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PubMed2004

Similarities and effectiveness of test environments in selecting and deploying desirable genotypes.

Rooted cuttings of 40 different clones (genotypes) of Picea abies (L.) Karst were planted in seven test environments (P, H, L, S, B, M and K) in northern Germany. Type-B genetic correlations between the pairs of test sites were estimated, and a cluster diagram based on inter-site genetic correlations for height was used to illustrate the general pattern of similarities among the test sites. Principal component analysis (PCA) showed that the first three principal components explained 97% of the variance in height, thereby providing a good summary of the relationships among the test sites. Test sites B and K accounted for a relatively high-and test sites H and M for a relatively low-proportion of genotype-environment interaction sums of squares and, consequently, for "ecovalence". "Moderator" and "instigator" test sites for interactions in different site combinations were detected. On the basis of several similarity measures, we observed two distinct groups: sites M-S-P formed one group, while sites K-L formed the other; sites H and B were closer to the first group. The empirical data indicated that a good test site should have the following features: (1) low interaction behaviour, (2) low coefficient of variation, (3) high genotypic selectivity, (4) high coefficient of determination, (5) high efficiency of expected gain. Based on these criteria, site M was determined to be the best test site for screening genotypes to be planted in other environments. We concluded that one broadly adapted vegetative propagation population of P. abies can be used for the potential planting environments in northern Germany.

Adaptation, Physiological↗
PubMed1989

Investigation of multiple simultaneously active brain sources in the electroencephalogram.

We present a method of investigating multiple simultaneously active brain sources that overlap both in space and time in the scalp electroencephalogram (EEG). In order to identify the contributions of the individual brain sources to measured potentials, we applied principal component analysis and various methods of rotating the principal components including a newly developed rotation procedure using frequency criteria. We related the results of these multivariate statistical techniques to a new physical model using multiple current dipoles with fixed anatomical locations and time-varying activities. We thus are able to study 3-dimensional location, time activity and interaction of multiple simultaneously active brain sources in the scalp EEG.

Brain↗
PubMed2006

Determination of PM2.5 sources using time-resolved integrated source and receptor models.

Multivariate statistical techniques are applied to particulate matter (PM) and meteorological data to identify the sources responsible for evening PM spikes at Sunland Park, NM (USA). The statistical techniques applied are principal components analysis (PCA), redundancy analysis (RDA), and absolute principal components scores analysis (APCSA), and the data evaluated are 3-h average (6-9 p.m.) PM(2.5) mass and chemical composition and 1-h average PM(2.5) and PM(10) mass and environmental data collected in the winter of 2002. Although the interpretation of the data was complicated by the presence of sources which are likely changing in time (e.g. brick kilns), the multivariate analyses indicate that the evening high PM(2.5) is associated with burning-activities occurring to the south of Sunland Park, and these emissions are characterized by elevated Sb, Cl(-), and elemental carbon; approximately 68% of the PM(2.5) mass can be attributed to this source. The PM(10) evening peaks, on the other hand, are mainly caused by resuspended dust generated by vehicular movements south of the site and transported by the local terrain-induced drainage flow.

Air Pollutants↗
PubMed2005

Multivariate analysis of selected metals in tannery effluents and related soil.

Effluent and relevant soil samples from 38 tanning units housed in Kasur, Pakistan, were obtained for metal analysis by flame atomic absorption spectrophotometric method. The levels of 12 metals, Na, Ca, K, Mg, Fe, Mn, Cr, Co, Cd, Ni, Pb and Zn were determined in the two media. The data were evaluated towards metal distribution and metal-to-metal correlations. The study evidenced enhanced levels of Cr (391, 16.7 mg/L) and Na (25,519, 9369 mg/L) in tannery effluents and relevant soil samples, respectively. The effluent versus soil trace metal content relationship confirmed that the effluent Cr was strongly correlated with soil Cr. For metal source identification the techniques of principal component analysis, and cluster analysis were applied. The principal component analysis yielded two factors for effluents: factor 1 (49.6% variance) showed significant loading for Ca, Fe, Mn, Cr, Cd, Ni, Pb and Zn, referring to a tanning related source for these metals, and factor 2 (12.6% variance) with higher loadings of Na, K, Mg and Co, was associated with the processes during the skin/hide treatment. Similarly, two factors with a cumulative variance of 34.8% were obtained for soil samples: factor 1 manifested the contribution from Mg, Mn, Co, Cd, Ni and Pb, which though soil-based is basically effluent-derived, while factor 2 was found associated with Na, K, Ca, Cr and Zn which referred to a tannery-based source. The dendograms obtained from cluster analysis, also support the observed results. The study exhibits a gross pollution of soils with Cr at levels far exceeding the stipulated safe limit laid down for tannery effluents.

