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PubMed2001

Latent semantic structure indexing (LaSSI) for defining chemical similarity.

A novel method for computing chemical similarity from chemical substructure descriptors is described. This new method, called LaSSI, uses the singular value decomposition (SVD) of a chemical descriptor-molecule matrix to create a low-dimensional representation of the original descriptor space. Ranking molecules by similarity to a probe molecule in the reduced-dimensional space has several advantages over analogous ranking in the original descriptor space: matching latent structures is more robust than matching discrete descriptors, choosing the number of singular values provides a rational way to vary the "fuzziness" of the search, and the reduction in the dimensionality of the chemical space increases searching speed. LaSSI also allows the calculation of the similarity between two descriptors and between a descriptor and a molecule.

Algorithms↗

PubMed2001

Reduction and alkylation of proteins in preparation of two-dimensional map analysis: why, when, and how?

The standard procedure adopted up to the present in proteome analysis calls for just reduction prior to the isoelectric focusing/immobilized pH gradient (IEF/IPG) step, followed by a second reduction/alkylation step in between the first and second dimension, in preparation for the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) step. This protocol is far from being optimal. It is here demonstrated, by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry, that failure to reduce and alkylate proteins prior to any electrophoretic step (including the first dimension) results in a large number of spurious spots in the alkaline pH region, due to "scrambled" disulfide bridges among like and unlike chains. This series of artefactual spots comprises not only dimers, but an impressive series of oligomers (up to nonamers) in the case of simple polypeptides such as the human alpha- and beta-globin chains, which possess only one (alpha-) or two (beta-) -SH groups. As a result, misplaced spots are to be found in the resulting two-dimensional (2-D) map, if performed with the wrong protocol. The number of such artefactual spots can be impressively large. In the case of analysis of complex samples, such as human plasma, it is additionally shown that failure to alkylate proteins results in a substantial loss of spots in the alkaline gel region, possibly due to the fact that these proteins, at their pI, regenerate their disulfide bridges with concomitant formation of macroaggregates which become entangled with and trapped within the polyacrylamide gel fibers. This strongly quenches their transfer in the subsequent SDS-PAGE step.

Alkylation↗

PubMed1988

[Correlation of left ventricular outflow obstruction with mitral regurgitation].

Our previous study of mitral regurgitation in obstructive hypertrophic cardiomyopathy suggested that left ventricular outflow obstruction due to systolic anterior motion of the distal residual anterior mitral leaflet may hydrodynamically induce mid-systolic mitral regurgitation. To test this hypothesis, we examined whether drug-induced left ventricular outflow obstruction in dogs might cause mitral regurgitation. Dobutamine, 20-60 micrograms/kg/min, induced the obstruction due to mitral systolic anterior motion with mitral-septal contact in 11 of 18 dogs. Pulsed Doppler and contrast echocardiography demonstrated that mitral regurgitation was concomitantly induced in the 11 dogs. The regurgitation was prominent during mid-systole from the onset to the end of mitral-septal contact. Two-dimensional echocardiography showed reduction of the mitral annular dimension and anterior shifts of the mitral valve coaptation during drug infusion in the 11 dogs. Accordingly, the distal portion of the mitral valve, especially of its anterior leaflet, became residual, and moved anteriorly in early systole and protruded into the outflow tract during mid-systole. Catheter-tip pressure recordings simultaneous with two-dimensional echocardiographic observation revealed that the outflow pressure gradient occurred across the protruding distal residual mitral valve. The onset and the end of the pressure gradient were nearly simultaneous with those of the mitral-septal contact. After cessation of the infusion, the mid-systolic mitral regurgitation disappeared together with the obstruction. These results indicate a close relationship between left ventricular outflow obstruction and mid-systolic mitral regurgitation, and strongly support the hypothesis that the obstruction due to systolic anterior motion of the distal residual anterior mitral leaflet is responsible for mitral regurgitation.

Animals↗

PubMed2006

Reduction of proteins during sample preparation and two-dimensional gel electrophoresis of woody plant samples.

