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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↗
PubMed1994

Tomographic time-of-flight optical imaging device.

Time-resolved optical imaging has been used to image phantoms, animals, and humans, and offers the potential for the production of functional images of human tissues, such as the oxygenation of brain during stroke. We had previously reported a transmission scanner, and now give an early report on conversion to a rotational tomographic scanner with a non-parallel ray geometry similar to early CAT scanners. Initial scans show that 1) spatial imaging in turbid media using time-of-flight measurements, non-recursive algorithms, and standard tomographic geometry is possible, 2) separation of absorbance and scattering as an image is attainable, a key step in performing spatially-resolved chemometric analysis, 3) imaging of multiple objects buried within scattering material is feasible, demonstrating that equations derived for homogeneous media can be applied in at least some cases to inhomogeneous media such as tissue-like phantoms, and 4) imaging of brain pathology produces recognizable images with sufficient resolution for diagnostic decisions. We conclude that optical tomography is feasible for clinical use and that conversion of the present mechanically scanning device to a clinical scanner should be possible with retention of the current processing algorithms. Such a clinical scanner should ultimately be able to generate images in a few minutes with centimeter resolution at the center of living human brain.

Algorithms↗
PubMed2000

Celloidin mounting (embedding without infiltration) - a new, simple and reliable method for producing serial sections of high thickness through complete human brains and its application to stereological and immunohistochemical investigations.

Celloidin mounting (embedding without infiltration) of the human central nervous system (CNS) proved to be superior to gelatin embedding for the production of serial sections ranging in thickness from 220 to 500 microm. After gallocyanin-staining, a comprehensive neuroanatomical as well as neuropathological survey of the human brain is possible, including diagnosis of Alzheimer's disease. Details of a fractionator analysis of the total striatal neuron number are described and the possible quantitative analysis of parallel immunohistochemically stained sections is discussed.

Adult↗
PubMed2001

The free energy landscape for beta hairpin folding in explicit water.

The folding free energy landscape of the C-terminal beta hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and OPLSAA force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the beta strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The beta hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature.

Amino Acid Sequence↗
PubMed2002

Identification of K(+) channels in the plasma membrane of maize subsidiary cells.

The stomatal complex of Zea mays consists of two guard cells with the pore in between them and two flanking subsidiary cells. Both guard cells and subsidiary cells are important elements for stoma physiology because a well-coordinated transmembrane shuttle transport of potassium and chloride ions occurs between these cells during stomatal movement. To shed light upon the corresponding transport systems from subsidiary cells, subsidiary cell protoplasts were enzymatically isolated and in turn, analyzed with the patch-clamp technique. Thereby, two K(+)-selective channel types were identified in the plasma membrane of subsidiary cells. With regard to their voltage-dependent gating behavior, they may act as hyperpolarization-dependent K(+) uptake and depolarization-activated K(+) release channels during stomatal movement. Interestingly, the K(+) channels from subsidiary cells and guard cells similarly responded to membrane voltage as well as to changes in the K(+) gradient. Further, the inward- and outward-rectifying K(+) current amplitude decreased upon a rise in the intracellular free Ca(2+) level from 2 nM to the micro M-range. The results indicate that the plasma membrane of subsidiary cells and guard cells has to be inversely polarized in order to achieve the anti-parallel direction of K(+) fluxes between these cell types during stomatal movement.

Algorithms↗
PubMedDate not supplied

Calculation of the uncertainty in the dose delivered during radiation therapy.

There is, inevitably, uncertainty in our knowledge of the dose at any point within an irradiated patient. A technique is presented for estimating this uncertainty by performing three parallel calculations, one using nominal values and the others extreme values of the parameters upon which the dose depends. Such calculations can be made with almost any algorithm for calculating dose. They result in an estimate, at some specified confidence level which is determined by the data used, of the range of dose likely at any point. Such calculations should help therapists to avert over- or underdosage which might not be evident in conventional calculations of the nominal dose.

Humans↗
PubMed1993

Magnocellular pathway for rotation invariant Neocognitron.

In the mammalian visual system, magnocellular pathway and parvocellular pathway cooperatively process visual information in parallel. The magnocellular pathway is more global and less particular about the details while the parvocellular pathway recognizes objects based on the local features. In many aspects, Neocognitron may be regarded as the artificial analogue of the parvocellular pathway. It is interesting then to model the magnocellular pathway. In order to achieve "rotation invariance" for Neocognitron, we propose a neural network model after the magnocellular pathway and expand its roles to include surmising the orientation of the input pattern prior to recognition. With the incorporation of the magnocellular pathway, a basic shift in the original paradigm has taken place. A pattern is now said to be recognized when and only when one of the winners of the magnocellular pathway is validified by the parvocellular pathway. We have implemented the magnocellular pathway coupled with Neocognitron parallel on transputers; our simulation programme is now able to recognize numerals in arbitrary orientation.

Algorithms↗
PubMed2004

Multigrid approach to predictive wave-front reconstruction in adaptive optical systems.

A computationally efficient approach, based on the principles of multigrid methods, to predictive wave-front reconstruction in adaptive optical systems is described. Local predictive estimators are computed by use of recursive least squares on multiple grids. Each grid is increasingly coarse, allowing for temporal prediction of the behavior of both high- and low-spatial-frequency aberrations. Example numerical simulation results are given, showing that implementing the recursive least-squares algorithm for predictive estimation in a multigrid fashion greatly accelerates convergence to the steady-state optimal estimator condition. By implementation of the multigrid predictive reconstructor in parallel, the computational cost of implementing a predictive wave-front reconstruction scheme that uses recursive least squares for each processor at each cycle can be reduced from [symbol: see text](m2) to [symbol: see text](2m), where m is the number of actuators.

Journal Article↗
PubMed2004

Compensation of distant phase-distorting layers. II. Extended-field-of-view adaptive receiver system.

We analyze the anisoplanatic adaptive receiver system field of view (FOV) and the possibility of controlling the system FOV by using an adaptive optics system with multiple wave-front sensors that sense wave-front phase aberrations of reference waves with different arrival angles. The conventional decoupled stochastic parallel gradient descent (D-SPGD) technique is generalized to include output signals from multiple wave-front sensors. The multiple-reference D-SPGD control algorithm introduced here is applied to obtain an anisotropic FOV in adaptive receiver systems by using two and three reference waves.

Journal Article↗