non-homogeneous DNA Markov chain models by cluster analysis algorithm minimizing multiple alignment entropy.

Non-homogeneous Markov chain models can represent biologically important regions of DNA sequences. The statistical pattern that is described by these models is usually weak and was found primarily because of strong biological indications. The general method for extracting similar patterns is presented in the current paper. The algorithm incorporates cluster analysis, multiple alignment and entropy minimization. The method was first tested using the set of DNA sequences produced by Markov chain generators. It was shown that artificial gene sequences, which initially have been randomly set up along the multiple alignment panels, are aligned according to the hidden triplet phase. Then the method was applied to real protein-coding sequences and the resulting alignment clearly indicated the triplet phase and produced the parameters of the optimal 3-periodic non-homogeneous Markov chain model. These Markov models were already employed in the GeneMark gene prediction algorithm, which is used in genome sequencing projects. The algorithm can also handle the case in which the sequences to be aligned reveal different statistical patterns, such as Escherichia coli protein-coding sequences belonging to Class II and Class III. The algorithm accepts a random mix of sequences from different classes, and is able to separate them into two groups (clusters), align each cluster separately, and define a non-homogeneous Markov chain model for each sequence cluster.

Algorithms↗

PubMed1996

Parallel processing of chemical information in a local area network--III. Using genetic algorithms for conformational analysis of biomacromolecules.

Multi-dimensional nuclear magnetic resonance experiments are an excellent means of revealing the three-dimensional structure of biomacromolecules in solution. However, the search space in the conformational analysis of biomacromolecules, using multi-dimensional NMR data, is huge and complex. This calls for global optimization techniques with good sampling properties. This paper describes a genetic algorithm that optimizes the fit between (simulated) experimental two-dimensional Nuclear Overhauser Effect spectra and the corresponding calculated spectra for trial structures. This is a very computational intensive procedure. Speed-up of performance is achieved by parallelizing the algorithm, i.e. creating small subpopulations of trial structures, each of which can be processed on different processors. Good sampling behavior is obtained by initializing each subpopulation with its own random seed and the introduction of a migration operator. The latter replaces the best performing individual from one subpopulation with the worst performing individual from another subpopulation after a predetermined number of generations. A parallel genetic algorithm for the conformational analysis of nucleic acids is developed using the software package HYDRA. It is demonstrated that, for the data sets used in the study, a considerable reduction in computation time is obtained for the parallel genetic algorithm as compared to a sequential implementation, while the same optimal solutions are found.

Algorithms↗

PubMed1988

Selection of class I MHC-restricted peptides with the strip-of-helix hydrophobicity algorithm.

A strip-of-helix hydrophobicity algorithm to predict class II MHC-restricted peptides, on the basis of their structural similarity to an amphipathic, alpha-helix in Ii, also predicted peptides which were presented to cytotoxic T-cells by class I MHC molecules. This algorithm ranked peptides according to mean Kyte-Doolittle hydrophobicity values of amino acids at positions n, n + 4, n + 7, n + 11, n + 14 and n + 18 in a sequence which when coiled as a putative alpha-helix, had the indicated residues in an axial strip along one side of the helix. Sequences selected for highly scoring, hydrophobic strips were required to have at least 1 of the 4 adjacent strips scoring more negatively than -1 in the strip-of-helix hydrophobicity index and the entire sequence could contain no prolines. This algorithm predicted the class I MHC-restricted, T-cell-presented peptides in sequences of 4 proteins from which some class I MHC-restricted, T-cell-presented sequences had been experimentally determined. Since both class I and class II MHC-restricted peptides could be identified with this algorithm, one can propose that: (1) foreign peptide-binding sites (desetopes) of the class I and class II MHC molecules are structurally similar; and (2) any one T-cell-presented peptide can be presented by some specific allele of both a class I and a class II MHC antigen.

Algorithms↗

PubMed1990

Experimental verification of an algorithm for inverse radiation therapy planning.

In inverse radiotherapy planning, the traditional dose planning sequence is reversed. This makes it possible to calculate the optimal incident beam profiles required to produce the desired dose distribution in the target volume by solving an integral equation with an iterative algorithm. The major advantage, compared with conventional treatment planning, is that the trial and error part is avoided, and replaced by a deterministic calculation of the optimal treatment plan. In the present paper this algorithm is briefly described and compared with experimental results and an analytical inversion formula which is valid for a cylindrical geometry. The experiments were performed with non-homogeneous beams shaped with compensators designed using the algorithm. The agreement between the experimental results and the predictions of the algorithm are quite good, generally within about 5%. The differences are caused by discretization noise due to the finite resolution of the calculation matrix, imperfections in the experimental situation, and by the assumption of spatial invariant dose distribution kernels.

