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PubMed1989

[Value of enzymuria during antibacterial therapy].

Enzymuria is a well known parameter of evaluation of drugs nephrotoxicity, particularly of antibiotics. Alanine aminopeptidase (AAP), gamma-glutamyltransferase (GGT) and N-acetyl-bêta-D-glucosaminidase activities were measured in native urine. This study included 19 patients treated by an association of netilmicin-vancomycin. Enzymuria was measured on 24 hours urines at J0 then every two days during treatment. Enzymuria increased 24 or 48 hours after the beginning of the treatment. The Principal Components Analysis (PCA) of the results of enzymuria, seric urea and creatininemia shows the presence of two groups of responses. The first principal component exhibits two populations: the patients with pathological seric urea and pathological seric creatinine and the others. The PCA does not allow this discrimination using only the results of enzymuria; in contrast, with these results, the patients may be classified by the PCA on the basis of treatment duration. The enzymuria allows the clear identification of nephrotoxic drugs but does not allow the prediction of renal injury or of its aggravation.

Acetylglucosaminidase↗
PubMed1993

Nutritional epidemiological study on mineral intake and mortality from cardiovascular disease.

To clarify the relationship between mortality from cardiovascular disease and mineral intake in Japan, we performed statistical analysis on the intake of 4 minerals, magnesium (Mg), calcium (Ca), sodium (Na) and potassium (K) calculated from the National Nutritional Survey. Their association with age-adjusted mortality from ischemic heart disease (IHD), cerebral hemorrhage (CH) and cerebral infarction (CI) during 15 years between 1971-1985 was examined. Ca/Mg ratio increased in all Japan. Mg intake, Na/K ratio and Na*Ca/K*Mg ratio decreased in all Japan. Geographical correlations among mineral intake were generally highly positive, and a high inverse correlation was observed between Na intake and Ca/Mg ratio. Mineral intake was closely correlated highly positively with mortality from CH and CI for almost all 15 years in men and women. Correlation between mortality from IHD and mineral intake was positively significant only in the period of 1971-75 in some cases. Principal component analysis using the intake in each food group showed the intake of all 4 minerals to be correlated highly with first principal component comprising the Japanese traditional diet. Thus, in Japan, it may be necessary to devise certain aspects of food intake such as lower Na in the Japanese traditional diet and additional Mg in the modern diet.

Calcium↗
PubMed2003

Analysis of terpenoids from hemlock (Tsuga) species by solid-phase microextraction/gas chromatography/ion-trap mass spectrometry.

A sampling method for determining the volatile terpenoid composition from single needles of seven Tsuga species was developed using headspace solid-phase microextraction (SPME). A reproducible sampling method for the volatile components was generated by examination of sample storage, method of needle cutting, and headspace sampling duration. Following SPME collection of the volatile compounds from the seven Tsuga species, gas chromatography/ion-trap mass spectrometry was used to identify 51 terpenoids present in the needle headspace. A semiquantitative method was devised to express individual terpenoid amounts as a percentage of all of the identified peaks in the chromatogram. The semiquantitative results permitted facile interspecies comparison using principal component analysis. Two components were able to account for 90% of the variance and were interpreted as a "species" component and a "resistance/susceptibility" component. Three interspecies groupings were evident from the principal component analysis: (1) Tsuga canadensis and Tsuga caroliniana; (2) Tsuga chinesnsis, Tsuga diversifolia, Tsuga heterophylla, and Tsuga sieboldii; and (3) Tsuga mertensiana. The finding that T. mertensiana was grouped alone and far removed from the other species adds to the morphological evidence that this species should be segregated from other Tsuga.

Bicyclic Monoterpenes↗
PubMed2002

[The naphtha composing characteristics of geoherbs of Atractylodes lancea].

