Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Parallel Algorithms”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8Linked to original sources
PubMed1991

Clustering a large number of compounds. 2. Using the Connection Machine.

About 230,000 compounds in the National Cancer Institute Repository are available for screening under a new protocol. This paper is the second on an project to extract a representative sample of these compounds by clustering. The clustering program was implemented on the Connection Machine, a massively parallel computer with 16K processing elements. This implementation reduced a formidable task to a relatively routine run.

Algorithms↗
PubMed1986

[SPECT images using a multislice fan beam collimator].

Several methods to improve the image resolution of single photon emission computed tomography (SPECT) occur to us. It is one method to use multislice fan beam collimators which have the parallel collimation along the cephalic-caudul axis of a patient and the conversing collimation within planes parpendicular to that axis. It is impossible to obtain corrective image when we used the algorithm which is commonly used for reconstruction of SPECT images. We proposed a reconstruction algorithm for multislice fan beam collimator in this paper. An interpolation method developed for fan beam type X-ray CT was modified to reconstruct images from SPECT with multislice fan beam collimator. This algorithm was confirmed by means of computer simulation studies. Beside improving the system resolution by effectively reducing the intrinsic resolution of the cameras, this collimator also increases the system sensitivity by utilizing a large fraction of the crystal area. We have thought that to use multislice fan beam collimator is beneficial for SPECT images.

Tomography, Emission-Computed↗
PubMed1988

Visual and auditory association areas of the cat's posterior ectosylvian gyrus: thalamic afferents.

The feline posterior ectosylvian gyrus contains a broad band of association cortex that is bounded anteriorly by tonotopic auditory areas and posteriorly by retinotopic visual areas. To characterize the possible functions of this cortex and to throw light on its pattern of internal divisions, we have carried out an analysis of its thalamic afferents. Deposits of differentiable retrograde tracers were placed at 17 cortical sites in nine cats. The deposit sites spanned the crown of the posterior ectosylvian gyrus and adjacent cortex in the suprasylvian sulcus. We compiled counts of retrogradely labeled neurons in 12 thalamic nuclei delineated by use of Nissl and acetylcholinesterase stains. We then employed a statistical clustering algorithm to identify groups of injections that gave rise to similar patterns of thalamic labeling. The results suggest that the posterior ectosylvian gyrus contains 3 fundamentally different cortical districts that have the form of parallel vertical bands. Very anterior cortex, overlapping previously identified tonotopic auditory areas (AI, P and VP) receives a dense projection from the laminated division of the medial geniculate body (MGl). An intermediate strip, to which we refer as the auditory belt, is innervated by axons from nontonotopic divisions of the medial geniculate body (MGds, MGvl, MGm, and MGd), from the lateral division of the posterior group (Pol), and from the posterior suprageniculate nucleus (SGp). A posterior strip, to which we refer as EPp, receives strong projections from the LM-SG complex (LM-SGa and LMp), and lighter projections from the intralaminar and lateroposterior (LPm and LPl) nuclei. On grounds of thalamic connectivity, EPp is not obviously distinguishable from adjacent retinotopic visual areas (PLLS, DLS, and VLS), and may be regarded as forming, together with these areas, a connectionally homogeneous visual belt.

Animals↗
PubMed1989

A dosimetric comparison of three compensator design methods for the mantle field.

The mid-plane dose was measured in an anthropomorphic phantom for parallel opposed mantle fields as typically used in the treatment of Hodgkin's Disease. Doses were measured for four cases: no compensator, a compensator designed by a three-dimensional CT based treatment planning algorithm, a compensator designed from a port film, and a compensator designed from surface topography. The results showed all three compensators gave a significant better dose distribution than using no compensator at all. Without a compensator, doses varied from 92 percent to 131 percent, with a standard deviation of 10.9 percent for 65 measured points. The treatment planning algorithm gave the best performance with a standard deviation of 3.2 percent with all points but three within 5 percent out of the 65 points measured, and no points outside of 10 percent. The port film compensator was next best with a standard deviation of 4.4 percent, with 19 points outside of 5 percent, and doses from 88 to 106 percent. The surface topography compensator had a standard deviation of 6.1 percent with 31 points outside of 5% and doses from 89 to 114 percent.

