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PubMed1988

Efficient algorithms for generating interpolated (zoomed) MR images.

This paper discusses the two-dimensional implementation of a number of modified fast Fourier transform (FFT) algorithms that efficiently interpolate (zoom) magnetic resonance (MR) images. If the original image was sampled at a rate satisfying the Nyquist criterion, these algorithms would effectively increase the sampling rate, permitting image details to be more easily discerned. The Skinner interpolating fast Fourier transform (SIFFT) avoids many of the computationally unnecessary complex multiplications that occur when interpolating using the normal fast Fourier transform algorithm. The novel interpolating fast Fourier transform (NIFFT) offers further savings when a subimage is required. Theoretical and experimental timings that compare the use of the normal FFT, SIFFT, and NIFFT algorithms for interpolation are given using magnetic resonance image reconstruction examples. Time savings of a factor of 2 to 4 are possible in typical experimental situations. Time savings of factors of 5 to 20 are possible when zooming images using two-dimensional band selectable digital filtering (2D-BSDF) in combination with decimation and the SIFFT algorithm. In 2D-BSDF, the original MRI data set is reduced in size to retain only those frequency components corresponding to a desired subimage, thereby decreasing the computational load associated with further processing. A significant reduction in computation time is achieved when modeling is combined with 2D-BSDF and SIFFT as fewer points require modeling.

Algorithms↗

PubMed1995

The diminishing variance algorithm for real-time reduction of motion artifacts in MRI.

A technique has been developed whereby motion can be detected in real time during the acquisition of data. This enables the implementation of several algorithms to reduce or eliminate motion effects from an image as it is being acquired. One such algorithm previously described is the acceptance/rejection method. This paper deals with another real-time algorithm called the diminishing variance algorithm (DVA). With this method, a complete set of preliminary data is acquired along with information about the relative motion position of each frame of data. After all the preliminary data are acquired, the position information is used to determine which data frames are most corrupted by motion. Frames of data are then reacquired, starting with the most corrupted one. The position information is continually updated in an iterative process; therefore, each subsequent reacquisition is always done on the worst frame of data. The algorithm has been implemented on several different types of sequences. Preliminary in vivo studies indicate that motion artifacts are dramatically reduced.

Algorithms↗

PubMed1996

Algorithms for extracting motion information from navigator echoes.

Algorithms to reliably detect motion in navigator echoes are crucial to many MRI motion suppression techniques. The accuracy of these algorithms is affected by noise and deformation of navigator echo profile caused by physiologic motion. This study compared the performance of algorithms based on correlation and least squares for extracting displacement information from motion-monitoring navigator echoes, using computer simulation and in vivo imaging. The least squares algorithm was determined to be of higher accuracy than the correlation algorithm against errors caused by noise and profile deformation.

Algorithms↗

PubMed1996

Contact interactions method: a new algorithm for protein folding simulations.

Computer simulations of simple exact lattice models are an aid in the study of protein folding process; they have sometimes resulted in predictions experimentally proved. The contact interactions (CI) method is here proposed as a new algorithm for the conformational search in the low-energy regions of protein chains modeled as copolymers of hydrophobic and polar monomers configured as self-avoiding walks on square or cubic lattices. It may be regarded as an extension of the standard Monte Carlo method improved by the concept of cooperativity deriving from nonlocal contact interactions. A major difference with respect to other algorithms is that criteria for the acceptance of new conformations generated during the simulations are not based on the energy of the entire molecule, but cooling factors associated with each residue define regions of the model protein with higher or lower mobility. Nine sequences of length ranging from 20 to 64 residues were used on the square lattice and 15 sequences of length ranging from 46 to 136 residues were used on the cubic lattice. The CI algorithm proved very efficient both in two and three dimensions, and allowed us to localize energy minima not localized by other searching algorithms described in the literature. Use of this algorithm is not limited to the conformational search, because it allows the exploration of thermodynamic and kinetic behavior of model protein chains.

Algorithms↗

PubMed1994

Presentation of a general algorithm to include effect assessment on secondary poisoning in the derivation of environmental quality criteria. 2. Terrestrial food chains.

