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PubMed2005

Experimental verification of lung dose with radiochromic film: comparison with Monte Carlo simulations and commercially available treatment planning systems.

The purpose of this study was to assess the absorbed dose in and around lung tissue by performing radiochromic film measurements, Monte Carlo simulations and calculations with superposition convolution algorithms. We considered a layered polystyrene phantom of 12 x 12 x 12 cm3 containing a central cavity of 6 x 6 x 6 cm3 filled with Gammex RMI lung-equivalent material. Two field configurations were investigated, a small 1 x 10 cm2 field and a larger 10 x 10 cm2 field. First, we performed Monte Carlo simulations to investigate the influence of radiochromic film itself on the measured dose distribution when the film intersects a lung-equivalent region and is oriented parallel to the central beam axis. To that end, the film and the lung-equivalent materials were modelled in detail, taking into account their specific composition. Next, measurements were performed with the film oriented both parallel and perpendicular to the central beam axis to verify the results of our Monte Carlo simulations. Finally, we digitized the phantom in two commercially available treatment planning systems, Helax-TMS version 6.1A and Pinnacle version 6.2b, and calculated the absorbed dose in the phantom with their incorporated superposition convolution algorithms to compare with the Monte Carlo simulations. Comparing Monte Carlo simulations with measurements reveals that radiochromic film is a reliable dosimeter in and around lung-equivalent regions when the film is positioned perpendicular to the central beam axis. Radiochromic film is also able to predict the absorbed dose accurately when the film is positioned parallel to the central beam axis through the lung-equivalent region. However, attention must be paid when the film is not positioned along the central beam axis, in which case the film gradually attenuates the beam and decreases the dose measured behind the cavity. This underdosage disappears by offsetting the film a few centimetres. We find deviations of about 3.6% between Monte Carlo and the superposition convolution algorithm of Pinnacle behind the lung region, for both field configurations. Pinnacle is quite accurate in the lung region. Deviations up to 5.6% for the small field are found in the lung region between Monte Carlo and the superposition convolution algorithm of Helax-TMS. Behind the lung region, Helax-TMS is in better agreement with Monte Carlo. Radiochromic film measurements or Monte Carlo simulations are reliable methods to establish the dose in and around lung tissue.

Algorithms↗
PubMed1998

Edge detection in medical images using a genetic algorithm.

An algorithm is developed that detects well-localized, unfragmented, thin edges in medical images based on optimization of edge configurations using a genetic algorithm (GA). Several enhancements were added to improve the performance of the algorithm over a traditional GA. The edge map is split into connected subregions to reduce the solution space and simplify the problem. The edge-map is then optimized in parallel using incorporated genetic operators that perform transforms on edge structures. Adaptation is used to control operator probabilities based on their participation. The GA was compared to the simulated annealing (SA) approach using ideal and actual medical images from different modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound. Quantitative comparisons were provided based on the Pratt figure of merit and on the cost-function minimization. The detected edges were thin, continuous, and well localized. Most of the basic edge features were detected. Results for different medical image modalities are promising and encourage further investigation to improve the accuracy and experiment with different cost functions and genetic operators.

Algorithms↗
PubMed2006

Dynamic coil selection for real-time imaging in interventional MRI.

MR-guided intravascular interventions require image update rates of up to 10 images per second, which can be achieved using parallel imaging. However, parallel imaging requires many coil elements, which increases reconstruction times and thus compromises real-time image reconstruction. In this study a dynamic coil selection (DCS) algorithm is presented that selects a subset of receive coils to reduce image reconstruction times. The center-of-sensitivity coordinates and the relative signal intensities are determined for each coil in a prescan. During the intervention m coils are selected for reconstruction using a coil ranking based on the distance to the current slice or catheter position. In a phantom experiment for m = 6, an optimal signal-to-background ratio (SBR) was achieved and foldover artifacts were avoided. In three animal experiments involving catheter manipulation in the aorta and the right heart chamber, the anatomy was successfully visualized at frame rates of about 5 Hz using active catheter tracking.

Algorithms↗
PubMed2004

Marching along ridges. An extrapolatable approach to locating conical intersections.

A conical intersection is a singular point in nuclear coordinate space. As result of this singularity the parameters used to search for energy minimized conical intersections, energy gradients, energy difference gradients and coupling vectors, vary irregularly along the search path. This irregular variation precludes the efficient use of extrapolation procedures to speed convergence. In this work we show how a previously introduced orthogonalization procedure for the branching or g-h space can be used to design search algorithms in which the key parameters are slowly varying functions of the search path. From a topographical perspective this approach amounts to walking along a path parallel the ridge of conical intersections.

Journal Article↗
PubMed2006

TLQP-21, a VGF-derived peptide, increases energy expenditure and prevents the early phase of diet-induced obesity.

