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PubMed2005

Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression.

A multiple linear regression method was applied to predict real values of solvent accessibility from the sequence and evolutionary information. This method allowed us to obtain coefficients of regression and correlation between the occurrence of an amino-acid residue at a specific target and its sequence neighbor positions on the one hand, and the solvent accessibility of that residue on the other. Our linear regression model based on sequence information and evolutionary models was found to predict residue accessibility with 18.9% and 16.2% mean absolute error respectively, which is better than or comparable to the best available methods. A correlation matrix for several neighbor positions to examine the role of evolutionary information at these positions has been developed and analyzed. As expected, the effective frequency of hydrophobic residues at target positions shows a strong negative correlation with solvent accessibility, whereas the reverse is true for charged and polar residues. The correlation of solvent accessibility with effective frequencies at neighboring positions falls abruptly with distance from target residues. Longer protein chains have been found to be more accurately predicted than their smaller counterparts.

Amino Acids↗

PubMed2000

Life expectancy as an indicator of environmental health.

Whether or not life expectancy at birth is related to the quality of life as expressed by global economical, environmental and nutritional measures is the primarily studied question in this article. Two models, set of independent variables and multivariate analysis was performed. An attempt to estimate the role of studied variables in overall life expectancy was done, too. A descriptive, ecological study design was used. The population of 156 countries have been taken into account, using data from published databases [7, 9]. Access to safe drinking water, per capita gross domestic product, literacy, calories available as percentage of needs and per capita public health expenditures were taken as exposure, and compared with life expectancy at birth. A linear regression model was used to estimate the role of different exposures on life expectancy at birth. A correlation matrix for all variables and life expectancy at birth is presented in the article. Literacy and access to safe drinking water are statistically significant variables (p < 0.001) also after fitting a linear regression model. The correlation coefficient for the linear model was 0.8823 (R2 = 0.7784). Shares of years of life from overall life expectancy attributed to studied variables were 28.06, 9.42, 2.04 and 1.93% for literacy, access to safe drinking water, GDP and calories available as percentage of needs, respectively.

Educational Status↗

PubMedDate not supplied

Eigenvector-based spatial filtering for reduction of physiological interference in diffuse optical imaging.

Diffuse optical imaging is an effective technique for noninvasive functional brain imaging. However, the measurements respond to systemic hemodynamic fluctuations caused by the cardiac cycle, respiration, and blood pressure, which may obscure or overwhelm the desired stimulus-evoked response. Previous work on this problem employed temporal filtering, estimation of systemic effects from background pixels, or modeling of interference signals with predefined basis functions, with some success. However, weak signals are still lost in the interference, and other complementary methods are desirable. We use the spatial behavior of measured baseline signals to identify the interference subspaces. We then project signals components in this subspace out of the stimulation data. In doing so, we assume that systemic interference components will be more global spatially, with higher energy, than the stimulus-evoked signals of interest. Thus, the eigenvectors corresponding to the largest eigenvalues of an appropriate correlation matrix form the basis for an interference subspace. By projecting the data onto the orthogonal nullspace of these eigenvectors, we can obtain more localized response, as reflected in improved contrast-to-noise ratio and correlation coefficient maps.

Artifacts↗

PubMedDate not supplied

[Validation of the French version of a pleasure scale for children (The Pleasure Scale for Children, PSC, Kazdin, 1989) in 214 hospitalized children in pediatrics].

UNLABELLED: The aim of this study was to determine the metrological parameters of a french version of the Pleasure Scale for Children (PSC): 214 (121 males and 93 females) with a mean age of 8.69 years (sd: 1.95) ranging from 6 years to 12 years were included in the study. The children were inpatients presenting various somatic disorders. STATISTICAL ANALYSIS: First a principal component analysis was done on the 39 items of the correlation matrix. Several guidelines were used to limit the number of factors (Kaiser criteria, Cattell scree test, Horn parallel analysis). Secondly the construct validity was studied using the alpha Cronbach coefficient and by calculing the Pearson correlation coefficient between each item and the total score. Thirdly the concurrent validity was determinated using two items of the Children Depression Rating Scale--Revised (CDRS-R) measuring pleasure (social withdrawal and enjoyment capacity). Fourthly the discriminant validity of the PSC was studied by comparing non depressive children (score lower than 30 to the CDRS-R) and depressive children (score higher than 30 to the CDRS-R). RESULTS: The principal component analysis showed a one factor solution with 33 items among the 39 having a higher than 0.3 saturation. The Cronbach alpha coefficient was 0.84. All the items correlated with the total score. The mean value was 0.37. The correlations between the total score of the scale and the CDRS-R enjoyment capacity and social withdrawal items were respectively -0.37 (p < 0.01) and -0.38 (p < 0.01). PSC score were significantly lower in depressive children (m = 86.96; sd = 8.33) than in non depressive children (m = 94.67; sd = 10) (t = 5.32; df = 212; p < 0.001).

