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PubMed2004

A comparison of methods for characterizing the event-related BOLD timeseries in rapid fMRI.

Information about the shape and temporal duration of the blood oxygenation level dependent (BOLD) response can inform both functional neuroanatomy and psychological theory. However, the BOLD response evolves over 20 s or more, making it difficult to distinguish the unique characteristics of the response evoked by temporally adjacent stimuli. Fortunately, event-related BOLD signals can be extracted given that there is adequate variance in the distribution of inter-stimulus intervals (ISI). Unfortunately, the ISI distribution that yields the highest statistical efficiency is not always optimal from a psychological perspective; variability in the stimulus timing may complicate the interpretation of neuroimaging data in terms of underlying cognitive operations. In the present paper, Monte Carlo simulations are used to evaluate two techniques for estimating the event-related BOLD timeseries-event-related averaging and deconvolution using the Ordinary Least Squares estimate -with respect to maintaining acceptable levels of statistical power and experimental validity. While the unbiased deconvolution technique more robustly estimates the shape of the BOLD response functions, both methods succeed in accurately re-producing known differences between evoked BOLD responses when the stimulus ordering is randomized. However, the deconvolution method is more effective at preserving differences when there are sequential dependencies in the stimulus presentation order and restricted ISI distributions are used; particularly if the second of two sequentially dependent stimuli is omitted on some portion of the trials. Importantly, the successful re-production of the evoked BOLD response using restricted ISI distributions often maximizes the ability to make psychologically valid experimental conclusions.

Brain↗
PubMed2006

Enhancement of resolution in core-loss and low-loss spectroscopy in a monochromated microscope.

The significant enhancement of the energy resolution in the new generation of commercially available monochromated transmission electron microscopes presents new challenges in term of selecting the correct experimental conditions and understanding the various effects that can potentially influence the quality of the EELS data. In this respect we investigated the effect of point spread function of the detector and spectrum-diffraction mixing on the energy resolution and the intensity of the zero loss peak tails. Alternative approaches to improve the energy resolution by mathematical methods have been tested. By using a simple and commonly available test case (Si L(2,3) edges) we assessed the efficiency of the deconvolution algorithms to improve the resolution. The results show that the deconvolution is not always successful in improving the resolution of the core loss EELS data and the results may not always be reliable. Contrary to this, the application of the Richardson-Lucy deconvolution algorithm on some bandgap measurements data appears to be very effective. The procedure proved successful in removing the contribution of the zero-loss peak tails and allows an easier access to spectroscopic information starting at energy losses as low as of 0.5 eV with monochromated spectra and 1 eV with the non-monochromated spectra.

Journal Article↗
PubMed2003

Optimized determination of T cell epitope responses.

Pools of overlapping peptides corresponding to specific antigens are frequently used to identify T cell immune responses to vaccines or pathogens. While the response to the entire pool of peptides provides important information, it is often desirable to also know to which individual peptides within the pool the immune responses are directed. In this report, we analyzed various ways of deconvoluting an immune response to a pool of peptides to determine the number of different peptides to which the T cells are responding. We used a Monte Carlo simulation to optimize the construction of peptide pools that could identify responses to individual peptides using the fewest numbers of assays and patient material. We find that the number of assays required to deconvolute a pool increases by the logarithm of the number of peptides within the pool; however, the optimum configuration of pools changes dramatically according to the number of responses to individual peptides that are expected to be in the sample. Our simulation will help in the design of clinical trials in which the breadth of the response is being measured, by allowing a calculation for the minimum amount of blood that needs to be collected. In addition, our results guide the design and implementation of the experiments to deconvolute the responses to individual peptide epitopes.

Computer Simulation↗
PubMed1996

CXT-MAIN: a software package for determination of the analytical form of the pharmacokinetic system weighting function.