Algorithms↗

PubMed1989

Software manipulations to speed up a real-valued fast Fourier transform algorithm.

It is described how a real-valued fast Fourier transform (RFFT) algorithm can be converted quite easily into a computer program in which loops, evaluation of subscripts, exchange of data, and logical operations are completely avoided. The resulting program runs considerably faster than the original algorithm. The actual saving of execution time depends upon both the computer system and the length of the RFFT. In the majority of the investigated cases the execution time was reduced by a factor between 1.8 and 5. The described technique can be recommended especially for critical real-time tasks and for applications requiring a huge amount of RFFT evaluations. Other algorithms as for example the complex-valued FFT, the inverse RFFT or correlation algorithms can be treated in a similar way.

Algorithms↗

PubMedDate not supplied

The influence of different generations of computer algorithms on diabetes control.

With all control schedules, the management of diabetes is possible using Skyler's algorithm. In general, those control algorithms which do not allow the individual adaptation to changing conditions lead to overinsulinisation. So-called meal-related algorithms do usually minimise the fluctuations in blood sugar. The introduction of self-adapting algorithms, detecting peripheral insulin resistance, may further improve metabolic diabetes control.

Algorithms↗

PubMed1993

Meta-analysis of clinical trials based on censored end-points: simplified theory and implementation of the statistical algorithms on a microcomputer.

Meta-analysis is increasingly being used in clinical research. While the meta-analytical algorithms for pooling the results of studies using non-censored end-points are now sufficiently standardized, the management of trials based on censored end-points is still controversial, and specific algorithms of meta-analysis are still needed (for example, censored end-points are commonly used in survival studies of cancer patients). In the present article we review the various algorithms that have thus far been utilized to perform a meta-analysis based on censored end-points, and we propose a new and original approach that combines two of the existing algorithms. Our approach is designed to formulate any meta-analysis of survival studies in terms of the calculation of an odds ratio. The meta-analytical odds ratio proposed here is called the 'log-rank' odds ratio of meta-analysis. A microcomputer program is described that implements the various methods of meta-analysis that can handle clinical trials based on censored end-points. Some examples are presented to illustrate the use of the program.

Algorithms↗

PubMed1994

An algorithm for estimating the terminal half-life in pharmacokinetic studies.

An algorithm is developed for automating the process of identifying the terminal phase in plasma concentration-time curves for non-compartmental estimation of the terminal elimination rate and half-life. The manual process of plotting each curve, selecting the observations in the terminal phase, performing the regressions and plotting the fitted regression lines can be very time-consuming in cases where many curves are to be processed. The algorithm makes use of single-row regression diagnostics to determine the first observed time point in the terminal phase. An example is used to illustrate the calculations, and a simulation study was conducted to evaluate the performance of the algorithm. The algorithm has been implemented in a computer program.

Algorithms↗

PubMed1994

Fast algorithms for computing and displaying dose-distributions in tomogram-oriented brachy-radiotherapy.

This paper describes in detail a dose calculation algorithm tailored to the needs of tomogram-oriented brachy-radiotherapy and a general-purpose dose visualization for displaying the dose distribution as isolines (or rather interval planes). The verbal description of the algorithms is accompanied by structograms. However, the intention of the authors is to present very fast algorithms that are easy to implement and to give a ready-to-use example formulated in 68020 assembler code. Execution times are estimated theoretically by counting clock cycles and practically by measuring the execution time of sample calculations. It turns out that both the dose calculation as well as the visualization algorithm need less than 1 s when applied to a radioactive point source lying on an arbitrary 320 x 256 grid of three-dimensional space.

Algorithms↗

PubMed1995

Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences.

We have designed two computer-based algorithms for T cell epitope prediction, OptiMer and EpiMer, which incorporate current knowledge of MHC-binding motifs. OptiMer locates amphipathic segments of protein antigens with a high density of MHC-binding motifs. EpiMer identifies peptides with a high density of MHC-binding motifs alone. These algorithms exploit the striking tendency for MHC-binding motifs to cluster within short segments of each protein. Putative epitopes predicted by these algorithms contain motifs corresponding to many different MHC alleles, and may contain both class I and class II motifs, features thought to be ideal for the peptide components of synthetic subunit vaccines. In this study, we describe the use of OptiMer and EpiMer for the prediction of putative T cell epitopes from Mycobacterium tuberculosis and human immunodeficiency virus protein antigens, and demonstrate that these two algorithms may provide sensitive and efficient means for the prediction of promiscuous T cell epitopes that may be critical to the development of vaccines against these and other pathogens.