The vgf gene has been identified as an energy homeostasis regulator. Vgf encodes a 617-aa precursor protein that is processed to yield an incompletely characterized panel of neuropeptides. Until now, it was an unproved assumption that VGF-derived peptides could regulate metabolism. Here, a VGF peptide designated TLQP-21 was identified in rat brain extracts by means of immunoprecipitation, microcapillary liquid chromatography-tandem MS, and database searching algorithms. Chronic intracerebroventricular (i.c.v.) injection of TLQP-21 (15 mug/day for 14 days) increased resting energy expenditure (EE) and rectal temperature in mice. These effects were paralleled by increased epinephrine and up-regulation of brown adipose tissue beta2-AR (beta2 adrenergic receptor) and white adipose tissue (WAT) PPAR-delta (peroxisome proliferator-activated receptor delta), beta3-AR, and UCP1 (uncoupling protein 1) mRNAs and were independent of locomotor activity and thyroid hormones. Hypothalamic gene expression of orexigenic and anorexigenic neuropeptides was unchanged. Furthermore, in mice that were fed a high-fat diet for 14 days, TLQP-21 prevented the increase in body and WAT weight as well as hormonal changes that are associated with a high-fat regimen. Biochemical and molecular analyses suggest that TLQP-21 exerts its effects by stimulating autonomic activation of adrenal medulla and adipose tissues. In conclusion, we present here the identification in the CNS of a previously uncharacterized VGF-derived peptide and prove that its chronic i.c.v. infusion effected an increase in EE and limited the early phase of diet-induced obesity.

Adipose Tissue, Brown↗
PubMed2005

Parallel imaging of head with a dedicated multi-coil on a 0.4T open MRI.

BACKGROUND: Parallel imaging is widely used for cylindrical magnetic resonance imaging (MRI); however, few studies apply parallel imaging to open MRI. We previously developed a parallel method called "RAPID" (rapid acquisition through a parallel imaging design) for imaging the heart on a 0.7T open MRI apparatus, and we have now developed a RAPID head coil and shading correction algorithm for imaging the brain with a 0.4T open MRI apparatus. Images acquired with RAPID were compared with those acquired using a conventional quadrature-detection (QD) head coil. MATERIALS AND METHODS: The images were acquired using a dedicated 4-channel RF receiving coil consisting of a solenoid coil and surface coils. For MRI of the brain, we developed 2 methods to acquire the necessary calibration data: a pre-scan method that acquires the calibration data before the main scans and a self-calibration method that acquires the calibration data and imaging data simultaneously. We also modified the algorithm for calculating the shading distribution so that it only uses acquired image data and then corrects the shading. RESULTS: RAPID was applied for T1-weighted, T2-weighted, fluid-attenuation inversion recovery (FLAIR), time-of-flight (TOF), and diffusion-weighted echo-planar (DW-EPI) imaging. The RAPID images had no visible unfolded artifacts or motion artifacts. Images with the same contrast as that with a conventional QD coil were acquired using the RAPID coil and shading correction. CONCLUSION: These preliminary results show that RAPID can be applied to imaging of the head using a 0.4T open MRI apparatus.

Algorithms↗
PubMed1995

Hyperinducibility of HLA class II expression of thyroid follicular cells from Graves' disease. A primary defect?

Thyroid follicular cells (thyrocytes) from Graves' disease (GD) patients' thyroid glands express HLA class II molecules "ectopically." This phenomenon has been attributed to induction by locally produced cytokines and may be relevant to disease pathogenesis. We have compared IFN-gamma-mediated induction of HLA class II in thyrocytes from glands affected with GD and a nonautoimmune disease (MNG), to investigate a possible differential regulation of HLA expression between these two pathologies. HLA induction has been measured in primary thyrocyte cultures and control autologous macrophages stimulated or not stimulated with IFN-gamma. Comparison of flow cytometric data using an improved algorithm demonstrated that expression of HLA class II molecules is more readily induced in thyrocytes from GD than from MNG thyroid glands. This higher inducibility was parallel to a faster and stronger induction of HLA class II message in GD thyrocytes but did not correlate with the levels of HLA class II or class I originally expressed by thyrocytes in the tissue or with the degree of lymphocytic infiltration of the gland. There was no association with a particular HLA class II allele or with the presence of IFN-gamma and IL-2 in the tissue, as assessed by reverse transcription-PCR. No differences in the induction of class II were found in macrophages from each group of patients. These results suggest that an intrinsic feature of thyrocytes from GD patients is an up-regulation of HLA class II expression and that this is a characteristic that may facilitate the triggering of autoimmunity to "hyperinducible" thyroid glands.

Adolescent↗
PubMed2005

Reconstruction of large phylogenetic trees: a parallel approach.

