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Pixel-by-pixel deconvolution of bolus-tracking data: optimization and implementation.

Quantification of haemodynamic parameters with a deconvolution analysis of bolus-tracking data is an ill-posed problem which requires regularization. In a previous study, simulated data without structural errors were used to validate two methods for a pixel-by-pixel analysis: standard-form Tikhonov regularization with either the L-curve criterion (LCC) or generalized cross validation (GCV) for selecting the regularization parameter. However, problems of image artefacts were reported when the methods were applied to patient data. The aim of this study was to investigate the nature of these problems in more detail and evaluate strategies of optimization for routine application in the clinic. In addition we investigated to which extent the calculation time of the algorithm can be minimized. In order to ensure that the conclusions are relevant for a larger range of clinical applications, we relied on patient data for evaluation of the algorithms. Simulated data were used to validate the conclusions in a more quantitative manner. We conclude that the reported problems with image quality can be removed by appropriate optimization of either LCC or GCV. In all examples this could be achieved with LCC without significant perturbation of the values in pixels where the regularization parameter was originally selected accurately. GCV could not be optimized for the renal data, and in the CT data only at the cost of image resolution. Using the implementations given, calculation times were sufficiently short for routine application in the clinic.

Algorithms↗

Statistical evaluation of a self-deconvoluting matrix strategy for high-throughput screening of the CXCR3 receptor.

In high-throughput screening (HTS), compounds can be tested in self-deconvoluting matrices (SDMs) of 10 compounds per well. The SDM setup is based upon a systematic mixing of compound samples such that each compound appears twice in the screening assay, in two independent mixtures. In order to test the quality of the SDM approach, we compared it with a standard single-compound screening approach. In a CXCR3 scintillation proximity assay, we performed five multiple screening trials of 26,400 compounds at a 10 microM screening concentration to estimate false positive and false negative rates in the compound population. No potent hits (<6.2 microM IC50) were missed in any screening method. Forty-eight percent of all actives were found in every screening trial independent of compound handling method. The SDM strategy had an average of 25 false positives and 15 false negatives as compared with an average of 34 false positives and 15 false negatives with a more conventional single-compound screening approach. Most of the variability resulted from day-to-day variation around the hit cutoff criterion, rather than from any particular screening technique. In the two most extreme examples, a compound with a 7.5 microM IC50 was missed in one out of two mixture trials, and a compound with a 6.2 microM IC50 was missed in one out of three single-compound trials. In the CXCR3 assay presented herein, the SDM screening method had better predictive value than the single-compound screening approach.

Animals↗

Signal deconvolution based expression-detection and background adjustment for microarray data.

Background adjustment is an essential stage in analyzing DNA microarrays. Discriminating expressed genes from unexpressed ones (expression detection), and estimating the expression levels of weakly expressed genes, critically depend on accurate treatment of the background intensity. Current methods for background adjustment either do not deal with nonspecific hybridization or strongly depend on the reliability of control probes. Existing model-based methods have limited accuracy. A new platform-independent background adjustment algorithm is presented. The algorithm relies on the deconvoluted experimental signal distribution for evaluating the expression probability and adjusting the background of each probe. Considering expression detection, it is shown, for two-channels cDNA arrays and for the Affymetrix GeneChip platform, that the algorithm performs at least as good or better than control-probes-based algorithms. For the Affymetrix GeneChip arrays, it is further shown that the algorithm outperforms the robust multiarray (RMA) expression measure in estimating genomewide expression levels.

Algorithms↗

Extension of HRTEM resolution by semi-blind deconvolution method and Gerchberg-Saxton algorithm: application to grain boundary and interface.

A generalized maximum entropy method coupled with Gerchberg-Saxton algorithm has been developed to extend the resolution from high-resolution TEM image(s) for weak objects. The Gerchberg-Saxton algorithm restores spatial resolution by operating real space and reciprocal space projections cyclically. In our methodology, a generalized maximum entropy method (Kullback-Leibler cross entropy) dealing with weak objects is used as a real space (P1) projection. After P1 projection, not only are the phases within the input spatial frequencies improved, but also the phases in the next higher frequencies are extrapolated. An example of semi-blind deconvolution (P1 project only) to improve the resolution in SiC twin boundary is shown. The nature of the bonding in this twin boundary is Si-C but it was rotated 180 degrees along the boundary normal. The optimum solution from P1 projection can be further improved by a P2 projection. The square roots of diffraction intensities from a diffraction pattern are then substituted to complete a cycle operation of the Gerchberg-Saxton algorithm. Application examples of Gerchberg-Saxton algorithm to solve the atomic structure of defects (2 x 1 interfacial reconstruction and dislocation) in NiSi2/Si interfaces will be shown also.

