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PubMed1995

Automatic analysis of cortical signals recorded with voltage-sensitive dyes using a forward-backward non-linear filtering technique and deconvolution.

A method for automatically analyzing cortical signals recorded with voltage-sensitive dyes and a photodiode array is described. First, a forward-backward non-linear filtering technique is used to eliminate the background noise and preserve the fast transients of the signals. Then the filtered signals are deconvoluted from their maximal values by using a gaussian function. The different components of the signals can be identified and characterized by their respective latencies, amplitudes, plateau durations, and slopes. These parameters can be used for subsequent statistical analysis. This automated method is much faster than a manual analysis because of the large number of responses that are optically recorded. Moreover, it can be easily applied to different experimental protocols and to other signals such as field potentials.

Animals↗
PubMed1993

Estimation of the secondary structure and conformation of bovine lens crystallins by infrared spectroscopy: quantitative analysis and resolution by Fourier self-deconvolution and curve fit.

The secondary structure of six bovine lens protein fractions (two alpha, three beta and one gamma-crystallin) are examined in solution and in solid forms for the first time using FTIR spectroscopy. Films of the nuclear and cortical regions of the bovine lens are also examined. The structure is quantitatively estimated from the vibrational analysis of the resolution-enhanced amide-I profile achieved by Fourier self-deconvolution and linear least-squares curve-fit algorithm. All the protein fractions fold predominantly in a beta-pleated sheet structure with little or no alpha-helical domains in solution or in lyophilized solid form. These proteins also retain their predominant beta-sheet conformation in the cellular phospholipid environment of the lens, in conformity with the structure obtained for all the mammalian species examined to date. Despite structural homology, vibrational data indicate subtle structural differences within each class of the crystallins probably due to presence of several minor substructures/subconformations. Substantial high amounts of turns (approx. 40%) observed in the beta-fractions may have a fundamental implication in stabilizing the tertiary structure of the uniquely folded-proteins vital for the transparency of the lens. These proteins in solid KBr-matrix undergo a major structural change, induced primarily by ionic interactions which refold them in a helical conformation. IR spectroscopy together with band-narrowing procedures has proven to be an effective tool to obtain structural information of proteins in solution, as solid substrates or in a complex biological tissue, such as ocular lens.

Algorithms↗
PubMedDate not supplied

Combined deficits in the somatotropic and gonadotropic axes in healthy aging men: an appraisal of neuroendocrine mechanisms by deconvolution analysis.

We have employed deconvolution analysis of 24-h serum GH, LH, and FSH concentration profiles to evaluate the nature of age-associated changes in GH, LH, and FSH secretion and disappearance in healthy older individuals. Our findings indicate that healthy aging results in a diminished frequency of detectable GH secretory episodes and an apparent decrease in estimated GH half life in men. These combined effects lead to a significant reduction in mean serum GH concentrations over 24 h. In contrast, we find that LH secretory burst frequency tends to increase with a reciprocal decrease in amplitude as serum total and free testosterone concentrations decline during healthy aging. There is also a prolongation of LH secretory burst duration, and a putative increase in basal LH secretion rates. The changes in LH secretory dynamics are specific, because the half life of immunoradiometric LH and the mass of hormone secreted per burst are not altered. In contrast, the apparent half life of FSH increases with age, and the secretory burst duration may decrease. This spectrum of distinct neuroendocrine sequelae of aging has interesting implications to both investigative and therapeutic strategies for modifying the somatotropic and gonadotropic axes in aging individuals.

Adult↗
PubMed1997

Noise deconvolution based on the L1-metric and decomposition of discrete distributions of postsynaptic responses.

A statistical approach to analysis of amplitude fluctuations of postsynaptic responses is described. This includes (1) using a L1-metric in the space of distribution functions for minimisation with application of linear programming methods to decompose amplitude distributions into a convolution of Gaussian and discrete distributions; (2) deconvolution of the resulting discrete distribution with determination of the release probabilities and the quantal amplitude for cases with a small number (< 5) of discrete components. The methods were tested against simulated data over a range of sample sizes and signal-to-noise ratios which mimicked those observed in physiological experiments. In computer simulation experiments, comparisons were made with other methods of 'unconstrained' (generalized) and constrained reconstruction of discrete components from convolutions. The simulation results provided additional criteria for improving the solutions to overcome 'over-fitting phenomena' and to constrain the number of components with small probabilities. Application of the programme to recordings from hippocampal neurones demonstrated its usefulness for the analysis of amplitude distributions of postsynaptic responses.

Animals↗
PubMed1988

Quantitation of collagen fragments and gelatin by deconvolution of polarimetry denaturation curves.

A method for quantitating nicked or shortened molecules (fragments) in pepsinized bovine type I collagen preparations using polarimetry thermal denaturation curves is described. The shortened molecules denature about 4 degrees C lower than intact collagen molecules. The analog output of a polarimeter was digitized and stored on a microcomputer disk. A BASIC program was written which retrieves the specific rotation data from the disk, smooths the data with a boxcar average, and plots the derivative of the denaturation curve. The derivative curve was deconvoluted by fitting three Gaussian curves to the derivative curve using published algorithms. The area of the Gaussian centered at 37 degrees C was proportional to the amount of collagen fragments. A good correlation between the amount of fragments determined by polarimetry and by a trypsin sensitivity assay was observed. The overall precision of the method was about 10% RSD, and the method was repeatable by multiple analysts. Application of the method to reconstituted fibrillar collagen samples showed that more fragments are generated when pepsin digestion time is lengthened. By fitting a fourth Gaussian component to the derivative curve, the method can also be used to determine relative amounts of denatured collagen (helix partially unwound but alpha chains not nicked). The detection limit for denatured collagen is about 20%.

Algorithms↗
PubMed1996

Quantitative analysis of multivariate data using artificial neural networks: a tutorial review and applications to the deconvolution of pyrolysis mass spectra.

The implementation of artificial neural networks (ANNs) to the analysis of multivariate data is reviewed, with particular reference to the analysis of pyrolysis mass spectra. The need for and benefits of multivariate data analysis are explained followed by a discussion of ANNs and their optimisation. Finally, an example of the use of ANNs for the quantitative deconvolution of the pyrolysis mass spectra of Staphylococcus aureus mixed with Escherichia coli is demonstrated.

Escherichia coli↗
PubMed1998

Bimodal granulocyte transit time through the human lung demonstrated by deconvolution analysis.

The lungs are an important site of granulocyte pooling. The aim of the study is to quantify pulmonary vascular granulocyte transit time using deconvolution analysis, as has previously been performed to measure pulmonary red cell transit time. Granulocyte and red cell studies were performed in separate groups of patients. Both cell types were labelled with Tc-99m, which for granulocyte labelling was complexed with hexamethylpropyleneamine oxime (HMPAO). The red cell impulse response function (IRF) was monoexponential with a median transit time of 4.3 s. The granulocyte IRF was biexponential in 19 of 22 subjects, 18 of whom had systemic inflammation (inflammatory bowel disease, systemic vasculitis or graft-vs-host disease) and four were controls without inflammatory disease. The median transit time of the fast component ranged from 20 to 25 s and of the slow component 120-138 s in the four patient groups. The fraction of cells undergoing slow transit correlated significantly with (a) mean granulocyte transit time and (b) the fraction showing shape change in vitro. We conclude that granulocyte transit time through the pulmonary circulation is bimodal and that shape-changed (activated) cells transit more slowly that non-activated cells. The size of the fraction undergoing slow transit is closely related to mean granulocyte transit time and is an important determinant of the size of the pulmonary vascular granulocyte pool.

Cell Movement↗
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↗
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↗
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↗