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Results for “deconvolution”

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PubMed2026

Cell cycle-dependent protein dynamics in budding yeast resolved by deconvolution of bulk proteomics.

The cell division cycle is characterised by oscillatory dynamics in regulatory mechanisms and biosynthesis, coordinated with genome replication and segregation. To understand these dynamics, quantitative cell cycle-dependent protein concentration data are essential. Unfortunately, accurately resolving cell cycle-dependent protein dynamics is challenging because single-cell proteomics is currently infeasible and bulk proteomics requires - inherently imperfect - cell synchronisation. Here, we developed a computational method to deconvolve cell cycle-dependent protein concentration dynamics and applied it to new budding yeast bulk proteome data. Key to this method was a yeast population model, parameterised with experimental cell cycle progression and volume growth data, for quantifying the desynchronisation in sampled populations. We performed deconvolution on 3272 proteins, using cross-validation to determine regularisation parameters, and identified 539 proteins with cell cycle-dependent dynamics. Many of these dynamics were consistent with known yeast biology and dynamic proteins were enriched for several metabolic process, extending previous observations and supporting the emerging picture of metabolic activity as varying substantially over cell cycle phases. We consider the generated cell cycle-resolved budding yeast proteome data a key resource.

Journal Article↗

PubMed2001

Approach to the determination of insulin-like-growth-factor-I (IGF-I) concentration in plasma by high-performance liquid chromatography-ion trap mass spectrometry: use of a deconvolution algorithm for the quantification of multiprotonated molecules in electrospray ionization.

The insulin-like-growth-factor-I (IGF-I) peptide is known to be a marker for growth hormone administration. The development of a quantification method by electrospray ionization mass spectrometry (ESI-MS) coupled with high-performance liquid chromatography (HPLC) is required. This paper describes a method to quantify IGF-I using the internal standard R3 IGF-I in its oxidized forms. A deconvolution software was used to quantify the set of multi-charged molecules recorded on an ESI ion trap mass spectrometer. The results (i.e., linearity, reproducibility and concentration range) were obtained on standard samples and the described LC-ESI-MS method should be applicable to biological samples.

Algorithms↗

PubMed1972

Rates of plasma protein synthesis by deconvolution.

The plasma specific radioactivity of arginine guanidine (14)C-labelled protein has been measured at various times after the injection of labelled protein precursor (Na(2) (14)CO(3)). The resulting ;appearance' curve is a balance between the rate of synthesis and delivery of new protein and the rate of destruction and distribution of new plus existing protein. The measured appearance curve can be corrected to give a measure solely of the rate of synthesis of the plasma protein concerned, if the amplitude of the curve at every point is increased by an amount that compensates for the destruction and distribution processes. The decrease of plasma specific radioactivity of labelled plasma protein after an injection of exogenously labelled protein is termed the ;disappearance' curve, and the method of correcting the appearance curve by using the disappearance curve is shown to take the form of a deconvolution.

Arginine↗

PubMed1997

Deconvolution analysis of bioassayable LH secretion and half-life in men with idiopathic oligoasthenospermia.

To further investigate the nature of neuroendocrine disturbances of the hypothalamopituitary-gonadal axis in idiopathic male infertility, we studied 12 infertile men with oligoasthenozoospermia and 13 euspermic controls, matched for age and body mass index, by blood withdrawal at 10-min intervals for 8 h to analyse pulsatile release of bioactive LH (b-LH). The rat interstitial cell testosterone (RICT) bioassay was used in conjunction with a recently validated multiparameter deconvolution algorithm, to estimate the endogenous half-life of b-LH, its secretory burst frequency, amplitude, duration and mass. Oligoasthenospermic men exhibited significant (p < 0.05) alterations within the LH axis; namely: (1) a prolonged half-life of b-LH (92 min in euspermic men, 127 min in oligoasthenospermic men); (2) a reduced b-LH secretory burst amplitude (2.2 +/- 1.2 IU/l/min in euspermic men, 1.7 +/- 0.8 IU/l/min in oligoasthenospermic men); (3) a lower bioactive/immunoactive (b/i) ratio for LH secretory burst amplitude (14 in euspermic men, 4 in oligoasthenospermic men); (4) a reduced b/i ratio in the mass of LH secreted per burst (5.4 in euspermic men, 4.1 in oligoasthenospermic men) and (5) decreased coordinate release of b-LH and testosterone in infertile men, as assessed by cross-correlation analysis. These disturbances differ from the neuroendocrine dysregulation described in other states of male hypogonadotrophism.