Environmental Monitoring↗
PubMed2006

Raman spectroscopy of coated pharmaceutical tablets and physical models for multivariate calibration to tablet coating thickness.

Raman spectra of a set of coated pharmaceutical tablets were analyzed for the purpose of calibrating the spectra to tablet coating thickness. Acetaminophen tablets were coated with a hydroxypropylmethylcellulose/polyethylene glycol film coating whose thickness was varied from 0 to 6% weight gain. Coatings were also prepared with two concentrations of TiO2 at several film thicknesses. The resulting spectral data set was analyzed using several different multivariate calibration procedures. The procedures examined in this study included spectral correction followed by target factor analysis, spectral correction with baseline subtraction followed by principal component regression, and first derivative computation followed by principal component regression. The results demonstrate that target factor analysis is a viable method for calibration of Raman spectra to tablet coating thickness. Calibration based on derivative spectra resulted in linear correlation that was equal to that of the results of target factor analysis for coatings without TiO2. However, target factor analysis was found to be superior to other methods when TiO2 was present in the tablet coatings. The effect of sample fluorescence on each of these chemometric methods was also examined. It was found that when photobleaching of fluorescent impurities due to exposure to the Raman excitation source was controlled, the tablet coating thickness could be calibrated to the intensity of the fluorescence signal. The results also demonstrate that for the samples examined here, calibration by target factor analysis is insensitive to variation in fluorescent intensity when the tablet coating emission spectrum is included in the matrix of target vectors.

Acetaminophen↗
PubMed2006

Pathological reactions and recovery of hepatopancreatic digestive cells from the marine snail Littorina littorea following exposure to a polycyclic aromatic hydrocarbon.

The aim of this study was to investigate the cellular pathological responses of hepatopancreatic digestive cells from the periwinkle Littorina littorea exposed to the polycyclic aromatic hydrocarbon (PAH) fluoranthene and to ascertain whether any injurious effects were reversible within the experimental time scale. A secondary objective was to establish the relationship of the various reactions to animal health status, using lysosomal stability as an index of well-being. Exposure of snails to a concentration of 335 microgl(-1) (1.7 microM) fluoranthene (seawater renewed and spiked daily with fluoranthene) for 5 days resulted in a reduction in lysosomal stability (neutral red retention) and endocytosis; and an increase in smooth endoplasmic reticulum (ER) and 7-ethoxycoumarin-o-deethylase (ECOD; measured as cyano-ECOD) activity measured in isolated live digestive cells. Exposed snails treated with clean seawater for a further 8 days resulted in a return to control levels of lysosomal stability, ECOD and ER; endocytosis showed only a partial recovery. Multi-variate and uni-variate analysis showed that there were strong correlations between the various cellular biomarker responses. These findings are interpretable within the current framework of molluscan biomarker responses to PAHs. Principal component analysis was used to derive the first principal component for endocytosis, ER and ECOD reactions and these were plotted against lysosomal stability as a measure of cellular well-being. The resulting significant regression represents the mapping of the individual biomarkers within health status space for a gradient of fluoranthene toxicity. From this analysis, we concluded that endocytosis is an indicator of healthy snails while proliferation of ER and to a lesser extent induced ECOD are indicative of dysfunction and reduced health. Finally, the results indicate that stress induced by chronic exposure to a PAH is reversible.

7-Alkoxycoumarin O-Dealkylase↗
PubMed2006

Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.

A method for flexible fitting of molecular models into three-dimensional electron microscopy (3D-EM) reconstructions at a resolution range of 8-12 A is proposed. The approach uses the evolutionarily related structural variability existing among the protein domains of a given superfamily, according to structural databases such as CATH. A structural alignment of domains belonging to the superfamily, followed by a principal components analysis, is performed, and the first three principal components of the decomposition are explored. Using rigid body transformations for the secondary structure elements (SSEs) plus the cyclic coordinate descent algorithm to close the loops, stereochemically correct models are built for the structure to fit. All of the models are fitted into the 3D-EM map, and the best one is selected based on crosscorrelation measures. This work applies the method to both simulated and experimental data and shows that the flexible fitting was able to produce better results than rigid body fitting.

