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Results for “Parallel Algorithms”

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At least 127 records · Page 7Linked to original sources

PubMed1991

A software-controlled EKG simulator.

This design allows generation of a wide range of waveforms from subaudio to ultrasonic directly via software. Waveforms may be calculated on the fly by suitable algorithms or produced from previously created lookup tables. The heart of the design is a fast 16-bit processor which directly executes the Forth programming language. A simple R/2R digital-to-analog converter is coupled to a parallel output port to produce the desired waveforms. This device has been used to generate realistic-appearing normal and abnormal EKG tracings in the lab.

Algorithms↗

PubMed1989

Standard forms of dentition and mandible for applications in rotational panoramic radiography.

Mathematical expressions describing the average form and size of the dentition and the mandible are presented. These expressions should be of value in applications of panoramic radiography when reference to an average standard jaw form is of interest. Data were collected from axial radiographs of 35 males and 35 females of three ethnic groups: Mexican-Americans, black Americans and American and Scandinavian Caucasians. Curves were traced on the axial radiographs representing the dentition and the mandible and points along these curves digitized. Mathematical expressions were established using advanced algorithms for orthogonal polynomial curve fitting, i.e. perpendicular distances to the curved dentition and mandible were minimized rather than distances parallel to the y-axis in an arbitrarily chosen coordinate system. The standard deviations around the polynomials defining the average curves are demonstrated and expressions for calculating the continuously varying standard deviations are given.

Dentition↗

PubMed1989

Fully automated measurements by light microscopy of tissue sections using a cellular array computer.

Software was developed for the acquisition, segmentation and analysis of microscopic OD-images on a VICOM digital image processor, extended with a VISIOMORPH morphoprocessor board. The delineation algorithms for peroxisomes, lysosomes, and nuclei in liver, kidney, and adrenal gland sections start by thresholding the difference between the original image and a low pass filtered version. The resulting binary mask is then processed by morphological operations in order to produce an object overlay. The efficiency of the programs is evaluated by comparing delineated objects at different OD-levels, created by varying the stain or by multiplying the original pixel values with constant factors. Manual delineation on some images is also used as a reference. More complex algorithms are used for the delineation of muscle fibres in ATP-ase-stained sections and immunocytochemically labelled cells in monolayer preparations. Muscle images from parallel sections with different stainings are matched with a coordinate transform, enabling the transfer of the object mask from a single delineated image to the unprocessed images and thus obtain all necessary information for fibre classification. After segmentation, the OD-images and their object overlays are fed into a data extraction program, measuring for each delineated object user-selected features. Data are sent to a VAX for statistical interpretation.

Adrenal Cortex↗

PubMed1986

Eye-hand-coordination: a model for computing reaction times in a visually guided reach task.

A model is described which provides a simple algorithm to compute the reaction times of saccadic eye movements and reach movements aimed at a single visual target. It is assumed, that the two movements are prepared in parallel and initiated independently unless the preparation of the saccade for some reason takes longer than the preparation of the reach movement. In the latter case the final command to execute the reach movement is synchronized with that to execute the eye movement and therefore the corresponding reaction times are highly correlated in a one-to-one relationship. Random variables are used to predict sets of data that are directly comparable with the experimental results. The algorithm includes the effects of daily practice (learning). The structure of the model and its computational results will be compared with the physiological data from monkey and man.

Algorithms↗

PubMed1992

Combined therapy for obese type 2 diabetes: suppertime mixed insulin with daytime sulfonylurea.

