Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “spatial analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,261 records · Page 70Linked to original sources
PubMed2002

Spatial filtering efficiency of monostatic biaxial lidar: analysis and applications.

Results of lidar modeling based on spatial-angular filtering efficiency criteria are presented. Their analysis shows that the low spatial-angular filtering efficiency of traditional visible and near-infrared systems is an important cause of low signal/background-radiation ratio (SBR) at the photodetector input The low SBR may be responsible for considerable measurement errors and ensuing the low accuracy of the retrieval of atmospheric optical parameters. As shown, the most effective protection against sky background radiation for groundbased biaxial lidars is the modifying of their angular field according to a spatial-angular filtering efficiency criterion. Some effective approaches to achieve a high filtering efficiency for the receiving system optimization are discussed.

Journal Article↗
PubMed2006

Short-term retinal vessel diameter variability in relation to the history of cold extremities.

PURPOSE: To test whether the regularity and short-term changes of retinal vessel diameter are related to the history of cold hands and feet and to nailfold circulatory response to cooling. METHODS: In 13 vasospastic and 13 nonvasospastic young healthy women (based on their history of cold extremities and nailfold capillaroscopy) 20- to 30-second recordings of the ocular fundus was obtained with a retinal vessel analyzer. The spatial regularity of arterioles and venules was analyzed by means of the coefficient of variation of vessel diameter and by exploratory Fourier analysis of spatial frequencies. Temporal variability was analyzed as excursion amplitude of the vessel diameter, as a correlation of means and standard deviations of vessel diameter within a defined time period, and by Fourier analysis of temporal diameter change in the heartbeat frequency range. RESULTS: Mean diameters of selected segments of arterioles (129.9 +/- 15.3 and 124.4 +/- 24.4 microm) and venules (150.8 +/- 14.6 and 149.3 +/- 19.6 microm) were not different between the vasospastic and nonvasospastic groups, respectively. Spatial variability: The coefficient of variation in arterioles was 8.8% +/- 2.8% and 6.1% +/- 1.7%, in venules 3.8% +/- 1.4%, and 3.6% +/- 0.9% in the vasospastic and nonvasospastic groups, respectively (difference by ANOVA, P = 0.017). Fourier analysis revealed differences between arterioles in the two groups, with relative Fourier power spectrum amplitudes of spatial frequencies higher in vasospastic eyes (Mann-Whitney P = 0.029). Temporal variability: The excursion amplitudes of vessel diameters were comparable in the two groups. Individual coefficients of correlation of successive means and standard deviations of the vessel diameter were 0.11 +/- 0.23 and 0.09 +/- 0.23 in the nonvasospastic group, and 0.25 +/- 0.40 and 0.24 +/- 0.22 in the vasospastic group, in the arterioles and venules, respectively (ANOVA: vasospastic versus nonvasospastic; P = 0.038). Fourier analysis in the heartbeat frequency range revealed differences in relative power spectrum amplitudes of temporal frequencies between arterioles in the two groups (higher in the vasospastic group, Mann-Whitney P = 0.029). CONCLUSIONS: Retinal arterioles in healthy vasospastic women show higher spatial irregularity and an increased vessel diameter variation within the temporal frequency of the heartbeat than do arterioles in nonvasospastic women.

Adult↗
PubMed2026

Spatially resolved multi-omics analysis of indigenous Bacillus-fortified high-temperature Daqu.

Layer-dependent patterns associated with indigenous Bacillus fortification on high-temperature Daqu remain unclear. Here, six indigenous functional Bacillus strains were combined to fortify Daqu at three inoculation levels (QH4, QH5, QH6), with non-fortified as the control (CK). Upper, middle, and lower shelf-layer samples were profiled by physicochemical measurements, volatilomics, organic acid analysis, untargeted metabolomics, 16S/ITS amplicon sequencing, and metagenomics. PERMANOVA showed significant effects of treatment, spatial layer, and their interaction on physicochemical, volatile, bacterial, and fungal profiles (P = 0.001). Among the three inoculation levels, QH5 showed the most balanced performance: QH5_M exhibited the highest observed mean peak temperature (63.3 °C; +4.5 °C relative to CK_M), and its group-mean temperature remained ≥ 60 °C for seven consecutive days. Multi-omics analyses indicated coordinated, non-linear, and layer-dependent differences associated with indigenous Bacillus fortification, with QH5_M showing the most pronounced combined thermal, pyrazine, substrate, microbial, and predicted functional profile. These findings indicate that moderate indigenous Bacillus fortification was associated with distinct layer-dependent thermal and flavor profiles and coordinated microbial, metabolic, and predicted functional differences.

Bacillus↗
PubMed2003

The use of Geographic Information System (GIS) in the frame of the contingency plan implemented during the 1999-2001 avian influenza (AI) epidemic in Italy.

