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PubMed2002

Two-dimensional viscous flow between slowly expanding or contracting walls with weak permeability.

Since the transport of biological fluids through contracting or expanding vessels is characterized by low seepage Reynolds numbers, the current study focuses on the viscous flow driven by small wall contractions and expansions of two weakly permeable walls. The scope is limited to two-dimensional symmetrical solutions inside a simulated channel with moving porous walls. In seeking an exact solution, similarity transformations are used in both space and time. The problem is first reduced to a nonlinear differential equation that is later solved both numerically and analytically. The analytical procedure is based on double perturbations in the permeation Reynolds number R and the wall expansion ratio alpha. Results are correlated and compared via variations in R and alpha. Under the auspices of small [R] and [alpha], the analytical result constitutes a practical equivalent to the numerical solution. We find that, when suction is coupled with wall contraction, rapid flow turning is precipitated near the wall where the boundary layer is formed. Conversely, when injection is paired with wall expansion, the flow adjacent to the wall is delayed. In this case, the viscous boundary layer thickens as injection or expansion rates are reduced. Furthermore, the pressure drop along the plane of symmetry increases when the rate of contraction is increased and when either the rate of expansion or permeation is reduced. As nonlinearity is retained, our solutions are valid from a large cross-section down to the state of a completely collapsed system.

Computer Simulation↗

PubMed2005

Maximal use of minimal libraries through the adaptive substituent reordering algorithm.

This paper describes an adaptive algorithm for interpolation over a library of molecules subjected to synthesis and property assaying. Starting with a coarse sampling of the library compounds, the algorithm finds the optimal substituent orderings on all of the functionalized scaffold sites to allow for accurate property interpolation over all remaining compounds in the full library space. A previous paper introduced the concept of substituent reordering and a smoothness-based criterion to search for optimal orderings (Shenvi, N.; Geremia, J. M.; Rabitz, H. J. Phys. Chem. A 2003, 107, 2066). Here, we propose a data-driven root-mean-squared (RMS) criteria and a combined RMS/smoothness criteria as alternative methods for the discovery of optimal substituent orderings. Error propagation from the property measurements of the sampled compounds is determined to provide confidence intervals on the interpolated molecular property values, and a substituent rescaling technique is introduced to manage poorly designed/sampled libraries. Finally, various factors are explored that can influence the applicability and interpolation quality of the algorithm. An adaptive methodology is proposed to iteratively and efficiently use laboratory experiments to optimize these algorithmic factors, so that the accuracy of property predictions is maximized. The enhanced algorithm is tested on copolymer and transition metal complex libraries, and the results demonstrate the capability of the algorithm to accurately interpolate various properties of both molecular libraries.

Algorithms↗

PubMed2002

Mg2+ transport in the kidney.

Magnesium is abundant in biological systems and an important divalent cation in the human body. Mg2+ helps mediate cellular energy metabolism, ribosomal and membrane integrity. Additionally Mg2+ modulates the activity of several membrane transport and signal transduction systems. Despite its importance however, little is known about the molecular mechanisms of Mg2+ transport and homeostasis in mammals. In mammals the amount of Mg2+ absorption is about the same as the amount of Mg2+ excretion in urine. Additionally, when total Mg2+ intake is deficient, the kidney is capable of reabsorbing all filtered Mg2+. This balance between intake and excretion indicates that the kidney plays a principal role in maintenance of total body Mg2+ homeostasis. Within the kidney, Mg2+ filtered by the glomerulus is handled in different ways along the nephron. About 10-20% of Mg2+ is reabsorbed by the proximal tubule. the bulk of Mg2+ (about 50-70%) is reabsorbed by the cortical thick ascending limb of the loop of Henle. In this region, Mg2+ moves across the epithelium through the paracellular pathway, driven by the positive lumenal transepithelial voltage. A recently cloned human gene, paracellin-1 was shown to encode a protein localized to the tight junctions of the cortical thick ascending limb and is thought to mediate Mg2+ transport via the paracellular space of this epithelium. The distal convoluted tubule reabsorbs the remaining 5-10% of filtered Mg2+. This segment seems to play an important role in determining final urinary excretion, since there is no evidence for significant Mg2+ absorption beyond the distal tubule. Although many renal Mg2+ transport activities have been characterized, no Mg2+ transporter cDNAs have been cloned from mammalian tissues. Recent research has certainly expanded our knowledge of Mg2+ transport in kidney; but details of the transport processes and the mechanisms by which they control Mg2+ excretion must await cloning of renal Mg2+ transporters and/or channels. Such information would provide new concepts in our understanding of renal Mg2+ handling.

