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PubMed2004

Parallel processing across neural systems: implications for a multiple memory system hypothesis.

A common conceptualization of the organization of memory systems in brain is that different types of memory are mediated by distinct neural systems. Strong support for this view comes from studies that show double (or triple) dissociations between spatial, response, and emotional memories following selective lesions of hippocampus, striatum, and the amygdala. Here, we examine the extent to which hippocampal and striatal neural activity patterns support the multiple memory systems view. A comparison is made between hippocampal and striatal neural correlates with behavior during asymptotic performance of spatial and response maze tasks. Location- (or place), movement, and reward-specific firing patterns were found in both structures regardless of the task demands. Many, but not all, place fields of hippocampal and striatal neurons were similarly affected by changes in the visual and reward context regardless of the cognitive demands. Also, many, but not all, hippocampal and striatal movement-sensitive neurons showed significant changes in their behavioral correlates after a change in visual context, irrespective of cognitive strategy. Similar partial reorganization was observed following manipulations of the reward condition for cells recorded from both structures, again regardless of task. Assuming that representations that persist across context changes reflect learned information, we make the following conclusions. First, the consistent pattern of partial reorganization supports a view that the analysis of spatial, response, and reinforcement information is accomplished via an error-driven, or match-mismatch, algorithm across neural systems. Second, task-relevant processing occurs continuously within hippocampus and striatum regardless of the cognitive demands of the task. Third, given the high degree of parallel processing across allegedly different memory systems, we propose that different neural systems may effectively compete for control of a behavioral expression system. The strength of the influence of any one neural system on behavioral output is likely modulated by factors such as motivation, experience, or hormone status.

Animals↗
PubMed1996

A self-organizing cognitive network of antibody repertoire development.

A self-organizing cognitive network is mapped here onto the Id network model. The weight-vectors in this network represent some important topographical and biophysical parameters in the antibody-antigen affinity landscape. The Kohonen layers in the network correspond to affinity clones and the involved algorithm simulates the operations of clonal selection, hypermutation, differentiation, diversity, and affinity maturation. Two significant features of this model are: (i) a computationally feasible and biophysically informative representation of the para/epitopes, and (ii) the ability to perform simultaneous (parallel) and associative computations in a multidimensional shape-space. Computational experiments with real data have shown cognitive properties of this network. The results also indicate scope in quantitative characterization of the metadynamics of the above operations/weights in the adaptive development of the antibody repertoire.

Algorithms↗
PubMed1996

Investigating shape-from-shading illusions using solid objects.

Recent growth in the shape-from-shading psychophysics literature has been paralleled by an increasing availability of computer graphics hardware and software, to the extent that most psychophysical studies in this area now employ computer lighting algorithms. The most widely used of these algorithms in shape-from-shading psychophysics is the Phong lighting model. This model, and other shading models of its genre, produce readily interpretable images of three-dimensional scenes. However, such algorithms are only approximations of how light interacts with real objects in the natural environment. Nevertheless, the results from psychophysical experiments using these techniques have been used to infer the processes underlying the perception of shape-from-shading in natural environments. It is important to establish whether this substitution is ever valid. We report a series of experiments investigating whether two recently reported illusions seen in computer-generated, Phong shaded images occur for solid objects under real illuminants. The two illusions investigated are three-dimensional curvature contrast and the illuminant-position effect on perceived curvature. We show that both effects do occur for solid objects, and that the magnitude of these effects are equivalent regardless of whether subjects are presented with ray traced or solid objects.

Algorithms↗
PubMedDate not supplied

A distributed and interactive three-dimensional medical image system.

Three-dimensional (3D) arrays of digital data representing spatial volumes arise in many scientific applications, such as computed tomography (CT) and magnetic resonance imaging (MRI) created by imaging a series of cross sections of human bodies in medical applications. In this article, a software system architecture, called DISCOVER (a Distributed Interactive Scientific COmputing and Visualization EnviRonment), which can take advantage of the power of parallel processing, is proposed and implemented for interactive visualization and manipulation of the 3D digital data. The surface-rendering and the volume-rendering algorithms are implemented. The same software program can be executed on several different hardware platforms. We also propose a new rendering algorithm, called volume-surface rendering, for medical applications. The algorithm enables users to visualize the external and internal structures of medical objects simultaneously. The network version of the DISCOVER, as it stands today, is in practical use in the Hospital of National Cheng Kung University in Taiwan for real clinical applications.

Algorithms↗
PubMed2006

Recognition of external object features in gas media using ultrasound transmission tomography.