OBJECTIVE: To find the chemical diversity and characteristics of A. lancea on two levels--individuals and populations, and to discover the chemical essentials for forming geoherbs. METHOD: 47 rhizomes of A. lancea were collected in 7 populations, and 6 naphtha components (1. elemol, 2. hinesol, 3. beta-eudesmol, 4. atractylone, 5. atractylodin, 6. atractylenolid I) in the rhizomes were determined by GC-MS combination. Principal Component Analysis and Cluster Analysis were carried out by SPSS. RESULT: Cluster Analysis of the 6 main components indicated that the chemical components of geoherbs were different from those of the non-geonerbs of A. lancea. Other analysis showed as follows: 1. The general oil of geoberbs were lower than that of non-geoherbs(P < 0.01), but components yielding more than 1% (% of the total oil) were more than non-geoherbs(P < 0.01); 2. Hinesol mixing beta-eudesmol was more in non-geoherbs, which atractylodin mixing atractylone was more in geoherbs(P < 0.001); 3. Principal Component Analysis implied that atractylone was the most important component to discriminate geoherbs and non-geoherbs of A. Lancea. CONCLUSION: The naphtha composing characteristics of geoherbs was the special proportionment sale, viz. atractylone: hinesol: beta-eudesmol: atractylodin being(0.70~2.00):(0.04~0.35):(0.09~0.40):1.

Atractylodes↗
PubMed1997

A first application of independent component analysis to extracting structure from stock returns.

This paper explores the application of a signal processing technique known as independent component analysis (ICA) or blind source separation to multivariate financial time series such as a portfolio of stocks. The key idea of ICA is to linearly map the observed multivariate time series into a new space of statistically independent components (ICs). We apply ICA to three years of daily returns of the 28 largest Japanese stocks and compare the results with those obtained using principal component analysis. The results indicate that the estimated ICs fall into two categories, (i) infrequent large shocks (responsible for the major changes in the stock prices), and (ii) frequent smaller fluctuations (contributing little to the overall level of the stocks). We show that the overall stock price can be reconstructed surprisingly well by using a small number of thresholded weighted ICs. In contrast, when using shocks derived from principal components instead of independent components, the reconstructed price is less similar to the original one. ICA is shown to be a potentially powerful method of analyzing and understanding driving mechanisms in financial time series. The application to portfolio optimization is described in Chin and Weigend (1998).

Algorithms↗
PubMed1998

Predictions of protein secondary structures using factor analysis on Fourier transform infrared spectra: effect of Fourier self-deconvolution of the amide I and amide II bands.

Fourier self-deconvolution (FSD) was performed on protein amide I and II Fourier transform infrared (FTIR) spectra to test if the resultant increased band shape variation would lead to improvements in protein secondary structure prediction with our factor analysis based restricted multiple regression (RMR) methods. FTIR spectra of 23 proteins dissolved in H2O were measured and normalized to a constant amide I peak absorbance. The deconvolved spectra were renormalized by area so that the deconvolved spectra sets had the same area as before. Principal component analysis of the deconvolved spectra sets was carried out, which was followed by a selective multiple linear regression (RMR) analysis of the principal component loadings with regard to the fractional components (FC) of secondary structure. As compared to analyses based on the original spectra set, helix and sheet predictions were not noticeably improved by FSD; but, if a very large number of component spectra (16) were retained in the pool to select which loadings to be used in the RMR optimization, better predictions of turn and "other" resulted. The prediction quality varied depending on the deconvolution parameters used.

Animals↗
PubMed2004

Explorative data analysis of two-dimensional electrophoresis gels.

Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.

Diagnostic Imaging↗
PubMed2006

Spatial and temporal trends of physicochemical parameters in the water of the Reconquista river (Buenos Aires, Argentina).