Protein extraction procedure and the reducing agent content (DTT, dithioerythritol, tributyl phosphine and tris (2-carboxyethyl) phosphine (TCEP)) of the sample and rehydration buffers were optimised for European beech leaves and roots and Norway spruce needles. Optimal extraction was achieved with 100 mM DTT for leaves and needles and a mixture of 2 mM TCEP and 50 mM DTT for roots. Performing IEF in buffers containing hydroxyethyldisulphide significantly enhanced the quality of separation for all proteins except for acidic root proteins, which were optimally focused in the same buffer as extracted.

Buffers↗

PubMed2006

The dynamic structure underlying subthreshold oscillatory activity and the onset of spikes in a model of medial entorhinal cortex stellate cells.

Medial entorhinal cortex layer II stellate cells display subthreshold oscillations (STOs). We study a single compartment biophysical model of such cells which qualitatively reproduces these STOs. We argue that in the subthreshold interval (STI) the seven-dimensional model can be reduced to a three-dimensional system of equations with well differentiated times scales. Using dynamical systems arguments we provide a mechanism for generations of STOs. This mechanism is based on the "canard structure," in which relevant trajectories stay close to repelling manifolds for a significant interval of time. We also show that the transition from subthreshold oscillatory activity to spiking ("canard explosion") is controlled in the STI by the same structure. A similar mechanism is invoked to explain why noise increases the robustness of the STO regime. Taking advantage of the reduction of the dimensionality of the full stellate cell system, we propose a nonlinear artificially spiking (NAS) model in which the STI reduced system is supplemented with a threshold for spiking and a reset voltage. We show that the synchronization properties in networks made up of the NAS cells are similar to those of networks using the full stellate cell models.

Action Potentials↗

PubMed1997

Radiofrequency volumetric reduction of the tongue. A porcine pilot study for the treatment of obstructive sleep apnea syndrome.

STUDY OBJECTIVE: To investigate, in an animal model, the feasibility of radiofrequency (RF) volumetric tongue reduction for the future purpose of determining its clinical applications in obstructive sleep apnea syndrome (OSAS). DESIGN: The study was performed in three stages, one in vitro bovine stage and two in vivo porcine stages. The last stage was a prospective investigation with histologic and volumetric analyses to establish outcomes. SETTING: Laboratory and operating room of veterinary research center. PARTICIPANTS: A homogeneous population of porcine animal models, including seven in stage 2 and 12 in stage 3. INTERVENTION: RF energy was delivered by a custom-fabricated needle electrode and RF generator to the tongue tissue of both the in vitro and in vivo models. MEASUREMENTS AND RESULTS: Microultransonic crystals were used to measure three-dimensional changes (volumetric reduction). Lesion size correlated well with increasing RF energy delivery (Sperman correlation coefficient of 0.986; p = 0.0003). Histologic assessments done serially over time (1 h through 3 weeks) showed a well-circumscribed lesion with a normal healing progression and no peripheral damage to nerves. Volumetric analysis documented a very mild initial edematous response that promptly tapered at 24 h. At 10 days after RF, a 26.3% volume reduction was documented at the treatment site (circumscribed by the microultrasonic crystals). CONCLUSION: RF, in a porcine animal model, can safely reduce tongue volume in a precise and controlled manner. Further studies will validate the use of RF in the treatment of OSAS.

Animals↗

PubMed1995

The human MUC2 mucin apoprotein appears to dimerize before O-glycosylation and shares epitopes with the 'insoluble' mucin of rat small intestine.

