SEARCH · PubMed Health

Results for “spatial structure”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37Linked to original sources

PubMed2005

Merging spatial and temporal structure within a metapopulation model.

Current research recognizes that both the spatial and temporal structure of the landscape influence species persistence. Patch models that incorporate the spatial structure of the landscape have been used to investigate static habitat destruction by comparing persistence results within nested landscapes. Other researchers have incorporated temporal structure into their models by making habitat suitability a dynamic feature of the landscape. In this article, we present a spatially realistic patch model that allows patches to be in one of three states: uninhabitable, habitable, or occupied. The model is analytically tractable and allows us to explore the interactions between the spatial and temporal structure of the landscape as perceived by the target species. Extinction thresholds are derived that depend on habitat suitability, mean lifetime of a patch, and metapopulation capacity. We find that a species is able to tolerate more ephemeral destruction, provided that the rate of the destruction does not exceed the scale of its own metapopulation dynamics, which is dictated by natural history characteristics and the spatial structure of the landscape. This model allows for an expansion of the classic definition of a patch and should prove useful when considering species inhabiting complex dynamic landscapes, for example, agricultural landscapes.

Ecosystem↗

PubMed2003

Ecotoxicology and spatial modeling in population dynamics: an illustration with brown trout.

We developed a multiregion matrix population model to explore how the demography of a hypothetical brown trout population living in a river network varies in response to different spatial scenarios of cadmium contamination. Age structure, spatial distribution, and demographic and migration processes are taken into account in the model. Chronic or acute cadmium concentrations affect the demographic parameters at the scale of the river range. The outputs of the model constitute population-level end points (the asymptotic population growth rate, the stable age structure, and the asymptotic spatial distribution) that allow comparing the different spatial scenarios of contamination regarding the demographic response at the scale of the whole river network. An analysis of the sensitivity of these end points to lower order parameters enables us to link the local effects of cadmium to the global demographic behavior of the brown trout population. Such a link is of broad interest in the point of view of ecotoxicological management.

Animal Migration↗

PubMed1983

Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance.

"Pseudo-structures" of the 20 common amino acid residues are introduced for use in protein spatial structure determinations, which rely on the use of intramolecular proton-proton distance constraints determined by nuclear Overhauser effects as input for distance geometry calculations. The proposed structures satisfy requirements for the initial structural interpretation of the nuclear magnetic resonance data that arise from the absence of stereospecific assignments and/or limited spectral resolution for certain resonance lines. The pseudo-atoms used as reference points for the experimental distance constraints can be used in conjunction with the real amino acid structures representing the van der Waals' constraints on the spatial molecular structure, or with simplified models in order to reduce the computing time for the distance geometry calculations.

Amino Acids↗

PubMed1980

Spatial characteristics of movement detection mechanisms in human vision. I. Achromatic vision.

Threshold illumination levels, It, for visual detection of white light targets, moving across spatially structured background fields, have been measured and it is shown that, for a given background illumination level, It depends upon the spatial characteristics of the background field structure. Thus, with the background composed of a square-waveform grating of fundamental spatial frequency f cycles/deg, It is maximum for an intermediate value of f, and falls as f increases or decreases from this value. The relationship between It and f characterizes the interaction between movement detection and the background grating, and is designated the IMG function. The parametric properties of the IMG functions are described and it is established that the mechanisms which give rise to these functions are sensitive to the movement, but not the spatial structure of the target. They correspond, therefore, to the movement-sensitive Y-type mechanisms, observed in electrophysiological studies of cat and primate visual pathways. The spatial distribution of sensitivity associated with the IMG functions has been computed by 2-D transform methods, the computation yielding circularly symmetric, centre-surround antagonistic "receptive field" distributions.

Adult↗

PubMed2005

Item organization in three-dimensional space and their discriminability in a mouse operant behavioral task.

In order to study spatial cognition as well as operant/instrumental conditioning or attention processes in the same experimental context in mice, we have designed and constructed an operant chamber that contains a large number of nose poke holes distributed over its inner walls. The nose poke holes were placed three in a horizontal row on one left wall, five in a form of an X on the front wall, and three in a vertical column on one right wall in a hexagonal shaped chamber. This organization of nose poke holes was intended to provide mice with spatially structured environmental cues. Here, we report on an experiment in which providing additional structuring to the standard condition, favoring either further spatial grouping or perceptual/visual clustering of subsets of holes, tremendously facilitated nose poke discrimination learning in normal C57BL/6 mice. More interestingly, mice were able to use their (spatial or mental) representation of holes organization elaborated under spatially or visually structured environment, to improve their learning of a new discrimination under the standard less-structured environment. These findings support the idea that mice are sensitive to subtle visual background information, in addition to spatial information, to organize nose poke items, process similar to both pattern separation and chunking process, in order to minimize interference and to increase items discriminability and their capacity for (long-term) memory.

