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PubMed1991

An algorithm for the DNA sequence generation from k-tuple word contents of the minimal number of random fragments.

An algorithm is described for generation of the long sequence written in a four letter alphabet from the constituent k-tuple words in the minimal number of separate, randomly defined fragments of the starting sequence. It is primarily intended for use in sequencing by hybridization (SBH) process- a potential method for sequencing human genome DNA (Drmanac et al., Genomics 4, pp. 114-128, 1989). The algorithm is based on the formerly defined rules and informative entities of the linear sequence. The algorithm requires neither knowledge on the number of appearances of a given k-tuple in sequence fragments, nor the information on which k-tuple words are on the ends of a fragment. It operates with the mixed content of k-tuples of the various lengths. The concept of the algorithm enables operations with the k-tuple sets containing false positive and false negative k-tuples. The content of the false k-tuples primarily affects the completeness of the generated sequence, and its correctness in the specific cases only. The algorithm can be used for the optimization of SBH parameters in the simulation experiments, as well as for the sequence generation in the real SBH experiments on the genomic DNA.

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PubMed1992

Evaluation of a 3D reconstruction algorithm for multi-slice PET scanners.

A fully 3D reconstruction algorithm based on filtered backprojection was evaluated for the reconstruction of data obtained with multi-slice positron emission tomography (PET) scanners which have had the septa removed. This algorithm uses forward-projection through the reconstructed images of a 2D subset of the data to complete the 3D dataset thus satisfying the condition of shift invariance. This is followed by 3D filtered backprojection. Axial sampling was doubled by combining adjacent polar angles, thus improving reconstructed axial resolution. The algorithm was tested using real and simulated datasets and gave high quality reconstructions without artifacts over a wide range of imaging conditions. Events are placed accurately throughout the imaging volume as determined by measurements with a MRI/PET registration phantom. The forward-projection step leads to degradation in image resolution due to insufficient axial and transaxial sampling. This effect is amplified if multiple iterations of the algorithm are used, with little decrease in image noise. Changing the filter employed in the initial 2D reconstruction can be used to alter the noise and resolution characteristics of the 3D images. This algorithm has proved very robust at reconstructing 3D PET data and is relatively fast. Those small problems which exist can be attributed to detector sampling problems, especially in the axial direction, which is a consequence of the geometry of these scanners, which are designed primarily for 2D data acquisition.

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PubMed1996

Prediction of HIV peptide epitopes by a novel algorithm.

Identification of promiscuous or multideterminant T cell epitopes is essential for HIV vaccine development, however, current methods for T cell epitope identification are both cost intensive and labor intensive. We have developed a computer-driven algorithm, named EpiMer, which searches protein amino acid sequences for putative MHC class I- and/or class II-restricted T cell epitopes. This algorithm identifies peptides that contain multiple MHC-binding motifs from protein sequences. To evaluate the predictive power of EpiMer, the amino acid sequences of the HIV-1 proteins nef, gp160, gag p55, and tat were searched for regions of MHC-binding motif clustering. We assessed the algorithm's predictive power by comparing the EpiMer-predicted peptide epitopes to T cell epitopes that have been published in the literature. The EpiMer method of T cell epitope identification was compared to the standard method of synthesizing short, overlapping peptides and testing them for immunogenicity (overlapping peptide method), and to an alternate algorithm that has been used to identify putative T cell epitopes from primary structure (AMPHI). For the four HIV-1 proteins analyzed, the in vitro testing of EpiMer peptides for immunogenicity would have required the synthesis of fewer total peptides than either AMPHI or the overlapping peptide method. The EpiMer algorithm proved to be more efficient and more sensitive per amino acid than both the overlapping peptide method and AMPHI. The EpiMer predictions for these four HIV proteins are described. Since EpiMer-predicted peptides have the potential to bind to multiple MHC alleles, they are strong candidates for inclusion in a synthetic HIV vaccine.

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PubMed1996

An algorithm for finding maximal common subtopologies in a set of protein structures.

For the comparison and analysis of protein structures, it is of interest to find maximal common substructures in a given set of proteins. This question is also relevant for motif definition and structure classification. In this paper we describe first a new suitable representation of the secondary structure topology of a protein by an undirected labeled graph. Based on this representation we developed a new fast algorithm that finds all common subtopologies in a set of protein structures. Our method is based on the algorithm by Bron and Kerbosch (1973), which enumerates all maximal cliques in a graph. The main improvement of our algorithm is to restrict the search process to cliques that represent connected substructures. This restriction reduces the number of cliques to be considered during the search process and the size of the search tree drastically. Thus we are able to handle large proteins. Experiments show the efficiency and superiority of our algorithm in comparison with other existing algorithms basing on graph-theoretical methods.