In a previous study a simple algorithm was presented for effect assessment on secondary poisoning of birds and mammals. This algorithm (MPC = NOECfish-eater/BCFfish) was drawn up by analyzing a two-step aquatic food chain (water-fish-bird/mammal). The algorithm was used to test whether quality criteria set for surface water, based on effect assessment for aquatic organisms, constitute a "safe" level for secondary poisoning. The present study analyzes whether this algorithm can equally well be used for effect assessment in a terrestrial food chain. The pathway soil-earthworm-bird/mammal was used as an example for a terrestrial food chain. Literature data of six selected compounds (lindane, dieldrin, DDT, PCP, cadmium, and mercury) on both bioconcentration factors for earthworms and toxicity data for birds and mammals were studied. Important differences were found between BCFs for this terrestrial pathway and BCFs for the aquatic pathway analyzed in the previous study. It was found that BCFs for earthworms were more dependent on soil-related properties than on compound-specific properties. Hence, it was concluded that the algorithm MPC = NOECworm-eater/BCFworm can be used only for effect assessment on terrestrial food chain in defined situations. By calculating maximum permissible concentrations for secondary poisoning (MPCsp) for a standard soil situation and comparing these to MPCs for soil organisms, it was concluded that secondary poisoning could be a critical pathway for cadmium and methyl mercury. For methyl mercury secondary poisoning in an aquatic food chain was also a critical pathway. Secondary poisoning of fish-eating birds and mammals is not likely to occur for cadmium at concentrations in water below the MPC calculated for aquatic organisms.

Algorithms↗

PubMed1994

Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package.

The peptide sequential assignment algorithm presented here was implemented as a macro within the CONnectivity TRacing ASsignment Tools (CONTRAST) computer software package. The algorithm provides a semi- or fully automated global means of sequentially assigning the NMR backbone resonances of proteins. The program's performance is demonstrated here by its analysis of realistic computer-generated data for IIIGlc, a 168-residue signal-transducing protein of Escherichia coli [Pelton et al. (1991) Biochemistry, 30, 10043-10057]. Missing experimental data (19 resonances) were generated so that a complete assignment set could be tested. The algorithm produces sequential assignments from appropriate peak lists of nD NMR data. It quantifies the ambiguity of each assignment and provides ranked alternatives. A 'best first' approach, in which high-scoring local assignments are made before and in preference to lower scoring assignments, is shown to be superior (in terms of the current set of CONTRAST scoring routines) to approaches such as simulated annealing that seek to maximize the combined scores of the individual assignments. The robustness of the algorithm was tested by evaluating the effects of imposed frequency imprecision (scatter), added false signals (noise), missing peaks (incomplete data), and variation in user-defined tolerances on the performance of the algorithm.

Algorithms↗

PubMed1996

Optimisation of metric matrix embedding by genetic algorithms.

To improve the convergence properties of 'embedding' distance geometry, a new approach was developed by combining the distance-geometry methodology with a genetic algorithm. This new approach is called DG-OMEGA (DG omega, optimised metric matrix embedding by genetic algorithms). The genetic algorithm was used to combine well-defined parts of individual structures generated by the distance-geometry program, and to identify new lower and upper distance bounds within the original experimental restraints in order to restrict the sampling of the metrisation algorithm to promising regions of the conformational space. The algorithm was tested on cyclosporin A, which is notorious for its intrinsic difficult sampling properties. A set of 58 distance restraints was employed. It was shown that DG omega resulted in an improvement of convergence behaviour as well as sampling properties with respect to the standard distance-geometry protocol.

Algorithms↗

PubMed1995

Noninvasive blood pressure monitoring from the supraorbital artery using an artificial neural network oscillometric algorithm.

