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PubMed2003

Accuracy of CT-based thickness measurement of thin structures: modeling of limited spatial resolution in all three dimensions.

Measurement of the width of thin structures such as the cortical shell of the vertebral body or femoral neck with computed tomography (CT) is limited by the spatial resolution of the CT system. Limited spatial resolution exists both within the CT image plane and perpendicular to it and can be described by the in-plane point spread function (PSF) and the across-plane slice sensitivity profile (SSP), respectively. The goal of this study was to confirm that errors of thickness measurement of thin structures critically depend on the spatial positioning of the object and the spatial resolution limitations of CT in all three dimensions, and to assess the size of the errors themselves. We compared computer models that incorporated both effects to experimentally assessed cortical thicknesses of the European Spine Phantom. Analysis included varying CT slice width, the orientation of measurement and angle beta of misalignment of longitudinal scanner and phantom axes. Agreement of models with measurements was good in all configurations with an overall error of 0.17 mm. This showed that PSF and SSP are adequate system characteristics to predict deviation of measured values from true widths. Errors between measurements and true cortical thickness values delta(true) averaged to 1.5 mm were strongly positively correlated with slice width d and beta. When the across-plane partial volume effect was eliminated, limited in-plane resolution still accounted for overestimation of delta(true) by 0.68 (137%), 0.27 (27%), and 0.06 mm (4%) for delta(true)=0.5, 1.0, and 1.5 mm, respectively. For delta(true) of 1.0 mm and above, it was shown that although the absolute cortical thickness values might not be accurately measurable, relative differences between two values are reflected in measurement. Implications for cortical thickness measurement are that the spinal cortical shell is too thin, whereas accurate assessment at locations of the femoral neck exhibiting a thicker cortical shell of both difference and absolute values should be possible with CT even for larger misalignment angles, especially when a smaller CT slice width is chosen.

Computer Simulation↗
PubMed2004

Maximum-likelihood estimation of low-rank signals for multiepoch MEG/EEG analysis.

A maximum-likelihood-based algorithm is presented for reducing the effects of spatially colored noise in evoked response magneto- and electro-encephalography data. The repeated component of the data, or signal of interest, is modeled as the mean, while the noise is modeled as the Kronecker product of a spatial and a temporal covariance matrix. The temporal covariance matrix is assumed known or estimated prior to the application of the algorithm. The spatial covariance structure is estimated as part of the maximum-likelihood procedure. The mean matrix representing the signal of interest is assumed to be low-rank due to the temporal and spatial structure of the data. The maximum-likelihood estimates of the components of the low-rank signal structure are derived in order to estimate the signal component. The relationship between this approach and principal component analysis (PCA) is explored. In contrast to prestimulus-based whitening followed by PCA, the maximum-likelihood approach does not require signal-free data for noise whitening. Consequently, the maximum-likelihood approach is much more effective with nonstationary noise and produces better quality whitening for a given data record length. The efficacy of this approach is demonstrated using simulated and real MEG data.

Algorithms↗
PubMed2004

Pollinator community structure and sources of spatial variation in plant--pollinator interactions in Clarkia xantiana ssp. xantiana.

The structure of diverse floral visitor assemblages and the nature of spatial variation in plant-pollinator interactions have important consequences for floral evolution and reproductive interactions among pollinator-sharing plant species. In this study, I use surveys of floral visitor communities across the geographic range of Clarkia xantiana ssp. xantiana (hereafter C. x. xantiana) (Onagraceae) to examine the structure of visitor communities, the specificity of the pollination system, and the role of variation in the abiotic vs. biotic environment in contributing to spatial variation in pollinator abundance and community composition. Although the assemblage of bee visitors to C. x. xantiana is very diverse (49 species), few were regular visitors and likely to act as pollinators. Seventy-four percent of visitor species accounted for only 11% of total visitor abundance and 69% were collected in three or fewer plant populations (of ten). Of the few reliable visitors, Clarkia pollen specialist bees were the most frequent visitors, carried more Clarkia pollen compared to generalist foragers, and were less likely to harbor foreign pollen. Overall, the core group of pollinators was obscured by high numbers of incidental visitors that are unlikely to contribute to pollination. In a geographic context, the composition of specialist pollinator assemblages varied considerably along the abiotic gradient spanning the subspecies' range. However, the overall abundance of specialist pollinators in plant populations was not influenced by the broad-scale abiotic gradient but strongly affected by local plant community associations. C. x. xantiana populations sympatric with pollinator-sharing congeners were visited twice as often by specialists compared to populations occurring alone. These positive indirect interactions among plant species may promote population persistence and species coexistence by enhancing individual reproductive success.