Journal Article↗

Restoring atomic configuration at interfaces by image deconvolution.

The image deconvolution technique in combination with dynamical scattering effect correction developed previously for crystal defect investigation has been modified to meet the needs of interface studies and applied to a [111] twin model of Si. Elliptical windows are utilized as a new means for Fourier filtering and correcting the amplitudes of reflections. Images were simulated with a 200 kV field-emission high-resolution electron microscope. After image restoration, four images simulated with different defocus values were transformed into structure images with atomic columns revealed individually at correct positions. The effectiveness of the technique is discussed.

Journal Article↗

Computerised glow curve deconvolution using general and mixed order kinetics.

Some accurate glow curve fitting functions for general and mixed order kinetics glow peaks are proposed and discussed. These mathematical expressions are used together with peak search and non-linear minimisation algorithms in order to provide a fast glow curve deconvolution for those materials which cannot be well fitted using first order kinetics. To test the accuracy of the proposed method. the result of the fitting of synthetic glow curves is compared with the original data giving negligible errors for values of parameters currently found in TL materials.

Computer Simulation↗

Glow curve analysis of composite peak 5 in LiF:Mg,Ti (TLD-100) using optical bleaching, thermal annealing and computerised glow curve deconvolution.

The relative intensity of glow peak 5a in the composite glow peak 5 of LiF:Mg,Ti (TLD-100) is very weak following gamma irradiation, and has been estimated at approximately 0.1 of the intensity of peak 5. Typical glow curve analysis using computerised glow curve deconvolution with unconstrained variation of the peak shape parameters, yields values of the relative intensity of glow peak 5a varying from 0 to 15%. Due to the potential of peak 5a to fulfil the criteria of a quasi-tissue-equivalent nanodosemeter which estimates quality factor, considerable efforts have been invested in ancilliary techniques to improve the reliability of the estimation of the intensity of peak 5a. Optical bleaching and thermal annealing techniques were used to obtain single-peak glow curves consisting of peak 4 only and peak 5 only. A multi-stage CGCD protocol was then constructed using these peak shape parameters for peaks 4 and 5, which allows more accurate estimation of the relative intensity of peak 5a. Following 60Co irradiation of ten chips to a dose level of 1 Gy, the technique yields a relative intensity of 0.08 +/- 0.008 (1 SD).

Equipment Design↗

On the possibility of using commercial software packages for thermoluminescence glow curve deconvolution analysis.

This paper explores the possibility of using commercial software for thermoluminescence glow curve deconvolution (GCD) analysis. The program PEAKFIT has been used to perform GCD analysis of complex glow curves of quartz and dosimetric materials. First-order TL peaks were represented successfully using the Weibull distribution function. Second-order and general-order TL peaks were represented accurately by using the Logistic asymmetric functions with varying symmetry parameters. Analytical expressions were derived for determining the energy E from the parameters of the Logistic asymmetric functions. The accuracy of these analytical expressions for E was tested for a wide variety of kinetic parameters and was found to be comparable to the commonly used expressions in the TL literature. The effectiveness of fit of the analytical functions used here was tested using the figure of merit (FOM) and was found to be comparable to the accuracy of recently published GCD expressions for first- and general-order kinetics.

Kinetics↗

Thermoluminescence glow curve deconvolution and its statistical analysis using the flexibility of spreadsheet programs.

Analysing thermoluminescence glow curves involves the solving of a system of non-linear equations. These equations are either differential equations that must be solved numerically or functional approximations for their solution. The current paper presents software with the functions needed for the study of glow curves that is not a stand-alone computer program but an extension of MS Excel. It supplies functions that solve the general one trap model for the thermoluminescence process without the use of approximating functions. Combined with the Solver utility of Excel this gives a very flexible system for the analysis of glow curves. Functions for analysing the statistics of the deconvolution results are included.

Algorithms↗

Characterization of attenuated proestrous luteinizing hormone surges in middle-aged rats by deconvolution analysis.