Algorithms↗

PubMed1995

A genetic algorithm to search for optimal and suboptimal RNA secondary structures.

Genetic algorithms are a search method used in solving problems by selection, recombination and mutation of tentative solutions, until the better ones are achieved. They are very efficient when the 'building block' hypothesis is effective for the solutions, which means that a better solution can be obtained by assembling short 'motifs' or 'schemata' that can be retrieved in some other worse solutions. The additive nature of the secondary structure free energy rules suggests the validity of this hypothesis, and therefore the likely power of a genetic algorithm approach to search for RNA secondary structures. We describe in detail an original genetic algorithm specific for this problem. The sharing function used to obtain differentiated solutions is also described. It results in a greater effectiveness of the algorithm in retrieving a large number of suboptimal RNA foldings besides the optimal one. RNA sequences of different length are used to test the method. The PSTV viroid sequence has been studied.

Algorithms↗

PubMed1995

A comparison of methods for self-adaptation in evolutionary algorithms.

Evolutionary algorithms, including evolutionary programming and evolution strategies, have often been applied to real-valued function optimization problems. These algorithms generally operate directly on the real values to be optimized, in contrast with genetic algorithms which usually operate on a separately coded transformation of the objective variables. Evolutionary algorithms often rely on a second-level optimization of strategy parameters, tunable variables that in part determine how each parent will generate offspring. Two alternative methods for performing this second-level optimization have been proposed and are compared across a series of function optimization tasks. The results appear to favor the approach offered originally in evolution strategies, although the applicability of the findings may be limited to the case where each parameter of a parent solution is perturbed independently of all others.

Algorithms↗

PubMed1986

A computer algorithm to determine the nadir and rise time in nocturnal cortisol secretion.

The nadir concentration value and the time of the circadian rise are two important characteristics of the nocturnal cortisol secretory pattern. A computer algorithm has been developed which objectively determines these parameters, supplementing the subjective evaluating methods previously used. The algorithm smooths the cortisol values and incorporates the intra-assay variability when calculating the nadir and rise. It was tested on 156 nights of cortisol data for healthy control and depressed subjects. The algorithm results closely matched the nadir and rise time subjectively determined by the investigators. With careful screening of the computer generated results, the algorithm decreases the reliance on subjective methods to determine the actual nocturnal cortisol nadir and rise time.

Adolescent↗

PubMed1992

Random search algorithm (RONSC) for optimization of radiation therapy with both physical and biological end points and constraints.

A new algorithm for the optimization of 3-dimensional radiotherapy plans is presented. The RONSC algorithm (Random Optimization with Non-linear Score functions and Constraints) is based on the idea of random search in the space of feasible solutions. RONSC takes advantage of some specific properties of the dose distribution and derivable information such as dose-volume histograms and calculated estimates of tumor control and normal tissue complication probabilities. The performance of the algorithm for clinical and test cases is discussed and compared with the performance of the simulated annealing algorithm, which is also based on the idea of random search.

Algorithms↗

PubMed1993

Clinical experience with antitachycardia pacing and improved detection algorithms in a new implantable cardioverter-defibrillator.

OBJECTIVES: This study was conducted to assess the effectiveness of antitachycardia pacing modes and detection algorithms in patients with a new third-generation implantable cardioverter-defibrillator. METHODS: Twenty-three of 42 consecutive patients had coronary artery disease, 14 had dilated cardiomyopathy, 2 had prior valve replacement and 3 had arrhythmogenic right ventricular dysplasia. The mean ejection fraction was 41 +/- 14%; there were 31 men (74%) and 11 women, with a mean age of 53 years. On the basis of preoperative and postoperative electrophysiologic studies, in 28 patients antitachycardia pacing was postoperatively programmed randomly as "burst" (66%) or autodecremental "ramp" (34%) stimulation with a first coupling interval of 81% of tachycardia cycle length and up to 8 sequences with 3 to 10 stimuli. RESULTS: During a follow-up interval of 6.3 +/- 2.2 months, 15 patients were treated by antitachycardia pacing for a median of 6 (range 1 to 59) hemodynamically stable ventricular tachycardias (175 +/- 12 beats/min). In 5 patients, 22 ventricular tachycardias (9%) were not terminated by antitachycardia pacing but by cardioversion. Seven (3%) of these episodes accelerated (> 50 ms) during antitachycardia pacing. Syncope did not occur during these episodes. In seven patients initial antitachycardia pacing in cases of supraventricular tachycardias delayed charging and redetection prevented inappropriate discharges. Additional detection algorithms were programmed only after inappropriate therapy. The sudden "onset" and "sustained rate duration" criteria were programmed in three patients and the cycle length "stability" criteria in six patients, respectively. After activation of these detection algorithms only two of the seven patients had further inappropriate device discharges. CONCLUSIONS: Thus, antitachycardia pacing by this implantable cardioverter-defibrillator effectively and appropriately terminated 91% of hemodynamically stable ventricular tachycardias. Inappropriate device discharges were prevented in some patients by antitachycardia pacing and additional detection algorithms.