Analysis of Variance↗
PubMed2003

Genetic structure of age classes in Camellia japonica (Theaceae).

Camellia japonica L. (Theaceae), an insect- and bird-pollinated, broad-leaved evergreen tree, is widely distributed in Japan and the southern Korean peninsula. The species has a relatively even age distribution within populations, which may influence the spatial genetic structure of different age classes relative to species with typical L-shaped age distributions. To determine whether the internal spatial genetic structure found in seedlings and young individuals carries over into adults, we used allozyme loci, F-statistics, spatial autocorrelation statistics (Moran's I), and coancestry measures to examine changes in genetic structure among seven age classes in a population (60-m x 100-m area) in southern Korea. In seedlings, weak but significant positive values of Moran's I-statistics and coancestry measures were found for distances less than 14 m, which is consistent with a mechanism of limited seed dispersal combined with overlapping seed shadows. This spatial structure, however, dissipates in older age classes, and in adults genetic variation has an essentially random spatial distribution. Morisita's index of dispersion of individuals in each age class showed that seedlings and juveniles are more highly clustered than are older individuals. These results suggest that self-thinning changes the spatial relationships of individuals, and thus genotypes. A multilocus estimate of FST (0.008) shows a small but statistically significant difference in allele frequencies among age classes. In summary, intrapopulation genetic structure within and among age classes of C. japonica was significant but weak. Despite presumably limited seed dispersal, weak spatial genetic structure in juveniles suggests overlapping seed shadows followed by self-thinning during recruitment. The present study also demonstrates that studies of spatial genetic structure focusing on limited numbers of generations may not be sufficient to reveal the entire picture of genetic structure in populations with overlapping generations.

Electrophoresis↗
PubMed2005

Identification of spatial genetic boundaries using a multifractal model in human population genetics.

There are two purposes in displaying spatial genetic structure. One is that a visual representation of the variation of the genetic variable should be provided in the contour map. The other is that spatial genetic structure should be reflected by the patterns or the gradients with genetic boundaries in the map. Nevertheless, most conventional interpolation methods, such as Cavalli-Sforza's method in genography, inverse distance-weighted methods, and the Kriging technique, focus only on the first primary purpose because of their arbitrary thresholds marked on the maps. In this paper we present an application of the contour area multifractal model (CAMM) to human population genetics. The method enables the analysis of the geographic distribution of a genetic marker and provides an insight into the spatial and geometric properties of obtained patterns. Furthermore, the CAMM may overcome some of the limitations of other interpolation techniques because no arbitrary thresholds are necessary in the computation of genetic boundaries. The CAMM is built by establishing power law relationships between the area A (> or =rho) in the contour map and the value p itself after plotting these values on a log-log graph. A series of straight-line segments can be fitted to the points on the log-log graph, each representing a power law relationship between the area A (> or =rho) and the cutoff genetic variable value for rho in a particular range. These straight-line segments can yield a group of cutoff values, which can be identified as the genetic boundaries that can classify the map of genetic variable into discrete genetic zones. These genetic zones usually correspond to spatial genetic structure on the landscape. To provide a better understanding of the interest in the CAMM approach, we analyze the spatial genetic structures of three loci (ABO, HLA-A, and TPOX) in China using the CAMM. Each synthetic principal component (SPC) contour map of the three loci is created by using both Han and minority groups data together. These contour maps all present an obvious geographic diversity, which gradually increases from north to south, and show that the genetic differences among populations in different districts of the same nationality are greater than those among different nationalities of the same district. It is surprising to find that both the value of p and the fractal dimension alpha have a clear north to south gradient for each locus, and the same clear boundary between southern and northern Asians in each contour map is still seen in the zone of the Yangtze River, although substantial population migrations have occurred because of war or famine in the last 2,000 or 3,000 years. A clear genetic boundary between Europeans and Asians in each contour map is still seen in northwestern China with a small value of alpha, although the genetic gradient caused by gene flow between Europeans and Asians has tended to show expansion from northwestern China. From the three contour maps another interesting result can be found: The values of alpha north of the Yangtze River are generally less than those south of the Yangtze River. This indicates that the genetic differences among the populations north of the Yangtze River are generally smaller than those in populations south of the Yangtze River.