Hodgkin Disease↗
PubMed2026

A novel method for across-chromosome phasing without relative data.

MOTIVATION: Across-chromosome phasing identifies which haplotypes of different chromosomes come from the same parent. This differs from within-chromosome phasing, which uses linkage disequilibrium patterns to determine which alleles were co-inherited within each chromosome but does not match haplotypes across different chromosomes. While across-chromosome phasing can be conducted using genotypes from parents or close relatives, current methods perform poorly for samples of unrelated individuals. Here, we introduce a novel approach for across-chromosome phasing that employs a window-based SNP-similarity metric, eliminating the need for data from close relatives or detection of identical-by-descent haplotypes. RESULTS: Using UK Biobank offspring with both parents genotyped as a gold standard, we evaluated the performance of our method by phasing the offspring without using parental data. In genomic data with no within-chromosome phase errors, our algorithm achieved a mean across-chromosome phasing accuracy of 95%, with 53% of individuals phased perfectly. When data was pre-phased computationally using a standard within-chromosome phasing algorithm, mean accuracy for across-chromosome phasing dropped to 83.1%. Thus, our method is limited primarily by the accuracy of within-chromosome phasing accuracy and can approach near-perfect across-chromosome phasing accuracy as within-chromosome phasing accuracy improves. AVAILABILITY AND IMPLEMENTATION: The implementation was executed within a multi-node computational environment of University of Colorado Boulder Research Computing (Blanca Cluster: https://www.colorado.edu/rc/resources/blanca), employing parallelization techniques in the C programming language. The source code has been made publicly accessible online at https://github.com/emmanuelsapin/AcrossChromosomesPhasing, thereby facilitating reproducibility of the results for researchers with authorized access to the UK Biobank dataset.

Algorithms↗
PubMed1991

Cone beam tomography of the heart using single-photon emission-computed tomography.

The authors evaluated cone beam single-photon emission-computed tomography (SPECT) of the heart. A new cone beam reconstruction algorithm was used to reconstruct data collected from "short scan" acquisitions (of slightly more than 180 degrees) of a detector anteriorally traversing a noncircular orbit. The less than 360 degrees acquisition was used to minimize the attenuation artifacts that result from reconstructing posterior projections of 201T1 emissions from the heart. The algorithm includes a new method for reconstructing truncated projections of background tissue activity that eliminates reconstruction ring artifacts. Phantom and patient results are presented which compare a high-resolution cone beam collimator (50-cm focal length; 6.0-mm full width at half maximum [FWHM] at 10 cm) to a low-energy general purpose (LEGP) parallel hole collimator (8.2-mm FWHM at 10 cm) which is 1.33 times more sensitive. The cone beam tomographic results are free of reconstruction artifacts and show improved spatial and contrast resolution over that obtained with the LEGP parallel hole collimator. The limited angular sampling restrictions and truncation problems associated with cone beam tomography do not deter from obtaining diagnostic information. However, even though these preliminary results are encouraging, a thorough clinical study is still needed to investigate the specificity and sensitivity of cone beam tomography.

Algorithms↗
PubMed1991

Simultaneous multinuclear magnetic resonance imaging and spectroscopy.

A technique has been developed to perform simultaneous multinuclear magnetic resonance imaging and spatially localized spectroscopy. It is inherently superior in terms of time efficiency over current approaches which use sequential or interleaved methods. The pulse sequence uses a parallel excitation and acquisition scheme to acquire multislice proton images concurrently with phosphorus-31 spectroscopic images. Because the phosphorus signal is necessarily collected in the presence of a gradient, an essential element of the technique is an algorithm to extract pure chemical-shift information.

