Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “deconvolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50Linked to original sources
PubMed1989

Fourier transform infrared spectroscopic investigation of rhodopsin structure and its comparison with bacteriorhodopsin.

FT-IR spectroscopy has been used to investigate the conformation of rhodopsin in bovine rod outer segment membranes, dispersed in aqueous suspension in both 2H2O and H2O. Detailed analysis of the amide I band was made, using second-derivative and deconvolution procedures. The frequency of the major amide I component is consistent with the presence of predominantly alpha-helices within the rhodopsin structure. A spectroscopic change occurs at acidic pH with the membranes in both 2H2O and H2O. The results for the membranes dispersed in H2O at pH 7 were used to estimate a value of 0.67 for w (amide II/amide I intensity ratio in H2O). This value of w gives an estimate of the unexchanged amide protons, in rhodopsin, of 51%. The extent of amide proton exchange at acidic p2H (p2H 5 and 2), in 2H2O was also determined. The conformation of rhodopsin in its unbleached and bleached states was investigated but no significant difference in the secondary structure was observed. A comparison, after second-derivative and deconvolution analysis, of the spectra of rhodopsin with that of bacteriorhodopsin shows that both proteins exhibit a similar number of amide I components. However, with bacteriorhodopsin the amide I band occurs at a higher frequency. Bacteriorhodopsin under similar conditions, in 2H2O, has 20% more unexchanged amide protons than does rhodopsin.

Animals↗
PubMed1989

A thermodynamic study on rA7U7.

Ultraviolet absorbance spectroscopy and differential scanning calorimetry were employed to study the heat-induced helix-to-coil transition of the oligoribonucleotide rA7U7. The analysis of concentration-dependent ultraviolet 'melting' profiles was used to derive the van't Hoff transition enthalpy delta HUVvH (-458 kJ/mol cooperative unit). From the DSC data we calculated the calorimetric transition enthalpy delta Hcal (-412.6 kJ/mol duplex) as well as delta HcalvH (-447.9 kJ/mol cooperative unit). For the size of the cooperative unit we obtained lambda approximately 1. In contrast to this result, by means of statistical numerical deconvolution we show that intermediate states are significantly populated; at the maximum the fraction of these states reaches 25.4% of the total population. Therefore, this DSC-deconvolution technique offers a more appropriate way to register amounts of populated intermediate states which are not sufficient to obtain a value of lambda which is essentially lower than unity.

Calorimetry, Differential Scanning↗
PubMed1995

Interaction of cytochrome c with cardiolipin: an infrared spectroscopic study.

The interactions of cytochrome c (cyt c) with cardiolipin, a major anionic phospholipid of mitochondrial membranes, and dioleoylphosphatidylglycerol (DOPG), have been compared by infrared (IR) spectroscopy. The Fourier self-deconvoluted IR spectra of the lipid carbonyl groups indicate that both cyt c3+ and cyt c2+ perturb and/or dehydrate the interfacial region of cardiolipin bilayers. Only a slight perturbation, if any, is observed in the interfacial region of DOPG bilayers. However, the phosphate head region of DOPG is perturbed by cyt c3+, which was not detected in cardiolipin. The results suggest that cytochrome c in both redox states can partially penetrate into cardiolipin but not into DOPG bilayers. The interaction of cyt c with cardiolipin and DOPG is mainly hydrophobic and electrostatic, respectively. The Fourier self-deconvoluted IR spectra in the amide I region reveal that ca. 10% of the cyt c3+ alpha-helix unfolds to random coil upon binding to cardiolipin bilayers. However, only very slight secondary structural changes, if any, were detected when cyt c3+ binds to DOPG bilayers.

Amides↗
PubMed1991

A protocol for 3D image reconstruction from a single image of an oblique section.

