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PubMed1993

Use of automated smoothing and deconvolution procedures for the determination of human breast cancer estrogen and progesterone receptor isoforms, after high-performance size-exclusion chromatography.

Automated smoothing and deconvolution procedures were used to analyse complex chromatographic patterns of human breast cancer estrogen and progesterone receptors, obtained by size-exclusion chromatography. By injecting, first, different known amounts of a radio-iodinated protein in a TSK G-3000 SW column, constructed complex chromatograms (twelve chromatograms) with known peak positions were obtained, and were further treated by mathematical functions to determine a smooth-deconvolution strategy, which could be used with unknown chromatographic patterns. The determination of peak areas by a "curve-fit" program showed a good correlation with the amounts of protein injected (r = 0.91). Human breast cancer estrogen receptors (56 cases) and progesterone receptors (45 cases) were chromatographed in a TSK G-3000 SW column, and further analysed with the smoothing and deconvolution procedures: eight different estrogen receptor isoforms were detected with molecular masses ranging from 530,000 [Stoke's radius (Rs) = 7.7 nm] to 23,000 (Rs = 2.6 nm), and eight progesterone receptor isoforms were observed with masses ranging from 680,000 (Rs = 8.6 nm) to 50,000 (Rs = 3.1 nm). The dissociation effect of KCl (0 to 1 M) on receptor structure yielded different proportions of receptor isoforms, but did not modify their different peak positions.

Breast Neoplasms↗
PubMed2006

Imaged deconvolution: a method for extracting high-resolution NMR spectra from inhomogeneous fields.

We present a novel method for obtaining high resolution NMR spectra in the presence of grossly inhomogeneous magnetic fields, such as those encountered in one-sided access NMR. Our method combines the well-known principle of reference deconvolution with NMR imaging in order to resolve spectral features with frequency resolution orders of magnitude smaller than the prevailing line-broadening due to field inhomogeneity. We demonstrate that, in cases of inhomogeneous field line-broadening more than an order of magnitude larger than the spectral features to be resolved, rather than performing reference deconvolution on the sample as a whole, it is more favourable in terms of SNR to divide the target region of a sample into smaller sub-regions, by means of chemical shift imaging, and then to perform reference deconvolution on the individual sub-region spectra, finally summing the results In this way, significant resolution enhancements can be obtained in the presence of severe magnetic field inhomogeneity without an unacceptable loss in SNR.

Algorithms↗
PubMed2005

Maximum entropy image deconvolution applied to structure determination for crystal Nd1.85Ce0.15CuO4-delta.

Eight [100] images from a through-focus series of tetragonal crystal Nd1.85Ce0.15CuO4-delta were transformed separately into the structure images by means of maximum entropy image deconvolution. The constructed projected structure model based on the deconvoluted image is confirmed by image simulation. It is demonstrated that the image deconvolution is still successful even when some reflections fall in the vicinity of zero cross of contrast transfer function. The effectiveness and advantages of the technique are discussed.

Journal Article↗
PubMed2001

Image restoration for confocal microscopy: improving the limits of deconvolution, with application to the visualization of the mammalian hearing organ.

Deconvolution algorithms have proven very effective in conventional (wide-field) fluorescence microscopy. Their application to confocal microscopy is hampered, in biological experiments, by the presence of important levels of noise in the images and by the lack of a precise knowledge of the point spread function (PSF) of the system. We investigate the application of wavelet-based processing tools to deal with these problems, in particular wavelet denoising methods, which turn out to be very effective in application to three-dimensional confocal images. When used in combination with more classical deconvolution algorithms, these methods provide a robust and efficient restoration scheme allowing one to deal with difficult imaging conditions. To make our approach applicable in practical situations, we measured the PSF of a Biorad-MRC1024 confocal microscope under a large set of imaging conditions, including in situ acquisitions. As a specific biological application, we present several examples of restorations of three-dimensional confocal images acquired inside an intact preparation of the hearing organ. We also provide a quantitative assessment of the gain in quality achieved by wavelet-aided restorations over classical deconvolution schemes, based on a set of numerical experiments that we performed with test images.