The Reconquista river is one of the most polluted watercourses in Argentina. More than 3 million people and over 10,000 industries are settled on its basin. The available data show that pollution is mainly related to the discharge of domestic and industrial liquid wastes that are poured into the river almost untreated. At present no site of the river can be characterized as free of pollutants. Samples were taken monthly from 5 sites of the river; some 18-20 physicochemical parameters were determined in each sample. Analyses revealed significant differences in the degree of deterioration between sites. Two of them, close to the source of the river (Cascallares-S(1) and Paso del Rey-S(2)) resulted less polluted than the two points located close to the mouth of the river (San Martin-S(4) and Bancalari-S(5)). The worsening of the water quality in S(4)-S(5) was attributed to the discharges of the Moron stream, a tributary that flows into the main course of the river a complex mixture of non treated waste waters. PCA was used in the ordination of samples (sites, season and physicochemical parameters). In the PCA performed using all variables, the first principal component showed positive correlation with N-NH(4) (+), conductivity, orthophosphate, BOD(5), COD and alkalinity, and negative correlation with DO. The second principal component was positively correlated with pH, temperature and chlorophyll a and negatively with phenols and hardness. In respect to the spatial distribution, the plot of the scores for the first two components of samples taken in each sampling station showed S(1) and S(2) values displayed farthest at the left side of the X axis with high DO. In contrast, S(4) and S(5) values stayed at the right side of this axis with high N-NH(4) (+), conductivity, orthophosphate, BOD(5), COD and alkalinity; data of S(3) were "intermediate". In order to identify seasonal trends in the concentration of contaminants scores of cases labeled by season were plotted. The line drawn on the ordination plane showed that summer samples tended to converge to the upper right portion of the graph where pollution variables had more importance on the first axis, and along the second axis with high correlation with pH, temperature and chlorophyll a. Winter scores were settled in the left lower part of the plot with minor contribution of pollution parameters and more importance of DO on the first axis. Samples of autumn and spring did not fit a clear cut pattern.

Argentina↗
PubMed1999

Modeling the inhibitory effects of organic acids on bacteria.

The inhibitory effect of acids on microbial growth has long been used to preserve foods from spoilage. While much of the effect can be accounted for by pH, it is well known that different organic acids vary considerably in their inhibitory effects. Because organic acids are not members of a homologous series, but vary in the numbers of carboxy groups, hydroxy groups and carbon-carbon double bonds in the molecule, it has typically not been possible to predict the magnitude, or in some cases even the direction, of the change in inhibitory effect upon substituting one acid for another or to predict the net result in food systems containing more than one acid. The objective of this investigation was to attempt to construct a mathematical model that would enable such prediction as a function of the physical and chemical properties of organic acids. Principal Components Analysis (PCA) was applied to 11 properties for each of 17 acids commonly found in food systems; this resulted in four significant principal components (PCs), presumably representing fundamental properties of the acids and indicating each acid's location along each of these four scales. These properties correspond to polar groups, the number of double bonds, molecular size, and solubility in non-polar solvents. Minimum inhibitory concentrations (MICs) for each of eight acids for six test microorganisms were determined at pH 5.25. The MICs for each organism were modeled as a function of the four PCs using partial least squares (PLS) regression. This produced models with high correlations for five of the bacteria (R2 = 0.856, 0.941, 0.968, 0.968 and 0.970) and one with a slightly lower value (R2 = 0.785). Acid susceptible organisms (Bacillus cereus, Bacillus subtilis, and Alicyclobacillus) exhibited a similar response pattern. There appeared to be two separate response patterns for acid resistant organisms; one was exhibited by the two lactobacilli studied and the other by E. coli. Predicting the inhibitory effects of the organic acids as a function of their chemical and physical properties is clearly possible.

Bacillaceae↗
PubMed2002

Comparative study of stromal cell lines derived from embryonic, fetal, and postnatal mouse blood-forming tissues.