Activity Cycles↗

PubMed2001

Improved spatial discrimination of protein reaction states in cells by global analysis and deconvolution of fluorescence lifetime imaging microscopy data.

The deconvolution of fluorescence lifetime imaging microscopy (FLIM) data that were processed with global analysis techniques is described. Global analysis of FLIM data enables the determination of relative numbers of molecules in different protein reaction states on a pixel-by-pixel basis in cells. The three-dimensional fluorescence distributions of each protein state can then be calculated and deconvolved. High-resolution maps of the relative concentrations of each state are then obtained from the deconvolved images. We applied these techniques to quantitatively image the phosphorylation state of ErbB1 receptors tagged with green fluorescent protein in MCF7 cells.

Cell Line↗

PubMed2005

Deconvolution of the relaxations associated with local and segmental motions in poly(methacrylate)s containing dichlorinated benzyl moieties in the ester residue.

The relaxation behavior of poly(2,3-dichlorobenzyl methacrylate) is studied by broadband dielectric spectroscopy in the frequency range of 10(-1)-10(9) Hz and temperature interval of 303-423 K. The isotherms representing the dielectric loss of the glassy polymer in the frequency domain present a single absorption, called beta process. At temperatures close to Tg, the dynamical alpha relaxation already overlaps with the beta process, the degree of overlapping increasing with temperature. The deconvolution of the alpha and beta relaxations is facilitated using the retardation spectra calculated from the isotherms utilizing linear programming regularization parameter techniques. The temperature dependence of the beta relaxation presents a crossover associated with a change in activation energy of the local processes. The distance between the alpha and beta peaks, expressed as log(fmax;beta/fmax;alpha) where fmax is the frequency at the peak maximum, follows Arrhenius behavior in the temperature range of 310-384 K. Above 384 K, the distance between the peaks remains nearly constant and, as a result, the a onset temperature exhibited for many polymers is not reached in this system. The fraction of relaxation carried out through the alpha process, without beta assistance, is larger than 60% in the temperature range of 310-384 K where the so-called Williams ansatz holds.

Journal Article↗

PubMed1987

The pituitary gland secretes in bursts: appraising the nature of glandular secretory impulses by simultaneous multiple-parameter deconvolution of plasma hormone concentrations.

To investigate patterns of endogenous hormone release, we have proposed a biophysical model in which measured hormone concentrations at any given instant reflect the operation of a suitable cumulation function (secretory input) convolved with an appropriate elimination mechanism (metabolic clearance). The cumulation function underlying a macroscopic hormone secretory burst can be represented by a random (Gaussian) distribution of instantaneous molecular secretory rates, which are centered with some finite and determinable standard deviation about a particular moment in time. The hormone elimination mechanism is described by a mono- or biexponential clearance function. The resultant convolution integral is solved by iterative nonlinear least-squares parameter estimation, in which all plasma hormone concentrations and their variances are considered simultaneously. Experiments with human endocrine time series revealed that the spontaneous secretory patterns of any of multiple distinct anterior pituitary hormones (luteinizing hormone, follicle-stimulating hormone, growth hormone, prolactin, thyrotropin, and adrenocorticotropic hormone) can be described effectively by this parsimonious model. In addition, endogenous hormone disappearance rates determined by deconvolution agreed well with those reported earlier that were determined after exogenous hormone injections. Moreover, this model predicted that durations of underlying secretory impulses are extremely brief; i.e., the standard deviations of the Gaussian distributions of instantaneous secretory rates range from 4.5 min (luteinizing hormone) to 16 min (growth hormone) compared to plasma hormone concentration peaks of 90-140 min in duration. Accordingly, we conclude that observed physiological patterns of fluctuating plasma hormone concentrations can be accounted for by distinct, highly delimited, random bursts of hormone release separated by intervals of secretory quiescence.

