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At least 361 records · Page 20Linked to original sources
PubMed2005

Computer-aided analysis of spatial structure of some hydrolytic enzymes.

Using the MolScript version 2.1 computer program for protein molecule modeling and X-ray structure analysis data the spatial structures of several hydrolytic enzymes have been compared. These include glucoamylase from Aspergillus awamori and Saccharomycopsis fibuligera and lipases from Rhizopus japonicus. Results on homology of amino acid sequences and topology of secondary structure elements were obtained. 3D models of these enzymes with positioning of functionally important groups in the active site cavity were built.

Amino Acid Sequence↗
PubMed2006

An approach based on spatial multicriteria analysis to map the nature conservation value of agricultural land.

Knowledge of the nature conservation value of agricultural land provides a useful input to land-use planning. However, the scarcity of suitable data causes this component to rarely play a role. The paper proposes a methodology based on commonly available data to assess the nature conservation value of agricultural landscapes, and to generate cartographic results to be used as decision variables in planning. The approach relies on landscape ecological indicators and on the application of multicriteria analysis in a Geographical Information System (GIS) context. Four criteria were selected: the agricultural landscape type, the cover of vegetation remnants and marginal features, the length of forest-agriculture ecotones, and the proximity to nature reserves. These criteria were assessed directly or by means of specific indicators, generating maps that were subsequently aggregated through spatial multicriteria analysis. The approach was tested in an alpine area located in Trentino (northern Italy).

Agriculture↗
PubMed2004

Improving permutation test power for group analysis of spatially filtered MEG data.

Non-parametric statistical methods, such as permutation, are flexible tools to analyze data when the population distribution is not known. With minimal assumptions and better statistical power compared to the parametric tests, permutation tests have recently been applied to the spatially filtered magnetoencephalography (MEG) data for group analysis. To perform permutation tests on neuroimaging data, an empirical maximal null distribution has to be found, which is free from any activated voxels, to determine the threshold to classify the voxels as active at a given probability level. An iterative procedure is used to determine the distribution by computing the null distribution, which is recomputed when a possible activated voxel is found within the current distributions. Besides the high computational costs associated with this approach, there is no guarantee that all activated voxels are excluded when constructing the maximal null distribution, which may reduce the statistical power. In this study, we propose a novel way to construct the maximal null distribution from the data of the resting period. The approach is tested on the MEG data from a somatosensory experiment, and demonstrated that the approach could improve the power of the permutation test while reducing the computational cost at the same time.

Adult↗
PubMed2002

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

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

Algorithms↗
PubMed2005

Semi-blind ICA of fMRI: A method for utilizing hypothesis-derived time courses in a spatial ICA analysis.

Independent component analysis (ICA) is a data-driven approach utilizing high-order statistical moments to find maximally independent sources that has found fruitful application in functional magnetic resonance imaging (fMRI). Being a blind source separation technique, ICA does not require any explicit constraints upon the fMRI time courses. However, for some fMRI data analysis applications, such as for the analysis of an event-related paradigm, it would be useful to flexibly incorporate paradigm information into the ICA analysis. In this paper, we present an approach for constrained or semi-blind ICA (sbICA) analysis of event-related fMRI data by imposing regularization on certain estimated time courses using the paradigm information. We demonstrate the performance of our approach using both simulations and fMRI data from a three-stimulus auditory oddball paradigm. Simulation results suggest that (1) a regression approach slightly outperforms ICA when prior information is accurate and ICA outperforms the general linear model (GLM)-based approach when prior information is not completely accurate, (2) prior information improves the robustness of ICA in the presence of noise, and (3) ICA analysis using prior information with temporal constraints can outperform a regression approach when the prior information is not completely accurate. Using fMRI data, we compare a regression-based conjunction analysis of target and novel stimuli, both of which elicit an orienting response, to an sbICA approach utilizing both the target and novel stimuli to constrain the ICA time courses. Results show similar positive associations for both GLM and sbICA, but sbICA detects additional negative associates consistent with regions implicated in a default mode of brain activity. This suggests that task-related default mode decreases have a more "complex" signal that benefits from a flexible modeling approach. Compared with a traditional GLM approach, the sbICA approach provides a flexible way to analyze fMRI data that reduces the assumptions placed upon the hemodynamic response of the brain. The advantages and limitations of our technique are discussed in detail in the manuscript to provide guidelines to the reader for developing useful applications. The use of prior time course information in a spatial ICA analysis, which combines elements of both a regression approach and a blind ICA approach, may prove to be a useful tool for fMRI analysis.

Auditory Perception↗
PubMedDate not supplied

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

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

Animals↗
PubMed1989

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

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

Alleles↗
PubMed2006

[Spatial variability analysis of soil arsenic in Zibo maize producing area, Shandong Province].

Spatial variability and distribution of soil arsenic in Zibo maize producing area, Shandong Province were studied using geostatistics and geographic information system (GIS) techniques. Positive skewed distribution was observed; Logarithm transformation was applied in order to achieve normality in the data set and to reduce the affect of outliers. The results show that experimental semi-variogram exists distinct anisotropic and has the strongest continuity in the direction of northeastern 70 degrees. Exponential model was used to fit experimental semi-variogram. Normal kriging was used to predict the spatial distribution of soil arsenic in Zibo maize producing area. It can be concluded that there is clear special heterogeneity in soil arsenic and wastewater irrigation is the main reason affected spatial variability. In fact, the concentrations of soil arsenic in Zibo maize producing area decrease in the pass 20 years.

Arsenic↗
PubMed2003

Localization of human somatosensory cortex using spatially filtered magnetoencephalography.