OBJECTIVE: Our objective was to overcome the limitations of linear models of oscillometric blood pressure determination by using a nonlinear technique to model the relationship between the oscillometric envelope and systolic and diastolic blood pressures, and then to use that technique for near-continuous arterial pressure monitoring at the supraorbital artery. METHODS: An adhesive pressure pad and transducer were used to collect oscillometric data from the supraorbital artery of 85 subjects. These data were then used to train an artificial neural network (ANN) to report diastolic or systolic pressure. Arterial pressure measurements defined by brachial artery auscultation were used as a reference. ANN results were compared with those obtained using a standard oscillometric algorithm that determined pressures based on fixed percentages of the maximum oscillometric amplitude. RESULTS: The ANN produced better estimates of reference blood pressures than the standard oscillometric algorithm. Mean difference between target and actual output for the ANN was 0.50 +/- 5.73 mm Hg for systolic pressures, compared to the mean difference of the standard algorithm of 2.78 +/- 19.38 mm Hg. For diastolic pressures, the ANN had a mean difference of 0.04 +/- 4.70 mm Hg, while the mean difference of the standard algorithm was -0.34 +/- 9.75 mm Hg. CONCLUSIONS: The ANN produced a better model of the relationship between the oscillometric envelope and reference systolic and diastolic pressures than did the standard oscillometric algorithm. Noninvasive blood pressure measured from the supraorbital artery agreed with pressure measured by auscultation in the brachial artery, and may sometimes be more clinically useful than an arm cuff device.

Adult↗

PubMed1989

Prototype ventilator and alarm algorithm for the NASA space station.

An alarm algorithm was developed to monitor the ventilator on the National Aeronautics and Space Administration space station. The algorithm automatically identifies and interprets critical events so that an untrained user can manage the mechanical ventilation of a critically injured crew member. The algorithm was tested in two healthy volunteers by simulating 260 critical events in each volunteer while the volunteer breathed via the ventilator. Thirteen critical events were induced eight times in random order, for the five different modes of ventilation. These events included various ventilator tubing disconnects, leaks, and occlusions, as well as power and gas supply failures. The algorithm identified the critical events and generated alarms in response to 99.2% (516 of 520, total) of the events. The alarm textual messages were correct 98% (505 of 516 messages) of the time. The alarm algorithm is an improvement over current alarms found on most ventilators because its alarm messages specifically identify failures in the patient breathing circuit or ventilator. The system may improve patient care by helping critical care personnel respond more rapidly and correctly to critical events.

Algorithms↗

PubMed1994

Spectra of data sampled at frequency-modulated rates in application to cardiovascular signals: Part 2. Evaluation of Fourier transform algorithms.

For three direct Fourier transform algorithms we quantified the influence of pulse frequency modulation (PFM) on the spectral estimation of pulse amplitude modulation (PAM). The simulation study is based on sinusoid functions sampled according to a pulse sequence which is the output of an integral pulse frequency modulator (IPFM). One algorithm exactly reproduces the theoretical spectrum derived in Part 1. The other two, including the classical FFT, scale all PFM-induced components in a different way, and in addition, generate higher modulating frequency harmonics. For a PFM depth below 30%, the sum of spurious PFM components is almost linearly dependent on this modulation depth, for all three algorithms. Dividing the effect of PFM in a 'harmonic' and 'aliasing' distortion, we found that the FFT has a relatively high harmonic distortion, compared to an algorithm that takes into account the non-uniform character of the data. In the cardiovascular (worst) case of 30% modulation in heart rate (PFM) at a frequency of 0.1 Hz, the FFT spectrum of beat-to-beat systolic blood pressure variations contains approximately 20% of spurious components caused solely by the modulation in time occurrences of the blood pressure samples. The 'non-uniform' algorithm performs twice as well in this case.

Algorithms↗

PubMed1994

The geriatric medication algorithm: a pilot study.

A geriatric medication algorithm designed to reduce inappropriate prescribing was tested in a resident outpatient clinic. The medications of patients over 65 years old taking more than three medications (n = 41) were compared pre- and post-algorithm using the paired t-test. Pre-algorithm, the average number of drugs was 5.8 per patient (SD 1.62). Fifteen medications (6.4%) were discontinued, seven were substituted for a less toxic medication, and five were added. Post-algorithm, the average number of drugs was 5.6 (SD 1.69), mean difference 0.3 (SD 0.67), p < 0.025. Drugs discontinued were more likely to be high risk compared with drugs used at baseline; drugs added were less likely to be high risk. In this pilot study, the authors conclude that the algorithm helps resident physicians reduce inappropriate prescribing.

