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Results for “Dimensionality Reduction”

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PubMedDate not supplied

Elemental classification in multi-detector stem images using image analysis clustering techniques.

The multi-detector STEM images form a multi-dimensional measurement space where picture elements of morphologically distinct regions cluster and can be separated for classification using image processing clustering techniques. These images are highly correlated and improve the classification only at the high cost of adding dimensionality. Data reduction techniques which take the class separation into account can be used to compress the useful information carried by these images into a few components to which clustering techniques can be successfully applied. At high magnification, a slight displacement is sometimes observed, which can slightly impair the classification result. The redundancy of the information in the quadrant images suggests their use for phase retrieval - which, added to an energy loss data channel, may greatly improve the classification.

Animals↗
PubMed1988

Stimulus equalization: temporary reduction of stimulus complexity to facilitate discrimination learning.

Learners with limited behavioral repertoires often have difficulty discriminating complex, multidimensional stimuli. Procedures that use gradual stimulus change have been developed to facilitate such discrimination, but these procedures are often difficult to implement and costly in terms of teacher time and expertise. This study investigated the effectiveness of stimulus equalization, an error reduction procedure involving an abrupt but temporary reduction of dimensional complexity. A microcomputer was used for stimulus presentation, data collection, and response analyses. Preschool children's responding to groups of four stimuli differing along several dimensions was analyzed on four discrimination tasks under several conditions. On each task, one element from a different dimension was programmed as correct. When trial-and-error training failed to establish the discrimination, equalization training began in which differences in the irrelevant dimensions were eliminated. When correct responding developed, the differences were reinstated, and correct performance was maintained in all but one instance. In a repeated acquisition design, stimulus equalization was found to be generally effective and superior to the trial-and-error method. Implications for computer-assisted instruction are discussed.

Attention↗
PubMedDate not supplied

Segmentation of multivariate medical images via unsupervised clustering with "adaptive resolution".

The need for quantitative information is becoming increasingly important in the clinical field. In this paper we present an interactive X11 based system, devoted to segmentation of multivariate medical images, including an unsupervised neural network approach to clustering. The following steps are considered in the analysis sequence: feature extraction, reduction of dimensionality, unsupervised data clustering, voxel classification, interactive post-processing refinement. The environment turns out to be extremely interactive, thus making the user able to display and modify data during processing, to set parameters, to choose different methods and different tools for each step, and to define online the whole analysis sequence.

Algorithms↗
PubMed2006

Binding of the dystrophin second repeat to membrane di-oleyl phospholipids is dependent upon lipid packing.

Dystrophin is the genetically deficient protein in Duchenne Muscular Dystrophy. Its C- and N-terminal ends interact with cytoskeletal and membrane proteins, establishing a link between the cytoskeleton and the extracellular matrix. In a previous study, we showed that there is an interaction between the second repeat of the rod domain and membrane phospholipids, which places tryptophan residues in close contact with the membrane. Here, we examine the binding of the dystrophin repeat-2 to small unilamellar vesicles with varying composition. We find that the protein binds predominantly to di-oleyl-phosphatidylserine. The binding as a function of increasing mol% of DOPS appears to be cooperative due to reduction of dimensionality, greatly enhanced in the absence of salts, and partly modulated by pH. Substituting small by large unilamellar vesicles induces a 30-fold lower affinity of the protein for the membrane phospholipids. However, modifying the packing of the acyl chains by introducing lipids such as phosphatidylethanolamine and cholesterol to the vesicle leads to an approximately 7-fold increase in affinity. Taken together, these results show that the binding involves electrostatic forces in addition to hydrophobic ones.

Dystrophin↗
PubMed2005

The statistical analysis of multivariate serological frequency data.

Data occurring in the form of frequencies are common in genetics-for example, in serology. Examples are provided by the AB0 group, the Rhesus group, and also DNA data. The statistical analysis of tables of frequencies is carried out using the available methods of multivariate analysis with usually three principal aims. One of these is to seek meaningful relationships between the components of a data set, the second is to examine relationships between populations from which the data have been obtained, the third is to bring about a reduction in dimensionality. This latter aim is usually realized by means of bivariate scatter diagrams using scores computed from a multivariate analysis. The multivariate statistical analysis of tables of frequencies cannot safely be carried out by standard multivariate procedures because they represent compositions and are therefore embedded in simplex space, a subspace of full space. Appropriate procedures for simplex space are compared and contrasted with simple standard methods of multivariate analysis ("raw" principal component analysis). The study shows that the differences between a log-ratio model and a simple logarithmic transformation of proportions may not be very great, particularly as regards graphical ordinations, but important discrepancies do occur. The divergencies between logarithmically based analyses and raw data are, however, great. Published data on Rhesus alleles observed for Italian populations are used to exemplify the subject.

