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At least 55 records · Page 3Linked to original sources

PubMed2006

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

Algorithms↗

PubMed2005

Systematic analysis of group identification in stock markets.

We propose improved methods to identify stock groups using the correlation matrix of stock price changes. By filtering out the market-wide effect and the random noise, we construct the correlation matrix of stock groups in which nontrivial high correlations between stocks are found. Using the filtered correlation matrix, we successfully identify the multiple stock groups without any extra knowledge of the stocks by the optimization of the matrix representation and the percolation approach to the correlation-based network of stocks. These methods drastically reduce the ambiguities while finding stock groups using the eigenvectors of the correlation matrix.

Journal Article↗

PubMed1987

Serum protein binding of phenytoin, diazepam and propranolol in age-related decrease in renal function.

The serum protein binding of phenytoin, diazepam and propranolol was investigated in vitro in 32 elderly people with an age-related decrease in renal function by a pressure ultrafiltration method at 37 degrees C. The mean age of the patients was 88 +/- 1 years (mean +/- SE), and their mean 51Cr-EDTA clearance 46 +/- 4 ml/min. The main reason for hospitalization of these patients was their age. The free fraction of phenytoin correlated negatively with the serum albumin concentration, and that of propranolol with the alpha 1-acid glycoprotein (alpha 1-AGP) concentration. The free fraction of diazepam did not correlate with either of these binding proteins. In stepwise multiple regression analysis, the most significant variable for phenytoin free fraction was serum albumin concentration, with the serum urea concentration coming in second place. For the diazepam free fraction, the only significant variable was the serum urea level, although in the correlation matrix the correlation with creatinine was also significant. When the effect of serum albumin level was corrected mathematically, the urea level was the best determinant in regression analysis for both the phenytoin and diazepam free fractions. It can be concluded that an age-dependent decrease in renal function increases the free fraction of phenytoin and diazepam and is, together with hypoalbuminaemia, responsible for the increased free fraction of these drugs in the elderly. For propranolol the only important factor is the serum alpha 1-acid glycoprotein concentration.

Aged↗

PubMedDate not supplied

An electron microscopic study of the origin of osteoblasts in implants of demineralized bone matrix.

Correlated light microscope and ultrastructural observations of allogeneic intramuscular implants of rat demineralized bone matrix demonstrate the interrelationships between various osteogenetic and non-osteogenetic cell types and suggest that the bone morphogenetic response is evoked from cells of a common origin. Endothelial cells may play a prominent, essential, as well as primary role in the bone morphogenetic response.

Animals↗

PubMed1980

Reassessment of factor solution of Halstead's Matrix.

Halstead's correlational matrix of 13 neuropsychological tests was reanalyzed with the objective of obtaining a more neuropsychologically meaningful solution. The emphasis was on solving for different numbers of factors (three and five). The three-factor solution supported and perhaps refined two of Halstead's original factors (P and A). The third factor loadings resulted in a considerably different concept that Halstead's D. The three factors (psychological vigilance, abstraction, and perception and memory for incidental stimuli) may be an essential factor pattern in recovery from head traumas. It was concluded that the investigator should not a priori be committed to a structure involving a particular number of factors. Experimentation with factor number or method would allow evaluation of the best psychological fit to the data.

Brain Damage, Chronic↗

PubMed2002

Over-expression of K-FGF or bFGF results in altered expression of matrix metalloproteinases: correlations with malignant progression and cellular invasion.

Matrix metalloproteinase (MMP) expression was investigated in NIH-3T3 fibroblasts that secrete K-FGF and in NIH-3T3 cells which express chimeric bFGF with a signal sequence targeting bFGF to the secretory pathway. Correlations between altered MMPs' and other proteases' expression and malignant potential were determined. Correlations between the expression of MMPs and the invasion ability of K-FGF and bFGF over-expressing cells were also determined. The resulting correlation between alterations in proteases and malignant progression supports a model which suggests that growth factor modulation of protease expression is part of the altered growth regulatory program associated with cellular transformation and malignant progression.

