Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Principal component”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,387 records · Page 77Linked to original sources

An overview of OSPAR priority compounds and selection of a representative training set.

The aim of our study was to chemically characterize a set of priority substances in order to systematically select a representative set of heterogeneous substances for experimental studies of their persistence, bioaccumulation and toxicity (PBT). By including structurally diverse compounds in a PBT-screening protocol, structure-based knowledge would be achieved as a basis for more detailed studies of specific compounds from certain regions of the chemical domain. Initially compounds on the Draft Preliminary List of Substances of Possible Concern presented by the Oslo & Paris Commission (OSPAR) were subjected to broad chemical characterization using Principal Component Analysis (PCA). Molecular weight and seven physico-chemical descriptors collected from the literature, five calculated properties and 25 constitutional descriptors were used in this characterization. The OSPAR list represents a broad spectrum of substances, and thus provides a good basis for selecting heterogeneous substances. D-optimal design was applied to the first four principal components derived in the PCA. In total, 19 structurally diverse substances were chosen as representatives of the chemical domain including 353 substances.

Hazardous Substances↗

A genome-wide scan of symptom dimensions in bipolar disorder pedigrees of adult probands.

Although twin and adoption show bipolar disorder (BP) has a strong genetic component, few chromosomal regions have been consistently implicated by molecular genetic studies. To address this issue, we sought to determine if quantitative dimensions of bipolar disorder symptoms would be useful for detecting genes that underlie the susceptibility to bipolar disorder. Subjects were 520 individuals diagnosed with bipolar I, bipolar II or schizoaffective disorder, bipolar type who had participated in the NIMH genetics initiative for bipolar disorder. We constructed symptom scores from 29 psychiatric symptoms recorded in the Diagnostic Interview for Genetic Studies (DIGS). Principal components factor analysis followed by a varimax rotation was used to extract symptom dimensions. Factor scores were calculated for all genotyped individuals in the sample, regardless of affection status. Heritable factors were used in a variance-components linkage analysis, which utilized the exact likelihoods of allele-sharing identical-by-descent for each pair of relatives within each pedigree. The principal components factor analysis resulted in five independent dimensions: depressed state, psychosis, sleep disturbances, psychomotor acceleration, and irritability. Two factors were significantly heritable: depression (h2=0.53, p<0.001) and irritable vs. euphoric mania (h2=0.35, p=0.03). These were subsequently used in a linkage analysis that resulted in LOD scores of <2.0, which are not statistically significant. The five constructs developed through factor analysis appear to be consistent with previous factor analyses. Notably, only the dimensions associated with the type of mood disturbance showed high heritability, which suggests that careful measurements of depression, euphoria and irritability may be particularly useful in clarifying the genetic etiology of bipolar disorder in future studies.

Adult↗

Cranial movements during suction feeding in teleost fishes: Are they modified to enhance suction production?

Suction is produced during prey capture by most teleost fishes. Here, we ask two questions about the functional basis of suction feeding. First, is there variation in the kinematic pattern produced by different species while suction feeding? Second, do species termed 'suction specialists' demonstrate similar modifications to their feeding behavior? We used 10 kinematic variables in a principal component analysis to identify axes of variation among 14 suction feeding teleost species (representing nine families and five orders within the Euteleostei) that demonstrate different feeding habits and habitats. MANOVA and Tukey post hoc tests were used to assess differences among species. Most species clustered together on the principal component axes, suggesting a generalized mechanism that facilitates unidirectional flow. Typically, only one species stood out as 'extreme' on each functional axis, and a species that stood out on one axis did not stand out on others. Only one species, the flatfish Pleuronichthys verticalis, an obligate benthic feeder, demonstrated modifications consistent with enhanced suction production. This species displayed a suite of changes that should enhance suction production, including large hyoid depression, large cranial rotation, and small gape. We suggest that suction performance may be greatest in such obligate benthic feeders because cranial morphology is highly modified and prey are captured from the substrate.

Analysis of Variance↗

Interrelationship and familiality of dyslexia related quantitative measures.

