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Results for “correlation matrix”

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PubMed1993

Markers of osteoarthritis and cartilage research in animal models.

Research in the past year on evaluating serum and synovial fluid markers in osteoarthritis has helped to define more precisely how the components of cartilage extracellular matrix correlate with disease progression. Novel, cartilage-specific markers, such as the cartilage oligomeric matrix protein, have been detected in serum and synovial fluid, and their relevance in the pathogenesis of osteoarthritis must now be determined. Precisely defined cartilage matrix protein changes in surgically induced and spontaneously occurring animal models of osteoarthritis have contributed to a better understanding of the dynamics of cartilage and bone reparative and degradative pathways.

Animals↗

PubMed2001

Global mapping analysis: stochastic approximation for multidimensional scaling.

In this paper, we propose global mapping analysis (GMA) as a new method to solve multidimensional scaling (MDS). By GMA, MDS is done by an online learning rule based on stochastic approximation. GMA need not directly calculate the disparity matrix for carrying out MDS, as Oja's PCA network do not calculate the correlation matrix. So, GMA is expected to be useful for multivariate data analysis on a large scale. Actually, it was verified by numerical experiments based on artificial data that GMA can work well even if the number of the attribute N is quite large (N=10,000.)

Data Interpretation, Statistical↗

PubMedDate not supplied

Time-resolved fluorometry (TRF)-based immunoassay concept for rapid and quantitative determination of biochemical myocardial infarction markers from whole blood, serum and plasma.

We report the development of a time-resolved fluorometry-based immunoassay concept for the rapid measurement of three cardiac markers from whole blood, serum or plasma. Using a universal all-in-one (AIO) dry reagent concept, all the analyte specific reagents are built into a single microtire well, to which an identical assay protocol is applied. Addition of 5-20 microL sample (whole blood, serum or plasma) together with a universal buffer initiates the reaction, which is brought close to equilibrium in 15 min. After the wash step the Eu chelate-derived signal is measured directly from the dried surface. Application of this concept to the three cardiac markers illustrates its ability to provide rapid, highly sensitive and fully quantitative results over a large dynamic range with good reproducibility. Such a performance, especially when using whole blood specimens, is largely a consequence of the inherently fluorescent and stable Eu-chelate employed in the system. Correlation to commercial assays was excellent for all three analytes, as was between-sample matrix correlation using the AIO assays. The presented assay concept enabling a simple automation is particularly suited for point-of-care applications, where the performance characteristics are fully comparable to state-of-the-art central laboratory immunoassays.

Biomarkers↗

PubMed1991

Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles.

A set of "similarity-parameters" was calculated that reflects the influence of the proteinogenic amino acids on the structure of the protein backbone. The parameters were derived from a detailed analysis of the amino acid specific main-chain torsion angle distributions as they are found in proteins (highly resolved protein structures from the Brookhaven Protein Data Bank). The purpose of these parameters is threefold: (1) they should help in estimating the structural effect of an amino acid substitution during the design of new mutants in protein-engineering; (2) in modeling by homology they should mark places in the protein where changes in the folding are expected; and (3) they should form a scoring matrix in protein sequence alignment superior to identity scoring. The usability of the "structure derived correlation matrix (SCM)" for these purposes is assessed and demonstrated for some examples in the paper.

Amino Acid Sequence↗

PubMed2004

Relationship between thirty post-thaw spermatozoal characteristics and the field fertility of 11 high-use Australian dairy AI sires.