Oblique section 3D reconstruction can produce a 3D image of a sectioned crystal from a single electron micrograph. We describe here in detail a reconstruction protocol applicable to an electron micrograph of an oblique section through a 3D crystal. The protocol is described in six steps: (1) selection criteria for images, (2) preprocessing steps to correct for image defects, (3) determination of unit cell coordinates, (4) interpolation of strip images with correction for image distortions and crystal disorder, (5) production of a crystallographic serial section reconstruction, (6) correction for skewed sampling to produce an oblique section reconstruction. In addition, we explore Wiener filter deconvolution of the section thickness. We describe a method for determining the section thickness by comparing data from projections of the oblique section reconstruction with corresponding data from a thick longitudinal section. Several schemes for Wiener filter deconvolution are described that differ in the way information on the signal-to-noise ratio is used in the filter.

Animals↗
PubMedDate not supplied

3D reconstruction from the Fourier transform of a single superlattice image of an oblique section.

An image of a thin oblique section through a 3D crystal exhibits superlattice periods much larger than the unit cell dimensions of the crystal. Within a superlattice period the contents of the unit cell of the 3D crystal are sampled at different levels, so that a 2D image of the section contains 3D information about the crystal. The 2D Fourier transform of an electron micrograph of such an oblique section thus exhibits superlattice spots, which provide an estimate of the 3D transform of the original crystal. The strengths of the observed spots are reduced from their true values by convolution with a weighting function that depends on section thickness. A method is described that uses phase relationships among symmetry-related structure factors to determine the section thickness and hence the weighting function. Wiener filter deconvolution of the section thickness is performed, in which the filter level is set by the ratio of diffraction spot intensity to background intensity. From the deconvoluted set of structure factors a 3D map of the unit cell can be computed by a standard crystallographic Fourier program. The approach is illustrated with images of oblique sections through rigor insect flight muscle.

Animals↗
PubMed1996

Transmission dosimetry with a liquid-filled electronic portal imaging device.

PURPOSE: To assess the accuracy of transmission dose rate measurements for various phantom-detector geometries, performed with an electronic portal imaging device (EPID) and to compare these transmission dose rate values with exit dose rate data. METHODS AND MATERIALS: Transmission dose rate values on the central beam axis and beam profiles were measured with an EPID consisting of a matrix of liquid-filled ionization chambers. These data were compared with transmission and exit dose rate values, obtained using air-filled ionization chambers for a number of field sizes, phantom thickness, and phantom-detector distances. Various homogeneous and inhomogeneous phantoms were applied. RESULTS: The increase in dose rate with field size is larger for the EPID than in air, due to the larger amount of side scatter in the EPID. The difference has been taken into account by a deconvolution of the EPID images. An additional build-up layer on top of the commercial device is needed to reach dose maximum at the liquid ionization chambers for photon beam energies higher than about 4 MV. The transmission off-axis ratios (OAR) determined with the EPID and in air agreed within 2% for all tested cases, after deconvolution of the EPID signal. The agreement between the EPID-and exit-OAR decreased with increasing phantom-detector distance and the presence of inhomogeneities. For a phantom-detector distance of about 10 cm, the EPID- and exit-OARs agree within 2.5%. The difference could be up to 8% for an air inhomogeneity and a phantom-detector distance of 30 cm. CONCLUSIONS: The difference between EPID measurements and measurements in air can be explained by side scatter effects in the EPID and lack of adequate buildup, and can easily be taken into account. The loss of scatter compared with the situation at the exit side of the phantom explains the difference between transmission and exit dose values. At short phantom-detector distances, good agreement exists between transmission and exit dose rate. This implies that at this distance, the EPID can be used for simple comparison with exit dose calculations during patient treatments. At larger distances, more sophisticated conversion methods are required.

Models, Anatomic↗
PubMed1987

Mathematical analysis of VIIIth nerve cap with a linearly-fitted experimental unit response.

