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Results for “spatial structure”

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PubMed1999

All maps of parameter estimates are misleading.

Maps are frequently used to display spatial distributions of parameters of interest, such as cancer rates or average pollutant concentrations by county. It is well known that plotting observed rates can have serious drawbacks when sample sizes vary by area, since very high (and low) observed rates are found disproportionately in poorly-sampled areas. Unfortunately, adjusting the observed rates to account for the effects of small-sample noise can introduce an opposite effect, in which the highest adjusted rates tend to be found disproportionately in well-sampled areas. In either case, the maps can be difficult to interpret because the display of spatial variation in the underlying parameters of interest is confounded with spatial variation in sample sizes. As a result, spatial patterns occur in adjusted rates even if there is no spatial structure in the underlying parameters of interest, and adjusted rates tend to look too uniform in areas with little data. We introduce two models (normal and Poisson) in which parameters of interest have no spatial patterns, and demonstrate the existence of spatial artefacts in inference from these models. We also discuss spatial models and the extent to which they are subject to the same artefacts. We present examples from Bayesian modelling, but, as we explain, the artefacts occur generally.

Bayes Theorem↗

PubMed1992

Diagnosis of malignancy in thyroid nodules by factor analysis of spectral and dynamic structures: a simultaneous dual-isotope dynamic study with thallium-201 and iodine-131.

The aim of this study was to identify malignant thyroid nodules using iodine-123 and thallium-201 simultaneous dynamic acquisition. The image sequences acquired were processed by factor analysis of spectral and dynamic structures (FASDS). Some 49 patients were investigated, and their diagnoses were confirmed by histological examination. Data processing enables the estimation of the spectra of the two isotopes and the evaluation of the kinetics and spatial structures related to each tracer. The superimposition of thallium and iodide sum images allowed us to delineate the nodule accurately. Two groups were defined: 21 patients who had 201Tl uptake in the nodule, and 28 who had none. In the first group, 5 nodules were carcinomas, whereas all nodules in the second group were benign. The results of the 201Tl dynamic study improved the diagnosis of carcinoma as the number of false-positive cases decreased. FASDS succeeds in extracting spectral and kinetic information, proving its usefulness in clinical diagnosis.

Adenoma↗

PubMed2004

Scale-dependent relationships between the spatial distribution of a limiting resource and plant species diversity in an African grassland ecosystem.

One cornerstone of ecological theory is that nutrient availability limits the number of species that can inhabit a community. However, the relationship between the spatial distribution of limiting nutrients and species diversity is not well established because there is no single scale appropriate for measuring variation in resource distribution. Instead, the correct scale for analyzing resource variation depends on the range of species sizes within the community. To quantify the relationship between nutrient distribution and plant species diversity, we measured NO(3)(-) distribution and plant species diversity in 16 paired, modified Whittaker grassland plots in Serengeti National Park, Tanzania. Semivariograms were used to quantify the spatial structure of NO(3)(-) from scales of 0.4-26 m. Plant species diversity (Shannon-Weiner diversity index; H ') was quantified in 1-m(2) plots, while plant species richness was measured at multiple spatial scales between 1 and 1000 m(2). Small-scale variation in NO(3)(-) (<0.4 m) was positively correlated with 1-m(2) H ', while 1000-m(2) species richness was a log-normal function of average NO(3)(-) patch size. Nine of the 16 grassland plots had a fractal (self-similar across scales) NO(3)(-) spatial distribution; of the nine fractal plots, five were adjacent to plots that had a non-fractal distribution of NO(3)(-). This finding offered the unique opportunity to test predictions of Ritchie and Olff (1999): when the spatial distribution of limiting resources is fractal, communities should display a left-skewed log-size distribution and a log-normal relationship between net primary production and species richness. These predictions were supported by comparisons of plant size distributions and biomass-richness relationships in paired plots, one with a fractal and one with a non-fractal distribution of NO(3)(-). In addition, fractal plots had greater large-scale richness than paired non-fractal plots (1,0-1000 m(2)), but neither species diversity ( H') nor richness was significantly different at small scales (1 m(2)). This result is most likely explained by differences in the scale of resource variation among plots: fractal and non-fractal plots had equivalent NO(3)(-) variation at small scales but differed in NO(3)(-) variation at large scales (as measured by the fractal dimension). We propose that small-scale variation in NO(3)(-) is largely due to the direct effects of plants on soil, while patterns of species richness at large scales is controlled by the patch size and fractal dimension of NO(3)(-) in the landscape. This study provides an important empirical step in understanding the relationship between the spatial distribution of resources and patterns of species diversity across multiple spatial scales.

