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PubMed1995

A novel transverse gradient coil design for high-resolution MR imaging.

The authors describe a new gradient coil design for high resolution human, animal, specimen, or phantom imaging with high gradient efficiency and a large region of excellent gradient uniformity. Important features of our new design are the simple analytical description of the wire patterns that comprise the design, and ease of construction. Wires are spaced in a sinusoidal distribution around the circumference of the cylinder, and curved in an arcsin shape along the length of the cylinder. This coil produces a magnetic field pointing in a direction transverse to the axis of the coil with a gradient in the direction parallel to the axis of the coil. The same arcsin coil can be used to create a magnetic field pointing in a direction parallel to its axis with a gradient in a direction perpendicular to the coil axis. A prototype coil was constructed; field and inductance calculations were verified. Geometric variations on this coil design were modeled and their performance characteristics compared. This coil design is ideal for rapid implementation of a transverse gradient coil, since no specialized design software is required.

Algorithms↗
PubMed1995

Role of prostate-specific antigen density after applying age-specific prostate-specific antigen reference ranges.

OBJECTIVES: To determine the potential role of prostate-specific antigen (PSA) density (PSAD) in the early detection of prostate carcinoma if we apply age-specific PSA reference ranges (2.5 ng/mL or less for ages 40 to 49 years, 3.5 or less for ages 50 to 59, 4.5 or less for ages 60 to 69, and 6.5 or less for ages 70 to 79. METHODS: We retrospectively reviewed 3234 cases referred to us by urologists for transrectal ultrasound (TRUS) between January 1, 1991, and September 28, 1993. We included 2429 patients in the study, ages 40 to 79 years, with Hybritech or Abbott IMx serum PSA determinations and without previously diagnosed prostate cancer. We performed digital rectal examination (DRE) and TRUS in all cases, and TRUS-guided biopsies when indicated. We used stringent criteria to define 736 cases without clinical evidence of malignancy that were designated as a "benign group." RESULTS: In the benign group, we found serum PSA to increase with age in parallel with the increase in prostate volume with age (r = 0.25 and r = 0.26, respectively). The association between serum PSA and prostate volume was stronger (r = 0.46). Using multiple regression analysis, prostate volume accounted for 18% of the variation in serum PSA, whereas age accounted for only an additional 2%. PSAD, which directly relates serum PSA to prostate volume, showed a weak association with age (r = 0.1). In the entire study population of 2429 cases, 555 patients had negative DRE and TRUS results and a serum PSA level between the age-specific upper limit of normal and 10.0 ng/mL. According to the proposed age-specific algorithm, these patients would have required automatic biopsies. Of these, 315 cases (56.8%) still had a PSAD of less than 0.15. We performed biopsies in 108 of these 315 and detected only two cancers, for a positive biopsy rate (PBR) of 1.9%. The remaining 240 cases had a PSAD of 0.15 or higher, and we performed biopsies in 217 of these cases and detected 59 cancers, for a PBR of 27.2%. CONCLUSIONS: The use of age-specific PSA reference ranges does not totally account for the effect of prostate volume on serum PSA. Therefore PSAD can still be used to reduce safely the number of biopsies performed in patients with negative DRE and TRUS results and a serum PSA level 10.0 ng/mL or less and above the age-specific upper limit of normal.

Adult↗
PubMed1994

Some approaches to the analysis of recurrent event data.

Methodological research in biostatistics has been dominated over the last twenty years by further development of Cox's regression model for life tables and of Nelder and Wedderburn's formulation of generalized linear models. In both of these areas the need to address the problems introduced by subject level heterogeneity has provided a major motivation, and the analysis of data concerning recurrent events has been widely discussed within both frameworks. This paper reviews this work, drawing together the parallel development of 'marginal' and 'conditional' approaches in survival analysis and in generalized linear models. Frailty models are shown to be a special case of a random effects generalization of generalized linear models, whereas marginal models for multivariate failure time data are more closely related to the generalized estimating equation approach to longitudinal generalized linear models. Computational methods for inference are discussed, including the Bayesian Markov chain Monte Carlo approach.