3T3 Cells↗

PubMed2001

Expression of tissue inhibitor of matrix metalloproteinase-2 correlates with activation of matrix metalloproteinase-2 and predicts poor prognosis in tongue squamous cell carcinoma.

Matrix metalloproteinase 2 (MMP-2) plays a crucial role in invasion and metastasis of malignant tumors. Membrane type 1-MMP (MT1-MMP) was originally identified as an activator of MMP-2. Tissue inhibitor of MMP-2 (TIMP-2) was identified as an inhibitor of MMP-2 and MT1-MMP. However, TIMP-2 was reported to be essential for cell-mediated activation of MMP-2 and thus, the contribution of TIMP-2 to tumor invasion has remained controversial. This study was designed to analyze the role of TIMP-2 for activation of MMP-2 and its prognostic value in tongue squamous cell carcinoma (SCC). Expression of MMP-2, MT1-MMP and TIMP-2 protein was analyzed by immunohistochemistry, and their association with clinical factors was evaluated in 51 patients treated surgically for tongue SCC. Expression of MMP-2, MT1-MMP and TIMP-2 was significantly correlated with local and distant metastatic tumor recurrence and poor prognosis (MMP-2 and MT1-MMP, p < 0.0001; TIMP-2, p = 0.0002). Activation of MMP-2, analyzed by gelatin zymography in 17 fresh specimens, was remarkably associated with expression of MMP-2 (r = 0.779, p < 0.0001), MT1-MMP (r = 0.674, p < 0.0022) and TIMP-2 (r = 0.858, p < 0.0001). Increased expression of TIMP-2, as well as MMP-2 and MT1-MMP, was an important prognostic factor in patients with tongue SCC.

Adult↗

PubMed1995

Efficient calculation of the principal components of imaging data.

Principal components analysis (PCA) of images is important in many applications such as positron emission tomography and functional magnetic resonance imaging. PCA is difficult for image data because the correlation matrix is very large. We present a direct method of calculating the PCA of the voxels from the small matrix expressing the correlations between images, instead of the larger matrix representing the correlations between voxels. The method is fast and accurate. It is faster and requires less memory than a singular value decomposition, although it is less accurate. It is much faster and more accurate than iterative and other approximate methods developed for this problem.

Algorithms↗

PubMed2000

How good is good enough in path analysis of fMRI data?

This paper is concerned with the problem of evaluating goodness-of-fit of a path analytic model to an interregional correlation matrix derived from functional magnetic resonance imaging (fMRI) data. We argue that model evaluation based on testing the null hypothesis that the correlation matrix predicted by the model equals the population correlation matrix is problematic because P values are conditional on asymptotic distributional results (which may not be valid for fMRI data acquired in less than 10 min), as well as arbitrary specification of residual variances and effective degrees of freedom in each regional fMRI time series. We introduce an alternative approach based on an algorithm for automatic identification of the best fitting model that can be found to account for the data. The algorithm starts from the null model, in which all path coefficients are zero, and iteratively unconstrains the coefficient which has the largest Lagrangian multiplier at each step until a model is identified which has maximum goodness by a parsimonious fit index. Repeating this process after bootstrapping the data generates a confidence interval for goodness-of-fit of the best model. If the goodness of the theoretically preferred model is within this confidence interval we can empirically say that the theoretical model could be the best model. This relativistic and data-based strategy for model evaluation is illustrated by analysis of functional MR images acquired from 20 normal volunteers during periodic performance (for 5 min) of a task demanding semantic decision and subvocal rehearsal. A model including unidirectional connections from frontal to parietal cortex, designed to represent sequential engagement of rehearsal and monitoring components of the articulatory loop, is found to be irrefutable by hypothesis-testing and within confidence limits for the best model that could be fitted to the data.

Adult↗

PubMed2005

Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS).