Data Interpretation, Statistical↗
PubMed2006

The usefulness of artificial neural networks in the evaluation of pulmonary efficiency and antioxidant capacity of welders.

OBJECTIVE: The aim of the study was to determine if artificial neural networks (ANNs) may be useful to analyse a complex and large set of data derived from smoking welders for the purpose of finding relationships between parameters describing respiratory system efficiency and antioxidant defence. METHODS: A group of 94 welders employed in a big metallurgic enterprise in Krakow, Poland (men only, aged 29-57 years, all active smokers) occupationally exposed to O(3) and NO(x), were the subjects of this study. They underwent biochemical measurements including total antioxidant status (TAS) and the anti-oxidative defence enzymes superoxide dismutase (SOD) and catalase (CT); biominerals: Fe, Cu, Zn, Mg in blood serum and in hair; the concentrations of albumin, bilirubin, uric acid in blood. The determination of respiratory efficiency was based on a "flow-volume" curve and spirometry. The dependant variables for ANNs were: TAS, SOD, CT. Thirty-one subjects with normal values of all spirometric parameters were selected for the final analysis. RESULTS: Statistically valid relationship between TAS and albumin, Zn and Cu in blood and the two pulmonary parameters forced expiratory volume after 1s (FEV(1)) and middle expiratory flow of 25-75% of vital capacity (MEF(25/75)) were found. Zn concentration almost linearly influenced TAS. For Cu a sigmoid curve was obtained. For albumin concentration as well as for FEV(1) a two-stage curve was observed. CONCLUSIONS: ANNs are useful for the reduction of dimensionality and are suited to analyse a complex and relatively large set of parameters when it is unknown which of these are related. ANNs were useful for finding the relationship between the antioxidant defence and the respiratory system capacity in welders who smoke.

Adult↗
PubMed2004

Multivariate statistical techniques for the evaluation of spatial and temporal variations in water quality of Gomti River (India)--a case study.

This case study reports different multivariate statistical techniques applied for evaluation of temporal/spatial variations and interpretation of a large complex water-quality data set obtained during monitoring of Gomti River in Northern part of India. Water quality of the Gomti River, a major tributary of the Ganga River was monitored at eight different sites selected in relatively low, moderate and high pollution regions, regularly over a period of 5 years (1994-1998) for 24 parameters. The complex data matrix (17,790 observations) was treated with different multivariate techniques such as cluster analysis, factor analysis/principal component analysis (FA/PCA) and discriminant analysis (DA). Cluster analysis (CA) showed good results rendering three different groups of similarity between the sampling sites reflecting the different water-quality parameters of the river system. FA/PCA identified six factors, which are responsible for the data structure explaining 71% of the total variance of the data set and allowed to group the selected parameters according to common features as well as to evaluate the incidence of each group on the overall variation in water quality. However, significant data reduction was not achieved, as it needed 14 parameters to explain 71% of both the temporal and spatial changes in water quality. Discriminant analysis showed the best results for data reduction and pattern recognition during both temporal and spatial analysis. Discriminant analysis showed five parameters (pH, temperature, conductivity, total alkalinity and magnesium) affording more than 88% right assignations in temporal analysis, while nine parameters (pH, temperature, alkalinity, Ca-hardness, DO, BOD, chloride, sulfate and TKN) to afford 91% right assignations in spatial analysis of three different regions in the basin. Thus, DA allowed reduction in dimensionality of the large data set, delineating a few indicator parameters responsible for large variations in water quality. This study presents necessity and usefulness of multivariate statistical techniques for evaluation and interpretation of large complex data sets with a view to get better information about the water quality and design of monitoring network for effective management of water resources.

Data Collection↗
PubMed2001

Kinetics of diffusion-assisted reactions in microheterogeneous systems.

