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PubMed2001

Finite element modeling of the 3D otolith structure.

A 3D finite element model (FEM) of the mammalian utricular otolith corresponding to spatial structure, shape and size of the otolith from the guinea pig was developed. The otolithic membrane (OM) was considered as consisting of gel and otoconial layers. The macular surface was approximated as a plane. The deformation of the OM under static loads such as gravity and the change of endolymphatic pressure was analyzed using the FEM for different mechanical parameters of the OM and for different gravity vector orientations. The analytical dependence of OM displacements caused by the acceleration parallel to the macular plane was obtained. By comparison of the results of calculations with the known experimental data Young's modulus of the gel layer was estimated to be of order of 10 N/m(2). It was shown that static loads result in 3D local otolith displacements inhomogeneously distributed along the macular surface and across otolith thickness. Their distribution depends on the geometrical and mechanical parameters of the otolith components. The influences of the finite size of the OM, the Young's modulus, Poisson's ratio and thickness of the gel layer on the local displacements distribution of the OM were analyzed. The results of simulation suggest that: a) the Young's modulus of the thin lowest part of the gel layer adjacent to the macular surface is much smaller than that of the rest of the OM; b) the structure of the border is designed to reduce the spatial inhomogeneity of the gel layer displacement; c) a change of the endolymphatic pressure may result in significant deformation of the OM.

Animals↗

PubMed1992

Human vision combines oriented filters to compute edges.

The experiments examined the perceived spatial structure of plaid patterns, composed of two or three sinusoidal gratings of the same spatial frequency, superimposed at different orientations. Perceived structure corresponded well with the pattern of zero crossings in the output of a circular spatial filter applied to the image. This lends some support to Marr & Hildreth's (Proc. R. Soc. Lond. B 207, 187 (1980)) theory of edge detection as a model for human vision, but with a very different implementation. The perceived structure of two-component plaids was distorted by prior exposure to a masking or adapting grating, in a way that was perceptually equivalent to reducing the contrast of one of the plaid components. This was confirmed by finding that the plaid distortion could be nulled by increasing the contrast of the masked or adapted component. A corresponding reduction of perceived contrast for single gratings was observed after adaptation and in some masking conditions. I propose the outlines of a model for edge finding in human vision. The plaid components are processed through cortical, orientation-selective filters that are subject to attenuation by forward masking and adaptation. The outputs of these oriented filters are then linearly summed to emulate circular filtering, and zero crossings (zcs) in the combined output are used to determine edge locations. Masking or adapting to a grating attenuates some oriented filters more than others, and although this changes only the effective contrast of the components, it results in a geometric distortion at the zc level after different filters have been combined. The orientation of zcs may not correspond at all with the orientation of Fourier components, but they are correctly predicted by this two-stage model. The oriented filters are not 'orientation detectors', but are precursors to a more subtle stage that locates and represents spatial features.

Adaptation, Ocular↗

PubMed1991

Epitope mapping of human thyroglobulin reveals a central immunodominant region.

Thyroglobulin is the thyroid hormone precursor and the major antigen frequently involved in autoimmune diseases. The primary structure of human thyroglobulin is known but the spatial structure remains largely undetermined. By using fusion protein produced in prokaryotic system we have characterized seven short immunoreactive peptides carrying at least one epitope. None of them includes hormonogenic sites, but five are concentrated in the central part of the monomeric molecule, which thus emerges as the major immunogenic region of this protein.

Epitopes↗

PubMed2000

Structure elucidation of glycoprotein glycans and of polysaccharides by NMR spectroscopy.

The applicability of 1H-NMR spectroscopy for the determination of the primary and tertiary structure of carbohydrate-containing molecules is demonstrated. For classes of known compounds the characterization can be based on chemical shifts observed in 1D NMR spectra with or without the aid of a computer database. For more complex structure determinations 2D NMR techniques are required. Here the application of 2D NMR is demonstrated for the primary structure determination of two bacterial exopolysaccharides, for the spatial structure determination of a disaccharide and a glycoprotein hormone.

Bacterial Proteins↗

PubMed2002

The evolving market structures of gambling: case studies modelling the socioeconomic assignment of gaming machines in Melbourne and Sydney, Australia.

