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 1,621 records · Page 90Linked to original sources
PubMed1997

X-ray crystal structure of cytotoxic oxidized cholesterols: 7-ketocholesterol and 25-hydroxycholesterol.

The cytotoxic cholesterol derivative, 7-ketocholesterol, crystallizes in a monoclinic unit cell, space group P2(1) with a = 11.405 A, b = 6.288 A, c = 35.393 A and beta = 92.75 degrees (Z = 4). Its room temperature crystal structure was solved by direct methods, i.e., the minimal principle via the Shake-and-Bake (SnB) algorithm. In contrast to the continuous chain pattern found for the cholesterol monohydrate structure, hydrogen bonding in the 7-ketocholesterol structure is localized to specific sites via one water molecule that forms linkages between two O3 hydroxyl groups and one keto oxygen. The final weighted R factor for 4562 reflections was 0.144. The 25-hydroxycholesterol also crystallizes in a monoclinic unit cell (P2(1)), with a = 10.840 A, b = 14.533 A, c = 16.093 A and beta = 95.91 degrees (Z = 4). The low temperature structure was solved by DIRDIF. In this instance, molecular packing is anti-parallel in layers stabilized by hydrogen bonding networks via both hydroxyl functions, differing both from cholesterol monohydrate and the 7-ketocholesterol. The final weighted R-factor for 6566 reflections was 0.034. Functional differences of the oxysterols therefore, may be expressed by observed variations in the molecular packing and geometry.

Crystallization↗
PubMed2000

Evaluation of the cervical spine in the polytrauma patient.

STUDY DESIGN: Two-part study. Part One: the analysis of surveys distributed to members of the Orthopaedic Trauma Association (OTA) and 1000 surgeon members of NASS. Part Two: a prospective clinical study evaluating a new algorithm to evaluate the cervical spine in polytrauma patients. OBJECTIVES: To determine if there is a consensus of the optimal method for "clearing the cervical spine"; to assess the safety and efficacy of a newly proposed algorithm. SUMMARY OF BACKGROUND DATA: There is no uniformly accepted algorithm for "clearing the cervical spine" in the polytrauma patient or those patients with altered mental status secondary to the influence of alcohol, drugs or a closed head injury. METHODS: All members of the OTA and 1000 surgeon members of NASS were sent questionnaires to assess their methods of "clearing the cervical spine" in the polytrauma patient. Their answers were collated, analyzed and compared to standard ATLS protocol guidelines. A new protocol, which includes a surgeon, controlled stretch test and flouroscopically visualized flexion-extension views, was initiated and evaluated for safety and efficacy. RESULTS SURVEY: Fifty-five percent of the members of the OTA and 31% of the NASS surgeons responded to the questionnaire. Among the responses from the NASS members, the ratio of orthopaedic spine surgeons to neurosurgeons accurately parallels the society's membership (77% ortho, 23% neuro). Sixty-nine of the OTA and 54% of the NASS responders replied that they followed ATLS guidelines. Analysis of their responses showed only 40% compliance. Eighty-one percent of the OTA respondents utilize the standard three view cervical spine trauma series, only 31% of the NASS members adhere to this guideline. Nearly 90% of all respondents identified the presence of neck pain or retropharygeal soft tissue swelling as an indicator to expand their initial radiographic evaluation. There was no consensus as to management of the polytrauma patient with a closed head injury. Eighty-two percent of all respondents has seen or treated a purely ligamentous injury of the c-spine. SPECTIVE STUDY: Prospective clinical protocol. 35-month period: enrolled 153 patients, 12,000 patients seen in trauma unit. Completed data 149/153. 8/153 unable to be cleared due to poor visualization of cervical-thoracic junction. 3/153 positive findings identified during fluoro examination. All three instability patterns verified in surgery (true positives). No untoward events to date. CONCLUSIONS: A standardized protocol to safely and effectively clear the cervical spine has yet to be established. Preliminary results of a new protocol to safely evaluate the cervical spine in the polytrauma patient are promising.

Adult↗
PubMed2004

Theoretical and practical advances in genome halving.

MOTIVATION: Duplication of an organism's entire genome is a rare but spectacular event, enabling the rapid emergence of multiple new gene functions. Over time, the parallel linkage of duplicated genes across chromosomes may be disrupted by reciprocal translocations, while the intra-chromosomal order of genes may be shuffled by inversions and transpositions. Some duplicate genes may evolve unrecognizably or be deleted. As a consequence, the only detectable signature of an ancient duplication event in a modern genome may be the presence of various chromosomal segments containing parallel paralogous genes, with each segment appearing exactly twice in the genome. The problem of reconstructing the linkage structure of an ancestral genome before duplication is known as genome halving with unordered chromosomes. RESULTS: In this paper, we derive a new upper bound on the genome halving distance that is tighter than the best known, and a new lower bound that is almost always tighter than the best known. We also define the notion of genome halving diameter, and obtain both upper and lower bounds for it. Our tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome. We create a software package GenomeHalving based on this new algorithm and test it on the yeast genome, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.

