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PubMed2003

Analysis of protein interactions using fluorescence technologies.

Biophotonics techniques, especially those involving fluorescence, are widely used in proteomics to characterize the in vitro interactions between proteins in high-throughput mode. On the other hand, fluorescence-based imaging studies often show that protein activity is regulated through large protein complexes that transiently form at specific sites in the cell. One could therefore argue that a systematic functional analysis of the human proteome requires technologies that are capable of time and spatially resolved, multiplexed analysis of protein interactions within cells.

Fluorescence Resonance Energy Transfer↗
PubMed2006

Transcriptional profiling of the Arabidopsis embryo.

We have used laser-capture microdissection to isolate RNA from discrete tissues of globular, heart, and torpedo stage embryos of Arabidopsis (Arabidopsis thaliana). This was amplified and analyzed by DNA microarray using the Affymetrix ATH1 GeneChip, representing approximately 22,800 Arabidopsis genes. Cluster analysis showed that spatial differences in gene expression were less significant than temporal differences. Time course analysis reveals the dynamics and complexity of gene expression in both apical and basal domains of the developing embryo, with several classes of synexpressed genes identifiable. The transition from globular to heart stage is associated in particular with an up-regulation of genes involved in cell cycle control, transcriptional regulation, and energetics and metabolism. The transition from heart to torpedo stage is associated with a repression of cell cycle genes and an up-regulation of genes encoding storage proteins, and pathways of cell growth, energy, and metabolism. The torpedo stage embryo shows strong functional differentiation in the root and cotyledon, as inferred from the classes of genes expressed in these tissues. The time course of expression of the essential EMBRYO-DEFECTIVE genes shows that most are expressed at unchanging levels across all stages of embryogenesis. We show how identified genes can be used to generate cell type-specific markers and promoter activities for future application in cell biology.

Arabidopsis↗
PubMed1986

Analysis of the changes in the proportion of clustered labelled cells in epidermis.

A new cell kinetic approach is presented from which the duration of the S and G2 + M phases can be estimated. The technique involves an analysis of the spatial distribution of labelled cells in sections or sheets of epithelium (i.e. an analysis of clustered labelled cells). The technique is largely independent of the absolute number of labelled cells and hence is not influenced by factors which affect the absolute number of labelled cells. The technique is described and experimental data from dorsal murine skin are presented. The technique has also been simulated mathematically so that the phase durations and their variances could be estimated. The advantages of the technique are: it is technically simple; it provides at least two independent estimates of the phase durations; unlabelled cells need not be counted (compare with LI or PLM analysis); it is independent of variations in the absolute yield of labelled cells, and it is applicable if the LI is low and the S phase is short (where the PLM technique tends to fail).

Animals↗
PubMed1999

Effects of spatial segmentation in the continuous model of excitation propagation in cardiac muscle.

INTRODUCTION: Spatial segmentation is essential for the numerical simulation of excitation propagation in cardiac muscle. METHODS AND RESULTS: This study evaluated the effects of spatial segmentation on action potential and on the velocity of propagation in a continuous one-dimensional model of cardiac muscle [intracellular and extracellular resistivities along (L) and transverse (T) to the muscle fibers: 402 omega(cm) (R(e), L), 3,620 omega(cm) (R(e), T), 48 omega(cm) (R(e), L), and 126 omega(cm) (R(e), T), J of Physiol 255:335-346, 1976) and either Luo-Rudy (L-R, Circ Res 68:1501-1526, 1991) or Beeler-Reuter (B-R, J Physiol 268:177-210, 1977) ionic currents. Related cable equations for active membrane are derived. Spatial segmentations of < 31.2 microm (L, L-R), < 11.5 microm (T, L-R), < 44.7 microm (L, B-R), and < 16.5 microm (T, B-R) were required for < 1% errors in the characteristic parameters of action potential. Similarly, spatial segmentations of < 54.5 microm (L, L-R), < 20.1 microm (T, L-R), < 84.3 microm (L, B-R), and < 31.2 microm (T, B-R) were required for < 1 % errors in the velocity of conduction. CONCLUSION: In general, spatial segmentations of < 26.9% and < 50.8% of the space constant of a fully activated membrane gave < 1.0% errors in the characteristic parameters of action potential and in the velocity of propagation, respectively, for both membranes. The action potential duration was relatively insensitive to the spatial segmentation. Our analysis suggests that lambda(full is a better criterion for the selection of spatial segmentation in numerical simulation than the space constant of the resting membrane.