This study determined the relationship between two measures of field fertility of 11 high-use Australian artificial insemination (AI) dairy bulls and thirty standard laboratory assessments of spermatozoal post-thaw viability. The two measures of field fertility used, conception rates (cCR) and non-return rates (cNRR), were both corrected for all major non-bull variables. Sperm viability assessments were conducted on semen collected within the same season as that used to derive the field fertility estimates. These assessments measured sperm concentration, motility, morphology and membrane integrity at thawing, after 2h incubation and after the swim-up sperm selection procedure. Derivations of these measures and in vitro embryo fertilizing and developmental capacity were also determined. The Genstat Statistical Package [Genstat 5 Release 4.2 Reference Manual, VSN International, Oxford, 2000] was used to conduct an analysis of variance on the viability parameters across semen straws and bulls, and to calculate the strength of correlation between each semen parameter, cNRR and cCR in a correlation matrix. Step forward multiple regression identified the combination of semen parameters that were most highly correlated with cCR and with cNRR. The sperm parameters identified as being most predictive of cCR were the percentage of morphologically normal sperm immediately post-thaw (zeroNorm), the number of morphologically normal sperm after the swim-up procedure (nSuNorm), and the rate of zygote cleavage in vitro (Clv); the predictive equation formed by these parameters accounted for 70% of variance. The predictive equation produced for cNRR contained the variables zeroNorm, the proportion of membrane intact sperm after 2h incubation at 37 degrees C (twoMem) and Clv and accounted for 76.5% of the variation. ZeroNorm was found to be consistent across straws and semen batches within-bull and the sperm parameter with the strongest individual predictive capacity for both cCR (P=0.1) and cNRR (P=0.001). Post-thaw sperm parameters can be used to predict field fertility of Australian dairy sires; the calculated predictive equations are particularly useful for identifying and monitoring bulls of very high and very low potential fertility within a group.

Animals↗

PubMed1995

A two-stage estimation of structural equation models with continuous and polytomous variables.

This paper develops a computationally efficient procedure for analysis of structural equation models with continuous and polytomous variables. A partition maximum likelihood approach is used to obtain the first stage estimates of the thresholds and the polyserial and polychoric correlations in the underlying correlation matrix. Then, based on the joint asymptotic distribution of the first stage estimator and an appropriate weight matrix, a generalized least squares approach is employed to estimate the structural parameters in the correlation structure. Asymptotic properties of the estimators are derived. Some simulation studies are conducted to study the empirical behaviours and robustness of the procedure, and compare it with some existing methods.

Humans↗

PubMed1999

Maternal animal model with correlation between maternal environmental effects of related dams.

A procedure to take into account the nongenetic relationship between maternal effects in adjacent generations is presented. It considers a correlation between maternal environments provided by a dam and its daughters (lambda). The dispersion structure of the maternal animal model was modified to include a correlation matrix (E) that relates the maternal permanent environmental effects. The structures of the E matrix and its inverse (E(-1)) are described. Both matrices are completely defined by the correlation coefficient lambda. An algorithm to compute these matrices from pedigree information was also developed. Furthermore, a Bayesian analysis of this model including the lambda parameter was developed using Gibbs sampling, with Metropolis steps for the nonstandard conditional distributions. With simulated data, the proposed model reduced the bias in all estimates of dispersion parameters when an antagonism between the maternal effects received by a daughter and its future maternal environment existed. This model also provides an estimate of the environmental relationship between the maternal effects of dams and daughters by the lambda parameter. The same Bayesian analysis was also carried out with weaning weight data of the Bruna dels Pirineus breed. The posterior means (standard deviation) of (co)variance ratios were .214 (.081) for direct heritability (h2d), .107 (.033) for maternal heritability (h2m), .047 (.020) for the proportion of variance due to maternal environmental effects (c2m), and -.034 (.043) for the genetic correlation between direct and maternal effects (r(dm)). The posterior mean of lambda parameter was -.190, and 76% of its marginal posterior distribution took negative values. As occurred with simulated data, considering the maternal environmental correlation in the analysis implied higher h2m estimates, lower c2m and h2d estimates, and less negative values for the marginal posterior distribution of r(dm). These results were considered as evidence of the environmental antagonism between maternal effects provided by a dam and its daughters to weaning weight of their progeny in the Bruna dels Pirineus breed.

Animal Husbandry↗

PubMed1994

Principal descriptors of body condition score in Holstein cows.

The objective of this study was to assess objectively the ability of observers to assess body condition of dairy cows. Four observers independently assigned a body condition score (five-point scale, .25 increments) and described the appearance of seven body regions of 225 Holstein cows. Areas described were the thurl region, ischial and ileal tuberosities, ilio-sacral and ischio-coccygeal ligaments, transverse processes of the lumbar vertebrae, and spinous processes of the lumbar vertebrae. An absolute body condition score was designated for each cow based on the modal body condition score for all observers. If there was no modal body condition score, the mean score was used for the absolute body condition score. Statistical analysis of principal components was used to examine the relationship between body region description and absolute body condition score. Descriptions of body regions were highly correlated across all absolute body condition scores. Four principal component vectors explained 83.6% of the variation of the body region correlation matrix. The first principal latent vector accounted for 55% of the variation and was uniformly correlated with all body regions. Analysis of variance of first principal latent vector as the dependent variable and absolute body condition score as the class variable indicated that body condition could be separated into .25 units between 2.5 and 4.0, inclusively. Below 2.5 and > 4.0, body condition could only be separated by .5 units. Distinct changes in specific body regions were associated with change in absolute body condition score. Observers agreed with the absolute score 58.1% of the time, deviating by .25 units 32.6% of the time. A body condition score can be given to a cow based on principal descriptors of specific body regions between 2.5 and 4.0 by .25 units.

