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At least 667 records · Page 37Linked to original sources
PubMed2002

Deconvolution estimation of motor unit conduction velocity distribution.

A conduction velocity distribution (CVD) estimator that incorporates volume conductor modeling of the muscle voluntary response is introduced in this paper. The CVD estimates are obtained from two correlation functions, an autocorrelation and a cross, computed from myoelectric signal recorded at the skin surface. The performance of the proposed estimator is evaluated for simulated and experimental data. The study includes assessment of the estimator bias and standard deviation, as well as its sensitivity to errors in the model parameters. Simulations show its good performance in terms of estimator bias. A filtering technique also helps reduce its variance. However, the inaccuracy introduced in the estimation of model parameters considerably deteriorates the estimator performance.

Action Potentials↗
PubMed2005

Multichannel blind deconvolution of spatially misaligned images.

Existing multichannel blind restoration techniques assume perfect spatial alignment of channels, correct estimation of blur size, and are prone to noise. We developed an alternating minimization scheme based on a maximum a posteriori estimation with a priori distribution of blurs derived from the multichannel framework and a priori distribution of original images defined by the variational integral. This stochastic approach enables us to recover the blurs and the original image from channels severely corrupted by noise. We observe that the exact knowledge of the blur size is not necessary, and we prove that translation misregistration up to a certain extent can be automatically removed in the restoration process.

Algorithms↗
PubMed2000

Thermal stability of Clostridium pasteurianum rubredoxin: deconvoluting the contributions of the metal site and the protein.

To provide a framework for understanding the hyperthermostability of some rubredoxins, a comprehensive analysis of the thermally induced denaturation of rubredoxin (Rd) from the mesophile, Clostridium pasteurianum was undertaken. Rds with three different metals in its M(SCys)4 site (M = Fe3+/2+, Zn2+, or Cd2+) were examined. Kinetics of metal ion release were monitored anaerobically at several fixed temperatures between 40 and 100 degrees C, and during progressive heating of the iron-containing protein. Both methods gave a thermal stability of metal binding in the order Fe2+ << Fe3+ < Zn2+ < Cd2+. The temperature at which half of the iron was released from the protein in temperature ramp experiments was 69 degrees C for Fe2+ Rd and 83 degrees C for Fe3+ Rd. Temperature-dependent changes in the protein structure were monitored by differential scanning calorimetry, tryptophan fluorescence, binding of a fluorescent hydrophobic probe, and 1H NMR. Major but reversible structural changes, consisting of swelling of the hydrophobic core and opening of a loop region, were found to occur at temperatures (50-70 degrees C) much lower than those required for loss of the metal ion. For the three divalent metal ions, the results suggest that the onset of the reversible, lower-temperature structural changes is dependent on the size of the MS4 site, whereas the final, irreversible loss of metal ion is dependent on the inherent M-SCys bond strength. In the case of Fe3+ Rd, stoichiometric Fe3+/cysteine-ligand redox chemistry also occurs during metal ion loss. The results indicate that thermally induced unfolding of the native Cp Rd must surmount a significant kinetic barrier caused by stabilizing interactions both within the protein and within the M(SCys)4 site.

Bacterial Proteins↗
PubMedDate not supplied

Fast model-free deconvolution of fluorescence decay for analysis of biological systems.

For complex biological systems, conventional analysis of fluorescence intensity decay in terms of discrete exponential components cannot readily provide a true representation of the underlying fluorescence dynamics. We investigate an alternative nonparametric method for the analysis of time-resolved fluorescence data from biochemical and biological systems based on the expansion of fluorescence decay in a discrete Laguerre basis. We report that a unique Laguerre expansion can be found for fluorescence intensity decays of arbitrary form with convergence to a correct solution significantly faster than conventional multiexponential approximation methods. The Laguerre expansion coefficients are shown to be highly correlated with intrinsic fluorescence lifetimes and allow direct characterization of the fluorescence dynamics. A novel method for prediction of concentrations in mixtures of biochemical components using these coefficients is developed and successfully tested (prediction error <2%) using data from different mixtures of fluorescence lifetime standards. These findings suggest that the use of Laguerre expansion coefficients is a fast approach for the characterization and discrimination of complex biological systems such as tissues and cells, and that the method has potential for applications of fluorescence lifetime techniques to tissue diagnostics and imaging microscopy of living cells.

Algorithms↗
PubMed2002

Deblurring of x-ray spectra acquired with a Nal-photomultiplier detector by constrained least-squares deconvolution.