Reconstruction of phylogenetic trees for very large datasets is a known example of a computationally hard problem. In this paper, we present a parallel computing model for the widely used Multiple Instruction Multiple Data (MIMD) architecture. Following the idea of divide-and-conquer, our model adapts the recursive-DCM3 decomposition method [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dataset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] to divide datasets into smaller subproblems. It distributes computation load over multiple processors so that each processor constructs subtrees on each subproblem within a batch in parallel. It finally collects the resulting trees and merges them into a supertree. The proposed model is flexible as far as methods for dividing and merging datasets are concerned. We show that our method greatly reduces the computational time of the sequential version of the program. As a case study, our parallel approach only takes 22.1h on four processors to outperform the best score to date (Found at 123.7h by the Rec-I-DCM3 program [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dataset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] on one dataset. Developed with the standard message-passing library, MPI, the program can be recompiled and run on any MIMD systems.

Journal Article↗
PubMed1997

SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements.

This paper discusses the implementation of a three-dimensional (3D) structure motif search of proteins. Each protein structure is represented by a set of secondary structure elements (SSEs) which involves alpha-helix segments and beta-strand segments. In describing it, every SSE is further reduced into a two-node graph that consists of the starting amino acid residue, the ending residue and a pseudo-bond between them. The searching algorithm is based on a graph theoretical clique-finding algorithm that has been used for 3D substructure searching in small organic molecules. The program SS3D-P2 was validated using proteins that have well-known 3D motifs, and it correctly found the Greek key motif within an eye lens protein, crystallin, that consists of four anti-parallel beta strands. The program was also successfully applied to searching for the more complex 3D motif, TIM-type beta-barrel motif, with a protein structure database from the Protein Data Bank.

Algorithms↗
PubMed2000

[Non-invasive ventilation in acute respiratory insufficiency].

Non invasive mechanical ventilation represents all the techniques of mechanical ventilation not using endotracheal connection to the respirator. Non invasive mechanical ventilation is essentially represented nowadays by facial (generally used for acute respiratory failure) and nasal ventilation (widely used for long term mechanical ventilation at home). Following in France the first studies of Rideau in the '80 in patients with chronic respiratory failure secondary to muscular dystrophy, Meduri, then Brochard demonstrated the interest of non invasive mechanical ventilation in the management of acute on chronic respiratory failure. A simple algorithm is thus able to recommend in first attempt use of non invasive mechanical ventilation in acute on chronic respiratory failure except if the patient presents in a severe respiratory status imposing in first line endotracheal ventilation. In parallel, more recent studies have demonstrated the interest of that technique in immediate ventilatory link in the spectrum of weaning of endotracheal mechanical ventilation. In hypoxic acute respiratory failure, non invasive mechanical ventilation remains controversial and seems to be better indicated in moderate to severe respiratory status.

Acute Disease↗
PubMed2003

A robust statistics-based global energy function for the alignment of serially acquired autoradiographic sections.

Autoradiographic analysis of the functional changes occurring in the rat brain are most often performed on coronal sections that allow a good insight into the events occurring at the structural level but lacks the 3D context which is necessary to fully understand the involvement of the brain structures in specific situations like focal seizures with or without generalization. Therefore a robust, fully-automated algorithm for the registration of serially acquired autoradiographic sections is presented. The method accounts for the main difficulties of autoradiographic alignment: corrupted data (cuts and tears), dissimilarities or discontinuities between slices, non parallel or missing slices. The approach relies on the minimization of a global energy function based on robust statistics. The energy function measures the similarity between a slice and its neighborhood in the 3D volume. No particular direction is privileged in the method, so that global offsets, biases in the estimation or error propagations are avoided. The method is evaluated qualitatively and quantitatively on real autoradiographic data. Rat brain autoradiographic volumes are reconstructed with registration errors less than 1 degree in rotation and less than 1 pixel in translation.

Algorithms↗
PubMed2003

General surface reconstruction for cone-beam multislice spiral computed tomography.

A new family of cone-beam reconstruction algorithm, the General Surface Reconstruction (GSR), is proposed and formulated in this paper for multislice spiral computed tomography (CT) reconstructions. It provides a general framework to allow the reconstruction of planar or nonplanar surfaces on a set of rebinned short-scan parallel beam projection data. An iterative surface formation method is proposed as an example to show the possibility to form nonplanar reconstruction surfaces to minimize the adverse effect between the collected cone-beam projection data and the reconstruction surfaces. The improvement in accuracy of the nonplanar surfaces over planar surfaces in the two-dimensional approximate cone-beam reconstructions is mathematically proved and demonstrated using numerical simulations. The proposed GSR algorithm is evaluated by the computer simulation of cone-beam spiral scanning geometry and various mathematical phantoms. The results demonstrate that the GSR algorithm generates much better image quality compared to conventional multislice reconstruction algorithms. For a table speed up to 100 mm per rotation, GSR demonstrates good image quality for both the low-contrast ball phantom and thorax phantom. All other performance parameters are comparable to the single-slice 180 degrees LI (linear interpolation) algorithm, which is considered the "gold standard." GSR also achieves high computing efficiency and good temporal resolution, making it an attractive alternative for the reconstruction of next generation multislice spiral CT data.

