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Measurement of thickness and density of thin structures by computed tomography: a simulation study.

The limited spatial resolution of clinical CT systems causes difficulties in the measurement of the density and thickness of thin structures such as the vertebral cortical shell. We simulated the imaging process by convolving experimentally determined point spread functions with rectangular and Gaussian profiles, for various fields of view or pixel sizes and reconstruction kernels. The simulations successfully explained the reported overestimation of thickness and underestimation of density when imaging thin structures. Both effects are larger for Gaussian profiles. For the rectangular profiles, experimental estimates of thickness and density will only be accurate when the true thickness is greater than about 1.5 times (for the bone reconstruction kernel) or 2.0 times (for the standard kernel) the full width at half maximum of the point spread function (PSF) of the imaging system. For Gaussian profiles imaged by a system with a Gaussian PSF, there are straightforward analytical expressions for the overestimation of thickness and underestimation of density: and these are useful approximations to the simulations of Gaussian profiles with experimental (pseudo-Gaussian) PSFs. We have demonstrated that thresholding of the vertebral image cannot provide accurate estimates of cortical thickness and density because the appropriate threshold level requires foreknowledge of the cortical thickness. To circumvent such difficulties we suggest that the average value of the peak CT numbers measured along the medial axis of the cortical shell be adopted as an index of cortical shell strength, since its value depends on both the density and the thickness of the shell.

Computer Simulation↗

Cartographic mapping of health data.

Health is a primary, individual interest of the population. The observation of health standard and health risks requires the consideration of geographical information. The cartographic visualization of health data is used to show spatial relations and correlations. A presupposition is that health data has local references. There are various local references: the local reference by domicile is most important in investigating the spatio-temporal occurrence, the geographically spread, the intensity and temporal periodicity of diseases. Cartographic visualization allows a quick and intuitive recognition of the situation in a geographical region.

Data Collection↗

[Studies of distribution of phosphorylated H3 in human MCF-7 cells by immunofluroescence labeling].

One of the prominent cell cycle-related modifications of histone proteins whose function is correlated with chromosome condensation is the phosphorylation of histone H3. In this work we used immunofluorescence labeling on human MCF-7 cells with the antibody that was specific for phosphorylated histone H3 at Ser10 to examine the cellular distribution of this protein. The acid-soluble proteins from interphase and mitotic cells were separated by SDS-PAGE and the transferred proteins were probed with the antibody. A strong H3-specific band was only detected in the acid-soluble proteins from mitotic cells, demonstrating the correlation between H3 phosphorylation and mitosis. With confocal microscopy on whole cells, our results showed that mitotic phosphorylation of H3 initiated in discrete foci near the nuclear envelope in early prophase cells. Following initiation, H3 phosphorylation appeared to spread throughout the condensing chromatin and reached maximum in early metaphase cells. Dephosphorylation of H3 began in anaphase cells and was complete immediately prior to detectable chromosome decondensation in telophase cells. There was a precise spatial and temporal correlation between H3 phosphorylation and initial stages of chromatin condensation. The possible functions of the singular phosphorylation of the amino-terminus of H3 were discussed.

Breast Neoplasms↗

Standards for measuring spatial resolution in biological X-ray microanalysis.

Lateral resolution in biological X-ray microanalysis is usually severely limited by the necessity to obtain an adequate number of X-ray counts, which requires the use of a relatively large electron beam spot size. Resolution is further degraded by spreading of the beam within the specimen. Although it is possible to make theoretical calculations of resolution, no straightforward and general method of measuring lateral resolution in biological X-ray microanalysis appears to have been proposed hitherto. In this paper, standards are proposed consisting of distinctive protein-bound elements embedded in araldite, and their use is described.

Egg Proteins↗

Temperature topography of the brain cortex: thermoencephaloscopy.