Combined insulin and sulfonylurea therapy for type 2 diabetes may improve the effectiveness of a single injection of insulin, thereby postponing the need for multiple injections. This concept was tested in 21 obese subjects imperfectly controlled by 20 mg of glyburide daily in a double masked, placebo-controlled, parallel design, 16-week protocol. Premixed 70% NPH/30% Regular insulin was taken before supper, and the dosage was adjusted weekly by an algorithm seeking nearly normal fasting glycemia. Eleven subjects using insulin plus 10 mg glyburide before breakfast had lower mean fasting glucose at 10-16 weeks than 10 subjects using insulin with placebo (mean +/- SEM; 5.9 +/- 0.3 versus 7.5 +/- 0.7 mmol/L; p less than 0.05), and had a greater decrement of glycosylated hemoglobin from baseline values (1.3 +/- 0.1 versus 0.8 +/- 0.2% A1, p less than 0.05). After 16 weeks the combined therapy group used half as much insulin as the insulin-only group (50 +/- 5 versus 101 +/- 13 units/d; p less than 0.01). Fasting serum free insulin values increased 58% from baseline after insulin therapy in the insulin-only group (p less than 0.05) but did not increase with combined therapy. Weight gain was similar in the two groups. These data support this form of combined therapy as one option for treating obese persons with type 2 diabetes no longer responsive to oral therapy alone.

Adult↗

PubMed1991

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations.

Algorithms↗

PubMed1992

An algorithm for protein engineering: simulations of recursive ensemble mutagenesis.

An algorithm for protein engineering, termed recursive ensemble mutagenesis, has been developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Starting from partially randomized "wild-type" DNA sequences, a highly parallel search of sequence space for peptides fitting an experimenter's criteria is performed. Each iteration uses information gained from the previous rounds to search the space more efficiently. Simulations of the technique indicate that, under a variety of conditions, the algorithm can rapidly produce a diverse population of proteins fitting specific criteria. In the experimental analog, genetic selection or screening applied during recursive ensemble mutagenesis should force the evolution of an ensemble of mutants to a targeted cluster of related phenotypes.

Algorithms↗

PubMed1987

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.

The crystal structure of M4 apo-lactate dehydrogenase from the spiny dogfish (Squalus acanthius) was initially refined by a constrained-restrained, and subsequently restrained, least-squares technique. The final structure contained 286 water molecules and two sulfate ions per subunit and gave an R-factor of 0.202 for difraction data between 8.0 and 2.0 A resolution. The upper limit for the co-ordinate accuracy of the atoms was estimated to be 0.25 A. The elements of secondary structure of the refined protein have not changed from those described previously, except for the appearance of a one-and-a-half turn 3(10) helix immediately after beta J. There is also a short segment of 3(10) helix between beta C and beta D in the part of the chain that connects the two beta alpha beta alpha beta units of the six-stranded parallel sheet (residues Tyr83 to Ala87). Examination of the interactions among the different elements of secondary structure by means of a surface accessibility algorithm supports the four structural clusters in the subunit. The first of the two sulfate ions is in the active site and occupies a cavity near the essential His195. Its nearest protein ligands are Arg171, Asp168 and Asn140. The second sulfate ion is located near the P-axis subunit interface. It is liganded by His188 and Arg173. These two residues are conserved in bacterial lactate dehydrogenase and form part of the fructose 1,6-bisphosphate effector binding site. Two other data sets in which one (collected at pH 7.8) or both (collected at pH 6.0) sulfate ions were replaced by citrate ions were also analyzed. Five cycles of refinement with respect to the pH 6.0 data (25 to 2.8 A resolution) resulted in an R value of 0.191. Only water molecules occupy the subunit boundary anion binding site at pH 7.8. The amino acid sequence was found to be in poor agreement with (2Fobs-Fcalc) electron density maps for the peptide between residues 207 and 211. The original sequence WNALKE was replaced by NVASIK. The essential His195 is hydrogen bonded to Asp168 on one side and Asn140 on the other. The latter residue is part of a turn that contains the only cis peptide bond of the structure at Pro141. The "flexible loop" (residues 97 to 123), which folds down over the active center in ternary complexes of the enzyme with substrate and coenzyme, has a well-defined structure. Analysis of the environment of Tyr237 suggests how its chemical modification inhibits the enzyme.

