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PubMedDate not supplied

Memory for a geometrical configuration in the cognitively impaired elderly.

The objective of this study was to analyze the mnemonic reconstruction of a complex spatial configuration in a group of 10 men and women, 70-88 years, with a diagnosis of organic brain syndrome and 10 controls matched for age, sex and educational background. A Piagetian model of a geometrical configuration with contingent and non-contingent properties was used to establish a heirarchical order of memorial organization for spatial structures. Subjects were evaluated one hour and one week after learning in reconstruction tasks. Although individuals with dementia performed more poorly than the age-matched controls, the hierarchy of chosen characteristics reflected a schematic progression in the organization of spatial memory in both groups.

Aged↗

PubMed1987

[Localization of the antigenic determinants in carcinoembryonic antigen: the role of the carbohydrate component].

The majority of topographic antigenic determinants of the carcinoembryonic antigen (CEA) representing a glycoprotein were shown to contain sugar residues of the CEA carbohydrate chains. Periodate oxidation of CEA followed by reduction afforded a corresponding CEA derivate (CEA-POR), which retained 3% antigenic activity of CEA. In secondary and tertiary structures CEA-POR was proved to be close to CEA pre heated to 80 degrees C. Formation of borate complexes with sugar residues of CEA decreased the CEA antigenic activity to 5% while a but did not affect the spatial structure of its protein core.

Carbohydrate Conformation↗

PubMed2001

Parametrically forced pattern formation.

Pattern formation in a nonlinear damped Mathieu-type partial differential equation defined on one space variable is analyzed. A bifurcation analysis of an averaged equation is performed and compared to full numerical simulations. Parametric resonance leads to periodically varying patterns whose spatial structure is determined by amplitude and detuning of the periodic forcing. At onset, patterns appear subcritically and attractor crowding is observed for large detuning. The evolution of patterns under the increase of the forcing amplitude is studied. It is found that spatially homogeneous and temporally periodic solutions occur for all detuning at a certain amplitude of the forcing. Although the system is dissipative, spatial solitons are found representing domain walls creating a phase jump of the solutions. Qualitative comparisons with experiments in vertically vibrating granular media are made. (c) 2001 American Institute of Physics.

Journal Article↗

PubMed2003

Spatial dynamics in model plant communities: what do we really know?

A variety of models have shown that spatial dynamics and small-scale endogenous heterogeneity (e.g., forest gaps or local resource depletion zones) can change the rate and outcome of competition in communities of plants or other sessile organisms. However, the theory appears complicated and hard to connect to real systems. We synthesize results from three different kinds of models: interacting particle systems, moment equations for spatial point processes, and metapopulation or patch models. Studies using all three frameworks agree that spatial dynamics need not enhance coexistence nor slow down dynamics; their effects depend on the underlying competitive interactions in the community. When similar species would coexist in a nonspatial habitat, endogenous spatial structure inhibits coexistence and slows dynamics. When a dominant species disperses poorly and the weaker species has higher fecundity or better dispersal, competition-colonization trade-offs enhance coexistence. Even when species have equal dispersal and per-generation fecundity, spatial successional niches where the weaker and faster-growing species can rapidly exploit ephemeral local resources can enhance coexistence. When interspecific competition is strong, spatial dynamics reduce founder control at large scales and short dispersal becomes advantageous. We describe a series of empirical tests to detect and distinguish among the suggested scenarios.

Ecosystem↗

PubMed2004

Spatial and temporal properties of visual responses in the thalamus of the developing ferret.

Spatiotemporal patterning of neural activity is thought to influence the development of connections in the visual pathway. This patterning can arise spontaneously or through sensory experience. Here, we use a combination of natural and simple stimuli to investigate which elements of the visual environment modulate the earliest responses in the primary visual pathway of developing ferrets. Recordings were made during the first 2 weeks of visual responsiveness, which, in the ferret, overlaps with the period that the eyelids have not yet opened. Even when the eyelids are closed, both thalamic and cortical activity was found to be temporally modulated under conditions of natural visual stimulation. The modulations correlated with temporal changes in stimulus contrast but also reflected spatial structure in the visual scene. Simple stimuli were used to show that early responses to naturalistic stimuli are influenced by the localization and structure of through-the-eyelid receptive fields. The early visual responses were also characterized by substantial variability in the ability of the cells to detect stimuli of different duration and different intensity, in a temporally precise manner. These temporal and spatial properties should constrain how plasticity mechanisms interpret naturally patterned activity.

