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PubMed1996

A comprehensive appraisal of 241Am in soils around Rocky Flats, Colorado.

Soils east of Rocky Flats Plant (RFETS) near Golden, Colorado, were contaminated with actinides because of accidental release of oils laden with plutonium isotopes. Consequently, these soils were contaminated by 241Am due to radioactive decay of 241Pu (t1/2 = 14.4 y). A spatial analysis of 241Am activity in soils east of RFETS was conducted to elucidate the magnitude and the mode of 241Am dispersion in the soil environment. 241Am activity of 178 soil samples ranged from 0.037 Bq kg-1 to 10,004 Bq kg-1 with a mean of 214 Bq kg-1, median of 7.28 Bq kg-1, standard deviation of 942 Bq kg-1, and a coefficient of variation of 4.3. Spatial analysis of 241Am in soils around RFETS was conducted using indicator kriging, which is a nonparametric technique especially suitable to model a conditional cumulative distribution function (ccdf) of highly skewed environmental data such as 241Am. The ccdf was used to generate an E-type (mean of the conditional cdf) surface. The resulted surfaces were consistent with the hypothesis that the westerly winds were the dominant mechanism of americium dispersal. The spatial distribution and dispersal mechanisms of 241Am were similar to those of 239+240Pu. The ccdf was also used to construct probability of exceedence maps of 241Am in soils. For the purpose of this report two threshold values for the probability maps were selected: (1) the mean measured background activity of 241Am (0.4 Bq kg-1), and (2) the programmatic preliminary remediation goal for residential occupancy scenario (87.7 Bq kg-1). The probability-of-exceedance maps provide estimates of spatial uncertainty associated with each threshold. The E-type maps in conjunction with the probability-of-exceedance maps provide a robust framework for future cleanup options and land use decisions.

Americium↗
PubMed1992

Analysis of spatial structure of thymocytes and of their contacts with thymic non-lymphoid cells.

The study aimed et determining morphological relations between thymic cells and thymocytes. The studies were performed on 16 days old rats of Wistar strain. The material was processed for ultrastructural studies in a routine manner. For 50 thymocytes computer reconstruction was performed which allowed to define cell volume, volume of cell nucleus and of condensed chromatin. The value characterizing three-dimensional morphology of thymocytes provided grounds for analysis using graph theory. The stereological methods allowed to examine microarchitecture of individual thymic zones. Thymocytes in contact with dendritic cells or with macrophages were found to differ in morphology from thymocytes with no such contacts. The results indicated direct effect of dendritic cells and of macrophages on thymocytes.

Animals↗
PubMed2006

Genome-wide analysis of spatial and temporal gene expression in rice panicle development.

The basic structure of a rice inflorescence (the panicle) is determined by the pattern of branch formation, which is established at the early stages of panicle development. In this study we conducted global transcriptome profiling of the early stages of rice panicle development from phase transition to floral organ differentiation. To generate a meristem-specific gene-expression profile, shoot apical meristems (SAMs) and subsequently formed, very young panicles were collected manually and used for cDNA microarray analysis. We identified 357 out of 22,000 genes that are expressed differentially in the early stages of panicle development, and the 357 genes were classified into seven groups based on their temporal expression patterns. The most noticeable feature is that a fairly small number of genes, which are extensively enriched in transcription factors, are upregulated in the SAM immediately after phase transition. In situ hybridization analysis showed that each gene analysed exhibits a unique and interesting localization of mRNA. Remarkably, one of the transcription factors was proven to be a close downstream component of the pathway in which LAX, a major regulator of panicle branching, acts. These results suggest that our strategy--careful collection of meristems, global transcriptome analysis and subsequent in situ hybridization analysis--is useful not only to obtain a genome-wide view of gene expression, but also to reveal genetic networks controlling rice panicle development.

Gene Expression Profiling↗
PubMed1996

Soil-transmitted helminthiases in China: a spatial statistical analysis.

