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PubMed2003

Parallel tempering simulations of HP-36.

We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins and points out the need for improved energy functions.

Algorithms↗
PubMed2006

Design and analysis of stepped wedge cluster randomized trials.

Cluster randomized trials (CRT) are often used to evaluate therapies or interventions in situations where individual randomization is not possible or not desirable for logistic, financial or ethical reasons. While a significant and rapidly growing body of literature exists on CRTs utilizing a "parallel" design (i.e. I clusters randomized to each treatment), only a few examples of CRTs using crossover designs have been described. In this article we discuss the design and analysis of a particular type of crossover CRT - the stepped wedge - and provide an example of its use.

Adolescent↗
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↗
PubMed2002

Chemogenomics: bridging a drug discovery gap.

With the successful completion of the human genome sequencing and the resulting plethora of genetic information now available novel technologies and applications have to be established to translate the huge amount of data generated into successful biological and biomedical research programs. The integration of various drug discovery disciplines within the parallel quest for novel targets and new molecular entities has meanwhile given rise to a quite popular term in pharmaceutical research named "chemogenomics". This review article gives an overview of the disciplines involved in this field and discusses the possible implications of this novel paradigm in drug discovery for the near future.

Algorithms↗
PubMed2004

Development of methods for beam angle optimization for IMRT using an accelerated exhaustive search strategy.

PURPOSE: The purpose of this article is to explore the use of the accelerated exhaustive search strategy for developing and validating methods for optimizing beam orientations for intensity-modulated radiation therapy (IMRT). Combining beam-angle optimization (BAO) with intensity distribution optimization is expected to improve the quality of IMRT treatment plans. However, BAO is one of the most difficult problems to solve adequately because of the huge hyperspace of possible beam configurations (e.g., selecting 7 of 36 uniformly spaced coplanar beams would require the intercomparison of 8,347,680 IMRT plans). METHODS AND MATERIALS: An "influence vector" (IV) approximation technique for high-speed estimation of IMRT dose distributions was used in combination with a fast gradient search algorithm (Newton's method) for IMRT optimization. In the IV approximation, it is assumed that the change in intensity of a ray (or bixel) proportionately changes dose along the ray. Evidence is presented that the IV approximation is valid for BAO. The scatter contribution at points away from the ray is accounted for fully in IMRT optimization after the optimum beam orientation has been determined. IVs for all candidate beam angles are generated before the start of optimization. For all subsets of beams selected from a given pool of beams (e.g., 5 of 24 uniformly spaced beams), the distribution of planning scores for the best and the worst plans, optimum angle distributions, dose distributions, and dose-volume histograms (DVH) were analyzed for one prostate and two lung cancer cases. The results of the exhaustive search technique were used to develop a "multiresolution" search strategy. In this approach, a smaller number of beams (e.g., three) is first used to explore the hyperspace of solutions to determine the most preferred and the least preferred directions. The results of such exploration are then used as a starting point for determining an optimum configuration comprising a larger number of beams (e.g., seven). This two-step process is considerably faster than full exhaustive search. The question to be answered was whether the two methods lead to the same or similar solutions. The results of exhaustive search and multiresolution approaches were also compared with a previously published approach that used beam's-eye-view dosimetrics (BEVD). RESULTS: The relative ranks of plans optimized by an accurate dose calculation method were highly correlated with those of the plans optimized by the fast calculation method (i.e., using the IV approximation), which suggests that an approximate dose calculation algorithm can be used effectively for ranking of plans during BAO. We found that dose distributions and DVH of many beam configurations within a specified subset from a given pool of beams (e.g., 5 of 18) may be clinically indistinguishable and acceptable. Their optimized IMRT scores fall in a narrow range, although beam configurations and dose distributions may be different. We used the frequency distributions as a function of beam angles for the best 100 and the worst 100 plans to determine the most and the least preferred beam angles. We found that the most and the least preferred angle distributions for 3 of 18 configurations were very similar to those for 5, 6, 7, or 8 of 18 or 24 configurations, but the size of the search space was much smaller for the 3 of 18 case. Using fewer than three beams was discovered to be inadequate. This information was used to select the most preferred angles and eliminate the least preferred ones before searching for the optimum angles for the remaining beams. For the cases we studies, the multiresolution strategy produced very similar results to the full exhaustive search. Based on the observation that the worst plans had at least one parallel-opposed pair of beams and virtually all of the best plans had none, we were able to further reduce the size of the search space dramatically by using a pool of only nonparallel-opposed equispaced beams (i.e., 7 of 19 instead of 7 of 36). Another observation was that the probability of finding an optimum configuration in a smaller beam pool is substantially lower than in a larger pool (e.g., 5 of 18 vs. 5 of 24). The implication of this BAO is not very important when a large number of beams (nine or more) is used and vice versa. Our results showed that the plans with fewer but optimally placed beams could be as good as or better than plans using a larger number of unoptimized or uniformly placed beams. CONCLUSION: Exhaustive search with fast IMRT algorithms provides a novel and realistic approach to study the characteristics of IMRT dose distributions as a function of beam angles and to design practical BAO strategies for IMRT planning.