Amino Acid Sequence↗
PubMed1996

Developing a subject-derived terminology to describe perceptions of chemicals in foods.

Risk perception may be influenced by a number of factors, such as unfamiliarity, lack of control, perceived consequences, and hazards being seen as catastrophic and having risk for future generations. Risk perception researchers have typically used such investigator-selected characteristics to assess hazards. In the first study reported here, the repertory grid method was used to elicit the terminology that subjects (n = 30) use to distinguish between 30 different chemicals. The data were submitted to generalized Procrustes analysis. The first principal axis of the resulting consensus plot separated the chemicals ranging from "poisonous or toxic," "harmful or dangerous," and "sounds negative" at one end, to "positive effect on health," "often present in food nowadays," and "sounds positive" at the other end. The second principal axis ranged from "familiar with or knowledge of" and "chemical" to "natural." A second study (n = 226) was carried out to look at the general validity of the results of the repertory grid interviews using a fixed questionnaire. The data were submitted to principal components analysis and internal preference mapping. The first principal component ranged from "safe" and "healthy" at one end, to "poisonous" and "harmful" at the other end. The chemicals also separated in terms of "familiar," "chemical," and "natural." All three methods of data collection and analysis yield essentially similar results.

Attitude↗
PubMed1986

Psychologic correlates of dental anxiety.

In an attempt to establish the relationships between dental anxiety and personality traits, such as neuroticism and locus of control, a survey has been carried out among 30-40-yr-olds in a Dutch town. In the first instance, the questionnaires comprising the psychologic items were treated by Non-Metric Principal Components analysis to detect the underlying structure. The principal components found were then used in a second-stage analysis. The results appear to be at variance with the literature, i.e. subgroups discernible in the sample by sets of psychologic features were not associated with dental anxiety categories.

Adult↗
PubMed1997

Nevill's explanation of Kleiber's 0.75 mass exponent: an artifact of collinearity problems in least squares models?

Intraspecific allometric modeling (Y = a.mass(b), where Y is the physiological dependent variable and a is the proportionality coefficient) of peak oxygen uptake (VO2peak) has frequently revealed a mass exponent (b) greater than that predicted from dimensionality theory, approximating Kleiber's 3/4 exponent for basal metabolic rate. Nevill (J. Appl. Physiol. 77: 2,870-2,873, 1994) proposed an explanation and a method that restores the inflated exponent to the anticipated 2/3. In human subjects, the method involves the addition of "stature" as a continuous predictor variable in a multiple log-linear aggression model: ln Y = a + c. ln stature + b. ln mass + ln epsilon, where c is the general body size exponent and epsilon is the error term. It is likely that serious collinearity confounds may adversely affect the reliability and validity of the model. The aim of this study was to critically examine Nevill's method in modeling VO2peak in prepubertal, teenage, and adult men. A mean exponent of 0.81 (95% confidence interval, 0.65-0.97) was found when scaling by mass alone. Nevill's method reduced the mean mass exponent to 0.67 (95% confidence interval, 0.44-0.9). However, variance inflation factors and tolerance for the log-transformed stature and mass variables exceeded published criteria for severe collinearity. Principal components analysis also diagnosed severe collinearity in two principal components, with condition indexes > 30 and variance decomposition proportions exceeding 50% for two regression coefficients. The derived exponents may thus be numerically inaccurate and unstable. In conclusion, the restoration of the mean mass exponent to the anticipated 2/3 may be a fortuitous statistical artifact.

Adolescent↗
PubMed2003

Space-time maps and two-bar interactions of different classes of direction-selective cells in macaque V-1.

We used one-dimensional sparse noise stimuli to generate first-order spatiotemporal maps and second-order two-bar interaction maps for 65 simple and 124 complex direction-selective cells in alert macaque V1. Spatial and temporal phase differences between light and dark space-time maps clearly distinguished simple and complex cell populations. Complex cells usually showed similar direction preferences to light and dark bars, but many of the directional simple cells were much more direction selective to one sign of contrast than the reverse. We show that this is predicted by a simple energy model. Some of the direction-selective simple cells showed multiple space-time-slanted subregions, but others (previously described as S1 cells) had space-time maps that looked like just one subregion of an ordinary simple cell. Both simple and complex cells showed directional interactions (nonlinearities) to pairs of flashed bars (a 2-bar apparent-motion stimulus). The space-time slant of the simple cells correlated with the optimum dX/dT (velocity) of the paired-bar interactions. Some complex cells also showed a space-time slant; the direction of the slant usually correlated with the preferred direction of motion, but the degree of slant correlated with the inferred velocity tuning only when measured by a weighted-centroid calculation. Principal components analysis of the simple-cell space-time maps yielded one fast temporally biphasic component and a slower temporally monophasic component. We saw no consistent pattern for the spatial phase of the components, unlike previous reports; however, we show that principal components analysis may not distinguish between spatial offsets and phase offsets.

