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Critical conceptualism in environmental modeling and prediction.

Many important problems in environmental science and engineering are of a conceptual nature. Research and development, however, often becomes so preoccupied with technical issues, which are themselves fascinating, that it neglects essential methodological elements of conceptual reasoning and theoretical inquiry. This work suggests that valuable insight into environmental modeling can be gained by means of critical conceptualism which focuses on the software of human reason and, in practical terms, leads to a powerful methodological framework of space-time modeling and prediction. A knowledge synthesis system develops the rational means for the epistemic integration of various physical knowledge bases relevant to the natural system of interest in order to obtain a realistic representation of the system, provide a rigorous assessment of the uncertainty sources, generate meaningful predictions of environmental processes in space-time, and produce science-based decisions. No restriction is imposed on the shape of the distribution model or the form of the predictor (non-Gaussian distributions, multiple-point statistics, and nonlinear models are automatically incorporated). The scientific reasoning structure underlying knowledge synthesis involves teleologic criteria and stochastic logic principles which have important advantages over the reasoning method of conventional space-time techniques. Insight is gained in terms of real world applications, including the following: the study of global ozone patterns in the atmosphere using data sets generated by instruments on board the Nimbus 7 satellite and secondary information in terms of total ozone-tropopause pressure models; the mapping of arsenic concentrations in the Bangladesh drinking water by assimilating hard and soft data from an extensive network of monitoring wells; and the dynamic imaging of probability distributions of pollutants across the Kalamazoo river.

Air Pollutants↗

Transport with multiple-rate exchange in disordered media.

We investigate transport of particles subject to exchange using the continuous-time random-walk framework. Transition is controlled by macroscale, and exchange by both macroscale and microscale disorder. A wide class of exchange mechanisms is represented using the multiple-rate exchange model. Particles are transported along random trajectories viewed as one-dimensional lattices. The solution of the transport problem is obtained in the form of the crossing-time density, h(t;L), at an exit surface L; h is dependent on two functions, g and f. g characterizes exchange controlled by microscale disorder. The joint density f is central for the solution as it relates the microscale and macroscale disorder along random trajectories. For the case of transition and exchange disorder, we show that power-law exponent eta (characterizing microscale disorder) and power-law exponents alpha(tau) and alpha(mu) (characterizing macroscale disorder), define two regions delimited by a line alpha(tau)=alpha(mu)(eta+1): One in which the asymptotic transport is dominated by transition, and one in which it is dominated by the exchange. For the case of transition disorder with uniform exchange, both transition and exchange can influence the late-time behavior of h(t). Microscale exchange processes will unconditionally influence the late-time behavior of h(t) only if eta<0. If eta>0, exchange will dominate at late time provided that transition is asymptotically Gaussian.

Journal Article↗

Membrane elasticity in giant vesicles with fluid phase coexistence.

Biological membranes are known to contain compositional heterogeneities, often termed rafts, with distinguishable composition and function, and these heterogeneities participate in vigorous transport processes. Membrane lipid phase coexistence is expected to modulate these processes through the differing mechanical properties of the bulk domains and line tension at phase boundaries. In this contribution, we compare the predictions from a shape theory derived for vesicles with fluid phase coexistence to the geometry of giant unilamellar vesicles with coexisting liquid-disordered (L(d)) and liquid-ordered (L(o)) phases. We find a bending modulus for the L(o) phase higher than that of the L(d) phase and a saddle-splay (Gauss) modulus difference with the Gauss modulus of the L(o) phase being more negative than the L(d) phase. The Gauss modulus critically influences membrane processes that change topology, such as vesicle fission or fusion, and could therefore be of significant biological relevance in heterogeneous membranes. Our observations of experimental vesicle geometries being modulated by Gaussian curvature moduli differences confirm the prediction by the theory of Juelicher and Lipowsky.

Biomechanical Phenomena↗

The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns.

We describe here a computer system for the analysis of high-resolution two-dimensional gel-electrophoresis patterns, with some initial applications. The system (called TYCHO) comprises programs for image acquisition, background subtraction and smoothing, spot detection, gaussian spot modeling, and pattern matching and comparison. It is based on a conventional minicomputer, but makes extensive use of a high-speed array processor in the image-processing and -modeling steps. Used in concert with the ISO-DALT two-dimensional electrophoresis system (Anal. Biochem. 85:331-354, 1978), TYCHO allows quantitative measurement of hundreds of proteins in complex biological samples, and constitutes the initial data-reduction system required for work towards a Human Protein Index.

