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At least 253 records · Page 14Linked to original sources
PubMed2001

One approach for doublet deconvolution to improve reliability in spectra analysis for in vivo lead measurement.

Calculation of lead concentration from K-series X-ray fluorescent studies uses a robust normalization technique based on the amplitude or area of the elastic signal. Parameter estimation of the elastic signal can be affected by the overlap of the Kbeta2 line, especially for concentrations greater than 40 ppm where the Kbeta2 amplitude can be greater than 1% of the elastic signal. We tested the combination of estimation by method of least moduli and doublet deconvolution. We found that the estimation of the area of the elastic signal is more robust to changes in the low-energy end of the region of interest with the combined method than with method of least-squares estimation and singlet processing. We recommend use of the combined method for creation of calibration curves at concentrations greater than or equal to 40 ppm.

Bone and Bones↗
PubMedDate not supplied

Determination of the 243 Cm/244 Cm ratio alpha spectrometry and spectral deconvolution in environmental samples exposed to discharges from the nuclear fuel cycle.

The presence of curium nuclides in irradiated nuclear fuel is well known, as is their occurrence in environmental materials exposed to liquid waste discharges from reprocessing plants and to fallout following the Chernobyl accident. Knowledge of the 242 Cm/244 Cm and 243 Cm/244 Cm atom ratios can be a useful tool for characterizing a source-term and assessing the burn-up history of nuclear fuel. Here, a practical technique, based on high-resolution alpha spectrometry and spectral deconvolution, is described by which the 243, 244 Cm multiplet can be resolved at the low activities typical of most environmental samples. The resulting 243 Cm/244 Cm ratio is then used to correct for any interference by 243 Cm in the 242 Cm window. The technique has been applied to the determination of the 243 Cm/244 Cm ratio in samples of seabed sediment collected near the Sellafield outfall, riverine sediment sampled downstream of the Mayak reprocessing plant and soil and lichen from within the Chernobyl exclusion zone. Near Sellafield, the 243 Cm/244 Cm ratio was found to be < 2%, while near Mayak and Chernobyl it was considerably higher, being approximately 6-8%.

Americium↗
PubMed2001

MoWeD, a computer program to rapidly deconvolute low resolution electrospray liquid chromatography/mass spectrometry runs to determine component molecular weights.

A computer program is described that can rapidly process low-resolution electrospray liquid chromatography/mass spectrometry (LC/MS) for peptides and proteins and assign molecular weights for observed components. The program first analyzes individual scans using a deconvolution algorithm similar to that previously described by Zhang and Marshall. Results for the entire run are then sorted by mass and those values found in adjacent scans are grouped together. The list of found components can also be compared to a user defined list of target molecular weight values making it easy to compare the results from different analyses. The program also has the capability to process a rolling average of scans that improves the performance when analyzing high molecular weight components. Other program features facilitate closer examination of selected spectra or regions of the chromatogram to check the MoWeD mass assignments. The utility of the program was demonstrated by the analysis of LC/MS data derived from a complex mixture of proteins derived from a bacterial whole cell lysate that had previously been analyzed manually. The MoWeD analysis was 30 times faster and provided a more comprehensive list of the components present.

Bacillus anthracis↗
PubMed2000

Recent developments in the encoding and deconvolution of combinatorial libraries.

The value of molecular libraries generated by combinatorial methods is largely dependent on the ease and ability to deconvolute or decode the structure of compounds of interest after screening the library. Following the introduction of promising concepts in the early 1990s, there has been considerable progress in the development and refinement of methodologies to address this issue.

Combinatorial Chemistry Techniques↗
PubMed1989

Evidence for radical anion formation during liquid secondary ion mass spectrometry analysis of oligonucleotides and synthetic oligomeric analogues: a deconvolution algorithm for molecular ion region clusters.

It is shown that one-electron reduction is a common process that occurs in negative ion liquid secondary ion mass spectrometry (LSIMS) of oligonucleotides and synthetic oligonucleosides and that this process is in competition with proton loss. Deconvolution of the molecular anion cluster reveals contributions from (M-2H).-, (M-H)-, M.-, and (M + H)-. A model based on these ionic species gives excellent agreement with the experimental data. A correlation between the concentration of species arising via one-electron reduction [M.- and (M + H)-] and the electron affinity of the matrix has been demonstrated. The relative intensity of M.- is mass-dependent; this is rationalized on the basis of base-stacking. Base sequence ion formation is theorized to arise from M.- radical anion among other possible pathways.

Algorithms↗
PubMed1985

Determination of rotational correlation times from deconvoluted fluorescence anisotropy decay curves. Demonstration with 6,7-dimethyl-8-ribityllumazine and lumazine protein from Photobacterium leiognathi as fluorescent indicators.