Analysis of Variance↗

PubMed1987

Cranial variation in European populations: a spatial autocorrelation study at three time periods.

This study reports on spatial variation of 10 cranial variables in European populations at 3 time periods. Means for these variables, based on 137, 108, and 183 samples from the Early Medieval, Late Medieval, and Recent periods, were subjected to one-dimensional and directional spatial autocorrelation analyses. Significant spatial structure was found for most variables. It becomes more pronounced as time progresses. The spatial patterns are not strongly clinal. Correlograms based on distances computed from all variables are monotonic only to 900, 1,650, and 1,350 km for the three periods. Regional patterns are seen for most variables and become more structured and significant with time. There is little similarity among the correlograms of the variables at any one period and virtually none among periods. Inferences about spatial structure of these populations, based on spatial autocorrelation analysis, suggest a pattern dominated by migration, followed by expansion and admixture rather than selection or chance fluctuations. The patterns of morphometric change seem to reflect the patterns of linguistic change in these areas.

Cephalometry↗

PubMed2003

Spatially mapping the spectral density of a single C60 molecule.

We have used scanning tunneling spectroscopy to spatially map the energy-resolved local density of states of individual C60 molecules on the Ag(100) surface. Spectral maps were obtained for molecular states derived from the C60 HOMO, LUMO, and LUMO+1 orbitals, revealing new details of the spatially inhomogeneous C60 local electronic structure. Spatial inhomogeneities are explained using ab initio pseudopotential density functional calculations. These calculations emphasize the need for explicitly including the C60-Ag interaction and STM tip trajectory to understand the observed C60 local electronic structure.

Journal Article↗

PubMed1990

The blue oxidases, ascorbate oxidase, laccase and ceruloplasmin. Modelling and structural relationships.

On the basis of the spatial structure of ascorbate oxidase [Messerschmidt, A., Rossi, A., Ladenstein, R., Huber, R., Bolognesi, M., Gatti, G., Marchesini, A., Petruzzelli, R. & Finazzi-Agro, A. (1989) J. Mol. Biol. 206, 513-529], an alignment of the amino acid sequence of the related blue oxidases, laccase and ceruloplasmin is proposed. This strongly suggests a three-domain structure for laccase closely related to ascorbate oxidase and a six-domain structure of ceruloplasmin. These domains demonstrate homology with the small blue copper proteins. The relationships suggest that laccase, like ascorbate oxidase, has a mononuclear blue copper in domain 3 and a trinuclear copper between domain 1 and 3 and ceruloplasmin has mononuclear copper ions in domains 2, 4 and 6 and a trinuclear copper between domains 1 and 6.

Amino Acid Sequence↗

PubMed2006

Three-dimensional reconstruction and quantitative analysis of the brain stem nuclei based on fast centroid auto-registration.

This paper introduces a three-dimensional (3D) reconstruction algorithm of the brain stem nuclei based on fast centroid auto-registration. The research is based on methods and theories of computer stereo vision, and by image information processing three-point pattern local search, registration and auto-tracing for the centroids of the brain stem nuclei were accomplished. We adopt two-peak threshold, edge detection and grayscale image enhancement to extract contours of the nuclei's structures. The experimental results obtain the spatial structure information and 3D image of the brain stem nuclei, show spatial relationship between 14 pairs of nuclei, and quantitate morphological parameters of each type of nuclei's 3D structure. This work is significant to neuroanatomy research and clinic applications. Furthermore, a software system named BRAIN.HUK is established.

Algorithms↗

PubMed1987

Punctualism, non-adaptationism, neutralism and evolution.

In its further development the theory of evolution will incorporate molecular biology, synergetics and the theory of information. Using a simple model it is shown that speciation can be similar to phase transition. This is a thermodynamical statement which does not say anything concerning the sharpness and kinetic features of transition. Hence there is no contradiction between punctuated equilibrium and phyletic gradualism. The notion of punctualism can be used in the sense of phase transition. Evolution is directional because of constraints of natural selection due to the structure of organisms already existing and to the possible pathways of development. Correspondingly many characters are non-adaptative. Not only are the structures of proteins important for speciation but also the exact answers to the questions: "how much", "where" and "when"? These answers can be obtained as the results of regulation of genes, particularly of homeiotic regulation. The basis features of the structure of proteins are considered and the sense of the neutral theory is discussed in connection with degeneracy of correlation between the primary structure of a protein, its spatial structure and biological function. Informational aspects of evolution are discussed. Punctualism, non-adaptationism and neutralism form the triad of internally connected features of evolution. The Darwinian theory preserves its fundamental significance.

