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PubMedDate not supplied

Texturing of layered surfaces for optimal viewing.

This paper is a contribution to the literature on perceptually optimal visualizations of layered three-dimensional surfaces. Specifically, we develop guidelines for generating texture patterns, which, when tiled on two overlapped surfaces, minimize confusion in depth-discrimination and maximize the ability to localize distinct features. We design a parameterized texture space and explore this texture space using a "human in the loop" experimental approach. Subjects are asked to rate their ability to identify Gaussian bumps on both upper and lower surfaces of noisy terrain fields. Their ratings direct a genetic algorithm, which selectively searches the texture parameter space to find fruitful areas. Data collected from these experiments are analyzed to determine what combinations of parameters work well and to develop texture generation guidelines. Data analysis methods include ANOVA, linear discriminant analysis, decision trees, and parallel coordinates. To confirm the guidelines, we conduct a post-analysis experiment, where subjects rate textures following our guidelines against textures violating the guidelines. Across all subjects, textures following the guidelines consistently produce high rated textures on an absolute scale, and are rated higher than those that did not follow the guidelines.

Journal Article↗
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↗
PubMed2006

Base deficit estimation in umbilical cord blood is influenced by gestational age, choice of fetal fluid compartment, and algorithm for calculation.

OBJECTIVE: The purpose of this study was to explore the influences of gestational age, the choice of fetal fluid compartment, and the algorithm for calculation on the estimation of the base deficit in umbilical cord arterial blood at birth. STUDY DESIGN: From 1995 to 2002, cord arterial blood gases and obstetric data were available for 43,551 newborn infants at 37+ weeks of gestation (cohort I). The mean base deficit in blood and the base deficit in extracellular fluid were estimated from pH and PCO2 values in 28,213 newborn infants with a 5-minute Apgar score of > or = 9 (cohort II) with the use of 3 different calculation algorithms (base deficit in blood, base deficit in extracellular fluid [A], and base deficit in extracellular fluid [B]). RESULTS: In cohort II, the base deficit in blood, the base deficit in extracellular fluid (A), and the base deficit in extracellular fluid (B) increased with advancing gestational age (linear regression; P < .0001). The curves run almost parallel, with the base deficit in blood being higher than the base deficit in extracellular fluid (A) and (B). With the use of receiver operating characteristic curves in cohort I, the area under curve to indicate a 5-minute Apgar score of < 7 and < 4 showed the area under curve-pH to be greater than the area under curve-base deficit in extracellular fluid (A) and (B), the area under curve-base deficit in blood to be greater than the area under curve-base deficit in extracellular fluid (A) and (B) for a 5-minute Apgar score of < 7, and the area under curve-base deficit in blood to be greater than the area under curve-base deficit in extracellular fluid (A) and (B) for an Apgar score of < 4. The cutoffs with highest sensitivity and lowest false-positive rate for a 5-minute Apgar score of < 7 and < 4 were, for both scores, a pH value of 7.15, a base deficit in blood of 10 mmol/L, a base deficit in extracellular fluid (A) of 8 mmol/L, and a base deficit in extracellular fluid (B) of 6 mmol/L. CONCLUSION: The calculated values of the base deficit in umbilical cord arterial blood are influenced decisively by gestational age, the choice of fetal fluid compartment, and the calculation algorithms that are used. The power of the base deficit to indicate neonatal distress depends on the choices of fluid compartment and the algorithm that is used to calculate the base deficit.

Acidosis↗
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↗
PubMed2004

Patient specific dynamic geometric models from sequential volumetric time series image data.

Generating patient specific dynamic models is complicated by the complexity of the motion intrinsic and extrinsic to the anatomic structures being modeled. Using a physics-based sequentially deforming algorithm, an anatomically accurate dynamic four-dimensional model can be created from a sequence of 3-D volumetric time series data sets. While such algorithms may accurately track the cyclic non-linear motion of the heart, they generally fail to accurately track extrinsic structural and non-cyclic motion. To accurately model these motions, we have modified a physics-based deformation algorithm to use a meta-surface defining the temporal and spatial maxima of the anatomic structure as the base reference surface. A mass-spring physics-based deformable model, which can expand or shrink with the local intrinsic motion, is applied to the metasurface, deforming this base reference surface to the volumetric data at each time point. As the meta-surface encompasses the temporal maxima of the structure, any extrinsic motion is inherently encoded into the base reference surface and allows the computation of the time point surfaces to be performed in parallel. The resultant 4-D model can be interactively transformed and viewed from different angles, showing the spatial and temporal motion of the anatomic structure. Using texture maps and per-vertex coloring, additional data such as physiological and/or biomechanical variables (e.g., mapping electrical activation sequences onto contracting myocardial surfaces) can be associated with the dynamic model, producing a 5-D model. For acquisition systems that may capture only limited time series data (e.g., only images at end-diastole/end-systole or inhalation/exhalation), this algorithm can provide useful interpolated surfaces between the time points. Such models help minimize the number of time points required to usefully depict the motion of anatomic structures for quantitative assessment of regional dynamics.

Algorithms↗
PubMedDate not supplied

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↗
PubMed2002

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↗
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↗
PubMed2006

System characteristics of SPECT with a slat collimated strip detector.

