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PubMed2003

Motion detection and the coincidence of structure at high and low spatial frequencies.

We used filtered random dot kinematograms and natural images to examine how motion detection depends the relative locations of structures defined at low and high spatial frequencies. The upper displacement limit of motion (D(max)), the lower displacement limit (D(min)) and motion coherence thresholds were unaffected by the degree of spatial coincidence between high and low spatial frequency structures i.e. whether they were consistent or inconsistent with a single feature. However motion detection was possible between band-pass filtered random dot patterns whose peak frequencies were separated by up to 4 octaves. The first result implicates spatial frequency selective motion detectors that operate independently. The second result implicates a motion system that can integrate the displacements of edges defined by widely separated spatial frequencies. Both are required to account for the two results, and they appear to operate under very similar conditions.

Contrast Sensitivity↗
PubMed1997

Twist grain boundaries in three-dimensional lamellar Turing structures.

Steady spatial self-organization of three-dimensional chemical reaction-diffusion systems is discussed with the emphasis put on the possible defects that may alter the Turing patterns. It is shown that one of the stable defects of a three-dimensional lamellar Turing structure is a twist grain boundary embedding a Scherk minimal surface.

Journal Article↗
PubMed1989

Calculating three-dimensional molecular structure from atom-atom distance information: cyclosporin A.

In recent years methods for deriving spatial molecular structure from atom-atom distance information have gained in importance due to the emergence of two-dimensional nuclear magnetic resonance (n.m.r) techniques, which make it possible to obtain such distance information for polypeptides, small proteins, sugars, and DNA fragments in solution. Distance geometry (DG) and restrained molecular dynamics (MD) refinement are applied to a cyclic polypeptide, the immunosuppressive drug cyclosporin A, and the results are compared. Two different procedures, DG followed by restrained MD, and straightforward restrained MD starting from the X-ray structure, both lead to a unique conformation that satisfies the 58 experimentally determined distance constraints. The results nicely show the relative merits of DG and restrained MD techniques for determining spatial molecular structure from distance information.

Cyclosporins↗
PubMed1999

Recognition of spatial motifs in protein structures.

As the structural database continues to expand, new methods are required to analyse and compare protein structures. Whereas the recognition, comparison, and classification of folds is now more or less a solved problem, tools for the study of constellations of small numbers of residues are few and far between. In this paper, two programs are described for the analysis of spatial motifs in protein structures. The first, SPASM, can be used to find the occurrence of a motif consisting of arbitrary main-chain and/or side-chains in a database of protein structures. The program also has a unique capability to carry out "fuzzy pattern matching" with relaxed requirements on the types of some or all of the matching residues. The second program, RIGOR, scans a single protein structure for the occurrence of any of a set of pre-defined motifs from a database. In one application, spatial motif recognition combined with profile analysis enabled the assignment of the structural and functional class of an uncharacterised hypothetical protein in the sequence database. In another application, the occurrence of short left-handed helical segments in protein structures was investigated, and such segments were found to be fairly common. Potential applications of the techniques presented here lie in the analysis of (newly determined) structures, in comparative structural analysis, in the design and engineering of novel functional sites, and in the prediction of structure and function of uncharacterised proteins.

Algorithms↗
PubMed2000

Non-destructive determination of local strain with 100-nanometre spatial resolution

Structure sizes of approximately 180 nm are now standard in microelectronics, and state-of-the-art fabrication techniques can reduce these to just a few tens of nanometres. But at these length scales, the strain induced at interfaces can locally distort the crystal lattice, which may in turn affect device performance in an unpredictable way. A means of non-destructively characterizing such strain fields with high spatial resolution and sensitivity is therefore highly desirable. One approach is to use Raman spectroscopy, but this is limited by the intrinsic approximately 0.5-microm resolution limit of visible light probes. Techniques based on electron-beam diffraction can achieve the desired nanometre-scale resolution. But either they require complex sample preparation procedures (which may alter the original strain field) or they are sensitive to distortional (but not dilational) strain within only the top few tens of nanometres of the sample surface. X-rays, on the other hand, have a much greater penetration depth, but have not hitherto achieved strain analysis with sub-micrometre resolution. Here we describe a magnifying diffraction imaging procedure for X-rays which achieves a spatial resolution of 100nm in one dimension and a sensitivity of 10(-4) for relative lattice variations. We demonstrate the suitability of this procedure for strain analysis by measuring the strain depth profiles beneath oxidized lines on silicon crystals.