Africa↗

PubMed1999

Hepatitis B core particles as a universal display model: a structure-function basis for development.

Because it exhibits a remarkable capability to accept mutational intervention and undergo correct folding and self-assembly in all viable prokaryotic and eukaryotic expression systems, hepatitis B core (HBc) protein has been favored over other proposed particulate carriers. Structurally, the unusual alpha-helical organization of HBc dimeric units allows introduction of foreign peptide sequences into several areas of HBc shells, including their most protruding spikes. Progress toward full resolution of the spatial structure as well as accumulation of chimeric HBc-based structures has brought closer the knowledge-based design of future vaccines, gene therapy tools and other artificial particulate objects.

Animals↗

PubMed2000

Pressure effect on the dynamics of an isolated alpha-helix studied by 15N-1H NMR relaxation.

Dynamics and structure of (1-36)bacteriorhodopsin solubilized in chloroform/methanol mixture (1:1) were investigated by 1H-15N NMR spectroscopy under a hydrostatic pressure of 2000 bar. It was shown that the peptide retains its spatial structure at high pressure. 15N transverse and longitudinal relaxation times, 15N[1H] nuclear Overhauser effects, chemical shifts and the translation diffusion rate of the peptide at 2000 bar were compared with the respective data at ambient pressure [Orekhov et al. (1999) J. Biomol. NMR, 14, 345-356]. The model free analysis of the relaxation data for the helical 9-31 fragment revealed that the high pressure decreases the overall rotation and translation diffusion, as well as apparent order parameters of fast picosecond internal motions (S2) but has no effect on internal nanosecond motions (S2 and taus) of the peptide. The decrease of translation and overall rotation diffusion was attributed to the increase in solvent viscosity and the decrease of apparent order parameters S2f to a compression of hydrogen bonds. It is suggested that this compression causes an elongation of H-N bonds and a decrease of absolute values of chemical shift anisotropy (CSA). In particular, the observed decrease of S2f at 2000 bar can be explained by 0.001 nm increase of N-H bond lengths and 10 ppm decrease of 15N CSA values.

Anisotropy↗

PubMed2006

Crystal structure of obelin after Ca2+-triggered bioluminescence suggests neutral coelenteramide as the primary excited state.

The crystal structure at 1.93-A resolution is determined for the Ca2+-discharged obelin containing three bound calcium ions as well as the product of the bioluminescence reaction, coelenteramide. This finding extends the series of available spatial structures of the ligand-dependent conformations of the protein to four, the obelin itself, and those after the bioluminescence reaction with or without bound Ca2+ and/or coelenteramide. Among these structures, global conformational changes are small, typical of the class of "calcium signal modulators" within the EF-hand protein superfamily. Nevertheless, in the active site there are significant repositions of two residues. The His-175 imidazole ring flips becoming almost perpendicular to the original orientation corroborating the crucial importance of this residue for triggering bioluminescence. Tyr-138 hydrogen bonded to the coelenterazine N1-atom in unreacted obelin is moved away from the binding cavity after reaction. However, this Tyr is displaced by a water molecule from within the cavity, which now forms a hydrogen bond to the same atom, the amide N of coelenteramide. From this observation, a reaction scheme is proposed that would result in the neutral coelenteramide as the primary excited state product in photoprotein bioluminescence. From such a higher energy state it is now energetically feasible to account for the shorter wavelength bioluminescence spectra obtained from some photoprotein mutants or to populate the lower energy state of the phenolate anion to yield the blue bioluminescence ordinarily observed from native photoproteins.

Amides↗

PubMed1997

The spatial dimension in population fluctuations

Theoretical research into the dynamics of coupled populations has suggested a rich ensemble of spatial structures that are created and maintained either by external disturbances or self-reinforcing interactions among the populations. Long-term data of the Canadian lynx from eight Canadian provinces display large-scale spatial synchrony in population fluctuations. The synchronous dynamics are not time-invariant, however, as pairs of populations that are initially in step may drift out of phase and back into phase. These observations are in agreement with predictions of a spatially-linked population model and support contemporary population ecology theory.

Journal Article↗

PubMedDate not supplied

[Effect of the rate of phytoplankton growth on the spaced-time dynamics of plankton communities in an homogeneous environment].