Amino Acid Sequence↗

PubMed1989

Nuclear medicine in the 1990s: a quantitative physiological approach.

This paper describes the potential advantages to medical diagnosis and treatment that might be obtained from the wider application of positron emission tomography as a clinical tool. Developments along the lines suggested here will require a radical change in thinking from both clinicians and the medically related scientific community in the UK and some enlightened and resourceful funding from a mixture of charitable, industrial and government sources. If these ideas are to be pursued successfully, then the work must start now on a much wider scale than is presently perceived in the UK, and close collaboration between physicists, engineers, chemists, biochemists, clinicians and industrialists is needed. Furthermore, it is imperative that the scientific developments now underway in silicon technology, parallel data processors, biochemical and pharmacological processes and even high-temperature superconductors be kept under close and constant review by those associated with the technological advancements of medicine, so that the value of such developments is rapidly transferred to applications to medicine. This must include closer relationships between academic medicine and science than is the general rule in the UK at present. In conclusion, the scenario presented here includes the installation of regional cyclotron facilities to provide a large number of institutions in the UK with positron-emitter labelled radiopharmaceuticals. Additionally, agents labelled with radionuclides from in-house generators and other already existing higher-energy cyclotrons will provide a versatile and valuable range of radiopharmaceuticals for the study of human disease. These developments must be supported by the manufacture of lower-cost positron camera systems, as suggested here, connected to high-data-rate parallel processors to provide images of body function and to determine the effects brought about by disease. These images may then be processed using algorithms based on kinetic models of the body systems to provide information about the basic biochemical and physiological processes of the body. Such a development could have a profound effect on our knowledge of human disease and on our ability to control and treat it successfully.

Forecasting↗

PubMed1991

Parallel simulated annealing for emission tomography.

A method for implementing simulated annealing in parallel to speed up the execution of emission tomography (ET) image reconstruction is presented. A high degree of parallelism can be attained by using a parallel-acceptance partitioning strategy, in which perturbations to subsets of the estimate are evaluated in parallel. However because the point spread function in ET imaging systems is globally dependent, processors cannot update the current estimate independently. Consequently, processors must be synchronized each time a perturbation is accepted to avoid introducing error. This can produce excessive communications overhead, especially when the acceptance rate is high. In this paper an energy function is constructed to reduce the synchronization requirements by using a reformulation of the log-likelihood function from the expectation maximization (EM) algorithm. The approach is to change the global dependence in the energy function from the current estimate to the estimate generated during the last iteration. The synchronization requirements for guaranteed convergence are then significantly reduced from once per acceptance to once per iteration. This parallel implementation on 54 Inmos T800 transputers connected in a ring topology resulted in execution times that were almost 50 times faster than on a VAX 8600.

Algorithms↗

PubMed1989

A low-cost single-board solution for real-time, unsupervised waveform classification of multineuron recordings.

We describe a low-cost single-board system for unsupervised, real-time spike sorting of recordings from a number of neurons on a single microelectrode. The maximum number of spike classes depends on the quality of the recording; it will typically be between 2 and 5. The spike sorter communicates with a conventional microcomputer through a standard serial port (RS232). For typical firing rates as measured in the mammalian central nervous system, this set-up will accommodate up to some 10 parallel spike sorters for as many separate microelectrodes.

Algorithms↗

PubMed1988

Refined evaluation of the exponential curve parameters and initial exchange rate constant for 22Na+ washout in cultured human skin fibroblasts.