Adrenocorticotropic Hormone↗

PubMed1998

Deconvolution of the fluorescence emission spectrum of human antithrombin and identification of the tryptophan residues that are responsive to heparin binding.

Heparin causes an allosterically transmitted conformational change in the reactive center loop of antithrombin and a 40% enhancement of tryptophan fluorescence. We have expressed four human antithrombins containing single Trp --> Phe mutations and determined that the fluorescence of antithrombin is a linear combination of the four tryptophans. The contributions to the spectrum of native antithrombin at 340 nm were 8% for Trp-49, 10% for Trp-189, 19% for Trp-225, and 63% for Trp-307. Trp-225 and Trp-307 accounted for the majority of the heparin-induced fluorescence enhancement, contributing 37 and 36%, respectively. Trp-49 and Trp-225 underwent spectral shifts of 15 nm to blue and 5 nm to red, respectively, in the antithrombin-heparin complex. The blue shift for Trp-49 is consistent with partial burial by contact with heparin, whereas the red shift for Trp-225 and large enhancement probably result from increased solvent access upon heparin-induced displacement of the contact residue Ser-380. The enhancement for Trp-307 may result from the heparin-induced movement of helix H seen in the crystal structure. The time-resolved fluorescence properties of individual tryptophans of wild-type antithrombin were also determined using the four variants and showed that Trp-225 and Trp-307 experienced the largest change in lifetime upon heparin binding, providing support for the steady-state fluorescence deconvolution.

Antithrombin III↗

PubMed2005

Deconvolution of a complex target using DNA aptamers.

In vitro selection of single-stranded nucleic acid aptamers from large random sequence libraries is now a straightforward process particularly when screening with a single target molecule. These libraries contain considerable shape diversity as evident by the successful isolation of aptamers that bind with high affinity and specificity to chemically diverse targets. We propose that aptamer libraries contain sufficient shape diversity to allow deconvolution of a complex mixture of targets. Using unfractionated human plasma as our experimental model, we aim to develop methods to obtain aptamers against as many proteins as possible. To begin, it is critical that we understand how aptamer populations change with increasing rounds of in vitro selection when using complex mixtures. Our results show that sequence representation in the selected population changes dramatically with increasing rounds of selection. Certain aptamer families were apparent after only three selection rounds. Two additional cycles saw a decline in the relative abundance of these families and the emergence of yet another family that accounted for more than 60% of sequences in the pool. To overcome this population convergence, an aptamer-based target depletion method was developed, and the library screen was repeated. The previous dominant family effectively disappeared from the selected populations but was replaced by other aptamer families. Insights gained from these initial experiments are now being applied in the creation of second generation plasma protein screens and also to the analysis of other complex biological targets.

Aptamers, Nucleotide↗

PubMed1979

A study of the application of a deconvolution method to scintigraphy.

It is shown that an Anger-type gamma camera can be considered as a linear filter. The image is therefore the convolution of the object by the camera point spread function. An important property of the objects is the fact that they are basically positive (count-rates as a function of space variables). The proposed deconvolution method (due to Biraud) is shown to work satisfactorily on a 1-D scintigraphic signal which is a particular cross-section of a 2-D image. This is a preliminary study of the enhancement of real scintigraphic images.

Image Enhancement↗

PubMed1979

On the deconvolution of exponential response functions.

