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At least 1,171 records · Page 65Linked to original sources
PubMed2002

A large scale molecular dynamics simulation code using the fast multipole algorithm (FMD): performance and application.

We present the performance of the fast classical molecular dynamics (MD) code, fast molecular dynamics (FMD), designed for efficient, object-oriented, and scalable large scale simulations, and summarize its application to a liquid crystalline cluster. FMD uses an implementation of the three-dimensional fast multipole method, developed in our group. The fast multipole method offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus, enabling more realistic simulations of large molecular systems. Performance testing was carried out on IBM SP2, SGI Origin 2000, and CRAY T3E massively parallel systems using the MPI massage passing library. The electrostatic forces were tested on models of up to 100,000 randomly placed charges, and on protein and liquid crystalline molecular systems of over 99,000 atoms. Tests on the stability of the method are presented, along with comparisons with direct calculations, the NAMD2 code, and the physical multipole-based cell-multipole method.

Algorithms↗
PubMed1987

Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase.

The tertiary structure of the alpha-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the alpha/beta-class of supersecondary structures. The two-domain structure of the alpha-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a beta-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the alpha-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the beta-sheet eliminated all but one structure. The native structure is predicted to have a parallel beta-sheet flanked on both sides by alpha-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for beta 2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.

Amino Acid Sequence↗
PubMed2006

Statistically integrated metabonomic-proteomic studies on a human prostate cancer xenograft model in mice.

A novel statistically integrated proteometabonomic method has been developed and applied to a human tumor xenograft mouse model of prostate cancer. Parallel 2D-DIGE proteomic and 1H NMR metabolic profile data were collected on blood plasma from mice implanted with a prostate cancer (PC-3) xenograft and from matched control animals. To interpret the xenograft-induced differences in plasma profiles, multivariate statistical algorithms including orthogonal projection to latent structure (OPLS) were applied to generate models characterizing the disease profile. Two approaches to integrating metabonomic data matrices are presented based on OPLS algorithms to provide a framework for generating models relating to the specific and common sources of variation in the metabolite concentrations and protein abundances that can be directly related to the disease model. Multiple correlations between metabolites and proteins were found, including associations between serotransferrin precursor and both tyrosine and 3-D-hydroxybutyrate. Additionally, a correlation between decreased concentration of tyrosine and increased presence of gelsolin was also observed. This approach can provide enhanced recovery of combination candidate biomarkers across multi-omic platforms, thus, enhancing understanding of in vivo model systems studied by multiple omic technologies.

Animals↗
PubMed1999

An objective function for radiation treatment optimization based on local biological measures.

The implementation of biological optimization of radiation treatment plans is impeded by both computational and modelling problems. We derive an objective function from basic model assumptions which includes the normal tissue constraints as interior penalty functions. For organs that are composed of parallel subunits, a mean response model is proposed which leads to constraints similar to dose-volume constraints. This objective function is convex in the case when no parallel organs lie in the treatment volume. Otherwise, an argument is given to show that a number of local minima may exist which are near degenerate to the global minimum. Thus, together with the measure quality of the objective function, highly efficient gradient algorithms can be used. The number of essential biological model parameters could be reduced to a minimum. However, if the optimization constraints are given as TCP/NTCP values, Lagrange multiplier updates have to be performed by invoking comprehensive biological models.

Humans↗
PubMed2004

Speed-accuracy characteristics of human-machine cooperative manipulation using virtual fixtures with variable admittance.

This work explores the effect of virtual fixture admittance on the performance, defined by error and time, of task execution with a human-machine cooperative system. A desired path is obtained using computer vision, and virtual fixtures for assistance in planar path following were implemented on an admittance-controlled robot. The admittance controller uses a velocity gain, so that the speed of the robot is proportional to the force applied by the operator. The level of virtual fixture guidance is determined by the admittance ratio, which is the ratio of the admittance gain of the force components orthogonal to the path to the gain of the force components parallel to the path. In Experiment 1, we found a linear relationship between admittance ratio and performance. In Experiment 2, we examined the effect of admittance ratio on the performance of three tasks: path following, off-path targeting, and obstacle avoidance. An algorithm was developed to select an appropriate admittance ratio based on the nature of the task. Automatic admittance ratio tuning is recommended for next-generation virtual fixtures. Actual or potential applications of this research include surgery, assembly, and manipulation at the macro and micro scales.