Journal Article↗
PubMed1999

Isolation by distance in a continuous population: reconciliation between spatial autocorrelation analysis and population genetics models.

Analysis of the spatial genetic structure within continuous populations in their natural habitat can reveal acting evolutionary processes. Spatial autocorrelation statistics are often used for this purpose, but their relationships with population genetics models have not been thoroughly established. Moreover, it has been argued that the dependency of these statistics on variation in mutation rates among loci strongly limits their interest for inferential purposes. In the context of an isolation by distance process, we describe relationships between a descriptor of the spatial genetic structure used in empirical studies, Moran's I statistic and population genetics parameters. In particular, we point out that, when Moran's I statistic is used to describe correlation in allele frequencies at the individual level, it provides an estimator of Wright's coefficient of relationship. We also show that the latter parameter, as a descriptor of genetic structure, is not influenced by selfing rate or ploidy level. Under specific finite population models, numerical simulations show that values of Moran's I statistic can be predicted from analytical theory. These simulations are also used to estimate the time taken to approach a structure at equilibrium. Finally, we discuss the conditions under which spatial autocorrelation statistics are little influenced by variation in mutation rates, so that they could be used to estimate gene dispersal parameters.

Genetics, Population↗
PubMed2006

A sensitive method for measuring spatial orientation in bone structures.

OBJECTIVES: This article introduces the newly developed line frequency deviation (LFD) method for measuring the orientation of the trabecular structure and shows that it is more sensitive than the mean intercept length (MIL) method that is commonly used. METHODS: The LFD method, which has been developed to measure the orientation of bone on two-dimensional X-ray images, was expanded to handle three-dimensional shapes. For the purpose of comparison, both the LFD and the MIL methods were applied to micro CT scans of 24 trabecular bone samples as well as to 24 simple synthetic samples. LFD and MIL values were calculated in various directions and collected in polar plots. Next, the anisotropy was quantified by calculating the coefficient of variation as well as by fitting ellipsoids through the plots. RESULTS: The MIL method yielded smooth rather spherical ellipsoidal polar plots with almost no sensitivity for changes in structure. The LFD method yielded more slender polar plots and more sensitivity for geometrical changes. The LFD method yielded significantly more anistropy and larger variation in anisotropy. CONCLUSIONS: The LFD method is a more sensitive descriptor of spatial orientation of bone structures than the MIL method.

Anisotropy↗
PubMed2006

Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites.

Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S-locus.

Alleles↗
PubMed2003

Properties of spike train spectra in two parietal reach areas.

In the lateral intraparietal area (LIP), a saccade-related region of the posterior parietal cortex (PPC), spiking activity recorded during the memory period of an instructed-delay task exhibits temporal structure that is spatially tuned. These results provide evidence for the existence of 'dynamic memory fields' which can be read-out by other brain areas, along with information contained in the mean firing rate, to give the direction of a planned movement. We looked for evidence of dynamic memory fields in spiking activity in two parietal reach areas, the parietal reach region (PRR) and area 5. Monkeys made center-out reaches to eight target locations in an instructed-delay task with a memory component. Neurons in both areas exhibited sustained activity during the delay period that was spatially tuned. Many single cell PRR spectra exhibited spatially tuned temporal structure, as evidenced by a significant and spatially tuned peak in the 20-50 Hz band. The PRR population spectrum of spike trains was also tuned, with the peak power centered on approximately 25 Hz. In contrast, area 5 spiking activity did not exhibit any significant temporal structure. These results suggest that different mechanisms underlie sustained delay period activity in these two areas and that dynamic memory fields, as revealed by our techniques, are more prominent in PRR than in area 5. Temporal structure in the spike train and local field potential (LFP) are related in at least one other brain area (LIP). The present results suggest then that LFP activity obtained from PRR may be better suited than area 5 LFP activity for use in neural prosthetic systems that incorporate analysis of temporal structure as part of a decode mechanism for extracting intended movement goals.

