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Software acceleration techniques for the simulation of scanning electron microscope images.

A scanning electron microscope (SEM) simulator was developed based on the models used in the MONSEL software. This simulator extends earlier work by introducing an object-oriented framework and adding optimization methods based on precomputation of electron trajectories. Several optimizations enable speedup by factors of 5-100 on a single processor over unoptimized simulations without introducing additional approximations. The speedup for a particular surface depends on the self-similarity of the surface at the scale of the electron penetration depth. We further accelerate by parallelizing the calculations for a total speedup of about 100-2000 on 30 processors. The goal of this work was to create a system capable of simulating a quantitatively accurate SEM image of a relatively unconstrained surface. Results of this work include simulation software, optimization algorithms, performance measurements with various optimizations, and examples of simulated images.

Algorithms↗

New approaches to high-throughput phasing.

Recent progress in macromolecular phasing, in part stimulated by the high-throughput structural biology initiatives, has made this crucial stage of the elucidation of crystal structures easier and more automatic. A quick soak in various salts leads to the rapid incorporation of the anomalously scattering ions, suitable for phasing by MAD (multiwavelength anomalous dispersion), SAD (single-wavelength anomalous dispersion) or MIR (multiple isomorphous replacement) methods. The availability of stable synchrotron beam lines equipped with elaborate hardware control and sophisticated data processing programs makes it possible to collect very accurate diffraction data and to solve structures from the very weak anomalous signal of such atoms as sulfur or phosphorus, inherently present in macromolecules. The current progress in phasing, coupled with the parallel advances in protein crystallization, diffraction data collection and so on, suggests that, in the near future, the process of macromolecular crystal structure elucidation may become fully automatic.

Algorithms↗

A distributed, developmental model of word recognition and naming.

A parallel distributed processing model of visual word recognition and pronunciation is described. The model consists of sets of orthographic and phonological units and an interlevel of hidden units. Weights on connections between units were modified during a training phase using the back-propagation learning algorithm. The model simulates many aspects of human performance, including (a) differences between words in terms of processing difficulty, (b) pronunciation of novel items, (c) differences between readers in terms of word recognition skill, (d) transitions from beginning to skilled reading, and (e) differences in performance on lexical decision and naming tasks. The model's behavior early in the learning phase corresponds to that of children acquiring word recognition skills. Training with a smaller number of hidden units produces output characteristic of many dyslexic readers. Naming is simulated without pronunciation rules, and lexical decisions are simulated without accessing word-level representations. The performance of the model is largely determined by three factors: the nature of the input, a significant fragment of written English; the learning rule, which encodes the implicit structure of the orthography in the weights on connections; and the architecture of the system, which influences the scope of what can be learned.

Dyslexia↗

A synchrotron radiation microtomography system for the analysis of trabecular bone samples.

X-ray computed microtomography is particularly well suited for studying trabecular bone architecture, which requires three-dimensional (3-D) images with high spatial resolution. For this purpose, we describe a three-dimensional computed microtomography (microCT) system using synchrotron radiation, developed at ESRF. Since synchrotron radiation provides a monochromatic and high photon flux x-ray beam, it allows high resolution and a high signal-to-noise ratio imaging. The principle of the system is based on truly three-dimensional parallel tomographic acquisition. It uses a two-dimensional (2-D) CCD-based detector to record 2-D radiographs of the transmitted beam through the sample under different angles of view. The 3-D tomographic reconstruction, performed by an exact 3-D filtered backprojection algorithm, yields 3-D images with cubic voxels. The spatial resolution of the detector was experimentally measured. For the application to bone investigation, the voxel size was set to 6.65 microm, and the experimental spatial resolution was found to be 11 microm. The reconstructed linear attenuation coefficient was calibrated from hydroxyapatite phantoms. Image processing tools are being developed to extract structural parameters quantifying trabecular bone architecture from the 3-D microCT images. First results on human trabecular bone samples are presented.

Aged↗

Neural cost functions and search strategies for the generation of block designs: an experimental evaluation.

