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 1,567 records · Page 87Linked to original sources
PubMed1994

Neural network for control of rearrangeable Clos networks.

Rapid evolution in the field of communication networks requires high speed switching technologies. This involves a high degree of parallelism in switching control and routing performed at the hardware level. The multistage crossbar networks have always been attractive to switch designers. In this paper a neural network approach to controlling a three-stage Clos network in real time is proposed. This controller provides optimal routing of communication traffic requests on a call-by-call basis by rearranging existing connections, with a minimum length of rearrangement sequence so that a new blocked call request can be accommodated. The proposed neural network controller uses Paull's rearrangement algorithm, along with the special (least used) switch selection rule in order to minimize the length of rearrangement sequences. The functional behavior of our model is verified by simulations and it is shown that the convergence time required for finding an optimal solution is constant, regardless of the switching network size. The performance is evaluated for random traffic with various traffic loads. Simulation results show that applying the least used switch selection rule increases the efficiency in switch rearrangements, reducing the network convergence time. The implementation aspects are also discussed to show the feasibility of the proposed approach.

Algorithms↗
PubMed1991

A simulation study comparing designs for dose ranging.

Only with knowledge of the (prior) distribution of dose-response parameters in a population, can one determine both the initial dose of a drug for chronic administration to an individual (such as the dose producing a fixed degree of response in a fixed proportion of the population) and an appropriate subsequent (adjusted) dose (such as the dose yielding a desirable response according to the posterior parameter distribution, given an observed response to an initial dose). The currently FDA-sanctioned design for a dose-ranging study, the parallel-dose design, assigns just one of several doses to each patient. It does not provide good information on the distribution of individual dose-response parameters. A cross-over design assigns several dose levels to each patient. It therefore can provide better information, but does not resemble clinical practice. Consequently, study participants must be restricted to patients who can tolerate such non-therapeutic drug exposure, posing problems in extrapolation of study results to other types of patients. A titration or dose-escalation design begins all patients on placebo and, except for those patients assigned to a placebo-only group, escalates the dose for a patient at preset intervals only when clinical response at lower doses is inadequate. It both exposes patients to several dose levels and resembles good clinical practice, allowing study of a representative patient sample. We report here the simulation results of parameter estimation for the three designs when the data arise from complex and realistic dose-response models and/or with certain complications in study execution. The dose-escalation design clearly performs better overall than the parallel-dose design for the models considered here, and generally, just a little worse than the cross-over design. These results support the conclusion that for dose ranging, depending on the demands of the clinical situation, one should use either the cross-over or the dose-escalation design.

Algorithms↗
PubMed2004

On the errors in assessment of severity of involuntary movements using surface EMG.

Surface electromyogram (SEMG) is a useful tool to depict involuntary movements, but evaluation of the intensity of such movements with SEMG over multiple recording instances requires awareness of factors influencing quantified SEMG signals. We investigated the differences in the amplitude of SEMGs due to electrode displacement in isometric voluntary contraction in the upper arm, forearm and lower leg in 8 healthy men. The SEMGs of gross muscle activity simultaneously recorded with 4 electrode pairs from the agonist and antagonist sides in 3 displacement conditions with respect to parallel position, interelectrode distance, and rotation were compared. The amount of EMG integration (equivalent to the average SEMG amplitude) of each electrode pair was compared to the reference electrode pair with interelectrode distance of 40 mm placed on the center of the tested muscles. The average EMG difference ratios ranged 1.1-2.2%/mm in parallel shift, 1.0-1.9%/mm in distance shift, and 0.3-0.6%/degree in rotation shift. Displacement error of electrodes in separate recording instances should be reduced using anatomical landmarks, when SEMG is applied as a quantitative method to evaluate change in the states of involuntary movements.

Adult↗
PubMed2000

Seed misplacement and stabilizing needles in transperineal permanent prostate implants.

