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Results for “deconvolution”

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PubMed1997

Selection of a histidine-containing inhibitor of gelatinases through deconvolution of combinatorial tetrapeptide libraries.

A fully automated peptide synthesizer was used to generate tetrapeptide sublibraries from 24 natural and nonnatural amino acids, from which new inhibitors of gelatinases (matrix metalloproteinases MMP-2 and MMP-9) were selected as potential anticancer drugs. MMP-2 and MMP-9 from mouse Balbc/3T3 fibroblasts conditioned media were assayed in their linear range response by zymography to quantify inhibition at each step of the tetrapeptide library deconvolution. The histidine-epsilon-amino caproic acid-beta-alanine-histidine (His-epsilon Ahx-beta Ala-His) sequence was found to yield optimal inhibition of both MMP-2 and MMP-9. Inhibition by selected tetrapeptides was also evaluated with two other techniques, a native type IV collagen degradation assay and a fluorogenic enzymatic assay, confirming the tetrapeptide potency. The His-epsilon Ahx-beta Ala-His tetrapeptide also inhibited purified human MMP-2 and MMP-9 and the corresponding enzymes present in conditioned media from human tumour cells. Finally, the length of the spacer between the two terminal histidines was found to be crucial to the inhibitory potential. This approach may thus be considered as a-successful strategy to yield specific peptide or pseudopeptide inhibitors, although their potency remains moderate, since it was measured before any chemical optimization was undertaken.

3T3 Cells↗

PubMed1996

A comparison of six deconvolution techniques.

We present results for the comparison of six deconvolution techniques. The methods we consider are based on Fourier transforms, system identification, constrained optimization, the use of cubic spline basis functions, maximum entropy, and a genetic algorithm. We compare the performance of these techniques by applying them to simulated noisy data, in order to extract an input function when the unit impulse response is known. The simulated data are generated by convolving the known impulse response with each of five different input functions, and then adding noise of constant coefficient of variation. Each algorithm was tested on 500 data sets, and we define error measures in order to compare the performance of the different methods.

Algorithms↗

PubMed2007

Reversible jump Markov chain Monte Carlo for deconvolution.

To solve the problem of estimating an unknown input function to a linear time invariant system we propose an adaptive non-parametric method based on reversible jump Markov chain Monte Carlo (RJMCMC). We use piecewise polynomial functions (splines) to represent the input function. The RJMCMC algorithm allows the exploration of a large space of competing models, in our case the collection of splines corresponding to alternative positions of breakpoints, and it is based on the specification of transition probabilities between the models. RJMCMC determines: the number and the position of the breakpoints, and the coefficients determining the shape of the spline, as well as the corresponding posterior distribution of breakpoints, number of breakpoints, coefficients and arbitrary statistics of interest associated with the estimation problem. Simulation studies show that the RJMCMC method can obtain accurate reconstructions of complex input functions, and obtains better results compared with standard non-parametric deconvolution methods. Applications to real data are also reported.

Algorithms↗

PubMed2005

A statistical mechanical deconvolution of the differential scanning calorimetric profiles of the thermal denaturation of cyanomethemoglobin.

A differential scanning calorimetric study of the thermal unfolding of horse cyanomethemoglobin (as an irreversible protein system) was carried out in phosphate-EDTA buffer (20 mM phosphate, 1 mM EDTA) pH 7.2. The calorimetric rescanning of the protein solution was found to be irreversible and the process unfolded state --> final state appears to follow first order kinetic. Assuming the system to be comprised of n reversible states and one irreversible final state, the number of particles participating in the reversible states changes with time because they ultimately transit to the final irreversible denatured state. Hence, we carried out the deconvolution analysis using the grand canonical ensembles instead of just the canonical ensembles. This change was effected by introducing a correction term into the related equations which determines the outlet share of those particles exiting from the reversible states and converting into the final irreversible state. This approach provided an improved interpretation of the experimental data, which supports the following two-step process for the thermal denaturation of cyanomethemoglobin: alpha(2)beta(2) --> (alpha + alphabeta + beta)(excited) --> alpha(melt) + (alphabeta)(melt) + (beta(melt).

Animals↗

PubMed1982

A method for in situ characterization of b- and c-type cytochromes in Escherichia coli and in complex III from beef heart mitochondria by combined spectrum deconvolution and potentiometric analysis.