Animals↗

PubMed2003

Construct validity of a kinesiophysical functional capacity evaluation administered within a worker's compensation environment.

The construct validity of a kinesiophysical Functional Capacity Evaluation (FCE) administered within a worker's compensation context was examined. A cross-sectional study design was employed. Clinical and demographic information on workers' compensation claimants was extracted from a rehabilitation facility's database. Measures of interest were the Isernhagen Work Systems' (Duluth, MN) FCE, the Pain Disability Index (PDI), and a pain visual analogue scale (VAS). A multitrait Pearson correlation matrix was created to observe the pattern of relationships between variables. The sample consisted of 321 subjects with work-related, medically stable low back pain of median duration of 307 days. FCE performance was moderately correlated with the PDI (r = -0.44-0.52) and with the pain VAS (r = 0.34-0.45). Pain intensity was correlated highly with the PDI (r = 0.79). The moderate relationship between FCE and the PDI supports the construct validity of FCE as a functional measure. However, kinesiophysical FCE performance was not unrelated to pain severity ratings as purported.

Chronic Disease↗

PubMed2003

Dynamics of market correlations: taxonomy and portfolio analysis.

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the "asset tree" has been studied in order to reflect the financial market taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer. During crashes, due to the strong global correlation in the market, the tree shrinks topologically, and this is shown by a low value of the mean occupation layer. The tree seems to have a scale-free structure where the scaling exponent of the degree distribution is different for "business as usual" and "crash" periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects such as the window size dependence of the investigated quantities are also discussed.

Journal Article↗

PubMedDate not supplied

Anatomical and physiologic characteristics to predict football ability. Report of study methods and correlations, University of Arkansas, 1976.

In a prospective study of 56 scholarship players at the University of Arkansas in 1976, 14 anatomical and physiologic measurements were carried out on each of the 56 players, to include certain orthopaedic strength, power, and balance tests, and compared to the coaches' subjective ratings of football ability in an effort to determine which characteristics best correlate to the athlete's true performance. The correlation matrix for the criterion measure and the predictor variables of selected anatomical strength, balance, and power measures are presented, and the results of the study indicate that genu varum (0.445) and tibial torsion (-0.33) had the highest correlation with the coaching criterion variable. The average tibial torsion was 42.6 for these scholarship athletes, while normal average tibial torsion among a nonscholarship group was 27.40 degrees. Other anatomical characteristics measured, as well as strength and power measure, could not reach the critical level of +/- 0.263 to be significant at the 0.05 level, although horsepower was close (0.255). The Margaria-Kalamen power test was significantly related to the 40-yard dash, and a moderately good measure of football ability.

Anthropometry↗

PubMed1987

Characterization of olfactory dysfunction.

Management of dysosmic patients frequently is hampered by an incomplete description of their chief complaint and sometimes inadequate qualitative analysis of their symptoms. Qualitative analysis of olfactory dysfunction by an Odorant Confusion Matrix helps to characterize more fully sense of smell in the dysosmic patient. It is well grounded in psychophysical theory, thereby permitting physiological inferences about specific neural dysfunctions. The quantitative measure derived from the matrix correlates well with another quantitative measure of olfactory ability, the Smell identification Test, and provides the opportunity for valid comparisons among and within patients. Examination of illustrative case reports demonstrates that the qualitative features of the Odorant Confusion Matrix offer additional insights to support etiologic diagnoses of disturbances in sense of smell.

Adult↗

PubMed2006

Three-dimensional study of pelvic asymmetry on anatomical specimens and its clinical perspectives.

