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At least 217 records · Page 12Linked to original sources
PubMed1992

Distance and risk measures for the analysis of spatial data: a study of childhood cancers.

Three statistical approaches, used to detect spatial clusters of disease associated with a point source exposure, are applied to childhood cancer data for the city of San Francisco (1973-88). The distributions of incident cases of leukemia (51 cases), brain cancer (35 cases), and lymphatic cancer (37 cases) among individuals less than 21 years of age are described using three measures of clustering: distance on a geopolitical map, distance on a density equalized transformed map, and relative risk. The point source of exposure investigated is a large microwave tower located southwest of the center of the city (Sutro Tower). The three analytic approaches indicate that the patterns of the major childhood cancers are essentially random with respect to the point source. These results and a statistical model for spatial clustering are used to explore distance and risk measures in the analysis of spatial data. Both types of measures of spatial clustering are shown to perform similarly when a specific area of exposure can be defined.

Adolescent↗
PubMed2001

New double-tracer digital radiography for analysis of spatial and temporal myocardial flow heterogeneity.

A new high-resolution digital radiographic technique based on the deposition of (125)I- and (3)H-labeled desmethylimipramine (IDMI and HDMI, respectively) was developed for the assessment of spatial and temporal myocardial flow heterogeneity at a microvascular level. The density distributions of two tracers, or relative flow distributions, were determined by subtraction digital radiography using two imaging plates of different sensitivity. The regions resolved are comparable in size to vascular regulatory units (400 x 400 microm(2)). This method was applied to the measurement of within-layer myocardial flow distributions in Langendorff-perfused rabbit hearts. The validity of this method was confirmed by the strong correlation between regional densities of two tracers injected simultaneously (r = 0.89 +/- 0.03, n = 8). The temporal flow stability was evaluated by a 90-s continuous IDMI injection and subsequent bolus HDMI injection (n = 8). Regional densities of the two tracers were fairly correlated (r = 0.86 +/- 0.03), indicating that the spatial pattern of flow distribution was stable even at a microvascular level over a 90-s period. The effect of microsphere embolization on the flow distribution was also investigated by the sequential injections of IDMI, 15-microm microspheres, and HDMI at 20-s intervals (n = 8). Microembolization increased the coefficient of variation of tracer density from 19 to 25% (P < 0.05), whereas the regional densities of two tracers were still correlated substantially, as in the case of no embolization (r = 0.84 +/- 0.06). Thus the microsphere embolization enhanced flow heterogeneity with increasing flow differences between control high-flow and control low-flow regions but rather maintained the pattern of flow distribution. In conclusion, double-tracer digital radiography will be a promising method for the spatial and temporal myocardial flow analysis at microvascular levels.

Animals↗
PubMed2003

Spatial autocorrelation analysis offers new insights into gene flow in the Australian bush rat, Rattus fuscipes.

Dispersal is a fundamental process that influences the response of species to landscape change and habitat fragmentation. In an attempt to better understand dispersal in the Australian bush rat, Rattus fuscipes, we have combined a new multilocus autocorrelation method with hypervariable microsatellite genetic markers to investigate fine-scale (< or = 1 km) patterns of spatial distribution and spatial genetic structure. The study was conducted across eight trapping transects at four sites, with a total of 270 animals sampled. Spatial autocorrelation analysis of bush rat distribution revealed that, in general, animals occurred in groups or clusters of higher density (< or = 200 m across), with intervening gaps or lower density areas. Spatial genetic autocorrelation analysis, based on seven hypervariable microsatellite loci (He = 0.8) with a total of 80 alleles, revealed a consistent pattern of significant positive local genetic structure. This genetic pattern was consistent for all transects, and for adults and sub-adults, males and females. By testing for autocorrelation at multiple scales from 10 to 800 m we found that the extent of detectable positive spatial genetic structure exceeded 500 m. Further analyses detected significantly weaker spatial genetic structure in males compared with females, but no significant differences were detected between adults and sub adults. Results from Mantel tests and hierarchical AMOVA further support the conclusion that the distribution of bush rat genotypes is not random at the scale of our study. Instead, proximate bush rats are more genetically alike than more distant animals. We conclude that in bush rats, gene flow per generation is sufficiently restricted to generate the strong positive signal of local spatial genetic structure. Although our results are consistent with field data on animal movement, including the reported tendency for males to move further than females, we provide the first evidence for restricted gene flow in bush rats. Our study appears to be the first microsatellite-based study of fine-scale genetic variation in small mammals and the first to report consistent positive local genetic structure across sites, age-classes, and sexes. The combination of new forms of autocorrelation analyses, hypervariable genetic markers and fine-scale analysis (< 1 km) may thus offer new evolutionary insights that are overlooked by more traditional larger scaled (> 10 km) population genetic studies.