Action Potentials↗
PubMed2003

Spatial and demographic population genetic structure in Catasetum viridiflavum across a human-disturbed habitat.

Spatial and temporal genetic structures were examined across sites on islands and mainland (continuous forest) populations of an epiphytic orchid, Catasetum viridiflavum, using 17 polymorphic allozyme loci. I tested whether patches on islands or at mainland sites comprised small local populations or a large population. Low among population differentiation was observed across the landscape suggesting that the species-specific pollinator and tiny wind-dispersed seeds maintain interconnections among distant patches. Temporal genetic structure among stage classes, and among breeding individuals are important components of the maintenance of genetic variation in this orchid. The natural history of this species including small breeding populations, probable high frequency of mating among relatives, and the high rates of seed movement among sites contribute to the high FIS. These data show that physically isolated patches in this epiphytic orchid comprise a single larger genetic population, which is independent of the physical distances among sites. Although quite different in ecological and life history characteristics, the genetic structure of this orchid demonstrates a pattern similar to temperate and tropical trees in fragmented landscapes.

Ecology↗
PubMed2005

Local genetic population structure in an endangered plant species, Silene tatarica (Caryophyllaceae).

Genetic substructuring in plant populations may evolve as a consequence of sampling events that occur when the population is founded or regenerated, or if gene dispersal by pollen and seeds is restricted within a population. Silene tatarica is an endangered, perennial plant species growing along periodically disturbed riverbanks in northern Finland. We investigated the mechanism behind the microspatial genetic structure of S. tatarica in four subpopulations using amplified fragment length polymorphism markers. Spatial autocorrelation revealed clear spatial genetic structure in each subpopulation, even though the pattern diminished in older subpopulations. Parentage analysis in an isolated island subpopulation indicated a very low level of selfing and avoidance of breeding between close relatives. The mean estimated pollen dispersal distance (24.10 m; SD = 10.5) was significantly longer and the mean seed dispersal distance (9.07 m; SD = 9.23) was considerably shorter than the mean distance between the individuals (19.20 m; SD = 13.80). The estimated indirect and direct estimates of neighbourhood sizes in this subpopulation were very similar, 32.1 and 37.6, respectively. Our results suggested that the local spatial genetic structure in S. tatarica was attributed merely to the isolation-by-distance process rather than founder effect, and despite free pollen movement across population, restricted seed dispersal maintains local genetic structure in this species.

DNA, Plant↗
PubMed1997

A spatial equilibrium model for region size, urbanization ratio, and rural structure.

"Earlier economic models of city size have either focused on urban agglomeration effects while ignoring the spatial structure of the rural hinterland, or made unrealistic assumptions (for example, uniform rural population distribution) so as to simplify the problem. Following the classic von Thunen framework, we present a two-sector spatial equilibrium model of a city located at the center of an agricultural hinterland. The city produces industrial goods, and the rural area produces agricultural goods. Both goods are consumed both by urban and by rural residents. Market equilibrium for these goods determines: (1) the spatial size of the region, (2) the urbanization ratio (urban to total population) and the population size of the city, and (3) the rural spatial structure (wage, population distribution, land rent, and agricultural yield). Given various sets of exogenous parameters pertaining to the industrial, agricultural, and transportation production functions and to population preferences, the model is solved numerically, and response functions are estimated and analyzed."

Agriculture↗
PubMed2005

Clonal and fine-scale genetic structure in populations of a restricted Korean endemic, Hosta jonesii (Liliaceae) and the implications for conservation.

BACKGROUND AND AIMS: In plant populations the magnitude of spatial genetic structure of apparent individuals (including clonal ramets) can be different from that of sexual individuals (genets). Thus, distinguishing the effects of clonal versus sexual individuals in population genetic analyses could provide important insights for evolutionary biology and conservation. To investigate the effects of clonal spread on the fine-scale spatial genetic structure within plant populations, Hosta jonesii (Liliaceae), an endemic species to Korea, was chosen as a study species. METHODS: Using allozymes as genetic markers, spatial autocorrelation analysis of ramets and of genets was conducted to quantify the spatial scale of clonal spread and genotype distribution in two populations of H. jonesii. KEY RESULTS: Join-count statistics revealed that most clones are significantly aggregated at < 3-m interplant distance. Spatial autocorrelation analysis of all individuals resulted in significantly higher Moran's I values at 0-3-m interplant distance than analyses of population samples in which clones were excluded. However, significant fine-scale genetic structure was still observed when clones were excluded. CONCLUSIONS: These results suggest that clones enhance the magnitude of spatial autocorrelation due to localized clonal spread. The significant fine-scale genetic structure detected in samples excluding clones is consistent with the biological and ecological traits exhibited by H. jonesii including bee pollination and limited seed dispersal. For conservation purposes, genetic diversity would be maximized in local populations of H. jonesii by collecting or preserving individuals that are spaced at least 5 m apart.