Algorithms↗
PubMed2006

Near infrared spectrometry for the quantification of human dermal absorption of econazole nitrate and estradiol.

PURPOSE: The purpose of this study was to demonstrate the use of near-infrared (NIR) spectrometry for the in vitro quantification of econazole nitrate (EN) and estradiol (EST) in human skin. METHODS: NIR spectra were collected from EN and EST powders to verify the presence of NIR chromophores. One percent EN cream, a saturated solution of EN, or 0.25% EST solution was applied to human skin. NIR spectra were collected and one-point net analyte signal (NAS) multivariate calibration was used to predict the drug concentrations. NIR results were validated against known skin concentrations measured by high-pressure liquid chromatography (HPLC) analysis of solvent extracts. RESULTS: NIR spectroscopy measured dermal absorption from saturated solutions of EN on human skin with an r2=0.990, standard error of estimation (SEE)=2.46%, and a standard error of performance (SEP)=3.55%, EN cream on skin with an r2=0.987, SEE=2.30%, and SEP=2.66%, and 0.25% solutions of EST on skin with an r2=0.987, SEE=3.30%, and SEP=5.66%. Despite low permeation amounts of both drugs through the stratum corneum into human tissue, the NIR signal-to-noise ratio was greater than three, even for the lowest concentrations. CONCLUSION: NIR analyses paralleled the results obtained from HPLC, and thus could serve as a viable alternative for measuring the topical bioavailability/bioequivalence of different EN and EST formulations. Because these experiments were conducted in human tissue, this research suggests an all-optical in vivo method of measurement for dermal absorption could be developed.

Administration, Topical↗
PubMed1994

An architecture for EEG signal processing and interpretation during sleep (ESPIS).

The project's aim is to develop a dedicated workstation in order to process multiple channels of electrophysiological signals in real-time during sleep. In ESPIS we are aiming to define both an architecture and an environment for EEG signal interpretation in medicine based on computer science gold standards (Unix, XWindow, Motif). Signal processing and pattern recognition analysis are provided by parallel processing on a specific developed acquisition architecture (DSP) based on transputers. The main result is a high performance prototype demonstrating signal interpretation during sleep which has already been tested in a medical environment. The overall specifications allow this biomedical device to be extended to other types of medical signals.

Algorithms↗
PubMed2005

Thermal conductivity of leaf compost used in biofilters: an experimental and theoretical investigation.

Thermal conductivity is an important property that governs the behaviour of leaf compost biofilters used in treating gaseous pollutants. Measurements were carried out for the thermal conductivity (K) of 44 samples of leaf compost, covering wide ranges of the volume fractions of water (xi(w)), solids (xi(s)) and air (xi(a)), at 20 degrees C using an unsteady state thermal probe. The results indicated that the compost thermal conductivity increased with an increase in xi(w), with a decrease in xi(a), and with an increase in the degree of saturation (defined as the volumetric fraction of water in the total void space). The predictions from the Woodside-Messmer quadratic parallel (QP) model for the thermal conductivity of leaf compost were higher than the experimental values. A simple linear relationship was developed between the thermal conductivity and the degree of saturation, which provided a satisfactory correlation for the data measured in this study as well as those reported recently for sandy and clay loams.

Air Pollutants↗
PubMed2002

NMRKIN: simulating line shapes from two-dimensional spectra of proteins upon ligand binding.

The analysis of the shape of signals in NMR spectra is a powerful tool to study exchange and reaction kinetics. Line shapes in two-dimensional spectra of proteins recorded for titrations with ligands provide information about binding rates observed at individual residues. Here we describe a fast method to simulate a series of line shapes derived from two-dimensional spectra of a protein during a ligand titration. This procedure, which takes the mutual effects of two dimensions into account, has been implemented in MATLAB as an add-on to NMRLab (Gunther et al., 2000). In addition, more complex kinetic models, including sequential and parallel reactions, were simulated to demonstrate common features of more complex line shapes which could be encountered in protein-ligand interactions. As an example of this method, we describe its application to line shapes obtained for a titration of the p85 N-SH2 domain of PI3-kinase with a peptide derived from polyomavirus middle T antigen (MT).