The experimental and analytical protocols required for obtaining rotational correlation times of biological macromolecules from fluorescence anisotropy decay measurements are described. As an example, the lumazine protein from Photobacterium leiognathi was used. This stable protein (Mr 21 200) contains the noncovalently bound, natural fluorescent marker 6,7-dimethyl-8-ribityllumazine, which has in the bound state a long fluorescence lifetime (tau = 14 ns). Shortening of the fluorescence lifetime to 2.6 ns at room temperature was achieved by addition of the collisional fluorescence quencher potassium iodide. The shortening of tau had virtually no effect on the rotational correlation time of the lumazine protein (phi = 9.4 ns, 19 degrees C). The ability to measure biexponential anisotropy decay was tested by the addition of Photobacterium luciferase (Mr 80 000), which forms an equilibrium complex with lumazine protein. Under the experimental conditions used (2 degrees C) the biexponential anisotropy decay can best be described with correlation times of 20 and 60 ns, representing the uncomplexed and luciferase-associated lumazine proteins, respectively. The unbound 6,7-dimethyl-8-ribityllumazine itself (tau = 9 ns) was used as a model compound for determining correlation times in the picosecond time range. In the latter case rigorous deconvolution from the excitation profile was required to recover the correlation time, which was shorter (100-200 ps) than the measured laser excitation pulse width (500 ps).

Bacterial Proteins↗
PubMed1995

Deconvolution of combinatorial libraries for drug discovery: a model system.

Iterative synthesis and screening strategies have recently been used to identify unique active molecules from complex synthetic combinatorial libraries. These techniques have many advantages over traditional screening methods, including the potential to screen large numbers of compounds to identify an active molecule while avoiding analytical separations and structural determination of unknown compounds. It is not clear, however, whether these techniques identify the most active molecular species in the mixtures and, if so, how often. Two key factors which may affect success of the selection process are the presence of many active compounds in the library with a range of activities and the chosen order of unrandomization. The importance of these factors has not been previously studied. Moreover, the impact of experimental errors in determination of subset activities or in randomization during library synthesis is not known. We describe here a model system based on oligonucleotide hybridization that addresses these questions using computer simulations. The results suggested that, within achievable experimental and library synthesis error, iterative deconvolution methods generally find either the best molecule or one with activity very close to the best. The presence of many active compounds in a library influenced the profile of subset activities, but did not preclude selection of a molecule with near optimal activity.

Base Sequence↗
PubMed1996

Deconvolution of combinatorial libraries for drug discovery: experimental comparison of pooling strategies.

An experimental evaluation of several different pooling strategies for combinatorial libraries was conducted using a library of 810 compounds and an enzyme inhibition assay (phospholipase A2). The library contained compounds with varying degrees of activity as well as inactive compounds. The compounds were synthesized in groups of three and pooled together in various formats to realize different pooling strategies. With one exception, all iterative deconvolution strategies and position scanning resulted in identification of the same compound. The results are in good agreement with the predicted outcome from theoretical and computational methods. These data support the tenet that active compounds for pharmaceutically relevant targets can be successfully identified from combinatorial libraries organized in mixtures.

Drug Evaluation, Preclinical↗
PubMed1996

Rediscovering an endothelin antagonist (BQ-123): a self-deconvoluting cyclic pentapeptide library.

A "self-deconvoluting" cyclic pentapeptide library, designed to produce 82,944 head-to-tail-linked peptides in 48 vials, has been prepared. The mixture included amino acids found in a recently optimized endothelin antagonist, BQ-123, originally isolated from microbial sources by Banyu investigators. Using a positional scan approach, the most potent of 12 residues at each of the four variable positions uniquely rediscovered the BQ-123 sequence or cyclo(L-Pro-D-Val-L-Leu-D-Trp-D-Asp). Resynthesis of the four most potent amino acid combinations gave the following values of relative potency: cyclo(L-Pro-D-Val-L-Leu-D-Trp-D-Asp) or BQ-123 = 1.0, cyclo(L-Pro-D-Pro-L-Leu-D-Trp-D-Asp) = 0.0, cyclo(L-Pro-D-Pro-L-Trp-D-Trp-D-Asp) = 0.0, and cyclo(L-Pro-D-Val-L-Trp-D-Trp-D-Asp) = 0.1. This study reflects the first time that the positional scan approach has been applied to cyclic peptide libraries using a known target. Although no analogs more potent than BQ-123 were discovered, our results provide verification of our synthetic methods for preparing head-to-tail cyclic peptide libraries and also lend support to the use of carefully designed sublibraries for the rapid elucidation of potential leads within a relatively constrained set of peptide macrocycles.

Amino Acid Sequence↗
PubMed1996

Determination of tablet coating distribution by deconvolution of uncoated and coated tablet weight distributions.

PURPOSE: The purpose of this research is to obtain the tablet coating distribution from weight distributions of uncoated and coated tablets. METHODS: The method of deconvolution with digital smoothing was used to calculate the distribution of coating applied to a tablet population from separate random measurements of individual uncoated and coated tablets. RESULTS: It was demonstrated that the calculated coating weight distribution agrees well with the measured distribution. The effect of the smoothing factor on the solution is illustrated. CONCLUSIONS: This method can be used during development to facilitate process scale-up/optimization. In routine production, the method can assess the reproducibility and consistency of a coating process.

Chemistry, Pharmaceutical↗
PubMed1995

The application of Fourier deconvolution to reaction time data: a cautionary note.

The Fourier transform method in conjunction with frequency domain smoothing techniques has been suggested as a powerful tool for examining components in a serial, additive reaction time model (P. L. Smith, 1990). Robustness and sensitivity to violations of the assumptions of serial model of this method are evaluated. When an incorrect distribution was used in recovering an unobserved component, results gave no information to show that an incorrect distribution was used, and the results were just as interpretable as those obtained using the correct distribution. These results demonstrate that the assumptions underlying the method cannot be assessed by the result of deconvolution, and the method cannot show that the purported component is actually from the serial combination.

Fourier Analysis↗
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↗
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↗