ABO Blood-Group System↗
PubMed2005

Fast similarity search for protein 3D structures using topological pattern matching based on spatial relations.

Similarity search for protein 3D structures become complex and computationally expensive due to the fact that the size of protein structure databases continues to grow tremendously. Recently, fast structural similarity search systems have been required to put them into practical use in protein structure classification whilst existing comparison systems do not provide comparison results on time. Our approach uses multi-step processing that composes of a preprocessing step to represent geometry of protein structures with spatial objects, a filter step to generate a small candidate set using approximate topological string matching, and a refinement step to compute a structural alignment. This paper describes the preprocessing and filtering for fast similarity search using the discovery of topological patterns of secondary structure elements based on spatial relations. Our system is fully implemented by using Oracle 8i spatial. We have previously shown that our approach has the advantage of speed of performance compared with other approach such as DALI. This work shows that the discovery of topological relations of secondary structure elements in protein structures by using spatial relations of spatial databases is practical for fast structural similarity search for proteins.

Algorithms↗
PubMed1999

Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements.

We carry out a systematic analysis of the correlation between similarity of protein three-dimensional structures and their evolutionary relationships. The structural similarity is quantitatively identified by an all-against-all comparison of the spatial arrangement of secondary structural elements in nonredundant 967 representative proteins, and the evolutionary relationship is judged according to the definition of superfamily in the SCOP database. We find the following symmetry rule: a protein pair that has similar folds but belong to different superfamilies has (with a very rare exception) certain internal symmetry in its common similar folds. Possible reasons behind the symmetry rule are discussed.

Models, Molecular↗
PubMed2006

Separate modulations of human V1 associated with spatial attention and task structure.

Functional magnetic resonance imaging (fMRI) was used while normal human volunteers engaged in simple detection and discrimination tasks, revealing separable modulations of early visual cortex associated with spatial attention and task structure. Both modulations occur even when there is no change in sensory stimulation. The modulation due to spatial attention is present throughout the early visual areas V1, V2, V3, and VP, and varies with the attended location. The task structure activations are strongest in V1 and are greater in regions that represent more peripheral parts of the visual field. Control experiments demonstrate that the task structure activations cannot be attributed to visual, auditory, or somatosensory processing, the motor response for the detection/discrimination judgment, or oculomotor responses such as blinks or saccades. These findings demonstrate that early visual areas are modulated by at least two types of endogenous signals, each with distinct cortical distributions.

Adult↗
PubMed2006

Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers.

Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic, Mediterranean and Black Sea populations are genetically disjunct. The present study used a higher sampling intensity and a combination of mitochondrial and four microsatellite markers to reveal population structuring between and within basins. Between basins, both marker sets indicated significant differentiation confirming earlier results that gene flow is probably absent between the respective S. setosa populations. At the within-basin scale, we found no evidence of spatial or temporal structuring within the NE Atlantic. In the Mediterranean basin, both marker sets indicated significant structuring, but only the mtDNA data indicated a sharp genetic division between Adriatic and all other Mediterranean populations. Data were inconclusive about population structuring in the Black Sea. The levels of differentiation indicated by the two marker sets differed substantially, with far less pronounced structure detected by microsatellite than mtDNA data. This study also uncovered the presence of highly divergent mitochondrial lineages that were discordant with morphology, geography and nuclear DNA. We thus propose the hypothesis that highly divergent mitochondrial lineages may be present within interbreeding S. setosa populations.