Blood Proteins↗

Drift-controlled anomalous diffusion: a solvable Gaussian model

We introduce a Langevin equation characterized by a time-dependent drift. By assuming a temporal power-law dependence of the drift, we show that a great variety of behavior is observed in the dynamics of the variance of the process. In particular, diffusive, subdiffusive, superdiffusive, and stretched exponentially diffusive processes are described by this model for specific values of the two control parameters. The model is also investigated in the presence of an external harmonic potential. We prove that the relaxation to the stationary solution has a power-law behavior in time with an exponent controlled by one of the model parameters.

Journal Article↗

Bhattacharyya distance as a contrast parameter for statistical processing of noisy optical images.

In many imaging applications, the measured optical images are perturbed by strong fluctuations or boise. This can be the case, for example, for coherent-active or low-flux imagery. In such cases, the noise is not Gaussian additive and the definition of a contrast parameter between two regions in the image is not always a straightforward task. We show that for noncorrelated noise, the Bhattacharyya distance can be an efficient candidate for contrast definition when one uses statistical algorithms for detection, location, or segmentation. We demonstrate with numerical simulations that different images with the same Bhattacharyya distance lead to equivalent values of the performance criterion for a large number of probability laws. The Bhattacharyya distance can thus be used to compare different noisy situations and to simplify the analysis and the specification of optical imaging systems.

Journal Article↗

Structure analysis of fibrinogen by electron microscopy and image processing.

Human fibrinogen was observed by electron microscopy following rotary shadowing with tungsten. Structure analysis of the molecules was performed by image processing of electron micrographs. A method is described for selection, alignment, and classification of molecules. The widely accepted overall trinodular structure of the protein was observed. The flexibility about the central domain of the molecule was quantitatively analyzed. A Gaussian distribution of this conformational parameter was obtained having an average corresponding to a maximally extended structure. Correspondence analysis applied to the aligned images showed that the degree of folding of the molecule was continuously distributed. The averaged structure of fibrinogen was estimated to be 450 A long. The central domain had a diameter of 50 A and the peripheral domains were 90 A long and 50 A wide. The latter regions had two separated maxima of scattering density.

Fibrinogen↗

Sex differences in face gender recognition in humans.

Human faces are ecologically-salient stimuli. Face sex is particularly relevant for human interactions and face gender recognition is an extremely efficient cognitive process that is acquired early during childhood. To measure the minimum information required for correct gender classification, we have used a pixelation filter and reduced frontal pictures (28,672 pixels) of male and female faces to 7168, 1792, 448 and 112 pixels. We then addressed the following questions: Is gender recognition of male and female faces equally efficient? Are male and female subjects equally efficient at recognising face gender? We found a striking difference in categorisation of male and female faces. Categorisation of female faces reduced to 1792 pixels is at chance level whereas categorisation of male faces is above chance even for 112 pixel images. In addition, the same difference in the efficiency of categorisation of male and female faces was detected using a Gaussian noise filter. A clear sex difference in the efficiency of face gender categorisation was detected as well. Female subject were more efficient in recognising female faces. These results indicate that recognition of male and female faces are different cognitive processes and that in general females are more efficient in this cognitive task.

Adolescent↗

Multi-adaptive filtering technique for surface somatosensory evoked potentials processing.

Somatosensory evoked potential (SEP) testing has been widely applied to diagnosis of various neurological disorders. However, SEP recorded using surface electrodes is buried in noises, which makes the signal-to-noise ratio (SNR) very poor. Conventional averaging method usually requires up to thousands of raw SEP input trials to increase the SNR so that an identifiable waveform can be produced for latency and amplitude measurement. In this study, a multi-adaptive filtering (MAF) technique, emerging from the combination of well-developed adaptive noise canceller and adaptive signal enhancer, is introduced for fast and accurate surface SEP extraction. The MAF technique first processes the raw surface recorded SEP by the Canceller with a reference noise channel of background noise for adaptive subtraction before entering the Enhancer. The MAF was verified by filtering simulated SEP signals in which electroencephalography and Gaussian noise of different SNRs were added. It was found that the MAF could effectively suppress the noise and enhance the SEP components such that the SNR of the SEP is improved. Results showed that MAF with 50 input trials could provide similar performance in SEP detection to those extracted by the conventional averaging method with 1000 trials even at an SNR of -20 dB.

Algorithms↗

A stochastic model of pulmonary platelet production.