Action Potentials↗

PubMedDate not supplied

[Accessible surface and intramolecular mobility of proteins: study by method of tritium planigraphy].

The method of tritium planigraphy is used for determination of the accessible surface of a globular protein--lysozyme--and the accessibility of particular types of amino acid residues as a function of temperature in the range of 77-193 K. Protein powder with humidity 10 +/- 1% was used. As the temperature is changed from 77 to 160 K for all types of amino acid residues was obtained decreasing of inclusion of tritium label. All types of amino acid residues may be divided on the three groups: I. Accessibility rises under increasing temperature from 160 to 293 K (K, R, H, P, L); II. Accessibility not depends or slightly increases with the growth of temperature (C, V, A, I, Y, F); III. Accessibility strongly increases in the range of the temperature 260-293 K (S, T, G, D + N, E + Q). The reason of "cold denaturation" is perhaps the difference of behaviour of structural water molecules. Under increasing of temperature from 160 to 293 K change of accessibility was explained the growing of intramolecular flexibility of molecule. Under transition from 160 to 77 K for all types of residues is observed sensible change of spatial structure of the protein, which cannot be explained by only participation of dynamical characteristics.

Animals↗

PubMed1993

[Structure-function organization of the angiotensin II molecule. II. Reverse structural problem].

A number of modifications of the amido acids sequence of the peptide hormone angiotensin II leading to the hormone's analogues with restricted conformational properties are considered. The relative conformational energies for all the analogues were evaluated in conformations similar to the low-energy conformations of the native hormone. Presented is the comparative analysis of the spatial structures of the native hormone and its analogues.

Amino Acid Sequence↗

PubMed2004

Crystal structure of a Ca2+-discharged photoprotein: implications for mechanisms of the calcium trigger and bioluminescence.

Ca2+-regulated photoproteins are members of the EF-hand calcium-binding protein family. The addition of Ca2+ produces a blue bioluminescence by triggering a decarboxylation reaction of protein-bound hydroperoxycoelenterazine to form the product, coelenteramide, in an excited state. Based on the spatial structures of aequorin and several obelins, we have postulated mechanisms for the Ca2+ trigger and for generation of the different excited states that are the origin of the different colors of bioluminescence. Here we report the crystal structure of the Ca2+-discharged photoprotein obelin at 1.96-A resolution. The results lend support to the proposed mechanisms and provide new structural insight into details of these processes. Global conformational changes caused by Ca2+ association are typical of the class of calcium signal modulators within the EF-hand protein superfamily. Accommodation of the Ca2+ ions into the loops of the EF-hands is seen to propagate into the active site of the protein now occupied by the coelenteramide where there is a significant repositioning and flipping of the His-175 imidazole ring as crucially required in the trigger hypothesis. Also the H-bonding between His-22 and the coelenterazine found in the active photoprotein is preserved at the equivalent position of coelenteramide, confirming the proposed rapid excited state proton transfer that would lead to the excited state of the phenolate ion pair, which is responsible for the blue emission of bioluminescence.

Calcium↗

PubMed2006

Correlation and response in a driven dissipative model.

We consider a simple dissipative system with spatial structure in contact with a heat bath. The system always exhibits correlations except in the cases of zero and maximal dissipation. We explicitly calculate the correlation function and the nonlocal response function of the system and show that they have the same spatial dependence.

Journal Article↗

PubMed1998

Population and employment density functions revisited: a spatial interaction approach.

"This article proposes a generalized urban spatial structure and transportation network, and adapts the Garin-Lowry model to simulate both population and service employment densities in this hypothetical, yet realistic, city. The model is solved numerically while varying exogenous factors such as the distance friction coefficients and the spatial distribution of basic employment.... The results are generalized by estimating, via regression analysis, density functions over a large sample of simulated density patterns, pointing to the critical importance of transportation costs and basic employment distribution, and providing a basis for further empirical studies."

Demography↗

PubMedDate not supplied

[Proteolytic degradation of native hemoglobin and its constituent parts--isolated subunits and globin. II. Correlation with the hydrogen exchange data and the mechanism of the burst-like proteolytic breakdown of native proteins].