Acceleration↗
PubMed2001

Input minimization: a model of cerebellar learning without climbing fiber error signals.

The cerebellum is critical for motor learning. Current cerebellar learning models follow the Marr/Albus paradigm, in which climbing fibers provide error signals that shape plastic synapses between parallel fibers and Purkinje cells. However, climbing fibers have slow and largely random discharge, and seem unlikely to provide error signals with resolution sufficient to guide cerebellar learning. Parallel fibers carry error signals and could direct the plasticity of their own synapses, but the error signals are carried along with other signals. This report presents the new input minimization (InMin) model, in which Purkinje cells reduce error by minimizing their overall parallel fiber input. The slowly, randomly firing climbing fiber provides only synchronization pulses. InMin offers an alternative that can unify cerebellar findings.

Action Potentials↗
PubMed2005

Ion recombination correction for very high dose-per-pulse high-energy electron beams.

The parallel-plate ionization chamber is the recommended tool for the absorbed dose measurement in pulsed high-energy electron beams. Typically, the electron beams used in radiotherapy have a dose-per-pulse value less then 0.1 cGy/pulse. In this range the factor to correct the response of an ionization chamber for the lack of complete charge collection due to ion recombination (ksat) can be properly evaluated with the standard "two voltage" method proposed by the international dosimetric reports. Very high dose-per-pulse electron beams are employed in some special Linac dedicated to the Intra-Operatory-Radiation-Therapy (IORT). The high dose-per-pulse values (3-13 cGy/pulse) characterizing the IORT electron beams allow to deliver the therapeutic dose (10-20 Gy) in less than a minute. This considerably reduces the IORT procedure time, but some dosimetric problems arise because the standard method to evaluate ksat overestimates its value by 20%. Moreover, if the dose-per-pulse value >1 cGy/pulse, the dependence of ksat on the dose-per-pulse value cannot be neglected for relative dosimetry. In this work the dependence of ksat on the dose-per-pulse value is derived, based on the general equation that describes the ion recombination in the Boag theory. A new equation for ksat, depending on known or measurable quantities, is presented. The new ksat equation is experimentally tested by comparing the absorbed doses to water measured with parallel-plate ionization chambers (Roos and Markus) to that measured using dose-per-pulse independent dosimeters, such as radiochromic films and chemical Fricke dosimeters. These measurements are performed in the high dose-per-pulse (3-13 cGy/pulse) electron beams of the IORT dedicated Linac Hitesys Novac7 (Aprilia-Latina, Italy). The dose measurements made using the parallel-plate chambers and those made using the dose-per-pulse independent dosimeters are in good agreement (<3%). This demonstrates the possibility of using the parallel-plate ionization chambers also for the very high dose-per-pulse (> 1 cGy/pulse) electron-beam dosimetry.

Algorithms↗
PubMed2006

Transcriptome analysis of Aspergillus nidulans exposed to camptothecin-induced DNA damage.