The expansion of gambling industries worldwide is intertwined with the growing government dependence on gambling revenue for fiscal assignments. In Australia, electronic gaming machines (EGMs) have dominated recent gambling industry growth. As EGMs have proliferated, growing recognition has emerged that EGM distribution closely reflects levels of socioeconomic disadvantage. More machines are located in less advantaged regions. This paper analyses time-series socioeconomic distributions of EGMs in Melbourne, Australia, an immature EGM market, and then compares the findings with the mature market in Sydney. Similar findings in both cities suggest that market assignment of EGMs transcends differences in historical and legislative environments. This indicates that similar underlying structures are evident in both markets. Modelling the spatial structures of gambling markets provides an opportunity to identify regions most at risk of gambling related problems. Subsequently, policies can be formulated which ensure fiscal revenue from gambling can be better targeted towards regions likely to be most afflicted by excessive gambling-related problems.

Australia↗

PubMed1981

Systematic application of two-dimensional 1H nuclear-magnetic-resonance techniques for studies of proteins. 2. Combined use of correlated spectroscopy and nuclear Overhauser spectroscopy for sequential assignments of backbone resonances and elucidation of polypeptide secondary structures.

This paper describes a new nuclear magnetic resonance approach for the determination of secondary structure in globular proteins. To illustrate the practical application of the new procedure, two-dimensional correlated spectroscopy and two-dimensional nuclear Overhauser enhancement spectroscopy were used to obtain individual assignments for all the backbone protons of the beta-sheet secondary structures in the basic pancreatic trypsin inhibitor. First, combined connectivity diagrams of these two methods recorded in both 2H2O solution and H2O solution of the inhibitor were employed to obtain sequential, individual resonance assignments for the separate strands in the beta sheet. Second, a 2D nuclear Overhauser enhancement spectrum recorded with a long mixing time was used to determine how the separate, extended polypeptide strands are linked by hydrogen bonds in the sheet structures. By combination of these results with the identifications of the amino acid side-chain resonances described in the preceding paper, the beta-sheet structures can, without reference to data on the spatial structure obtained with other techniques, be localized in the amino acid sequence. This investigation confirms results on limited regions of the beta sheet in the inhibitor obtained previously with one-dimensional nuclear magnetic resonance experiments and demonstrates that the entire beta-sheet structure seen in single crystals of the inhibitor is preserved in aqueous solution.

Amino Acids↗

PubMed2005

Impaired spatial coding within objects but not between objects in prosopagnosia.

BACKGROUND: Patients with prosopagnosia from occipitotemporal lesions have impaired perception of the configuration of facial features. This may be an example of impaired "within-object" spatial coding, which others propose to be distinct from "between-object" spatial coding. OBJECTIVE: To determine whether the prosopagnosic deficit in perceiving spatial configuration was specific to within-face and not between-face spatial coding and whether the deficit was face-selective or extended to objects other than faces. METHODS: Six prosopagnosic patients were tested using an oddity paradigm in which they detected which of three simultaneously seen stimuli was an altered target. In the "within-face" task, the target face had altered interocular distance or mouth position. In the "between-face" task, the target face was located farther away from the other two. In the "within-object" task, the stimulus was a two-dot pattern, and the target pattern had altered interdot distance. RESULTS: Spatial judgments were impaired within faces for all six patients and within the two-dot pattern for five of six patients. However, all six had normal between-face spatial perception. CONCLUSIONS: Impaired perception of spatial relations in prosopagnosia is selective to the spatial structure within individual objects and spares the perception of spatial location of objects. It is not specific to faces. It reveals a process involved in analyzing object structure, consistent with the patients' deficits in recognizing facial identity, and illustrates a different type of "visuospatial" defect.

Adult↗

PubMed2006

Feature-specific structured imaging.

We present a feature-specific imaging system based on the use of structured light. Feature measurements are obtained by projecting spatially structured illumination onto an object and collecting all the reflected light onto a single photodetector. Principal component features are used to define the illumination patterns. The optimal linear minimum mean-square error (LMMSE) operator is used to generate object estimates from the measured features. We study the optimal allocation of illumination energy into each feature measurement in the presence of additive white Gaussian detector noise and optical blur. We demonstrate that this new imaging approach reduces imager complexity and provides improved image quality in high noise environments. Compared to the optimal LMMSE postprocessing of a conventional image, feature-specific structured imaging provides a 38% rms error reduction and requires 400 times fewer measurements for a noise standard deviation of sigma = 2 x 10(-3). Experimental results validate these theoretical predictions.

Algorithms↗

PubMed1987

Reductive alkylation of lysine residues in subtilisin DY.