BACKGROUND AND PURPOSE: Seed misplacement occurring in transperineal permanent implants contributes to the degradation in dose coverage. It has been suggested that needles could be used to immobilize the prostate and help reduce misplacement. This study investigates the effects of parallel stabilizing needles on seed misplacement. MATERIALS AND METHODS: A group of ten patients implanted with stabilizing needles was compared with a group of 20 patients implanted without stabilization. Measurements were performed on the displacement of individual seeds and needles. The needle measurements are: insertion angle, the ratio of post-implant over pre-implant lengths and the clustering tendency, a measure of relative misplacement among the seeds of the same needle. RESULTS: No difference was observed in seed misplacement. No difference was observed in needle insertion angle, a measure which was expected to improve with the use of stabilizing needles. CONCLUSION: None of the expected effects from the use of parallel stabilizing needles have been observed. This method of prostate contention appears to be without benefits. Seed misplacement is most pronounced along the insertion axis and is caused by friction between prostatic tissues and implantation needles. Reducing friction could be a promising alternative to prostate contention in trying to reduce misplacement.

Algorithms↗
PubMed2004

Distance-driven projection and backprojection in three dimensions.

Projection and backprojection are operations that arise frequently in tomographic imaging. Recently, we proposed a new method for projection and backprojection, which we call distance-driven, and that offers low arithmetic cost and a highly sequential memory access pattern. Furthermore, distance-driven projection and backprojection avoid several artefact-inducing approximations characteristic of some other methods. We have previously demonstrated the application of this method to parallel and fan beam geometries. In this paper, we extend the distance-driven framework to three dimensions and demonstrate its application to cone beam reconstruction. We also present experimental results to demonstrate the computational performance, the artefact characteristics and the noise-resolution characteristics of the distance-driven method in three dimensions.

Algorithms↗
PubMed1998

Electrical stimulation of cardiac tissue by a bipolar electrode in a conductive bath.

A three-dimensional (3-D) computer simulation of the electrical stimulation of passive cardiac tissue from a bipolar electrode placed within a conductive bath is presented. Through the bidomain model, the syncytial and anisotropic properties of cardiac tissue are taken into account; tissues with equal anisotropy and no transverse coupling are also considered. The membrane is represented by a capacitor and passive resistor in parallel. Located within an isotropic bath, the bipolar electrode is oriented either perpendicular or parallel to the tissue surface. For anisotropic tissue with a small cathode-tissue separation, the tissue surface is highly depolarized under the cathode with the depolarization persisting a considerable distance from the electrode in the transverse fiber direction. Adjacent to this region in the longitudinal direction, areas of hyperpolarization exist. At large distances from the cathode, the tissue surface is hyperpolarized in all directions when the electrode axis is perpendicular to the tissue. In the parallel case, surface depolarization creates buried regions of hyperpolarization. For the perpendicular configuration, the ratio of the steady-state maximum depolarization to steady-state maximum hyperpolarization, an estimate of the ratio of anodal to cathodal threshold, decreases rapidly with increasing cathode-tissue separation. In the parallel case, the depth of the conductive bath significantly affected the transmembrane potential distribution in the tissue. The use of a 3-D model more realistically simulates real-life electrical stimulation (such as stimulation with an implantable pacemaker) and provides insight into the effect of the volume conductor adjacent to the tissue.

Algorithms↗
PubMed1989

[Clinico-pathogenetic substantiation of medical tactics in combined benign hyperplastic processes in the uterus of patients of reproductive age].

The definition of concomitant benign hyperplastic diseases of the uterus relates to the abnormalities of the female reproductive system which are accompanied with a simultaneous development of uterine hyperplasias or endometrial polyps, myomas and/or endometriosis. The investigation of 290 patients of reproductive age revealed a multifactorial origin of the aforementioned diseases. Anamnestic, gynecological, dermatoglyphic, hormonal and receptor investigation techniques used in parallel with a routine general clinical examination evidenced systemic lesions and defined clinical and pathogenetic differences in the conditions associated with hyperplasia or endometrial polyps. The authors substantiated the use of various methods in the system of treatment: the use of nonsteroidal drugs with gestagen properties and cryogenic application to the walls of the uterus.

Adult↗
PubMed2002

[Ultrasound differentiation between benign enlargement of the subarachnoid space and brain atrophy].