Atlantic Ocean↗
PubMed2002

Population genetic structure of the cyclic snowshoe hare (Lepus americanus) in southwestern Yukon, Canada.

Spatial population structure has important ecological and evolutionary consequences. Little is known about the population structure of snowshoe hares (Lepus americanus), despite their ecological importance in North American boreal forests. We used seven variable microsatellite DNA loci to determine the spatial genetic structure of snowshoe hares near Kluane Lake, Yukon during a cyclic population peak. We sampled 317 hares at 12 sites separated by distances ranging from 3 to 140 km, and used 46 additional samples from Alaska and Montana. The level of genetic variation was high (13.4 alleles/locus, 0.67 expected heterozygosity) and the distribution of alleles and genotypes was not homogeneous across the sites. The degree of differentiation was low among Yukon sites (FST = 0.015) and between Yukon and Alaska (FST = 0.012), but the Montana site was highly differentiated (FST = 0.20). A weak pattern of isolation by distance was found over the Yukon study area, with an indication that local genetic drift may be important in shaping the regional genetic structure. Landscape barriers expected to influence gene flow did not consistently affect genetic structure, although there was evidence for a partial barrier effect of Kluane Lake. The high level of inferred gene flow confirms that snowshoe hare dispersal is widespread, successful and equal between the sexes. A stepping-stone model of gene flow, potentially influenced by the synchronous density cycle, appears to best explain the observed genetic structure. Our results suggest that despite their dramatic fluctuations in density, snowshoe hares in the northern boreal forest have a large evolutionary effective population size and are not strongly subdivided by either physical or social barriers to gene flow.

Alaska↗
PubMed2026

Spatial habitat radiomics predicts tertiary lymphoid structure status and identifies an IDO1+ migratory dendritic cell axis in breast cancer.

BACKGROUND: Tertiary lymphoid structures (TLS) are spatially organized immune niches associated with therapeutic response and favorable outcomes in breast cancer (BC). However, TLS assessment currently relies on invasive tissue-based analyses, and the biological mechanisms underlying imaging-based TLS prediction remain poorly understood. METHODS: We developed and validated a spatial heterogeneity-based radiomic TLS signature (shTLS) using dynamic contrast-enhanced MRI to non-invasively predict TLS status across multicenter BC cohorts. Spatial habitat radiomics were used to capture intratumoral and peritumoral immune-related heterogeneity. Integrated multi-omics analyses, including transcriptomics, pathomics, genomics, single-cell RNA sequencing, immunohistochemistry, and multiplex immunofluorescence, were performed to biologically interpret shTLS-defined subgroups. Functional drug-sensitivity assays were conducted to assess therapeutic implications. RESULTS: The shTLS model achieved robust predictive performance across independent cohorts and molecular subtypes. High shTLS scores were associated with immune-inflamed tumors characterized by spatially clustered activated T cells and dendritic cells (DCs). In contrast, shTLS-low tumors exhibited an immunosuppressive spatial niche with peripheral accumulation of CD4+ PD-1+ T cells and plasma cells, increased immune-tumor separation, and enhanced inflammatory and immunoregulatory signaling. An indoleamine 2,3-dioxygenase 1 (IDO1)-associated immunoregulatory program was observed in the shTLS-low tumors, which appeared to be preferentially expressed by LAMP3+CCR7+ migratory DCs. Pharmacologic inhibition of IDO1 enhanced chemotherapy and CDK4/6 inhibitor sensitivity in vitro. CONCLUSION: This study establishes spatial radiomics as a non-invasive approach to decode TLS-associated immune ecosystems and supports the presence of an IDO1-associated immunosuppressive phenotype, providing biological insight and translational rationale for patient stratification and future combination strategies.

Humans↗
PubMed2005

Do distances among host patches and host density affect the distribution of a specialist parasitoid?