We use a conceptual mathematical reaction-diffusion model to investigate the mechanisms of spatial structure formation and complex temporal dynamics of plankton in a heterogeneous environment. We take into account basic trophic interactions, namely, "prey-predator" interactions between phytoplankton, zooplankton, and fish in upper layers of natural waters. We consider plankton as a passive contaminant in turbulent waters. We show that plankton structure formation can result from the difference in phytoplankton growth rate in neighboring habitats. Phytoplankton and zooplankton biomass is shown to undergo both regular and chaotic oscillations. The fish predation rate substantially affects the spatial and temporal dynamics of plankton in a heterogeneous environment.

Animals↗

PubMed2001

Van der Waals locks: loop-n-lock structure of globular proteins.

In a globular protein the polypeptide chain returns to itself many times, making numerous chain-to-chain contacts. The stability of these contacts is maintained primarily by van der Waals interactions. In this work we isolated and analysed van der Waals contacts that stabilise spatial structures of nine major folds. We suggest a specific way to identify the tightest contacts of prime importance for the stability of a given crystallized protein and introduce the notion of the van der Waals lock. The loops closed by the van der Waals interactions provide a basically novel view of protein globule organization: the loop-n-lock structure. This opens a new perspective in understanding protein folding as well: the consecutive looping of the polypeptide chain and the locking of the loop ends by tight van der Waals interactions.

Binding Sites↗

PubMed1988

Thermodynamic study of the apomyoglobin structure.

Sperm whale apomyoglobin has been studied thermodynamically in solutions with different pH and temperature by scanning microcalorimetry, viscosimetry, nuclear magnetic resonance and circular dichroism spectrometry, and by electrometric and calorimetric titration. It has been shown that apomyoglobin in solutions with pH close to neutral has a compact and unique spatial structure with an extended hydrophobic core. This structure is maximally stable at about 30 degrees C and breaks down reversibly both upon heating or cooling from this temperature. The process of breakdown of this structure is highly co-operative and can be regarded as a transition between two macroscopic states of protein, the native and denatured states. In contrast to the native state, which is specified by definite values of compactness and ellipticity, the compactness and ellipticity of the denatured state of apomyoglobin depend strongly on pH; with a decrease of pH below 4.0, these parameters gradually approach the values of the random coil.

Animals↗

PubMed1994

The generalized cone in human spatial organization.

The generalized cone is one of the newer concepts useful for describing spatial structures, and it has become popular as a volumetric primitive in models of object recognition. Apart from this use of the concept (or perhaps underlying it), the generalized cone can be considered a species of spatial regularity. In the general definition of symmetry as invariance across transformation, the generalized cone is a combination of translation and dilation symmetry. In such symmetry, there is homogeneity both of the slants of edges and surfaces of an object about an axis and the radial positions of these features about the axis. The results of two research projects are reviewed suggesting that the generalized cone is useful in human spatial organization. In the first instance, each of the three simpler regular polyhedra, the Platonic Solids, are easiest to perceive and imaging when they are organized as generalized cones. In the second instance, people imagine simple rotations best when the symmetric space that would be traced by the motion is aligned with salient spatial reference systems.

Form Perception↗

PubMed2000

[Photoactivated derivatives of peptide and protein ligands in the studies of neuroreceptors].

The application of photoactivatable derivatives for studies of different types of neuroreceptors belonging to two superfamilies, G-protein dependent receptors and ligand-gated ionic channels, is discussed. Studies of the structure of voltage-gated and ion-gated channels with the use of specific photoactivatable derivatives of neurotoxins are also described. Possibilities and prospects for the application of photoactivatable ligands in studies of the spatial structure of neuroreceptors are reviewed.

Animals↗

PubMed1993

Socio-demographic structure of Sydney's perimetropolitan region.

"The paper conceptualizes processes driving change in perimetropolitan regions then, using Sydney [Australia] as a case study, analyses population growth rates and internal migration patterns between 1981 and 1991. Next, a set of social and demographic variables derived from the 1986 Census is analysed to derive four key dimensions of socio-spatial structure, namely: disadvantage, rurality, socio-economic status and retirement."

Australia↗

PubMed2006

Spatio-temporal modelling and assessment of within-species phenological variability using thermal time methods.

Phenological observations of flowering date, budding date or senescence provide very valuable time series. They hold out the prospect for relating plant growth to environmental and climatic factors and hence for engendering a better understanding of plant physiology under natural conditions. The statistical establishment of associations between time series of phenological data and climatic factors provides a means of aiding forecasts of the biological impacts of future climatic change. However, it must be kept in mind that plant growth and behaviour vary spatially as well as temporally. Environmental, climatic and genetic diversity can give rise to spatially structured variation on a range of scales. The variations extend from large-scale geographical (clinal) trends, through medium-scale population and sub-population fluctuations, to micro-scale differentiation among neighbouring plants, where spatially close individuals are found to be genetically more alike than those some distance apart. We developed spatio-temporal phenological models that allow observations from multiple locations to be analysed simultaneously. We applied the models to the first-flowering dates of Prunus padus and Tilia cordata from localities as far apart as Norway and the Caucasus. Our growing-degree-day approach yielded a good fit to the available phenological data and yet involved only a small number of model parameters. It indicated that plants should display different sensitivities to temperature change according to their geographical location and the time of year at which they flower. For spring-flowering plants, we found strong temperature sensitivities for islands and archipelagos with oceanic climates, and low sensitivities in the interiors of continents.