Algorithms↗
PubMed1994

Evaluation and quality control of a commercial 3-D dose compensator system.

A commercially available software/hardware system for automated design and fabrication of three-dimensional dose compensator molds has been tested for accuracy and precision as well as for its ability to provide adequate dose compensation at depth. To date, we have used this system to treat more than 50 patients with either head and neck or lung malignancies. In 19 head and neck patients (38 compensators) the use of a customized compensator resulted in an average reduction of dose variance in the target volume from 13.8% (range of 7%-21%) with uncompensated parallel-opposed fields to 4.5% (2%-7%) with custom-compensated parallel-opposed fields. A similar reduction was seen in the dose variation across lung tumor volumes. The custom compensators were also tested for accuracy of fabrication and positioning; both were found to be accurate within +/- 1 mm of the design specifications for all compensators tested. Last, the dosimetric properties of the compensators were studied. The ratios of measured open-beam dose profiles to measured compensated-beam dose profiles were compared with the ratio of similar profiles calculated with a treatment planning system. These ratios were equal within +/- 2.9%, thus providing evidence of the fidelity of the compensator to its design and the accuracy of the treatment planning algorithm that designs 34 each compensator.

Algorithms↗
PubMed1996

GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space.

GEOMETRY is a software package for the analysis of nucleotide sequences using the method of statistical geometry in sequence space. The package consists of programs performing estimation of the average geometry of sequence quartets, analysis of positional variability and computer simulation of parallel and tree-like sequence divergence with user-defined parameters. It provides an independent tool for evaluation of the reliability of conventional phylogenetic trees and calibration of the time of sequence divergence. GEOMETRY may be of interest for all scientists engaged in the study of molecular phylogeny. The package is available by anonymous FTP from ftp.bionet.nsk.su, directory /incoming/molevol/geom.exe, and will be available from EMBL file server (URL: http://@www.ebi.ac.uk)

Algorithms↗
PubMed1991

Parallel cascade identification and kernel estimation for nonlinear systems.

We consider the representation and identification of nonlinear systems through the use of parallel cascades of alternating dynamic linear and static nonlinear elements. Building on the work of Palm and others, we show that any discrete-time finite-memory nonlinear system having a finite-order Volterra series representation can be exactly represented by a finite number of parallel LN cascade paths. Each LN path consists of a dynamic linear system followed by a static nonlinearity (which can be a polynomial). In particular, we provide an upper bound for the number of parallel LN paths required to represent exactly a discrete-time finite-memory Volterra functional of a given order. Next, we show how to obtain a parallel cascade representation of a nonlinear system from a single input-output record. The input is not required to be Gaussian or white, nor to have special autocorrelation properties. Next, our parallel cascade identification is applied to measure accurately the kernels of nonlinear systems (even those with lengthy memory), and to discover the significant terms to include in a nonlinear difference equation model for a system. In addition, the kernel estimation is used as a means of studying individual signals to distinguish deterministic from random behaviour, in an alternative to the use of chaotic dynamics. Finally, an alternate kernel estimation scheme is presented.

Algorithms↗
PubMed1992

Detection, classification and 3D reconstruction of biological macromolecules on hypercube computers.

In this work we present results of the mapping on hypercube computers of some of the key steps involved in the procedure for 3D structural determination from transmission electron microscopy images. The goal is the introduction of parallel processing tools in the field of electron microscopy image processing. We show how the rich topology of the hypercube, combined with an efficient programming strategy, allows for order-of-magnitude increase in computational capacity for such time-consuming tasks as calculation of multidimensional FFT's, cross-correlation coefficients, fuzzy partitioning functionals and the filtered back-projection 3D reconstruction method.

Algorithms↗
PubMed1992

Insect motion perception.