The deconvolution or unfolding of exponential response functions from experimental data has been examined through the use of a Bayesian based algorithm. The algorithm, which is founded upon the concepts of probability, ensures positivity of solution. This constraint leads to a significant reduction in the growth of statistical noise in deconvolved data when compared with the more common linear unfolding techniques. The algorithm is an iterative procedure which, in the absence of statistical noise, can ultimately result in complete signal recovery. When noise is present one must balance the degree with which the response function is removed against the growth in the noise and, at some point, terminate the iterative process. Criteria for determining the point at which this 'best estimate' is attained are examined and an operationally realisable test is given. Comparison of results is made with the inverse filter solution which, for an exponential response function, is shown to consist of the sum of the observed data and its first derivative.

Mathematics↗

PubMed1988

On the possibility of obtaining non-diffused proximity functions from cloud-chamber data: I. Fourier deconvolution.

A mathematical procedure, using Fourier deconvolution, is described whereby diffusion-free proximity functions can be obtained from cloud-chamber data. Such non-diffused distributions can be used to obtain further microdosimetric and nanodosimetric quantities hitherto not available from experiments, thus making the cloud chamber an almost ideal nanodosimeter.

Fourier Analysis↗

PubMed1988

Optimal filtering values in renogram deconvolution.

The evaluation of the isotopic renogram by means of the renal retention function (RRF) is a technique that supplies valuable information about renal function. It is not unusual to perform a smoothing of the data because of the sensitivity of the deconvolution algorithms with respect to noise. The purpose of this work is to confirm the existence of an optimal smoothing which minimises the error between the calculated RRF and the theoretical value for two filters (linear and non-linear). In order to test the effectiveness of these optimal smoothing values, some parameters of the calculated RRF were considered using this optimal smoothing. The comparison of these parameters with the theoretical ones revealed a better result in the case of the linear filter than in the non-linear case. The study was carried out simulating the input and output curves which would be obtained when using hippuran and DTPA as tracers.

Humans↗

PubMed1988

Extravascular background subtraction using deconvolution analysis of the renogram.

The effect of the intravascular background in the renogram on the calculated renal retention function is known and can be removed. However, the effect of the extravascular background (EVB) has not been thoroughly investigated using patient data. By varying the size of the region of interest containing a single kidney and by deconvolving the 131I-hippuran and 99Tcm-DTPA renograms so generated, the following has been found: (a) the effect of EVB on the mean transit time (MTT) is negligible and EVB subtraction is not necessary, (b) the EVB overestimates the lower relative kidney function (RKF) and underestimates the higher RKF, so that EVB subtraction should be performed if the RKFs are asymmetric. A new method is described in which the correction for EVB is performed following deconvolution. If the RKFs are greater than about 30%, the correction can be performed using a regression equation between the RKFs corrected for EVB and those that are not corrected. When the RKFs are asymmetric to a greater extent, the correction should be performed for each study separately. The proposed method includes a small systematic error due to the inherent limitations of nuclear medicine equipment.

Adult↗

PubMed1991

Perfect-mixer retention function by analytical deconvolution of tracer histograms: application to evaluation of left-ventricular contractility and competence.

The analytical solution for the perfect-mixer retention function, r(t), was developed from tracer histograms sampled at the system input, i(t), and its output, y(t), linked by the convolution integral y = i * r. Theories were developed for both continuous-output mixer and pulsatile, discrete mixer. The latter method was applied in first-pass radioangiography (FPRA) to calculate the forward ejection fraction of the left ventricle (LVFEF). Curves generated over the lungs and the ventricle provided system input and output respectively. LVFEF correlated strongly with the reference values obtained with simultaneously acquired gated FPRA(LVGEF) in 32 non-regurgitant patients: LVGEF = 0.90LVFEF + 5.93, r = 0.96, SEE = 3.98, p less than 0.001. In 14 patients with left-side valvular incompetence LVFEF values (0.41 +/- 0.13) were consistently lower than the corresponding LVGEF values (0.63 +/- 0.11). The method is free from instability inherent in numerical deconvolution. Applied in FPRA it yielded accurate estimates of LV contractility and competence. The continuous-mixer theory may apply to arbitrary compartmental models studied via tracer kinetics.