A new procedure specific for the determination of the analytical form of the model weighting function of a complex multicomponent pharmacokinetic system with or without a shunt and time delays is described. The procedure is based on the theory of linear dynamic systems and on a circulatory pharmacokinetic model of the living body. The model transfer function of the system under study was obtained by the frequency response method in the form of the ratio of two frequency dependent polynomials. Subsequently, the technique of the partial fraction inversion was employed to determine the analytical form of the model weighting function. Two examples from bioavailability studies in pharmacokinetics are given. The first example presents two estimates of the model weighting function of a pharmacokinetic system obtained by the new procedure and by a polyexponential deconvolution method. To compare these results, two models of the measured system output were determined using the two estimates of the model weighting function, the actual system input and a convolution method. The model weighting function obtained by the new procedure yielded a better model approximation of the output data than that obtained by the polyexponential deconvolution method. The second example, using the new procedure, presents the determination of the model weighting function of such a system that the deconvolution methods, commonly used in pharmacokinetics, cannot be applied to.

Administration, Oral↗
PubMed2001

Noncompartmentally-based pharmacokinetic modeling.

OBJECTIVE: To present an overview of noncompartmentally-based modeling which is a modeling that makes use of systems analysis, predominantly linear systems analysis (LSA). FINDINGS: Fundamental elements of LSA presented from a linear operational viewpoint have a sound foundation in molecular stochastic independence (MSI). Powerful LSA procedures based on MSI presented such as convolution, deconvolution and disposition decomposition analysis (DDA) enable PK predictions and evaluations of drug input and delivery using models with simple general structures and few verifiable assumptions. DDA nonparametrically differentiates the unit impulse response (UIR) into generalized elimination and distribution functions. DDA applied in a linear and nonlinear context is central to many LSA procedures such as analytically exact direct deconvolution, nonparametric evaluation of drug elimination and distribution, steady state predictions, evaluation of mean time parameters for drug delivery and disposition (mean residence time, mean transit time, mean arrival time), relative tissue affinity (residence time coefficients), nonparametric exact clearance correction of UIR, and time variant convolution and deconvolution. The general response mapping operation procedure of LSA presented provides a powerful rational alternative to problematic structured modeling of multivariate PK systems. CONCLUSION: The wide arsenal of underutilized LSA-based kinetic analysis tools provide a rational, powerful alternative to traditional kinetic modeling.

Linear Models↗
PubMed1998

Effect of charge interactions on the carboxylate vibrational stretching frequency in c-type cytochromes investigated by continuum electrostatic calculations and FTIR spectroscopy.

The FTIR spectra of the asymmetric carboxylate absorption region of three c-type cytochromes--namely horse heart, yeast and bonito cytochromes c--as well as continuum electrostatic calculations performed on their respective protein matrices, show that these combined methods can target specific protein regions and yield pertinent protein charge information that correlates with the observed spectral data. Deconvolution of the IR carboxylate stretch frequency region (1525-1675 cm-1) in the three cytochromes yield different v(oco)a distributions. In the case of the bonito cytochrome c carboxylates, two v(oco)a populations are clearly distinguishable in the deconvoluted spectra--which is not the case for the more complex v(oco)a deconvolutions of the other two cytochromes. The frequency distributions of the calculated potentials are consistent with the experimental observations and we conclude that the IR carboxylate absorption in proteins can be modified by the electrostatic environment.

Animals↗
PubMed2003

Transfer function analysis of ultrasonic time-intensity measurements.

Time-intensity measurements of ultrasonic-contrast microbubbles based on the dilution theory have been used to assist blood flow estimation. The compartment model has been employed to describe the dilution process. Under the linear and time-invariant assumption, the time-intensity curve measured at the output of a compartment (i.e., blood mixing chamber) is the convolution of the input time-intensity curve with the compartment's transfer function. Thus, transfer function analysis is possible using deconvolution when the temporal variations in both the input and the output intensities are available. Note that the linear and time-invariant assumption requires a constant flow rate because, with flow pulsation, the flow rate changes with time and the mixing process becomes time varying. Thus, the purpose of this paper was to study the effects of flow pulsation on time-intensity measurements. In addition, a deconvolution technique based on a recursive least squares approach is used for transfer function analysis. Both simulations and experiments were performed; the results from which indicate that the pulsation generally does not affect the validity of time-intensity-based flow estimation. The proposed deconvolution technique is also effective for both constant and pulsatile flows; thus, permitting transfer function analysis in various flow conditions. One potential application of this transfer function analysis is to remove the effects of a noninstantaneous input function. The results from this paper lead to future work in brain-perfusion estimation based on extracranial time-intensity measurements.

