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 793 records · Page 44Linked to original sources

Strategy execution in cognitive skill learning: an item-level test of candidate models.

This article investigates the transition to memory-based performance that commonly occurs with practice on tasks that initially require use of a multistep algorithm. In an alphabet arithmetic task, item response times exhibited pronounced step-function decreases after moderate practice that were uniquely predicted by T. C. Rickard's (1997) component power laws model. The results challenge parallel strategy execution models as developed to date and they demonstrate that the shift to retrieval is an item-specific, as opposed to task-general, learning phenomenon. The results also call into question the entire class of smooth speed-up functions as global empirical learning laws. It is shown that overlaying of averaged item fits on averaged data can provide a sensitive test for model sufficiency. Strategy probes agreed with strategy inferences that were based on step-function speed-up patterns, supporting the validity of the probing technique.

Cognition↗

Pre-clinical evaluation of a two-channel microwave hyperthermia system with adaptive phase control in a large animal.

A pre-clinical assessment of the heating capabilities of a two-channel 915 MHz Microfocus-1000 hyperthermia system, with adaptive phase control, was carried out in a series of experiments using a large animal model. The results of the experimental measurements of specific absorption rate (SAR) and tissue temperature show that when muscle tissue of the hind legs of pigs was compressed to 6.5-7 cm, then a pair of parallel opposed, coherently driven, transverse electromagnetic wave applicators could elevate the temperature in deep tissue to therapeutic levels without overheating superficial tissues when the phase difference between applicators was determined by the adaptive phase control algorithm.

Animals↗

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.

We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix workstations to massively parallel systems, and is available from the Ribosomal Database Project (RDP) by anonymous FTP. Our program uses a maximum likelihood approach and is based on version 3.3 of Felsenstein's dnaml program. Several enhancements, including algorithmic changes, significantly improve performance and reduce memory usage, making it feasible to construct even very large trees. Trees containing 40-100 taxa have been easily generated, and phylogenetic estimates are possible even when hundreds of sequences exist. We are currently using the tool to construct a phylogenetic tree based on 473 small subunit rRNA sequences from prokaryotes.

Algorithms↗

[Use of voxel-oriented femur models for stress analysis. Generation, calculation and validation of CT-based FEM models].

A means of interfacing computed tomography with the finite element method for the analysis of stress distribution in human femurs is described. With the aid of data transfer and image processing programs, three-dimensional voxel models of four macerated and a fresh-frozen cadaveric femur were generated from CT data sets. The underlying basic principle is direct generation of model elements from one or more adjacent CT-voxels, which are characterised by their coordinates and local absorption coefficients. A new algorithm was used for smoothing the edges of the model. All the models were analysed with respect to their stress distribution under different load situations, and the results were compared with the data of a parallel study utilizing the strain-gauge technique. Using the method of linear regression, a high correlation (coefficient of determination r2: 0.80-0.91) was found between the calculated and experimentally measured principal stresses at the surface of the bones.

Biomechanical Phenomena↗

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↗

Distributed data mining on grids: services, tools, and applications.

Data mining algorithms are widely used today for the analysis of large corporate and scientific datasets stored in databases and data archives. Industry, science, and commerce fields often need to analyze very large datasets maintained over geographically distributed sites by using the computational power of distributed and parallel systems. The grid can play a significant role in providing an effective computational support for distributed knowledge discovery applications. For the development of data mining applications on grids we designed a system called Knowledge Grid. This paper describes the Knowledge Grid framework and presents the toolset provided by the Knowledge Grid for implementing distributed knowledge discovery. The paper discusses how to design and implement data mining applications by using the Knowledge Grid tools starting from searching grid resources, composing software and data components, and executing the resulting data mining process on a grid. Some performance results are also discussed.

Algorithms↗

Value of a screening algorithm for celiac disease using tissue transglutaminase antibodies as first level in a population-based study.

