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PubMed2005

Quantifying IOHDR brachytherapy underdosage resulting from an incomplete scatter environment.

PURPOSE: Most brachytherapy planning systems are based on a dose calculation algorithm that assumes an infinite scatter environment surrounding the target volume and applicator. Dosimetric errors from this assumption are negligible. However, in intraoperative high-dose-rate brachytherapy (IOHDR) where treatment catheters are typically laid either directly on a tumor bed or within applicators that may have little or no scatter material above them, the lack of scatter from one side of the applicator can result in underdosage during treatment. This study was carried out to investigate the magnitude of this underdosage. METHODS: IOHDR treatment geometries were simulated using a solid water phantom beneath an applicator with varying amounts of bolus material on the top and sides of the applicator to account for missing tissue. Treatment plans were developed for 3 different treatment surface areas (4 x 4, 7 x 7, 12 x 12 cm(2)), each with prescription points located at 3 distances (0.5 cm, 1.0 cm, and 1.5 cm) from the source dwell positions. Ionization measurements were made with a liquid-filled ionization chamber linear array with a dedicated electrometer and data acquisition system. RESULTS: Measurements showed that the magnitude of the underdosage varies from about 8% to 13% of the prescription dose as the prescription depth is increased from 0.5 cm to 1.5 cm. This treatment error was found to be independent of the irradiated area and strongly dependent on the prescription distance. Furthermore, for a given prescription depth, measurements in planes parallel to an applicator at distances up to 4.0 cm from the applicator plane showed that the dose delivery error is equal in magnitude throughout the target volume. CONCLUSION: This study demonstrates the magnitude of underdosage in IOHDR treatments delivered in a geometry that may not result in a full scatter environment around the applicator. This implies that the target volume and, specifically, the prescription depth (tumor bed) may get a dose significantly less than prescribed. It might be clinically relevant to correct for this inaccuracy.

Algorithms↗
PubMed2001

Neuronal population codes and the perception of object distance in weakly electric fish.

Weakly electric fish use an electric sense to navigate and capture prey in the dark. Objects in the surroundings of the fish produce distortions in their self-generated electric field; these distortions form a two-dimensional Gaussian-like electric image on the skin surface. To determine the distance of an object, the peak amplitude and width of its electric image must be estimated. These sensory features are encoded by a neuronal population in the early stages of the electrosensory pathway, but are not represented with classic bell-shaped neuronal tuning curves. In contrast, bell-shaped tuning curves do characterize the neuronal responses to the location of the electric image on the body surface, such that parallel two-dimensional maps of this feature are formed. In the case of such two-dimensional maps, theoretical results suggest that the width of neural tuning should have no effect on the accuracy of a population code. Here we show that although the spatial scale of the electrosensory maps does not affect the accuracy of encoding the body surface location of the electric image, maps with narrower tuning are better for estimating image width and those with wider tuning are better for estimating image amplitude. We quantitatively evaluate a two-step algorithm for distance perception involving the sequential estimation of peak amplitude and width of the electric image. This algorithm is best implemented by two neural maps with different tuning widths. These results suggest that multiple maps of sensory features may be specialized with different tuning widths, for encoding additional sensory features that are not explicitly mapped.

Algorithms↗
PubMed2006

The study of neural network-based controller for controlling dissolved oxygen concentration in a sequencing batch reactor.

The design and development of the neural network (NN)-based controller performance for the activated sludge process in sequencing batch reactor (SBR) is presented in this paper. Here we give a comparative study of various neural network (NN)-based controllers such as the direct inverse control, internal model control (IMC) and hybrid NN control strategies to maintain the dissolved oxygen (DO) level of an activated sludge system by manipulating the air flow rate. The NN inverse model-based controller with the model-based scheme represents the controller, which relies solely upon the simple NN inverse model. In the IMC, both the forward and inverse models are used directly as elements within the feedback loop. The hybrid NN control consists of a basic NN controller in parallel with a proportional integral (PI) controller. Various simulation tests involving multiple set-point changes, disturbances rejection and noise effects were performed to review the performances of these various controllers. From the results it can be seen that hybrid controller gives the best results in tracking set-point changes under disturbances and noise effects.

