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PubMed2003

Genome scale mapping of brain gene expression.

Two new approaches, voxelation and gene expression tomography (GET), permit multiplex acquisition of gene expression patterns in the brain. Both methods result in volumetric images of gene expression analogous to those produced in biomedical imaging systems. Voxelation employs analysis of spatially registered cubes from the brain, whereas GET entails analysis of parallel slices obtained by rotation about multiple axes. These methods have been used to investigate neurologic diseases and their models in both humans and mice. The results of these studies are discussed, as is the future of high-throughput gene expression mapping in the brain.

Animals↗

PubMed1995

Analysis of DNA diversity by spatial autocorrelation.

Two statistics are proposed for summarizing spatial patterns of DNA diversity. These autocorrelation indices for DNA analysis, or AIDAs, can be applied to RFLP and sequence data; the resulting set of autocorrelation coefficients, or correlogram, measures whether, and to what extent, individual DNA sequences or haplotypes resemble the haplotypes sampled at arbitrarily chosen spatial distances. Analyses of computer-generated sets of data, and of RFLP data from two natural populations, show that AIDAs allow one to objectively and simply identify basic patterns in the spatial distribution of haplotypes. These statistics, therefore, seem to be a useful tool both to explore the genetic structure of a population and to suggest hypotheses on the evolutionary processes that shaped the observed patterns.

DNA↗

PubMed2001

Sector analysis of prostate implants.

The analysis of treatment plans generated following prostate implants (post plans) is an essential part of the patient's treatment regimen. The results are used to determine the adequacy of the individual implant and, just as importantly, to provide an evaluation of the institution's brachytherapy technique. Compiled post plan results can be used to compare data from different institutions and help determine guidelines that should be established as dosimetric goals. Sector analysis, or spatial dose mapping, is a novel method of analyzing brachytherapy results that has been developed for this purpose. The display of isodose curves provides spatial information pertaining to the dosimetric evaluation of post plans but is an unwieldy tool; ill suited to the creation of general conclusions for comparative efforts. Dose-volume histogram (DVH) analysis is an excellent tool for examining dosimetric results, but the spatial information is lost. Sector analysis bridges the gap between isodose curves and DVH analysis in post plan analysis. To perform sector analysis we divide the gland into three regions in the cranial-caudal direction (base, midgland, and apex) and four regions on each transverse slice (anterior, posterior, left and right). This gives twelve sectors, each identified by its location in the cranial-caudal direction and position on the transverse slice, e.g., posterior midgland. DVH analysis is performed for each region separately and compiled for display. We present an example of the use of this technique wherein we have analyzed a sequential series of 118 implants performed by a single practitioner (BRP) at two institutions over a calendar year. The implants were performed using two different techniques at the two institutions. Sector analysis was used to compare the results of the implants at the two institutions.

Biophysical Phenomena↗

PubMed1999

Common spatial subspace decomposition applied to analysis of brain responses under multiple task conditions: a simulation study.

A method, called common spatial subspace decomposition, is presented which can extract signal components specific to one condition from multiple magnetoencephalography/electroencephalography data sets of multiple task conditions. Signal matrices or covariance matrices are decomposed using spatial factors common to multiple conditions. The spatial factors and corresponding spatial filters are then dissociated into specific and common parts, according to the common spatial subspace which exists among the data sets. Finally, the specific signal components are extracted using the corresponding spatial filters and spatial factors. The relationship between this decomposition and spatio-temporal source models is described in this paper. Computer simulations suggest that this method can facilitate the analysis of brain responses under multiple task conditions and merits further application.

Brain↗

PubMedDate not supplied

[The spatial relationships and social structure of gerbils in the genus Meriones (Gerbillinae, Rodentia)].

Comparative analysis of spatial relations of 4 gerbil species (M. tamariscinus M. meridianus, M. libycus, M. unguiculatus) shows differences in the system of space use between species and within a species--between individuals of different sex. During reproduction period females are inclined to isolation, small overlap of home ranges and high degree of individualisation. Males occupy large home ranges overlapping with territories of several reproductive females. The territories occupied by the males of midday and tamarisk gerbils do not have clear boundaries and the level of their individualization is quite low. The males of Mongolian gerbil (M. unguiculatus) occupy well defined territories with high level of individualization. Spatial relations of M. libycus males are intermediate. The relationships of the males of three investigated species (M. meridianus, M. libycus, M. tamariscinus) being characterised by the high degree of asymmetry of pair connections, are organised according to the principle of agonistic dominance. Relationships between individuals of different family groups of Mongolian gerbils are based on the locus-dependent dominance, while within one family group-on principle of hierarchical subordination. The meaning of specific peculiarities in use of space and dominance relations are discussed in terms of reproductive strategies.