OBJECTIVE: Serological screening for celiac disease (CD) can detect a large number of otherwise undiagnosed patients based on the sequential evaluation of serological tests and intestinal biopsy. The aim of this study was to compare the screening value for CD of two different protocols for the same community-based population. METHODS: We screened 1,000 consecutive subjects (497 women, age range 16-71 yr) attending a centralized laboratory for obligatory prenuptial blood tests. Serum samples obtained from all subjects were processed using two different protocols: I) a three-level classic screening consisting of the parallel use of IgG and IgA antigliadin antibodies as first level, followed by endomysial antibodies and total serum IgA for positive patients, and finally, intestinal biopsy of positive patients; and 2) a study screening protocol consisting of the parallel use of a commercial guinea pig antitissue transglutaminase antibody and total serum IgA as first line, endomysial antibodies (type IgA and/or IgG) for positive patients, and finally, intestinal biopsy. RESULTS: The classic screening protocol identified five subjects who were eligible for intestinal biopsy, which confirmed the presence of CD in all (prevalence 5.0 x 1,000, 95% CI = 1.6-11.6). Using the study algorithm, we detected seven new patients including the five patients detected by the first protocol (prevalence 7.0 x 1,000, 95% CI = 2.8-14.4). The two additional patients diagnosed using the proposed algorithm had positive IgG antigliadin antibodies and normal total serum IgA and were not detected by the classic protocol. Both patients were endomysial antibodies positive. The comparative analysis showed that the classic approach was more expensive (U.S. $4,687 per new patient detected) compared with the proposed study algorithm (U.S. $3,006). CONCLUSIONS: Our data showed that a new screening protocol using antitissue transglutaminase as first line followed by endomysial antibodies is a cost-effective screening and yielded more realistic figures of prevalence for CD in a community setting than the classic three-level sequential evaluation using antigliadin antibodies.

Adolescent↗

Automated feature extraction and identification of colon carcinoma.

OBJECTIVE: To assess an automated algorithm, developed for the classification of normal and cancerous colonic mucosa, using geometric analysis of features and texture analysis. STUDY DESIGN: Twenty-one images were analyzed, 10 from normal and 11 from cancerous mucosa. The classification was based on a regularity index dependent on shape, object orientation for establishing parallelism and five texture features derived using the co-occurrence image analysis method. RESULTS: Geometric analysis yielded an overall classification accuracy of 80%. The corresponding sensitivity and specificity were 94% and 64%, respectively. Using texture analysis, the overall classification accuracy was 90%, with a sensitivity and specificity of 82% and 100%, respectively. CONCLUSION: This initial study demonstrated that geometric and texture analysis techniques show promise for automated analysis of colon cancer.

Algorithms↗

Cardiac material markers from tagged MR images.

Tagged magnetic resonance imaging (MRI) has shown great promise in non-invasive analysis of heart motion. To replace implanted markers as a gold standard, however, tagged MRI must be able to track a sparse set of material points, so-called material markers, with high accuracy. This paper presents a new method for generating accurate motion estimates over a sparse set of material points using standard, parallel-tagged MR images. Each tracked point is located at the intersection of three tag surfaces, each of which is estimated using a thin-plate spline. The intersections are determined by an iterative alternating projections algorithm for which a proof of convergence is provided. The resulting data sets are compatible with applications developed to exploit implanted marker data. One set of these material markers from a normal human volunteer is examined in detail using several methods to visualize the markers. Numerical results that include additional studies are also discussed. Finally, an error analysis is presented using a computer-simulated left ventricle for which material markers are tracked with an RMS error of approximately 0.2 mm for typical imaging parameters and noise levels.

Algorithms↗

A sticker-based model for DNA computation.