Action Potentials↗
PubMedDate not supplied

Using geographic information systems to evaluate cardiac arrest survival.

OBJECTIVE: To evaluate cardiac arrest survival using geographical information systems (GIS) methodology. METHODS: Patient data were obtained from a fire district Utstein-style adult cardiac arrest registry that also included address data. All incident locations were geocoded and fire station first-due areas were mapped by using the new computer-aided dispatch geographic data. Retrospective assignment of first-due versus second-due fire response unit was done by using a GIS "point-in-polygon" algorithm Survival to hospital admission was the primary outcome measure for incidents responded to by first-due versus second-due apparatus controlling for other potential predictors of survival using logistic regression. Cluster analysis was also performed to evaluate potential areas of high or low rates of survival. RESULTS: There were 461 eligible patients with an average age of 67+/-17 years, 63% were male, 53% had a witnessed arrest, bystander cardiopulmonary resuscitation was performed in 38%, bystander automatic external defibrillator (AED) Page: 1 was used in 0.01%, ventricular fibrillation or ventricular tachycardia were the presenting rhythms in 44%, the average response time was 5.5+/-2.1 minutes, and survival to hospital admission was 17%. There was no significant difference in response time between survivors (4.97 minutes) and non-survivors (5.52 minutes), (difference 0.55 minutes, 95%CI -0.08 to 1.18 min). The number of cardiac arrest calls varied from 1 to 49 for each station and the rate of second-due response varied from 0 to 19%. There was a nonsignificant association of survival to hospital admission for the first-due area cohort: odds ratio 0.70, 95% CI 0.38-1.29. CONCLUSION: GIS is a new methodology for analyzing EMS incident data. It adds a spatial component of analysis to traditional statistical techniques. No spatial difference was found on patient survival in this analysis.

Aged↗
PubMed1994

The geographic variation of cancer incidence in Ontario.

OBJECTIVES: Our objectives were (1) to describe an analysis of the spatial pattern of cancer incidence in Ontario and (2) to discuss the quality of data in the Ontario Cancer Registry with respect to the accuracy of local cancer rates. METHODS: Cancer incidence rates were calculated for 22 cancer sites in 49 counties of Ontario during 1976 to 1986. Capture-recapture methods were used to estimate completeness of case registration, and completeness of residence information was also assessed. Spatial autocorrelation was used in measuring the geographic pattern of incidence rates. Comparisons were also made between sexes and with earlier data from 1966 to 1975. RESULTS: The quality of the geographic data in the registry appeared good, and corrections for incomplete or inaccurate registration had little impact. About one third of the sex-site combinations showed some evidence of spatial patterning in the cancer rate. Particularly strong regional variation was noted for cancers of the stomach, lung, uterus, and prostate. CONCLUSIONS: The analysis revealed a number of cancers with significant spatial patterning of risk. Further work is needed to relate the cancer data to other information on potential life-style and environmental factors.

Female↗
PubMed2004

Spatiotemporal wavelet analysis for functional MRI.

Characterizing the spatiotemporal behavior of the BOLD signal in functional Magnetic Resonance Imaging (fMRI) is a central issue in understanding brain function. While the nature of functional activation clusters is fundamentally heterogeneous, many current analysis approaches use spatially invariant models that can degrade anatomic boundaries and distort the underlying spatiotemporal signal. Furthermore, few analysis approaches use true spatiotemporal continuity in their statistical formulations. To address these issues, we present a novel spatiotemporal wavelet procedure that uses a stimulus-convolved hemodynamic signal plus correlated noise model. The wavelet fits, computed by spatially constrained maximum-likelihood estimation, provide efficient multiscale representations of heterogeneous brain structures and give well-identified, parsimonious spatial activation estimates that are modulated by the temporal fMRI dynamics. In a study of both simulated data and actual fMRI memory task experiments, our new method gave lower mean-squared error and seemed to result in more localized fMRI activation maps compared to models using standard wavelet or smoothing techniques. Our spatiotemporal wavelet framework suggests a useful tool for the analysis of fMRI studies.

Algorithms↗
PubMed1998

Fast Fourier transform analysis of ventricular fibrillation intervals to predict ventricular refractoriness and its spatial dispersion.