Algorithms↗
PubMed2005

An improved MCNP version of the NORMAN voxel phantom for dosimetry studies.

In recent years voxel phantoms have been developed on the basis of tomographic data of real individuals allowing new sets of conversion coefficients to be calculated for effective dose. Progress in radiation studies brought ICRP to revise its recommendations and a new report, already circulated in draft form, is expected to change the actual effective dose evaluation method. In the present paper the voxel phantom NORMAN developed at HPA, formerly NRPB, was employed with MCNP Monte Carlo code. A modified version of the phantom, NORMAN-05, was developed to take into account the new set of tissues and weighting factors proposed in the cited ICRP draft. Air kerma to organ equivalent dose and effective dose conversion coefficients for antero-posterior and postero-anterior parallel photon beam irradiations, from 20 keV to 10 MeV, have been calculated and compared with data obtained in other laboratories using different numerical phantoms. Obtained results are in good agreement with published data with some differences for the effective dose calculated employing the proposed new tissue weighting factors set in comparison with previous evaluations based on the ICRP 60 report.

Algorithms↗
PubMed2005

Pattern reconstruction and sequence processing in feed-forward layered neural networks near saturation.

The dynamics and the stationary states for the competition between pattern reconstruction and asymmetric sequence processing are studied here in an exactly solvable feed-forward layered neural network model of binary units and patterns near saturation. Earlier work by Coolen and Sherrington on a parallel dynamics far from saturation is extended here to account for finite stochastic noise due to a Hebbian and a sequential learning rule. Phase diagrams are obtained with stationary states and quasiperiodic nonstationary solutions. The relevant dependence of these diagrams and of the quasiperiodic solutions on the stochastic noise and on initial inputs for the overlaps is explicitly discussed.

Algorithms↗
PubMed2005

Optimizing the acquisition time profile for a planar integral measurement system with a spinning slat collimator.

This article considers a hypothetical imaging device with a spinning slat collimator that measures parallel-planar-integral data from an object. This device rotates around the object 180 degrees and stops at N positions uniformly distributed over this 180 degrees. At each stop, the device spins on its own axis 180 degrees and acquires measurements at M positions uniformly distributed over this 180 degrees. For a fixed total imaging time, an optimal distribution of the scanning time among the data measurement locations is searched by a nonlinear programming method: Nelder-Mead's simplex method. The optimal dwell time is approximately proportional to the weighting factor in the backprojector of the reconstruction algorithm. By using an optimal dwell-time profile, the reconstruction signal-to-noise ratio has a gain of 23%-24% for the filtered backprojection algorithm and a gain of 10%-18% for the iterative algorithms, compared with the situation when a constant dwell-time profile is used.

Algorithms↗
PubMed2001

Enhanced EPR sensitivity from a ferroelectric cavity insert.

We report the development of a simple ferroelectric cavity insert that increases the electron paramagnetic resonance (EPR) sensitivity by an order of magnitude when a sample is placed within it. The insert is a hollow cylinder (length 4.8 mm, outside diameter 1.7 mm, inside diameter 0.6 mm) made from a single crystal of KTaO(3), which has a dielectric constant of 230 at X-band (9.5 GHz). Its outside dimensions were chosen to produce a resonant frequency in the X-band range, based on electromagnetic field modeling calculations. The insert increases the microwave magnetic field (H(1)) at the center of the insert by a factor of 7.4 when placed in an X-band TM(110) cavity. This increases the EPR signal for a small (volume 0.13 microL) unsaturated nitroxide spin label sample by a factor of 64 at constant microwave power, and by a factor of 9.8 at constant H(1). The insert does not significantly affect the cavity quality factor Q, indicating that this device simply redistributes the microwave fields within the cavity, focusing H(1) onto the sample inside the insert, thus increasing the filling factor. A similar signal enhancement is obtained in the TM(110) and TE(102) cavities, and when the insert is oriented either vertically (parallel to the microwave field) or horizontally (parallel to the DC magnetic field) in the TM(110) cavity. This order-of-magnitude sensitivity enhancement allows EPR spectroscopy to be performed in conventional high-Q cavities on small EPR samples previously only measurable in loop-gap or dielectric resonators. This is of particular importance for small samples of spin-labeled biomolecules.

Algorithms↗
PubMed1995

An approach to validation of a leg simulation by the comparison of two dynamic models.

The dynamics of a jointed leg were simulated using two different models, one based on a recursive Newton-Euler method and one on a closed-form Lagrange method. To validate the models, the simulations were run in parallel and the intermediate steps and output of the two methods were compared to one another to reveal the presence and locations of errors. Sources of error and the use of this method for the detection of errors are discussed. Some errors could not have been detected using only a single simulation.