We introduce a new model of molecular computation that we call the sticker model. Like many previous proposals it makes use of DNA strands as the physical substrate in which information is represented and of separation by hybridization as a central mechanism. However, unlike previous models, the stickers model has a random access memory that requires no strand extension and uses no enzymes; also (at least in theory), its materials are reusable. The paper describes computation under the stickers model and discusses possible means for physically implementing each operation. Finally, we go on to propose a specific machine architecture for implementing the stickers model as a microprocessor-controlled parallel robotic workstation. In the course of this development a number of previous general concerns about molecular computation (Smith, 1996; Hartmanis, 1995; Linial et al., 1995) are addressed. First, it is clear that general-purpose algorithms can be implemented by DNA-based computers, potentially solving a wide class of search problems. Second, we find that there are challenging problems, for which only modest volumes of DNA should suffice. Third, we demonstrate that the formation and breaking of covalent bonds is not intrinsic to DNA-based computation. Fourth, we show that a single essential biotechnology, sequence-specific separation, suffices for constructing a general-purpose molecular computer. Concerns about errors in this separation operation and means to reduce them are addressed elsewhere (Karp et al., 1995; Roweis and Winfree, 1999). Despite these encouraging theoretical advances, we emphasize that substantial engineering challenges remain at almost all stages and that the ultimate success or failure of DNA computing will certainly depend on whether these challenges can be met in laboratory investigations.

Computer Simulation↗

DNA microarrays of the complex human cytomegalovirus genome: profiling kinetic class with drug sensitivity of viral gene expression.

We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the largest member of the herpesvirus family, human cytomegalovirus (HCMV). In this study, an HCMV chip was fabricated and used to characterize the temporal class of viral gene expression. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of oligonucleotides on glass for ORFs in the HCMV genome. Viral gene expression was monitored by hybridization to the oligonucleotide microarrays with fluorescently labelled cDNAs prepared from mock-infected or infected human foreskin fibroblast cells. By using cycloheximide and ganciclovir to block de novo viral protein synthesis and viral DNA replication, respectively, the kinetic classes of array elements were classified. The expression profiles of known ORFs and many previously uncharacterized ORFs provided a temporal map of immediate-early (alpha), early (beta), early-late (gamma1), and late (gamma2) genes in the entire genome of HCMV. Sequence compositional analysis of the 5' noncoding DNA sequences of the temporal classes, performed by using algorithms that automatically search for defined and recurring motifs in unaligned sequences, indicated the presence of potential regulatory motifs for beta, gamma1, and gamma2 genes. In summary, these fabricated microarrays of viral DNA allow rapid and parallel analysis of gene expression at the whole viral genome level. The viral chip approach coupled with global biochemical and genetic strategies should greatly speed the functional analysis of established as well as newly discovered large viral genomes.

Base Sequence↗

Neural activity in monkey dorsal and ventral cingulate motor areas: comparison with the supplementary motor area.

The cingulate motor areas are a recently discovered group of discrete cortical regions located in the cingulate sulcus with direct connections to the primary motor cortex and spinal cord. Although much is known about their anatomical relationship with other motor areas, relatively little is known about their functional neurophysiology. We investigated neural mechanisms of motor processing in the dorsal and ventral cingulate motor areas (CMAd and CMAv) during two-dimensional visually guided arm movements. Single-neuron activity in CMAd and CMAv was recorded during an instructed delay task requiring combined elbow and shoulder movements. Neural activity associated with the onset of a visual cue (signal activity), delay (set activity), and motor response (movement activity) were assessed, and their onset time, duration, magnitude, and parameters of directional specificity were calculated. To determine how CMAd and CMAv compared with other premotor areas, we also analyzed the activity of neurons in the supplementary motor area (SMA) during the same task in the same monkeys. Comparison of CMAd, CMAv, and SMA revealed remarkably similar response properties. All three areas contained signal, set, and movement activity in similar proportions and in all possible combinations within single neurons. The average onset time of signal and set activity and the duration of signal activity were not significantly different across areas. The directional tuning of activities in all three areas were uniformly distributed and highly correlated within the same neuron. There were, however, some notable differences in movement activity between motor areas. Neurons with only movement activity were more numerous in CMAd and CMAv, whereas neurons with both set and movement activity were more prevalent in SMA. Furthermore, movement activity in SMA began earlier and had a shorter duration than movement activity in CMAd and CMAv, although there was substantial overlap in their distributions. These results indicate that CMAd and CMAv participate in the visual guidance of limb movements using similar neurophysiological mechanisms as SMA. The earlier average onset and shorter duration of movement activity in SMA suggest a more prominent role for this area in movement initiation, whereas the later onset and longer duration of movement activity in CMAd and CMAv suggest a more influential role in movement execution. Notwithstanding these differences, however, the remarkable similarities in response types and their combinatorial organization within single neurons across all cortical areas attests to the parallel organization and distributed nature of information processing in these three motor areas.