Animals↗
PubMed2001

Spherical harmonic decomposition applied to spatial-temporal analysis of human high-density electroencephalogram.

We demonstrate an application of spherical harmonic decomposition to the analysis of the human electroencephalogram (EEG). We implement two methods and discuss issues specific to the analysis of hemispherical, irregularly sampled data. Spatial sampling requirements and performance of the methods are quantified using simulated data. The analysis is applied to experimental EEG data, confirming earlier reports of an approximate frequency-wave-number relationship in some bands.

Biophysical Phenomena↗
PubMed1986

Sampling-theory analysis of spatial vision.

Spatial-vision research has been largely concerned with measuring and understanding the consequences of receptive-field properties measured by single-unit recording. However, in order to understand spatial-information processing in the visual system, it is equally essential to know the densities and the distribution patterns of the receptive fields. If the receptive fields are not arrayed properly across the visual field, spatial information will be lost. It has been argued, on the basis of the Whittaker-Shannon sampling theorem, that the receptors of the fovea sample the retinal image at a high enough rate to preserve essentially all the available spatial information. In this paper we show how two-dimensional sampling theory can be used to determine which combinations of receptive-field shapes and sampling patterns would preserve all spatial information from the receptors. This analysis will prove useful for determining, in conjunction with electrophysiological and anatomical evidence, what spatial information is or is not being transmitted by a given stage of the visual pathway. It may also prove useful for developing and testing theories of spatial vision.

Humans↗
PubMed1995

Contrast sensitivity in Alzheimer's disease: a 1-year longitudinal analysis.

Spatial contrast sensitivity was evaluated in normal elderly adults and a group with probable Alzheimer's disease (AD) in three sessions over a 1-year period. There was evidence of a reduction over 1 year in contrast sensitivity for static, high spatial frequencies in both groups of subjects. A striking difference between the subject groups was observed in their response to flickered stimuli. Although normal elderly adults yielded good stability in sensitivity for both static and flickered spatial frequencies over the 1 year, AD patients experienced a significant decline in response to flickered (7.5 Hz) stimuli. The significant decline in sensitivity for low contrast, high temporal events in AD patients is consistent with reports of cell loss at the retinal and cortical levels of the magnocellular (M) channel in AD. Thus, the spatial contrast sensitivity change in AD may reflect a more rapid loss of cells specifically in the M channel over a 1-year period.

Adult↗
PubMedDate not supplied

[Hemispheric organization of verbal memory functions in seasonal winter depression: electrophysiological analysis].

Spatial organization of EEG power and coherence during memorization of dichotically presented lists of words were studied in patients with winter depression (N = 17) and control subjects (N = 22). In contrast to the control subjects, the depressed patients were characterized by the higher theta power in the right parietal and posterior temporal regions and the dominance of the alpha 2 in the left midfrontal area. The patients also differed in the lower theta 2 coherence in the left hemisphere and lower alpha 1 coherence in the right hemisphere. These effects showed different intrahemispheric distribution. The interhemispheric EEG coherence in the theta 2 range between the frontal areas and alpha 1 coherence between the left frontal and right posterior areas was lower in the patients than in the control subjects. Verbal-emotional interaction in depressions are discussed.

Adult↗
PubMedDate not supplied

[Comparative analysis of spatial organization of myoglobins. II. Secondary structure].

An analysis of probability of distribution curves of alpha-helical sites and bends of polypeptide chains of myoglobins in half-water mammals (beaver, nutria, muskrat, otter) carried out in comparison with those of myoglobins of the horse and Sperm whale (X-ray diffraction analysis has revealed their tertiary structure) has revealed a coincidence of the secondary structure sites end bends of the chain in the studied respiratory hemoproteins of muscles. Despite a considerable number of amino acid substitutions the profiles of alpha-helicity and B-bends of the compared proteins are practically identical. This indicates to the "resistance" of the probability curves to amino acid substitutions and to retention of the tertiary structure of myoglobins in evolutionary remote species of the animals.

Amino Acid Sequence↗
PubMed1993

A compiled BASIC program for analysis of spatial point patterns: application to retinal studies.