A constrained least-squares technique to correct diagnostic x-ray tube energy spectra for inherent blurring by scintillation detectors was developed. The measured detector response function to monoenergetic sources was used to construct a matrix that modeled the energy broadening in the crystal. This blurring operator, along with an estimate of statistical noise in the count data, comprised the a priori system knowledge required for application of the method. Tungsten anode spectra up to 90 kVp were acquired with a Nal-photomultiplier detector system at a source-to-detector distance of 30 cm. X-ray tube output was collimated at the detector by a 0.5 mm diameter pinhole collimator. Measured Nal spectra were compared to both published reference data and to spectra acquired in our laboratory with a Ge detector system. Application of the constrained least-squares technique involved first defining a criterion function that combined an assessment of the goodness of fit with a weighted measure of the smoothness of the solution. Minimization of this function resulted in the corrected spectrum. While it is not possible to recover the characteristic tungsten peaks, the success of our method in deconvolving the measured spectra was demonstrated by a significant improvement in agreement with reference data. To provide a measure of this agreement, a histogram of the differences between the two curves was generated. The full width at half maximum (FWHM) of the Gaussian distribution fit to the histogram was used to quantify the similarity between the spectra and the reference data, both before and after correction. As spectral agreement improves, the FWHM becomes smaller. We show that application of the constrained least-squares technique improved spectral matching by 20%-60%.

Biophysical Phenomena↗
PubMedDate not supplied

Constrained deconvolution of SPECT liver tomograms by direct digital image restoration.

Several techniques for performing digital image restoration are reviewed and the problems associated with evaluating image processing are discussed. An application of constrained deconvulution to images of the liver produced by single-photon emission computed tomography is presented. Specific evaluation criteria are suggested and based on these, the choice of conditions best suited for processing liver images is proposed. Typically cold tumor contrast can be improved by a factor of greater than 2 whilst image mottle increases negligibly.

Filtration↗
PubMed1998

Magnetic resonance quantification of the myocardial perfusion reserve with a Fermi function model for constrained deconvolution.

The myocardial perfusion reserve, defined as the ratio of hyperemic and basal myocardial blood flow, is a useful indicator of the functional significance of a coronary artery lesion. Rapid magnetic resonance (MR) imaging for the noninvasive detection of a bolus-injected contrast agent as a MR tracer is applied to the measurement of regional tissue perfusion during rest and hyperemia, in patients with microvascular dysfunction. A Fermi function model for the distribution of tracer residence times in the myocardium is used to fit the MR signal curves. The myocardial perfusion reserve is calculated from the impulse response amplitudes for rest and hyperemia. The assumptions of the model are tested with Monte Carlo simulations, using a multiple path, axially distributed mathematical model of blood tissue exchange, which allows for systematic variation of blood flow, vascular volume, and capillary permeability. For a contrast-to-noise ratio of 6:1, and over a range of flows from 0.5 to 4.0 ml/min per g of tissue, the ratio of the impulse response amplitudes for hyperemic and basal flows is linearly proportional to the ratio of model blood flows, if the mean transit time of the input function is shorter than approximately 9 s. The uncertainty in the blood flow reserve estimates grows both at low (< 1.0 ml/min/g) and high (> 3-4 ml/min/g) flows. The predictions of the Monte Carlo simulations agree with the results of MR first pass studies in patients without significant coronary artery lesions and microvascular dysfunction, where the perfusion reserve in the territory of the left anterior descending coronary artery (LAD) correlates linearly with the intracoronary Doppler ultrasound flow reserve in the LAD (r = 0.84), in agreement with previous PET studies.

Capillaries↗
PubMed2006

Deconvolution of the factors contributing to the increase in global hurricane intensity.

To better understand the change in global hurricane intensity since 1970, we examined the joint distribution of hurricane intensity with variables identified in the literature as contributing to the intensification of hurricanes. We used a methodology based on information theory, isolating the trend from the shorter-term natural modes of variability. The results show that the trend of increasing numbers of category 4 and 5 hurricanes for the period 1970-2004 is directly linked to the trend in sea-surface temperature; other aspects of the tropical environment, although they influence shorter-term variations in hurricane intensity, do not contribute substantially to the observed global trend.

Journal Article↗
PubMed1996

Metaphase and interphase mapping by FISH: improvement of chromosome banding and signal resolution in interphase nuclei by means of iterative deconvolution.

FISH images obtained with conventional epifluorescence microscopes are always blurred by glare and out of focus light emissions. In order to restore high contrast images, a procedure based on a modelling of the optical system in the microscope was developed and used for the processing of images acquired with a cooled CCD camera mounted on a fluorescence microscope. This procedure was tested on images of both mouse and human chromosomes stained with DAP1 and on images of interphase nuclei hybridized with pairs of cosmid probes. This method improves the definition and the sharpness of the DAPI G-banding and thus facilitates and speeds up the identification of chromosomes. When performed on images of interphase cell nuclei, this procedure allows the discrimination of fluorescent signals which appear partially overlapping on raw images. This significant improvement of spatial resolution is of particular interest for ordering sets of probes on DNA fibers.