A Geographic Information System (GIS) is a very powerful and flexible software tool for effective management of spatially referenced data (e.g., geodata). Coupling database and GIS technology provides the tools for a detailed analysis of spatial patterns and distributions in veterinary applications. A specific veterinary GIS (VetGIS) toolbox was developed to perform the calculation of indices such as Lorenz curve, GINI index, and a kernel-based animal density estimation. This software was employed for the analysis and management of avian influenza in Italy during the 1999-2000 epidemic.

Animals↗
PubMed2004

Mechanisms of coexistence in competitive metacommunities.

Although there is a large body of theory on spatial competitive coexistence, very little of it involves comparative analyses of alternative mechanisms. We thus have limited knowledge of the conditions under which multiple spatial mechanisms can operate or of emergent properties arising from interactions between mechanisms. Here we present a mathematical framework that allows for comparative analysis of spatial coexistence mechanisms. The basis for comparison is mechanisms operating in spatially homogeneous competitive environments (e.g., life-history trade-offs) versus mechanisms operating in spatially heterogeneous competitive environments (e.g., source-sink dynamics). Our comparative approach leads to several new insights about spatial coexistence. First, we show that spatial variation in the expression of a life-history trade-off leads to a unique regional pattern that cannot be predicted by considering trade-offs or source-sink dynamics alone. This result represents an instance where spatial heterogeneity constrains rather than promotes coexistence, and it illustrates the kind of counterintuitive emergent properties that arise due to interactions between different classes of mechanisms. Second, we clarify the role of dispersal mortality in spatial coexistence. Previous studies have shown that coexistence can be constrained or facilitated by dispersal mortality. Our broader analysis distinguishes situations where dispersal mortality is not necessary for coexistence from those where such mortality is essential for coexistence because it preserves spatial variation in the strength of competition. These results form the basis for two important future directions: evolution of life-history traits in spatially heterogeneous environments and elucidation of the cause and effect relationship(s) between biodiversity and ecosystem functioning.

Animals↗
PubMed2004

GM haplotype diversity of 82 populations over the world suggests a centrifugal model of human migrations.

This study investigates the GM genetic relationships of 82 human populations, among which 10 represent original data, within and among the main broad geographic areas of the world. Different approaches are used: multidimensional scaling analysis and test for isolation by distance, to assess the correlation between genetic variation and spatial distributions; analysis of variance, to investigate the genetic structure at different hierarchical levels of population subdivision; genetic similarity map (geographic map distorted by available genetic information), to identify regions of high and low genetic variation; and minimal spanning network, to point out possible migration routes across continental areas. The results show that the GM polymorphism is characterized by one of the highest amounts of genetic variation observed so far among populations of different continents (Fct=0.3915, P < 0.0001). GM diversity can be explained by a model of isolation by distance (IBD) at most continental levels, with a particularly significant fit to IBD for the Middle East and Europe. Five peripheral regions of the world (Europe, west and south sub-Saharan Africa, Southeast Asia, and America) exhibit a low level of genetic diversity both within and among populations. By contrast, East and North African, Southwest Asian, and Northeast Asian populations are highly diverse and interconnected genetically by large genetic distances. Therefore, the observed GM variation can be explained by a "centrifugal model" of modern humans peopling history, involving ancient dispersals across a large intercontinental area spanning from East Africa to Northeast Asia, followed by recent migrations in peripheral geographic regions.

Demography↗
PubMed2003

Neuron recognition by parallel Potts segmentation.

Identifying neurons and their spatial coordinates in images of the cerebral cortex is a necessary step in the quantitative analysis of spatial organization in the brain. This is especially important in the study of Alzheimer's disease (AD), in which spatial neuronal organization and relationships are highly disrupted because of neuronal loss. To automate neuron recognition by using high-resolution confocal microscope images from human brain tissue, we propose a recognition method based on statistical physics that consists of image preprocessing, parallel image segmentation, and cluster selection on the basis of shape, optical density, and size. We segment a preprocessed digital image into clusters by applying Monte Carlo simulations of a q-state inhomogeneous Potts model. We then select the range of Potts segmentation parameters to yield an ideal recognition of simplified objects in the test image. We apply our parallel segmentation method to control individuals and to AD patients and achieve recognition of 98% (for a control) and 93% (for an AD patient), with at most 3% false clusters.

Alzheimer Disease↗
PubMed2005

Spatiotemporal activity patterns during respiratory rhythmogenesis in the rat ventrolateral medulla.