Animals↗

PubMed2006

Discrete and analogue quantity processing in the parietal lobe: a functional MRI study.

The human intraparietal sulcus (IPS) is implicated in processing symbolic number information and possibly in nonsymbolic number information. Specific IPS activity for discrete quantities (numerosities) as compared with continuous, analogue quantity has not been demonstrated. Here we use a stimulus-driven paradigm to distinguish automatic estimation of "how many things" from "how much" and "how long." The discrete analogue response task (DART) uses the perception of hues which can change either abruptly (discrete, numerous stimuli) or smoothly (analogue, nonnumerous stimuli) in space or in time. Subjects decide whether they saw more green or more blue. A conjunction analysis of spatial and temporal conditions revealed that bilateral IPS was significantly more active during the processing of discrete stimuli than during analogue stimuli, as was a parietal-occipital transition zone. We suggest that processing numerosity is a distinct process from processing analogue quantity, whether extended in space or time, and that an intraparietal network connects objects' segmentation to the estimation of their numerosity.

Adolescent↗

PubMed2003

Generating neural circuits that implement probabilistic reasoning.

We extend the hypothesis that neuronal populations represent and process analog variables in terms of probability density functions (PDFs). Aided by an intermediate representation of the probability density based on orthogonal functions spanning an underlying low-dimensional function space, it is shown how neural circuits may be generated from Bayesian belief networks. The ideas and the formalism of this PDF approach are illustrated and tested with several elementary examples, and in particular through a problem in which model-driven top-down information flow influences the processing of bottom-up sensory input.

Action Potentials↗

PubMed2005

Pattern formation in parametric sound generation.

Pattern formation of sound is predicted in a driven resonator where subharmonic generation takes place. A model allowing for diffraction of the fields (large-aspect-ratio limit) is derived by means of the multiple-scale expansion technique. An analysis of the solutions and its stability against space-dependent perturbations is performed in detail considering the distinctive peculiarities of the acoustical system. Numerical integration confirms the analytical predictions and shows the possibility of patterns in the form of stripes and squares.

Journal Article↗

PubMed2001

Strong "quantum" chaos in the global ballooning mode spectrum of three-dimensional plasmas.

The spectrum of ideal magnetohydrodynamic (MHD) pressure-driven (ballooning) modes in strongly nonaxisymmetric toroidal systems is difficult to analyze numerically owing to the singular nature of ideal MHD caused by lack of an inherent scale length. In this paper, ideal MHD is regularized by using a k-space cutoff, making the ray tracing for the WKB ballooning formalism a chaotic Hamiltonian billiard problem. The minimum width of the toroidal Fourier spectrum needed for resolving toroidally localized ballooning modes with a global eigenvalue code is estimated from the Weyl formula. This phase-space-volume estimation method is applied to two stellarator cases.

Journal Article↗

PubMed2003

Foveal versus full-field visual stabilization strategies for translational and rotational head movements.

Because we view the world from a constantly shifting platform when our head and body move in space, vestibular and visuomotor reflexes are critical to maintain visual acuity. In contrast to the phylogenetically old rotational vestibulo-ocular reflex (RVOR), it has been proposed that the translational vestibulo-ocular reflex (TVOR) represents a newly developed vestibular-driven mechanism that is important for foveal vision and stereopsis. To investigate the hypothesis that the function of the TVOR is indeed related to foveal (as opposed to full-field) image stabilization, we compared the three-dimensional ocular kinematics during lateral translation and rotational movements with those during pursuit of a small moving target in four rhesus monkeys. Specifically, we tested whether TVOR rotation axes tilt with eye position as in visually driven systems such as pursuit, or whether they stay relatively fixed in the head as in the RVOR. We found a significant dependence of three-dimensional eye velocity on eye position that was independent of viewing distance and viewing conditions (full-field, single target, or complete darkness). The slopes for this eye-position dependence averaged 0.7 +/- 0.07 for the TVOR, compared with 0.6 +/- 0.07 for visually guided pursuit eye movements and 0.18 +/- 0.09 for the RVOR. Because the torsional tilt versus vertical gaze slopes during translation were slightly higher than those during pursuit, three-dimensional eye movements during translation could partly reflect a compromise between the two different solutions for foveal gaze control, that of Listing's law and minimum velocity strategies. These results with respect to three-dimensional kinematics provide additional support for a functional difference in the two vestibular-driven mechanisms for visual stability during rotations and translations and establish clearly the functional goal of the TVOR as that for foveal visual acuity.