Rabbit antiserum against a synthetic peptide corresponding to a tandemly repeated amino acid sequence in the human intestinal mucin apoprotein MUC2 was used in immunoprecipitation to study the biosynthesis of MUC2 in the colon-carcinoma cell line LS 174T. Under non-reducing conditions, two bands were precipitated, the smaller with an apparent size of about 700 kDa on SDS/PAGE. When analysed by two-dimensional electrophoresis after reduction, the larger band migrated to the same position as the smaller band and was interpreted as a putative disulphide-bond-stabilized dimer. Pulse-chase experiments showed only the monomer after 5 min and the appearance of the putative dimer after 30 min. The MUC2 apoprotein was also precipitated by antisera against the HF-deglycosylated peptides of the two highly glycosylated domains of the 'insoluble' mucin complex of rat small intestine [Carlstedt, Herrmann, Karlsson, Sheehan, Fransson and Hansson (1993) J. Biol. Chem. 268, [18771-18781]. Endoprotease Lys-C cleavage of the immunopurified apoprotein gave a large fragment of about 250 kDa that was detected by both the antiserum against the MUC2 tandem repeat and one of the glycopeptide antisera. This supports the view that the 'insoluble' mucin of rat small intestine is encoded by the Muc2 gene, as recently indicated by a partial cDNA sequence [Hansson, Baeckström, Carlstedt and Klinga-Levan (1994) Biochem. Biophys. Res. Commun. 198, 181-190] and that parts of the apoprotein are conserved between the species. A lectin from the snail Helix pomatia that detects terminal alpha-GalNAc residues did not bind to the monomer or putative dimer, suggesting that O-glycosylation starts after dimerization. The results indicate that the biosynthetic pathway of the MUC2 mucin may be similar to that of the von Willebrand factor with which MUC2 shares sequence similarities at its C- and N-termini.

Amino Acid Sequence↗

PubMed1984

Quantitative analysis and pattern recognition of two-dimensional electrophoresis gels.

We describe a system, both hardware and software, that provides quantitative analysis and data reduction of two-dimensional electrophoresis gels. Image-analysis techniques are used to determine spot intensities and to match spot patterns among many gels. A pattern-recognition program is used to extract the useful information contained in the spot lists. The application of this technology to a study of supernates from bacterial cultures is described.

Bacterial Proteins↗

PubMed1992

Analyzing the normal mode dynamics of macromolecules by the component synthesis method.

This paper presents a general method for studying the harmonic dynamics of large biomolecules and molecular complexes. The performance and accuracy of the method applied to a number of molecules are also reported. The basic approach of the method is to divide a macromolecule into a number of smaller components. The local normal modes of the components are first calculated by treating individual components and the interactions between nearest neighboring components. The physical displacements of all atoms are then represented in the local normal mode space, in which a selected range of high-frequency local modes is neglected. The equation of motion of the molecule in the local normal mode space will then have a smaller dimension, and consequently the normal modes of the whole structure, particularly for large molecules, can be solved much more easily. The normal modes of two polypeptides--(Ala)6 and (Ala)12--and a double-helical DNA--d(ATATA).d(TATAT)--are analyzed with this method. Reductions on the dimensions of harmonic dynamic equations for these molecules have been made, with the fraction of the deleted high-frequency modes ranging from 1/2 to 5/6. The calculated low-frequency normal modes are found to be very accurate as compared to the exact solutions by standard procedure. The major advantage of the present approach on macromolecule harmonic dynamics is that the reduction on the dimensionality of the eigenvalue problems can be varied according to the size of molecules, so the method can be easily applied to large macromolecules with controlled accuracy.

DNA↗

PubMed2006

Application of multivariate statistical methods to water quality assessment of the watercourses in Northwestern New Territories, Hong Kong.

Multivariate statistical methods, i.e., cluster analysis (CA) and discriminant analysis (DA), were used to assess temporal and spatial variations in the water quality of the watercourses in the Northwestern New Territories, Hong Kong, over a period of five years (2000-2004) using 23 parameters at 23 different sites (31,740 observations). Hierarchical CA grouped the 12 months into two periods (the first and second periods) and classified the 23 monitoring sites into three groups (group A, group B, and group C) based on similarities of water quality characteristics. DA provided better results with great discriminatory ability for both temporal and spatial analysis. DA also provided an important data reduction because it only used six parameters (pH, temperature, five-day biochemical oxygen demand, fecal coliforms, Fe, and Ni) for temporal analysis, affording about 84% correct assignations, and seven parameters (pH, ammonia-nitrogen, nitrate nitrogen, fecal coliforms, Fe, Ni, and Zn) for spatial analysis, affording more than 90% correct assignations. Therefore, DA allowed a reduction in the dimensionality of the large data set and indicated a few significant parameters that were responsible for most of the variations in water quality. Thus, this study demonstrated that the multivariate statistical methods are useful for interpreting complex data sets in the analysis of temporal and spatial variations in water quality and the optimization of regional water quality monitoring network.

