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At least 343 records · Page 19Linked to original sources
PubMed2007

A method for quantitative analysis of spatially variable physiological processes across leaf surfaces.

Many physiological processes are spatially variable across leaf surfaces. While maps of photosynthesis, stomatal conductance, gene expression, water transport, and the production of reactive oxygen species (ROS) for individual leaves are readily obtained, analytical methods for quantifying spatial heterogeneity and combining information gathered from the same leaf but with different instruments are not widely used. We present a novel application of tools from the field of geographical imaging to the multivariate analysis of physiological images. Procedures for registration and resampling, cluster analysis, and classification provide a general framework for the analysis of spatially resolved physiological data. Two experiments were conducted to illustrate the utility of this approach. Quantitative analysis of images of chlorophyll fluorescence and the production of ROS following simultaneous exposure of soybean leaves to atmospheric O3 and soybean mosaic virus revealed that areas of the leaf where the operating quantum efficiency of PSII was depressed also experienced an accumulation of ROS. This correlation suggests a causal relationship between oxidative stress and inhibition of photosynthesis. Overlaying maps of leaf surface temperature and chlorophyll fluorescence following a photoinhibition treatment indicated that areas with low operating quantum efficiency of PSII also experienced reduced stomatal conductance (high temperature). While each of these experiments explored the covariance of two processes by overlaying independent images gathered with different instruments, the same procedures can be used to analyze the covariance of information from multiple images. The application of tools from geographic image analysis to physiological processes occurring over small spatial scales will help reveal the mechanisms generating spatial variation across leaves.

Algorithms↗
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↗
PubMed2005

A modelling framework describing the enzyme regulation of membrane lipids underlying gradient perception in Dictyostelium cells II: input-output analysis.

Spatial sensing in Dictyostelium involves localization of the phosphoinositide lipids PI(3,4,5)P3 and PI(3,4)P2 at the leading edge of the cell in response to an external gradient. We have previously proposed a modelling framework describing the regulation of these lipids by the enzymes PI3K and PTEN. In this paper we analyse this regulation from an input-output perspective. When the inputs are homogeneous, we obtain explicit analytical expressions for the lipid concentrations as a function of enzyme concentrations and model parameters. We also show that the system can be cast as an open-loop bilinear control system, and employ control engineering tools to show that a local three-dimensional region in the four-dimensional phase space can be accessed by temporally varying either or both enzyme concentrations. For spatially graded enzyme profiles, we show that diffusion limits the extent to which lipid profiles can be manipulated by enzymes. However, we also demonstrate that for certain ranges of network parameters, increasing lipid diffusion can lead to an increase in steady-state leading-edge concentrations of PI(3,4,5)P3 or PI(3,4)P2, even though all lipid diffusion coefficients are equal. Finally, in order to determine the extent to which lipid profiles can be regulated by the enzymes, we formulate and solve inverse problems, where we determine the enzyme profiles required to realize particular lipid profiles at steady state.

Animals↗
PubMed2005

Improved background removal method using principal components analysis for spatially resolved electron energy loss spectroscopy.

Principal components analysis (PCA) factor filtering is implemented for the improvement of background removal in noisy spectra. When PCA is used as a method for filtering before background removal in electron energy loss spectroscopy elemental maps, an improvement in the accuracy of the background fit with very short fitting intervals is achieved, leading to improved quality of elemental maps from noisy spectra. This opens the possibility to use shorter exposure times for elemental mapping, leading to fewer problems with, for example, drift and beam damage.

Journal Article↗
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↗
PubMed2004

Exploratory spatial data analysis for the identification of risk factors to birth defects.

BACKGROUND: Birth defects, which are the major cause of infant mortality and a leading cause of disability, refer to "Any anomaly, functional or structural, that presents in infancy or later in life and is caused by events preceding birth, whether inherited, or acquired (ICBDMS)". However, the risk factors associated with heredity and/or environment are very difficult to filter out accurately. This study selected an area with the highest ratio of neural-tube birth defect (NTBD) occurrences worldwide to identify the scale of environmental risk factors for birth defects using exploratory spatial data analysis methods. METHODS: By birth defect registers based on hospital records and investigation in villages, the number of birth defects cases within a four-year period was acquired and classified by organ system. The neural-tube birth defect ratio was calculated according to the number of births planned for each village in the study area, as the family planning policy is strictly adhered to in China. The Bayesian modeling method was used to estimate the ratio in order to remove the dependence of variance caused by different populations in each village. A recently developed statistical spatial method for detecting hotspots, Getis's 7, was used to detect the high-risk regions for neural-tube birth defects in the study area. RESULTS: After the Bayesian modeling method was used to calculate the ratio of neural-tube birth defects occurrences, Getis's statistics method was used in different distance scales. Two typical clustering phenomena were present in the study area. One was related to socioeconomic activities, and the other was related to soil type distributions. CONCLUSION: The fact that there were two typical hotspot clustering phenomena provides evidence that the risk for neural-tube birth defect exists on two different scales (a socioeconomic scale at 6.84 km and a soil type scale at 22.8 km) for the area studied. Although our study has limited spatial exploratory data for the analysis of the neural-tube birth defect occurrence ratio and for finding clues to risk factors, this result provides effective clues for further physical, chemical and even more molecular laboratory testing according to these two spatial scales.