Algorithms↗
PubMed2005

A dynamic fuzzy neural filter for separation of discontinuous adventitious sounds from vesicular sounds.

This paper presents a recurrent filter that performs real-time separation of discontinuous adventitious sounds from vesicular sounds. The filter uses two Dynamic Fuzzy Neural Networks, operating in parallel, to perform the task of separation of the lung sounds, obtained from patients with pulmonary pathology. Extensive experimental results, including fine/coarse crackles and squawks, are given, and a performance comparison with a series of other models is conducted, underlining the separation capabilities of the proposed filter and its improved performance with respect to its competing rivals.

Algorithms↗
PubMed2004

Synthesis and optical properties of anisotropic metal nanoparticles.

In this paper we overview our recent studies of anisotropic noble metal (e.g. gold and silver) nanoparticles, in which a combination of theory and experiment has been used to elucidate the extinction spectra of the particles, as well as information related to their surface enhanced Raman spectroscopy. We used wet-chemical methods to generate several structurally well-defined nanostructures other than solid spheres, including silver nanodisks and triangular nanoprisms, and gold nanoshells and multipods. When solid spheres are transformed into one of these shapes, the surface plasmon resonances in these particles are strongly affected, typically red-shifting and even splitting into distinctive dipole and quadrupole plasmon modes. In parallel, we have developed computational electrodynamics methods based on the discrete dipole approximation (DDA) method to determine the origins of these intriguing optical features. This has resulted in considerable insight concerning the variation of plasmon wavelength with nanoparticle size, shape and dielectric environment, as well as the use of these particles for optical sensing applications.

Algorithms↗
PubMed2006

The midpoint method for parallelization of particle simulations.

The evaluation of interactions between nearby particles constitutes the majority of the computational workload involved in classical molecular dynamics (MD) simulations. In this paper, we introduce a new method for the parallelization of range-limited particle interactions that proves particularly suitable to MD applications. Because it applies not only to pairwise interactions but also to interactions involving three or more particles, the method can be used for evaluation of both nonbonded and bonded forces in a MD simulation. It requires less interprocessor data transfer than traditional spatial decomposition methods at all but the lowest levels of parallelism. It gains an additional practical advantage in certain commonly used interprocessor communication networks by distributing the communication burden more evenly across network links and by decreasing the associated latency. When used to parallelize MD, it further reduces communication requirements by allowing the computations associated with short-range nonbonded interactions, long-range electrostatics, bonded interactions, and particle migration to use much of the same communicated data. We also introduce certain variants of this method that can significantly improve the balance of computational load across processors.

Algorithms↗
PubMed2005

Brain shift estimation in image-guided neurosurgery using 3-D ultrasound.

Intraoperative brain deformation is one of the most important causes affecting the overall accuracy of image-guided neurosurgical procedures. One option for correcting for this deformation is to acquire three-dimensional (3-D) ultrasound data during the operation and use this data to update the information provided by the preoperatively acquired MR data. For 12 patients 3-D ultrasound images have been reconstructed from freehand sweeps acquired during neurosurgical procedures. Ultrasound data acquired prior to and after opening the dura, but prior to surgery, have been quantitatively compared to the preoperatively acquired MR data to estimate the rigid component of brain shift at the first stages of surgery. Prior to opening the dura the average brain shift measured was 3.0 mm parallel to the direction of gravity, with a maximum of 7.5 mm, and 3.9 mm perpendicular to the direction of gravity, with a maximum of 8.2 mm. After opening the dura the shift increased on average 0.2 mm parallel to the direction of gravity and 1.4 mm perpendicular to the direction of gravity. Brain shift can be detected by acquiring 3-D ultrasound data during image-guided neurosurgery. Therefore, it can be used as a basis for correcting image data and preoperative planning for intraoperative deformations.

Algorithms↗
PubMed2002

Clinical experience with infliximab for Crohn's disease: the first 100 patients in Edmonton, Alberta.