The pattern of distribution of a population of cells is of considerable interest to biologists and neurobiologists. However, the labor involved in collecting and analyzing the data often requires a significant amount of time. This paper presents a compiled BASIC program written using the Microsoft QuickBasic compiler for Apple Macintosh to facilitate such studies. The program allows collection and analysis of data that can be introduced either with the aid of a digitizing tablet of directly imported as x,y coordinates from different sources as, for example, word processors or image analysis software. Subsequently the program provides a quick, easy and interactive way of access to statistical, mathematical and graphical techniques used in the analysis of spatial point patterns. These techniques include several measures of dispersion (quadrat count, nearest neighbor and a 2-dimensional point autocorrelogram analysis) and arrangement. Although the program has been tested on spatial organization of retinal cells, it can be used to study the distribution of other cells in the nervous system and for different projects, as for example the distribution of microtubules and neurofilaments inside the axons. This software is available from the authors.

Animals↗
PubMed2002

In situ analysis of spatial relationships between proteins of the nuclear pore complex.

Macromolecular transport between the nucleus and cytoplasm occurs through the nuclear pore complexes (NPCs). The NPC in the budding yeast Saccharomyces cerevisiae is a 60-MDa structure embedded in the nuclear envelope and composed of ~30 proteins, termed nucleoporins or nups. Here we present a large-scale analysis of spatial relationships between nucleoporins using fluorescence resonance energy transfer (FRET) in living yeast cells. Energy transfer was measured in a panel of strains, each of which coexpresses the enhanced cyan and yellow fluorescent proteins as fusions to distinct nucleoporins. With this approach, we have determined 13 nucleoporin pairs yielding FRET signals. Independent experiments are consistent with the FRET results: Nup120 localization is perturbed in the nic96-1 mutant, as is Nup82 localization in the nup116Delta mutant. To better understand the spatial relationship represented by an in vivo FRET signal, we have investigated the requirements of these signals. We demonstrate that in one case FRET signal is lost upon insertion of a short spacer between the nucleoporin and its enhanced yellow fluorescent protein label. We also show that the Nup120 FRET signals depend on whether the fluorescent moiety is fused to the N- or C-terminus of Nup120. Combined with existing data on NPC structure, the FRET pairs identified in this study allow us to propose a refined molecular model of the NPC. We suggest that the approach may serve as a prototype for the in situ study of other large macromolecular complexes.

Bacterial Proteins↗
PubMed2025

Colorectal Liver Metastasis Pathomics Model: Integrating Single-Cell and Spatial Transcriptome Analysis With Pathomics for Predicting Liver Metastasis in Colorectal Cancer.

The liver is the primary target organ for hematologic metastasis of colorectal cancer (CRC), and CRC liver metastasis (CRLM) often precludes radical resection, making it the leading cause of death in patients with CRC. To improve the identification and prediction of liver metastasis risk, we identified a cell type of liver metastasis--triggering malignant cells (LMTMCs) through integrating single-cell RNA sequencing and spatial transcriptome analysis. Multiomics cell communication analysis indicated that the interaction between fibroblasts and LMTMCs through the COL1A1-CD44/SDC4 and LAMA4-CD44 signaling axes could promote CRLM. By applying the one-class logistic regression algorithm, we developed a CRLM scoring system in the bulk RNA-sequencing data according to the abundance of LMTMCs in each individual. Using the grouping labels derived from the CRLM scoring system in the bulk data and the corresponding whole-slide images without any manual annotations at the region or pixel level, processed via slide-level weakly supervised learning, a deep-learning model based on the ResNet18 architecture, called Colorectal Liver Metastasis Pathomics Model, was developed to predict the risk of liver metastasis in patients with CRC. The Colorectal Liver Metastasis Pathomics Model achieved an area under the curve of 0.84 at the internal test set of The Cancer Genome Atlas-CRC histology images. In the external independent validation sets, namely the Affiliated Hospital of Southwest Medical University and the Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University cohorts, the areas under the curve were 0.89 and 0.72, respectively, indicating effective classification performances. This study provided new insights and tools for the early identification of CRLM and demonstrated the potential of combining multiomics with deep learning-based pathomics in cancer research.

Humans↗
PubMed2002

Improved parametric image generation using spatial-temporal analysis of dynamic PET studies.