We have used an Aspergillus nidulans macroarray carrying sequences of 2,787 genes from this fungus to monitor gene expression of both wild-type and uvsB(ATR) (the homologue of the ATR gene) deletion mutant strains in a time course exposure to camptothecin (CPT). The results revealed a total of 1,512 and 1,700 genes in the wild-type and uvsB(ATR) deletion mutant strains that displayed a statistically significant difference at at least one experimental time point. We characterized six genes that have increased mRNA expression in the presence of CPT in the wild-type strain relative to the uvsB(ATR) mutant strain: fhdA (encoding a forkhead-associated domain protein), tprA (encoding a hypothetical protein that contains a tetratrico peptide repeat), mshA (encoding a MutS homologue involved in mismatch repair), phbA (encoding a prohibitin homologue), uvsC(RAD51) (the homologue of the RAD51 gene), and cshA (encoding a homologue of the excision repair protein ERCC-6 [Cockayne's syndrome protein]). The induced transcript levels of these genes in the presence of CPT require uvsB(ATR). These genes were deleted, and surprisingly, only the DeltauvsC mutant strain was sensitive to CPT; however, the others displayed sensitivity to a range of DNA-damaging and oxidative stress agents. These results indicate that the selected genes when inactivated display very complex and heterogeneous sensitivity behavior during growth in the presence of agents that directly or indirectly cause DNA damage. Moreover, with the exception of UvsC, deletion of each of these genes partially suppressed the sensitivity of the DeltauvsB strain to menadione and paraquat. Our results provide the first insight into the overall complexity of the response to DNA damage in filamentous fungi and suggest that multiple pathways may act in parallel to mediate DNA repair.

Algorithms↗
PubMed2004

General reconstruction theory for multislice X-ray computed tomography with a gantry tilt.

This paper discusses image reconstruction with a tilted gantry in multislice computed tomography (CT) with helical (spiral) data acquisition. The reconstruction problem with gantry tilt is shown to be transformable into the problem of reconstructing a virtual object from multislice CT data with no gantry tilt, for which various algorithms exist in the literature. The virtual object is related to the real object by a simple affine transformation that transforms the tilted helical trajectory of the X-ray source into a nontilted helix, and the real object can be computed from the virtual object using one-dimensional interpolation. However, the interpolation may be skipped since the reconstruction of the virtual object on a Cartesian grid provides directly nondistorted images of the real object on slices parallel to the tilted plane of the gantry. The theory is first presented without any specification of the detector geometry, then applied to the curved detector geometry of third-generation CT scanners with the use of Katsevich's formula for example. Results from computer-simulated data of the FORBILD thorax phantom are given in support of the theory.

Algorithms↗
PubMed2000

Implementation of FFT convolution and multigrid superposition models in the FOCUS RTP system.

In radiotherapy treatment planning, convolution/superposition algorithms currently represent the best practical approach for accurate photon dose calculation in heterogeneous tissues. In this work, the implementation, accuracy and performance of the FFT convolution (FFTC) and multigrid superposition (MGS) algorithms are presented. The FFTC and MGS models use the same 'TERMA' calculation and are commissioned using the same parameters. Both models use the same spectra, incorporate the same off-axis softening and base incident lateral fluence on the same measurements. In addition, corrections are explicitly applied to the polyenergetic and parallel kernel approximations, and electron contamination is modelled. Spectra generated by Monte Carlo (MC) modelling of treatment heads are used. Calculations using the MC spectra were in excellent agreement with measurements for many linear accelerator types. To speed up the calculations, a number of calculation techniques were implemented, including separate primary and scatter dose calculation, the FFT technique which assumes kernel invariance for the convolution calculation and a multigrid (MG) acceleration technique for the superposition calculation. Timing results show that the FFTC model is faster than MGS by a factor of 4 and 8 for small and large field sizes, respectively. Comparisons with measured data and BEAM MC results for a wide range of clinical beam setups show that (a) FFTC and MGS doses match measurements to better than 2% or 2 mm in homogeneous media; (b) MGS is more accurate than FFTC in lung phantoms where MGS doses are within 3% or 3 mm of BEAM results and (c) FFTC overestimates the dose in lung by a maximum of 9% compared to BEAM.

Algorithms↗
PubMed1986

Toward computerized morphometric facilities: a review of 58 software packages for computer-aided three-dimensional reconstruction, quantification, and picture generation from parallel serial sections.

This review gives an inventory of 58 computer-aided three-dimensional reconstruction applications in the domain of biomedical research. It is devoted to the formulation of a set of recommendations thought to be necessary for improved performance of software packages in this field. These recommendations can be used to select packages and to guide future developments of existing reconstruction systems. The survey is restricted to three-dimensional reconstructions based upon a series of parallel sections of an object. Subjects treated are programming languages, resolution and sampling, input preparation, realignment, local deformation of slices, numerical quantifications, topological complexity, internal representation, display complexity (hidden surfaces, shading, smoothing), structure extraction, descriptive elements, database, data compression, time efficiency of systems and algorithms, hardware configuration, input devices, input media, interactive aids, display devices, and output devices. Information for this survey comes from articles that appeared between 1965 and 1985.