Animals↗
PubMed2004

Deconvoluting lung evolution using functional/comparative genomics.

Parathyroid Hormone-related Protein (PTHrP) is a highly evolutionarily conserved, stretch-regulated gene that is necessary for the embryonic transition from branching morphogenesis to alveolization of the lung. It is expressed throughout vertebrate phylogeny, beginning with its expression in the fish swim bladder as an adaptation to gravity; microgravity downregulates the expression of PTHrP by alveolar type II cells, and by bones from rats exposed to 0 x g, suggesting that PTHrP signaling has been exploited for adaptation to 1 x g. PTHrP/PTHrP receptor signaling is upregulated by stretching alveolar type II cells and intersitial lung fibroblasts, whereas overdistension downregulates PTHrP and PTHrP receptor mRNA, further suggesting an evolutionary adaptation. Both surfactant homeostasis and alveolar capillary perfusion are under PTHrP control, indicating that alveolization and ventilation/perfusion matching may have evolved under the influence of PTHrP signaling. Phylogenetic analysis of lung evolution reflects the concomitant increases in alveolar surface area and surfactant production by "amplifying" the PTHrP pathway signal. This mechanism is discussed as a function of increased evolutionary respiratory demand to keep up with the increased metabolic demand for oxygen, and the role of the PTHrP signaling mechanism in leveraging this process.

Animals↗
PubMed1992

Deconvolution of ultrasound images.

Based on physical models, it is indicated that the received pressure field in ultrasound B-mode images can be described by a convolution between a tissue reflection signal and the emitted pressure field. This result is used in a description of current image formation and in formulating a new processing scheme. The suggested estimator can take into account the dispersive attenuation, the temporal and spatial variation of the pulse, and the change in reflection strength and signal-to-noise ratio. Details of the algorithm and the estimation of parameters to be used are given. The performance is indicated by two examples. One is for a synthetic signal and the other is for data measured from a tissue mimicking phantom. The last example shows a finer speckle pattern, giving an increased resolution.

Algorithms↗
PubMed2006

Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity.

BACKGROUND: MHC Class I molecules present antigenic peptides to cytotoxic T cells, which forms an integral part of the adaptive immune response. Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions. RESULTS: A large dataset comprising MHC-peptide structural complexes was created by re-modelling pre-determined x-ray crystallographic structures. Static energetic analysis, following energy minimisation, was performed on the dataset in order to characterise interactions between bound peptides and the MHC Class I molecule, partitioning the interactions within the groove into van der Waals, electrostatic and total non-bonded energy contributions. CONCLUSION: The QSAR techniques of Genetic Function Approximation (GFA) and Genetic Partial Least Squares (G/PLS) algorithms were used to identify key interactions between the two molecules by comparing the calculated energy values with experimentally-determined BL50 data. Although the peptide termini binding interactions help ensure the stability of the MHC Class I-peptide complex, the central region of the peptide is also important in defining the specificity of the interaction. As thermodynamic studies indicate that peptide association and dissociation may be driven entropically, it may be necessary to incorporate entropic contributions into future calculations.

Binding Sites↗
PubMed2004

Numerical deconvolution of cDNA microarray signal: simulation study.

A computational model for simulation of the cDNA microarray experiments has been created. The simulation allows one to foresee the statistical properties of replicated experiments without actually performing them. We introduce a new concept, the so-called bio-weight, which allows for reconciliation between conflicting meanings of biological and statistical significance in microarray experiments. It is shown that, for a small sample size, the bio-weight is a more powerful criterion of the presence of a signal in microarray data as compared to the standard approach based on t test. Joint simulation of microarray and quantitative PCR data shows that the genes recovered by using the bio-weight have better chances to be confirmed by PCR than those obtained by the t test technique. We also employ extreme value considerations to derive plausible cutoff levels for hypothesis testing.

Cell Line, Tumor↗
PubMed2002

Live cell imaging using wide-field microscopy and deconvolution.

The use of fluorescence imaging methods, most recently based on fluorescent protein technology, and the availability of high quality fluorescence imaging systems have driven a revolution in cell and molecular biology. Live cell imaging, especially using fluorescence, is now used in a wide variety of assays in academic and commercial laboratories. The use of this technology requires particular attention to be paid to cell engineering, the design of the image acquisition system, the imaging protocol, and subsequent processing and analytic methods. In this review, we discuss each of these steps, highlighting practical techniques developed by us and others.

Algorithms↗