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Results for “Dimensionality Reduction”

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At least 307 records · Page 17Linked to original sources
PubMed1995

Use of principal component analysis for the evaluation of the retention behaviour of monoamine oxidase inhibitory drugs on beta-cyclodextrin column.

The retention of 17 monoamine oxidase inhibitory drugs (proparlgylamine derivatives) were determined on a beta-cyclodextrin polymer (beta CDP)-coated silica column using ethanol-0.05 M K2HPO4 (6:4 v/v) as the eluent. The relative strength of interaction between the drugs and a water soluble beta-cyclodextrin polymer was determined by charge-transfer chromatography carried out on reversed-phase TLC layers. The relationship between capacity factors, physicochemical parameters and inclusion complex forming capacity of the monoamine oxidase inhibitory drugs were evaluated by stepwise regression analysis and by principal component analysis (PCA) followed by two-dimensional nonlinear mapping and varimax rotation. Calculations indicated that the retention of monoamine oxidase inhibitory drugs on beta CDP column is mainly governed by their steric and lipophylic parameters. Significant linear correlations were found between the corresponding coordinates of varimax rotation and two-dimensional nonlinear maps proving the suitability of both methods for the reduction of dimensionality of complicated data matrices.

Chemical Phenomena↗
PubMed1997

Checking the projection display of multivariate data with colored graphs.

Projection methods such as principal component analysis (PCA), nonlinear mapping (NLM), and the self-organizing map (SOM) are valuable algorithms for visualizing multidimensional data in a two-dimensional plane. Unfortunately, the reduction of the dimensionality involves distortions. In an attempt to graphically localize the distortions of the projected data, we suggest superposing colored graphs onto the 2D plots. The color of the edges of these graphs encodes the original high-dimensional distances between the connected points. The method is applied to a cluster analysis of 37 biologically active compounds and 471 molecules represented by a structural 3D descriptor.

Computer Graphics↗
PubMed1998

Folding of beta-sheet membrane proteins: a hydrophobic hexapeptide model.

Beta-sheets, in the form of the beta-barrel folding motif, are found in several constitutive membrane proteins (porins) and in several microbial toxins that assemble on membranes to form oligomeric transmembrane channels. We report here a first step towards understanding the principles of beta-sheet formation in membranes. In particular, we describe the properties of a simple hydrophobic hexapeptide, acetyl-Trp-Leu5 (AcWL5), that assembles cooperatively into beta-sheet aggregates upon partitioning into lipid bilayer membranes from the aqueous phase where the peptide is strictly monomeric and random coil. The aggregates, containing 10 to 20 monomers, undergo a relatively sharp and reversible thermal unfolding at approximately 60 degreesC. No pores are formed by the aggregates, but they do induce graded leakage of vesicle contents at very high peptide to lipid ratios. Because beta-sheet structure is not observed when the peptide is dissolved in n-octanol, trifluoroethanol or sodium dodecyl sulfate micelles, aggregation into beta-sheets appears to be an exclusive property of the peptide in the bilayer membrane interface. This is an expected consequence of the hypothesis that a reduction in the free energy of partitioning of peptide bonds caused by hydrogen bonding drives secondary structure formation in membrane interfaces. But, other features of interfacial partitioning, such as side-chain interactions and reduction of dimensionality, must also contribute. We estimate from our partitioning data that the free energy reduction per residue for aggregation is about 0.5 kcal mol-1. Although modest, its aggregate effect on the free energy of assembling beta-sheet proteins can be huge. This surprising finding, that a simple hydrophobic hexapeptide readily assembles into oligomeric beta-sheets in membranes, reveals the potent ability of membranes to promote secondary structure in peptides, and shows that the formation of beta-sheets in membranes is more facile than expected. Furthermore, it provides a basis for understanding the observation that membranes promote self-association of beta-amyloid peptides. AcWL5 and related peptides thus provide a good starting point for designing peptide models for exploring the principles of beta-sheet formation in membranes.

Circular Dichroism↗
PubMed1998

Asymmetric sampling along k(slice-select) in two-dimensional multislice MRI.