Algorithms↗
PubMed2006

Performances of Wang-Landau algorithms for continuous systems.

The relative performances of different implementations of the Wang-Landau method are assessed on two classes of systems with continuous degrees of freedom, namely, two polypeptides and two atomic Lennard-Jones clusters. Parallel tempering Monte Carlo simulations serve as a reference, and we pay particular attention to the variations of the multiplicative factor f during the course of the simulation. For the systems studied, the Wang-Landau method is found to be of comparable accuracy as parallel tempering, but has significant difficulties in reproducing low-temperature transitions exhibited by the Lennard-Jones clusters at low temperature. Using a complementary order parameter and calculating a two-dimensional joint density of states significantly improves the situation, especially for the notoriously difficult LJ(38) system. However, while parallel tempering easily converges for LJ(31), we have not been able to get data of comparable accuracy with Wang-Landau multicanonical sampling.

Journal Article↗
PubMed2000

Malignant melanoma on the sole: how to detect the early lesions efficiently.

Early detection of malignant melanoma (MM) is essential to improve the prognosis. In non-white populations, including Japanese, the sole is the most prevalent site of MM. On the sole, however, melanocytic nevus is also frequently found. Clinical differentiation of early MM from benign melanocytic nevus on the sole is sometimes difficult because both are observed as a brownish-black macule. For the effective early detection of MM on the sole, the author has proposed guidelines based on the data of hundreds of melanocytic lesions on the sole. The algorithmic guidelines are as follows: when you see a pigmented lesion on the sole, first exclude congenital melanocytic nevus and some other specified disorders, and then measure the maximum diameter of the lesion. If it is more than 7 mm, biopsy it for histopathologic evaluation. If it is 7 mm or less, just follow the course of the lesion and advise the patient to come back if it enlarges to more than 7 mm. Even when the lesion is 7 mm or less, a biopsy is recommended on it, if it shows marked irregularity in shape and/or color or it shows the parallel ridge pattern with epiluminescence microscopy (ELM). The author believes the guidelines surely work efficiently in screening early MM on the sole.

Algorithms↗
PubMed2005

Using points at infinity for parameter decoupling in camera calibration.

The majority of camera calibration methods, including the Gold Standard algorithm, use point-based information and simultaneously estimate all calibration parameters. In contrast, we propose a novel calibration method that exploits line orientation information and decouples the problem into two simpler stages. We formulate the problem as minimization of the lateral displacement between single projected image lines and their vanishing points. Unlike previous vanishing point methods, parallel line pairs are not required. Additionally, the invariance properties of vanishing points mean that multiple images related by pure translation can be used to increase the calibration data set size without increasing the number of estimated parameters. We compare this method with vanishing point methods and the Gold Standard algorithm and demonstrate that it has comparable performance.

Algorithms↗
PubMed1990

Evaluation of a human immunodeficiency virus test algorithm utilizing a recombinant protein enzyme immunoassay.

Many truly human immunodeficiency virus (HIV) antibody-negative serum samples may be unnecessarily subjected to costly and time-consuming Western blots (immunoblots). An investigation was undertaken to evaluate the efficiency of using a recombinant protein-based enzyme immunosorbent assay (EIA; Cambridge BioScience [CBC] Recombigen HIV EIA) as an adjunct to whole viral lysate EIA. A total of 2,212 serum samples which had been screened by viral lysate EIA were tested by CBC EIA in parallel with the Western blot. The sensitivity and specificity of the CBC kit were 99.9 and 99.7%, respectively. Positive and negative predictive values were 99.7 and 99.9%, respectively. The high sensitivity of this kit and its high negative predictive value make it an attractive addition to an HIV testing algorithm by reducing the number of Western blot tests on truly antibody negative serum samples.

Acquired Immunodeficiency Syndrome↗
PubMed2005

Scalable molecular dynamics with NAMD.

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

Algorithms↗
PubMed2005

3D freehand ultrasound reconstruction based on probe trajectory.

3D freehand ultrasound imaging is a very attractive technique in medical examinations and intra-operative stage for its cost and field of view capacities. This technique produces a set of non parallel B-scans which are irregularly distributed in the space. Reconstruction amounts to computing a regular lattice volume and is needed to apply conventional computer vision algorithms like registration. In this paper, a new 3D reconstruction method is presented, taking explicitly into account the probe trajectory. Experiments were conducted on different data sets with various probe motion types and indicate that this technique outperforms classical methods, especially on low acquisition frame rate.

Algorithms↗