The effect of spatial habitat structure and patchiness may differ among species within a multi-trophic system. Theoretical models predict that species at higher trophic levels are more negatively affected by fragmentation than are their hosts or preys. The absence or presence of the higher trophic level, in turn, can affect the population dynamics of lower levels and even the stability of the trophic system as a whole. The present study examines different effects of spatial habitat structure with two field experiments, using as model system the parasitoid Cotesia popularis which is a specialist larval parasitoid of the herbivore Tyria jacobaeae. One experiment examines the colonisation rate of the parasitoid and the percentage parasitism at distances occurring on a natural scale; the other experiment examines the dispersal rate and the percentage parasitism in relation to the density of the herbivore and its host plant. C. popularis was able to reach artificial host populations at distances up to the largest distance created (at least 80 m from the nearest source population). Also, the percentage parasitism did not differ among the distances. The density experiment showed that the total number of herbivores parasitised was higher in patches with a high density of hosts, regardless of the density of the host plant. The percentage parasitism, however, was not related to the density of the host. The density of the host plant did have a (marginally) significant effect on the percentage parasitism, probably indicating that the parasitoid uses the host plant of the herbivore as a cue to find the herbivore itself. In conclusion, the parasitoid was not affected by the spatial habitat structure on spatial scales that are typical of local patches.

Animals↗
PubMed2003

Phylogenetic analysis of bacterial populations in an anaerobic microbial consortium capable of degrading saturation concentrations of tetrachloroethylene.

An anaerobic microbial consortium able to biodegrade saturation levels of perchloroethylene (PCE) in a column containing a source zone of PCE was examined phylogenetically to determine microbial community structure and spatial variation in relation to the PCE source. The consortium was comprised of at least 34 members with 7 organisms sharing affiliations with known respiratory or cometabolic dechlorinators. Seven other organisms had their closest phylogenetic relative detected in other environments containing chlorinated compounds. Based on denaturing gradient gel electrophoresis, significant Bacteria were Dehalococcoides ethenogenes, Shewanella putrefaciens, and an Acetobacterium species. Spatial variations in community structure of the consortium relative to the PCE source zone were observed. A Pseudomonas species was predominant in a zone 30 cm from the PCE source. A Methanothrix species was predominant at points over 85 cm from the source zone. A Trichlorobacter species was detected where PCE concentrations were highest, up to 85 cm from the PCE source, whereas D. ethenogenes was ubiquitous to over 128 cm from the PCE source.

Anaerobiosis↗
PubMed1998

Spatial arrangement of the structural elements of vocal fold layers: an adjustment to the vibration process.

It is well established that the multilayered structure of the vocal fold is highly adjusted to the requirements of the vibration process during phonation. There is also some partial data indicating that the spatial arrangement of each vocal fold layer corresponds to the functional requirements, and thus facilitate the phonation process. Nevertheless, all reports on the spatial arrangement of the vocal fold structures deal only with an individual element of the vocal fold histologic structure. The present study encompasses the spatial histologic analysis of all major elements of the vocal fold layers. It was demonstrated that the vocal fold epithelial cells, the connective and muscle fibers, and even the blood vessels run parallel to the vocal fold free edge, which indicates a high adjustment to the phonation requirements and the vibration process.

Humans↗
PubMed1993

The spatial organization of epidermal structures: hairy establishes the geometrical pattern of Drosophila leg bristles by delimiting the domains of achaete expression.

The spatial organization of Drosophila melanogaster epidermal structures in embryos and adults constitutes a classic model system for understanding how the two dimensional arrangement of particular cell types is generated. For example, the legs of the Drosophila melanogaster adult are covered with bristles, which in most segments are arranged in longitudinal rows. Here we elucidate the key roles of two regulatory genes, hairy and achaete, in setting up this periodic bristle pattern. We show that achaete is expressed during pupal leg development in a dynamic pattern which changes, by approximately 6 hours after puparium formation, into narrow longitudinal stripes of 3-4 cells in width, each of which represents a field of cells (proneural field) from which bristle precursor cells are selected. This pattern of gene expression foreshadows the adult bristle pattern and is established in part through the function of the hairy gene, which also functions in patterning other adult sense organs. In pupal legs, hairy is expressed in four longitudinal stripes, located between every other pair of achaete stripes. We show that in the absence of hairy function achaete expression expands into the interstripe regions that normally express hairy, fusing the two achaete stripes and resulting in extra-wide stripes of achaete expression. This misexpression of achaete, in turn, alters the fields of potential bristle precursor cells which leads to the misalignment of bristle rows in the adult. This function of hairy in patterning achaete expression is distinct from that in the wing in which hairy suppresses late expression of achaete but has no effect on the initial patterning of achaete expression. Thus, the leg bristle pattern is apparently regulated at two levels: a global regulation of the hairy and achaete expression patterns which partitions the leg epidermis into striped zones (this study) and a local regulation (inferred from other studies on the selection of neural precursor cells) that involves refinement steps which may control the alignment and spacing of bristle cells within these zones.

