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At least 541 records · Page 30Linked to original sources
PubMed2002

Localization of the transmembrane proteoglycan syndecan-4 and its regulatory kinases in costameres of rat cardiomyocytes: a deconvolution microscopic study.

Syndecan-4 (syn-4), a transmembrane heparan sulfate-containing proteoglycan, is unique among the four members of the syndecan family in its specific cellular localization to complex cytoskeletal adhesion sites, i.e., focal adhesions. During early phenotypic redifferentiation of neonatal cardiomyocytes in culture, immunolocalization reveals syn-4 to be heavily concentrated in the perinuclear endoplasmic reticulum-Golgi region, with little found at the peripheral regions. Subsequently, syn-4 becomes localized to a cytoskeletal adhesion complex unique to striated muscle, the costamere. Soon after redifferentiation of myofibrils in cultured neonatal cardiomyocytes, syn-4 is present only in costameres, not in focal adhesions. In cultured adult cardiomyocytes, it is present in both costameres and focal adhesions-the latter in two distinct regions of the spread cardiomyocytes, reflecting localization with two types of actin-containing filaments. The fact that syn-4 is observed early in the costameric regions, as opposed to later in the focal adhesions, suggests that it may play an initial role in early adhesion/signal transduction mechanisms in close proximity to the contractile apparatus, as well as in transmission of contractile force to the collagenous extracellular matrix (ECM) which surrounds the cardiac myofibers in situ. With respect to possible regulatory mechanisms of syn-4, we localized syn-4 with both the epsilon isoform of protein kinase C and the tyrosine kinase pp60(csrc) in costameric regions. These findings suggest that syn-4 may not only play a role in cellular adhesion and contractile force transmission, it may also, through ser, thr, and tyr phosphorylation, be part of an interactive signal transduction mechanism in myocardial functioning via these adhesive cytoskeletal complexes.

Animals↗
PubMed2007

Determination of community structure through deconvolution of PLFA-FAME signature of mixed population.

Phospholipid fatty acids (PLFAs) as biomarkers are well established in the literature. A general method based on least square approximation (LSA) was developed for the estimation of community structure from the PLFA signature of a mixed population where biomarker PLFA signatures of the component species were known. Fatty acid methyl ester (FAME) standards were used as species analogs and mixture of the standards as representative of the mixed population. The PLFA/FAME signatures were analyzed by gas chromatographic separation, followed by detection in flame ionization detector (GC-FID). The PLFAs in the signature were quantified as relative weight percent of the total PLFA. The PLFA signatures were analyzed by the models to predict community structure of the mixture. The LSA model results were compared with the existing "functional group" approach. Both successfully predicted community structure of mixed population containing completely unrelated species with uncommon PLFAs. For slightest intersection in PLFA signatures of component species, the LSA model produced better results. This was mainly due to inability of the "functional group" approach to distinguish the relative amounts of the common PLFA coming from more than one species. The performance of the LSA model was influenced by errors in the chromatographic analyses. Suppression (or enhancement) of a component's PLFA signature in chromatographic analysis of the mixture, led to underestimation (or overestimation) of the component's proportion in the mixture by the model. In mixtures of closely related species with common PLFAs, the errors in the common components were adjusted across the species by the model.

Bacteria↗
PubMed2006

Ab initio and experimental thermodynamic and kinetic study of proton-assisted bond activation in gaseous hydrocarbons: deconvolution of reaction efficiencies in the case of adamantane.

1) Protonation at all possible sites of adamantane (C(10)H(16)) was studied at the MP2/6-311++G(3df,2p)//MP2/6-311++G(d,p) level. This provided values of the changes in the thermodynamic state functions for these processes. Whenever direct comparison was possible, the agreement with experimental data was very good. 2) By the same means, the reaction paths linking the various species obtained in these reactions were analyzed. 3) Fourier transform ion cyclotron resonance (FT-ICR) spectroscopy was used to determine the rate constants for proton transfer from 16 protonated reference bases to adamantane in the gas phase. Also, the rate constants for the formation of ionic products in these reactions were determined. 4) The experimental reaction rates were successfully predicted and refined on the basis of a simple mechanistic model based on the reaction profiles indicated above. 5) Our results hint at the potential usefulness of this approach for mechanistic studies.

Journal Article↗
PubMed2006

Deconvoluting the memory effect in Pd-catalyzed allylic alkylation: Effect of leaving group and added chloride.

An analysis of product distributions in the Tsuji-Trost reaction indicates that several instances of reported "memory effects" can be attributed to slow interconversion of the initially formed syn- and anti-[Pd(eta3-allyl)] complexes. Addition of chloride triggers a true memory effect, in which the allylic terminus originally bearing the leaving group has a higher reactivity. The latter effect, termed regioretention, can be rationalized by ionization from a palladium complex bearing a chloride ion, forming an unsymmetrically substituted [Pd(eta3-allyl)] complex. DFT calculations verify that the position trans to the phosphine ligand is more reactive both in the initial ionization and in the subsequent nucleophilic attack.