The compound action potential (CAP) recorded at the round window has for some time been investigated in order to determine the underlying temporal spike sequence: the firing probability density (FPD) function of the fibres. Charlet de Sauvage et al. [(1980) Hear. Res. 2, 343-346; (1983) J. Acoust. Soc. Am. 73, 616-627] have previously described a close estimate of the far-field unit response (UR) by presenting to the ear a transient electrical stimulation combined with an acoustical masking noise. A linear model of UR, free of noise or extrinsic potentials and based on both experimental data and on the dipole principle of Teas et al. [(1962) J. Acoust. Soc. Am. 34, 1438-1459], was proposed [(1985) Hear. Res. 18, 121-125]. Using the UR model, deconvolutions were performed on CAPs recorded in various conditions of stimulation and of cochlear pathologies in the guinea pig. The principal findings were: (1) a plateau was observed in the amplitude function around 60-70 dB above normal threshold both for click-evoked CAPs and for the corresponding FPDs; (2) FPDs resulting from the deconvolution of high-frequency derived responses showed 2 main peaks with a 0.7 ms interval followed by a second homologous pair with lower amplitude. Convolution computations confirmed the need for the second set with peaks 2 and 3 being only 0.3 ms apart. These findings are interpreted in terms of mechanical excitation pattern.

Animals↗
PubMed1983

Novel applications of multichannel spectroscopy in pharmaceutical analysis.

Multichannel detectors based on the linear photodiode array, the silicon vidicon tube and charge coupled (or injection) devices are reviewed with reference to their applications in analytical spectroscopy and high-performance liquid chromatography (HPLC). The use of computer-aided techniques, including second derivative spectroscopy and spectral deconvolution methods, for the multichannel spectroscopic analysis of pharmaceuticals is discussed, and applications are reviewed in clinical chemistry, enzyme analysis and studies on aromatic amino acids in proteins. In HPLC, the principles and applications of digital algorithms for validation of peak homogeneity are considered, with reference to spectral suppression, spectral deconvolution, absorbance ratio and the second derivative of the elution profile. The isometric projections of (A, lambda, t) data, and their cartographically equivalent contour plots, are discussed and the impact of multicolour graphics is assessed. The implications of two-dimensional multichannel detectors for detection of luminescence radiation are considered in the context of analytical spectroscopy, and detection in both HPLC and thin-layer chromatography. The potential contribution of charge coupled and charge injection devices as the next generation of multichannel detectors is considered.

Journal Article↗
PubMed2004

The effect of varying user-selected input parameters on quantitative values in CT perfusion maps.

RATIONALE AND OBJECTIVES: Deconvolution-based software can be used to calculate quantitative maps of cerebral blood flow (CBF), cerebral blood volume (CBV), and mean transit time (MTT) from first-pass computed tomography perfusion (CTP) datasets. The application of this software requires the user to select multiple input variables. The purpose of this study was to investigate the degree to which both major and minor variations of these user-defined inputs would affect the final quantitative values of CBF, CBV, and MTT. MATERIALS AND METHODS: A neuroradiologist constructed CBF, CBV, and MTT maps using standard methodology with commercially available software (GE Functool Version 1.9s) from CTP datasets of three acute stroke patients. Each map was reconstructed multiple times by systematically and independently varying the following parameters: postenhancement and preenhancement cutoff values, arterial and venous region-of-interest (ROI) placement, and arterial and venous ROI size. The resulting quantitative CTP values were compared using identical ROIs placed at the infarct core. RESULTS: Major variations of either arterial ROI placement or arterial and venous ROI size had no significant effect on the mean CBF, CBV, and MTT values at the infarct core (p > .05). Even minor variations, however, in the choice of venous ROI placement or in pre- and postenhancement cutoff values significantly altered the quantitative values for each of the CTP maps, by as much as threefold. CONCLUSION: Even minor variations of user-defined inputs can significantly influence the quantitative, deconvolution-based CTP map values of acute stroke patients. Although quantitation was robust to the choice of arterial ROI placement and arterial or venous ROI size, it was strongly dependent on the choice of venous ROI location and pre- and postenhancement cut-off values. Awareness of these results by clinicians may be important in the creation of quantitatively accurate CTP maps.

Adult↗
PubMed2006

Spectral and kinetic resolution of the bc1 complex components in situ: a simple and robust alternative to the traditional difference wavelength approach.