Animals↗
PubMedDate not supplied

[The spatial relationships and social structure of gerbils in the genus Meriones (Gerbillinae, Rodentia)].

Comparative analysis of spatial relations of 4 gerbil species (M. tamariscinus M. meridianus, M. libycus, M. unguiculatus) shows differences in the system of space use between species and within a species--between individuals of different sex. During reproduction period females are inclined to isolation, small overlap of home ranges and high degree of individualisation. Males occupy large home ranges overlapping with territories of several reproductive females. The territories occupied by the males of midday and tamarisk gerbils do not have clear boundaries and the level of their individualization is quite low. The males of Mongolian gerbil (M. unguiculatus) occupy well defined territories with high level of individualization. Spatial relations of M. libycus males are intermediate. The relationships of the males of three investigated species (M. meridianus, M. libycus, M. tamariscinus) being characterised by the high degree of asymmetry of pair connections, are organised according to the principle of agonistic dominance. Relationships between individuals of different family groups of Mongolian gerbils are based on the locus-dependent dominance, while within one family group-on principle of hierarchical subordination. The meaning of specific peculiarities in use of space and dominance relations are discussed in terms of reproductive strategies.

Aging↗
PubMed1999

Spatial and temporal genetic structure in chloroplast and allozyme markers in phacelia dubia implicate genetic drift

For neutral genes, uniparental inheritance is expected to reduce effective population size relative to biparentally inherited genes. In finite populations, the ensuing genetic drift can cause stronger spatial and temporal differentiation. An intrapopulation polymorphism in chloroplast DNA was used to examine relative spatial and temporal population structure of chloroplast and allozyme markers in the annual plant Phacelia dubia. There was significant differentiation among populations at chloroplast markers but not for allozyme loci. A fine-scale analysis showed significant structure among sites within populations for chloroplast markers and local heterozygote deficiencies at allozyme loci. These spatial analyses suggest that gene flow via pollen exceeds that via seed. Temporal variation in chloroplast markers, assessed over a 10-year period, was evident in two of four populations, and allozyme loci were characterized by temporal variation in rare-allele frequencies. Population structure appeared to be related to the intensity and type of human disturbance influencing each population. Habitat destruction promoted isolation and enhanced differentiation, whereas mowing increased seed dispersal and reduced differentiation for chloroplast markers. At this time, genetic drift appears to be the primary force shaping chloroplast gene frequencies.

Journal Article↗
PubMed1989

Subjective hierarchies in spatial memory.

Two experiments investigated the structure of spatial memories. Subjects learned locations of objects in spatial layouts (Experiment 1) or locations of object names on maps (Experiment 2). Physical and perceptual boundaries were absent in these spatial arrays. Subjects then participated in three tasks: item recognition, in which the variable of interest was spatial priming; free and cued recall; and Euclidean distance estimation. Ordered-tree analysis of individual subjects' recall protocols produced hierarchical trees consistent with regularities in output order. Spatial priming and distance estimations depended on whether pairs of objects appeared in the same subtree or in different subtrees. These findings indicate that spatial memories have a hierarchical component, even when physical and perceptual boundaries are nonexistent. Priming also increased with depth of clustering in ordered trees. This result supports spreading-activation theories of retrieval but provides evidence against several "non-spreading-activation" theories.

Adult↗