A constraint satisfaction problem, namely the generation of Balanced Incomplete Block Designs (v, b, r, kappa, lambda)-BIBDs, is cast in terms of function optimization. A family of cost functions that both suit the problem and admit a neural implementation is defined. An experimental comparison spanning this repertoire of cost functions and three neural relaxation strategies (Down-Hill search, Simulated Annealing and a new Parallel Mean Search procedure), as applied to all BIBDs of up to 1000 entries, has been undertaken. The experiments were performed on a Connection Machine CM-200 and their analysis required a careful study of performance measures. The simplest cost function stood out as the best one for the three strategies. Parallel Mean Search, with several processors searching cooperatively in parallel, could solve a larger number of problems than the same number of processors working independently, but Simulated Annealing yielded overall the best results. Other conclusions, as detailed in the paper, could be drawn from the comparison, BIBDs remaining a challenging problem for neural optimization algorithms.

Algorithms↗

Arterial imaging with a new forward-viewing intravascular ultrasound catheter, II. Three-dimensional reconstruction and display of data.

BACKGROUND: Current intravascular ultrasound (IVUS) catheters provide transverse imaging at the level of the ultrasound transducer. This limits imaging to large-diameter segments without critical atherosclerotic narrowings. We have developed a prototype 20-MHz forward-viewing IVUS catheter that provides two-dimensional sector imaging distal to the catheter tip. A present limitation of this technique is that the catheter must be manually rotated to obtain multiple longitudinal views required to integrate the segment into a three-dimensional matrix. To overcome this, we have developed an algorithm that reconstructs these multiple two-dimensional forward-viewing IVUS images into a three-dimensional matrix for more complete depiction of the segment distal to the ultrasound catheter. This algorithm allows display and multidimensional slicing of the three-dimensional reconstruction. METHODS AND RESULTS. To test our algorithms, five arterial segments (three canine aortas, two human femoral arteries) were evaluated in vitro. In each segment, 36 forward-viewing longitudinal slices were collected, digitized, processed, and reoriented to produce a three-dimensional reconstruction (3DR) matrix. The matrix data were sliced into parallel transverse sections and compared with morphometric interpretation of histological sections (Histo). As a result, image data could be reconstructed for a distance of 2.0 cm ahead of the catheter. 3DR easily demonstrated wall and luminal morphology and provided transverse IVUS images comparable to the histological specimens. A good correlation was noted between Histo- and 3DR-determined luminal diameters (LD) and luminal areas: 3DR LD = 1.4 Histo LD-0.4, r = .86; 3DR LD = 0.7 +/- 0.20 cm (mean +/- SD); and Histo LD = 0.7 +/- 0.13 cm. CONCLUSIONS: These preliminary data demonstrate the feasibility of 3DR of forward-viewing IVUS data. This method allows rapid, detailed analysis of diseased arterial segments previously unavailable with standard IVUS and may permit better targeting of interventional techniques.

Animals↗

Anatomy and physiology of a color system in the primate visual cortex.

Staining for the mitochondrial enzyme cytochrome oxidase reveals an array of dense regions (blobs) in the primate primary visual cortex. They are most obvious in the upper layers, 2 and 3, but can also be seen in layers 4B, 5, and 6, in register with the blobs in layers 2 and 3. We compared cells inside and outside blobs in macaque and squirrel monkeys, looking at their physiological responses and anatomical connections. Cells within blobs did not show orientation selectivity, whereas cells between blobs were highly orientation selective. Receptive fields of blob cells had circular symmetry and were of three main types, Broad-Band Center-Surround, Red-Green Double-Opponent, and Yellow-Blue Double-Opponent. Double-Opponent cells responded poorly or not at all to white light in any form, or to diffuse light at any wavelength. In contrast to blob cells, none of the cells recorded in layer 4C beta were Double-Opponent: like the majority of cells in the parvocellular geniculate layers, they were either Broad-Band or Color-Opponent Center-Surround, e.g., red-on-center green-off-surround. To our surprise cells in layer 4C alpha were orientation selective. In tangential penetrations throughout layers 2 and 3, optium orientation, when plotted against electrode position, formed long, regular, usually linear sequences, which were interrupted but not perturbed by the blobs. Staining area 18 for cytochrome oxidase reveals a series of alternating wide and narrow dense stripes, separated by paler interstripes. After small injections of horseradish peroxidase into area 18, we saw a precise set of connections from the blobs in area 17 to thin stripes in area 18, and from the interblob regions in area 17 to interstripes in area 18. Specific reciprocal connections also ran from thin stripes to blobs and from interstripes to interblobs. We have not yet determined the area 17 connections to thick stripes in area 18. In addition, within area 18 there are stripe-to-stripe and interstripe-to-interstripe intrinsic connections. These results suggest that a system involved in the processing of color information, especially color-spatial interactions, runs parallel to and separate from the orientation-specific system. Color, encoded in three coordinates by the major blob cell types, red-green, yellow-blue, and black-white, can be transformed into the three coordinates, red, green, and blue, of the Retinex algorithm of Land.