Fluid collections surrounding the brain (pericerebral fluid collections) in infants can be caused by a variety of conditions: benign enlargement of the subarachnoid space, passive dilatation of the subarachnoid space due to brain atrophy, subdural hygroma and subdural effusion as a result of meningitis or subdural haematoma. An enlarged frontal subarachnoid space and normal or minimally enlarged ventricular size, with normal or increase head circumference is relatively common finding in infancy. Without associated brain anomalies, this finding predicts normal development of the child. In our study, we have followed up psychomotor development of 22 children, with increased diameters of subarachnoid spaces, detected by ultrasound examination of the brain, without associated brain anomalies. The inclusion criterion for study was enlarged subarachnoid space, measured at the conventional coronal section at the level of the interventricular foramen. The upper limits of each measurements were: 3 mm for sinocortical width, 4 mm for craniocortical width and 6 mm for the interhespheric width. The patients have been followed up to the age of 24 months. Each of them had normal development. 16 of them had normal head circumference. 6 of them had head circumference above the 97th percentile and their head circumference measurements have been plotted for the next 6 months after the diagnosis, to be certain that growth is paralleling the normal curve. It is important to differ benign enlargement of subarachnoid space from brain atrophy, which is quite "serious" diagnosis, with poor neurodevelopmental prognosis. The brain atrophy has been presented with passive dilatation of subarachnoid space and ventriculomegaly, as well. In the case of benign enlargement of subarachnoid space normal or minimally enlarged ventricular size is present. For proper interpretation of this ultrasound finding, correlation with head circumference is necessary. We recommend the head circumference percentile chart to be enclosed to the each brain sonography finding. The algorithm of the further neurological evaluation differs significantly in the case of benign enlargement of subarachnoid space and brain atrophy. In the case of benign enlargement of subarachnoid space further neuroimaging procedures are not needed (in our study it has been done for 6 patients). If the brain atrophy is suspected, further complete neurological examination is necessary.

Atrophy↗
PubMed1999

Flow injection with chemical reaction interface-isotope ratio mass spectrometry: an alternative to off-line combustion for detecting low levels of enriched 13C in mass balance studies.

We have evaluated the potential of flow injection chemical reaction interface isotope-ratio mass spectrometry to replace radioactive labeling techniques in material balance studies. A sample is flow injected and transmitted through a desolvation system followed by combustion to form 13CO2 with a microwave-powered chemical reaction interface. We can detect trace amounts of a 13C-labeled drug (3'-azido-3'-deoxythymidine, AZT) in urine or feces. Our ability to quantify less than 100 ng/mL of excess 13C (approximately 1 microgram/mL of 13C-labeled AZT) from a sample equivalent to 10 microL of urine is superior to previous detection limits for 13C in urine that use off-line combustion methods. Parallel studies using 14C-labeled AZT showed that our stable isotope method provides comparable percent excretion data for urine and feces. These results support previous findings that mass balance studies could be carried out with isotope-ratio mass spectrometer, here using doses as low as 1-2 mg/kg.

Algorithms↗
PubMed2004

Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.

The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in gas phase, the iterative quantum mechanical/molecular mechanical (QM/MM) optimization method developed earlier in our laboratory and the introduction of a new metric defining the distance between different structures in the configuration space. In this method we represent the reaction path by a discrete set of structures. For each structure we partition the atoms into a core set that usually includes the QM subsystem and an environment set that usually includes the MM subsystem. These two sets are optimized iteratively: the core set is optimized to approximate the reaction path while the environment set is optimized to the corresponding energy minimum. In the optimization of the core set of atoms for the reaction path, we introduce a new metric to define the distances between the points on the reaction path, which excludes the soft degrees of freedom from the environment set and includes extra weights on coordinates describing chemical changes. Because the reaction path is represented by discrete structures and the optimization for each can be performed individually with very limited coupling, our method can be executed in a natural and efficient parallelization, with each processor handling one of the structures. We demonstrate the applicability and efficiency of our method by testing it on two systems previously studied by our group, triosephosphate isomerase and 4-oxalocrotonate tautomerase. In both cases the minimum energy paths for both enzymes agree with the previously reported paths.