The first step in this work of reconstruction of a theory of insect vision was to demonstrate that visual behaviour relies on scanning by self-motion and apparently involves measurement of angular velocities of contrasts moving across the eye. The next step was to demonstrate that parallax is also significant as a way of segmenting the visual scene into separate objects. There followed a series of experiments to rule out the existing theory that motion perception depends on autocorrelation, and at the same time an alternative theory was developed. The new theory assumes that at the level of the optic medulla there are numerous parallel channels on each visual axis, representing different neurons, all looking out for their specific combination of signals. The combinations are formed by positive, negative or no-change temporal contrasts at two adjacent visual axes at two successive times, forming 3(4) = 81 possible templates. Simulation of this highly parallel system shows that it can represent the moving image in a compact form that would be adequate to explain what is known for motion and form vision (but not colour vision) in insects. Form, like colour, would be seen as the ratio of numbers of responses of particular templates, in the same way that colours are seen as ratios of responses of receptors for different wavelengths.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed1989

Assessment of the vasomotility of epicardial coronary arteries with quantitative coronary angiography.

Quantitative in vivo analysis of the vasomotility of epicardial coronary arteries is based on the measurement of changes of the vessel diameters. Vessel contours can be determined with the help of a precision caliper by the investigator or with computer-assisted geometrical analysis systems applying a contour detection algorithm; the variability of the results from repeated coronary diameter measurements in the identical film frame is comparably low with all systems (less than or equal to 0.12 mm standard deviation). When investigating the influence of an intervention on coronary vasomotility the variability of the measurements can only be kept low by careful standardization of the entire method. Repeated coronary angiograms are performed in identical angiographic projections (mono- or biplane) with standardization of the inspiratory status of the patient and of the rate of contrast material injection (automatic injection pump). For quantitative analysis all coronary segments with a diameter greater than 1 mm which are clearly outlined, free from overlaps, and mainly run parallel to the image plane, are selected by the investigator in preferably end-diastolic cineframes. Whereas with a caliper and with most of the semi-automatic edge detection systems the segment diameter can only be measured at particular sites defined by the investigator, few systems are able to analyze and average the diameter over the entire segment length. The variability of measurements of the minimal diameters of coronary stenoses in different cine frames is particularly high; therefore, only distinct changes of this parameter (e.g. with the CAAS-system greater than 0.24 mm) may be considered significant.(ABSTRACT TRUNCATED AT 250 WORDS)

Cineangiography↗
PubMed1994

Combination (multiple) testing for myocardial infarction using myoglobin, creatine kinase-2 (mass), and troponin T.

We retrospectively determined the mass concentrations of myoglobin, creatine kinase-2 (CK-2), and troponin T in serial samples from 80 patients with confirmed myocardial infarction (MI) and 60 non-MI patients. Results from receiver operating characteristic curve analyses show that all three tests are comparable in their diagnostic utility within the first 12 h of infarction. Decision thresholds were selected at a constant rule-in specificity of 95% and rule-out sensitivities of 95% at, respectively, 3-6, 6-9, and 9-12 h intervals after the onset of symptoms. Test sensitivities and specificities were compared for each, used as: a single test; two-test parallel combination; three-test parallel combination; two-test series combination; and three-test series combination. Our results from combination testing indicate what for the early diagnosis of MI, a single serum myoglobin measurement has diagnostic utility at 3 h after the onset of symptoms, and myoglobin and CK-2 (mass) in combination later than 3 h following the onset of symptoms. Serum troponin T is diagnostically similar to CK-2 (mass), although it has superior cardiac-tissue specificity, but it is not as yet commercially available as a "stat" test. Therefore, we recommend using troponin T as a confirmatory test 9 h after the onset of MI. Based on our findings, we suggest a testing algorithm for the early biochemical diagnosis of MI.

Adult↗
PubMed2026

FFC: a scalable FASTA compressor.

SUMMARY: FASTA is a widely used text-based format for storing nucleotide and protein sequences. The existing FASTA compressors usually focus on (slightly) improving the compression ratio, not on practical performance. We present FFC, a scalable FASTA compressor that achieves average compression speeds 4.7× and 11.4× higher than two high-performance compressors, zstd and NAF, respectively, across a benchmark set of seven single genomes. It also delivers average decompression speeds 3.5× and 2.7× higher than zstd and NAF, respectively. Although a chunk-based zstd variant with parallel decompression, pzstd, almost matches FFC speed, its compression ratio is on average by 23% worse than FFC's. For the experiment, a 14-core workstation and a RAM disk (to reduce the impact of I/O) were used. AVAILABILITY AND IMPLEMENTATION: FFC is freely available at github.com/kowallus/ffc and also as a Zenodo repository at 10.5281/zenodo.18892353, and the used datasets at 10.5281/zenodo.18873744.