Thermoencephaloscopy (TES) - a new method of functional imaging of the cerebral cortex by its infrared radiation was advanced and developed since 1984. Improved thermovision and image processing techniques allow 2D, contact-free, dynamic and non-invasive recording of background and evoked cortical activity through an unopened skull. Activated (heated) and deactivated (cooled) zones of the cerebral cortex are revealed. The temporal resolution of TES is 40 msec (25 maps/sec), the spatial resolution is up to 70 x 70 microns/pixel. The diameter of the smallest recordable active region of the cortex is 200-300 microns. The minimal time needed for a session used for averaging of 4-9 responses varied from 40 sec up to 18 min. TES allows to detect the position, size and sequence of operation of precisely located specific cortical zones, and to measure their dynamics before, during and after sensory and direct cortical stimulation, motor acts and conditioning (associative learning). TES-effects were recorded in rats, rabbits, cats, monkeys and humans. Waves were found spreading over the cortex with a speed of up to 30 mm/sec along trajectories specific for the sensory modality and the site of stimulation. Some pathological processes in the brain are detectable by TES: experimental tumours and epileptic foci. There are many sources for local heating: neural activity, local metabolism of units, local cerebral blood flow and thermoconductivity in the activated zones of the cortex. Thermoencephaloscopy is a dynamic, non-invasive, contact-free method with a relatively high temporal and spatial resolution and sensitivity. It can be a useful tool in basic neuroscience and medicine.

Acoustic Stimulation↗

Intrinsic optical signals in vitro: a tool to measure alterations in extracellular space with two-dimensional resolution.

In excitable tissues, extensive neuronal activity or pathophysiological conditions, such as spreading depression, ischemic infarct, or epileptic seizure, are accompanied by changes in extracellular space volume. Extracellular space volume, in turn, influences neuronal excitability and extracellular ion concentrations and is, therefore, an important parameter of brain activity. Unfortunately, determination of changes in extracellular space by ion-selective microelectrodes is tedious, restricted to one spot in space at a time and limited in time resolution. In this study we present intrinsic optical signals in vitro as a tool to measure relative changes in extracellular space volume in brain slice preparations with two-dimensional spatial and sufficient time resolution. Evidence is given that the intensity of intrinsic optical signals is linearly correlated to the amplitude of extracellular space volume changes. In contrast, the optical signal is poorly correlated to the concomitant increase in extracellular potassium concentration. We conclude that intrinsic optical signals in vitro are a useful tool to measure the spread of changes in extracellular space volume with high resolution in time and space. In combination with the measurement of the extracellular space at one location using ion-selective microelectrodes, it is possible to calibrate the optical signal to percentile alterations of extracellular space volume.

Animals↗

Saturation modified point spread functions in two-photon microscopy.

Excitation saturation can dramatically alter the effective imaging point spread function (PSF) in two-photon fluorescence microscopy. The saturation-modified PSF can have important implications for resolution in fluorescence imaging as saturation leads to both an increased fluorescence observation volume and an altered spatial profile for the PSF. We introduce here a computational approach to accurately quantify molecular excitation profiles that represent the modified imaging PSF in two-photon microscopy under the influence of excitation saturation. An analytical model that accounts for pulsed laser excitation is developed to calculate the influence of saturation at any location within the excitation laser profile. The overall saturation modified molecular excitation profiles are then evaluated numerically. Our results demonstrate that saturation can play an important role in two-photon fluorescence microscopy even with relatively modest excitation levels.

Fluorescent Dyes↗

Allee effects can both conserve and create spatial heterogeneity in population densities.

In order to determine conditions which allow the Allee effect (caused by biparental reproduction) to conserve and create spatial heterogeneity in population densities, we studied a deterministic model of a symmetric two-patch metapopulation. We proved that under certain conditions there exist stable equilibria with unequal population densities in the two patches, a situation which can be interpreted as conserved heterogeneity. Furthermore, the Allee effect can lead to instability of the equilibrium with equal population densities if some degree of competition is assumed to occur between the subpopulations (non-local competition). This indicates the potential of the Allee effect to create spatial heterogeneity. Neither of these effects appear under biologically realistic parameter values in a model where uniparental reproduction is assumed. We proved that both the between-patch migration intensity and the degree of non-local competition are decisive in determining boundaries between these types of behaviour of the spatial system with Allee effect. Therefore, we propose that the Allee effect, migration intensity, and non-local competition should be considered jointly in studies focusing on problems like pattern formation in space and invasions of spreading species.