Animals↗

Analysis of interaction between number of implant catheters and dose-volume histograms in prostate high- dose-rate brachytherapy using a computer model.

PURPOSE: In prostate high-dose-rate brachytherapy, to determine before implant, using the standard geometric optimization algorithm, whether there is an optimal number of catheters. MATERIALS AND METHODS: Transrectal ultrasound images of the prostate from 24 patients were transferred into the brachytherapy planning system. Urethra and prostate contours were digitized onto each axial slice of a CT scan, as well as hypothetical locations of the catheters (2/3 of the catheters along the prostate contour, 1/3 around the urethra). Each prostate was implanted with 9, 12, 15, 18, and 21 catheters. Dosimetry was optimized using a geometric optimization algorithm; prescription isodose was chosen so that 95% of planning target volume was covered by the 100% isodose. RESULTS: A significant increase in mean volume of prostate receiving 150% of the dose (V150) when the number of catheters decreased (p < 0.0001). The 9-catheter group significantly differed from each of the other groups; no difference was seen in V150 among the 21-, 18-, and 15-catheter groups. Parallel results were observed for urethra V150 and homogeneity index; there was no difference in conformity index by catheter group. CONCLUSION: V150 increased when fewer catheters were used. There was no significant difference among the 21-, 18-, and 15-catheter groups: the geometric optimization routine probably compensated for the larger distance between dwell positions. Based on the technique described in our study, we conclude that 15 to 21 catheters seem to cover the prostate adequately without creating excess hot spots.

Algorithms↗

Quantitative phase microscopy: a new tool for measurement of cell culture growth and confluency in situ.

Quantitative phase microscopy (QPM) is a recently developed computational approach that provides quantitative phase measurements of specimen images obtained under bright-field conditions without phase- or interference-contrast optics. To perform QPM, an in-focus bright-field image is acquired, together with one positive and one negative de-focus image. An algorithm is then applied to produce a specimen phase map. In this investigation we demonstrate that manipulation of the phase map intensity histogram using novel, non-subjective thresholding and segmentation methods provides enhanced delineation of cells in culture. QPM was utilised to measure the growth behaviour of cultured airway smooth muscle cells over a 92-h period. There was a high degree of correlation between parallel QPM-derived confluency measurements and haemocytometry-derived counts of airway smooth muscle cells over this time period. Using QPM, translucent cells can be visualised with improved cell boundary definition allowing precise and reproducible measurements of cell culture confluency. Quantitative phase imaging provides a rapid, optically simple and non-destructive approach for measurement of cellular morphology. Further development of the QPM-based analysis methodology has the potential to provide even more refined measures of cellular growth.

Algorithms↗

Solid state 2H-NMR as a method for determining the orientation of cannabinoid analogs in membranes.

In order to investigate the correlation between the pharmacological activities of cannabinoids and the geometric features of their interactions with membranes, we have calculated the molecular orientations of five analogs in model membrane bilayers. The studies involved the stereospecific 2H-labeling of each analog in different positions and the use of solid state 2H-NMR. The cannabinoids included in our study are (-)-delta 9-tetrahydrocannabinol (THC), (-)-delta 8-THC and its methylated ether analog (-)-O-methyl-delta 8-THC, as well as two hexahydrocannabinols (HHC) having an additional hydroxyl in the 11-position, (-)-11-OH-9 alpha-HHC and (-)-11-OH-9 beta-HHC. A new algorithm is used to circumvent the problem of deuterium quadrupolar splitting signs. The method has general applicability for calculating the orientation of a molecule in a anisotropic environment. Our calculations show that the biological inactive O-methyl-delta 8-THC orients with its long axis parallel to the lipid acyl chains, whereas the psychoactive cannabinoids assume "awkward" orientations in which the hydroxyl groups are pointing towards the bilayer interface, presumably to maximize the amphipathic interaction with the membrane. To produce their biological effects, cannabinoids may need to acquire an appropriate location and orientation in the membrane bilayer so that, through lateral diffusion, they can reach their sites of action and interact productively with these sites.