Algorithms↗
PubMed1991

Mathematical resolution of mixed in vivo voltammetry signals. Models, equipment, assessment by simultaneous microdialysis sampling.

A microcomputer-assisted curve-fitting procedure was developed for the quantitative estimation of the components of the mixed "catechol peak" recorded with differential normal pulse voltammetry (DNPV) at electrochemically pretreated carbon fiber microelectrodes in the living brain. The contribution of each of the relevant electroactive species is fitted by a normal probability function, the parameters of which are previously determined in vitro for each electrode and substance. The voltammogram is thus modeled as a mixture of normal curves corresponding to the individual oxidizable substances plus a low order polynomial approximating the baseline. In a former approach the function was solved by linear least squares techniques. As a further improvement, we now propose a non-linear model of the voltammogram and a Gauss-Newton iterative algorithm with stepwise regression for parameter estimation. This report shows the application of the method for the resolution of the dopamine (DA) and dihydroxyphenylacetic acid (DOPAC) components of the DNPV signal recorded from the striatum of freely moving animals in response to amphetamine and pargyline. The method was validated by the chemical assay of contralateral microdialysates collected simultaneously. The changes detected by both methodologies were closely parallel, with highly significant correlation coefficients (0.87 and 0.99 for DA and DOPAC, respectively, P less than 0.001). This study further illustrates that the in vivo voltammetry methodology can be improved substantially by incorporating a suitable mathematical treatment of the electrochemical signals.

3,4-Dihydroxyphenylacetic Acid↗
PubMed1989

Scattered wave inversion by image projections.

A three-dimensional diffraction tomography algorithm based on image projections is implemented. For each view, the measured scattered field is directly backpropagated onto a single plane in the image space. The backpropagated field evaluated on the plane is defined as the image projection because it closely approximates the straight line projection of the object. The object is then reconstructed by parallel slices using conventional straight ray tomographic techniques. This approach permits practical three-dimensional reconstruction using a limited number of views. The reconstructions made with image projections are of comparable quality to ideal diffraction-limited images. By backpropagating the field prior to filtering, curved or misaligned recording surfaces can be used. The limits on the image projection technique for multiple object systems are explored. A diffuse structure is reconstructed.

Algorithms↗
PubMed2026

Integrating NECTIN4 Amplification With Membranous Nectin-4 Expression to Develop a Scoring System for Predicting Enfortumab Vedotin Response in Urothelial Carcinoma.

PURPOSE: Enfortumab vedotin (EV) is standard therapy for metastatic urothelial carcinoma (mUC), yet the predictive relevance of NECTIN4 expression-especially membranous versus cytoplasmic-remains unclear. Here, we sought to extend previous findings on NECTIN4 gene amplification in parallel with a systematic subcellular evaluation of NECTIN4 expression. EXPERIMENTAL DESIGN: We retrospectively analyzed 179 EV-treated mUC patients. NECTIN4 amplification was assessed by FISH and NECTIN4 protein levels by IHC. A four-tier membranous scoring algorithm (0,1+,2+,3+) adapted from CAP HER2 gastric guidelines was benchmarked against H-score. We integrated amplification status with membranous staining to refine predictive stratification and compared associations with objective response rate (ORR) to EV-301 data. RESULTS: Combining membranous and cytoplasmic compartments resulted in a median composite H-score of 260 (78.2% &#x2265;150), closely matching NECTIN4 expression prevalence reported in EV-301 (median 250; 82.6% &#x2265; 150). A &#x2265;150 cut-off enriched for EV responders in both cohorts; in EV-301 with ORR of 45.8% vs. 20% (P = 0.001). High membranous expression based on the scoring (2+/3+) predicted response (ORR 55.1% vs. 25.5%; P < 0.001), with longer PFS (7.1 vs. 2.9 months; HR 0.45) and OS (12.3 vs. 6.9 months; HR 0.57), whereas cytoplasmic expression lacked predictive value. NECTIN4-amplified tumors showed particularly favorable outcomes (PFS 12.2 months; OS 30.1 months). An integrated three-tier model-amplified, non-amplified/high-membranous, and non-amplified/low-membranous-yielded ORRs of 77.2%, 42.9%, and 26.1% and separated survival outcomes. CONCLUSIONS: Our NECTIN4 scoring system integrating NECTIN4 amplification with membranous NECTIN4 expression accurately predicts outcomes, supporting combined genomic and membranous assessment as complementary biomarkers for optimizing EV selection.