OBJECTIVE: To determine whether the clinical efficacy and safety of infliximab in diverse clinical referral practices was similar to that seen in the randomized, controlled clinical trials. METHODS: Data were gathered from a review of charts of 109 consecutive patients with inflammatory and/or fistulizing Crohn's disease who received infliximab infusions. Responses were recorded based on the physician's global clinical assessment and classified as complete, partial or nonresponse. RESULTS: One hundred nine patients were treated with one to nine infusions of infliximab at a dose of 5 mg/kg and followed up for a median of 24 weeks (range one to 40 weeks). Fifty-four patients were treated for inflammatory disease, 38 for fistulizing disease and 17 for both. Clinical response occurred in 73% (17% complete response, 55% partial response). The clinical response rate did not vary relative to patient demographics, disease distribution, indication for infliximab, or the concomitant use of corticosteroids or immune modifiers. For those taking concomitant immune modifiers, the response rate was 75%. The median time to response was two weeks (range one to six weeks). The median duration of response was 12 weeks (range six to 88 weeks). Reduction or cessation of steroids was possible in 17 of 32 patients. Adverse events related to infliximab occurred in 7% of patients. These events were characterized as mild and did not require stoppage of infliximab therapy, except in one patient who had a treatable anaphylactic-like infusion reaction. CONCLUSIONS: The patient group in the present study realized significant clinical benefit, with minimal adverse effects, following treatment with infliximab. Clinical response rates paralleled those previously described in placebo controlled trials and retrospective clinical practice reviews. Nevertheless, the complete response rate (ie, remission) in this patient group was lower than that previously described.

Adolescent↗
PubMed1990

An optimal control model for maximum-height human jumping.

To understand how intermuscular control, inertial interactions among body segments, and musculotendon dynamics coordinate human movement, we have chosen to study maximum-height jumping. Because this activity presents a relatively unambiguous performance criterion, it fits well into the framework of optimal control theory. The human body is modeled as a four-segment, planar, articulated linkage, with adjacent links joined together by frictionless revolutes. Driving the skeletal system are eight musculotendon actuators, each muscle modeled as a three-element, lumped-parameter entity, in series with tendon. Tendon is assumed to be elastic, and its properties are defined by a stress-strain curve. The mechanical behavior of muscle is described by a Hill-type contractile element, including both series and parallel elasticity. Driving the musculotendon model is a first-order representation of excitation-contraction (activation) dynamics. The optimal control problem is to maximize the height reached by the center of mass of the body subject to body-segmental, musculotendon, and activation dynamics, a zero vertical ground reaction force at lift-off, and constraints which limit the magnitude of the incoming neural control signals to lie between zero (no excitation) and one (full excitation). A computational solution to this problem was found on the basis of a Mayne-Polak dynamic optimization algorithm. Qualitative comparisons between the predictions of the model and previously reported experimental findings indicate that the model reproduces the major features of a maximum-height squat jump (i.e. limb-segmental angular displacements, vertical and horizontal ground reaction forces, sequence of muscular activity, overall jump height, and final lift-off time).

Biomechanical Phenomena↗
PubMed2006

Computer simulation of polypeptides in a confinement.

A coarse-grained model of polypeptide chains confined in a slit formed by two parallel impenetrable surfaces was studied. The chains were flexible heteropolymers (polypeptides) built of two kinds of united atoms-hydrophobic and hydrophilic. The positions of the united atoms were restricted to the vertices of a [310] lattice. The force field consisted of a rigorous excluded volume, a long-distance potential between a pair of amino-acid residues and a local preference for forming secondary structure (helices). The properties of the chains were studied at a wide range of temperatures from good to bad solvent conditions. Monte-Carlo simulations were carried out using the algorithm based on the chain's local changes of conformation and employing the Replica Exchange technique. The influence of the chain length, the distances between the confining surfaces, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that the presence of the confinement chain complicates the process of the chain collapse to low-temperature structures. For some conditions, one can find a rapid decrease of chain size and a second transition indicated by the rapid decrease of the total energy of the system.

Computer Simulation↗
PubMed2006

k-space inherited parallel acquisition (KIPA): application on dynamic magnetic resonance imaging thermometry.