Algorithms↗
PubMed1984

Quantitative analysis of nucleic acids, proteins, and viruses by Raman band deconvolution.

A constrained, iterative Fourier deconvolution method is employed to enhance the resolution of Raman spectra of biological molecules for quantitative assessment of macromolecular secondary structures and hydrogen isotope exchange kinetics. In an application to the Pf1 filamentous bacterial virus, it is shown that the Raman amide I band contains no component other than that due to alpha-helix, indicating the virtual 100% helicity of coat proteins in the native virion. Comparative analysis of the amide I band of six filamentous phages (fd, If1, IKe, Pf1, Xf, and Pf3), all at the same experimental conditions, indicates that the subunit helix-percentage ranges from a high of 100% in Pf1 to a low of 71% in Xf. Deconvolution of amide I of Pf3 at elevated temperatures, for which an alpha-to-beta transition was previously reported (Thomas, G. J., Jr., and L. A. Day, 1981, Proc. Natl. Acad. Sci. USA., 78:2962-2966), allows quantitative evaluation of the contributions of both alpha-helix and beta-strand conformations to the structure of the thermally perturbed viral coat protein. Weak Raman lines of viral DNA bases and coat protein side chains, which are poorly resolved instrumentally, are also distinguished for all viruses by the deconvolution procedure. Application to the carbon-8 hydrogen isotope exchange reaction of a purine constituent of transfer RNA permits accurate determination of the exchange rate constant, which is in agreement with calculations based upon curve-fitting methods.

Bacteriophages↗
PubMed2001

On the equations describing chromatographic peaks and the problem of the deconvolution of overlapped peaks.

The problem of the appropriate choice of the function that describes a chromatographic peak is examined in combination with the deconvolution of overlapped peaks by means of the non-linear least-squares method. It is shown that the majority of the functions proposed in the literature to describe chromatographic peaks are not suitable for this purpose. Only the polynomial modified Gaussian function can describe almost every peak but it is mathematically incorrect unless it is redefined properly. Two new functions are proposed and discussed. It is also shown that the deconvolution of an overlapping peak can be done with high accuracy using a non-linear least-squares procedure, like Microsoft Solver, but this target is attained only if we use as fitted parameters the position of the peak maximum and the peak area (or height) of every component in the unresolved chromatographic peak. In case we use as fitted parameters all the parameters that describe each single peak enclosed in the multi-component peak, then Solver leads to better fits, which though do not correspond to the best deconvolution of the peak. Finally, it is found that Solver gives much better results than those of modern methods, like the immune and genetic algorithms.

Artifacts↗
PubMed1999

Maximum a posteriori deconvolution of sparse ultrasonic signals using genetic optimization.

Deconvolution of sparse spike sequences has received much attention in the field of seismic exploration. In certain situations in ultrasonic non-destructive testing (NDT) of materials, similar conditions as those found in seismic exploration occur. One example is the problem of detecting disbonds in layered aluminum structures. The reflection sequence convolved with the impulse response of the transducer results in masking closely spaced reflections. Deconvolution of these signals may reveal the reflection sequence and thus make the interpretation easier. In this paper we use the Bernoulli-Gaussian (BG) distribution for modeling the signal generation. This relatively simple model allows maximum a posteriori (MAP) estimation of the reflection sequence. A derivation of the MAP criterion is given for clarity. We propose a genetic algorithm for optimizing the MAP criterion. The genetic algorithm approach is motivated by the fact that the criterion is non-convex, implying that the criterion may have more than one local minimum point. The probability of obtaining the global optimal solution is increased by using the proposed genetic algorithm. One of the key features in genetic algorithms, the so-called cross-over operator, has been modified and adapted to the structure of the BG deconvolution problem to improve the efficiency of the search. The algorithm is tested on simulated data using the probability of detection (PD) and probability of false alarm (PFA) as evaluation criteria. The algorithm is also tested on real ultrasonic data from a layered aluminum structure. The results show considerable improvements in the possibility of interpreting the signals.

Algorithms↗
PubMed2000

Deconvolution can be used in electrooptic studies to correct for non-ideal electric excitation pulses only when the electric dipole moment of the studied molecules is predominantly induced.