The kinetics of the cytochrome (cyt) components of the bc(1) complex (ubiquinol: cytochrome c oxidoreductase, Complex III) are traditionally followed by using the difference of absorbance changes at two or more different wavelengths. However, this difference-wavelength (DW) approach is of limited accuracy in the separation of absorbance changes of components with overlapping spectral bands. To resolve the kinetics of individual components in Rhodobacter sphaeroides chromatophores, we have tested a simplified version of a least squares (LS) analysis, based on measurement at a minimal number of different wavelengths. The success of the simplified LS analysis depended significantly on the wavelengths used in the set. The "traditional" set of 6 wavelengths (542, 551, 561, 566, 569 and 575 nm), normally used in the DW approach to characterize kinetics of cyt c(tot) (cyt c(1)+cyt c(2)), cyt b(L), cyt b(H), and P870 in chromatophores, could also be used to determine these components via the simplified LS analysis, with improved resolution of the individual components. However, this set is not sufficient when information about cyts c(1) and c(2) is needed. We identified multiple alternative sets of 5 and 6 wavelengths that could be used to determine the kinetics of all 5 components (P870 and cyts c(1), c(2), b(L), and b(H)) simultaneously, with an accuracy comparable to that of the LS analysis based on a full set of wavelengths (1 nm intervals). We conclude that a simplified version of LS deconvolution based on a small number of carefully selected wavelengths provides a robust and significant improvement over the traditional DW approach, since it accounts for spectral interference of the different components, and uses fewer measurements when information about all five individual components is needed. Using the simplified and complete LS analyses, we measured the simultaneous kinetics of all cytochrome components of bc(1) complex in the absence and presence of specific inhibitors and found that they correspond well to those expected from the modified Q-cycle. This is the first study in which the kinetics of all cytochrome and reaction center components of the bc(1) complex functioning in situ have been measured simultaneously, with full deconvolution over an extended time range.

Electron Transport Complex III↗
PubMed2004

Quantitative spectroscopy analysis of prokaryotic cells: vegetative cells and spores.

Multiwavelength ultraviolet/visible (UV-Vis) spectra of microorganisms and cell suspensions contain quantitative information on properties such as number, size, shape, chemical composition, and internal structure of the suspended particles. These properties are essential for the identification and classification of microorganisms and cells. The complexity of microorganisms in terms of their chemical composition and internal structure make the interpretation of their spectral signature a difficult task. In this paper, a model is proposed for the quantitative interpretation of spectral patterns resulting from transmission measurements of prokaryotic microorganism suspensions. It is also demonstrated that different organisms give rise to spectral differences that may be used for their identification and classification. The proposed interpretation model is based on light scattering theory, spectral deconvolution techniques, and on the approximation of the frequency dependent optical properties of the basic constituents of living organisms. The quantitative deconvolution in terms of the interpretation model yields critical information necessary for the detection and identification of microorganisms, such as size, dry mass, dipicolinic acid concentration, nucleotide concentration, and an average representation of the internal scattering elements of the organisms. E. coli, P. agglomerans, B. subtilis spores, and vegetative cells and spores of Bacillus globigii are used as case studies. It is concluded that spectroscopy techniques coupled with effective interpretation models are applicable to a wide range of cell types found in diverse environments.

Algorithms↗
PubMed2004

Vacuum-ultraviolet circular dichroism study of saccharides by synchrotron radiation spectrophotometry.

Vacuum-ultraviolet circular dichroism (VUVCD) spectra of five monosaccharides (D-glucose, D-mannose, D-galactose, D-xylose, and D-lyxose) and five disaccharides (maltose, isomaltose, cellobiose, gentiobiose, and lactose) were measured to 160 nm using a synchrotron-radiation VUVCD spectrophotometer in aqueous solution under high vacuum at 25 degrees C. Most of the saccharides show a positive peak with some shoulders at around 170 nm, except for D-galactose and lactose, which show two distinct negative peaks at around 165 and 177 nm. These spectra are influenced by such structural factors as alpha and beta anomers at C-1, axial and equatorial hydroxyl groups at C-2 and C-4, trans (T) and gauche (G) conformations of the hydroxymethyl group at C-5, and the type of glycosidic linkage. Deconvolution of the VUVCD spectra of D-glucose, D-mannose, and D-galactose into six independent Gaussian components for alpha-GG, alpha-GT, alpha-TG, beta-GG, beta-GT, and beta-TG conformations suggests that the alpha anomer has red-shifted spectra relative to the beta anomer, and that GG and GT conformations have positive and negative circular dichroism signs, respectively, while the sign for TG conformation is anomer dependent. These speculations from the deconvolution analyses are also supported by the VUVCD spectra of disaccharides. These results give new insight into the equilibrium conformations of saccharides, demonstrating the usefulness of synchrotron-radiation VUVCD spectroscopy.