Data Compression↗
PubMed1996

Criticality and parallelism in combinatorial optimization.

Local search methods constitute one of the most successful approaches to solving large-scale combinatorial optimization problems. As these methods are increasingly parallelized, optimization performance initially improves but then abruptly degrades to no better than that of random search beyond a certain point. The existence of this transition is demonstrated for a family of generalized spin-glass models and the traveling salesman problem. Finite-size scaling is used to characterize size-dependent effects near the transition, and analytical insight is obtained through a mean-field approximation.

Algorithms↗
PubMed1994

An evaluation of lesion detectability with cone-beam, fanbeam and parallel-beam collimation in SPECT by continuous ROC study.

UNLABELLED: To evaluate lesion detectability for clinical evaluation of cone-beam (CB), fanbeam (FB) and parallel-beam (PB) collimator sensitivity, experimentally acquired phantom data were used to assess the advantage of CB collimation over conventional collimation. METHODS: Lesion detectability with CB, FB and PB collimation in SPECT was compared using a three-dimensional brain phantom and continuous receiver operating characteristic (CROC) analysis. A simulated cold lesion was located near the posterior portion of the thalamus. High count density scans of this phantom were acquired with CB, FB and PB collimators with similar resolution. These projections were scaled to count levels which reflected the measured sensitivities of the three collimators. Computer-generated Poisson noise was added to the projections to produce uncorrelated data sets. Images were reconstructed using a filtered backprojection algorithm. All reconstructions used a Hann filter with multiplicative attenuation correction. Each of seven trained observers viewed 288 sets of images and indicated the certainty of perceiving a cold lesion at a specified location by a rating of 0-100. Each image set contained four adjacent slices centered on the lesion to minimize partial volume effects. The program LABROC4 was used to fit CROC curves to individual observers' ratings. A t-test for paired data was performed on the individual areas. RESULTS: The average areas (standard deviations) under CROC curves for CB, FB and PB were 0.89 (0.03), 0.83 (0.05) and 0.76 (0.04), respectively. The differences of the areas were statistically significant with all two-tailed p values < 0.02. CONCLUSION: These results demonstrate that cold lesions in the posterior portion of the thalamus are best detected by images obtained using CB followed by FB and PB collimation.

Brain↗
PubMedDate not supplied

3D base: a geometrical data base system for the analysis and visualisation of 3D-shapes obtained from parallel serial sections including three different geometrical representations.

In this paper we discuss a geometrical data base that includes three different geometrical representations of one and the same reconstructed 3D shape: the contour-pile, the voxel enumeration, and the triangulation of a surface. The data base is tailored for 3D shapes obtained from plan-parallel serial sections. It is explained how this geometrical data base is useful with the different processing approaches of a 3D shape, such as analysis and visualisation. Methods of conversion between the geometrical representations are discussed. Examples of the operation of the data base as it is embedded in a data base management system are given by illustrations of retrieval of geometrical information.

Algorithms↗
PubMed1995

Recognition of Telugu characters using neural networks.

The aim of the present work is to recognize printed and handwritten Telugu characters using artificial neural networks (ANNs). Earlier work on recognition of Telugu characters has been done using conventional pattern recognition techniques. We make an initial attempt here of using neural networks for recognition with the aim of improving upon earlier methods which do not perform effectively in the presence of noise and distortion in the characters. The Hopfield model of neural network working as an associative memory is chosen for recognition purposes initially. Due to limitation in the capacity of the Hopfield neural network, we propose a new scheme named here as the Multiple Neural Network Associative Memory (MNNAM). The limitation in storage capacity has been overcome by combining multiple neural networks which work in parallel. It is also demonstrated that the Hopfield network is suitable for recognizing noisy printed characters as well as handwritten characters written by different "hands" in a variety of styles. Detailed experiments have been carried out using several learning strategies and results are reported. It is shown here that satisfactory recognition is possible using the proposed strategy. A detailed preprocessing scheme of the Telugu characters from digitized documents is also described.