In this study, a novel method for dynamic parallel image acquisition and reconstruction is presented. In this method, called k-space inherited parallel acquisition (KIPA), localized reconstruction coefficients are used to achieve higher reduction factors, and lower noise and artifact levels compared to that of generalized autocalibrating partially parallel acquisition (GRAPPA) reconstruction. In KIPA, the full k-space for the first frame and the partial k-space for later frames are required to reconstruct a whole series of images. Reconstruction coefficients calculated for different segments of k-space from the first frame data set are used to estimate missing k-space lines in corresponding k-space segments of other frames. The local determination of KIPA reconstruction coefficients is essential to adjusting them according to the local signal-to-noise ratio characteristics of k-space data. The proposed algorithm is applicable to dynamic imaging with arbitrary k-space sampling trajectories. Simulations of magnetic resonance thermometry using the KIPA method with a reduction factor of 6 and using dynamic imaging studies of human subjects with reduction factors of 4 and 6 have been performed to prove the feasibility of our method and to show apparent improvement in image quality in comparison with GRAPPA for dynamic imaging.

Algorithms↗
PubMedDate not supplied

Efficacy and safety of excimer laser photorefractive keratectomy and radial keratotomy for bilateral myopia.

PURPOSE: To compare the safety and efficacy of radial keratotomy (RK) and photorefractive keratectomy (PRK) to correct myopia. METHODS: In this randomized, prospective, parallel-group study, 33 patients with bilateral myopia of 1.00 to 5.00 diopters (D) had PRK in one eye and RK in the other. The order of surgeries and treatment assignments were randomized, and the bilateral surgeries were within 1 week for each patient. Data were collected using standardized procedures. Clinical measurements and satisfaction surveys were taken in masked fashion. RESULTS: Eyes that had PRK had statistically significantly more residual myopia than RK-treated eyes at 3, 6, and 12 months postoperatively. This result was attributed to the use of an older excimer laser PRK algorithm that was used at the initiation of the study. No eye that had PRK was overcorrected by 0.50 D or more at 1 year postoperatively, while seven eyes that had RK were overcorrected by at least 0.50 D and six were overcorrected by 1.00 D. Eyes that had PRK had a statistically significant mean shift in the myopic direction between 6 and 12 months postoperatively; two RK eyes had hyperopic shifts of 1.00 D. Three RK eyes and two PRK eyes failed to achieve an uncorrected visual acuity of 20/40 or better by 12 months postoperatively. No eye lost any best corrected visual acuity. CONCLUSION: The two procedures were comparably safe and effective in treating mild to moderate myopia under this protocol. Eyes that had PRK were somewhat more myopic at 1 year after surgery, attributable to the older PRK ablation algorithm. Adoption of newer (current) laser algorithms has improved the predictability of PRK. There was also evidence of reduced variability of outcome in the PRK group. The PRK eyes did not exhibit hyperopic shifts during the 1 year follow-up.

Adolescent↗
PubMed2003

Clustering ensembles of neural network models.

We show that large ensembles of (neural network) models, obtained e.g. in bootstrapping or sampling from (Bayesian) probability distributions, can be effectively summarized by a relatively small number of representative models. In some cases this summary may even yield better function estimates. We present a method to find representative models through clustering based on the models' outputs on a data set. We apply the method on an ensemble of neural network models obtained from bootstrapping on the Boston housing data, and use the results to discuss bootstrapping in terms of bias and variance. A parallel application is the prediction of newspaper sales, where we learn a series of parallel tasks. The results indicate that it is not necessary to store all samples in the ensembles: a small number of representative models generally matches, or even surpasses, the performance of the full ensemble. The clustered representation of the ensemble obtained thus is much better suitable for qualitative analysis, and will be shown to yield new insights into the data.

Algorithms↗
PubMed2001

Informatics and multiplexing of intact protein identification in bacteria and the archaea.