The aim of this study was to assess pelvic asymmetry (i.e. to determine whether the right iliac bone and the right part of the sacrum are mirror images of the left), both quantitatively and qualitatively, using three-dimensional measurements. Pelvic symmetry was described osteologically using a common reference coordinate system for a large sample of pelvises. Landmarks were established on 12 anatomical specimens with an electromagnetic Fastrak system. Seventy-one paired variables were tested with a paired t-test and a non-parametric test (Wilcoxon). A Pearson correlation matrix between the right and left values of the same variable was applied exclusively to values that were significantly asymmetric in order to calculate a dimensionless asymmetry index, ABGi, for each variable. Fifteen variables were significantly asymmetric and correlated with the right vs. left sides for the following anatomical regions: sacrum, iliac blades, iliac width, acetabulum and the superior lunate surface of the acetabulum. ABGi values above a threshold of +/- 4.8% were considered significantly asymmetric in seven variables of the pelvic area. Total asymmetry involving the right and the left pelvis seems to follow a spiral path in the pelvis; in the upper part, the iliac blades rotate clockwise, and in the lower part, the pubic symphysis rotates anticlockwise. Thus, pelvic asymmetry may be evaluated in clinical examinations by measuring iliac crest orientation.

Acetabulum↗

PubMed1979

HLA--D typing with lymphoblastoid cell lines. IV. Allelic relationships.

Responses of approximately 200 persons were measured by mixed leukocyte cultures against 41 lymphoblastoid cell lines which were thought to be homozygous for HLA--D (i.e. LCL-HTCs). These responses were standardized by computer analysis and the resultant Interaction Indices for each LCL-HTC were compared with those of every other LCL-HTC in a correlation matrix of 861 independent analyses. Only those analyses involving LCL-HTCs of defined HLA--D types are reported here. In general, these studies confirmed many allelic relationships of reputedly similar LCL-HTCs; however, several unexpected groups of correlations suggested that groups Dw1 and 3 overlap to form Groups "1a-3," "1b-3" and "true 3." The "1b-3" group also included Dw8. Segregation of the "1b-3" allelic group was also observed in a family study. These preliminary analyses suggest a working model for further investigation of HLA--D allelic relationships (Fig. 3). On the other hand, they may also be interpreted to suggest that "typing" with LCL-HTCs may be controlled by a separate HLA locus which is closely related to, but distinct from, HLA--D.

Alleles↗

PubMed2005

Linear scaling computation of the Fock matrix. VII. Periodic density functional theory at the Gamma point.

Linear scaling quantum chemical methods for density functional theory are extended to the condensed phase at the Gamma point. For the two-electron Coulomb matrix, this is achieved with a tree-code algorithm for fast Coulomb summation [M. Challacombe and E. Schwegler, J. Chem. Phys. 106, 5526 (1997)], together with multipole representation of the crystal field [M. Challacombe, C. White, and M. Head-Gordon, J. Chem. Phys. 107, 10131 (1997)]. A periodic version of the hierarchical cubature algorithm [M. Challacombe, J. Chem. Phys. 113, 10037 (2000)], which builds a telescoping adaptive grid for numerical integration of the exchange-correlation matrix, is shown to be efficient when the problem is posed as integration over the unit cell. Commonalities between the Coulomb and exchange-correlation algorithms are discussed, with an emphasis on achieving linear scaling through the use of modern data structures. With these developments, convergence of the Gamma-point supercell approximation to the k-space integration limit is demonstrated for MgO and NaCl. Linear scaling construction of the Fockian and control of error is demonstrated for RBLYP6-21G* diamond up to 512 atoms.

Journal Article↗

PubMed2002

Comments on the Meehl-Waller (2002) procedure for appraisal of path analysis models.

P. E. Meehl and N. G. Waller (2002) proposed an innovative method for assessing path analysis models wherein they subjected a given model, along with a set of alternatives, to risky tests using selected elements of a sample correlation matrix. Although the authors find much common ground with the perspective underlying the Meehl-Waller approach, they suggest that there are aspects of the proposed procedure that require close examination and further development. These include the selection of only one subset of correlations to estimate parameters when multiple solutions are generally available, the fact that the risky tests may test only a subset of parameters rather than the full model of interest, and the potential for different results to be obtained from analysis of equivalent models.