Journal Article↗
PubMed1987

Accuracy in clinical electron beam dose planning using pencil beam algorithms.

The accuracy of two different pencil beam models for electron beam dose planning is shown by comparisons with measured dose distributions. The investigation is restricted to two-dimensional geometries. In one model the multiple scattering of the electrons is considered by the small angle Gaussian approximation of Fermi and Eyges. In the other, the generalized Gaussian model, the large angle single scattering events are also considered. The parallel slab approximation is used in both models. The comparisons have been made for two different anatomical phantoms. One phantom was constructed to simulate a transversal cross-section through the chest wall and lung in radiotherapy of breast cancer. The other phantom was made to simulate the head at the level of the nose. The measurements in these phantoms were made with thermoluminescence dosimetry, LiF rods. The accuracy of the oblique incidence case was investigated in a homogenous water phantom. The results show that for oblique incidence and geometries where the semi-infinite slab approximation is reasonably good, the generalized Gaussian model is more accurate. Within and behind low density cavities, in the phantom, the Gaussian model often gives a better agreement to experimental data. This is shown to be due to mutually balancing errors from the semi-infinite slab approximation and the Gaussian approximation.

Algorithms↗
PubMed1979

Rapid analysis of hematology image data: the ADC-500 preprocessor.

A sequential, pipeline processor (that we have named the ADC-500 preprocessor) has been developed which scene segments the three color image data from the ADC-500 optics one image element at a time, groups together image elements from each object in the scene and extracts features from each object. The processing occurs at television frame rates, requiring 16.7 msec to process the entire image. This speed was instrumental in allowing the ADC-500 automated differential analyzer to perform routine 500-cell differentials. The preprocessor also contains hardware which simplifies compilation of the three color histograms. The segmentation algorithms implemented in the preprocessor are multicolor extensions of the classical monochrome density histogram threshold method. For most cell image analysis tasks, a sequential pipeline processor of this type should be more economical and as fast or faster than a parallel processor.

Blood Cells↗
PubMedDate not supplied

Similarity searching in databases of three-dimensional molecules and macromolecules.

This paper discusses algorithmic techniques for measuring the degree of similarity between pairs of three-dimensional (3-D) chemical molecules represented by interatomic distance matrices. A comparison of four methods for the calculation of 3-D structural similarity suggests that the most effective one is a procedure that identifies pairs of atoms, one from each of the molecules that are being compared, that lie at the center of geometrically-related volumes of 3-D space. This atom mapping method enables the calculation of a wide range of types of intermolecular similarity coefficient, including measures that are based on physicochemical data. Massively-parallel implementations of the method are discussed, using the AMT Distributed Array Processor, that achieve a substantial increase in performance when compared with a sequential implementation on a UNIX workstation. Current work involves the use of angular information and the extension of the method to field-based similarity searching. Similarity searching in 3-D macromolecules is effected by the use of a maximal common subgraph (MCS) isomorphism algorithm with a novel, graph-based representation of the tertiary structures of proteins. This algorithm is being used to identify similarities between the 3-D structures of proteins in the Brookhaven Protein Data Bank; its use is exemplified by searches involving the NAD-binding fold motif.

Algorithms↗
PubMed1985

Cortical ultrastructure of Coleps bicuspis Noland, 1925 and the phylogeny of the class Prostomatea (Ciliophora).