Reduction of the slice-select refocusing gradient in two-dimensional multislice imaging results in asymmetry of the k-space representation of collected data along the slice-select direction. Standard methods of partial Fourier reconstruction developed for other methods of asymmetric k-space sampling can be used to reconstruct these data with final through-plane resolution smaller than the collected slice thickness. This method can be used for reducing scan time in the same manner as asymmetric sampling in the phase-encoded direction. In addition, the reduced refocusing gradient reduces minimum TE and motion artifacts in the same manner as for asymmetric sampling in the frequency-encoded direction (fractional echoes). Results using a resolution phantom and a flow phantom illustrate these concepts.

Algorithms↗
PubMed2002

Nonparametric discriminant analysis of phytoplankton species using data from analytical flow cytometry.

BACKGROUND: Analytical flow cytometry (AFC) provides rapid and accurate measurement of particles from heterogeneous populations. AFC has been used to classify and identify phytoplankton species, but most methods of discriminant analysis of resulting data have depended on normality assumptions and outcomes have been disappointing. METHODS AND RESULTS: In this study, we consider nonparametric methods based on density estimation. In addition to the familiar kernel method, methods based on wavelets are also implemented. Full five-dimensional wavelet estimation proves to be computationally prohibitive with current workstation power, so we employ projection pursuit for reduction of dimensionality. AFC typically produces very large samples, so we also investigate data simplification through binning. Further modifications to the discrimination strategy are suggested by specific features of phytoplankton data, namely, a hierarchical group structure, the possible presence of many groups, and the likelihood of encountering an aberrant group in a test sample. CONCLUSIONS: We apply all the resultant procedures to appropriate subsets of a very large data set, demonstrate their efficacy, and compare their error rates with those of more conventional methods. We further show that incorporation of the specific features of phytoplankton data into the analysis leads to improved results and provides a general framework for analysis of such data.

Animals↗
PubMed2004

Formation process of two-dimensional networked gold nanowires by citrate reduction of AuCl4- and the shape stabilization.

Gold nanowires with a two-dimensional (2-D) network structure were formed by citrate reduction of AuCl4- with a low concentration of citrate. The structure change during the growth processes was observed by transmission electron microscopy (TEM) and the variation in concentrations of gold species in the aqueous solution was monitored by UV-vis spectra and Inductively Coupled Argon Plasma Emission Spectrophotometer (ICAP). The formation of 2-D gold nanowires was induced by the small amount of reducing agent because the preliminary gold nanoparticles formed by reduction of AuCl4- were thermodynamically unstable in the aqueous solution due to the insufficient capping of citrate. One of the key points of nanowire formation is the preferential adsorption of AuCl4- instead of citrate ions on the surface of the preliminary gold particles, which results in an attracting force between gold nanoparticles. We propose a hit-to-stick-to-fusion model, in which gold nanoparticles adhere by the attraction force and stick together, causing selective deposition of reduced gold metallic species on the concave surface of the two sticking particles, followed by fusion into nanowires. Nanowires then connect with each other, forming a network structure. The evidence obtained from TEM observation of transformation from gold nanowires on a TEM grid to large nanoparticles by hydrogen gas reduction and time-resolved measurements of gold ions suggest that gold ions not only are crucial for the growth of gold nanowires but also play an important role in stabilizing the shape of gold nanowires during the formation process. This method for synthesizing 2-D gold nanowires is simple and relatively easy application to the synthesis of other metallic nanowires such as silver or platinum is expected.

Adsorption↗
PubMed2003

Performance of three-phase three-dimensional electrode reactor for the reduction of COD in simulated wastewater-containing phenol.