The prevalence of the soil-transmitted helminthiases is extremely high in some rural areas in China. The endemic foci of these human parasites constitute one of the most neglected public health problems. A large scale survey on human parasites (1988-1992) was conducted in China. The prevalences of the soil-transmitted helminthiases in the 30 provinces, autonomous regions and municipalities were reported and correlated with ecological factors (Yu et al, 1994; Xu et al, 1995). In this paper, we re-examined and analyzed the reported results with a spatial pattern test statistic, the D statistic. The values of the D statistic indicated that the spatial correlation of the prevalence of the soil-transmitted helminthiases in China was significant. We also found that the spatial correlation of the prevalence could largely be explained by the paddy field area per capita. The correlation of the prevalence of the soil-transmitted helminthiases and the paddy field area per capita was higher than the correlation of the prevalence with the factors found previously by Xu et al (1995).

China↗
PubMed2003

Advanced factor analysis of spatial distributions of PM2.5 in the eastern United States.

This work analyzes PM2.5 24-h average concentrations measured every third day at over 300 locations in the eastern United States during 2000. The non-negative factor analytic model, Positive Matrix Factorization, has been enhanced by modeling the dependence of PM2.5 concentrations on temperature, humidity, pressure, ozone concentrations, and wind velocity vectors. The model comprises 12 general factors, augmented by 5 urban-only factors intended to represent excess concentration present in urban locations only. The computed factor components or concentration fields are displayed as concentration maps, one for each factor, showing how much each factor contributes to the average concentration at each location. The factors are also displayed as flux maps that illustrate the spatial movement of PM2.5 aerosol, thus enabling one to pinpoint potential source areas of PM2.5. The quality of the results was investigated by examining how well the model reproduces especially high concentrations of PM2.5 on specific days at specific locations. Delimiting the spatial extent of all such factors that exhibit a clear regional maximum surrounded by an almost-zero outer domain lowered the uncertainty in the computed results.

Aerosols↗
PubMed2002

[Geostatiscal analysis on spatial patterns of Schizaphis granarium and Aphidius sp].

The spatial construction and correlation of Schizaphis granarium and Aphidius sp. at different stages were investigated using geostatistical method. The results showed that the semivariogram of S. granarium was described by a spherical model, and indicated an aggregated special pattern ranging from 21 to 61 cm. The semivariogram of Aphidius sp. could be also well described by spherical model, and indicated an aggregated spatial pattern ranging from 36 to 55 cm. The amount and spatial distribution of Aphidius sp. were closely related to those of Schizaphis granarium, which reveals that Aphidius sp. was the dominant natural enemies influencing the population of S. granarium.

Analysis of Variance↗
PubMedDate not supplied

A genetic and spatial Bayesian analysis of mastitis resistance.

A nationwide health card recording system for dairy cattle was introduced in Norway in 1975 (the Norwegian Cattle Health Services). The data base holds information on mastitis occurrences on an individual cow basis. A reduction in mastitis frequency across the population is desired, and for this purpose risk factors are investigated. In this paper a Bayesian proportional hazards model is used for modelling the time to first veterinary treatment of clinical mastitis, including both genetic and environmental covariates. Sire effects were modelled as shared random components, and veterinary district was included as an environmental effect with prior spatial smoothing. A non-informative smoothing prior was assumed for the baseline hazard, and Markov chain Monte Carlo methods (MCMC) were used for inference. We propose a new measure of quality for sires, in terms of their posterior probability of being among the, say 10% best sires. The probability is an easily interpretable measure that can be directly used to rank sires. Estimating these complex probabilities is straightforward in an MCMC setting. The results indicate considerable differences between sires with regards to their daughters disease resistance. A regional effect was also discovered with the lowest risk of disease in the south-eastern parts of Norway.

Animals↗
PubMed2005

The health status of southern children: a neglected regional disparity.