Journal Article↗
PubMed2002

Deconvolution of surface topology for quantification of initial wear in highly cross-linked acetabular components for THA.

Evaluation of the surface morphology of short-term retrieved cross-linked acetabular components requires differentiation between the features generated during machining and the smaller-scale morphologies generated during the in vivo wear process. Previously, the distinction between the waviness of machining and the roughness of wear has been related to the grain size of the UHMWPE. Here a low-frequency cutoff is proposed, based on the maximum spectral frequency of machining marks, rather than on the grain size of the bulk UHMWPE material, as a reliable method for deconvolving machining marks from in vivo wear following short-term implantation. To this end, as-machined articulating surfaces of conventional (GUR 1050) and two groups of highly cross-linked UHMWPE acetabular components were examined to determine whether they exhibited a periodic surface morphology with a well-defined spatial frequency. The surface frequency spectra revealed low-frequency peaks associated with the machining marks, which were unique to each type of implant. Furthermore, the surface frequency spectra appeared uniform within a single group of implants. Statistically significant differences in the surface roughness and waviness were observed between the three groups of new implants. Our research suggests that machining marks can be effectively deconvolved from the articulating surface with the use of a Fourier transform algorithm with a single cutoff frequency of 0.08 1/microm, corresponding to a wavelength of 12.5 microm. The results of this study provide a unified conceptual framework for discriminating between waviness and roughness of the articulating surface for machined orthopedic components. The distinction between waviness and roughness is expected to be crucial for the comprehensive evaluation of wear surfaces after short-term implantation, when machining marks may be partially worn away or plastically deformed in vivo.

Acetabulum↗
PubMed2004

Improvement in volume estimation from confocal sections after image deconvolution.

The confocal microscope can image a specimen in its natural environment forming a 3D image of the whole structure by scanning it and collecting light through a small aperture (pinhole), allowing in vivo and in vitro observations. So far, the confocal fluorescence microscope (CFM) is considered a true volume imager because of the role of the pinhole that rejects information coming from out-of-focus planes. Unfortunately, intrinsic imaging properties of the optical scheme presently employed yield a corrupted image that can hamper quantitative analysis of successive image planes. By a post-image collection restoration, it is possible to obtain an estimate, with respect to a given optimization criterium, of the true object, utilizing the impulse response of system or Point Spread Function (PSF). The PSF can be measured or predicted so as to have a mathematical and physical model of the image-formation process. Further modelling and recording noise as an additive Gaussian process has used the regularized Iterative Constrained Tykhonov Miller (ICTM) restoration algorithm for solving the inverse problem. This algorithm finds the best estimate iteratively searching among the possible positive solutions; in the Fourier domain, such an approach is relatively fast and elegant. In order to compare the effective improvement in the quantitative image information analysis, we measured the volume of reference objects before and after image restoration, using the isotropic Fakir method.

Animals↗
PubMed2001

A semiparametric deconvolution model to establish in vivo-in vitro correlation applied to OROS oxybutynin.

In vitro-in vivo correlation (IVIVC) models may be used to predict in vivo drug concentration-time profiles given in vitro release characteristics of a drug. This prediction is accomplished by incorporating in vitro release characteristics as an input function (A(vitro)) to a pharmacokinetics model. This simple approach often results in biased predictions of observed in vivo drug concentrations, and it can result in rejecting IVIVC. To solve this problem we propose a population IVIVC model that incorporates the in vitro information and allows one to quantify possibly changed in vivo release characteristic. The model assumes linear kinetics and describes the in vivo release as a sum of A(vitro) and a nonparametric function (A(d), a spline) representing the difference in release due to in vivo conditions. The function A(vitro) and its variability enter the model as a prior distribution. The function A(d) is estimated together with its intersubject variability. The number of parameters associated with A(d) defines the model: no parameters indicates perfect IVIVC, a large number of parameters indicates poor IVIVC. The number of parameters is determined using statistical model selection criteria. We demonstrate the approach to solve the IVIVC problem of an oral extended release oxybutynin form (OROS), administered in three pharmacokinetic studies. These studies present a particular challenging case; that is, the relative bioavailability for the OROS administration is >100% compared with that of the immediate-release form. The result of our modeling shows that the apparent lack of IVIVC can be overcome: in vivo concentration can be predicted (within or across data sets) based on in vitro release rate together with a simple form of systematic deviation from the in vitro release.

Biological Availability↗
PubMed1980

Novel approach to bioavailability testing: statistical method for comparing drug input calculated by a least-squares deconvolution technique.

A novel approach to bioavailability testing is presented. The approach is model independent because it does not assume a specific pharmacokinetic model and does not use absorption, distribution, or elimination rate constants or a volume term. The method, which requires intravenous administration, is compared to classical bioavailability evaluation methods. Evaluation of drug input is based on the same assumptions required for using the area under the curve. No extrapolation beyond the last data point is required. Two statistics are derived that enable a comparison of the rate and the cumulative amount of input of two inputs for various times. A differential confidence profile is calculated that allows a more detailed and intrinsic bioavailability comparison than previous methods. The approach is demonstrated on simulated data containing random noise and shows satisfactory performance.