Carbohydrate Conformation↗
PubMed2004

PNA-encoded protease substrate microarrays.

Our current understanding of the role and regulation of protease activity in normal and pathogenic processes is limited by our ability to measure and deconvolute their enzymatic activity. To address this limitation, an approach was developed that utilizes rhodamine-based fluorogenic substrates encoded with PNA tags. The PNA tags address each of the substrates to a predefined location on an oligonucleotide microarray through hybridization, thus allowing the deconvolution of multiple signals from a solution. A library of 192 protease substrates was prepared by split and mix combinatorial synthesis. The methodology and validation of this approach for profiling proteolytic activity from single proteases and from those in crude cell lysates as well as clinical blood samples is described.

Humans↗
PubMed2004

High-throughput automated post-processing of separation data.

The development of an efficient method for high-throughput analysis of multiple electropherograms or chromatograms collected in series is presented. The method, encoded in a computer program designated "Cutter", utilizes batch processing for determining chromatographic figures of merit (CFOM) including peak centroid times, heights, areas, signal-to-noise ratios (S/N), variance (sigma2), skew, excess, and plate number (N) across a set of separations collected serially. The software was validated using simulated data with varying S/N, skew, and excess. The accuracy of the analysis was comparable to or improved over commercial software with area calculation relative errors (RE) below 5% for simulated data with S/N = 5. File sets containing 1300 electropherograms were analyzed in 5 min, representing a nearly 200-fold reduction in analysis time from other methods. Incorporated within the program is a novel method for automated peak deconvolution using an Empirically Transformed Gaussian function. Area measurements of deconvoluted peaks were within 3% of the true value of a simulated data set with S/N = 5 and resolution (R(S)) = 1 for equivalent peaks, and within 10% when the ratio of the overlapped peak heights was 10:1.

Automation↗
PubMed2005

Characterization and pattern recognition of oil-sand naphthenic acids using comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry.

Oil-sand naphthenic acids (NAs) are organic wastes produced during the oil-sand digestion and extraction processes and are very difficult to separate and analyze as individual components due to their complex compositions. A comprehensive two-dimensional gas chromatography/time of flight mass spectrometry (GC x GC/TOF-MS) system was applied for the characterization of two commercial mixtures of naphthenic acids (Fluka and Acros) and a naphthenic acid sample extracted from the Syncrude tailings. Contour plots of chromatographic distributions of different Z homologous series of the Fluka, Acros and Syncrude NAs were constructed using fragment ions that were characteristic of the NA's molecular structures. Well-ordered patterns were observed for NAs of Z= 0 and -2 which corresponded to acyclic acids and monocyclic acids, respectively. For NAs of Z= -4, -6, and -8, specific zones were observed which would allow the pattern recognition of these NAs obtained from different origins. As expected, gas chromatographic retention times increase with the number of the carbons and the number of rings in the molecules. Little signal was obtained for NAs with Z numbers of -10, or lower. Deconvoluted mass spectra of various NA isomers were derived from the reconstructed GC x GC chromatogram, permitting detailed structural elucidations for NAs in the future. The current study demonstrated that the combination of GC x GC and the TOF-MS is a powerful to identify origins of the NAs in an effective manner. GC x GC/TOF-MS alone, however, may not be enough to characterize each individual isomer in a complex mixture such as NAs. The use of mass deconvolution software followed by library search have thus become necessary to separate and study the mass spectrum of each individual NA component, allowing a detailed identification of the toxic components within the NAs mixture.

Carboxylic Acids↗
PubMed2004

Regiospecificity in deuterium labeling determined by mass spectrometry.