PURPOSE: Great variations exist in child health outcomes among states in the United States, with southern states consistently ranked among the lowest in the country. Investigation of the geographical distribution of children's health status and the regional factors contributing to these outcomes has been neglected. We attempted to identify the degree to which region of residence may be linked to health outcomes for children with the specific aim of determining whether living in the southern region of the United States is adversely associated with children's health status. METHODS: A child health index (CHI) that ranked each state in the United States was computed by using state-specific composite scores generated from outcome measures for a number of indicators of child health. Five indicators for physical health were chosen (percent low birth weight infants, infant mortality rate, child death rate, teen death rate, and teen birth rates) based on their historic and routine use to define health outcomes in children. Indicators were calculated as rates or percentages. Standard scores were calculated for each state for each health indicator by subtracting the mean of the measures for all states from the observed measure for each state. Indicators related to social and economic status were considered to be variables that impact physical health, as opposed to indicators of physical health, and therefore were not used to generate the composite child health score. These variables were subsequently examined in this study as potential confounding variables. Mapping was used to redefine regional groupings of states, and parametric tests (2-sample t test, analysis of means, and analysis-of-variance F tests) were used to compare the means of the CHI scores for the regional groupings and test for statistical significance. Multiple-regression analysis computed the relationship of region, social and economic indicators, and race to the CHI. Simple linear-regression analyses were used to assess the individual effect of each indicator. RESULTS: A geographic region of contiguous states, characterized by their poor child health outcomes relative to other states and regions of the United States, exists within the "Deep South" (Mississippi, Louisiana, Arkansas, Tennessee, Alabama, Georgia, North Carolina, South Carolina, and Florida). This Deep-South region is statistically different in CHI scores from the US Census Bureau-defined grouping of states in the South. The mean of CHI scores for the Deep-South region was >1 SD below the mean of CHI scores for all states. In contrast, the CHI score means for each of the other 3 regions were all above the overall mean of CHI scores for all states. Regression analysis showed that living in the Deep-South region is a stronger predictor of poor child health outcomes than other consistently collected and reported variables commonly used to predict children's health. CONCLUSIONS: The findings of this study indicate that region of residence in the United States is statistically related to important measures of children's health and may be among the most powerful predictors of child health outcomes and disparities. This clarification of the poorer health status of children living in the Deep South through spatial analysis is an essential first step for developing a better understanding of variations in the health of children. Similar to early epidemiology work linking geographic boundaries to disease, discovering the mechanisms/pathways/causes by which region influences health outcomes is a critical step in addressing disparities and inequities in child health and one that is an important and fertile area for future research. The reasons for these disparities may be complex and synergistically related to various economic, political, social, cultural, and perhaps even environmental (physical) factors in the region. This research will require the use and development of new approaches and applications of spatial analysis to develop insights into the societal, environmental, and historical determinants of child health that have been neglected in previous child health outcomes and policy research. The public policy implications of the findings in this study are substantial. Few, if any, policies identify these children as a high-risk group on the basis of their region of residence. A better understanding of the depth and breadth of disparities in health, education, and other social outcomes among and within regions of the United States is necessary for the generation of policies that enable policy makers to address and mitigate the factors that influence these disparities. Defining and clarifying the regional boundaries is also necessary to better inform public policy decisions related to resource allocation and the prevention and/or mitigation of the effects of region on child health. The identification of the Deep South as a clearly defined subregion of the Census Bureau's regional definition of the South suggests the need to use more culturally and socially relevant boundaries than the Census Bureau regions when analyzing regional data for policy development.

Adolescent↗
PubMed1989

Analysis of spatial aggregation.

While cancer maps are a convenient way of conveying quickly such information as the presence of clusters of areas at high or low risk, the level of statistical significance of these occurrences cannot be easily derived. A method of measuring the "spatial aggregation," based on rank, was presented in the Atlas of Cancer in Scotland (Kemp et al. 1985) and further expanded in the Atlas of Cancer Mortality in Italy (Cislaghi et al. 1986). A refined version of this method is presented and compared with others.