One of the most important brain rhythms is that which generates involuntary breathing movements. The lower brain stem contains neural circuitry for respiratory rhythm generation in mammals. To date, microsectioning and selective lesioning studies have revealed anatomical regions necessary for respiratory rhythmogenesis. Although respiratory neurons distributed within these regions can be identified by their firing patterns in different phases of the respiratory cycle, conventional electrophysiology techniques have limited the study of spatial organization within this network. Optical imaging techniques offer the potential for monitoring the spatiotemporal activity of large groups of neurons simultaneously. Using high-speed voltage-sensitive dye imaging and spatial correlation analysis in an arterially perfused in situ preparation of the juvenile rat, we determined the spatial distribution of respiratory neuronal activity in a region of the ventrolateral respiratory group containing the pre-Bötzinger complex (pBC) during spontaneous eupneic breathing. While distinctly pre- and postinspiratory-related responses were spatially localizable on length scales less than 100 microm, we found the studied area on whole exhibited a spatial mixture of phase-spanning and postinspiratory-related activity. Additionally, optical recordings revealed significant widespread hyperpolarization, suggesting inhibition in the same region during expiration. This finding is consistent with the hypothesis that inhibitory neurons play a crucial role in the inspiration-expiration phase transition in the pBC. To our knowledge this is the first optical imaging of a near fully intact in situ preparation that exhibits both eupneic respiratory activity and functional reflexes.

Action Potentials↗
PubMed1999

Recognition of spatial motifs in protein structures.

As the structural database continues to expand, new methods are required to analyse and compare protein structures. Whereas the recognition, comparison, and classification of folds is now more or less a solved problem, tools for the study of constellations of small numbers of residues are few and far between. In this paper, two programs are described for the analysis of spatial motifs in protein structures. The first, SPASM, can be used to find the occurrence of a motif consisting of arbitrary main-chain and/or side-chains in a database of protein structures. The program also has a unique capability to carry out "fuzzy pattern matching" with relaxed requirements on the types of some or all of the matching residues. The second program, RIGOR, scans a single protein structure for the occurrence of any of a set of pre-defined motifs from a database. In one application, spatial motif recognition combined with profile analysis enabled the assignment of the structural and functional class of an uncharacterised hypothetical protein in the sequence database. In another application, the occurrence of short left-handed helical segments in protein structures was investigated, and such segments were found to be fairly common. Potential applications of the techniques presented here lie in the analysis of (newly determined) structures, in comparative structural analysis, in the design and engineering of novel functional sites, and in the prediction of structure and function of uncharacterised proteins.

Algorithms↗
PubMed1998

On the modularity of recognition memory for object form and spatial location: a topographic ERP analysis.

Event-related potentials from 61 scalp sites were used to examine the brain processes subserving recognition memory for object forms and spatial locations. Subjects memorized line drawings of highly familiar objects and their spatial locations within a two-dimensional matrix. Prior to the test phases a cue indicated whether object-based or spatially-based recognition judgements were required. Recognition judgements were faster and more accurate for spatially-based than for object-based judgements. A variety of topographical differences in the ERP waveforms as a function of recognition task emerged: First, when the cue indicated that object-based judgements were required, negative slow wave activity extending for several hundred ms with a maximum at frontal recording sites was obtained. Conversely when spatially-based judgements were required, slow wave activity developed over parieto-occipital areas. Second, early portions of the old/new effects evoked by the test items (i.e. 300-600 ms after stimulus onset) showed a similar anterior-posterior dissociation as a function of recognition task. Third, for object-based, but not for spatially-based, judgements, late old/new effects (i.e. 700-1600 ms) were found with a clear maximum at right frontal recordings. The results are consistent with the view that functionally and anatomically different brain systems are involved in recognition memory for object form and spatial location. They further suggest that the retrieval of object forms involves conceptual semantic integration processes.

Adult↗
PubMed2003

Identification of geographic factors associated with early spread of foot-and-mouth disease.

OBJECTIVE: To explore whether early analysis of spatial data may result in identification of variables associated with epidemic spread of foot and mouth disease. SAMPLE POPULATION: 37 farms with infected cattle (ie, case farms) reported within the first 6 days of the 2001 Uruguayan foot-and-mouth disease epidemic. PROCEDURE: A georeferenced database was created and retrospective analysis was performed on case farm location in relation to farm density, cattle density, farm type (ie, beef vs dairy cattle production), road density, case farm distance to the nearest road, farm size, farm ownership, and day of infection. Mean or median results of 1 to 3 day versus 4 to 6 day spatial data were compared. Spatial-temporal associations were investigated by correlation analysis. RESULTS: Comparison of mean or median values between the first 3 days and days 4 to 6 of the epidemic and results of correlation analysis indicated a significant increase in road density, cattle density, and dairy cattle production and a significant decrease in farm size and case farm distance to the nearest road that developed over time. A route that linked most case farms by the shortest possible distance and also considered significantly associated variables was created. It included 86.1% of all case farms reported by 60 days into the epidemic. CONCLUSIONS AND CLINICAL RELEVANCE: Epidemic direction can be assessed on the basis of road density and other spatial variables as early as 6 days into an epidemic. Epidemic control areas may be more effectively identified if local and regional georeferenced data are considered.