Animals↗

PubMed1988

Sodium-gradient-driven, high-affinity, uphill transport of succinate in human placental brush-border membrane vesicles.

Brush-border membrane vesicles isolated from normal human term placentas were shown to accumulate succinate transiently against a concentration gradient, when an inward-directed Na+ gradient was imposed across the membrane. This uptake was almost totally due to transport into intravesicular space, non-specific binding to the membranes being negligible. The dependence of the initial uptake rate of succinate on Na+ concentration exhibited sigmoidal kinetics, indicating interaction of more than one Na+ ion with the carrier system. The Hill coefficient for this ion was calculated to be 2.7. The Na+-dependent uptake of succinate was electrogenic, resulting in the transfer of positive charge across the membrane. Kinetic analysis showed that succinate uptake in these vesicles occurred via a single transport system, with an apparent affinity constant of 4.8 +/- 0.2 microM and a maximal velocity of 274 +/- 4 pmol/20 s per mg of protein. Uptake of succinate was strongly inhibited by various C4 or C5 dicarboxylic acids, whereas monocarboxylic acids, amino acids and glucose showed little or no effect. Li+ and K+ could not substitute for Na+ in the uptake process. Instead, Li+ was found to have a significant inhibitory effect on the Na+-dependent uptake of succinate.

Biological Transport, Active↗

PubMed1992

Multielement visual tracking: attention and perceptual organization.

Two types of theories have been advanced to account for how attention is allocated in performing goal-directed visual tasks. According to location-based theories, visual attention is allocated to spatial locations in the image; according to object-based theories, attention is allocated to perceptual objects. Evidence for the latter view comes from experiments demonstrating the importance of perceptual grouping in selective-attention tasks. This article provides further evidence concerning the importance of perceptual organization in attending to objects. In seven experiments, observers tracked multiple randomly moving visual elements under a variety of conditions. Ten elements moved continuously about the display for several seconds; one to five of them were designated as targets before movement initiation. At the end of movement, one element was highlighted, and subjects indicated whether or not it was a target. The ease with which the elements in the target set could be perceptually grouped was systematically manipulated. In Experiments 1-3, factors that influenced the initial formation of a perceptual group were manipulated; this affected performance, but only early in practice. In Experiments 4-7, factors that influenced the maintenance of a perceptual group during motion were manipulated; this affected performance throughout practice. The results suggest that observers spontaneously grouped the target elements and directed attention toward this coherent but nonrigid virtual object. This supports object-based theories of attention and demonstrates that perceptual grouping, which is usually conceived of as a purely stimulus-driven process, can also be governed by goal-directed mechanisms.

Adult↗

PubMed2003

When does the Titchener Circles illusion exert an effect on grasping?. Two- and three-dimensional targets.

This study used the Titchener Circles illusion to investigate the functional dissociation of the dorsal visuomotor and ventral perceptual systems. In order to investigate the visual requirements for an action to be driven by the dorsal stream, two-dimensional (2D) and three-dimensional (3D) targets were compared. Thirteen subjects made visual open loop manual estimations or grasping actions towards 2D and 3D versions of the illusion. No illusion effect was found for immediate grasping, but the illusion did influence manual estimation, irrespective of whether the target was 2D or 3D. It is suggested that the underlying representations used to drive grasping actions towards 2D targets are fundamentally the same as those used to drive natural grasping actions. While stereoscopically specified depth may be important to the dorsal visuomotor system, it does not appear to be necessary in order for an action to be based on dorsal representations. It is suggested that an action must be goal directed in order for that action to be driven by dorsal stream processes.