Animals↗

Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation.

We have generated and characterized a novel site-specific antibody highly specific for the phosphorylated form of the amino-terminus of histone H3 (Ser10). In this study, we used this antibody to examine in detail the relationship between H3 phosphorylation and mitotic chromosome condensation in mammalian cells. Our results extend previous biochemical studies by demonstrating that mitotic phosphorylation of H3 initiates nonrandomly in pericentromeric heterochromatin in late G2 interphase cells. Following initiation, H3 phosphorylation appears to spread throughout the condensing chromatin and is complete in most cell lines just prior to the formation of prophase chromosomes, in which a phosphorylated, but nonmitotic, chromosomal organization is observed. In general, there is a precise spatial and temporal correlation between H3 phosphorylation and initial stages of chromatin condensation. Dephosphorylation of H3 begins in anaphase and is complete immediately prior to detectable chromosome decondensation in telophase cells. We propose that the singular phosphorylation of the amino-terminus of histone H3 may be involved in facilitating two key functions during mitosis: (1) regulate protein-protein interactions to promote binding of trans-acting factors that "drive" chromatin condensation as cells enter M-phase and (2) coordinate chromatin decondensation associated with M-phase.

Amino Acid Sequence↗

A method of dynamic chromatic aberration correction in low-voltage scanning electron microscopes.

A time-of-flight concept that dynamically corrects for chromatic aberration effects in scanning electron microscopes (SEMs) is presented. The method is predicted to reduce the microscope's chromatic aberration by an order of magnitude. The scheme should significantly improve the spatial resolution of low-voltage scanning electron microscopes (LVSEMs). The dynamic means of correcting for chromatic aberration also allows for the possibility of obtaining high image resolution from electron guns that have relatively large energy spreads.

Journal Article↗

Effects of horizontal cell network architecture on signal spread in the turtle outer retina. Experiments and simulations.

In the Pseudemys turtle retina five functionally distinct, electrically coupled networks of horizontal cells distribute signals in the outer plexiform layer. These networks differ significantly in their architecture, as determined by intracellular labeling with Neurobiotin after physiological recording and identification. The density of H1 horizontal cells is highest, ranging around 1800 cells/mm2 at approximately 2.3 mm eccentricity. H1 horizontal cell somata are connected via 6-10 thin, short dendrites. The H1 horizontal cell axon terminal network is composed of thick axon terminals, forming a three-dimensional, sheath-like structure. Networks of coupled H2 and H3 horizontal cells have cell densities of around 210 cells/mm2 and 350 cells/mm2, respectively, at the same eccentricity of 2.3 mm. Cell bodies are connected with 6-12 long, thin dendrites. Here we report for the first time H4 horizontal cell networks. Cell density is approximately 970 cells/mm2 at 2 mm eccentricity, and cell bodies are connected with 6-10 thin, short dendrites. General properties of passive voltage spread were compared for three of these horizontal cell networks using NeuronC. Realistic network architectures were obtained by digitizing the intracellularly labeled networks, respectively. One network obtained from coupled H1 horizontal cell bodies, one from coupled H1 horizontal cell axon terminals, and one from H2 horizontal cells were simulated. These three realistic networks were compared with an artificial, electrically coupled regular triangular network. Passive signal spread in these networks strongly depended on the exact network architecture using otherwise identical parameters. Changes in coupling strength affected signal spread in these networks differently. As in the experimental situation, changes in synaptic conductance influenced signal spread. Some principal effects of extensively coupled horizontal cells on photoreceptor signal processing were simulated with one type of photoreceptor connected by telodendria, synapsing onto an underlying triangular network and receiving feedback synapses. Under certain conditions, spatial information is coded in single photoreceptors. This was also the case in the experimental situation. In the simulation, spatial filter adjustment for optimal spatial coding in photoreceptors can be achieved by changing coupling strength in the horizontal cell network.