This review is focused on the basic theory of diffusion-assisted reactions in microheterogeneous systems, from porous solids to self-organized colloids and biomolecules. Rich kinetic behaviors observed experimentally are explained in a unified fashion using simple concepts of competing distance and time scales of the reaction and the embedding structure. We mainly consider pseudo-first-order reactions, such as luminescence quenching, described by the Smoluchowski type of equation for the reactant pair distribution function with a sink term defined by the reaction mechanism. Microheterogeneity can affect the microscopic rate constant. It also enters the evolution equation through various spatial constraints leading to complicated boundary conditions and, possibly, to the reduction of dimensionality of the diffusion space. The reaction coordinate and diffusive motion along this coordinate are understood in a general way, depending on the problem at hand. Thus, the evolution operator can describe translational and rotational diffusion of molecules in a usual sense, it can be a discrete random walk operator when dealing with hopping of adsorbates in solids, or it can correspond to conformational fluctuations in proteins. Mathematical formulation is universal but physical consequences can be different. Understanding the principal features of reaction kinetics in microheterogeneous systems enables one to extract important structural and dynamical information about the host environments by analyzing suitably designed experiments, it helps building effective strategies for computer simulations, and ultimately opens possibilities for designing systems with controllable reactivity properties.

Animals↗
PubMed1994

Phosphorylation reverses the membrane association of peptides that correspond to the basic domains of MARCKS and neuromodulin.

Several groups have observed that phosphorylation causes the MARCKS (Myristoylated Alanine-Rich C Kinase Substrate) protein to move off cell membranes and phospholipid vesicles. Our working hypothesis is that significant membrane binding of MARCKS requires both hydrophobic insertion of the N-terminal myristate into the bilayer and electrostatic association of the single cluster of basic residues in the protein with acidic lipids and that phosphorylation reverses this electrostatic association. Membrane binding measurements with myristoylated peptides and phospholipid vesicles show this hydrophobic moiety could, at best, barely attach proteins to plasma membranes. We report here membrane binding measurements with basic peptides that correspond to the phosphorylation domains of MARCKS and neuromodulin. Binding of these peptides increases sigmoidally with the percent acidic lipid in the phospholipid vesicle and can be described by a Gouy-Chapman/mass action theory that explains how electrostatics and reduction of dimensionality produce apparent cooperativity. The electrostatic affinity of the MARCKS peptide for membranes containing 10% acidic phospholipids (10(4) M-1 = chi/[P], where chi is the mole ratio of peptide bound to the outer monolayer of the vesicles and [P] is the concentration of peptide in the aqueous phase) is the same as the hydrophobic affinity of the myristate moiety for bilayer membranes. Phosphorylation decreases the affinity of the MARCKS peptide for membranes containing 15% acidic lipid about 1000-fold and produces a rapid (t1/2 < 30 s) dissociation of the peptide from phospholipid vesicles.

Amino Acid Sequence↗
PubMed1996

Resonance energy transfer in a model system of membranes: application to gel and liquid crystalline phases.

Resonance energy transfer between octadecyl rhodamine B (donor) and 1,1',3,3,3',3'-hexamethylindotricarbocyanine (acceptor) was studied in a model system of membranes (large unilamellar vesicles of dipalmitoylphosphatidylcholine), using both steady-state and time-resolved techniques. In the fluid phase (temperature = 50 degrees C) the decay law and the steady-state theoretical curve for energy transfer in two dimensions are verified. In the gel phase (temperature = 25 degrees C) an apparent reduction of dimensionality is observed, which is explained on the basis of probe segregation to the defect lines (grain boundaries). An estimation of the domain size from the model recovered linear probe concentrations is approximately 1750-2000 lipid molecules. In both phases, the existence of a fractal geometry was ruled out.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1992

Binding of basic peptides to acidic lipids in membranes: effects of inserting alanine(s) between the basic residues.

We studied the binding of peptides containing five basic residues to membranes containing acidic lipids. The peptides have five arginine or lysine residues and zero, one, or two alanines between the basic groups. The vesicles were formed from mixtures of a zwitterionic lipid, phosphatidylcholine, and an acidic lipid, either phosphatidylserine or phosphatidylglycerol. Measuring the binding using equilibrium dialysis, ultrafiltration, and electrophoretic mobility techniques, we found that all peptides bind to the membranes with a sigmoidal dependence on the mole fraction of acidic lipid. The sigmoidal dependence (Hill coefficient greater than 1 or apparent cooperativity) is due to both electrostatics and reduction of dimensionality and can be described by a simple model that combines Gouy-Chapman-Stern theory with mass action formalism. The adjustable parameter in this model is the microscopic association constant k between a basic residue and an acidic lipid (1 less than k less than 10 M-1). The addition of alanine residues decreases the affinity of the peptides for the membranes; two alanines inserted between the basic residues reduces k 2-fold. Equivalently, the affinity of the peptide for the membrane decreases 10-fold, probably due to a combination of local electrostatic effects and the increased loss of entropy that may occur when the more massive alanine-containing peptides bind to the membrane. The arginine peptides bind more strongly than the lysine peptides: k for an arginine residue is 2-fold higher than for a lysine residue. Our results imply that a cluster of arginine and lysine residues with interspersed electrically neutral amino acids can bind a significant fraction of a cytoplasmic protein to the plasma membrane if the cluster contains more than five basic residues.