Adolescent↗

PubMed2003

The invasion and coexistence of competing Wolbachia strains.

Cytoplasmic incompatibility between arthropods infected with different strains of Wolbachia has been proposed as an important mechanism for speciation. However, a basic requirement for this mechanism is the coexistence of different strains in neighbouring populations. Here we test whether this required coexistence is possible in a spatial context. Continuous-time models for the behaviour of one and two strains of Wolbachia within a single well-mixed population demonstrate the Allee effect and founder control, such that one strain is always driven extinct. In contrast, discretised spatial models show patchy persistence of the two strains although coexistence within the same habitat is rare. A simplified model of such founder control suggests that it is fragmentation of (or barriers within) the habitat rather than space itself that leads to persistence.

Models, Biological↗

PubMed1997

Dynamic cell structures for the evaluation of keypoints in facial images.

In this contribution Dynamic Cell Structures (DCS network) are applied to classify local image structures at particular facial landmarks. The facial landmarks such as the corners of the eyes or intersections of the iris with the eyelid are computed in advance by a combined model and data driven sequential search strategy. To reduce the detection error after the processing of the sequential search strategy, the computed image positions are verified applying a DCS network. The DCS network is trained by supervised learning with feature vectors which encode spatially arranged edge and structural information at the keypoint position considered. The model driven localization as well as the data driven verification are based on steerable filters, which build a representation comparable with one provided by a receptive field in the human visual system. We apply a DCS based classifier because of its ability to grasp the topological structure of complex input spaces and because it has proved successful in a number of other classification tasks. In our experiments the average error resulting from false positive classifications is less than 1%.

Algorithms↗

PubMed2006

Nonparaxial scalar treatment of sinusoidal phase gratings.

Scalar diffraction theory is frequently considered inadequate for predicting diffraction efficiencies for grating applications where lambda/d>0.1. It has also been stated that scalar theory imposes energy upon the evanescent diffracted orders. These notions, as well as several other common misconceptions, are driven more by an unnecessary paraxial approximation in the traditional Fourier treatment of scalar diffraction theory than by the scalar limitation. By scaling the spatial variables by the wavelength, we have previously shown that diffracted radiance is shift invariant in direction cosine space. Thus simple Fourier techniques can now be used to predict a variety of wide-angle (nonparaxial) diffraction grating effects. These include (1) the redistribution of energy from the evanescent orders to the propagating ones, (2) the angular broadening (and apparent shifting) of wide-angle diffracted orders, and (3) nonparaxial diffraction efficiencies predicted with an accuracy usually thought to require rigorous electromagnetic theory.

Journal Article↗

PubMedDate not supplied

Current sheet applicator arrays for superficial hyperthermia of chestwall lesions.

The current sheet applicator is an electromagnetic heating device whose size may be chosen virtually independent of frequency even though practical limitations may restrict it to VHF and UHF bands. In this paper we investigate absorbed power distributions in muscle tissue from current sheet applicators when used as elements of a planar array intended for superficial hyperthermic treatment of tumours. Advantages offered by current sheet applicators for tissue heating include compact size, a linear polarization of the induced electric field and relatively large heating area. It is shown that the effective field produced by a pair of these elements is continuous regardless of whether the common edges of the elements are perpendicular or parallel to the direction of impressed current. The feasibility of customizing the shape and size of the field is also illustrated. The absorbed power distribution patterns due to a coherently driven array operating around 434 MHz is relatively insensitive to phase variations of about 20 degrees but is sensitive to relative power level variations as low as 10%. Mutual coupling between array elements may be reduced to acceptable levels by incorporating suitable spacing between them. It is also demonstrated that there is good agreement between measurements of absorbed power distributions and predictions using the Gaussian beam model.

Biomedical Engineering↗

PubMed2004

Odor-driven attractor dynamics in the antennal lobe allow for simple and rapid olfactory pattern classification.