Animals↗

Role of NMDA receptors in the propagation of excitation in rat visual cortex as studied by optical imaging.

To examine the role of the N-methyl-D-aspartate (NMDA) type of glutamate receptors in the propagation of information in visual cortex, optical imaging with high spatial and temporal resolution of neuronal activity was used in cortical slices of rats. Single-shock stimulation of the white matter elicited a vertical propagation of excitation toward the cortical surface simultaneously with a horizontal spread of excitation in lower layers. The horizontal spread in upper layers occurred subsequent to the vertical spread reaching these layers. The results from perfusion of Ca2+-free medium and application of an antagonist of non-NMDA receptors indicated that this intracortical propagation of signals is due mostly, if not exclusively, to the postsynaptic excitation of cortical neurons. Blockade of NMDA receptors attenuated the rising and peak phases of the upper horizontal spread, but did not affect those of the lower horizontal or vertical propagation of excitation. Perfusion with Mg2+-free solution enhanced the upper horizontal spread, but in most cases did not significantly change the spread of excitation in the other pathways. These results indicate that NMDA receptors are involved in the flow of information in the upper layers of visual cortex, and further suggest that this propagation of activity is mediated mainly by horizontal connections intrinsic to the upper layers.

2-Amino-5-phosphonovalerate↗

Efficient sampling for three-dimensional atom probe microscopy data.

The best calculation of concentration profiles, isoconcentration surfaces or Gibbsian interfacial excesses from three-dimensional atom-probe microscopy data requires a compromise between spatial positioning error and statistical sampling error. For example, sampling from larger spatial regions decreases the statistical error, but increases the error in spatial positioning. Finding the appropriate balance for a particular calculation can be tricky, especially when the three-dimensional nature of the data presents an infinite number of degrees of freedom in defining surfaces, and when the statistical error is changing from one region of a sample to another due to differences in collection efficiency or atomic density. We present some strategies for approaching these problems, focusing on efficient algorithms for generating different spatial samplings. We present a unique double-splat algorithm, in which an initial, fine-grained sampling is taken to convert the data to a regular grid, followed by a second, variable width splat, to spread the effective sampling distance to any value desired. The first sampling is time consuming for a large dataset, but needs only be performed once. The second splat is done on a regular grid, so it is efficient, and can be repeated as many times as necessary to find the correct balance of statistical and positioning error. The net effect is equivalent to a Gaussian spreading of each data point, without the necessity of calculating Gaussian coefficients for millions of data points. We show examples of isoconcentration surfaces calculated under different circumstances from the same dataset.

Journal Article↗

Spatial resolution in echo planar imaging: shifting the acquisition window in k-space.

Single-shot echo planar imaging (EPI) is one of the most suitable techniques for very fast image acquisition, especially in functional MRI. In standard EPI schemes the k-space center is sampled in the middle of the acquisition train. This leads to longer echo times for higher spatial resolutions, as well as reduced signal intensity and signal-to-noise ratio. Therefore, echo shifting to lower echo times is often used. After a brief overview on the theoretical background of various point-spread-functions (PSF) computational simulations are presented, which quantify the modulation amplitude of a binary test object sampled with either standard, zero-filled or shifted k-space acquisition. The results suggest that echo-shifting with zero-filling is not advantageous, not even with small matrix sizes, and that echo-shifting with additional acquisition of outer k-space lines decreases the modulation amplitude only slightly. Simulations were also performed on noise-corrupted test objects, indicating that the use of the echo-shifted scheme causes resolution loss of up to 30% compared to the standard scheme for a 128 by 128 pixel matrix at a noise level of 20%. Finally, in vivo experiments using different echo shifts are presented and the characteristics of signal and noise with varying TE are quantified.