Normally, cells reproduce by mitosis. In mammals, a system has evolved that is unique to cell biology. The circulating blood cells called platelets are produced from parent cells called megakaryocytes, but the mechanism of platelet production is not mitosis. At present, both the site and mechanism of production are still debated. This article describes a production mechanism based on a sequence of random binary divisions of the megakaryocyte cytoplasm as it traverses the pulmonary microcirculation. Using the measured megakaryocyte cytoplasmic volumes circulating in the blood of three different mammals, rat, rabbit, and man, a computer simulation of this process is developed. The simulation depends on two separate stochastic processes. The first involves the probability that a division of a cytoplasmic particle of a specified size will occur. The second relates to the relative sizes of the two particles produced by the binary division. These two processes are controlled by three parameters only: a lower threshold L on the platelet volume, below which the probability of a binary division is zero; a parameter lambda which defines the probability of division for volumes larger than this lower threshold; and the standard deviation S of the Gaussian distribution of possible volumes created by the binary division. A minimization scheme is used to establish those values of L, lambda, and S which provide the best fit to the experimental data obtained from the different mammals.

Animals↗

The effect of finite spatial resolution on the measurement of cardiac phantom wall thickness in single photon emission computerized tomographic imaging.

OBJECTIVE: To devise and validate a method of estimating accurately myocardial wall thickness from cardiac images acquired with single photon emission tomography (SPECT). MATERIALS AND METHODS: We simulated the imaging process by convolving a spatial resolution function, experimentally determined for a clinical SPECT system, with rectangular profiles mimicking the myocardial walls for different thicknesses and separations. Wall thicknesses were estimated by fitting the resulting profiles to a linear superposition of two offset Gaussians. The method was validated by extensive computer simulation and by testing on real phantom images. RESULTS: Accurate estimates of the wall thickness of SPECT phantoms were obtained when the estimated thickness (using fitting to Gaussians) was deconvolved with the point spread function (PSF) of the imaging system using a look-up table. CONCLUSIONS: This method is a novel method of estimating wall thickness from cardiac images. It is particularly useful for small separations (e.g. at end systole and/or towards the apex of the heart) of walls that are narrow compared to the PSF of the imaging system.

Computer Simulation↗

Efficient algorithm for computation of the second-order moment of the subpixel-edge position.

Subpixel-edge detection is the first stage in processing many high-level vision algorithms. However, the study of the statistical properties of such data has remained incomplete in most research. We present a method for estimating the second-order moments of the subpixel-edge position, computed by a deterministic algorithm based on three quadratic interpolations. The algorithm is tested on different types of noise (Gaussian, impulse, colored) and compared with two methods in the literature. The results show that this approach remains accurate even at high noise levels.

Algorithms↗

Wavelet packet denoising of magnetic resonance images: importance of Rician noise at low SNR.

Wavelet packet analysis is a mathematical transformation that can be used to post-process images, for example, to remove image noise ("denoising"). At a very low signal-to-noise ratio (SNR <5), standard magnitude magnetic resonance images have skewed Rician noise statistics that degrade denoising performance. Since the quadrature images have approximately Gaussian noise, it was postulated that denoising would produce better contrast and sharper edges if performed before magnitude image formation. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and edge blurring effects of these two approaches were examined in synthetic, phantom, and human MR images. While magnitude and complex denoising both significantly improved SNR and CNR, complex denoising yielded sharper edges and better low-intensity feature contrast.

Artifacts↗

Geometry of phage head construction.

The process of phage capsid assembly is reviewed, with particular attention to the probable role of curvature in helping to determine head size and shape. Both measures of curvature (mean curvature and Gaussian curvature, explained in Appendix I), should act best when the assembling shell is spherical, which could account for procapsids having this shape. Procapsids are also relatively thick, which should help head size determination by the mean curvature. The accessory role of inner and outer scaffolds in size determination and head nucleation is also reviewed. Nucleation failure generates various malformations, including non-closure, but the most common is the tube or polyhead, where the subunits' inherent curvature is expressed as a constant mean curvature. This induces lattice distortions that only partly understood. An extra tubular section in normal heads leads to the prolate shape, with a more complex and variable geometry. Newly assembled procapsids are both enlarged and toughened by the head transformation. In the procapsid the Gaussian curvature is uniformly distributed. But toughening tends to equalize bond lengths, so all the Gaussian curvature gets concentrated in the vertices, being zero elsewhere. This explains head angularization. Because of this change in Gaussian curvature, the regular subunit packing in the polyhedral head cannot be mapped onto the procapsid. This explains part of the hexon distortions found in this region. The implications of translocase-induced DNA twist, end rotation and the coiling of packaged DNA, are discussed. The symmetry mismatches between the head, connector and tail are discussed in relation to the possible alpha-helical structures of their DNA channels.