Biological Availability↗
PubMed2004

Use of spherical harmonic deconvolution methods to compensate for nonlinear gradient effects on MRI images.

Spatial encoding in MR techniques is achieved by sampling the signal as a function of time in the presence of a magnetic field gradient. The gradients are assumed to generate a linear magnetic field gradient, and typical image reconstruction relies upon this approximation. However, high-speed gradients in the current generation of MRI scanners often sacrifice linearity for improvements in speed. Such nonlinearity results in distorted images. The problem is presented in terms of first principles, and a correction method based on a gradient field spherical harmonic expansion is proposed. In our case, the amount of distortion measured within a typical field of view (FOV) required for head imaging is sufficiently large that without the use of some distortion correction technique, the images would be of limited use for stereotaxy or longitudinal studies, where precise volumetric information is required.

Brain↗
PubMed2006

Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise.

The dominant ions in MS/MS spectra of peptides, which have been fragmented by low-energy CID, are often b-, y-ions and their derivatives resulting from the cleavage of the peptide bonds. However, MS/MS spectra typically contain many more peaks. These can result not only from isotope variants and multiply charged replicates of the peptide fragmentation products but also from unknown fragmentation pathways, sample-specific or systematic chemical contaminations or from noise generated by the electronic detection system. The presence of this background complicates spectrum interpretation. Besides dramatically prolonged computation time, it can lead to incorrect protein identification, especially in the case of de novo sequencing algorithms. Here, we present an algorithm for detection and transformation of multiply charged peaks into singly charged monoisotopic peaks, removal of heavy isotope replicates, and random noise. A quantitative criterion for the recognition of some noninterpretable spectra has been derived as a byproduct. The approach is based on numerical spectral analysis and signal detection methods. The algorithm has been implemented in a stand-alone computer program called MS Cleaner that can be obtained from the authors upon request.

Adenosine Triphosphatases↗
PubMed1998

Measurement of R'2 in the presence of multiple spectral components using reference spectrum deconvolution.

A method is described for measuring R'2, the RF reversible contribution to the effective transverse relaxation rate in yellow trabecular marrow, as a means to evaluate trabecular bone structure and density. The method exploits the similarity in spectral composition of the marrow and fat in subcutaneous tissue. Under these conditions the gradient echo envelope of the marrow signal can be regarded as a convolution of a function describing the bone marrow intravoxel line broadening (R'2) with a function expressing chemical shift modulation, which is obtained from the echo envelope of the subcutaneous fat signal in a reference region. Simple division of each of a series of echoes by the reference signal is shown to afford a smooth decay which can be fitted to a model to extract R'2. The method has been evaluated in the upper femur of test subjects and a strong correlation of the thus derived R'2 values with those obtained by the GESFIDE technique is demonstrated. The close correspondence in spectral composition of proximal femur marrow and subcutaneous fat is further illustrated by means of localized spectroscopy. The major potential error source is global inhomogeneity in the reference region which can lead to an underestimation of the demodulation-derived R'2.

Absorptiometry, Photon↗
PubMed2002

Deconvolution of compartmental water diffusion coefficients in yeast-cell suspensions using combined T(1) and diffusion measurements.

An NMR method is presented for measuring compartment-specific water diffusion coefficient (D) values. It uses relaxography, employing an extracellular contrast reagent (CR) to distinguish intracellular (IC) and extracellular (EC) (1)H(2)O signals by differences in their respective longitudinal (T(1)) relaxation times. A diffusion-weighted inversion-recovery spin-echo (DW-IRSE) pulse sequence was used to acquire IR data sets with systematically and independently varying inversion time (TI) and diffusion-attenuation gradient amplitude (g) values. Implementation of the DW-IRSE technique was demonstrated and validated using yeast cells suspended in 3 mM Gd-DTPA(2-) with a wet/dry mass ratio of 3.25:1.0. Two-dimensional (2D) NMR data were acquired at 2.0 T and analyzed using numerical inverse Laplace transformation (2D- and sequential 1D-ILT) and sequential exponential fitting to yield T(1) and water D values. All three methods gave substantial agreement. Exponential fitting, deemed the most accurate and time efficient, yielded T(1):D (relative contribution) values of 304 ms:0.023x10(-5) cm(2)/s (47%) and 65 ms:1.24x10(-5) cm(2)/s (53%) for the IC and EC components, respectively. The compartment-specific D values derived from direct biexponential fitting of diffusion-attenuation data were also in good agreement. Extension of the DW-IRSE method to in vivo models should provide valuable insights into compartment-specific water D changes in response to injury or disease. (c) 2002 Elsevier Science (USA).

Contrast Media↗