Discriminant Analysis↗

PubMed1982

A morphometric study of cultured rat cerebral synapses exposed to different cationic media.

Quantitative techniques have been applied to compare the effects of high-K+, Mg2+ and Li+ media on the ultrastructure of cultured synapses alongside Na+-incubated controls. The explant cultures were prepared from 18-day-old embryonic rat cerebral cortices and maintained for 19 days in vitro. K+ -Stimulation for 25 min resulted in an increase in the mean perimeter and area of presynaptic terminals. Of these, the perimeter increase was the more pronounced, as indicated by a decrease in the value of the two-dimensional form factor. Reductions were also observed in the number of synaptic vesicles per presynaptic terminal, in the vesicle-terminal area ratio and in the synaptic vesicle density in an area adjacent to the presynaptic membrane, the latter two parameters being in positive linear correlation. The frequency of presynaptic cisternal/vacuolar profiles increased, and the synaptic curvature shifted in a positive direction. Synaptic length did not change following K+-exposure. Qualitative assessment indicated the presence of a network subjacent to the post-synaptic thickening and swelling of the postsynaptic ending after K+-stimulation. Incubation and fixation in Mg2+-media of two concentrations resulted in an increase in the number and area ratio of synaptic vesicles per terminal, and an elevation in the synaptic vesicle density in the higher Mg2+ concentration medium. Li+-treatment reduced the number of synaptic vesicles per terminal, the vesicle-terminal area ratio, and the vesicle density in the vicinity of the presynaptic membrane, while the synaptic curvature shifted in the positive direction. These changes were less pronounced than those characteristic of synapses in the K+ medium.

Animals↗

PubMed1985

Tensorial computer model of gaze--I. Oculomotor activity is expressed in non-orthogonal natural coordinates.

The central nervous system expresses its function in natural frames of reference. A most conspicuous feature of such frames is their non-orthogonality. Gaze stabilization and, in particular, the sensorimotor transformations performed by the vestibulo-ocular reflex, are prime examples of such general coordinate transformations between and within multidimensional non-orthogonal frames. Since such operations can be described by tensor formalisms in an abstract manner, this methodology is applied here to develop a tensorial computer model of gaze stabilization. The representation of sensorimotor transformations by a reference-frame independent method obviates the necessity to simplify the intrinsic coordinate systems either by a reduction of the dimensionality or by a presumption of orthogonality. The frames of reference intrinsic to vestibulo-ocular reflex transformation (the vestibular semicircular canals and extraocular muscles) as well as the covariant character of the sensory input and the contravariant character of the motor output are physically obvious. A model built on these intrinsic systems of coordinates first serves to quantitate the degree of non-orthogonality in the extraocular muscle system, and thus to demonstrate both the necessity and the applicability of representing them by a formalism suitable for non-orthogonal systems, such as tensor network theory. The actual non-orthogonality of the gaze-stabilization system can be quantitated on the basis of the difference of covariant and contravariant expressions as follows. Tensor network theory describes sensorimotor transformations by employing a covariant embedding procedure. This, however, yields a covariant intention-type motor vector. If the central nervous system were to transmit these sensory-type components directly to the extraocular muscle motor mechanism, an error-angle would occur since covariants do not physically compose the intended movement. The error in every direction of gaze would be zero only if the extraocular muscle system would constitute an orthogonal set of rotation axes. Otherwise, the error, called refraction angle, is a measure of non-orthogonality. The complexity of the quantitation of non-orthogonality is compounded by the fact that these rotation axes change with the moving eye. Calculation of eye movements, executed both by covariant and contravariant vectors from primary and secondary eye positions, is based on the simplest assumption that the central nervous system establishes the covariant-contravariant transformation in the retinal tangent plane.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed2005

Signal identification in NMR spectra with coupled evolution periods.