Several mass spectrometry methods were explored to determine the regiospecificity of deuterium substitutions in hydrocarbon mixtures. The case investigated in this work was that of ethane mixtures obtained by catalytic HD exchange between either C(2)H(6) and D(2) or C(2)D(6) and H(2) over platinum surfaces. A total of ten isotopologs are possible, and were indeed detected in all cases. Deconvolution of low-resolution mass spectra was found sufficient to determine the composition of the gas mixtures in terms of the total number of deuterium substitutions, but not to identify symmetric versus asymmetric substitutions in the C(2)D(2)H(4), C(2)D(3)H(3), and C(2)D(4)H(2) products. High-resolution mass spectrometry allowed the separation of the intensities due to C(2)X(4)(+) fragments from those from molecular C(2)X(6)(+) signals (X = H or D), and with that for a more accurate determination of the composition of the mixtures. Relative probabilities were determined for the symmetric versus asymmetric removal of X(2) from C(2)X(6)(+) ions and for isotope scrambling in the mass spectrometer, and with that information fairly good cracking patterns were then calculated for the C(2)X(4)(+) fragments produced by each individual pure C(2)X(6) isotopologue. However, total deconvolution of all ten components in the ethane mixtures obtained by HD exchange catalysis was beyond the experimental accuracy of the measurements. Tandem mass spectrometry/collision-induced decomposition mass spectrometry (MS/CID-MS) proved more useful for this task. In particular, it was possible to determine the proportion of symmetric versus asymmetric double HD exchange in samples for which the total ethane-d(2) (in the case of C(2)H(6) + D(2)) or ethane-d(4) (with C(2)D(6) + H(2)) amounted to only approximately 3% on the ethane mix. A comparison with other analytical methods, NMR in particular, is provided.

Journal Article↗
PubMed2006

Mass spectrometric separation and quantitation of overlapping isotopologues. H2O/HOD/D2O and H2Se/HDSe/D2Se mixtures.

Three conceptually different mathematical methods are presented for accurate mass spectrometric determination of H2O/HOD/D2O and H2Se/HDSe/D2Se concentrations from mixtures. These are alternating least-squares, weighted two-band target entropy minimization, and a statistical mass balance model. The otherwise nonmeasurable mass spectra of partially deuterated isotopologues (HOD and HDSe) are mathematically constructed. Any recorded isotopologue mixture mass spectra are then deconvoluted by least-squares into their components. This approach is used to study the H2O/D2O exchange reaction, and is externally validated gravimetrically. The H2O/D2O exchange equilibrium constant is also measured from the deconvoluted 70 eV electron impact GC/MS data (K = 3.85 +/- 0.03).

Algorithms↗
PubMed2006

Improving mass accuracy of high performance liquid chromatography/electrospray ionization time-of-flight mass spectrometry of intact antibodies.

The glycosylation profile of intact antibody due to the galactose and fucose heterogeneity in the N-linked sugars was determined with instrument resolution of 5000 and 10,000. After deconvolution of electrospray ionization mass spectra to complete convergence, several extra peaks appeared in addition to the peaks observed in the original mass spectra. The artificial peaks were avoided if deconvolution was stopped after a smaller number of iterations. A standard antibody was used as an external calibrant to minimize mass measurement errors during long-period experiments. Precision of four consecutive LC/MS measurements of the same antibody was 10 ppm (+/-1.5 Da). By using this approach, the masses of 11 intact antibodies were measured. All antibodies containing N-terminal glutamines had a negative mass shift due to the formation of pyroglutamate (-17 Da). Although the pyroglutamate variant of intact antibody was not resolved from the unmodified variant, this modification led to a mass shift proportional to the percentage of N-terminal pyroglutamate. By accurately measuring the mass shift we were able to quantify the abundance of pyroglutamic acid on intact antibodies. Mass accuracy in measuring different antibodies was below 30 ppm (+/-4 Da). The accurate mass measurement can be an effective tool for monitoring chemical degradations in therapeutic antibodies.

Antibodies, Monoclonal↗