Adipose Tissue↗

PubMed2001

Multivariate correlations of geochemical binding phases of heavy metals in contaminated river sediment.

Distributions of geochemical binding phases of seven heavy metals (Cr, Cu, Co, Zn, Ni, Pb, and Cd) in sediment cores taken from six heavily polluted sites of the Ell-Ren River in Southern Taiwan were studied. Sequential extraction procedures (SEP) were used to determine the variations of heavy metal binding phases (exchangeable, bound to carbonates, bound to manganese-oxides, bound to iron-oxides, and bound to organic matter) in different sediment depths. Multivariate analyses were used to explore the correlations among these geochemical binding phases of heavy metals. Results showed that the total amounts of various binding phases of heavy metals significantly varied with sediment depth, but their binding behaviors in various phases did not significantly change with depth. The organic matter content in the sediments increased with increasing Fe-oxide content. In addition, the binding affinities of carbonates with Zn, Pb, and Ni were higher than the affinities of carbonates with the other heavy metals. The binding affinity of Fe-oxides with Cr was higher than the affinities of Fe-oxides with the other heavy metals. Both correlation matrixes and principal component analyses demonstrated that distributions of Cu, Zn, Ni, and Cd had significant correlations with each other in both different depth horizons and various geochemical binding phases. The results indicate that these heavy metals might be discharged from the same pollution sources in the past, and also showed stable geochemical binding behaviors with the high silt sediment. However, Co had a poor correlation with the other six heavy metals in various binding phases, except with organic matter. Binding behaviors of Pb in the phases of bound to carbonates and exchangeable were different from the other six heavy metals. Cu was inversly correlated with the other six heavy metals in its binding behavior with reducible phases (Fe-/Mn-oxides).

Carbonates↗

PubMedDate not supplied

A conversational program for hierarchic and non-hierarchic cluster analysis.

The theoretical basis and the features of some cluster analysis programs are described in this paper. These programs use as input data an N x M matrix. For the N' less than or equal to N set of individuals, the cross-correlation matrix, R = (rij), is then calculated. The dissimilarity matrix, D = (dhk), and the distribution histogram of the distances between each pair is worked out. Hierarchic and non-hierarchic clustering techniques are allowed. Using the non-hierarchic strategy, the non-overlapping clusters are then separated into different groups. The distances between these groups are calculated and statistical tests of significance are performed. In the hierarchic case, a dendrogram is drawn using an agglomerative algorithm. As an example the programs (written in FORTRAN, batch or TSS version) were used to classify human mitotic chromosomes.

Classification↗

PubMed2001

Delaying S-phase progression rescues cells from heat-induced S-phase hypertoxicity.

The mechanism by which a cell protects itself from the lethal effects of heat shock and other stress-inducing agents is the subject of much research. We have investigated the relationship between heat-induced damage to DNA replication machinery and the lethal effects of heat shock, in S-phase cells, which are more sensitive to heat shock than either G1 or G2. We found that maintaining cells in aphidicolin, which prevents the passage of cells through S-phase, can rescue S-phase HeLa cells from the lethal effects of heat shock. When S-phase, HeLa cells were held for 5-6 h in 3 microM aphidicolin the measured clonogenic survival was similar to that for exponentially growing cells. It is known, that heat shock induces denaturation or unfolding of proteins, rendering them less soluble and more likely to co-isolate with the nuclear matrix. Here, we show that enhanced binding of proteins involved in DNA replication (PCNA, RPA, and cyclin A), with the nuclear matrix, correlates with lethality of S-phase cells following heat shock under four different experimental conditions. Specifically, the amounts of RPA, PCNA, and cyclin A associated with the nuclear matrix when cells resumed progression through S-phase correlated with cell killing. Heat-induced enhanced binding of nuclear proteins involved with other aspects of DNA metabolism, (Mrell, PDI), do not show this correlation. These results support the hypothesis that heat-induced changes in the binding of proteins associated with DNA replication factories are the potentially lethal lesions, which become fixed to lethal lesions by S-phase progression but are repairable if S-phase progression is delayed.