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PubMed1995

Cost-reducing treatment algorithms for antineoplastic drug-induced nausea and vomiting.

A treatment algorithm and preprinted order form developed to reduce the cost of treating antineoplastic drug-induced nausea and vomiting are described. A team including pharmacists, oncologists, and oncology nurses developed a treatment algorithm to reduce the cost of antiemetic therapy for patients receiving antineoplastic therapy at a 719-bed academic medical center. The algorithm incorporated the following concepts: matching antiemetic therapy with the emetogenic potential of the antineoplastic regimen, reducing ondansetron dosages, increasing the ratio of oral to intravenous therapy, and treating delayed-onset nausea and vomiting without using serotonin-receptor antagonists. To help physicians learn and use the treatment algorithm, it was incorporated into an order form for both antineoplastic and antiemetic drugs. Separate order forms were created for pediatric and adult patients. A comparison of outcome data before and after implementation of the practice guidelines showed that the patient outcomes were at least as good after implementation as before. More than a year after the guidelines were implemented, more than 85% of antiemetic regimens prescribed for antineoplastic drug-induced nausea and vomiting were in compliance with the guidelines. A cost avoidance of nearly $205,000 was realized in the first year. Collaboration with oncologists at the start of the care plan was a key element in its success. An antiemetic treatment algorithm, integrated with a preprinted physician order form, was well accepted and has reduced expenses for antiemetic therapy.

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PubMed1994

An algorithm for identifying regions of a DNA sequence that satisfy a content requirement.

We present a dynamic programming algorithm for identifying regions of a DNA sequence that meet a user-specified compositional requirement. Applications of the algorithm include finding C + G-rich regions, locating TA + CG-deficient regions, identifying CpG islands, and finding regions rich in periodical three-base patterns. The algorithm has an advantage over the simple window method in that the algorithm shows the exact location of each identified region. The algorithm has been implemented as a portable C program called LCP (Local Content Program). LCP is extremely efficient in computer time and memory; it instantly locates all regions of a long DNA sequence meeting a given requirement. The LCP program was used to analyze the rabbit alpha-like globin gene cluster sequence.

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PubMed1996

A polynomial-time algorithm for a class of protein threading problems.

This paper presents an algorithm for constructing an optimal alignment between a three-dimensional protein structure template and an amino acid sequence. A protein structure template is given as a sequence of amino acid residue positions in three-dimensional space, along with an array of physical properties attached to each position; these residue positions are sequentially grouped into a series of core secondary structures (central helices and beta sheets). In addition to match scores and gap penalties, as in a traditional sequence-sequence alignment problem, the quality of a structure-sequence alignment is also determined by interaction preferences among amino acids aligned with structure positions that are spatially close (we call these 'long-range interactions'). Although it is known that constructing such a structure-sequence alignment in the most general form is NP-hard, our algorithm runs in polynomial time when restricted to structures with a 'modest' number of long-range amino acid interactions. In the current work, long-range interactions are limited to interactions between amino acids from different core secondary structures. Dividing the series of core secondary structures into two subseries creates a cut set of long-range interactions. If we use N, M and C to represent the size of an amino acid sequence, the size of a structure template, and the maximum cut size of long-range interactions, respectively, the algorithm finds an optimal structure-sequence alignment in O(21C NM) time, a polynomial function of N and M when C = O(log(N + M)). When running on structure-sequence alignment problems without long-range intersections, i.e. C = 0, the algorithm achieves the same asymptotic computational complexity of the Smith-Waterman sequence-sequence alignment algorithm.

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PubMed1997

Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.

Comparison of the secondary structure of the 5' non-coding region of poliovirus 3 RNA derived from the genetic algorithm with the model of Skinner et al. (J. Mol. Biol., 207, 379-392, 1989) demonstrates many of the confirmed structural elements. The genetic algorithm (Shapiro and Navetta, J. Supercomput., 8, 195-201, 1994) generates a population of all possible stems, then mixes, combines, and recombines these stems in multiple iterations on a massively parallel computer, ultimately selecting a most fit structure based on its energy. The secondary structure of the region containing the determinants of neurovirulence was better predicted using the genetic algorithm, whereas the dynamic programming algorithm (Zuker, Science, 244, 48-52, 1989) required phylogenetic comparative sequence analysis to arrive at the correct conclusion. In addition, artificial mutations were introduced throughout this region of the genome and although rearrangements in structure may occur, many structures persisted, suggesting that the given structures thus selected may have evolved to withstand isolated mutations. The genetic algorithm-derived structure for the 5' non-coding region compares favorably with the biological data and functions previously described, and contains all of the 'persistent' structures, suggesting also that the persistence factor may be an aid to validating structures.

