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Results for “Spatial Analysis”

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At least 289 records · Page 16Linked to original sources

PubMed2005

Study of temporal stationarity and spatial consistency of fMRI noise using independent component analysis.

Spatial independent component analysis (ICA) was used to study the temporal stationarity and spatial consistency of structured functional MRI (fMRI) noise. Spatial correlations have been used in the past to generate filters for the removal of structured noise for each time-course in an fMRI dataset. It would be beneficial to produce a multivariate filter based on the same principles. ICA is examined to determine if it has properties that are beneficial for this type of filtering. Six fMRI baseline datasets were decomposed via spatial ICA. The time-courses associated with each component were tested for wide-sense stationarity using the wide sense stationarity quotient (WSS). Each dataset was divided into three subsets and each subset was decomposed. The components of first and third subset were matched by the strength of their correlation. The components produced by ICA were found to have largely nonstationary time-courses. Despite the temporal nonstationarity in the data, ICA was found to produce consistent spatial components. The degree of correlation among components differed depending on the amount of dimension reduction performed on the data. It was found that a relatively small number of dimensions produced components that are potentially useful for generating a spatial fMRI filter.

Algorithms↗

PubMed2025

Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.

Emerging spatial multiomics technologies provide an increasingly large amount of information content at multiple scales. However, it remains challenging to efficiently represent and harmonize diverse spatial datasets. Here we present Giotto Suite, a suite of modular packages that provides scalable and extensible end-to-end solutions for multiscale and multiomic data analysis, integration and visualization. At its core, Giotto Suite is centered around an innovative data framework, allowing the representation and integration of spatial omics data in a technology-agnostic manner. Giotto Suite integrates molecular, morphology, spatial and annotated feature information to create a responsive and flexible workflow, as demonstrated by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science in R, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive and multiscale ecosystem for spatial multiomic data analysis.

Genomics↗

PubMed2003

Proper multivariate conditional autoregressive models for spatial data analysis.

In the past decade conditional autoregressive modelling specifications have found considerable application for the analysis of spatial data. Nearly all of this work is done in the univariate case and employs an improper specification. Our contribution here is to move to multivariate conditional autoregressive models and to provide rich, flexible classes which yield proper distributions. Our approach is to introduce spatial autoregression parameters. We first clarify what classes can be developed from the family of Mardia (1988) and contrast with recent work of Kim et al. (2000). We then present a novel parametric linear transformation which provides an extension with attractive interpretation. We propose to employ these models as specifications for second-stage spatial effects in hierarchical models. Two applications are discussed; one for the two-dimensional case modelling spatial patterns of child growth, the other for a four-dimensional situation modelling spatial variation in HLA-B allele frequencies. In each case, full Bayesian inference is carried out using Markov chain Monte Carlo simulation.

Alleles↗

PubMed1998

Breast cancer in West Islip, NY: a spatial clustering analysis with covariates.

This paper presents the results of an exploratory spatial analysis of breast cancer clustering in the community of West Islip on Long Island. Using address-level data from a survey of women in West Islip, we analyze the existence and locations of breast cancer clusters among long-term community residents. Statistical and geographical methods are used to first, estimate a logistic regression model of disease as a function of known risk factors and second, analyze spatial clustering among the cases of breast cancer not explained by the modeled risk factors. The method determines the actual locations of clusters so that if there is a potential causal factor in the environment it can be identified for further study. Although little evidence of clustering is uncovered, the methods described here have utility for exploratory spatial analysis in many health contexts.

Adult↗

PubMedDate not supplied

SGS--Spatial Genetic Software: a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations.

We have developed a program called Spatial Genetic Software (SGS), which provides a user-friendly Windows tool to analyze both local and broad scale genetic and phenotypic structure. It can deal with nearly any type of genetic data, codominant (allozyme, PCR-RFLP, microsatellite) or dominant (RAPD, AFLP) markers, or biparentally (nuclear) or uniparentally (cpDNA and mtDNA) inherited markers. Data based on any of these markers can be analyzed, either as individual genotypes within a single population (local scale) or as allele or haplotype frequencies from different populations (broad scale). We also include a simple approach to analysis of spatial structure for continuous quantitative traits. The program implements various parameters to analyze spatial genetic and phenotypic structure: Moran's index, Geary's index, number of alleles in common, and approaches using genetic distances and F(ST) values. The statistical significance of all measures is verified by the use of a permutation test. The results are assessed by graphics that can be integrated, via the clipboard, to other Windows programs. The details of the computations are given in a table and can be stored as ASCII files.