The removal of chemical oxygen demand (COD) from wastewater-containing phenol was investigated using three-phase three-dimensional electrode reactor. Special attention was paid to experimentally probe the performance of the reactor in COD removal in the process of repeated batch runs. The experimental results showed that the reactor could remove COD from phenol-containing wastewater much more efficiently than both granulated activated carbon (GAC) adsorption bed and conventional three-dimensional electrode. For 200th batch run, the three-phase three-dimensional electrode reactor with an airflow of 5 l min(-1) and a cell voltage of 30 V could remove 1350 ppm COD from the wastewater in 30 min while conventional three-dimensional electrode reactor with a same cell voltage and GAC adsorption bed with a same airflow only could remove 610 and 1000 ppm, respectively, at the same reaction duration. Although it was found that COD removal decreased with increasing repeated batch runs in our experimental range, due to adsorption saturation of GAC and electrode passivation, the extent of decrease for the three-phase three-dimensional electrode is much less than those for conventional three-dimensional electrodes and GAC adsorption beds. The passivated reactor could be partly re-activated by electrolysis in the presence of MnO2.

Electrodes↗
PubMed2004

Two-dimensional correlation analysis of spectroelectrochemical data for p-benzoquinone reduction in acetonitrile.

Two-dimensional (2D) spectral correlation analysis has been employed to interpret the complex spectroelectrochemical data obtained from an electrochemical system undergoing following reactions after electron transfer. The system used was electrochemical reduction of p-benzoquinone (p-BQ) in acetonitrile, which produces anion radicals and dianions at its first and second reduction potentials. The dianions undergo a fast comproporationation reaction with neutral p-BQ molecules to produce anion radicals back, complicating the spectral analysis. Upon application of 2D correlation analysis in conjunction with the self-modeling curve resolution technique, we were able not only to resolve the spectra and determine the sequence of spectral emergence but also to extract the individual spectra. The techniques offer a very powerful tool for interpreting highly convoluted spectra obtained from a system where a series of chemical reactions occur following the electron transfer at the electrode/electrolyte interface.

Journal Article↗
PubMed1981

Double-label reductive methylation of tissue proteins for precision two-dimensional polyacrylamide-gel electrophoretic analysis.

Reductive methylation has been used to radioactively label crude-extract proteins with 3H or 14C. The procedure achieved good isotope incorporation and resolution of proteins on two-dimensional polyacrylamide gels. It allows high-precision comparison of tissue samples by double-labelling and should facilitate the study of tissue proteins by two-dimensional gel electrophoresis.

Animals↗
PubMed2000

Three-dimensional tailored RF pulses for the reduction of susceptibility artifacts in T(*)(2)-weighted functional MRI.

A three-dimensional tailored RF pulse method for reducing intravoxel dephasing artifacts in T *(2)-weighted functional MRI is presented. A stack of spirals k-space trajectory is employed to excite a disk of magnetization for small tip angles. Smaller disks with a linear through-plane phase are inserted into the disk to locally refocus regions which are normally dephased due to susceptibility variations. Numerical simulations and imaging experiments which use the tailored RF pulses are presented. Limitations of the method and improvements are also discussed.

Artifacts↗
PubMed1997

A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins.

A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four C alpha atoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudodihedral involving four sequential C alpha atoms, as well as the triple scalar product for the vectors describing the orientation of the three intervening peptide groups. The method provides a reduction in dimensionality, from the usual combination of multiple phi,psi pairs to a single pair, yielding valuable information concerning the structure and dynamics of these important elements. The new two-dimensional surface is explored by reference to 63 selected protein crystal structures together with a comparison of model built peptides representing the common secondary structural elements. Dynamical aspects on this new surface are examined using a molecular dynamics trajectory of Basic Pancreatic Trypsin Inhibitor.

Aprotinin↗
PubMed2004

Modelling a spatially heterogeneous biofilm and the bulk fluid: selected results from benchmark problem 2 (BM2).

The numerical simulation of mass transfer and conversion in spatially heterogeneous biofilms on the meso-scale requires an accurate description of the hydrodynamics in the biofilm systems and of spatial effects. This leads to systems of three-dimensional nonlinear partial differential equations that are numerically very expensive to solve and to data requirements that are not easy to meet. In this paper several modeling approaches to reduce the physical complexity and, hence, accelerate the computation are compared. They range from a mere reduction of dimensionality by lumping the problem along a secondary flow direction to global mass balances or empirical correlations, at the core of which a one-dimensional boundary value problem must be solved. It is found that even strongly simplified models can describe the qualitative behaviour of the model with regard to variations in the geometrical and hydrodynamic model parameters quite well. In order to obtain also quantitatively reliable results the hydrodynamics must be considered in an appropriate manner.