The electric field pulses used for most measurements of transient electrooptic properties such as birefringence and dichroism, are rectangular and assumed to be ideal, but in practice do all such pulses have non-zero rise and fall times. Claims have been made that this non-ideality may be taken into account by employing standard deconvolution techniques. We find that this approach yields exact results in the zero electric field limit when the electric dipole moment of the studied macromolecules is predominantly induced. However, for finite electric field strengths and/or macromolecules with partly or fully permanent electric dipole moments, we find that the deconvolution method yields erroneous estimates of the electrooptic relaxation times. When the decay time of the electric pulse and the electrooptic decay time are equal, and the system is operated in the Kerr domain, this systematic error for macromolecules with purely permanent electric dipole moment equals 37%. In a research field where the uncertainty of the reported relaxation times normally is assumed to be only a few percent this is an error that may seriously mislead unsuspecting users. We find that this systematic error can readily be avoided by employing standard numerical integration of a set of coupled first-order differential equations instead of the standard deconvolution techniques.

Birefringence↗
PubMed2002

WINSTODEC: a stochastic deconvolution interactive program for physiological and pharmacokinetic systems.

Deconvolution allows the reconstruction of non-accessible inputs (e.g. hormone secretion rate) from their causally-related measurable effects (e.g. hormone plasma concentration). Deconvolution is challenging under several aspects both general (e.g. determination of a suitable trade-off between data fit and solution smoothness in order to contrast ill-conditioning, assessment of the confidence intervals) as well as specific of physiological systems (e.g. non-uniform and infrequent data sampling). Recently, a stochastic regularization approach has been proposed and validated to handle these difficulties (De Nicolao et al., Automatica 33 (1997) 851-870). In this paper, an interactive program, WINSTODEC, is presented to allow the clinical investigator to easily obtain the solution of a deconvolution problem by this approach.

Humans↗
PubMed2002

Deconvolution processing of HAADF STEM images.

A deconvolution processing of high-resolution high-angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images, combined with maximum entropy method, is applied to two experimental [0 11]-Si images; one having unresolved dumbbells and the other having resolved dumbbells and artificial bright spots. The deconvoluted images for these images show bright spots corresponding to the projected atomic columns and no artificial bright spots. Thus, the deconvolution processing provides almost a real projected atomic structure by eliminating effects of the probe function from HAADF STEM images.

Journal Article↗
PubMed1999

A comparison between direct determination of in vivo dissolution and the deconvolution technique in humans.

AIM: The primary objective of this study was to investigate the in vivo dissolution of carbamazepine in humans and to compare it with the dissolution estimated by deconvolution of plasma concentrations as well as the in vitro dissolution. METHODS: The in vivo study included six healthy volunteers, and consisted of two sequential parts. In part 1 the dissolution was measured by perfusing a semi-open segment in the proximal jejunum in humans. In part 2 the volunteers were given a solution of carbamazepine orally. In both parts of the study, plasma samples were collected up to 48 h after administration of the dose. The in vitro dissolution was measured in a flow-through cell using dissolution medium with and without the addition of bile acids (3 mM). RESULTS: The direct measured in vivo dissolution profile of carbamazepine and the deconvoluted profile were found to be similar. The two dissolution profiles of carbamazepine obtained in vitro were statistically lower than the two in vivo dissolution profiles. The higher in vivo dissolution rate is probably due to efficient sink conditions as a consequence of the high permeability of carbamazepine and more pronounced intestinal motility. CONCLUSION: The jejunal perfusion system was successfully used for in vivo dissolution measurements of carbamazepine and agreed with the deconvoluted plasma profile regarding rate and extent of dissolution. Single-pass perfusion is therefore a meaningful tool for further studies of in vivo dissolution.

Algorithms↗
PubMed1999

Deconvolution of 40 Hz steady-state fields reveals two overlapping source activities of the human auditory cortex.