Blood Flow Velocity↗
PubMed1999

Investigation of S-farnesyl transferase substrate specificity with combinatorial tetrapeptide libraries.

Using biased tetrapeptide libraries made up of proteinogenic amino acids of the general formula Cys-O2-X3-X4, we searched for new substrates of partly purified rat brain S-farnesyl transferase (FTase). To achieve this task, an assay was developed in which the consumption of the co-substrate (farnesyl pyrophosphate) was measured. After three steps of deconvolution including each synthesis and enzymatic assay, the most efficient substrates found under these particular conditions were Cys-Lys-Gln-Gln (peptide I) and Cys-Lys-Gln-Met (peptide II). As a control, we used another tetrapeptide library (Cys-Val-O3-X4) in which the valine position was arbitrarily fixed, corresponding to Cys-Val-Ile-Met in the CAAX box of K-RasB, although this sublibrary was only marginally active compared with Cys-Lys-X3-X4 in the first round of deconvolution. The best substrate sublibrary was Cys-Val-Thr-X4, threonine being more favourable than the aliphatic amino acids (Val, Ile, Leu, Ala) in this position. Deconvolution finally led to Cys-Val-Thr-Gln, -Met, -Thr and -Ser as the most efficient substrates of FTase. Those tetrapeptides were not substrates of a partly purified geranylgeranyl transferase 1 (GGTase1). We also investigated the influence of the -1 position (at the N-terminus of cysteine) on the specificity of the enzyme, by using a series of pentapeptides constructed on the basis of the best tetrapeptide core (peptide 1). Among this family of analogues, only His-Cys-Lys-Gln-Gln did not behave as a substrate, whereas all the other pentapeptides were measurable substrates, with Gly-, Asn- and Thr-Cys-Lys-Gln-Gln displaying kinetic constants similar to that of Cys-Lys-Gln-Gln. The present work provides strong evidence that the best tetrapeptide substrates of FTase do not necessarily belong to the classical CAAX box, in which A's are lipophilic residues, but rather contain hydrophilic amino acids in the middle of their sequences. Among them, peptides I and II are potent FTase in vitro substrates that are not recognised by GGTase1 and might be new starting points for the design of FTase inhibitors.

Alkyl and Aryl Transferases↗
PubMed2002

A numerical method for estimating blood flow by dynamic functional imaging.

We present a numerical deconvolution scheme for estimating regional blood flow and tissue retention functions by dynamic functional imaging. The present approach implements the Tikhonov-Miller regularization in general form, which allows for prior knowledge or assumptions to be incorporated during the deconvolution process, so as to stabilize the solution against variations due to noise. Appropriate approximations and simplifications in the context of functional imaging, were also introduced to ease numerical computations. Monte Carlo simulation experiments were carried out to study the applicability of the present approach and to compare with other deconvolution techniques previously studied.

Algorithms↗
PubMed2002

Response times of carbon fiber microelectrodes to dynamic changes in catecholamine concentration.

The electrode response time and the measured concentrations during dynamic catecholamine changes were compared using constant potential amperometry and fast-scan cyclic voltammetry. The amperometric response to a rectangular pulse of catecholamine is more rectangular than the cyclic voltammetric response; however, the response times are very similar when, during cyclic voltammetry, the temporal lag due to adsorption and desorption of catecholamine to the electrode is removed by deconvolution. Deconvolution of cyclic voltammetry data was applied to stimulated dopamine release in vivo, allowing for modeling of release and uptake kinetics and to measure catecholamine release from single cells, resulting in better resolution of peaks from single vesicles. In vitro postcalibrations were performed to calculate concentrations of catecholamine measured with cyclic voltammetry and amperometry. The addition of 600 microM ascorbic acid to the postcalibration buffer, allowing a catalytic reaction to regenerate dopamine, resulted in similar calculated concentrations for stimulated release of dopamine using amperometry and cyclic voltammetry. Using deconvoluted cyclic voltammetry to remove the response time lag and adding ascorbic acid to the calibration buffer, the shape and concentration of dynamic catecholamine changes are very similar when measured with constant potential amperometry and cyclic voltammetry.