A technique is proposed to evaluate the exponential curve parameters and the initial exchange rate constant (kie) for 22Na+ washout from cultured human skin fibroblasts. After loading with the isotope, the cells were subjected to cold washing and warming steps. A desaturation curve for 22Na+ washout was developed including the activity in the warming medium that corresponded to t = 0 min. Using nonlinear regression analysis, a general three exponential function adequately described the 22Na+ washout in the time interval of 0-70 min. A back extrapolation was performed to estimate the initial time (ti; a negative number) when the total activity was present in the cells. The ti was substituted into the first derivative function of the three exponents to yield the kie. Calculated from the equilibrium distribution of 22Na+ and the specific activity of the medium, the concentration of Na+ (in mM; mean +/- SD) for fibroblasts of two individuals were 13.3 +/- 2.3, n = 3, and 19.0 +/- 5.2, n = 4. This indicates that the washout originated mainly or exclusively from the cellular milieu. Therefore, the kie represents the equilibrium exchange rate constant for Na+ washout from an inhomogeneous cell-related space. Multiple experiments demonstrated that the kie value for the two subjects were significantly higher than the initial slopes of the washout curves (kA), a commonly used parameter to characterize Na+ washout, and significantly lower than the slopes of the fastest exponential components (k3): kie = 0.531 +/- 0.017, kA = 0.502 +/- 0.019, and k3 = 0.557 +/- 0.017 min-1 (n = 3) for one subject, and kie = 0.567 +/- 0.065, kA = 0.479 +/- 0.031, and k3 = 0.667 +/- 0.094 min-1 (n = 6) for the other subject. The respective equilibrium exchange rates for these cells, namely the products of kie and cellular Na+ contents, were 1.10 +/- 0.16 and 1.19 +/- 0.24 nmole/10(5) cells. Using the exponential curve parameters, analytical solutions of a serial model and a parallel model with three compartments were performed. According to these analyses the major portion of the cellular Na+ comprises a fast exchangeable cellular compartment. The relative size of this compartment (expressed as a fraction of total cellular Na+ content) for fibroblasts of the two subjects was 96.2 and 89.2% for the serial model and 96.1 and 89.3% according to the parallel model.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMed1990

Evaluation of a human immunodeficiency virus test algorithm utilizing a recombinant protein enzyme immunoassay.

Many truly human immunodeficiency virus (HIV) antibody-negative serum samples may be unnecessarily subjected to costly and time-consuming Western blots (immunoblots). An investigation was undertaken to evaluate the efficiency of using a recombinant protein-based enzyme immunosorbent assay (EIA; Cambridge BioScience [CBC] Recombigen HIV EIA) as an adjunct to whole viral lysate EIA. A total of 2,212 serum samples which had been screened by viral lysate EIA were tested by CBC EIA in parallel with the Western blot. The sensitivity and specificity of the CBC kit were 99.9 and 99.7%, respectively. Positive and negative predictive values were 99.7 and 99.9%, respectively. The high sensitivity of this kit and its high negative predictive value make it an attractive addition to an HIV testing algorithm by reducing the number of Western blot tests on truly antibody negative serum samples.

Acquired Immunodeficiency Syndrome↗

PubMedDate not supplied

Calculation of the uncertainty in the dose delivered during radiation therapy.

There is, inevitably, uncertainty in our knowledge of the dose at any point within an irradiated patient. A technique is presented for estimating this uncertainty by performing three parallel calculations, one using nominal values and the others extreme values of the parameters upon which the dose depends. Such calculations can be made with almost any algorithm for calculating dose. They result in an estimate, at some specified confidence level which is determined by the data used, of the range of dose likely at any point. Such calculations should help therapists to avert over- or underdosage which might not be evident in conventional calculations of the nominal dose.

Humans↗

PubMed1992

Effect of the signal-to-noise ratio on the quality of linear estimation reconstructions of distributed current sources.

Currently, linear estimation reconstruction is the only feasible method for extracting information about spatially distributed current sources from measurements of neural magnetic fields. We present the results of a systematic study of the effect of the signal-to-noise ratio on the imaging quality of one such algorithm in over-as well as undetermined circumstances. In particular, we will discuss the necessary trade-off between the contradictory goals of a minimum norm of the reconstructed current density distribution and of a minimal deviation of the reconstructed fields from the measured fields. As an example, we show the reconstruction of a simple arrangement of two nearly parallel dipoles in two different depths inside a spherical volume conductor, discussing the differences between the computer simulation without noise and simulation with a realistic noise level.