Only lysine epsilon-amino groups (and the N-terminal alpha-amino group) in native subtilisin DY were reductively alkylated by glyceraldehyde in the presence of sodium cyanoborohydride. The modified protein molecule was cleaved by TosPheCH2Cl-trypsin or cyanogen bromide and the two sets of peptides obtained were fractionated and purified by gel filtration and HPLC. For determination of the degree of modification of each lysine residue, selected peptides were subjected to sequence analysis combined with quantitative estimation of the containing PTH-Lys and PTH-epsilon-DHP-Lys. The data obtained showed that the lysine residues in positions 12, 15, 27, 43, 136, 141, 265 were entirely modified, those in positions 170, 184, 237 were partially modified, and Lys22 and Lys94 were unaccessible for the reagent. The caseinolytic activity decreased by 23% when the maximum number of lysine residues (8.6 of the total 12 residues) in subtilisin DY were modified. The CD-spectra of native and modified enzyme showed only slight differences. Both these experiments suggest that the lysine residues do not take part directly in the catalytic reaction but are responsible for maintaining the native three-dimensional enzyme structure. The data obtained for the accessibility of the different lysine residues in subtilisin DY correlated very well with the positions of these residues in a video model of the structure of subtilisin Carlsberg, thus suggesting that the spatial structures of these two enzymes are very similar.

Alkylation↗

PubMedDate not supplied

[The spatial ordering of the brain electrical processes as an index of its functional organization].

Analysis of constraints, which are imposed on correctness of conclusions drawn from the studies of the spectrum-correlation model of cortex electrical activity, and necessity of enlarging interaction forms which have to be studied, brought to development a new index for estimating spatial order of cortex electrical processes. This index and the technique were called "multiple entropy" (ME). The algorithm of calculating ME and its properties are discussed. The results of studying spatial structure of cortex electrical processes by estimating their spatial synchronization and ME were compared. It was shown that these approaches complemented each other. Using both these techniques in combination gives more complete picture of integration of cortex processes.

Brain↗

PubMed1995

Perceived motion of contrast-modulated gratings: predictions of the multi-channel gradient model and the role of full-wave rectification.

The paper examines the perception of motion in contrast-modulated sine-wave grating patterns. These non-rigid motion patterns give rise to a spatially-structured motion percept in which perceived speed varies with spatial position. We measured the perceived motion of the low contrast regions of amplitude-modulated gratings as a function of the carrier frequency, the carrier speed, the shape of the modulation signal and the modulation depth. We found that for static carriers perceived speed was greatest in the low contrast regions of the display. The speed of the low contrast regions was underestimated and perceived speed decreased as the spatial frequency of the carrier increased. When the direction of the motion of the carrier was opposite to that of the contrast modulation, the low contrast regions could appear to be stationary. The perceived speed of the contrast modulation increased with modulation depth. The brightness contrast of the carrier grating had little effect on perceived speed of contrast-modulated patterns for average contrasts of over 10%. A motion model which had full-wave rectification as an explicit pre-processing stage followed by low-pass filtering or some other selection criterion, would predict that the motion of contrast-modulated gratings should appear rigid and that the motion of the envelope should be judged correctly. The Multi-channel Gradient Model however predicts both the structured motion field experienced when viewing these second-order motion patterns and the reductions in perceived speed as a function of carrier spatial frequency and carrier speed.

Contrast Sensitivity↗

PubMed2003

Habitat fragmentation resulting in overgrazing by herbivores.

Habitat fragmentation sometimes results in outbreaks of herbivorous insect and causes an enormous loss of primary production. It is hypothesized that the driving force behind such herbivore outbreaks is disruption of natural enemy attack that releases herbivores from top-down control. To test this hypothesis I studied how trophic community structure changes along a gradient of habitat fragmentation level using spatially implicit and explicit models of a tri-trophic (plant, herbivore and natural enemy) food chain. While in spatially implicit model number of trophic levels gradually decreases with increasing fragmentation, in spatially explicit model a relatively low level of habitat fragmentation leads to overgrazing by herbivore to result in extinction of the plant population followed by a total system collapse. This provides a theoretical support to the hypothesis that habitat fragmentation can lead to overgrazing by herbivores and suggests a central role of spatial structure in the influence of habitat fragmentation on trophic communities. Further, the spatially explicit model shows (i) that the total system collapse by the overgrazing can occur only if herbivore colonization rate is high; (ii) that with increasing natural enemy colonization rate, the fragmentation level that leads to the system collapse becomes higher, and the frequency of the collapse is lowered.

Animals↗

PubMed1989

Receptive field properties of human motion detector units inferred from spatial frequency masking.