Echo-Planar Imaging↗

Hadamard encoding with surface coils for high SNR MR spectroscopy.

The advantages of Hadamard over phase encoding in magnetic resonance spectroscopy (MRS) applied with surface coils in the direction perpendicular to the coil are demonstrated experimentally. With the recently introduced, time-shifted adiabatic pulses, the application of Hadamard encoding with surface coils results with almost ideal point spread function for pixels up to a distance of a radius from the coil. Comparison to phase encoding with equal region of interest size shows the significant advantage of Hadamard encoding in slice sharpness, overlapping, and spatial contamination. In addition, since there is no aliasing in Hadamard space, the total experimental time for the same region of interest is much shorter. We conclude that the hybrid of Hadamard encoding in the direction perpendicular to the coil and phase encoding in other directions is the method of choice to obtain reliable high signal to noise ratio MRS in vivo.

Magnetic Resonance Spectroscopy↗

Inhibition of pp125FAK in cultured fibroblasts results in apoptosis.

The tyrosine kinase called pp125FAK is believed to play an important role in integrin-mediated signal transduction. pp125FAK is associated both functionally and spatially with integrins, which are the cell surface receptors for extracellular matrix components. Although the precise function of pp125FAK is not known, two possibilities have been proposed: pp125FAK may regulate the assembly of focal adhesions in spreading or migrating cells, or pp125FAK may participate in a signal transduction cascade to inform the nucleus that the cell is anchored. To test these models in living cells, a peptide representing the focal adhesion kinase (FAK)-binding site of the beta 1 tail was coupled to carrier protein and injected into cultured cells to competitively inhibit the binding of pp125FAK to endogenous integrin, thus inhibiting activation of pp125FAK on a cell-by-cell basis. In addition, an antibody directed against an epitope adjacent to the focal adhesion targeting sequence on pp125FAK was microinjected, as an alternative means of inhibiting pp125FAK activation. It was observed that when rounded cells were injected with either the integrin peptide or the anti-FAK antibody, the cells rapidly began to apoptose, within 4 h after injection. These results indicate that pp125FAK may play a critical role in suppressing apoptosis in fibroblasts.

Amino Acid Sequence↗

Metabolic activity patterns in the monkey visual cortex as revealed by spectral analysis.

The metabolic activity pattern of the monkey visual cortex was mapped quantitatively with [14C]-2-deoxyglucose during the performance of a visually guided reaching task. After bandpass filtering of the reconstructed two-dimensional metabolic maps of areas V1 and V2, alternating bands of high and low metabolic activity were apparent in control and experimental hemispheres. The spatial arrangement of active bands was studied with two-dimensional spectral analysis, and bands were found to be more organized in the experimental monkey. In area V1 of the control monkey the spectral amplitude was spread over a wider range of directions and frequencies than in the experimental subject. The finding that layer IV is characterized by more complex spectra than layers I through III suggests the coexistence of more than one active columnar system in the geniculorecipient layer. In area V2, stripes running almost perpendicular to the V1/V2 border were found along with superimposed patches of enhanced metabolic activity. In the experimental hemispheres, the corresponding spectra were extremely sharp yielding a constant periodicity. It is suggested that the well-organized columnar arrangement within areas V1 and V2 of the experimental hemispheres emerges from the diffusely organized background network of activity patterns in the control state.

Algorithms↗

The effects of local spatial structure on epidemiological invasions.

Predicting the likely success of invasions is vitally important in ecology and especially epidemiology. Whether an organism can successfully invade and persist in the short-term is highly dependent on the spatial correlations that develop in the early stages of invasion. By modelling the correlations between individuals, we are able to understand the role of spatial heterogeneity in invasion dynamics without the need for large-scale computer simulations. Here, a natural methodology is developed for modelling the behaviour of individuals in a fixed network. This formulation is applied to the spread of a disease through a structured network to determine invasion thresholds and some statistical properties of a single epidemic.

Communicable Disease Control↗