The ultrastructure of Coleps bicuspis Noland, 1925 is described. The ciliate is a typical prostomate: the somatic kinetid is a monokinetid with a postciliary ribbon at triple 9, a kinetodesmal fibril originating near triplets 5, 6, 7 and an apparently radial transverse ribbon at triplet 4. The oral area is circular and has three brosse kineties associated with it. The brosse kineties are composed of dikinetids whose anterior kinetosome bears a tangential transverse ribbon and whose posterior kinetosome bears the fibrillar associates typical of a somatic monokinetid. The oral dikinetids are oriented parallel to the circumference of the oral cavity, which is surrounded by oral papillae and oral ridges. Pairs of nematodesmata, originating from oral dikinetid kinetosomes, are typically triangular in transection. A phylogeny of rhabdophoran ciliates is presented using the mixed parsimony algorithm and is discussed with reference to the systematic revisions of the phylum Ciliophora.

Animals↗
PubMed1987

Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase.

The tertiary structure of the alpha-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the alpha/beta-class of supersecondary structures. The two-domain structure of the alpha-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a beta-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the alpha-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the beta-sheet eliminated all but one structure. The native structure is predicted to have a parallel beta-sheet flanked on both sides by alpha-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for beta 2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.

Amino Acid Sequence↗
PubMed1986

Toward computerized morphometric facilities: a review of 58 software packages for computer-aided three-dimensional reconstruction, quantification, and picture generation from parallel serial sections.

This review gives an inventory of 58 computer-aided three-dimensional reconstruction applications in the domain of biomedical research. It is devoted to the formulation of a set of recommendations thought to be necessary for improved performance of software packages in this field. These recommendations can be used to select packages and to guide future developments of existing reconstruction systems. The survey is restricted to three-dimensional reconstructions based upon a series of parallel sections of an object. Subjects treated are programming languages, resolution and sampling, input preparation, realignment, local deformation of slices, numerical quantifications, topological complexity, internal representation, display complexity (hidden surfaces, shading, smoothing), structure extraction, descriptive elements, database, data compression, time efficiency of systems and algorithms, hardware configuration, input devices, input media, interactive aids, display devices, and output devices. Information for this survey comes from articles that appeared between 1965 and 1985.

Computers↗
PubMed1990

The cellular computer DNA: program or data.

The classical metaphor of the genetic program written in the DNA nucleotidic sequences is reconsidered. Recent works on algorithmic complexity and logical properties of computer programs and data are used to question the explanatory value of that metaphor. Structural properties of strings are looked for which would be necessary to apply to DNA sequences if the metaphor is to be taken literally. The notion of sophistication is used to quantify meaningful complexity and to distinguish it from classical computational complexity. In this context, the distinction between program and data becomes relevant and an alternative metaphor of DNA as data to a parallel computing network embedded in the global geometrical and biochemical structure of the cell is discussed. An intermediate picture of an evolving network emerges as the most likely where the output of the cellular computing network can produce, at a different time scale, changes in the structure of the network itself by means of changes in the DNA activity patterns.

Algorithms↗
PubMed1989

A distributed, developmental model of word recognition and naming.

A parallel distributed processing model of visual word recognition and pronunciation is described. The model consists of sets of orthographic and phonological units and an interlevel of hidden units. Weights on connections between units were modified during a training phase using the back-propagation learning algorithm. The model simulates many aspects of human performance, including (a) differences between words in terms of processing difficulty, (b) pronunciation of novel items, (c) differences between readers in terms of word recognition skill, (d) transitions from beginning to skilled reading, and (e) differences in performance on lexical decision and naming tasks. The model's behavior early in the learning phase corresponds to that of children acquiring word recognition skills. Training with a smaller number of hidden units produces output characteristic of many dyslexic readers. Naming is simulated without pronunciation rules, and lexical decisions are simulated without accessing word-level representations. The performance of the model is largely determined by three factors: the nature of the input, a significant fragment of written English; the learning rule, which encodes the implicit structure of the orthography in the weights on connections; and the architecture of the system, which influences the scope of what can be learned.

Dyslexia↗