The paper presents and analyzes a new way of recognizing external object features (shape, size, location) in gas media using ultrasound transmission tomography (UTT) with parallel-ray-projection scanning geometry. The concept of UTT in a gas medium is close to classical tomography, however because of the nature of the measurement environment, visualizing the internal structure of solid objects is difficult; whereas it is possible to image their external features: their shape, size and spatial location. The paper presents the results of examining the shape, size and location of different objects in the air in the form of tomographic images, obtained in parallel-ray-projection geometry, using a specially elaborated research setup for UTT. Applying parallel-ray-projection geometry enabled us to investigate the influence of scanning resolution on image quality. In order to test the operation of the elaborated algorithm of tomographic image reconstruction on the basis of correct measurement data, special software was written for simulating the binary matrix of the measurements for a set of a dozen or so solid objects of different shapes and a few simulations were performed.

Journal Article↗
PubMed1997

Validation of the central-ray approximation for attenuated depth-dependent convolution in quantitative SPECT reconstruction.

In order to model photon attenuation and detector resolution variation as a depth-dependent convolution for efficient reconstruction of quantitative SPECT, a central-ray approximation is necessary. This work investigates the impact of the approximation upon reconstruction accuracy and computational efficiency. A patient chest CT image was acquired and converted into an object-specific attenuation map. From a segmentation of the map, an emission thorax phantom was constructed with a cardiac insert. To generate a system-specific resolution-variant kernal, a point source was measured at several depths from the surface of a low-energy, high-resolution, parallel-hole collimator of a SPECT system. Projections of parallel-beam geometry were simulated from the phantom, the map, and the kernel on an elliptical orbit. Reconstruction was performed by the ML-EM algorithm with and without the central-ray approximation. The approximation cuts down dramatically (more than 100 fold) the computing time with a negligible loss (less than 1%) of reconstruction accuracy.

Algorithms↗
PubMed2005

Data pre-processing in liquid chromatography-mass spectrometry-based proteomics.

MOTIVATION: In a liquid chromatography-mass spectrometry (LC-MS)-based expressional proteomics, multiple samples from different groups are analyzed in parallel. It is necessary to develop a data mining system to perform peak quantification, peak alignment and data quality assurance. RESULTS: We have developed an algorithm for spectrum deconvolution. A two-step alignment algorithm is proposed for recognizing peaks generated by the same peptide but detected in different samples. The quality of LC-MS data is evaluated using statistical tests and alignment quality tests. AVAILABILITY: Xalign software is available upon request from the author.

Algorithms↗
PubMed2005

Genetic-based fuzzy image filter and its application to image processing.

In this paper, we propose a Genetic-based Fuzzy Image Filter (GFIF) to remove additive identical independent distribution (i.i.d.) impulse noise from highly corrupted images. The proposed filter consists of a fuzzy number construction process, a fuzz filtering process, a genetic learning process, and an image knowledge base. First, the fuzzy number construction process receives sample images or the noise-free image and then constructs an image knowledge base for the fuzzy filtering process. Second, the fuzzy filtering process contains a parallel fuzzy inference mechanism, a fuzzy mean process, and a fuzzy decision process to perform the task of noise removal. Finally, based on the genetic algorithm, the genetic learning process adjusts the parameters of the image knowledge base. By the experimental results, GFIF achieves a better performance than the state-of-the-art filters based on the criteria of Peak-Signal-to-Noise-Ratio (PSNR), Mean-Square-Error (MSE), and Mean-Absolute-Error (MAE). On the subjective evaluation of those filtered images, GFIF also results in a higher quality of global restoration.

Algorithms↗
PubMed2005

libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

SUMMARY: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES, to facilitate a fast implementation of computer software for study of non-linear biochemical pathways. This library implements a (mu, lambda)-ES evolutionary optimization algorithm that uses stochastic ranking as the constraint handling technique. Considering the amount of computing time it might require to solve a parameter-estimation problem, an MPI version of libSRES is provided for parallel implementation, as well as a simple user interface. libSRES is freely available and could be used directly in any C program as a library function. We have extensively tested the performance of libSRES on various pathway parameter-estimation problems and found its performance to be satisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/

Algorithms↗
PubMed2001

Value of flow diagrams in reports of randomized controlled trials.