Computers↗
PubMed2005

Technical complications are rising as common duct exploration is becoming rare.

BACKGROUND: Both hospital and surgeon volume influence outcomes. With introduction of new technologies, some procedures are now performed less frequently. ERCP has replaced the need for common duct exploration (CDE) in most cases of choledocholithiasis. We explored the secular trends and outcomes of CDE and how they have changed relative to introduction of ERCP. STUDY DESIGN: The National Hospital Discharge Survey database was analyzed for the years 1979 to 2001. Procedural frequency of ERCP and CDE was determined. Charlson and Elixhauser comorbidity indices were used to characterize patients' disease burden for the years 1993 to 2001. Length of stay, mortality, and complication rates for each procedure were determined. RESULTS: At the beginning of the study period, an estimated 47,000 CDEs were performed annually. These declined to 7,700 per year as ERCP increased to 42,500 procedures per year at the end of the study period. CDE complication rates increased from 3.4% to 17.4% over the same period. Comorbidity analysis for the years 1993 to 2001 revealed that ERCP and CDE patients had equivalent disease burdens. Technical complication rates rose in parallel to the increased overall CDE complication rate. CONCLUSIONS: ERCP has replaced the need for most but not all CDE. With diminished CDE experience at a national level, the complication rate has markedly increased, at least in part from technical complications. Both choledocholithiasis treatment algorithms and clinical training paradigms need to account for the rarity of CDE and high complication rates associated with it, by incorporation of training modules in surgical residencies and advocating referral to centers having expertise in biliary tract operations from surgeons with little CDE experience.

Age Factors↗
PubMed1982

Clinical management of acute and chronic cocaine poisoning.

At the Haight-Ashbury Free Medical Clinics in San Francisco, the recreational use of cocaine is on a precipitous incline of popularity. Intensified symptoms of intoxication and the possibility of overdose parallel the current fad of smoking "freebase." We examined the "cocaine reaction," an adrenergic storm affecting CNS, respiratory and cardiovascular systems, which may proceed to generalized collapse and death within minutes. The physiologic and pharmacologic mechanisms of the reaction are elaborated, and a logical algorithm of treatment is outlined. The psychodynamics of the "armed" cocaine personality is discussed, as is the proper psychological approach to these patients. A specific indicated technical and pharmacologic approach, as well as several caveats of therapy that have been clinically developed in the treatment of several hundred cases of cocaine overdose, are presented.

Brain↗
PubMed1997

A triple-head SPECT system with parallel-hole collimators of different acceptance angles.

We proposed to use three different parallel-hole collimators for a triple-head SPECT system. One of the collimators had a small collimator acceptance angle to provide ultra-high spatial resolution and the other two had larger collimator acceptance angles to achieve high counts. A new 2D reconstruction algorithm that combined the data acquired from different collimators was derived to take advantages of both high resolution and high sensitivity. The algorithm was evaluated using a computer-simulated matrix of spherical sources. For noise-free data, the accuracy (mainly determined by spatial resolution) obtained from combination of the collimator acceptance angles of 1.35, 4.05 and 6.75 degrees (or 1.35, 5.40 and 9.45 degrees) was slightly inferior to that obtained from three same LEHR collimators (with a 2.70 degrees collimator acceptance angle). This is because the modulation transfer function (MTF) resulting from three different collimators decreases more quickly at low frequencies but becomes comparable at high frequencies as compared with the MTF of the 2.70 degrees collimator. With noisy data, however, the image quality obtained with three different collimators was better than that resulting from any combinations of three same collimators. The improvement was only achieved by using the derived algorithm, while the conventional FBP algorithm did not improve image quality even with the same collimator configuration.