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PubMed1997

Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences.

MOTIVATION: Compression algorithms can be used to analyse genetic sequences. A compression algorithm tests a given property on the sequence and uses it to encode the sequence: if the property is true, it reveals some structure of the sequence which can be described briefly, this yields a description of the sequence which is shorter than the sequence of nucleotides given in extenso. The more a sequence is compressed by the algorithm, the more significant is the property for that sequence. RESULTS: We present a compression algorithm that tests the presence of a particular type of dosDNA (defined ordered sequence-DNA): approximate tandem repeats of small motifs (i.e. of lengths < 4). This algorithm has been experimented with on four yeast chromosomes. The presence of approximate tandem repeats seems to be a uniform structural property of yeast chromosomes.

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PubMed1995

Management of vaginal discharge in women treated at a Jamaican sexually transmitted disease clinic: use of diagnostic algorithms versus laboratory testing.

The management of cervical infections is difficult in developing countries because laboratory facilities for diagnosing these infections are seldom available; therefore, syndrome-based management has been recommended by the World Health Organization (WHO). However, such alternative approaches need to be evaluated in real field settings. We used algorithms (flowcharts) for syndromic management of abnormal vaginal discharge to treat 752 women who presented at a Jamaican sexually transmitted disease (STD) clinic. Laboratory testing revealed cervical infection (gonococcal and/or chlamydial) in 34% of these women; trichomoniasis was documented for 25%; and at least one STD was documented for 54% of the women. Use of a clinical algorithm for diagnosing cervical infection was 73% sensitive (95% CI, 67-78) and 55% specific (95% CI, 49-62) when compared with laboratory testing. The risk-assessment-inclusive flowchart developed by WHO was 84% sensitive (95% CI, 80-89) and 40% specific (95% CI, 34-46) for diagnosing cervical infection. Positive predictive values for diagnosing cervical infection with use of the algorithms ranged from 42% to 43%, and negative predictive values ranged from 78% to 81%. The sensitivity of the algorithms for diagnosing trichomoniasis ranged from 85% to 88%. To treat as many infected women as possible, the most sensitive algorithm was selected for routine use in Jamaican STD clinics.

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PubMed1996

A stepwise algorithm for finding minimum evolution trees.

A stepwise algorithm for reconstructing minimum evolution (ME) trees from evolutionary distance data is proposed. In each step, a taxon that potentially has a neighbor (another taxon connected to it with a single interior node) is first chosen and then its true neighbor searched iteratively. For m taxa, at most (m-1)!/2 trees are examined and the tree with the minimum sum of branch lengths (S) is chosen as the final tree. This algorithm provides simple strategies for restricting the tree space searched and allows us to implement efficient ways of dynamically computing the ordinary least squares estimates of S for the topologies examined. Using computer simulation, we found that the efficiency of the ME method in recovering the correct tree is similar to that of the neighbor-joining method (Saitou and Nei 1987). A more exhaustive search is unlikely to improve the efficiency of the ME method in finding the correct tree because the correct tree is almost always included in the tree space searched with this stepwise algorithm. The new algorithm finds trees for which S values may not be significantly different from that of the ME tree if the correct tree contains very small interior branches or if the pairwise distance estimates have large sampling errors. These topologies form a set of plausible alternatives to the ME tree and can be compared with each other using statistical tests based on the minimum evolution principle. The new algorithm makes it possible to use the ME method for large data sets.

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PubMed1995

A simple protein folding algorithm using a binary code and secondary structure constraints.

We describe an algorithm to predict tertiary structures of small proteins. In contrast to most current folding algorithms, it uses very few energy parameters. Given the secondary structural elements in the sequence--alpha-helices and beta-strands--the algorithm searches the remaining conformational space of a simplified real-space representation of chains to find a minimum energy of an exceedingly simple potential function. The potential is based only on a single type of favorable interaction between hydrophobic residues, an unfavorable excluded volume term of spatial overlaps and, for sheet proteins, an interstrand hydrogen bond interaction. Where appropriate, the known disulfide bonds are constrained by a square-law potential. Conformations are searched by a genetic algorithm. The model predicts reasonably well the known tertiary folds of seven out of the 10 small proteins we consider. We draw two conclusions. First, for the proteins we tested, this exceedingly simple potential function is no worse than others having hundreds of energy parameters in finding the right general tertiary structures. Second, despite its simplicity, the potential function is not the weak link in this algorithm. Differences between our predicted structures and the correct targets can be ascribed to shortcomings in our search strategy. This potential function may be useful for testing other conformational search strategies.