Alanine↗
PubMed2003

Contribution of the C1A and C1B domains to the membrane interaction of protein kinase C.

The hallmark for protein kinase C activation is its "translocation" to membranes following generation of lipid second messengers. This translocation is mediated by the C1 and C2 domains, two membrane-targeting modules, whose engagement on membranes provides the energy for an activating conformational change in which an autoinhibitory pseudosubstrate sequence is released from the active site. Novel and conventional protein kinase C isozymes contain a tandem repeat of C1 domains, the C1A and C1B, which each contain a binding pocket for phorbol esters/diacylglycerol. This study addresses the contribution of the C1A and C1B domains in the regulation of protein kinase C's membrane interaction using bisfunctional (dimeric) phorbol myristate acetate (PMA) molecules. We show that dimeric bisphorbols are an order of magnitude more effective at recruiting full-length PKC betaII to membranes compared with monomeric PMA and that the effectiveness of the interaction depends on the nature and length of the cross-link between the PMA moieties. Most effective were dimeric phorbol 12-acetate 13-esters linked at the 13 position with a 14 carbon spacer. The increased potency of dimeric phorbol esters is reduced if either the C1A or C1B domains are mutated so that they are unable to bind PMA, if one moiety of the dimer contains a nonfunctional phorbol, or if the binding to the isolated C1B domain is measured. Thus, the increased potency of the dimeric phorbol esters results primarily from their ability to engage, to a limited extent, both C1 modules on the same molecule. Although dimeric phorbols were more potent than monomeric phorbol esters in recruiting protein kinase C to membranes, the magnitude of the increase was still several orders of magnitude lower than what would be predicted on the basis of the reduction in dimensionality that occurs when the first C1 domain is engaged on the membrane. Thus, engaging both domains can be forced but is highly unfavored. In summary, our data reveal that both C1 domains are oriented for potential membrane interaction but only one C1 domain binds ligand in a physiological context.

Amino Acid Substitution↗
PubMed2006

Visualization of transient encounter complexes in protein-protein association.

Kinetic data on a number of protein-protein associations have provided evidence for the initial formation of a pre-equilibrium encounter complex that subsequently relaxes to the final stereospecific complex. Site-directed mutagenesis and brownian dynamics simulations have suggested that the rate of association can be modulated by perturbations in charge distribution outside the direct interaction surfaces. Furthermore, rate enhancement through non-specific binding may occur by either a reduction in dimensionality or the presence of a short-range, non-specific attractive potential. Here, using paramagnetic relaxation enhancement, we directly demonstrate the existence and visualize the distribution of an ensemble of transient, non-specific encounter complexes under equilibrium conditions for a relatively weak protein-protein complex between the amino-terminal domain of enzyme I and the phosphocarrier protein HPr. Neither the stereospecific complex alone nor any single alternative conformation can account fully for the intermolecular paramagnetic relaxation enhancement data. Restrained rigid-body simulated annealing refinement against the paramagnetic relaxation enhancement data enables us to obtain an atomic probability distribution map of the non-specific encounter complex ensemble that qualitatively correlates with the electrostatic surface potentials on the interacting proteins. Qualitatively similar results are presented for two other protein-protein complexes.

Bacterial Proteins↗
PubMed2006

Depletion "skraps" and dynamic buffering inside the cellular calcium store.

Ca2+ signals, produced by Ca2+ release from cellular stores, switch metabolic responses inside cells. In muscle, Ca2+ sparks locally exhibit the rapid start and termination of the cell-wide signal. By imaging Ca2+ inside the store using shifted excitation and emission ratioing of fluorescence, a surprising observation was made: Depletion during sparks or voltage-induced cell-wide release occurs too late, continuing to progress even after the Ca2+ release channels have closed. This finding indicates that Ca2+ is released from a "proximate" compartment functionally in between store lumen and cytosol. The presence of a proximate compartment also explains a paradoxical surge in intrastore Ca2+, which was recorded upon stimulation of prolonged, cell-wide Ca2+ release. An intrastore surge upon induction of Ca2+ release was first reported in subcellular store fractions, where its source was traced to the store buffer, calsequestrin. The present results update the evolving concept, largely due to N. Ikemoto and C. Kang, of calsequestrin as a dynamic store. Given the strategic location and reduction of dimensionality of Ca2+-adsorbing linear polymers of calsequestrin, they could deliver Ca2+ to the open release channels more efficiently than the luminal store solution, thus constituting the proximate compartment. When store depletion becomes widespread, the polymers would collapse to increase store [Ca2+] and sustain the concentration gradient that drives release flux.