Demography↗

PubMed1998

Hypoxia and hypothermia enhance spatial heterogeneities of repolarization in guinea pig hearts: analysis of spatial autocorrelation of optically recorded action potential durations.

INTRODUCTION: Regional dispersions of repolarization (DOR) are arrhythmogenic perturbations that are closely associated with reentry. However, the characteristics of DOR have not been well defined or adequately analyzed because previous algorithms did not take into account spatial heterogeneities of action potential durations (APDs). Earlier simulations proposed that pathologic conditions enhance DOR by decreasing electrical coupling between cells, thereby unmasking differences in cellular repolarization between neighboring cells. Optical mapping indicated that gradients of APD and DOR are associated with fiber structure and are largely independent of activation. We developed an approach to quantitatively characterize APD gradients and DOR to determine how they are influenced by tissue anisotropy and cell coupling during diverse arrhythmogenic insults such as hypoxia and hypothermia. METHODS AND RESULTS: Voltage-sensitive dyes were used to map APs from 124 sites on the epicardium of Langendorff-perfused guinea pig hearts during (1) cycles of hypoxia and reoxygenation and (2) after 30 minutes of hypothermia (32 degrees to 25 degrees C). We introduce an approach to quantitate DOR by analyzing two-dimensional spatial autocorrelation of APDs along directions perpendicular and parallel to the longitudinal axis of epicardial fibers. A spatial correlation length L was derived as a statistical measure of DOR. It corresponds to the distance over which APDs had comparable values, where L is inversely related to DOR. Hypoxia (30 min) caused a negligible decrease in longitudinal thetaL (from 0.530 +/- 0.138 to 0.478 +/- 0.052 m/sec) and transverse thetaT (from 0.225 +/- 0.034 to 0.204 +/- 0.021 m/sec) conduction velocities and did not alter thetaL/thetaT or activation patterns. In paced hearts (cycle length [CL] = 300 msec), hypoxia decreased APDs (123 +/- 18.2 to 46 +/- 0.6 msec; P < 0.001) within 10 to 15 minutes and enhanced DOR, as indicated by reductions of L from 1.8 +/- 0.9 to 1.1 +/- 0.5 mm (P < 0.005). Hypothermia caused marked reductions of thetaL (0.53 +/- 0.138 to 0.298 +/- 0.104 m/sec) and thetaT (0.225 +/- 0.034 to 0.138 +/- 0.027 m/sec), increased APDs (128 +/- 4.4 to 148 +/- 14.5 msec), and reduced L from 2.0 +/- 0.3 to 1.3 +/- 0.6 mm (P < 0.05). L decreased with increased time of hypoxia and recovered upon reoxygenation. Hypoxia and hypothermia reduced L measured along the longitudinal (L(L)) and transverse (L(T)) axes of cardiac fibers while the ratio of L(L)/L(T) remained constant. CONCLUSION: Conventional indexes of DOR (i.e., APD "range" or "standard deviation," evaluated with extracellular electrodes) did not convey the spatial inhomogeneities of repolarization revealed by L. Spatial autocorrelation analysis provides a statistically significant measurement of DOR, which can take into account intrinsic heterogeneities of APDs and fiber orientation. The data show that hypoxia and hypothermia produce reductions of L, even though they have different effects on mean APD and conduction velocity. The preservation of a constant L(L)/L(T) ratio during hypoxia and hypothermia, despite large reductions in L, is consistent with a mechanism in which reduced cell-to-cell coupling unmasks intrinsic dispersions of APD and reduces L(L) and L(T) by the same factor. Thus, the spatial autocorrelation of APDs provides a sensitive index of DOR under normal and arrhythmogenic conditions. It incorporates the anisotropic nature of the myocardium and therefore is preferable to conventional indexes of DOR.