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PubMed1997

A digital filterbank hearing aid: predicting user preference and performance for two signal processing algorithms.

OBJECTIVE: In a series of experiments with a wearable binaural digital hearing aid, two hearing aid processing algorithms were compared. Both algorithms provided individual frequency shaping via a seven-band filterbank with compression limiting in the high-frequency channel. They differed in the processing of the low-frequency channel, using dynamic range compression for one (DynEar) and linear processing with compression limiting for the other (LinEar). In a pilot field test we found that LinEar/ DynEar preference based on use time could be predicted from auditory dynamic range data. For the subjects who preferred DynEar, the mean dynamic range was broader for low and mid frequencies and narrower for high frequencies, as compared with the LinEar preference subjects. These groupings were tested as predictors of user preference and performance in a main field test. DESIGN: The main study included 26 hearing aid users with symmetrical sensorineural losses. The algorithms were compared in a one-mo-long blind field test. A data logger function was included for objective recording of the total time each algorithm was used and how the volume controls were used. The preference was based on the time used for each algorithm and on subjective statements. Threshold signal-to-noise ratio (S/N-threshold) for speech was tested, and sound quality ratings were obtained through a questionnaire. We also tested the S/N-thresholds for the subjects' conventional (own) aids. RESULTS: The preference was correctly predicted by the dynamic range data on 12 out of 15 new cases. S/N-thresholds were lower for the preferred fittings compared with the nonpreferred fittings and with the subjects' own aids. In the questionnaire the preferred fittings were rated significantly higher in terms of overall impression and clearness. Because of the systematic way the DynEar-preference subjects adjusted the high-frequency DynEar gain, we speculate that upward spread of masking may have been a factor in preference and performance. Additionally, LinEar-preference subjects' preference and performance might have been influenced by excessive compression ratios with the DynEar processing in these cases. CONCLUSIONS: 1. Preference for DynEar versus LinEar depends on the auditory dynamic range. 2. S/N-thresholds for speech were better for the preferred fittings, which also were rated higher in terms of overall impression of sound quality and clearness.

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PubMedDate not supplied

Retrospective registration of PET and MR brain images: an algorithm and its stereotactic validation.

OBJECTIVE: We present a validation study of an algorithm for retrospective registration of PET and MR brain images. MATERIALS AND METHODS: This algorithm involves two steps. In the first step, the two volumes are reformatted by aligning their interhemispheric fissure planes (midsagittal plane). In the second step, the corresponding planes parallel to the midsagittal plane are further aligned in the reformatted volumes to produce a 3D rigid body registration of the two original volumes. It is an efficient algorithm because both steps are performed in 2D spaces, and in each step only a small number of landmarks are required. A user-friendly system has been implemented to facilitate easy and fast processing of registration and reformatting of image volumes. The accuracy of this algorithm is validated using clinical scans of neurosurgical patients with a stereotaxic frame attached to their skull. The frame-based stereotaxic system provides an effective method for transforming image coordinates from different image volumes into a common coordinate system. This common coordinate system is used for assessing the spatial correspondence of each pixel in the registered image volumes. Validation using the stereotaxic image volumes enables objective estimation of retrospective registration accuracy. RESULTS: Analysis of 11 MR/PET image pairs indicates that our registration method not only is efficient but also provides adequate accuracy for most clinical evaluation of PET studies. CONCLUSION: We have implemented and validated an efficient algorithm for retrospective registration of PET and MR brain images.

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PubMedDate not supplied

A fully automatic multimodality image registration algorithm.

OBJECTIVE: A fully automatic multimodality image registration algorithm is presented. The method is primarily designed for 3D registration of MR and PET images of the brain. However, it has also been successfully applied to CT-PET, MR-CT, and MR-SPECT registrations. MATERIALS AND METHODS: The head contour is detected on the MR image using a gradient threshold method. The head region in the MR image is then segmented into a set of connected components using the K-means clustering algorithm. When the two image sets are registered, the segmentation of the MR image indirectly generates a segmentation of the PET image. The best registration is taken to be the one that optimizes the segmentation induced on the PET image. In this article, the K-means minimum variance criterion is used as a cost function, and the optimization is performed using the method of coordinate descent. RESULTS: The algorithm was tested on 80 H2 15O PET and MR image pairs from 10 subjects. Qualitatively correct results were obtained in all cases. With use of external markers visible in both image modalities, the average registration error was estimated to be < 3 mm. CONCLUSION: The algorithm presented in this article requires no user interaction and can be applied to a wide range of registration problems. Quantitative and qualitative evaluations of the algorithm indicate a high degree of accuracy.