Animals↗
PubMed1997

Calicheamicin derivatives conjugated to monoclonal antibodies: determination of loading values and distributions by infrared and UV matrix-assisted laser desorption/ionization mass spectrometry and electrospray ionization mass spectrometry.

Calicheamicin derivatives (MW approximately 1500) and monoclonal antibodies (MoAbs) conjugated to calicheamicin derivatives (MW approximately 150,000) were analyzed by UV-MALDI/MS, IR-MALDI/MS, and ESI/MS. These materials are potent anticancer agents. Calicheamicin derivatives and conjugates rapidly degrade upon UV irradiation but are relatively stable during IR irradiation and under ESI conditions. A unique feature of IR-MALDI/MS is a 2 times enhancement in resolution relative to UV-MALDI/MS for masses above approximately 50,000 Da resulting in a molecular ion envelope containing a series of partially resolved peaks of the calicheamicin-MoAb conjugates. The mass shift difference between the peak maxima corresponded to the mass change due to the covalent addition of calicheamicin derivatives to the monoclonal antibody. The distribution of the calicheamicin derivatives in the monoclonal antibodies was computed by deconvoluting the partially resolved peak envelope. A unique feature of the ESI mass spectra, under unit resolution conditions, is that the distribution of the carbohydrates can be well resolved for pure MoAbs and can be only partially resolved for conjugated MoAbs. Average loading values for calicheamicia derivatives when conjugated to MoAbs were computed from UV-MALDI/MS, IR-MALDI/MS, and ESI/MS data and the results compared with the average loading values obtained by UV absorption spectrometry. Very low average loading values were computed from UV-MALDI/MS data due to the degradation of the conjugated calicheamicin derivatives during the UV irradiation process. The IR-MALDI/MS average loading values, obtained with glycerol as the matrix, were consistent with the UV absorption spectrometry values for conjugates having hydrolytically stable linkers, but not when the linker contained a hydrolytically labile hydrazone. ESI/MS average loading values were generally lower than the corresponding values obtained by IR-MALDI/MS. The average loading values and distributions obtained using IR-MALDI/MS were more reliable than the corresponding ESI/MS values because the partially resolved, singly and doubly charged peaks in the IR-MALDI spectra can be mathematically deconvoluted, while the overlapping, highly multiply charged peaks of the electrospray spectra can only be partially deconvoluted.

Aminoglycosides↗
PubMed2001

The secondary structure of the inhibited mitochondrial ADP/ATP transporter from yeast analyzed by FTIR spectroscopy.

Fourier transform infrared spectroscopy has been applied to the study of the carboxyatractyloside-inhibited mitochondrial ADP/ATP transporter from the yeast Saccharomyces cerevisiae, either solubilized in dodecyl maltoside or reconstituted in phosphatidylcholine liposomes. Its secondary structure has been estimated by means of Fourier self-deconvolution followed by curve fit. A Voigt function was used to fit the components of the deconvoluted spectrum, aiming to account for any distortions introduced by deconvolution. For any of the states analyzed, reconstituted or solubilized, in solution or in dry films, 60-70% of the amino acids are found to adopt alpha-helix plus unordered structures, coherent with the six transmembrane spanning helix model. Moreover, the problem of structure preservation on drying was addressed, and several observations pointed to a maintenance of the protein structure in dry films. Comparison of reconstituted and solubilized samples indicated the presence of both lipid-induced changes in the protein (decrease of the beta-sheets and increase of unordered structures) and protein-induced changes in the lipids (strong hydrogen bonding of lipid C=O groups). To obtain a better discrimination of alpha-helix and unordered structure contributions for the reconstituted form, H/D exchange experiments were performed. Between 35% and 45% of the amino acids were finally assigned to alpha-helix structures, compatible with the existence of five or six transmembrane spanning helices in the transporter. The level of H/D exchange was determined after 15 h of exposure to D(2)O vapor to be 85%, reflecting a high accessibility of the amide hydrogens even for the carboxyatractyloside-inhibited state.