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

Adult↗
PubMed2006

Spatial clustering analysis in neuroanatomy: applications of different approaches to motor nerve fiber distribution.

Spatial organization of the nerve fibers in the peripheral nerves may be important for the studies of axonal regeneration, the degenerative nerve diseases and the construction of interfaces with peripheral nerves, such as nerve prostheses. Functional topography of motor axons related to the gastrocnemius muscle was revealed in the ventral spinal roots by retrograde tracing. Gastrocnemius muscles of adult rats were injected with the tracer Fluoro-Gold. After 3 days of survival the animals were sacrificed and their ventral roots were harvested, sectioned, and imaged on a fluorescence microscope. Maps of the traced fibers were automatically analyzed using a novel approach, local spatial clustering statistics, that tested for occurrences of clusters of motor fibers and visualized them. Thresholds indicating the presence of clustering at various scales of observation were computed based on series of Monte Carlo simulations of random spatial point patterns. Clusters were visualized by kernel interpolation. The approach was tested on simulated data and subsequently applied to the motor fiber maps in the ventral roots. Results revealed clustering of the motor fibers innervating the gastrocnemius muscle at the level of the L6 ventral spinal root. The analysis was validated using Voronoi tessellation and nearest neighbor analysis.

Animals↗
PubMed1986

Spatial resolution analysis of computed tomographic images.

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

Humans↗
PubMed2004

An accident waiting to happen: a spatial approach to proactive pedestrian planning.

There are about 75,000 pedestrian crashes in the United States each year. Approximately 5000 of these crashes are fatal, accounting for 12% of all roadway deaths. On college campuses, pedestrian exposure and crash-risk can be quite high. Therefore, we analyzed pedestrian crashes on the campus of the University of North Carolina at Chapel Hill (UNC) as a test case for our spatially-oriented prototype tool that combines perceived-risk (survey) data with police-reported crash data to obtain a more complete picture of pedestrian crash-risk. We use spatial analysis techniques combined with regression models to understand factors associated with risk. The spatial analysis is based on comparing two distributions, i.e. the locations of perceived-risk with police-reported crash locations. The differences between the two distributions are statistically significant, implying that certain locations on campus are perceived as dangerous, though pedestrian crashes have not yet occurred there, and there are actual locations of police-reported crashes that are not perceived to be dangerous by pedestrians or drivers. Furthermore, we estimate negative binomial regression models to combine pedestrian and automobile exposure with roadway characteristics and spatial/land use information. The models show that high exposure, incomplete sidewalks and high crosswalk density are associated with greater observed and perceived pedestrian crash-risk. Additionally, we found that people perceive a lower risk near university libraries, stadiums, and academic buildings, despite the occurrence of crashes.

Accidents, Traffic↗
PubMed2003

Spatial distribution analysis of AT- and GC-rich regions in nuclei using corrected fluorescence resonance energy transfer.

We employed microscopic intensity-based fluorescence resonance energy transfer (FRET) images with correction by donor and acceptor concentrations to obtain unbiased maps of spatial distribution of the AT- and GC-rich DNA regions in nuclei. FRET images of 137 bovine aortic endothelial cells stained by the AT-specific donor Hoechst 33258 and the GC-specific acceptor 7-aminoactinomycin D were acquired and corrected for the donor and acceptor concentrations by the Gordon's method based on the three fluorescence filter sets. The corrected FRET images were quantitatively analyzed by texture analysis to correlate the spatial distribution of the AT- and GC-rich DNA regions with different phases of the cell cycle. Both visual observation and quantitative texture analysis revealed an increased number and size of the low FRET efficiency centers for cells in the G(2)/M-phases, compared to the G(1)-phase cells. We have detected cell cycle-dependent changes of the spatial organization and separation of the AT- and GC-rich DNA regions. Using the corrected FRET (cFRET) technique, we were able to detect early DNA separation stages in late interphase nuclei.

AT Rich Sequence↗
PubMed1991

Spatial Fourier analysis of video photobleaching measurements. Principles and optimization.

The major use of the fluorescence recovery after photobleaching (FRAP) technique is to measure the translational motion of the molecular components in various condensed media. In a conventional laser spot photobleaching experiment, a photomultiplier is used to measure the total brightness levels of the bleached region in the sample, so no spatial information can be directly obtained. In video-FRAP, a series of images after photobleaching is acquired, allowing the spatial character of the recovery to be determined; this permits direct detection of both anisotropic diffusion and flow. To utilize all of the available image data to determine the transport coefficients, a two-dimensional spatial Fourier transform analysis of the images after photobleaching was employed. The change in the transform between two time points reflects the action of diffusion during the interim. An important advantage of this method, which involves taking the ratio of image transforms at different time points, is that it does not require a specific initial condition to be created by laser photobleaching. The ability of the analysis to extract transport coefficients from computer-simulated diffusional recovery is assessed in the presence of increasing amounts of noise. Experimental data analysis from the diffusion of proteins in viscous solutions and from the diffusion of protein receptors on cell surfaces demonstrate the feasibility of the Fourier analysis to obtain transport coefficients from the video FRAP measurement.

Biophysical Phenomena↗
PubMed1998

What is line bisection in unilateral spatial neglect? Analysis of perceptual and motor aspects in line bisection tasks.

Three patients with unilateral spatial neglect could detect the difference of length between the right and left segments when a line had a transection mark. To examine the effect of response mode, the manual line bisection task and a new "line bisection task by fixation" were given to the patients. In tasks that used lines with no landmark, they showed apparent rightward errors. The results suggest that line bisection is not a task that examines the ability of patients with neglect to compare the right and left extents of a line. Where to fixate as the subjective midpoint may determine the rightward errors of bisection, whether manual response is used or not.

Aged↗