CONTEXT: Diagrams of the flow of participants through a clinical trial are recommended in the Consolidated Standards for Reporting of Trials (CONSORT) statement, but it is unclear whether such flow diagrams improve the quality of trial reports. OBJECTIVE: To examine the information contributed by flow diagrams and the completeness of reporting overall in reports of randomized controlled trials (RCTs) published in 5 general and internal medicine journals. DESIGN AND SETTING: Analysis of 270 reports of RCTs published in 1998 in the Annals of Internal Medicine (AIM; n = 19), BMJ (n = 42), JAMA (n = 45), The Lancet (n = 81), and The New England Journal of Medicine (NEJM; n = 83). MAIN OUTCOME MEASURES: Proportion of reports that included a flow diagram, information provided in flow diagrams, and completeness of reporting about flow of participants overall in flow diagrams or text. RESULTS: A total of 139 reports (51.5%) of RCTs included a flow diagram, but this varied widely among journals (AIM, 21.0%; BMJ, 38.1%; JAMA, 80.0%; The Lancet, 93.8%; and NEJM, 8.4%). Diagrams generally provided useful information, but only 73 (52.5%) included the number of participants who received allocated interventions and only 32 (23.0%) included the number of participants included in the analysis. In logistic regression analysis, overall completeness of reporting about flow of study participants was associated with publication of a flow diagram. CONCLUSIONS: Flow diagrams are associated with improved quality of reporting of randomized controlled trials. However, the structure of current flow diagrams is less than ideal. We propose a revised flow diagram that includes all important counts through the stages of parallel group trials.

Algorithms↗
PubMed2005

Videomicroscopy, image processing, and analysis of whole histologic sections of the human brain.

Serial histologic sections of a whole human brain may have extensions of up to 130 x 130 mm within the coronal plane around the temporal lobe. To date, however, technology has not provided a bright field microscope that is able to shift the object holder continuously in the x- and y-direction over such distances and still possess the same optical capabilities as comparable devices. We developed a new light microscope to continuously quantify such sections. We also developed the computing environment for controlling the device and for analyzing the data produced. In principle, we are now able to quantify each neuron of a human brain. The data ultimately will provide the most detailed structural information about the human brain ascertained thus far. Such detailed information of the spatial distribution of neurons is essential to develop realistic models for simulation of large-scale neuronal networks and to investigate the significance of neuronal arrangements with respect to neuronal signal processing in the CNS. After preprocessing of the data produced by the new microscope, we are able to detect lamination patterns in the spatial distribution of gravity centers of cells. Furthermore, morphological features like size of the projection area and mean staining intensity are visualized as a particle process. The particle process presents the sizes and staining intensity of perikaryons and allows a distinction of gray matter and white matter. These results provide evidence that the system works correctly and can be applied to a systematic analysis of a larger sequence of serial histologic sections. The objective of this study is to introduce the very large section analyzing microscope (VLSAM) and to present the initial data produced by the system. Moreover, we will discuss workload and future developments of the parallel image analysis system that are associated with the microscope.

Aged↗
PubMed2006

Encoding and reconstruction in parallel MRI.

The advent of parallel MRI over recent years has prompted a variety of concepts and techniques for performing parallel imaging. A main distinguishing feature among these is the specific way of posing and solving the problem of image reconstruction from undersampled multiple-coil data. The clearest distinction in this respect is that between k-space and image-domain methods. The present paper reviews the basic reconstruction approaches, aiming to emphasize common principles along with actual differences. To this end the treatment starts with an elaboration of the encoding mechanisms and sampling strategies that define the reconstruction task. Based on these considerations a formal framework is developed that permits the various methods to be viewed as different solutions of one common problem. Besides the distinction between k-space and image-domain approaches, special attention is given to the implications of general vs lattice sampling patterns. The paper closes with remarks concerning noise propagation and control in parallel imaging and an outlook upon key issues to be addressed in the future.

Algorithms↗
PubMed1989

A low-cost single-board solution for real-time, unsupervised waveform classification of multineuron recordings.

We describe a low-cost single-board system for unsupervised, real-time spike sorting of recordings from a number of neurons on a single microelectrode. The maximum number of spike classes depends on the quality of the recording; it will typically be between 2 and 5. The spike sorter communicates with a conventional microcomputer through a standard serial port (RS232). For typical firing rates as measured in the mammalian central nervous system, this set-up will accommodate up to some 10 parallel spike sorters for as many separate microelectrodes.

Algorithms↗
PubMed2004

Magnetoencephalographic gamma-band responses to illusory triangles in humans.

Electroencephalography studies have suggested that the perception of illusory figures is associated with increases in gamma-band activity putatively reflecting the formation of synchronously firing neuronal assemblies. Here we assessed magnetoencephalographic gamma-band activity, which has been shown to be topographically more focal than in electroencephalogram. In line with functional brain imaging findings, we hypothesized gamma-band activity over ventral visual stream areas. In addition, we expected that the analysis of oscillatory activity would provide information on the time courses and connectivity patterns of these activations. Following a paradigm previously assessed with electroencephalography, 16 adults were presented four types of stimuli at equal probabilities: illusory (Kanizsa) triangles, real triangles, no-triangle stimuli with rotated inducer disks, and curved illusory triangles serving as targets that subjects had to respond to. Induced oscillatory responses were compared between illusory triangles and no-triangle stimuli and between illusory and real triangles using a statistical probability mapping method. Illusory triangles were distinguished from no-triangles by increased activity at around 70 Hz over midline occipital cortex peaking at 240 ms after stimulus onset. This was followed by activations over bilateral lateral occipital areas at 430 ms. Illusory triangles differed from real triangles by increased spectral activity at 90 Hz over posterior parietal cortex between 100 and 450 ms after stimulus onset, suggesting an involvement of visual dorsal stream regions. Coherence analysis showed increased connectivity between posterior parietal and lateral occipital cortex. These findings suggest that illusory triangles are encoded in parallel by networks along the visual ventral and dorsal streams.