Aging↗

PubMed1995

[Spatial distribution of cancer incidence by anatomic site in Quebec].

Knowledge of the spatial distribution of diseases provides useful information in etiologic research and in implementation of preventive activities in community health. Spatial autocorrelation analysis is one of the various methods that enables to determine spatial clustering of diseases. This method has not been applied to lung, stomach and colon cancer in Québec. These cancers are frequent and are associated with environmental factors. The objectives of the study are to determine spatial distribution of incidence rates of these cancer sites by sex and to help generate etiologic hypotheses. Community health departments (CHDs) of residence are considered as risk markers since their population and environment may be related to the selected cancer sites. Data were obtained from Québec Cancer Registry. Rates were standardized by the direct method. Autocorrelation analysis was done through BW coefficient and Moran's coefficient I for correlograms. Results of standardized rates were compared to those of non standardized rates. Rates yielded the same results for the BW coefficient. Conversely, results were quite different for the correlograms. This implies that results from standardized rates should be kept since the age structure of CHD populations are different. Important variation in the level of spatial autocorrelation was found among the six sex-specific cancer sites. For male lung cancer and male stomach cancer first-order neighbouring CHDs showed similar incidence rates according to a geographic gradient. Female lung cancer exhibited spatial autocorrelation. Absence of spatial autocorrelation for colon cancer suggests that CHD is not the appropriate scale for study of this cancer and allows use of conventional epidemiologic methods. These results are discussed in relation to current etiologic hypotheses.(ABSTRACT TRUNCATED AT 250 WORDS)

Cluster Analysis↗

PubMed2003

Technique to study three-dimensional spatial arrangement of synaptic vesicles using data from single sections.

Synaptic vesicles are membrane-bound organelles storing neurotransmitters in presynaptic terminals and releasing them into the synaptic cleft. Coordinated movements of synaptic vesicles relate to synaptic function and their spatial arrangement can provide useful information about the activity of a synapse. This article presents a technique to extract quantitative information about three-dimensional (3D) spatial arrangement of synaptic vesicles from measurements performed on single ultrathin random sections of a presynaptic terminal. The technique presumes quantification of a 2D density as well as 2D spatial pattern formed by vesicle profiles using a minimum spanning tree (MST) algorithm, in digitized micrographs of a presynaptic terminal. Further, original software was used to simulate a 3D spatial arrangement of synaptic vesicles and their random sectioning. A 3D density and pattern of synaptic vesicles were used as basic input parameters of the model, while a 2D density and MST quantities for vesicle profiles served as output, model-derived parameters allowing one to compare and fit simulated distributions to experimental ones. Pilot simulations performed to check the validity of the technique have shown that a 2D density and MST quantities of vesicle profiles closely relate to a 3D density and spatial pattern of vesicles. The technique was demonstrated in the analysis of spatial distribution of synaptic vesicles in axonal terminals forming asymmetric synaptic densities in the stratum radiatum of the CA1 subfield of the murine hippocampus.

Animals↗

PubMed2005

Local genetic differentiation among populations of the mass-flowering tropical shrub Erythroxylum havanense (Erythroxylaceae).

This study is aimed to understand the role of life-history traits in determining the genetic structure of populations. We used Erythroxylum havanense, a distylous shrub with synchronous and massive patterns of flowering and fruiting. We suggest that the high concentration of ephemeral resources produced by mass flowering satiates both pollinators and frugivores, restricting gene flow and leading to genetic differentiation among populations. Using random amplified polymorphic DNAs as genetic markers, we estimated genetic diversity and structure statistics to quantify the amount and distribution of genetic variation within and among five populations from the Pacific coast of Mexico. High levels of genetic variation within populations and significant differentiation among populations located very near to each other were found. Furthermore, spatial autocorrelation analysis indicated the presence of significant genetic structure at short spatial distances. We suggest that by influencing the foraging behavior of pollinators and frugivores, mass flowering may produce the observed patterns of genetic structure, while small differences in flowering or fruiting phenology could further reinforce the isolation of nearby populations.

Animals↗

PubMed2006

Independent component analysis of high-resolution imaging data identifies distinct functional domains.