Dyslexia is a complex gene-environment disorder with poorly understood etiology that affects about 5% of school-age children. Dyslexia occurs in all languages and is associated with a high level of social and psychological morbidity for the individual and their family; approximately 40-50% have persistent disability into adulthood. The core symptoms are word reading and spelling deficits, but several other cognitive components influence the core phenotype. A broad spectrum of dyslexia related phenotypes, including phonological decoding, phoneme awareness, orthographic processing, short-term memory, rapid naming and basic mathematical abilities, were investigated in large sample of 287 German dyslexia families. We explored the interrelationship between the component phenotypes using correlation and principal component analyses (PCA). In addition, we estimated familiality for phenotypes as well as for the factors suggested by PCA. The correlation between the component phenotypes varied between -0.1 and 0.7. The PCA resulted in three factors: a general dyslexia factor, a speed of processing factor and a mathematical abilities factor. The familiality estimates of single components and factors ranged between 0.25 and 0.63. Instead of analyzing single dyslexia-related components, multivariate analyses including factor analytic approaches may help in the identification of susceptibility genes.

Adolescent↗

Psychometric analysis of a scale assessing self-efficacy for cultural competence in patient counseling.

BACKGROUND: The Accreditation Council for Pharmacy Education adopted revised accreditation standards and guidelines for the PharmD degree program in January 2006. The revised standards mandate the inclusion of cultural competence in pharmacy curricula. Assessment tools to evaluate the impact of training are needed. OBJECTIVE: To examine the psychometric properties of a 12 item scale designed to estimate the impact of cultural competence training on pharmacy students' self-efficacy in providing culturally appropriate patient care. METHODS: A 12 item scale to assess the impact of an elective course on pharmacy students' (N = 175; 173 analyzable) perceived self-efficacy in providing culturally competent patient care was used before and after students completed the training. Principal components analysis was conducted to examine the underlying structure of the scale, and the Cronbach alpha statistic was computed as an estimate of internal consistency. Pre-versus posttraining responses for each item and for the total scale scores were compared as an indicator of concurrent validity. RESULTS: The principal components analysis yielded a one-component solution, "self-efficacy for cultural competence," which included all 12 contributing items and accounted for 46% of the total variance. Item communalities ranged from 0.25 to 0.58. Component loadings ranged from 0.50 to 0.76. Overall, the scale exhibited a Cronbach alpha estimate of internal consistency of 0.89. Posttraining scores were significantly higher than pretraining scores for both the total scale scores (posttest and pretest mean +/- SD score = 47.96 +/- 5.15 and 34.21 +/- 6.19, respectively; p < 0.001) and for each item (p values < 0.001). These comparisons provide evidence of concurrent validity. CONCLUSIONS: Our results suggest that our 12 item scale exhibits acceptable psychometric properties and is a useful tool for estimating the impact of cultural competence training on pharmacy students' perceived self-efficacy for providing culturally competent care and services.

Cultural Diversity↗

Chemometric exploration of an amperometric biosensor array for fast determination of wastewater quality.

Four wastewater samples of different treatment qualities; untreated, alarm, alert and normal, from a Swedish chemi-thermo-mechanical pulp mill and pure water were investigated using an amperometric bio-electronic tongue in a batch cell. The aim was to explore enzymatically modified screen-printed amperometric sensors for the discrimination of wastewater quality and to counteract the inherent drift. Seven out of eight platinum electrodes on the array were modified with four different enzymes; tyrosinase, horseradish peroxidase, acetyl cholinesterase and butyryl cholinesterase. At a constant potential the current intensity on each sensor was measured for 200s, 100s before injection and 100s after injection of the sample. The dynamic biosensor response curves from the eight sensors were used for principal component analysis (PCA). A simple baseline and sensitivity correction equivalent to multiplicative drift correction (MDC), using steady state intensities of reference sample (catechol) recordings, was employed. A clear pattern emerged in perfect agreement with prior knowledge of the samples explaining 97% of the variation in the data by two principal components (PCs). The first PC described the treatment quality of the samples and the second PC described the difference between treated and untreated samples. Horseradish peroxidase and pure platinum sensors were found to be the determinant sensors, while the rest did not contribute much to the discrimination. The wastewater samples were characterized by the chemical oxygen demand (COD), biological oxygen demand (BOD), total organic carbon (TOC), inhibition of nitrification, inhibition of respiration and toxicity towards Vibrio fischeri using Microtox, the freshwater alga Pseudokirchneriella subcapita and the freshwater crustacean Daphnia magna.

Algorithms↗

A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data.