Cluster Analysis↗
PubMed2006

Geographical clustering of mortality from systemic lupus erythematosus in the United States: contributions of poverty, Hispanic ethnicity and solar radiation.

The objective was to investigate whether spatial variation in poverty, Hispanic ethnicity, and solar radiation explains the strong pattern of geographical clustering of mortality from systemic lupus erythematosus (SLE) in the United States. SLE mortality counts for women and men of black and white race in US counties, 1979-1998, were obtained from the National Center for Health Statistics. County-level poverty rates and proportions of Hispanic residents were drawn from the 1990 national census. The annual cumulative level of ambient ultraviolet 'B' radiation (UVB) was estimated for each county according to latitude, longitude, and elevation. Maps for the full study population and for sex - and race-specific subpopulations showed that the national pattern of geographical variation in SLE mortality primarily reflected the experience of white women. Formal spatial analysis of the data for white women identified 10 statistically significant, multi-county clusters--four with elevated and six with reduced SLE mortality rates. Multivariate regression modeling established that higher levels of poverty, Hispanic ethnicity, and UVB were each associated with elevated local rates of SLE mortality among white women. Statistical adjustment via the regression model was used to remove effects of these factors on local rates. In a re-application of spatial analysis to the adjusted rates, four clusters 'disappeared'. In those clusters, poverty, Hispanic ethnicity and UVB had explained an average of 58.2% of the deviations between local and national SLE mortality rates. In six clusters (including three that disappeared with adjustment), Hispanic ethnicity explained a larger percentage of the deviations between local and national rates than either poverty or UVB. In multivariate models based on data for black women and for men of both races, poverty and UVB had similar effects on SLE mortality rates to those observed among white women. However, Hispanic ethnicity was not a significant predictor of SLE mortality in any of these other groups. The contributions of poverty, Hispanic ethnicity and solar radiation to geographical variation of SLE mortality in the United States are substantial, but these factors do not fully account for the clustering phenomenon.

Black or African American↗
PubMed2005

Fabrication and analysis of spatially uniform field electrokinetic flow devices: theory and experiment.

A uniform-field design approach can improve the performance of microanalytical, chip-based devices for a number of applications, including separations and sample preparation. The faceted prism paradigm allows the design of microfluidic devices possessing spatially uniform fields in electrokinetically driven flows. We present the first quantitative study of the velocity fields obtained using faceted interfaces between deep and shallow channel sections. Electrokinetic flows were generated in a series of wet-etch fabricated microfluidic channels. The resulting velocity fields were analyzed by particle image velocimetry and compared with simulations of the two-dimensional Laplace equation using both the designed channel geometry and the as-fabricated channel geometry. This analysis found localized differences between the designed and observed flow fields that were directly attributable to the limitations of isotropic substrate etching. Simulations using the as-fabricated channel geometry reproduced the experimental electrokinetic velocity field, quantitatively accounting for speed field variations due to the limits of the fabrication method. The electrokinetic speed fields were also compared to corresponding pressure-driven speed fields.

Electrochemistry↗
PubMed2002

Lacunarity analysis of spatial pattern in CT images of vertebral trabecular bone for assessing osteoporosis.

The structural integrity of vertebral trabecular bone is determined by the continuity of its trabecular network and the size of the holes comprising its marrow space, both of which determine the apparent size of the marrow spaces in a transaxial CT image. A model-independent assessment of the trabeculation pattern was determined from the lacunarity of thresholded CT images. Using test images of lumbar vertebrae from human cadavers, acquired at different slice thicknesses, we determined that both median thresholding and local adaptive thresholding (using a 7 x 7 window) successfully segmented the grey-scale images. Lacunarity analysis indicated a multifractal nature to the images, and a range of marrow space sizes with significant structure around 14-18 mm(2). Preliminary studies of in vivo images from a clinical CT scanner indicate that lacunarity analysis can follow the pattern of bone loss in osteoporosis by monitoring the homogeneity of the marrow spaces, which is related to the connectivity of the trabecular bone network and the marrow space sizes. Although the patient sample was small, derived parameters such as the maximum deviation of the lacunarity from a neutral (fractal) model, and the maximum derivative of this deviation, seem to be sufficiently sensitive to distinguish a range of bone conditions. Our results suggest that these parameters, used with bone mineral density values, may have diagnostic value in characterizing osteoporosis and predicting fracture risk.