Adaptation, Biological↗

PubMed2006

Hierarchical modeling and other spatial analyses in prostate cancer incidence data.

BACKGROUND: State central cancer registries are often asked to respond to questions about the spatial distribution of cancer cases. Spatial analysis methods and technology are evolving rapidly, and can be a considerable challenge to registries that do not have staff with training in this area. The purpose of this article is to describe a general methodological approach that potentially might be a starting point for many cancer registry spatial analyses at the county level. METHODS: Prostate cancer incident cases (N=31,159) from the Louisiana Tumor Registry from 1988 to 1999 were used for illustrative purposes. To explore spatio-temporal patterns, analyses focused on four time periods, each 3 years in length: 1998-1990, 1991-1993, 1994-1996, and 1997-1999. For each time period, race-specific (white and black), direct age-adjusted incidence rates and indirect standardized incidence ratios (SIRs) were calculated, smoothed using Bayesian methods, and assessed for evidence of spatial autocorrelation using global and local Moran's I. Hierarchical generalized linear models (HGLM) were fitted to identify significant covariates. Clusters of elevated and lower rates were identified using a spatial scan statistic (SaTScan). RESULTS: Temporal trends in SIRs in both race groups were consistent with the introduction of prostate specific antigen (PSA) testing in Louisiana during the late 1980s and early 1990s, but possibly with a lag in black males. Clusters of lower than expected values were observed for white males in the central (p=0.001) and southeastern coastal areas (p=0.001), and to a greater extent for black males in the central (p=0.001), southwestern and southeastern coastal parishes (p=0.001). CONCLUSIONS: Mapping disease occurrence by time period is an effective way to explore spatio-temporal patterns. HGLM models and software are available to control for covariates and for unstructured and spatially structured variability that may confound spatial variability patterns.

Adult↗

PubMed2004

Imposing structure on a Corsi-type task: evidence for hierarchical organisation based on spatial proximity in serial-spatial memory.

Structure was imposed on a tapping task by requiring participants to reproduce sequences of responses to icons organised in spatial clusters. A first experiment featured sequences either segregated or not segregated by clusters. Accuracy was higher for sequences segregated by clusters. Moreover, inter-response times were longer at cluster boundaries than within cluster boundaries. To rule out possible confounding effects of movement length, this temporal pattern was replicated in a second experiment requiring a single response indicating the next sequential step, following the presentation of a portion of a previously practised sequence. These results suggest that sequence reproduction can be sustained by a hierarchical representation based on spatial proximity and provide a first indication of the role of spatial structure in serial-spatial memory.

Adolescent↗

PubMed2000

Improved estimation of the pair correlation function of random sets.

The texture of binary spatial structures can be characterized by second-order methods of spatial statistics. The pair correlation function, which describes the structure in terms of spatial correlation as a function of distance, is of central importance in this context. Conventionally, the pair correlation function of stationary and isotropic random sets is estimated as the ratio of the covariance to the square of volume fraction of the phase of interest. In the present paper, an improved estimator of the pair correlation function is presented, where the covariance is divided by the square of a distance-adapted estimator of volume fraction. The new estimator is explained mathematically and applied to simulated images of the Boolean model and to microscopic images from neoplastic and non-neoplastic human glandular tissues. It leads to a considerable reduction of bias and variance of estimated pair correlation functions, in particular for large distances.

Animals↗

PubMed1997

Influences on the global structure of cortical maps.

Cortical maps often contain global spatial structure: however, theoretical accounts for their development have generally concentrated on reproducing only local structure. We show that the elastic net model of cortical map formation can closely approximate the global structure of the ocular dominance column map observed in macaque primary visual cortex. A key component is the assumption of spatially non-uniform and anisotropic correlations in the retina. This work shows how genetic and epigenetic effects could combine to establish characteristic global structure in cortical maps.

Animals↗

PubMed2006

Spatial organization and evolution period of the epidemic model using cellular automata.

We investigate epidemic models with spatial structure based on the cellular automata method. The construction of the cellular automata is from the study by Weimar and Boon about the reaction-diffusion equations [Phys. Rev. E 49, 1749 (1994)]. Our results show that the spatial epidemic models exhibit the spontaneous formation of irregular spiral waves at large scales within the domain of chaos. Moreover, the irregular spiral waves grow stably. The system also shows a spatial period-2 structure at one dimension outside the domain of chaos. It is interesting that the spatial period-2 structure will break and transform into a spatial synchronous configuration in the domain of chaos. Our results confirm that populations embed and disperse more stably in space than they do in nonspatial counterparts.