OBJECTIVE: To better understand the differentiation of stromal cells of the hematopoietic microenvironment, we set out to characterize stromal cells from the different developmental sites of hematopoiesis in the mouse (30 bone marrow, 7 spleen, 3 embryonic and 15 fetal liver, 6 yolk sac, and 6 aorta-gonad-mesonephros lines) for expression of 22 cytoskeletal, membrane, and extracellular matrix proteins. MATERIALS AND METHODS: Western blotting, immunofluorescence, and flow cytometry were used. Statistical methods included principal components analysis and analysis of variance. RESULTS: Stromal cells from 11 dpc mouse embryos express mesenchymal and vascular smooth muscle cell (VSMC) markers. Principal components analysis on the 70 stromal cell lines isolated from different anatomic sites and developmental stages allows classification of stromal lines along a mesenchymal to VSMC differentiation pathway. Stromal cells do not express endothelial and hematopoietic differentiation membrane antigens, but they do express integrin alpha(5), alpha(6), and beta(1) subunits, vascular cell adhesion molecule-1, CD44, stem cell antigen-1, Thy-1, CD34, and endoglin. The intensity of expression of certain markers differs between lines according to the anatomic site of origin. CONCLUSIONS: This study indicates that stromal cells, whatever their anatomic site of origin, follow a VSMC differentiation pathway, suggesting a blood-forming tissue-specific differentiation of mesenchymal stem cells. Differential quantitative expression of distinct sets of markers appears to be correlated with the anatomic sites of origin of the stromal cells.

Aging↗
PubMedDate not supplied

Intact chemoreceptor-based biosensors.

A receptrode biosensor is presented that uses intact chemoreceptor-based molecular recognition from antennular structures of the Hawaiian swimming crab species Portunis sanguinolentus. The sensor is coupled to a learning, pattern recognition calculation for performing analytical chemistry. Action potential waveforms are used to establish the identity of individual action potential types that can be associated to particular analytes. The pattern recognition calculations used are referred to as cluster analysis (CA) and principal component analysis (PCA). Action potential similarities are determined by using a dendrogram plot of the cluster analysis results and further elucidated by using principal component scores plots. Quantitative analysis was performed after classification of analyte and background responses. Chemoresponses to salinity and trimethylamine N-oxide, two chemical constituents that are found in the crustacean living environment, were investigated and gave analytic responses over several orders of magnitude.

Action Potentials↗
PubMed2001

An analysis of 14 molecular markers for monitoring osteoarthritis. Relationship of the markers to clinical end-points.

OBJECTIVE: To investigate whether any of 14 serum and urine molecular markers (MMs) used to monitor osteoarthritis (OA) would be associated with particular clinical end-points. DESIGN: Thirty-nine OA patients were bled and urine collected at five time points: at baseline visit and at visits 1, 3, 6 and 12 months later. Twelve clinical measurements were made and the concentrations of each of 14 MMs were determined. Principal component analysis, stepwise linear regression with backward elimination, and logistic regression were used to determine the correlations between MMs and clinical measures. RESULTS: Principal component analysis was used to reduce the 12 clinical measurements into three independent clinical clusters: baseline clinical assessments, changes in clinical assessments and signal joint measurements. The 14 MMs were similarly reduced to five MM clusters. Each of the three clinical clusters was correlated with a single but different MM cluster. Baseline clinical assessments were correlated with bone markers typified by hydroxylysyl pyridinoline (HP) crosslinks, swelling of the signal joint was correlated with inflammation markers, especially CRP, and the change in clinical assessments over the 1 year evaluation was correlated with TGFbeta1. There was no correlation between any of the skeletal markers and the clinical measures, a situation which draws attention to the need for a direct assessment of cartilage damage in OA to validate the use of cartilage markers. CONCLUSIONS: This study demonstrates statistical methodology for analysis of clinical trials using multiple MMs and clinical end-points. The patient numbers are sufficient to test hypotheses of relationships of single MMs such as CRP, TGFbeta1 and HP to clinical measures, but larger clinical trials are needed to validate hypotheses.

Biomarkers↗
PubMed2006

Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species.