Aged↗

PubMedDate not supplied

The early diagnosis of acute myocardial infarction. Comparison of a simple algorithm with a computer program for electrocardiogram interpretation.

The sensitivity and specificity of electrocardiographic (ECG) interpretation by a simple algorithm was compared with a computer read ECG machine. Clinical data and ECG findings on 264 consecutive patients admitted to a coronary care unit with suspected acute myocardial infarction were prospectively entered into an algorithm with 13 end-points. These end-points were compared with the interpretations of a computer read ECG machine (Marquette MAC PC). 86 patients (32.5%) had confirmed acute infarction. 85% of those with infarction had some form of ST elevation on their initial ECG. Patients with ST elevation presented earlier (4.9 +/- 4.9 versus 8.0 +/- 9.7 hours after symptom onset, p < 0.001), and were older (66.5 +/- 11.0 versus 62.0 +/- 12.5 years, p < 0.01) than those without infarction. According to the algorithm 94.2% of patients with infarction had some form of ECG abnormality, compared with 55.6% of those without infarction (p < 0.001). The area under the receiver operating characteristic (ROC) curve of the algorithm was 92.3% of the area of the graph. This was more (p < 0.01) than the area under the ROC curve of the interpretations of the computer read ECG machine (83.9%). Marked ST elevation with reciprocal changes was the most specific indicators of infarction (Likelihood ratio 51.7). The algorithm, therefore, was comparatively sensitive and specific in the early diagnosis of acute infarction.

Adult↗

PubMed1986

Parallel algorithms for the analysis of two-dimensional electrophoresis gels.

This paper describes some parallel processing algorithms for the analysis of two-dimensional electrophoresis images. The machine used for the processing was the CLIP4 Cellular Array Computer at University College, London, one of the largest processor arrays in the world. Included in this paper are an algorithm for centroid detection, Gaussian fitting algorithms, and an algorithm for the extraction of data out of the cellular array machine. It is shown that these parallel algorithms can run at a speed almost completely independent of the number of spots in the gel images.

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PubMed1995

Neuromagnetic source imaging with FOCUSS: a recursive weighted minimum norm algorithm.

The paper describes a new algorithm for tomographic source reconstruction in neural electromagnetic inverse problems. Termed FOCUSS (FOCal Underdetermined System Solution), this algorithm combines the desired features of the two major approaches to electromagnetic inverse procedures. Like multiple current dipole modeling methods, FOCUSS produces high resolution solutions appropriate for the highly localized sources often encountered in electromagnetic imaging. Like linear estimation methods, FOCUSS allows current sources to assume arbitrary shapes and it preserves the generality and ease of application characteristic of this group of methods. It stands apart from standard signal processing techniques because, as an initialization-dependent algorithm, it accommodates the non-unique set of feasible solutions that arise from the neuroelectric source constraints. FOCUSS is based on recursive, weighted norm minimization. The consequence of the repeated weighting procedure is, in effect, to concentrate the solution in the minimal active regions that are essential for accurately reproducing the measurements. The FOCUSS algorithm is introduced and its properties are illustrated in the context of a number of simulations, first using exact measurements in 2- and 3-D problems, and then in the presence of noise and modeling errors. The results suggest that FOCUSS is a powerful algorithm with considerable utility for tomographic current estimation.

Algorithms↗

PubMed1995

An expectation maximization reconstruction algorithm for emission tomography with non-uniform entropy prior.