Algorithms↗
PubMed1990

On the control of automatic processes: a parallel distributed processing account of the Stroop effect.

Traditional views of automaticity are in need of revision. For example, automaticity often has been treated as an all-or-none phenomenon, and traditional theories have held that automatic processes are independent of attention. Yet recent empirical data suggest that automatic processes are continuous, and furthermore are subject to attentional control. A model of attention is presented to address these issues. Within a parallel distributed processing framework, it is proposed that the attributes of automaticity depend on the strength of a processing pathway and that strength increases with training. With the Stroop effect as an example, automatic processes are shown to be continuous and to emerge gradually with practice. Specifically, a computational model of the Stroop task simulates the time course of processing as well as the effects of learning. This was accomplished by combining the cascade mechanism described by McClelland (1979) with the backpropagation learning algorithm (Rumelhart, Hinton, & Williams, 1986). The model can simulate performance in the standard Stroop task, as well as aspects of performance in variants of this task that manipulate stimulus-onset asynchrony, response set, and degree of practice. The model presented is contrasted against other models, and its relation to many of the central issues in the literature on attention, automaticity, and interference is discussed.

Attention↗
PubMed2005

An image-analysis system based on support vector machines for automatic grade diagnosis of brain-tumour astrocytomas in clinical routine.

An image-analysis system based on the concept of Support Vector Machines (SVM) was developed to assist in grade diagnosis of brain tumour astrocytomas in clinical routine. One hundred and forty biopsies of astrocytomas were characterized according to the WHO system as grade II, III and IV. Images from biopsies were digitized, and cell nuclei regions were automatically detected by encoding texture variations in a set of wavelet, autocorrelation and parzen estimated descriptors and using an unsupervised SVM clustering methodology. Based on morphological and textural nuclear features, a decision-tree classification scheme distinguished between different grades of tumours employing an SVM classifier. The system was validated for clinical material collected from two different hospitals. On average, the SVM clustering algorithm correctly identified and accurately delineated 95% of all nuclei. Low-grade tumours were distinguished from high-grade tumours with an accuracy of 90.2% and grade III from grade IV with an accuracy of 88.3% The system was tested in a new clinical data set, and the classification rates were 87.5 and 83.8%, respectively. Segmentation and classification results are very encouraging, considering that the method was developed based on every-day clinical standards. The proposed methodology might be used in parallel with conventional grading to support the regular diagnostic procedure and reduce subjectivity in astrocytomas grading.

Astrocytoma↗
PubMed1987

Deformation analyses in cell and developmental biology. Part II--Mechanical experiments on cells.