The domestication and improvement of fruit-bearing crops resulted in a large diversity of fruit form. To facilitate consistent terminology pertaining to shape, a controlled vocabulary focusing specifically on fruit shape traits was developed. Mathematical equations were established for the attributes so that objective, quantitative measurements of fruit shape could be conducted. The controlled vocabulary and equations were integrated into a newly developed software application, Tomato Analyzer, which conducts semiautomatic phenotypic measurements. To demonstrate the utility of Tomato Analyzer in the detection of shape variation, fruit from two F2 populations of tomato (Solanum spp.) were analyzed. Principal components analysis was used to identify the traits that best described shape variation within as well as between the two populations. The three principal components were analyzed as traits, and several significant quantitative trait loci (QTL) were identified in both populations. The usefulness and flexibility of the software was further demonstrated by analyzing the distal fruit end angle of fruit at various user-defined settings. Results of the QTL analyses indicated that significance levels of detected QTL were greatly improved by selecting the setting that maximized phenotypic variation in a given population. Tomato Analyzer was also applied to conduct phenotypic analyses of fruit from several other species, demonstrating that many of the algorithms developed for tomato could be readily applied to other plants. The controlled vocabulary, algorithms, and software application presented herein will provide plant scientists with novel tools to consistently, accurately, and efficiently describe two-dimensional fruit shapes.

Algorithms↗
PubMed2005

Immunological characteristics of patients infected with common intestinal helminths: results of a study based on reverse-transcriptase PCR.

To determine whether common helminth infections could modify the intestinal immunopathological status of the host, the expression in the human duodenal mucosa of cytokines, eosinophil- and mast-cell-specific molecules and monosaccharide transporters of the glucose-transporter (GLUT) family was explored. The 31 subjects were all patients at the gastro-intestinal disease unit of Nongkhai Hospital, Thailand. Four of the 10 patients who presented with eosinophilia (> or = 6.0% of their leucocytes were eosinophils), and five of the other 21 patients, had intestinal infections with helminths when they presented or within the previous 3 months. Studies based on semi-quantitative, reverse-transcriptase PCR revealed that the interleukin-5/interferon-gamma ratio was significantly higher in the noneosinophilic, helminth-infected patients than in the non-eosinophilic, uninfected patients, whereas the IgE receptor type I (Fc epsilon RI)/mast-cell tryptase ratio was significantly higher in the eosinophilic, helminth-infected patients than in the eosinophilic, uninfected patients. Expression of Charcot-Leyden-crystal protein, GLUT-1 and GLUT-5, however, showed no significant inter-group differences. Principal-components analysis of the data on eosinophils, interleukin-5, interferon-gamma, Fc epsilon RI and mast-cell tryptase revealed that one principal component could discriminate the patients who had helminth infection from the non-eosinophilic, uninfected patients, but not from the eosinophilic, uninfected patients. These results indicate that, whatever the intestinal pathology, patients infected with common intestinal helminths tend to develop a mucosal immunological response of the Th2 type.

Adult↗
PubMed2001

[Relevance and validity of a new French composite index to measure poverty on a geographical level].

BACKGROUND: A number of disease conditions are influenced by deprivation. Geographical measurement of deprivation can provide an independent contribution to individual measures by accounting for the social context. Such a geographical approach, based on deprivation indices, is classical in Great Britain but scarcely used in France. The objective of this work was to build and validate an index readily usable in French municipalities and cantons. METHODS: Socioeconomic data (unemployment, occupations, housing specifications, income, etc.) were derived from the 1990 census of municipalities and cantons in the Doubs departement. A new index was built by principal components analysis on the municipality data. The validity of the new index was checked and tested for correlations with British deprivation indices. RESULTS: Principal components analysis on municipality data identified four components (explaining 76% of the variance). Only the first component (CP1 explaining 42% of the variance) was retained. Content validity (wide choice of potential deprivation items, correlation between items and CP1: 0.52 to 0.96) and construct validity (CP1 socially relevant; Cronbach's alpha=0.91; correlation between CP1 and three out of four British indices ranging from 0.73 to 0.88) were sufficient. Analysis on canton data supported that on municipality data. CONCLUSION: The validation of the new index being satisfactory, the user will have to make a choice. The new index, CP1, is closer to the local background and was derived from data from a French departement. It is therefore better adapted to more descriptive approaches such as health care planning. To examine the relationship between deprivation and health with a more etiological approach, the British indices (anteriority, international comparisons) would be more appropriate, but CP1, once validated in various health problem situations, should be most useful for French studies.