Climate↗

PubMed2004

Spatial interactions within modular organisms: genetic heterogeneity and organism fitness.

Modular organisms are composed of iterated units of construction that vary in their spatial arrangement. This variation is expected to affect the fitness of modular organisms due to interactions among neighboring modules and the potential for such organisms to be genetically heterogeneous. We devise a spatially explicit model to investigate how spatial interactions among neighboring modules affect organism fitness. We show that fitness is strongly dependent on the spatial arrangement of modules in both genetically homogeneous and heterogeneous organisms, and that the magnitude of the variation is dependent on the strength of interactions among modules. Organism fitness is more variable with interactions among modules that are symmetrical (each affects each other in the same directions) than with asymmetrical interactions (neighbors affect each other in different directions). We conclude by discussing potential extension of the present framework to a general dynamic model of spatially structured organism development.

Adaptation, Physiological↗

PubMed2003

Pattern selection in a cooperative biochemical in vitro amplification system: the role of parasites.

Previously, numerical simulations have shown that evolving systems can be stabilized against emerging parasites by pattern formation in spatially extended flow reactors. Hence, it can be argued that pattern formation is a prerequisite for any experimental investigation of the biochemical evolution of cooperative function. Here, we study a model of an experimental biochemical system for the cooperative in vitro amplification of DNA strands and show that emerging parasites can induce a complex pattern formation even when no pattern formation occurs without parasites. In an adiabatic approximation where the cooperative amplification reaction is assumed to adapt fast to slowly emerging parasites, the parasite concentration itself acts as a Steuer parameter for the selection of various complex patterns. Without such an adiabatic approximation only transient patterns emerge. As any species can grow for very low concentrations, the parasite is able to infect the entire reactor and the system is finally diluted out. In the experimental biochemical system, however, the species are individual molecules and the growth of spatially separated, non-infected regions becomes feasible. Hence a cutoff threshold for the minimal concentration is applied. In these simulations the otherwise lethal infection by parasites induces the formation of spatiotemporal spirals, and this spatial structure help the host and parasitoid species to survive together. These theoretical results describe an inherent property of cooperative reactions and have an important impact on experimental investigations on the molecular evolution and complex function in spatially extended reactors. Since the formation of the complex pattern is restricted either to a rather large cutoff value or a special choice of the kinetic parameters, we, however, conclude that the persistence of evolving cooperative amplification is not possible in a simple reaction-diffusion reactor. Experimental set-ups with patchy environments, e.g. biomolecular amplification in coupled microstructured flow chambers or in microemulsion, are eligible candidates for the observation of such a self-organized pattern selection.

Animals↗

PubMed1992

Search for the stable state of a short chain in a molecular field.

A general approach is developed to search for stable structures of short chain fragments (e.g. of loops or bound oligopeptides) in a given molecular field. This molecular field is produced by the remaining part of a globule or by any other surface with a defined spatial structure. The fragment must be short enough to have no pronounced long-range interactions within itself. The method is illustrated by calculation of the 3-D structures of two loops of bovine pancreatic trypsin inhibitor (BPTI). Computations are based on a lattice model of conformational space and on strict and fast algorithms of 1-D statistical mechanics and dynamic programming (which are very similar in essence). This makes a search of oligopeptide structures only several times (and not several orders of magnitude) longer than that of a dipeptide.

Algorithms↗

PubMed1982

[Localization of emergency psychiatric services in Montréal.].

The validity of using a < > criterion as the organizing principle for the provision of emergency psychiatric services is examined both from the standpoint of the scientific literature on the subject and through a quantitative analysis of Montreal - based data. Given the lack of agreement as to the relative importance of distance between the consumer and the supply of services, the analysis attempts to test two hypotheses : 1) that there is a spatially structured response to the supply of emergency psychiatric services provided by Montreal hospitals and 2) the geographical distribution of the users of these services is linked to three variables of which the most important is the spatial distance between the patient and the closest emergency services. The study tends to confirm both hypotheses.

English Abstract↗