This study employs the finite element approach developed in Part I to analyze mechanical experiments on cells. It views cells as axisymmetric membrane structures containing a body of incompressible material, and models the mechanical contact between a cell and the loading apparatus by a contact algorithm. Since the method is valid for analyzing axisymmetric shell-like bodies with arbitrary shapes, it treates various mechanical experiments on cells in a unified manner. For demonstration purposes, three commonly used mechanical experiments on cells are considered; the compression experiment; the suction (micropipette aspiration) experiment; and the magnetic particle experiment. Based on an estimate of the mechanical property data for unfertilized sea urchin eggs, this analysis method predicts the responses for all three experiments using the same assumptions and approximations. This parallel treatment gives a broad basis for data correlation with experiments. The method also provides insights into mechanical experiments not offered by other approximate methods. For example, it gives the distributions of tensions and stretches on the cell cortex, and suggests the role of friction in the suction experiment.

Animals↗
PubMed2000

Postprocessing technique to correct for background gradients in image-based R*(2) measurements.

Background static magnetic field gradients are a source of signal loss in gradient-echo imaging, as they typically result from discontinuity in the magnetic susceptibility at air-tissue boundaries. Moreover, these induced gradients severely compromise the measurement of R*(2), the effective transverse relaxation rate, which is of interest in many biomedical applications of MRI. Since the slice thickness is usually larger than the in-plane pixel dimensions, gradients parallel to the slice-select direction are of particular concern. In this work, a post-processing technique is introduced which attempts to correct the signal on the assumption that the background gradients are approximately linear across the voxel and the signal decay in the absence of these gradients is exponential. In this case, the time-domain signal is weighted by a sinc function characterized by the amplitude G(b) of the background gradient, which is typically not known a priori. The algorithm searches for the estimate of G(b) which yields the optimum fit of the corrected experimental data to an exponential. It is shown to be effective as long as this gradient is below a critical threshold. Evaluation in a phantom and in the human brain at 1.5 and 4 T demonstrates that this method can restore R(2)* in spite of the apparent rate constant exceeding the true value by up to 100%. Contrary to prospective correction techniques, the approach presented in this study does not prolong scan time.

Adult↗
PubMed1994

Operations research survey and computer simulation of waiting times in two medical outpatient clinic structures.

Outpatient services are increasingly recognised as an important component of health care provision and may be improved through the application of modern management techniques. We have performed a time and role audit of consultation and waiting times in two medical clinics using different queuing systems: namely, a serial processing clinic where patients wait in a single queue and a quasi-parallel processing clinic where patients are directed to the shortest queue to maintain clinic flow. Data collected were used to construct a computer simulation of patient flows in clinic. Assessment of patient satisfaction in the clinic process was determined using a self-administered questionnaire. Mean waiting time was shorter in the quasi-parallel processing clinic: 26 (SD 17) minutes compared with 36(24) minutes in the serial processing clinic. In the serial processing clinic 61% of patients waited more than 30 minutes compared with 41% in the quasi-parallel processing clinic. In the serial processing clinic 8% of 142 patients surveyed complained of the time spent waiting. The computer simulation we produced was able to determine waiting times with different clinic structures. The simulation showed that reductions in waiting time up to 30% might be achieved by changing our serial processing clinic to a quasi-parallel processing one. Performance of medical outpatient clinics can be improved by examining and changing clinic management. Computer simulation of outpatient clinics offers a means of assessing the impact of such changes on waiting time in clinic and on waiting lists.

Algorithms↗
PubMed2006

Near-infrared spectrometry for the quantification of dermal absorption of econazole nitrate and 4-cyanophenol.