The value of parametric images that represent both spatial distribution and quantification of the physiological parameters of tracer kinetics has long been recognized. However, the inherent high noise level of pixel kinetics of dynamic PET makes it unsuitable to generate parametric images of the microparameters of tracer kinetic model by conventional weighted nonlinear least squares (WNLS) fitting. Based on the concept that both spatial and temporal information should be integrated to improve parametric image quality, a nonlinear ridge regression with spatial constraint (NLRRSC) parametric imaging algorithm was proposed in this study. For NLRRSC, a term that penalizes local spatial variation of parameters was added to the cost function of WNLS fitting. The initial estimates and spatial constraint were estimated by component representation model (CRM) with cluster analysis. A hierarchical cluster with average linkage method was used to extract components. The ridge parameter was determined by linear ridge regression theory at each iteration, and a modified Gauss-Newton algorithm was used for minimizing the cost function. Results from a computer simulation showed that the percent mean square error of estimates obtained by NLRRSC can be decreased by 60-80% compared to that of WNLS. The parametric images estimated by NLRRSC are significantly better than the ones generated by WNLS. A highly correlated linear relationship was found between the ROI values calculated from the microparametric images generated by NLRRSC and estimates from ROI kinetic fitting. NLRRSC provided a reliable estimate of glucose metabolite uptake rate with a comparable image quality compared to Patlak analysis. In conclusion, NLRRSC is a reliable and robust parametric imaging algorithm for dynamic PET studies.

Algorithms↗
PubMedDate not supplied

Mitochondrial DNA variation in the European otter (Lutra lutra) and the use of spatial autocorrelation analysis in conservation.

To add genetic information to the international conservation efforts on European otters Lutra lutra, we investigated the genetic population structure in and around a known "source" population of the otter, the Oberlausitz (OL) in eastern Germany. This was complemented by a first survey of genetic variation levels in the Central European otter population. Sequence analysis of 300bp of the mitochondrial control region in 76 specimens from the eastern German study region and 53 individuals from several other European populations revealed a low level of genetic variation, with only 5 haplotypes present and nucleotide diversities within populations ranging from 0.00% to 0.17%. Apart from eastern Germany, one haplotype was by far the most abundant one, from which other, only locally occurring types, could be derived by a single point mutation. This suggests a single Pleistocene refugium from which the analyzed European regions have been reinvaded after the glaciations. Within eastern Germany, two abundant haplotypes were found. Their occurrence differed significantly among subregions of eastern Germany. The uneven distribution of a locally restricted but abundant haplotype could be explained by isolation-by-distance and might reflect emigration from the OL source population to surrounding regions. This suggests that vital local populations can indeed serve as "sources" for the invasion of surrounding areas. Given a suitable genetic marker, we suggest a spatial autocorrelation analysis to monitor the genetic effect of such an emigration from a source population.

Animals↗
PubMed1989

Spatial autocorrelation analysis of the distribution of genotypes within populations of lodgepole pine.

Spatial autocorrelation analyses of point samples within two populations of lodgepole pine (Pinus contorta ssp. latifolia) indicate that single-locus mature tree and pollen genotypes are distributed in a nearly random fashion for most of the allozyme loci assayed. This lack of structure in the distributions of most genotypes is consistent with outcrossing rates that are very nearly 1.0 and with estimates indicating that both pollen and seed are dispersed over long distances in lodgepole pine. However, spatial autocorrelation of genotypes for a few loci suggests that genotypes at these loci may be under natural selection.

Alleles↗
PubMed2003

Localization of human somatosensory cortex using spatially filtered magnetoencephalography.

A spatial filter algorithm based on minimum-variance beamforming (synthetic aperture magnetometry (SAM)) was applied to single trial neuromagnetic recordings in order to localize primary somatosensory cortex. Magnetoencephalography (MEG) responses to electrical stimulation of the right and left median nerve were recorded using a whole-head MEG system and localized using both SAM spatial filtering and dipole analysis. Spatial filtering was applied to single trial neuromagnetic recordings to produce 3-dimensional difference images of source power between active (0-50 ms) and control states (-50-0 ms) in the range of 15-300 Hz. Average difference between N20m dipole location and location of maximal increase in power in the SAM images was 3.7 mm (1.5 mm SD) and localized to primary somatosensory cortex. Time-frequency analysis of spatially filtered output for the peak SAM locations showed a brief (10 ms) increase in the 60-100 Hz band coincident with the N20m response and a longer duration (approx. 80 ms) increase in power in the 10-40 Hz band following N20m onset. These results indicate that beamformer based spatial filter methods such as SAM can be used to localize temporally discrete cortical activity produced by median nerve stimulation.

Adult↗
PubMed1986

Spatial resolution analysis of computed tomographic images.

Methods are presented for the quantification of spatial resolution in x-ray computed tomographic (CT) images. Model-dependent methods are derived and compared with model independent methods for computation of the Modulation Transfer Function (MTF). These techniques are applied to phantom images of point, line, edge, and ring discontinuities. The model-dependent methods utilize multiparameter fits of a two-dimensional model function to the image data. Model predictions are compared with results obtained in a model-independent way by numerical transformation of the data. Results of resolution measurements of an Imatron C-100 CT scanner at UCSF and a second experimental scanner at the UCSF Physics Research Laboratory are presented.

Humans↗