In the vertebrate brain external stimuli are often represented in distinct functional domains distributed across the cortical surface. Fast imaging techniques used to measure patterns of population activity record movies with many pixels and many frames, i.e., data sets with high dimensionality. Here we demonstrate that principal component analysis (PCA) followed by spatial independent component analysis (sICA), can be exploited to reduce the dimensionality of data sets recorded in the olfactory bulb and the somatosensory cortex of mice as well as the visual cortex of monkeys, without loosing the stimulus-specific responses. Different neuronal populations are separated based on their stimulus-specific spatiotemporal activation. Both, spatial and temporal response characteristics can be objectively obtained, simultaneously. In the olfactory bulb, groups of glomeruli with different response latencies can be identified. This is shown for recordings of olfactory receptor neuron input measured with a calcium-sensitive axon tracer and for network dynamics measured with the voltage-sensitive dye RH 1838. In the somatosensory cortex, barrels responding to the stimulation of single whiskers can be automatically detected. In the visual cortex orientation columns can be extracted. In all cases artifacts due to movement, heartbeat or respiration were separated from the functional signal by sICA and could be removed from the data set. sICA following PCA is therefore a powerful technique for data compression, unbiased analysis and dissection of imaging data of population activity, collected with high spatial and temporal resolution.

Animals↗

PubMed2001

Topographic time-frequency decomposition of the EEG.

Frequency-transformed EEG resting data has been widely used to describe normal and abnormal brain functional states as function of the spectral power in different frequency bands. This has yielded a series of clinically relevant findings. However, by transforming the EEG into the frequency domain, the initially excellent time resolution of time-domain EEG is lost. The topographic time-frequency decomposition is a novel computerized EEG analysis method that combines previously available techniques from time-domain spatial EEG analysis and time-frequency decomposition of single-channel time series. It yields a new, physiologically and statistically plausible topographic time-frequency representation of human multichannel EEG. The original EEG is accounted by the coefficients of a large set of user defined EEG like time-series, which are optimized for maximal spatial smoothness and minimal norm. These coefficients are then reduced to a small number of model scalp field configurations, which vary in intensity as a function of time and frequency. The result is thus a small number of EEG field configurations, each with a corresponding time-frequency (Wigner) plot. The method has several advantages: It does not assume that the data is composed of orthogonal elements, it does not assume stationarity, it produces topographical maps and it allows to include user-defined, specific EEG elements, such as spike and wave patterns. After a formal introduction of the method, several examples are given, which include artificial data and multichannel EEG during different physiological and pathological conditions.

Adult↗

PubMedDate not supplied

[Residual dipolar couplings and molecular dynamic calculations as a source for refinement of protein spatial structures].

The precision of techniques and factors affecting the interpretation of residual dipolar couplings (RDCs) in analysis of spatial structures of partially aligned proteins are discussed. Experimental RDC values were obtained for pairs of 1H-15N nuclei of the protein barstar partially aligned in a liquid crystalline matrix of bicelles composed of dimiristoylphosphatidylcholine and dihexanoylphosphatidylcholine. The observed couplings agree well with the spatial structures of barstar determined earlier by X-ray and NMR methods. However, the differences between the experimental and calculated RDCs that were calculated on the basis of the known spatial structures of barstar, exceed the experimental errors three- to fourfold. These discrepancies can be explained by differences in the protein structures in solution and in crystal, a limited precision of the X-ray analysis, and the intramolecular mobility of the protein molecule. A comparison of the results of modeling of the molecular dynamics of barstar in solution, crystal structures, and the experimental RDCs showed that the methods of molecular dynamics provide for a reasonable description of the character and amplitudes of internal motions and they should be considered for the correct determination of protein spatial structures from NMR spectroscopic data.

Amino Acid Substitution↗

PubMed1998

Spatial structure, environmental heterogeneity, and population dynamics: analysis of the coupled logistic map.

