Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computing Methodologies”

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 433 records · Page 24Linked to original sources
PubMed1999

Accounting for treatment delays when treating highly proliferative tumours.

This study was undertaken to investigate the possibility of increasing the dose per fraction or increasing the number of fractions to account for treatment delays occurring during radiotherapy treatments for highly proliferative tumours. The linear quadratic model with time was used to determine the difference in biological effective dose (BED) for the original schedule and the schedule including a treatment delay. Tables of extra fractions and extra dose per fraction required to account for a number of possible delays have been determined. It has been shown that for tumours with very short potential doubling times it is best to deliver the extra dose as an increase in dose per fraction rather than an increase in the number of fractions, while for tumours with moderately short potential doubling times (above 7 days) the reverse is true. The equivalent uninterrupted schedules, which would have delivered the same effects to the tumour, have also been determined.

Cell Division↗
PubMed2003

A vectorized Monte Carlo code for radiotherapy treatment planning dose calculation.

How to speed up Monte Carlo (MC) simulation in dose calculation without losing its intrinsic accuracy is one of the key issues of making a clinical MC dose engine. In this study we intensively investigated a special parallel computation technique, the vectorization technique, to boost simulation efficiency on a personal computer (PC) without extra hardware investment. A MC code, dose planning method (DPM), was extensively modified into a vectorized code, V-DPM, using the streaming single-instruction-multiple-data extension (SSE) parallel computation model. Comparative simulations were conducted for typical simulation cases in both DPM and V-DPM codes. We found that in every case the V-DPM code runs 1.5 times faster than the DPM code with variance of 0.6%.

Algorithms↗
PubMed2004

Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference.

MOTIVATION: Bayesian estimation of phylogeny is based on the posterior probability distribution of trees. Currently, the only numerical method that can effectively approximate posterior probabilities of trees is Markov chain Monte Carlo (MCMC). Standard implementations of MCMC can be prone to entrapment in local optima. Metropolis coupled MCMC [(MC)(3)], a variant of MCMC, allows multiple peaks in the landscape of trees to be more readily explored, but at the cost of increased execution time. RESULTS: This paper presents a parallel algorithm for (MC)(3). The proposed parallel algorithm retains the ability to explore multiple peaks in the posterior distribution of trees while maintaining a fast execution time. The algorithm has been implemented using two popular parallel programming models: message passing and shared memory. Performance results indicate nearly linear speed improvement in both programming models for small and large data sets.

Algorithms↗
PubMed2005

Incremental communication for adaptive resonance theory networks.

We have proposed earlier the incremental internode communication method to reduce the communication cost as well as the time of the learning process in artificial neural networks (ANNs). In this paper, the limited precision incremental communication method is applied to a class of recurrent neural networks, the adaptive resonance theory 2 (ART2) networks. Simulation studies are carried out to examine the effects of the incremental communication method on the convergence behavior of ART2 networks. We have found that, 7-13-b precision is sufficient to obtain almost the same results as those with full (32-b) precision conventional communication. A theoretical error analysis is also carried out to analyze the effects of the limited precision incremental communication. The simulation and analytical results show that the limited precision errors are bounded and do not seriously degrade the convergence of ART2 networks. Therefore, the incremental communication can be incorporated in parallel and special-purpose very large scale integration (VLSI) implementations of the ART2 networks.

Algorithms↗
PubMed2005

Are artificial neural networks white boxes?

In this paper, we introduce a novel Mamdani-type fuzzy model, referred to as the all-permutations fuzzy rule base (APFRB), and show that it is mathematically equivalent to a standard feedforward neural network. We describe several applications of this equivalence between a neural network and our fuzzy rule base (FRB), including knowledge extraction from and knowledge insertion into neural networks.

Algorithms↗
PubMed1999

Ovarian dysplasia in prophylactic oophorectomy specimens: cytogenetic and morphometric correlations.