Amides↗
PubMed2006

In situ kinetics of cytochromes c1 and c2.

In Rhodobacter sphaeroides chromatophores, cytochromes (cyt) c(1) and c(2) have closely overlapping spectra, and their spectral deconvolution provides a challenging task. As a result, analyses of the kinetics of different cytochrome components of the bc(1) complex in purple bacteria usually report only the sum cyt c(1) + cyt c(2) kinetics. Here we used newly determined difference spectra of individual components to resolve the kinetics of cyt c(1) and c(2) in situ via a least-squares (LS) deconvolution. We found that the kinetics of cyt c(1) and c(2) are significantly different from those measured using the traditional difference wavelength (DW) approach, based on the difference in the absorbance at two different wavelengths specific for each component. In particular, with the wavelength pairs previously recommended, differences in instrumental calibration led to kinetics of flash-induced cyt c(1) oxidation measured with the DW method which were faster than those determined by the LS method (half-time of approximately 120 micros vs half-time of approximately 235 micros, in the presence of antimycin). In addition, the LS approach revealed a delay of approximately 50 micros in the kinetics of cyt c(1) oxidation, which was masked when the DW approach was used. We attribute this delay to all processes leading to the oxidation of cyt c(1) after light activation of the photosynthetic reaction center, especially the dissociation of cyt c(2) from the reaction center. We also found that kinetics of both cyt c(1) and c(2) measured by the DW approach were significantly distorted at times longer than 1 ms, due to spectral contamination from changes in the b hemes. The successful spectral deconvolution of cyt c(1) and c(2), and inclusion of both cytochromes in the kinetic analysis, significantly increase the data available for mechanistic understanding of bc(1) turnover in situ.

Antimycin A↗
PubMed2001

Computer Aided Analysis of Split and Mix Combinatorial Libraries.

Combinatorial chemistry using split and pool synthesis involves making and testing mixtures of compounds in pools which are subsets of the larger compound collection. These subsets are created during the synthesis of the collection through a resin splitting and mixing method. Tests are conducted on each of the final pools of mixtures and the individual compounds within a mixture of interest are then identified through some deconvolution scheme, originally involving selective re-synthesis. It is possible that different schemes for splitting and mixing will have different consequences on the overall effort necessary to deconvolute interesting mixtures. The evaluation of different protocols of splitting and mixing involves consideration of more possibilities than can be exhaustively or optimally determined manually in a realistic time frame for most compound collections. We present herein a computational scheme to aid in this analysis. The approach exhaustively examines possible splitting and mixing strategies for the interrelated values of total library size, number of combinatorial steps, number of reaction vessels, and number of compounds per final pool. Weighting factors may be introduced into the various steps. The resulting complete list of splitting and mixing options is scored based on a variable weighting strategy for the total effort of synthesis and deconvolution. The results indicate the splitting/mixing strategy used has an impact on overall efficiency and should be considered in the design of compound libraries.

Journal Article↗
PubMed2005

29Si NMR study of structural ordering in aluminosilicate geopolymer gels.