Algorithms↗
PubMed2004

Whole-genome expression profiling through fragment display and combinatorial gene identification.

There is a growing demand for highly parallel gene expression analysis with whole genome coverage, high sensitivity and high accuracy. Open systems such as differential display are capable of analyzing most of the expressed genome but are not quantitative and generally require manual identification of differentially expressed genes by sequencing. Closed systems such as microarrays use gene-specific probes and are, therefore, limited to studying specific genes in well-characterized species. Here, we describe Tangerine, a PCR-based system that combines the scope and generality of open systems with a robust and immediate identification algorithm using publicly available sequence information. By combinatorial analysis of three independent and complete DNA indexing profiles, each displaying the complete set of expressed transcripts on capillary electrophoresis, the method allows transcripts to be simultaneously quantified and identified. The method is sensitive, accurate and reproducible, and is amenable to high-throughput automated operation.

Animals↗
PubMed1993

Typing of serum-soluble HLA-B27 antigen by ELISA.

An ELISA using serum as soluble HLA antigen source was developed for HLA-B27 typing. Two sandwich assays were run in parallel. The first assay utilized a monoclonal antibody (mAb) reacting with a determinant expressed by both HLA-B7 and B27 antigens; the other assay utilized a mAb reactive with HLA-B7 antigens but not with HLA-B27 antigens. After incubation with serum samples, bound HLA antigen was detected using an anti-beta 2m antibody conjugated to peroxidase and a chromogenic substrate. Absorbance of each well was measured at 490 nm. Based on analysis of absorbances obtained with panels of specimens of known HLA phenotypes, a mathematical algorithm was developed to derive the specimen HLA-B27 phenotype from its ELISA absorbance values. Despite the lack of monospecific mAb, an accurate HLA-B27 typing was possible. 362 specimens (including 151 HLA-B27-positive) were tested. Agreement between microlymphocytotoxicity and ELISA was 99.2%. No correlation between the level of HLA-B27 antigen reactivity and the amount of total HLA class I antigen in serum was observed. This report demonstrates the possibility of using serum-soluble HLA antigen and ELISA technology for histocompatibility testing. The assay offers several significant advantages over microlymphocytotoxicity: no need for cell preparation, batch testing capabilities and objective, reproducible interpretation of results.

Algorithms↗
PubMed2004

Acid-base cosolvent method for determining aqueous permeability of amiodarone, itraconazole, tamoxifen, terfenadine and other very insoluble molecules.

A high-throughput, UV-detection PAMPA (parallel artificial membrane permeability assay) cosolvent procedure is described, based on the use of 20% v/v acetonitrile in aqueous buffer. A training set of 32 drugs (17 bases, 13 acids, 2 ampholytes) was studied both in aqueous buffer and in cosolvent-buffer solutions. A procedure was devised, where intrinsic permeability values, log P(o)(COS), measured in cosolvent solution, are converted to values expected under cosolvent-free conditions, using an in silico model based on Abraham H-bond acidity (alpha) and basicity (beta) descriptors, developed with the Algorithm Builder computer program, to obtain aqueous intrinsic permeability values: log P(o)=0.738+0.885 log P(o)(COS)-1.262alpha+0.436beta, r(2)=0.97, q(2)=0.96, s=0.38, n=32, F=279. Five sparingly-soluble weak bases (solubility <1 microg/ml), which could not be characterized without cosolvent, had their aqueous intrinsic permeability, P(o), estimated: miconazole 0.32 cm/s; itraconazole 3.2 cm/s; amiodarone 13 cm/s; tamoxifen 28 cm/s; terfenadine 162 cm/s.

Acids↗
PubMed2004

Improved watershed transform for medical image segmentation using prior information.

The watershed transform has interesting properties that make it useful for many different image segmentation applications: it is simple and intuitive, can be parallelized, and always produces a complete division of the image. However, when applied to medical image analysis, it has important drawbacks (oversegmentation, sensitivity to noise, poor detection of thin or low signal to noise ratio structures). We present an improvement to the watershed transform that enables the introduction of prior information in its calculation. We propose to introduce this information via the use of a previous probability calculation. Furthermore, we introduce a method to combine the watershed transform and atlas registration, through the use of markers. We have applied our new algorithm to two challenging applications: knee cartilage and gray matter/white matter segmentation in MR images. Numerical validation of the results is provided, demonstrating the strength of the algorithm for medical image segmentation.