Bayes Theorem↗
PubMed2005

Component spatial pattern analysis of chemicals by use of two-dimensional electro-optic terahertz imaging.

We demonstrate a method of chemical mapping by using the transillumination terahertz (THz) images obtained by two-dimensional electro-optic THz imaging. The images and spectral data were measured between 0.1 and 1.0 THz. An experimental sample consisting of three chemicals was prepared, with one in two concentrations. By introducing the component spatial pattern analysis based on the least-squares method, the chemical composition, spatial distribution, and difference in concentration were clearly determined.

Journal Article↗
PubMed2006

Application of multivariate statistical methods to water quality assessment of the watercourses in Northwestern New Territories, Hong Kong.

Multivariate statistical methods, i.e., cluster analysis (CA) and discriminant analysis (DA), were used to assess temporal and spatial variations in the water quality of the watercourses in the Northwestern New Territories, Hong Kong, over a period of five years (2000-2004) using 23 parameters at 23 different sites (31,740 observations). Hierarchical CA grouped the 12 months into two periods (the first and second periods) and classified the 23 monitoring sites into three groups (group A, group B, and group C) based on similarities of water quality characteristics. DA provided better results with great discriminatory ability for both temporal and spatial analysis. DA also provided an important data reduction because it only used six parameters (pH, temperature, five-day biochemical oxygen demand, fecal coliforms, Fe, and Ni) for temporal analysis, affording about 84% correct assignations, and seven parameters (pH, ammonia-nitrogen, nitrate nitrogen, fecal coliforms, Fe, Ni, and Zn) for spatial analysis, affording more than 90% correct assignations. Therefore, DA allowed a reduction in the dimensionality of the large data set and indicated a few significant parameters that were responsible for most of the variations in water quality. Thus, this study demonstrated that the multivariate statistical methods are useful for interpreting complex data sets in the analysis of temporal and spatial variations in water quality and the optimization of regional water quality monitoring network.

Discriminant Analysis↗
PubMed2005

Information processing flow and neural activations in the dorsolateral prefrontal cortex in the Stroop task in schizophrenic patients. A spatially filtered MEG analysis with high temporal and spatial resolution.

Using a spatially filtered magnetoencephalography analysis (synthetic aperture magnetometry), we estimated neural activations in the Stroop task in nearly real time for schizophrenic patients with/without auditory hallucinations and for normal control subjects. In addition, auditory hallucinations were examined through the information processing flow of the brain neural network, including the frontal regions. One hundred unaveraged magnetoencephalography signals during the incongruent stimulus responses were analyzed with a time window of 200 ms in steps of 50 ms. In the 25-60-Hz band, cortical regions that showed significant current source density changes were examined for each time window. The three groups showed significantly decreased current source density, corresponding to neural activation, with temporal overlap along the fundamental cognitive information processing flow: sensory input system, executive control system, motor output system. Transient neural activations in the dorsolateral prefrontal cortex were bilateral with left-side dominancy for normal controls, left-lateralized for nonhallucinators and right-lateralized for hallucinators. Our results suggest that the dysfunction in the left dorsolateral prefrontal cortex was related to auditory hallucinations, while the information processing flow was unaffected in the schizophrenic subjects in the Stroop task.

Adolescent↗
PubMed2006

Spatial correlation analysis of isotropic microvessels: methodology and application to thyroid capillaries.

The study of relations between structural organization and functions of microcirculatory networks is a major aim of modern microangiology. Such a structural aspect of microvessels (MVs) as their spatial arrangement has substantial influence on their transport and other functional properties. This paper describes a methodology of spatial correlation analysis for isotropic blood and lymphatic MVs which is based on a stereological estimator of the pair correlation function [g3D(r)] created recently by the authors for systems of elongated objects. The following main features of the methodology are presented: (i) interpretation of the shape of g3D(r) curves, (ii) their quantitative description by numerical parameters, and (iii) limitations of the method arising from statistical requirements to MVs under investigation. The methodology is considered in the light of multilevel sampling designs, which are typical for biomedical morphology. The estimator with its methodological framework is applied to perifollicular blood capillaries in the adult rat thyroid. Related methods for studying the spatial arrangement of MVs are thoroughly discussed in the paper.

Albinism↗
PubMed2005

Geographical information system (GIS) in investigation of an outbreak.

An outbreak of fever in a village in southern India was reported on 1st September, 2001. The first reported case presented with epistaxis and a platelet count of 27000h(1)/mm3. Clinical, laboratory and entomological evidence supported a diagnosis of dengue fever. One third of the village was affected and 3.7 % of the population presented with haemorrhagic symptoms; none were fatal. Five acute cases tested for dengue specific IgM showed that two were positive. The larvae of Aedes aegypti were discovered from domestic water collections in the village. Spatial analysis done with the help of Geographical Information Systems software (GIS) demonstrated a centrifugal spread of cases from the most affected street until it involved the entire village. Spatial analysis revealed that cases occurred in clusters and that these could not have occurred by chance. This was our first experience in producing a geo-referenced map of a village area and in spatial analysis. GIS is a novel and simple tool for outbreak investigations and the spatial analyst adds additional information to the data collected. Control of adult mosquitoes and larvae prevented the outbreak from spreading to an adjacent village.

Adolescent↗
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↗