BACKGROUND: Proteomic profiling of complex biological mixtures by the ProteinChip technology of surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) is one of the most promising approaches in toxicological, biological, and clinic research. The reliable identification of protein expression patterns and associated protein biomarkers that differentiate disease from health or that distinguish different stages of a disease depends on developing methods for assessing the quality of SELDI-TOF mass spectra. The use of SELDI data for biomarker identification requires application of rigorous procedures to detect and discard low quality spectra prior to data analysis. RESULTS: The systematic variability from plates, chips, and spot positions in SELDI experiments was evaluated using biological and technical replicates. Systematic biases on plates, chips, and spots were not found. The reproducibility of SELDI experiments was demonstrated by examining the resulting low coefficient of variances of five peaks presented in all 144 spectra from quality control samples that were loaded randomly on different spots in the chips of six bioprocessor plates. We developed a method to detect and discard low quality spectra prior to proteomic profiling data analysis, which uses a correlation matrix to measure the similarities among SELDI mass spectra obtained from similar biological samples. Application of the correlation matrix to our SELDI data for liver cancer and liver toxicity study and myeloma-associated lytic bone disease study confirmed this approach as an efficient and reliable method for detecting low quality spectra. CONCLUSION: This report provides evidence that systematic variability between plates, chips, and spots on which the samples were assayed using SELDI based proteomic procedures did not exist. The reproducibility of experiments in our studies was demonstrated to be acceptable and the profiling data for subsequent data analysis are reliable. Correlation matrix was developed as a quality control tool to detect and discard low quality spectra prior to data analysis. It proved to be a reliable method to measure the similarities among SELDI mass spectra and can be used for quality control to decrease noise in proteomic profiling data prior to data analysis.

Female↗

PubMed2005

Ontogenetic integration of the hominoid face.

By investigating similarity in cranial covariation patterns, it is possible to locate underlying functional and developmental causes for the patterning, and to make inferences about the evolutionary forces that have acted to produce the patterns. Furthermore, establishing where these covariation patterns may diverge in ontogeny can offer insight into when selection may have acted on development. Here, covariation patterns are compared among adult and non-adult members of the African ape/human clade, in order to address three questions. First, are integration patterns constant among adult African apes and humans? Second, are they are constant in non-adults--i.e. throughout ontogeny? Third, if they are not constant, when do they diverge? Measurements are obtained from 677 crania of adult and non-adult African apes and humans. In order to address the first two questions, correlation matrices and theoretical integration matrices are compared using matrix correlation methods. The third question is evaluated by comparing correlation and variance/covariance patterns, using matrix correlation and random skewers methods, respectively, between adjacent age categories within each species, and between equivalent age categories among the four species. Results show that the hominoids share a similar pattern of ontogenetic integration, suggesting that common developmental/functional integrative processes may play an important role in keeping covariance structure stable across this lineage. However, there are some important differences in the magnitude of integration and in phenotypic covariance structure among the species, which may provide some insight into how selection acted to differentiate humans from the great apes.

Adolescent↗

PubMed2005

Stainable hepatic iron in 341 African American adults at coroner/medical examiner autopsy.