A technique of fast Fourier transform analysis has been used to derive mean ventricular fibrillation (VF) intervals, and to confirm that these VF intervals predict ventricular refractory periods. Twenty episodes of VF were induced by a rapid ventricular pacing in 12 sheep. VF activations in a 10-second period were simultaneously acquired from 64 epicardial sites with an electrode sock. The VF electrograms were analyzed by a fast Fourier transform analysis. The dominant peak frequency of the VF spectrum in each epicardial site was converted into milliseconds and served as a mean VF interval. The dominant peak frequency of VF electrograms ranged from 8.1 to 11.5 Hz, and the corresponding mean VF intervals were 87 to 124 ms. In five sheep, the mean VF intervals and the effective refractory periods were determined by the extrastimulus technique obtained from 29 epicardial sites. There was a very good correlation between the two parameters when the effective refractory periods were determined at a basic cycle length of 300 ms (r = 0.89, P < 0.001) and 400 ms (r = 0.87, P < 0.001), respectively. VF was induced twice in eight sheep. The maximum difference in the mean VF intervals between the two VF episodes in the same sheep was 3 ms (P > 0.05). In conclusion, mean VF intervals determined by the fast Fourier transform analysis have a good reproducibility and a good correlation with ventricular refractory periods measured by the classic extrastimulus technique. The mean VF intervals could serve as an index of ventricular refractoriness.

Animals↗
PubMed2001

Measurement of electron beam broadening in stainless steels during EDS analysis in the FEG-TEM.

The effect of electron beam broadening on spatial resolution of EDS analysis in a 200 kV cold-FEG-TEM has been investigated for Type 316L stainless steel. Platinum (Pt) was evaporated on half the 316L TEM foil surface, and the difference in Pt concentration profiles obtained by the EDS method from the Pt evaporated surface and its opposite side was analysed as a function of foil thickness. Advantages of Pt use are that Pt is not included in the 316L steel, and it is easily formed as a stable and continuous thin evaporated film on the stainless steel. No change of spatial resolution caused by electron beam broadening was observed in stainless steel foils of less than about 140 nm thick subjected to EDS analysis with the FEG-TEM (incident probe size 1.6 +/- 0.2 nm diameter). Specimens of about 160 nm and more thick had a decrease in spatial resolution, but the decrease was smaller than that predicted from theoretical calculations of beam broadening for stainless steels. It is suggested that only the central part of the broadened electron beam with high intensity influences the spatial resolution of EDS analysis with the FEG-TEM.

Journal Article↗
PubMed2000

Spatial risk factors related to outbreaks of contagious bovine pleuropneumonia in northern Italy (1990-1993).

In October 1990, an outbreak of contagious bovine pleuropneumonia (CBPP) was reported in Italy after an absence of approximately one century. Since October 1990, ninety-four outbreaks have occurred in Italy, of which forty-seven were concentrated in three areas of northern Italy (Lombardy region). The disease was eradicated in September 1993. The data used for the analysis were obtained from the epidemiological investigations undertaken during the outbreaks of 1990-1993. The unit of interest for the analysis is the farm. Spatial segregation of infected and uninfected farms within the study area was determined through the Pielou index of segregation. Data from herds within the same set of outbreaks were analysed through logistic regression to identify factors which could be used to discriminate between infected and uninfected herds. The study indicated a clear spatial segregation between infected and uninfected herds. The results of the analysis do not indicate the mode of disease spread. However, the study demonstrated that both aerosol and indirect transmission of the infection could have occurred, as previously documented in Africa. The possibility that indirect transmission played a prominent role in the spread of CBPP in the region of Lombardy is a completely new suggestion. Further studies are required to understand the epidemiology of CBPP in regions with intensive farming and a relatively cold climate. In particular, three aspects require consideration; firstly, animal movement among neighbouring herds could produce a pattern of disease similar to the one produced by indirect transmission (this possibility was excluded in the epidemiological outbreak investigations conducted by field veterinarians). Secondly, the methods of spatial analysis used in this study have not been previously used in the field of veterinary epidemiology. Further validation of the efficacy of these methods is thus required. Thirdly, the epidemiology of CBPP under conditions of high animal density and a relatively cool climate, as encountered in Lombardy, requires further investigation.