Basing on comparison of the data on the rate of proteolytic breakdown and hydrogen exchange for hemoglobin and its constituent parts, we discuss the problem of the mechanism of the burst-like ("one-by-one") proteolytic breakdown of native proteins in conditions which are not close to extreme denaturational. The rate of proteolytic breakdown by different proteases decreases in the same order as the local conformational mobility according to the hydrogen exchange data: globin greater than oxy-alpha-chain greater than metHb much greater than oxy-beta-chain greater than HbO2 congruent to CNmetHb. For native globin and and metHb, the rates of hydrogen exchange and proteolytic breakdown depend weakly on the temperature in the range of 5-25 degrees, not much stronger than for flexible "unstructured" peptides and proteins. These correlations as well as other data allow a conclusion to be made that the process of the proteolytic breakdown of native proteins study is governed by spontaneous local conformational transitions of the same type as for the hydrogen exchange processes. A similar correlation between the changes in the rates of hydrogen exchange and proteolytic thought that the discussed mechanism of the burst-like proteolytic breakdown has a common character. Alongside with similarities, we consider distinctions between the role of the dynamical structure of the proteins in the realization of reactions of proteolytic degradation and the hydrogen exchange. Upon proteolytic degradation of stable native proteins, the significance of conformational rearrangement of the protein substrate induced by proteases and also that of distortions in the spatial structure of proteases under the action of the protein substrate increase. It is pointed that the actual concentration of the dynamic conformers of native proteins which serve as substrate for proteases can be much lower than the nominal concentration of the protein substrate. The mechanisms of the influence of the cofactor splitting and the dissociation of the oligomeric structure on the rate of proteolytic degradation are discussed.

Drug Stability↗

PubMed1997

[New structural motifs in alpha-helical proteins].

Four novel structural motifs were found and characterized in alpha-helical proteins. One of them consists of three alpha helices and can be represented as a combination of an alpha-alpha corner and an L-shaped structure. Its second alpha helix is a part of both one of the two alpha helices of the alpha-alpha corner and one of the two L-structure helices. The second structural motif, named the ABCD unit, consists of four alpha helices A, B, C, and D. These are consecutive in sequence and arranged in space in such a manner that the helices B, C, and D form a left-handed superhelix and the helix A is located between the helices B and D and is approximately antiparallel to them. The third motif, alpha helix-loop-alpha helix, consists of two alpha helices and a long connection. Its alpha helices are arranged in an approximately parallel manner and together with the long connection, form a left-handed alpha-1-alpha superhelix in space. The fourth structural motif considered is formed by four consecutive alpha helices. It is named the phi motif, because its overall shape is reminiscent of the Greek letter phi. Various variants of these motifs are analyzed on numerous examples of proteins with the known spatial structures.

Protein Conformation↗

PubMed2002

Local adaptation in the Linum marginale-Melampsora lini host-pathogen interaction.

The potential for local adaptation between pathogens and their hosts has generated strong theoretical and empirical interest with evidence both for and against local adaptation reported for a range of systems. We use the Linum marginale-Melampsora lini plant-pathogen system and a hierarchical spatial structure to investigate patterns of local adaptation within a metapopulation characterised by epidemic dynamics and frequent extinction of pathogen populations. Based on large sample sizes and comprehensive cross-inoculation trials, our analyses demonstrate strong local adaptation by Melampsora to its host populations, with this effect being greatest at regional scales, as predicted from the broader spatial scales at which M. lini disperses relative to L. marginale. However, there was no consistent trend for more distant pathogen populations to perform more poorly. Our results further show how the coevolutionary interaction between hosts and pathogens can be influenced by local structure such that resistant hosts select for generally virulent pathogens, while susceptible hosts select for more avirulent pathogens. Empirically, local adaptation has generally been tested in two contrasting ways: (1) pathogen performance on sympatric versus allopatric hosts; and (2) sympatric versus allopatric pathogens on a given host population. In situations where no host population is more resistant or susceptible than others when averaged across pathogen populations (and likewise, no pathogen population is more virulent or avirulent than others), results from these tests should generally be congruent. We argue that this is unlikely to be the case in the metapopulation situations that predominate in natural host-pathogen interactions, thus requiring tests that control simultaneously for variation in plant and pathogen populations.

Adaptation, Physiological↗

PubMed1999

Modes selection in polymer mixtures undergoing phase separation by photochemical reactions.