Steady-state auditory evoked fields were recorded from 15 subjects using a whole head MEG system. Stimuli were 800 ms trains of binaural clicks with constant stimulus onset asynchrony (SOA). Seven different SOA settings (19, 21, 23, 25, 27, 29 and 31 ms) were used to give click rates near 40 Hz. Transient responses to each click were reconstructed using a new algorithm that deconvoluted the averaged responses to the different trains. Spatio-temporal multiple dipole modelling in relation to 3D MRI scans revealed two overlapping source components in both the left and right auditory cortex. The primary sources in the medial part of Heschl's gyrus exhibited a N19-P30-N40 m pattern. The secondary, weaker sources at more lateral sites on Heschl's gyrus showed a N24-P36-N46 m pattern. When applied to transient middle latency auditory evoked fields (MAEFs) recorded at SOAs of 95-135 ms, the primary sources imaged activities similar to the deconvoluted steady-state responses, but the secondary source activities were inconsistent. Linear summation of the deconvoluted source waveforms accounted for more than 96% of the steady-state variance. This indicates that the primary activity of the auditory cortex remains constant up to high stimulation rates and is not specifically enhanced around 40 Hz.

Acoustic Stimulation↗
PubMed1990

Accuracy of peak deconvolution algorithms within chromatographic integrators.

The soundness of present-day algorithms to deconvolve overlapping skewed peaks was investigated. From simulated studies based on the exponentially modified Gaussian model (EMG), chromatographic peak area inaccuracies for unresolved peaks are presented for the two deconvolution methods, the tangent skim and the perpendicular drop method. These inherent inaccuracies, in many cases exceeding 50%, are much greater than those calculated from ideal Gaussian profiles. Multiple linear regression (MLR) was used to build models that predict the relative error for either peak deconvolution method. MLR also provided a means for determining influential independent variables, defining the required chromatographic relationships needed for prediction. Once forecasted errors for both methods are calculated, selection of either peak deconvolution method can be made by minimum errors. These selection boundaries are contrasted to method selection criteria of present data systems' algorithms.

Algorithms↗
PubMed2003

Characterization and quantitative analysis with GC/TOFMS comparing enhanced separation with tandem-column stop-flow GC and spectral deconvolution of overlapping peaks.

Time-of-flight mass spectrometry is unique in that ion abundance ratios are constant over the chromatographic peak profile provided that the peak contains only one component. This provides the means for the automated finding and spectral deconvolution of overlapping chromatographic peaks from completely unknown mixtures if the mass spectra for the overlapping components are sufficiently unique. This can greatly reduce the chromatographic resolution requirements, which allows for very rapid quantitative analysis as well as for high-speed mixture characterization. High-speed GC with stop-flow operation of a series-coupled column ensemble can be used to completely separate some component pairs that coelute from the column ensemble, thus eliminating the need for spectral deconvolution of those mixture components. This provides two options for high-speed qualitative and quantitative analysis, using either the mass spectra from deconvoluted overlapping peaks or the mass spectra from the completely separated peaks obtained with stop-flow operation of the tandem column ensemble. These options are compared with respect to the similarity for spectral matching with a library and to peak area linearity with concentration, calibration plot correlation coefficients, and shot-to-shot reproducibility.

Journal Article↗
PubMed2006

Automatic deconvolution of isotope-resolved mass spectra using variable selection and quantized peptide mass distribution.

We present an algorithm for the deconvolution of isotope-resolved mass spectra of complex peptide mixtures where peaks and isotope series often overlap. The algorithm formulates the problem of mass spectrum deconvolution as a classical statistical problem of variable selection, which aims to interpret the spectrum with the least number of peptides. The LASSO method is used to perform automatic variable selection. The algorithm also makes use of the quantized distribution of peptide masses in the NCBInr database after in silico trypsin digestion as filters to aid the deconvolution process. Errors in the expected isotope pattern are accounted for to avoid spurious isotope series. The effectiveness of the algorithm is demonstrated with annotated ESI spectrum of known peptides for which the peaks and isotope series are highly overlapping. The algorithm successfully finds all correct masses in the experimental spectrum, except for one spectrum where an additional refinement procedure is required to obtain the correct results. Our results compare favorably to those from a widely used commercial program.