Journal Article↗

PubMed2002

Spatial autocorrelation and linkage of Mendelian RAPD markers in a population of Picea abies Karst.

The spatial clustering of single- and di-locus genotypes in a natural, continuous population of Norway spruce was investigated using 69 Mendelian Random Amplified Polymorphic DNA (RAPD) markers that covered about 15 of the species genome, and whose linkage relationships were known. Spatial autocorrelation techniques and randomization tests, applied to both single- and di-locus genotypes, revealed a weak, though significant, spatial structure at the scale 0-200 m (5 of single-locus and 7 of di-locus genotypes). To assess the relative importance of isolation by distance and linkage between markers on their spatial genetic structuring, we grouped joins between sampled trees into equivalence categories expected to show similar, specific patterns of spatial distribution under isolation by distance. Results from both single- and di-locus analyses were consistent with the existence of patches of like homozygotes (about 8 and 11 of loci at the single- and di-locus level, respectively) surrounded by a mix of like heterozygotes. Similar structuring has been predicted by simulation models under isolation by distance and selective neutrality. Overall, linkage between markers accounted for an increase of spatial clumping of di-locus genotypes involving tightly linked loci with recombination fractions up to 0.1, a consequence of limited, stochastic spread of single-locus genotypes in space. Our results support the hypothesis that isolation by distance and linkage have a small, though significant, effect even within continuous forest tree populations. In general, the spatial distribution of multilocus genotypes within populations should be interpreted with caution when linkage relationships among the markers used are unknown.

DNA↗

PubMed2006

A micro-tomography method based on X-ray diffraction enhanced imaging for the visualization of micro-organs and soft tissues.

Diffraction enhanced imaging (DEI) is one of the phase contrast imaging methods using the monochromatic X-ray from synchrotron, which provides information on the out-of-plane angular deviation of X-ray. DEI allows the investigation of micro-structures inside weakly absorbing samples at high spatial resolution without serious radiation exposure. Tomographic techniques can be applied readily to phase contrast images. The combination of DEI and tomography allows for a reconstruction of refractive index gradient distribution inside weakly absorbing samples with micrometer resolution, particularly suited for the 3D observation of micro-organisms and tissues. The existing phase contrast tomography methods based on DEI use phase contrast images as projections, such images contain not only the phase information, but also the absorption information. A novel method (DEI in the tomography mode) was developed to greatly increase the proportion of refraction information in phase contrast images by computing the difference between the two sets of images acquired at different angles of the rocking curve to adopt the projections with a complete set (2pi) for reconstruction. The reconstructed images of cochlea of a guinea pig showed the spatial structures and the micro-features inside the samples. The new method reveals higher spatial resolution compared to the conventional phase contrast tomography methods and is more suitable to the investigation of micro-structures of micro-organisms and tissue materials.

Algorithms↗

PubMed2006

On the use of bipolar montages for time-series analysis of intracranial electroencephalograms.

OBJECTIVE: Bipolar montages are routinely employed for the interpretation of scalp and intracranial EEGs (icEEGs). In this manuscript we consider the assumptions that support the use of a bipolar montage and question the universal appropriateness of bipolar representation of icEEGs for the time-series analysis of these signals. Bipolar montages introduce an element of spatial processing into the observed time-series. In the case of icEEGs, we argue ambiguity may be introduced in some settings through this operation because of a lack of certifiability of local differentiability and continuity of the spatial structure of icEEGs, and their suboptimal spatial sampling. METHODS: Example icEEGs were collected from three patients being studied for possible resective epilepsy surgery. Referential and bipolar representations of these signals were subjected to different visual and time-series analysis. The time-series measures calculated were the power spectral density and magnitude squared coherence. RESULTS: Visual analysis and time-series measures revealed that the icEEG time-series was altered by the use of a bipolar montage. The changes resulted from either the introduction of unrelated information from the two referential time-series into the bipolar time-series, or from the removal or alteration of information common to the two referential time-series in the bipolar time-series. The changes could not be predicted without prior knowledge of the relationship between measurement sites that form the bipolar montage. CONCLUSIONS: In certain settings, bipolar montages alter icEEGs and can confound the time-series analysis of these signals. In such settings, bipolar montages should be used with caution in the time-series analysis of icEEGs. SIGNIFICANCE: This manuscript addresses the representation of the intracranial EEG for time-series analysis. There may be contexts where the assumptions underpinning correct application of the bipolar montage to the intracranial EEG are not satisfied.

Brain↗