Novel multidimensional NMR experiments rely on modified time-domain sampling schemes to provide significant savings of experimental time. Several approaches are based on the coupling of evolution times resulting in a reduction of the dimensionality of the recorded spectra, and a concomitant saving of experimental time. We present a consistent and general tool, called EVOCOUP, for the analysis of these reduced dimensionality spectra. The approach is flexible in the sense that the input can consist of various forms of reduced dimensionality spectra, that any piece of information can be removed (provided enough information is left), e.g., signals undetectable due to poor signal-to-noise or covered by artifacts, and that it can be applied to spectra involving any number of nuclei. The use of a general optimization procedure and an appropriate target function provides for a robust approach with well-defined results and ensures optimal use of redundant information normally present in the input. Spectral overlap in the directly detected dimension is resolved in a fully automated manner, avoiding the assessment of signal quality and its use in combinatorial trials. The positions of all peaks in a corresponding full-dimensional spectrum are obtained without need for reconstruction of this spectrum. In a systematic analysis of a complete spectrum recorded for the 14 kDa protein azurin and involving five different nuclei, only four spin systems were missed and no false spins systems were detected.

Artifacts↗

PubMed2005

Fully-automated detection of cerebral water content changes: study of age- and gender-related H2O patterns with quantitative MRI.

We present a simple and robust method for the automated image analysis of quantitative cerebral water content maps acquired with MRI. The method is based on a new approach for the absolute and quantitative mapping of water content in vivo. Water content maps were automatically segmented into grey and white matter by employing the quantitative T1 information acquired as part of the water content mapping procedure. Based on the segmented maps, twenty-two parameters sensitive to both absolute water content and its spatial organisation are automatically extracted without user interaction. The parameters include, amongst others, absolute water content in grey and white matter and spatial asymmetries of the cerebral water content distribution. Significant age- and gender-related changes in the parameters determined were observed in a study of forty-four healthy subjects. Most notably, the grey matter water content decreases at a rate of 0.034%/year for females between the 3rd and 8th decade of life, whilst a much stronger decrease is observed in males which sets in after the 5th decade of life. In addition, female grey matter water content is, on average, 1.2% higher than the respective male grey matter water content. In contrast to the heterogeneity observed in grey matter, no significant physiological variation was observed for white matter water content. In addition to absolute grey matter water content, characteristic age- and gender-specific variations were also observed in most of the other variables. To check the potential loss of information associated with the large reduction of the dimensionality of the dataset to 22 parameters only, the age and gender of each individual subject were predicted by employing robust linear discriminant analysis based on only the determined twenty-two variables. The median deviation between predicted and real age was 6.3 years resulting in a high correlation coefficient between both values (r = 0.69). Gender is correctly predicted in 68.2% of all cases which improves to 87.5% when age-dependent effects are first corrected, demonstrating the high information content present in the variables even though the dimension of the dataset was significantly reduced. These results form the baseline for future studies of cerebral pathology. The method presented is fully automated, robust and flexible, making it an ideal tool for routine application in both neuroscientific studies and clinical diagnosis based on the quantitative measurement of cerebral water content.

Adult↗

PubMed1996

Iatrogenic myocardial edema: increased diastolic compliance and time course of resolution in vivo.

BACKGROUND: Perfusion-induced edema reduces diastolic compliance in isolated hearts, but this effect and the time for edema to resolve after blood reperfusion have not been defined in large animals. METHODS: Edema was induced by coronary perfusion with Plegisol (750 mL, 289 mOsm/L) during a 1-minute aortic occlusion in 6 pigs. This was followed by whole blood reperfusion, inotropic support, and circulatory assistance until sinus rhythm and contractile function were restored. A control group (n = 6) was treated similarly, with 1 minute of electrically induced ventricular fibrillation and no coronary perfusion. Recorded data included electrocardiogram, left ventricular pressure and conductance, aortic flow, and two-dimensional echocardiography. Preload reduction by vena caval occlusion was used to define systolic and diastolic properties. Data were recorded at baseline and at 15-minute intervals for 90 minutes after reperfusion. RESULTS: In the edema group, average left ventricular mass (132 +/- 7 [standard error of the mean] versus 106 +/- 4 g) and ventricular stiffness constant (0.15 +/- 0.02 versus 0.05 +/- 0.01) increased after Plegisol versus baseline (p < 0.05), returning to normal after 45 minutes of reperfusion. In controls, mass (118 +/- 6 versus 116 +/- 4 g) and ventricular stiffness (0.06 +/- 0.01 versus 0.05 +/- 0.01) did not change significantly. There was no significant change in systolic function. Myocardial water content at the end of the study was not different for the two groups. CONCLUSIONS: Crystalloid-induced edema and diastolic stiffness resolve after 45 minutes in pigs. This suggests that edema caused solely by cardioplegia during cardiac operations should not cause significant perioperative ventricular dysfunction.

