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PubMed1986

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

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

Computers↗
PubMed1982

Clinical management of acute and chronic cocaine poisoning.

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

Brain↗
PubMed1997

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

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

Algorithms↗
PubMed1998

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

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

Animals↗
PubMed1995

Using the Potts glass for solving the clustering problem.

We present an application of a Potts glass to the clustering problem. Simulated annealing in the mean field approximation is used in order to avoid local minima. The resulting updating equations are completely parallel, and very easy to implement. The model has no free parameters except for the annealing parameters. We show how the model can be implemented for some special clustering problems. The T-->0 limit of the Potts glass is identical to the vector quantization algorithm with certain increments. A comparative study of the Potts glass and vector quantization is also made, and it is shown that for difficult clustering problems, the Potts glass is far better than vector quantization.

Algorithms↗
PubMed1993

Bilateral inhibition generates neuronal responses tuned to interaural level differences in the auditory brainstem of the barn owl.

I investigated the neural algorithms by which neurons gain selectivity for interaural level difference in the brainstem of the barn owl (Tyto alba). Differences in the timing and in the level of sounds at the ears are used by this owl to encode, respectively, azimuthal and vertical position of sound sources in space. These two cues are processed in two parallel neural pathways. Below the level of the inferior colliculus, all neurons in the pathway that processes level differences show responses to this cue that are monotonic, and thus not selective for a particular level difference. Only in the inferior colliculus, which contains a map of auditory space, are neurons sharply tuned to specific interaural level differences. How are these response properties generated from those of the nuclei that provide input to the inferior colliculus? I show that the posterior subdivision of the nucleus ventralis lemnisci lateralis (VLVp) projects bilaterally to the lateral shell of the central nucleus of the inferior colliculus, the input stage to the map of auditory space. Both these nuclei are part of the pathway that processes interaural level differences. Manipulations of the responses in VLVp affected the responses to level differences in the inferior colliculus; responses to time differences were unaffected. By systematically increasing or decreasing neural activity in VLVp, I show that the VLVp on each side provides inhibition to the colliculus at large level differences. This results in a peaked response that is tuned to level differences in the inferior colliculus. Some cells in the lateral shell of the inferior colliculus appear to receive direct GABAergic inhibition from VLVp. I suggest that this circuitry and the algorithms it supports are the neural substrates that allow the barn owl to exploit level differences for computation of sound source elevation.

Acoustic Stimulation↗
PubMed1990

The cellular computer DNA: program or data.

The classical metaphor of the genetic program written in the DNA nucleotidic sequences is reconsidered. Recent works on algorithmic complexity and logical properties of computer programs and data are used to question the explanatory value of that metaphor. Structural properties of strings are looked for which would be necessary to apply to DNA sequences if the metaphor is to be taken literally. The notion of sophistication is used to quantify meaningful complexity and to distinguish it from classical computational complexity. In this context, the distinction between program and data becomes relevant and an alternative metaphor of DNA as data to a parallel computing network embedded in the global geometrical and biochemical structure of the cell is discussed. An intermediate picture of an evolving network emerges as the most likely where the output of the cellular computing network can produce, at a different time scale, changes in the structure of the network itself by means of changes in the DNA activity patterns.

Algorithms↗
PubMed1989

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↗
PubMed1999

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↗
PubMed1994

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↗
PubMed1984

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↗
PubMed1991

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↗
PubMed1995

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↗
PubMed1999

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↗
PubMed2000

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↗
PubMed1988

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↗
PubMed2001

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↗
PubMed1990

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↗