Action Potentials↗

PubMed2002

Multiple sclerosis distribution in northern Sardinia: spatial cluster analysis of prevalence.

BACKGROUND: A heterogeneous geographic distribution of MS has been reported among different ethnic groups, and also within small communities. Epidemiologic studies conducted over the past two decades using repeated assessments clearly show that Sardinia is at high risk for MS, with a prevalence of 150 per 100,000 in 1997. OBJECTIVE: To present spatial analysis of the disease prevalence to disclose possible "hot" or "cold" spots of disease, further allowing correlations with risk factors. METHODS: A spatial analysis of the whole province of Sassari, in northern Sardinia, at a microgeographic level (i.e., in the 89 administrative communes and 6 linguistic areas) was conducted. Because of the small number of cases per commune and to overcome random variability, a hierarchical Bayesian approach was adopted. The distribution of prevalent cases by commune of residence on December 31, 1997 and from age 5 to 15 years was analyzed. RESULTS: A clustering pattern was found in the southwestern communes of the province based on geographic distribution by both prevalence and residence at age 5 to 15 years. A west-to-east gradient also was observed. CONCLUSIONS: This study highlights a hot spot of MS in the southwestern part of Sassari province, bordering with the commune of Macomer, where MS was once hypothesized as having occurred as an epidemic. Interestingly, these areas of MS clustering comprise the Common Logudorese linguistic domain. The Catalan area, linguistically and genetically distant from the remaining Sardinian domains, does not show such high estimates. Because MS is not a single-source infectious disease, this study may help test the hypothesis that a widely and evenly spread environmental (infectious?) agent may produce disease in subgroups of genetically more susceptible individuals in areas at higher inbreeding rates, wherein a disease mode of inheritance could be better investigated.

Adolescent↗

PubMed1995

[Temporal and spatial pattern analysis of pharyngeal swallowing in patients with abnormal sensation in the throat].

There are many patients who complain of abnormal sensations, such as an obstructive sensation, foreign body sensation, difficulty in swallowing, etc., in the throat, which do not have an obvious cause. The causes of such unpleasant symptoms have not been adequately investigated. As one of the potential factors in volved in abnormal sensations in the throat, we considered the existence of subclinical dysphagia. We then performed videofluoroscopic analysis in patients with an abnormal sensation in the throat to examine whether or not there were functional disorders in swallowing. Videofluoroscopy was performed in 42 subjects, 30 patients with abnormal sensation in the throat and 12 volunteers without swallowing problems. We devised a temporal and spatial analysis system of swallowing using personal computer technology. Videofluoroscopic swallowing sequences during spoon feeding (3-5ml) and drinking from a cup (15-20ml) of liquid barium, were analyzed. The results suggest that two temporal measurements of swallow from videofluoroscopic studies are appropriate for parameter of subclinical dysphagia: the time it takes the bolus to move through pharynx from the point at which the bolus head passes the tongue base until the bolus head extends caudally beyond the piriform sinus while feeding from a spoon (S2), and the time it takes the bolus to move through the upper esophagus from the point at which the bolus head passes the bottom of the piriform sinus until the bolus tail passes the same point while drinking from a cup (C1). Then, we selected C1 and S2 for variables and detect the patients who have subclinical dysphagia with cluster analysis. Forty-two subjects were divided into two groups: those composed of 14 patients (cluster 1), and those composed of 16 patients and 12 controls (cluster 2). We thought 14 patients in cluster 1 would have subclinical dysphagia for the cause of abnormal sensation in the throat. Temporal and spatial analysis revealed three forms of pharyngeal swallow in cluster 1. In 6 patients, the bolus stall in the valleculae prior to the onset of the pharyngeal swallow. In other 6 patients, the bolus stall in the piriform sinus before swallowing reflex. In the other 2 patients, the bolus moved smoothly but slowly without delay in pharynx. Our results indicate that a delayed swallowing reflex is the main functional finding in videofluoroscopy in patients with subclinical dysphagia contributing to an abnormal sensatin in the throat.

Adult↗

PubMed2001

Marine eutrophication: a proposed data analysis procedure for assessing spatial trends.