Algorithms↗

PubMed1990

Order-disorder phenomena in myelinated nerve sheaths. I. A physical model and its parametrization: exact and approximate determination of the parameters.

An algorithm is developed for the analysis of the X-ray scattering spectra of lamellar systems, by reference to a precise physical model. The model consists of identical planar lamellae (the motif), all parallel and stacked in a one-dimensional crystal with four types of defect: stacking disorder, finite size of the crystallites, and presence of diffuse and blank scattering. In addition, the spectra are distorted by collimation aberrations. In order to evaluate the effects of these distortions, the following assumptions are made: (1) beyond some point Slimit the intensity curve can be expressed as a function of a (small) number of parameters; (2) the blank scattering, restricted to very small angles, can be identified and eliminated; and (3) the diffuse scattering is entirely defined by the values of idiff(h/D) at the lattice Sh = h/D (h is a positive integer less than or equal to DSlimit). These assumptions lead to an expression of the whole of the intensity curve as a function of a finite number of parameters: the average D and the variance sigma 2D of the repeat distance, the average number [N] of lamellae per crystallite, the set [idiff(h/D)] and the set [imotif(k/2D)] (where k is a positive integer), which defines the structure of the motif. An algorithm is proposed to determine the value of the various parameters. The derivation of the algorithm involves several operations: construction in real space of periodic functions whose motifs are step-sections of the autocorrelation function; expression in reciprocal space, and in terms of the experimental scattering curves, of the Fourier transform of those periodic functions; analysis of the properties of the two functions. The algorithm is tested using a variety of simulated scattering curves whose parameters [imotif(k/2D)], [idiff(2/D)], D, sigma D, [N] (and collimation distortions) are within the range commonly encountered in experimental conditions. The results show that the values of the parameters retrieved by the algorithms are very close to those used in the simulation. The calculations are fast and easy to implement on a computer. The main virtues of the algorithm are (1) to determine the values of all the parameters at once, eliminating most of the intermediate (and questionable) manipulations (separation of signal from noise, discrimination of overlapping reflections, integration of the intensities) and (2) to yield the continuous intensity curve of a single motif.

Algorithms↗

PubMed1987

Arbitrary oblique image sections for 3-D radiation treatment planning.

Methods for selecting and computing arbitrary image sections for displaying anatomic and isodose information for three-dimensional treatment planning are investigated. Selection of the desired plane may be made by defining a plane that is perpendicular to an existing image section (called the base image) and passing through a line on the base image. Alternatively, the anatomic structures displayed perspectively in three dimensions as a series of contours that can be rotated and translated may be used to define an arbitrary plane for image reconstruction. The viewing screen is considered to be the plane of interest. As a typical three-dimensional image of 30 to 60 sections requires considerable computer storage (on the order of 25 megabytes), a reconstruction algorithm may need extensive memory space or CPU and disk I/O time. Of the schemes examined, we believe the following is the most efficient. One pair of images is read from the disk at a time in sequence and intersections of the rows of the cutting plane with the box formed by the consecutive images are computed. Pixel values of all points between the given images are computed by interpolation. Special cases, such as the cutting plane being parallel to or coincident with an existing image, must be considered separately.

Algorithms↗

PubMed1979

A computerized rotating laminar radionuclide camera.

We have constructed a radionuclide camera that embodies a unique detector-collimator concept and provides a radically new approach to imaging. The heart of the instrument is a linear array of semiconductor detectors separated by thin tungsten plates that confine the field of view of each detector to one dimension. This collimator design has a higher collection efficiency than the standard parallel-hole collimator but cannot directly produce a two-dimensional image. When multiple measurements are taken as the array rotates through 180 degrees, a computerized image restoration algorithm can then produce two-dimensional images with resolution determined by the width of the detectors. A small prototype camera has produced images with resolution superior to conventional Anger cameras.

Computers↗