Adult↗
PubMed2003

Exploratory data analysis using set operations and ordinal mapping.

Exploratory data analysis requires the ability to issue ad hoc queries to filter and summarise data sets. As the sizes of health data sets grow, traditional methods of processing data have difficulty in providing acceptable response times for such queries. An alternative method is described which combines complete vertical partitioning of data with set operations on ordinal mappings (SOOM). An initial implementation of the technique provides significantly better performance than a conventional SQL database on typical exploratory data analysis queries. The use of parallel, distributed computation to further increase the performance of the technique appears to be feasible.

Algorithms↗
PubMed2001

A model of oxidative phosphorylation in mammalian skeletal muscle.

A dynamic computer model of oxidative phosphorylation in oxidative mammalian skeletal muscle was developed. The previously published model of oxidative phosphorylation in isolated skeletal muscle mitochondria was extended by incorporation of the creatine kinase system (creatine kinase plus phosphocreatine/creatine pair), cytosolic proton production/consumption system (proton production/consumption by the creatine kinase-catalysed reaction, efflux/influx of protons), physiological size of the adenine nucleotide pool and some additional minor changes. Theoretical studies performed by means of the extended model demonstrated that the CK system, which allows for large changes in P(i) in relation to isolated mitochondria system, has no significant influence on the kinetic properties of oxidative phosphorylation, as inorganic phosphate only slightly modifies the relationship between the respiration rate and [ADP]. Computer simulations also suggested that the second-order dependence of oxidative phosphorylation on [ADP] proposed in the literature refers only to the ATP synthesis flux, but not to the oxygen consumption flux (the difference between these two fluxes being due to the proton leak). Next, time courses of changes in fluxes and metabolite concentrations during transition between different steady-states were simulated. The model suggests, in accordance with previous theoretical predictions, that activation of oxidative phosphorylation by an increase in [ADP] can (roughly) explain the behaviour of the system only at low work intensities, while at higher work intensities parallel activation of different steps of oxidative phosphorylation is involved.

Adenosine Diphosphate↗
PubMed2002

Parallel computing in microwave heating analysis.

The use of parallel computing in the finite element analysis of microwave heating applicators is discussed. Numerical results for a multiple feed cavity at 896 MHz and a cavity with a mode stirrer at 2.45 GHz are presented, and it is shown that for the two structures parallelism is most effectively introduced at different levels in the analysis.

Algorithms↗
PubMed2003

Dynamics of deterministic and stochastic paired excitatory-inhibitory delayed feedback.

We examine the effects of paired delayed excitatory and inhibitory feedback on a single integrate-and-fire neuron with reversal potentials embedded within a feedback network. These effects are studied using bifurcation theory and numerical analysis. The feedback occurs through modulation of the excitatory and inhibitory conductances by the previous firing history of the neuron; as a consequence, the feedback also modifies the membrane time constant. Such paired feedback is ubiquitous in the nervous system. We assume that the feedback dynamics are slower than the membrane time constant, which leads to a rate model formulation. Our article provides an extensive analysis of the possible dynamical behaviors of such simple yet realistic neural loops as a function of the balance between positive and negative feedback, with and without noise, and offers insight into the potential behaviors such loops can exhibit in response to time-varying external inputs. With excitatory feedback, the system can be quiescent, can be periodically firing, or can exhibit bistability between these two states. With inhibitory feedback, quiescence, oscillatory firing rates, and bistability between constant and oscillatory firing-rate solutions are possible. The general case of paired feedback exhibits a blend of the behaviors seen in the extreme cases and can produce chaotic firing. We further derive a condition for a dynamically balanced paired feedback in which there is neither bistability nor oscillations. We also show how a biophysically plausible smoothing of the firing function by noise can modify the existence and stability of fixed points and oscillations of the system. We take advantage in our mathematical analysis of the existence of an invariant manifold, which reduces the dimensionality of the dynamics, and prove the stability of this manifold. The novel computational challenges involved in analyzing such dynamics with and without noise are also described. Our results demonstrate that a paired delayed feedback loop can act as a sophisticated computational unit, capable of switching between a variety of behaviors depending on the input current, the relative strengths and asymmetry of the two parallel feedback pathways, and the delay distributions and noise level.

Action Potentials↗