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PubMed1986

A microcomputer algorithm for solving compartmental models involving radionuclide transformations.

An algorithm for solving first-order non-recycling compartment models is described. Given the initial amounts of a radioactive material in each compartment and the fundamental transfer rate constants between each compartment, the algorithm gives both the amount of material remaining at any time t and the integrated number of transformations that would occur up to time t. The method is analytical, and consequently, is ideally suited for implementation on a microcomputer. For a typical microcomputer with 64 kilobytes of random access memory, a model containing up to 100 compartments, with any number of interconnecting translocation routes, can be solved in a few seconds; providing that no recycling occurs. An example computer program, written in 30 lines of Microsoft BASIC, is included in an appendix to demonstrate the use of the algorithm. A detailed description is included to show how the algorithm is modified to satisfy the requirements commonly encountered in compartment modelling, for example, continuous intake, partitioning of activity, and transformations from radioactive progeny. Although the algorithm does not solve models involving recycling, it is often possible to represent such cases by a non-recycling model which is mathematically equivalent.

Computers↗

PubMed1985

A new scan conversion algorithm for ultrasound compound scanning.

An improved scan conversion algorithm for ultrasound compound scanning is proposed. In this algorithm, the input data in the spatial domain is sampled by the concentric square raster sampling (CSRS) method, and the display pixel data are filled by one-dimensional linear interpolation. The reconstruction error of the proposed algorithm is much smaller than that of other algorithms, because only one-dimensional, rather than two-dimensional, interpolation is involved. This algorithm greatly simplifies implementation of a real-time digital scan converter (DSC) for spatial compounding of ultrasound images.

Mathematics↗

PubMed1985

Image reconstruction from coded data: I. Reconstruction algorithms and experimental results.

Two algorithms have been developed for reconstructing objects from their coded images and a priori knowledge of the object class. Reconstructions from both algorithms are presented, but the results appear to be largely independent of the algorithm used. One of the algorithms, a Monte Carlo approach, is used to investigate the quality of the reconstruction of two- and three-dimensional objects from simulated coded-image data with respect to viewing geometry and multiplexing (mixing) of the data. The cases examined include reconstructions from data with and without signal-dependent photon noise. It is found that reconstructing from multiplexed data is not so serious a problem as reconstructing from data obtained with a limited viewing angle. Also, when photon noise is included in the data, reconstructions obtained from multiplexed data are better than those obtained from unmultiplexed data because of the higher photon count made available by multiplexing. It appears that the fidelity of a reconstruction depends much more strongly on the design of the data-taking system (the coded apertures) than on the reconstruction algorithm.

Models, Structural↗

PubMed1991

Comparison of analytic algorithms for detecting glaucomatous visual field loss.

The sensitivity and specificity of alternate analytic strategies for recognizing glaucomatous visual field loss from automated threshold perimetry (C-30-2 test of the Humphrey Field Analyzer) were compared among one eye each of 106 patients with glaucoma and 249 normal subjects. Algorithms included commercially available global indexes and cross-meridional differences (Statpac 1 and Statpac 2), as well as cross-meridional and cluster analyses that were developed independently for natural history studies and clinical trials. The sensitivity of most algorithms was high, except for those that used only diffuse loss as an indicator of abnormality. Specificity was acceptably high for all algorithms. Subjects who failed to meet the manufacturer's standard for reliability had much reduced specificity, but sensitivity was also affected. Algorithms that were based on any of the alternate definitions of localized reduction in retinal sensitivity performed equally well, which suggests that any of these approaches is useful in searching for glaucomatous visual loss as typified by this database. Availability, familiarity, and convenience may govern the selection of any one analytic approach for use in a particular setting.

Algorithms↗

PubMed1987

A comparative study of attenuation correction algorithms in single photon emission computed tomography (SPECT).

A computer based simulation method was developed to assess the relative effectiveness and availability of various attenuation compensation algorithms in single photon emission computed tomography (SPECT). The effect of the nonuniformity of attenuation coefficient distribution in the body, the errors in determining a body contour and the statistical noise on reconstruction accuracy and the computation time in using the algorithms were studied. The algorithms were classified into three groups: precorrection, post correction and iterative correction methods. Furthermore, a hybrid method was devised by combining several methods. This study will be useful for understanding the characteristics, limitations and strengths of the algorithms and searching for a practical correction method for photon attenuation in SPECT.

Algorithms↗

PubMed1991

New algorithm for the detection of the ECG fiducial point in the averaging technique.