An analytical technique for the in situ characterization of b- and c-type cytochromes has been developed. From evaluation of the results of potentiometric measurements and spectrum deconvolutions, it was concluded that an integrated best-fit analysis of potentiometric and spectral data gave the most reliable results. In the total cytochrome b content of cytoplasmic membranes from aerobically grown Escherichia coli, four major components are distinguished with alpha-band maxima at 77 K of 555.7, 556.7, 558.6 and 563.5 nm, and midpoint potentials at pH 7.0 of 46, 174, -75 and 187 mV, respectively. In addition, two very small contributions to the alpha-band spectrum at 547.0 and 560.2 nm, with midpoint potentials of 71 and 169 mV, respectively, have been distinguished. On the basis of their spectral properties they should be designated as a cytochrome c and a cytochrome b, respectively. In Complex III, isolated from beef heart mitochondria, five cytochromes are distinguished: cytochrome c1 (lambda m (25 degrees C) = 553.5 nm; E'0 = 238 mV) and four cytochromes b (lambda m (25 degrees C) = 558.6, 561.2, 562.1, 566.1 nm and E'0 = -83, 26, 85, -60 mV).

Animals↗

PubMed1988

Applications of a general method for deconvolution using compartmental analysis.

A method of deconvolution is illustrated using compartmental models. The approach can be used to determine an arbitrary unknown input function from a measured response and the impulse response of the system. Compartmental models are constructed to specify (a) the function fitting the response data and (b) the impulse response of the system. Simulation of these models is then used to construct the unknown input function.

Alanine↗

PubMed1983

Model-free deconvolution techniques for estimating vascular transport functions.

In this paper we present two methods which can be used to numerically deconvolve indicator dilution curves to obtain vascular transport functions. In the first method, direct algebraic deconvolution is made stable and practical by the damped least squares method. The second method involves a time-shift of the output curve which is based on the first and second moments of the input and output curves. This method is stable, computationally simple and can provide reasonable estimates of the transport function.

Animals↗

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↗

PubMed2006

Use of mixture distributions to deconvolute the behavior of "hits" and controls in high-throughput screening data.

The stochastic nature of high-throughput screening (HTS) data indicates that information may be gleaned by applying statistical methods to HTS data. A foundation of parametric statistics is the study and elucidation of population distributions, which can be modeled using modern spreadsheet software. The methods and results described here use fundamental concepts of statistical population distributions analyzed using a spreadsheet to provide tools in a developing armamentarium for extracting information from HTS data. Specific examples using two HTS kinase assays are analyzed. The analyses use normal and gamma distributions, which combine to form mixture distributions. HTS data were found to be described well using such mixture distributions, and deconvolution of the mixtures to the constituent gamma and normal parts provided insight into how the assays performed. In particular, the proportion of hits confirmed was predicted from the original HTS data and used to assess screening assay performance. The analyses also provide a method for determining how hit thresholds--values used to separate active from inactive compounds--affect the proportion of compounds verified as active and how the threshold can be chosen to optimize the selection process.

Chemistry, Pharmaceutical↗

PubMed2006

Instrumental method for automated on-line fraction analysis and peak deconvolution in multicomponent-overloaded high-performance liquid chromatography.

A bi-dimensional (non-orthogonal) chromatographic system made of two columns of different length (longer along the first direction and shorter on the second) but packed with identical (or similar) materials has been employed to perform automated on-line fraction analysis and peak deconvolution of multicomponent overloaded band profiles. Multicomponent overloaded peaks, eluted from the first column, are sampled through a remotely-controlled switching valve and fractions are injected, under analytical conditions, directly into the second direction. This set-up serves a twofold purpose. First of all, it has been possible to use linear calibration curves for detector calibration (DC). Secondly, since single component peaks were resolved on the second direction, individual concentration profiles have been obtained beneath the envelop of overlapping bands. All the information necessary to operate the bi-dimensional system can be achieved by analyzing the chromatographic behavior of the mixture on the shorter column under linear conditions. Therefore, solutions of unknown concentration can be prepared and their composition reconstructed with a simple chromatographic run. Two- and three-component overloaded mixtures have been employed to validate the system.

Automation↗

PubMed2004

The use of QSD (q-sequence deconvolution) to recover superposed, transient evoked-responses.

OBJECTIVE: We describe q-sequence deconvolution (QSD), a new data acquisition/analysis method for evoked-responses that solves the problem of waveform distortion at high stimulus repetition-rates, due to response overlap. QSD can increase the sensitivity of clinically useful evoked-responses because it is well known that high stimulus repetition-rates are better for detecting pathophysiology. METHODS: QSD is applicable to a variety of experimental conditions. Because some QSD-parameters must be chosen by the experimenter, the underlying principles and assumptions of the method are described in detail. The theoretical and mathematical bases of the QSD method are also described, including some equivalent computational formulations. RESULTS: QSD was applied to recordings of the human auditory brainstem response (ABR) at stimulus repetition-rates that overlapped the responses. The transient ABR was recovered at all rates tested (highest 160/s), and showed systematic changes with stimulus repetition-rate within a single subject. CONCLUSIONS: QSD offers a new method of recovering brain evoked-response activity having a duration longer than the time between stimuli. SIGNIFICANCE: The use of this new technique for analysis of evoked responses will permit examination of brain activation patterns across a broad range of stimulus repetition-rates, some never before studied. Such studies will improve the sensitivity of evoked-responses for the detection of brain pathophysiology. New measures of brain activity may be discovered using QSD. The method also permits the recovery of the transient brain waveforms that overlap to form 'steady-state' waveforms. An additional benefit of the QSD method is that repetition-rate can be isolated as a variable, independent of other stimulus characteristics, even if the response is a nonlinear function of rate.