Aphidicolin↗

PubMed2001

Principal component analysis of polarity and interaction parameters in inverse gas chromatography.

Inverse gas chromatography is used in the characterization of aliphatic-aromatic and aromatic ketones, their oximes, and ketone-oxime or oxime-oxime mixtures. All these organic materials are used as liquid stationary phases in gas chromatographic columns. A series of polarity and Flory-Huggins interaction parameters are determined and used to describe the physicochemical properties of examined materials, metal extractants, and products of their degradation. Principal component analysis (PCA) is performed on a data matrix consisting of polarity and interaction parameters for ketones, their oximes, and mixtures. The calculations are carried out on the correlation matrix. It is found that seven principal components account for more than 95% of the total variance in the data, indicating that the polarity (interaction) parameters are not correlating well. Physical meanings are attributed to the principal components, the most influential ones being that the first and the second principal components account for several Flory-Huggins interaction parameters, whereas the fifth is correlated with criterion "A". The plots of component loadings show characteristic groupings of polarity indicators, whereas that of component scores show several groupings of stationary phases. Cluster analysis provides mainly the same groupings. PCA allows for the grouping of polarity and solubility parameters based on the information carried within those parameters. There is no need to use more than one parameter from each cluster. McReynolds polarity and the partial molar excess Gibbs free energy of solution per methylene group carry the same information. The groups of ketones, oximes, and their mixtures can be distinguished with the use of PCA on the basis of the measured polarity, solubility parameters, or both.

Chemical Phenomena↗

PubMed2002

Patterns of covariation in the hominoid craniofacial skeleton: implications for paleoanthropological models.

Living species are often used as analogues for fossil ones. When this is done, the implicit assumption is made that hominids and living hominoids vary in the same way. This paper addresses the validity of this assumption by comparing patterns of facial variation among humans and African apes. In particular, it addresses three major questions that underlie approaches to reconstructing hominid relationships. First, is phenotypic variation similar between closely related species? Second, if it is dissimilar, why? Third, is it feasible to use analogue species for modeling purposes? Measurements are obtained from 542 crania of adult apes and humans. Care is taken to choose homologous data, and account for differences in population size and structure. Variance/covariance and correlation matrices among the species are compared using common principal component (CPC) analysis, random skewers methods and matrix correlations. Morphological distances (D(2)) are calculated between population means, and between randomized pairs of individuals within each population, to evaluate intraspecific variation. Morphological distances are also calculated between randomized pairs of individuals using the variation patterns of analogue populations, in order to evaluate the efficacy of such substitutions. Results show that while the hominoids share a similar pattern of facial variation overall, the patterns do diverge. This difference generally corresponds to the phylogenetic relationships among these species, suggesting that patterns of variation may have diverged through time in the large bodied hominoids. Because interpretation of relationships in the fossil record is confounded by a lack of understanding of how variation changes through time, exploration of such patterns of divergence can provide important clues to understanding human evolution. Additionally, neglecting to account for this divergence when using living analogues as variation "yardsticks" can give rise to interpretations of the fossil record that are more speciose than is warranted.

Animals↗

PubMed1978

Assessment of protein-calorie malnutrition in surgical patients from plasma proteins and anthropometric measurements.

Six plasma proteins, two anthropometric measurements, hemoglobin and total lymphocytes were determined in 54 surgical patients and 19 normal individuals. Preoperative patients had a low mean values for prealbumin, retinol binding protein, and arm muscle circumference. In postoperative patients, plasma transferrin, albumin, hemoglobin, total lymphocytes and body weight were also low and complement C3 was higher than normal. A correlation matrix for 10 variables showed interrelationships between the biochemical and anthropometric data. Prealbumin and transferrin were highly correlated with most of the variables. The effects of protein-calorie malnutrition were analyzed from the data ranked and grouped according to the plasma prealbumin or transferrin concentration. Those groups with low mean values for these proteins also had low values for most of the other variables. Protein calorie malnutrition in surgical patients may be conveniently assessed from plasma prealbumin, transferrin, arm muscle circumference, percentage weight loss, and hemoglobin.