Algorithms↗
PubMed2006

Dehydroepiandrosterone secretion in healthy older men and women: effects of testosterone and growth hormone administration in older men.

CONTEXT: Aging is associated with diminished gonadal steroid and GH/IGF-I axis activity; whether these changes contribute to the parallel declines of dehydroepiandrosterone (DHEA) and DHEA sulfate (DHEAS) production is unknown, as are the effects of sex steroid and/or GH administration on DHEA and DHEAS production. OBJECTIVE: Our objective was to evaluate morning DHEAS concentrations and nocturnal DHEA secretory dynamics in healthy older men and women, before and after chronic administration of sex steroid(s) alone, GH alone, sex steroid(s) combined with GH, or placebo alone. DESIGN: We compared nocturnal DHEA secretory dynamics (2000 h to 0800 h, sampling every 20 min, analyzed by multiparameter deconvolution and approximate entropy algorithms) in healthy older (65-88 yr) men (n = 68) and women (n = 36), both before and after 26 wk of administration of sex steroid(s) alone [testosterone (T) in men or estrogen/progesterone in women], GH alone, sex steroid(s) combined with GH, or placebo alone. RESULTS: Morning concentrations of DHEAS were lower; nocturnal DHEA pulsatile production rate, burst frequency, and amplitude were higher; and half-life was shorter in women (P < 0.05). Nocturnal integrated DHEA concentrations, total production rate, and approximate entropy did not differ significantly by sex. Because of small treatment group sizes in women, only hormone intervention results in men are presented. In men, T and T plus GH administration significantly decreased nocturnal integrated DHEA but not morning DHEAS concentrations. GH alone exerted no significant effects on nocturnal DHEA secretion or morning DHEAS. CONCLUSIONS: Spontaneous nocturnal DHEA secretion is sexually dimorphic in healthy older individuals, and T administration decreases nocturnal DHEA secretion in older men. The clinical significance of sex steroid modulation of DHEA secretion in older persons remains to be elucidated.

Aged↗
PubMed1996

Local computed tomography via iterative deblurring.

X-ray computed tomography is a major imaging modality. An iterative deblurring method is adapted for local reconstruction in parallel-beam and cone-beam geometries, utilizing only x-rays passing through a region of interest. The feasibility is demonstrated in numerical simulation with noise-free and noisy projection data. The iterative deblurring method has the theoretical advantages of maintaining nonnegativity, converging monotonically and minimizing Csiszàr's I-divergence.

Algorithms↗
PubMed2002

Grouped-neural network modeling for model predictive control.

A group of feed-forward neural networks (NNs), each providing the prediction of an individual process output at a future step, is used as the dynamic prediction model for the model-based predictive control (MPC) scheme in the proposed work. These NNs are parallel (independent) rather than cascaded--they are trained and implemented in parallel. Therefore, the complexity and effort in the training stage is decreased and compounded error propagation is eliminated from the prediction. A new strategy of compensating for the process-model mismatch under this grouped-NN model structure is also developed. Effectiveness of the scheme as a general nonlinear MPC is demonstrated by simulation results.

Algorithms↗
PubMed2001

Optimization of view ordering for motion artifact suppression.

Motion artifacts in MRI may be reduced by optimized view ordering. Extensive simulations of view-ordering techniques were performed on high-resolution phantom images to determine the best strategy for distributing motion in k-space. Although not exhaustive, simulation results indicate that minimizing motion at the center of k-space is critical to overall image quality. For 2D imaging, using edge-center-edge view order and setting the readout direction parallel to the direction of the motion produces the sharpest point spread function and the lowest image energy error. For 3D imaging, using an edge-center-edge view order proves to be the optimum choice in general. Given these observations, several important issues regarding the measurement of motion effects are discussed.

Algorithms↗