Analysis of Variance↗
PubMed1980

Antibacterial antibodies in swine colostrum.

Antibacterial antibody activities were examined in 138 samples of swine colostrum by O-agglutinin test with serotypes of Escherichia coli (O-6, 0-45, 0-81, 0-83, 0-115, 0-138, O-139, and O-126), Salmonella typhimurium, and Salmonella cholerae suis. The mean agglutinin titer of E coli O-83 was the highest; E coli O-115 was next highest. The mean agglutinin titer of S cholerae suis was lowest; S typhimurium was next to lowest. Correlation coefficients among these O-agglutinin titers were between 0.109 and 0.693. Correlations of S typhimurium were the poorest; those of E coli O83, E coli O-138, and S cholerae suis were also poor. By principal component analysis, it was possible to classify ten kinds of O-agglutinins into four groups. The cumulative proportion of the first four principal components accounted for 77.97% of the total variance. Cumulative coefficients of factor loadings were from 65.25% to 99.50% of these O-agglutinins.

Agglutinins↗
PubMed2003

Geochemical evidences of the anthropogenic alteration of trace metal composition of the sediments of Chiricahueto marsh (SE Gulf of California).

Seven sediment cores (60-80 cm) were collected at Chiricahueto marsh, a salt marsh influenced by agrochemical, domestic and industrial effluents. The concentrations of Ag, Al, Cd, Co, Cu, Fe, Li, Mn, Pb, V and Zn were studied in the solid phase at each 1-cm section. The profiles of Ag, Cd, Cu, Mn, Ni, Pb and Zn showed a slight recent pollution in the site with enrichment and anthropogenic factors higher than unity; and correlation analysis indicated a direct association with organic carbon. Al, Co, Cr, Fe, Li, and V concentration profiles displayed a negative correlation with organic C and positive with mud content and no consistent enrichment at surface. Based on the principal component analysis and correlation analysis, two principal groups of metals were identified. The first group includes Al, Co, Cr, Fe and Li, that are derived predominantly from the weathering of parent materials in the local bedrock; and the second group include most of the metals, which were relatively enriched at surficial sediments, that are produced mainly by anthropogenic activities such as agriculture (Cd, Cu and Zn), sewage effluents (Ag, Cd, Cu, Ni, Pb and Zn) and in lesser extent atmospheric deposition (Cd and Pb).

Agrochemicals↗
PubMed1995

MR image classification algorithms for neurosurgical and stereotactic radiosurgical trajectory planning and volumetric analysis.

Neurosurgical and stereotactic radiosurgical trajectory planning involves a phase of image data acquisition followed by localization of tissues to be avoided or crossed during the procedure. Success of the procedure is often assessed during follow-up by performing volumetric analysis of tissues of interest. Both localization and volumetric analysis can be facilitated by classifying the input data into different tissue types. This study compares classification results based on four different input image data: (1) MR data obtained with one TR and TE parameter combination, (2) MR data acquired with eight combinations of TR and TE parameters, (3) input data compressed into four principal components, and (4) the input data (3) together with first- and second-order texture features. The algorithms (a) to reduce the dimensionality using principal components, (b) to generate texture features, (c) to determine feature usefulness in classification using the Wilk's lambda criterion, and (d) to classify the input set are described. Classification results are found to be poor for input data 1 and much improved (qualitatively and quantatively) for input data 2. Input data 3 produces classification results (quantitatively and qualitatively) similar to that of 2. Input data 4 is found to produce quantitative results similar to those of 2 and 3, but the qualitative results show enhanced classification of some tissues and distortion of others.

Algorithms↗