Algorithms↗
PubMed1990

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. I. Generation of partition functions and mass balance equations.

The thermodynamics of binding of a ligand A and/or proton H to a macromolecule M is treated by the partition function method. In complex systems, the representation of the equilibria by means of cumulative constants beta PQR used as coefficients in partition functions ZM, ZA, and ZH is ill-suited to least-squares refinement procedures because the cumulative constants are interrelated by common cooperativity functions gamma j(i) and common site affinity constants kappa j. There is therefore the need to express ZM, ZA, ZH as functions of site constants kappa j and cooperativity coefficients bj. This is done by developing an algebra of partition functions based on the following concepts: (i) factorability of partition functions; (ii) binary generating function Jj = (1 + kappa j[Y])i tau for each class j of sites, represented by column (Jj) and row (Jj) vectors; (iii) cooperativity between sites of one class described by functions gamma j(i), represented by diagonal matrices gamma j; (iv) probability of finding microspecies represented by elements of tensor product matrix Ll = (J1)[J2]; (v) statistical factors mij obtained from Newton polynomials, Jj; (vi) power operators Oi', O(i-l)', and O(i tau-l)', transforming vectors Jj; and (vii) operators Oi or O(i-l) indicating tensor products of i or (i-l) vectors Jj. Vectors Jj combined in tensors Ll give rise to both an affinity/cooperativity space and a parallel index space. The partition functions ZM, ZA, and ZH and the total amounts TM, TA, and TH can be obtained as an appropriate sum of elements of matrices Ll, each of which is represented in an index space by a combination p1, p2,...q1, q2,...r1, r2,... of indices ij. From these indices the contribution of that element to partition function ZM, ZA, or ZH and to total amount TM, TA, or TH is calculated in the affinity/cooperativity space as product of factors: [i tau !/i !(i tau-i)!]kappa ij(exp[bj (i-1)i])[X]i, i being any index p, q, r and X any component M, A, or H. Future applications of this algorithm to practical problems of macromolecule-ligand-proton equilibria are outlined.

Binding Sites↗
PubMed1993

Higher-order structure in regularity detection.

In three experiments a simple Euclidean transformation (reflection, translation, rotation) was applied to collections of twelve dots in such a way that they contained equal lower-order structure, defined on the pairwise grouping of elements with their partner following transformation (e.g. parallel virtual lines), but differed in the presence vs absence of higher-order structure, defined on pairs of pairwise groupings (e.g. virtual quadrangles with correlated angles). Based on the much better performance levels (d') in the case of additional higher-order structure, we conclude that global regularities are easier to detect when the local correspondences are supported by higher-order ones formed between them. These enable the lower-order groupings to spread out across the whole pattern very rapidly (called bootstrapping). As a preliminary attempt to specify these principles, we proposed a working model with two basic components: first, a function expressing the cost of a perceptual grouping or the lack of regularity, and, secondly, an algorithm based on simulated annealing to minimize the cost function. The simulation results obtained with our current implementation of these principles showed satisfactory qualitative agreement with human regularity detection performance. Finally, the theory was shown to capture the essence of a large number of grouping phenomena taken from diverse domains such as detection of symmetry in dot patterns, global structure in Glass and vector patterns, correspondence in stereoscopic transparency and apparent motion. Therefore, we are convinced that, in principle, the mechanism used by the human visual system to detect regularity incorporates something like bootstrapping based on higher-order structure. We regard this as a promising step towards unraveling the intriguing mechanisms of classic Gestalt phenomena.

Cues↗
PubMed1995

Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer.

Rapid growth of protein structures database in recent years requires an effective approach for objective comparison and classification of deposited protein structures. We describe a novel method for structure comparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the OCCO pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acid residues) from protein three-dimensional coordinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of letter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to rapidly align and classify these one-dimensional structure profiles. We have developed and implemented weighted scoring matrix to identify structural classes based on commonly found structural motifs. The results of our experiments are in good agreement with the traditional protein structure classification schemes. One-dimensional structure profiles significantly improve efficiency of structure comparison and classification.

Algorithms↗