The antennal lobe plays a central role for odor processing in insects, as demonstrated by electrophysiological and imaging experiments. Here we analyze the detailed temporal evolution of glomerular activity patterns in the antennal lobe of honeybees. We represent these spatiotemporal patterns as trajectories in a multidimensional space, where each dimension accounts for the activity of one glomerulus. Our data show that the trajectories reach odor-specific steady states (attractors) that correspond to stable activity patterns at about 1 second after stimulus onset. As revealed by a detailed mathematical investigation, the trajectories are characterized by different phases: response onset, steady-state plateau, response offset, and periods of spontaneous activity. An analysis based on support-vector machines quantifies the odor specificity of the attractors and the optimal time needed for odor discrimination. The results support the hypothesis of a spatial olfactory code in the antennal lobe and suggest a perceptron-like readout mechanism that is biologically implemented in a downstream network, such as the mushroom body.

Animals↗

PubMed2004

Gibbs adsorption isotherm combined with Monte Carlo sampling to see action of cosolutes on protein folding.

Driven by conditions set by smaller solutes, proteins fold and unfold. Experimentally, these conditions are stated as intensive variables--pH and other chemical potentials--as though small solutes were infinite resources that come at an externally varied free energy cost. Computationally, the finite spaces of simulation allow only fixed numbers of these solutes. By combining the analytic Gibbs adsorption isotherm with the computational Monte Carlo sampling of polymer configurations, we have been able to overcome an inherent limitation of computer simulation. The idea is to compute analytically the free energy changes wrought by solutes on each particular configuration. Then numerical computation is needed only to sample the set of configurations as efficiently as when no bathing solute is present. For illustration, the procedure is applied to an idealized two-dimensional heteropolymer to yield lessons about the effect of cosolutes on protein stability.

Adsorption↗

PubMed1998

Model Analysis of Spatial Patterns in Mountain Pine Beetle Outbreaks.

The mountain pine beetle [MPB, Dendroctonus ponderosae Hopkins (Coleoptera: Scolytidae)] is an aggressive bark beetle, one that typically needs to kill host trees in order to successfully reproduce. This ecological adaptation has resulted in an organism that is both economically important and ecologically significant. Even though significant resources have been expended on MPB research, and a great deal of knowledge exists regarding individual aspects of MPB ecology, some of the most basic questions regarding outbreaks remain unanswered. In our opinion, one reason for the lack of synthesis and predictive power is the inadequate treatment of spatial dynamics in outbreak theories. This paper explicitly addresses the role of spatial dynamics in the precipitation and propagation of MPB outbreaks. We first describe a spatially dynamic model of the MPB/forest interaction that includes chemical ecology, spatial redistribution of beetles, attack, and resulting host mortality. The model is a system of 6 coupled, partial differential equations with 7 state variables and 20 parameters. It represents an attempt to capture the relatively complex predator/prey interaction between MPB and host trees by including the minimum phenomenological descriptions necessary for ecological credibility. This system of equations describes the temporal dynamics of: beetle attraction as a function of pheromone concentration; the change in numbers of flying and nesting beetles; tree resistance/susceptibility; and tree recovery from attack. Spatial dynamics are modeled by fluxes due to gradients in pheromones and kairomones, and the random redistribution of beetles in absence of semiochemicals. We then use the parameterized model to explore three issues central to the ecology of MPB/forest interaction. The first of these is in response to the need for objective ways to compare patterns of successful beetle attacks as they evolve in space. Simulation results indicate that at endemic levels, the pattern of successful attacks are determined almost exclusively by the underlying distribution of susceptible host trees (environmental determinism). As an outbreak develops, the pattern of successfully attacked trees switches to one that is dynamically driven by the self-generated semiochemical landscape (dynamic determinism). This switch from an environmentally determined spatial pattern to a dynamically driven pattern is the hallmark of an outbreak. We discuss the application of a spatial correlation coefficient that can be used to differentiate between the spatial distribution of killed trees in endemic and outbreak phases. The second issue we address through simulation is synchrony in adult emergence. Synchronous adult emergence is critical for the mass attack strategy necessary for overcoming tree defenses. Results from these simulations indicate that the degree of synchrony in adult emergence can have important consequences for assessing the risk of an outbreak. The final issue we investigate through simulation is the effect of spatial pattern of nurse trees (those successfully attacked the previous year) on outbreak potential. Simulations indicated that the spatial proximity of nurse trees was an important determinant of subsequent successful attacks. We conclude with a discussion of the general implications of our simulation experiments. Copyright 1998 Academic Press.

Journal Article↗