Spatial extent can have two important consequences for population dynamics: It can generate spatial structure, in which individuals interact more intensely with neighbors than with more distant conspecifics, and it allows for environmental heterogeneity, in which habitat quality varies spatially. Studies of these features are difficult to interpret because the models are complex and sometimes idiosyncratic. Here we analyze one of the simplest possible spatial population models, to understand the mathematical basis for the observed patterns: two patches coupled by dispersal, with dynamics in each patch governed by the logistic map. With suitable choices of parameters, this model can represent spatial structure, environmental heterogeneity, or both in combination. We synthesize previous work and new analyses on this model, with two goals: to provide a comprehensive baseline to aid our understanding of more complex spatial models, and to generate predictions about the effects of spatial structure and environmental heterogeneity on population dynamics. Spatial structure alone can generate positive, negative, or zero spatial correlations between patches when dispersal rates are high, medium, or low relative to the complexity of the local dynamics. It can also lead to quasiperiodicity and hyperchaos, which are not present in the nonspatial model. With density-independent dispersal, spatial structure cannot destabilize equilibria or periodic orbits that would be stable in the absence of space. When densities in the two patches are uncorrelated, the probability that the population in a patch reaches extreme low densities is reduced relative to the same patch in isolation; this "rescue effect" would reduce the probability of metapopulation extinction beyond the simple effect of spreading of risk. Pure environmental heterogeneity always produces positive spatial correlations. The dynamics of the entire population is approximated by a nonspatial model with mean patch characteristics. This approximation worsens as the difference between the patches increases and the dispersal rate decreases: Under extreme conditions, destabilization of equilibria and periodic orbits occurs at mean parameter values lower than those predicted by the mean parameters. Apparent within-patch dynamics are distorted: The local population appears to have the wrong growth parameter and a constant number of immigrants (or emigrants) per generation. Adding environmental heterogeneity to spatial structure increases the occurrence of spatially correlated population dynamics, but the resulting temporal dynamics are more complex than would be predicted by the mean parameter values. The three classes of spatial pattern (positive, negative, and zero correlation), while still mathematically distinct, become increasingly similar phenomenologically.

Animals↗

PubMed2006

[Objectivity of therapeutic results following skull base surgery using virtual model analysis].

BACKGROUND: Virtual model analysis of patient head tracking allows for objectivity and the monitoring of therapeutic results of pathologies in the skull base region. The introduction of these models in clinical routine has been impaired by the extended time needed for the preparation of radiological data. METHODS: Quality control analysis was carried out for seven cases with different pathological findings in the skull base region in patients who had undergone virtual model analysis. RESULTS: Preparation time of radiological data for the process of segmentation required, under optimal conditions, a minimum of 30 min. Virtual model analysis enables spatial visualization of regions of interest and adjacent anatomical structures. This improves case-specific pathoanatomical understanding as well as preoperative planning of surgical strategies. CONCLUSIONS: Virtual model analysis improves the physician's spatial comprehension of localized pathological findings at the dysmorphic interface of bone and soft tissue across the skull base. Therefore, it seems to be an adequate tool for quality control analysis of therapeutic results after extended skull base surgery.

Adolescent↗

PubMed2006

How does the perception of a lesion influence visual search strategy in mammogram reading?

RATIONALE AND OBJECTIVES: Radiologists do not decide whether to report or to dismiss a perceived finding based solely on the conspicuity of the finding itself, but rather, they compare the finding with selected areas of the background. In this article, we examined how the perception of a malignant mass changed the background sampling strategy of experienced mammographers when searching mammograms for breast cancer. We determined whether these changes were different for correctly reported masses and for both visually inspected but unreported masses (ie, misses) and for lesion-free areas that were interpreted as containing a malignant mass (ie, false-positive decisions). MATERIALS AND METHODS: Four experienced mammographers read a case set of 20 two-view mammograms on two trials. Fifteen cases contained one biopsy-proven malignant mass, and five cases were lesion-free. Each cancer case had two sets of images: 1) the ones in which the lesion was reported at mammography screening, and 2) the first prior mammogram. On each trial, for each cancer case, only one set of images was shown to the observer in a balanced mix of current and prior cases per trial. The complementary set was shown in the next trial. The lesion-free cases were shown in both trials. The observers' eye positions were recorded. Spatial frequency analysis was used to represent the observers' background sampling strategy, and analysis of variance and correlation analysis were used to evaluate whether there were significant differences in the background areas sampled before and after the observers' eyes hit for the first time the location of the lesion. RESULTS: We found statistically significant differences (analysis of variance F(1,19) = 12.812, P = .0003) in the spatial frequency representation of the background areas sampled before and after the observers' eyes first hit the location of a true malignant mass. There were no statistically significant differences in the spatial frequency representation of background areas sampled before and after the observers' eyes first hit the location of a correctly reported malignant mass, but there were significant differences when either the observer did not report the mass (a miss) or the observer reported a lesion-free area as containing a mass (a false positive). CONCLUSION: A true malignant mass that the observers correctly report may be perceived immediately after image onset, thus biasing background sampling from the start, whereas areas that yield both false-negative and false-positive decisions may only be perceived during visual examination of the parenchyma. For the false negatives, our data suggest that after fixating the location of the lesion, the observers actively tried to reconcile the perception of the lesion with its background, whereas for the false positives, which represent a "true" lesion for the observers, background sampling was clearly different before and after the location was fixated for the first time. Hence, the perception of a finding effectively biases any further analysis of the case.