Acceleration↗
PubMed2002

Optimization of artificial neural networks used for retention modelling in ion chromatography.

The aim of this work is the development of an artificial neural network model, which can be generalized and used in a variety of applications for retention modelling in ion chromatography. Influences of eluent flow-rate and concentration of eluent anion (OH-) on separation of seven inorganic anions (fluoride, chloride, nitrite, sulfate, bromide, nitrate, and phosphate) were investigated. Parallel prediction of retention times of seven inorganic anions by using one artificial neural network was applied. MATLAB Neural Networks ToolBox was not adequate for application to retention modelling in this particular case. Therefore the authors adopted it for retention modelling by programming in MATLAB metalanguage. The following routines were written; the division of experimental data set on training and test set; selection of data for training and test set; Dixon's outlier test; retraining procedure routine; calculations of relative error. A three-layer feed forward neural network trained with a Levenberg-Marquardt batch error back propagation algorithm has been used to model ion chromatographic retention mechanisms. The advantage of applied batch training methodology is the significant increase in speed of calculation of algorithms in comparison with delta rule training methodology. The technique of experimental data selection for training set was used allowing improvement of artificial neural network prediction power. Experimental design space was divided into 8-32 subspaces depending on number of experimental data points used for training set. The number of hidden layer nodes, the number of iteration steps and the number of experimental data points used for training set were optimized. This study presents the very fast (300 iteration steps) and very accurate (relative error of 0.88%) retention model, obtained by using a small amount of experimental data (16 experimental data points in training set). This indicates that the method of choice for retention modelling in ion chromatography is the artificial neural network.

Chromatography, Liquid↗
PubMed1991

A distributed-parameter model of the myelinated nerve fiber.

This paper presents a new model for the characterization of electrical activity in the nodal, paranodal and internodal regions of isolated amphibian and mammalian myelinated nerve fibers. It differs from previous models in the following ways: (1) in its ability to incorporate detailed anatomical and electrophysiological data; (2) in its approach to the myelinated nerve fiber as a multi-axial cable; and (3) in the numerical algorithm used to obtain distributed model equation solutions for potential and current. The morphometric properties are taken from detailed electron microscopic anatomical studies (Berthold & Rydmark, 1983a, Experientia 39, 964-976). The internodal axolemma is characterized as an excitable membrane and model-generated nodal and internodal membrane action potentials are presented. A system of describing equations for the equivalent network model is derived, based on the application of Kirchoff's Current Law, which take the form of multiple cross-coupled parabolic partial differential equations. An implicit numerical integration method is developed and the numerical solution implemented on a parallel processor. Non-uniform spatial step sizes are used, enabling detailed representation of the nodal region while minimizing the number of total segments necessary to represent the overall fiber. Conduction velocities of 20.2 m sec-1 at 20 degrees C for a 15 microns diameter amphibian fiber and 57.6 m sec-1 at 37 degrees C for a 17.5 microns diameter mammalian fiber are achieved, which agrees qualitatively with published experimental data at similar temperatures (Huxley & Stämpfli, 1949, J. Physiol., Lond. 108, 315-339; Rasminsky, 1973, Arch, Neurol. 28, 287-292). The simulation results demonstrate the ability of this model to produce detailed representations of the transaxonal, transmyelin and transfiber potentials and currents, as well as the longitudinal extra-axonal, periaxonal and intra-axonal currents. Also indicated is the potential contribution of the paranodal axolemma to nodal activity as well as the presence of significant longitudinal currents in the periaxonal space adjacent to the node of Ranvier.

Action Potentials↗
PubMed2000

An intelligent rapid odour recognition model in discrimination of Helicobacter pylori and other gastroesophageal isolates in vitro.