Reproductive aging in female rats is associated with attenuated preovulatory LH surges. In this study, detailed analyses of the episodic characteristics of the proestrous LH surge were conducted in young and middle-aged regularly cyclic rats. On proestrus, blood samples were withdrawn at 3-min intervals for 6 h and analyzed for LH concentrations by RIA in triplicate. Deconvolution analysis of immunoreactive LH concentrations revealed that there was no difference in the detectable LH secretory burst frequency between young and middle-aged rats. However, in middle-aged rats with an attenuated LH surge on proestrus, the mass of LH secreted per burst and the maximal rate of LH secretion per burst were only one fourth (p < 0.01) of those in young and middle-aged rats with normal LH surges. Furthermore, middle-aged rats with attenuated LH surges had a 4-fold decrease (p < 0.01) in the maximal rate of LH secretion per burst compared to young and middle-aged females with normal LH surges. The apparent half-life of endogenous LH was similar among the 3 groups. The attenuated LH surges of middle-aged rats were related specifically to a decrease in LH burst amplitude with no change in pulse frequency. The orderliness of moment-to-moment LH release as quantified by the regularity statistic, approximate entropy, was comparable in the 3 groups. Our findings of a markedly decreased amount of LH released per burst and preserved orderliness of the LH release process strongly suggest that a deficient GnRH drive and/or reduced responsivity to the GnRH signal, rather than altered timing of the signal, accounts for the age-related decline in reproductive function in female rats as presaged by an attenuated proestrous LH surge in middle age.

Aging↗

Scatter compensation in digital chest radiography using Fourier deconvolution.

The authors present a numerical deconvolution technique to compensate for image degrading effects caused by scattered photons in radiographic chest images. Fourier transform techniques are used to deconvolve a shift invariant model of the two dimensional point spread response functions of the scattered radiation. This approach uses a digitized radiograph acquired with a standard chest imaging protocol, so no specialized imaging equipment is required. While the shift variant shape of the scatter model is optimized for the lung field, effective compensation is provided when this model shape is applied to other chest regions. Preliminary evaluation suggests that this technique can provide improved image contrast over the entire chest region.

Computer Simulation↗

99Tcm-TDG renography with deconvolution analysis: a comparative study with 99Tcm-DTPA and 123I-hippuran.

TDG has been compared with hippuran and DTPA in normal subjects and the derived gamma camera renograms of both the whole kidney and parenchymal regions subjected to deconvolution analysis using the matrix algorithm. The transit time of TDG was found to be longer than both hippuran and DTPA. The parenchymal mean transit time of TDG was 3.0 +/- 0.6 min (mean +/- S.D.). That of hippuran was 2.2 +/- 0.7 min and DTPA, 2.6 +/- 0.5 min. It is thought that a small fraction of the TDG is bound to the renal parenchyma thus prolonging both the mean and maximum transit times.

Adult↗

The reduction of renogram deconvolution to a direct method of transit time determination.

It is known that the intrarenal mean transit time (MTT) can be determined using renography by first deconvoluing the kidney retention function from the obtained time-activity curve and then integrating the retention function. A direct and approximate calculational method, based on an integral mathematical model, has also been employed to estimate the MTT. In this work it is shown that the direct approximate method is equivalent to the standard deconvolution method applied with the assumption of a time independent retention function. Potential errors incurred using the direct method are thus quantified and assessed over a range of representative decay parameters.

Humans↗

99Tcm-MAG3 renogram deconvolution in normal subjects and in normal functioning kidney grafts.

This study provides values of transit times obtained by 99Tcm- mercaptoacetyl triglycine (99Tcm-MAG3) renogram deconvolution for both normal subjects and kidney graft recipients. The analysis included 50 healthy kidney units from 25 volunteers and 28 normal functioning kidney grafts. The parameters calculated for the whole kidney (WK) and for the renal parenchyma (P) were: mean transit time (MTT) and times at 20% (T20) and 80% (T80) of renal retention function initial height. For healthy kidneys the WK MTT was 174 +/- 27 s and P MTT 148 +/- 22 s. The WK T20 values were 230 +/- 33 s and P T20 231 +/- 34 s. The WK T80 was 108 +/- 19 s and P T80 106 +/- 12 s. Whole kidney and parenchymal values of transit times for normal functioning kidney grafts do not present significant differences with respect to healthy kidneys.