Bacteriophages↗

Fading time of retinally-stabilized images as a function of background luminance and target width.

Fading time of a retinally-stabilized difference-of-Gaussian (DOG) stimulus depends on the background luminance, contrast and spatial frequency content of the stimulus. A model of the visual system including a nonlinear multiplicative, non-local and fast process followed by a linear subtractive, local and slower process accounts for these effects. Analysis of the fading time data allows us to estimate the spatiotemporal characteristics of the proposed adaptation processes. The model is consistent with recent models of normal light adaptation from the probe-flash paradigm.

Adaptation, Ocular↗

Is the site of non-linear filtering in stereopsis before or after binocular combination?

There is recent evidence that both linear and non-linear filtering operations subserve stereoscopic localization. For example, for spatially band-pass stimuli, the overall Gaussian envelope, which is not explicitly represented by the output of linear filters, can provide coarse disparity information. Here we ask three questions about the nature of this non-linear processing in stereopsis. First, is the site of the non-linearity before or after binocular combination? Second, is the stimulus envelope extracted by orientation or non-orientation selective spatial filters? Finally, we ask whether the envelope-based 3-D localization performance is similar to that for monocular 2-D localization as would be the case if the localization of the monocular contrast envelope was common to both operations. Our results suggest that envelope extraction occurs before binocular combination and that the filters involved are orientation selective. Finally, we provide preliminary evidence that is compatible with the proposal that 3-D and 2-D localization use the same envelope extraction operations.

Contrast Sensitivity↗

Orientation tuning of the transient-stereopsis system.

Stereo-perception appears to be mediated by at least two systems: a transient system that processes stimuli presented briefly and a sustained one that processes stimuli presented for longer durations. In this paper we investigated the tuning of the transient-stereopsis system to stimulus orientation. Narrowband-gabor targets with a constant envelope size (Gaussian standard deviation of 1 degree) were presented for brief (140 ms) durations at large (from 4 to 8 degrees) disparities. The results were as follows: (1) while observers could extract depth from orthogonally-oriented gabors at above chance levels, their performance was worse than that with gabors of matched orientation; (2) varying the relative contrasts of the two orthogonally oriented gabors of the same spatial frequency resulted in a reduction in performance; (3) varying the relative spatial frequencies of the orthogonally-oriented gabors impaired performance, relative to that for matched frequencies; and (4) varying the relative contrasts of orthogonal gabors that were at different spatial frequencies could improve performance. These results indicate that transient stereo-performance in the orthogonal condition was not mediated by the channels that extracted depth in either the horizontal- or vertically-matched gabor conditions. This apparent lack of orientation tuning is indicative of a second-order pathway. That this performance was mediated by a binocular, as opposed to a monocular channel, is supported by the finding that performance decreased as the contrast of one of the gabors was reduced. The finding that performance with orthogonal gabors of unmatched spatial frequency (0.5 and 4 cpd) could be improved by varying their relative contrasts suggests that the binocular spatial-frequency tuning exhibited by this channel is broadband in nature. Finally, the observation that lowering the contrast of either the high or low spatial-frequency gabor improved performance suggests the presence of at least two broadband channels: one with its peak sensitivity at a low and the other at a high spatial-frequency.

Contrast Sensitivity↗

Modified Fuzzy ARTMAP Approaches Bayes Optimal Classification Rates: An Empirical Demonstration.

This paper investigates the effectiveness of the Fuzzy ARTMAP (FAM) neural network in classifying statistical data and compares the results with Bayesian decision theory. Binary classification problems are used to assess the performance of FAM operating autonomously and on-line in statistical settings. The results illustrate the limitations of FAM in this context. Novel modifications are, therefore, proposed for the category formation process and the category selection process of FAM, which allow the modified system to minimize the misclassification rates. A number of simulations with randomly generated data sets have been carried out. First, two continuous-valued Gaussian sources are used with various source (mean) separations, prior probabilities, and variances. Then, multi-dimensional discrete patterns are employed to examine the classification ability of modified FAM in both stationary and non-stationary environments. Simulation results consistently demonstrate that modified FAM is able to approach the Bayes optimal classification rates on-line, and thereby justify the rationale behind the modifications. Copyright 1997 Elsevier Science Ltd.

Journal Article↗