Adult↗

PubMed2004

Health-related quality of life and hand eczema--a comparison of two instruments, including factor analysis.

Hand eczema is a disease of long duration, affecting the individual and society. The purpose of this study of 100 patients (51 females and 49 males) at an occupational dermatology clinic was to investigate whether the generic questionnaire Short Form-36 (SF-36), and the dermatology-specific Dermatology Life Quality Index (DLQI) are appropriate for assessing health-related quality of life (HRQL) in patients with hand eczema, and whether gender differences in HRQL could be detected. HRQL was affected by hand eczema, measured with both SF-36 and DLQI. The SF-36 showed more impaired HRQL for females than for males, in the mental health dimension, whereas no gender-related differences were detected with the DLQI. To compare the instruments we used factor analysis, with a polychoric correlation matrix as input, thus taking the ordinal aspect of the data into account. There was a high correlation between the instruments for physical health, but lower for mental health. In this context our interpretation of the factor analysis is that the SF-36 measures mental health better than the DLQI. The SF-36 therefore appears suitable for use in future studies for measuring HRQL, and gender differences in HRQL, in persons with reported hand eczema.

Adult↗

PubMed1984

PCAVR: a portable laboratory program for performing varimax-rotated principal components analysis of event-related potentials.

A portable laboratory computer program for performing varimax-rotated principal components analysis (PCA) of event-related potentials (ERPs) is described. The program is written in FORTRAN 77; its compiled version requires 429, 140 bytes of memory. The program reads a matrix of numbers from an input file. The PCA can be performed on either the variance/covariance or the correlation matrix. The program computes the first six principal components. The user is given the option of rotating as many of the principal components as desired based upon the percentages of variance that they account for. Eigenvalues, percentages of variance, cumulative percentages of variance, factor loadings, and factor scores are written to an output file. Description of the program is preceded by a conceptual overview both of PCA as a factor analytic technique and of the application of PCA to ERP data analysis.

Brain↗

PubMed1986

Screening for antimicrobial activity of some essential oils by the agar overlay technique.

Fifty-three essential oils were tested against five micro-organisms (Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Candida albicans) using the agar overlay technique. The essential oils were randomly selected and not on the basis of a supposed activity. It was found that all oils showed an activity against at least one micro-organism, and that substantial activities against P. aeruginosa were scarce. Combined activities against C. albicans, the Gram-positive bacteria and E. coli, and an activity against C. albicans were most often observed. Secondly a combined activity against C. albicans, B. subtilis and S. aureus was found. The differences between the inhibition zones were too small for a differentiation of the antimicrobial activities of the essential oils. A correlation matrix shows the relationships of the micro-organisms as to the activity patterns of the essential oils. High correlations were found for all the micro-organisms, except for P. aeruginosa.

Anti-Bacterial Agents↗

PubMed2005

Genetics and geometry of canalization and developmental stability in Drosophila subobscura.

BACKGROUND: Many properties of organisms show great robustness against genetic and environmental perturbations. The terms canalization and developmental stability were originally proposed to describe the ability of an organism to resist perturbations and to produce a predictable target phenotype regardless of random developmental noise. However, the extent to which canalization and developmental stability are controlled by the same set of genes and share underlying regulatory mechanisms is largely unresolved. RESULTS: We have analyzed the effects of clinical genetic variation (inversion polymorphism) on wing asymmetry by applying the methods of geometric morphometrics in the context of quantitative genetics using isochromosomal lines of Drosophila subobscura. For the analysis of overall size, developmental stability was positively correlated with levels of heterozygosity and development at the optimal temperature. For analyses of shape, the overall comparisons by matrix correlations indicate that inter- and intraindividual variation levels were poorly correlated, a result also supported when comparing the vectors describing patterns of variation of landmark position. The lack of similarity was basically due to the discrepancy between the genetic and environmental components of the interindividual variation. Finally, the analyses have also underscored the presence of genetic variation for directional asymmetry. CONCLUSIONS: The results strongly support the hypothesis that environmental canalization and developmental stability share underlying regulatory mechanisms, but environmental and genetic canalization are not functionally the same. A likely explanation for this lack of association is that natural wing shape variation in Drosophila populations is loosely related to individual fitness.

Analysis of Variance↗