Animals↗

PubMed2002

On the solution of mixed-integer nonlinear programming models for computer aided molecular design.

This paper addresses the efficient solution of computer aided molecular design (CAMD) problems, which have been posed as mixed-integer nonlinear programming models. The models of interest are those in which the number of linear constraints far exceeds the number of nonlinear constraints, and with most variables participating in the nonconvex terms. As a result global optimization methods are needed. A branch-and-bound algorithm (BB) is proposed that is specifically tailored to solving such problems. In a conventional BB algorithm, branching is performed on all the search variables that appear in the nonlinear terms. This translates to a large number of node traversals. To overcome this problem, we have proposed a new strategy for branching on a set of linear branchingfunctions, which depend linearly on the search variables. This leads to a significant reduction in the dimensionality of the search space. The construction of linear underestimators for a class of functions is also presented. The CAMD problem that is considered is the design of optimal solvents to be used as cleaning agents in lithographic printing.

Journal Article↗

PubMed2005

Role of angular momentum conservation in unimolecular translational energy release: validity of the orbiting transition state theory.

The translational kinetic energy release distribution (KERD) for the halogen loss reaction of the bromobenzene and iodobenzene cations has been reinvestigated on the microsecond time scale. Two necessary conditions of validity of the orbiting transition state theory (OTST) for the calculation of kinetic energy release distributions (KERDs) have been formulated. One of them examines the central ion-induced dipole potential approximation. As a second criterion, an adiabatic parameter is derived. The lower the released translational energy and the total angular momentum, the larger the reduced mass, the rotational constant of the molecular fragment, and the polarizability of the released atom, the more valid is the OTST. Only the low-energy dissociation of the iodobenzene ion (E approximately 0.45 eV, where E is the internal energy above the reaction threshold) is found to fulfill the criteria of validity of the OTST. The constraints that act on the dissociation dynamics have been studied by the maximum entropy method. Calculations of entropy deficiencies (which measure the deviation from a microcanonical distribution) show that the pair of fragments does not sample the whole of the phase space that is compatible with the mere specification of the internal energy. The major constraint that results from conservation of angular momentum is related to a reduction of the dimensionality of the dynamics of the translational motion to a two-dimensional space. A second and minor constraint that affects the KERD leads to a suppression of small translational releases, i.e., accounts for threshold behavior. At high internal energies, the effects of curvature of the reaction path and of angular momentum conservation are intricately intermeddled and it is not possible to specify the share of each effect.

Journal Article↗

PubMed2006

A variational approach to the stochastic aspects of cellular signal transduction.

Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process noisy signals. The essential difficulty associated with the master equation approach to solving the stochastic chemical kinetics problem is the enormous number of ordinary differential equations involved. In this work, we show how to achieve tremendous reduction in the dimensionality of specific reaction cascade dynamics by solving variationally an equivalent quantum field theoretic formulation of stochastic chemical kinetics. The present formulation avoids cumbersome commutator computations in the derivation of evolution equations, making the physical significance of the variational method more transparent. We propose novel time-dependent basis functions which work well over a wide range of rate parameters. We apply the new basis functions to describe stochastic signaling in several enzymatic cascades and compare the results so obtained with those from alternative solution techniques. The variational Ansatz gives probability distributions that agree well with the exact ones, even when fluctuations are large and discreteness and nonlinearity are important. A numerical implementation of our technique is many orders of magnitude more efficient computationally compared with the traditional Monte Carlo simulation algorithms or the Langevin simulations.

Cells↗