Cannabinoids↗

A parallel neural network simulator on the connection machine CM-5.

We here present a parallel implementation of artificial neural networks on the connection machine CM-5 and compare it with other parallel implementations on SIMD and MIMD architectures. This parallel implementation was developed with the goal of efficiently training large neural networks with huge training pattern sets for applications in molecular biology, in particular the prediction of coding regions in DNA sequences. The implementation uses training pattern parallelism and makes use of the parallel I/O facilities of the CM-5 and its efficient reduction operations available within the control network to achieve a high scalability. The parallel simulator obtains a maximum speed of 149.25 MCUPS for training feedforward networks with backpropagation on a 512 processor CM-5 system without using the CM-5 vector facility. The implementation poses no restriction on the type of network topology and works with different batch training algorithms like BP. Quickprop and Rprop.

Algorithms↗

The incipient stage in thrombin-induced fibrin polymerization detected by FCS at the single molecule level.

We used fluorescence correlation spectroscopy (FCS) to study the activation of fibrinogen by thrombin and the subsequent aggregation of fibrin monomers into fibrin polymers at a very low and at physiological fibrinogen concentrations. In the labeling procedure used the fibrinogen was randomly labeled and the label was bound to the fibrinopeptide A and/or to the part of fibrinogen which after activation takes part in fibrin formation. We measured a diffusion coefficient for fibrinogen of 2.48 x 10(-7) +/- 0.10 x 10(-7) cm2/s. After activation with thrombin both fibrinopeptide A and fibrin polymerization products could be demonstrated. From our findings we suggest a model for the formation of a three-dimensional network as two parallel processes, elongation and branching and that fibrin oligomers are not only intermediates in the polymerization process but also are substrates for branching.

Algorithms↗

Forecasts using neural network versus Box-Jenkins methodology for ambient air quality monitoring data.

This study explores ambient air quality forecasts using the conventional time-series approach and a neural network. Sulfur dioxide and ozone monitoring data collected from two background stations and an industrial station are used. Various learning methods and varied numbers of hidden layer processing units of the neural network model are tested. Results obtained from the time-series and neural network models are discussed and compared on the basis of their performance for 1-step-ahead and 24-step-ahead forecasts. Although both models perform well for 1-step-ahead prediction, some neural network results reveal a slightly better forecast without manually adjusting model parameters, according to the results. For a 24-step-ahead forecast, most neural network results are as good as or superior to those of the time-series model. With the advantages of self-learning, self-adaptation, and parallel processing, the neural network approach is a promising technique for developing an automated short-term ambient air quality forecast system.

Air Pollution, Indoor↗

Interaction of carotid chemoreceptor and baroreceptor reflexes in anesthetized dogs.

Interaction between baroreceptors and chemoreceptors during simultaneous activation of the reflexes was studied in eight pentobarbital sodium-anesthetized vagotomized dogs. The carotid sinus reflexogenic area was isolated and perfused at controlled carotid sinus pressure (CSP), PO2, and PCO2. Random combinations of CSP, PO2, and PCO2 were delivered to the carotid sinus. Results were analyzed by multiple linear regression. For the arterial pressure response, increasing CO2 resulted in an upward shift of the baroreceptor reflex response curve and an increased slope of the linear portion of the curve. The heart rate-CSP curve was also shifted upward by CO2, with the effect being greatest at high levels of CSP. The respiratory frequency-CO2 relationship had an increased slope and was shifted upward when CSP was decreased. The responses of tidal volume and ventilation (VE) depended on all three inputs. At any level of PO2, decreasing CSP resulted in a parallel shift of the VE-CO2 relationship. The results indicate that there is a significant interaction between chemoreceptor and baroreceptor reflex sensitivities.

Algorithms↗

Detection of motion in hybrid PET/SPECT imaging based on the correlation of partial sinograms.