Two series of experiments are reported which result in the discrimination between Helicobacter pylori and other bacterial gastroesophageal isolates using a newly developed odour generating system, an electronic nose and a hybrid intelligent odour recognition system. In the first series of experiments, after 5 h of growth (37 degrees C), 53 volatile 'sniffs' were collected over the headspace of complex broth cultures of the following clinical isolates: Staphylococcus aureus, Klebsiella sp., H. pylori, Enterococcus faecalis (10(7) ml(-1)), Mixed infection (Proteus mirabilis, Escherichia coli, and E. faecalis 3 x 10(6) ml each) and sterile cultures. Fifty-six normalised variables were extracted from 14 conductive polymer sensor responses and analysed by a 3-layer back propagation neural network (NN). The NN prediction rate achieved was 98% and the test data (37.7% of all data) was recognised correctly. Successful clustering of bacterial classes was also achieved by discriminant analysis (DA) of a normalised subset of sensor data. Cross-validation identified correctly seven 'unknown' samples. In the second series of experiments after 150 min of microaerobic growth at 37 degrees C, 24 volatile samples were collected over the headspace of H. pylori cultures in enriched (HPP) and normal (HP) media and 11 samples over sterile (N) cultures. Forty-eight sensor parameters were extracted from 12 sensor responses and analysed by a 3-layer NN previously optimised by a genetic algorithm (GA). GA-NN analysis achieved a 94% prediction rate of 'unknown' data. Additionally the 'genetically' selected 16 input neurones were used to perform DA-cross validation that showed a clear clustering of three groups and reclassified correctly nine 'sniffs'. It is concluded that the most important factors that govern the performance of an intelligent bacterial odour detection system are: (a) an odour generation mechanism, (b) a rapid odour delivery system similar to the mammalian olfactory system, (c) a gas sensor array of high reproducibility and (d) a hybrid intelligent model (expert system) which will enable the parallel use of GA-NNs and multivariate techniques.

Culture Media↗
PubMed2000

Importance of multiple-scattering phenomena in XAS structural determinations of [Ni(CN)4]2- in condensed phases.

A quantitative analysis of the XAS spectra of the tetracyanonickelate complex [Ni(CN)4]2- has been carried out. The simultaneous study of the EXAFS and XANES regions yielded complementary information regarding the geometric and electronic structures of the complex. XANES spectra were modeled by applying recently developed self-consistent, full multiple-scattering algorithms in the FEFF8 code (version 8 x 34). XANES spectra for clusters of different sizes (from 9 to 125 atoms) were computed and compared with experimental spectra. This region of the spectra was proportional to a broadened Ni p-density of states diagram above the Fermi level. Although the main features of the XANES spectra were reasonably reproduced by computations, the weak dependence of the theoretical spectra on cluster size contrasts with the close similarity between the experimental spectra of the solid and solution systems. Because of the special geometry of the complex, calculations with polarized light parallel and perpendicular to the molecular plane were carried out, yielding a reasonable reproduction of the experimental data from another report for cluster sizes equal to or higher than 45 atoms. The highly symmetric square planar structure of the complex was found to be responsible for the unusual amplitude of the multiple-scattering (MS) contributions to the EXAFS spectra. Spectra in this region were fitted using the FEFFIT EXAFS analysis program, taking into account only the MS paths that simultaneously have both a high amplitude, as calculated with the ab initio code FEFF, and a small Debye-Waller factor, as estimated by the independent-vibration approximation model. Fitting results yielded very similar structures for the Ni2+ complex in the solid state and in solution, though the larger Debye-Waller factors found for the solid suggest higher static disorder in this state.

Journal Article↗
PubMed2001

Electrostatics of nanosystems: application to microtubules and the ribosome.

Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.

Algorithms↗
PubMed1998

Porcine cerebroside sulfate activator (saposin B) secondary structure: CD, FTIR, and NMR studies.

Cerebroside sulfate activator protein (CSAct or saposin B) is one of a group of heat stable, low-molecular-weight proteins that appear to share a common structural motif. These have been referred to as saposin-like proteins and are thought to share a multiple amphipathic helical barrel structure with a conserved pattern of disulfide linkages. Porcine kidney CSAct was prepared in high purity and consisted of three major glycosylated subforms. The protein was studied by physical-chemical methods and evaluated by various methods for structural prediction. All suggest that CSAct has high amounts of alpha-helical conformation and little if any beta-sheet. Circular dichroism (CD) studies indicate 45-50% helical conformation depending on buffer and temperature. There was only a moderate loss in helical content with increasing temperature and no indication of thermal denaturation. Fourier transform infrared spectroscopy (FTIR) measurements on deuterium hydrated self-films also indicated a predominantly helical structure. Helical axis orientation was investigated by both oriented CD and FTIR dichroism, which suggested that the helical axes were roughly parallel and oriented along the axis of the surface on which the self-films had been deposited. One-dimensional nuclear magnetic resonance spectra showed large chemical shift dispersion, indicating a defined tertiary structure with little variation between 6 and 85 degrees C. NOESY spectra failed to show the strong NOE cross peaks expected for a highly helical conformation. This may indicate short-term conformational flexibility within the helices or molecular aggregation at the high protein concentrations employed. These observations are consistent with the 3-4-helix bundle motif suggested for saposin-like proteins by various predictive algorithms.

Algorithms↗