Alleles↗
PubMed2002

Old-growth red spruce forests as reservoirs of genetic diversity and reproductive fitness.

Old-growth forests are assumed to be potential reservoirs of genetic diversity for the dominant tree species, yet there is little empirical evidence for this assumption. Our aim was to characterize the relationship of stand traits, such as age, height and stem diameter, with the genetic and reproductive status of old-growth and older second-growth stands of red spruce (Picea rubens Sarg.) in eastern Canada. We found strong relationships between height growth (a fitness trait) and measures of genetic diversity based on allozyme analyses in red spruce. The negative relationship between height and the proportion of rare alleles suggests that high proportions of these rare alleles may be deleterious to growth performance. Latent genetic potential, however, showed a significant and positive relationship with height. Stand age was not correlated to height, but was correlated to seedling progeny height. In late-successional species such as red spruce, age and size (e.g., height and stem diameter) relationships may be strongly influenced by local stand disturbance dynamics that determine availability of light, growing space, moisture and nutrients. In larger and older stands, age appeared to provide a good surrogate measure or indicator for genetic diversity and progeny height growth. However, in smaller and more isolated populations, these age and fitness relationships may be strongly influenced by the effects of inbreeding and genetic drift. Therefore, older populations or old-growth forests may represent superior seed sources, but only if they are also of sufficient size and structure (e.g., stem density and spatial family structure) to avoid the effects of inbreeding and genetic drift. Thus, larger and older forests appear to have an important evolutionary role as reservoirs of both genetic diversity and reproductive fitness. Given the rapid environmental changes anticipated (as a result of climate change, increasing population isolation through fragmentation, or following the introduction of exotic pests and diseases) these older populations of trees may have a valuable function in maintaining the adaptive potential of tree species.

Genetic Variation↗
PubMed1993

Rhythmic and patterned neuronal firing in visual cortex.

We present evidence from multi-electrode recordings that the stimulus driven activity in a region of monkey visual cortex displays synchronous, oscillatory behaviour with temporally changing patterns of firing. The spatial-temporal patterns are dependent on cortical layer and on visual stimulus, 'build up and die down' with a period of 70-100 msec, and cannot be factorized into separate spatial and temporal components. This finding supports neural network models which explicitly incorporate spatial-temporal structure, ruling against a purely spatial code for information processing. The new type of analysis presented here is also suitable for direct on-line interactive analysis during multi-electrode recording experiments. Further, it could be modified for use in human EEG or evoked response recordings.

Action Potentials↗
PubMed2000

Spatial distribution of allozyme polymorphisms following clonal and sexual reproduction in populations of Rhus javanica (Anacardiaceae).

Rhus javanica L. (Anacardiaceae), a dioecious tree with both sexual reproduction and clonal growth, is widely distributed in warm temperate, subtropical, and tropical regions in east Asia. We used allozyme loci and spatial autocorrelation statistics to examine clonal structure and the spatial distribution of allozyme polymorphisms in two Korean populations. Populations of the species maintain moderate levels of allozyme variability (mean He=0.175, GST=0.060), and high levels of multilocus genotypic diversity (mean DG=0.971). Clone-pair distances ranged from 1.4 m to 57.4 m, and had high mean values of 24.0 m and 25.6 m in the two study populations. Approximate genetic patch widths were inferred to be 23-25 m. The results indicated that within populations there is moderate (one study population) or no (other study population) spatial genetic structure among sexually reproduced individuals, and vegetatively reproduced genotypes also are almost randomly distributed. The spatial genetic structure among sexually reproduced trees in the one case is probably caused by limited pollen dispersal in that population, and the lack of structure in the other probably results from the short time elapsed since founding. It appears that clonal reproduction also does not contribute substantially to genetic isolation by distance neither among the sexually reproduced individuals nor the total population. Ramets often establish long distances from their progenitors and thus do not substantially increase the degree of local consanguineous matings.