Bacteria↗
PubMed2000

Dimensional complexity and power spectral measures of the EEG during functional versus predicative problem solving.

Electroencephalograms were recorded in 22 men while solving tasks of visual-pattern completion and during mental relaxation. They were primed (by foregoing trials) to solve these tasks either in a predicative or functional mode of thinking. Predicative thinking required that in order to complete the pattern the subject had to get involved with the logic of the static structure of the pattern and therefore had to recognize the recurrence of certain features of the elements (e.g., shape, color, and size). Functional thinking required involvement in a dynamic reading of the logic of the pattern and therefore to search for operations and actions to be performed on the pattern elements (e.g., pushing, mirroring, and rotating). The EEG complexity during predicative thinking decreased in comparison to functional thinking and mental relaxation, with this reduction being most pronounced over the right parietal cortex. A reduction in dimensional complexity during functional thinking as compared to mental relaxation, which was concentrated over the left central cortex, although significant, was less clear. The reduced EEG complexity during predicative thought, dominant over the right hemisphere, could reflect increased competitive inhibition among respective cortical neuron assemblies in association with the visual analysis of static element features, converging upon those predicates relevant for the solution.

Adult↗
PubMed2000

Reduction in sample size for studies of remodeling in heart failure by the use of cardiovascular magnetic resonance.

Fast breathhold cardiovascular magnetic resonance (CMR) has become a reference standard for the measurement of cardiac volumes, function, and mass. The implications of this for sample sizes for remodeling studies in heart failure (HF) have not been elucidated. We determined the reproducibility of CMR in HF and calculated the sample size requirements and compared them with published values for echocardiography. Breathhold gradient echo cines of the left ventricle were acquired in 20 patients with HF and 20 normal subjects. Sample size values were calculated from the interstudy standard deviation of the difference. The percentage variability of the measured parameters in our HF group of intraobserver (2.0-7.4%), interobserver (3.3-7.7%), and interstudy (2.5-4.8%) measurements was slightly larger than for our normal group (1.6-6.6%, 1.6-7.3%, and 2.0-7.3%, respectively) but remained comparable with previous studies in normal subjects. The calculated sample sizes in patients with HF for CMR to detect a 10-ml change in end-diastolic volume (n = 12) and end-systolic volume (n = 10), a 3% change in ejection fraction (n = 15), and a 10-g change in mass was (n = 9) were substantially smaller than recently published values for two-dimensional echocardiography (reduction of 81-97%). Breathhold CMR is a fast comprehensive technique for the assessment of cardiac volumes, function, and mass in HF that is accurate but also highly reproducible. This allows a considerable reduction in the patient numbers required to prove a hypothesis in research studies, which suggests a potential for important research cost savings.

Cardiac Volume↗
PubMed1997

Radionuclide imaging in emphysema after lung volume reduction surgery.

Three dimensional (3D) surface displays of dynamic Xe-133 and Tc-99m MAA SPECT were performed to evaluate regional lung function in two patients with pulmonary emphysema before and after thoracoscopic lung volume reduction surgery. The 3D displays were reconstructed using a color-illuminated, surface-rendering technique. For the Xe-133 studies, a fusion display of 3D equilibrium (EQ) and 3-minute washout (WO) images was used to show the distribution of Xe-133 retention, which were transparently seen within the entire lung contours delineated by the EQ image. In both patients, these 3D displays allowed an overview of the localized poorly functioning lungs with Xe-133 retention or reduced perfusion with geometric realism. The location and extent were more easily comprehended on the displays compared to the slice-by-slice presentations of tomograms. Postoperatively, the displays efficiently revealed restored function in the remaining lungs. The 3D surface displays of the two SPECT procedures providing topographic information of regional lung function appears to contribute to the treatment strategy of this surgery.

Aged↗
PubMed2006

Effect of membrane mimicking environment on the conformation of a pore-forming (xSxG)6 peptide.