Algorithms↗
PubMed2003

Differentiation of species of the Baccharis genus by HPLC and chemometric methods.

Phytochemical investigation of the aerial parts of three Baccharis species (Asteraceae family) was performed using HPLC and chemometric methods, with the objective of distinguishing between three morphologically very similar species: Baccharis genistelloides Persoon var. trimera (Less.) DC, B. milleflora (Less.) DC and B. articulata (Lam.) Persoon. With the help of Principal Component Analysis (PCA) and variance weights, it was possible to characterize the chromatographic profiles of the alcoholic extracts of the three species. Application of Soft Independent Modeling of Class Analogy (SIMCA) and K-Nearest Neighbor (KNN) methods on a training set of 74 extracts resulted in models that correctly classified all eight samples in an independent test set.

Baccharis↗
PubMed2002

Development of rats' maternally directed orienting behaviors from birth to day 2.

We previously observed 2- to 3-day-old (P2-3) rats perform maternally directed orienting behaviors (MDOBs)-locomotion, torso flexion, rotation to the supine orientation, and snout probing, accompanied by audible vocalizations (barking)-under surfaces having properties of the dam's ventrum, which result in close contact between the pup's ventrum and the surface. We now report on the development of MDOBs from birth through P2. Wistar rats (24 litters) were tested at one of four times: 1 hr after birth before the first nursing bout (P0pre), on the day of birth after the first nursing bout (P0post), on postnatal Day 1 (P1), or on postnatal Day 2 (P2). Pups were placed prone on a warmed platform inside a corral where, for 4 min, they encountered one of two motherlike surfaces at head height: (a) a soft cotton roof or (b) a patch of the pup's own anesthetized dam's ventrum. Control pups received no overhead stimulus. The behaviors we had identified as MDOBs and others, including limb behaviors, are easily recognized at P0pre, and, in aggregate, are more frequent then than at any later age. The differential responsiveness of most of the behaviors to the dam's ventrum compared to the cotton roof or open condition is relatively low at P0pre, but rises rapidly through P2. Behavioral structure develops quickly from a rudimentary principal component with two behaviors at P0pre to two principal components incorporating seven behavior classes by P2. MDOBs are discussed in relation to late-term fetal behaviors, early postnatal righting responses, and the oral nipple grasp, and as a model of the development of filial attachment in an altricial mammal.

Animals↗
PubMedDate not supplied

[Low-molecular-weight autoregulatory factors in bacteria Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum].

The haloalkaliphilic, lithoautotrophic, sulfur-oxidizing gram-negative bacteria Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum were found to possess a special system for the autoregulation of their growth. The system includes the extracellular autoinducers of anabiosis (the d1 factor) and autolysis (the d2 factor). The principal components of the d1 factor are alkylhydroxybenzenes. The principal components of the d2 factor are free unsaturated fatty acids dominated by oleic acid isomers. Like the respective autoregulators of neutrophilic bacteria, the d1 factor of haloalkaliphilic bacteria presumably controls their growth and transition to a anabiotic state, while the d2 factor controls autolytic processes. Alkylhydroxybenzenes of both microbial and chemical origin were found to influence bacterial respiration. The low-molecular-weight osmoprotectant glycine betaine enhanced the thermostability of trypsin. This suggests that glycine betaine, like the d1 factor, serves as a molecular chaperone.

Adaptation, Physiological↗
PubMed2004

Electrostatic potential of nucleotide-free protein is sufficient for discrimination between adenine and guanine-specific binding sites.