BACKGROUND: Ovarian dysplasia, a potential precursor to ovarian carcinoma, has been described in ovarian tissue obtained by prophylactic oophorectomy and also adjacent to ovarian carcinoma. Women with a family history of ovarian carcinoma, especially those of Jewish Ashkenazi descent, often test positive for BRCA mutant genes. Prophylactically removed ovaries, generally described as normal on macroscopic examination, can exhibit a "preneoplastic phenotype" and unsuspected neoplasm. METHODS: Histologic slides of ovarian tissue from 54 Ashkenazi Jewish women were reviewed. All had a family history of ovarian carcinoma and all were tested for BRCA mutations. Forty-four women tested positive. Thirty-one women underwent prophylactic oophorectomy and 23 underwent oophorectomy for ovarian carcinoma. Normal, dysplastic, and ovarian carcinoma epithelial cells were analyzed morphometrically combining nuclear area measurements with chromatin texture assessment using a novel method based on the computation of autocorrelation coefficients and a derived parameter (Beta). Discriminant analysis between classificatory algorithms was used to obtain results. RESULTS: Ovarian dysplasia was identified in 77.6% of the prophylactic oophorectomy specimens. An unsuspected ovarian carcinoma was diagnosed in one prophylactic oophorectomy specimen. Of 10 women who underwent prophylactic oophorectomy and were negative for BRCA mutations, three had ovarian dysplasia. The average nuclear measurements of the dysplastic cells were similar to those published previously. The new autocorrelation-based method evaluating nuclear texture, as revealed by tridimensional surface plots, demonstrated high discriminatory potential. Discriminant analysis based on nuclear area and nuclear texture information resulted in the correct classification of nearly all the cases in the three diagnostic categories. CONCLUSIONS: Ovaries removed by prophylactic oophorectomy examined in their entirety often reveal ovarian dysplasia and occasionally ovarian carcinoma. The new morphometric method used was highly discriminatory in the evaluation of nuclear texture. Ovarian dysplasia in women with risk factors for ovarian carcinoma is significant in early ovarian carcinogenesis.

Adult↗
PubMed2005

Using parallel evolutionary development for a biologically-inspired computer vision system for mobile robots.

We describe a new approach to attacking the problem of robust computer vision for mobile robots. The overall strategy is to mimic the biological evolution of animal vision systems. Our basic imaging sensor is based upon the eye of the common house fly, Musca domestica. The computational algorithms are a mix of traditional image processing, subspace techniques, and multilayer neural networks.

Algorithms↗
PubMed2006

Advantages of parallel imaging in conjunction with hyperpolarized helium--a new approach to MRI of the lung.

Hyperpolarized helium (3He) gas MRI has the potential to assess pulmonary function. The non-equilibrium state of hyperpolarized 3He results in the continual depletion of the signal level over the course of excitations. Under non-equilibrium conditions the relationship between the signal-to-noise ratio (SNR) and the number of excitations significantly deviates from that established in the equilibrium state. In many circumstances the SNR increases or remains the same when the number of data acquisitions decreases. This provides a unique opportunity for performing parallel MRI in such a way that both the temporal and spatial resolution will increase without the conventional decrease in the SNR. In this study an analytical relationship between the SNR and the number of excitations for any flip angle was developed. Second, the point-spread function (PSF) was utilized to quantitatively demonstrate the unconventional SNR behavior for parallel imaging in hyperpolarized gas MRI. Third, a 24-channel (24ch) receive and two-channel (2ch) transmit phased-array system was developed to experimentally prove the theoretical predictions with 3He MRI. The in vivo experimental results prove that significant temporal resolution can be gained without the usual SNR loss in an equilibrium system, and that the entire lung can be scanned within one breath-hold (approximately 13 s) by applying parallel imaging to 3D data acquisition.

Administration, Inhalation↗
PubMed2006

Band-selective 13C homonuclear 3D spectroscopy for solid proteins at high field with rotor-synchronized soft pulses.

We demonstrate improved 3D 13C-13C-13C chemical shift correlation experiments for solid proteins, utilizing band-selective coherence transfer, scalar decoupling and homonuclear zero-quantum polarization transfer. Judicious use of selective pulses and a z-filter period suppress artifacts with a two-step phase cycle, allowing higher digital resolution in a fixed measurement time. The novel correlation of C(ali)-C(ali)-CX (C(ali) for aliphatic carbons, CX for any carbon) reduces measurement time by an order of magnitude without sacrificing digital resolution. The experiment retains intensity from side-chain carbon resonances whose chemical shift dispersion is critical to minimize spectral degeneracy for large proteins with a predominance of secondary structure, such as beta-sheet rich fibrillar proteins and alpha-helical membrane proteins. We demonstrate the experiment for the beta1 immunoglobulin binding domain of protein G (GB1) and fibrils of the A30P mutant of alpha-synuclein, which is implicated in Parkinson's disease. Selective pulses of duration comparable the rotor period give optimal performance, but must be synchronized with the spinning in non-trivial ways to minimize chemical shift anisotropy recoupling effects. Soft pulses with a small bandwidth-duration product are best for exciting the approximately 70 ppm bandwidth required for aliphatic-only dimensions.