A Bayesian image reconstruction algorithm is proposed for emission tomography. It incorporates the Poisson nature of the noise in the projection data and uses a non-uniform entropy as an a priori probability distribution of the image in a maximum a posteriori (MAP) approach. The expectation maximization (EM) method was applied to find the MAP estimator. The Newton-Raphson numerical method whose convergence and positive solutions are proven, was used to solve the EM problem. The prior mean at iteration k was determined by smoothing the image obtained at iteration k-1. Comparisons between the ML and the MAP algorithm were carried out with a numerical phantom that contains a narrow valley region. The ML solution after 50 iterations was chosen as the initial solution for the MAP algorithm, since the global performance of the ML algorithm deteriorates with increasing number of iterations while its local performance in the valley region is always improving. The resulting algorithm is a compromise between ML who has the best local performance in the valley region and the MAP who has the best global performance.

Algorithms↗

PubMed1992

Mathematical characterization of Chaos Game Representation. New algorithms for nucleotide sequence analysis.

Chaos Game Representation (CGR) can recognize patterns in the nucleotide sequences, obtained from databases, of a class of genes using the techniques of fractal structures and by considering DNA sequences as strings composed of four units, G, A, T and C. Such recognition of patterns relies only on visual identification and no mathematical characterization of CGR is known. The present report describes two algorithms that can predict the presence or absence of a stretch of nucleotides in any gene family. The first algorithm can be used to generate DNA sequences represented by any point in the CGR. The second algorithm can simulate known CGR patterns for different gene families by setting the probabilities of occurrence of different di- or trinucleotides by a trial and error process using some guidelines and approximate rules-of-thumb. The validity of the second algorithm has been tested by simulating sequences that can mimic the CGRs of vertebrate non-oncogenes, proto-oncogenes and oncogenes. These algorithms can provide a mathematical basis of the CGR patterns obtained using nucleotide sequences from databases.

Algorithms↗

PubMed1995

A simulation algorithm for ultrasound liver backscattered signals.

In this study, we present a simulation algorithm for the backscattered ultrasound signal from liver tissue. The algorithm simulates backscattered signals from normal liver and three different liver abnormalities. The performance of the algorithm has been tested by statistically comparing the simulated signals with corresponding signals obtained from a previous in vivo study. To verify that the simulated signals can be classified correctly we have applied a classification technique based on an artificial neural network. The acoustic features extracted from the spectrum over a 2.5 MHz bandwidth are the attenuation coefficient and the change of speed of sound with frequency (dispersion). Our results show that the algorithm performs satisfactorily. Further testing of the algorithm is conducted by the use of a data acquisition and analysis system designed by the authors, where several simulated signals are stored in memory chips and classified according to their abnormalities.

Acoustics↗

PubMed1992

Dynamic programming algorithms for biological sequence comparison.

Efficient dynamic programming algorithms are available for a broad class of protein and DNA sequence comparison problems. These algorithms require computer time proportional to the product of the lengths of the two sequences being compared [O(N2)] but require memory space proportional only to the sum of these lengths [O(N)]. Although the requirement for O(N2) time limits use of the algorithms to the largest computers when searching protein and DNA sequence databases, many other applications of these algorithms, such as calculation of distances for evolutionary trees and comparison of a new sequence to a library of sequence profiles, are well within the capabilities of desktop computers. In particular, the results of library searches with rapid searching programs, such as FASTA or BLAST, should be confirmed by performing a rigorous optimal alignment. Whereas rapid methods do not overlook significant sequence similarities, FASTA limits the number of gaps that can be inserted into an alignment, so that a rigorous alignment may extend the alignment substantially in some cases. BLAST does not allow gaps in the local regions that it reports; a calculation that allows gaps is very likely to extend the alignment substantially. Although a Monte Carlo evaluation of the statistical significance of a similarity score with a rigorous algorithm is much slower than the heuristic approach used by the RDF2 program, the dynamic programming approach should take less than 1 hr on a 386-based PC or desktop Unix workstation. For descriptive purposes, we have limited our discussion to methods for calculating similarity scores and distances that use gap penalties of the form g = rk. Nevertheless, programs for the more general case (g = q+rk) are readily available. Versions of these programs that run either on Unix workstations, IBM-PC class computers, or the Macintosh can be obtained from either of the authors.

Algorithms↗