Despite sharing many common features, adenine-binding and guanine-binding sites in proteins often show a clear preference for the cognate over the non-cognate ligand. We have analyzed electrostatic potential (ESP) patterns at adenine and guanine-binding sites of a large number of non-redundant proteins where each binding site was first annotated as adenine/guanine-specific or non-specific from a survey of primary literature. We show that more than 90% of ESP variance at the binding sites is accounted for by only two principal component ESP vectors, each aligned to molecular dipoles of adenine and guanine. Projected on these principal component vectors, the adenine/guanine-specific and non-specific binding sites, including adenine-containing dinucleotides, show non-overlapping distributions. Adenine or guanine specificities of the binding sites also show high correlation with the corresponding electrostatic replacement (cognate by non-cognate ligand) energies. High correlation coefficients (0.94 for 35 adenine-binding sites and 1.0 for 20 guanine-binding sites) were obtained when adenine/guanine specificities were predicted using the replacement energies. Our results demonstrate that ligand-free protein ESP is an excellent indicator for discrimination between adenine and guanine-specific binding sites and that ESP of ligand-free protein can be used as a tool to annotate known and putative purine-binding sites in proteins as adenine or guanine-specific.

Adenine↗
PubMed2006

Use of factor analysis in Journal of Advanced Nursing: literature review.

AIM: This paper reports a review analysing the use of factor analysis in papers in Journal of Advanced Nursing. BACKGROUND: Factor analysis is a multivariate statistical method for reducing large numbers of variables to fewer underlying dimensions. There are several methods of factor analysis with principal components analysis being the most commonly applied. Factor analysis has been used by researchers in nursing for many years but the standards for use and reporting are variable. METHOD: Papers using factor analysis in Journal of Advanced Nursing were retrieved from 1982 to the end of 2004. The search term 'factor analysis' was used in the CINAHL database and applied specifically to Journal of Advanced Nursing in December 2004. Retrieved papers were included in the review if they came from Journal of Advanced Nursing and used factor analysis as part of the method of the reported study. RESULTS: One hundred and twenty-four papers were retrieved as a result of the initial search criteria of which 116 were from Journal of Advanced Nursing. Screening of papers for the use of factor analysis left 100 papers for review. Principal components analysis was the most commonly used method of factor analysis; Eigenvalues greater than one was the most commonly applied criterion for selecting the number of factors followed by orthogonal rotation to achieve simple structure. The majority of papers did not report the whole factor solution and there were papers that did not specify anything beyond the fact that they carried out factor analysis. Confirmatory factor analysis was rarely used and exploratory methods other than principal components analysis were also rarely used. CONCLUSIONS: Factor analysis is quite commonly used in nursing research reported in Journal of Advanced Nursing. While some papers are exemplary there is room for improvement in the reporting of all aspects of factor analysis.

Bibliometrics↗
PubMed2004

Prediction of ozone concentration in ambient air using multivariate methods.

Multivariate statistical methods including pattern recognition (Principal Component Analysis--PCA) and modeling (Multiple Linear Regression--MLR, Partial Least Squares--PLS, as well as Principal Component Regression--PCR) methods were carried out to evaluate the state of ambient air in Miskolc (second largest city in Hungary). Samples were taken from near the ground at a place with an extremely heavy traffic. Although PCA is not able to determine the significance of variables, it can uncover their similarities and classify the cases. PCA revealed that it is worth to separate day and night data because different factors influence the ozone concentrations during all day. Ozone concentration was modeled by MLR and PCR with the same efficiency if the conditions of meteorological parameters were not changed (i.e. morning and afternoon). Without night data, PCR and PLS suggest that the main process is not a photochemical but a chemical one.

Air↗
PubMed2002

Structural characterization of the metabolites of hydroxytyrosol, the principal phenolic component in olive oil, in rats.

Hydroxytyrosol is quantitatively and qualitatively the principal phenolic antioxidant in olive oil. Recently it was shown that hydroxytyrosol and five metabolites were excreted in urine when hydroxytyrosol was dosed intravenously or orally in an olive oil solution to rats. The conclusive identification of three metabolites of hydroxytyrosol by MS/MS as a monosulfate conjugate, a 3-O-glucuronide conjugate, and 4-hydroxy-3-methoxyphenylacetic acid (homovanillic acid) has been established in this investigation. The structural configurations of the glucuronide conjugate and 4-hydroxy-3-methoxyphenylacetic acid were confirmed by (1)H NMR. The radical scavenging potencies of homovanillic acid, homovanillic alcohol, hydroxytyrosol, and the metabolites were examined with the radical 2,2-diphenyl-1-picrylhydrazyl. These studies showed them to be potent antioxidants with SC(50) values of 14.8 and 11.4 microM for homovanillic acid and homovanillic alcohol, respectively. The 3-O-glucuronide conjugate was more potent than hydroxytyrosol, with an SC(50) of 2.3 in comparison to 11.0 microM, and the monosulfate conjugate was almost devoid of radical scavenging activity.

Animals↗