The use of the coherent averaging technique applied to the electrocardiographic signal implies the location of a fiducial point as a synchronisation reference. An algorithm easily adaptable to a personal computer, operable in real time, insensitive to mains and to ECG-baseline fluctuations, with a low jitter value and the capacity to trigger any ECG signal wave or complex, has been developed. The algorithm detects those waveforms which, within certain confidence intervals, are morphologically equal to a reference wave. This wave is chosen by the user as the repetitive waveform within which the fiducial point is to be located. A two-window template and differential parameters are used. The possibility of building the template permits the user to adapt the algorithm to each patient's ECG. To evaluate its accuracy objectively, a software simulation was built of a generator capable of producing test signals as the sum of the 'useful' signal plus 'noise'. A jitter standard deviation of 1.65 ms was obtained in the worst test (SNR = 10 dB; noiseband = 0-50 Hz), which shows the excellent recognition accuracy of the algorithm.

Algorithms↗

PubMed1992

A local algorithm for DNA sequence alignment with inversions.

A dynamic programming algorithm to find all optimal alignments of DNA subsequences is described. The alignments use not only substitutions, insertions and deletions of nucleotides but also inversions (reversed complements) of substrings of the sequences. The inversion alignments themselves contain substitutions, insertions and deletions of nucleotides. We study the problem of alignment with non-intersecting inversions. To provide a computationally efficient algorithm we restrict candidate inversions to the K highest scoring inversions. An algorithm to find the J best non-intersecting alignments with inversions is also described. The new algorithm is applied to the regions of mitochondrial DNA of Drosophila yakuba and mouse coding for URF6 and cytochrome b and the inversion of the URF6 gene is found. The open problem of intersecting inversions is discussed.

Algorithms↗

PubMed1987

A microcomputer implementation of status and alarm algorithms in a cardiac surgical intensive care unit.

Algorithms have been developed for monitoring the cardiovascular status of patients on their return to an intensive care unit after cardiac surgery and also for giving an immediate alarm of a critical deterioration in this status. The two systems for implementing these algorithms were initially developed on Z80 based microprocessor systems and preliminary clinical trials based on the resulting instruments proved encouraging. For further clinical trials of the algorithms the systems have been integrated and implemented on a BBC microcomputer with a 6502 second processor. The development and structure of the programs for implementing the algorithms are described, together with the program input and output facilities and diagnostic techniques used to analyse the information output from the program.

Algorithms↗

PubMed1992

Validation of an adaptive software trigger and arrhythmia diagnostic algorithm.

The authors have developed an algorithm for the identification of arrhythmias using intracardiac atrial and ventricular leads. The algorithm is based on the rate of the depolarizations and a measure of the organization of electrical activity in each of the cardiac chambers. The most important requirement of the algorithm is to identify the occurrence of each cardiac event correctly. A robust amplitude-adaptive software trigger is developed, which accurately detects depolarizations in both chambers. With this reliable trigger the authors demonstrate the veracity of the arrhythmia identification algorithm.

Algorithms↗

PubMed1992

Comparison of logistic regression and Bayesian-based algorithms to estimate posttest probability in patients with suspected coronary artery disease undergoing exercise ECG.

Two multivariate methods, a logistic regression-derived algorithm and a Bayesian independence-assuming method (CADENZA), were compared concerning their abilities to estimate posttest probability of coronary disease in patients with suspected coronary disease. All patients underwent exercise testing within 3 months prior to coronary angiography. Coronary disease was defined as the presence of one or more vessels with greater than or equal to 50% luminal diameter narrowing. A group of 300 patients (disease prevalence = 37%) was used to derive the algorithm. Another group of 950 patients was used to validate the algorithm and compare it to CADENZA. Seven variables (age, sex, symptoms, diabetes, mm ST depression, ST slope, and peak heart rate) were used to generate posttest probabilities for each method. The receiver operating characteristic curve area for the logistic regression method (0.81 +/- 0.01) was significantly higher than CADENZA (0.75 +/- 0.01; p less than 0.05). There was, however, no difference in the calibration of the two methods. When given equivalent variable information, the logistic regression algorithm had better discrimination than CADENZA for estimating the probability of coronary disease following exercise electrocardiography.

Algorithms↗

PubMed1990

Speeding up the dynamic algorithm for planar RNA folding.

The simplest dynamic algorithm for planar RNA folding searches for the maximum number of base pairs. The algorithm uses O(n3) steps. The more general case, where different weights (energies) are assigned to stacked base pairs and to the various types of single-stranded region topologies, requires a considerably longer computation time because of the partial backtracking involved. Limiting the loop size reduces the running time back to O(n3). Reduction in the number of steps in the calculations of the various RNA topologies has recently been suggested, thereby improving the time behavior. Here we show how a "jumping" procedure can be used to speed up the computation, not only for the maximal number of base pairs algorithm, but for the minimal energy algorithm as well.

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↗

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↗

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↗