Phase separation kinetics and morphology of binary polymer mixtures (A/B) in the presence of photochemical reactions were investigated by using phase-contrast optical microscopy combined with digital image analysis. The polymers were chemically designed in such a way that two types of chemical reactions, intermolecular photodimerization and intramolecular photoisomerization, of polymer segments can be induced and controled by irradiation with ultraviolet light. Unlike the conventional case, the phase separation in the presence of these reactions is spontaneously frozen due to the suppression of the long-wavelength instabilities, resulting in stationary spatial structures with intrinsic periodicities. These characteristic length scales are determined by the competition between the two antagonistic interactions: phase separation as a relatively short-range activation and the photochemical reaction as a long-range inhibition. Furthermore, it was found that the spatial symmetry breaking of concentration fluctuations can emerge from the elastic stress associated with the nonhomogeneous kinetics of the reactions. Experimental data obtained with three types of reactions: A-A only cross-link, A-A and B-B simultaneous cross-links and the reversible A<-->B photoisomerization are described. These results do not only indicate that combination of chemical reactions and phase separation could provide a novel method to control the morphology of multiphase polymer materials, but also suggest that photoreactive polymers can be used as a chemical system to study the mode-selection process in polymers far from thermodynamic equilibrium. (c) 1999 American Institute of Physics.

Journal Article↗

PubMedDate not supplied

[Analysis of spatial frequency characteristics of complex receptive fields].

The difference fB2-fB1=deltaf and ratio fB2/fB1=R of the bandwidth boundary frequencies fB1, fB2 of spatial frequency characteristic of complex receptive field depends on the size of RF and spatial structure of excitatory and inhibitory zones. deltaf and r are independent of the weighting functions of excitatory and inhibitory zones. The theoretical value of r is similar to data which was obtained in psychophysical and physiologycal experiments. The dependence of contrast sensitivity on spatial frequency can be explained by dependence of the envelope of weighting functions of exitatory (inhibitory) zones on the spatial frequency.

Animals↗

PubMed2001

Population dynamics advected by chaotic flows: A discrete-time map approach.

A discrete-time model of reacting evolving fields, transported by a bidimensional chaotic fluid flow, is studied. Our approach is based on the use of a Lagrangian scheme where fluid particles are advected by a two-dimensional symplectic map possibly yielding Lagrangian chaos. Each fluid particle carries concentrations of active substances which evolve according to its own reaction dynamics. This evolution is also modeled in terms of maps. Motivated by the question, of relevance in marine ecology, of how a localized distribution of nutrients or preys affects the spatial structure of predators transported by a fluid flow, we study a specific model in which the population dynamics is given by a logistic map with space-dependent coefficient, and advection is given by the standard map. Fractal and random patterns in the Eulerian spatial concentration of predators are obtained under different conditions. Exploiting the analogies of this coupled-map (advection plus reaction) system with a random map, some features of these patterns are discussed. (c) 2001 American Institute of Physics.

Journal Article↗

PubMed2004

Spatial patterns of infant mortality in Mali: the effect of malaria endemicity.

A spatial analysis was carried out to identify factors related to geographic differences in infant mortality risk in Mali by linking data from two spatially structured databases: the Demographic and Health Surveys of 1995-1996 and the Mapping Malaria Risk in Africa database for Mali. Socioeconomic factors measured directly at the individual level and site-specific malaria prevalence predicted for the Demographic and Health Surveys' locations by a spatial model fitted to the Mapping Malaria Risk in Africa database were examined as possible risk factors. The analysis was carried out by fitting a Bayesian hierarchical geostatistical logistic model to infant mortality risk, by Markov chain Monte Carlo simulation. It confirmed that mother's education, birth order and interval, infant's sex, residence, and mother's age at infant's birth had a strong impact on infant mortality risk in Mali. The residual spatial pattern of infant mortality showed a clear relation to well-known foci of malaria transmission, especially the inland delta of the Niger River. No effect of estimated parasite prevalence could be demonstrated. Possible explanations include confounding by unmeasured covariates and sparsity of the source malaria data. Spatial statistical models of malaria prevalence are useful for indicating approximate levels of endemicity over wide areas and, hence, for guiding intervention strategies. However, at points very remote from those sampled, it is important to consider prediction error.

Adult↗

PubMed2005

Topological structure of a vortex in the Fulde-Ferrell-Larkin-Ovchinnikov state.

We find theoretically that the vortex core in the Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) state is quite different from the ordinary core for a simple topological reason. The intersection point of a vortex and nodal plane of the FFLO state empties the excess spins. This leads to observable consequences in the spatial structure of the spontaneous magnetization. We analyze this topological structure based on the low lying excitation spectrum by solving a microscopic Bogoliubov-de Gennes equation to clarify its physical origin.

Journal Article↗