A suite of Mathematica notebooks has been designed to ease the analysis of protein main chain 15N NMR relaxation data collected at a single magnetic field strength. Individual notebooks were developed to perform the following tasks: nonlinear fitting of 15N-T1 and -T2 relaxation decays to a two parameter exponential decay, calculation of the principal components of the inertia tensor from protein structural coordinates, nonlinear optimization of the principal components and orientation of the axially symmetric rotational diffusion tensor, model-free analysis of 15N-T1, -T2, and {1H}-15N NOE data, and reduced spectral density analysis of the relaxation data. The principle features of the notebooks include use of a minimal number of input files, integrated notebook data management, ease of use, cross-platform compatibility, automatic visualization of results and generation of high-quality graphics, and output of analyses in text format.

Anisotropy↗

Constitutional and echocardiographic variability of the normal electrocardiogram in children.

To understand better the normal electrocardiogram and to improve the diagnosis of left ventricular hypertrophy (LVH), the authors examined RV5 and SV1 + RV5, using a special computational technique, in relation to body size, heart size, and the distance between the heart and the chest wall in 7-year-old normal subjects. Boys and girls were analyzed separately. Using multiple regression analysis with a total of 16 constitutional and echocardiographic parameters as the predictor variable, the authors selected a minimum set of parameters and found that the greater the left ventricular mass (LVM) and the left ventricular cavity and the shorter the distance between the heart and the chest wall, the greater the RV5 and SV1 + RV5. In subjects with LVH in whom these parameters vary, SV1 + RV5 is preferable to RV5 for the electrocardiographic diagnosis of LVH, because LVM correlates more significantly with SV1 + RV5. In a similar analysis, using principal components as the predictor variable, no significance level was reached for the first principal component that represented size. This indicates that RV5 and SV1 + RV5 are in a constant range, irrespective of the body size and accompanying heart size.

Body Constitution↗

Maternal-infant interactions at one-year adjusted age in infants at low- and high-risk as newborns.

To compare maternal-infant interactions in high- and low-risk groups, we observed infants who had required neonatal intensive care and otherwise similar infants with normal perinatal histories in a follow-up clinic at one year adjusted age. The developmental level as assessed by the Bayley Scales of Infant Development was significantly lower for the high-risk infants than for the control infants at one year of age. Principal component analyses were used to define interaction patterns in each of five situations. Principal component analyses allow a more meaningful analysis of interrelated maternal and infant behaviors than do standard statistical analyses and minimize the likelihood of misleading 'significant' findings resulting from multiple comparisons. Prior to being examined, mothers of control infants were more likely to adopt an 'en face' position, play with, comfort, talk to, and smile at their infants than were mothers of high-risk infants. Control infants were more likely to smile in return. These differences between control and high-risk mother-infant dyads disappeared when the infants' developmental level was statistically controlled. Group differences in maternal-infant interactions independent of the infants' developmental level were observed in only one situation (collection of blood). Specific medical risk factors had little relation to findings at one year. Maternal-infant interaction should be interpreted in relation to the postconceptional and developmental age as well as the postnatal age of the infant.

Child Behavior↗

Molecular dynamics simulations of evolved collective motions of atoms in the myosin motor domain upon perturbation of the ATPase pocket.

A crucial point for mechanical force generation in actomyosin systems is how the energy released by ATP hydrolysis in the myosin motor domain gives rise to the movement of the myosin head along the actin filament. We assumed the signal of the ATP hydrolysis to be transmitted as modulated atomic vibrations from the nucleotide-binding site throughout the myosin head, and carried out 1-ns all-atom molecular dynamics simulations for that signal transmission. We distributed the released energy to atoms located around the ATPase pocket as kinetic energies and examined how the effect of disturbance extended throughout the motor domain. The result showed that the disturbance signal extended over the motor domain in 150 ps and induced slowly varying collective motions of atoms at the actin-binding site and the junction with the neck, both of which are relevant to the movement of the myosin head along the actin filament. We also performed a principal component analysis of thermal atomic motions for the motor domain, and the first principal component was consistent with the response to the disturbance given to the ATPase pocket.

Adenosine Triphosphatases↗

3D laser surface scanning and geometric morphometric analysis of craniofacial shape as an index of cerebro-craniofacial morphogenesis: initial application to sexual dimorphism.