Algorithms↗

A new algorithm for computational image analysis of deformable motion at high spatial and temporal resolution applied to root growth. Roughly uniform elongation in the meristem and also, after an abrupt acceleration, in the elongation zone.

A requirement for understanding morphogenesis is being able to quantify expansion at the cellular scale. Here, we present new software (RootflowRT) for measuring the expansion profile of a growing root at high spatial and temporal resolution. The software implements an image processing algorithm using a novel combination of optical flow methods for deformable motion. The algorithm operates on a stack of nine images with a given time interval between each (usually 10 s) and quantifies velocity confidently at most pixels of the image. The root does not need to be marked. The software calculates components of motion parallel and perpendicular to the local tangent of the root's midline. A variation of the software has been developed that reports the overall root growth rate versus time. Using this software, we find that the growth zone of the root can be divided into two distinct regions, an apical region where the rate of motion, i.e. velocity, rises gradually with position and a subapical region where velocity rises steeply with position. In both zones, velocity increases almost linearly with position, and the transition between zones is abrupt. We observed this pattern for roots of Arabidopsis, tomato (Lycopersicon lycopersicum), lettuce (Lactuca sativa), alyssum (Aurinia saxatilis), and timothy (Phleum pratense). These velocity profiles imply that relative elongation rate is regulated in a step-wise fashion, being low but roughly uniform within the meristem and then becoming high, but again roughly uniform, within the zone of elongation. The executable code for RootflowRT is available from the corresponding author on request.

Algorithms↗

Algorithm for semi-automatic sorting of objects to specified tissue domains. An aid for co-ordinating morphometric data with identified tissue components.

A personal computer-based technique was developed that reduces the extent of human efforts in obtaining data, like numerical density of profiles on area, describing the distribution of specific features of histological sections, e.g., density of synaptic profiles or of histochemical reaction products in specified tissue compartments. The procedure consists of (i) marking the objects to be counted, (ii) recording the borderlines of (reference) tissue domains of interest, and (iii) allocating the marked objects to the corresponding domains automatically. This automatic sorting of objects into defined tissue domains is achieved by an algorithm operating on two sets of coordinates: (i) coordinates of points that constitute the boundary of tissue domains (perimeter points) and (ii) coordinates of points marking the particular objects to be sorted. The principle of the sorting calculation is to construct 'segments' of the loop by lines parallel to the ordinate which pass through neighbouring perimeter points. The 'items' to be sorted are classified by the sign of marker flags allocated to each point depending on which side of the perimeter segment they are located. Segmentation and classification procedures are sequentially repeated along the entire perimeter of each domain specified by the operator which may result during the procedure in multiple changes of the sign of the flags. The internal or external location of each item finally is represented by the last sign of its flag. Objects, allocated to domains can be counted and processed further for numerical density determination.

Algorithms↗

Honey characterization and adulteration detection by pattern recognition applied on HPAEC-PAD profiles. 1. Honey floral species characterization.