The mechanism of membrane interaction by beta-sheet peptides is important to understand fundamental principles of folding of beta-barrel proteins and various beta-amyloid proteins. Here, we examined the conformational characteristics of a porin-like channel forming (xSxG)(6) peptide in solution and membrane-mimicking environments (CD and ATR-IR) to understand the structural changes of the peptide during membrane association and channel formation. A comparison of the peptide conformations in different microenvironments showed that beta-sheet formation is enhanced in membrane-mimicking liposomes and SDS-micelles. The lipid-induced beta-sheet formation was confirmed by the formation of a characteristic beta-sheet structure on mixing a methanolic solution of the peptide (partially folded) with preformed liposomes. The amphipathicity of the peptide; increased hydrogen bonding, hydrophilicity, and reduction in dimensionality of the membrane surface; membrane-peptide interaction-forces; and presence of flexible glycines might facilitate beta-sheet formation in membranes. Though the CD spectra of both the peptide-bound and peptide-incorporated lipids are reminiscent of a beta-sheet structure, a significant variation in the peak positions of the two beta-sheet structures was noticed. The channel characteristics of (xSxG)(6) in the presence of low ionic strength solutions of NEt(3)BzCl and glucosammonium chloride are comparable to those reported under high ionic strength solutions. Altogether the data suggest that the channel formation by (xSxG)(6) proceeds via beta-sheet aggregate formation at the membrane surface, beta-sheet insertion, and rearrangement into a beta-barrel-like structure. The beta-barrel-like channel formation most likely arises from a sequence similarity to beta-barrel porins whereas the lipid-induced beta-sheet formation is governed by the above-mentioned factors.

2-Propanol↗
PubMed2003

Efficient principal component analysis for multivariate 3D voxel-based mapping of brain functional imaging data sets as applied to FDG-PET and normal aging.

Principal component analysis (PCA) is a well-known technique for reduction of dimensionality of functional imaging data. PCA can be looked at as the projection of the original images onto a new orthogonal coordinate system with lower dimensions. The new axes explain the variance in the images in decreasing order of importance, showing correlations between brain regions. We used an efficient, stable and analytical method to work out the PCA of Positron Emission Tomography (PET) images of 74 normal subjects using [(18)F]fluoro-2-deoxy-D-glucose (FDG) as a tracer. Principal components (PCs) and their relation to age effects were investigated. Correlations between the projections of the images on the new axes and the age of the subjects were carried out. The first two PCs could be identified as being the only PCs significantly correlated to age. The first principal component, which explained 10% of the data set variance, was reduced only in subjects of age 55 or older and was related to loss of signal in and adjacent to ventricles and basal cisterns, reflecting expected age-related brain atrophy with enlarging CSF spaces. The second principal component, which accounted for 8% of the total variance, had high loadings from prefrontal, posterior parietal and posterior cingulate cortices and showed the strongest correlation with age (r = -0.56), entirely consistent with previously documented age-related declines in brain glucose utilization. Thus, our method showed that the effect of aging on brain metabolism has at least two independent dimensions. This method should have widespread applications in multivariate analysis of brain functional images.

Adult↗
PubMed1987

Lipid fluidity and membrane protein dynamics.

Membrane fluidity plays an important role in cellular functions. Membrane proteins are mobile in the lipid fluid environment; lateral diffusion of membrane proteins is slower than expected by theory, due to both the effect of protein crowding in the membrane and to constraints from the aqueous matrix. A major aspect of diffusion is in macromolecular associations: reduction of dimensionality for membrane diffusion facilitates collisional encounters, as those concerned with receptor-mediated signal transduction and with electron transfer chains. In mitochondrial electron transfer, diffusional control is prevented by the excess of collisional encounters between fast-diffusing ubiquinone and the respiratory complexes. Another aspect of dynamics of membrane proteins is their conformational flexibility. Lipids may induce the optimal conformation for catalytic activity. Breaks in Arrhenius plots of membrane-bound enzymes may be related to lipid fluidity: the break could occur when a limiting viscosity is reached for catalytic activity. Viscosity can affect protein conformational changes by inhibiting thermal fluctuations to the inner core of the protein molecule.

Diffusion↗