A methodology for the discrimination of the different trophic levels at a spatial scale in the marine environment is proposed using spatial analysis methods and non-parametric statistics. Phytoplankton cell number, being a representative parameter to express trophic trends in the marine ecosystem is selected for the methodology development; Saronicos Gulf, Greece is used for the case study. The proposed stepwise methodology includes interpolation for assessing the spatial distribution of phytoplankton cell number, division of the Gulf into a number of quadrates, development of a scale characterising trophic levels and finally characterisation of the trophic state of each quadrate using non-parametric statistics. The advantages of this methodology and the potential applications in coastal management studies are also discussed.

Cell Count↗

PubMed1989

Analysis of spatial structure in eccentric vision.

The analysis of spatial structure, ie, the encoding of relative positions between pattern elements, was studied in central and eccentric vision. In a two-alternative forced-choice task the observer had to discriminate between two patterns consisting of short line segments. At each trial the two patterns were flashed for 140 msec and the observer indicated whether the patterns were identical or mirror symmetric. Psychometric functions were measured by changing pattern size at each eccentricity in order to find the threshold size allowing 75% of correct responses. The scaling factor, required for discriminating between mirror symmetric and identical patterns independent of eccentricity, was found to be similar to the size-scaling proposed by Levi et al (Vision Res 25:963, 1985) for vernier acuity tasks.

Differential Threshold↗

PubMed2001

On the analysis of spatial binary images.

This paper deals with the analysis of spatial images taken from microscopically heterogeneous but macroscopically homogeneous microstructures. A new method is presented, which is strictly based on integral-geometric formulae such as Crofton's intersection formulae and Hadwiger's recursive definition of the Euler number. By means of this approach the quermassdensities can be expressed as the inner products of two vectors where the first vector carries the 'integrated local knowledge' about the microstructure and the second vector depends on the lateral resolution of the image as well as the quadrature rules used in the discretization of the integral-geometric formulae. As an example of application we consider the analysis of spatial microtomographic images obtained from natural sandstones.

Journal Article↗

PubMed2004

An experimental characterization of elastographic spatial resolution: analysis of the trade-offs between spatial resolution and contrast-to-noise ratio.

An experimental study of the spatial resolution in elastography was conducted. Models that involved two cylindrical inclusions arranged as a wedge were used to characterize the axial and lateral resolution of the axial strain elastograms. A study of the dependence of the spatial resolution on several factors such as the algorithmic parameters, the applied strain and the modulus contrast was performed. The axial resolution was found to show a linear dependence with respect to the algorithmic parameters, namely the window length and the window shift used for strain estimation. The lateral resolution showed a weak dependence on the algorithmic parameters. A weak dependence of the spatial resolution on factors such as the modulus contrast and the applied strain was found. The trade-offs between the spatial resolution and the elastographic contrast-to-noise ratio (CNR(e)) were then analyzed. A nonlinear trade-off between the CNR(e) and the axial and lateral resolution was shown for conventional strain estimation techniques, with the CNR(e) improving at a more than linear rate with respect to a linear degradation in the resolution. This study provided an experimental framework for characterizing the spatial resolution in elastography and facilitating a comparison of the CNR(e) with spatial resolution.

Elasticity↗

PubMed2004

Multilinear model for spatial pattern analysis of the Measurement of Haze and Visual Effects project.

A multilinear model was developed for the analysis of the spatial patterns and possible sources affecting haze and its visual effects in the southwestern United States. The data from the project Measurement of Haze and Visual Effects (MOHAVE) collected during the late winter and mid-summer of 1992 at the monitoring sites in four states (i.e., California, Arizona, Nevada and Utah) were used in the study. The three-way data array was analyzed by a four-product-term model. This study makes a direct effort to include wind patterns as a component in the model in order to obtain the information of the spatial patterns of source contributions. The solution is computed using the conjugate gradient algorithm with applied non-negativity constraints. For the winter data set, reasonable solutions contained six sources and six wind patterns. The analysis of summer data required seven sources and seven wind patterns. The ME results are compared to the prior single-species empirical orthogonal function analysis results--and prior work describing the transport pathways.

Air Pollutants↗

PubMed1994

Detecting clinical and balanced selection using spatial autocorrelation analysis under kin-structured migration.