BACKGROUND: Over early fetal life, when disturbances in schizophrenia have been posited and craniofacial dysmorphogenesis reported, cerebral morphogenesis proceeds in embryological intimacy with craniofacial morphogenesis. Digitization technologies now allow 3D recording of craniofacial surface landmarks and modeling of craniofacial shape differences using geometric morphometrics. METHODS: Using normal sexual dimorphism as an exemplar, facial surfaces of 131 Medical School employees [82 females, 49 males] were recorded in 3D using a portable, hand-held laser scanner; 3D coordinate data were then analyzed using geometric morphometrics. RESULTS: Males and females differed markedly on an omnibus test of craniofacial shape. Logistic regression analysis of 16 principal components of shape variability, explaining 84.9% of the overall sample variance, generated 8 principal components as significant and independent discriminators. On visualization, the female face is wider and flatter; the eyes are more lateral, anterior and are further apart, and nasal bridge is posterior; the nose is smaller; the lips are fuller and the chin more forward. These findings are complementary to sexual dimorphism in cerebral structures. CONCLUSIONS: This technique reliably discriminates geometric features of craniofacial morphology that are associated with aspects of cerebral morphology, and may inform on putative neurodevelopmental disorders characterised by dysmorphogenesis.

Adult↗

Source identification of underground fuel spills by solid-phase microextraction/high-resolution gas chromatography/genetic algorithms.

Solid-phase microextraction (SPME), capillary column gas chromatography, and pattern recognition methods were used to develop a potential method for typing jet fuels so a spill sample in the environment can be traced to its source. The test data consisted of gas chromatograms from 180 neat jet fuel samples representing common aviation turbine fuels found in the United States (JP-4, Jet-A, JP-7, JPTS, JP-5, JP-8). SPME sampling of the fuel's headspace afforded well-resolved reproducible profiles, which were standardized using special peak-matching software. The peak-matching procedure yielded 84 standardized retention time windows, though not all peaks were present in all gas chromatograms. A genetic algorithm (GA) was employed to identify features (in the standardized chromatograms of the neat jet fuels) suitable for pattern recognition analysis. The GA selected peaks, whose two largest principal components showed clustering of the chromatograms on the basis of fuel type. The principal component analysis routine in the fitness function of the GA acted as an information filter, significantly reducing the size of the search space, since it restricted the search to feature subsets whose variance is primarily about differences between the various fuel types in the training set. In addition, the GA focused on those classes and/or samples that were difficult to classify as it trained using a form of boosting. Samples that consistently classify correctly were not as heavily weighted as samples that were difficult to classify. Over time, the GA learned its optimal parameters in a manner similar to a perceptron. The pattern recognition GA integrated aspects of strong and weak learning to yield a "smart" one-pass procedure for feature selection.

Algorithms↗

Comparative study on the triglyceride composition of almond kernel oil. A new basis for cultivar chemometric characterization.

Nine triglycerides (LLL, OLL, PLL, OLO, PLO, PLP, OOO, POO, and SOO; triglycerides are abbreviated using L, O, P, and S for linoleoyl, oleoyl, palmitoyl, and stearoyl fat acid radicals, respectively) in the almond kernel of 19 different cultivars have been determined by high-performance liquid chromatography. Multivariate techniques have been applied to the data from 114 chromatographic determinations. Principal component analysis efficiently reduces the number of variables so that the first two principal components explain 84.4% of the total variance. The classification obtained by the application of cluster analysis to triglyceride composition differentiates the American cultivar Texas from the rest of the cultivars. The Italian cultivars are grouped. The cultivars Achaak, Del Cid, Malagueña, Desmayo Largueta, and Chellaston form another group, and the largest group includes most of the Spanish cultivars. Discriminant analysis provides convenient functions to describe the four groups previously established by cluster analysis. The calculated classification functions correctly assign samples from the testing set to their respective groups.

Fatty Acids↗

Effect of leavening microflora on pizza dough properties.

Fourteen different starter cultures containing one strain of Saccharomyces cerevisiae with and without individual or combinations of lactic acid bacteria (Lactobacillus plantarum, Lact. sanfrancisco, Enterococcus faecium, Leuconostoc mesenteroides) were employed to investigate the role of leavening microflora on the properties of pizza doughs. Microbiological, chemical and physical characteristics of doughs prepared with the same flour and under the same processing conditions were determined. Leavening times and acidification properties depended on the microbial association used. The proportions of lactic and acetic acid produced by lactic acid bacteria were consistent with the metabolic properties of the strains employed. The bacteria/yeast ratios arising from microbial counts at the end of the leavening process were always lower in comparison to sour- or bread-doughs. The size of the yeast population did not change much, while bacteria showed from one to four duplications. Rheologically, the fermented doughs could only be significantly distinguished from the control dough with regard to the elastic modulus. Principal Component Analysis was applied to the acidimetric data. The scattergram of the two principal components effectively discriminated 13 of the 14 pizza dough types.