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PubMed1997

Evaluation of a screening algorithm for the diagnosis of genital infections with Neisseria gonorrhoeae and Chlamydia trachomatis among female sexworkers in Bénin.

BACKGROUND AND OBJECTIVES: In developing countries, simple and cheap procedures for the diagnosis of sexually transmitted diseases (STDs) are urgently needed, especially for screening purposes in high risk groups. GOALS: To evaluate the sensitivity and specificity of a screening algorithm for STDs among 364 female sex workers in Bénin, in comparison with reference laboratory tests. STUDY DESIGN: The algorithm relied on the following criteria, which were evaluated in sequence: the presence of endocervical mucopus on visual inspection of the cervix, a positive swab test, or a microscopic examination of vaginal fluid showing more than 10 polymorphonuclear cells per field. The algorithm diagnosed an infection if any one of these criteria was fulfilled. True infectious status was determined by the combined results of culture for Neisseria gonorrhoeae, enzyme immunoassay for Chlamydia trachomatis, and polymerase chain reaction assays for both infections. RESULTS: Gonococcal or chlamydial infection was diagnosed in 39.8% of the study population according to the reference tests. The algorithm had a sensitivity of 57.9% and a specificity of 61.2%. In the presence of Candida sp or Trichomonas vaginalis, specificity decreased to 39.1%, but sensitivity increased to 67.5%. CONCLUSIONS: These results underscore the limitations of simple, nonlaboratory diagnostic tools for screening STDs in high-risk groups in developing countries. Further research is needed to increase the validity--especially the sensitivity--of these algorithms.

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PubMed1989

Development and evaluation of spectral classification algorithms for fluorescence guided laser angioplasty.

Laser angioplasty, or the ablation of atherosclerotic plaque using laser energy, has tremendous potential to expand the scope of nonsurgical treatment of obstructive vascular disease. Clinical laser angioplasty, however, has been hindered by an unacceptable risk of vessel perforation. Laser-induced fluorescence spectroscopy can discriminate atherosclerotic from normal artery and may therefore be capable of guiding selective plaque ablation. To assess the feasibility of utilizing spectral information to discriminate arterial tissue type, several classification algorithms were developed and evaluated. Arterial fluorescence spectra from 350 to 700 nm were obtained from 100 human aortic specimens. Seven spectral classification algorithms were developed with the following techniques: multivariate linear regression, stepwise multivariate linear regression, principal components analysis, decision plane analysis, Bayes decision theory, principal peak ratio, and spectral width. The classification ability of each algorithm was evaluated by its application to the training set and to a validation set containing 82 additional spectra. All seven spectral classification algorithms prospectively classified atherosclerotic and normal aorta with an accuracy greater than 80 percent (range: 82-96 percent). Laser angioplasty systems incorporating spectral classification algorithms may therefore be capable of detection and selective ablation of atherosclerotic plaque.

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PubMed1991

A fast and simple algorithm for the calculation of convective heat transfer by large vessels in three-dimensional inhomogeneous tissues.

A fast and simple algorithm has been presented for the calculation of time-dependent temperature distributions in inhomogeneous vascularized tissue. Three-dimensional anatomical data of tissues and vessel structures are decomposed into elementary cubic nodes by a special digitizing routine with vessels represented by connected strings of vessel nodes. Vessel cross sections may be irregular shaped and/or tapered. Conductive and convective heat transfer was calculated through use of the heat balance technique on each cubic node resulting in an explicit finite difference computational scheme. Employing a three time level scheme, the Fourier stability criterion is circumvented allowing arbitrary time steps to be defined in the algorithm. Time steps as large as 100 times the Fourier restricted one still result in stable and convergent calculations of the stationary temperature distribution. Vessels with different flows and diameters are incorporated by performing a vessel specific second discretization step in time. Using the new algorithm as a mathematical tool the thermal equilibration length of vessel segments have been established under a broad range of geometrical and flow conditions. Validation followed from comparing transient and stationary temperature distributions derived by the proposed algorithm to those from an accurate cylindrical numerical model. Predicted values for the thermal equilibration lengths are compared to an analytical expression and phantom experiments. The algorithm is incorporated in a thermal model being the main part of our hyperthermia treatment planning system.

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