Carbon Isotopes↗
PubMed2004

Potential for enlarging DNA memory: the validity of experimental operations of scaled-up nested primer molecular memory.

DNA is an attractive memory unit because of its immense information density. Here, we describe a memory model made of DNA, called Nested Primer Molecular Memory (NPMM). NPMM consists of many DNA strands, and each DNA strand consists of two areas: a data area and a data address area. When the address of target data is specified, only the target data can be extracted from NPMM. In this paper, we evaluate the validity of the basic operations of NPMM and then discuss the feasibility of scaled-up NPMM through some laboratory experiments. In the latter, we deal with scaled-up NPMM simulated by the Concentration Scaling method.

Algorithms↗
PubMed2003

Software objects in distributed flow measurements.

Increasing complexity of the contemporary industrial measurement systems is a common characteristic. Partitioning of the measurement process into software components that can be realized as separate objects facilitates the development of the measurement system. Using a client/server approach, the measurement system components become shareable and accessible across the network. The components can be deployed anywhere on the network and shared by a considerable number of applications. The paper describes a realization of the flow measurement system with distributed software components, i.e., measurement procedures, which include the concurrent calculation of the measurement results and the corresponding uncertainties.

Computer Communication Networks↗
PubMed2006

A proposed computational biomechanics cyber-infrastructure for multi-phase and multi-scale problems: delivering biomechanics to the surgeon.

This paper presents a new direction for practitioners of computational biomechanics. It provides a description of three prototype software platforms, which demonstrate how the cyber-infrastructure can be used to integrate the algorithms of computational biomechanics to solve multi-phase and multi-scale problems. Then, a development platform is presented. This platform can also deliver integrated biomechanics into the surgical ward for surgical planning. This platform performs these tasks without the need for advanced network software tools: an appendix provides all the simple and fundamental open source and CI technologies that are required. The overarching goal of this paper is to make the potential of the emerging cyber-infrastructure comprehensible and accessible to practitioners of computational biomechanics.

Biomechanical Phenomena↗
PubMed1999

Intensity modulation methods for proton radiotherapy.

The characteristic Bragg peak of protons or heavy ions provides a good localization of dose in three dimensions. Through their ability to deliver laterally and distally shaped homogenous fields, protons have been shown to be a precise and practical method for delivering highly conformal radiotherapy. However, in an analogous manner to intensity modulation for photons, protons can be used to construct dose distributions through the application of many individually inhomogeneous fields, but with the localization of dose in the Bragg peak providing the possibility of modulating intensity within each field in two or three dimensions. We describe four different methods of intensity modulation for protons and describe how these have been implemented in an existing proton planning system. As a preliminary evaluation of the efficacy of these methods, each has been applied to an example case using a variety of field combinations. Dose-volume histogram analysis of the resulting dose distributions shows that when large numbers of fields are used, all techniques exhibit both good target homogeneity and sparing of neighbouring critical structures, with little difference between the four techniques being discerned. As the number of fields is decreased, however, only a full 3D modulation of individual Bragg peaks can preserve both target coverage and sparing of normal tissues. We conclude that the 3D method provides the greatest flexibility for constructing conformal doses in challenging situations, but that when large numbers of beam ports are available, little advantage may be gained from the additional modulation of intensity in depth.

Computing Methodologies↗
PubMed1998

Computer assistance for pelvic osteotomies.

To assist surgeons performing pelvic osteotomies for the treatment of dysplastic hips, an image guided freehand navigation system has been developed. Preoperative computed tomographic scan images are presented in various ways to the surgeon together with real time display of the instruments and surgical action on the computer screen. The system supports the preoperative plan and provides optimized control of surgical action. The main focus of the image guidance has been placed on the execution of the different required cuts and the reorientation of the acetabular fragment. Special attention also has been given to the development of a sophisticated surgeon-machine interface. Fourteen surgeries have been performed with image guidance so far. The visualization aids provided by the system are able to help reduce potential risk and thus increase safety and accuracy for this difficult class of surgical interventions.

Acetabulum↗