Acoustic Stimulation↗

PubMed2006

Deconvoluting the effects of P-glycoprotein on intestinal CYP3A: a major challenge.

Metabolism by cytochrome P4503A (CYP3A) and P-glycoprotein (P-gp)-mediated efflux are two important biochemical barriers to drug absorption from the intestine. CYP3A, the most important family of drug-metabolizing enzymes, shares many substrates with the efflux transporter P-gp. Although the individual impact of these two systems on drug disposition is routinely assessed, the effect of both systems acting together during intestinal absorption is difficult to ascertain. Pharmacokinetic theory predicts that the effect of efflux on overall metabolism depends on substrate concentrations relative to the respective kinetic parameters of these processes (i.e. affinities for transport and metabolism, as well as the capacities of these processes). Researchers have published conflicting findings on how efflux affects metabolism. Furthermore, the in vitro parameters that have been used to explain or predict this interation are more relevant for describing overall changes in extraction efficiency of the system (intestinal epithelium), rather than deconvoluting the effect of P-gp on CYP3A-mediated metabolism. Developing a more refined way to understand this interplay and its potential relevance to drug absorption is an important goal, as a large proportion of marketed drugs and many modern drug discovery candidates are known to be affected by one or both of these proteins.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2005

Rapid-scan EPR with triangular scans and fourier deconvolution to recover the slow-scan spectrum.

Direct-detected rapid-scan EPR signals were recorded using triangular field scan rates between 1.7 and 150 kG/s for deoxygenated samples of lithium phthalocyanine (LiPc) and Nycomed trityl-CD3. These scan rates are rapid relative to the reciprocals of the electron spin relaxation times and cause characteristic oscillations in the signals. Fourier deconvolution with an analytical function permitted recovery of lineshapes that are in good agreement with experimental slow-scan spectra. Unlike slow-scan EPR, direct detection rapid-scan EPR does not use phase sensitive detection and records the absorption signal directly instead of the first derivative of the absorption signal. The amplitude of the signal decreases approximately linearly with applied magnetic field gradient. Images of phantoms constructed from samples of LiPc and trityl-CD3 were reconstructed by filtered back-projection from data sets with a missing angle. The lineshapes in spectral slices from the image are in good agreement with slow-scan spectra and the spacing between sample tubes matches well with the known sample geometry.

Algorithms↗

PubMed2006

High-resolution NMR with resistive and hybrid magnets: deconvolution using a field-fluctuation signal.

A method for compensating effect of field fluctuation is examined to attain high-resolution NMR spectra with resistive and hybrid magnets. In this method, time dependence of electromotive force induced for a pickup coil attached near a sample is measured synchronously with acquisition of NMR. Observed voltage across the pickup coil is converted to field fluctuation data, which is used to deconvolute NMR signals. The feasibility of the method is studied by (79)Br MAS NMR of KBr under a 30T magnetic field of a hybrid magnet. Twenty single-scan NMR signals were accumulated after the manipulation, resulting in a high-resolution NMR spectrum.

Algorithms↗

PubMed2003

Combining deconvolution and fluctuation analysis to determine quantal parameters and release rates.

Analysis methods are described which integrate information from fluctuation analysis with that from deconvolution. Together the two approaches allow to derive a consistent quantitative description of quantal release (both evoked, spontaneous and asynchronous) under conditions in which quantal parameters may change during a repetitively applied stimulation protocol. Specifically, our methods take into account the effects of accumulating transmitter in the synaptic cleft and postsynaptic receptor desensitization, which may develop during strong stimulation. Several ways to handle non-stationarities are described. Examples are provided for the Calyx of Held, a glutamatergic synapse, in which both the pre- and the postsynaptic compartments can be voltage-clamped.

Algorithms↗

PubMed2006

A novel fluorescence imaging technique combining deconvolution microscopy and spectral analysis for quantitative detection of opportunistic pathogens.

A novel fluorescence imaging technique based on deconvolution microscopy and spectral analysis is presented here as an alternative to confocal laser scanning microscopy. It allowed rapid, specific and simultaneous identification of five major opportunistic pathogens, relevant for public health, in suspension and provided quantitative results.

Bacteria↗