Animals↗
PubMed2004

A primer on the study of transitory dynamics in ecological series using the scale-dependent correlation analysis.

Here we describe a practical, step-by-step primer to scale-dependent correlation (SDC) analysis. The analysis of transitory processes is an important but often neglected topic in ecological studies because only a few statistical techniques appear to detect temporary features accurately enough. We introduce here the SDC analysis, a statistical and graphical method to study transitory processes at any temporal or spatial scale. SDC analysis, thanks to the combination of conventional procedures and simple well-known statistical techniques, becomes an improved time-domain analogue of wavelet analysis. We use several simple synthetic series to describe the method, a more complex example, full of transitory features, to compare SDC and wavelet analysis, and finally we analyze some selected ecological series to illustrate the methodology. The SDC analysis of time series of copepod abundances in the North Sea indicates that ENSO primarily is the main climatic driver of short-term changes in population dynamics. SDC also uncovers some long-term, unexpected features in the population. Similarly, the SDC analysis of Nicholson's blowflies data locates where the proposed models fail and provides new insights about the mechanism that drives the apparent vanishing of the population cycle during the second half of the series.

Animals↗
PubMed2003

Analysis of fMRI data by blind separation of data in a tiny spatial domain into independent temporal component.

Independent Component Analysis (ICA) is a promising tool for the analysis of functional magnetic resonance imaging (fMRI) time series. In these studies, mostly assumed is a spatially independent component map of fMRI data (spatial ICA). In this paper, we assume that the temporal courses of the signal and noises are independent within a Tiny spatial domain (temporal ICA). Then with fast-ICA algorithm, spatially neighboring fMRI data were blindly separated into several temporal courses and were preassumed to be formed by a signal time course and several noise time courses where the signal has the largest correlation coefficient with the reference signal. The final functional imaging was completed for the signals obtained from each voxel. Simulations showed that compared with the spatial ICA method, the new temporal ICA method is more effective than the spatial ICA in detecting weak signal in a fMRI dataset. As background noise, the simulations include simulated Gaussian noise and fMRI data without stimulation. Finally, vivo fMRI tests showed that the excited areas evoked by a visual stimuli are mainly in the region of the primary visual cortex and that evoked by auditory stimuli are mainly in the region of the primary temporal cortex.

Algorithms↗
PubMed2003

Spatial navigation in virtual reality environments: an EEG analysis.

Past research has linked theta oscillations (electroencephalographic activity in the 4-8-Hz range) to spatial navigation in rodents and humans, and to the encoding and retrieval of spatial information in rodents. In the present study, electroencephalographic activity was measured while humans navigated through virtual mazes. Results confirmed previous findings that the frequency of theta episodes is directly related to the difficulty of maze navigation. We were also able to show that theta episodes occur most likely at points in a maze where new hallways come into view, or after navigational mistakes have been realized and are being corrected. This indicates that, just as in rodents, theta episodes in humans are related to the encoding and retrieval of spatial information.

Adult↗
PubMed1994

Molecular scene analysis: application of a topological approach to the automated interpretation of protein electron-density maps.

Methods to assist in the spatial and visual analysis of electron-density maps have been investigated as part of a project in molecular scene analysis [Fortier, Castleden, Glasgow, Conklin, Walmsley, Leherte & Allen (1993). Acta Cryst. D49, 168-178]. In particular, the usefulness of the topological approach for the segmentation of medium-resolution (3 A) maps of proteins and their interpretation in terms of structural motifs has been assessed. The approach followed is that proposed by Johnson [Johnson (1977). ORCRIT. The Oak Ridge Critical Point Network Program. Chemistry Division, Oak Ridge National Laboratory, USA] which provides a global representation of the electron-density distribution through the location, identification and linkage of its critical points. In the first part of the study, the topological approach was applied to calculated maps of three proteins of small to medium size so as to develop a methodology that could then be used for analyzing maps of medium resolution. The methodology was then applied to both calculated and experimental maps of penicillopepsin at 3 A resolution. The study shows that the networks of critical points can provide a useful segmentation of the maps, tracing the protein main chains and capturing their conformation. In addition, these networks can be parsed in terms of secondary-structure motifs, through a geometrical analysis of the critical points. The procedure adopted for secondary-structure recognition, which was phrased in terms of geometry-based rules, provides a basis for a further automated implementation of a more complete set of recognition operations through the use of artificial-intelligence techniques.