Algorithms↗
PubMed1992

The plastic coupled map lattice: A novel image-processing paradigm.

Coupled map lattices (CML) can describe many relaxation and optimization algorithms currently used in image processing. We recently introduced the "plastic-CML" as a paradigm to extract (segment) objects in an image. Here, the image is applied by a set of forces to a metal sheet which is allowed to undergo plastic deformation parallel to the applied forces. In this paper we present an analysis of our "plastic-CML" in one and two dimensions, deriving the nature and stability of its stationary solutions. We also detail how to use the CML in image processing, how to set the system parameters and present examples of it at work. We conclude that the plastic-CML is able to segment images with large amounts of noise and large dynamic range of pixel values, and is suitable for a very large scale integration (VLSI) implementation.

Journal Article↗
PubMed2005

Frontostriatal microstructure modulates efficient recruitment of cognitive control.

Many studies have linked activity in a frontostriatal network with the capacity to suppress inappropriate thoughts and actions, but relatively few have examined the role of connectivity between these structures. Here, we use diffusion tensor imaging to assess frontostriatal connectivity in 21 subjects (ages 7-31 years). Fifteen subjects were tested on a go/no-go task, where they responded with a button press to a visual stimulus and inhibited a response to a second infrequent stimulus. An automated fiber tracking algorithm was used to delineate white matter fibers adjacent to ventral prefrontal cortex and the striatum, and the corticospinal tract, which was not expected to contribute to control per se. Diffusion in frontostriatal and corticospinal tracts became more restricted with age. This shift was paralleled by an increase in efficiency of task performance. Frontostriatal radial diffusivities predicted faster reaction times, independent of age and accuracy, and this correlation grew stronger for trials expected to require greater control. This was not observed in the corticospinal tract. On trials matched for speed of task performance, adults were significantly more accurate, and accuracies were correlated with frontostriatal, but not corticospinal, diffusivities. These findings suggest that frontostriatal connectivity may contribute to developmental and individual differences in the efficient recruitment of cognitive control.

Adolescent↗
PubMed2003

Subsystem identification through dimensionality reduction of large-scale gene expression data.

The availability of parallel, high-throughput biological experiments that simultaneously monitor thousands of cellular observables provides an opportunity for investigating cellular behavior in a highly quantitative manner at multiple levels of resolution. One challenge to more fully exploit new experimental advances is the need to develop algorithms to provide an analysis at each of the relevant levels of detail. Here, the data analysis method non-negative matrix factorization (NMF) has been applied to the analysis of gene array experiments. Whereas current algorithms identify relationships on the basis of large-scale similarity between expression patterns, NMF is a recently developed machine learning technique capable of recognizing similarity between subportions of the data corresponding to localized features in expression space. A large data set consisting of 300 genome-wide expression measurements of yeast was used as sample data to illustrate the performance of the new approach. Local features detected are shown to map well to functional cellular subsystems. Functional relationships predicted by the new analysis are compared with those predicted using standard approaches; validation using bioinformatic databases suggests predictions using the new approach may be up to twice as accurate as some conventional approaches.

Algorithms↗
PubMed1998

Dynamic tracking in interventional MRI using wavelet-encoded gradient-echo sequences.

This work describes a newly developed magnetic resonance imaging (MRI) data-acquisition strategy which replaces the standard Fourier phase-encoding with the spatially localized coefficients of wavelet-encoding and offers a new technique for image guidance when combined with a dynamic tracking algorithm. By using this new technique, only a specific fraction of the entire raw data set needs to be updated and reconstructed to visualize the movement of an interventional device during an MR guided procedure. The combination of wavelet-encoding and a dynamic tracking algorithm was implemented in two-dimensional and three-dimensional gradient-echo sequences on a 0.2-T open C-arm-shaped MR system (Siemens, Erlangen Germany) and tested in phantom and in vitro experiments. When applying the wavelet-encoding direction parallel to the movement of a straight interventional device, only those spatially localized wavelet-coefficients mainly affected by the interventional device are updated. This led to potential increases of the image frame rate by a factor of up to seven.

Animals↗