Breast Neoplasms↗

PubMed1993

Functional organization of the main olfactory bulb.

Complete understanding of the role of the mammalian main olfactory bulb in sensory processing has remained elusive despite many detailed studies on its anatomy and physiology. Several lines of recent evidence viewed in the context of earlier knowledge have provided new insights into the bulbar mechanisms of olfactory coding. The output cells of the olfactory bulb receive a localized olfactory nerve input and interneuronal input via dendrodendritic synapses on distinct sets of dendrites. The spatial arrangement of granule cell contacts on output cell basal dendrites suggests that lateral inhibitory interactions may occur between neighboring output cells. The input from olfactory receptor cell axons to the bulb also has spatial order, but does not represent a precise map of the receptor surface. Recent studies with antibodies and lectins suggest that different groups of axons from chemically similar receptor cells collect into certain glomeruli, even if the axons originate from cells that are not contiguous in the mucosa. Electrophysiological studies have begun to explore the participation of spatially organized circuits in olfactory processing. The degree to which neighboring output cells respond similarly to odor stimulation, for example, depends on the distance between the cells, with those further apart showing complementary responses. Also, a single output cell can show 2 or more different temporal response patterns when different odors are presented. Intracellular recordings indicate that these responses are shaped by IPSPs. Electrical stimulation during such recordings shows that some mitral cells are excited by nerve inputs close to their glomerular tufts, while they are inhibited by nerve inputs to other parts of the bulb. Finally, recordings from granule and periglomerular cells indicate their potential in mediating components of output cell odor responses. These considerations suggest that the olfactory bulb performs a spatially based analysis on the information coming from the receptor cells. While the spatial organization of the olfactory bulb is probably not faithfully represented in the projections to the olfactory cortex, bulbocortical projections are not random. The fact that spatial factors exist at each of these levels in the olfactory system must be considered in developing models of central olfactory processing.

Animals↗

PubMed1995

[Structural organization of rimorphin and its synthetic analogs].

The spatial structure and conformations of rimorphin were investigated using theoretical conformational analysis. The spatial organization of the peptide can be described by a set of 11 low-energy conformations of the backbone. By solving the reverse conformational problem, a number of modified amino acid sequences ([Ala2], [Ala3], [MePhe9], [MeLys10], [MeVal11], and [MeVal12]-analogs of rimorphin) were determined that have spatial structures corresponding to the set of low-energy conformations and should, therefore, possess physiological activity.

Amino Acid Sequence↗

PubMedDate not supplied

Quadrat analysis software for the detection of spatial or temporal clustering.

A software program is presented which automates the quadrat analysis procedure for detecting spatial or temporal clustering outlined by Boots and Getis. The software essentially compares observed values within areal or temporal sampling units to those values that would have been obtained were the values distributed randomly. A chi-square test of significance is used to assess whether the values are dispersed in a non-random pattern and a t-test is used to assess whether the values are dispersed in a non-regular pattern. The software requires DOS 3.3 or higher and reads dBase-compatible data files.

Chi-Square Distribution↗

PubMed2003

Alike performance during nonverbal episodic learning from diversely imprinted neural networks.

Performance on neuropsychological testing permits inferences to be made regarding neural networks required to solve the task. In healthy young human subjects it is common sense that differential performance in cognitive tasks results from recruitment of different neural networks and that alike performance results from recruitment of alike neural networks. It was the goal of the present study to investigate whether these assumptions are also valid in cross-cultural studies. To address this, we used functional MRI during a nonverbal episodic memory task with repeated learning of abstract geometric patterns. Behavioural performance in this task was alike over repeated trials in native Chinese and Caucasian subjects. Given this equivalent performance, the distinct pattern of neuronal activation observed is interpreted as the outcome of different culturally imprinted processing routines. In the 'what' and 'where' framework of visuo-spatial processing initial learning in Chinese subjects activated the dorsal stream for analysis of spatial features whereas Caucasians recruited the ventral stream for object identification. With repeated learning Chinese subjects integrated visuo-spatial processing to object coding and vice versa. Thus, imprints of culture result in activation of distinct neural networks and mandate monitoring of both behavioural performance and neural recruitment in cross-cultural studies of cognition.

Adult↗