Animals↗
PubMed1993

Estimating pesticide field half-lives from a backpropagation neural network.

The field half-lives of 110 pesticides were modelled using a backpropagation neural network (NN). The molecules were described by means of the frequency of 17 structural fragments. Before training the NN, different scaling transformations were assayed. Best results were obtained with correspondence factor analysis which also allowed a reduction of dimensionality. The training and testing sets of the NN analysis gave 95.5% and 84.6% of good classifications, respectively. Comparison with discriminant factor analysis showed that a backpropagation NN was more appropriate to model the field half-lives of pesticides.

Discriminant Analysis↗
PubMed2003

Nematostatics of triple lines.

The Landau-de Gennes model for nematic liquid crystal bulk and interfaces has been extended to nematic triple lines involving the intersection of two isotropic fluids and one nematic liquid crystalline phase. A complete set of bulk, interface, and triple line force and torque balance equations has been formulated. The triple line force and torque balance equations have linear, interfacial, and bulk contributions. The bulk contributions appear as junction integrals, the surface contributions as junctions sums, and the line contributions as gradients of stresses. Reduction of dimensionality from three to one dimensional creates the following effects: (a) bulk terms enter interfacial balances as surface jumps and line balances as junction integrals, and (b) surface terms enter linear balances as junction sums. Line stress and torque equations are derived using classical liquid crystal models. The correspondence between line stress and line torque and their surface and bulk analogs is established. The triple line force and torque balance equations are use to analyze the contact angle in a nematic lens lying at the interface between two isotropic fluids, when the preferred surface orientation is tangential. The effect of anisotropy and long range elasticity on triple line phases is established. Under weak anchoring the contact angle is shown to be a function of the anchoring energy at the nematic-isotropic interface, while under strong anchoring conditions the contact angle is a function of the Peach-Koehler force that originates from bulk long range elasticity and acts on the triple line. The use of the complete set of balance equations removes the classical inconsistency in force balances at a contact line by properly taking into account long range (bulk gradient elasticity) and anisotropic (interfacial anchoring elasticity) effects.

Journal Article↗
PubMed1988

Brownian dynamics of cytochrome c and cytochrome c peroxidase association.

Brownian dynamics computer simulations of the diffusional association of electron transport proteins cytochrome c (cyt c) and cytochrome c peroxidase (cyt c per) were performed. A highly detailed and realistic model of the protein structures and their electrostatic interactions was used that was based on an atomic-level spatial description. Several structural features played a role in enhancing and optimizing the electron transfer efficiency of this reaction. Favorable electrostatic interactions facilitated long-lived nonspecific encounters between the proteins that allowed the severe orientational criteria for reaction to be overcome by rotational diffusion during encounters. Thus a "reduction-in-dimensionality" effect operated. The proteins achieved plausible electron transfer orientations in a multitude of electrostatically stable encounter complexes, rather than in a single dominant complex.

Chemical Phenomena↗
PubMed1985

Two-dimensional echocardiographic image texture analysis: reduction of regional variability using polar coordinates.

Factors inherent to the ultrasound imaging system can influence quantitative ultrasound image texture and may produce changes that mask or mimic those due to alterations in tissue structure. In this study, we assessed the effect of the method of image data acquisition and analysis on the variations in quantitative texture measures that occurred solely due to the position of a region of interest (ROI) within the field of view. When ROI's, which varied in range and azimuth within the image of a tissue equivalent phantom (of uniform composition), were assessed by conventional analysis of scan-converted (rectangular coordinate) data, over 50 percent of all texture measures showed significant differences. Pseudo polar analysis reduced the number of texture measures showing regional variation by 80 percent (p less than 0.01) and true polar coordinate data analysis reduced the number by 74 percent (p less than 0.01). True polar analysis completely abolished differences in texture measures between ROI's separated in azimuth. Acquisition and analysis of tissue texture data using polar coordinates should allow a more definitive identification of abnormal tissue.

Echocardiography↗