Adolescent↗

Renogram deconvolution in the management of diabetic nephropathy: utility of the measurement of initial tracer uptake.

Our objective was to assess mean transit time (MTT) and initial uptake, both parameters derived from the renal retention function (RRF), in the study of renal function in patients with diabetic nephropathy. We studied 25 patients, 7 with type I diabetes mellitus and 18 with type II diabetes mellitus, all of whom fulfilled the criteria for diabetic nephropathy with proteinuria and/or retinopathy. We found a statistically significant correlation between initial uptake and the other biochemical and renographic parameters studied except proteinuria: serum creatinine (r = 0.66, P < 0.002), creatinine clearance (r = 0.61, P < 0.003), glomerular filtration rate (r = 0.74, P < 0.003) and effective renal plasma flow (r = 0.66, P < 0.003). The other renographic parameters studied (maximal activity of the conventional renogram and MTT of the deconvoluted renogram) did not show any correlation. Initial uptake is a semi-quantitative renographic parameter that can provide complementary information to biochemical data and it may be useful in the management of diabetic nephropathy, especially in patients with high serum creatinine or creatinine clearance.

Adult↗

Improved quantification in 123I cardiac SPECT imaging with deconvolution of septal penetration.

OBJECTIVES: (123)I is becoming an important radionuclide for cardiac imaging. Multiple, low-abundance, high-energy photons associated with (123)I imaging can cause septal penetration in the collimators and degrade quantification of the (123)I cardiac uptake. This study presents a method for the deconvolution of septal penetration (DSP) for improving quantification in (123)I cardiac single photon emission computed tomography (SPECT). METHODS: Distance-dependent point spread functions were measured for low-energy high-resolution collimators on a dual-head SPECT system. The measured point spread functions were used in two-dimensional (2-D) and three-dimensional (3-D) models of the collimator response, respectively. 2-D DSP and 3-D DSP were then developed and implemented using iterative reconstruction. A cardiac torso phantom with an internal calibration source was designed with various heart-to-calibration ratios (HCRs) simulating different levels of a patient's uptake. SPECT acquisitions of the phantom were performed using optimized acquisition and processing parameters for (123)I cardiac SPECT. HCRs were calculated using planar projection and tomographic reconstructions. The paired t-test and regression analysis were used to compare the HCRs given by different calculation methods. RESULTS: SPECT produced more accurate HCRs than planar imaging. The slopes of the regression lines for SPECT using filtered back-projection were statistically significantly higher than those for planar imaging (0.2118 +/- 0.0297 vs. 0.0819 +/- 0.0070, P = 0.0001). 2-D DSP and 3-D DSP yielded similar HCRs that were close to the true HCR. The slopes of the regression lines for 2-D DSP and 3-D DSP were 0.9203 +/- 0.0523 and 0.9101 +/- 0.0304, respectively. The DSP HCRs were significantly more accurate than those calculated without DSP (P < 0.0001). CONCLUSION: DSP significantly improves quantification in (123)I cardiac SPECT imaging. 2-D DSP with its less computational burden shows promise for implementation in clinical practice so as to allow the use of the widely available low-energy, high-resolution collimators for quantitative I cardiac SPECT imaging.

Algorithms↗

Atomic spectral line free parameter deconvolution procedure.

We report an advanced numerical procedure for deconvolution of theoretical asymmetric convolution integral of a Gaussian and a plasma broadened spectral line profile j(A,R)(lambda) for spectal lines. Our method determines all broadening parameters, self-consistently and directly from the line profile with minimal assumptions or prior knowledge. This method is useful for obtaining complete information on all plasma parameters directly from the recorded shape of a single line, which is very important in case no other diagnostic methods are available. The method is also convenient for determination of plasma parameters in the case of a symmetrical profile such as Voigt one.

Journal Article↗

[Delimiting the molecular envelope of a protein by deconvolution of the Patterson function for native proteins].

A process, based on the superposition method, is described to delimit the molecular envelope of a protein by deconvolution of the Patterson function. The object is to obtain a preliminary set of phases from native structure-factor amplitudes with only native intensity data. The method has been tested with data from two immunoglobulin Fab fragments, Fab NEW and Fab R19.9. Several zones of resolution were explored.

Immunoglobulin Fragments↗