An improved COFRAC (COmité FRançais d'ACréditation) method for the analysis and evaluation of the quality of honey by high-performance anion-exchange chromatography of sugar profiles is proposed. With this method, both minor and major sugars are simultaneously analyzed and the technique is integrated in a new chemometric approach, which uses the entire chromatographic sugars profile of each analyzed sample to characterize honey floral species. Sixty-eight authentic honey samples (6 varieties) were analyzed by high-performance anion-exchange chromatography-pulsed amperometric detection. A new algorithm was developed to create automatically the corresponding normalized data matrix, ready-to-use in various chemometric procedures. This algorithm transforms the analytical profiles to produce the corresponding calibrated table of the surfaces or intensities according to retention times of peaks. The possibility of taking into account unknown peaks (those for which no standards are available) allows the maximum chemical information provided by the chromatograms to be retained. The parallel application of principal component analysis (PCA)/linear discriminant analysis (LDA) and artificial neural networks (ANN) shows a high capability in the classification of the analyzed samples (LDA, 93%; ANN, 100%) and a very good discrimination of honey groups. This work is the starting point of the elaboration of a new system designed for the automatic pattern recognition of food samples (first application on honey samples) from chromatographic analyses for food characterization and adulteration detection.

Algorithms↗

Fast fragments: the development of a parallel effective fragment potential method.

The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute plus some number of solvent molecules, if desired, and an "effective fragment" region that contains the remaining solvent molecules. Interactions introduced with this fragment region (for example, Coulomb and polarization interactions) are added as one-electron terms to the total system Hamiltonian. As larger systems and dynamics are just starting to be studied with the EFP method, more needs to be done to decrease the calculation time of the method. This article considers parallelization of both the EFP fragment-fragment and mixed quantum mechanics (QM)-EFP interaction energy and gradient computation within the GAMESS suite of programs. The iteratively self-consistent polarization term is treated with a new algorithm that makes use of nonblocking communication to obtain better scalability. Results show that reasonable speedup is achieved with a variety of sizes of water clusters and number of processors.

Journal Article↗

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↗

Initial evaluation of commercial optical CT-based 3D gel dosimeter.

We evaluated the OCTOPUS-ONE research laser CT scanner developed and manufactured by MGS Research, Inc. (Madison, CT). The scanner is designed for imaging 3D optical density distributions in BANG gels. The scanner operates in a translate-rotate configuration with a single scanning laser beam. The rotating cylindrical gel phantom is immersed in a refractive index matching solution and positioned at the center of a square tank made of plastic and glass. A stationary polarized He-Ne laser beam (633 nm) is reflected from a mirror moving parallel to the tank wall and scans the gel. Another mirror moves synchronously along the opposite side of the tank and collects the transmitted light and sends it to a single stationary silicon photodetector. A filtered backprojection algorithm is used to reconstruct projection data in a plane. The laser-mirrors-detector assembly is mounted on a horizontal platform that moves vertically for slice selection. We have tested the mechanical and optical setup, projection centering on the axis of rotation, linearity, and spatial resolution. We found the optical detector to respond linearly to transmitted light from control samples. The spatial resolution of the scanner was determined by employing a split field resolution technique. We obtained the horizontal and vertical full widths at half maxima of the laser beam intensity profiles as 0.6 and 0.8 mm, respectively. Dose calibration tests of the gel were performed using a nine-field (2 x 2 cm2 each) dose pattern irradiated at different dose levels. Finally, we compared gel-derived 2D planar dose distribution against radiochromic film measured dose distribution for both the nine-field and a uniform 5 x 5 cm2 field of 6 MV x rays. Very similar dose distributions were observed in gel and radiochromic film except in regions of steep dose gradient and highest dose. A dose normalization of 15.6% was required between the two dosimeters due to differences in overall radiation response. After normalization, analysis using the gamma evaluation showed that the radiochromic film and gel-measured dose distributions differed by a maximum gamma of 1.3 using 5% and 1.5 mm dose difference and distance-to-agreement criteria. The optical CT scanner has great potential as a 3D dosimeter, but a few refinements and further testing are necessary before its routine clinical use.

Algorithms↗