In classical SPECT with parallel hole collimation, the sensitivity is constant over the field of view (FOV). This is no longer the case if a rotating slat collimator with planar photon collection is used: there will be a significant variation of the sensitivity within the FOV. Since not compensating for this inhomogeneous sensitivity distribution would result in non-quantitative images, an accurate knowledge of the sensitivity is mandatory to account for it during reconstruction. On the other hand, the spatial resolution versus distance dependency remains unaltered compared to parallel hole collimation. For deriving the sensitivity, different factors have to be taken into account: a first factor concerns the intrinsic detector properties and will be incorporated into the calculations as a detection efficiency term depending on the incident angle. The calculations are based on a second and more pronounced factor: the collimator and detector geometry. Several assumptions will be made for the calculation of the sensitivity formulae and it will be proven that these calculations deliver a valid prediction of the sensitivity at points far enough from the collimator. To derive a close field model which also accounts for points close to the collimator surface, a modified calculation method is used. After calculating the sensitivity in one plane it is easy to obtain the tomographic sensitivity. This is done by rotating the sensitivity maps for spin and camera rotation. The results derived from the calculations are then compared to simulation results and both show good agreement after including the aforementioned detection efficiency term. The validity of the calculations is also proven by measuring the sensitivity in the FOV of a prototype rotating slat gamma camera. An expression for the resolution of these planar collimation systems is obtained. It is shown that for equal collimator dimensions the same resolution-distance relationship is obtained as for parallel hole collimators. Although, a better spatial resolution can be obtained with our prototype camera due to the smaller pitch of the slats. This can be achieved without a major drop in system sensitivity due to the fact that the slats consist of less collimator material compared to a parallel hole collimator. The accuracy of the calculated resolution is proven by comparison with Monte Carlo simulation and measurement resolution values.

Algorithms↗
PubMed2006

Methods for the accurate estimation of confidence intervals on protein folding phi-values.

Phi-values provide an important benchmark for the comparison of experimental protein folding studies to computer simulations and theories of the folding process. Despite the growing importance of phi measurements, however, formulas to quantify the precision with which phi is measured have seen little significant discussion. Moreover, a commonly employed method for the determination of standard errors on phi estimates assumes that estimates of the changes in free energy of the transition and folded states are independent. Here we demonstrate that this assumption is usually incorrect and that this typically leads to the underestimation of phi precision. We derive an analytical expression for the precision of phi estimates (assuming linear chevron behavior) that explicitly takes this dependence into account. We also describe an alternative method that implicitly corrects for the effect. By simulating experimental chevron data, we show that both methods accurately estimate phi confidence intervals. We also explore the effects of the commonly employed techniques of calculating phi from kinetics estimated at non-zero denaturant concentrations and via the assumption of parallel chevron arms. We find that these approaches can produce significantly different estimates for phi (again, even for truly linear chevron behavior), indicating that they are not equivalent, interchangeable measures of transition state structure. Lastly, we describe a Web-based implementation of the above algorithms for general use by the protein folding community.

Algorithms↗
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↗
PubMed2001

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↗
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↗
PubMed2003

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↗
PubMed2005

Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis.

MOTIVATION: Robust computer algorithms are required to interpret the vast amounts of proteomic data currently being produced and to generate generalized models which are applicable to 'real world' scenarios. One such scenario is the classification of bacterial species. These vary immensely, some remaining remarkably stable whereas others are extremely labile showing rapid mutation and change. Such variation makes clinical diagnosis difficult and pathogens may be easily misidentified. RESULTS: We applied artificial neural networks (Neuroshell 2) in parallel with cluster analysis and principal components analysis to surface enhanced laser desorption/ionization (SELDI)-TOF mass spectrometry data with the aim of accurately identifying the bacterium Neisseria meningitidis from species within this genus and other closely related taxa. A subset of ions were identified that allowed for the consistent identification of species, classifying >97% of a separate validation subset of samples into their respective groups. AVAILABILITY: Neuroshell 2 is commercially available from Ward Systems.

Algorithms↗
PubMed2005

Biological master games: using biologists' reasoning to guide algorithm development for integrated functional genomics.

We review some powerful new algorithms that build on the intuitive biological interpretation techniques for statistical analysis of functional genomics experiments. Although they were originally designed for transcriptomics, we argue that these algorithms are applicable to any type of -omics study (transcriptomics, proteomics, metabolomics). Rank Products (RP), a strictly non-parametric test statistic to detect differentially regulated elements (genes, proteins, metabolites) in genome-wide screens. RP is particularly powerful for noisy data and low numbers of replicates and makes full use of the availability of a large number of parallel measurements that is typical of modern large-scale experiments. Iterative Group Analysis (iGA), a statistical method that makes the transition from regulated single elements to significant classes of elements, and thus provides an automatic functional annotation of an experiment. Graph-based iGA (GiGA), an extension of iGA that combines experimental data with a broad variety of biological annotations to highlight physiologically relevant regions in a given "evidence graph" (e.g., metabolic networks, signaling pathway diagrams, protein interaction maps). The sequential application of these techniques yields an increasingly abstract interpretation of experimental data that is at the same time quantitative, statistically rigorous, and biologically significant. The results can be used either as helpful tools to guide data visualization and exploration, or as the input for downstream computational applications in a systems biology framework.

Algorithms↗