BACKGROUND: Results of previous autopsy studies indicate that increased hepatic iron stores or hepatic iron overload is common in African Americans dying in hospitals, but there are no reports of hepatic iron content in other cohorts of African Americans. METHODS: We investigated the prevalence of heavy liver iron deposition in African American adults. Using established histochemical criteria, we graded Perls' acid ferrocyanide-reactive iron in the hepatocytes and Kupffer cells of 341 consecutive African American adults who were autopsied in the coroner/medical examiner office. Heavy staining was defined as grade 3 or 4 hepatocyte iron or grade 3 Kupffer cell iron. RESULTS: There were 254 men and 85 women (mean age ± 1 SD: 44 ± 13 y vs. 48 ± 14 y, respectively; p = 0.0255); gender was unstated or unknown in two subjects. Approximately one-third of subjects died of natural causes. Heavy staining was observed in 10.2% of men and 4.7% of women. 23 subjects had heavy hepatocyte staining only, six had heavy Kupffer cell staining only, and one had a mixed pattern of heavy staining. 15 subjects had histories of chronic alcoholism; three had heavy staining confined to hepatocytes. We analyzed the relationships of three continuous variables (age at death in years, hepatocyte iron grade, Kupffer cell iron grade) and two categorical variables (sex, cause of death (natural and non-natural causes)) in all 341 subjects using a correlation matrix with Bonferroni correction. This revealed two positive correlations: hepatocyte with Kupffer cell iron grades (p < 0.01), and male sex with hepatocyte iron grade (p < 0.05). We also analyzed the relationship of steatosis, inflammation, and fibrosis/cirrhosis in 30 subjects with heavy iron staining using a correlation matrix with Bonferroni correction. There were significant positive correlations of steatosis with inflammation (r = 0.5641; p < 0.01), and of inflammation with fibrosis/cirrhosis (r = 0.6124; p < 0.01). CONCLUSIONS: The present results confirm and extend previous observations that heavy liver iron staining is relatively common in African Americans. The pertinence of these observations to genetic and acquired causes of iron overload in African Americans is discussed.

Journal Article↗

PubMed2005

Detection and characterization of changes of the correlation structure in multivariate time series.

We propose a method based on the equal-time correlation matrix as a sensitive detector for phase-shape correlations in multivariate data sets. The key point of the method is that changes of the degree of synchronization between time series provoke level repulsions between eigenstates at both edges of the spectrum of the correlation matrix. Consequently, detailed information about the correlation structure of the multivariate data set is imprinted into the dynamics of the eigenvalues and into the structure of the corresponding eigenvectors. The performance of the technique is demonstrated by application to N(f)-tori, autoregressive models, and coupled chaotic systems. The high sensitivity, the comparatively small computational effort, and the excellent time resolution of the method recommend it for application to the analysis of complex, spatially extended, nonstationary systems.

Journal Article↗

PubMed1975

Taxonomic congruence in Eskimoid populations.

The study compares distance relationships in Eskimoid populations based on metric and attribute data with linguistic relationships based on structural and lexicostatistical data. Taxonomic congruence and the non-specificity hypothesis are investigated by matrix correlations and by a clustering procedure. The matrix correlation approaches employed are the Pearson product-moment correlation coefficient and the Spearman rank-order correlation coefficient. An unweighted pair-group clustering procedure provides a visual comparison of biological and linguistic relationships. Data consist of 74 craniometric measurements and 28 cranial observations taken on 12 Eskimoid populations. Mahalanobis' D2 and Balakrishnan and Sanghvi's B2 were used to compute the metric and attribute distances, respectively. The results indicate that a strict adherence to the non-specificity hypothesis is untenable. Also, there is better concordance between the sexes for metric distances than for attribute distances, and the metric data are more concordant with linguistic relationships than are the attribute data.

Cephalometry↗

PubMed1998

[Relationship between dietary fiber intake and food intake patterns of the general population, evaluated by a regional nutrition survey].

This study was performed to estimate the dietary fiber intake calculated using individual food intake data and the dietary fiber tables, and to ascertain the relationship between food intake patterns and dietary fiber intake of the general population. The 805 subjects over 15 years old were obtained from the Tottori Prefecture Nutrition Survey. The results are summarized as follows: 1. The average dietary fiber intake per capita per day was 18.19 g; 18.67 g in men, and 17.81 g in women. Dietary fiber intake per energy was different among sexes and ages: women had more dietary fiber than men and the aged had more than the young. Those who had high fiber intake per energy took green vegetables, fruits, milk, soybean products, seaweed and potatoes more frequently, and did not take oil so frequently. 2. Total dietary fiber intake from 20 food-group sources was analyzed by Multiple Regression Analysis. For both men and women fruits, vegetables and soybean products mostly influenced dietary fiber intake. 3. Based on the intake of the 20 food-groups obtained from 356 men and 449 women, the correlation matrix among these foods was calculated. The correlation matrix was also submitted to a Principal Component Analysis. The result of the Principal Component Analysis told that food intake patterns were different among the levels of dietary fiber intake. Food intake patterns of men and women who had high fiber intake per energy had an eating pattern characterized by relatively more non-processed vegetable food, bread and milk. 4. The level of blood pressure was significantly related to dietary fiber intake per energy in men over 60 years old. In the hypertensive men over 60 years old, 23.3% were in the low fiber intake group, 37.2% in the middle group, and 39.5% in the high group. But in the normal blood pressure men over 60 years old, 50.0% were in the low fiber intake group, 8.3% in the middle group, and 41.7% in the high group.