This paper describes a motion detection method specific to hybrid positron emission tomography/single photon emission computed tomography systems. The method relies on temporal fractionation of the acquisition into three data sets followed by an algorithm based on the cross correlation (CC) of partial sinograms from successive sets at different rotations of the camera. Spatial inconsistencies due to motion are detected by decreases in the CC between two sets. This permits to separate data into premotion and postmotion sets of consistent data that are reconstructed independently then registered and summed. Rigid motions greater than 1-cm translation or 10 degrees rotation were detected with this method from experimental data obtained by manually moving phantoms made of radioactive spheres as well as from a patient lung study corrupted by artificial motion. The different motion studies showed that the image contrast does not seem to be a limiting factor and that the motion is best detected when the gantry is parallel to the direction of motion. The registration and fusion of the reconstructed premotion and postmotion sets lead in all cases to a reduction of the motion artifacts and an increase in signal-to-noise ratio.

Algorithms↗

Image analysis techniques for automatic evaluation of two-dimensional electrophoresis.

Techniques for automatic analysis of two-dimensional electrophoresis gels by computer-aided image analysis are described. Original gels or photographic films are scanned using a laser scanner and the files are transferred to a microcomputer. The program package first performs a compression and preevaluation of the files. Spot identification and quantification is performed by the chain code algorithm after appropriate zooming and cutting. Labeling facilitates spot identification and quantification in numerical and graphical (pseudocolor) representation on peripheral devices for camera ready output. Interpolation between measured basepoints is performed by cubic spline algorithms which are automatically switched on and off, depending on the need by the program. High speed analysis and graphic representation is achieved using fast Assembler language routines rather than high level languages. One-dimensional gels can be analyzed using the same software. Spot matching between parallel two-dimensional gels has not yet been implemented.

Electrophoresis, Gel, Two-Dimensional↗

On-line laser-photometric monitoring of aerosol deposition in ventilated rabbit lungs.

A photometric technique was developed for on-line measurement of aerosol deposition in isolated, ventilated, and perfused rabbit lungs. A jet nebulizer was used for aerosolization of saline (hygroscopic particles) and di(2-ethylhexyl) sebacate (nonhygroscopic particles). Aerosol concentration (laser photometer, constructed for measurements in rabbit lungs) and flow rate (commercial pneumotachograph) were continuously monitored at the inlet of the tracheal cannula. Computer-assisted data processing allowed the breath-by-breath calculation of inhaled and exhaled aerosol mass, thus providing the deposition fraction. With the use of hygroscopic particles, however, this approach was hampered by the humidity-induced particle growth in the airways, leading to an overestimation of the aerosol concentration in exhaled air. This effect was corrected by an algorithm using a "particle growth factor" derived breath by breath from the photometer signal. To test the reliability of this approach, saline particles carrying technetium-99m label were aerosolized into rabbit lungs with the use of various ventilator settings, and the aerosol deposition was assessed in parallel by photometry and by radioactivity detection over the lung and over a trap in the exhaled-air circuit. Superimposable curves of cumulative aerosol deposition, with changes in kinetics dependent on the ventilator mode, were obtained. For a given ventilator setting, absolute values of the deposition fraction were 0.32 +/- 0.04 (radiotracer quantification) and 0.36 +/- 0.04 (photometry; means +/- SD; n = 4). We conclude that the presented laser-photometric technique allows reliable on-line monitoring of the deposition of both nonhygroscopic and hygroscopic aerosol particles in ventilated lungs.

Aerosols↗

[Pathogenetic rationale and diagnostic methods in allergic tuberculous synovitis of the knee joint].

The pathogenesis of tuberculous allergic synovitis was specified in the experiments on 44 rabbits by applying original simulation methods, including bivalent sensibilization, parallel study of the synovial fluid and serum of laboratory animals. A role of the synovial layer as an organ of immunogenesis and its impact on antibody titers were defined. A new diagnostic test, involving a diagnostic parameter and an equation for its calculation was developed. An algorithm was proposed for examining patients with synovitis (arthritis) of unknown etiology, which includes a set of significant clinical and laboratory parameters. Its testing in 64 patients enabled the tuberculous nature of the disease to be identified in 30% of cases.

Algorithms↗