Acetic Acid↗

Application of gravitational clustering analysis to liquid gastric emptying.

A gravitational clustering analysis was applied to principal component weighting factors and t1/2 values from 100 liquid gastric emptying studies. Using principal components, groups of patients with clinical features in common were identified, whereas the analysis of the t1/2 values failed to differentiate them.

Duodenal Ulcer↗

Interrelationships between electrical properties and microstructure of human trabecular bone.

Microstructural changes, such as reduction of trabecular thickness and number, are characteristic signs of osteoporosis leading to diminished bone strength. Electrical and dielectric parameters might provide diagnostically valuable information on trabecular bone microstructure not extractable from bone mineral density measurements. In this study, structural properties of human trabecular bone samples (n=26) harvested from the distal femur and proximal tibia were investigated using the computed microtomography (microCT) technique. Quantitative parameters, e.g. structural model index (SMI) or trabecular bone volume fraction (BV/TV), were calculated. In addition, the samples were examined electrically over a wide frequency range (50 Hz-5 MHz) using a two-electrode impedance spectroscopy set-up. Relative permittivity, loss factor, conductivity, phase angle, specific impedance and dissipation factor were determined. Significant linear correlations were obtained between the dissipation factor and BV/TV or SMI (|r| 0.70, p<0.01, n=26). Principal component analyses, conducted on electrical and structural parameters, revealed that the high frequency principal component of the dissipation factor was significantly related to SMI (r=0.72, p<0.01, n=26). The linear combination of high and low frequency relative permittivity predicted 73% of the variation in BV/TV. To conclude, electrical and dielectric parameters of trabecular bone, especially relative permittivity and dissipation factor, were significantly and specifically related to a trabecular microstructure as characterized with microCT. The data gathered in this study constitute a useful basis for theoretical and experimental work towards the development of impedance spectroscopy techniques for detection of bone quality in vitro or in special cases of open surgery.

Bone Density↗

Is major depressive disorder in adolescence a distinct diagnostic entity?

The concept of major depressive disorder in childhood and adolescence is reviewed and it is suggested that contemporary enthusiasm for this diagnosis may have outrun the evidence that it is a distinct categorical entity. To test the hypothesis that major depression is not a qualitatively distinct disorder in adolescence, but rather a continuously distributed, noncategorical syndrome, the behavioral rating scales (CBCL-P) of 216 hospitalized adolescent patients were analyzed first by principal components analysis and then by cluster analysis. Three behavioral syndromes were isolated by principal components analysis. Of three groups of patients identified by a subsequent cluster analysis, one was consistent with the concept of a categorically distinct "nuclear" depression. However, a noncategorical continuously distributed depressive syndrome appears to affect a larger number of patients in this age group, and the "nuclear" disorder may be less prevalent than is currently assumed. One explanation of these findings would combine a categorical model of nuclear depression with a dimensional model of dysthymia.

Adjustment Disorders↗

Sub-cutaneous fat thickness measured by magnetic resonance imaging, ultrasound, and calipers.

Sub-cutaneous fat thickness was measured at 12 sites on the body surface of 24 males and 26 females using magnetic resonance imaging (MRI), skinfold calipers, and A-mode ultrasound. The mean of the 12 fat thickness measurements and individual site thicknesses were compared between individuals using analysis of variance. In males, the mean thicknesses for ultrasound and calipers were similar (P greater than 0.05) but both were less than the MRI (P less than 0.001). MRI and ultrasound were similar in females but less than calipers (P less than 0.001). A good between-subject correlation was found between all three methods in the males but only the calipers and MRI were well correlated in females. Within-subject correlations are poor for all measures and in both sexes. Factor loadings for a varimax rotation of two principal components indicate that the fat is distributed in 1 of 2 patterns: either principally on the trunk or on the limbs. The principal component analysis and the result of canonical correlations obtained from the factor loadings confirm the findings of the analysis of variance, in that a general level of fatness is measurable by all three methods over a range of subjects. However, the pattern of fat thicknesses measured over a number of specific sites by one method of measurement is unlikely to be duplicated by either of the other two methods on the same individual.

Adipose Tissue↗