Adolescent↗

PubMed1986

Analysis of interspecific relationships in mesostigmatid mites (Acari: Mesostigmata) in the nests of the bank vole (Clethrionomys glareolus (Schreber, 1780)).

An analysis is presented of a community of mesostigmatid mites from the nests of Clethrionomys glareolus found in the forest biotopes of Vsetínské Beskydy Mts. (North Moravia) throughout all seasons of the year. Main attention was paid to the structure of the nest community, relationships of mites to their host and interspecific relationships in the mites themselves. Primarily cluster and factor analyses based on correlation matrix were used for mathematical assessment. The particular elements of correlation matrix were Spearman's non-parametric correlation coefficients computed from frequencies of species in the nests studied.

Animals↗

PubMed2004

A neural network learning for adaptively extracting cross-correlation features between two high-dimensional data streams.

This paper proposes a novel cross-correlation neural network (CNN) model for finding the principal singular subspace of a cross-correlation matrix between two high-dimensional data streams. We introduce a novel nonquadratic criterion (NQC) for searching the optimum weights of two linear neural networks (LNN). The NQC exhibits a single global minimum attained if and only if the weight matrices of the left and right neural networks span the left and right principal singular subspace of a cross-correlation matrix, respectively. The other stationary points of the NQC are (unstable) saddle points. We develop an adaptive algorithm based on the NQC for tracking the principal singular subspace of a cross-correlation matrix between two high-dimensional vector sequences. The NQC algorithm provides a fast online learning of the optimum weights for two LNN. The global asymptotic stability of the NQC algorithm is analyzed. The NQC algorithm has several key advantages such as faster convergence, which is illustrated through simulations.

Algorithms↗

PubMed1975

On the soluble phase of adrenergic nerve vesicles: correlation of matrix density and biochemical composition.

Highly purified sympathetic nerve vesicles isolated from bovine splenic nerves were treated by hypo-osmotic shocks, freeze-thawing or incubation in the absence or presence of ATP and MgCl. The vesicle preparations were then studied morphologically by electron microscopy and their content of noradrenaline (NA), and soluble proteins analyzed biochemically with special regard to dopamine beta-hydroxylase (DBH). Hypo-osmotic shocks released about 25 per cent of the NA and protein content and about 8 per cent of the DBH activity. This treatment induced swelling of the vesicles but their membranes remained unruptured and they still contained dense cores. Freeze-thawing released about 35 per cent of the NA, 25 per cent of the proteins and 11 per cent of the DBH. After the latter treatment some matrix material still remained in most vesicles but many were less stainable than the intact vesicles in cold control preparations. During incubation at 30 degrees C in an isotonic sucrose-phosphate medium for 30 min the vesicles released most of their NA and soluble DBH activity as well as much of their matrix density. After incubation at 37 degrees C for 30 min most vesicles appeared translucent. After incubation at 30 degrees C for 30 min in the presence of ATP and MgCl the vesicles lost most of their original NA content but retained their DBH activity and most of their matrix density. The results indicate that there is not always a correlation between NA content and retention of matrix density which suggests that DBH might be a component of a macro-molecular complex responsible for the staining reaction taking place in the maxtrix of NA depleted vesicles. This hypothesis is further supported by the finding of striking similarities between DBH isolated from chromaffin granules and the granular and fibrillar material surrounding the nerve vesicles after depletion.

Adenosine Triphosphate↗