Recently spatial autocorrelation has been employed to infer microevolutionary processes from patterns of genetic variation. In theory, different processes should show characteristic signature correlograms; e.g., clinal selection should produce correlograms decreasing from positive to negative autocorrelation, whereas uniform balanced selection should lead to no spatial autocorrelation. The ability of a statistical method such as spatial autocorrelation analysis to distinguish between these selective regimes or even to detect departures from neutrality is dependent on the strength of the evolutionary force and the population structure. Weak selection or migration will not be apparent against the expected background of stochastic noise. Moreover, the population structure may generate sufficient stochastic variation such that even strong evolutionary forces may fail to be detected. This study uses computer simulation to examine the effects of kin-structured migration and three different selective regimes on the shape of spatial correlograms to assess the ability of this technique to detect different microevolutionary processes. Genetic variation among 8 loci is simulated in a linear set of 25 artificial populations. Kin-structured stepping-stone migration among adjacent populations is modeled; directional, balanced, and clinal selection, as well as neutral loci are considered. These experiments show that strong selection produces correlograms of the predicted shape. However, with an anthropologically reasonable population structure, considerable stochastic variation among correlograms for different alleles may still exist. This suggests the need for caution in inferring genetic process from spatial patterns.

Bias↗

PubMed2004

Spatial-temporal analysis of non-stationary fMEG data.

Magnetoencephalography (MEG) is a technique used to non-invasively record neuromagnetic fields generated by the human brain. Our new SARA (SQUID Array for Reproductive Assessment) is a unique MEG device designed specifically for the study of the fetal neurophysiology. During the acquistion of fetal magnetoencephalography (fMEG), many other interfering bio-magnetic signals are collected as well. Examples include the movement of fetus or muscle contraction of the mother. As a result, the recorded signals may show unexpected patterns, other than the target signal of interest. These interventions makes it difficult for a physician to assess the exact fetal condition, including its response to various stimuli. We propose using intervention analysis and spatial-temporal autoregressive moving average (STARMA) modeling to address the problem. STARMA is a statistical method that examines the relationship between the current observations as a linear combination of past observations, as well as observations at neighboring sites. Through intervention analysis, the change in pattern due to interfering signals can be well accounted for. When these interferences are removed, the end product is a template time series, or a typical signal from the target of interest thus providing a more reliable means to monitor the actual signals generated by the fetal brain and other organs of interest.

Female↗

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↗

PubMed1997

Geographic information systems, spatial network analysis, and contraceptive choice.

How does family planning accessibility affect contraceptive choice? In this paper we use techniques of spatial analysis to develop measures of family planning accessibility, and evaluate the effects of these geographically derived measures in a multilevel statistical model of temporary method choice in Nang Rong, Thailand. In our analyses we combine spatial data obtained from maps and Global Positioning System (GPS) readings with sociodemographic data from surveys and administrative records. The new measures reveal (1) important travel time effects even when family planning outlets are close by; (2) independent effects of road composition; (3) the relevance of alternative sources of family planning supply; and (4) the importance of the local history of program placement.

Choice Behavior↗

PubMedDate not supplied

[Ultrasound spatial clinical analysis of the orbital part of the lacrimal gland in health].

The paper presents an algorithm of ultrasound spatial analysis of the unaltered lacrimal gland. The algorithm has been used to define its shape, size, density, structural features and the pattern of blood supply, as well as the anatomic and topographic position in the orbit. The study was conducted in the B- and 3D-modes of color and energy Doppler mapping on both sides. The procedure was based on the clinical examination of 40 healthy individuals aged 20 to 75 years who had no systemic vascular and lymphoid tissue lesions or functional impairments of the lacrimal gland itself. The study defined the mean values of the ultrasound section of the lacrimal gland: 1-1.8 and 0.5-0.8 cm for vertical and horizontal ones, respectively; the mean volume of the lacrimal gland of 0.66 to 1 cm(3) and the densitometric parameters (density and vasculogenicity index); three types of structural manifestations of the unaltered lacrimal gland were identified. The proposed algorithm of ultrasound study of the lacrimal gland may enhance the accuracy and validity of results in the differential diagnosis of various orbital diseases.

Adult↗