Cadaver↗
PubMed1988

Objective evidence for phase-independent spatial frequency analysis in the human visual pathway.

Electrophysiological responses in human index an interaction between responses to two gratings that is relatively independent of the distribution of light in the retinal image. Two 5 cycle/deg sinewave gratings were superimposed, one counterphase-modulated at F1 Hz and the other at F2 Hz. Nonlinear interaction terms of frequency (nF1 +/- mF2) were recorded that could not be produced by superimposing the F1 Hz grating on blank-field 7 Hz flicker. A local luminance origin could be excluded for the (2F1 + 2F2) term and for the suppression of 2F1 and 4F1, but not for the (F1 + F2), (F1 + 3F2) and (5F2 - F1) terms. The relative spatial phase of the two gratings was varied, thus altering the light distribution in the retinal image without changing its spatial power spectrum. The (2F1 + 2F2) Hz contrast-specific grating-grating interaction term was almost unaffected by these substantial changes in retinal image light distribution providing that the spatial frequency power spectrum of the retinal image was held constant. The (2F1 + 2F2) term and the suppression of 2F1 were both tuned to spatial frequency.

Evoked Potentials, Visual↗
PubMed1995

Spatial data analysis in the quantitative assessment of cerebral white matter pathology on MRI in HIV infection.

This study was carried out using MRI (proton density--and T2-weighted) on 16 HIV-negative controls, 9 symptom-free HIV-positive patients and 25 with CDC IV HIV disease. The studies from this last group had previously been allocated by a radiologist to the following categories: 8 with focal mass lesions and normal-appearing white matter; 9 with diffuse encephalopathy (high signal on T2-weighted images, affecting most or all of the white matter) and 8 with patchy encephalopathy (high signal affecting only one or two areas within the white matter). Moran's I, a statistic of spatial autocorrelation, was calculated for the grey-scale values of a sampled pixel array from a central white matter region of each of the images. All values of Moran's I calculated in this study showed a large positive excess over the expected value under randomisation, indicating highly significant positive auto-correlation in the spatial arrangement of the grey-scale values. On T2-weighted images a statistically significant increase in the mean value of Moran's I, compared with controls, was found in the diffuse encephalopathy group, indicating that quantifiable changes in the spatial autocorrelation of pixel data can be related to recognised qualitative changes in the appearance of white matter in subjects with HIV disease. A lesser, but significant, rise in the mean value of Moran's I was also found in the focal mass lesion group, suggesting that changes in spatial autocorrelation may indicate pathological change in advance of qualitative MRI changes.

AIDS Dementia Complex↗
PubMed2025

Integrative spatial transcriptomic analysis pinpoints the role of the ferroxidase, TaMCO3, in wheat root tip iron mobilization.

Roots play a critical role in the sensing and absorption of essential minerals from the rhizosphere. Iron (Fe) deficiency, for example, triggers a well-known series of physiological and molecular responses within roots that facilitate uptake, which differs between monocots and dicots. In monocots, little is known about the molecular responses that occur within specific root development zones in response to iron deprivation, and how these differences result in overall nutrient uptake. Here, we conducted a transcriptome analysis of wheat root tips under Fe deficiency (-Fe) and performed a comparative transcriptome analysis with the previous datasets generated from the whole root. Gene ontology analysis of differentially expressed genes highlighted the significance of oxidoreductase activity and metal/ion transport in the root tip, which are critical for Fe mobilization. Interestingly, wheat, an allohexaploid species consisting of three different genomes (A, B, and D) displayed varying gene expression levels arising from the three genomes that contributed to similar molecular functions. Detailed analysis of oxidoreductase function at the root tip revealed multiple multicopper oxidase (MCO) proteins, such as Fe-responsive TaMCO3, that likely contribute to the overall ferroxidase activity. Further characterization of TaMCO3 shows that it complements the yeast FET3 mutant and rescues the -Fe sensitivity phenotype of Arabidopsis atmco3 mutants by enhancing vascular Fe loading. Transgenic wheat lines overexpressing TaMCO3 exhibited increased root Fe accumulation and improved tolerance to -Fe by augmenting the expression of Fe-mobilizing genes. Our findings highlight the role of spatially resolved gene expression in -Fe responses, suggesting strategies to reprogram cells for improved nutrient stress tolerance.