Adult↗

PubMed1994

Underdetection of ventricular tachycardia by algorithms to enhance specificity in a tiered-therapy cardioverter-defibrillator.

OBJECTIVES: The goal of this study was to determine the incidence and clinical significance of underdetection in 125 patients treated with a tiered-therapy cardioverter-defibrillator, the Medtronic PCD. BACKGROUND: Underdetection, distinct from undersensing, is a unique, potential complication of new algorithms that enhance specificity in tiered-therapy cardioverter-defibrillators. These algorithms may delay or prevent recognition of ventricular tachycardia even though electrograms are sensed accurately and RR intervals meet the programmed interval criterion. METHODS: Underdetection was defined as delay in detection > 5 s at electrophysiologic study or symptomatic delay or detection failure at follow-up of 15 +/- 8 months. RESULTS: We identified six specific mechanisms of underdetection caused by algorithms to discriminate sustained ventricular tachycardia from sinus tachycardia, atrial fibrillation, ventricular fibrillation and nonsustained ventricular tachycardia. Underdetection caused detection delays in 13 (1.9%) of 677 induced ventricular tachyarrhythmia episodes in 12 patients (9.6%). During follow-up, underdetection occurred in 7 (9.9%) of 71 patients in whom ventricular tachycardia therapies were programmed. Failure to detect ventricular tachycardia occurred in 6 (0.6%) of 988 spontaneous ventricular tachycardia episodes in four patients (5.6%); 2 episodes required external cardioversion. After defibrillator reprogramming, underdetection did not occur. CONCLUSIONS: Algorithms to enhance specificity cause underdetection of ventricular tachycardia in a significant minority of patients with tiered-therapy cardioverter-defibrillators. Optimal programming can minimize underdetection.

Algorithms↗

PubMed1991

Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.

The sensitivity and selectivity of the FASTA and the Smith-Waterman protein sequence comparison algorithms were evaluated using the superfamily classification provided in the National Biomedical Research Foundation/Protein Identification Resource (PIR) protein sequence database. Sequences from each of the 34 superfamilies in the PIR database with 20 or more members were compared against the protein sequence database. The similarity scores of the related and unrelated sequences were determined using either the FASTA program or the Smith-Waterman local similarity algorithm. These two sets of similarity scores were used to evaluate the ability of the two comparison algorithms to identify distantly related protein sequences. The FASTA program using the ktup = 2 sensitivity setting performed as well as the Smith-Waterman algorithm for 19 of the 34 superfamilies. Increasing the sensitivity by setting ktup = 1 allowed FASTA to perform as well as Smith-Waterman on an additional 7 superfamilies. The rigorous Smith-Waterman method performed better than FASTA with ktup = 1 on 8 superfamilies, including the globins, immunoglobulin variable regions, calmodulins, and plastocyanins. Several strategies for improving the sensitivity of FASTA were examined. The greatest improvement in sensitivity was achieved by optimizing a band around the best initial region found for every library sequence. For every superfamily except the globins and immunoglobulin variable regions, this strategy was as sensitive as a full Smith-Waterman. For some sequences, additional sensitivity was achieved by including conserved but nonidentical residues in the lookup table used to identify the initial region.

Algorithms↗

PubMed1995

Separation of fetal and maternal ECG complexes from a mixed signal using an algorithm based on linear regression.

Fetal scalp ECG and Doppler ultrasound are the two methods universally used to derive the fetal heart rate (FHR) for cardiotocography. Other fetal signal sources have not been used successfully because of the complexity of the signal and the need for an additional maternal ECG input. In this paper, we present an algorithm for separating the fetal and maternal ECG signals obtained from intrauterine electrodes during labour. The algorithm detects all occurrences of ECG complexes and uses linear regression functions to compare each complex with a set templates. Sets of templates are identified as either maternal or fetal in origin and two signals are output for heart rate measurement. The outputs are also processed to eliminate artefacts that may occur when the maternal and fetal complexes are coincident. The algorithm processes 10 seconds of data at a time (in about 200 ms on a standard PC) while a further 10 s of data is being acquired. It has the advantage that no extra input is required, such as maternal ECG obtained from chest leads, and only assumes that two different populations of complexes of two different shapes are present in the input signal. The algorithm could also be used for the separation of fetal and maternal signals obtained from abdominal electrodes.

Algorithms↗