Genetic Markers↗
PubMed2004

Characterization of land contaminated by past heavy metal mining using geostatistical methods.

Aspects of mining operations, including production, processing, transportation, and, finally, abandoned mine workings, can undoubtedly cause varying degrees of environmental pollution and contamination. Characterization of the spatial distribution of pollutants in contaminated soil is important for risk assessment and soil remediation. This study has been carried out using both conventional statistics and geostatistical methods which are useful for site assessment, characterization, and monitoring situations where data are collected spatially. These methods are particularly suited to cases where spatial dependence structure and contour maps of contaminant concentration or other variables are needed. The aims of this paper were to determine the extent and severity of the pollution levels on land contaminated by past mining activity through using geostatistical techniques, assess sampling strategy, and interpret data for potentially contaminated land. In the study, a total of 329 soil samples was collected at 1-, 5-, and 10-m regular grid intervals of 100 x 1 00-m area of Carsington Pasture in the UK and analyzed using an automatic X-ray fluorescence machine for a large number of elements. Only a few elements (Cu, Pb, Zn, and Ba) were subsequently studied in detail because of their association with the mining operation. Directional and omnidirectional experimental semivariograms of elements Cu, Pb, Zn, and Ba for 10-m grid intervals, pooled data of 10- and 5-m grid intervals (S10+5), and pooled data of 10-, 5-, and 1-m grid interval (S10+5+1) showed that neither geometric nor zonal anisotropy exits in the data. The most evident spatial dependence structure of the continuity for omnidirectional experimental semivariogram, characterized by a spherical model, of each element was obtained for the pooled data set of S10+5. Pooling 1-m grid data to S10+5 shaded the spatial dependence structure. The spherical model adopted for each element embodied no nugget effect, indicating that mineralization did not occur as nuggets in the study area, but it did show different ranges of influence and sill values. Spherical semivariogram model of each element for the pooled data set of S10+5 passed the cross validation tests. Graphs of cross validation test results proved that the isotropic spherical model, with its parameters and kriging search parameters, is representative for the area under study. The values of 10,000 grid nodes established regularly over the study area were estimated by kriging interpolation technique to smooth out the contours. Kriged maps for the Cu, Pb, Zn, and Ba elements were plotted. Anomalies such as bull's-eyes and drift did not observed in the maps generated. Contour maps of estimated element concentrations revealed the extent and severity of contamination. Spatial distribution maps of the elements might be used in the remediation studies and help decision-makers and others involved in the abandoned heavy metal mining site in the UK.

Data Interpretation, Statistical↗
PubMed1999

Dynamic characteristics of spatial mechanisms coding contour structures.

Psychophysical thresholds for the detection of luminance targets improve significantly when the targets are presented in a specific context of spatially separated, collinear inducing stimuli defining visual contours. This phenomenon is generally referred to as a special case of detection facilitation called spatial facilitation. Spatial facilitation has been observed with luminance-defined. achromatic stimuli on achromatic backgrounds as well as with targets and inducers defined by colour contrast. This paper reviews psychophysical results from detection experiments with human observers showing the conditions under which spatially separated contour inducers facilitate the detection of simultaneously presented target stimuli. The findings point towards two types of spatial mechanisms: (i) Short-range mechanisms that are sensitive to narrowly spaced stimuli of small size and, at distinct target locations, selective to the contrast polarity of targets and inducers. (ii) Long-range mechanisms that are triggered by longer stimuli, generate facilitation across wider spatial gaps between targets and inducers, and are insensitive to their contrast polarity. Spatial facilitation with chromatic stimuli requires a longer inducer exposure than spatial facilitation with achromatic stimuli, which is already fully effective at inducer exposures of 30 ms. This difference in temporal dynamics indicates some functional segregation between mechanisms for colour and luminance contrast in spatial coding. In general, spatially induced detection facilitation can to a large extent be explained by mechanisms involving from-short-to-long-range interactions between cortical detectors.

Humans↗

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