Animals↗
PubMed1997

Strategies for rapid deconvolution of combinational libraries: comparative evaluation using a model system.

Synthesis and testing of complex mixtures maximize the number of compounds that can be prepared and tested in a combinatorial library. When mixtures of compounds are screened, however, the identity of the compound(s) selected may depend on the deconvolution procedure employed. Previously, we developed a model system for evaluation of deconvolution procedures and used it to compare pooling strategies for iterative and noniterative deconvolution [Freier et al. J. Med. Chem. 1995, 38, 344-352]. We have now extended the model studies to include simulations of procedures with overlapping subsets such as subtractive pooling [Carell et al. Angew, Chem., Int. Ed. Engl. 1994, 33, 2061-2064], bogus coin pooling [Blake and Litzi-Davis. Bioconjugate Chem. 1992, 3, 510-513], and orthogonal pooling [D'Prez et al. J. Am. Chem. Soc. 1995, 117, 5405-5406]. These strategies required synthesis and testing of fewer subsets than did the more traditional nonoverlapping iterative strategies. The compounds identified using simulations of these strategies, however, were not the most active compounds in the library and were substantially less active than those identified by simulations of more traditional strategies.

Computer Simulation↗
PubMed1996

Mean input times of three oral chlorprothixene formulations assessed by an enhanced least-squares deconvolution method.

The efficacy and quality of drug formulations are determined mainly by their bioavailability, which is defined by the rate and extent of drug absorption. The zero and first moments of the serum concentration time profile provide relevant information on the bioavailability. On the basis of the body residence time distributions, mean input times may be used as drug absorption rate parameters, but due to computational errors the statistical moments procedure is in some instances of limited value. To circumvent these problems we have developed a procedure to calculate mean input times from input profiles obtained by least-squares deconvolution. We enhanced the performance of the deconvolution method by directly generating initial estimates of one input rate for each sampling interval and compared the statistical properties of various input rate characteristics using data from a bioavailability study on four chlorprothixene preparations. The analysis of variance revealed that estimates of mean input times depended on the calculation procedure. Mean input times estimated by the least-squares deconvolution method were more reliable and less variable than those computed as differences of mean body residence times.

Administration, Oral↗
PubMed1997

Analysis of metabolite kinetics by deconvolution and in vivo-in vitro correlations of metabolite formation rates: studies of fibrinogen receptor antagonist ester prodrugs.

The pharmacokinetics of L-767,679, a potent fibrinogen receptor antagonist, were characterized following administration of its ethyl ester prodrug to dogs and monkeys. Deconvolution analysis was performed to determine the rate and extent of (1) the formation of L-767,679 from the prodrug in the systemic circulation, (2) the composite input (systemic and presystemic) of L-767,679 to the general circulation after oral administration of the prodrug, (3) the oral input of the prodrug, and (4) the input of the presystemically formed L-767,679 following oral administration of the prodrug. The results indicated that there were species differences in the kinetics of the disposition of L-767,679 and its prodrug. In dogs, the prodrug was absorbed faster than it was converted to the active drug, and the presystemic formation of L-767,679 contributed to about one-half of the total input of L-767,679 following oral administration of the prodrug. In monkeys, the low input of L-767,679 following oral administration of the prodrug was not due to an inefficient formation of L-767,679 in the systemic circulation but rather to the low oral bioavailability of the prodrug. Virtually all of the total oral input of L-767,679 following administration of its prodrug to monkeys resulted from the presystemic metabolism of the prodrug. These results were consistent with the finding in monkeys that the ester prodrug underwent extensive transformation to metabolites other than L-767,679. In addition, the present study also demonstrated a correlation between in vivo formation rates of L-767,679 determined using deconvolution analysis following its ethyl, methyl, and isopropyl esters in dogs and the ethyl ester in monkeys and in vitro formation rates of L-767,679 obtained following incubations of the corresponding esters with dog and monkey liver microsomes. The results suggested that deconvolution and/or convolution analysis together with in vitro metabolism results could potentially be used to predict in vivo formation rates of other ester prodrugs of L-767,679 and also plasma concentrations of L-767,679 as a function of time, following administration of its prodrugs.

Animals↗