Although direct fragmentation of protein ions in a mass spectrometer is far more efficient than exhaustive mapping of 1-3 kDa peptides for complete characterization of primary structures predicted from sequenced genomes, the development of this approach is still in its infancy. Here we describe a statistical model (good to within approximately 5%) that shows that the database search specificity of this method requires only three of four fragment ions to match (at +/-0.1 Da) for a 99.8% probability of being correct in a database of 5,000 protein forms. Software developed for automated processing of protein ion fragmentation data and for probability-based retrieval of whole proteins is illustrated by identification of 18 archaeal and bacterial proteins with simultaneous mass-spectrometric (MS) mapping of their entire primary structures. Dissociation of two or three proteins at once for such identifications in parallel is also demonstrated, along with retention and exact localization of a phosphorylated serine residue through the fragmentation process. These conceptual and technical advances should assist future processing of whole proteins in a higher throughput format for more robust detection of co- and post-translational modifications.

Algorithms↗
PubMed2002

Internet2-based 3D PET image reconstruction using a PC cluster.

We describe an approach to fast iterative reconstruction from fully three-dimensional (3D) PET data using a network of PentiumIII PCs configured as a Beowulf cluster. To facilitate the use of this system, we have developed a browser-based interface using Java. The system compresses PET data on the user's machine, sends these data over a network, and instructs the PC cluster to reconstruct the image. The cluster implements a parallelized version of our preconditioned conjugate gradient method for fully 3D MAP image reconstruction. We report on the speed-up factors using the Beowulf approach and the impacts of communication latencies in the local cluster network and the network connection between the user's machine and our PC cluster.

Algorithms↗
PubMed2006

Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome.

UNLABELLED: Linkage disequilibrium (LD) maps increase power and precision in association mapping, define optimal marker spacing and identify recombination hot-spots and regions influenced by natural selection. Phase II of HapMap provides approximately 2.8-fold more single nucleotide polymorphisms (SNPs) than phase I for constructing higher resolution maps. LDMAP-cluster, is a parallel program for rapid map construction in a Linux environment used here to construct genome-wide LD maps with >8.2 million SNPs from the phase II data. AVAILABILITY: The LD maps, LDMAP-cluster and documentation are available from: http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/LDMAP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗
PubMed1981

Analysis and predication of structural motifs in the glycolytic enzymes.

Protein crystallography has determined the three-dimensional structures of 10 of the 13 enzymes of the glycolytic pathway. Diagrams and details of these enzyme structures are given in the paper. Most of the enzyme domains are variations and extensions of a many (4--9)-stranded, predominantly or totally parallel, beta-sheet that is shielded from solvent by alpha-helices (i.e. alpha/beta structures). There are strong structural similarities between the domains of some, but not all, of the enzymes. In particular the dinucleotide binding fold of lactate dehydrogenase and the beta-barrel of triose phosphate isomerase are found in other domains. General rules governing the topology and packing of alpha-helices against a beta-sheet provide a basis for the combinatorial prediction of the tertiary fold of glycolytic domains from their amino acid sequence and observed secondary structure. The predication algorithm demonstrates that there are severe restrictions on the number of possible structures. However, these restrictions do not fully explain some of the remarkable structural similarities between different enzymes that probably result from evolution from a common ancestor.

Animals↗
PubMed2001

Numerical studies of backscattering enhancement of electromagnetic waves from two-dimensional random rough surfaces with the forward-backward/novel spectral acceleration method.

The forward-backward method with a novel spectral acceleration algorithm (FB/NSA) has been shown to be a highly efficient O(Ntot) iterative method of moments, where Ntot is the total number of unknowns to be solved, for the computation of electromagnetic (EM) wave scattering from both one-dimensional and two-dimensional (2-D) rough surfaces. The efficiency of the method makes studies of backscattering enhancement from moderately rough impedance surfaces at large incident angles tractable. Variations in the characteristics of backscattering enhancement with incident angle, surface impedance, polarization, and surface statistics are investigated by use of the 2-D FB/NSA method combined with parallel computing techniques. The surfaces considered are Gaussian random processes with an isotropic Gaussian spectrum and root-mean-square surface heights and slopes ranging from 0.5 lambda to lambda and from 0.5 to 1.0, respectively, where lambda is the EM wavelength in free space. Incident angles ranging from normal incidence up to 70 degrees are considered in this study. It is found that backscattering enhancement depends strongly on all parameters of interest. America

Journal Article↗