Humans↗

PubMed1990

[Correlation between morphologies of mandibular vertical sections and linear measurements of the skull].

The purpose of this study is to evaluate the relationships between the sectional forms of the mandible and the craniofacial morphology. Vertical sections were made at the symphysis (SY) and at the second molar region (M2R). Materials were dried human skulls which were measured in three dimensional co-ordinate system. The correlation matrix of 24 measurements was examined in the male and the female. The difference of these measurements between the low angle group and the high angle group of gonial angle was also examined. Results obtained were as follows: 1. Gonial angle was negatively correlated with the height, width, breadth of ramus and the breadth of second molars. SY form was related to the facial height and size of the mandible. On the other hand, M2R form was related to the height, width and breadth of ramus. 2. The differences of measurements between the low angle group and the high angle group of gonial angle were as follows: 1) The ramal height, ramal width, bicondylar width and breadth of second molars in the low angle group were significantly larger than those in the high angle group. 2) The measurements of SY in the high angle group and the low angle group showed no significant difference. 3) The height and area of M2R in the low angle group were significantly larger than those in the high angle group. This study demonstrated that SY form might relate to vertical factors of the face (facial height), the size of mandible and the types of occlusions. On the other hand, M2R form being nearer to the attachment of masseter and medial pterygoid muscles than SY was related to the form of ramus and the gonial angle.

Cephalometry↗

PubMed1989

Differential adhesion of metastatic rat mammary carcinoma cells to organ-derived microvessel endothelial cells and subendothelial matrix.

The in vitro adhesion rates of rat 13762NF mammary adenocarcinoma cell clones of different spontaneous metastatic potentials to cloned microvessel endothelial cell monolayers and their subendothelial extracellular matrix were investigated. In this system, high rates of adhesion of the cloned tumor cell lines to syngeneic target (lung) organ-derived subendothelial matrix correlated with spontaneous metastatic potential, whereas adhesion to the lung microvessel endothelial cell apical surfaces occurred at lower rates and was not highly significantly different among the tumor cell lines. Adhesion rates to bovine aortic large vessel, and human brain and human meningeal microvessel endothelial cell monolayers were, in general, lower than those found with syngeneic lung microvessel endothelial cells, and did not correlate with spontaneous metastatic potential. Growth of endothelial cells in fetal bovine serum or platelet-poor horse serum did not affect the results, suggesting that in this system metastasis-associated organ-adhesive specificity is determined at the level of the subendothelial matrix.

Adenocarcinoma↗

PubMed1999

Generating correlation matrices with model error for simulation studies in factor analysis: a combination of the Tucker-Koopman-Linn model and Wijsman's algorithm.

Most simulation studies in factor analysis follow a process of constructing population correlation matrices from the common-factor model and generating sample correlation matrices from the population matrices. In the common-factor model, the population correlation matrix is perfectly fit by the model's containing common and unique factors. However, since no mathematical model accounts exactly for the real-world phenomena that it is intended to represent, the Tucker-Koopman-Linn model (1969) is more realistic for generating correlation matrices than the conventional common-factor model because the former incorporates model error. In this paper, a procedure for generating population and sample correlation matrices with model error by combining the Tucker-Koopman-Linn model and Wijsman's algorithm (1959) is presented. The SAS/IML program for generating correlation matrices is described, and an example is also provided.

Algorithms↗

PubMed2000

Relationships between plantar flexor muscle stiffness, strength, and range of motion in subjects with diabetes-peripheral neuropathy compared to age-matched controls.