PURPOSE: The purpose of this study was to demonstrate the utility of near-infrared (NIR) spectroscopy for the in vitro quantification of econazole nitrate (EN) and 4-cyanophenol (4-CP) in hairless guinea pig skin. METHODS: NIR spectra were collected from each of the following: EN and 4-CP powders, EN and 4-CP in solution, and skin samples following topical exposure to either 4-CP in water or EN in propylene glycol and topical creams. To predict drug concentration from NIR spectra, principal component regression (PCR), interval PCR, and uninformative variable elimination PCR were each used with a leave-one-out cross-validation, and results were compared. NIR results were validated against known skin concentrations measured by high-pressure liquid chromatography (HPLC) analysis of solvent extracts. RESULTS: NIR results matched the HPLC results for the quantification of 4-CP and EN in skin exposed to saturated solutions and topical creams with an r2 > 0.90, a standard error of estimation < 7.0%, and a standard error of performance < 8.0%. CONCLUSION: This experiment demonstrated that NIR closely parallels results obtained from tissue extraction and HPLC analysis, proving its potential utility for the rapid and noninvasive determination of topical bioavailability/bioequivalence of EN and quantification of the model chemical 4-CP. Investigation of drugs in human skin is now justified.

Algorithms↗
PubMed1989

Frequency domain analysis of contrast echocardiographic images.

Sequences of echocontrastographic images of the dog's myocardium are analysed in the frequency domain for the identification of underperfused areas. Owing to the fact that echo images are contaminated by noise and artifacts, we have applied filtering techniques based on Fourier's methods in sequences of raw frames recorded during perfusion with a contrast agent. Thus we have been able to assess correctly the spatial and temporal distribution of the contrast, i.e. the agent kinetics which parallel the distribution of coronary blood flow, in terms of the time necessary for the flow gradient to reach its maximum value, and to describe such a distribution by a functional image obtained by means of an original procedure.

Algorithms↗
PubMed2005

Evaluation of pathways for progression of heterogeneous breast tumors.

To better understand the progression of heterogeneous breast cancers, four models of progession pathways have been evaluated. The models describe the progression through the grades of ductal carcinoma in situ (DCIS) 1, 2, and 3, and through the grades of invasive ductal carcinoma (IDC) 1, 2, and 3. The first three pathways, termed linear, nonlinear, and branched, describe DCIS as a progenitor of IDC, and grades of DCIS progressing into grades of IDC. The fourth pathway, termed parallel, describes DCIS and IDC as diverging from a common progenitor and progressing through grades in parallel. The best transition rates for the linear, nonlinear, and branched pathways were sought using a random search in combination with a directed search based on the Nelder-Mead simplex method. Parameter values for the parallel pathway were determined with heuristic graphs. Results of computer simulation were compared with clinically observed frequencies of grades of DCIS and grades of IDC that were reported to occur together in heterogeneous tumors. Each of the four pathways could simulate frequencies that resembled, to varying degrees, the clinical observations. The parallel pathway produced the best correspondence with clinical observations. These results quantify the traditional descriptions in which grades of DCIS are the progenitors of grades of IDC. The results also raise the alternative possibility that, in some tumors with both components, DCIS and IDC may have diverged from a common progenitor.

Algorithms↗
PubMed2006

TOM: a web-based integrated approach for identification of candidate disease genes.

The massive production of biological data by means of highly parallel devices like microarrays for gene expression has paved the way to new possible approaches in molecular genetics. Among them the possibility of inferring biological answers by querying large amounts of expression data. Based on this principle, we present here TOM, a web-based resource for the efficient extraction of candidate genes for hereditary diseases. The service requires the previous knowledge of at least another gene responsible for the disease and the linkage area, or else of two disease associated genetic intervals. The algorithm uses the information stored in public resources, including mapping, expression and functional databases. Given the queries, TOM will select and list one or more candidate genes. This approach allows the geneticist to bypass the costly and time consuming tracing of genetic markers through entire families and might improve the chance of identifying disease genes, particularly for rare diseases. We present here the tool and the results obtained on known benchmark and on hereditary predisposition to familial thyroid cancer. Our algorithm is available at http://www-micrel.deis.unibo.it/~tom/.

Algorithms↗
PubMed2003

Semiautomatic three-dimensional segmentation of the prostate using two-dimensional ultrasound images.