A systematic series of aluminosilicate geopolymer gels was synthesized and then analyzed using 29Si magic-angle spinning nuclear magnetic resonance (MAS NMR) in combination with Gaussian peak deconvolution to characterize the short-range ordering in terms of T-O-T bonds (where T is Al or Si). The effect of nominal Na2O/(Na2O + K2O) and Si/Al ratios on short-range network ordering was quantified by deconvolution of the 29Si MAS NMR spectra into individual Gaussian peaks representing different Q4(mAl) silicon centers. The deconvolution procedure developed in this work is applicable to other aluminosilicate gel systems. The short-range ordering observed here indicates that Loewenstein's Rule of perfect aluminum avoidance may not apply strictly to geopolymeric gels, although further analyses are required to quantify the degree of aluminum avoidance. Potassium geopolymers appeared to exhibit a more random Si/Al distribution compared to that of mixed-alkali and sodium systems. This work provides a quantitative account of the silicon and aluminum ordering in geopolymers, which is essential for extending our understanding of the mechanical strength, chemical and thermal stability, and fundamental structure of these systems.

Journal Article↗
PubMed1992

A comparison between the semisimultaneous and the stable isotope techniques for bioavailability estimation of terbutaline in humans.

A recently proposed bioavailability estimation procedure, the "semisimultaneous" method, in which the test and reference dose administrations are separated by a short time interval and total concentrations are analyzed, was compared with the stable isotope method for precision and accuracy. By administering isotope-labeled (reference) and unlabeled (test) terbutaline in a semisimultaneous fashion, the bioavailability could be determined with both methods at the same time. The extent and rate of bioavailability of oral terbutaline was determined in eight healthy volunteers by use of both model fitting, AUC methods, and deconvolution. The AUC ratio and the deconvolution methods, by use of the separate isotope data, gave bioavailability estimates of 14.5% +/- 4.1% and 12.2% +/- 3.9%, respectively. According to the semisimultaneous method, bioavailability estimates with the same data sets were 11.8% +/- 4.5% obtained from fitting a model to the data and 11.0% +/- 3.7% by use of a combined model fitting-deconvolution procedure. An excellent agreement between the semisimultaneous and the stable isotope methods was also obtained in the estimation of the rate of absorption.

Administration, Oral↗
PubMed1978

The measurement of calcium absorption and absorption rate with an external arm radioactivity counter.

1. A large-volume scintillation counter was used to measure calcium absorption from the ratio of forearm uptake of 47Ca after oral 47CaCl2 (administered with milk) to forearm uptake after intravenously administered 47CaCl2. 2. In some subjects serial measurements of both forearm uptake of 47Ca and blood 47Ca radioactivity were also recorded, and by using deconvolution both total calcium absorption and calcium absorption rate were determined. 3. The forearm ratio determination of 47Ca absorption correlated well with that obtained by deconvolution of either serial blood 47Ca or forearm 47Ca measurements provided that the forearm radioactivity measurements were made at least 8 h after the administration of 47CaCL2. 4. Although the two deconvolution techniques gave similar estimates of total calcium absorption there were discrepancies between their measurements of calcium absorption rate. These discrepancies were reduced but not eliminated by the use of additional lead shielding around the Armac counter.

Absorption↗
PubMed1981

Comparison of radioisotope methods for the measurement of phosphate absorption in normal subjects and in patients with chronic renal failure.

1. Intestinal phosphate absorption was measured in normal subjects, in patients with chronic renal failure, and in post-transplant patients, by a double isotope technique involving oral administration of 32P and simultaneous intravenous injection of 33P with subsequent deconvolution analysis. 2. By this technique intestinal phosphate absorption has been shown to have two components: an initial rapid phase, which is completed by 3 h, and a slower more prolonged phase, which continues beyond 7 1/2 h. 3. Phosphate malabsorption has been demonstrated in chronic renal failure and transplant patients, which is accounted for by impairment of the initial rapid phase of absorption. 4. Results obtained by deconvolution analysis have been compared with other estimates of phosphate absorption obtained from analysis of 32P radioactivity curves alone. 5. The fractional hourly rate of absorption and the plasma 32P radioactivity at 60 min corrected for extracellular fluid volume provided the best approximations to the result obtained by deconvolution analysis, with respect to both the maximal rate of phosphate absorption and cumulative percentage phosphate absorption.

Administration, Oral↗