Journal Article↗
PubMed1987

Evaluating the aggregate spatial structure of Canadian metropolitan areas.

"Few attempts have been made to develop and test a conceptual framework for the comparative analysis of urban spatial structure and growth. This paper offers one aggregate approach as well as a series of empirical tests based on Canada's 27 largest urban areas. Six composite indices are introduced: population densities, rates of change, intraurban population redistribution, mobility rates, incidence of low-income populations, and degree of social polarization. Regression analyses reveal that differences among urban areas in spatial patterning and structural change are consistent with the hypothesized effects of city size, age, transport usage, social heterogeneity, production base, and physical setting. Yet immense regional and intraurban diversity remains. No single model of urban structure is sufficient to capture this diversity." (SUMMARY IN FRE)

Americas↗
PubMed1994

Spatial non-uniformities in [Ca2+]i during excitation-contraction coupling in cardiac myocytes.

The intracellular calcium ([Ca2+]i) transient in adult rat heart cells was examined using the fluorescent calcium indicator fluo-3 and a laser scanning confocal microscope. We find that the electrically evoked [Ca2+]i transient does not rise at a uniform rate at all points within the cell during the [Ca2+]i transient. These spatial non-uniformities in [Ca2+]i are observed immediately upon depolarization and largely disappear by the time the peak of the [Ca2+]i transient occurs. Importantly, some of the spatial non-uniformity in [Ca2+]i varies randomly in location from beat to beat. Analysis of the spatial character of the non-uniformities suggests that they arise from the stochastic nature of the activation of SR calcium-release channels. The non-uniformities in [Ca2+]i are markedly enhanced by low concentrations of Cd2+, suggesting that activation of L-type calcium channels is the primary source of activator calcium for the calcium transient. In addition, the pattern of calcium release in these conditions was very similar to the spontaneous calcium sparks that are observed under resting conditions and which are due to spontaneous calcium release from the SR. The spatial non-uniformity in the evoked [Ca2+]i transient under normal conditions can be explained by the temporal and spatial summation of a large number of calcium sparks whose activation is a stochastic process. The results are discussed with respect to a stochastic local control model for excitation-contraction (E-C) coupling, and it is proposed that the fundamental unit of E-C coupling consists of one dihydropyridine receptor activating a small group of ryanodine receptors (possibly four) in a square packing model.

Animals↗
PubMed2002

A probabilistic methodology to assess the risk of groundwater quality degradation.

An approach to assess the risk of groundwater quality degradation with regard to fixed standards. based on Disjunctive Kriging (DK) is presented. The DK allows one to evaluate the Conditional Probability (CP) of overriding a given threshold of concentration of a pollutant at a given time, and at a generic point in a considered groundwater system. The result of such investigation over the considered area can be plotted in form of maps of spatial risk. By repeating this analysis at different times, several spatial risk maps will be produced, one for each considered time. By means of non-parametric statistics, the temporal trend of the CPs can be evaluated at every point of the considered area. The trend index, assessed by means of a sort of classification of the trend values obtained as described above, can be superimposed on the most recent values of the spatial risk (i.e.: the most recent values of probability). Consequently a classification of the risk of groundwater quality degradation results with which to weigh both the spatial distribution and the temporal behaviour of the probability to exceed a given standard threshold. The methodology has been applied to values of nitrate concentration sampled in the monitoring well network of the Modena plain, northern Italy. This area is characterised by intensive agricultural exploitation and hog breeding along with industrial and civil developments. The influence of agriculture on groundwater results in a high nitrate pollution that limits its use for potable purposes.

Agriculture↗
PubMed1995

Linkage of the 1981 and 1991 U.K. censuses using surface modelling concepts.

Problems involving the comparative analysis of data for the 1981 and 1991 U.K. censuses are explored. The authors note that "the integration of 1981 and 1991 data is far from straightforward because of changes in census geography and definitions, in the administration of the census, and in the format and nature of the data. It is explained how, by a further refinement of population surface modelling concepts, these two data sets can be transformed into a single, consistent geographical database independent of the two original and inconsistent zonal structures....The resulting models permit intercensal analysis with considerable spatial flexibility and a number of computational advantages. Illustration is made of the types of analysis that can be supported, and attention is drawn to the availability of the remodelled data to the academic community."

Censuses↗

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