In this paper, we report on two methods for semiautomatic three-dimensional (3-D) prostate boundary segmentation using 2-D ultrasound images. For each method, a 3-D ultrasound prostate image was sliced into the series of contiguous 2-D images, either in a parallel manner, with a uniform slice spacing of 1 mm, or in a rotational manner, about an axis approximately through the center of the prostate, with a uniform angular spacing of 5 degrees. The segmentation process was initiated by manually placing four points on the boundary of a selected slice, from which an initial prostate boundary was determined. This initial boundary was refined using the Discrete Dynamic Contour until it fit the actual prostate boundary. The remaining slices were then segmented by iteratively propagating this result to an adjacent slice and repeating the refinement, pausing the process when necessary to manually edit the boundary. The two methods were tested with six 3-D prostate images. The results showed that the parallel and rotational methods had mean editing rates of 20% and 14%, and mean (mean absolute) volume errors of -5.4% (6.5%) and -1.7% (3.1%), respectively. Based on these results, as well as the relative difficulty in editing, we conclude that the rotational segmentation method is superior.

Algorithms↗
PubMed2004

Gridding-based direct Fourier inversion of the three-dimensional ray transform.

We describe a fast and accurate direct Fourier method for reconstructing a function f of three variables from a number of its parallel beam projections. The main application of our method is in single particle analysis, where the goal is to reconstruct the mass density of a biological macromolecule. Typically, the number of projections is extremely large, and each projection is extremely noisy. The projection directions are random and initially unknown. However, it is possible to determine both the directions and f by an iterative procedure; during each stage of the iteration, one has to solve a reconstruction problem of the type considered here. Our reconstruction algorithm is distinguished from other direct Fourier methods by the use of gridding techniques that provide an efficient means to compute a uniformly sampled version of a function g from a nonuniformly sampled version of Fg, the Fourier transform of g, or vice versa. We apply the two-dimensional reverse gridding method to each available projection of f, the function to be reconstructed, in order to obtain Ff on a special spherical grid. Then we use the three-dimensional gridding method to reconstruct f from this sampled version of Ff. This stage requires a proper weighting of the samples of Ff to compensate for their nonuniform distribution. We use a fast method for computing appropriate weights that exploits the special properties of the spherical sampling grid for Ff and involves the computation of a Voronoi diagram on the unit sphere. We demonstrate the excellent speed and accuracy of our method by using simulated data.

Algorithms↗
PubMed2004

Zinc sulphate release and morphology of matrices prepared for the individual therapy of Wilson's disease.

Hydrophobic zinc sulphate wax matrices with different drug loadings were prepared for the individual hospital therapy of Wilson's disease. The drug release parameters, scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS) of the samples were analysed. The release mechanisms from matrices of 75% and 80% w/w zinc sulphate loadings were described with good correlation by the semi-empirical Fikkian diffusion based release model. Besides the zinc sulphate diffusion through the pores of the wax matrices, the parallel diffusion of zinc sulphate from the matrix surface is dominant in the case of samples of 83% and 90%w/w drug loadings. The combination of SEM and EDS analysis visualizes the morphology of the matrices and the related composition thus explaining the differences in the release characteristics.

Algorithms↗
PubMed2005

Partial fourier partially parallel imaging.

The techniques of partial Fourier (PF) and partially parallel imaging have been combined using a constrained reconstruction technique. The benefits compared with the individual techniques are reduced imaging time and/or an increase in signal-to-noise ratio. Low-resolution phase maps and coil sensitivities may be obtained using autocalibration or from a prescan followed by additional processing. Minor phase artifacts that are introduced by relying on conjugate symmetry can be reduced using a novel regularization scheme to vary the degree to which PF is used in the reconstruction. A nonrectilinear reconstruction algorithm is presented and the potential for motion artifact reduction is investigated using robust reconstruction.

Algorithms↗