Triticum↗
PubMed1997

Topographical analysis of spatial patterns generated by a cellular automaton model of the proliferation of a cancer cell line in vitro.

A well-suited model to simulate cellular population dynamics is the two-dimensional cellular automaton model, which consists of a lattice of sites, the value ai,j of each site being updated in discrete time steps according to an identical deterministic rule depending on a neighbourhood of sites around it. A cellular automaton is described which mimics cell population proliferation by replacing the site values by the age and the cycle phase of cells. The model takes into account the size of the cells. It is used to simulate the proliferation of the human breast cancer cell line MCF-7 and the results of the simulation are compared with experimental data obtained from a light microscopic image analysis of the proliferation process. The initial configuration of the cellular automaton is obtained from the discretization of the results of the initial stage of the image processing. After each day of proliferation the pattern obtained from the simulation is compared to the experimental result of the corresponding image analysis. The comparison is made from a topographical point of view through the concept of the minimal spanning tree graph. The agreement between experiment and model is a good starting point to complex models such as cell proliferation under growth effectors or drugs.

Breast Neoplasms↗
PubMed2002

Analysis of spatial and temporal gene expression patterns in blastula and gastrula stage chick embryos.

Studies on the genetic basis of rostral-caudal specification, neural induction, and head development require knowledge of the relevant gene expression patterns. Gaps in our understanding of gene expression have led us to examine the detailed spatiotemporal expression patterns of 19 genes implicated in early development, to learn more about their potential role in specifying and patterning early developmental processes leading to head formation. Here, we report the expression patterns of these markers in blastula- and gastrula-stage chick embryos, using whole-mount in situ hybridisation. Nodal, Fgf8, Bmp7, Chordin, Lim1, Hnf3beta, Otx2, Goosecoid, Cerberus, Hex, Dickkopf1, and Crescent are all already expressed by the time the egg is laid. When the primitive streak has reached its full length, a later group of genes, including Ganf, Six3, Bmp2, Bmp4, Noggin, Follistatin, and Qin (BF1), begins to be expressed. We reassess current models of early rostral patterning based on the analysis of these dynamic spatiotemporal expression patterns.

Animals↗
PubMed2006

Analysis of spatial orientation strategies of male and female Wistar rats in a Morris water escape task.

In the present study we investigated spatial navigation in male and female Wistar rats in the Morris water escape task. Rats were subjected to procedures which required the use of a place (PLACE), cue (CUE) and egocentric (EGO) response to learn the task efficiently. In a first experiment rats were successively tested in the PLACE, CUE and EGO condition and in a second experiment the order of tasks was reversed. The first experiment showed that female rats swam longer distances and took more time to find the platform in the PLACE task. Further, the female rats spent less time near the previous platform position than the male rats during probe trial. No sex difference was found in the CUE and EGO task. In the second experiment, the female rats took longer to find the platform than the male rats in the EGO task. In the CUE and PLACE task no differences between the sexes was found during acquisition. However, the male rats spent more time near the previous platform position than the female rats during the probe trial of the PLACE task. On basis of present data it is concluded that the use of a PLACE-based strategy is better in male Wistar rats. CUE learning is not sex-dependent. The ability to use EGO strategies appears not to be different between male and female Wistar rats, but appears dependent on pre-exposure to the task.

Analysis of Variance↗