STUDY DESIGN: Descriptive study to compare relationships between muscle performance measures in 2 subject groups. OBJECTIVES: To determine the relationships between plantar flexor (PF) muscle stiffness, strength (concentric peak torque), and dorsiflexion (DF) range of motion (ROM) in subjects with diabetes who have peripheral neuropathy (n = 17, 10 men, 7 women; age = 58 +/- 11 years) and age-matched controls (n = 17, 10 men, 7 women; age = 62 +/- 6 years). BACKGROUND: The relationships between muscle stiffness, strength, and joint ROM have not been clearly established. Furthermore, the effect of neuromuscular pathology on these relationships is unknown. METHODS AND MEASURES: PF stiffness and strength measurements were obtained with an isokinetic dynamometer. DF ROM was measured with a goniometer. A Pearson correlation matrix was constructed for each subject group using stiffness, strength, and ROM variables. The percent contribution of passive torque to total torque was computed at 2 joint angles. RESULTS: In subjects with diabetes and peripheral neuropathy (DM-PN) peak concentric PF torque was positively correlated with passive torque at 5 degrees DF (r = 0.77), Stiffness #1 (r = 0.58), and Stiffness #2 (r = 0.50). The percentage of passive PF torque at 5 degrees DF was greater in subjects with DM-PN, compared to control subjects (29.3 +/- 9.4% versus 12.6 +/- 5.9%). CONCLUSIONS: The positive correlation between PF stiffness and strength, and the greater percentage of passive PF torque in subjects with DM-PN suggest that patients with decreased strength may use passive torque to maximize total torque. Therefore, treatment methods designed to decrease stiffness should be used cautiously.

Aged↗

PubMed2000

The hypothalamic-pituitary-adrenal axis activity as a predictor of cardiovascular disease, type 2 diabetes and stroke.

OBJECTIVES: The hypothalamic-pituitary-adrenal (HPA) axis, the mediator of cortisol, plays a central role in the homeostatic processes. In this study, we addressed the potential impact of HPA axis activity on established anthropometric, metabolic and haemodynamic risk factors for cardiovascular disease (CVD), type 2 diabetes mellitus and stroke. DESIGN: A cross-sectional study. SUBJECTS: A subgroup of 284 men from a population sample of 1040 at the age of 51 years. MAIN OUTCOME MEASURES: Anthropometric measurements included body mass index (BMI, kg m-2), waist/hip circumference ratio (WHR) and abdominal sagittal diameter (D). Overnight fasting values of blood glucose, serum insulin, triglycerides, total, low (LDL) and high density (HDL) lipoprotein cholesterol, as well as resting heart rate and blood pressure, were also determined. By using repeated diurnal salivary cortisol measurements during everyday conditions, methods were developed to characterize the status of the HPA axis, and set in relation to the anthropometric, metabolic and haemodynamic measurements. RESULTS: In bivariate analyses, risk factors intercorrelated in clusters of anthropometric (BMI, WHR, D), metabolic (insulin, glucose and their ratio, triglycerides, cholesterol [total and LDL], HDL cholesterol [negative]) and haemodynamic (systolic and diastolic blood pressure and heart rate) measurements. This was also the case in the two-dimensional scaling analysis, where, however, HDL separated out. A normal HPA axis status, characterized by high variability and morning cortisol values, as well as a clear response to a standardized lunch and dexamethasone suppression test, was then introduced by a statistical weighting procedure. This did not essentially change the results of either the bivariate correlation matrix or the two-dimensional scaling analysis. A similar introduction of a pathological HPA axis, characterized by low variability and morning cortisol values, a poor lunch-induced cortisol response and a blunted dexamethasone suppression of cortisol, changed the results markedly. Now strong and consistent correlations were found not only within but also between different clusters of risk factors, which also congregated into one distinct cluster, again except for HDL cholesterol. CONCLUSIONS: These results disclose the prospect of an overriding function of a pathological HPA axis on other, established risk factors for CVD, type 2 diabetes and stroke. Its close association to HPA axis dysfunction may explain the previously reported powerful risk indication of abdominal obesity for the diseases mentioned. The HPA axis abnormality has been reported to be a characteristic consequence of frequently repeated or chronic environmental stress challenges.

Adipose Tissue↗

PubMed1993

Application of generalized estimating equations to a study of in vitro radiation sensitivity.

We describe an application of the generalized estimating equation (GEE) method (Liang and Zeger, 1986, Biometrika 73, 13-22) for regression analysis of correlated Poisson data from a split-plot design with a small number of experimental units. As an alternative to the use of an arbitrarily chosen working correlation matrix, we demonstrate the use of GEE with a reasonable model for the true covariance structure among repeated observations within individuals. We show that, under such a split-plot design with large clusters, the asymptotic relative efficiency of GEE with simple (independence or exchangeable) working correlation matrices is rather low. We conclude by summarizing issues and needs for further work concerning efficiency of the GEE parameter estimates in practice.

Biometry↗