Adolescent↗

PubMed1994

Quantitative reconstruction for myocardial perfusion SPECT: an efficient approach by depth-dependent deconvolution and matrix rotation.

An efficient reconstruction method for myocardial perfusion single-photon emission computed tomography (SPECT) has been developed which compensates simultaneously for attenuation, scatter, and resolution variation. The scattered photons in the primary-energy-window measurements are approximately removed by subtracting the weighted scatter-energy-window samples. The resolution variation is corrected by deconvolving the subtracted data with the detector-response kernel in frequency space using the depth-dependent frequency relation. The attenuated photons are compensated by recursively tracing the attenuation factors through the object-specific attenuation map. An experimental chest phantom with defects inside myocardium was used to test the method. The attenuation map of the phantom was reconstructed from transmission scans using a flat external source and a high-resolution parallel-hole collimator of a single-detector system. The detector-response kernel was approximated from measurements of a point source in air at several depths from the collimator surface. The emission data were acquired by the same detector setting. A computer simulation using similar protocols as in the experiment was performed. Both the simulation and experiment showed significant improvement in quantification with the proposed method, as compared to the conventional filtered-backprojection technique. The quantitative gain by the additional deconvolution was demonstrated. The computation time was less than 20 min on a HP/730 desktop computer for reconstruction of a 1282 x 64 array from 128 projections of 128 x 64 samples.

Algorithms↗

PubMed2001

Accuracy of deconvolution analysis based on singular value decomposition for quantification of cerebral blood flow using dynamic susceptibility contrast-enhanced magnetic resonance imaging.

Deconvolution analysis (DA) based on singular value decomposition (SVD) has been widely accepted for quantification of cerebral blood flow (CBF) using dynamic susceptibility contrast-enhanced magnetic resonance imaging (DSC-MRI). When using this method, the elements in the diagonal matrix obtained by SVD are set to zero when they are smaller than the threshold value given beforehand. In the present study, we investigated the effect of the threshold value on the accuracy of the CBF values obtained by this method using computer simulations. We also investigated the threshold value giving the CBF closest to the assumed value (optimal threshold value) under various conditions. The CBF values obtained by this method largely depended on the threshold value. Both the mean and the standard deviation of the estimated CBF values decreased with increasing threshold value. The optimal threshold value decreased with increasing signal-to-noise ratio and CBF, and increased with increasing cerebral blood volume. Although delay and dispersion in the arterial input function also affected the relationship between the estimated CBF and threshold values, the optimal threshold value tended to be nearly constant. In conclusion, our results suggest that the threshold value should be carefully considered when quantifying CBF in terms of absolute values using DSC-MRI for DA based on SVD. We believe that this study will be helpful in selecting the threshold value in SVD.

Algorithms↗

PubMed2004

Mammographic image restoration using maximum entropy deconvolution.

An image restoration approach based on a Bayesian maximum entropy method (MEM) has been applied to a radiological image deconvolution problem, that of reduction of geometric blurring in magnification mammography. The aim of the work is to demonstrate an improvement in image spatial resolution in realistic noisy radiological images with no associated penalty in terms of reduction in the signal-to-noise ratio perceived by the observer. Images of the TORMAM mammographic image quality phantom were recorded using the standard magnification settings of 1.8 magnification/fine focus and also at 1.8 magnification/broad focus and 3.0 magnification/fine focus; the latter two arrangements would normally give rise to unacceptable geometric blurring. Measured point-spread functions were used in conjunction with the MEM image processing to de-blur these images. The results are presented as comparative images of phantom test features and as observer scores for the raw and processed images. Visualization of high resolution features and the total image scores for the test phantom were improved by the application of the MEM processing. It is argued that this successful demonstration of image de-blurring in noisy radiological images offers the possibility of weakening the link between focal spot size and geometric blurring in radiology, thus opening up new approaches to system optimization.

Algorithms↗