This study was designed to investigate the spatial frequency selectivity and spatial structure of receptive fields of motion sensitive mechanisms in human vision. Spatial frequency selectivity was inferred from masking measurements, using dynamic test and mask stimuli. For test frequencies between 0.025 and 15.0 c/deg, maximal masking occurred when the mask frequency matched that of the test, suggesting that the test was detected by mechanisms tuned to (or near to) that frequency. For tests below 0.025 c/deg or above 15.0 c/deg, maximal masking occurred at 0.025 and 15.0 c/deg, respectively, suggesting that there exist no mechanisms selective to frequencies outside these limits. A masking model, suitable for interpreting results obtained with drifting test stimuli, was developed and used to calculate spatial frequency selectivity functions from masking data. Assuming small signal linearity, and a constant phase spectrum, the selectivity functions were inverse-Fourier transformed to yield estimates of the extent and structure of receptive fields. Field width was found to vary with test spatial frequency from 5.8 deg at 0.03 c/deg to 0.05 deg at 10.0 c/deg. These estimates were compared with width estimates previously obtained by a summation technique (Anderson & Burr, 1987), and found to be similar over a wide range of spatial frequencies (2.5 log units). Gabor functions provided a reasonable fit to the calculated field profiles at high spatial frequencies (above 1.0 c/deg), but not at low frequencies.

Fourier Analysis↗

PubMed1993

[Structure-activity organization of angiotensin II molecules. I. The structural problem].

Conformational energy calculations were carried out for angiotensin II. Its spatial structure can be described by two groups of low-energy conformations. The values of all dihedral angles of the backbone and side chains as well as intra- and inter-residual interaction energies were calculated for all potential physiologically active conformations.

Amino Acid Sequence↗

PubMed2000

Heterogeneity in biofilms.

Biofilms, accumulations of microorganisms at interfaces, have been described for every aqueous system supporting life. The structure of these microbial communities ranges from monolayers of scattered single cells to thick, mucous structures of macroscopic dimensions (microbial mats; algal-microbial associations; trickling filter biofilms). During recent years the structure of biofilms from many different environments has been documented and evaluated by use of a broad variety of microscopic, physico-chemical and molecular biological techniques, revealing a generally complex 3D structure. Parallel to these investigations more and more complex mathematical models and simulations were developed to explain the development, structures, and interactions of biofilms. The forces determining the spatial structure of biofilms, including microcolonies, extracellular polymeric substances (EPS), and channels, are still the subject of controversy. To achieve conclusive explanations for the structures observed in biofilms the cooperation of both fields of investigation, modelling and experimental research, is necessary. The expanding field of molecular techniques not only allows more and more detailed documentation of the spatial distribution of species, but also of functional activities of single cells in their biofilm environment. These new methods will certainly reveal new insights in the mechanisms involved in the developmental processes involved in the formation and behavior of biofilms.

Bacteria↗

PubMed1984

Illusory motion in visual displays.

The apparent motion of a change in the structure of a random check pattern is studied by spatially masking it with another noise pattern and it is compared with phi motion. A fundamental difference with phi motion is the insensitivity of second order correlators (Reichardt mechanisms) to this apparent motion. The following experimental characteristics distinguish this motion from phi motion: it induces no motion after-effect, it is not transparent to another simultaneous motion, it is strongly influenced by spatial masking and it does not evoke optokinetic nystagmus. A fourth order detector is introduced which is sensitive to this illusory motion as well as to phi motion. Simulation experiments with this detector together with the subjective reports of the observers lead us to the conclusion that human subjects inadvertently treat the coarsest spatial structures as signal and the finest as the disturbing noise.

Adult↗

PubMed1997

COOH-terminal decamers in proteins are non-random.

We have undertaken an exhaustive statistical analysis of the amino acid sequences at the carboxyl-terminal (C) ends of proteins. The composition of the C-terminal decapeptides differs from that expected for the given proteins from the overall amino acid composition. For E. coli, yeast, and H. sapiens it was shown that positively charged amino acid residues are over-represented while Gly residues are under-represented. The C-terminal bias, a novel feature of protein structure, should be taken into account when molecular evolution, spatial structure, translational termination and protein folding are concerned.

Amino Acid Sequence↗

PubMed2003

The spatial tuning of chromatic adaptation.

A key question in colour research is how the colour and spatial analysis of an image interact. Traditionally, colour and form analysis have been regarded as parallel and separate processes, and documented effects of image complexity on chromatic adaptation have been attributed to a temporal integration process during eye movements. Evidence is presented here for a spatial mechanism, which tunes chromatic adaptation to the luminance structure (spatial frequency and orientation) of an image. This in turn suggests a close cooperation between colour and form analysis during chromatic adaptation. The results are discussed in relation to the "segregated pathway hypothesis" and the role of spatial aspects for the computation of colour constancy and adaptation to natural scenes.

Adaptation, Ocular↗