Agriculture↗
PubMed2004

Improving the spatial specificity of canonical correlation analysis in fMRI.

The contrast-to-noise ratio (CNR) is often very low in fMRI data, and standard univariate methods suffer from a loss of sensitivity in the context of noise. The increased power of a multivariate statistical analysis method known as canonical correlation analysis (CCA) in fMRI studies with low CNR was established previously. However, CCA in its conventional form has weak spatial specificity. In this work we propose a new assignment scheme to rectify this problem. It is shown that the new method has improved spatial specificity as well as sensitivity compared to conventional CCA for detecting activation patterns in fMRI.

Adult↗
PubMed2003

Interferometric analysis of reorientational nonlinear phenomena at 10.6 microm in a nematic liquid crystal.

We describe an infrared interferometric technique based on a two-dimensional spatial fringe analysis Fourier method for investigating the characteristic ring diffraction pattern generated by the self-phase-modulation effect induced in nematic liquid crystals (NLCs) by an infrared laser beam and for measuring the nonlinear refractive index of the NLCs. The experimental setup employs a Mach-Zehnder interferometer with a cw CO2 laser emitting at 10.6 microm and a pyroelectric optoelectronic sensor matrix to detect the modulated ring-pattern intensity distribution formed in the far field by a nematic E7 sample. A Fourier-transform-based analysis of the interference fringe pattern allows comparison of the measurements with the theoretical ring-pattern intensity distribution. We show that accurate determination of the nonlinear refractive index can be obtained by analyzing the two-dimensional phase distribution of the modulated ring pattern.

Journal Article↗
PubMedDate not supplied

[Spatial distribution of rare species: statistical approach].

Many species are locally rare (have low occurrences in a given region). The method is proposed for the analysis of spatial distribution of such species. The procedure is based on the comparison of actual mean distances between records with Monte-Carlo-simulated mean distances expected for random occurrence pattern. The method was applied to two datasets: benthic macrofauna from the Barents and Kara Seas (Kucheruk, Kotov, 2002) and the Black Sea interstitial ciliates (original data). For both datasets, the number of rare species positively correlates with number of common species per site and with the total number of species. Furthermore (and irrespectively of total diversity pattern), rare species usually were locally clumped in their distribution: each of the species was mostly found at sites that were close together. This tendency, however, was significant for the macrofauna species but not for ciliates.

Animals↗
PubMed2004

Investigation of different transcript quantitation tools for high-throughput mapping of brain gene expression using voxelation.

Voxelation is a new approach for genome scale acquisition of brain gene expression patterns. The method employs high-throughput analysis of spatially registered voxels (cubes) to create multiple volumetric images of brain gene expression, similar to those obtained from biomedical imaging systems. The spatial resolution of voxelation depends on voxel size, with smaller voxels giving higher resolution. An important question is the applicability of different transcript profiling tools for the various levels of resolution that can be employed. Here, we describe the use of three methods to analyze voxel transcript abundance: real-time PCR, microarray analysis and linear amplification coupled with microarrays. We show statistically significant concordance between real-time PCR and microarray analysis for the myelin basic protein gene in human brain specimens at differing levels of spatial resolution. In addition, we also demonstrate the feasibility of using linear amplification coupled with microarray analysis to create voxelation maps from the mouse brain at high resolution, 1 microl. These data indicate the suitability of a number of transcript profiling tools for various levels of spatial resolution in voxelation.

Brain↗
PubMed2003

The neural representation of speed in macaque area MT/V5.

Tuning for speed is one key feature of motion-selective neurons in the middle temporal visual area of the macaque cortex (MT, or V5). The present paper asks whether speed is coded in a way that is invariant to the shape of the moving stimulus, and if so, how. When tested with single sine-wave gratings of different spatial and temporal frequencies, MT neurons show a continuum in the degree to which preferred speed depends on spatial frequency. There is some dependence in 75% of MT neurons, and the other 25% maintain speed tuning despite changes in spatial frequency. When tested with stimuli constructed by adding two superimposed sine-wave gratings, the preferred speed of MT neurons becomes less dependent on spatial frequency. Analysis of these responses reveals a speed-tuning nonlinearity that selectively enhances the responses of the neuron when multiple spatial frequencies are present and moving at the same speed. Consistent with the presence of the nonlinearity, MT neurons show speed tuning that is close to form-invariant when the moving stimuli comprise square-wave gratings, which contain multiple spatial frequencies moving at the same speed. We conclude that the neural circuitry in and before MT makes no explicit attempt to render MT neurons speed-tuned for sine-wave gratings, which do not occur in natural scenes. Instead, MT neurons derive form-invariant speed tuning in a way that takes advantage of the multiple spatial frequencies that comprise moving objects in natural scenes.

Action Potentials↗